Site built with pkgdown 2.0.7.
+Site built with pkgdown 2.0.9.
diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html index edfbd9db..c024836a 100644 --- a/docs/LICENSE-text.html +++ b/docs/LICENSE-text.html @@ -1,5 +1,5 @@ -License
diff --git a/docs/articles/abfit-baseline-opts.html b/docs/articles/abfit-baseline-opts.html index 159a271c..9da9b524 100644 --- a/docs/articles/abfit-baseline-opts.html +++ b/docs/articles/abfit-baseline-opts.html @@ -12,7 +12,7 @@ - + @@ -40,7 +40,7 @@ @@ -237,7 +237,7 @@Custom analyses
-Site built with pkgdown 2.0.7.
+Site built with pkgdown 2.0.9.
diff --git a/docs/articles/abfit-baseline-opts_files/figure-html/abfit_aic-1.png b/docs/articles/abfit-baseline-opts_files/figure-html/abfit_aic-1.png
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diff --git a/docs/articles/index.html b/docs/articles/index.html
index 10698206..cbcb747e 100644
--- a/docs/articles/index.html
+++ b/docs/articles/index.html
@@ -1,5 +1,5 @@
-Articles • Spectroscopy Analysis Tools (spant) Articles • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -95,7 +95,7 @@ All vignettes
diff --git a/docs/articles/spant-basis-simulation.html b/docs/articles/spant-basis-simulation.html
index f1b9d819..e3bc5346 100644
--- a/docs/articles/spant-basis-simulation.html
+++ b/docs/articles/spant-basis-simulation.html
@@ -12,7 +12,7 @@
-
+
@@ -40,7 +40,7 @@
@@ -189,7 +189,7 @@ Basis simulation
-Site built with pkgdown 2.0.7.
+Site built with pkgdown 2.0.9.
diff --git a/docs/articles/spant-intro.html b/docs/articles/spant-intro.html
index aa3da6d1..f91bcb30 100644
--- a/docs/articles/spant-intro.html
+++ b/docs/articles/spant-intro.html
@@ -12,7 +12,7 @@
-
+
@@ -40,7 +40,7 @@
@@ -178,78 +178,79 @@ Basis simulation#> GSH,Glu,GPC,Ins,Lac,Lip09,
#> Lip13a,Lip13b,Lip20,MM09,MM12,
#> MM14,MM17,MM20,NAA,NAAG,PCh,
-#> PCr,sIns,Tau
-stackplot(basis, xlim = c(4, 0.5), labels = basis$names, y_offset = 5)
+#> PCr,sIns,Tau
+
Perform ABfit analysis of the processed data
(mrs_proc):
-
+
fit_res <- fit_mrs(mrs_proc, basis)
Plot the fit result:
-
+
plot(fit_res)
Unscaled amplitudes, CRLB error estimates and other useful fitting
diagnostics, such as SNR, are given in the fit_res results
table:
-
+
fit_res$res_tab
-#> X Y Z Dynamic Coil X.CrCH2 Ala Asp Cr
-#> 1 1 1 1 1 1 0 8.228912e-06 3.548337e-05 4.020305e-05
-#> GABA Glc Gln GSH Glu GPC
-#> 1 1.706754e-05 2.442067e-06 3.029726e-06 2.227786e-05 6.499645e-05 1.603288e-05
-#> Ins Lac Lip09 Lip13a Lip13b Lip20 MM09
-#> 1 5.902957e-05 5.818739e-06 2.362972e-05 2.635502e-06 0 0 9.887557e-06
-#> MM12 MM14 MM17 MM20 NAA NAAG
-#> 1 6.546986e-06 2.59994e-05 2.245507e-05 9.207418e-05 5.981787e-05 1.556188e-05
-#> PCh PCr sIns Tau tNAA tCr tCho
-#> 1 0 2.101297e-05 6.508636e-06 0 7.537975e-05 6.121601e-05 1.603288e-05
-#> Glx tLM09 tLM13 tLM20 X.CrCH2.sd Ala.sd
-#> 1 6.802617e-05 3.351728e-05 3.518189e-05 9.207418e-05 2.383751e-06 4.353306e-06
+#> X Y Z Dynamic Coil X.CrCH2 Ala Asp Cr GABA
+#> 1 1 1 1 1 1 0 8.133932e-06 3.547065e-05 4.02672e-05 1.697281e-05
+#> Glc Gln GSH Glu GPC Ins
+#> 1 2.446596e-06 3.036132e-06 2.228048e-05 6.503217e-05 1.606706e-05 5.906155e-05
+#> Lac Lip09 Lip13a Lip13b Lip20 MM09 MM12
+#> 1 5.802284e-06 2.387704e-05 2.670653e-06 0 0 9.630788e-06 6.511381e-06
+#> MM14 MM17 MM20 NAA NAAG PCh
+#> 1 2.603855e-05 2.238405e-05 9.203743e-05 6.011109e-05 1.536531e-05 0
+#> PCr sIns Tau tNAA tCr tCho
+#> 1 2.101921e-05 6.504098e-06 0 7.54764e-05 6.12864e-05 1.606706e-05
+#> Glx tLM09 tLM13 tLM20 X.CrCH2.sd Ala.sd
+#> 1 6.80683e-05 3.350783e-05 3.522059e-05 9.203743e-05 2.386861e-06 4.343919e-06
#> Asp.sd Cr.sd GABA.sd Glc.sd Gln.sd GSH.sd
-#> 1 9.243626e-06 3.715175e-06 4.580082e-06 4.427045e-06 5.089143e-06 2.022836e-06
+#> 1 9.235326e-06 3.689004e-06 4.574407e-06 4.421681e-06 5.083001e-06 2.020426e-06
#> Glu.sd GPC.sd Ins.sd Lac.sd Lip09.sd Lip13a.sd
-#> 1 5.086888e-06 2.525936e-06 2.091039e-06 5.311855e-06 4.118786e-06 1.328562e-05
+#> 1 5.082976e-06 2.602651e-06 2.093225e-06 5.301703e-06 4.119256e-06 1.328305e-05
#> Lip13b.sd Lip20.sd MM09.sd MM12.sd MM14.sd MM17.sd
-#> 1 6.477225e-06 7.510915e-06 3.827221e-06 4.597884e-06 7.234429e-06 3.810268e-06
+#> 1 6.474481e-06 7.510908e-06 3.827554e-06 4.594019e-06 7.223367e-06 3.811301e-06
#> MM20.sd NAA.sd NAAG.sd PCh.sd PCr.sd sIns.sd
-#> 1 8.602464e-06 1.015226e-06 1.215672e-06 2.174697e-06 3.108036e-06 7.233855e-07
-#> Tau.sd tNAA.sd tCr.sd tCho.sd Glx.sd tLM09.sd
-#> 1 3.777984e-06 7.031059e-07 5.881706e-07 2.1135e-07 3.165045e-06 1.006532e-06
-#> tLM13.sd tLM20.sd phase lw shift asym
-#> 1 1.572003e-06 3.018189e-06 11.15087 5.038937 -0.003427612 0.1764497
+#> 1 8.595853e-06 1.017712e-06 1.208985e-06 2.236873e-06 3.084598e-06 7.240068e-07
+#> Tau.sd tNAA.sd tCr.sd tCho.sd Glx.sd tLM09.sd
+#> 1 3.759956e-06 7.031383e-07 5.890481e-07 2.110662e-07 3.16966e-06 1.006794e-06
+#> tLM13.sd tLM20.sd phase lw shift asym
+#> 1 1.573147e-06 3.016809e-06 11.10963 5.023681 -0.00376505 0.1771067
#> res.deviance res.niter res.info
-#> 1 7.300317e-05 28 2
+#> 1 7.307669e-05 28 2
#> res.message bl_ed_pppm
#> 1 Relative error between `par' and the solution is at most `ptol'. 2.364083
-#> max_bl_flex_used full_res fit_pts ppm_range SNR SRR FQN
-#> 1 FALSE 7.745303e-05 497 3.8 62.79191 51.44068 1.490027
+#> max_bl_flex_used full_res fit_pts ppm_range SNR SRR FQN
+#> 1 FALSE 7.754368e-05 497 3.8 62.71687 51.3328 1.492722
#> tNAA_lw tCr_lw tCho_lw auto_bl_crit_7 auto_bl_crit_5.901
-#> 1 0.04565271 0.05199592 0.05438808 -8.904402 -8.947808
+#> 1 0.04562445 0.05189506 0.05438237 -8.900349 -8.944159
#> auto_bl_crit_4.942 auto_bl_crit_4.12 auto_bl_crit_3.425 auto_bl_crit_2.844
-#> 1 -8.980941 -9.003463 -9.016574 -9.023969
+#> 1 -8.977355 -9.000064 -9.013367 -9.02055
#> auto_bl_crit_2.364 auto_bl_crit_1.969 auto_bl_crit_1.647 auto_bl_crit_1.384
-#> 1 -9.027876 -9.027566 -9.014311 -8.963287
+#> 1 -9.024177 -9.023462 -9.009854 -8.958654
#> auto_bl_crit_1.17 auto_bl_crit_0.997 auto_bl_crit_0.856 auto_bl_crit_0.743
-#> 1 -8.848747 -8.694785 -8.565992 -8.488415
+#> 1 -8.844271 -8.690744 -8.562631 -8.485471
#> auto_bl_crit_0.654 auto_bl_crit_0.593 auto_bl_crit_0.558 auto_bl_crit_0.54
-#> 1 -8.449874 -8.432813 -8.425648 -8.42266
+#> 1 -8.447136 -8.430174 -8.423053 -8.420086
#> auto_bl_crit_0.532 auto_bl_crit_0.529
-#> 1 -8.421406 -8.420875
+#> 1 -8.418839 -8.418312
Note that signal names appended with “.sd” are the CRLB estimates for
the uncertainty (standard deviation) in the metabolite quantity
estimate. e.g. to calculate the percentage s.d. for tNAA:
-
+
fit_res$res_tab$tNAA.sd / fit_res$res_tab$tNAA * 100
-#> [1] 0.9327517
+#> [1] 0.9316001
Spectral SNR:
-
+
fit_res$res_tab$SNR
-#> [1] 62.79191
+#> [1] 62.71687
Linewidth of the tNAA resonance in PPM:
-
+
fit_res$res_tab$tNAA_lw
-#> [1] 0.04565271
+#> [1] 0.04562445
Ratios to total-creatine
@@ -258,45 +259,45 @@ Ratios to total-creatine
-
+
fit_res_tcr_sc <- scale_amp_ratio(fit_res, "tCr")
amps <- fit_amps(fit_res_tcr_sc)
print(t(amps))
#> [,1]
#> X.CrCH2 0.00000000
-#> Ala 0.13442417
-#> Asp 0.57964197
-#> Cr 0.65674069
-#> GABA 0.27880838
-#> Glc 0.03989262
-#> Gln 0.04949238
-#> GSH 0.36392207
-#> Glu 1.06175561
-#> GPC 0.26190670
-#> Ins 0.96428305
-#> Lac 0.09505257
-#> Lip09 0.38600560
-#> Lip13a 0.04305248
+#> Ala 0.13272001
+#> Asp 0.57876874
+#> Cr 0.65703313
+#> GABA 0.27694252
+#> Glc 0.03992071
+#> Gln 0.04954005
+#> GSH 0.36354683
+#> Glu 1.06111906
+#> GPC 0.26216356
+#> Ins 0.96369746
+#> Lac 0.09467490
+#> Lip09 0.38959768
+#> Lip13a 0.04357660
#> Lip13b 0.00000000
#> Lip20 0.00000000
-#> MM09 0.16151913
-#> MM12 0.10694891
-#> MM14 0.42471563
-#> MM17 0.36681686
-#> MM20 1.50408643
-#> NAA 0.97716047
-#> NAAG 0.25421252
+#> MM09 0.15714395
+#> MM12 0.10624512
+#> MM14 0.42486672
+#> MM17 0.36523688
+#> MM20 1.50175937
+#> NAA 0.98082268
+#> NAAG 0.25071313
#> PCh 0.00000000
-#> PCr 0.34325931
-#> sIns 0.10632244
+#> PCr 0.34296687
+#> sIns 0.10612627
#> Tau 0.00000000
-#> tNAA 1.23137299
+#> tNAA 1.23153582
#> tCr 1.00000000
-#> tCho 0.26190670
-#> Glx 1.11124799
-#> tLM09 0.54752473
-#> tLM13 0.57471702
-#> tLM20 1.50408643
+#> tCho 0.26216356
+#> Glx 1.11065912
+#> tLM09 0.54674163
+#> tLM13 0.57468844
+#> tLM20 1.50175937
Water reference scaling, AKA “absolute-quantification”
@@ -304,29 +305,29 @@ Water reference sca
A more sophisticated approach to scaling metabolite values involves
the use of a separate water-reference acquisition - which can be
imported in the standard way:
-
+
fname_wref <- system.file("extdata", "philips_spar_sdat_W.SDAT", package = "spant")
mrs_data_wref <- read_mrs(fname_wref)
The following code assumes the voxel contains 100% white matter
tissue and scales the metabolite values into molal (mM) units (mol / kg
tissue water) based on the method described by Gasparovic et al MRM 2006
55(6):1219-26:
-
+
p_vols <- c(WM = 100, GM = 0, CSF = 0)
TE = 0.03
TR = 2
fit_res_molal <- scale_amp_molal_pvc(fit_res, mrs_data_wref, p_vols, TE, TR)
fit_res_molal$res_tab$tNAA
-#> [1] 12.58176
+#> [1] 12.59789
An alternative method scales the metabolite values into molar (mM)
units (mol / Litre of tissue) based on assumptions outlined in the
LCModel manual and references therein (section 10.2). This approach may
be preferred when comparing results to those obtained LCModel or
TARQUIN.
-
+
fit_res_molar <- scale_amp_molar(fit_res, mrs_data_wref)
fit_res_molar$res_tab$tNAA
-#> [1] 6.817594
+#> [1] 6.826336
Note, while “absolute” units are attractive, a large number of
assumptions about metabolite and water relaxation rates are necessary to
arrive at these mM estimates. If you’re not confident at being able to
@@ -354,7 +355,7 @@
Water reference sca
diff --git a/docs/articles/spant-intro_files/figure-html/unnamed-chunk-10-1.png b/docs/articles/spant-intro_files/figure-html/unnamed-chunk-10-1.png
index b84cd2d5..a8160510 100644
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diff --git a/docs/articles/spant-metabolite-simulation.html b/docs/articles/spant-metabolite-simulation.html
index e6efca00..564fa989 100644
--- a/docs/articles/spant-metabolite-simulation.html
+++ b/docs/articles/spant-metabolite-simulation.html
@@ -12,7 +12,7 @@
-
+
@@ -40,7 +40,7 @@
@@ -279,8 +279,9 @@ Custom molecules#> L/G lineshape : 0
#>
#> nucleus chem_shift
-#> 1 1H 2.5
-custom_mol |> sim_mol() |> lb(2) |> zf() |> plot(xlim = c(4.4, 0.5))
+#> 1 1H 2.5
+
Once your happy the new molecule is correct, please consider
contributing it to the package if you think others would benefit.
@@ -304,7 +305,7 @@ Custom molecules
-Site built with pkgdown 2.0.7.
+Site built with pkgdown 2.0.9.
diff --git a/docs/articles/spant-preprocessing.html b/docs/articles/spant-preprocessing.html
index 28e38762..9544cf71 100644
--- a/docs/articles/spant-preprocessing.html
+++ b/docs/articles/spant-preprocessing.html
@@ -12,7 +12,7 @@
-
+
@@ -40,7 +40,7 @@
@@ -179,7 +179,7 @@ Reading raw data and plotting
-Site built with pkgdown 2.0.7.
+Site built with pkgdown 2.0.9.
diff --git a/docs/articles/spant-preprocessing_files/figure-html/unnamed-chunk-10-1.png b/docs/articles/spant-preprocessing_files/figure-html/unnamed-chunk-10-1.png
index 02bdd7ca..d9d919b3 100644
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diff --git a/docs/articles/spant-preprocessing_files/figure-html/unnamed-chunk-8-1.png b/docs/articles/spant-preprocessing_files/figure-html/unnamed-chunk-8-1.png
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diff --git a/docs/authors.html b/docs/authors.html
index fd4064a4..34e6b241 100644
--- a/docs/authors.html
+++ b/docs/authors.html
@@ -1,5 +1,5 @@
-Authors and Citation • Spectroscopy Analysis Tools (spant) Authors and Citation • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -69,7 +69,7 @@
diff --git a/docs/index.html b/docs/index.html
index 6e715d8e..c58968f6 100644
--- a/docs/index.html
+++ b/docs/index.html
@@ -12,16 +12,13 @@
-
+
-
+
Changelog • Spectroscopy Analysis Tools (spant) Changelog • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -73,7 +73,13 @@ Changelog
-spant 2.21.0
+spant 2.22.0
+- Added find_bids_mrs and mrs_data2bids helper functions.
+- Improved handling of CMRR semi-LASER SVS water reference scans.
+- Added functions for GLS coil combination.
+
+
+spant 2.21.02024-05-30
- Fixed compiler warnings for Fortran code.
- Added glm_spec function.
- Added add_noise_spec_snr function.
@@ -584,7 +590,7 @@ spant 0.1.02
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml
index 510f032e..8099ddc1 100644
--- a/docs/pkgdown.yml
+++ b/docs/pkgdown.yml
@@ -1,5 +1,5 @@
-pandoc: 3.1.1
-pkgdown: 2.0.7
+pandoc: 3.1.11
+pkgdown: 2.0.9
pkgdown_sha: ~
articles:
abfit-baseline-opts: abfit-baseline-opts.html
@@ -7,7 +7,7 @@ articles:
spant-intro: spant-intro.html
spant-metabolite-simulation: spant-metabolite-simulation.html
spant-preprocessing: spant-preprocessing.html
-last_built: 2024-05-29T18:39Z
+last_built: 2024-07-11T11:18Z
urls:
reference: https://martin3141.github.io/spant/reference
article: https://martin3141.github.io/spant/articles
diff --git a/docs/reference/Arg.mrs_data.html b/docs/reference/Arg.mrs_data.html
index 1372d866..4eba752f 100644
--- a/docs/reference/Arg.mrs_data.html
+++ b/docs/reference/Arg.mrs_data.html
@@ -1,5 +1,5 @@
-Apply Arg operator to an MRS dataset. — Arg.mrs_data • Spectroscopy Analysis Tools (spant) Apply Arg operator to an MRS dataset. — Arg.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -107,7 +107,7 @@ Value
diff --git a/docs/reference/Conj.mrs_data.html b/docs/reference/Conj.mrs_data.html
index 794d446f..10ea0ef1 100644
--- a/docs/reference/Conj.mrs_data.html
+++ b/docs/reference/Conj.mrs_data.html
@@ -1,5 +1,5 @@
-Apply Conj operator to an MRS dataset. — Conj.mrs_data • Spectroscopy Analysis Tools (spant) Apply Conj operator to an MRS dataset. — Conj.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -107,7 +107,7 @@ Value
diff --git a/docs/reference/Im.mrs_data.html b/docs/reference/Im.mrs_data.html
index 4c9a70eb..e0e26588 100644
--- a/docs/reference/Im.mrs_data.html
+++ b/docs/reference/Im.mrs_data.html
@@ -1,5 +1,5 @@
-Apply Im operator to an MRS dataset. — Im.mrs_data • Spectroscopy Analysis Tools (spant) Apply Im operator to an MRS dataset. — Im.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -107,7 +107,7 @@ Value
diff --git a/docs/reference/Imzap.html b/docs/reference/Imzap.html
index a3eeaed6..cf1b088d 100644
--- a/docs/reference/Imzap.html
+++ b/docs/reference/Imzap.html
@@ -1,7 +1,5 @@
-Complex rounding function taken from complexplus package to reduce the number
-of spant dependencies. — Imzap • Spectroscopy Analysis Tools (spant) Complex rounding function taken from complexplus package to reduce the number of spant dependencies. — Imzap • Spectroscopy Analysis Tools (spant) Apply Mod operator to an MRS dataset. — Mod.mrs_data • Spectroscopy Analysis Tools (spant) Apply Mod operator to an MRS dataset. — Mod.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -107,7 +107,7 @@ Value
diff --git a/docs/reference/Ncoils.html b/docs/reference/Ncoils.html
index 503ce5c0..09d22662 100644
--- a/docs/reference/Ncoils.html
+++ b/docs/reference/Ncoils.html
@@ -1,5 +1,5 @@
-Return the total number of coil elements in an MRS dataset. — Ncoils • Spectroscopy Analysis Tools (spant) Return the total number of coil elements in an MRS dataset. — Ncoils • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/Ndyns.html b/docs/reference/Ndyns.html
index 49c3ebb2..26ca34a7 100644
--- a/docs/reference/Ndyns.html
+++ b/docs/reference/Ndyns.html
@@ -1,5 +1,5 @@
-Return the total number of dynamic scans in an MRS dataset. — Ndyns • Spectroscopy Analysis Tools (spant) Return the total number of dynamic scans in an MRS dataset. — Ndyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/Npts.html b/docs/reference/Npts.html
index c63fe64e..7e8af89e 100644
--- a/docs/reference/Npts.html
+++ b/docs/reference/Npts.html
@@ -1,5 +1,5 @@
-Return the number of data points in an MRS dataset. — Npts • Spectroscopy Analysis Tools (spant) Return the number of data points in an MRS dataset. — Npts • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/Nspec.html b/docs/reference/Nspec.html
index e5f2464a..ff6c4dcd 100644
--- a/docs/reference/Nspec.html
+++ b/docs/reference/Nspec.html
@@ -1,5 +1,5 @@
-Return the total number of spectra in an MRS dataset. — Nspec • Spectroscopy Analysis Tools (spant) Return the total number of spectra in an MRS dataset. — Nspec • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/Ntrans.html b/docs/reference/Ntrans.html
index 3d3ce629..32ae3ad6 100644
--- a/docs/reference/Ntrans.html
+++ b/docs/reference/Ntrans.html
@@ -1,5 +1,5 @@
-Return the total number of acquired transients for an MRS dataset. — Ntrans • Spectroscopy Analysis Tools (spant) Return the total number of acquired transients for an MRS dataset. — Ntrans • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/Nx.html b/docs/reference/Nx.html
index beb130b8..461192b3 100644
--- a/docs/reference/Nx.html
+++ b/docs/reference/Nx.html
@@ -1,5 +1,5 @@
-Return the total number of x locations in an MRS dataset. — Nx • Spectroscopy Analysis Tools (spant) Return the total number of x locations in an MRS dataset. — Nx • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/Ny.html b/docs/reference/Ny.html
index 5c23ee37..530efde4 100644
--- a/docs/reference/Ny.html
+++ b/docs/reference/Ny.html
@@ -1,5 +1,5 @@
-Return the total number of y locations in an MRS dataset. — Ny • Spectroscopy Analysis Tools (spant) Return the total number of y locations in an MRS dataset. — Ny • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/Nz.html b/docs/reference/Nz.html
index 2a28bfbb..15295f98 100644
--- a/docs/reference/Nz.html
+++ b/docs/reference/Nz.html
@@ -1,5 +1,5 @@
-Return the total number of z locations in an MRS dataset. — Nz • Spectroscopy Analysis Tools (spant) Return the total number of z locations in an MRS dataset. — Nz • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/Re.mrs_data.html b/docs/reference/Re.mrs_data.html
index bbdcd3e7..37608c36 100644
--- a/docs/reference/Re.mrs_data.html
+++ b/docs/reference/Re.mrs_data.html
@@ -1,5 +1,5 @@
-Apply Re operator to an MRS dataset. — Re.mrs_data • Spectroscopy Analysis Tools (spant) Apply Re operator to an MRS dataset. — Re.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -107,7 +107,7 @@ Value
diff --git a/docs/reference/abfit_opts.html b/docs/reference/abfit_opts.html
index d501fc2a..5524db43 100644
--- a/docs/reference/abfit_opts.html
+++ b/docs/reference/abfit_opts.html
@@ -1,5 +1,5 @@
-Return a list of options for an ABfit analysis. — abfit_opts • Spectroscopy Analysis Tools (spant) Return a list of options for an ABfit analysis. — abfit_opts • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -125,7 +125,8 @@ Return a list of options for an ABfit analysis.
input_paras_raw = NULL,
optim_lw_only = FALSE,
optim_lw_only_limit = 20,
- lb_init = 0.001
+ lb_init = 0.001,
+ zf_offset = NULL
)
@@ -347,6 +348,12 @@ Arguments
basis signals. Setting to 0 will clash with the minimum allowable value
(eg hard constraint) during the detailed fit.
+
+zf_offset
+offset in number of data points from the end of the FID to
+zero-fill. Default is NULL and will automatically set this to 50 points when
+the FID distortion flag is set for the mrs_data.
Value
@@ -372,7 +379,7 @@ Examples
diff --git a/docs/reference/abfit_opts_v1_9_0.html b/docs/reference/abfit_opts_v1_9_0.html
index 1c128a05..975f7a0a 100644
--- a/docs/reference/abfit_opts_v1_9_0.html
+++ b/docs/reference/abfit_opts_v1_9_0.html
@@ -1,7 +1,5 @@
-Return a list of options for an ABfit analysis to maintain comparability with
-analyses performed with version 1.9.0 (and earlier) of spant. — abfit_opts_v1_9_0 • Spectroscopy Analysis Tools (spant) Return a list of options for an ABfit analysis to maintain comparability with analyses performed with version 1.9.0 (and earlier) of spant. — abfit_opts_v1_9_0 • Spectroscopy Analysis Tools (spant) Simulate pulse sequence acquisition. — acquire • Spectroscopy Analysis Tools (spant) Simulate pulse sequence acquisition. — acquire • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/add_noise.html b/docs/reference/add_noise.html
index 5c395587..c2ded890 100644
--- a/docs/reference/add_noise.html
+++ b/docs/reference/add_noise.html
@@ -1,5 +1,5 @@
-Add noise to an mrs_data object. — add_noise • Spectroscopy Analysis Tools (spant) Add noise to an mrs_data object. — add_noise • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -116,7 +116,7 @@ Value
diff --git a/docs/reference/add_noise_spec_snr.html b/docs/reference/add_noise_spec_snr.html
index f0072ef4..92a0fab3 100644
--- a/docs/reference/add_noise_spec_snr.html
+++ b/docs/reference/add_noise_spec_snr.html
@@ -1,5 +1,5 @@
-Add noise to an mrs_data object to match a given SNR. — add_noise_spec_snr • Spectroscopy Analysis Tools (spant) Add noise to an mrs_data object to match a given SNR. — add_noise_spec_snr • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -78,7 +78,12 @@ Add noise to an mrs_data object to match a given SNR.
- add_noise_spec_snr(mrs_data, target_snr, sig_region = c(4, 0.5))
+ add_noise_spec_snr(
+ mrs_data,
+ target_snr,
+ sig_region = c(4, 0.5),
+ ref_data = NULL
+)
@@ -97,6 +102,11 @@ Arguments
spectral limits to search for the strongest spectral data
point.
ref_data
+measure the signal from the first scan in this reference data
+and apply the same target noise level to mrs_data.
Value
@@ -117,7 +127,7 @@ Value
diff --git a/docs/reference/align.html b/docs/reference/align.html
index f61afc9f..53697923 100644
--- a/docs/reference/align.html
+++ b/docs/reference/align.html
@@ -1,5 +1,5 @@
-Align spectra to a reference frequency using a convolution based method. — align • Spectroscopy Analysis Tools (spant) Align spectra to a reference frequency using a convolution based method. — align • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -146,7 +146,7 @@ Value
diff --git a/docs/reference/apodise_xy.html b/docs/reference/apodise_xy.html
index 35121da6..9f622f56 100644
--- a/docs/reference/apodise_xy.html
+++ b/docs/reference/apodise_xy.html
@@ -1,5 +1,5 @@
-Apodise MRSI data in the x-y direction with a k-space filter. — apodise_xy • Spectroscopy Analysis Tools (spant) Apodise MRSI data in the x-y direction with a k-space filter. — apodise_xy • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -88,7 +88,7 @@ Arguments
func
-must be "hamming" or "gaussian".
must be "hamming", "hanning" or "gaussian".
w
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/append_basis.html b/docs/reference/append_basis.html
index cf58e336..c32f7be3 100644
--- a/docs/reference/append_basis.html
+++ b/docs/reference/append_basis.html
@@ -1,5 +1,5 @@
-Combine a pair of basis set objects. — append_basis • Spectroscopy Analysis Tools (spant) Combine a pair of basis set objects. — append_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/append_coils.html b/docs/reference/append_coils.html
index 6e2ead5b..99c8c3cf 100644
--- a/docs/reference/append_coils.html
+++ b/docs/reference/append_coils.html
@@ -1,7 +1,5 @@
-Append MRS data across the coil dimension, assumes they matched across the
-other dimensions. — append_coils • Spectroscopy Analysis Tools (spant) Append MRS data across the coil dimension, assumes they matched across the other dimensions. — append_coils • Spectroscopy Analysis Tools (spant) Append MRS data across the dynamic dimension, assumes they matched across the
-other dimensions. — append_dyns • Spectroscopy Analysis Tools (spant) Append MRS data across the dynamic dimension, assumes they matched across the other dimensions. — append_dyns • Spectroscopy Analysis Tools (spant) Append multiple regressor data frames into a single data frame. — append_regs • Spectroscopy Analysis Tools (spant) Append multiple regressor data frames into a single data frame. — append_regs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/apply_axes.html b/docs/reference/apply_axes.html
index 0f2f4d55..b5a7e296 100644
--- a/docs/reference/apply_axes.html
+++ b/docs/reference/apply_axes.html
@@ -1,5 +1,5 @@
-Apply a function over specified array axes. — apply_axes • Spectroscopy Analysis Tools (spant) Apply a function over specified array axes. — apply_axes • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -130,7 +130,7 @@ Examples
diff --git a/docs/reference/apply_mrs.html b/docs/reference/apply_mrs.html
index 22bc1933..1e2ea9ed 100644
--- a/docs/reference/apply_mrs.html
+++ b/docs/reference/apply_mrs.html
@@ -1,5 +1,5 @@
-Apply a function across given dimensions of a MRS data object. — apply_mrs • Spectroscopy Analysis Tools (spant) Apply a function across given dimensions of a MRS data object. — apply_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -116,7 +116,7 @@ Arguments
diff --git a/docs/reference/apply_pulse.html b/docs/reference/apply_pulse.html
index cae875cf..17c6e3ae 100644
--- a/docs/reference/apply_pulse.html
+++ b/docs/reference/apply_pulse.html
@@ -1,5 +1,5 @@
-Simulate an RF pulse on a single spin. — apply_pulse • Spectroscopy Analysis Tools (spant) Simulate an RF pulse on a single spin. — apply_pulse • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -126,7 +126,7 @@ Value
diff --git a/docs/reference/array2mrs_data.html b/docs/reference/array2mrs_data.html
index 26278811..c5f77129 100644
--- a/docs/reference/array2mrs_data.html
+++ b/docs/reference/array2mrs_data.html
@@ -1,7 +1,5 @@
-Convert a 7 dimensional array in into a mrs_data object. The array dimensions
-should be ordered as : dummy, X, Y, Z, dynamic, coil, FID. — array2mrs_data • Spectroscopy Analysis Tools (spant) Convert a 7 dimensional array in into a mrs_data object. The array dimensions should be ordered as : dummy, X, Y, Z, dynamic, coil, FID. — array2mrs_data • Spectroscopy Analysis Tools (spant) Perform zeroth-order phase correction based on the minimisation of the
-squared difference between the real and magnitude components of the
-spectrum. — auto_phase • Spectroscopy Analysis Tools (spant) Perform zeroth-order phase correction based on the minimisation of the squared difference between the real and magnitude components of the spectrum. — auto_phase • Spectroscopy Analysis Tools (spant) Back extrapolate time-domain data points using an autoregressive model. — back_extrap_ar • Spectroscopy Analysis Tools (spant) Back extrapolate time-domain data points using an autoregressive model. — back_extrap_ar • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -136,7 +136,7 @@ Value
diff --git a/docs/reference/basis2dyn_mrs_data.html b/docs/reference/basis2dyn_mrs_data.html
index 1e334800..ef466e85 100644
--- a/docs/reference/basis2dyn_mrs_data.html
+++ b/docs/reference/basis2dyn_mrs_data.html
@@ -1,5 +1,5 @@
-Convert a basis object to a dynamic mrs_data object. — basis2dyn_mrs_data • Spectroscopy Analysis Tools (spant) Convert a basis object to a dynamic mrs_data object. — basis2dyn_mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Value
diff --git a/docs/reference/basis2mrs_data.html b/docs/reference/basis2mrs_data.html
index d712d28f..dd0f65d9 100644
--- a/docs/reference/basis2mrs_data.html
+++ b/docs/reference/basis2mrs_data.html
@@ -1,7 +1,5 @@
-Convert a basis object to an mrs_data object - where basis signals are spread
-across the dynamic dimension. — basis2mrs_data • Spectroscopy Analysis Tools (spant) Convert a basis object to an mrs_data object - where basis signals are spread across the dynamic dimension. — basis2mrs_data • Spectroscopy Analysis Tools (spant) Generate a spline basis, slightly adapted from : "Splines, knots, and
-penalties", Eilers 2010. — bbase • Spectroscopy Analysis Tools (spant) Baseline correction using the ALS method. — bc_als • Spectroscopy Analysis Tools (spant) Baseline correction using the ALS method. — bc_als • Spectroscopy Analysis Tools (spant) Remove a constant baseline offset based on a reference spectral region. — bc_constant • Spectroscopy Analysis Tools (spant) Remove a constant baseline offset based on a reference spectral region. — bc_constant • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/bc_gauss.html b/docs/reference/bc_gauss.html
index 265fce5e..29fee72a 100644
--- a/docs/reference/bc_gauss.html
+++ b/docs/reference/bc_gauss.html
@@ -1,5 +1,5 @@
-Apply and subtract a Gaussian smoother in the spectral domain. — bc_gauss • Spectroscopy Analysis Tools (spant) Apply and subtract a Gaussian smoother in the spectral domain. — bc_gauss • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/bc_poly.html b/docs/reference/bc_poly.html
index e4f74fea..50b824de 100644
--- a/docs/reference/bc_poly.html
+++ b/docs/reference/bc_poly.html
@@ -1,5 +1,5 @@
-Fit and subtract a polynomial to each spectrum in a dataset. — bc_poly • Spectroscopy Analysis Tools (spant) Fit and subtract a polynomial to each spectrum in a dataset. — bc_poly • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/bc_spline.html b/docs/reference/bc_spline.html
index 09d7fc51..33239c4a 100644
--- a/docs/reference/bc_spline.html
+++ b/docs/reference/bc_spline.html
@@ -1,5 +1,5 @@
-Fit and subtract a smoothing spline to each spectrum in a dataset. — bc_spline • Spectroscopy Analysis Tools (spant) Fit and subtract a smoothing spline to each spectrum in a dataset. — bc_spline • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/beta2lw.html b/docs/reference/beta2lw.html
index 331a5c0b..d6afbc92 100644
--- a/docs/reference/beta2lw.html
+++ b/docs/reference/beta2lw.html
@@ -1,7 +1,5 @@
-Covert a beta value in the time-domain to an equivalent linewidth in Hz:
-x * exp(-i * t * t * beta). — beta2lw • Spectroscopy Analysis Tools (spant) Covert a beta value in the time-domain to an equivalent linewidth in Hz: x * exp(-i * t * t * beta). — beta2lw • Spectroscopy Analysis Tools (spant) Bin equally spaced spectral regions. — bin_spec • Spectroscopy Analysis Tools (spant) Bin equally spaced spectral regions. — bin_spec • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/calc_coil_noise_cor.html b/docs/reference/calc_coil_noise_cor.html
index beeab373..935cf09f 100644
--- a/docs/reference/calc_coil_noise_cor.html
+++ b/docs/reference/calc_coil_noise_cor.html
@@ -1,5 +1,5 @@
-Calculate the noise correlation between coil elements. — calc_coil_noise_cor • Spectroscopy Analysis Tools (spant) Calculate the noise correlation between coil elements. — calc_coil_noise_cor • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/calc_coil_noise_sd.html b/docs/reference/calc_coil_noise_sd.html
index 2a788fc7..d5f47a93 100644
--- a/docs/reference/calc_coil_noise_sd.html
+++ b/docs/reference/calc_coil_noise_sd.html
@@ -1,5 +1,5 @@
-Calculate the noise standard deviation for each coil element. — calc_coil_noise_sd • Spectroscopy Analysis Tools (spant) Calculate the noise standard deviation for each coil element. — calc_coil_noise_sd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/calc_design_efficiency.html b/docs/reference/calc_design_efficiency.html
index 0fc73261..2975440c 100644
--- a/docs/reference/calc_design_efficiency.html
+++ b/docs/reference/calc_design_efficiency.html
@@ -1,5 +1,5 @@
-Calculate the efficiency of a regressor data frame. — calc_design_efficiency • Spectroscopy Analysis Tools (spant) Calculate the efficiency of a regressor data frame. — calc_design_efficiency • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/calc_ed_from_lambda.html b/docs/reference/calc_ed_from_lambda.html
index 56237859..7962e054 100644
--- a/docs/reference/calc_ed_from_lambda.html
+++ b/docs/reference/calc_ed_from_lambda.html
@@ -1,5 +1,5 @@
-Calculate the effective dimensions of a spline smoother from lambda. — calc_ed_from_lambda • Spectroscopy Analysis Tools (spant) Calculate the effective dimensions of a spline smoother from lambda. — calc_ed_from_lambda • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/calc_peak_info_vec.html b/docs/reference/calc_peak_info_vec.html
index 79914d1f..03813eb8 100644
--- a/docs/reference/calc_peak_info_vec.html
+++ b/docs/reference/calc_peak_info_vec.html
@@ -1,5 +1,5 @@
-Calculate the FWHM of a peak from a vector of intensity values. — calc_peak_info_vec • Spectroscopy Analysis Tools (spant) Calculate the FWHM of a peak from a vector of intensity values. — calc_peak_info_vec • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/calc_sd_poly.html b/docs/reference/calc_sd_poly.html
index 737d68c7..c2f6d1eb 100644
--- a/docs/reference/calc_sd_poly.html
+++ b/docs/reference/calc_sd_poly.html
@@ -1,7 +1,5 @@
-Perform a polynomial fit, subtract and return the standard deviation of the
-residuals. — calc_sd_poly • Spectroscopy Analysis Tools (spant) Perform a polynomial fit, subtract and return the standard deviation of the residuals. — calc_sd_poly • Spectroscopy Analysis Tools (spant) Calculate the sum of squares differences between two mrs_data objects. — calc_spec_diff • Spectroscopy Analysis Tools (spant) Calculate the sum of squares differences between two mrs_data objects. — calc_spec_diff • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/calc_spec_snr.html b/docs/reference/calc_spec_snr.html
index 702fc62d..972912a0 100644
--- a/docs/reference/calc_spec_snr.html
+++ b/docs/reference/calc_spec_snr.html
@@ -1,5 +1,5 @@
-Calculate the spectral SNR. — calc_spec_snr • Spectroscopy Analysis Tools (spant) Calculate the spectral SNR. — calc_spec_snr • Spectroscopy Analysis Tools (spant) Check LCModel can be run — check_lcm • Spectroscopy Analysis Tools (spant) Check LCModel can be run — check_lcm • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -94,7 +94,7 @@ Check LCModel can be run
diff --git a/docs/reference/check_tqn.html b/docs/reference/check_tqn.html
index 7cdb1d18..4bfd1977 100644
--- a/docs/reference/check_tqn.html
+++ b/docs/reference/check_tqn.html
@@ -1,5 +1,5 @@
-Check the TARQUIN binary can be run — check_tqn • Spectroscopy Analysis Tools (spant) Check the TARQUIN binary can be run — check_tqn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -94,7 +94,7 @@ Check the TARQUIN binary can be run
diff --git a/docs/reference/circ_mask.html b/docs/reference/circ_mask.html
index 462f90f1..4634256d 100644
--- a/docs/reference/circ_mask.html
+++ b/docs/reference/circ_mask.html
@@ -1,5 +1,5 @@
-Create a logical circular mask spanning the full extent of an n x n matrix. — circ_mask • Spectroscopy Analysis Tools (spant) Create a logical circular mask spanning the full extent of an n x n matrix. — circ_mask • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/coherence_filter.html b/docs/reference/coherence_filter.html
index 61141857..852d1489 100644
--- a/docs/reference/coherence_filter.html
+++ b/docs/reference/coherence_filter.html
@@ -1,5 +1,5 @@
-Zero all coherence orders other than the one supplied as an argument. — coherence_filter • Spectroscopy Analysis Tools (spant) Zero all coherence orders other than the one supplied as an argument. — coherence_filter • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/collapse_to_dyns.html b/docs/reference/collapse_to_dyns.html
index f4dc6b97..7668cb08 100644
--- a/docs/reference/collapse_to_dyns.html
+++ b/docs/reference/collapse_to_dyns.html
@@ -1,5 +1,5 @@
-Collapse MRS data by concatenating spectra along the dynamic dimension. — collapse_to_dyns • Spectroscopy Analysis Tools (spant) Collapse MRS data by concatenating spectra along the dynamic dimension. — collapse_to_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -117,7 +117,7 @@ Value
diff --git a/docs/reference/comb_coils.html b/docs/reference/comb_coils.html
index 2f1cd561..9253b058 100644
--- a/docs/reference/comb_coils.html
+++ b/docs/reference/comb_coils.html
@@ -1,5 +1,5 @@
-Combine coil data based on the first data point of a reference signal. — comb_coils • Spectroscopy Analysis Tools (spant) Combine coil data based on the first data point of a reference signal. — comb_coils • Spectroscopy Analysis Tools (spant) Combine MRSI coil data using the GLS method presented by An et al JMRI 37:1445-1450 (2013). — comb_coils_mrsi_gls • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Combine MRSI coil data using the GLS method presented by An et al JMRI 37:1445-1450 (2013).
+ Source: R/mrs_data_proc.R
+ comb_coils_mrsi_gls.Rd
+
+
+
+ Combine MRSI coil data using the GLS method presented by An et al
+JMRI 37:1445-1450 (2013).
+
+
+
+ comb_coils_mrsi_gls(metab, noise_pts = 30, noise_mrs = NULL)
+
+
+
+ Arguments
+ - metab
+MRSI data containing metabolite data.
- noise_pts
+number of points from the end of the FIDs to use for noise
+covariance estimation.
- noise_mrs
+MRS data containing noise information for each coil.
+
+ Value
+
+
+coil combined MRSI data.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/comb_coils_svs_gls.html b/docs/reference/comb_coils_svs_gls.html
new file mode 100644
index 00000000..05b14d6d
--- /dev/null
+++ b/docs/reference/comb_coils_svs_gls.html
@@ -0,0 +1,145 @@
+
+Combine SVS coil data using the GLS method presented by An et al JMRI 37:1445-1450 (2013). — comb_coils_svs_gls • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Combine SVS coil data using the GLS method presented by An et al JMRI 37:1445-1450 (2013).
+ Source: R/mrs_data_proc.R
+ comb_coils_svs_gls.Rd
+
+
+
+ Combine SVS coil data using the GLS method presented by An et al
+JMRI 37:1445-1450 (2013).
+
+
+
+ comb_coils_svs_gls(
+ metab,
+ ref = NULL,
+ noise_pts = 256,
+ noise_mrs = NULL,
+ use_mean_sens = TRUE
+)
+
+
+
+ Arguments
+ - metab
+MRS data containing metabolite data.
- ref
+MRS data containing reference data (optional).
- noise_pts
+number of points from the end of the FIDs to use for noise
+covariance estimation.
- noise_mrs
+MRS data containing noise information for each coil.
- use_mean_sens
+use the dynamic mean to estimate coil sensitivities.
+
+ Value
+
+
+coil combined MRS data.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/comb_fit_list_fit_tables.html b/docs/reference/comb_fit_list_fit_tables.html
index e88c513a..098dea6e 100644
--- a/docs/reference/comb_fit_list_fit_tables.html
+++ b/docs/reference/comb_fit_list_fit_tables.html
@@ -1,5 +1,5 @@
-Combine all fitting data points from a list of fits into a single data frame. — comb_fit_list_fit_tables • Spectroscopy Analysis Tools (spant) Combine all fitting data points from a list of fits into a single data frame. — comb_fit_list_fit_tables • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -137,7 +137,7 @@ Value
diff --git a/docs/reference/comb_fit_list_result_tables.html b/docs/reference/comb_fit_list_result_tables.html
index 9a9cd20f..82008f85 100644
--- a/docs/reference/comb_fit_list_result_tables.html
+++ b/docs/reference/comb_fit_list_result_tables.html
@@ -1,5 +1,5 @@
-Combine the fit result tables from a list of fit results. — comb_fit_list_result_tables • Spectroscopy Analysis Tools (spant) Combine the fit result tables from a list of fit results. — comb_fit_list_result_tables • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -117,7 +117,7 @@ Value
diff --git a/docs/reference/comb_fit_tables.html b/docs/reference/comb_fit_tables.html
index 52315125..5ab0b533 100644
--- a/docs/reference/comb_fit_tables.html
+++ b/docs/reference/comb_fit_tables.html
@@ -1,5 +1,5 @@
-Combine all fitting data points into a single data frame. — comb_fit_tables • Spectroscopy Analysis Tools (spant) Combine all fitting data points into a single data frame. — comb_fit_tables • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -116,7 +116,7 @@ Value
diff --git a/docs/reference/comb_metab_ref.html b/docs/reference/comb_metab_ref.html
index 40474562..ac6d5555 100644
--- a/docs/reference/comb_metab_ref.html
+++ b/docs/reference/comb_metab_ref.html
@@ -1,5 +1,5 @@
-Combine a reference and metabolite mrs_data object. — comb_metab_ref • Spectroscopy Analysis Tools (spant) Combine a reference and metabolite mrs_data object. — comb_metab_ref • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/conv_mrs.html b/docs/reference/conv_mrs.html
index 3c349299..298e9810 100644
--- a/docs/reference/conv_mrs.html
+++ b/docs/reference/conv_mrs.html
@@ -1,5 +1,5 @@
-Convolve two MRS data objects. — conv_mrs • Spectroscopy Analysis Tools (spant) Convolve two MRS data objects. — conv_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/crop_basis.html b/docs/reference/crop_basis.html
index 25adfcc2..8193c2fe 100644
--- a/docs/reference/crop_basis.html
+++ b/docs/reference/crop_basis.html
@@ -1,5 +1,5 @@
-Crop basis_set object based on a frequency range. — crop_basis • Spectroscopy Analysis Tools (spant) Crop basis_set object based on a frequency range. — crop_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -116,7 +116,7 @@ Value
diff --git a/docs/reference/crop_spec.html b/docs/reference/crop_spec.html
index bac28c4b..be5e2e87 100644
--- a/docs/reference/crop_spec.html
+++ b/docs/reference/crop_spec.html
@@ -1,5 +1,5 @@
-Crop mrs_data object based on a frequency range. — crop_spec • Spectroscopy Analysis Tools (spant) Crop mrs_data object based on a frequency range. — crop_spec • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -116,7 +116,7 @@ Value
diff --git a/docs/reference/crop_td_pts.html b/docs/reference/crop_td_pts.html
index c9c4a213..c810fa4b 100644
--- a/docs/reference/crop_td_pts.html
+++ b/docs/reference/crop_td_pts.html
@@ -1,5 +1,5 @@
-Crop mrs_data object data points in the time-domain. — crop_td_pts • Spectroscopy Analysis Tools (spant) Crop mrs_data object data points in the time-domain. — crop_td_pts • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/crop_td_pts_end.html b/docs/reference/crop_td_pts_end.html
index 3560fee2..45fd251f 100644
--- a/docs/reference/crop_td_pts_end.html
+++ b/docs/reference/crop_td_pts_end.html
@@ -1,5 +1,5 @@
-Crop mrs_data object data points at the end of the FID. — crop_td_pts_end • Spectroscopy Analysis Tools (spant) Crop mrs_data object data points at the end of the FID. — crop_td_pts_end • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/crop_td_pts_pot.html b/docs/reference/crop_td_pts_pot.html
index d6c77479..4e2c39de 100644
--- a/docs/reference/crop_td_pts_pot.html
+++ b/docs/reference/crop_td_pts_pot.html
@@ -1,9 +1,5 @@
-Crop mrs_data object data points in the time-domain rounding down to
-the next smallest power of two (pot). Data that already has a pot length will
-not be changed. — crop_td_pts_pot • Spectroscopy Analysis Tools (spant) Crop mrs_data object data points in the time-domain rounding down to the next smallest power of two (pot). Data that already has a pot length will not be changed. — crop_td_pts_pot • Spectroscopy Analysis Tools (spant) Crop an MRSI dataset in the x-y direction — crop_xy • Spectroscopy Analysis Tools (spant) Crop an MRSI dataset in the x-y direction — crop_xy • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/crossprod_3d.html b/docs/reference/crossprod_3d.html
index 417852cd..eaf22eac 100644
--- a/docs/reference/crossprod_3d.html
+++ b/docs/reference/crossprod_3d.html
@@ -1,7 +1,5 @@
-Compute the vector cross product between vectors x and y. Adapted from
-http://stackoverflow.com/questions/15162741/what-is-rs-crossproduct-function — crossprod_3d • Spectroscopy Analysis Tools (spant) Compute the vector cross product between vectors x and y. Adapted from http://stackoverflow.com/questions/15162741/what-is-rs-crossproduct-function — crossprod_3d • Spectroscopy Analysis Tools (spant) Decimate an MRS signal to half the original sampling frequency by filtering
-in the frequency domain before down sampling. — decimate_mrs_fd • Spectroscopy Analysis Tools (spant) Decimate an MRS signal to half the original sampling frequency by filtering in the frequency domain before down sampling. — decimate_mrs_fd • Spectroscopy Analysis Tools (spant) Decimate an MRS signal by filtering in the time domain before downsampling. — decimate_mrs_td • Spectroscopy Analysis Tools (spant) Decimate an MRS signal by filtering in the time domain before downsampling. — decimate_mrs_td • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -118,7 +118,7 @@ Value
diff --git a/docs/reference/deconv_mrs.html b/docs/reference/deconv_mrs.html
index 1640eb61..61ad2631 100644
--- a/docs/reference/deconv_mrs.html
+++ b/docs/reference/deconv_mrs.html
@@ -1,5 +1,5 @@
-Deconvolve two MRS data objects. — deconv_mrs • Spectroscopy Analysis Tools (spant) Deconvolve two MRS data objects. — deconv_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/def_N.html b/docs/reference/def_N.html
index 1b8c28e2..204d145b 100644
--- a/docs/reference/def_N.html
+++ b/docs/reference/def_N.html
@@ -1,5 +1,5 @@
-Return the default number of data points in the spectral dimension. — def_N • Spectroscopy Analysis Tools (spant) Return the default number of data points in the spectral dimension. — def_N • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Value
diff --git a/docs/reference/def_acq_paras.html b/docs/reference/def_acq_paras.html
index e5dfddab..b06e4d22 100644
--- a/docs/reference/def_acq_paras.html
+++ b/docs/reference/def_acq_paras.html
@@ -1,7 +1,5 @@
-Return (and optionally modify using the input arguments) a list of the
-default acquisition parameters. — def_acq_paras • Spectroscopy Analysis Tools (spant) Return (and optionally modify using the input arguments) a list of the default acquisition parameters. — def_acq_paras • Spectroscopy Analysis Tools (spant) Return the default sampling frequency in Hz. — def_fs • Spectroscopy Analysis Tools (spant) Return the default sampling frequency in Hz. — def_fs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Value
diff --git a/docs/reference/def_ft.html b/docs/reference/def_ft.html
index 715f0c1f..cb7a33fb 100644
--- a/docs/reference/def_ft.html
+++ b/docs/reference/def_ft.html
@@ -1,5 +1,5 @@
-Return the default transmitter frequency in Hz. — def_ft • Spectroscopy Analysis Tools (spant) Return the default transmitter frequency in Hz. — def_ft • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Value
diff --git a/docs/reference/def_nuc.html b/docs/reference/def_nuc.html
index cfffaa97..addd88b8 100644
--- a/docs/reference/def_nuc.html
+++ b/docs/reference/def_nuc.html
@@ -1,5 +1,5 @@
-Return the default nucleus. — def_nuc • Spectroscopy Analysis Tools (spant) Return the default nucleus. — def_nuc • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Value
diff --git a/docs/reference/def_ref.html b/docs/reference/def_ref.html
index 1aed7ccf..0ff90af1 100644
--- a/docs/reference/def_ref.html
+++ b/docs/reference/def_ref.html
@@ -1,5 +1,5 @@
-Return the default reference value for ppm scale. — def_ref • Spectroscopy Analysis Tools (spant) Return the default reference value for ppm scale. — def_ref • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Value
diff --git a/docs/reference/dicom_reader.html b/docs/reference/dicom_reader.html
index f27d6e7f..0d19c93c 100644
--- a/docs/reference/dicom_reader.html
+++ b/docs/reference/dicom_reader.html
@@ -1,5 +1,5 @@
-A very simple DICOM reader. — dicom_reader • Spectroscopy Analysis Tools (spant) A very simple DICOM reader. — dicom_reader • Spectroscopy Analysis Tools (spant) Apply the diff operator to an MRS dataset in the FID/spectral dimension. — diff_mrs • Spectroscopy Analysis Tools (spant) Apply the diff operator to an MRS dataset in the FID/spectral dimension. — diff_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/downsample_mrs_fd.html b/docs/reference/downsample_mrs_fd.html
index 9974daa5..abb34365 100644
--- a/docs/reference/downsample_mrs_fd.html
+++ b/docs/reference/downsample_mrs_fd.html
@@ -1,5 +1,5 @@
-Downsample an MRS signal by a factor of 2 using an FFT "brick-wall" filter. — downsample_mrs_fd • Spectroscopy Analysis Tools (spant) Downsample an MRS signal by a factor of 2 using an FFT "brick-wall" filter. — downsample_mrs_fd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/downsample_mrs_td.html b/docs/reference/downsample_mrs_td.html
index 1a131574..c8464ac5 100644
--- a/docs/reference/downsample_mrs_td.html
+++ b/docs/reference/downsample_mrs_td.html
@@ -1,9 +1,5 @@
-Downsample an MRS signal by a factor of 2 by removing every other data point
-in the time-domain. Note, signals outside the new sampling frequency will be
-aliased. — downsample_mrs_td • Spectroscopy Analysis Tools (spant) Downsample an MRS signal by a factor of 2 by removing every other data point in the time-domain. Note, signals outside the new sampling frequency will be aliased. — downsample_mrs_td • Spectroscopy Analysis Tools (spant) Return a time scale vector of acquisition times for a dynamic MRS scan. The
-first temporal scan is assigned a value of 0. — dyn_acq_times • Spectroscopy Analysis Tools (spant) Return a time scale vector of acquisition times for a dynamic MRS scan. The first temporal scan is assigned a value of 0. — dyn_acq_times • Spectroscopy Analysis Tools (spant) Eddy current correction. — ecc • Spectroscopy Analysis Tools (spant) Eddy current correction. — ecc • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -120,7 +120,7 @@ Details
diff --git a/docs/reference/elliptical_mask.html b/docs/reference/elliptical_mask.html
index 9736c7c1..0e8f2c72 100644
--- a/docs/reference/elliptical_mask.html
+++ b/docs/reference/elliptical_mask.html
@@ -1,5 +1,5 @@
-Create an elliptical mask stored as a matrix of logical values. — elliptical_mask • Spectroscopy Analysis Tools (spant) Create an elliptical mask stored as a matrix of logical values. — elliptical_mask • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -130,7 +130,7 @@ Value
diff --git a/docs/reference/est_noise_sd.html b/docs/reference/est_noise_sd.html
index d0bcbc47..287ec04c 100644
--- a/docs/reference/est_noise_sd.html
+++ b/docs/reference/est_noise_sd.html
@@ -1,7 +1,5 @@
-Estimate the standard deviation of the noise from a segment of an mrs_data
-object. — est_noise_sd • Spectroscopy Analysis Tools (spant) Estimate the standard deviation of the noise from a segment of an mrs_data object. — est_noise_sd • Spectroscopy Analysis Tools (spant) Transform frequency-domain data to the time-domain. — fd2td • Spectroscopy Analysis Tools (spant) Transform frequency-domain data to the time-domain. — fd2td • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/fd_conv_filt.html b/docs/reference/fd_conv_filt.html
index d419e680..daf83ea8 100644
--- a/docs/reference/fd_conv_filt.html
+++ b/docs/reference/fd_conv_filt.html
@@ -1,5 +1,5 @@
-Frequency-domain convolution based filter. — fd_conv_filt • Spectroscopy Analysis Tools (spant) Frequency-domain convolution based filter. — fd_conv_filt • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -108,7 +108,7 @@ Arguments
diff --git a/docs/reference/fd_gauss_smo.html b/docs/reference/fd_gauss_smo.html
index 43fbb24b..0e6f1a96 100644
--- a/docs/reference/fd_gauss_smo.html
+++ b/docs/reference/fd_gauss_smo.html
@@ -1,5 +1,5 @@
-Apply a Gaussian smoother in the spectral domain. — fd_gauss_smo • Spectroscopy Analysis Tools (spant) Apply a Gaussian smoother in the spectral domain. — fd_gauss_smo • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/find_bids_mrs.html b/docs/reference/find_bids_mrs.html
index 81ef7726..ec9106b3 100644
--- a/docs/reference/find_bids_mrs.html
+++ b/docs/reference/find_bids_mrs.html
@@ -1,5 +1,5 @@
-Search for MRS data files in a BIDS filesystem structure. — find_bids_mrs • Spectroscopy Analysis Tools (spant) Search for MRS data files in a BIDS filesystem structure. — find_bids_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -78,7 +78,7 @@ Search for MRS data files in a BIDS filesystem structure.
- find_bids_mrs(path)
+ find_bids_mrs(path, output_full_path = FALSE)
@@ -86,6 +86,10 @@ Arguments
- path
path to the directory containing the BIDS structure.
- output_full_path
+output the full normalised data paths.
Value
@@ -106,7 +110,7 @@ Value
diff --git a/docs/reference/find_mrs_files.html b/docs/reference/find_mrs_files.html
index aa88618b..675c6ef0 100644
--- a/docs/reference/find_mrs_files.html
+++ b/docs/reference/find_mrs_files.html
@@ -1,5 +1,5 @@
-Find valid MRS data files recursively from a directory path. — find_mrs_files • Spectroscopy Analysis Tools (spant) Find valid MRS data files recursively from a directory path. — find_mrs_files • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/fit_amps.html b/docs/reference/fit_amps.html
index 2190b708..af27c9c7 100644
--- a/docs/reference/fit_amps.html
+++ b/docs/reference/fit_amps.html
@@ -1,5 +1,5 @@
-Extract the fit amplitudes from an object of class fit_result. — fit_amps • Spectroscopy Analysis Tools (spant) Extract the fit amplitudes from an object of class fit_result. — fit_amps • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -124,7 +124,7 @@ Value
diff --git a/docs/reference/fit_diags.html b/docs/reference/fit_diags.html
index 9f940ff1..b7ce449b 100644
--- a/docs/reference/fit_diags.html
+++ b/docs/reference/fit_diags.html
@@ -1,5 +1,5 @@
-Calculate diagnostic information for object of class fit_result. — fit_diags • Spectroscopy Analysis Tools (spant) Calculate diagnostic information for object of class fit_result. — fit_diags • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/fit_mrs.html b/docs/reference/fit_mrs.html
index 9eb523df..e088a98f 100644
--- a/docs/reference/fit_mrs.html
+++ b/docs/reference/fit_mrs.html
@@ -1,5 +1,5 @@
-Perform a fit based analysis of MRS data. — fit_mrs • Spectroscopy Analysis Tools (spant) Perform a fit based analysis of MRS data. — fit_mrs • Spectroscopy Analysis Tools (spant) Write fit results table to a csv file. — fit_res2csv • Spectroscopy Analysis Tools (spant) Write fit results table to a csv file. — fit_res2csv • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -108,7 +108,7 @@ Arguments
diff --git a/docs/reference/fit_t1_ti_array.html b/docs/reference/fit_t1_ti_array.html
index 5360fbc3..c8e26e48 100644
--- a/docs/reference/fit_t1_ti_array.html
+++ b/docs/reference/fit_t1_ti_array.html
@@ -1,5 +1,5 @@
-Fit a T1 recovery curve, from multiple TIs, to a set of amplitudes. — fit_t1_ti_array • Spectroscopy Analysis Tools (spant) Fit a T1 recovery curve, from multiple TIs, to a set of amplitudes. — fit_t1_ti_array • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -136,7 +136,7 @@ Value
diff --git a/docs/reference/fit_t1_tr_array.html b/docs/reference/fit_t1_tr_array.html
index 42d6961a..0a1f6cf3 100644
--- a/docs/reference/fit_t1_tr_array.html
+++ b/docs/reference/fit_t1_tr_array.html
@@ -1,5 +1,5 @@
-Fit a T1 recovery curve, from multiple TRs, to a set of amplitudes. — fit_t1_tr_array • Spectroscopy Analysis Tools (spant) Fit a T1 recovery curve, from multiple TRs, to a set of amplitudes. — fit_t1_tr_array • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -136,7 +136,7 @@ Value
diff --git a/docs/reference/fit_t2_te_array.html b/docs/reference/fit_t2_te_array.html
index abfc708c..75983e35 100644
--- a/docs/reference/fit_t2_te_array.html
+++ b/docs/reference/fit_t2_te_array.html
@@ -1,5 +1,5 @@
-Fit a T2 relaxation curve, from multiple TEs, to a set of amplitudes. — fit_t2_te_array • Spectroscopy Analysis Tools (spant) Fit a T2 relaxation curve, from multiple TEs, to a set of amplitudes. — fit_t2_te_array • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -136,7 +136,7 @@ Value
diff --git a/docs/reference/fp_phase.html b/docs/reference/fp_phase.html
index 55b65a21..5053cca5 100644
--- a/docs/reference/fp_phase.html
+++ b/docs/reference/fp_phase.html
@@ -1,5 +1,5 @@
-Return the phase of the first data point in the time-domain. — fp_phase • Spectroscopy Analysis Tools (spant) Return the phase of the first data point in the time-domain. — fp_phase • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/fp_phase_correct.html b/docs/reference/fp_phase_correct.html
index 8f847ebf..8859b25b 100644
--- a/docs/reference/fp_phase_correct.html
+++ b/docs/reference/fp_phase_correct.html
@@ -1,7 +1,5 @@
-Perform a zeroth order phase correction based on the phase of the first data
-point in the time-domain. — fp_phase_correct • Spectroscopy Analysis Tools (spant) Perform a zeroth order phase correction based on the phase of the first data point in the time-domain. — fp_phase_correct • Spectroscopy Analysis Tools (spant) Scale the first time-domain data point in an mrs_data object. — fp_scale • Spectroscopy Analysis Tools (spant) Scale the first time-domain data point in an mrs_data object. — fp_scale • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/fs.html b/docs/reference/fs.html
index 9e576eef..cd022581 100644
--- a/docs/reference/fs.html
+++ b/docs/reference/fs.html
@@ -1,5 +1,5 @@
-Return the sampling frequency in Hz of an MRS dataset. — fs • Spectroscopy Analysis Tools (spant) Return the sampling frequency in Hz of an MRS dataset. — fs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/ft_dyns.html b/docs/reference/ft_dyns.html
index de5e96a4..b8838eba 100644
--- a/docs/reference/ft_dyns.html
+++ b/docs/reference/ft_dyns.html
@@ -1,5 +1,5 @@
-Apply the Fourier transform over the dynamic dimension. — ft_dyns • Spectroscopy Analysis Tools (spant) Apply the Fourier transform over the dynamic dimension. — ft_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -119,7 +119,7 @@ Value
diff --git a/docs/reference/ft_shift.html b/docs/reference/ft_shift.html
index 7b55740b..a91d15c4 100644
--- a/docs/reference/ft_shift.html
+++ b/docs/reference/ft_shift.html
@@ -1,5 +1,5 @@
-Perform a fft and ffshift on a vector. — ft_shift • Spectroscopy Analysis Tools (spant) Perform a fft and ffshift on a vector. — ft_shift • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/ft_shift_mat.html b/docs/reference/ft_shift_mat.html
index 7009d0b9..46b6e787 100644
--- a/docs/reference/ft_shift_mat.html
+++ b/docs/reference/ft_shift_mat.html
@@ -1,7 +1,5 @@
-Perform a fft and fftshift on a matrix with each column replaced by its
-shifted fft. — ft_shift_mat • Spectroscopy Analysis Tools (spant) Perform a fft and fftshift on a matrix with each column replaced by its shifted fft. — ft_shift_mat • Spectroscopy Analysis Tools (spant) Create a two dimensional Gaussian window function stored as a matrix. — gausswin_2d • Spectroscopy Analysis Tools (spant) Create a two dimensional Gaussian window function stored as a matrix. — gausswin_2d • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -130,7 +130,7 @@ Value
diff --git a/docs/reference/gen_F.html b/docs/reference/gen_F.html
index 0eee85ab..2bdbe201 100644
--- a/docs/reference/gen_F.html
+++ b/docs/reference/gen_F.html
@@ -1,5 +1,5 @@
-Generate the F product operator. — gen_F • Spectroscopy Analysis Tools (spant) Generate the F product operator. — gen_F • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/gen_F_xy.html b/docs/reference/gen_F_xy.html
index 67c141e0..34e0242c 100644
--- a/docs/reference/gen_F_xy.html
+++ b/docs/reference/gen_F_xy.html
@@ -1,5 +1,5 @@
-Generate the Fxy product operator with a specified phase. — gen_F_xy • Spectroscopy Analysis Tools (spant) Generate the Fxy product operator with a specified phase. — gen_F_xy • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/gen_I.html b/docs/reference/gen_I.html
index 546e31e0..3b071790 100644
--- a/docs/reference/gen_I.html
+++ b/docs/reference/gen_I.html
@@ -1,5 +1,5 @@
-Generate the I product operator for a single spin. — gen_I • Spectroscopy Analysis Tools (spant) Generate the I product operator for a single spin. — gen_I • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/gen_baseline_reg.html b/docs/reference/gen_baseline_reg.html
index 499cd905..6c061185 100644
--- a/docs/reference/gen_baseline_reg.html
+++ b/docs/reference/gen_baseline_reg.html
@@ -1,5 +1,5 @@
-Generate baseline regressor. — gen_baseline_reg • Spectroscopy Analysis Tools (spant) Generate baseline regressor. — gen_baseline_reg • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -78,7 +78,7 @@ Generate baseline regressor.
- gen_baseline_reg(mrs_data)
+ gen_baseline_reg(mrs_data = NULL, tr = NULL, Ndyns = NULL, Ntrans = NULL)
@@ -86,6 +86,19 @@ Arguments
- mrs_data
mrs_data object for timing information.
- tr
+repetition time.
- Ndyns
+number of dynamic scans stored, potentially less than Ntrans
+if block averaging has been performed.
- Ntrans
+number of dynamic scans acquired.
Value
@@ -106,7 +119,7 @@ Value
diff --git a/docs/reference/gen_bold_reg.html b/docs/reference/gen_bold_reg.html
index 56bf47b9..e8755630 100644
--- a/docs/reference/gen_bold_reg.html
+++ b/docs/reference/gen_bold_reg.html
@@ -1,5 +1,5 @@
-Generate BOLD regressors. — gen_bold_reg • Spectroscopy Analysis Tools (spant) Generate BOLD regressors. — gen_bold_reg • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -83,6 +83,9 @@ Generate BOLD regressors.
duration = NULL,
trial_type = NULL,
mrs_data = NULL,
+ tr = NULL,
+ Ndyns = NULL,
+ Ntrans = NULL,
match_tr = TRUE,
dt = 0.1,
normalise = FALSE
@@ -107,6 +110,19 @@ Arguments
mrs_data object for timing information.
tr
+repetition time.
Ndyns
+number of dynamic scans stored, potentially less than Ntrans
+if block averaging has been performed.
Ntrans
+number of dynamic scans acquired.
match_tr
match the output to the input mrs_data.
Value
diff --git a/docs/reference/gen_conv_reg.html b/docs/reference/gen_conv_reg.html
index e94d6114..2a62bfc6 100644
--- a/docs/reference/gen_conv_reg.html
+++ b/docs/reference/gen_conv_reg.html
@@ -1,7 +1,5 @@
-Generate regressors by convolving a specified response function with a
-stimulus. — gen_conv_reg • Spectroscopy Analysis Tools (spant) Generate regressors by convolving a specified response function with a stimulus. — gen_conv_reg • Spectroscopy Analysis Tools (spant) Expand a regressor matrix for a group analysis. — gen_group_reg • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+
+
+ Expand a regressor matrix for a group analysis.
+
+
+
+ gen_group_reg(regressor_df, n)
+
+
+
+ Arguments
+ - regressor_df
+input regressor data frame.
- n
+number of datasets n the group.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/gen_impulse_reg.html b/docs/reference/gen_impulse_reg.html
index a900c805..b31ec7ff 100644
--- a/docs/reference/gen_impulse_reg.html
+++ b/docs/reference/gen_impulse_reg.html
@@ -1,5 +1,5 @@
-Generate impulse regressors. — gen_impulse_reg • Spectroscopy Analysis Tools (spant) Generate impulse regressors. — gen_impulse_reg • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -78,7 +78,14 @@ Generate impulse regressors.
- gen_impulse_reg(onset, trial_type = NULL, mrs_data = NULL)
+ gen_impulse_reg(
+ onset,
+ trial_type = NULL,
+ mrs_data = NULL,
+ tr = NULL,
+ Ndyns = NULL,
+ Ntrans = NULL
+)
@@ -94,6 +101,19 @@ Arguments
mrs_data
mrs_data object for timing information.
tr
+repetition time.
Ndyns
+number of dynamic scans stored, potentially less than Ntrans
+if block averaging has been performed.
Ntrans
+number of dynamic scans acquired.
Value
@@ -114,7 +134,7 @@ Value
diff --git a/docs/reference/gen_poly_reg.html b/docs/reference/gen_poly_reg.html
index 44c2aee5..e90af45c 100644
--- a/docs/reference/gen_poly_reg.html
+++ b/docs/reference/gen_poly_reg.html
@@ -1,5 +1,5 @@
-Generate polynomial regressors. — gen_poly_reg • Spectroscopy Analysis Tools (spant) Generate polynomial regressors. — gen_poly_reg • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -78,17 +78,30 @@ Generate polynomial regressors.
- gen_poly_reg(mrs_data, degree)
+ gen_poly_reg(degree, mrs_data = NULL, tr = NULL, Ndyns = NULL, Ntrans = NULL)
Arguments
- - mrs_data
+ - degree
+the degree of the polynomial.
- mrs_data
mrs_data object for timing information.
- degree
-the degree of the polynomial.
- tr
+repetition time.
- Ndyns
+number of dynamic scans stored, potentially less than Ntrans
+if block averaging has been performed.
- Ntrans
+number of dynamic scans acquired.
@@ -110,7 +123,7 @@ Value
diff --git a/docs/reference/gen_trap_reg.html b/docs/reference/gen_trap_reg.html
index 6c3d083a..d624f730 100644
--- a/docs/reference/gen_trap_reg.html
+++ b/docs/reference/gen_trap_reg.html
@@ -1,5 +1,5 @@
-Generate trapezoidal regressors. — gen_trap_reg • Spectroscopy Analysis Tools (spant) Generate trapezoidal regressors. — gen_trap_reg • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -83,6 +83,9 @@ Generate trapezoidal regressors.
duration,
trial_type = NULL,
mrs_data = NULL,
+ tr = NULL,
+ Ndyns = NULL,
+ Ntrans = NULL,
rise_t = 0,
fall_t = 0,
exp_fall = FALSE,
@@ -112,6 +115,19 @@ Arguments
mrs_data object for timing information.
tr
+repetition time.
Ndyns
+number of dynamic scans stored, potentially less than Ntrans
+if block averaging has been performed.
Ntrans
+number of dynamic scans acquired.
rise_t
time to reach a plateau from baseline in seconds.
Value
diff --git a/docs/reference/get_1h_brain_basis_names.html b/docs/reference/get_1h_brain_basis_names.html
index a8496ee7..0f940926 100644
--- a/docs/reference/get_1h_brain_basis_names.html
+++ b/docs/reference/get_1h_brain_basis_names.html
@@ -1,7 +1,5 @@
-Return a character vector of common 1H molecules found in healthy human
-brain. — get_1h_brain_basis_names • Spectroscopy Analysis Tools (spant) Return a character vector of common 1H molecules found in healthy human brain. — get_1h_brain_basis_names • Spectroscopy Analysis Tools (spant) Return a list of mol_parameter objects suitable for 1H brain MRS
-analyses. — get_1h_brain_basis_paras • Spectroscopy Analysis Tools (spant) Return a list of mol_parameter objects suitable for 1H brain MRS analyses. — get_1h_brain_basis_paras • Spectroscopy Analysis Tools (spant) Return a list of mol_parameter objects suitable for 1H brain MRS
-analyses. — get_1h_brain_basis_paras_v1 • Spectroscopy Analysis Tools (spant) Return a list of mol_parameter objects suitable for 1H brain MRS analyses. — get_1h_brain_basis_paras_v1 • Spectroscopy Analysis Tools (spant) Return a list of mol_parameter objects suitable for 1H brain MRS
-analyses. — get_1h_brain_basis_paras_v2 • Spectroscopy Analysis Tools (spant) Return a list of mol_parameter objects suitable for 1H brain MRS analyses. — get_1h_brain_basis_paras_v2 • Spectroscopy Analysis Tools (spant) Return a list of mol_parameter objects suitable for 1H brain MRS
-analyses. — get_1h_brain_basis_paras_v3 • Spectroscopy Analysis Tools (spant) Return a list of mol_parameter objects suitable for 1H brain MRS analyses. — get_1h_brain_basis_paras_v3 • Spectroscopy Analysis Tools (spant) Return a character vector of molecules included in the GE BRAINO phantom. — get_1h_braino_basis_names • Spectroscopy Analysis Tools (spant) Return a character vector of molecules included in the GE BRAINO phantom. — get_1h_braino_basis_names • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Value
diff --git a/docs/reference/get_1h_spectre_basis_names.html b/docs/reference/get_1h_spectre_basis_names.html
index 14f088ac..1a559f2e 100644
--- a/docs/reference/get_1h_spectre_basis_names.html
+++ b/docs/reference/get_1h_spectre_basis_names.html
@@ -1,7 +1,5 @@
-Return a character vector of molecules included in the Gold Star Phantoms
-SPECTRE phantom. — get_1h_spectre_basis_names • Spectroscopy Analysis Tools (spant) Return a character vector of molecules included in the Gold Star Phantoms SPECTRE phantom. — get_1h_spectre_basis_names • Spectroscopy Analysis Tools (spant) Get the point spread function (PSF) for a 2D phase encoded MRSI scan. — get_2d_psf • Spectroscopy Analysis Tools (spant) Get the point spread function (PSF) for a 2D phase encoded MRSI scan. — get_2d_psf • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -129,7 +129,7 @@ Value
diff --git a/docs/reference/get_acq_paras.html b/docs/reference/get_acq_paras.html
index 5bb919aa..3050cfff 100644
--- a/docs/reference/get_acq_paras.html
+++ b/docs/reference/get_acq_paras.html
@@ -1,5 +1,5 @@
-Return acquisition parameters from a MRS data object. — get_acq_paras • Spectroscopy Analysis Tools (spant) Return acquisition parameters from a MRS data object. — get_acq_paras • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/get_basis_subset.html b/docs/reference/get_basis_subset.html
index b7c1b5ed..08340cca 100644
--- a/docs/reference/get_basis_subset.html
+++ b/docs/reference/get_basis_subset.html
@@ -1,5 +1,5 @@
-Return a subset of the input basis. — get_basis_subset • Spectroscopy Analysis Tools (spant) Return a subset of the input basis. — get_basis_subset • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Value
diff --git a/docs/reference/get_dyns.html b/docs/reference/get_dyns.html
index d4376131..f9ef2c85 100644
--- a/docs/reference/get_dyns.html
+++ b/docs/reference/get_dyns.html
@@ -1,5 +1,5 @@
-Extract a subset of dynamic scans. — get_dyns • Spectroscopy Analysis Tools (spant) Extract a subset of dynamic scans. — get_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/get_even_dyns.html b/docs/reference/get_even_dyns.html
index 85fac0a6..8869a5aa 100644
--- a/docs/reference/get_even_dyns.html
+++ b/docs/reference/get_even_dyns.html
@@ -1,5 +1,5 @@
-Return even numbered dynamic scans starting from 1 (2,4,6...). — get_even_dyns • Spectroscopy Analysis Tools (spant) Return even numbered dynamic scans starting from 1 (2,4,6...). — get_even_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/get_fh_dyns.html b/docs/reference/get_fh_dyns.html
index 80d45928..e040408f 100644
--- a/docs/reference/get_fh_dyns.html
+++ b/docs/reference/get_fh_dyns.html
@@ -1,5 +1,5 @@
-Return the first half of a dynamic series. — get_fh_dyns • Spectroscopy Analysis Tools (spant) Return the first half of a dynamic series. — get_fh_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/get_fit_map.html b/docs/reference/get_fit_map.html
index 9584babd..0a20e465 100644
--- a/docs/reference/get_fit_map.html
+++ b/docs/reference/get_fit_map.html
@@ -1,5 +1,5 @@
-Get a data array from a fit result. — get_fit_map • Spectroscopy Analysis Tools (spant) Get a data array from a fit result. — get_fit_map • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/get_fp.html b/docs/reference/get_fp.html
index cce9f222..f6a7c7e3 100644
--- a/docs/reference/get_fp.html
+++ b/docs/reference/get_fp.html
@@ -1,5 +1,5 @@
-Return the first time-domain data point. — get_fp • Spectroscopy Analysis Tools (spant) Return the first time-domain data point. — get_fp • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/get_guassian_pulse.html b/docs/reference/get_guassian_pulse.html
index 739ef620..a6b1117c 100644
--- a/docs/reference/get_guassian_pulse.html
+++ b/docs/reference/get_guassian_pulse.html
@@ -1,5 +1,5 @@
-Generate a gaussian pulse shape. — get_guassian_pulse • Spectroscopy Analysis Tools (spant) Generate a gaussian pulse shape. — get_guassian_pulse • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -108,7 +108,7 @@ Arguments
diff --git a/docs/reference/get_head_dyns.html b/docs/reference/get_head_dyns.html
index 075c37b7..b3eea046 100644
--- a/docs/reference/get_head_dyns.html
+++ b/docs/reference/get_head_dyns.html
@@ -1,5 +1,5 @@
-Return the first scans of a dynamic series. — get_head_dyns • Spectroscopy Analysis Tools (spant) Return the first scans of a dynamic series. — get_head_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/get_lcm_cmd.html b/docs/reference/get_lcm_cmd.html
index 84ae0186..df411eaf 100644
--- a/docs/reference/get_lcm_cmd.html
+++ b/docs/reference/get_lcm_cmd.html
@@ -1,5 +1,5 @@
-Print the command to run the LCModel command-line program. — get_lcm_cmd • Spectroscopy Analysis Tools (spant) Print the command to run the LCModel command-line program. — get_lcm_cmd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -94,7 +94,7 @@ Print the command to run the LCModel command-line program.
diff --git a/docs/reference/get_metab.html b/docs/reference/get_metab.html
index 8c345609..e4777661 100644
--- a/docs/reference/get_metab.html
+++ b/docs/reference/get_metab.html
@@ -1,5 +1,5 @@
-Extract the metabolite component from an mrs_data object. — get_metab • Spectroscopy Analysis Tools (spant) Extract the metabolite component from an mrs_data object. — get_metab • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/get_mol_names.html b/docs/reference/get_mol_names.html
index ac6a75b5..44c0460f 100644
--- a/docs/reference/get_mol_names.html
+++ b/docs/reference/get_mol_names.html
@@ -1,7 +1,5 @@
-Return a character array of names that may be used with the
-get_mol_paras function. — get_mol_names • Spectroscopy Analysis Tools (spant) Return a character array of names that may be used with the get_mol_paras function. — get_mol_names • Spectroscopy Analysis Tools (spant) Get a mol_parameters object for a named molecule. — get_mol_paras • Spectroscopy Analysis Tools (spant) Get a mol_parameters object for a named molecule. — get_mol_paras • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/get_mrs_affine.html b/docs/reference/get_mrs_affine.html
index ae0672bd..1f4c519f 100644
--- a/docs/reference/get_mrs_affine.html
+++ b/docs/reference/get_mrs_affine.html
@@ -1,5 +1,5 @@
-Generate an affine for nifti generation. — get_mrs_affine • Spectroscopy Analysis Tools (spant) Generate an affine for nifti generation. — get_mrs_affine • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -118,7 +118,7 @@ Value
diff --git a/docs/reference/get_mrsi2d_seg.html b/docs/reference/get_mrsi2d_seg.html
index c8d981cd..99e56c11 100644
--- a/docs/reference/get_mrsi2d_seg.html
+++ b/docs/reference/get_mrsi2d_seg.html
@@ -1,5 +1,5 @@
-Calculate the partial volume estimates for each voxel in a 2D MRSI dataset. — get_mrsi2d_seg • Spectroscopy Analysis Tools (spant) Calculate the partial volume estimates for each voxel in a 2D MRSI dataset. — get_mrsi2d_seg • Spectroscopy Analysis Tools (spant) Generate a MRSI VOI from an mrs_data object. — get_mrsi_voi • Spectroscopy Analysis Tools (spant) Generate a MRSI VOI from an mrs_data object. — get_mrsi_voi • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -119,7 +119,7 @@ Value
diff --git a/docs/reference/get_mrsi_voxel.html b/docs/reference/get_mrsi_voxel.html
index c4255416..9f082f05 100644
--- a/docs/reference/get_mrsi_voxel.html
+++ b/docs/reference/get_mrsi_voxel.html
@@ -1,5 +1,5 @@
-Generate a MRSI voxel from an mrs_data object. — get_mrsi_voxel • Spectroscopy Analysis Tools (spant) Generate a MRSI voxel from an mrs_data object. — get_mrsi_voxel • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/get_mrsi_voxel_xy_psf.html b/docs/reference/get_mrsi_voxel_xy_psf.html
index 04c90780..1af5dfd5 100644
--- a/docs/reference/get_mrsi_voxel_xy_psf.html
+++ b/docs/reference/get_mrsi_voxel_xy_psf.html
@@ -1,5 +1,5 @@
-Generate a MRSI voxel PSF from an mrs_data object. — get_mrsi_voxel_xy_psf • Spectroscopy Analysis Tools (spant) Generate a MRSI voxel PSF from an mrs_data object. — get_mrsi_voxel_xy_psf • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/get_odd_dyns.html b/docs/reference/get_odd_dyns.html
index d016c241..498c924f 100644
--- a/docs/reference/get_odd_dyns.html
+++ b/docs/reference/get_odd_dyns.html
@@ -1,5 +1,5 @@
-Return odd numbered dynamic scans starting from 1 (1,3,5...). — get_odd_dyns • Spectroscopy Analysis Tools (spant) Return odd numbered dynamic scans starting from 1 (1,3,5...). — get_odd_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/get_ref.html b/docs/reference/get_ref.html
index d8234a92..9cf13eab 100644
--- a/docs/reference/get_ref.html
+++ b/docs/reference/get_ref.html
@@ -1,5 +1,5 @@
-Extract the reference component from an mrs_data object. — get_ref • Spectroscopy Analysis Tools (spant) Extract the reference component from an mrs_data object. — get_ref • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/get_seg_ind.html b/docs/reference/get_seg_ind.html
index e97e51ac..68eaa5f1 100644
--- a/docs/reference/get_seg_ind.html
+++ b/docs/reference/get_seg_ind.html
@@ -1,5 +1,5 @@
-Get the indices of data points lying between two values (end > x > start). — get_seg_ind • Spectroscopy Analysis Tools (spant) Get the indices of data points lying between two values (end > x > start). — get_seg_ind • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/get_sh_dyns.html b/docs/reference/get_sh_dyns.html
index 932c4247..8ea1d7be 100644
--- a/docs/reference/get_sh_dyns.html
+++ b/docs/reference/get_sh_dyns.html
@@ -1,5 +1,5 @@
-Return the second half of a dynamic series. — get_sh_dyns • Spectroscopy Analysis Tools (spant) Return the second half of a dynamic series. — get_sh_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/get_slice.html b/docs/reference/get_slice.html
index e8b9fa7e..1fb729cc 100644
--- a/docs/reference/get_slice.html
+++ b/docs/reference/get_slice.html
@@ -1,5 +1,5 @@
-Return a single slice from a larger MRSI dataset. — get_slice • Spectroscopy Analysis Tools (spant) Return a single slice from a larger MRSI dataset. — get_slice • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/get_spin_num.html b/docs/reference/get_spin_num.html
index 021d4e60..acff1245 100644
--- a/docs/reference/get_spin_num.html
+++ b/docs/reference/get_spin_num.html
@@ -1,5 +1,5 @@
-Return the spin number for a given nucleus. — get_spin_num • Spectroscopy Analysis Tools (spant) Return the spin number for a given nucleus. — get_spin_num • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/get_subset.html b/docs/reference/get_subset.html
index 34df3128..ecab116c 100644
--- a/docs/reference/get_subset.html
+++ b/docs/reference/get_subset.html
@@ -1,5 +1,5 @@
-Extract a subset of MRS data. — get_subset • Spectroscopy Analysis Tools (spant) Extract a subset of MRS data. — get_subset • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -144,7 +144,7 @@ Value
diff --git a/docs/reference/get_svs_voi.html b/docs/reference/get_svs_voi.html
index 54de4821..97437d5d 100644
--- a/docs/reference/get_svs_voi.html
+++ b/docs/reference/get_svs_voi.html
@@ -1,5 +1,5 @@
-Generate a SVS acquisition volume from an mrs_data object. — get_svs_voi • Spectroscopy Analysis Tools (spant) Generate a SVS acquisition volume from an mrs_data object. — get_svs_voi • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/get_tail_dyns.html b/docs/reference/get_tail_dyns.html
index cace1556..cee1cec3 100644
--- a/docs/reference/get_tail_dyns.html
+++ b/docs/reference/get_tail_dyns.html
@@ -1,5 +1,5 @@
-Return the last scans of a dynamic series. — get_tail_dyns • Spectroscopy Analysis Tools (spant) Return the last scans of a dynamic series. — get_tail_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/get_td_amp.html b/docs/reference/get_td_amp.html
index ad9f3f71..5e2b5814 100644
--- a/docs/reference/get_td_amp.html
+++ b/docs/reference/get_td_amp.html
@@ -1,7 +1,5 @@
-Return an array of amplitudes derived from fitting the initial points in the
-time domain and extrapolating back to t=0. — get_td_amp • Spectroscopy Analysis Tools (spant) Return an array of amplitudes derived from fitting the initial points in the time domain and extrapolating back to t=0. — get_td_amp • Spectroscopy Analysis Tools (spant) Print the command to run the TARQUIN command-line program. — get_tqn_cmd • Spectroscopy Analysis Tools (spant) Print the command to run the TARQUIN command-line program. — get_tqn_cmd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -94,7 +94,7 @@ Print the command to run the TARQUIN command-line program.
diff --git a/docs/reference/get_uncoupled_mol.html b/docs/reference/get_uncoupled_mol.html
index 0747cc21..5fd5cb69 100644
--- a/docs/reference/get_uncoupled_mol.html
+++ b/docs/reference/get_uncoupled_mol.html
@@ -1,7 +1,5 @@
-Generate a mol_parameters object for a simple spin system with one
-resonance. — get_uncoupled_mol • Spectroscopy Analysis Tools (spant) Generate a mol_parameters object for a simple spin system with one resonance. — get_uncoupled_mol • Spectroscopy Analysis Tools (spant) Calculate the centre of gravity for an image containing 0 and 1's. — get_voi_cog • Spectroscopy Analysis Tools (spant) Calculate the centre of gravity for an image containing 0 and 1's. — get_voi_cog • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/get_voi_seg.html b/docs/reference/get_voi_seg.html
index 9f0f7f44..261f5aa2 100644
--- a/docs/reference/get_voi_seg.html
+++ b/docs/reference/get_voi_seg.html
@@ -1,5 +1,5 @@
-Return the white matter, gray matter and CSF composition of a volume. — get_voi_seg • Spectroscopy Analysis Tools (spant) Return the white matter, gray matter and CSF composition of a volume. — get_voi_seg • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/get_voi_seg_psf.html b/docs/reference/get_voi_seg_psf.html
index 2e632a30..7982a0a4 100644
--- a/docs/reference/get_voi_seg_psf.html
+++ b/docs/reference/get_voi_seg_psf.html
@@ -1,5 +1,5 @@
-Return the white matter, gray matter and CSF composition of a volume. — get_voi_seg_psf • Spectroscopy Analysis Tools (spant) Return the white matter, gray matter and CSF composition of a volume. — get_voi_seg_psf • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/get_voxel.html b/docs/reference/get_voxel.html
index cb474e6c..93a4b392 100644
--- a/docs/reference/get_voxel.html
+++ b/docs/reference/get_voxel.html
@@ -1,5 +1,5 @@
-Return a single voxel from a larger mrs dataset. — get_voxel • Spectroscopy Analysis Tools (spant) Return a single voxel from a larger mrs dataset. — get_voxel • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -126,7 +126,7 @@ Value
diff --git a/docs/reference/glm_spec.html b/docs/reference/glm_spec.html
index 20459117..e767ecbf 100644
--- a/docs/reference/glm_spec.html
+++ b/docs/reference/glm_spec.html
@@ -1,5 +1,5 @@
-Perform a GLM analysis of dynamic MRS data in the spectral domain. — glm_spec • Spectroscopy Analysis Tools (spant) Perform a GLM analysis of dynamic MRS data in the spectral domain. — glm_spec • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -78,7 +78,7 @@ Perform a GLM analysis of dynamic MRS data in the spectral domain.
- glm_spec(mrs_data, regressor_df)
+ glm_spec(mrs_data, regressor_df, full_output = FALSE)
@@ -91,6 +91,10 @@ Arguments
a data frame containing temporal regressors to be applied
to each spectral datapoint.
full_output
+append mrs_data and regressor_df to the output list.
Value
@@ -111,7 +115,7 @@ Value
diff --git a/docs/reference/glm_spec_fmrs_fl.html b/docs/reference/glm_spec_fmrs_fl.html
new file mode 100644
index 00000000..30584e18
--- /dev/null
+++ b/docs/reference/glm_spec_fmrs_fl.html
@@ -0,0 +1,149 @@
+
+Perform first-level spectral GLM analysis of an fMRS dataset. — glm_spec_fmrs_fl • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Perform first-level spectral GLM analysis of an fMRS dataset.
+ Source: R/fmrs.R
+ glm_spec_fmrs_fl.Rd
+
+
+
+ Perform first-level spectral GLM analysis of an fMRS dataset.
+
+
+
+
+
+
+
+ Arguments
+ - regressor_df
+a data frame containing temporal regressors to be applied
+to each spectral datapoint.
- analysis_dir
+directory containing preprocessed data generated by
+the preproc_svs_dataset function.
- exclude_labels
+vector of labels of scans to exclude, eg poor quality
+data.
- labels
+labels to describe each data set.
- xlim
+spectral range to include in the analysis.
- vline
+vertical lines to add to the plot.
- return_results
+function will return key outputs, defaults to FALSE.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/glm_spec_fmrs_group.html b/docs/reference/glm_spec_fmrs_group.html
new file mode 100644
index 00000000..527478e5
--- /dev/null
+++ b/docs/reference/glm_spec_fmrs_group.html
@@ -0,0 +1,134 @@
+
+Perform group-level spectral GLM analysis of an fMRS dataset. — glm_spec_fmrs_group • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Perform group-level spectral GLM analysis of an fMRS dataset.
+ Source: R/fmrs.R
+ glm_spec_fmrs_group.Rd
+
+
+
+ Perform group-level spectral GLM analysis of an fMRS dataset.
+
+
+
+ glm_spec_fmrs_group(
+ regressor_df,
+ analysis_dir = "spant_analysis",
+ exclude_labels = NULL,
+ labels = NULL
+)
+
+
+
+ Arguments
+ - regressor_df
+a data frame containing temporal regressors to be applied
+to each spectral datapoint.
- analysis_dir
+directory containing preprocessed data generated by
+the preproc_svs_dataset function.
- exclude_labels
+vector of labels of scans to exclude, eg poor quality
+data.
- labels
+labels to describe each data set.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/glm_spec_group_linhyp.html b/docs/reference/glm_spec_group_linhyp.html
new file mode 100644
index 00000000..747860d9
--- /dev/null
+++ b/docs/reference/glm_spec_group_linhyp.html
@@ -0,0 +1,119 @@
+
+Test a group-level spectral GLM linear hypothesis. — glm_spec_group_linhyp • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Test a group-level spectral GLM linear hypothesis.
+ Source: R/fmrs.R
+ glm_spec_group_linhyp.Rd
+
+
+
+ Test a group-level spectral GLM linear hypothesis.
+
+
+
+ glm_spec_group_linhyp(hmat, analysis_dir = "spant_analysis")
+
+
+
+ Arguments
+ - hmat
+linear hypothesis matrix.
- analysis_dir
+directory containing preprocessed data generated by
+the preproc_svs_dataset function.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/grid_shift_xy.html b/docs/reference/grid_shift_xy.html
index 592fa3ec..d0e05b1d 100644
--- a/docs/reference/grid_shift_xy.html
+++ b/docs/reference/grid_shift_xy.html
@@ -1,5 +1,5 @@
-Grid shift MRSI data in the x/y dimension. — grid_shift_xy • Spectroscopy Analysis Tools (spant) Grid shift MRSI data in the x/y dimension. — grid_shift_xy • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/gridplot.html b/docs/reference/gridplot.html
index ca385d91..54e40afe 100644
--- a/docs/reference/gridplot.html
+++ b/docs/reference/gridplot.html
@@ -1,5 +1,5 @@
-Arrange spectral plots in a grid. — gridplot • Spectroscopy Analysis Tools (spant) Arrange spectral plots in a grid. — gridplot • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/gridplot.mrs_data.html b/docs/reference/gridplot.mrs_data.html
index 1f4d09b5..8d68edae 100644
--- a/docs/reference/gridplot.mrs_data.html
+++ b/docs/reference/gridplot.mrs_data.html
@@ -1,5 +1,5 @@
-Arrange spectral plots in a grid. — gridplot.mrs_data • Spectroscopy Analysis Tools (spant) Arrange spectral plots in a grid. — gridplot.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -139,7 +139,7 @@ Arguments
diff --git a/docs/reference/hsvd.html b/docs/reference/hsvd.html
index 25734f49..41c28be8 100644
--- a/docs/reference/hsvd.html
+++ b/docs/reference/hsvd.html
@@ -1,5 +1,5 @@
-HSVD of an mrs_data object. — hsvd • Spectroscopy Analysis Tools (spant) HSVD of an mrs_data object. — hsvd • Spectroscopy Analysis Tools (spant) HSVD based signal filter. — hsvd_filt • Spectroscopy Analysis Tools (spant) HSVD based signal filter. — hsvd_filt • Spectroscopy Analysis Tools (spant) HSVD of a complex vector. — hsvd_vec • Spectroscopy Analysis Tools (spant) HSVD of a complex vector. — hsvd_vec • Spectroscopy Analysis Tools (spant) Return the frequency scale of an MRS dataset in Hz. — hz • Spectroscopy Analysis Tools (spant) Return the frequency scale of an MRS dataset in Hz. — hz • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/ift_shift.html b/docs/reference/ift_shift.html
index 9fba4a24..168b58dd 100644
--- a/docs/reference/ift_shift.html
+++ b/docs/reference/ift_shift.html
@@ -1,5 +1,5 @@
-Perform an iffshift and ifft on a vector. — ift_shift • Spectroscopy Analysis Tools (spant) Perform an iffshift and ifft on a vector. — ift_shift • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/ift_shift_mat.html b/docs/reference/ift_shift_mat.html
index 1a7c85ca..22a75c11 100644
--- a/docs/reference/ift_shift_mat.html
+++ b/docs/reference/ift_shift_mat.html
@@ -1,7 +1,5 @@
-Perform an ifft and ifftshift on a matrix with each column replaced by its
-shifted ifft. — ift_shift_mat • Spectroscopy Analysis Tools (spant) Perform an ifft and ifftshift on a matrix with each column replaced by its shifted ifft. — ift_shift_mat • Spectroscopy Analysis Tools (spant) Image plot method for objects of class mrs_data. — image.mrs_data • Spectroscopy Analysis Tools (spant) Image plot method for objects of class mrs_data. — image.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -92,8 +92,12 @@ Image plot method for objects of class mrs_data.
coil = 1,
restore_def_par = TRUE,
y_ticks = NULL,
- vline = NULL,
hline = NULL,
+ hline_lty = 2,
+ hline_col = "white",
+ vline = NULL,
+ vline_lty = 2,
+ vline_col = "white",
legend = FALSE,
...
)
@@ -154,12 +158,28 @@ Arguments
tick marks.
+hline
+add a horizontal line at the specified value.
hline_lty
+linetype for the horizontal line.
hline_col
+colour for the horizontal line.
vline
-draw a vertical line at the value of vline.
add a vertical line at the specified value.
hline
-draw a horizontal line at the value of hline.
vline_lty
+linetype for the vertical line.
vline_col
+colour for the vertical line.
legend
@@ -184,7 +204,7 @@ Arguments
diff --git a/docs/reference/img2kspace_xy.html b/docs/reference/img2kspace_xy.html
index db04668f..4b47cc32 100644
--- a/docs/reference/img2kspace_xy.html
+++ b/docs/reference/img2kspace_xy.html
@@ -1,5 +1,5 @@
-Transform 2D MRSI data to k-space in the x-y direction. — img2kspace_xy • Spectroscopy Analysis Tools (spant) Transform 2D MRSI data to k-space in the x-y direction. — img2kspace_xy • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/index.html b/docs/reference/index.html
index 1ef7cafd..689c02a5 100644
--- a/docs/reference/index.html
+++ b/docs/reference/index.html
@@ -1,5 +1,5 @@
-Function reference • Spectroscopy Analysis Tools (spant) Function reference • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -90,8 +90,7 @@ All functions
- Complex rounding function taken from complexplus package to reduce the number
-of spant dependencies.
Complex rounding function taken from complexplus package to reduce the number of spant dependencies.
@@ -139,8 +138,7 @@ All functions
- Return a list of options for an ABfit analysis to maintain comparability with
-analyses performed with version 1.9.0 (and earlier) of spant.
Return a list of options for an ABfit analysis to maintain comparability with analyses performed with version 1.9.0 (and earlier) of spant.
@@ -168,13 +166,11 @@ All functions
- Append MRS data across the coil dimension, assumes they matched across the
-other dimensions.
Append MRS data across the coil dimension, assumes they matched across the other dimensions.
- Append MRS data across the dynamic dimension, assumes they matched across the
-other dimensions.
Append MRS data across the dynamic dimension, assumes they matched across the other dimensions.
@@ -194,14 +190,11 @@ All functions
- Convert a 7 dimensional array in into a mrs_data object. The array dimensions
-should be ordered as : dummy, X, Y, Z, dynamic, coil, FID.
Convert a 7 dimensional array in into a mrs_data object. The array dimensions should be ordered as : dummy, X, Y, Z, dynamic, coil, FID.
- Perform zeroth-order phase correction based on the minimisation of the
-squared difference between the real and magnitude components of the
-spectrum.
Perform zeroth-order phase correction based on the minimisation of the squared difference between the real and magnitude components of the spectrum.
@@ -213,13 +206,11 @@ All functions
- Convert a basis object to an mrs_data object - where basis signals are spread
-across the dynamic dimension.
Convert a basis object to an mrs_data object - where basis signals are spread across the dynamic dimension.
- Generate a spline basis, slightly adapted from : "Splines, knots, and
-penalties", Eilers 2010.
Generate a spline basis, slightly adapted from : "Splines, knots, and penalties", Eilers 2010.
@@ -243,8 +234,7 @@ All functions
- Covert a beta value in the time-domain to an equivalent linewidth in Hz:
-x * exp(-i * t * t * beta).
Covert a beta value in the time-domain to an equivalent linewidth in Hz: x * exp(-i * t * t * beta).
@@ -272,8 +262,7 @@ All functions
- Perform a polynomial fit, subtract and return the standard deviation of the
-residuals.
Perform a polynomial fit, subtract and return the standard deviation of the residuals.
@@ -306,6 +295,14 @@ All functions comb_coils()
Combine coil data based on the first data point of a reference signal.
+
+
+ Combine MRSI coil data using the GLS method presented by An et al JMRI 37:1445-1450 (2013).
+
+
+ Combine SVS coil data using the GLS method presented by An et al JMRI 37:1445-1450 (2013).
@@ -345,9 +342,7 @@ All functions
- Crop mrs_data object data points in the time-domain rounding down to
-the next smallest power of two (pot). Data that already has a pot length will
-not be changed.
Crop mrs_data object data points in the time-domain rounding down to the next smallest power of two (pot). Data that already has a pot length will not be changed.
@@ -355,13 +350,11 @@ All functions
- Compute the vector cross product between vectors x and y. Adapted from
-http://stackoverflow.com/questions/15162741/what-is-rs-crossproduct-function
Compute the vector cross product between vectors x and y. Adapted from http://stackoverflow.com/questions/15162741/what-is-rs-crossproduct-function
- Decimate an MRS signal to half the original sampling frequency by filtering
-in the frequency domain before down sampling.
Decimate an MRS signal to half the original sampling frequency by filtering in the frequency domain before down sampling.
@@ -377,8 +370,7 @@ All functions
- Return (and optionally modify using the input arguments) a list of the
-default acquisition parameters.
Return (and optionally modify using the input arguments) a list of the default acquisition parameters.
@@ -410,14 +402,11 @@ All functions
- Downsample an MRS signal by a factor of 2 by removing every other data point
-in the time-domain. Note, signals outside the new sampling frequency will be
-aliased.
Downsample an MRS signal by a factor of 2 by removing every other data point in the time-domain. Note, signals outside the new sampling frequency will be aliased.
- Return a time scale vector of acquisition times for a dynamic MRS scan. The
-first temporal scan is assigned a value of 0.
Return a time scale vector of acquisition times for a dynamic MRS scan. The first temporal scan is assigned a value of 0.
@@ -429,8 +418,7 @@ All functions
- Estimate the standard deviation of the noise from a segment of an mrs_data
-object.
Estimate the standard deviation of the noise from a segment of an mrs_data object.
@@ -486,8 +474,7 @@ All functions
- Perform a zeroth order phase correction based on the phase of the first data
-point in the time-domain.
Perform a zeroth order phase correction based on the phase of the first data point in the time-domain.
@@ -507,8 +494,7 @@ All functions
- Perform a fft and fftshift on a matrix with each column replaced by its
-shifted fft.
Perform a fft and fftshift on a matrix with each column replaced by its shifted fft.
@@ -536,8 +522,11 @@ All functions
- Generate regressors by convolving a specified response function with a
-stimulus.
Generate regressors by convolving a specified response function with a stimulus.
+
+
+ Expand a regressor matrix for a group analysis.
@@ -553,28 +542,23 @@ All functions
- Return a character vector of common 1H molecules found in healthy human
-brain.
Return a character vector of common 1H molecules found in healthy human brain.
- Return a list of mol_parameter objects suitable for 1H brain MRS
-analyses.
Return a list of mol_parameter objects suitable for 1H brain MRS analyses.
- Return a list of mol_parameter objects suitable for 1H brain MRS
-analyses.
Return a list of mol_parameter objects suitable for 1H brain MRS analyses.
- Return a list of mol_parameter objects suitable for 1H brain MRS
-analyses.
Return a list of mol_parameter objects suitable for 1H brain MRS analyses.
- Return a list of mol_parameter objects suitable for 1H brain MRS
-analyses.
Return a list of mol_parameter objects suitable for 1H brain MRS analyses.
@@ -582,8 +566,7 @@ All functions
- Return a character vector of molecules included in the Gold Star Phantoms
-SPECTRE phantom.
Return a character vector of molecules included in the Gold Star Phantoms SPECTRE phantom.
@@ -635,8 +618,7 @@ All functions
- Return a character array of names that may be used with the
-get_mol_paras function.
Return a character array of names that may be used with the get_mol_paras function.
@@ -700,8 +682,7 @@ All functions
- Return an array of amplitudes derived from fitting the initial points in the
-time domain and extrapolating back to t=0.
Return an array of amplitudes derived from fitting the initial points in the time domain and extrapolating back to t=0.
@@ -709,8 +690,7 @@ All functions
- Generate a mol_parameters object for a simple spin system with one
-resonance.
Generate a mol_parameters object for a simple spin system with one resonance.
@@ -731,6 +711,18 @@ All functions glm_spec()
Perform a GLM analysis of dynamic MRS data in the spectral domain.
+
+
+ Perform first-level spectral GLM analysis of an fMRS dataset.
+
+
+ Perform group-level spectral GLM analysis of an fMRS dataset.
+
+
+ Test a group-level spectral GLM linear hypothesis.
@@ -766,8 +758,7 @@ All functions
- Perform an ifft and ifftshift on a matrix with each column replaced by its
-shifted ifft.
Perform an ifft and ifftshift on a matrix with each column replaced by its shifted ifft.
@@ -799,8 +790,7 @@ All functions
- Check if the chemical shift dimension of an MRS data object is in the
-frequency domain.
Check if the chemical shift dimension of an MRS data object is in the frequency domain.
@@ -820,18 +810,15 @@ All functions
- Covert a linewidth in Hz to an equivalent alpha value in the time-domain ie:
-x * exp(-t * alpha).
Covert a linewidth in Hz to an equivalent alpha value in the time-domain ie: x * exp(-t * alpha).
- Covert a linewidth in Hz to an equivalent beta value in the time-domain ie:
-x * exp(-t * t * beta).
Covert a linewidth in Hz to an equivalent beta value in the time-domain ie: x * exp(-t * t * beta).
- Make a basis-set object from a directory containing LCModel formatted RAW
-files.
Make a basis-set object from a directory containing LCModel formatted RAW files.
@@ -851,8 +838,7 @@ All functions
- Mask the voxels outside an elliptical region spanning the MRSI dataset in the
-x-y plane.
Mask the voxels outside an elliptical region spanning the MRSI dataset in the x-y plane.
@@ -860,13 +846,11 @@ All functions
- Convert a matrix (with spectral points in the column dimension and dynamics
-in the row dimensions) into a mrs_data object.
Convert a matrix (with spectral points in the column dimension and dynamics in the row dimensions) into a mrs_data object.
- Matrix exponential function taken from complexplus package to reduce the
-number of spant dependencies.
Matrix exponential function taken from complexplus package to reduce the number of spant dependencies.
@@ -914,31 +898,31 @@ All functions
- Convert an mrs_data object to basis object - where basis signals are spread
-across the dynamic dimension in the MRS data.
Convert an mrs_data object to basis object - where basis signals are spread across the dynamic dimension in the MRS data.
+
+
+ Create a BIDS file structure from a vector of MRS data paths or list of mrs_data objects.
- Convert mrs_data object to a matrix, with spectral points in the column
-dimension and dynamics in the row dimension.
Convert mrs_data object to a matrix, with spectral points in the column dimension and dynamics in the row dimension.
-
+
- Convert mrs_data object to a vector.
Convert mrs_data object to a matrix, with spectral points in the column dimension and dynamics in the row dimension.
-
+
- Create a BIDS directory and file structure from a list of mrs_data objects.
Convert mrs_data object to a vector.
- Perform a fftshift on a matrix, with each column replaced by its shifted
-result.
Perform a fftshift on a matrix, with each column replaced by its shifted result.
- Perform an ifftshift on a matrix, with each column replaced by its shifted
-result.
Perform an ifftshift on a matrix, with each column replaced by its shifted result.
@@ -946,9 +930,7 @@ All functions
- Flip the x data dimension order of a nifti image. This corresponds to
-flipping MRI data in the left-right direction, assuming the data in save in
-neurological format (can check with fslorient program).
Flip the x data dimension order of a nifti image. This corresponds to flipping MRI data in the left-right direction, assuming the data in save in neurological format (can check with fslorient program).
@@ -964,8 +946,7 @@ All functions
- Search for the highest peak in a spectral region and return the frequency,
-height and FWHM.
Search for the highest peak in a spectral region and return the frequency, height and FWHM.
@@ -974,6 +955,10 @@ All functions phase()
Apply phasing parameters to MRS data.
+
+
+ Corrected zero order phase and chemical shift offset in 1H MRS data from the brain.
@@ -1005,8 +990,7 @@ All functions
- Plot an interactive slice map from a data array where voxels can be selected
-to display a corresponding spectrum.
Plot an interactive slice map from a data array where voxels can be selected to display a corresponding spectrum.
@@ -1026,8 +1010,15 @@ All functions
- Save function results to file and load on subsequent calls to avoid repeat
-computation.
Save function results to file and load on subsequent calls to avoid repeat computation.
+
+
+ Preprocess and perform quality assessment of a single SVS data set.
+
+
+ Preprocess and perform quality assessment of one or more SVS data sets.
@@ -1055,15 +1046,11 @@ All functions
- Read a directory containing Siemens MRS IMA files and combine along the coil
-dimension. Note that the coil ID is inferred from the sorted file name and
-should be checked when consistency is required between two directories.
Read a directory containing Siemens MRS IMA files and combine along the coil dimension. Note that the coil ID is inferred from the sorted file name and should be checked when consistency is required between two directories.
- Read a directory containing Siemens MRS IMA files and combine along the
-dynamic dimension. Note that the coil ID is inferred from the sorted file
-name and should be checked when consistency is required.
Read a directory containing Siemens MRS IMA files and combine along the dynamic dimension. Note that the coil ID is inferred from the sorted file name and should be checked when consistency is required.
@@ -1103,13 +1090,11 @@ All functions
- Reconstruct complex time-domain data from the real part of frequency-domain
-data.
Reconstruct complex time-domain data from the real part of frequency-domain data.
- Reconstruct complex time-domain data from the real part of frequency-domain
-data.
Reconstruct complex time-domain data from the real part of frequency-domain data.
@@ -1141,8 +1126,7 @@ All functions
- Resample a VOI to match a target image space using nearest-neighbour
-interpolation.
Resample a VOI to match a target image space using nearest-neighbour interpolation.
@@ -1158,23 +1142,19 @@ All functions
- Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water).
Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / kg of tissue water).
- Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water).
Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / kg of tissue water).
- Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / Litre of tissue).
Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / Litre of tissue).
- Convert default LCM/TARQUIN concentration scaling to molal units with partial
-volume correction.
Convert default LCM/TARQUIN concentration scaling to molal units with partial volume correction.
@@ -1222,8 +1202,7 @@ All functions
- MEGA-PRESS sequence with ideal localisation pulses and Gaussian shaped
-editing pulse.
MEGA-PRESS sequence with ideal localisation pulses and Gaussian shaped editing pulse.
@@ -1251,13 +1230,11 @@ All functions
- STEAM sequence with ideal pulses and coherence order filtering to simulate
-gradient crushers.
STEAM sequence with ideal pulses and coherence order filtering to simulate gradient crushers.
- STEAM sequence with ideal pulses using the z-rotation gradient simulation
-method described by Young et al JMR 140, 146-152 (1999).
STEAM sequence with ideal pulses using the z-rotation gradient simulation method described by Young et al JMR 140, 146-152 (1999).
@@ -1293,8 +1270,7 @@ All functions
- Set the number of time-domain data points, truncating or zero-filling as
-appropriate.
Set the number of time-domain data points, truncating or zero-filling as appropriate.
@@ -1318,18 +1294,15 @@ All functions
- Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS
-sequence. Note, ideal pulses are assumed.
Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS sequence. Note, ideal pulses are assumed.
- Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS
-sequence. Note, ideal pulses are assumed.
Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS sequence. Note, ideal pulses are assumed.
- Simulate a macromolecular and lipid basis-set suitable for 1H brain MRS
-analysis.
Simulate a macromolecular and lipid basis-set suitable for 1H brain MRS analysis.
@@ -1353,8 +1326,7 @@ All functions
- Simulate an ideal pulse excitation profile by smoothing a top-hat function
-with a Gaussian.
Simulate an ideal pulse excitation profile by smoothing a top-hat function with a Gaussian.
@@ -1374,17 +1346,19 @@ All functions
- Simulate and fit some spectra with ABfit for benchmarking purposes. Basic
-timing and performance metrics will be printed.
Simulate and fit some spectra with ABfit for benchmarking purposes. Basic timing and performance metrics will be printed.
Example MEGA-PRESS data with significant B0 drift.
+
+
+ Simulate an example fMRS dataset for a block design fMRS experiment and export a BIDS structure.
- Simulate a typical metabolite basis set for benchmarking. Timing metrics will
-be printed on completion.
Simulate a typical metabolite basis set for benchmarking. Timing metrics will be printed on completion.
@@ -1400,8 +1374,7 @@ All functions
- Convert SPM style segmentation files to a single categorical image where
-the numerical values map as: 0) Other, 1) CSF, 2) GM and 3) WM.
Convert SPM style segmentation files to a single categorical image where the numerical values map as: 0) Other, 1) CSF, 2) GM and 3) WM.
@@ -1413,8 +1386,7 @@ All functions
- Plot the fitting results of an object of class fit_result with
-individual basis set components shown.
Plot the fitting results of an object of class fit_result with individual basis set components shown.
@@ -1459,6 +1431,10 @@ All functions svs_1h_brain_batch_analysis()
Batch interface to the standard SVS 1H brain analysis pipeline.
+
+
+ Perform a t-test on spectral data points.
@@ -1518,8 +1494,7 @@ All functions
- Fade a spectrum to zero by frequency domain multiplication with a tanh
-function. Note this operation distorts data points at the end of the FID.
Fade a spectrum to zero by frequency domain multiplication with a tanh function. Note this operation distorts data points at the end of the FID.
@@ -1549,7 +1524,7 @@ All functions
diff --git a/docs/reference/int_spec.html b/docs/reference/int_spec.html
index c7060fe7..783325a8 100644
--- a/docs/reference/int_spec.html
+++ b/docs/reference/int_spec.html
@@ -1,5 +1,5 @@
-Integrate a spectral region. — int_spec • Spectroscopy Analysis Tools (spant) Integrate a spectral region. — int_spec • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -118,7 +118,7 @@ Value
diff --git a/docs/reference/interleave_dyns.html b/docs/reference/interleave_dyns.html
index effe5543..441eff27 100644
--- a/docs/reference/interleave_dyns.html
+++ b/docs/reference/interleave_dyns.html
@@ -1,5 +1,5 @@
-Interleave the first and second half of a dynamic series. — interleave_dyns • Spectroscopy Analysis Tools (spant) Interleave the first and second half of a dynamic series. — interleave_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/inv_even_dyns.html b/docs/reference/inv_even_dyns.html
index 9f9d4fff..dcb781dc 100644
--- a/docs/reference/inv_even_dyns.html
+++ b/docs/reference/inv_even_dyns.html
@@ -1,5 +1,5 @@
-Invert even numbered dynamic scans starting from 1 (2,4,6...). — inv_even_dyns • Spectroscopy Analysis Tools (spant) Invert even numbered dynamic scans starting from 1 (2,4,6...). — inv_even_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/inv_odd_dyns.html b/docs/reference/inv_odd_dyns.html
index 26212e2b..78d64660 100644
--- a/docs/reference/inv_odd_dyns.html
+++ b/docs/reference/inv_odd_dyns.html
@@ -1,5 +1,5 @@
-Invert odd numbered dynamic scans starting from 1 (1,3,5...). — inv_odd_dyns • Spectroscopy Analysis Tools (spant) Invert odd numbered dynamic scans starting from 1 (1,3,5...). — inv_odd_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/is.def.html b/docs/reference/is.def.html
index f196ffd0..a67b9eba 100644
--- a/docs/reference/is.def.html
+++ b/docs/reference/is.def.html
@@ -1,5 +1,5 @@
-Check if an object is defined, which is the same as being not NULL. — is.def • Spectroscopy Analysis Tools (spant) Check if an object is defined, which is the same as being not NULL. — is.def • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/is_fd.html b/docs/reference/is_fd.html
index 3b0ca165..18a193aa 100644
--- a/docs/reference/is_fd.html
+++ b/docs/reference/is_fd.html
@@ -1,7 +1,5 @@
-Check if the chemical shift dimension of an MRS data object is in the
-frequency domain. — is_fd • Spectroscopy Analysis Tools (spant) Check if the chemical shift dimension of an MRS data object is in the frequency domain. — is_fd • Spectroscopy Analysis Tools (spant) Transform 2D MRSI data from k-space to image space in the x-y direction. — kspace2img_xy • Spectroscopy Analysis Tools (spant) Transform 2D MRSI data from k-space to image space in the x-y direction. — kspace2img_xy • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/l2_reg.html b/docs/reference/l2_reg.html
index 3d781d80..21aa9849 100644
--- a/docs/reference/l2_reg.html
+++ b/docs/reference/l2_reg.html
@@ -1,5 +1,5 @@
-Perform l2 regularisation artefact suppression. — l2_reg • Spectroscopy Analysis Tools (spant) Perform l2 regularisation artefact suppression. — l2_reg • Spectroscopy Analysis Tools (spant) Apply line-broadening (apodisation) to MRS data or basis object. — lb • Spectroscopy Analysis Tools (spant) Apply line-broadening (apodisation) to MRS data or basis object. — lb • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -123,7 +123,7 @@ Value
diff --git a/docs/reference/lofdc.html b/docs/reference/lofdc.html
index 5419b1ec..31347a25 100644
--- a/docs/reference/lofdc.html
+++ b/docs/reference/lofdc.html
@@ -1,5 +1,5 @@
-Correct linear frequency drift. — lofdc • Spectroscopy Analysis Tools (spant) Correct linear frequency drift. — lofdc • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -138,7 +138,7 @@ Value
diff --git a/docs/reference/lw2alpha.html b/docs/reference/lw2alpha.html
index b83db682..25da229b 100644
--- a/docs/reference/lw2alpha.html
+++ b/docs/reference/lw2alpha.html
@@ -1,7 +1,5 @@
-Covert a linewidth in Hz to an equivalent alpha value in the time-domain ie:
-x * exp(-t * alpha). — lw2alpha • Spectroscopy Analysis Tools (spant) Covert a linewidth in Hz to an equivalent alpha value in the time-domain ie: x * exp(-t * alpha). — lw2alpha • Spectroscopy Analysis Tools (spant) Covert a linewidth in Hz to an equivalent beta value in the time-domain ie:
-x * exp(-t * t * beta). — lw2beta • Spectroscopy Analysis Tools (spant) Covert a linewidth in Hz to an equivalent beta value in the time-domain ie: x * exp(-t * t * beta). — lw2beta • Spectroscopy Analysis Tools (spant) Make a basis-set object from a directory containing LCModel formatted RAW
-files. — make_basis_from_raw • Spectroscopy Analysis Tools (spant) Make a basis-set object from a directory containing LCModel formatted RAW files. — make_basis_from_raw • Spectroscopy Analysis Tools (spant) Mask an MRS dataset in the dynamic dimension. — mask_dyns • Spectroscopy Analysis Tools (spant) Mask an MRS dataset in the dynamic dimension. — mask_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/mask_fit_res.html b/docs/reference/mask_fit_res.html
index 97baaa3f..ebd91a99 100644
--- a/docs/reference/mask_fit_res.html
+++ b/docs/reference/mask_fit_res.html
@@ -1,5 +1,5 @@
-Mask fit result spectra depending on a vector of bool values. — mask_fit_res • Spectroscopy Analysis Tools (spant) Mask fit result spectra depending on a vector of bool values. — mask_fit_res • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -116,7 +116,7 @@ Value
diff --git a/docs/reference/mask_xy.html b/docs/reference/mask_xy.html
index 11bb577c..b0d38619 100644
--- a/docs/reference/mask_xy.html
+++ b/docs/reference/mask_xy.html
@@ -1,5 +1,5 @@
-Mask an MRSI dataset in the x-y direction — mask_xy • Spectroscopy Analysis Tools (spant) Mask an MRSI dataset in the x-y direction — mask_xy • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/mask_xy_corners.html b/docs/reference/mask_xy_corners.html
index 09b16cd2..2d13839d 100644
--- a/docs/reference/mask_xy_corners.html
+++ b/docs/reference/mask_xy_corners.html
@@ -1,5 +1,5 @@
-Mask the four corners of an MRSI dataset in the x-y plane. — mask_xy_corners • Spectroscopy Analysis Tools (spant) Mask the four corners of an MRSI dataset in the x-y plane. — mask_xy_corners • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/mask_xy_ellipse.html b/docs/reference/mask_xy_ellipse.html
index 1d8b02e4..e2e749ef 100644
--- a/docs/reference/mask_xy_ellipse.html
+++ b/docs/reference/mask_xy_ellipse.html
@@ -1,7 +1,5 @@
-Mask the voxels outside an elliptical region spanning the MRSI dataset in the
-x-y plane. — mask_xy_ellipse • Spectroscopy Analysis Tools (spant) Mask the voxels outside an elliptical region spanning the MRSI dataset in the x-y plane. — mask_xy_ellipse • Spectroscopy Analysis Tools (spant) Mask a 2D MRSI dataset in the x-y dimension. — mask_xy_mat • Spectroscopy Analysis Tools (spant) Mask a 2D MRSI dataset in the x-y dimension. — mask_xy_mat • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Value
diff --git a/docs/reference/mat2mrs_data.html b/docs/reference/mat2mrs_data.html
index 2e2895f3..ae55665f 100644
--- a/docs/reference/mat2mrs_data.html
+++ b/docs/reference/mat2mrs_data.html
@@ -1,7 +1,5 @@
-Convert a matrix (with spectral points in the column dimension and dynamics
-in the row dimensions) into a mrs_data object. — mat2mrs_data • Spectroscopy Analysis Tools (spant) Convert a matrix (with spectral points in the column dimension and dynamics in the row dimensions) into a mrs_data object. — mat2mrs_data • Spectroscopy Analysis Tools (spant) Matrix exponential function taken from complexplus package to reduce the
-number of spant dependencies. — matexp • Spectroscopy Analysis Tools (spant) Matrix exponential function taken from complexplus package to reduce the number of spant dependencies. — matexp • Spectroscopy Analysis Tools (spant) Apply the max operator to an MRS dataset. — max_mrs • Spectroscopy Analysis Tools (spant) Apply the max operator to an MRS dataset. — max_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/max_mrs_interp.html b/docs/reference/max_mrs_interp.html
index e4474764..52e63f3e 100644
--- a/docs/reference/max_mrs_interp.html
+++ b/docs/reference/max_mrs_interp.html
@@ -1,5 +1,5 @@
-Apply the max operator to an interpolated MRS dataset. — max_mrs_interp • Spectroscopy Analysis Tools (spant) Apply the max operator to an interpolated MRS dataset. — max_mrs_interp • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/mean.list.html b/docs/reference/mean.list.html
index b8eb3463..048306fd 100644
--- a/docs/reference/mean.list.html
+++ b/docs/reference/mean.list.html
@@ -1,5 +1,5 @@
-Calculate the mean spectrum from an mrs_data object. — mean.list • Spectroscopy Analysis Tools (spant) Calculate the mean spectrum from an mrs_data object. — mean.list • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/mean.mrs_data.html b/docs/reference/mean.mrs_data.html
index 5531a28d..79515014 100644
--- a/docs/reference/mean.mrs_data.html
+++ b/docs/reference/mean.mrs_data.html
@@ -1,5 +1,5 @@
-Calculate the mean spectrum from an mrs_data object. — mean.mrs_data • Spectroscopy Analysis Tools (spant) Calculate the mean spectrum from an mrs_data object. — mean.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/mean_dyn_blocks.html b/docs/reference/mean_dyn_blocks.html
index 10467098..4c042448 100644
--- a/docs/reference/mean_dyn_blocks.html
+++ b/docs/reference/mean_dyn_blocks.html
@@ -1,5 +1,5 @@
-Calculate the mean of adjacent dynamic scans. — mean_dyn_blocks • Spectroscopy Analysis Tools (spant) Calculate the mean of adjacent dynamic scans. — mean_dyn_blocks • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/mean_dyn_pairs.html b/docs/reference/mean_dyn_pairs.html
index 63e909ea..1a241126 100644
--- a/docs/reference/mean_dyn_pairs.html
+++ b/docs/reference/mean_dyn_pairs.html
@@ -1,5 +1,5 @@
-Calculate the pairwise means across a dynamic data set. — mean_dyn_pairs • Spectroscopy Analysis Tools (spant) Calculate the pairwise means across a dynamic data set. — mean_dyn_pairs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/mean_dyns.html b/docs/reference/mean_dyns.html
index 73fdbfa7..0daa27df 100644
--- a/docs/reference/mean_dyns.html
+++ b/docs/reference/mean_dyns.html
@@ -1,5 +1,5 @@
-Calculate the mean dynamic data. — mean_dyns • Spectroscopy Analysis Tools (spant) Calculate the mean dynamic data. — mean_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/mean_mrs_list.html b/docs/reference/mean_mrs_list.html
index 808b6c50..10d842c0 100644
--- a/docs/reference/mean_mrs_list.html
+++ b/docs/reference/mean_mrs_list.html
@@ -1,5 +1,5 @@
-Return the mean of a list of mrs_data objects. — mean_mrs_list • Spectroscopy Analysis Tools (spant) Return the mean of a list of mrs_data objects. — mean_mrs_list • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/mean_vec_blocks.html b/docs/reference/mean_vec_blocks.html
index 8fc92eaa..dd78b122 100644
--- a/docs/reference/mean_vec_blocks.html
+++ b/docs/reference/mean_vec_blocks.html
@@ -1,5 +1,5 @@
-Calculate the mean of adjacent blocks in a vector. — mean_vec_blocks • Spectroscopy Analysis Tools (spant) Calculate the mean of adjacent blocks in a vector. — mean_vec_blocks • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/median_dyns.html b/docs/reference/median_dyns.html
index 1039d4b5..9a085b10 100644
--- a/docs/reference/median_dyns.html
+++ b/docs/reference/median_dyns.html
@@ -1,5 +1,5 @@
-Calculate the median dynamic data. — median_dyns • Spectroscopy Analysis Tools (spant) Calculate the median dynamic data. — median_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/mod_td.html b/docs/reference/mod_td.html
index 76ad0a40..141ef09e 100644
--- a/docs/reference/mod_td.html
+++ b/docs/reference/mod_td.html
@@ -1,5 +1,5 @@
-Apply the Modulus operator to the time-domain MRS signal. — mod_td • Spectroscopy Analysis Tools (spant) Apply the Modulus operator to the time-domain MRS signal. — mod_td • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/mrs_data2basis.html b/docs/reference/mrs_data2basis.html
index 62f7d749..11797b91 100644
--- a/docs/reference/mrs_data2basis.html
+++ b/docs/reference/mrs_data2basis.html
@@ -1,7 +1,5 @@
-Convert an mrs_data object to basis object - where basis signals are spread
-across the dynamic dimension in the MRS data. — mrs_data2basis • Spectroscopy Analysis Tools (spant) Convert an mrs_data object to basis object - where basis signals are spread across the dynamic dimension in the MRS data. — mrs_data2basis • Spectroscopy Analysis Tools (spant) Create a BIDS file structure from a vector of MRS data paths or list of mrs_data objects. — mrs_data2bids • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Create a BIDS file structure from a vector of MRS data paths or list of mrs_data objects.
+ Source: R/fmrs.R
+ mrs_data2bids.Rd
+
+
+
+ Create a BIDS file structure from a vector of MRS data paths or list of
+mrs_data objects.
+
+
+
+ mrs_data2bids(
+ mrs_data,
+ output_dir,
+ suffix = NULL,
+ sub = NULL,
+ ses = NULL,
+ task = NULL,
+ acq = NULL,
+ nuc = NULL,
+ voi = NULL,
+ rec = NULL,
+ run = NULL,
+ echo = NULL,
+ inv = NULL,
+ skip_existing = TRUE
+)
+
+
+
+ Arguments
+ - mrs_data
+vector of MRS data paths or list of mrs_data objects.
- output_dir
+the base directory to create the BIDS structure.
- suffix
+optional vector of file suffixes. Default behaviour is to
+automatically determine these from the input data, however it is recommended
+that they are specified to allow more efficient skipping of existing data.
- sub
+optional vector of subject labels. If not specified, these will be
+automatically generated as a series of increasing zero-padded integer values
+corresponding to the mrs_data input indices.
- ses
+optional vector of session labels.
- task
+optional vector of task labels.
- acq
+optional vector of acquisition labels.
- nuc
+optional vector of nucleus labels.
- voi
+optional vector of volume of interest labels.
- rec
+optional vector of reconstruction labels.
- run
+optional vector of run indices.
- echo
+optional vector of echo time indices.
- inv
+optional vector of inversion indices.
- skip_existing
+skip any data files that have already been converted.
+Defaults to TRUE, set to FALSE to force an overwrite of any existing data
+files.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/mrs_data2mat.html b/docs/reference/mrs_data2mat.html
index cf5ff28c..9e47688a 100644
--- a/docs/reference/mrs_data2mat.html
+++ b/docs/reference/mrs_data2mat.html
@@ -1,7 +1,5 @@
-Convert mrs_data object to a matrix, with spectral points in the column
-dimension and dynamics in the row dimension. — mrs_data2mat • Spectroscopy Analysis Tools (spant) Convert mrs_data object to a matrix, with spectral points in the column dimension and dynamics in the row dimension. — mrs_data2mat • Spectroscopy Analysis Tools (spant) Convert mrs_data object to a matrix, with spectral points in the column dimension and dynamics in the row dimension. — mrs_data2spec_mat • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Convert mrs_data object to a matrix, with spectral points in the column dimension and dynamics in the row dimension.
+ Source: R/mrs_data_proc.R
+ mrs_data2spec_mat.Rd
+
+
+
+ Convert mrs_data object to a matrix, with spectral points in the column
+dimension and dynamics in the row dimension.
+
+
+
+ mrs_data2spec_mat(mrs_data, collapse = TRUE)
+
+
+
+ Arguments
+ - mrs_data
+MRS data object or list of MRS data objects.
- collapse
+collapse all other dimensions along the dynamic dimension, eg
+a 16x16 MRSI grid would be first collapsed across 256 dynamic scans.
+
+ Value
+
+
+MRS data matrix.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/mrs_data2vec.html b/docs/reference/mrs_data2vec.html
index fb172d68..a1fd654d 100644
--- a/docs/reference/mrs_data2vec.html
+++ b/docs/reference/mrs_data2vec.html
@@ -1,5 +1,5 @@
-Convert mrs_data object to a vector. — mrs_data2vec • Spectroscopy Analysis Tools (spant) Convert mrs_data object to a vector. — mrs_data2vec • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -126,7 +126,7 @@ Value
diff --git a/docs/reference/mvfftshift.html b/docs/reference/mvfftshift.html
index 92b0841b..976b3410 100644
--- a/docs/reference/mvfftshift.html
+++ b/docs/reference/mvfftshift.html
@@ -1,7 +1,5 @@
-Perform a fftshift on a matrix, with each column replaced by its shifted
-result. — mvfftshift • Spectroscopy Analysis Tools (spant) Perform a fftshift on a matrix, with each column replaced by its shifted result. — mvfftshift • Spectroscopy Analysis Tools (spant) Perform an ifftshift on a matrix, with each column replaced by its shifted
-result. — mvifftshift • Spectroscopy Analysis Tools (spant) Perform an ifftshift on a matrix, with each column replaced by its shifted result. — mvifftshift • Spectroscopy Analysis Tools (spant) Print fit coordinates from a single index. — n2coord • Spectroscopy Analysis Tools (spant) Print fit coordinates from a single index. — n2coord • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/nifti_flip_lr.html b/docs/reference/nifti_flip_lr.html
index 730abe3c..19860b3c 100644
--- a/docs/reference/nifti_flip_lr.html
+++ b/docs/reference/nifti_flip_lr.html
@@ -1,9 +1,5 @@
-Flip the x data dimension order of a nifti image. This corresponds to
-flipping MRI data in the left-right direction, assuming the data in save in
-neurological format (can check with fslorient program). — nifti_flip_lr • Spectroscopy Analysis Tools (spant) Flip the x data dimension order of a nifti image. This corresponds to flipping MRI data in the left-right direction, assuming the data in save in neurological format (can check with fslorient program). — nifti_flip_lr • Spectroscopy Analysis Tools (spant) Export a one-page pdf of a single fit result — one_page_pdf • Spectroscopy Analysis Tools (spant) Export a one-page pdf of a single fit result — one_page_pdf • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -108,7 +108,7 @@ Arguments
diff --git a/docs/reference/ortho3.html b/docs/reference/ortho3.html
index 13ade97d..5d7dd2fd 100644
--- a/docs/reference/ortho3.html
+++ b/docs/reference/ortho3.html
@@ -1,5 +1,5 @@
-Display an orthographic projection plot of a nifti object. — ortho3 • Spectroscopy Analysis Tools (spant) Display an orthographic projection plot of a nifti object. — ortho3 • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -172,7 +172,7 @@ Arguments
diff --git a/docs/reference/ortho3_inter.html b/docs/reference/ortho3_inter.html
index 090cc5e5..15948899 100644
--- a/docs/reference/ortho3_inter.html
+++ b/docs/reference/ortho3_inter.html
@@ -1,5 +1,5 @@
-Display an interactive orthographic projection plot of a nifti object. — ortho3_inter • Spectroscopy Analysis Tools (spant) Display an interactive orthographic projection plot of a nifti object. — ortho3_inter • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -132,7 +132,7 @@ Arguments
diff --git a/docs/reference/peak_info.html b/docs/reference/peak_info.html
index 09058bd8..41c8ffaf 100644
--- a/docs/reference/peak_info.html
+++ b/docs/reference/peak_info.html
@@ -1,7 +1,5 @@
-Search for the highest peak in a spectral region and return the frequency,
-height and FWHM. — peak_info • Spectroscopy Analysis Tools (spant) Search for the highest peak in a spectral region and return the frequency, height and FWHM. — peak_info • Spectroscopy Analysis Tools (spant) Papoulis-Gerchberg (PG) algorithm method for k-space extrapolation. — pg_extrap_xy • Spectroscopy Analysis Tools (spant) Papoulis-Gerchberg (PG) algorithm method for k-space extrapolation. — pg_extrap_xy • Spectroscopy Analysis Tools (spant) Apply phasing parameters to MRS data. — phase • Spectroscopy Analysis Tools (spant) Apply phasing parameters to MRS data. — phase • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/phase_ref_1h_brain.html b/docs/reference/phase_ref_1h_brain.html
new file mode 100644
index 00000000..8707a74a
--- /dev/null
+++ b/docs/reference/phase_ref_1h_brain.html
@@ -0,0 +1,131 @@
+
+Corrected zero order phase and chemical shift offset in 1H MRS data from the brain. — phase_ref_1h_brain • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Corrected zero order phase and chemical shift offset in 1H MRS data from the brain.
+ Source: R/rats.R
+ phase_ref_1h_brain.Rd
+
+
+
+ Corrected zero order phase and chemical shift offset in 1H MRS data from the
+brain.
+
+
+
+ phase_ref_1h_brain(mrs_data, mean_ref = FALSE, ret_corr_only = TRUE)
+
+
+
+ Arguments
+ - mrs_data
+MRS data to be corrected.
- mean_ref
+apply the phase and offset of the mean spectrum to all
+others. Default is FALSE.
- ret_corr_only
+return the corrected data only.
+
+ Value
+
+
+corrected MRS data.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/plot.fit_result.html b/docs/reference/plot.fit_result.html
index e54d3bc1..836a53ee 100644
--- a/docs/reference/plot.fit_result.html
+++ b/docs/reference/plot.fit_result.html
@@ -1,5 +1,5 @@
-Plot the fitting results of an object of class fit_result. — plot.fit_result • Spectroscopy Analysis Tools (spant) Plot the fitting results of an object of class fit_result. — plot.fit_result • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -207,7 +207,7 @@ Arguments
diff --git a/docs/reference/plot.mrs_data.html b/docs/reference/plot.mrs_data.html
index fabcc35b..bb2ec651 100644
--- a/docs/reference/plot.mrs_data.html
+++ b/docs/reference/plot.mrs_data.html
@@ -1,5 +1,5 @@
-Plotting method for objects of class mrs_data. — plot.mrs_data • Spectroscopy Analysis Tools (spant) Plotting method for objects of class mrs_data. — plot.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -287,7 +287,7 @@ Arguments
diff --git a/docs/reference/plot_bc.html b/docs/reference/plot_bc.html
index 4f8309b4..b48142cc 100644
--- a/docs/reference/plot_bc.html
+++ b/docs/reference/plot_bc.html
@@ -1,5 +1,5 @@
-Convenience function to plot a baseline estimate with the original data. — plot_bc • Spectroscopy Analysis Tools (spant) Convenience function to plot a baseline estimate with the original data. — plot_bc • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -108,7 +108,7 @@ Arguments
diff --git a/docs/reference/plot_reg.html b/docs/reference/plot_reg.html
index ae1acbe7..2addb2f6 100644
--- a/docs/reference/plot_reg.html
+++ b/docs/reference/plot_reg.html
@@ -1,5 +1,5 @@
-Plot regressors as an image. — plot_reg • Spectroscopy Analysis Tools (spant) Plot regressors as an image. — plot_reg • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/plot_slice_fit.html b/docs/reference/plot_slice_fit.html
index fbc7b560..57f1af8a 100644
--- a/docs/reference/plot_slice_fit.html
+++ b/docs/reference/plot_slice_fit.html
@@ -1,5 +1,5 @@
-Plot a 2D slice from an MRSI fit result object. — plot_slice_fit • Spectroscopy Analysis Tools (spant) Plot a 2D slice from an MRSI fit result object. — plot_slice_fit • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -129,7 +129,7 @@ Arguments
diff --git a/docs/reference/plot_slice_fit_inter.html b/docs/reference/plot_slice_fit_inter.html
index 4eed104a..da105a7d 100644
--- a/docs/reference/plot_slice_fit_inter.html
+++ b/docs/reference/plot_slice_fit_inter.html
@@ -1,5 +1,5 @@
-Plot a 2D slice from an MRSI fit result object. — plot_slice_fit_inter • Spectroscopy Analysis Tools (spant) Plot a 2D slice from an MRSI fit result object. — plot_slice_fit_inter • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -134,7 +134,7 @@ Arguments
diff --git a/docs/reference/plot_slice_map.html b/docs/reference/plot_slice_map.html
index 553e9ac8..ffb2a134 100644
--- a/docs/reference/plot_slice_map.html
+++ b/docs/reference/plot_slice_map.html
@@ -1,5 +1,5 @@
-Plot a slice from a 7 dimensional array. — plot_slice_map • Spectroscopy Analysis Tools (spant) Plot a slice from a 7 dimensional array. — plot_slice_map • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -153,7 +153,7 @@ Arguments
diff --git a/docs/reference/plot_slice_map_inter.html b/docs/reference/plot_slice_map_inter.html
index 40d33b42..90968f66 100644
--- a/docs/reference/plot_slice_map_inter.html
+++ b/docs/reference/plot_slice_map_inter.html
@@ -1,7 +1,5 @@
-Plot an interactive slice map from a data array where voxels can be selected
-to display a corresponding spectrum. — plot_slice_map_inter • Spectroscopy Analysis Tools (spant) Plot an interactive slice map from a data array where voxels can be selected to display a corresponding spectrum. — plot_slice_map_inter • Spectroscopy Analysis Tools (spant) Plot the spectral standard deviation. — plot_spec_sd • Spectroscopy Analysis Tools (spant) Plot the spectral standard deviation. — plot_spec_sd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Arguments
diff --git a/docs/reference/plot_voi_overlay.html b/docs/reference/plot_voi_overlay.html
index 9a782e88..bbbbf35e 100644
--- a/docs/reference/plot_voi_overlay.html
+++ b/docs/reference/plot_voi_overlay.html
@@ -1,5 +1,5 @@
-Plot a volume as an image overlay. — plot_voi_overlay • Spectroscopy Analysis Tools (spant) Plot a volume as an image overlay. — plot_voi_overlay • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -116,7 +116,7 @@ Arguments
diff --git a/docs/reference/plot_voi_overlay_seg.html b/docs/reference/plot_voi_overlay_seg.html
index 3d4e74ff..0e800ff2 100644
--- a/docs/reference/plot_voi_overlay_seg.html
+++ b/docs/reference/plot_voi_overlay_seg.html
@@ -1,5 +1,5 @@
-Plot a volume as an overlay on a segmented brain volume. — plot_voi_overlay_seg • Spectroscopy Analysis Tools (spant) Plot a volume as an overlay on a segmented brain volume. — plot_voi_overlay_seg • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Arguments
diff --git a/docs/reference/ppm.html b/docs/reference/ppm.html
index c352327a..ee4696e2 100644
--- a/docs/reference/ppm.html
+++ b/docs/reference/ppm.html
@@ -1,5 +1,5 @@
-Return the ppm scale of an MRS dataset or fit result. — ppm • Spectroscopy Analysis Tools (spant) Return the ppm scale of an MRS dataset or fit result. — ppm • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -132,7 +132,7 @@ Value
diff --git a/docs/reference/precomp.html b/docs/reference/precomp.html
index 822d7336..df3d2c6c 100644
--- a/docs/reference/precomp.html
+++ b/docs/reference/precomp.html
@@ -1,7 +1,5 @@
-Save function results to file and load on subsequent calls to avoid repeat
-computation. — precomp • Spectroscopy Analysis Tools (spant) Save function results to file and load on subsequent calls to avoid repeat computation. — precomp • Spectroscopy Analysis Tools (spant) Preprocess and perform quality assessment of a single SVS data set. — preproc_svs • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Preprocess and perform quality assessment of a single SVS data set.
+ Source: R/fmrs.R
+ preproc_svs.Rd
+
+
+
+ Preprocess and perform quality assessment of a single SVS data set.
+
+
+
+ preproc_svs(path, label = NULL, output_dir = NULL, ref_inds = NULL)
+
+
+
+ Arguments
+ - path
+path to the fMRS data file or IMA directory.
- label
+a label to describe the data set.
- output_dir
+output directory.
- ref_inds
+a vector of 1-based indices for any water reference dynamic
+scans.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/preproc_svs_dataset.html b/docs/reference/preproc_svs_dataset.html
new file mode 100644
index 00000000..07c3a29b
--- /dev/null
+++ b/docs/reference/preproc_svs_dataset.html
@@ -0,0 +1,148 @@
+
+Preprocess and perform quality assessment of one or more SVS data sets. — preproc_svs_dataset • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Preprocess and perform quality assessment of one or more SVS data sets.
+ Source: R/fmrs.R
+ preproc_svs_dataset.Rd
+
+
+
+ Preprocess and perform quality assessment of one or more SVS data sets.
+
+
+
+ preproc_svs_dataset(
+ paths,
+ labels = NULL,
+ output_dir = "spant_analysis",
+ exclude_labels = NULL,
+ overwrite = FALSE,
+ ref_inds = NULL,
+ return_results = FALSE
+)
+
+
+
+ Arguments
+ - paths
+paths to the fMRS data file or IMA directory.
- labels
+labels to describe each data set.
- output_dir
+output directory.
- exclude_labels
+vector of labels of scans to exclude, eg poor quality
+data.
- overwrite
+overwrite saved results, defaults to FALSE.
- ref_inds
+a vector of 1-based indices for any water reference dynamic
+scans.
- return_results
+function will return key outputs, defaults to FALSE.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/print.fit_result.html b/docs/reference/print.fit_result.html
index 297f28dc..5f434e57 100644
--- a/docs/reference/print.fit_result.html
+++ b/docs/reference/print.fit_result.html
@@ -1,5 +1,5 @@
-Print a summary of an object of class fit_result. — print.fit_result • Spectroscopy Analysis Tools (spant) Print a summary of an object of class fit_result. — print.fit_result • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -105,7 +105,7 @@ Arguments
diff --git a/docs/reference/print.mrs_data.html b/docs/reference/print.mrs_data.html
index 51199017..e1561eb2 100644
--- a/docs/reference/print.mrs_data.html
+++ b/docs/reference/print.mrs_data.html
@@ -1,5 +1,5 @@
-Print a summary of mrs_data parameters. — print.mrs_data • Spectroscopy Analysis Tools (spant) Print a summary of mrs_data parameters. — print.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -109,7 +109,7 @@ Arguments
diff --git a/docs/reference/qn_states.html b/docs/reference/qn_states.html
index 0f42f2f9..d7aa6715 100644
--- a/docs/reference/qn_states.html
+++ b/docs/reference/qn_states.html
@@ -1,5 +1,5 @@
-Get the quantum coherence matrix for a spin system. — qn_states • Spectroscopy Analysis Tools (spant) Get the quantum coherence matrix for a spin system. — qn_states • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/rats.html b/docs/reference/rats.html
index 5a39a396..93585e08 100644
--- a/docs/reference/rats.html
+++ b/docs/reference/rats.html
@@ -1,5 +1,5 @@
-Robust Alignment to a Target Spectrum (RATS). — rats • Spectroscopy Analysis Tools (spant) Robust Alignment to a Target Spectrum (RATS). — rats • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -207,7 +207,7 @@ Value
diff --git a/docs/reference/re_weighting.html b/docs/reference/re_weighting.html
index d21caf21..8b0b070a 100644
--- a/docs/reference/re_weighting.html
+++ b/docs/reference/re_weighting.html
@@ -1,5 +1,5 @@
-Apply a weighting to the FID to enhance spectral resolution. — re_weighting • Spectroscopy Analysis Tools (spant) Apply a weighting to the FID to enhance spectral resolution. — re_weighting • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/read_basis.html b/docs/reference/read_basis.html
index da9b94af..eb6f8557 100644
--- a/docs/reference/read_basis.html
+++ b/docs/reference/read_basis.html
@@ -1,5 +1,5 @@
-Read a basis file in LCModel .basis format. — read_basis • Spectroscopy Analysis Tools (spant) Read a basis file in LCModel .basis format. — read_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/read_ima_coil_dir.html b/docs/reference/read_ima_coil_dir.html
index 28c02de0..4f073cd8 100644
--- a/docs/reference/read_ima_coil_dir.html
+++ b/docs/reference/read_ima_coil_dir.html
@@ -1,9 +1,5 @@
-Read a directory containing Siemens MRS IMA files and combine along the coil
-dimension. Note that the coil ID is inferred from the sorted file name and
-should be checked when consistency is required between two directories. — read_ima_coil_dir • Spectroscopy Analysis Tools (spant) Read a directory containing Siemens MRS IMA files and combine along the coil dimension. Note that the coil ID is inferred from the sorted file name and should be checked when consistency is required between two directories. — read_ima_coil_dir • Spectroscopy Analysis Tools (spant) Read a directory containing Siemens MRS IMA files and combine along the
-dynamic dimension. Note that the coil ID is inferred from the sorted file
-name and should be checked when consistency is required. — read_ima_dyn_dir • Spectroscopy Analysis Tools (spant) Read a directory containing Siemens MRS IMA files and combine along the dynamic dimension. Note that the coil ID is inferred from the sorted file name and should be checked when consistency is required. — read_ima_dyn_dir • Spectroscopy Analysis Tools (spant) Read an LCModel formatted coord file containing fit information. — read_lcm_coord • Spectroscopy Analysis Tools (spant) Read an LCModel formatted coord file containing fit information. — read_lcm_coord • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -107,7 +107,7 @@ Value
diff --git a/docs/reference/read_mrs.html b/docs/reference/read_mrs.html
index 3ac2a36b..2cf36b20 100644
--- a/docs/reference/read_mrs.html
+++ b/docs/reference/read_mrs.html
@@ -1,5 +1,5 @@
-Read MRS data from a file. — read_mrs • Spectroscopy Analysis Tools (spant) Read MRS data from a file. — read_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -88,7 +88,8 @@ Read MRS data from a file.
full_fid = FALSE,
omit_svs_ref_scans = TRUE,
verbose = FALSE,
- extra = NULL
+ extra = NULL,
+ fid_filt_dist = NULL
)
@@ -140,6 +141,13 @@ Arguments
an optional data frame to provide additional variables for use
in subsequent analysis steps, eg id or grouping variables.
fid_filt_dist
+indicate if the data has a distorted FID due to a
+brick-wall filter being used to downsample the data. Default is to auto
+detect this from the data, but TRUE or FALSE options can be given to override
+detection.
Value
@@ -183,7 +191,7 @@ Examples
diff --git a/docs/reference/read_mrs_tqn.html b/docs/reference/read_mrs_tqn.html
index 5766362f..84bdaf3a 100644
--- a/docs/reference/read_mrs_tqn.html
+++ b/docs/reference/read_mrs_tqn.html
@@ -1,5 +1,5 @@
-Read MRS data using the TARQUIN software package. — read_mrs_tqn • Spectroscopy Analysis Tools (spant) Read MRS data using the TARQUIN software package. — read_mrs_tqn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -131,7 +131,7 @@ Examples
diff --git a/docs/reference/read_pulse_ascii.html b/docs/reference/read_pulse_ascii.html
index c9e0d43c..ab11c9cc 100644
--- a/docs/reference/read_pulse_ascii.html
+++ b/docs/reference/read_pulse_ascii.html
@@ -1,5 +1,5 @@
-Read an ASCII formatted pulse file. — read_pulse_ascii • Spectroscopy Analysis Tools (spant) Read an ASCII formatted pulse file. — read_pulse_ascii • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/read_pulse_bruker.html b/docs/reference/read_pulse_bruker.html
index c92bf76a..dbe9073b 100644
--- a/docs/reference/read_pulse_bruker.html
+++ b/docs/reference/read_pulse_bruker.html
@@ -1,5 +1,5 @@
-Read a Bruker formatted pulse file — read_pulse_bruker • Spectroscopy Analysis Tools (spant) Read a Bruker formatted pulse file — read_pulse_bruker • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/read_pulse_pta.html b/docs/reference/read_pulse_pta.html
index 72e1b6d4..a0fac3c3 100644
--- a/docs/reference/read_pulse_pta.html
+++ b/docs/reference/read_pulse_pta.html
@@ -1,5 +1,5 @@
-Read a .pta formatted pulse file compatible with Siemens PulseTool. — read_pulse_pta • Spectroscopy Analysis Tools (spant) Read a .pta formatted pulse file compatible with Siemens PulseTool. — read_pulse_pta • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/read_siemens_txt_hdr.html b/docs/reference/read_siemens_txt_hdr.html
index 23fb8c70..3a17d87c 100644
--- a/docs/reference/read_siemens_txt_hdr.html
+++ b/docs/reference/read_siemens_txt_hdr.html
@@ -1,5 +1,5 @@
-Read the text format header found in Siemens IMA and TWIX data files. — read_siemens_txt_hdr • Spectroscopy Analysis Tools (spant) Read the text format header found in Siemens IMA and TWIX data files. — read_siemens_txt_hdr • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -78,7 +78,7 @@ Read the text format header found in Siemens IMA and TWIX data files.
- read_siemens_txt_hdr(input, version = "vd", verbose, offset = 0)
+ read_siemens_txt_hdr(input, version = "vd", verbose = FALSE, offset = 0)
@@ -118,7 +118,7 @@ Value
diff --git a/docs/reference/read_tqn_fit.html b/docs/reference/read_tqn_fit.html
index 4da6c25e..a1630420 100644
--- a/docs/reference/read_tqn_fit.html
+++ b/docs/reference/read_tqn_fit.html
@@ -1,5 +1,5 @@
-Reader for csv fit results generated by TARQUIN. — read_tqn_fit • Spectroscopy Analysis Tools (spant) Reader for csv fit results generated by TARQUIN. — read_tqn_fit • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -113,7 +113,7 @@ Examples
diff --git a/docs/reference/read_tqn_result.html b/docs/reference/read_tqn_result.html
index 36659714..68a3e98c 100644
--- a/docs/reference/read_tqn_result.html
+++ b/docs/reference/read_tqn_result.html
@@ -1,5 +1,5 @@
-Reader for csv results generated by TARQUIN. — read_tqn_result • Spectroscopy Analysis Tools (spant) Reader for csv results generated by TARQUIN. — read_tqn_result • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -117,7 +117,7 @@ Examples
diff --git a/docs/reference/recon_imag.html b/docs/reference/recon_imag.html
index d2a72225..5bc3b1eb 100644
--- a/docs/reference/recon_imag.html
+++ b/docs/reference/recon_imag.html
@@ -1,7 +1,5 @@
-Reconstruct complex time-domain data from the real part of frequency-domain
-data. — recon_imag • Spectroscopy Analysis Tools (spant) Reconstruct complex time-domain data from the real part of frequency-domain data. — recon_imag • Spectroscopy Analysis Tools (spant) Reconstruct complex time-domain data from the real part of frequency-domain
-data. — recon_imag_vec • Spectroscopy Analysis Tools (spant) Reconstruct complex time-domain data from the real part of frequency-domain data. — recon_imag_vec • Spectroscopy Analysis Tools (spant) Reconstruct 2D MRSI data from a twix file loaded with read_mrs. — recon_twix_2d_mrsi • Spectroscopy Analysis Tools (spant) Reconstruct 2D MRSI data from a twix file loaded with read_mrs. — recon_twix_2d_mrsi • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/rectangular_mask.html b/docs/reference/rectangular_mask.html
index a2117283..6e469bc9 100644
--- a/docs/reference/rectangular_mask.html
+++ b/docs/reference/rectangular_mask.html
@@ -1,5 +1,5 @@
-Create a rectangular mask stored as a matrix of logical values. — rectangular_mask • Spectroscopy Analysis Tools (spant) Create a rectangular mask stored as a matrix of logical values. — rectangular_mask • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -130,7 +130,7 @@ Value
diff --git a/docs/reference/reexports.html b/docs/reference/reexports.html
index 694a75d1..a59e8379 100644
--- a/docs/reference/reexports.html
+++ b/docs/reference/reexports.html
@@ -1,5 +1,5 @@
-Objects exported from other packages — reexports • Spectroscopy Analysis Tools (spant) Objects exported from other packages — reexports • Spectroscopy Analysis Tools (spant)
Spectroscopy Analysis Tools (spant)
- 2.21.0
+ 2.22.0
@@ -103,7 +103,7 @@ Objects exported from other packages
diff --git a/docs/reference/rep_array_dim.html b/docs/reference/rep_array_dim.html
index b9c49b4a..48c0a5ed 100644
--- a/docs/reference/rep_array_dim.html
+++ b/docs/reference/rep_array_dim.html
@@ -1,5 +1,5 @@
-Repeat an array over a given dimension. — rep_array_dim • Spectroscopy Analysis Tools (spant) Repeat an array over a given dimension. — rep_array_dim • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/rep_dyn.html b/docs/reference/rep_dyn.html
index 6bbfb0ef..89a4bb9b 100644
--- a/docs/reference/rep_dyn.html
+++ b/docs/reference/rep_dyn.html
@@ -1,5 +1,5 @@
-Replicate a scan in the dynamic dimension. — rep_dyn • Spectroscopy Analysis Tools (spant) Replicate a scan in the dynamic dimension. — rep_dyn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/rep_mrs.html b/docs/reference/rep_mrs.html
index 67730b5c..becb8f00 100644
--- a/docs/reference/rep_mrs.html
+++ b/docs/reference/rep_mrs.html
@@ -1,5 +1,5 @@
-Replicate a scan over a given dimension. — rep_mrs • Spectroscopy Analysis Tools (spant) Replicate a scan over a given dimension. — rep_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -138,7 +138,7 @@ Value
diff --git a/docs/reference/resample_basis.html b/docs/reference/resample_basis.html
index b0f2ab17..c7a6222a 100644
--- a/docs/reference/resample_basis.html
+++ b/docs/reference/resample_basis.html
@@ -1,5 +1,5 @@
-Resample a basis-set to match a mrs_data acquisition. — resample_basis • Spectroscopy Analysis Tools (spant) Resample a basis-set to match a mrs_data acquisition. — resample_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -116,7 +116,7 @@ Value
diff --git a/docs/reference/resample_img.html b/docs/reference/resample_img.html
index f1e7beaf..b0cc8f71 100644
--- a/docs/reference/resample_img.html
+++ b/docs/reference/resample_img.html
@@ -1,5 +1,5 @@
-Resample an image to match a target image space. — resample_img • Spectroscopy Analysis Tools (spant) Resample an image to match a target image space. — resample_img • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/resample_voi.html b/docs/reference/resample_voi.html
index 8fbfa836..a29ab096 100644
--- a/docs/reference/resample_voi.html
+++ b/docs/reference/resample_voi.html
@@ -1,7 +1,5 @@
-Resample a VOI to match a target image space using nearest-neighbour
-interpolation. — resample_voi • Spectroscopy Analysis Tools (spant) Resample a VOI to match a target image space using nearest-neighbour interpolation. — resample_voi • Spectroscopy Analysis Tools (spant) Reslice a nifti object to match the orientation of mrs data. — reslice_to_mrs • Spectroscopy Analysis Tools (spant) Reslice a nifti object to match the orientation of mrs data. — reslice_to_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/reson_table2mrs_data.html b/docs/reference/reson_table2mrs_data.html
index d75579ee..c5a2167a 100644
--- a/docs/reference/reson_table2mrs_data.html
+++ b/docs/reference/reson_table2mrs_data.html
@@ -1,5 +1,5 @@
-Generate mrs_data from a table of single Lorentzian resonances. — reson_table2mrs_data • Spectroscopy Analysis Tools (spant) Generate mrs_data from a table of single Lorentzian resonances. — reson_table2mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -119,7 +119,7 @@ Value
diff --git a/docs/reference/rm_dyns.html b/docs/reference/rm_dyns.html
index 5d5ef692..573e1f51 100644
--- a/docs/reference/rm_dyns.html
+++ b/docs/reference/rm_dyns.html
@@ -1,5 +1,5 @@
-Remove a subset of dynamic scans. — rm_dyns • Spectroscopy Analysis Tools (spant) Remove a subset of dynamic scans. — rm_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/scale_amp_molal.html b/docs/reference/scale_amp_molal.html
index aaeee1f2..7acb8cb0 100644
--- a/docs/reference/scale_amp_molal.html
+++ b/docs/reference/scale_amp_molal.html
@@ -1,7 +1,5 @@
-Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water). — scale_amp_molal • Spectroscopy Analysis Tools (spant) Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / kg of tissue water). — scale_amp_molal • Spectroscopy Analysis Tools (spant)
Spectroscopy Analysis Tools (spant)
- 2.21.0
+ 2.22.0
@@ -76,8 +74,7 @@
- Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water).
+ Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / kg of tissue water).
Source: R/amp_scaling.R
scale_amp_molal.Rd
@@ -163,7 +160,7 @@ Value
diff --git a/docs/reference/scale_amp_molal_pvc.html b/docs/reference/scale_amp_molal_pvc.html
index 962d6afc..4d194abd 100644
--- a/docs/reference/scale_amp_molal_pvc.html
+++ b/docs/reference/scale_amp_molal_pvc.html
@@ -1,7 +1,5 @@
-Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water). — scale_amp_molal_pvc • Spectroscopy Analysis Tools (spant)
@@ -75,8 +73,7 @@
- Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water).
+ Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / kg of tissue water).
Source: R/amp_scaling.R
scale_amp_molal_pvc.Rd
@@ -141,7 +138,7 @@ Value
diff --git a/docs/reference/scale_amp_molar.html b/docs/reference/scale_amp_molar.html
index 02358d91..dc87a338 100644
--- a/docs/reference/scale_amp_molar.html
+++ b/docs/reference/scale_amp_molar.html
@@ -1,7 +1,5 @@
-Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / Litre of tissue). — scale_amp_molar • Spectroscopy Analysis Tools (spant) Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / Litre of tissue). — scale_amp_molar • Spectroscopy Analysis Tools (spant) Convert default LCM/TARQUIN concentration scaling to molal units with partial
-volume correction. — scale_amp_molar2molal_pvc • Spectroscopy Analysis Tools (spant) Convert default LCM/TARQUIN concentration scaling to molal units with partial volume correction. — scale_amp_molar2molal_pvc • Spectroscopy Analysis Tools (spant) Scale fitted amplitudes to a ratio of signal amplitude. — scale_amp_ratio • Spectroscopy Analysis Tools (spant) Scale fitted amplitudes to a ratio of signal amplitude. — scale_amp_ratio • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -116,7 +116,7 @@ Value
diff --git a/docs/reference/scale_amp_ratio_value.html b/docs/reference/scale_amp_ratio_value.html
index 2036837a..6af8ac51 100644
--- a/docs/reference/scale_amp_ratio_value.html
+++ b/docs/reference/scale_amp_ratio_value.html
@@ -1,5 +1,5 @@
-Scale fitted amplitudes to a ratio of signal amplitude. — scale_amp_ratio_value • Spectroscopy Analysis Tools (spant) Scale fitted amplitudes to a ratio of signal amplitude. — scale_amp_ratio_value • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/scale_amp_water_ratio.html b/docs/reference/scale_amp_water_ratio.html
index 5b25e884..35a76b00 100644
--- a/docs/reference/scale_amp_water_ratio.html
+++ b/docs/reference/scale_amp_water_ratio.html
@@ -1,5 +1,5 @@
-Scale metabolite amplitudes as a ratio to the unsuppressed water amplitude. — scale_amp_water_ratio • Spectroscopy Analysis Tools (spant) Scale metabolite amplitudes as a ratio to the unsuppressed water amplitude. — scale_amp_water_ratio • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/scale_basis_amp.html b/docs/reference/scale_basis_amp.html
index 9401c3f1..5a58b5e5 100644
--- a/docs/reference/scale_basis_amp.html
+++ b/docs/reference/scale_basis_amp.html
@@ -1,5 +1,5 @@
-Scale a basis object by a scalar. — scale_basis_amp • Spectroscopy Analysis Tools (spant) Scale a basis object by a scalar. — scale_basis_amp • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/scale_basis_from_singlet.html b/docs/reference/scale_basis_from_singlet.html
index 0d542bc8..c9a19e77 100644
--- a/docs/reference/scale_basis_from_singlet.html
+++ b/docs/reference/scale_basis_from_singlet.html
@@ -1,5 +1,5 @@
-Scale a basis-set to be consistent with spant assumptions for water scaling. — scale_basis_from_singlet • Spectroscopy Analysis Tools (spant) Scale a basis-set to be consistent with spant assumptions for water scaling. — scale_basis_from_singlet • Spectroscopy Analysis Tools (spant)
Spectroscopy Analysis Tools (spant)
- 2.21.0
+ 2.22.0
@@ -127,7 +127,7 @@ Value
diff --git a/docs/reference/scale_mrs_amp.html b/docs/reference/scale_mrs_amp.html
index b5501a0d..990f058a 100644
--- a/docs/reference/scale_mrs_amp.html
+++ b/docs/reference/scale_mrs_amp.html
@@ -1,5 +1,5 @@
-Scale an mrs_data object by a scalar or vector or amplitudes. — scale_mrs_amp • Spectroscopy Analysis Tools (spant) Scale an mrs_data object by a scalar or vector or amplitudes. — scale_mrs_amp • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/scale_spec.html b/docs/reference/scale_spec.html
index 4f6ea835..6b3ddba4 100644
--- a/docs/reference/scale_spec.html
+++ b/docs/reference/scale_spec.html
@@ -1,5 +1,5 @@
-Scale mrs_data to a spectral region. — scale_spec • Spectroscopy Analysis Tools (spant) Scale mrs_data to a spectral region. — scale_spec • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -141,7 +141,7 @@ Value
diff --git a/docs/reference/sd.html b/docs/reference/sd.html
index ea1eec9f..3ae4dfd4 100644
--- a/docs/reference/sd.html
+++ b/docs/reference/sd.html
@@ -1,5 +1,5 @@
-Calculate the standard deviation spectrum from an mrs_data object. — sd • Spectroscopy Analysis Tools (spant) Calculate the standard deviation spectrum from an mrs_data object. — sd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/sd.mrs_data.html b/docs/reference/sd.mrs_data.html
index 3f92a49f..13bdda85 100644
--- a/docs/reference/sd.mrs_data.html
+++ b/docs/reference/sd.mrs_data.html
@@ -1,5 +1,5 @@
-Calculate the standard deviation spectrum from an mrs_data object. — sd.mrs_data • Spectroscopy Analysis Tools (spant) Calculate the standard deviation spectrum from an mrs_data object. — sd.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/seconds.html b/docs/reference/seconds.html
index b34d6627..467ee17f 100644
--- a/docs/reference/seconds.html
+++ b/docs/reference/seconds.html
@@ -1,5 +1,5 @@
-Return a time scale vector to match the FID of an MRS data object. — seconds • Spectroscopy Analysis Tools (spant) Return a time scale vector to match the FID of an MRS data object. — seconds • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/seq_cpmg_ideal.html b/docs/reference/seq_cpmg_ideal.html
index 547e96ab..45727c86 100644
--- a/docs/reference/seq_cpmg_ideal.html
+++ b/docs/reference/seq_cpmg_ideal.html
@@ -1,5 +1,5 @@
-CPMG style sequence with ideal pulses. — seq_cpmg_ideal • Spectroscopy Analysis Tools (spant) CPMG style sequence with ideal pulses. — seq_cpmg_ideal • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/seq_mega_press_ideal.html b/docs/reference/seq_mega_press_ideal.html
index 0769b8b4..a9cd7fa0 100644
--- a/docs/reference/seq_mega_press_ideal.html
+++ b/docs/reference/seq_mega_press_ideal.html
@@ -1,7 +1,5 @@
-MEGA-PRESS sequence with ideal localisation pulses and Gaussian shaped
-editing pulse. — seq_mega_press_ideal • Spectroscopy Analysis Tools (spant) MEGA-PRESS sequence with ideal localisation pulses and Gaussian shaped editing pulse. — seq_mega_press_ideal • Spectroscopy Analysis Tools (spant) PRESS sequence with shaped refocusing pulses. — seq_press_2d_shaped • Spectroscopy Analysis Tools (spant) PRESS sequence with shaped refocusing pulses. — seq_press_2d_shaped • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -165,7 +165,7 @@ Value
diff --git a/docs/reference/seq_press_ideal.html b/docs/reference/seq_press_ideal.html
index 8c976856..72c3af3d 100644
--- a/docs/reference/seq_press_ideal.html
+++ b/docs/reference/seq_press_ideal.html
@@ -1,5 +1,5 @@
-PRESS sequence with ideal pulses. — seq_press_ideal • Spectroscopy Analysis Tools (spant) PRESS sequence with ideal pulses. — seq_press_ideal • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/seq_pulse_acquire.html b/docs/reference/seq_pulse_acquire.html
index 4a88fc64..ad80571e 100644
--- a/docs/reference/seq_pulse_acquire.html
+++ b/docs/reference/seq_pulse_acquire.html
@@ -1,5 +1,5 @@
-Simple pulse and acquire sequence with ideal pulses. — seq_pulse_acquire • Spectroscopy Analysis Tools (spant) Simple pulse and acquire sequence with ideal pulses. — seq_pulse_acquire • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/seq_slaser_ideal.html b/docs/reference/seq_slaser_ideal.html
index 74688f4d..eb83e8e3 100644
--- a/docs/reference/seq_slaser_ideal.html
+++ b/docs/reference/seq_slaser_ideal.html
@@ -1,5 +1,5 @@
-sLASER sequence with ideal pulses. — seq_slaser_ideal • Spectroscopy Analysis Tools (spant) sLASER sequence with ideal pulses. — seq_slaser_ideal • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -126,7 +126,7 @@ Value
diff --git a/docs/reference/seq_spin_echo_ideal.html b/docs/reference/seq_spin_echo_ideal.html
index e23271de..4248716f 100644
--- a/docs/reference/seq_spin_echo_ideal.html
+++ b/docs/reference/seq_spin_echo_ideal.html
@@ -1,5 +1,5 @@
-Spin echo sequence with ideal pulses. — seq_spin_echo_ideal • Spectroscopy Analysis Tools (spant) Spin echo sequence with ideal pulses. — seq_spin_echo_ideal • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/seq_steam_ideal.html b/docs/reference/seq_steam_ideal.html
index a60685a8..1c8115d7 100644
--- a/docs/reference/seq_steam_ideal.html
+++ b/docs/reference/seq_steam_ideal.html
@@ -1,5 +1,5 @@
-STEAM sequence with ideal pulses. — seq_steam_ideal • Spectroscopy Analysis Tools (spant) STEAM sequence with ideal pulses. — seq_steam_ideal • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -128,7 +128,7 @@ Value
diff --git a/docs/reference/seq_steam_ideal_cof.html b/docs/reference/seq_steam_ideal_cof.html
index 8f225740..cba7af91 100644
--- a/docs/reference/seq_steam_ideal_cof.html
+++ b/docs/reference/seq_steam_ideal_cof.html
@@ -1,7 +1,5 @@
-STEAM sequence with ideal pulses and coherence order filtering to simulate
-gradient crushers. — seq_steam_ideal_cof • Spectroscopy Analysis Tools (spant) STEAM sequence with ideal pulses and coherence order filtering to simulate gradient crushers. — seq_steam_ideal_cof • Spectroscopy Analysis Tools (spant) STEAM sequence with ideal pulses using the z-rotation gradient simulation
-method described by Young et al JMR 140, 146-152 (1999). — seq_steam_ideal_young • Spectroscopy Analysis Tools (spant) STEAM sequence with ideal pulses using the z-rotation gradient simulation method described by Young et al JMR 140, 146-152 (1999). — seq_steam_ideal_young • Spectroscopy Analysis Tools (spant) Set the number of transients for an mrs_data object. — set_Ntrans • Spectroscopy Analysis Tools (spant) Set the number of transients for an mrs_data object. — set_Ntrans • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/set_def_acq_paras.html b/docs/reference/set_def_acq_paras.html
index 3e1b4004..cc2ada9c 100644
--- a/docs/reference/set_def_acq_paras.html
+++ b/docs/reference/set_def_acq_paras.html
@@ -1,5 +1,5 @@
-Set the default acquisition parameters. — set_def_acq_paras • Spectroscopy Analysis Tools (spant) Set the default acquisition parameters. — set_def_acq_paras • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Arguments
diff --git a/docs/reference/set_lcm_cmd.html b/docs/reference/set_lcm_cmd.html
index 2056ed01..42bb2f24 100644
--- a/docs/reference/set_lcm_cmd.html
+++ b/docs/reference/set_lcm_cmd.html
@@ -1,5 +1,5 @@
-Set the command to run the LCModel command-line program. — set_lcm_cmd • Spectroscopy Analysis Tools (spant) Set the command to run the LCModel command-line program. — set_lcm_cmd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/set_lw.html b/docs/reference/set_lw.html
index b64ec851..bb176c62 100644
--- a/docs/reference/set_lw.html
+++ b/docs/reference/set_lw.html
@@ -1,5 +1,5 @@
-Apply line-broadening to an mrs_data object to achieve a specified linewidth. — set_lw • Spectroscopy Analysis Tools (spant) Apply line-broadening to an mrs_data object to achieve a specified linewidth. — set_lw • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -123,7 +123,7 @@ Value
diff --git a/docs/reference/set_mask_xy_mat.html b/docs/reference/set_mask_xy_mat.html
index 49dc5d4e..52c4b617 100644
--- a/docs/reference/set_mask_xy_mat.html
+++ b/docs/reference/set_mask_xy_mat.html
@@ -1,5 +1,5 @@
-Set the masked voxels in a 2D MRSI dataset to given spectrum. — set_mask_xy_mat • Spectroscopy Analysis Tools (spant) Set the masked voxels in a 2D MRSI dataset to given spectrum. — set_mask_xy_mat • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Value
diff --git a/docs/reference/set_precomp_mode.html b/docs/reference/set_precomp_mode.html
index f44bd5d3..47c28e3b 100644
--- a/docs/reference/set_precomp_mode.html
+++ b/docs/reference/set_precomp_mode.html
@@ -1,5 +1,5 @@
-Set the precompute mode. — set_precomp_mode • Spectroscopy Analysis Tools (spant) Set the precompute mode. — set_precomp_mode • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/set_precomp_verbose.html b/docs/reference/set_precomp_verbose.html
index 1453a231..9c613505 100644
--- a/docs/reference/set_precomp_verbose.html
+++ b/docs/reference/set_precomp_verbose.html
@@ -1,5 +1,5 @@
-Set the verbosity of the precompute function. — set_precomp_verbose • Spectroscopy Analysis Tools (spant) Set the verbosity of the precompute function. — set_precomp_verbose • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/set_ref.html b/docs/reference/set_ref.html
index 8953fa50..5436dfa2 100644
--- a/docs/reference/set_ref.html
+++ b/docs/reference/set_ref.html
@@ -1,5 +1,5 @@
-Set the ppm reference value (eg ppm value at 0Hz). — set_ref • Spectroscopy Analysis Tools (spant) Set the ppm reference value (eg ppm value at 0Hz). — set_ref • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/set_td_pts.html b/docs/reference/set_td_pts.html
index 8a80d42a..586459ff 100644
--- a/docs/reference/set_td_pts.html
+++ b/docs/reference/set_td_pts.html
@@ -1,7 +1,5 @@
-Set the number of time-domain data points, truncating or zero-filling as
-appropriate. — set_td_pts • Spectroscopy Analysis Tools (spant) Set the number of time-domain data points, truncating or zero-filling as appropriate. — set_td_pts • Spectroscopy Analysis Tools (spant) Set the command to run the TARQUIN command-line program. — set_tqn_cmd • Spectroscopy Analysis Tools (spant) Set the command to run the TARQUIN command-line program. — set_tqn_cmd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/set_tr.html b/docs/reference/set_tr.html
index b2109ab0..65c9df5f 100644
--- a/docs/reference/set_tr.html
+++ b/docs/reference/set_tr.html
@@ -1,5 +1,5 @@
-Set the repetition time of an MRS dataset. — set_tr • Spectroscopy Analysis Tools (spant) Set the repetition time of an MRS dataset. — set_tr • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/shift.html b/docs/reference/shift.html
index ab0fe724..034591d0 100644
--- a/docs/reference/shift.html
+++ b/docs/reference/shift.html
@@ -1,5 +1,5 @@
-Apply a frequency shift to MRS data. — shift • Spectroscopy Analysis Tools (spant) Apply a frequency shift to MRS data. — shift • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/shift_basis.html b/docs/reference/shift_basis.html
index 2884be19..f55a65e0 100644
--- a/docs/reference/shift_basis.html
+++ b/docs/reference/shift_basis.html
@@ -1,5 +1,5 @@
-Apply frequency shifts to basis set signals. — shift_basis • Spectroscopy Analysis Tools (spant) Apply frequency shifts to basis set signals. — shift_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Value
diff --git a/docs/reference/sim_basis.html b/docs/reference/sim_basis.html
index c7838c46..bb5fefc6 100644
--- a/docs/reference/sim_basis.html
+++ b/docs/reference/sim_basis.html
@@ -1,5 +1,5 @@
-Simulate a basis set object. — sim_basis • Spectroscopy Analysis Tools (spant) Simulate a basis set object. — sim_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -136,7 +136,7 @@ Value
diff --git a/docs/reference/sim_basis_1h_brain.html b/docs/reference/sim_basis_1h_brain.html
index 62ed7389..f71ffa0b 100644
--- a/docs/reference/sim_basis_1h_brain.html
+++ b/docs/reference/sim_basis_1h_brain.html
@@ -1,7 +1,5 @@
-Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS
-sequence. Note, ideal pulses are assumed. — sim_basis_1h_brain • Spectroscopy Analysis Tools (spant) Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS sequence. Note, ideal pulses are assumed. — sim_basis_1h_brain • Spectroscopy Analysis Tools (spant) Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS
-sequence. Note, ideal pulses are assumed. — sim_basis_1h_brain_press • Spectroscopy Analysis Tools (spant) Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS sequence. Note, ideal pulses are assumed. — sim_basis_1h_brain_press • Spectroscopy Analysis Tools (spant) Simulate a macromolecular and lipid basis-set suitable for 1H brain MRS
-analysis. — sim_basis_mm_lip_lcm • Spectroscopy Analysis Tools (spant) Simulate a macromolecular and lipid basis-set suitable for 1H brain MRS analysis. — sim_basis_mm_lip_lcm • Spectroscopy Analysis Tools (spant) Simulate a basis file using TARQUIN. — sim_basis_tqn • Spectroscopy Analysis Tools (spant) Simulate a basis file using TARQUIN. — sim_basis_tqn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -129,7 +129,7 @@ Examples
diff --git a/docs/reference/sim_brain_1h.html b/docs/reference/sim_brain_1h.html
index 2044cf1a..717ee289 100644
--- a/docs/reference/sim_brain_1h.html
+++ b/docs/reference/sim_brain_1h.html
@@ -1,5 +1,5 @@
-Simulate MRS data with a similar appearance to normal brain (by default). — sim_brain_1h • Spectroscopy Analysis Tools (spant) Simulate MRS data with a similar appearance to normal brain (by default). — sim_brain_1h • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -159,7 +159,7 @@ Value
diff --git a/docs/reference/sim_mol.html b/docs/reference/sim_mol.html
index 23bcef50..77f76a50 100644
--- a/docs/reference/sim_mol.html
+++ b/docs/reference/sim_mol.html
@@ -1,5 +1,5 @@
-Simulate a mol_parameter object. — sim_mol • Spectroscopy Analysis Tools (spant) Simulate a mol_parameter object. — sim_mol • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -143,7 +143,7 @@ Value
diff --git a/docs/reference/sim_noise.html b/docs/reference/sim_noise.html
index 23875f79..a71477d4 100644
--- a/docs/reference/sim_noise.html
+++ b/docs/reference/sim_noise.html
@@ -1,5 +1,5 @@
-Simulate an mrs_data object containing simulated Gaussian noise. — sim_noise • Spectroscopy Analysis Tools (spant) Simulate an mrs_data object containing simulated Gaussian noise. — sim_noise • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -84,6 +84,7 @@ Simulate an mrs_data object containing simulated Gaussian noise.
ft = def_ft(),
N = def_N(),
ref = def_ref(),
+ nuc = def_nuc(),
dyns = 1,
fd = TRUE
)
@@ -111,6 +112,10 @@ Arguments
reference value for ppm scale.
nuc
+resonant nucleus.
dyns
number of dynamic scans to generate.
Value
diff --git a/docs/reference/sim_resonances.html b/docs/reference/sim_resonances.html
index 19e9a8a4..d4f8d7c0 100644
--- a/docs/reference/sim_resonances.html
+++ b/docs/reference/sim_resonances.html
@@ -1,5 +1,5 @@
-Simulate a MRS data object containing a set of simulated resonances. — sim_resonances • Spectroscopy Analysis Tools (spant) Simulate a MRS data object containing a set of simulated resonances. — sim_resonances • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -161,7 +161,7 @@ Examples
diff --git a/docs/reference/sim_th_excit_profile.html b/docs/reference/sim_th_excit_profile.html
index 5535c5ef..e781cab1 100644
--- a/docs/reference/sim_th_excit_profile.html
+++ b/docs/reference/sim_th_excit_profile.html
@@ -1,7 +1,5 @@
-Simulate an ideal pulse excitation profile by smoothing a top-hat function
-with a Gaussian. — sim_th_excit_profile • Spectroscopy Analysis Tools (spant) Simulate an ideal pulse excitation profile by smoothing a top-hat function with a Gaussian. — sim_th_excit_profile • Spectroscopy Analysis Tools (spant) Simulate an mrs_data object containing complex zero valued samples. — sim_zero • Spectroscopy Analysis Tools (spant) Simulate an mrs_data object containing complex zero valued samples. — sim_zero • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -78,7 +78,14 @@ Simulate an mrs_data object containing complex zero valued samples.
-
+
@@ -99,6 +106,10 @@ Arguments
reference value for ppm scale.
nuc
+resonant nucleus.
dyns
number of dynamic scans to generate.
Value
diff --git a/docs/reference/smooth_dyns.html b/docs/reference/smooth_dyns.html
index 4cc8da50..accf3a51 100644
--- a/docs/reference/smooth_dyns.html
+++ b/docs/reference/smooth_dyns.html
@@ -1,5 +1,5 @@
-Smooth data across the dynamic dimension with a Gaussian kernel. — smooth_dyns • Spectroscopy Analysis Tools (spant) Smooth data across the dynamic dimension with a Gaussian kernel. — smooth_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/sort_basis.html b/docs/reference/sort_basis.html
index 6a676ea2..d25cc006 100644
--- a/docs/reference/sort_basis.html
+++ b/docs/reference/sort_basis.html
@@ -1,5 +1,5 @@
-Sort the basis-set elements alphabetically. — sort_basis • Spectroscopy Analysis Tools (spant) Sort the basis-set elements alphabetically. — sort_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/spant-package.html b/docs/reference/spant-package.html
index b3dd8e21..90f19ec3 100644
--- a/docs/reference/spant-package.html
+++ b/docs/reference/spant-package.html
@@ -1,5 +1,5 @@
-spant: spectroscopy analysis tools. — spant-package • Spectroscopy Analysis Tools (spant) spant: spectroscopy analysis tools. — spant-package • Spectroscopy Analysis Tools (spant) Simulate and fit some spectra with ABfit for benchmarking purposes. Basic
-timing and performance metrics will be printed. — spant_abfit_benchmark • Spectroscopy Analysis Tools (spant) Simulate and fit some spectra with ABfit for benchmarking purposes. Basic timing and performance metrics will be printed. — spant_abfit_benchmark • Spectroscopy Analysis Tools (spant) Example MEGA-PRESS data with significant B0 drift. — spant_mpress_drift • Spectroscopy Analysis Tools (spant) Example MEGA-PRESS data with significant B0 drift. — spant_mpress_drift • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -83,7 +83,7 @@ Example MEGA-PRESS data with significant B0 drift.
Format
- An object of class mrs_data of length 13.
+ An object of class mrs_data of dimension 1 x 1 x 1 x 1 x 40 x 1 x 1024.
@@ -98,7 +98,7 @@ Format
diff --git a/docs/reference/spant_sim_fmrs_dataset.html b/docs/reference/spant_sim_fmrs_dataset.html
new file mode 100644
index 00000000..00e48b56
--- /dev/null
+++ b/docs/reference/spant_sim_fmrs_dataset.html
@@ -0,0 +1,117 @@
+
+Simulate an example fMRS dataset for a block design fMRS experiment and export a BIDS structure. — spant_sim_fmrs_dataset • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Simulate an example fMRS dataset for a block design fMRS experiment and export a BIDS structure.
+ Source: R/fmrs.R
+ spant_sim_fmrs_dataset.Rd
+
+
+
+ Simulate an example fMRS dataset for a block design fMRS experiment and
+export a BIDS structure.
+
+
+
+ spant_sim_fmrs_dataset(output_dir = NULL)
+
+
+
+ Arguments
+ - output_dir
+output directory for the BIDS data. Defaults to :
+"HOME/sim_fmrs_dataset/data".
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/spant_simulation_benchmark.html b/docs/reference/spant_simulation_benchmark.html
index 32daa8bf..d8cc6841 100644
--- a/docs/reference/spant_simulation_benchmark.html
+++ b/docs/reference/spant_simulation_benchmark.html
@@ -1,7 +1,5 @@
-Simulate a typical metabolite basis set for benchmarking. Timing metrics will
-be printed on completion. — spant_simulation_benchmark • Spectroscopy Analysis Tools (spant) Simulate a typical metabolite basis set for benchmarking. Timing metrics will be printed on completion. — spant_simulation_benchmark • Spectroscopy Analysis Tools (spant) Decompose an mrs_data object into white and gray matter spectra. — spec_decomp • Spectroscopy Analysis Tools (spant) Perform a mathematical operation on a spectral region. — spec_op • Spectroscopy Analysis Tools (spant) Perform a mathematical operation on a spectral region. — spec_op • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -98,8 +98,8 @@ Arguments
operator
-can be "sum" (default), "mean", "l2", "max", "min" or
-"max-min".
can be "sum" (default), "mean", "l2", "max", "max_cplx,
+"min" or "max-min".
freq_scale
@@ -129,7 +129,7 @@ Value
diff --git a/docs/reference/spin_sys.html b/docs/reference/spin_sys.html
index 853423a4..1eaa9e76 100644
--- a/docs/reference/spin_sys.html
+++ b/docs/reference/spin_sys.html
@@ -1,5 +1,5 @@
-Create a spin system object for pulse sequence simulation. — spin_sys • Spectroscopy Analysis Tools (spant) Create a spin system object for pulse sequence simulation. — spin_sys • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/spm_pve2categorical.html b/docs/reference/spm_pve2categorical.html
index 23a1bad9..70f10729 100644
--- a/docs/reference/spm_pve2categorical.html
+++ b/docs/reference/spm_pve2categorical.html
@@ -1,7 +1,5 @@
-Convert SPM style segmentation files to a single categorical image where
-the numerical values map as: 0) Other, 1) CSF, 2) GM and 3) WM. — spm_pve2categorical • Spectroscopy Analysis Tools (spant) Convert SPM style segmentation files to a single categorical image where the numerical values map as: 0) Other, 1) CSF, 2) GM and 3) WM. — spm_pve2categorical • Spectroscopy Analysis Tools (spant) Signal space projection method for lipid suppression. — ssp • Spectroscopy Analysis Tools (spant) Signal space projection method for lipid suppression. — ssp • Spectroscopy Analysis Tools (spant) Plot the fitting results of an object of class fit_result with
-individual basis set components shown. — stackplot.fit_result • Spectroscopy Analysis Tools (spant) Plot the fitting results of an object of class fit_result with individual basis set components shown. — stackplot.fit_result • Spectroscopy Analysis Tools (spant) Produce a plot with multiple traces. — stackplot • Spectroscopy Analysis Tools (spant) Produce a plot with multiple traces. — stackplot • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/stackplot.mrs_data.html b/docs/reference/stackplot.mrs_data.html
index 17ff5648..64eea445 100644
--- a/docs/reference/stackplot.mrs_data.html
+++ b/docs/reference/stackplot.mrs_data.html
@@ -1,5 +1,5 @@
-Stackplot plotting method for objects of class mrs_data. — stackplot.mrs_data • Spectroscopy Analysis Tools (spant) Stackplot plotting method for objects of class mrs_data. — stackplot.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -255,7 +255,7 @@ Arguments
diff --git a/docs/reference/sub_first_dyn.html b/docs/reference/sub_first_dyn.html
index dbd7f831..493b7242 100644
--- a/docs/reference/sub_first_dyn.html
+++ b/docs/reference/sub_first_dyn.html
@@ -1,5 +1,5 @@
-Subtract the first dynamic spectrum from a dynamic series. — sub_first_dyn • Spectroscopy Analysis Tools (spant) Subtract the first dynamic spectrum from a dynamic series. — sub_first_dyn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/sub_mean_dyns.html b/docs/reference/sub_mean_dyns.html
index 6e3bb2df..221bd0c1 100644
--- a/docs/reference/sub_mean_dyns.html
+++ b/docs/reference/sub_mean_dyns.html
@@ -1,5 +1,5 @@
-Subtract the mean dynamic spectrum from a dynamic series. — sub_mean_dyns • Spectroscopy Analysis Tools (spant) Subtract the mean dynamic spectrum from a dynamic series. — sub_mean_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/sub_median_dyns.html b/docs/reference/sub_median_dyns.html
index 134c495d..1e834f14 100644
--- a/docs/reference/sub_median_dyns.html
+++ b/docs/reference/sub_median_dyns.html
@@ -1,5 +1,5 @@
-Subtract the median dynamic spectrum from a dynamic series. — sub_median_dyns • Spectroscopy Analysis Tools (spant) Subtract the median dynamic spectrum from a dynamic series. — sub_median_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/sum_coils.html b/docs/reference/sum_coils.html
index 7bf559f2..e1ab3cc0 100644
--- a/docs/reference/sum_coils.html
+++ b/docs/reference/sum_coils.html
@@ -1,5 +1,5 @@
-Calculate the sum across receiver coil elements. — sum_coils • Spectroscopy Analysis Tools (spant) Calculate the sum across receiver coil elements. — sum_coils • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/sum_dyns.html b/docs/reference/sum_dyns.html
index a0be19d3..bbda2ffc 100644
--- a/docs/reference/sum_dyns.html
+++ b/docs/reference/sum_dyns.html
@@ -1,5 +1,5 @@
-Calculate the sum of data dynamics. — sum_dyns • Spectroscopy Analysis Tools (spant) Calculate the sum of data dynamics. — sum_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/sum_mrs.html b/docs/reference/sum_mrs.html
index a22f215b..3cc3ab9e 100644
--- a/docs/reference/sum_mrs.html
+++ b/docs/reference/sum_mrs.html
@@ -1,5 +1,5 @@
-Sum two mrs_data objects. — sum_mrs • Spectroscopy Analysis Tools (spant) Sum two mrs_data objects. — sum_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Value
diff --git a/docs/reference/sum_mrs_list.html b/docs/reference/sum_mrs_list.html
index f4e09aea..c3584348 100644
--- a/docs/reference/sum_mrs_list.html
+++ b/docs/reference/sum_mrs_list.html
@@ -1,5 +1,5 @@
-Return the sum of a list of mrs_data objects. — sum_mrs_list • Spectroscopy Analysis Tools (spant) Return the sum of a list of mrs_data objects. — sum_mrs_list • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/svs_1h_brain_analysis.html b/docs/reference/svs_1h_brain_analysis.html
index 8ce514db..dff0ef7d 100644
--- a/docs/reference/svs_1h_brain_analysis.html
+++ b/docs/reference/svs_1h_brain_analysis.html
@@ -1,5 +1,5 @@
-Standard SVS 1H brain analysis pipeline. — svs_1h_brain_analysis • Spectroscopy Analysis Tools (spant) Standard SVS 1H brain analysis pipeline. — svs_1h_brain_analysis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -199,7 +199,7 @@ Value
diff --git a/docs/reference/svs_1h_brain_analysis_dev.html b/docs/reference/svs_1h_brain_analysis_dev.html
index d70a14d3..d71bfea2 100644
--- a/docs/reference/svs_1h_brain_analysis_dev.html
+++ b/docs/reference/svs_1h_brain_analysis_dev.html
@@ -1,5 +1,5 @@
-Standard SVS 1H brain analysis pipeline. — svs_1h_brain_analysis_dev • Spectroscopy Analysis Tools (spant) Standard SVS 1H brain analysis pipeline. — svs_1h_brain_analysis_dev • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -193,7 +193,7 @@ Examples
diff --git a/docs/reference/svs_1h_brain_batch_analysis.html b/docs/reference/svs_1h_brain_batch_analysis.html
index 5631e8cc..15f7223e 100644
--- a/docs/reference/svs_1h_brain_batch_analysis.html
+++ b/docs/reference/svs_1h_brain_batch_analysis.html
@@ -1,5 +1,5 @@
-Batch interface to the standard SVS 1H brain analysis pipeline. — svs_1h_brain_batch_analysis • Spectroscopy Analysis Tools (spant) Batch interface to the standard SVS 1H brain analysis pipeline. — svs_1h_brain_batch_analysis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -144,7 +144,7 @@ Value
diff --git a/docs/reference/t_test_spec.html b/docs/reference/t_test_spec.html
new file mode 100644
index 00000000..56a7ea1b
--- /dev/null
+++ b/docs/reference/t_test_spec.html
@@ -0,0 +1,124 @@
+
+Perform a t-test on spectral data points. — t_test_spec • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+
+
+ Perform a t-test on spectral data points.
+
+
+
+ t_test_spec(mrs_data, group)
+
+
+
+ Arguments
+ - mrs_data
+an mrs_data object with spectra in the dynamic dimension.
- group
+vector describing the group membership of each dynamic spectrum.
+
+ Value
+
+
+a list of statistical results.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/td2fd.html b/docs/reference/td2fd.html
index 6748a6a8..f31ed524 100644
--- a/docs/reference/td2fd.html
+++ b/docs/reference/td2fd.html
@@ -1,5 +1,5 @@
-Transform time-domain data to the frequency-domain. — td2fd • Spectroscopy Analysis Tools (spant) Transform time-domain data to the frequency-domain. — td2fd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/td_conv_filt.html b/docs/reference/td_conv_filt.html
index a9f340c3..106b9b00 100644
--- a/docs/reference/td_conv_filt.html
+++ b/docs/reference/td_conv_filt.html
@@ -1,5 +1,5 @@
-Time-domain convolution based filter. — td_conv_filt • Spectroscopy Analysis Tools (spant) Time-domain convolution based filter. — td_conv_filt • Spectroscopy Analysis Tools (spant) Time-domain spectral registration. — tdsr • Spectroscopy Analysis Tools (spant) Time-domain spectral registration. — tdsr • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -121,7 +121,7 @@ Value
diff --git a/docs/reference/te.html b/docs/reference/te.html
index 010361b1..4a65711d 100644
--- a/docs/reference/te.html
+++ b/docs/reference/te.html
@@ -1,5 +1,5 @@
-Return the echo time of an MRS dataset. — te • Spectroscopy Analysis Tools (spant) Return the echo time of an MRS dataset. — te • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/tr.html b/docs/reference/tr.html
index 0c0bd63b..2e749e02 100644
--- a/docs/reference/tr.html
+++ b/docs/reference/tr.html
@@ -1,5 +1,5 @@
-Return the repetition time of an MRS dataset. — tr • Spectroscopy Analysis Tools (spant) Return the repetition time of an MRS dataset. — tr • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/varpro_3_para_opts.html b/docs/reference/varpro_3_para_opts.html
index c2270a16..52d7cd84 100644
--- a/docs/reference/varpro_3_para_opts.html
+++ b/docs/reference/varpro_3_para_opts.html
@@ -1,5 +1,5 @@
-Return a list of options for VARPRO based fitting with 3 free parameters. — varpro_3_para_opts • Spectroscopy Analysis Tools (spant) Return a list of options for VARPRO based fitting with 3 free parameters. — varpro_3_para_opts • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -141,7 +141,7 @@ Value
diff --git a/docs/reference/varpro_basic_opts.html b/docs/reference/varpro_basic_opts.html
index 32c86d22..c5104891 100644
--- a/docs/reference/varpro_basic_opts.html
+++ b/docs/reference/varpro_basic_opts.html
@@ -1,5 +1,5 @@
-Return a list of options for a basic VARPRO analysis. — varpro_basic_opts • Spectroscopy Analysis Tools (spant) Return a list of options for a basic VARPRO analysis. — varpro_basic_opts • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -118,7 +118,7 @@ Value
diff --git a/docs/reference/varpro_opts.html b/docs/reference/varpro_opts.html
index 2aabf11d..6332f730 100644
--- a/docs/reference/varpro_opts.html
+++ b/docs/reference/varpro_opts.html
@@ -1,5 +1,5 @@
-Return a list of options for VARPRO based fitting. — varpro_opts • Spectroscopy Analysis Tools (spant) Return a list of options for VARPRO based fitting. — varpro_opts • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -177,7 +177,7 @@ Examples
diff --git a/docs/reference/vec2mrs_data.html b/docs/reference/vec2mrs_data.html
index 0cccd73b..f0d58bf0 100644
--- a/docs/reference/vec2mrs_data.html
+++ b/docs/reference/vec2mrs_data.html
@@ -1,5 +1,5 @@
-Convert a vector into a mrs_data object. — vec2mrs_data • Spectroscopy Analysis Tools (spant) Convert a vector into a mrs_data object. — vec2mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -80,10 +80,11 @@ Convert a vector into a mrs_data object.
vec2mrs_data(
vec,
- fs = def_fs(),
- ft = def_ft(),
- ref = def_ref(),
- nuc = def_nuc(),
+ mrs_data = NULL,
+ fs = NULL,
+ ft = NULL,
+ ref = NULL,
+ nuc = NULL,
dyns = 1,
fd = FALSE
)
@@ -95,6 +96,10 @@ Arguments
the data vector.
mrs_data
+example data to copy acquisition parameters from.
fs
sampling frequency in Hz.
Arguments
fd
-flag to indicate if the matrix is in the frequency domain (logical).
flag to indicate if the vector is in the frequency domain (logical).
Value
diff --git a/docs/reference/write_basis.html b/docs/reference/write_basis.html
index b6e27cbd..94c5e021 100644
--- a/docs/reference/write_basis.html
+++ b/docs/reference/write_basis.html
@@ -1,5 +1,5 @@
-Write a basis object to an LCModel .basis formatted file. — write_basis • Spectroscopy Analysis Tools (spant) Write a basis object to an LCModel .basis formatted file. — write_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -108,7 +108,7 @@ Arguments
diff --git a/docs/reference/write_basis_tqn.html b/docs/reference/write_basis_tqn.html
index 6aa51c1d..116c73ec 100644
--- a/docs/reference/write_basis_tqn.html
+++ b/docs/reference/write_basis_tqn.html
@@ -1,5 +1,5 @@
-Generate a basis file using TARQUIN. — write_basis_tqn • Spectroscopy Analysis Tools (spant) Generate a basis file using TARQUIN. — write_basis_tqn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Examples
diff --git a/docs/reference/write_mrs.html b/docs/reference/write_mrs.html
index fff25f15..124b9dc4 100644
--- a/docs/reference/write_mrs.html
+++ b/docs/reference/write_mrs.html
@@ -1,5 +1,5 @@
-Write MRS data object to file. — write_mrs • Spectroscopy Analysis Tools (spant) Write MRS data object to file. — write_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Arguments
diff --git a/docs/reference/write_mrs_nifti.html b/docs/reference/write_mrs_nifti.html
index f4bf1921..bd3ed4b7 100644
--- a/docs/reference/write_mrs_nifti.html
+++ b/docs/reference/write_mrs_nifti.html
@@ -1,5 +1,5 @@
-Write MRS data object to file in NIFTI format. — write_mrs_nifti • Spectroscopy Analysis Tools (spant) Write MRS data object to file in NIFTI format. — write_mrs_nifti • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/write_pulse_ascii.html b/docs/reference/write_pulse_ascii.html
index 067ae086..221f8ebb 100644
--- a/docs/reference/write_pulse_ascii.html
+++ b/docs/reference/write_pulse_ascii.html
@@ -1,5 +1,5 @@
-Write an ASCII formatted pulse file. — write_pulse_ascii • Spectroscopy Analysis Tools (spant) Write an ASCII formatted pulse file. — write_pulse_ascii • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/zero_fade_spec.html b/docs/reference/zero_fade_spec.html
index c703745c..c8b572c3 100644
--- a/docs/reference/zero_fade_spec.html
+++ b/docs/reference/zero_fade_spec.html
@@ -1,7 +1,5 @@
-Fade a spectrum to zero by frequency domain multiplication with a tanh
-function. Note this operation distorts data points at the end of the FID. — zero_fade_spec • Spectroscopy Analysis Tools (spant) Fade a spectrum to zero by frequency domain multiplication with a tanh function. Note this operation distorts data points at the end of the FID. — zero_fade_spec • Spectroscopy Analysis Tools (spant) Zero all coherences including and above a given order. — zero_higher_orders • Spectroscopy Analysis Tools (spant) Zero all coherences including and above a given order. — zero_higher_orders • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Value
diff --git a/docs/reference/zero_td_pts_end.html b/docs/reference/zero_td_pts_end.html
index 8c1123c8..71d24ebb 100644
--- a/docs/reference/zero_td_pts_end.html
+++ b/docs/reference/zero_td_pts_end.html
@@ -1,5 +1,5 @@
-Set mrs_data object data points at the end of the FID to zero. — zero_td_pts_end • Spectroscopy Analysis Tools (spant) Set mrs_data object data points at the end of the FID to zero. — zero_td_pts_end • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/zf.html b/docs/reference/zf.html
index 85e2013c..baf50256 100644
--- a/docs/reference/zf.html
+++ b/docs/reference/zf.html
@@ -1,5 +1,5 @@
-Zero-fill MRS data in the time domain. — zf • Spectroscopy Analysis Tools (spant) Zero-fill MRS data in the time domain. — zf • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -125,7 +125,7 @@ Value
diff --git a/docs/reference/zf_xy.html b/docs/reference/zf_xy.html
index ebca3999..c4104a74 100644
--- a/docs/reference/zf_xy.html
+++ b/docs/reference/zf_xy.html
@@ -1,5 +1,5 @@
-Zero-fill MRSI data in the k-space x-y direction. — zf_xy • Spectroscopy Analysis Tools (spant) Zero-fill MRSI data in the k-space x-y direction. — zf_xy • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -113,7 +113,7 @@ Value
diff --git a/docs/sitemap.xml b/docs/sitemap.xml
index e2139f71..4c39f515 100644
--- a/docs/sitemap.xml
+++ b/docs/sitemap.xml
@@ -216,6 +216,12 @@
https://martin3141.github.io/spant/reference/comb_coils_fp_pc.html
+
+ https://martin3141.github.io/spant/reference/comb_coils_mrsi_gls.html
+
+
+ https://martin3141.github.io/spant/reference/comb_coils_svs_gls.html
+
https://martin3141.github.io/spant/reference/comb_csv_results.html
@@ -411,6 +417,9 @@
https://martin3141.github.io/spant/reference/gen_conv_reg.html
+
+ https://martin3141.github.io/spant/reference/gen_group_reg.html
+
https://martin3141.github.io/spant/reference/gen_impulse_reg.html
@@ -555,6 +564,15 @@
https://martin3141.github.io/spant/reference/glm_spec.html
+
+ https://martin3141.github.io/spant/reference/glm_spec_fmrs_fl.html
+
+
+ https://martin3141.github.io/spant/reference/glm_spec_fmrs_group.html
+
+
+ https://martin3141.github.io/spant/reference/glm_spec_group_linhyp.html
+
https://martin3141.github.io/spant/reference/grid_shift_xy.html
@@ -690,9 +708,15 @@
https://martin3141.github.io/spant/reference/mrs_data2basis.html
+
+ https://martin3141.github.io/spant/reference/mrs_data2bids.html
+
https://martin3141.github.io/spant/reference/mrs_data2mat.html
+
+ https://martin3141.github.io/spant/reference/mrs_data2spec_mat.html
+
https://martin3141.github.io/spant/reference/mrs_data2vec.html
@@ -741,6 +765,9 @@
https://martin3141.github.io/spant/reference/phase.html
+
+ https://martin3141.github.io/spant/reference/phase_ref_1h_brain.html
+
https://martin3141.github.io/spant/reference/plot.fit_result.html
@@ -780,6 +807,12 @@
https://martin3141.github.io/spant/reference/precomp.html
+
+ https://martin3141.github.io/spant/reference/preproc_svs.html
+
+
+ https://martin3141.github.io/spant/reference/preproc_svs_dataset.html
+
https://martin3141.github.io/spant/reference/print.fit_result.html
@@ -1050,6 +1083,9 @@
https://martin3141.github.io/spant/reference/spant_mpress_drift.html
+
+ https://martin3141.github.io/spant/reference/spant_sim_fmrs_dataset.html
+
https://martin3141.github.io/spant/reference/spant_simulation_benchmark.html
@@ -1107,6 +1143,9 @@
https://martin3141.github.io/spant/reference/svs_1h_brain_batch_analysis.html
+
+ https://martin3141.github.io/spant/reference/t_test_spec.html
+
https://martin3141.github.io/spant/reference/td2fd.html
Site built with pkgdown 2.0.7.
+Site built with pkgdown 2.0.9.
diff --git a/docs/articles/spant-intro.html b/docs/articles/spant-intro.html index aa3da6d1..f91bcb30 100644 --- a/docs/articles/spant-intro.html +++ b/docs/articles/spant-intro.html @@ -12,7 +12,7 @@ - + @@ -40,7 +40,7 @@ @@ -178,78 +178,79 @@Basis simulation#> GSH,Glu,GPC,Ins,Lac,Lip09,
#> Lip13a,Lip13b,Lip20,MM09,MM12,
#> MM14,MM17,MM20,NAA,NAAG,PCh,
-#> PCr,sIns,Tau
-stackplot(basis, xlim = c(4, 0.5), labels = basis$names, y_offset = 5)
+#> PCr,sIns,Tau
+
Perform ABfit analysis of the processed data
(mrs_proc):
-
+
fit_res <- fit_mrs(mrs_proc, basis)
Plot the fit result:
-
+
plot(fit_res)
Unscaled amplitudes, CRLB error estimates and other useful fitting
diagnostics, such as SNR, are given in the fit_res results
table:
-
+
fit_res$res_tab
-#> X Y Z Dynamic Coil X.CrCH2 Ala Asp Cr
-#> 1 1 1 1 1 1 0 8.228912e-06 3.548337e-05 4.020305e-05
-#> GABA Glc Gln GSH Glu GPC
-#> 1 1.706754e-05 2.442067e-06 3.029726e-06 2.227786e-05 6.499645e-05 1.603288e-05
-#> Ins Lac Lip09 Lip13a Lip13b Lip20 MM09
-#> 1 5.902957e-05 5.818739e-06 2.362972e-05 2.635502e-06 0 0 9.887557e-06
-#> MM12 MM14 MM17 MM20 NAA NAAG
-#> 1 6.546986e-06 2.59994e-05 2.245507e-05 9.207418e-05 5.981787e-05 1.556188e-05
-#> PCh PCr sIns Tau tNAA tCr tCho
-#> 1 0 2.101297e-05 6.508636e-06 0 7.537975e-05 6.121601e-05 1.603288e-05
-#> Glx tLM09 tLM13 tLM20 X.CrCH2.sd Ala.sd
-#> 1 6.802617e-05 3.351728e-05 3.518189e-05 9.207418e-05 2.383751e-06 4.353306e-06
+#> X Y Z Dynamic Coil X.CrCH2 Ala Asp Cr GABA
+#> 1 1 1 1 1 1 0 8.133932e-06 3.547065e-05 4.02672e-05 1.697281e-05
+#> Glc Gln GSH Glu GPC Ins
+#> 1 2.446596e-06 3.036132e-06 2.228048e-05 6.503217e-05 1.606706e-05 5.906155e-05
+#> Lac Lip09 Lip13a Lip13b Lip20 MM09 MM12
+#> 1 5.802284e-06 2.387704e-05 2.670653e-06 0 0 9.630788e-06 6.511381e-06
+#> MM14 MM17 MM20 NAA NAAG PCh
+#> 1 2.603855e-05 2.238405e-05 9.203743e-05 6.011109e-05 1.536531e-05 0
+#> PCr sIns Tau tNAA tCr tCho
+#> 1 2.101921e-05 6.504098e-06 0 7.54764e-05 6.12864e-05 1.606706e-05
+#> Glx tLM09 tLM13 tLM20 X.CrCH2.sd Ala.sd
+#> 1 6.80683e-05 3.350783e-05 3.522059e-05 9.203743e-05 2.386861e-06 4.343919e-06
#> Asp.sd Cr.sd GABA.sd Glc.sd Gln.sd GSH.sd
-#> 1 9.243626e-06 3.715175e-06 4.580082e-06 4.427045e-06 5.089143e-06 2.022836e-06
+#> 1 9.235326e-06 3.689004e-06 4.574407e-06 4.421681e-06 5.083001e-06 2.020426e-06
#> Glu.sd GPC.sd Ins.sd Lac.sd Lip09.sd Lip13a.sd
-#> 1 5.086888e-06 2.525936e-06 2.091039e-06 5.311855e-06 4.118786e-06 1.328562e-05
+#> 1 5.082976e-06 2.602651e-06 2.093225e-06 5.301703e-06 4.119256e-06 1.328305e-05
#> Lip13b.sd Lip20.sd MM09.sd MM12.sd MM14.sd MM17.sd
-#> 1 6.477225e-06 7.510915e-06 3.827221e-06 4.597884e-06 7.234429e-06 3.810268e-06
+#> 1 6.474481e-06 7.510908e-06 3.827554e-06 4.594019e-06 7.223367e-06 3.811301e-06
#> MM20.sd NAA.sd NAAG.sd PCh.sd PCr.sd sIns.sd
-#> 1 8.602464e-06 1.015226e-06 1.215672e-06 2.174697e-06 3.108036e-06 7.233855e-07
-#> Tau.sd tNAA.sd tCr.sd tCho.sd Glx.sd tLM09.sd
-#> 1 3.777984e-06 7.031059e-07 5.881706e-07 2.1135e-07 3.165045e-06 1.006532e-06
-#> tLM13.sd tLM20.sd phase lw shift asym
-#> 1 1.572003e-06 3.018189e-06 11.15087 5.038937 -0.003427612 0.1764497
+#> 1 8.595853e-06 1.017712e-06 1.208985e-06 2.236873e-06 3.084598e-06 7.240068e-07
+#> Tau.sd tNAA.sd tCr.sd tCho.sd Glx.sd tLM09.sd
+#> 1 3.759956e-06 7.031383e-07 5.890481e-07 2.110662e-07 3.16966e-06 1.006794e-06
+#> tLM13.sd tLM20.sd phase lw shift asym
+#> 1 1.573147e-06 3.016809e-06 11.10963 5.023681 -0.00376505 0.1771067
#> res.deviance res.niter res.info
-#> 1 7.300317e-05 28 2
+#> 1 7.307669e-05 28 2
#> res.message bl_ed_pppm
#> 1 Relative error between `par' and the solution is at most `ptol'. 2.364083
-#> max_bl_flex_used full_res fit_pts ppm_range SNR SRR FQN
-#> 1 FALSE 7.745303e-05 497 3.8 62.79191 51.44068 1.490027
+#> max_bl_flex_used full_res fit_pts ppm_range SNR SRR FQN
+#> 1 FALSE 7.754368e-05 497 3.8 62.71687 51.3328 1.492722
#> tNAA_lw tCr_lw tCho_lw auto_bl_crit_7 auto_bl_crit_5.901
-#> 1 0.04565271 0.05199592 0.05438808 -8.904402 -8.947808
+#> 1 0.04562445 0.05189506 0.05438237 -8.900349 -8.944159
#> auto_bl_crit_4.942 auto_bl_crit_4.12 auto_bl_crit_3.425 auto_bl_crit_2.844
-#> 1 -8.980941 -9.003463 -9.016574 -9.023969
+#> 1 -8.977355 -9.000064 -9.013367 -9.02055
#> auto_bl_crit_2.364 auto_bl_crit_1.969 auto_bl_crit_1.647 auto_bl_crit_1.384
-#> 1 -9.027876 -9.027566 -9.014311 -8.963287
+#> 1 -9.024177 -9.023462 -9.009854 -8.958654
#> auto_bl_crit_1.17 auto_bl_crit_0.997 auto_bl_crit_0.856 auto_bl_crit_0.743
-#> 1 -8.848747 -8.694785 -8.565992 -8.488415
+#> 1 -8.844271 -8.690744 -8.562631 -8.485471
#> auto_bl_crit_0.654 auto_bl_crit_0.593 auto_bl_crit_0.558 auto_bl_crit_0.54
-#> 1 -8.449874 -8.432813 -8.425648 -8.42266
+#> 1 -8.447136 -8.430174 -8.423053 -8.420086
#> auto_bl_crit_0.532 auto_bl_crit_0.529
-#> 1 -8.421406 -8.420875
+#> 1 -8.418839 -8.418312
Note that signal names appended with “.sd” are the CRLB estimates for
the uncertainty (standard deviation) in the metabolite quantity
estimate. e.g. to calculate the percentage s.d. for tNAA:
-
+
fit_res$res_tab$tNAA.sd / fit_res$res_tab$tNAA * 100
-#> [1] 0.9327517
+#> [1] 0.9316001
Spectral SNR:
-
+
fit_res$res_tab$SNR
-#> [1] 62.79191
+#> [1] 62.71687
Linewidth of the tNAA resonance in PPM:
-
+
fit_res$res_tab$tNAA_lw
-#> [1] 0.04565271
+#> [1] 0.04562445
Ratios to total-creatine
@@ -258,45 +259,45 @@ Ratios to total-creatine
-
+
fit_res_tcr_sc <- scale_amp_ratio(fit_res, "tCr")
amps <- fit_amps(fit_res_tcr_sc)
print(t(amps))
#> [,1]
#> X.CrCH2 0.00000000
-#> Ala 0.13442417
-#> Asp 0.57964197
-#> Cr 0.65674069
-#> GABA 0.27880838
-#> Glc 0.03989262
-#> Gln 0.04949238
-#> GSH 0.36392207
-#> Glu 1.06175561
-#> GPC 0.26190670
-#> Ins 0.96428305
-#> Lac 0.09505257
-#> Lip09 0.38600560
-#> Lip13a 0.04305248
+#> Ala 0.13272001
+#> Asp 0.57876874
+#> Cr 0.65703313
+#> GABA 0.27694252
+#> Glc 0.03992071
+#> Gln 0.04954005
+#> GSH 0.36354683
+#> Glu 1.06111906
+#> GPC 0.26216356
+#> Ins 0.96369746
+#> Lac 0.09467490
+#> Lip09 0.38959768
+#> Lip13a 0.04357660
#> Lip13b 0.00000000
#> Lip20 0.00000000
-#> MM09 0.16151913
-#> MM12 0.10694891
-#> MM14 0.42471563
-#> MM17 0.36681686
-#> MM20 1.50408643
-#> NAA 0.97716047
-#> NAAG 0.25421252
+#> MM09 0.15714395
+#> MM12 0.10624512
+#> MM14 0.42486672
+#> MM17 0.36523688
+#> MM20 1.50175937
+#> NAA 0.98082268
+#> NAAG 0.25071313
#> PCh 0.00000000
-#> PCr 0.34325931
-#> sIns 0.10632244
+#> PCr 0.34296687
+#> sIns 0.10612627
#> Tau 0.00000000
-#> tNAA 1.23137299
+#> tNAA 1.23153582
#> tCr 1.00000000
-#> tCho 0.26190670
-#> Glx 1.11124799
-#> tLM09 0.54752473
-#> tLM13 0.57471702
-#> tLM20 1.50408643
+#> tCho 0.26216356
+#> Glx 1.11065912
+#> tLM09 0.54674163
+#> tLM13 0.57468844
+#> tLM20 1.50175937
Water reference scaling, AKA “absolute-quantification”
@@ -304,29 +305,29 @@ Water reference sca
A more sophisticated approach to scaling metabolite values involves
the use of a separate water-reference acquisition - which can be
imported in the standard way:
-
+
fname_wref <- system.file("extdata", "philips_spar_sdat_W.SDAT", package = "spant")
mrs_data_wref <- read_mrs(fname_wref)
The following code assumes the voxel contains 100% white matter
tissue and scales the metabolite values into molal (mM) units (mol / kg
tissue water) based on the method described by Gasparovic et al MRM 2006
55(6):1219-26:
-
+
p_vols <- c(WM = 100, GM = 0, CSF = 0)
TE = 0.03
TR = 2
fit_res_molal <- scale_amp_molal_pvc(fit_res, mrs_data_wref, p_vols, TE, TR)
fit_res_molal$res_tab$tNAA
-#> [1] 12.58176
+#> [1] 12.59789
An alternative method scales the metabolite values into molar (mM)
units (mol / Litre of tissue) based on assumptions outlined in the
LCModel manual and references therein (section 10.2). This approach may
be preferred when comparing results to those obtained LCModel or
TARQUIN.
-
+
fit_res_molar <- scale_amp_molar(fit_res, mrs_data_wref)
fit_res_molar$res_tab$tNAA
-#> [1] 6.817594
+#> [1] 6.826336
Note, while “absolute” units are attractive, a large number of
assumptions about metabolite and water relaxation rates are necessary to
arrive at these mM estimates. If you’re not confident at being able to
@@ -354,7 +355,7 @@
Water reference sca
diff --git a/docs/articles/spant-intro_files/figure-html/unnamed-chunk-10-1.png b/docs/articles/spant-intro_files/figure-html/unnamed-chunk-10-1.png
index b84cd2d5..a8160510 100644
Binary files a/docs/articles/spant-intro_files/figure-html/unnamed-chunk-10-1.png and b/docs/articles/spant-intro_files/figure-html/unnamed-chunk-10-1.png differ
diff --git a/docs/articles/spant-intro_files/figure-html/unnamed-chunk-7-1.png b/docs/articles/spant-intro_files/figure-html/unnamed-chunk-7-1.png
index 15bdc4e5..94a3f545 100644
Binary files a/docs/articles/spant-intro_files/figure-html/unnamed-chunk-7-1.png and b/docs/articles/spant-intro_files/figure-html/unnamed-chunk-7-1.png differ
diff --git a/docs/articles/spant-metabolite-simulation.html b/docs/articles/spant-metabolite-simulation.html
index e6efca00..564fa989 100644
--- a/docs/articles/spant-metabolite-simulation.html
+++ b/docs/articles/spant-metabolite-simulation.html
@@ -12,7 +12,7 @@
-
+
@@ -40,7 +40,7 @@
@@ -279,8 +279,9 @@ Custom molecules#> L/G lineshape : 0
#>
#> nucleus chem_shift
-#> 1 1H 2.5
-custom_mol |> sim_mol() |> lb(2) |> zf() |> plot(xlim = c(4.4, 0.5))
+#> 1 1H 2.5
+
Once your happy the new molecule is correct, please consider
contributing it to the package if you think others would benefit.
@@ -304,7 +305,7 @@ Custom molecules
-Site built with pkgdown 2.0.7.
+Site built with pkgdown 2.0.9.
diff --git a/docs/articles/spant-preprocessing.html b/docs/articles/spant-preprocessing.html
index 28e38762..9544cf71 100644
--- a/docs/articles/spant-preprocessing.html
+++ b/docs/articles/spant-preprocessing.html
@@ -12,7 +12,7 @@
-
+
@@ -40,7 +40,7 @@
@@ -179,7 +179,7 @@ Reading raw data and plotting
-Site built with pkgdown 2.0.7.
+Site built with pkgdown 2.0.9.
diff --git a/docs/articles/spant-preprocessing_files/figure-html/unnamed-chunk-10-1.png b/docs/articles/spant-preprocessing_files/figure-html/unnamed-chunk-10-1.png
index 02bdd7ca..d9d919b3 100644
Binary files a/docs/articles/spant-preprocessing_files/figure-html/unnamed-chunk-10-1.png and b/docs/articles/spant-preprocessing_files/figure-html/unnamed-chunk-10-1.png differ
diff --git a/docs/articles/spant-preprocessing_files/figure-html/unnamed-chunk-8-1.png b/docs/articles/spant-preprocessing_files/figure-html/unnamed-chunk-8-1.png
index f8a9f999..9cc14061 100644
Binary files a/docs/articles/spant-preprocessing_files/figure-html/unnamed-chunk-8-1.png and b/docs/articles/spant-preprocessing_files/figure-html/unnamed-chunk-8-1.png differ
diff --git a/docs/authors.html b/docs/authors.html
index fd4064a4..34e6b241 100644
--- a/docs/authors.html
+++ b/docs/authors.html
@@ -1,5 +1,5 @@
-Authors and Citation • Spectroscopy Analysis Tools (spant) Authors and Citation • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -69,7 +69,7 @@
diff --git a/docs/index.html b/docs/index.html
index 6e715d8e..c58968f6 100644
--- a/docs/index.html
+++ b/docs/index.html
@@ -12,16 +12,13 @@
-
+
-
+
Changelog • Spectroscopy Analysis Tools (spant) Changelog • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -73,7 +73,13 @@ Changelog
-spant 2.21.0
+spant 2.22.0
+- Added find_bids_mrs and mrs_data2bids helper functions.
+- Improved handling of CMRR semi-LASER SVS water reference scans.
+- Added functions for GLS coil combination.
+
+
+spant 2.21.02024-05-30
- Fixed compiler warnings for Fortran code.
- Added glm_spec function.
- Added add_noise_spec_snr function.
@@ -584,7 +590,7 @@ spant 0.1.02
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml
index 510f032e..8099ddc1 100644
--- a/docs/pkgdown.yml
+++ b/docs/pkgdown.yml
@@ -1,5 +1,5 @@
-pandoc: 3.1.1
-pkgdown: 2.0.7
+pandoc: 3.1.11
+pkgdown: 2.0.9
pkgdown_sha: ~
articles:
abfit-baseline-opts: abfit-baseline-opts.html
@@ -7,7 +7,7 @@ articles:
spant-intro: spant-intro.html
spant-metabolite-simulation: spant-metabolite-simulation.html
spant-preprocessing: spant-preprocessing.html
-last_built: 2024-05-29T18:39Z
+last_built: 2024-07-11T11:18Z
urls:
reference: https://martin3141.github.io/spant/reference
article: https://martin3141.github.io/spant/articles
diff --git a/docs/reference/Arg.mrs_data.html b/docs/reference/Arg.mrs_data.html
index 1372d866..4eba752f 100644
--- a/docs/reference/Arg.mrs_data.html
+++ b/docs/reference/Arg.mrs_data.html
@@ -1,5 +1,5 @@
-Apply Arg operator to an MRS dataset. — Arg.mrs_data • Spectroscopy Analysis Tools (spant) Apply Arg operator to an MRS dataset. — Arg.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -107,7 +107,7 @@ Value
diff --git a/docs/reference/Conj.mrs_data.html b/docs/reference/Conj.mrs_data.html
index 794d446f..10ea0ef1 100644
--- a/docs/reference/Conj.mrs_data.html
+++ b/docs/reference/Conj.mrs_data.html
@@ -1,5 +1,5 @@
-Apply Conj operator to an MRS dataset. — Conj.mrs_data • Spectroscopy Analysis Tools (spant) Apply Conj operator to an MRS dataset. — Conj.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -107,7 +107,7 @@ Value
diff --git a/docs/reference/Im.mrs_data.html b/docs/reference/Im.mrs_data.html
index 4c9a70eb..e0e26588 100644
--- a/docs/reference/Im.mrs_data.html
+++ b/docs/reference/Im.mrs_data.html
@@ -1,5 +1,5 @@
-Apply Im operator to an MRS dataset. — Im.mrs_data • Spectroscopy Analysis Tools (spant) Apply Im operator to an MRS dataset. — Im.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -107,7 +107,7 @@ Value
diff --git a/docs/reference/Imzap.html b/docs/reference/Imzap.html
index a3eeaed6..cf1b088d 100644
--- a/docs/reference/Imzap.html
+++ b/docs/reference/Imzap.html
@@ -1,7 +1,5 @@
-Complex rounding function taken from complexplus package to reduce the number
-of spant dependencies. — Imzap • Spectroscopy Analysis Tools (spant) Complex rounding function taken from complexplus package to reduce the number of spant dependencies. — Imzap • Spectroscopy Analysis Tools (spant) Apply Mod operator to an MRS dataset. — Mod.mrs_data • Spectroscopy Analysis Tools (spant) Apply Mod operator to an MRS dataset. — Mod.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -107,7 +107,7 @@ Value
diff --git a/docs/reference/Ncoils.html b/docs/reference/Ncoils.html
index 503ce5c0..09d22662 100644
--- a/docs/reference/Ncoils.html
+++ b/docs/reference/Ncoils.html
@@ -1,5 +1,5 @@
-Return the total number of coil elements in an MRS dataset. — Ncoils • Spectroscopy Analysis Tools (spant) Return the total number of coil elements in an MRS dataset. — Ncoils • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/Ndyns.html b/docs/reference/Ndyns.html
index 49c3ebb2..26ca34a7 100644
--- a/docs/reference/Ndyns.html
+++ b/docs/reference/Ndyns.html
@@ -1,5 +1,5 @@
-Return the total number of dynamic scans in an MRS dataset. — Ndyns • Spectroscopy Analysis Tools (spant) Return the total number of dynamic scans in an MRS dataset. — Ndyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/Npts.html b/docs/reference/Npts.html
index c63fe64e..7e8af89e 100644
--- a/docs/reference/Npts.html
+++ b/docs/reference/Npts.html
@@ -1,5 +1,5 @@
-Return the number of data points in an MRS dataset. — Npts • Spectroscopy Analysis Tools (spant) Return the number of data points in an MRS dataset. — Npts • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/Nspec.html b/docs/reference/Nspec.html
index e5f2464a..ff6c4dcd 100644
--- a/docs/reference/Nspec.html
+++ b/docs/reference/Nspec.html
@@ -1,5 +1,5 @@
-Return the total number of spectra in an MRS dataset. — Nspec • Spectroscopy Analysis Tools (spant) Return the total number of spectra in an MRS dataset. — Nspec • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/Ntrans.html b/docs/reference/Ntrans.html
index 3d3ce629..32ae3ad6 100644
--- a/docs/reference/Ntrans.html
+++ b/docs/reference/Ntrans.html
@@ -1,5 +1,5 @@
-Return the total number of acquired transients for an MRS dataset. — Ntrans • Spectroscopy Analysis Tools (spant) Return the total number of acquired transients for an MRS dataset. — Ntrans • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/Nx.html b/docs/reference/Nx.html
index beb130b8..461192b3 100644
--- a/docs/reference/Nx.html
+++ b/docs/reference/Nx.html
@@ -1,5 +1,5 @@
-Return the total number of x locations in an MRS dataset. — Nx • Spectroscopy Analysis Tools (spant) Return the total number of x locations in an MRS dataset. — Nx • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/Ny.html b/docs/reference/Ny.html
index 5c23ee37..530efde4 100644
--- a/docs/reference/Ny.html
+++ b/docs/reference/Ny.html
@@ -1,5 +1,5 @@
-Return the total number of y locations in an MRS dataset. — Ny • Spectroscopy Analysis Tools (spant) Return the total number of y locations in an MRS dataset. — Ny • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/Nz.html b/docs/reference/Nz.html
index 2a28bfbb..15295f98 100644
--- a/docs/reference/Nz.html
+++ b/docs/reference/Nz.html
@@ -1,5 +1,5 @@
-Return the total number of z locations in an MRS dataset. — Nz • Spectroscopy Analysis Tools (spant) Return the total number of z locations in an MRS dataset. — Nz • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/Re.mrs_data.html b/docs/reference/Re.mrs_data.html
index bbdcd3e7..37608c36 100644
--- a/docs/reference/Re.mrs_data.html
+++ b/docs/reference/Re.mrs_data.html
@@ -1,5 +1,5 @@
-Apply Re operator to an MRS dataset. — Re.mrs_data • Spectroscopy Analysis Tools (spant) Apply Re operator to an MRS dataset. — Re.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -107,7 +107,7 @@ Value
diff --git a/docs/reference/abfit_opts.html b/docs/reference/abfit_opts.html
index d501fc2a..5524db43 100644
--- a/docs/reference/abfit_opts.html
+++ b/docs/reference/abfit_opts.html
@@ -1,5 +1,5 @@
-Return a list of options for an ABfit analysis. — abfit_opts • Spectroscopy Analysis Tools (spant) Return a list of options for an ABfit analysis. — abfit_opts • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -125,7 +125,8 @@ Return a list of options for an ABfit analysis.
input_paras_raw = NULL,
optim_lw_only = FALSE,
optim_lw_only_limit = 20,
- lb_init = 0.001
+ lb_init = 0.001,
+ zf_offset = NULL
)
@@ -347,6 +348,12 @@ Arguments
basis signals. Setting to 0 will clash with the minimum allowable value
(eg hard constraint) during the detailed fit.
+
+zf_offset
+offset in number of data points from the end of the FID to
+zero-fill. Default is NULL and will automatically set this to 50 points when
+the FID distortion flag is set for the mrs_data.
Value
@@ -372,7 +379,7 @@ Examples
diff --git a/docs/reference/abfit_opts_v1_9_0.html b/docs/reference/abfit_opts_v1_9_0.html
index 1c128a05..975f7a0a 100644
--- a/docs/reference/abfit_opts_v1_9_0.html
+++ b/docs/reference/abfit_opts_v1_9_0.html
@@ -1,7 +1,5 @@
-Return a list of options for an ABfit analysis to maintain comparability with
-analyses performed with version 1.9.0 (and earlier) of spant. — abfit_opts_v1_9_0 • Spectroscopy Analysis Tools (spant) Return a list of options for an ABfit analysis to maintain comparability with analyses performed with version 1.9.0 (and earlier) of spant. — abfit_opts_v1_9_0 • Spectroscopy Analysis Tools (spant) Simulate pulse sequence acquisition. — acquire • Spectroscopy Analysis Tools (spant) Simulate pulse sequence acquisition. — acquire • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/add_noise.html b/docs/reference/add_noise.html
index 5c395587..c2ded890 100644
--- a/docs/reference/add_noise.html
+++ b/docs/reference/add_noise.html
@@ -1,5 +1,5 @@
-Add noise to an mrs_data object. — add_noise • Spectroscopy Analysis Tools (spant) Add noise to an mrs_data object. — add_noise • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -116,7 +116,7 @@ Value
diff --git a/docs/reference/add_noise_spec_snr.html b/docs/reference/add_noise_spec_snr.html
index f0072ef4..92a0fab3 100644
--- a/docs/reference/add_noise_spec_snr.html
+++ b/docs/reference/add_noise_spec_snr.html
@@ -1,5 +1,5 @@
-Add noise to an mrs_data object to match a given SNR. — add_noise_spec_snr • Spectroscopy Analysis Tools (spant) Add noise to an mrs_data object to match a given SNR. — add_noise_spec_snr • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -78,7 +78,12 @@ Add noise to an mrs_data object to match a given SNR.
- add_noise_spec_snr(mrs_data, target_snr, sig_region = c(4, 0.5))
+ add_noise_spec_snr(
+ mrs_data,
+ target_snr,
+ sig_region = c(4, 0.5),
+ ref_data = NULL
+)
@@ -97,6 +102,11 @@ Arguments
spectral limits to search for the strongest spectral data
point.
ref_data
+measure the signal from the first scan in this reference data
+and apply the same target noise level to mrs_data.
Value
@@ -117,7 +127,7 @@ Value
diff --git a/docs/reference/align.html b/docs/reference/align.html
index f61afc9f..53697923 100644
--- a/docs/reference/align.html
+++ b/docs/reference/align.html
@@ -1,5 +1,5 @@
-Align spectra to a reference frequency using a convolution based method. — align • Spectroscopy Analysis Tools (spant) Align spectra to a reference frequency using a convolution based method. — align • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -146,7 +146,7 @@ Value
diff --git a/docs/reference/apodise_xy.html b/docs/reference/apodise_xy.html
index 35121da6..9f622f56 100644
--- a/docs/reference/apodise_xy.html
+++ b/docs/reference/apodise_xy.html
@@ -1,5 +1,5 @@
-Apodise MRSI data in the x-y direction with a k-space filter. — apodise_xy • Spectroscopy Analysis Tools (spant) Apodise MRSI data in the x-y direction with a k-space filter. — apodise_xy • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -88,7 +88,7 @@ Arguments
func
-must be "hamming" or "gaussian".
must be "hamming", "hanning" or "gaussian".
w
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/append_basis.html b/docs/reference/append_basis.html
index cf58e336..c32f7be3 100644
--- a/docs/reference/append_basis.html
+++ b/docs/reference/append_basis.html
@@ -1,5 +1,5 @@
-Combine a pair of basis set objects. — append_basis • Spectroscopy Analysis Tools (spant) Combine a pair of basis set objects. — append_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/append_coils.html b/docs/reference/append_coils.html
index 6e2ead5b..99c8c3cf 100644
--- a/docs/reference/append_coils.html
+++ b/docs/reference/append_coils.html
@@ -1,7 +1,5 @@
-Append MRS data across the coil dimension, assumes they matched across the
-other dimensions. — append_coils • Spectroscopy Analysis Tools (spant) Append MRS data across the coil dimension, assumes they matched across the other dimensions. — append_coils • Spectroscopy Analysis Tools (spant) Append MRS data across the dynamic dimension, assumes they matched across the
-other dimensions. — append_dyns • Spectroscopy Analysis Tools (spant) Append MRS data across the dynamic dimension, assumes they matched across the other dimensions. — append_dyns • Spectroscopy Analysis Tools (spant) Append multiple regressor data frames into a single data frame. — append_regs • Spectroscopy Analysis Tools (spant) Append multiple regressor data frames into a single data frame. — append_regs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/apply_axes.html b/docs/reference/apply_axes.html
index 0f2f4d55..b5a7e296 100644
--- a/docs/reference/apply_axes.html
+++ b/docs/reference/apply_axes.html
@@ -1,5 +1,5 @@
-Apply a function over specified array axes. — apply_axes • Spectroscopy Analysis Tools (spant) Apply a function over specified array axes. — apply_axes • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -130,7 +130,7 @@ Examples
diff --git a/docs/reference/apply_mrs.html b/docs/reference/apply_mrs.html
index 22bc1933..1e2ea9ed 100644
--- a/docs/reference/apply_mrs.html
+++ b/docs/reference/apply_mrs.html
@@ -1,5 +1,5 @@
-Apply a function across given dimensions of a MRS data object. — apply_mrs • Spectroscopy Analysis Tools (spant) Apply a function across given dimensions of a MRS data object. — apply_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -116,7 +116,7 @@ Arguments
diff --git a/docs/reference/apply_pulse.html b/docs/reference/apply_pulse.html
index cae875cf..17c6e3ae 100644
--- a/docs/reference/apply_pulse.html
+++ b/docs/reference/apply_pulse.html
@@ -1,5 +1,5 @@
-Simulate an RF pulse on a single spin. — apply_pulse • Spectroscopy Analysis Tools (spant) Simulate an RF pulse on a single spin. — apply_pulse • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -126,7 +126,7 @@ Value
diff --git a/docs/reference/array2mrs_data.html b/docs/reference/array2mrs_data.html
index 26278811..c5f77129 100644
--- a/docs/reference/array2mrs_data.html
+++ b/docs/reference/array2mrs_data.html
@@ -1,7 +1,5 @@
-Convert a 7 dimensional array in into a mrs_data object. The array dimensions
-should be ordered as : dummy, X, Y, Z, dynamic, coil, FID. — array2mrs_data • Spectroscopy Analysis Tools (spant) Convert a 7 dimensional array in into a mrs_data object. The array dimensions should be ordered as : dummy, X, Y, Z, dynamic, coil, FID. — array2mrs_data • Spectroscopy Analysis Tools (spant) Perform zeroth-order phase correction based on the minimisation of the
-squared difference between the real and magnitude components of the
-spectrum. — auto_phase • Spectroscopy Analysis Tools (spant) Perform zeroth-order phase correction based on the minimisation of the squared difference between the real and magnitude components of the spectrum. — auto_phase • Spectroscopy Analysis Tools (spant) Back extrapolate time-domain data points using an autoregressive model. — back_extrap_ar • Spectroscopy Analysis Tools (spant) Back extrapolate time-domain data points using an autoregressive model. — back_extrap_ar • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -136,7 +136,7 @@ Value
diff --git a/docs/reference/basis2dyn_mrs_data.html b/docs/reference/basis2dyn_mrs_data.html
index 1e334800..ef466e85 100644
--- a/docs/reference/basis2dyn_mrs_data.html
+++ b/docs/reference/basis2dyn_mrs_data.html
@@ -1,5 +1,5 @@
-Convert a basis object to a dynamic mrs_data object. — basis2dyn_mrs_data • Spectroscopy Analysis Tools (spant) Convert a basis object to a dynamic mrs_data object. — basis2dyn_mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Value
diff --git a/docs/reference/basis2mrs_data.html b/docs/reference/basis2mrs_data.html
index d712d28f..dd0f65d9 100644
--- a/docs/reference/basis2mrs_data.html
+++ b/docs/reference/basis2mrs_data.html
@@ -1,7 +1,5 @@
-Convert a basis object to an mrs_data object - where basis signals are spread
-across the dynamic dimension. — basis2mrs_data • Spectroscopy Analysis Tools (spant) Convert a basis object to an mrs_data object - where basis signals are spread across the dynamic dimension. — basis2mrs_data • Spectroscopy Analysis Tools (spant) Generate a spline basis, slightly adapted from : "Splines, knots, and
-penalties", Eilers 2010. — bbase • Spectroscopy Analysis Tools (spant) Baseline correction using the ALS method. — bc_als • Spectroscopy Analysis Tools (spant) Baseline correction using the ALS method. — bc_als • Spectroscopy Analysis Tools (spant) Remove a constant baseline offset based on a reference spectral region. — bc_constant • Spectroscopy Analysis Tools (spant) Remove a constant baseline offset based on a reference spectral region. — bc_constant • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/bc_gauss.html b/docs/reference/bc_gauss.html
index 265fce5e..29fee72a 100644
--- a/docs/reference/bc_gauss.html
+++ b/docs/reference/bc_gauss.html
@@ -1,5 +1,5 @@
-Apply and subtract a Gaussian smoother in the spectral domain. — bc_gauss • Spectroscopy Analysis Tools (spant) Apply and subtract a Gaussian smoother in the spectral domain. — bc_gauss • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/bc_poly.html b/docs/reference/bc_poly.html
index e4f74fea..50b824de 100644
--- a/docs/reference/bc_poly.html
+++ b/docs/reference/bc_poly.html
@@ -1,5 +1,5 @@
-Fit and subtract a polynomial to each spectrum in a dataset. — bc_poly • Spectroscopy Analysis Tools (spant) Fit and subtract a polynomial to each spectrum in a dataset. — bc_poly • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/bc_spline.html b/docs/reference/bc_spline.html
index 09d7fc51..33239c4a 100644
--- a/docs/reference/bc_spline.html
+++ b/docs/reference/bc_spline.html
@@ -1,5 +1,5 @@
-Fit and subtract a smoothing spline to each spectrum in a dataset. — bc_spline • Spectroscopy Analysis Tools (spant) Fit and subtract a smoothing spline to each spectrum in a dataset. — bc_spline • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/beta2lw.html b/docs/reference/beta2lw.html
index 331a5c0b..d6afbc92 100644
--- a/docs/reference/beta2lw.html
+++ b/docs/reference/beta2lw.html
@@ -1,7 +1,5 @@
-Covert a beta value in the time-domain to an equivalent linewidth in Hz:
-x * exp(-i * t * t * beta). — beta2lw • Spectroscopy Analysis Tools (spant) Covert a beta value in the time-domain to an equivalent linewidth in Hz: x * exp(-i * t * t * beta). — beta2lw • Spectroscopy Analysis Tools (spant) Bin equally spaced spectral regions. — bin_spec • Spectroscopy Analysis Tools (spant) Bin equally spaced spectral regions. — bin_spec • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/calc_coil_noise_cor.html b/docs/reference/calc_coil_noise_cor.html
index beeab373..935cf09f 100644
--- a/docs/reference/calc_coil_noise_cor.html
+++ b/docs/reference/calc_coil_noise_cor.html
@@ -1,5 +1,5 @@
-Calculate the noise correlation between coil elements. — calc_coil_noise_cor • Spectroscopy Analysis Tools (spant) Calculate the noise correlation between coil elements. — calc_coil_noise_cor • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/calc_coil_noise_sd.html b/docs/reference/calc_coil_noise_sd.html
index 2a788fc7..d5f47a93 100644
--- a/docs/reference/calc_coil_noise_sd.html
+++ b/docs/reference/calc_coil_noise_sd.html
@@ -1,5 +1,5 @@
-Calculate the noise standard deviation for each coil element. — calc_coil_noise_sd • Spectroscopy Analysis Tools (spant) Calculate the noise standard deviation for each coil element. — calc_coil_noise_sd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/calc_design_efficiency.html b/docs/reference/calc_design_efficiency.html
index 0fc73261..2975440c 100644
--- a/docs/reference/calc_design_efficiency.html
+++ b/docs/reference/calc_design_efficiency.html
@@ -1,5 +1,5 @@
-Calculate the efficiency of a regressor data frame. — calc_design_efficiency • Spectroscopy Analysis Tools (spant) Calculate the efficiency of a regressor data frame. — calc_design_efficiency • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/calc_ed_from_lambda.html b/docs/reference/calc_ed_from_lambda.html
index 56237859..7962e054 100644
--- a/docs/reference/calc_ed_from_lambda.html
+++ b/docs/reference/calc_ed_from_lambda.html
@@ -1,5 +1,5 @@
-Calculate the effective dimensions of a spline smoother from lambda. — calc_ed_from_lambda • Spectroscopy Analysis Tools (spant) Calculate the effective dimensions of a spline smoother from lambda. — calc_ed_from_lambda • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/calc_peak_info_vec.html b/docs/reference/calc_peak_info_vec.html
index 79914d1f..03813eb8 100644
--- a/docs/reference/calc_peak_info_vec.html
+++ b/docs/reference/calc_peak_info_vec.html
@@ -1,5 +1,5 @@
-Calculate the FWHM of a peak from a vector of intensity values. — calc_peak_info_vec • Spectroscopy Analysis Tools (spant) Calculate the FWHM of a peak from a vector of intensity values. — calc_peak_info_vec • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/calc_sd_poly.html b/docs/reference/calc_sd_poly.html
index 737d68c7..c2f6d1eb 100644
--- a/docs/reference/calc_sd_poly.html
+++ b/docs/reference/calc_sd_poly.html
@@ -1,7 +1,5 @@
-Perform a polynomial fit, subtract and return the standard deviation of the
-residuals. — calc_sd_poly • Spectroscopy Analysis Tools (spant) Perform a polynomial fit, subtract and return the standard deviation of the residuals. — calc_sd_poly • Spectroscopy Analysis Tools (spant) Calculate the sum of squares differences between two mrs_data objects. — calc_spec_diff • Spectroscopy Analysis Tools (spant) Calculate the sum of squares differences between two mrs_data objects. — calc_spec_diff • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/calc_spec_snr.html b/docs/reference/calc_spec_snr.html
index 702fc62d..972912a0 100644
--- a/docs/reference/calc_spec_snr.html
+++ b/docs/reference/calc_spec_snr.html
@@ -1,5 +1,5 @@
-Calculate the spectral SNR. — calc_spec_snr • Spectroscopy Analysis Tools (spant) Calculate the spectral SNR. — calc_spec_snr • Spectroscopy Analysis Tools (spant) Check LCModel can be run — check_lcm • Spectroscopy Analysis Tools (spant) Check LCModel can be run — check_lcm • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -94,7 +94,7 @@ Check LCModel can be run
diff --git a/docs/reference/check_tqn.html b/docs/reference/check_tqn.html
index 7cdb1d18..4bfd1977 100644
--- a/docs/reference/check_tqn.html
+++ b/docs/reference/check_tqn.html
@@ -1,5 +1,5 @@
-Check the TARQUIN binary can be run — check_tqn • Spectroscopy Analysis Tools (spant) Check the TARQUIN binary can be run — check_tqn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -94,7 +94,7 @@ Check the TARQUIN binary can be run
diff --git a/docs/reference/circ_mask.html b/docs/reference/circ_mask.html
index 462f90f1..4634256d 100644
--- a/docs/reference/circ_mask.html
+++ b/docs/reference/circ_mask.html
@@ -1,5 +1,5 @@
-Create a logical circular mask spanning the full extent of an n x n matrix. — circ_mask • Spectroscopy Analysis Tools (spant) Create a logical circular mask spanning the full extent of an n x n matrix. — circ_mask • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/coherence_filter.html b/docs/reference/coherence_filter.html
index 61141857..852d1489 100644
--- a/docs/reference/coherence_filter.html
+++ b/docs/reference/coherence_filter.html
@@ -1,5 +1,5 @@
-Zero all coherence orders other than the one supplied as an argument. — coherence_filter • Spectroscopy Analysis Tools (spant) Zero all coherence orders other than the one supplied as an argument. — coherence_filter • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/collapse_to_dyns.html b/docs/reference/collapse_to_dyns.html
index f4dc6b97..7668cb08 100644
--- a/docs/reference/collapse_to_dyns.html
+++ b/docs/reference/collapse_to_dyns.html
@@ -1,5 +1,5 @@
-Collapse MRS data by concatenating spectra along the dynamic dimension. — collapse_to_dyns • Spectroscopy Analysis Tools (spant) Collapse MRS data by concatenating spectra along the dynamic dimension. — collapse_to_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -117,7 +117,7 @@ Value
diff --git a/docs/reference/comb_coils.html b/docs/reference/comb_coils.html
index 2f1cd561..9253b058 100644
--- a/docs/reference/comb_coils.html
+++ b/docs/reference/comb_coils.html
@@ -1,5 +1,5 @@
-Combine coil data based on the first data point of a reference signal. — comb_coils • Spectroscopy Analysis Tools (spant) Combine coil data based on the first data point of a reference signal. — comb_coils • Spectroscopy Analysis Tools (spant) Combine MRSI coil data using the GLS method presented by An et al JMRI 37:1445-1450 (2013). — comb_coils_mrsi_gls • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Combine MRSI coil data using the GLS method presented by An et al JMRI 37:1445-1450 (2013).
+ Source: R/mrs_data_proc.R
+ comb_coils_mrsi_gls.Rd
+
+
+
+ Combine MRSI coil data using the GLS method presented by An et al
+JMRI 37:1445-1450 (2013).
+
+
+
+ comb_coils_mrsi_gls(metab, noise_pts = 30, noise_mrs = NULL)
+
+
+
+ Arguments
+ - metab
+MRSI data containing metabolite data.
- noise_pts
+number of points from the end of the FIDs to use for noise
+covariance estimation.
- noise_mrs
+MRS data containing noise information for each coil.
+
+ Value
+
+
+coil combined MRSI data.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/comb_coils_svs_gls.html b/docs/reference/comb_coils_svs_gls.html
new file mode 100644
index 00000000..05b14d6d
--- /dev/null
+++ b/docs/reference/comb_coils_svs_gls.html
@@ -0,0 +1,145 @@
+
+Combine SVS coil data using the GLS method presented by An et al JMRI 37:1445-1450 (2013). — comb_coils_svs_gls • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Combine SVS coil data using the GLS method presented by An et al JMRI 37:1445-1450 (2013).
+ Source: R/mrs_data_proc.R
+ comb_coils_svs_gls.Rd
+
+
+
+ Combine SVS coil data using the GLS method presented by An et al
+JMRI 37:1445-1450 (2013).
+
+
+
+ comb_coils_svs_gls(
+ metab,
+ ref = NULL,
+ noise_pts = 256,
+ noise_mrs = NULL,
+ use_mean_sens = TRUE
+)
+
+
+
+ Arguments
+ - metab
+MRS data containing metabolite data.
- ref
+MRS data containing reference data (optional).
- noise_pts
+number of points from the end of the FIDs to use for noise
+covariance estimation.
- noise_mrs
+MRS data containing noise information for each coil.
- use_mean_sens
+use the dynamic mean to estimate coil sensitivities.
+
+ Value
+
+
+coil combined MRS data.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/comb_fit_list_fit_tables.html b/docs/reference/comb_fit_list_fit_tables.html
index e88c513a..098dea6e 100644
--- a/docs/reference/comb_fit_list_fit_tables.html
+++ b/docs/reference/comb_fit_list_fit_tables.html
@@ -1,5 +1,5 @@
-Combine all fitting data points from a list of fits into a single data frame. — comb_fit_list_fit_tables • Spectroscopy Analysis Tools (spant) Combine all fitting data points from a list of fits into a single data frame. — comb_fit_list_fit_tables • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -137,7 +137,7 @@ Value
diff --git a/docs/reference/comb_fit_list_result_tables.html b/docs/reference/comb_fit_list_result_tables.html
index 9a9cd20f..82008f85 100644
--- a/docs/reference/comb_fit_list_result_tables.html
+++ b/docs/reference/comb_fit_list_result_tables.html
@@ -1,5 +1,5 @@
-Combine the fit result tables from a list of fit results. — comb_fit_list_result_tables • Spectroscopy Analysis Tools (spant) Combine the fit result tables from a list of fit results. — comb_fit_list_result_tables • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -117,7 +117,7 @@ Value
diff --git a/docs/reference/comb_fit_tables.html b/docs/reference/comb_fit_tables.html
index 52315125..5ab0b533 100644
--- a/docs/reference/comb_fit_tables.html
+++ b/docs/reference/comb_fit_tables.html
@@ -1,5 +1,5 @@
-Combine all fitting data points into a single data frame. — comb_fit_tables • Spectroscopy Analysis Tools (spant) Combine all fitting data points into a single data frame. — comb_fit_tables • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -116,7 +116,7 @@ Value
diff --git a/docs/reference/comb_metab_ref.html b/docs/reference/comb_metab_ref.html
index 40474562..ac6d5555 100644
--- a/docs/reference/comb_metab_ref.html
+++ b/docs/reference/comb_metab_ref.html
@@ -1,5 +1,5 @@
-Combine a reference and metabolite mrs_data object. — comb_metab_ref • Spectroscopy Analysis Tools (spant) Combine a reference and metabolite mrs_data object. — comb_metab_ref • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/conv_mrs.html b/docs/reference/conv_mrs.html
index 3c349299..298e9810 100644
--- a/docs/reference/conv_mrs.html
+++ b/docs/reference/conv_mrs.html
@@ -1,5 +1,5 @@
-Convolve two MRS data objects. — conv_mrs • Spectroscopy Analysis Tools (spant) Convolve two MRS data objects. — conv_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/crop_basis.html b/docs/reference/crop_basis.html
index 25adfcc2..8193c2fe 100644
--- a/docs/reference/crop_basis.html
+++ b/docs/reference/crop_basis.html
@@ -1,5 +1,5 @@
-Crop basis_set object based on a frequency range. — crop_basis • Spectroscopy Analysis Tools (spant) Crop basis_set object based on a frequency range. — crop_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -116,7 +116,7 @@ Value
diff --git a/docs/reference/crop_spec.html b/docs/reference/crop_spec.html
index bac28c4b..be5e2e87 100644
--- a/docs/reference/crop_spec.html
+++ b/docs/reference/crop_spec.html
@@ -1,5 +1,5 @@
-Crop mrs_data object based on a frequency range. — crop_spec • Spectroscopy Analysis Tools (spant) Crop mrs_data object based on a frequency range. — crop_spec • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -116,7 +116,7 @@ Value
diff --git a/docs/reference/crop_td_pts.html b/docs/reference/crop_td_pts.html
index c9c4a213..c810fa4b 100644
--- a/docs/reference/crop_td_pts.html
+++ b/docs/reference/crop_td_pts.html
@@ -1,5 +1,5 @@
-Crop mrs_data object data points in the time-domain. — crop_td_pts • Spectroscopy Analysis Tools (spant) Crop mrs_data object data points in the time-domain. — crop_td_pts • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/crop_td_pts_end.html b/docs/reference/crop_td_pts_end.html
index 3560fee2..45fd251f 100644
--- a/docs/reference/crop_td_pts_end.html
+++ b/docs/reference/crop_td_pts_end.html
@@ -1,5 +1,5 @@
-Crop mrs_data object data points at the end of the FID. — crop_td_pts_end • Spectroscopy Analysis Tools (spant) Crop mrs_data object data points at the end of the FID. — crop_td_pts_end • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/crop_td_pts_pot.html b/docs/reference/crop_td_pts_pot.html
index d6c77479..4e2c39de 100644
--- a/docs/reference/crop_td_pts_pot.html
+++ b/docs/reference/crop_td_pts_pot.html
@@ -1,9 +1,5 @@
-Crop mrs_data object data points in the time-domain rounding down to
-the next smallest power of two (pot). Data that already has a pot length will
-not be changed. — crop_td_pts_pot • Spectroscopy Analysis Tools (spant) Crop mrs_data object data points in the time-domain rounding down to the next smallest power of two (pot). Data that already has a pot length will not be changed. — crop_td_pts_pot • Spectroscopy Analysis Tools (spant) Crop an MRSI dataset in the x-y direction — crop_xy • Spectroscopy Analysis Tools (spant) Crop an MRSI dataset in the x-y direction — crop_xy • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/crossprod_3d.html b/docs/reference/crossprod_3d.html
index 417852cd..eaf22eac 100644
--- a/docs/reference/crossprod_3d.html
+++ b/docs/reference/crossprod_3d.html
@@ -1,7 +1,5 @@
-Compute the vector cross product between vectors x and y. Adapted from
-http://stackoverflow.com/questions/15162741/what-is-rs-crossproduct-function — crossprod_3d • Spectroscopy Analysis Tools (spant) Compute the vector cross product between vectors x and y. Adapted from http://stackoverflow.com/questions/15162741/what-is-rs-crossproduct-function — crossprod_3d • Spectroscopy Analysis Tools (spant) Decimate an MRS signal to half the original sampling frequency by filtering
-in the frequency domain before down sampling. — decimate_mrs_fd • Spectroscopy Analysis Tools (spant) Decimate an MRS signal to half the original sampling frequency by filtering in the frequency domain before down sampling. — decimate_mrs_fd • Spectroscopy Analysis Tools (spant) Decimate an MRS signal by filtering in the time domain before downsampling. — decimate_mrs_td • Spectroscopy Analysis Tools (spant) Decimate an MRS signal by filtering in the time domain before downsampling. — decimate_mrs_td • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -118,7 +118,7 @@ Value
diff --git a/docs/reference/deconv_mrs.html b/docs/reference/deconv_mrs.html
index 1640eb61..61ad2631 100644
--- a/docs/reference/deconv_mrs.html
+++ b/docs/reference/deconv_mrs.html
@@ -1,5 +1,5 @@
-Deconvolve two MRS data objects. — deconv_mrs • Spectroscopy Analysis Tools (spant) Deconvolve two MRS data objects. — deconv_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/def_N.html b/docs/reference/def_N.html
index 1b8c28e2..204d145b 100644
--- a/docs/reference/def_N.html
+++ b/docs/reference/def_N.html
@@ -1,5 +1,5 @@
-Return the default number of data points in the spectral dimension. — def_N • Spectroscopy Analysis Tools (spant) Return the default number of data points in the spectral dimension. — def_N • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Value
diff --git a/docs/reference/def_acq_paras.html b/docs/reference/def_acq_paras.html
index e5dfddab..b06e4d22 100644
--- a/docs/reference/def_acq_paras.html
+++ b/docs/reference/def_acq_paras.html
@@ -1,7 +1,5 @@
-Return (and optionally modify using the input arguments) a list of the
-default acquisition parameters. — def_acq_paras • Spectroscopy Analysis Tools (spant) Return (and optionally modify using the input arguments) a list of the default acquisition parameters. — def_acq_paras • Spectroscopy Analysis Tools (spant) Return the default sampling frequency in Hz. — def_fs • Spectroscopy Analysis Tools (spant) Return the default sampling frequency in Hz. — def_fs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Value
diff --git a/docs/reference/def_ft.html b/docs/reference/def_ft.html
index 715f0c1f..cb7a33fb 100644
--- a/docs/reference/def_ft.html
+++ b/docs/reference/def_ft.html
@@ -1,5 +1,5 @@
-Return the default transmitter frequency in Hz. — def_ft • Spectroscopy Analysis Tools (spant) Return the default transmitter frequency in Hz. — def_ft • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Value
diff --git a/docs/reference/def_nuc.html b/docs/reference/def_nuc.html
index cfffaa97..addd88b8 100644
--- a/docs/reference/def_nuc.html
+++ b/docs/reference/def_nuc.html
@@ -1,5 +1,5 @@
-Return the default nucleus. — def_nuc • Spectroscopy Analysis Tools (spant) Return the default nucleus. — def_nuc • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Value
diff --git a/docs/reference/def_ref.html b/docs/reference/def_ref.html
index 1aed7ccf..0ff90af1 100644
--- a/docs/reference/def_ref.html
+++ b/docs/reference/def_ref.html
@@ -1,5 +1,5 @@
-Return the default reference value for ppm scale. — def_ref • Spectroscopy Analysis Tools (spant) Return the default reference value for ppm scale. — def_ref • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Value
diff --git a/docs/reference/dicom_reader.html b/docs/reference/dicom_reader.html
index f27d6e7f..0d19c93c 100644
--- a/docs/reference/dicom_reader.html
+++ b/docs/reference/dicom_reader.html
@@ -1,5 +1,5 @@
-A very simple DICOM reader. — dicom_reader • Spectroscopy Analysis Tools (spant) A very simple DICOM reader. — dicom_reader • Spectroscopy Analysis Tools (spant) Apply the diff operator to an MRS dataset in the FID/spectral dimension. — diff_mrs • Spectroscopy Analysis Tools (spant) Apply the diff operator to an MRS dataset in the FID/spectral dimension. — diff_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/downsample_mrs_fd.html b/docs/reference/downsample_mrs_fd.html
index 9974daa5..abb34365 100644
--- a/docs/reference/downsample_mrs_fd.html
+++ b/docs/reference/downsample_mrs_fd.html
@@ -1,5 +1,5 @@
-Downsample an MRS signal by a factor of 2 using an FFT "brick-wall" filter. — downsample_mrs_fd • Spectroscopy Analysis Tools (spant) Downsample an MRS signal by a factor of 2 using an FFT "brick-wall" filter. — downsample_mrs_fd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/downsample_mrs_td.html b/docs/reference/downsample_mrs_td.html
index 1a131574..c8464ac5 100644
--- a/docs/reference/downsample_mrs_td.html
+++ b/docs/reference/downsample_mrs_td.html
@@ -1,9 +1,5 @@
-Downsample an MRS signal by a factor of 2 by removing every other data point
-in the time-domain. Note, signals outside the new sampling frequency will be
-aliased. — downsample_mrs_td • Spectroscopy Analysis Tools (spant) Downsample an MRS signal by a factor of 2 by removing every other data point in the time-domain. Note, signals outside the new sampling frequency will be aliased. — downsample_mrs_td • Spectroscopy Analysis Tools (spant) Return a time scale vector of acquisition times for a dynamic MRS scan. The
-first temporal scan is assigned a value of 0. — dyn_acq_times • Spectroscopy Analysis Tools (spant) Return a time scale vector of acquisition times for a dynamic MRS scan. The first temporal scan is assigned a value of 0. — dyn_acq_times • Spectroscopy Analysis Tools (spant) Eddy current correction. — ecc • Spectroscopy Analysis Tools (spant) Eddy current correction. — ecc • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -120,7 +120,7 @@ Details
diff --git a/docs/reference/elliptical_mask.html b/docs/reference/elliptical_mask.html
index 9736c7c1..0e8f2c72 100644
--- a/docs/reference/elliptical_mask.html
+++ b/docs/reference/elliptical_mask.html
@@ -1,5 +1,5 @@
-Create an elliptical mask stored as a matrix of logical values. — elliptical_mask • Spectroscopy Analysis Tools (spant) Create an elliptical mask stored as a matrix of logical values. — elliptical_mask • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -130,7 +130,7 @@ Value
diff --git a/docs/reference/est_noise_sd.html b/docs/reference/est_noise_sd.html
index d0bcbc47..287ec04c 100644
--- a/docs/reference/est_noise_sd.html
+++ b/docs/reference/est_noise_sd.html
@@ -1,7 +1,5 @@
-Estimate the standard deviation of the noise from a segment of an mrs_data
-object. — est_noise_sd • Spectroscopy Analysis Tools (spant) Estimate the standard deviation of the noise from a segment of an mrs_data object. — est_noise_sd • Spectroscopy Analysis Tools (spant) Transform frequency-domain data to the time-domain. — fd2td • Spectroscopy Analysis Tools (spant) Transform frequency-domain data to the time-domain. — fd2td • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/fd_conv_filt.html b/docs/reference/fd_conv_filt.html
index d419e680..daf83ea8 100644
--- a/docs/reference/fd_conv_filt.html
+++ b/docs/reference/fd_conv_filt.html
@@ -1,5 +1,5 @@
-Frequency-domain convolution based filter. — fd_conv_filt • Spectroscopy Analysis Tools (spant) Frequency-domain convolution based filter. — fd_conv_filt • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -108,7 +108,7 @@ Arguments
diff --git a/docs/reference/fd_gauss_smo.html b/docs/reference/fd_gauss_smo.html
index 43fbb24b..0e6f1a96 100644
--- a/docs/reference/fd_gauss_smo.html
+++ b/docs/reference/fd_gauss_smo.html
@@ -1,5 +1,5 @@
-Apply a Gaussian smoother in the spectral domain. — fd_gauss_smo • Spectroscopy Analysis Tools (spant) Apply a Gaussian smoother in the spectral domain. — fd_gauss_smo • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/find_bids_mrs.html b/docs/reference/find_bids_mrs.html
index 81ef7726..ec9106b3 100644
--- a/docs/reference/find_bids_mrs.html
+++ b/docs/reference/find_bids_mrs.html
@@ -1,5 +1,5 @@
-Search for MRS data files in a BIDS filesystem structure. — find_bids_mrs • Spectroscopy Analysis Tools (spant) Search for MRS data files in a BIDS filesystem structure. — find_bids_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -78,7 +78,7 @@ Search for MRS data files in a BIDS filesystem structure.
- find_bids_mrs(path)
+ find_bids_mrs(path, output_full_path = FALSE)
@@ -86,6 +86,10 @@ Arguments
- path
path to the directory containing the BIDS structure.
- output_full_path
+output the full normalised data paths.
Value
@@ -106,7 +110,7 @@ Value
diff --git a/docs/reference/find_mrs_files.html b/docs/reference/find_mrs_files.html
index aa88618b..675c6ef0 100644
--- a/docs/reference/find_mrs_files.html
+++ b/docs/reference/find_mrs_files.html
@@ -1,5 +1,5 @@
-Find valid MRS data files recursively from a directory path. — find_mrs_files • Spectroscopy Analysis Tools (spant) Find valid MRS data files recursively from a directory path. — find_mrs_files • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/fit_amps.html b/docs/reference/fit_amps.html
index 2190b708..af27c9c7 100644
--- a/docs/reference/fit_amps.html
+++ b/docs/reference/fit_amps.html
@@ -1,5 +1,5 @@
-Extract the fit amplitudes from an object of class fit_result. — fit_amps • Spectroscopy Analysis Tools (spant) Extract the fit amplitudes from an object of class fit_result. — fit_amps • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -124,7 +124,7 @@ Value
diff --git a/docs/reference/fit_diags.html b/docs/reference/fit_diags.html
index 9f940ff1..b7ce449b 100644
--- a/docs/reference/fit_diags.html
+++ b/docs/reference/fit_diags.html
@@ -1,5 +1,5 @@
-Calculate diagnostic information for object of class fit_result. — fit_diags • Spectroscopy Analysis Tools (spant) Calculate diagnostic information for object of class fit_result. — fit_diags • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/fit_mrs.html b/docs/reference/fit_mrs.html
index 9eb523df..e088a98f 100644
--- a/docs/reference/fit_mrs.html
+++ b/docs/reference/fit_mrs.html
@@ -1,5 +1,5 @@
-Perform a fit based analysis of MRS data. — fit_mrs • Spectroscopy Analysis Tools (spant) Perform a fit based analysis of MRS data. — fit_mrs • Spectroscopy Analysis Tools (spant) Write fit results table to a csv file. — fit_res2csv • Spectroscopy Analysis Tools (spant) Write fit results table to a csv file. — fit_res2csv • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -108,7 +108,7 @@ Arguments
diff --git a/docs/reference/fit_t1_ti_array.html b/docs/reference/fit_t1_ti_array.html
index 5360fbc3..c8e26e48 100644
--- a/docs/reference/fit_t1_ti_array.html
+++ b/docs/reference/fit_t1_ti_array.html
@@ -1,5 +1,5 @@
-Fit a T1 recovery curve, from multiple TIs, to a set of amplitudes. — fit_t1_ti_array • Spectroscopy Analysis Tools (spant) Fit a T1 recovery curve, from multiple TIs, to a set of amplitudes. — fit_t1_ti_array • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -136,7 +136,7 @@ Value
diff --git a/docs/reference/fit_t1_tr_array.html b/docs/reference/fit_t1_tr_array.html
index 42d6961a..0a1f6cf3 100644
--- a/docs/reference/fit_t1_tr_array.html
+++ b/docs/reference/fit_t1_tr_array.html
@@ -1,5 +1,5 @@
-Fit a T1 recovery curve, from multiple TRs, to a set of amplitudes. — fit_t1_tr_array • Spectroscopy Analysis Tools (spant) Fit a T1 recovery curve, from multiple TRs, to a set of amplitudes. — fit_t1_tr_array • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -136,7 +136,7 @@ Value
diff --git a/docs/reference/fit_t2_te_array.html b/docs/reference/fit_t2_te_array.html
index abfc708c..75983e35 100644
--- a/docs/reference/fit_t2_te_array.html
+++ b/docs/reference/fit_t2_te_array.html
@@ -1,5 +1,5 @@
-Fit a T2 relaxation curve, from multiple TEs, to a set of amplitudes. — fit_t2_te_array • Spectroscopy Analysis Tools (spant) Fit a T2 relaxation curve, from multiple TEs, to a set of amplitudes. — fit_t2_te_array • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -136,7 +136,7 @@ Value
diff --git a/docs/reference/fp_phase.html b/docs/reference/fp_phase.html
index 55b65a21..5053cca5 100644
--- a/docs/reference/fp_phase.html
+++ b/docs/reference/fp_phase.html
@@ -1,5 +1,5 @@
-Return the phase of the first data point in the time-domain. — fp_phase • Spectroscopy Analysis Tools (spant) Return the phase of the first data point in the time-domain. — fp_phase • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/fp_phase_correct.html b/docs/reference/fp_phase_correct.html
index 8f847ebf..8859b25b 100644
--- a/docs/reference/fp_phase_correct.html
+++ b/docs/reference/fp_phase_correct.html
@@ -1,7 +1,5 @@
-Perform a zeroth order phase correction based on the phase of the first data
-point in the time-domain. — fp_phase_correct • Spectroscopy Analysis Tools (spant) Perform a zeroth order phase correction based on the phase of the first data point in the time-domain. — fp_phase_correct • Spectroscopy Analysis Tools (spant) Scale the first time-domain data point in an mrs_data object. — fp_scale • Spectroscopy Analysis Tools (spant) Scale the first time-domain data point in an mrs_data object. — fp_scale • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/fs.html b/docs/reference/fs.html
index 9e576eef..cd022581 100644
--- a/docs/reference/fs.html
+++ b/docs/reference/fs.html
@@ -1,5 +1,5 @@
-Return the sampling frequency in Hz of an MRS dataset. — fs • Spectroscopy Analysis Tools (spant) Return the sampling frequency in Hz of an MRS dataset. — fs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/ft_dyns.html b/docs/reference/ft_dyns.html
index de5e96a4..b8838eba 100644
--- a/docs/reference/ft_dyns.html
+++ b/docs/reference/ft_dyns.html
@@ -1,5 +1,5 @@
-Apply the Fourier transform over the dynamic dimension. — ft_dyns • Spectroscopy Analysis Tools (spant) Apply the Fourier transform over the dynamic dimension. — ft_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -119,7 +119,7 @@ Value
diff --git a/docs/reference/ft_shift.html b/docs/reference/ft_shift.html
index 7b55740b..a91d15c4 100644
--- a/docs/reference/ft_shift.html
+++ b/docs/reference/ft_shift.html
@@ -1,5 +1,5 @@
-Perform a fft and ffshift on a vector. — ft_shift • Spectroscopy Analysis Tools (spant) Perform a fft and ffshift on a vector. — ft_shift • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/ft_shift_mat.html b/docs/reference/ft_shift_mat.html
index 7009d0b9..46b6e787 100644
--- a/docs/reference/ft_shift_mat.html
+++ b/docs/reference/ft_shift_mat.html
@@ -1,7 +1,5 @@
-Perform a fft and fftshift on a matrix with each column replaced by its
-shifted fft. — ft_shift_mat • Spectroscopy Analysis Tools (spant) Perform a fft and fftshift on a matrix with each column replaced by its shifted fft. — ft_shift_mat • Spectroscopy Analysis Tools (spant) Create a two dimensional Gaussian window function stored as a matrix. — gausswin_2d • Spectroscopy Analysis Tools (spant) Create a two dimensional Gaussian window function stored as a matrix. — gausswin_2d • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -130,7 +130,7 @@ Value
diff --git a/docs/reference/gen_F.html b/docs/reference/gen_F.html
index 0eee85ab..2bdbe201 100644
--- a/docs/reference/gen_F.html
+++ b/docs/reference/gen_F.html
@@ -1,5 +1,5 @@
-Generate the F product operator. — gen_F • Spectroscopy Analysis Tools (spant) Generate the F product operator. — gen_F • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/gen_F_xy.html b/docs/reference/gen_F_xy.html
index 67c141e0..34e0242c 100644
--- a/docs/reference/gen_F_xy.html
+++ b/docs/reference/gen_F_xy.html
@@ -1,5 +1,5 @@
-Generate the Fxy product operator with a specified phase. — gen_F_xy • Spectroscopy Analysis Tools (spant) Generate the Fxy product operator with a specified phase. — gen_F_xy • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/gen_I.html b/docs/reference/gen_I.html
index 546e31e0..3b071790 100644
--- a/docs/reference/gen_I.html
+++ b/docs/reference/gen_I.html
@@ -1,5 +1,5 @@
-Generate the I product operator for a single spin. — gen_I • Spectroscopy Analysis Tools (spant) Generate the I product operator for a single spin. — gen_I • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/gen_baseline_reg.html b/docs/reference/gen_baseline_reg.html
index 499cd905..6c061185 100644
--- a/docs/reference/gen_baseline_reg.html
+++ b/docs/reference/gen_baseline_reg.html
@@ -1,5 +1,5 @@
-Generate baseline regressor. — gen_baseline_reg • Spectroscopy Analysis Tools (spant) Generate baseline regressor. — gen_baseline_reg • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -78,7 +78,7 @@ Generate baseline regressor.
- gen_baseline_reg(mrs_data)
+ gen_baseline_reg(mrs_data = NULL, tr = NULL, Ndyns = NULL, Ntrans = NULL)
@@ -86,6 +86,19 @@ Arguments
- mrs_data
mrs_data object for timing information.
- tr
+repetition time.
- Ndyns
+number of dynamic scans stored, potentially less than Ntrans
+if block averaging has been performed.
- Ntrans
+number of dynamic scans acquired.
Value
@@ -106,7 +119,7 @@ Value
diff --git a/docs/reference/gen_bold_reg.html b/docs/reference/gen_bold_reg.html
index 56bf47b9..e8755630 100644
--- a/docs/reference/gen_bold_reg.html
+++ b/docs/reference/gen_bold_reg.html
@@ -1,5 +1,5 @@
-Generate BOLD regressors. — gen_bold_reg • Spectroscopy Analysis Tools (spant) Generate BOLD regressors. — gen_bold_reg • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -83,6 +83,9 @@ Generate BOLD regressors.
duration = NULL,
trial_type = NULL,
mrs_data = NULL,
+ tr = NULL,
+ Ndyns = NULL,
+ Ntrans = NULL,
match_tr = TRUE,
dt = 0.1,
normalise = FALSE
@@ -107,6 +110,19 @@ Arguments
mrs_data object for timing information.
tr
+repetition time.
Ndyns
+number of dynamic scans stored, potentially less than Ntrans
+if block averaging has been performed.
Ntrans
+number of dynamic scans acquired.
match_tr
match the output to the input mrs_data.
Value
diff --git a/docs/reference/gen_conv_reg.html b/docs/reference/gen_conv_reg.html
index e94d6114..2a62bfc6 100644
--- a/docs/reference/gen_conv_reg.html
+++ b/docs/reference/gen_conv_reg.html
@@ -1,7 +1,5 @@
-Generate regressors by convolving a specified response function with a
-stimulus. — gen_conv_reg • Spectroscopy Analysis Tools (spant) Generate regressors by convolving a specified response function with a stimulus. — gen_conv_reg • Spectroscopy Analysis Tools (spant) Expand a regressor matrix for a group analysis. — gen_group_reg • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+
+
+ Expand a regressor matrix for a group analysis.
+
+
+
+ gen_group_reg(regressor_df, n)
+
+
+
+ Arguments
+ - regressor_df
+input regressor data frame.
- n
+number of datasets n the group.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/gen_impulse_reg.html b/docs/reference/gen_impulse_reg.html
index a900c805..b31ec7ff 100644
--- a/docs/reference/gen_impulse_reg.html
+++ b/docs/reference/gen_impulse_reg.html
@@ -1,5 +1,5 @@
-Generate impulse regressors. — gen_impulse_reg • Spectroscopy Analysis Tools (spant) Generate impulse regressors. — gen_impulse_reg • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -78,7 +78,14 @@ Generate impulse regressors.
- gen_impulse_reg(onset, trial_type = NULL, mrs_data = NULL)
+ gen_impulse_reg(
+ onset,
+ trial_type = NULL,
+ mrs_data = NULL,
+ tr = NULL,
+ Ndyns = NULL,
+ Ntrans = NULL
+)
@@ -94,6 +101,19 @@ Arguments
mrs_data
mrs_data object for timing information.
tr
+repetition time.
Ndyns
+number of dynamic scans stored, potentially less than Ntrans
+if block averaging has been performed.
Ntrans
+number of dynamic scans acquired.
Value
@@ -114,7 +134,7 @@ Value
diff --git a/docs/reference/gen_poly_reg.html b/docs/reference/gen_poly_reg.html
index 44c2aee5..e90af45c 100644
--- a/docs/reference/gen_poly_reg.html
+++ b/docs/reference/gen_poly_reg.html
@@ -1,5 +1,5 @@
-Generate polynomial regressors. — gen_poly_reg • Spectroscopy Analysis Tools (spant) Generate polynomial regressors. — gen_poly_reg • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -78,17 +78,30 @@ Generate polynomial regressors.
- gen_poly_reg(mrs_data, degree)
+ gen_poly_reg(degree, mrs_data = NULL, tr = NULL, Ndyns = NULL, Ntrans = NULL)
Arguments
- - mrs_data
+ - degree
+the degree of the polynomial.
- mrs_data
mrs_data object for timing information.
- degree
-the degree of the polynomial.
- tr
+repetition time.
- Ndyns
+number of dynamic scans stored, potentially less than Ntrans
+if block averaging has been performed.
- Ntrans
+number of dynamic scans acquired.
@@ -110,7 +123,7 @@ Value
diff --git a/docs/reference/gen_trap_reg.html b/docs/reference/gen_trap_reg.html
index 6c3d083a..d624f730 100644
--- a/docs/reference/gen_trap_reg.html
+++ b/docs/reference/gen_trap_reg.html
@@ -1,5 +1,5 @@
-Generate trapezoidal regressors. — gen_trap_reg • Spectroscopy Analysis Tools (spant) Generate trapezoidal regressors. — gen_trap_reg • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -83,6 +83,9 @@ Generate trapezoidal regressors.
duration,
trial_type = NULL,
mrs_data = NULL,
+ tr = NULL,
+ Ndyns = NULL,
+ Ntrans = NULL,
rise_t = 0,
fall_t = 0,
exp_fall = FALSE,
@@ -112,6 +115,19 @@ Arguments
mrs_data object for timing information.
tr
+repetition time.
Ndyns
+number of dynamic scans stored, potentially less than Ntrans
+if block averaging has been performed.
Ntrans
+number of dynamic scans acquired.
rise_t
time to reach a plateau from baseline in seconds.
Value
diff --git a/docs/reference/get_1h_brain_basis_names.html b/docs/reference/get_1h_brain_basis_names.html
index a8496ee7..0f940926 100644
--- a/docs/reference/get_1h_brain_basis_names.html
+++ b/docs/reference/get_1h_brain_basis_names.html
@@ -1,7 +1,5 @@
-Return a character vector of common 1H molecules found in healthy human
-brain. — get_1h_brain_basis_names • Spectroscopy Analysis Tools (spant) Return a character vector of common 1H molecules found in healthy human brain. — get_1h_brain_basis_names • Spectroscopy Analysis Tools (spant) Return a list of mol_parameter objects suitable for 1H brain MRS
-analyses. — get_1h_brain_basis_paras • Spectroscopy Analysis Tools (spant) Return a list of mol_parameter objects suitable for 1H brain MRS analyses. — get_1h_brain_basis_paras • Spectroscopy Analysis Tools (spant) Return a list of mol_parameter objects suitable for 1H brain MRS
-analyses. — get_1h_brain_basis_paras_v1 • Spectroscopy Analysis Tools (spant) Return a list of mol_parameter objects suitable for 1H brain MRS analyses. — get_1h_brain_basis_paras_v1 • Spectroscopy Analysis Tools (spant) Return a list of mol_parameter objects suitable for 1H brain MRS
-analyses. — get_1h_brain_basis_paras_v2 • Spectroscopy Analysis Tools (spant) Return a list of mol_parameter objects suitable for 1H brain MRS analyses. — get_1h_brain_basis_paras_v2 • Spectroscopy Analysis Tools (spant) Return a list of mol_parameter objects suitable for 1H brain MRS
-analyses. — get_1h_brain_basis_paras_v3 • Spectroscopy Analysis Tools (spant) Return a list of mol_parameter objects suitable for 1H brain MRS analyses. — get_1h_brain_basis_paras_v3 • Spectroscopy Analysis Tools (spant) Return a character vector of molecules included in the GE BRAINO phantom. — get_1h_braino_basis_names • Spectroscopy Analysis Tools (spant) Return a character vector of molecules included in the GE BRAINO phantom. — get_1h_braino_basis_names • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Value
diff --git a/docs/reference/get_1h_spectre_basis_names.html b/docs/reference/get_1h_spectre_basis_names.html
index 14f088ac..1a559f2e 100644
--- a/docs/reference/get_1h_spectre_basis_names.html
+++ b/docs/reference/get_1h_spectre_basis_names.html
@@ -1,7 +1,5 @@
-Return a character vector of molecules included in the Gold Star Phantoms
-SPECTRE phantom. — get_1h_spectre_basis_names • Spectroscopy Analysis Tools (spant) Return a character vector of molecules included in the Gold Star Phantoms SPECTRE phantom. — get_1h_spectre_basis_names • Spectroscopy Analysis Tools (spant) Get the point spread function (PSF) for a 2D phase encoded MRSI scan. — get_2d_psf • Spectroscopy Analysis Tools (spant) Get the point spread function (PSF) for a 2D phase encoded MRSI scan. — get_2d_psf • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -129,7 +129,7 @@ Value
diff --git a/docs/reference/get_acq_paras.html b/docs/reference/get_acq_paras.html
index 5bb919aa..3050cfff 100644
--- a/docs/reference/get_acq_paras.html
+++ b/docs/reference/get_acq_paras.html
@@ -1,5 +1,5 @@
-Return acquisition parameters from a MRS data object. — get_acq_paras • Spectroscopy Analysis Tools (spant) Return acquisition parameters from a MRS data object. — get_acq_paras • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/get_basis_subset.html b/docs/reference/get_basis_subset.html
index b7c1b5ed..08340cca 100644
--- a/docs/reference/get_basis_subset.html
+++ b/docs/reference/get_basis_subset.html
@@ -1,5 +1,5 @@
-Return a subset of the input basis. — get_basis_subset • Spectroscopy Analysis Tools (spant) Return a subset of the input basis. — get_basis_subset • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Value
diff --git a/docs/reference/get_dyns.html b/docs/reference/get_dyns.html
index d4376131..f9ef2c85 100644
--- a/docs/reference/get_dyns.html
+++ b/docs/reference/get_dyns.html
@@ -1,5 +1,5 @@
-Extract a subset of dynamic scans. — get_dyns • Spectroscopy Analysis Tools (spant) Extract a subset of dynamic scans. — get_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/get_even_dyns.html b/docs/reference/get_even_dyns.html
index 85fac0a6..8869a5aa 100644
--- a/docs/reference/get_even_dyns.html
+++ b/docs/reference/get_even_dyns.html
@@ -1,5 +1,5 @@
-Return even numbered dynamic scans starting from 1 (2,4,6...). — get_even_dyns • Spectroscopy Analysis Tools (spant) Return even numbered dynamic scans starting from 1 (2,4,6...). — get_even_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/get_fh_dyns.html b/docs/reference/get_fh_dyns.html
index 80d45928..e040408f 100644
--- a/docs/reference/get_fh_dyns.html
+++ b/docs/reference/get_fh_dyns.html
@@ -1,5 +1,5 @@
-Return the first half of a dynamic series. — get_fh_dyns • Spectroscopy Analysis Tools (spant) Return the first half of a dynamic series. — get_fh_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/get_fit_map.html b/docs/reference/get_fit_map.html
index 9584babd..0a20e465 100644
--- a/docs/reference/get_fit_map.html
+++ b/docs/reference/get_fit_map.html
@@ -1,5 +1,5 @@
-Get a data array from a fit result. — get_fit_map • Spectroscopy Analysis Tools (spant) Get a data array from a fit result. — get_fit_map • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/get_fp.html b/docs/reference/get_fp.html
index cce9f222..f6a7c7e3 100644
--- a/docs/reference/get_fp.html
+++ b/docs/reference/get_fp.html
@@ -1,5 +1,5 @@
-Return the first time-domain data point. — get_fp • Spectroscopy Analysis Tools (spant) Return the first time-domain data point. — get_fp • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/get_guassian_pulse.html b/docs/reference/get_guassian_pulse.html
index 739ef620..a6b1117c 100644
--- a/docs/reference/get_guassian_pulse.html
+++ b/docs/reference/get_guassian_pulse.html
@@ -1,5 +1,5 @@
-Generate a gaussian pulse shape. — get_guassian_pulse • Spectroscopy Analysis Tools (spant) Generate a gaussian pulse shape. — get_guassian_pulse • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -108,7 +108,7 @@ Arguments
diff --git a/docs/reference/get_head_dyns.html b/docs/reference/get_head_dyns.html
index 075c37b7..b3eea046 100644
--- a/docs/reference/get_head_dyns.html
+++ b/docs/reference/get_head_dyns.html
@@ -1,5 +1,5 @@
-Return the first scans of a dynamic series. — get_head_dyns • Spectroscopy Analysis Tools (spant) Return the first scans of a dynamic series. — get_head_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/get_lcm_cmd.html b/docs/reference/get_lcm_cmd.html
index 84ae0186..df411eaf 100644
--- a/docs/reference/get_lcm_cmd.html
+++ b/docs/reference/get_lcm_cmd.html
@@ -1,5 +1,5 @@
-Print the command to run the LCModel command-line program. — get_lcm_cmd • Spectroscopy Analysis Tools (spant) Print the command to run the LCModel command-line program. — get_lcm_cmd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -94,7 +94,7 @@ Print the command to run the LCModel command-line program.
diff --git a/docs/reference/get_metab.html b/docs/reference/get_metab.html
index 8c345609..e4777661 100644
--- a/docs/reference/get_metab.html
+++ b/docs/reference/get_metab.html
@@ -1,5 +1,5 @@
-Extract the metabolite component from an mrs_data object. — get_metab • Spectroscopy Analysis Tools (spant) Extract the metabolite component from an mrs_data object. — get_metab • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/get_mol_names.html b/docs/reference/get_mol_names.html
index ac6a75b5..44c0460f 100644
--- a/docs/reference/get_mol_names.html
+++ b/docs/reference/get_mol_names.html
@@ -1,7 +1,5 @@
-Return a character array of names that may be used with the
-get_mol_paras function. — get_mol_names • Spectroscopy Analysis Tools (spant) Return a character array of names that may be used with the get_mol_paras function. — get_mol_names • Spectroscopy Analysis Tools (spant) Get a mol_parameters object for a named molecule. — get_mol_paras • Spectroscopy Analysis Tools (spant) Get a mol_parameters object for a named molecule. — get_mol_paras • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/get_mrs_affine.html b/docs/reference/get_mrs_affine.html
index ae0672bd..1f4c519f 100644
--- a/docs/reference/get_mrs_affine.html
+++ b/docs/reference/get_mrs_affine.html
@@ -1,5 +1,5 @@
-Generate an affine for nifti generation. — get_mrs_affine • Spectroscopy Analysis Tools (spant) Generate an affine for nifti generation. — get_mrs_affine • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -118,7 +118,7 @@ Value
diff --git a/docs/reference/get_mrsi2d_seg.html b/docs/reference/get_mrsi2d_seg.html
index c8d981cd..99e56c11 100644
--- a/docs/reference/get_mrsi2d_seg.html
+++ b/docs/reference/get_mrsi2d_seg.html
@@ -1,5 +1,5 @@
-Calculate the partial volume estimates for each voxel in a 2D MRSI dataset. — get_mrsi2d_seg • Spectroscopy Analysis Tools (spant) Calculate the partial volume estimates for each voxel in a 2D MRSI dataset. — get_mrsi2d_seg • Spectroscopy Analysis Tools (spant) Generate a MRSI VOI from an mrs_data object. — get_mrsi_voi • Spectroscopy Analysis Tools (spant) Generate a MRSI VOI from an mrs_data object. — get_mrsi_voi • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -119,7 +119,7 @@ Value
diff --git a/docs/reference/get_mrsi_voxel.html b/docs/reference/get_mrsi_voxel.html
index c4255416..9f082f05 100644
--- a/docs/reference/get_mrsi_voxel.html
+++ b/docs/reference/get_mrsi_voxel.html
@@ -1,5 +1,5 @@
-Generate a MRSI voxel from an mrs_data object. — get_mrsi_voxel • Spectroscopy Analysis Tools (spant) Generate a MRSI voxel from an mrs_data object. — get_mrsi_voxel • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/get_mrsi_voxel_xy_psf.html b/docs/reference/get_mrsi_voxel_xy_psf.html
index 04c90780..1af5dfd5 100644
--- a/docs/reference/get_mrsi_voxel_xy_psf.html
+++ b/docs/reference/get_mrsi_voxel_xy_psf.html
@@ -1,5 +1,5 @@
-Generate a MRSI voxel PSF from an mrs_data object. — get_mrsi_voxel_xy_psf • Spectroscopy Analysis Tools (spant) Generate a MRSI voxel PSF from an mrs_data object. — get_mrsi_voxel_xy_psf • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/get_odd_dyns.html b/docs/reference/get_odd_dyns.html
index d016c241..498c924f 100644
--- a/docs/reference/get_odd_dyns.html
+++ b/docs/reference/get_odd_dyns.html
@@ -1,5 +1,5 @@
-Return odd numbered dynamic scans starting from 1 (1,3,5...). — get_odd_dyns • Spectroscopy Analysis Tools (spant) Return odd numbered dynamic scans starting from 1 (1,3,5...). — get_odd_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/get_ref.html b/docs/reference/get_ref.html
index d8234a92..9cf13eab 100644
--- a/docs/reference/get_ref.html
+++ b/docs/reference/get_ref.html
@@ -1,5 +1,5 @@
-Extract the reference component from an mrs_data object. — get_ref • Spectroscopy Analysis Tools (spant) Extract the reference component from an mrs_data object. — get_ref • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/get_seg_ind.html b/docs/reference/get_seg_ind.html
index e97e51ac..68eaa5f1 100644
--- a/docs/reference/get_seg_ind.html
+++ b/docs/reference/get_seg_ind.html
@@ -1,5 +1,5 @@
-Get the indices of data points lying between two values (end > x > start). — get_seg_ind • Spectroscopy Analysis Tools (spant) Get the indices of data points lying between two values (end > x > start). — get_seg_ind • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/get_sh_dyns.html b/docs/reference/get_sh_dyns.html
index 932c4247..8ea1d7be 100644
--- a/docs/reference/get_sh_dyns.html
+++ b/docs/reference/get_sh_dyns.html
@@ -1,5 +1,5 @@
-Return the second half of a dynamic series. — get_sh_dyns • Spectroscopy Analysis Tools (spant) Return the second half of a dynamic series. — get_sh_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/get_slice.html b/docs/reference/get_slice.html
index e8b9fa7e..1fb729cc 100644
--- a/docs/reference/get_slice.html
+++ b/docs/reference/get_slice.html
@@ -1,5 +1,5 @@
-Return a single slice from a larger MRSI dataset. — get_slice • Spectroscopy Analysis Tools (spant) Return a single slice from a larger MRSI dataset. — get_slice • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/get_spin_num.html b/docs/reference/get_spin_num.html
index 021d4e60..acff1245 100644
--- a/docs/reference/get_spin_num.html
+++ b/docs/reference/get_spin_num.html
@@ -1,5 +1,5 @@
-Return the spin number for a given nucleus. — get_spin_num • Spectroscopy Analysis Tools (spant) Return the spin number for a given nucleus. — get_spin_num • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/get_subset.html b/docs/reference/get_subset.html
index 34df3128..ecab116c 100644
--- a/docs/reference/get_subset.html
+++ b/docs/reference/get_subset.html
@@ -1,5 +1,5 @@
-Extract a subset of MRS data. — get_subset • Spectroscopy Analysis Tools (spant) Extract a subset of MRS data. — get_subset • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -144,7 +144,7 @@ Value
diff --git a/docs/reference/get_svs_voi.html b/docs/reference/get_svs_voi.html
index 54de4821..97437d5d 100644
--- a/docs/reference/get_svs_voi.html
+++ b/docs/reference/get_svs_voi.html
@@ -1,5 +1,5 @@
-Generate a SVS acquisition volume from an mrs_data object. — get_svs_voi • Spectroscopy Analysis Tools (spant) Generate a SVS acquisition volume from an mrs_data object. — get_svs_voi • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/get_tail_dyns.html b/docs/reference/get_tail_dyns.html
index cace1556..cee1cec3 100644
--- a/docs/reference/get_tail_dyns.html
+++ b/docs/reference/get_tail_dyns.html
@@ -1,5 +1,5 @@
-Return the last scans of a dynamic series. — get_tail_dyns • Spectroscopy Analysis Tools (spant) Return the last scans of a dynamic series. — get_tail_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/get_td_amp.html b/docs/reference/get_td_amp.html
index ad9f3f71..5e2b5814 100644
--- a/docs/reference/get_td_amp.html
+++ b/docs/reference/get_td_amp.html
@@ -1,7 +1,5 @@
-Return an array of amplitudes derived from fitting the initial points in the
-time domain and extrapolating back to t=0. — get_td_amp • Spectroscopy Analysis Tools (spant) Return an array of amplitudes derived from fitting the initial points in the time domain and extrapolating back to t=0. — get_td_amp • Spectroscopy Analysis Tools (spant) Print the command to run the TARQUIN command-line program. — get_tqn_cmd • Spectroscopy Analysis Tools (spant) Print the command to run the TARQUIN command-line program. — get_tqn_cmd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -94,7 +94,7 @@ Print the command to run the TARQUIN command-line program.
diff --git a/docs/reference/get_uncoupled_mol.html b/docs/reference/get_uncoupled_mol.html
index 0747cc21..5fd5cb69 100644
--- a/docs/reference/get_uncoupled_mol.html
+++ b/docs/reference/get_uncoupled_mol.html
@@ -1,7 +1,5 @@
-Generate a mol_parameters object for a simple spin system with one
-resonance. — get_uncoupled_mol • Spectroscopy Analysis Tools (spant) Generate a mol_parameters object for a simple spin system with one resonance. — get_uncoupled_mol • Spectroscopy Analysis Tools (spant) Calculate the centre of gravity for an image containing 0 and 1's. — get_voi_cog • Spectroscopy Analysis Tools (spant) Calculate the centre of gravity for an image containing 0 and 1's. — get_voi_cog • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/get_voi_seg.html b/docs/reference/get_voi_seg.html
index 9f0f7f44..261f5aa2 100644
--- a/docs/reference/get_voi_seg.html
+++ b/docs/reference/get_voi_seg.html
@@ -1,5 +1,5 @@
-Return the white matter, gray matter and CSF composition of a volume. — get_voi_seg • Spectroscopy Analysis Tools (spant) Return the white matter, gray matter and CSF composition of a volume. — get_voi_seg • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/get_voi_seg_psf.html b/docs/reference/get_voi_seg_psf.html
index 2e632a30..7982a0a4 100644
--- a/docs/reference/get_voi_seg_psf.html
+++ b/docs/reference/get_voi_seg_psf.html
@@ -1,5 +1,5 @@
-Return the white matter, gray matter and CSF composition of a volume. — get_voi_seg_psf • Spectroscopy Analysis Tools (spant) Return the white matter, gray matter and CSF composition of a volume. — get_voi_seg_psf • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/get_voxel.html b/docs/reference/get_voxel.html
index cb474e6c..93a4b392 100644
--- a/docs/reference/get_voxel.html
+++ b/docs/reference/get_voxel.html
@@ -1,5 +1,5 @@
-Return a single voxel from a larger mrs dataset. — get_voxel • Spectroscopy Analysis Tools (spant) Return a single voxel from a larger mrs dataset. — get_voxel • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -126,7 +126,7 @@ Value
diff --git a/docs/reference/glm_spec.html b/docs/reference/glm_spec.html
index 20459117..e767ecbf 100644
--- a/docs/reference/glm_spec.html
+++ b/docs/reference/glm_spec.html
@@ -1,5 +1,5 @@
-Perform a GLM analysis of dynamic MRS data in the spectral domain. — glm_spec • Spectroscopy Analysis Tools (spant) Perform a GLM analysis of dynamic MRS data in the spectral domain. — glm_spec • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -78,7 +78,7 @@ Perform a GLM analysis of dynamic MRS data in the spectral domain.
- glm_spec(mrs_data, regressor_df)
+ glm_spec(mrs_data, regressor_df, full_output = FALSE)
@@ -91,6 +91,10 @@ Arguments
a data frame containing temporal regressors to be applied
to each spectral datapoint.
full_output
+append mrs_data and regressor_df to the output list.
Value
@@ -111,7 +115,7 @@ Value
diff --git a/docs/reference/glm_spec_fmrs_fl.html b/docs/reference/glm_spec_fmrs_fl.html
new file mode 100644
index 00000000..30584e18
--- /dev/null
+++ b/docs/reference/glm_spec_fmrs_fl.html
@@ -0,0 +1,149 @@
+
+Perform first-level spectral GLM analysis of an fMRS dataset. — glm_spec_fmrs_fl • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Perform first-level spectral GLM analysis of an fMRS dataset.
+ Source: R/fmrs.R
+ glm_spec_fmrs_fl.Rd
+
+
+
+ Perform first-level spectral GLM analysis of an fMRS dataset.
+
+
+
+
+
+
+
+ Arguments
+ - regressor_df
+a data frame containing temporal regressors to be applied
+to each spectral datapoint.
- analysis_dir
+directory containing preprocessed data generated by
+the preproc_svs_dataset function.
- exclude_labels
+vector of labels of scans to exclude, eg poor quality
+data.
- labels
+labels to describe each data set.
- xlim
+spectral range to include in the analysis.
- vline
+vertical lines to add to the plot.
- return_results
+function will return key outputs, defaults to FALSE.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/glm_spec_fmrs_group.html b/docs/reference/glm_spec_fmrs_group.html
new file mode 100644
index 00000000..527478e5
--- /dev/null
+++ b/docs/reference/glm_spec_fmrs_group.html
@@ -0,0 +1,134 @@
+
+Perform group-level spectral GLM analysis of an fMRS dataset. — glm_spec_fmrs_group • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Perform group-level spectral GLM analysis of an fMRS dataset.
+ Source: R/fmrs.R
+ glm_spec_fmrs_group.Rd
+
+
+
+ Perform group-level spectral GLM analysis of an fMRS dataset.
+
+
+
+ glm_spec_fmrs_group(
+ regressor_df,
+ analysis_dir = "spant_analysis",
+ exclude_labels = NULL,
+ labels = NULL
+)
+
+
+
+ Arguments
+ - regressor_df
+a data frame containing temporal regressors to be applied
+to each spectral datapoint.
- analysis_dir
+directory containing preprocessed data generated by
+the preproc_svs_dataset function.
- exclude_labels
+vector of labels of scans to exclude, eg poor quality
+data.
- labels
+labels to describe each data set.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/glm_spec_group_linhyp.html b/docs/reference/glm_spec_group_linhyp.html
new file mode 100644
index 00000000..747860d9
--- /dev/null
+++ b/docs/reference/glm_spec_group_linhyp.html
@@ -0,0 +1,119 @@
+
+Test a group-level spectral GLM linear hypothesis. — glm_spec_group_linhyp • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Test a group-level spectral GLM linear hypothesis.
+ Source: R/fmrs.R
+ glm_spec_group_linhyp.Rd
+
+
+
+ Test a group-level spectral GLM linear hypothesis.
+
+
+
+ glm_spec_group_linhyp(hmat, analysis_dir = "spant_analysis")
+
+
+
+ Arguments
+ - hmat
+linear hypothesis matrix.
- analysis_dir
+directory containing preprocessed data generated by
+the preproc_svs_dataset function.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/grid_shift_xy.html b/docs/reference/grid_shift_xy.html
index 592fa3ec..d0e05b1d 100644
--- a/docs/reference/grid_shift_xy.html
+++ b/docs/reference/grid_shift_xy.html
@@ -1,5 +1,5 @@
-Grid shift MRSI data in the x/y dimension. — grid_shift_xy • Spectroscopy Analysis Tools (spant) Grid shift MRSI data in the x/y dimension. — grid_shift_xy • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/gridplot.html b/docs/reference/gridplot.html
index ca385d91..54e40afe 100644
--- a/docs/reference/gridplot.html
+++ b/docs/reference/gridplot.html
@@ -1,5 +1,5 @@
-Arrange spectral plots in a grid. — gridplot • Spectroscopy Analysis Tools (spant) Arrange spectral plots in a grid. — gridplot • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/gridplot.mrs_data.html b/docs/reference/gridplot.mrs_data.html
index 1f4d09b5..8d68edae 100644
--- a/docs/reference/gridplot.mrs_data.html
+++ b/docs/reference/gridplot.mrs_data.html
@@ -1,5 +1,5 @@
-Arrange spectral plots in a grid. — gridplot.mrs_data • Spectroscopy Analysis Tools (spant) Arrange spectral plots in a grid. — gridplot.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -139,7 +139,7 @@ Arguments
diff --git a/docs/reference/hsvd.html b/docs/reference/hsvd.html
index 25734f49..41c28be8 100644
--- a/docs/reference/hsvd.html
+++ b/docs/reference/hsvd.html
@@ -1,5 +1,5 @@
-HSVD of an mrs_data object. — hsvd • Spectroscopy Analysis Tools (spant) HSVD of an mrs_data object. — hsvd • Spectroscopy Analysis Tools (spant) HSVD based signal filter. — hsvd_filt • Spectroscopy Analysis Tools (spant) HSVD based signal filter. — hsvd_filt • Spectroscopy Analysis Tools (spant) HSVD of a complex vector. — hsvd_vec • Spectroscopy Analysis Tools (spant) HSVD of a complex vector. — hsvd_vec • Spectroscopy Analysis Tools (spant) Return the frequency scale of an MRS dataset in Hz. — hz • Spectroscopy Analysis Tools (spant) Return the frequency scale of an MRS dataset in Hz. — hz • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/ift_shift.html b/docs/reference/ift_shift.html
index 9fba4a24..168b58dd 100644
--- a/docs/reference/ift_shift.html
+++ b/docs/reference/ift_shift.html
@@ -1,5 +1,5 @@
-Perform an iffshift and ifft on a vector. — ift_shift • Spectroscopy Analysis Tools (spant) Perform an iffshift and ifft on a vector. — ift_shift • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/ift_shift_mat.html b/docs/reference/ift_shift_mat.html
index 1a7c85ca..22a75c11 100644
--- a/docs/reference/ift_shift_mat.html
+++ b/docs/reference/ift_shift_mat.html
@@ -1,7 +1,5 @@
-Perform an ifft and ifftshift on a matrix with each column replaced by its
-shifted ifft. — ift_shift_mat • Spectroscopy Analysis Tools (spant) Perform an ifft and ifftshift on a matrix with each column replaced by its shifted ifft. — ift_shift_mat • Spectroscopy Analysis Tools (spant) Image plot method for objects of class mrs_data. — image.mrs_data • Spectroscopy Analysis Tools (spant) Image plot method for objects of class mrs_data. — image.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -92,8 +92,12 @@ Image plot method for objects of class mrs_data.
coil = 1,
restore_def_par = TRUE,
y_ticks = NULL,
- vline = NULL,
hline = NULL,
+ hline_lty = 2,
+ hline_col = "white",
+ vline = NULL,
+ vline_lty = 2,
+ vline_col = "white",
legend = FALSE,
...
)
@@ -154,12 +158,28 @@ Arguments
tick marks.
+hline
+add a horizontal line at the specified value.
hline_lty
+linetype for the horizontal line.
hline_col
+colour for the horizontal line.
vline
-draw a vertical line at the value of vline.
add a vertical line at the specified value.
hline
-draw a horizontal line at the value of hline.
vline_lty
+linetype for the vertical line.
vline_col
+colour for the vertical line.
legend
@@ -184,7 +204,7 @@ Arguments
diff --git a/docs/reference/img2kspace_xy.html b/docs/reference/img2kspace_xy.html
index db04668f..4b47cc32 100644
--- a/docs/reference/img2kspace_xy.html
+++ b/docs/reference/img2kspace_xy.html
@@ -1,5 +1,5 @@
-Transform 2D MRSI data to k-space in the x-y direction. — img2kspace_xy • Spectroscopy Analysis Tools (spant) Transform 2D MRSI data to k-space in the x-y direction. — img2kspace_xy • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/index.html b/docs/reference/index.html
index 1ef7cafd..689c02a5 100644
--- a/docs/reference/index.html
+++ b/docs/reference/index.html
@@ -1,5 +1,5 @@
-Function reference • Spectroscopy Analysis Tools (spant) Function reference • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -90,8 +90,7 @@ All functions
- Complex rounding function taken from complexplus package to reduce the number
-of spant dependencies.
Complex rounding function taken from complexplus package to reduce the number of spant dependencies.
@@ -139,8 +138,7 @@ All functions
- Return a list of options for an ABfit analysis to maintain comparability with
-analyses performed with version 1.9.0 (and earlier) of spant.
Return a list of options for an ABfit analysis to maintain comparability with analyses performed with version 1.9.0 (and earlier) of spant.
@@ -168,13 +166,11 @@ All functions
- Append MRS data across the coil dimension, assumes they matched across the
-other dimensions.
Append MRS data across the coil dimension, assumes they matched across the other dimensions.
- Append MRS data across the dynamic dimension, assumes they matched across the
-other dimensions.
Append MRS data across the dynamic dimension, assumes they matched across the other dimensions.
@@ -194,14 +190,11 @@ All functions
- Convert a 7 dimensional array in into a mrs_data object. The array dimensions
-should be ordered as : dummy, X, Y, Z, dynamic, coil, FID.
Convert a 7 dimensional array in into a mrs_data object. The array dimensions should be ordered as : dummy, X, Y, Z, dynamic, coil, FID.
- Perform zeroth-order phase correction based on the minimisation of the
-squared difference between the real and magnitude components of the
-spectrum.
Perform zeroth-order phase correction based on the minimisation of the squared difference between the real and magnitude components of the spectrum.
@@ -213,13 +206,11 @@ All functions
- Convert a basis object to an mrs_data object - where basis signals are spread
-across the dynamic dimension.
Convert a basis object to an mrs_data object - where basis signals are spread across the dynamic dimension.
- Generate a spline basis, slightly adapted from : "Splines, knots, and
-penalties", Eilers 2010.
Generate a spline basis, slightly adapted from : "Splines, knots, and penalties", Eilers 2010.
@@ -243,8 +234,7 @@ All functions
- Covert a beta value in the time-domain to an equivalent linewidth in Hz:
-x * exp(-i * t * t * beta).
Covert a beta value in the time-domain to an equivalent linewidth in Hz: x * exp(-i * t * t * beta).
@@ -272,8 +262,7 @@ All functions
- Perform a polynomial fit, subtract and return the standard deviation of the
-residuals.
Perform a polynomial fit, subtract and return the standard deviation of the residuals.
@@ -306,6 +295,14 @@ All functions comb_coils()
Combine coil data based on the first data point of a reference signal.
+
+
+ Combine MRSI coil data using the GLS method presented by An et al JMRI 37:1445-1450 (2013).
+
+
+ Combine SVS coil data using the GLS method presented by An et al JMRI 37:1445-1450 (2013).
@@ -345,9 +342,7 @@ All functions
- Crop mrs_data object data points in the time-domain rounding down to
-the next smallest power of two (pot). Data that already has a pot length will
-not be changed.
Crop mrs_data object data points in the time-domain rounding down to the next smallest power of two (pot). Data that already has a pot length will not be changed.
@@ -355,13 +350,11 @@ All functions
- Compute the vector cross product between vectors x and y. Adapted from
-http://stackoverflow.com/questions/15162741/what-is-rs-crossproduct-function
Compute the vector cross product between vectors x and y. Adapted from http://stackoverflow.com/questions/15162741/what-is-rs-crossproduct-function
- Decimate an MRS signal to half the original sampling frequency by filtering
-in the frequency domain before down sampling.
Decimate an MRS signal to half the original sampling frequency by filtering in the frequency domain before down sampling.
@@ -377,8 +370,7 @@ All functions
- Return (and optionally modify using the input arguments) a list of the
-default acquisition parameters.
Return (and optionally modify using the input arguments) a list of the default acquisition parameters.
@@ -410,14 +402,11 @@ All functions
- Downsample an MRS signal by a factor of 2 by removing every other data point
-in the time-domain. Note, signals outside the new sampling frequency will be
-aliased.
Downsample an MRS signal by a factor of 2 by removing every other data point in the time-domain. Note, signals outside the new sampling frequency will be aliased.
- Return a time scale vector of acquisition times for a dynamic MRS scan. The
-first temporal scan is assigned a value of 0.
Return a time scale vector of acquisition times for a dynamic MRS scan. The first temporal scan is assigned a value of 0.
@@ -429,8 +418,7 @@ All functions
- Estimate the standard deviation of the noise from a segment of an mrs_data
-object.
Estimate the standard deviation of the noise from a segment of an mrs_data object.
@@ -486,8 +474,7 @@ All functions
- Perform a zeroth order phase correction based on the phase of the first data
-point in the time-domain.
Perform a zeroth order phase correction based on the phase of the first data point in the time-domain.
@@ -507,8 +494,7 @@ All functions
- Perform a fft and fftshift on a matrix with each column replaced by its
-shifted fft.
Perform a fft and fftshift on a matrix with each column replaced by its shifted fft.
@@ -536,8 +522,11 @@ All functions
- Generate regressors by convolving a specified response function with a
-stimulus.
Generate regressors by convolving a specified response function with a stimulus.
+
+
+ Expand a regressor matrix for a group analysis.
@@ -553,28 +542,23 @@ All functions
- Return a character vector of common 1H molecules found in healthy human
-brain.
Return a character vector of common 1H molecules found in healthy human brain.
- Return a list of mol_parameter objects suitable for 1H brain MRS
-analyses.
Return a list of mol_parameter objects suitable for 1H brain MRS analyses.
- Return a list of mol_parameter objects suitable for 1H brain MRS
-analyses.
Return a list of mol_parameter objects suitable for 1H brain MRS analyses.
- Return a list of mol_parameter objects suitable for 1H brain MRS
-analyses.
Return a list of mol_parameter objects suitable for 1H brain MRS analyses.
- Return a list of mol_parameter objects suitable for 1H brain MRS
-analyses.
Return a list of mol_parameter objects suitable for 1H brain MRS analyses.
@@ -582,8 +566,7 @@ All functions
- Return a character vector of molecules included in the Gold Star Phantoms
-SPECTRE phantom.
Return a character vector of molecules included in the Gold Star Phantoms SPECTRE phantom.
@@ -635,8 +618,7 @@ All functions
- Return a character array of names that may be used with the
-get_mol_paras function.
Return a character array of names that may be used with the get_mol_paras function.
@@ -700,8 +682,7 @@ All functions
- Return an array of amplitudes derived from fitting the initial points in the
-time domain and extrapolating back to t=0.
Return an array of amplitudes derived from fitting the initial points in the time domain and extrapolating back to t=0.
@@ -709,8 +690,7 @@ All functions
- Generate a mol_parameters object for a simple spin system with one
-resonance.
Generate a mol_parameters object for a simple spin system with one resonance.
@@ -731,6 +711,18 @@ All functions glm_spec()
Perform a GLM analysis of dynamic MRS data in the spectral domain.
+
+
+ Perform first-level spectral GLM analysis of an fMRS dataset.
+
+
+ Perform group-level spectral GLM analysis of an fMRS dataset.
+
+
+ Test a group-level spectral GLM linear hypothesis.
@@ -766,8 +758,7 @@ All functions
- Perform an ifft and ifftshift on a matrix with each column replaced by its
-shifted ifft.
Perform an ifft and ifftshift on a matrix with each column replaced by its shifted ifft.
@@ -799,8 +790,7 @@ All functions
- Check if the chemical shift dimension of an MRS data object is in the
-frequency domain.
Check if the chemical shift dimension of an MRS data object is in the frequency domain.
@@ -820,18 +810,15 @@ All functions
- Covert a linewidth in Hz to an equivalent alpha value in the time-domain ie:
-x * exp(-t * alpha).
Covert a linewidth in Hz to an equivalent alpha value in the time-domain ie: x * exp(-t * alpha).
- Covert a linewidth in Hz to an equivalent beta value in the time-domain ie:
-x * exp(-t * t * beta).
Covert a linewidth in Hz to an equivalent beta value in the time-domain ie: x * exp(-t * t * beta).
- Make a basis-set object from a directory containing LCModel formatted RAW
-files.
Make a basis-set object from a directory containing LCModel formatted RAW files.
@@ -851,8 +838,7 @@ All functions
- Mask the voxels outside an elliptical region spanning the MRSI dataset in the
-x-y plane.
Mask the voxels outside an elliptical region spanning the MRSI dataset in the x-y plane.
@@ -860,13 +846,11 @@ All functions
- Convert a matrix (with spectral points in the column dimension and dynamics
-in the row dimensions) into a mrs_data object.
Convert a matrix (with spectral points in the column dimension and dynamics in the row dimensions) into a mrs_data object.
- Matrix exponential function taken from complexplus package to reduce the
-number of spant dependencies.
Matrix exponential function taken from complexplus package to reduce the number of spant dependencies.
@@ -914,31 +898,31 @@ All functions
- Convert an mrs_data object to basis object - where basis signals are spread
-across the dynamic dimension in the MRS data.
Convert an mrs_data object to basis object - where basis signals are spread across the dynamic dimension in the MRS data.
+
+
+ Create a BIDS file structure from a vector of MRS data paths or list of mrs_data objects.
- Convert mrs_data object to a matrix, with spectral points in the column
-dimension and dynamics in the row dimension.
Convert mrs_data object to a matrix, with spectral points in the column dimension and dynamics in the row dimension.
-
+
- Convert mrs_data object to a vector.
Convert mrs_data object to a matrix, with spectral points in the column dimension and dynamics in the row dimension.
-
+
- Create a BIDS directory and file structure from a list of mrs_data objects.
Convert mrs_data object to a vector.
- Perform a fftshift on a matrix, with each column replaced by its shifted
-result.
Perform a fftshift on a matrix, with each column replaced by its shifted result.
- Perform an ifftshift on a matrix, with each column replaced by its shifted
-result.
Perform an ifftshift on a matrix, with each column replaced by its shifted result.
@@ -946,9 +930,7 @@ All functions
- Flip the x data dimension order of a nifti image. This corresponds to
-flipping MRI data in the left-right direction, assuming the data in save in
-neurological format (can check with fslorient program).
Flip the x data dimension order of a nifti image. This corresponds to flipping MRI data in the left-right direction, assuming the data in save in neurological format (can check with fslorient program).
@@ -964,8 +946,7 @@ All functions
- Search for the highest peak in a spectral region and return the frequency,
-height and FWHM.
Search for the highest peak in a spectral region and return the frequency, height and FWHM.
@@ -974,6 +955,10 @@ All functions phase()
Apply phasing parameters to MRS data.
+
+
+ Corrected zero order phase and chemical shift offset in 1H MRS data from the brain.
@@ -1005,8 +990,7 @@ All functions
- Plot an interactive slice map from a data array where voxels can be selected
-to display a corresponding spectrum.
Plot an interactive slice map from a data array where voxels can be selected to display a corresponding spectrum.
@@ -1026,8 +1010,15 @@ All functions
- Save function results to file and load on subsequent calls to avoid repeat
-computation.
Save function results to file and load on subsequent calls to avoid repeat computation.
+
+
+ Preprocess and perform quality assessment of a single SVS data set.
+
+
+ Preprocess and perform quality assessment of one or more SVS data sets.
@@ -1055,15 +1046,11 @@ All functions
- Read a directory containing Siemens MRS IMA files and combine along the coil
-dimension. Note that the coil ID is inferred from the sorted file name and
-should be checked when consistency is required between two directories.
Read a directory containing Siemens MRS IMA files and combine along the coil dimension. Note that the coil ID is inferred from the sorted file name and should be checked when consistency is required between two directories.
- Read a directory containing Siemens MRS IMA files and combine along the
-dynamic dimension. Note that the coil ID is inferred from the sorted file
-name and should be checked when consistency is required.
Read a directory containing Siemens MRS IMA files and combine along the dynamic dimension. Note that the coil ID is inferred from the sorted file name and should be checked when consistency is required.
@@ -1103,13 +1090,11 @@ All functions
- Reconstruct complex time-domain data from the real part of frequency-domain
-data.
Reconstruct complex time-domain data from the real part of frequency-domain data.
- Reconstruct complex time-domain data from the real part of frequency-domain
-data.
Reconstruct complex time-domain data from the real part of frequency-domain data.
@@ -1141,8 +1126,7 @@ All functions
- Resample a VOI to match a target image space using nearest-neighbour
-interpolation.
Resample a VOI to match a target image space using nearest-neighbour interpolation.
@@ -1158,23 +1142,19 @@ All functions
- Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water).
Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / kg of tissue water).
- Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water).
Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / kg of tissue water).
- Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / Litre of tissue).
Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / Litre of tissue).
- Convert default LCM/TARQUIN concentration scaling to molal units with partial
-volume correction.
Convert default LCM/TARQUIN concentration scaling to molal units with partial volume correction.
@@ -1222,8 +1202,7 @@ All functions
- MEGA-PRESS sequence with ideal localisation pulses and Gaussian shaped
-editing pulse.
MEGA-PRESS sequence with ideal localisation pulses and Gaussian shaped editing pulse.
@@ -1251,13 +1230,11 @@ All functions
- STEAM sequence with ideal pulses and coherence order filtering to simulate
-gradient crushers.
STEAM sequence with ideal pulses and coherence order filtering to simulate gradient crushers.
- STEAM sequence with ideal pulses using the z-rotation gradient simulation
-method described by Young et al JMR 140, 146-152 (1999).
STEAM sequence with ideal pulses using the z-rotation gradient simulation method described by Young et al JMR 140, 146-152 (1999).
@@ -1293,8 +1270,7 @@ All functions
- Set the number of time-domain data points, truncating or zero-filling as
-appropriate.
Set the number of time-domain data points, truncating or zero-filling as appropriate.
@@ -1318,18 +1294,15 @@ All functions
- Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS
-sequence. Note, ideal pulses are assumed.
Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS sequence. Note, ideal pulses are assumed.
- Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS
-sequence. Note, ideal pulses are assumed.
Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS sequence. Note, ideal pulses are assumed.
- Simulate a macromolecular and lipid basis-set suitable for 1H brain MRS
-analysis.
Simulate a macromolecular and lipid basis-set suitable for 1H brain MRS analysis.
@@ -1353,8 +1326,7 @@ All functions
- Simulate an ideal pulse excitation profile by smoothing a top-hat function
-with a Gaussian.
Simulate an ideal pulse excitation profile by smoothing a top-hat function with a Gaussian.
@@ -1374,17 +1346,19 @@ All functions
- Simulate and fit some spectra with ABfit for benchmarking purposes. Basic
-timing and performance metrics will be printed.
Simulate and fit some spectra with ABfit for benchmarking purposes. Basic timing and performance metrics will be printed.
Example MEGA-PRESS data with significant B0 drift.
+
+
+ Simulate an example fMRS dataset for a block design fMRS experiment and export a BIDS structure.
- Simulate a typical metabolite basis set for benchmarking. Timing metrics will
-be printed on completion.
Simulate a typical metabolite basis set for benchmarking. Timing metrics will be printed on completion.
@@ -1400,8 +1374,7 @@ All functions
- Convert SPM style segmentation files to a single categorical image where
-the numerical values map as: 0) Other, 1) CSF, 2) GM and 3) WM.
Convert SPM style segmentation files to a single categorical image where the numerical values map as: 0) Other, 1) CSF, 2) GM and 3) WM.
@@ -1413,8 +1386,7 @@ All functions
- Plot the fitting results of an object of class fit_result with
-individual basis set components shown.
Plot the fitting results of an object of class fit_result with individual basis set components shown.
@@ -1459,6 +1431,10 @@ All functions svs_1h_brain_batch_analysis()
Batch interface to the standard SVS 1H brain analysis pipeline.
+
+
+ Perform a t-test on spectral data points.
@@ -1518,8 +1494,7 @@ All functions
- Fade a spectrum to zero by frequency domain multiplication with a tanh
-function. Note this operation distorts data points at the end of the FID.
Fade a spectrum to zero by frequency domain multiplication with a tanh function. Note this operation distorts data points at the end of the FID.
@@ -1549,7 +1524,7 @@ All functions
diff --git a/docs/reference/int_spec.html b/docs/reference/int_spec.html
index c7060fe7..783325a8 100644
--- a/docs/reference/int_spec.html
+++ b/docs/reference/int_spec.html
@@ -1,5 +1,5 @@
-Integrate a spectral region. — int_spec • Spectroscopy Analysis Tools (spant) Integrate a spectral region. — int_spec • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -118,7 +118,7 @@ Value
diff --git a/docs/reference/interleave_dyns.html b/docs/reference/interleave_dyns.html
index effe5543..441eff27 100644
--- a/docs/reference/interleave_dyns.html
+++ b/docs/reference/interleave_dyns.html
@@ -1,5 +1,5 @@
-Interleave the first and second half of a dynamic series. — interleave_dyns • Spectroscopy Analysis Tools (spant) Interleave the first and second half of a dynamic series. — interleave_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/inv_even_dyns.html b/docs/reference/inv_even_dyns.html
index 9f9d4fff..dcb781dc 100644
--- a/docs/reference/inv_even_dyns.html
+++ b/docs/reference/inv_even_dyns.html
@@ -1,5 +1,5 @@
-Invert even numbered dynamic scans starting from 1 (2,4,6...). — inv_even_dyns • Spectroscopy Analysis Tools (spant) Invert even numbered dynamic scans starting from 1 (2,4,6...). — inv_even_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/inv_odd_dyns.html b/docs/reference/inv_odd_dyns.html
index 26212e2b..78d64660 100644
--- a/docs/reference/inv_odd_dyns.html
+++ b/docs/reference/inv_odd_dyns.html
@@ -1,5 +1,5 @@
-Invert odd numbered dynamic scans starting from 1 (1,3,5...). — inv_odd_dyns • Spectroscopy Analysis Tools (spant) Invert odd numbered dynamic scans starting from 1 (1,3,5...). — inv_odd_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/is.def.html b/docs/reference/is.def.html
index f196ffd0..a67b9eba 100644
--- a/docs/reference/is.def.html
+++ b/docs/reference/is.def.html
@@ -1,5 +1,5 @@
-Check if an object is defined, which is the same as being not NULL. — is.def • Spectroscopy Analysis Tools (spant) Check if an object is defined, which is the same as being not NULL. — is.def • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/is_fd.html b/docs/reference/is_fd.html
index 3b0ca165..18a193aa 100644
--- a/docs/reference/is_fd.html
+++ b/docs/reference/is_fd.html
@@ -1,7 +1,5 @@
-Check if the chemical shift dimension of an MRS data object is in the
-frequency domain. — is_fd • Spectroscopy Analysis Tools (spant) Check if the chemical shift dimension of an MRS data object is in the frequency domain. — is_fd • Spectroscopy Analysis Tools (spant) Transform 2D MRSI data from k-space to image space in the x-y direction. — kspace2img_xy • Spectroscopy Analysis Tools (spant) Transform 2D MRSI data from k-space to image space in the x-y direction. — kspace2img_xy • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/l2_reg.html b/docs/reference/l2_reg.html
index 3d781d80..21aa9849 100644
--- a/docs/reference/l2_reg.html
+++ b/docs/reference/l2_reg.html
@@ -1,5 +1,5 @@
-Perform l2 regularisation artefact suppression. — l2_reg • Spectroscopy Analysis Tools (spant) Perform l2 regularisation artefact suppression. — l2_reg • Spectroscopy Analysis Tools (spant) Apply line-broadening (apodisation) to MRS data or basis object. — lb • Spectroscopy Analysis Tools (spant) Apply line-broadening (apodisation) to MRS data or basis object. — lb • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -123,7 +123,7 @@ Value
diff --git a/docs/reference/lofdc.html b/docs/reference/lofdc.html
index 5419b1ec..31347a25 100644
--- a/docs/reference/lofdc.html
+++ b/docs/reference/lofdc.html
@@ -1,5 +1,5 @@
-Correct linear frequency drift. — lofdc • Spectroscopy Analysis Tools (spant) Correct linear frequency drift. — lofdc • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -138,7 +138,7 @@ Value
diff --git a/docs/reference/lw2alpha.html b/docs/reference/lw2alpha.html
index b83db682..25da229b 100644
--- a/docs/reference/lw2alpha.html
+++ b/docs/reference/lw2alpha.html
@@ -1,7 +1,5 @@
-Covert a linewidth in Hz to an equivalent alpha value in the time-domain ie:
-x * exp(-t * alpha). — lw2alpha • Spectroscopy Analysis Tools (spant) Covert a linewidth in Hz to an equivalent alpha value in the time-domain ie: x * exp(-t * alpha). — lw2alpha • Spectroscopy Analysis Tools (spant) Covert a linewidth in Hz to an equivalent beta value in the time-domain ie:
-x * exp(-t * t * beta). — lw2beta • Spectroscopy Analysis Tools (spant) Covert a linewidth in Hz to an equivalent beta value in the time-domain ie: x * exp(-t * t * beta). — lw2beta • Spectroscopy Analysis Tools (spant) Make a basis-set object from a directory containing LCModel formatted RAW
-files. — make_basis_from_raw • Spectroscopy Analysis Tools (spant) Make a basis-set object from a directory containing LCModel formatted RAW files. — make_basis_from_raw • Spectroscopy Analysis Tools (spant) Mask an MRS dataset in the dynamic dimension. — mask_dyns • Spectroscopy Analysis Tools (spant) Mask an MRS dataset in the dynamic dimension. — mask_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/mask_fit_res.html b/docs/reference/mask_fit_res.html
index 97baaa3f..ebd91a99 100644
--- a/docs/reference/mask_fit_res.html
+++ b/docs/reference/mask_fit_res.html
@@ -1,5 +1,5 @@
-Mask fit result spectra depending on a vector of bool values. — mask_fit_res • Spectroscopy Analysis Tools (spant) Mask fit result spectra depending on a vector of bool values. — mask_fit_res • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -116,7 +116,7 @@ Value
diff --git a/docs/reference/mask_xy.html b/docs/reference/mask_xy.html
index 11bb577c..b0d38619 100644
--- a/docs/reference/mask_xy.html
+++ b/docs/reference/mask_xy.html
@@ -1,5 +1,5 @@
-Mask an MRSI dataset in the x-y direction — mask_xy • Spectroscopy Analysis Tools (spant) Mask an MRSI dataset in the x-y direction — mask_xy • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/mask_xy_corners.html b/docs/reference/mask_xy_corners.html
index 09b16cd2..2d13839d 100644
--- a/docs/reference/mask_xy_corners.html
+++ b/docs/reference/mask_xy_corners.html
@@ -1,5 +1,5 @@
-Mask the four corners of an MRSI dataset in the x-y plane. — mask_xy_corners • Spectroscopy Analysis Tools (spant) Mask the four corners of an MRSI dataset in the x-y plane. — mask_xy_corners • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/mask_xy_ellipse.html b/docs/reference/mask_xy_ellipse.html
index 1d8b02e4..e2e749ef 100644
--- a/docs/reference/mask_xy_ellipse.html
+++ b/docs/reference/mask_xy_ellipse.html
@@ -1,7 +1,5 @@
-Mask the voxels outside an elliptical region spanning the MRSI dataset in the
-x-y plane. — mask_xy_ellipse • Spectroscopy Analysis Tools (spant) Mask the voxels outside an elliptical region spanning the MRSI dataset in the x-y plane. — mask_xy_ellipse • Spectroscopy Analysis Tools (spant) Mask a 2D MRSI dataset in the x-y dimension. — mask_xy_mat • Spectroscopy Analysis Tools (spant) Mask a 2D MRSI dataset in the x-y dimension. — mask_xy_mat • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Value
diff --git a/docs/reference/mat2mrs_data.html b/docs/reference/mat2mrs_data.html
index 2e2895f3..ae55665f 100644
--- a/docs/reference/mat2mrs_data.html
+++ b/docs/reference/mat2mrs_data.html
@@ -1,7 +1,5 @@
-Convert a matrix (with spectral points in the column dimension and dynamics
-in the row dimensions) into a mrs_data object. — mat2mrs_data • Spectroscopy Analysis Tools (spant) Convert a matrix (with spectral points in the column dimension and dynamics in the row dimensions) into a mrs_data object. — mat2mrs_data • Spectroscopy Analysis Tools (spant) Matrix exponential function taken from complexplus package to reduce the
-number of spant dependencies. — matexp • Spectroscopy Analysis Tools (spant) Matrix exponential function taken from complexplus package to reduce the number of spant dependencies. — matexp • Spectroscopy Analysis Tools (spant) Apply the max operator to an MRS dataset. — max_mrs • Spectroscopy Analysis Tools (spant) Apply the max operator to an MRS dataset. — max_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/max_mrs_interp.html b/docs/reference/max_mrs_interp.html
index e4474764..52e63f3e 100644
--- a/docs/reference/max_mrs_interp.html
+++ b/docs/reference/max_mrs_interp.html
@@ -1,5 +1,5 @@
-Apply the max operator to an interpolated MRS dataset. — max_mrs_interp • Spectroscopy Analysis Tools (spant) Apply the max operator to an interpolated MRS dataset. — max_mrs_interp • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/mean.list.html b/docs/reference/mean.list.html
index b8eb3463..048306fd 100644
--- a/docs/reference/mean.list.html
+++ b/docs/reference/mean.list.html
@@ -1,5 +1,5 @@
-Calculate the mean spectrum from an mrs_data object. — mean.list • Spectroscopy Analysis Tools (spant) Calculate the mean spectrum from an mrs_data object. — mean.list • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/mean.mrs_data.html b/docs/reference/mean.mrs_data.html
index 5531a28d..79515014 100644
--- a/docs/reference/mean.mrs_data.html
+++ b/docs/reference/mean.mrs_data.html
@@ -1,5 +1,5 @@
-Calculate the mean spectrum from an mrs_data object. — mean.mrs_data • Spectroscopy Analysis Tools (spant) Calculate the mean spectrum from an mrs_data object. — mean.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/mean_dyn_blocks.html b/docs/reference/mean_dyn_blocks.html
index 10467098..4c042448 100644
--- a/docs/reference/mean_dyn_blocks.html
+++ b/docs/reference/mean_dyn_blocks.html
@@ -1,5 +1,5 @@
-Calculate the mean of adjacent dynamic scans. — mean_dyn_blocks • Spectroscopy Analysis Tools (spant) Calculate the mean of adjacent dynamic scans. — mean_dyn_blocks • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/mean_dyn_pairs.html b/docs/reference/mean_dyn_pairs.html
index 63e909ea..1a241126 100644
--- a/docs/reference/mean_dyn_pairs.html
+++ b/docs/reference/mean_dyn_pairs.html
@@ -1,5 +1,5 @@
-Calculate the pairwise means across a dynamic data set. — mean_dyn_pairs • Spectroscopy Analysis Tools (spant) Calculate the pairwise means across a dynamic data set. — mean_dyn_pairs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/mean_dyns.html b/docs/reference/mean_dyns.html
index 73fdbfa7..0daa27df 100644
--- a/docs/reference/mean_dyns.html
+++ b/docs/reference/mean_dyns.html
@@ -1,5 +1,5 @@
-Calculate the mean dynamic data. — mean_dyns • Spectroscopy Analysis Tools (spant) Calculate the mean dynamic data. — mean_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/mean_mrs_list.html b/docs/reference/mean_mrs_list.html
index 808b6c50..10d842c0 100644
--- a/docs/reference/mean_mrs_list.html
+++ b/docs/reference/mean_mrs_list.html
@@ -1,5 +1,5 @@
-Return the mean of a list of mrs_data objects. — mean_mrs_list • Spectroscopy Analysis Tools (spant) Return the mean of a list of mrs_data objects. — mean_mrs_list • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/mean_vec_blocks.html b/docs/reference/mean_vec_blocks.html
index 8fc92eaa..dd78b122 100644
--- a/docs/reference/mean_vec_blocks.html
+++ b/docs/reference/mean_vec_blocks.html
@@ -1,5 +1,5 @@
-Calculate the mean of adjacent blocks in a vector. — mean_vec_blocks • Spectroscopy Analysis Tools (spant) Calculate the mean of adjacent blocks in a vector. — mean_vec_blocks • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/median_dyns.html b/docs/reference/median_dyns.html
index 1039d4b5..9a085b10 100644
--- a/docs/reference/median_dyns.html
+++ b/docs/reference/median_dyns.html
@@ -1,5 +1,5 @@
-Calculate the median dynamic data. — median_dyns • Spectroscopy Analysis Tools (spant) Calculate the median dynamic data. — median_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/mod_td.html b/docs/reference/mod_td.html
index 76ad0a40..141ef09e 100644
--- a/docs/reference/mod_td.html
+++ b/docs/reference/mod_td.html
@@ -1,5 +1,5 @@
-Apply the Modulus operator to the time-domain MRS signal. — mod_td • Spectroscopy Analysis Tools (spant) Apply the Modulus operator to the time-domain MRS signal. — mod_td • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/mrs_data2basis.html b/docs/reference/mrs_data2basis.html
index 62f7d749..11797b91 100644
--- a/docs/reference/mrs_data2basis.html
+++ b/docs/reference/mrs_data2basis.html
@@ -1,7 +1,5 @@
-Convert an mrs_data object to basis object - where basis signals are spread
-across the dynamic dimension in the MRS data. — mrs_data2basis • Spectroscopy Analysis Tools (spant) Convert an mrs_data object to basis object - where basis signals are spread across the dynamic dimension in the MRS data. — mrs_data2basis • Spectroscopy Analysis Tools (spant) Create a BIDS file structure from a vector of MRS data paths or list of mrs_data objects. — mrs_data2bids • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Create a BIDS file structure from a vector of MRS data paths or list of mrs_data objects.
+ Source: R/fmrs.R
+ mrs_data2bids.Rd
+
+
+
+ Create a BIDS file structure from a vector of MRS data paths or list of
+mrs_data objects.
+
+
+
+ mrs_data2bids(
+ mrs_data,
+ output_dir,
+ suffix = NULL,
+ sub = NULL,
+ ses = NULL,
+ task = NULL,
+ acq = NULL,
+ nuc = NULL,
+ voi = NULL,
+ rec = NULL,
+ run = NULL,
+ echo = NULL,
+ inv = NULL,
+ skip_existing = TRUE
+)
+
+
+
+ Arguments
+ - mrs_data
+vector of MRS data paths or list of mrs_data objects.
- output_dir
+the base directory to create the BIDS structure.
- suffix
+optional vector of file suffixes. Default behaviour is to
+automatically determine these from the input data, however it is recommended
+that they are specified to allow more efficient skipping of existing data.
- sub
+optional vector of subject labels. If not specified, these will be
+automatically generated as a series of increasing zero-padded integer values
+corresponding to the mrs_data input indices.
- ses
+optional vector of session labels.
- task
+optional vector of task labels.
- acq
+optional vector of acquisition labels.
- nuc
+optional vector of nucleus labels.
- voi
+optional vector of volume of interest labels.
- rec
+optional vector of reconstruction labels.
- run
+optional vector of run indices.
- echo
+optional vector of echo time indices.
- inv
+optional vector of inversion indices.
- skip_existing
+skip any data files that have already been converted.
+Defaults to TRUE, set to FALSE to force an overwrite of any existing data
+files.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/mrs_data2mat.html b/docs/reference/mrs_data2mat.html
index cf5ff28c..9e47688a 100644
--- a/docs/reference/mrs_data2mat.html
+++ b/docs/reference/mrs_data2mat.html
@@ -1,7 +1,5 @@
-Convert mrs_data object to a matrix, with spectral points in the column
-dimension and dynamics in the row dimension. — mrs_data2mat • Spectroscopy Analysis Tools (spant) Convert mrs_data object to a matrix, with spectral points in the column dimension and dynamics in the row dimension. — mrs_data2mat • Spectroscopy Analysis Tools (spant) Convert mrs_data object to a matrix, with spectral points in the column dimension and dynamics in the row dimension. — mrs_data2spec_mat • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Convert mrs_data object to a matrix, with spectral points in the column dimension and dynamics in the row dimension.
+ Source: R/mrs_data_proc.R
+ mrs_data2spec_mat.Rd
+
+
+
+ Convert mrs_data object to a matrix, with spectral points in the column
+dimension and dynamics in the row dimension.
+
+
+
+ mrs_data2spec_mat(mrs_data, collapse = TRUE)
+
+
+
+ Arguments
+ - mrs_data
+MRS data object or list of MRS data objects.
- collapse
+collapse all other dimensions along the dynamic dimension, eg
+a 16x16 MRSI grid would be first collapsed across 256 dynamic scans.
+
+ Value
+
+
+MRS data matrix.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/mrs_data2vec.html b/docs/reference/mrs_data2vec.html
index fb172d68..a1fd654d 100644
--- a/docs/reference/mrs_data2vec.html
+++ b/docs/reference/mrs_data2vec.html
@@ -1,5 +1,5 @@
-Convert mrs_data object to a vector. — mrs_data2vec • Spectroscopy Analysis Tools (spant) Convert mrs_data object to a vector. — mrs_data2vec • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -126,7 +126,7 @@ Value
diff --git a/docs/reference/mvfftshift.html b/docs/reference/mvfftshift.html
index 92b0841b..976b3410 100644
--- a/docs/reference/mvfftshift.html
+++ b/docs/reference/mvfftshift.html
@@ -1,7 +1,5 @@
-Perform a fftshift on a matrix, with each column replaced by its shifted
-result. — mvfftshift • Spectroscopy Analysis Tools (spant) Perform a fftshift on a matrix, with each column replaced by its shifted result. — mvfftshift • Spectroscopy Analysis Tools (spant) Perform an ifftshift on a matrix, with each column replaced by its shifted
-result. — mvifftshift • Spectroscopy Analysis Tools (spant) Perform an ifftshift on a matrix, with each column replaced by its shifted result. — mvifftshift • Spectroscopy Analysis Tools (spant) Print fit coordinates from a single index. — n2coord • Spectroscopy Analysis Tools (spant) Print fit coordinates from a single index. — n2coord • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/nifti_flip_lr.html b/docs/reference/nifti_flip_lr.html
index 730abe3c..19860b3c 100644
--- a/docs/reference/nifti_flip_lr.html
+++ b/docs/reference/nifti_flip_lr.html
@@ -1,9 +1,5 @@
-Flip the x data dimension order of a nifti image. This corresponds to
-flipping MRI data in the left-right direction, assuming the data in save in
-neurological format (can check with fslorient program). — nifti_flip_lr • Spectroscopy Analysis Tools (spant) Flip the x data dimension order of a nifti image. This corresponds to flipping MRI data in the left-right direction, assuming the data in save in neurological format (can check with fslorient program). — nifti_flip_lr • Spectroscopy Analysis Tools (spant) Export a one-page pdf of a single fit result — one_page_pdf • Spectroscopy Analysis Tools (spant) Export a one-page pdf of a single fit result — one_page_pdf • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -108,7 +108,7 @@ Arguments
diff --git a/docs/reference/ortho3.html b/docs/reference/ortho3.html
index 13ade97d..5d7dd2fd 100644
--- a/docs/reference/ortho3.html
+++ b/docs/reference/ortho3.html
@@ -1,5 +1,5 @@
-Display an orthographic projection plot of a nifti object. — ortho3 • Spectroscopy Analysis Tools (spant) Display an orthographic projection plot of a nifti object. — ortho3 • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -172,7 +172,7 @@ Arguments
diff --git a/docs/reference/ortho3_inter.html b/docs/reference/ortho3_inter.html
index 090cc5e5..15948899 100644
--- a/docs/reference/ortho3_inter.html
+++ b/docs/reference/ortho3_inter.html
@@ -1,5 +1,5 @@
-Display an interactive orthographic projection plot of a nifti object. — ortho3_inter • Spectroscopy Analysis Tools (spant) Display an interactive orthographic projection plot of a nifti object. — ortho3_inter • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -132,7 +132,7 @@ Arguments
diff --git a/docs/reference/peak_info.html b/docs/reference/peak_info.html
index 09058bd8..41c8ffaf 100644
--- a/docs/reference/peak_info.html
+++ b/docs/reference/peak_info.html
@@ -1,7 +1,5 @@
-Search for the highest peak in a spectral region and return the frequency,
-height and FWHM. — peak_info • Spectroscopy Analysis Tools (spant) Search for the highest peak in a spectral region and return the frequency, height and FWHM. — peak_info • Spectroscopy Analysis Tools (spant) Papoulis-Gerchberg (PG) algorithm method for k-space extrapolation. — pg_extrap_xy • Spectroscopy Analysis Tools (spant) Papoulis-Gerchberg (PG) algorithm method for k-space extrapolation. — pg_extrap_xy • Spectroscopy Analysis Tools (spant) Apply phasing parameters to MRS data. — phase • Spectroscopy Analysis Tools (spant) Apply phasing parameters to MRS data. — phase • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/phase_ref_1h_brain.html b/docs/reference/phase_ref_1h_brain.html
new file mode 100644
index 00000000..8707a74a
--- /dev/null
+++ b/docs/reference/phase_ref_1h_brain.html
@@ -0,0 +1,131 @@
+
+Corrected zero order phase and chemical shift offset in 1H MRS data from the brain. — phase_ref_1h_brain • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Corrected zero order phase and chemical shift offset in 1H MRS data from the brain.
+ Source: R/rats.R
+ phase_ref_1h_brain.Rd
+
+
+
+ Corrected zero order phase and chemical shift offset in 1H MRS data from the
+brain.
+
+
+
+ phase_ref_1h_brain(mrs_data, mean_ref = FALSE, ret_corr_only = TRUE)
+
+
+
+ Arguments
+ - mrs_data
+MRS data to be corrected.
- mean_ref
+apply the phase and offset of the mean spectrum to all
+others. Default is FALSE.
- ret_corr_only
+return the corrected data only.
+
+ Value
+
+
+corrected MRS data.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/plot.fit_result.html b/docs/reference/plot.fit_result.html
index e54d3bc1..836a53ee 100644
--- a/docs/reference/plot.fit_result.html
+++ b/docs/reference/plot.fit_result.html
@@ -1,5 +1,5 @@
-Plot the fitting results of an object of class fit_result. — plot.fit_result • Spectroscopy Analysis Tools (spant) Plot the fitting results of an object of class fit_result. — plot.fit_result • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -207,7 +207,7 @@ Arguments
diff --git a/docs/reference/plot.mrs_data.html b/docs/reference/plot.mrs_data.html
index fabcc35b..bb2ec651 100644
--- a/docs/reference/plot.mrs_data.html
+++ b/docs/reference/plot.mrs_data.html
@@ -1,5 +1,5 @@
-Plotting method for objects of class mrs_data. — plot.mrs_data • Spectroscopy Analysis Tools (spant) Plotting method for objects of class mrs_data. — plot.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -287,7 +287,7 @@ Arguments
diff --git a/docs/reference/plot_bc.html b/docs/reference/plot_bc.html
index 4f8309b4..b48142cc 100644
--- a/docs/reference/plot_bc.html
+++ b/docs/reference/plot_bc.html
@@ -1,5 +1,5 @@
-Convenience function to plot a baseline estimate with the original data. — plot_bc • Spectroscopy Analysis Tools (spant) Convenience function to plot a baseline estimate with the original data. — plot_bc • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -108,7 +108,7 @@ Arguments
diff --git a/docs/reference/plot_reg.html b/docs/reference/plot_reg.html
index ae1acbe7..2addb2f6 100644
--- a/docs/reference/plot_reg.html
+++ b/docs/reference/plot_reg.html
@@ -1,5 +1,5 @@
-Plot regressors as an image. — plot_reg • Spectroscopy Analysis Tools (spant) Plot regressors as an image. — plot_reg • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/plot_slice_fit.html b/docs/reference/plot_slice_fit.html
index fbc7b560..57f1af8a 100644
--- a/docs/reference/plot_slice_fit.html
+++ b/docs/reference/plot_slice_fit.html
@@ -1,5 +1,5 @@
-Plot a 2D slice from an MRSI fit result object. — plot_slice_fit • Spectroscopy Analysis Tools (spant) Plot a 2D slice from an MRSI fit result object. — plot_slice_fit • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -129,7 +129,7 @@ Arguments
diff --git a/docs/reference/plot_slice_fit_inter.html b/docs/reference/plot_slice_fit_inter.html
index 4eed104a..da105a7d 100644
--- a/docs/reference/plot_slice_fit_inter.html
+++ b/docs/reference/plot_slice_fit_inter.html
@@ -1,5 +1,5 @@
-Plot a 2D slice from an MRSI fit result object. — plot_slice_fit_inter • Spectroscopy Analysis Tools (spant) Plot a 2D slice from an MRSI fit result object. — plot_slice_fit_inter • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -134,7 +134,7 @@ Arguments
diff --git a/docs/reference/plot_slice_map.html b/docs/reference/plot_slice_map.html
index 553e9ac8..ffb2a134 100644
--- a/docs/reference/plot_slice_map.html
+++ b/docs/reference/plot_slice_map.html
@@ -1,5 +1,5 @@
-Plot a slice from a 7 dimensional array. — plot_slice_map • Spectroscopy Analysis Tools (spant) Plot a slice from a 7 dimensional array. — plot_slice_map • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -153,7 +153,7 @@ Arguments
diff --git a/docs/reference/plot_slice_map_inter.html b/docs/reference/plot_slice_map_inter.html
index 40d33b42..90968f66 100644
--- a/docs/reference/plot_slice_map_inter.html
+++ b/docs/reference/plot_slice_map_inter.html
@@ -1,7 +1,5 @@
-Plot an interactive slice map from a data array where voxels can be selected
-to display a corresponding spectrum. — plot_slice_map_inter • Spectroscopy Analysis Tools (spant) Plot an interactive slice map from a data array where voxels can be selected to display a corresponding spectrum. — plot_slice_map_inter • Spectroscopy Analysis Tools (spant) Plot the spectral standard deviation. — plot_spec_sd • Spectroscopy Analysis Tools (spant) Plot the spectral standard deviation. — plot_spec_sd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Arguments
diff --git a/docs/reference/plot_voi_overlay.html b/docs/reference/plot_voi_overlay.html
index 9a782e88..bbbbf35e 100644
--- a/docs/reference/plot_voi_overlay.html
+++ b/docs/reference/plot_voi_overlay.html
@@ -1,5 +1,5 @@
-Plot a volume as an image overlay. — plot_voi_overlay • Spectroscopy Analysis Tools (spant) Plot a volume as an image overlay. — plot_voi_overlay • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -116,7 +116,7 @@ Arguments
diff --git a/docs/reference/plot_voi_overlay_seg.html b/docs/reference/plot_voi_overlay_seg.html
index 3d4e74ff..0e800ff2 100644
--- a/docs/reference/plot_voi_overlay_seg.html
+++ b/docs/reference/plot_voi_overlay_seg.html
@@ -1,5 +1,5 @@
-Plot a volume as an overlay on a segmented brain volume. — plot_voi_overlay_seg • Spectroscopy Analysis Tools (spant) Plot a volume as an overlay on a segmented brain volume. — plot_voi_overlay_seg • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Arguments
diff --git a/docs/reference/ppm.html b/docs/reference/ppm.html
index c352327a..ee4696e2 100644
--- a/docs/reference/ppm.html
+++ b/docs/reference/ppm.html
@@ -1,5 +1,5 @@
-Return the ppm scale of an MRS dataset or fit result. — ppm • Spectroscopy Analysis Tools (spant) Return the ppm scale of an MRS dataset or fit result. — ppm • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -132,7 +132,7 @@ Value
diff --git a/docs/reference/precomp.html b/docs/reference/precomp.html
index 822d7336..df3d2c6c 100644
--- a/docs/reference/precomp.html
+++ b/docs/reference/precomp.html
@@ -1,7 +1,5 @@
-Save function results to file and load on subsequent calls to avoid repeat
-computation. — precomp • Spectroscopy Analysis Tools (spant) Save function results to file and load on subsequent calls to avoid repeat computation. — precomp • Spectroscopy Analysis Tools (spant) Preprocess and perform quality assessment of a single SVS data set. — preproc_svs • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Preprocess and perform quality assessment of a single SVS data set.
+ Source: R/fmrs.R
+ preproc_svs.Rd
+
+
+
+ Preprocess and perform quality assessment of a single SVS data set.
+
+
+
+ preproc_svs(path, label = NULL, output_dir = NULL, ref_inds = NULL)
+
+
+
+ Arguments
+ - path
+path to the fMRS data file or IMA directory.
- label
+a label to describe the data set.
- output_dir
+output directory.
- ref_inds
+a vector of 1-based indices for any water reference dynamic
+scans.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/preproc_svs_dataset.html b/docs/reference/preproc_svs_dataset.html
new file mode 100644
index 00000000..07c3a29b
--- /dev/null
+++ b/docs/reference/preproc_svs_dataset.html
@@ -0,0 +1,148 @@
+
+Preprocess and perform quality assessment of one or more SVS data sets. — preproc_svs_dataset • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Preprocess and perform quality assessment of one or more SVS data sets.
+ Source: R/fmrs.R
+ preproc_svs_dataset.Rd
+
+
+
+ Preprocess and perform quality assessment of one or more SVS data sets.
+
+
+
+ preproc_svs_dataset(
+ paths,
+ labels = NULL,
+ output_dir = "spant_analysis",
+ exclude_labels = NULL,
+ overwrite = FALSE,
+ ref_inds = NULL,
+ return_results = FALSE
+)
+
+
+
+ Arguments
+ - paths
+paths to the fMRS data file or IMA directory.
- labels
+labels to describe each data set.
- output_dir
+output directory.
- exclude_labels
+vector of labels of scans to exclude, eg poor quality
+data.
- overwrite
+overwrite saved results, defaults to FALSE.
- ref_inds
+a vector of 1-based indices for any water reference dynamic
+scans.
- return_results
+function will return key outputs, defaults to FALSE.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/print.fit_result.html b/docs/reference/print.fit_result.html
index 297f28dc..5f434e57 100644
--- a/docs/reference/print.fit_result.html
+++ b/docs/reference/print.fit_result.html
@@ -1,5 +1,5 @@
-Print a summary of an object of class fit_result. — print.fit_result • Spectroscopy Analysis Tools (spant) Print a summary of an object of class fit_result. — print.fit_result • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -105,7 +105,7 @@ Arguments
diff --git a/docs/reference/print.mrs_data.html b/docs/reference/print.mrs_data.html
index 51199017..e1561eb2 100644
--- a/docs/reference/print.mrs_data.html
+++ b/docs/reference/print.mrs_data.html
@@ -1,5 +1,5 @@
-Print a summary of mrs_data parameters. — print.mrs_data • Spectroscopy Analysis Tools (spant) Print a summary of mrs_data parameters. — print.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -109,7 +109,7 @@ Arguments
diff --git a/docs/reference/qn_states.html b/docs/reference/qn_states.html
index 0f42f2f9..d7aa6715 100644
--- a/docs/reference/qn_states.html
+++ b/docs/reference/qn_states.html
@@ -1,5 +1,5 @@
-Get the quantum coherence matrix for a spin system. — qn_states • Spectroscopy Analysis Tools (spant) Get the quantum coherence matrix for a spin system. — qn_states • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/rats.html b/docs/reference/rats.html
index 5a39a396..93585e08 100644
--- a/docs/reference/rats.html
+++ b/docs/reference/rats.html
@@ -1,5 +1,5 @@
-Robust Alignment to a Target Spectrum (RATS). — rats • Spectroscopy Analysis Tools (spant) Robust Alignment to a Target Spectrum (RATS). — rats • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -207,7 +207,7 @@ Value
diff --git a/docs/reference/re_weighting.html b/docs/reference/re_weighting.html
index d21caf21..8b0b070a 100644
--- a/docs/reference/re_weighting.html
+++ b/docs/reference/re_weighting.html
@@ -1,5 +1,5 @@
-Apply a weighting to the FID to enhance spectral resolution. — re_weighting • Spectroscopy Analysis Tools (spant) Apply a weighting to the FID to enhance spectral resolution. — re_weighting • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/read_basis.html b/docs/reference/read_basis.html
index da9b94af..eb6f8557 100644
--- a/docs/reference/read_basis.html
+++ b/docs/reference/read_basis.html
@@ -1,5 +1,5 @@
-Read a basis file in LCModel .basis format. — read_basis • Spectroscopy Analysis Tools (spant) Read a basis file in LCModel .basis format. — read_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/read_ima_coil_dir.html b/docs/reference/read_ima_coil_dir.html
index 28c02de0..4f073cd8 100644
--- a/docs/reference/read_ima_coil_dir.html
+++ b/docs/reference/read_ima_coil_dir.html
@@ -1,9 +1,5 @@
-Read a directory containing Siemens MRS IMA files and combine along the coil
-dimension. Note that the coil ID is inferred from the sorted file name and
-should be checked when consistency is required between two directories. — read_ima_coil_dir • Spectroscopy Analysis Tools (spant) Read a directory containing Siemens MRS IMA files and combine along the coil dimension. Note that the coil ID is inferred from the sorted file name and should be checked when consistency is required between two directories. — read_ima_coil_dir • Spectroscopy Analysis Tools (spant) Read a directory containing Siemens MRS IMA files and combine along the
-dynamic dimension. Note that the coil ID is inferred from the sorted file
-name and should be checked when consistency is required. — read_ima_dyn_dir • Spectroscopy Analysis Tools (spant) Read a directory containing Siemens MRS IMA files and combine along the dynamic dimension. Note that the coil ID is inferred from the sorted file name and should be checked when consistency is required. — read_ima_dyn_dir • Spectroscopy Analysis Tools (spant) Read an LCModel formatted coord file containing fit information. — read_lcm_coord • Spectroscopy Analysis Tools (spant) Read an LCModel formatted coord file containing fit information. — read_lcm_coord • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -107,7 +107,7 @@ Value
diff --git a/docs/reference/read_mrs.html b/docs/reference/read_mrs.html
index 3ac2a36b..2cf36b20 100644
--- a/docs/reference/read_mrs.html
+++ b/docs/reference/read_mrs.html
@@ -1,5 +1,5 @@
-Read MRS data from a file. — read_mrs • Spectroscopy Analysis Tools (spant) Read MRS data from a file. — read_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -88,7 +88,8 @@ Read MRS data from a file.
full_fid = FALSE,
omit_svs_ref_scans = TRUE,
verbose = FALSE,
- extra = NULL
+ extra = NULL,
+ fid_filt_dist = NULL
)
@@ -140,6 +141,13 @@ Arguments
an optional data frame to provide additional variables for use
in subsequent analysis steps, eg id or grouping variables.
fid_filt_dist
+indicate if the data has a distorted FID due to a
+brick-wall filter being used to downsample the data. Default is to auto
+detect this from the data, but TRUE or FALSE options can be given to override
+detection.
Value
@@ -183,7 +191,7 @@ Examples
diff --git a/docs/reference/read_mrs_tqn.html b/docs/reference/read_mrs_tqn.html
index 5766362f..84bdaf3a 100644
--- a/docs/reference/read_mrs_tqn.html
+++ b/docs/reference/read_mrs_tqn.html
@@ -1,5 +1,5 @@
-Read MRS data using the TARQUIN software package. — read_mrs_tqn • Spectroscopy Analysis Tools (spant) Read MRS data using the TARQUIN software package. — read_mrs_tqn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -131,7 +131,7 @@ Examples
diff --git a/docs/reference/read_pulse_ascii.html b/docs/reference/read_pulse_ascii.html
index c9e0d43c..ab11c9cc 100644
--- a/docs/reference/read_pulse_ascii.html
+++ b/docs/reference/read_pulse_ascii.html
@@ -1,5 +1,5 @@
-Read an ASCII formatted pulse file. — read_pulse_ascii • Spectroscopy Analysis Tools (spant) Read an ASCII formatted pulse file. — read_pulse_ascii • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/read_pulse_bruker.html b/docs/reference/read_pulse_bruker.html
index c92bf76a..dbe9073b 100644
--- a/docs/reference/read_pulse_bruker.html
+++ b/docs/reference/read_pulse_bruker.html
@@ -1,5 +1,5 @@
-Read a Bruker formatted pulse file — read_pulse_bruker • Spectroscopy Analysis Tools (spant) Read a Bruker formatted pulse file — read_pulse_bruker • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/read_pulse_pta.html b/docs/reference/read_pulse_pta.html
index 72e1b6d4..a0fac3c3 100644
--- a/docs/reference/read_pulse_pta.html
+++ b/docs/reference/read_pulse_pta.html
@@ -1,5 +1,5 @@
-Read a .pta formatted pulse file compatible with Siemens PulseTool. — read_pulse_pta • Spectroscopy Analysis Tools (spant) Read a .pta formatted pulse file compatible with Siemens PulseTool. — read_pulse_pta • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/read_siemens_txt_hdr.html b/docs/reference/read_siemens_txt_hdr.html
index 23fb8c70..3a17d87c 100644
--- a/docs/reference/read_siemens_txt_hdr.html
+++ b/docs/reference/read_siemens_txt_hdr.html
@@ -1,5 +1,5 @@
-Read the text format header found in Siemens IMA and TWIX data files. — read_siemens_txt_hdr • Spectroscopy Analysis Tools (spant) Read the text format header found in Siemens IMA and TWIX data files. — read_siemens_txt_hdr • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -78,7 +78,7 @@ Read the text format header found in Siemens IMA and TWIX data files.
- read_siemens_txt_hdr(input, version = "vd", verbose, offset = 0)
+ read_siemens_txt_hdr(input, version = "vd", verbose = FALSE, offset = 0)
@@ -118,7 +118,7 @@ Value
diff --git a/docs/reference/read_tqn_fit.html b/docs/reference/read_tqn_fit.html
index 4da6c25e..a1630420 100644
--- a/docs/reference/read_tqn_fit.html
+++ b/docs/reference/read_tqn_fit.html
@@ -1,5 +1,5 @@
-Reader for csv fit results generated by TARQUIN. — read_tqn_fit • Spectroscopy Analysis Tools (spant) Reader for csv fit results generated by TARQUIN. — read_tqn_fit • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -113,7 +113,7 @@ Examples
diff --git a/docs/reference/read_tqn_result.html b/docs/reference/read_tqn_result.html
index 36659714..68a3e98c 100644
--- a/docs/reference/read_tqn_result.html
+++ b/docs/reference/read_tqn_result.html
@@ -1,5 +1,5 @@
-Reader for csv results generated by TARQUIN. — read_tqn_result • Spectroscopy Analysis Tools (spant) Reader for csv results generated by TARQUIN. — read_tqn_result • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -117,7 +117,7 @@ Examples
diff --git a/docs/reference/recon_imag.html b/docs/reference/recon_imag.html
index d2a72225..5bc3b1eb 100644
--- a/docs/reference/recon_imag.html
+++ b/docs/reference/recon_imag.html
@@ -1,7 +1,5 @@
-Reconstruct complex time-domain data from the real part of frequency-domain
-data. — recon_imag • Spectroscopy Analysis Tools (spant) Reconstruct complex time-domain data from the real part of frequency-domain data. — recon_imag • Spectroscopy Analysis Tools (spant) Reconstruct complex time-domain data from the real part of frequency-domain
-data. — recon_imag_vec • Spectroscopy Analysis Tools (spant) Reconstruct complex time-domain data from the real part of frequency-domain data. — recon_imag_vec • Spectroscopy Analysis Tools (spant) Reconstruct 2D MRSI data from a twix file loaded with read_mrs. — recon_twix_2d_mrsi • Spectroscopy Analysis Tools (spant) Reconstruct 2D MRSI data from a twix file loaded with read_mrs. — recon_twix_2d_mrsi • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/rectangular_mask.html b/docs/reference/rectangular_mask.html
index a2117283..6e469bc9 100644
--- a/docs/reference/rectangular_mask.html
+++ b/docs/reference/rectangular_mask.html
@@ -1,5 +1,5 @@
-Create a rectangular mask stored as a matrix of logical values. — rectangular_mask • Spectroscopy Analysis Tools (spant) Create a rectangular mask stored as a matrix of logical values. — rectangular_mask • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -130,7 +130,7 @@ Value
diff --git a/docs/reference/reexports.html b/docs/reference/reexports.html
index 694a75d1..a59e8379 100644
--- a/docs/reference/reexports.html
+++ b/docs/reference/reexports.html
@@ -1,5 +1,5 @@
-Objects exported from other packages — reexports • Spectroscopy Analysis Tools (spant) Objects exported from other packages — reexports • Spectroscopy Analysis Tools (spant)
Spectroscopy Analysis Tools (spant)
- 2.21.0
+ 2.22.0
@@ -103,7 +103,7 @@ Objects exported from other packages
diff --git a/docs/reference/rep_array_dim.html b/docs/reference/rep_array_dim.html
index b9c49b4a..48c0a5ed 100644
--- a/docs/reference/rep_array_dim.html
+++ b/docs/reference/rep_array_dim.html
@@ -1,5 +1,5 @@
-Repeat an array over a given dimension. — rep_array_dim • Spectroscopy Analysis Tools (spant) Repeat an array over a given dimension. — rep_array_dim • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/rep_dyn.html b/docs/reference/rep_dyn.html
index 6bbfb0ef..89a4bb9b 100644
--- a/docs/reference/rep_dyn.html
+++ b/docs/reference/rep_dyn.html
@@ -1,5 +1,5 @@
-Replicate a scan in the dynamic dimension. — rep_dyn • Spectroscopy Analysis Tools (spant) Replicate a scan in the dynamic dimension. — rep_dyn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/rep_mrs.html b/docs/reference/rep_mrs.html
index 67730b5c..becb8f00 100644
--- a/docs/reference/rep_mrs.html
+++ b/docs/reference/rep_mrs.html
@@ -1,5 +1,5 @@
-Replicate a scan over a given dimension. — rep_mrs • Spectroscopy Analysis Tools (spant) Replicate a scan over a given dimension. — rep_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -138,7 +138,7 @@ Value
diff --git a/docs/reference/resample_basis.html b/docs/reference/resample_basis.html
index b0f2ab17..c7a6222a 100644
--- a/docs/reference/resample_basis.html
+++ b/docs/reference/resample_basis.html
@@ -1,5 +1,5 @@
-Resample a basis-set to match a mrs_data acquisition. — resample_basis • Spectroscopy Analysis Tools (spant) Resample a basis-set to match a mrs_data acquisition. — resample_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -116,7 +116,7 @@ Value
diff --git a/docs/reference/resample_img.html b/docs/reference/resample_img.html
index f1e7beaf..b0cc8f71 100644
--- a/docs/reference/resample_img.html
+++ b/docs/reference/resample_img.html
@@ -1,5 +1,5 @@
-Resample an image to match a target image space. — resample_img • Spectroscopy Analysis Tools (spant) Resample an image to match a target image space. — resample_img • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/resample_voi.html b/docs/reference/resample_voi.html
index 8fbfa836..a29ab096 100644
--- a/docs/reference/resample_voi.html
+++ b/docs/reference/resample_voi.html
@@ -1,7 +1,5 @@
-Resample a VOI to match a target image space using nearest-neighbour
-interpolation. — resample_voi • Spectroscopy Analysis Tools (spant) Resample a VOI to match a target image space using nearest-neighbour interpolation. — resample_voi • Spectroscopy Analysis Tools (spant) Reslice a nifti object to match the orientation of mrs data. — reslice_to_mrs • Spectroscopy Analysis Tools (spant) Reslice a nifti object to match the orientation of mrs data. — reslice_to_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/reson_table2mrs_data.html b/docs/reference/reson_table2mrs_data.html
index d75579ee..c5a2167a 100644
--- a/docs/reference/reson_table2mrs_data.html
+++ b/docs/reference/reson_table2mrs_data.html
@@ -1,5 +1,5 @@
-Generate mrs_data from a table of single Lorentzian resonances. — reson_table2mrs_data • Spectroscopy Analysis Tools (spant) Generate mrs_data from a table of single Lorentzian resonances. — reson_table2mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -119,7 +119,7 @@ Value
diff --git a/docs/reference/rm_dyns.html b/docs/reference/rm_dyns.html
index 5d5ef692..573e1f51 100644
--- a/docs/reference/rm_dyns.html
+++ b/docs/reference/rm_dyns.html
@@ -1,5 +1,5 @@
-Remove a subset of dynamic scans. — rm_dyns • Spectroscopy Analysis Tools (spant) Remove a subset of dynamic scans. — rm_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/scale_amp_molal.html b/docs/reference/scale_amp_molal.html
index aaeee1f2..7acb8cb0 100644
--- a/docs/reference/scale_amp_molal.html
+++ b/docs/reference/scale_amp_molal.html
@@ -1,7 +1,5 @@
-Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water). — scale_amp_molal • Spectroscopy Analysis Tools (spant) Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / kg of tissue water). — scale_amp_molal • Spectroscopy Analysis Tools (spant)
Spectroscopy Analysis Tools (spant)
- 2.21.0
+ 2.22.0
@@ -76,8 +74,7 @@
- Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water).
+ Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / kg of tissue water).
Source: R/amp_scaling.R
scale_amp_molal.Rd
@@ -163,7 +160,7 @@ Value
diff --git a/docs/reference/scale_amp_molal_pvc.html b/docs/reference/scale_amp_molal_pvc.html
index 962d6afc..4d194abd 100644
--- a/docs/reference/scale_amp_molal_pvc.html
+++ b/docs/reference/scale_amp_molal_pvc.html
@@ -1,7 +1,5 @@
-Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water). — scale_amp_molal_pvc • Spectroscopy Analysis Tools (spant)
@@ -75,8 +73,7 @@
- Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water).
+ Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / kg of tissue water).
Source: R/amp_scaling.R
scale_amp_molal_pvc.Rd
@@ -141,7 +138,7 @@ Value
diff --git a/docs/reference/scale_amp_molar.html b/docs/reference/scale_amp_molar.html
index 02358d91..dc87a338 100644
--- a/docs/reference/scale_amp_molar.html
+++ b/docs/reference/scale_amp_molar.html
@@ -1,7 +1,5 @@
-Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / Litre of tissue). — scale_amp_molar • Spectroscopy Analysis Tools (spant) Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / Litre of tissue). — scale_amp_molar • Spectroscopy Analysis Tools (spant) Convert default LCM/TARQUIN concentration scaling to molal units with partial
-volume correction. — scale_amp_molar2molal_pvc • Spectroscopy Analysis Tools (spant) Convert default LCM/TARQUIN concentration scaling to molal units with partial volume correction. — scale_amp_molar2molal_pvc • Spectroscopy Analysis Tools (spant) Scale fitted amplitudes to a ratio of signal amplitude. — scale_amp_ratio • Spectroscopy Analysis Tools (spant) Scale fitted amplitudes to a ratio of signal amplitude. — scale_amp_ratio • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -116,7 +116,7 @@ Value
diff --git a/docs/reference/scale_amp_ratio_value.html b/docs/reference/scale_amp_ratio_value.html
index 2036837a..6af8ac51 100644
--- a/docs/reference/scale_amp_ratio_value.html
+++ b/docs/reference/scale_amp_ratio_value.html
@@ -1,5 +1,5 @@
-Scale fitted amplitudes to a ratio of signal amplitude. — scale_amp_ratio_value • Spectroscopy Analysis Tools (spant) Scale fitted amplitudes to a ratio of signal amplitude. — scale_amp_ratio_value • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/scale_amp_water_ratio.html b/docs/reference/scale_amp_water_ratio.html
index 5b25e884..35a76b00 100644
--- a/docs/reference/scale_amp_water_ratio.html
+++ b/docs/reference/scale_amp_water_ratio.html
@@ -1,5 +1,5 @@
-Scale metabolite amplitudes as a ratio to the unsuppressed water amplitude. — scale_amp_water_ratio • Spectroscopy Analysis Tools (spant) Scale metabolite amplitudes as a ratio to the unsuppressed water amplitude. — scale_amp_water_ratio • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/scale_basis_amp.html b/docs/reference/scale_basis_amp.html
index 9401c3f1..5a58b5e5 100644
--- a/docs/reference/scale_basis_amp.html
+++ b/docs/reference/scale_basis_amp.html
@@ -1,5 +1,5 @@
-Scale a basis object by a scalar. — scale_basis_amp • Spectroscopy Analysis Tools (spant) Scale a basis object by a scalar. — scale_basis_amp • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/scale_basis_from_singlet.html b/docs/reference/scale_basis_from_singlet.html
index 0d542bc8..c9a19e77 100644
--- a/docs/reference/scale_basis_from_singlet.html
+++ b/docs/reference/scale_basis_from_singlet.html
@@ -1,5 +1,5 @@
-Scale a basis-set to be consistent with spant assumptions for water scaling. — scale_basis_from_singlet • Spectroscopy Analysis Tools (spant) Scale a basis-set to be consistent with spant assumptions for water scaling. — scale_basis_from_singlet • Spectroscopy Analysis Tools (spant)
Spectroscopy Analysis Tools (spant)
- 2.21.0
+ 2.22.0
@@ -127,7 +127,7 @@ Value
diff --git a/docs/reference/scale_mrs_amp.html b/docs/reference/scale_mrs_amp.html
index b5501a0d..990f058a 100644
--- a/docs/reference/scale_mrs_amp.html
+++ b/docs/reference/scale_mrs_amp.html
@@ -1,5 +1,5 @@
-Scale an mrs_data object by a scalar or vector or amplitudes. — scale_mrs_amp • Spectroscopy Analysis Tools (spant) Scale an mrs_data object by a scalar or vector or amplitudes. — scale_mrs_amp • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/scale_spec.html b/docs/reference/scale_spec.html
index 4f6ea835..6b3ddba4 100644
--- a/docs/reference/scale_spec.html
+++ b/docs/reference/scale_spec.html
@@ -1,5 +1,5 @@
-Scale mrs_data to a spectral region. — scale_spec • Spectroscopy Analysis Tools (spant) Scale mrs_data to a spectral region. — scale_spec • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -141,7 +141,7 @@ Value
diff --git a/docs/reference/sd.html b/docs/reference/sd.html
index ea1eec9f..3ae4dfd4 100644
--- a/docs/reference/sd.html
+++ b/docs/reference/sd.html
@@ -1,5 +1,5 @@
-Calculate the standard deviation spectrum from an mrs_data object. — sd • Spectroscopy Analysis Tools (spant) Calculate the standard deviation spectrum from an mrs_data object. — sd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/sd.mrs_data.html b/docs/reference/sd.mrs_data.html
index 3f92a49f..13bdda85 100644
--- a/docs/reference/sd.mrs_data.html
+++ b/docs/reference/sd.mrs_data.html
@@ -1,5 +1,5 @@
-Calculate the standard deviation spectrum from an mrs_data object. — sd.mrs_data • Spectroscopy Analysis Tools (spant) Calculate the standard deviation spectrum from an mrs_data object. — sd.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/seconds.html b/docs/reference/seconds.html
index b34d6627..467ee17f 100644
--- a/docs/reference/seconds.html
+++ b/docs/reference/seconds.html
@@ -1,5 +1,5 @@
-Return a time scale vector to match the FID of an MRS data object. — seconds • Spectroscopy Analysis Tools (spant) Return a time scale vector to match the FID of an MRS data object. — seconds • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/seq_cpmg_ideal.html b/docs/reference/seq_cpmg_ideal.html
index 547e96ab..45727c86 100644
--- a/docs/reference/seq_cpmg_ideal.html
+++ b/docs/reference/seq_cpmg_ideal.html
@@ -1,5 +1,5 @@
-CPMG style sequence with ideal pulses. — seq_cpmg_ideal • Spectroscopy Analysis Tools (spant) CPMG style sequence with ideal pulses. — seq_cpmg_ideal • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/seq_mega_press_ideal.html b/docs/reference/seq_mega_press_ideal.html
index 0769b8b4..a9cd7fa0 100644
--- a/docs/reference/seq_mega_press_ideal.html
+++ b/docs/reference/seq_mega_press_ideal.html
@@ -1,7 +1,5 @@
-MEGA-PRESS sequence with ideal localisation pulses and Gaussian shaped
-editing pulse. — seq_mega_press_ideal • Spectroscopy Analysis Tools (spant) MEGA-PRESS sequence with ideal localisation pulses and Gaussian shaped editing pulse. — seq_mega_press_ideal • Spectroscopy Analysis Tools (spant) PRESS sequence with shaped refocusing pulses. — seq_press_2d_shaped • Spectroscopy Analysis Tools (spant) PRESS sequence with shaped refocusing pulses. — seq_press_2d_shaped • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -165,7 +165,7 @@ Value
diff --git a/docs/reference/seq_press_ideal.html b/docs/reference/seq_press_ideal.html
index 8c976856..72c3af3d 100644
--- a/docs/reference/seq_press_ideal.html
+++ b/docs/reference/seq_press_ideal.html
@@ -1,5 +1,5 @@
-PRESS sequence with ideal pulses. — seq_press_ideal • Spectroscopy Analysis Tools (spant) PRESS sequence with ideal pulses. — seq_press_ideal • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/seq_pulse_acquire.html b/docs/reference/seq_pulse_acquire.html
index 4a88fc64..ad80571e 100644
--- a/docs/reference/seq_pulse_acquire.html
+++ b/docs/reference/seq_pulse_acquire.html
@@ -1,5 +1,5 @@
-Simple pulse and acquire sequence with ideal pulses. — seq_pulse_acquire • Spectroscopy Analysis Tools (spant) Simple pulse and acquire sequence with ideal pulses. — seq_pulse_acquire • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/seq_slaser_ideal.html b/docs/reference/seq_slaser_ideal.html
index 74688f4d..eb83e8e3 100644
--- a/docs/reference/seq_slaser_ideal.html
+++ b/docs/reference/seq_slaser_ideal.html
@@ -1,5 +1,5 @@
-sLASER sequence with ideal pulses. — seq_slaser_ideal • Spectroscopy Analysis Tools (spant) sLASER sequence with ideal pulses. — seq_slaser_ideal • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -126,7 +126,7 @@ Value
diff --git a/docs/reference/seq_spin_echo_ideal.html b/docs/reference/seq_spin_echo_ideal.html
index e23271de..4248716f 100644
--- a/docs/reference/seq_spin_echo_ideal.html
+++ b/docs/reference/seq_spin_echo_ideal.html
@@ -1,5 +1,5 @@
-Spin echo sequence with ideal pulses. — seq_spin_echo_ideal • Spectroscopy Analysis Tools (spant) Spin echo sequence with ideal pulses. — seq_spin_echo_ideal • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/seq_steam_ideal.html b/docs/reference/seq_steam_ideal.html
index a60685a8..1c8115d7 100644
--- a/docs/reference/seq_steam_ideal.html
+++ b/docs/reference/seq_steam_ideal.html
@@ -1,5 +1,5 @@
-STEAM sequence with ideal pulses. — seq_steam_ideal • Spectroscopy Analysis Tools (spant) STEAM sequence with ideal pulses. — seq_steam_ideal • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -128,7 +128,7 @@ Value
diff --git a/docs/reference/seq_steam_ideal_cof.html b/docs/reference/seq_steam_ideal_cof.html
index 8f225740..cba7af91 100644
--- a/docs/reference/seq_steam_ideal_cof.html
+++ b/docs/reference/seq_steam_ideal_cof.html
@@ -1,7 +1,5 @@
-STEAM sequence with ideal pulses and coherence order filtering to simulate
-gradient crushers. — seq_steam_ideal_cof • Spectroscopy Analysis Tools (spant) STEAM sequence with ideal pulses and coherence order filtering to simulate gradient crushers. — seq_steam_ideal_cof • Spectroscopy Analysis Tools (spant) STEAM sequence with ideal pulses using the z-rotation gradient simulation
-method described by Young et al JMR 140, 146-152 (1999). — seq_steam_ideal_young • Spectroscopy Analysis Tools (spant) STEAM sequence with ideal pulses using the z-rotation gradient simulation method described by Young et al JMR 140, 146-152 (1999). — seq_steam_ideal_young • Spectroscopy Analysis Tools (spant) Set the number of transients for an mrs_data object. — set_Ntrans • Spectroscopy Analysis Tools (spant) Set the number of transients for an mrs_data object. — set_Ntrans • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/set_def_acq_paras.html b/docs/reference/set_def_acq_paras.html
index 3e1b4004..cc2ada9c 100644
--- a/docs/reference/set_def_acq_paras.html
+++ b/docs/reference/set_def_acq_paras.html
@@ -1,5 +1,5 @@
-Set the default acquisition parameters. — set_def_acq_paras • Spectroscopy Analysis Tools (spant) Set the default acquisition parameters. — set_def_acq_paras • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Arguments
diff --git a/docs/reference/set_lcm_cmd.html b/docs/reference/set_lcm_cmd.html
index 2056ed01..42bb2f24 100644
--- a/docs/reference/set_lcm_cmd.html
+++ b/docs/reference/set_lcm_cmd.html
@@ -1,5 +1,5 @@
-Set the command to run the LCModel command-line program. — set_lcm_cmd • Spectroscopy Analysis Tools (spant) Set the command to run the LCModel command-line program. — set_lcm_cmd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/set_lw.html b/docs/reference/set_lw.html
index b64ec851..bb176c62 100644
--- a/docs/reference/set_lw.html
+++ b/docs/reference/set_lw.html
@@ -1,5 +1,5 @@
-Apply line-broadening to an mrs_data object to achieve a specified linewidth. — set_lw • Spectroscopy Analysis Tools (spant) Apply line-broadening to an mrs_data object to achieve a specified linewidth. — set_lw • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -123,7 +123,7 @@ Value
diff --git a/docs/reference/set_mask_xy_mat.html b/docs/reference/set_mask_xy_mat.html
index 49dc5d4e..52c4b617 100644
--- a/docs/reference/set_mask_xy_mat.html
+++ b/docs/reference/set_mask_xy_mat.html
@@ -1,5 +1,5 @@
-Set the masked voxels in a 2D MRSI dataset to given spectrum. — set_mask_xy_mat • Spectroscopy Analysis Tools (spant) Set the masked voxels in a 2D MRSI dataset to given spectrum. — set_mask_xy_mat • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Value
diff --git a/docs/reference/set_precomp_mode.html b/docs/reference/set_precomp_mode.html
index f44bd5d3..47c28e3b 100644
--- a/docs/reference/set_precomp_mode.html
+++ b/docs/reference/set_precomp_mode.html
@@ -1,5 +1,5 @@
-Set the precompute mode. — set_precomp_mode • Spectroscopy Analysis Tools (spant) Set the precompute mode. — set_precomp_mode • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/set_precomp_verbose.html b/docs/reference/set_precomp_verbose.html
index 1453a231..9c613505 100644
--- a/docs/reference/set_precomp_verbose.html
+++ b/docs/reference/set_precomp_verbose.html
@@ -1,5 +1,5 @@
-Set the verbosity of the precompute function. — set_precomp_verbose • Spectroscopy Analysis Tools (spant) Set the verbosity of the precompute function. — set_precomp_verbose • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/set_ref.html b/docs/reference/set_ref.html
index 8953fa50..5436dfa2 100644
--- a/docs/reference/set_ref.html
+++ b/docs/reference/set_ref.html
@@ -1,5 +1,5 @@
-Set the ppm reference value (eg ppm value at 0Hz). — set_ref • Spectroscopy Analysis Tools (spant) Set the ppm reference value (eg ppm value at 0Hz). — set_ref • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/set_td_pts.html b/docs/reference/set_td_pts.html
index 8a80d42a..586459ff 100644
--- a/docs/reference/set_td_pts.html
+++ b/docs/reference/set_td_pts.html
@@ -1,7 +1,5 @@
-Set the number of time-domain data points, truncating or zero-filling as
-appropriate. — set_td_pts • Spectroscopy Analysis Tools (spant) Set the number of time-domain data points, truncating or zero-filling as appropriate. — set_td_pts • Spectroscopy Analysis Tools (spant) Set the command to run the TARQUIN command-line program. — set_tqn_cmd • Spectroscopy Analysis Tools (spant) Set the command to run the TARQUIN command-line program. — set_tqn_cmd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/set_tr.html b/docs/reference/set_tr.html
index b2109ab0..65c9df5f 100644
--- a/docs/reference/set_tr.html
+++ b/docs/reference/set_tr.html
@@ -1,5 +1,5 @@
-Set the repetition time of an MRS dataset. — set_tr • Spectroscopy Analysis Tools (spant) Set the repetition time of an MRS dataset. — set_tr • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/shift.html b/docs/reference/shift.html
index ab0fe724..034591d0 100644
--- a/docs/reference/shift.html
+++ b/docs/reference/shift.html
@@ -1,5 +1,5 @@
-Apply a frequency shift to MRS data. — shift • Spectroscopy Analysis Tools (spant) Apply a frequency shift to MRS data. — shift • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/shift_basis.html b/docs/reference/shift_basis.html
index 2884be19..f55a65e0 100644
--- a/docs/reference/shift_basis.html
+++ b/docs/reference/shift_basis.html
@@ -1,5 +1,5 @@
-Apply frequency shifts to basis set signals. — shift_basis • Spectroscopy Analysis Tools (spant) Apply frequency shifts to basis set signals. — shift_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Value
diff --git a/docs/reference/sim_basis.html b/docs/reference/sim_basis.html
index c7838c46..bb5fefc6 100644
--- a/docs/reference/sim_basis.html
+++ b/docs/reference/sim_basis.html
@@ -1,5 +1,5 @@
-Simulate a basis set object. — sim_basis • Spectroscopy Analysis Tools (spant) Simulate a basis set object. — sim_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -136,7 +136,7 @@ Value
diff --git a/docs/reference/sim_basis_1h_brain.html b/docs/reference/sim_basis_1h_brain.html
index 62ed7389..f71ffa0b 100644
--- a/docs/reference/sim_basis_1h_brain.html
+++ b/docs/reference/sim_basis_1h_brain.html
@@ -1,7 +1,5 @@
-Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS
-sequence. Note, ideal pulses are assumed. — sim_basis_1h_brain • Spectroscopy Analysis Tools (spant) Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS sequence. Note, ideal pulses are assumed. — sim_basis_1h_brain • Spectroscopy Analysis Tools (spant) Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS
-sequence. Note, ideal pulses are assumed. — sim_basis_1h_brain_press • Spectroscopy Analysis Tools (spant) Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS sequence. Note, ideal pulses are assumed. — sim_basis_1h_brain_press • Spectroscopy Analysis Tools (spant) Simulate a macromolecular and lipid basis-set suitable for 1H brain MRS
-analysis. — sim_basis_mm_lip_lcm • Spectroscopy Analysis Tools (spant) Simulate a macromolecular and lipid basis-set suitable for 1H brain MRS analysis. — sim_basis_mm_lip_lcm • Spectroscopy Analysis Tools (spant) Simulate a basis file using TARQUIN. — sim_basis_tqn • Spectroscopy Analysis Tools (spant) Simulate a basis file using TARQUIN. — sim_basis_tqn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -129,7 +129,7 @@ Examples
diff --git a/docs/reference/sim_brain_1h.html b/docs/reference/sim_brain_1h.html
index 2044cf1a..717ee289 100644
--- a/docs/reference/sim_brain_1h.html
+++ b/docs/reference/sim_brain_1h.html
@@ -1,5 +1,5 @@
-Simulate MRS data with a similar appearance to normal brain (by default). — sim_brain_1h • Spectroscopy Analysis Tools (spant) Simulate MRS data with a similar appearance to normal brain (by default). — sim_brain_1h • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -159,7 +159,7 @@ Value
diff --git a/docs/reference/sim_mol.html b/docs/reference/sim_mol.html
index 23bcef50..77f76a50 100644
--- a/docs/reference/sim_mol.html
+++ b/docs/reference/sim_mol.html
@@ -1,5 +1,5 @@
-Simulate a mol_parameter object. — sim_mol • Spectroscopy Analysis Tools (spant) Simulate a mol_parameter object. — sim_mol • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -143,7 +143,7 @@ Value
diff --git a/docs/reference/sim_noise.html b/docs/reference/sim_noise.html
index 23875f79..a71477d4 100644
--- a/docs/reference/sim_noise.html
+++ b/docs/reference/sim_noise.html
@@ -1,5 +1,5 @@
-Simulate an mrs_data object containing simulated Gaussian noise. — sim_noise • Spectroscopy Analysis Tools (spant) Simulate an mrs_data object containing simulated Gaussian noise. — sim_noise • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -84,6 +84,7 @@ Simulate an mrs_data object containing simulated Gaussian noise.
ft = def_ft(),
N = def_N(),
ref = def_ref(),
+ nuc = def_nuc(),
dyns = 1,
fd = TRUE
)
@@ -111,6 +112,10 @@ Arguments
reference value for ppm scale.
nuc
+resonant nucleus.
dyns
number of dynamic scans to generate.
Value
diff --git a/docs/reference/sim_resonances.html b/docs/reference/sim_resonances.html
index 19e9a8a4..d4f8d7c0 100644
--- a/docs/reference/sim_resonances.html
+++ b/docs/reference/sim_resonances.html
@@ -1,5 +1,5 @@
-Simulate a MRS data object containing a set of simulated resonances. — sim_resonances • Spectroscopy Analysis Tools (spant) Simulate a MRS data object containing a set of simulated resonances. — sim_resonances • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -161,7 +161,7 @@ Examples
diff --git a/docs/reference/sim_th_excit_profile.html b/docs/reference/sim_th_excit_profile.html
index 5535c5ef..e781cab1 100644
--- a/docs/reference/sim_th_excit_profile.html
+++ b/docs/reference/sim_th_excit_profile.html
@@ -1,7 +1,5 @@
-Simulate an ideal pulse excitation profile by smoothing a top-hat function
-with a Gaussian. — sim_th_excit_profile • Spectroscopy Analysis Tools (spant) Simulate an ideal pulse excitation profile by smoothing a top-hat function with a Gaussian. — sim_th_excit_profile • Spectroscopy Analysis Tools (spant) Simulate an mrs_data object containing complex zero valued samples. — sim_zero • Spectroscopy Analysis Tools (spant) Simulate an mrs_data object containing complex zero valued samples. — sim_zero • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -78,7 +78,14 @@ Simulate an mrs_data object containing complex zero valued samples.
-
+
@@ -99,6 +106,10 @@ Arguments
reference value for ppm scale.
nuc
+resonant nucleus.
dyns
number of dynamic scans to generate.
Value
diff --git a/docs/reference/smooth_dyns.html b/docs/reference/smooth_dyns.html
index 4cc8da50..accf3a51 100644
--- a/docs/reference/smooth_dyns.html
+++ b/docs/reference/smooth_dyns.html
@@ -1,5 +1,5 @@
-Smooth data across the dynamic dimension with a Gaussian kernel. — smooth_dyns • Spectroscopy Analysis Tools (spant) Smooth data across the dynamic dimension with a Gaussian kernel. — smooth_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/sort_basis.html b/docs/reference/sort_basis.html
index 6a676ea2..d25cc006 100644
--- a/docs/reference/sort_basis.html
+++ b/docs/reference/sort_basis.html
@@ -1,5 +1,5 @@
-Sort the basis-set elements alphabetically. — sort_basis • Spectroscopy Analysis Tools (spant) Sort the basis-set elements alphabetically. — sort_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/spant-package.html b/docs/reference/spant-package.html
index b3dd8e21..90f19ec3 100644
--- a/docs/reference/spant-package.html
+++ b/docs/reference/spant-package.html
@@ -1,5 +1,5 @@
-spant: spectroscopy analysis tools. — spant-package • Spectroscopy Analysis Tools (spant) spant: spectroscopy analysis tools. — spant-package • Spectroscopy Analysis Tools (spant) Simulate and fit some spectra with ABfit for benchmarking purposes. Basic
-timing and performance metrics will be printed. — spant_abfit_benchmark • Spectroscopy Analysis Tools (spant) Simulate and fit some spectra with ABfit for benchmarking purposes. Basic timing and performance metrics will be printed. — spant_abfit_benchmark • Spectroscopy Analysis Tools (spant) Example MEGA-PRESS data with significant B0 drift. — spant_mpress_drift • Spectroscopy Analysis Tools (spant) Example MEGA-PRESS data with significant B0 drift. — spant_mpress_drift • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -83,7 +83,7 @@ Example MEGA-PRESS data with significant B0 drift.
Format
- An object of class mrs_data of length 13.
+ An object of class mrs_data of dimension 1 x 1 x 1 x 1 x 40 x 1 x 1024.
@@ -98,7 +98,7 @@ Format
diff --git a/docs/reference/spant_sim_fmrs_dataset.html b/docs/reference/spant_sim_fmrs_dataset.html
new file mode 100644
index 00000000..00e48b56
--- /dev/null
+++ b/docs/reference/spant_sim_fmrs_dataset.html
@@ -0,0 +1,117 @@
+
+Simulate an example fMRS dataset for a block design fMRS experiment and export a BIDS structure. — spant_sim_fmrs_dataset • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Simulate an example fMRS dataset for a block design fMRS experiment and export a BIDS structure.
+ Source: R/fmrs.R
+ spant_sim_fmrs_dataset.Rd
+
+
+
+ Simulate an example fMRS dataset for a block design fMRS experiment and
+export a BIDS structure.
+
+
+
+ spant_sim_fmrs_dataset(output_dir = NULL)
+
+
+
+ Arguments
+ - output_dir
+output directory for the BIDS data. Defaults to :
+"HOME/sim_fmrs_dataset/data".
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/spant_simulation_benchmark.html b/docs/reference/spant_simulation_benchmark.html
index 32daa8bf..d8cc6841 100644
--- a/docs/reference/spant_simulation_benchmark.html
+++ b/docs/reference/spant_simulation_benchmark.html
@@ -1,7 +1,5 @@
-Simulate a typical metabolite basis set for benchmarking. Timing metrics will
-be printed on completion. — spant_simulation_benchmark • Spectroscopy Analysis Tools (spant) Simulate a typical metabolite basis set for benchmarking. Timing metrics will be printed on completion. — spant_simulation_benchmark • Spectroscopy Analysis Tools (spant) Decompose an mrs_data object into white and gray matter spectra. — spec_decomp • Spectroscopy Analysis Tools (spant) Perform a mathematical operation on a spectral region. — spec_op • Spectroscopy Analysis Tools (spant) Perform a mathematical operation on a spectral region. — spec_op • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -98,8 +98,8 @@ Arguments
operator
-can be "sum" (default), "mean", "l2", "max", "min" or
-"max-min".
can be "sum" (default), "mean", "l2", "max", "max_cplx,
+"min" or "max-min".
freq_scale
@@ -129,7 +129,7 @@ Value
diff --git a/docs/reference/spin_sys.html b/docs/reference/spin_sys.html
index 853423a4..1eaa9e76 100644
--- a/docs/reference/spin_sys.html
+++ b/docs/reference/spin_sys.html
@@ -1,5 +1,5 @@
-Create a spin system object for pulse sequence simulation. — spin_sys • Spectroscopy Analysis Tools (spant) Create a spin system object for pulse sequence simulation. — spin_sys • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/spm_pve2categorical.html b/docs/reference/spm_pve2categorical.html
index 23a1bad9..70f10729 100644
--- a/docs/reference/spm_pve2categorical.html
+++ b/docs/reference/spm_pve2categorical.html
@@ -1,7 +1,5 @@
-Convert SPM style segmentation files to a single categorical image where
-the numerical values map as: 0) Other, 1) CSF, 2) GM and 3) WM. — spm_pve2categorical • Spectroscopy Analysis Tools (spant) Convert SPM style segmentation files to a single categorical image where the numerical values map as: 0) Other, 1) CSF, 2) GM and 3) WM. — spm_pve2categorical • Spectroscopy Analysis Tools (spant) Signal space projection method for lipid suppression. — ssp • Spectroscopy Analysis Tools (spant) Signal space projection method for lipid suppression. — ssp • Spectroscopy Analysis Tools (spant) Plot the fitting results of an object of class fit_result with
-individual basis set components shown. — stackplot.fit_result • Spectroscopy Analysis Tools (spant) Plot the fitting results of an object of class fit_result with individual basis set components shown. — stackplot.fit_result • Spectroscopy Analysis Tools (spant) Produce a plot with multiple traces. — stackplot • Spectroscopy Analysis Tools (spant) Produce a plot with multiple traces. — stackplot • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/stackplot.mrs_data.html b/docs/reference/stackplot.mrs_data.html
index 17ff5648..64eea445 100644
--- a/docs/reference/stackplot.mrs_data.html
+++ b/docs/reference/stackplot.mrs_data.html
@@ -1,5 +1,5 @@
-Stackplot plotting method for objects of class mrs_data. — stackplot.mrs_data • Spectroscopy Analysis Tools (spant) Stackplot plotting method for objects of class mrs_data. — stackplot.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -255,7 +255,7 @@ Arguments
diff --git a/docs/reference/sub_first_dyn.html b/docs/reference/sub_first_dyn.html
index dbd7f831..493b7242 100644
--- a/docs/reference/sub_first_dyn.html
+++ b/docs/reference/sub_first_dyn.html
@@ -1,5 +1,5 @@
-Subtract the first dynamic spectrum from a dynamic series. — sub_first_dyn • Spectroscopy Analysis Tools (spant) Subtract the first dynamic spectrum from a dynamic series. — sub_first_dyn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/sub_mean_dyns.html b/docs/reference/sub_mean_dyns.html
index 6e3bb2df..221bd0c1 100644
--- a/docs/reference/sub_mean_dyns.html
+++ b/docs/reference/sub_mean_dyns.html
@@ -1,5 +1,5 @@
-Subtract the mean dynamic spectrum from a dynamic series. — sub_mean_dyns • Spectroscopy Analysis Tools (spant) Subtract the mean dynamic spectrum from a dynamic series. — sub_mean_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/sub_median_dyns.html b/docs/reference/sub_median_dyns.html
index 134c495d..1e834f14 100644
--- a/docs/reference/sub_median_dyns.html
+++ b/docs/reference/sub_median_dyns.html
@@ -1,5 +1,5 @@
-Subtract the median dynamic spectrum from a dynamic series. — sub_median_dyns • Spectroscopy Analysis Tools (spant) Subtract the median dynamic spectrum from a dynamic series. — sub_median_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/sum_coils.html b/docs/reference/sum_coils.html
index 7bf559f2..e1ab3cc0 100644
--- a/docs/reference/sum_coils.html
+++ b/docs/reference/sum_coils.html
@@ -1,5 +1,5 @@
-Calculate the sum across receiver coil elements. — sum_coils • Spectroscopy Analysis Tools (spant) Calculate the sum across receiver coil elements. — sum_coils • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/sum_dyns.html b/docs/reference/sum_dyns.html
index a0be19d3..bbda2ffc 100644
--- a/docs/reference/sum_dyns.html
+++ b/docs/reference/sum_dyns.html
@@ -1,5 +1,5 @@
-Calculate the sum of data dynamics. — sum_dyns • Spectroscopy Analysis Tools (spant) Calculate the sum of data dynamics. — sum_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/sum_mrs.html b/docs/reference/sum_mrs.html
index a22f215b..3cc3ab9e 100644
--- a/docs/reference/sum_mrs.html
+++ b/docs/reference/sum_mrs.html
@@ -1,5 +1,5 @@
-Sum two mrs_data objects. — sum_mrs • Spectroscopy Analysis Tools (spant) Sum two mrs_data objects. — sum_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Value
diff --git a/docs/reference/sum_mrs_list.html b/docs/reference/sum_mrs_list.html
index f4e09aea..c3584348 100644
--- a/docs/reference/sum_mrs_list.html
+++ b/docs/reference/sum_mrs_list.html
@@ -1,5 +1,5 @@
-Return the sum of a list of mrs_data objects. — sum_mrs_list • Spectroscopy Analysis Tools (spant) Return the sum of a list of mrs_data objects. — sum_mrs_list • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/svs_1h_brain_analysis.html b/docs/reference/svs_1h_brain_analysis.html
index 8ce514db..dff0ef7d 100644
--- a/docs/reference/svs_1h_brain_analysis.html
+++ b/docs/reference/svs_1h_brain_analysis.html
@@ -1,5 +1,5 @@
-Standard SVS 1H brain analysis pipeline. — svs_1h_brain_analysis • Spectroscopy Analysis Tools (spant) Standard SVS 1H brain analysis pipeline. — svs_1h_brain_analysis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -199,7 +199,7 @@ Value
diff --git a/docs/reference/svs_1h_brain_analysis_dev.html b/docs/reference/svs_1h_brain_analysis_dev.html
index d70a14d3..d71bfea2 100644
--- a/docs/reference/svs_1h_brain_analysis_dev.html
+++ b/docs/reference/svs_1h_brain_analysis_dev.html
@@ -1,5 +1,5 @@
-Standard SVS 1H brain analysis pipeline. — svs_1h_brain_analysis_dev • Spectroscopy Analysis Tools (spant) Standard SVS 1H brain analysis pipeline. — svs_1h_brain_analysis_dev • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -193,7 +193,7 @@ Examples
diff --git a/docs/reference/svs_1h_brain_batch_analysis.html b/docs/reference/svs_1h_brain_batch_analysis.html
index 5631e8cc..15f7223e 100644
--- a/docs/reference/svs_1h_brain_batch_analysis.html
+++ b/docs/reference/svs_1h_brain_batch_analysis.html
@@ -1,5 +1,5 @@
-Batch interface to the standard SVS 1H brain analysis pipeline. — svs_1h_brain_batch_analysis • Spectroscopy Analysis Tools (spant) Batch interface to the standard SVS 1H brain analysis pipeline. — svs_1h_brain_batch_analysis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -144,7 +144,7 @@ Value
diff --git a/docs/reference/t_test_spec.html b/docs/reference/t_test_spec.html
new file mode 100644
index 00000000..56a7ea1b
--- /dev/null
+++ b/docs/reference/t_test_spec.html
@@ -0,0 +1,124 @@
+
+Perform a t-test on spectral data points. — t_test_spec • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+
+
+ Perform a t-test on spectral data points.
+
+
+
+ t_test_spec(mrs_data, group)
+
+
+
+ Arguments
+ - mrs_data
+an mrs_data object with spectra in the dynamic dimension.
- group
+vector describing the group membership of each dynamic spectrum.
+
+ Value
+
+
+a list of statistical results.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/td2fd.html b/docs/reference/td2fd.html
index 6748a6a8..f31ed524 100644
--- a/docs/reference/td2fd.html
+++ b/docs/reference/td2fd.html
@@ -1,5 +1,5 @@
-Transform time-domain data to the frequency-domain. — td2fd • Spectroscopy Analysis Tools (spant) Transform time-domain data to the frequency-domain. — td2fd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/td_conv_filt.html b/docs/reference/td_conv_filt.html
index a9f340c3..106b9b00 100644
--- a/docs/reference/td_conv_filt.html
+++ b/docs/reference/td_conv_filt.html
@@ -1,5 +1,5 @@
-Time-domain convolution based filter. — td_conv_filt • Spectroscopy Analysis Tools (spant) Time-domain convolution based filter. — td_conv_filt • Spectroscopy Analysis Tools (spant) Time-domain spectral registration. — tdsr • Spectroscopy Analysis Tools (spant) Time-domain spectral registration. — tdsr • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -121,7 +121,7 @@ Value
diff --git a/docs/reference/te.html b/docs/reference/te.html
index 010361b1..4a65711d 100644
--- a/docs/reference/te.html
+++ b/docs/reference/te.html
@@ -1,5 +1,5 @@
-Return the echo time of an MRS dataset. — te • Spectroscopy Analysis Tools (spant) Return the echo time of an MRS dataset. — te • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/tr.html b/docs/reference/tr.html
index 0c0bd63b..2e749e02 100644
--- a/docs/reference/tr.html
+++ b/docs/reference/tr.html
@@ -1,5 +1,5 @@
-Return the repetition time of an MRS dataset. — tr • Spectroscopy Analysis Tools (spant) Return the repetition time of an MRS dataset. — tr • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/varpro_3_para_opts.html b/docs/reference/varpro_3_para_opts.html
index c2270a16..52d7cd84 100644
--- a/docs/reference/varpro_3_para_opts.html
+++ b/docs/reference/varpro_3_para_opts.html
@@ -1,5 +1,5 @@
-Return a list of options for VARPRO based fitting with 3 free parameters. — varpro_3_para_opts • Spectroscopy Analysis Tools (spant) Return a list of options for VARPRO based fitting with 3 free parameters. — varpro_3_para_opts • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -141,7 +141,7 @@ Value
diff --git a/docs/reference/varpro_basic_opts.html b/docs/reference/varpro_basic_opts.html
index 32c86d22..c5104891 100644
--- a/docs/reference/varpro_basic_opts.html
+++ b/docs/reference/varpro_basic_opts.html
@@ -1,5 +1,5 @@
-Return a list of options for a basic VARPRO analysis. — varpro_basic_opts • Spectroscopy Analysis Tools (spant) Return a list of options for a basic VARPRO analysis. — varpro_basic_opts • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -118,7 +118,7 @@ Value
diff --git a/docs/reference/varpro_opts.html b/docs/reference/varpro_opts.html
index 2aabf11d..6332f730 100644
--- a/docs/reference/varpro_opts.html
+++ b/docs/reference/varpro_opts.html
@@ -1,5 +1,5 @@
-Return a list of options for VARPRO based fitting. — varpro_opts • Spectroscopy Analysis Tools (spant) Return a list of options for VARPRO based fitting. — varpro_opts • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -177,7 +177,7 @@ Examples
diff --git a/docs/reference/vec2mrs_data.html b/docs/reference/vec2mrs_data.html
index 0cccd73b..f0d58bf0 100644
--- a/docs/reference/vec2mrs_data.html
+++ b/docs/reference/vec2mrs_data.html
@@ -1,5 +1,5 @@
-Convert a vector into a mrs_data object. — vec2mrs_data • Spectroscopy Analysis Tools (spant) Convert a vector into a mrs_data object. — vec2mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -80,10 +80,11 @@ Convert a vector into a mrs_data object.
vec2mrs_data(
vec,
- fs = def_fs(),
- ft = def_ft(),
- ref = def_ref(),
- nuc = def_nuc(),
+ mrs_data = NULL,
+ fs = NULL,
+ ft = NULL,
+ ref = NULL,
+ nuc = NULL,
dyns = 1,
fd = FALSE
)
@@ -95,6 +96,10 @@ Arguments
the data vector.
mrs_data
+example data to copy acquisition parameters from.
fs
sampling frequency in Hz.
Arguments
fd
-flag to indicate if the matrix is in the frequency domain (logical).
flag to indicate if the vector is in the frequency domain (logical).
Value
diff --git a/docs/reference/write_basis.html b/docs/reference/write_basis.html
index b6e27cbd..94c5e021 100644
--- a/docs/reference/write_basis.html
+++ b/docs/reference/write_basis.html
@@ -1,5 +1,5 @@
-Write a basis object to an LCModel .basis formatted file. — write_basis • Spectroscopy Analysis Tools (spant) Write a basis object to an LCModel .basis formatted file. — write_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -108,7 +108,7 @@ Arguments
diff --git a/docs/reference/write_basis_tqn.html b/docs/reference/write_basis_tqn.html
index 6aa51c1d..116c73ec 100644
--- a/docs/reference/write_basis_tqn.html
+++ b/docs/reference/write_basis_tqn.html
@@ -1,5 +1,5 @@
-Generate a basis file using TARQUIN. — write_basis_tqn • Spectroscopy Analysis Tools (spant) Generate a basis file using TARQUIN. — write_basis_tqn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Examples
diff --git a/docs/reference/write_mrs.html b/docs/reference/write_mrs.html
index fff25f15..124b9dc4 100644
--- a/docs/reference/write_mrs.html
+++ b/docs/reference/write_mrs.html
@@ -1,5 +1,5 @@
-Write MRS data object to file. — write_mrs • Spectroscopy Analysis Tools (spant) Write MRS data object to file. — write_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Arguments
diff --git a/docs/reference/write_mrs_nifti.html b/docs/reference/write_mrs_nifti.html
index f4bf1921..bd3ed4b7 100644
--- a/docs/reference/write_mrs_nifti.html
+++ b/docs/reference/write_mrs_nifti.html
@@ -1,5 +1,5 @@
-Write MRS data object to file in NIFTI format. — write_mrs_nifti • Spectroscopy Analysis Tools (spant) Write MRS data object to file in NIFTI format. — write_mrs_nifti • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/write_pulse_ascii.html b/docs/reference/write_pulse_ascii.html
index 067ae086..221f8ebb 100644
--- a/docs/reference/write_pulse_ascii.html
+++ b/docs/reference/write_pulse_ascii.html
@@ -1,5 +1,5 @@
-Write an ASCII formatted pulse file. — write_pulse_ascii • Spectroscopy Analysis Tools (spant) Write an ASCII formatted pulse file. — write_pulse_ascii • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/zero_fade_spec.html b/docs/reference/zero_fade_spec.html
index c703745c..c8b572c3 100644
--- a/docs/reference/zero_fade_spec.html
+++ b/docs/reference/zero_fade_spec.html
@@ -1,7 +1,5 @@
-Fade a spectrum to zero by frequency domain multiplication with a tanh
-function. Note this operation distorts data points at the end of the FID. — zero_fade_spec • Spectroscopy Analysis Tools (spant) Fade a spectrum to zero by frequency domain multiplication with a tanh function. Note this operation distorts data points at the end of the FID. — zero_fade_spec • Spectroscopy Analysis Tools (spant) Zero all coherences including and above a given order. — zero_higher_orders • Spectroscopy Analysis Tools (spant) Zero all coherences including and above a given order. — zero_higher_orders • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Value
diff --git a/docs/reference/zero_td_pts_end.html b/docs/reference/zero_td_pts_end.html
index 8c1123c8..71d24ebb 100644
--- a/docs/reference/zero_td_pts_end.html
+++ b/docs/reference/zero_td_pts_end.html
@@ -1,5 +1,5 @@
-Set mrs_data object data points at the end of the FID to zero. — zero_td_pts_end • Spectroscopy Analysis Tools (spant) Set mrs_data object data points at the end of the FID to zero. — zero_td_pts_end • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/zf.html b/docs/reference/zf.html
index 85e2013c..baf50256 100644
--- a/docs/reference/zf.html
+++ b/docs/reference/zf.html
@@ -1,5 +1,5 @@
-Zero-fill MRS data in the time domain. — zf • Spectroscopy Analysis Tools (spant) Zero-fill MRS data in the time domain. — zf • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -125,7 +125,7 @@ Value
diff --git a/docs/reference/zf_xy.html b/docs/reference/zf_xy.html
index ebca3999..c4104a74 100644
--- a/docs/reference/zf_xy.html
+++ b/docs/reference/zf_xy.html
@@ -1,5 +1,5 @@
-Zero-fill MRSI data in the k-space x-y direction. — zf_xy • Spectroscopy Analysis Tools (spant) Zero-fill MRSI data in the k-space x-y direction. — zf_xy • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -113,7 +113,7 @@ Value
diff --git a/docs/sitemap.xml b/docs/sitemap.xml
index e2139f71..4c39f515 100644
--- a/docs/sitemap.xml
+++ b/docs/sitemap.xml
@@ -216,6 +216,12 @@
https://martin3141.github.io/spant/reference/comb_coils_fp_pc.html
+
+ https://martin3141.github.io/spant/reference/comb_coils_mrsi_gls.html
+
+
+ https://martin3141.github.io/spant/reference/comb_coils_svs_gls.html
+
https://martin3141.github.io/spant/reference/comb_csv_results.html
@@ -411,6 +417,9 @@
https://martin3141.github.io/spant/reference/gen_conv_reg.html
+
+ https://martin3141.github.io/spant/reference/gen_group_reg.html
+
https://martin3141.github.io/spant/reference/gen_impulse_reg.html
@@ -555,6 +564,15 @@
https://martin3141.github.io/spant/reference/glm_spec.html
+
+ https://martin3141.github.io/spant/reference/glm_spec_fmrs_fl.html
+
+
+ https://martin3141.github.io/spant/reference/glm_spec_fmrs_group.html
+
+
+ https://martin3141.github.io/spant/reference/glm_spec_group_linhyp.html
+
https://martin3141.github.io/spant/reference/grid_shift_xy.html
@@ -690,9 +708,15 @@
https://martin3141.github.io/spant/reference/mrs_data2basis.html
+
+ https://martin3141.github.io/spant/reference/mrs_data2bids.html
+
https://martin3141.github.io/spant/reference/mrs_data2mat.html
+
+ https://martin3141.github.io/spant/reference/mrs_data2spec_mat.html
+
https://martin3141.github.io/spant/reference/mrs_data2vec.html
@@ -741,6 +765,9 @@
https://martin3141.github.io/spant/reference/phase.html
+
+ https://martin3141.github.io/spant/reference/phase_ref_1h_brain.html
+
https://martin3141.github.io/spant/reference/plot.fit_result.html
@@ -780,6 +807,12 @@
https://martin3141.github.io/spant/reference/precomp.html
+
+ https://martin3141.github.io/spant/reference/preproc_svs.html
+
+
+ https://martin3141.github.io/spant/reference/preproc_svs_dataset.html
+
https://martin3141.github.io/spant/reference/print.fit_result.html
@@ -1050,6 +1083,9 @@
https://martin3141.github.io/spant/reference/spant_mpress_drift.html
+
+ https://martin3141.github.io/spant/reference/spant_sim_fmrs_dataset.html
+
https://martin3141.github.io/spant/reference/spant_simulation_benchmark.html
@@ -1107,6 +1143,9 @@
https://martin3141.github.io/spant/reference/svs_1h_brain_batch_analysis.html
+
+ https://martin3141.github.io/spant/reference/t_test_spec.html
+
https://martin3141.github.io/spant/reference/td2fd.html
mrs_proc):+fit_res <- fit_mrs(mrs_proc, basis)Plot the fit result:
-+plot(fit_res)
Unscaled amplitudes, CRLB error estimates and other useful fitting diagnostics, such as SNR, are given in the
-fit_resresults table:++#> 1 -8.418839 -8.418312fit_res$res_tab -#> X Y Z Dynamic Coil X.CrCH2 Ala Asp Cr -#> 1 1 1 1 1 1 0 8.228912e-06 3.548337e-05 4.020305e-05 -#> GABA Glc Gln GSH Glu GPC -#> 1 1.706754e-05 2.442067e-06 3.029726e-06 2.227786e-05 6.499645e-05 1.603288e-05 -#> Ins Lac Lip09 Lip13a Lip13b Lip20 MM09 -#> 1 5.902957e-05 5.818739e-06 2.362972e-05 2.635502e-06 0 0 9.887557e-06 -#> MM12 MM14 MM17 MM20 NAA NAAG -#> 1 6.546986e-06 2.59994e-05 2.245507e-05 9.207418e-05 5.981787e-05 1.556188e-05 -#> PCh PCr sIns Tau tNAA tCr tCho -#> 1 0 2.101297e-05 6.508636e-06 0 7.537975e-05 6.121601e-05 1.603288e-05 -#> Glx tLM09 tLM13 tLM20 X.CrCH2.sd Ala.sd -#> 1 6.802617e-05 3.351728e-05 3.518189e-05 9.207418e-05 2.383751e-06 4.353306e-06 +#> X Y Z Dynamic Coil X.CrCH2 Ala Asp Cr GABA +#> 1 1 1 1 1 1 0 8.133932e-06 3.547065e-05 4.02672e-05 1.697281e-05 +#> Glc Gln GSH Glu GPC Ins +#> 1 2.446596e-06 3.036132e-06 2.228048e-05 6.503217e-05 1.606706e-05 5.906155e-05 +#> Lac Lip09 Lip13a Lip13b Lip20 MM09 MM12 +#> 1 5.802284e-06 2.387704e-05 2.670653e-06 0 0 9.630788e-06 6.511381e-06 +#> MM14 MM17 MM20 NAA NAAG PCh +#> 1 2.603855e-05 2.238405e-05 9.203743e-05 6.011109e-05 1.536531e-05 0 +#> PCr sIns Tau tNAA tCr tCho +#> 1 2.101921e-05 6.504098e-06 0 7.54764e-05 6.12864e-05 1.606706e-05 +#> Glx tLM09 tLM13 tLM20 X.CrCH2.sd Ala.sd +#> 1 6.80683e-05 3.350783e-05 3.522059e-05 9.203743e-05 2.386861e-06 4.343919e-06 #> Asp.sd Cr.sd GABA.sd Glc.sd Gln.sd GSH.sd -#> 1 9.243626e-06 3.715175e-06 4.580082e-06 4.427045e-06 5.089143e-06 2.022836e-06 +#> 1 9.235326e-06 3.689004e-06 4.574407e-06 4.421681e-06 5.083001e-06 2.020426e-06 #> Glu.sd GPC.sd Ins.sd Lac.sd Lip09.sd Lip13a.sd -#> 1 5.086888e-06 2.525936e-06 2.091039e-06 5.311855e-06 4.118786e-06 1.328562e-05 +#> 1 5.082976e-06 2.602651e-06 2.093225e-06 5.301703e-06 4.119256e-06 1.328305e-05 #> Lip13b.sd Lip20.sd MM09.sd MM12.sd MM14.sd MM17.sd -#> 1 6.477225e-06 7.510915e-06 3.827221e-06 4.597884e-06 7.234429e-06 3.810268e-06 +#> 1 6.474481e-06 7.510908e-06 3.827554e-06 4.594019e-06 7.223367e-06 3.811301e-06 #> MM20.sd NAA.sd NAAG.sd PCh.sd PCr.sd sIns.sd -#> 1 8.602464e-06 1.015226e-06 1.215672e-06 2.174697e-06 3.108036e-06 7.233855e-07 -#> Tau.sd tNAA.sd tCr.sd tCho.sd Glx.sd tLM09.sd -#> 1 3.777984e-06 7.031059e-07 5.881706e-07 2.1135e-07 3.165045e-06 1.006532e-06 -#> tLM13.sd tLM20.sd phase lw shift asym -#> 1 1.572003e-06 3.018189e-06 11.15087 5.038937 -0.003427612 0.1764497 +#> 1 8.595853e-06 1.017712e-06 1.208985e-06 2.236873e-06 3.084598e-06 7.240068e-07 +#> Tau.sd tNAA.sd tCr.sd tCho.sd Glx.sd tLM09.sd +#> 1 3.759956e-06 7.031383e-07 5.890481e-07 2.110662e-07 3.16966e-06 1.006794e-06 +#> tLM13.sd tLM20.sd phase lw shift asym +#> 1 1.573147e-06 3.016809e-06 11.10963 5.023681 -0.00376505 0.1771067 #> res.deviance res.niter res.info -#> 1 7.300317e-05 28 2 +#> 1 7.307669e-05 28 2 #> res.message bl_ed_pppm #> 1 Relative error between `par' and the solution is at most `ptol'. 2.364083 -#> max_bl_flex_used full_res fit_pts ppm_range SNR SRR FQN -#> 1 FALSE 7.745303e-05 497 3.8 62.79191 51.44068 1.490027 +#> max_bl_flex_used full_res fit_pts ppm_range SNR SRR FQN +#> 1 FALSE 7.754368e-05 497 3.8 62.71687 51.3328 1.492722 #> tNAA_lw tCr_lw tCho_lw auto_bl_crit_7 auto_bl_crit_5.901 -#> 1 0.04565271 0.05199592 0.05438808 -8.904402 -8.947808 +#> 1 0.04562445 0.05189506 0.05438237 -8.900349 -8.944159 #> auto_bl_crit_4.942 auto_bl_crit_4.12 auto_bl_crit_3.425 auto_bl_crit_2.844 -#> 1 -8.980941 -9.003463 -9.016574 -9.023969 +#> 1 -8.977355 -9.000064 -9.013367 -9.02055 #> auto_bl_crit_2.364 auto_bl_crit_1.969 auto_bl_crit_1.647 auto_bl_crit_1.384 -#> 1 -9.027876 -9.027566 -9.014311 -8.963287 +#> 1 -9.024177 -9.023462 -9.009854 -8.958654 #> auto_bl_crit_1.17 auto_bl_crit_0.997 auto_bl_crit_0.856 auto_bl_crit_0.743 -#> 1 -8.848747 -8.694785 -8.565992 -8.488415 +#> 1 -8.844271 -8.690744 -8.562631 -8.485471 #> auto_bl_crit_0.654 auto_bl_crit_0.593 auto_bl_crit_0.558 auto_bl_crit_0.54 -#> 1 -8.449874 -8.432813 -8.425648 -8.42266 +#> 1 -8.447136 -8.430174 -8.423053 -8.420086 #> auto_bl_crit_0.532 auto_bl_crit_0.529 -#> 1 -8.421406 -8.420875Note that signal names appended with “.sd” are the CRLB estimates for the uncertainty (standard deviation) in the metabolite quantity estimate. e.g. to calculate the percentage s.d. for tNAA:
-++#> [1] 0.9316001fit_res$res_tab$tNAA.sd / fit_res$res_tab$tNAA * 100 -#> [1] 0.9327517Spectral SNR:
-++#> [1] 62.71687fit_res$res_tab$SNR -#> [1] 62.79191Linewidth of the tNAA resonance in PPM:
-++#> [1] 0.04562445fit_res$res_tab$tNAA_lw -#> [1] 0.04565271Ratios to total-creatine @@ -258,45 +259,45 @@
Ratios to total-creatine -
++#> tCho 0.26216356 +#> Glx 1.11065912 +#> tLM09 0.54674163 +#> tLM13 0.57468844 +#> tLM20 1.50175937fit_res_tcr_sc <- scale_amp_ratio(fit_res, "tCr") amps <- fit_amps(fit_res_tcr_sc) print(t(amps)) #> [,1] #> X.CrCH2 0.00000000 -#> Ala 0.13442417 -#> Asp 0.57964197 -#> Cr 0.65674069 -#> GABA 0.27880838 -#> Glc 0.03989262 -#> Gln 0.04949238 -#> GSH 0.36392207 -#> Glu 1.06175561 -#> GPC 0.26190670 -#> Ins 0.96428305 -#> Lac 0.09505257 -#> Lip09 0.38600560 -#> Lip13a 0.04305248 +#> Ala 0.13272001 +#> Asp 0.57876874 +#> Cr 0.65703313 +#> GABA 0.27694252 +#> Glc 0.03992071 +#> Gln 0.04954005 +#> GSH 0.36354683 +#> Glu 1.06111906 +#> GPC 0.26216356 +#> Ins 0.96369746 +#> Lac 0.09467490 +#> Lip09 0.38959768 +#> Lip13a 0.04357660 #> Lip13b 0.00000000 #> Lip20 0.00000000 -#> MM09 0.16151913 -#> MM12 0.10694891 -#> MM14 0.42471563 -#> MM17 0.36681686 -#> MM20 1.50408643 -#> NAA 0.97716047 -#> NAAG 0.25421252 +#> MM09 0.15714395 +#> MM12 0.10624512 +#> MM14 0.42486672 +#> MM17 0.36523688 +#> MM20 1.50175937 +#> NAA 0.98082268 +#> NAAG 0.25071313 #> PCh 0.00000000 -#> PCr 0.34325931 -#> sIns 0.10632244 +#> PCr 0.34296687 +#> sIns 0.10612627 #> Tau 0.00000000 -#> tNAA 1.23137299 +#> tNAA 1.23153582 #> tCr 1.00000000 -#> tCho 0.26190670 -#> Glx 1.11124799 -#> tLM09 0.54752473 -#> tLM13 0.57471702 -#> tLM20 1.50408643+#> 1 1H 2.5Water reference scaling, AKA “absolute-quantification” @@ -304,29 +305,29 @@
Water reference sca
A more sophisticated approach to scaling metabolite values involves the use of a separate water-reference acquisition - which can be imported in the standard way:
-@@ -279,8 +279,9 @@+fname_wref <- system.file("extdata", "philips_spar_sdat_W.SDAT", package = "spant") mrs_data_wref <- read_mrs(fname_wref)The following code assumes the voxel contains 100% white matter tissue and scales the metabolite values into molal (mM) units (mol / kg tissue water) based on the method described by Gasparovic et al MRM 2006 55(6):1219-26:
-++#> [1] 12.59789p_vols <- c(WM = 100, GM = 0, CSF = 0) TE = 0.03 TR = 2 fit_res_molal <- scale_amp_molal_pvc(fit_res, mrs_data_wref, p_vols, TE, TR) fit_res_molal$res_tab$tNAA -#> [1] 12.58176An alternative method scales the metabolite values into molar (mM) units (mol / Litre of tissue) based on assumptions outlined in the LCModel manual and references therein (section 10.2). This approach may be preferred when comparing results to those obtained LCModel or TARQUIN.
-++#> [1] 6.826336fit_res_molar <- scale_amp_molar(fit_res, mrs_data_wref) fit_res_molar$res_tab$tNAA -#> [1] 6.817594Note, while “absolute” units are attractive, a large number of assumptions about metabolite and water relaxation rates are necessary to arrive at these mM estimates. If you’re not confident at being able to @@ -354,7 +355,7 @@
Water reference sca diff --git a/docs/articles/spant-intro_files/figure-html/unnamed-chunk-10-1.png b/docs/articles/spant-intro_files/figure-html/unnamed-chunk-10-1.png index b84cd2d5..a8160510 100644 Binary files a/docs/articles/spant-intro_files/figure-html/unnamed-chunk-10-1.png and b/docs/articles/spant-intro_files/figure-html/unnamed-chunk-10-1.png differ diff --git a/docs/articles/spant-intro_files/figure-html/unnamed-chunk-7-1.png b/docs/articles/spant-intro_files/figure-html/unnamed-chunk-7-1.png index 15bdc4e5..94a3f545 100644 Binary files a/docs/articles/spant-intro_files/figure-html/unnamed-chunk-7-1.png and b/docs/articles/spant-intro_files/figure-html/unnamed-chunk-7-1.png differ diff --git a/docs/articles/spant-metabolite-simulation.html b/docs/articles/spant-metabolite-simulation.html index e6efca00..564fa989 100644 --- a/docs/articles/spant-metabolite-simulation.html +++ b/docs/articles/spant-metabolite-simulation.html @@ -12,7 +12,7 @@ - + @@ -40,7 +40,7 @@
Custom molecules#> L/G lineshape : 0 #> #> nucleus chem_shift -#> 1 1H 2.5 -custom_mol |> sim_mol() |> lb(2) |> zf() |> plot(xlim = c(4.4, 0.5))
Site built with pkgdown 2.0.7.
+Site built with pkgdown 2.0.9.
diff --git a/docs/articles/spant-preprocessing.html b/docs/articles/spant-preprocessing.html index 28e38762..9544cf71 100644 --- a/docs/articles/spant-preprocessing.html +++ b/docs/articles/spant-preprocessing.html @@ -12,7 +12,7 @@ - + @@ -40,7 +40,7 @@ @@ -179,7 +179,7 @@Reading raw data and plotting
-Site built with pkgdown 2.0.7.
+Site built with pkgdown 2.0.9.
diff --git a/docs/articles/spant-preprocessing_files/figure-html/unnamed-chunk-10-1.png b/docs/articles/spant-preprocessing_files/figure-html/unnamed-chunk-10-1.png
index 02bdd7ca..d9d919b3 100644
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diff --git a/docs/articles/spant-preprocessing_files/figure-html/unnamed-chunk-8-1.png b/docs/articles/spant-preprocessing_files/figure-html/unnamed-chunk-8-1.png
index f8a9f999..9cc14061 100644
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diff --git a/docs/authors.html b/docs/authors.html
index fd4064a4..34e6b241 100644
--- a/docs/authors.html
+++ b/docs/authors.html
@@ -1,5 +1,5 @@
-Authors and Citation • Spectroscopy Analysis Tools (spant) Authors and Citation • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -69,7 +69,7 @@
diff --git a/docs/index.html b/docs/index.html
index 6e715d8e..c58968f6 100644
--- a/docs/index.html
+++ b/docs/index.html
@@ -12,16 +12,13 @@
-
+
-
+
Changelog • Spectroscopy Analysis Tools (spant) Changelog • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -73,7 +73,13 @@ Changelog
-spant 2.21.0
+spant 2.22.0
+- Added find_bids_mrs and mrs_data2bids helper functions.
+- Improved handling of CMRR semi-LASER SVS water reference scans.
+- Added functions for GLS coil combination.
+
+
+spant 2.21.02024-05-30
- Fixed compiler warnings for Fortran code.
- Added glm_spec function.
- Added add_noise_spec_snr function.
@@ -584,7 +590,7 @@ spant 0.1.02
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml
index 510f032e..8099ddc1 100644
--- a/docs/pkgdown.yml
+++ b/docs/pkgdown.yml
@@ -1,5 +1,5 @@
-pandoc: 3.1.1
-pkgdown: 2.0.7
+pandoc: 3.1.11
+pkgdown: 2.0.9
pkgdown_sha: ~
articles:
abfit-baseline-opts: abfit-baseline-opts.html
@@ -7,7 +7,7 @@ articles:
spant-intro: spant-intro.html
spant-metabolite-simulation: spant-metabolite-simulation.html
spant-preprocessing: spant-preprocessing.html
-last_built: 2024-05-29T18:39Z
+last_built: 2024-07-11T11:18Z
urls:
reference: https://martin3141.github.io/spant/reference
article: https://martin3141.github.io/spant/articles
diff --git a/docs/reference/Arg.mrs_data.html b/docs/reference/Arg.mrs_data.html
index 1372d866..4eba752f 100644
--- a/docs/reference/Arg.mrs_data.html
+++ b/docs/reference/Arg.mrs_data.html
@@ -1,5 +1,5 @@
-Apply Arg operator to an MRS dataset. — Arg.mrs_data • Spectroscopy Analysis Tools (spant) Apply Arg operator to an MRS dataset. — Arg.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -107,7 +107,7 @@ Value
diff --git a/docs/reference/Conj.mrs_data.html b/docs/reference/Conj.mrs_data.html
index 794d446f..10ea0ef1 100644
--- a/docs/reference/Conj.mrs_data.html
+++ b/docs/reference/Conj.mrs_data.html
@@ -1,5 +1,5 @@
-Apply Conj operator to an MRS dataset. — Conj.mrs_data • Spectroscopy Analysis Tools (spant) Apply Conj operator to an MRS dataset. — Conj.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -107,7 +107,7 @@ Value
diff --git a/docs/reference/Im.mrs_data.html b/docs/reference/Im.mrs_data.html
index 4c9a70eb..e0e26588 100644
--- a/docs/reference/Im.mrs_data.html
+++ b/docs/reference/Im.mrs_data.html
@@ -1,5 +1,5 @@
-Apply Im operator to an MRS dataset. — Im.mrs_data • Spectroscopy Analysis Tools (spant) Apply Im operator to an MRS dataset. — Im.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -107,7 +107,7 @@ Value
diff --git a/docs/reference/Imzap.html b/docs/reference/Imzap.html
index a3eeaed6..cf1b088d 100644
--- a/docs/reference/Imzap.html
+++ b/docs/reference/Imzap.html
@@ -1,7 +1,5 @@
-Complex rounding function taken from complexplus package to reduce the number
-of spant dependencies. — Imzap • Spectroscopy Analysis Tools (spant) Complex rounding function taken from complexplus package to reduce the number of spant dependencies. — Imzap • Spectroscopy Analysis Tools (spant) Apply Mod operator to an MRS dataset. — Mod.mrs_data • Spectroscopy Analysis Tools (spant) Apply Mod operator to an MRS dataset. — Mod.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -107,7 +107,7 @@ Value
diff --git a/docs/reference/Ncoils.html b/docs/reference/Ncoils.html
index 503ce5c0..09d22662 100644
--- a/docs/reference/Ncoils.html
+++ b/docs/reference/Ncoils.html
@@ -1,5 +1,5 @@
-Return the total number of coil elements in an MRS dataset. — Ncoils • Spectroscopy Analysis Tools (spant) Return the total number of coil elements in an MRS dataset. — Ncoils • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/Ndyns.html b/docs/reference/Ndyns.html
index 49c3ebb2..26ca34a7 100644
--- a/docs/reference/Ndyns.html
+++ b/docs/reference/Ndyns.html
@@ -1,5 +1,5 @@
-Return the total number of dynamic scans in an MRS dataset. — Ndyns • Spectroscopy Analysis Tools (spant) Return the total number of dynamic scans in an MRS dataset. — Ndyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/Npts.html b/docs/reference/Npts.html
index c63fe64e..7e8af89e 100644
--- a/docs/reference/Npts.html
+++ b/docs/reference/Npts.html
@@ -1,5 +1,5 @@
-Return the number of data points in an MRS dataset. — Npts • Spectroscopy Analysis Tools (spant) Return the number of data points in an MRS dataset. — Npts • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/Nspec.html b/docs/reference/Nspec.html
index e5f2464a..ff6c4dcd 100644
--- a/docs/reference/Nspec.html
+++ b/docs/reference/Nspec.html
@@ -1,5 +1,5 @@
-Return the total number of spectra in an MRS dataset. — Nspec • Spectroscopy Analysis Tools (spant) Return the total number of spectra in an MRS dataset. — Nspec • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/Ntrans.html b/docs/reference/Ntrans.html
index 3d3ce629..32ae3ad6 100644
--- a/docs/reference/Ntrans.html
+++ b/docs/reference/Ntrans.html
@@ -1,5 +1,5 @@
-Return the total number of acquired transients for an MRS dataset. — Ntrans • Spectroscopy Analysis Tools (spant) Return the total number of acquired transients for an MRS dataset. — Ntrans • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/Nx.html b/docs/reference/Nx.html
index beb130b8..461192b3 100644
--- a/docs/reference/Nx.html
+++ b/docs/reference/Nx.html
@@ -1,5 +1,5 @@
-Return the total number of x locations in an MRS dataset. — Nx • Spectroscopy Analysis Tools (spant) Return the total number of x locations in an MRS dataset. — Nx • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/Ny.html b/docs/reference/Ny.html
index 5c23ee37..530efde4 100644
--- a/docs/reference/Ny.html
+++ b/docs/reference/Ny.html
@@ -1,5 +1,5 @@
-Return the total number of y locations in an MRS dataset. — Ny • Spectroscopy Analysis Tools (spant) Return the total number of y locations in an MRS dataset. — Ny • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/Nz.html b/docs/reference/Nz.html
index 2a28bfbb..15295f98 100644
--- a/docs/reference/Nz.html
+++ b/docs/reference/Nz.html
@@ -1,5 +1,5 @@
-Return the total number of z locations in an MRS dataset. — Nz • Spectroscopy Analysis Tools (spant) Return the total number of z locations in an MRS dataset. — Nz • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/Re.mrs_data.html b/docs/reference/Re.mrs_data.html
index bbdcd3e7..37608c36 100644
--- a/docs/reference/Re.mrs_data.html
+++ b/docs/reference/Re.mrs_data.html
@@ -1,5 +1,5 @@
-Apply Re operator to an MRS dataset. — Re.mrs_data • Spectroscopy Analysis Tools (spant) Apply Re operator to an MRS dataset. — Re.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -107,7 +107,7 @@ Value
diff --git a/docs/reference/abfit_opts.html b/docs/reference/abfit_opts.html
index d501fc2a..5524db43 100644
--- a/docs/reference/abfit_opts.html
+++ b/docs/reference/abfit_opts.html
@@ -1,5 +1,5 @@
-Return a list of options for an ABfit analysis. — abfit_opts • Spectroscopy Analysis Tools (spant) Return a list of options for an ABfit analysis. — abfit_opts • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -125,7 +125,8 @@ Return a list of options for an ABfit analysis.
input_paras_raw = NULL,
optim_lw_only = FALSE,
optim_lw_only_limit = 20,
- lb_init = 0.001
+ lb_init = 0.001,
+ zf_offset = NULL
)
@@ -347,6 +348,12 @@ Arguments
basis signals. Setting to 0 will clash with the minimum allowable value
(eg hard constraint) during the detailed fit.
+
+zf_offset
+offset in number of data points from the end of the FID to
+zero-fill. Default is NULL and will automatically set this to 50 points when
+the FID distortion flag is set for the mrs_data.
Value
@@ -372,7 +379,7 @@ Examples
diff --git a/docs/reference/abfit_opts_v1_9_0.html b/docs/reference/abfit_opts_v1_9_0.html
index 1c128a05..975f7a0a 100644
--- a/docs/reference/abfit_opts_v1_9_0.html
+++ b/docs/reference/abfit_opts_v1_9_0.html
@@ -1,7 +1,5 @@
-Return a list of options for an ABfit analysis to maintain comparability with
-analyses performed with version 1.9.0 (and earlier) of spant. — abfit_opts_v1_9_0 • Spectroscopy Analysis Tools (spant) Return a list of options for an ABfit analysis to maintain comparability with analyses performed with version 1.9.0 (and earlier) of spant. — abfit_opts_v1_9_0 • Spectroscopy Analysis Tools (spant) Simulate pulse sequence acquisition. — acquire • Spectroscopy Analysis Tools (spant) Simulate pulse sequence acquisition. — acquire • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/add_noise.html b/docs/reference/add_noise.html
index 5c395587..c2ded890 100644
--- a/docs/reference/add_noise.html
+++ b/docs/reference/add_noise.html
@@ -1,5 +1,5 @@
-Add noise to an mrs_data object. — add_noise • Spectroscopy Analysis Tools (spant) Add noise to an mrs_data object. — add_noise • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -116,7 +116,7 @@ Value
diff --git a/docs/reference/add_noise_spec_snr.html b/docs/reference/add_noise_spec_snr.html
index f0072ef4..92a0fab3 100644
--- a/docs/reference/add_noise_spec_snr.html
+++ b/docs/reference/add_noise_spec_snr.html
@@ -1,5 +1,5 @@
-Add noise to an mrs_data object to match a given SNR. — add_noise_spec_snr • Spectroscopy Analysis Tools (spant) Add noise to an mrs_data object to match a given SNR. — add_noise_spec_snr • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -78,7 +78,12 @@ Add noise to an mrs_data object to match a given SNR.
- add_noise_spec_snr(mrs_data, target_snr, sig_region = c(4, 0.5))
+ add_noise_spec_snr(
+ mrs_data,
+ target_snr,
+ sig_region = c(4, 0.5),
+ ref_data = NULL
+)
@@ -97,6 +102,11 @@ Arguments
spectral limits to search for the strongest spectral data
point.
ref_data
+measure the signal from the first scan in this reference data
+and apply the same target noise level to mrs_data.
Value
@@ -117,7 +127,7 @@ Value
diff --git a/docs/reference/align.html b/docs/reference/align.html
index f61afc9f..53697923 100644
--- a/docs/reference/align.html
+++ b/docs/reference/align.html
@@ -1,5 +1,5 @@
-Align spectra to a reference frequency using a convolution based method. — align • Spectroscopy Analysis Tools (spant) Align spectra to a reference frequency using a convolution based method. — align • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -146,7 +146,7 @@ Value
diff --git a/docs/reference/apodise_xy.html b/docs/reference/apodise_xy.html
index 35121da6..9f622f56 100644
--- a/docs/reference/apodise_xy.html
+++ b/docs/reference/apodise_xy.html
@@ -1,5 +1,5 @@
-Apodise MRSI data in the x-y direction with a k-space filter. — apodise_xy • Spectroscopy Analysis Tools (spant) Apodise MRSI data in the x-y direction with a k-space filter. — apodise_xy • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -88,7 +88,7 @@ Arguments
func
-must be "hamming" or "gaussian".
must be "hamming", "hanning" or "gaussian".
w
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/append_basis.html b/docs/reference/append_basis.html
index cf58e336..c32f7be3 100644
--- a/docs/reference/append_basis.html
+++ b/docs/reference/append_basis.html
@@ -1,5 +1,5 @@
-Combine a pair of basis set objects. — append_basis • Spectroscopy Analysis Tools (spant) Combine a pair of basis set objects. — append_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/append_coils.html b/docs/reference/append_coils.html
index 6e2ead5b..99c8c3cf 100644
--- a/docs/reference/append_coils.html
+++ b/docs/reference/append_coils.html
@@ -1,7 +1,5 @@
-Append MRS data across the coil dimension, assumes they matched across the
-other dimensions. — append_coils • Spectroscopy Analysis Tools (spant) Append MRS data across the coil dimension, assumes they matched across the other dimensions. — append_coils • Spectroscopy Analysis Tools (spant) Append MRS data across the dynamic dimension, assumes they matched across the
-other dimensions. — append_dyns • Spectroscopy Analysis Tools (spant) Append MRS data across the dynamic dimension, assumes they matched across the other dimensions. — append_dyns • Spectroscopy Analysis Tools (spant) Append multiple regressor data frames into a single data frame. — append_regs • Spectroscopy Analysis Tools (spant) Append multiple regressor data frames into a single data frame. — append_regs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/apply_axes.html b/docs/reference/apply_axes.html
index 0f2f4d55..b5a7e296 100644
--- a/docs/reference/apply_axes.html
+++ b/docs/reference/apply_axes.html
@@ -1,5 +1,5 @@
-Apply a function over specified array axes. — apply_axes • Spectroscopy Analysis Tools (spant) Apply a function over specified array axes. — apply_axes • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -130,7 +130,7 @@ Examples
diff --git a/docs/reference/apply_mrs.html b/docs/reference/apply_mrs.html
index 22bc1933..1e2ea9ed 100644
--- a/docs/reference/apply_mrs.html
+++ b/docs/reference/apply_mrs.html
@@ -1,5 +1,5 @@
-Apply a function across given dimensions of a MRS data object. — apply_mrs • Spectroscopy Analysis Tools (spant) Apply a function across given dimensions of a MRS data object. — apply_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -116,7 +116,7 @@ Arguments
diff --git a/docs/reference/apply_pulse.html b/docs/reference/apply_pulse.html
index cae875cf..17c6e3ae 100644
--- a/docs/reference/apply_pulse.html
+++ b/docs/reference/apply_pulse.html
@@ -1,5 +1,5 @@
-Simulate an RF pulse on a single spin. — apply_pulse • Spectroscopy Analysis Tools (spant) Simulate an RF pulse on a single spin. — apply_pulse • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -126,7 +126,7 @@ Value
diff --git a/docs/reference/array2mrs_data.html b/docs/reference/array2mrs_data.html
index 26278811..c5f77129 100644
--- a/docs/reference/array2mrs_data.html
+++ b/docs/reference/array2mrs_data.html
@@ -1,7 +1,5 @@
-Convert a 7 dimensional array in into a mrs_data object. The array dimensions
-should be ordered as : dummy, X, Y, Z, dynamic, coil, FID. — array2mrs_data • Spectroscopy Analysis Tools (spant) Convert a 7 dimensional array in into a mrs_data object. The array dimensions should be ordered as : dummy, X, Y, Z, dynamic, coil, FID. — array2mrs_data • Spectroscopy Analysis Tools (spant) Perform zeroth-order phase correction based on the minimisation of the
-squared difference between the real and magnitude components of the
-spectrum. — auto_phase • Spectroscopy Analysis Tools (spant) Perform zeroth-order phase correction based on the minimisation of the squared difference between the real and magnitude components of the spectrum. — auto_phase • Spectroscopy Analysis Tools (spant) Back extrapolate time-domain data points using an autoregressive model. — back_extrap_ar • Spectroscopy Analysis Tools (spant) Back extrapolate time-domain data points using an autoregressive model. — back_extrap_ar • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -136,7 +136,7 @@ Value
diff --git a/docs/reference/basis2dyn_mrs_data.html b/docs/reference/basis2dyn_mrs_data.html
index 1e334800..ef466e85 100644
--- a/docs/reference/basis2dyn_mrs_data.html
+++ b/docs/reference/basis2dyn_mrs_data.html
@@ -1,5 +1,5 @@
-Convert a basis object to a dynamic mrs_data object. — basis2dyn_mrs_data • Spectroscopy Analysis Tools (spant) Convert a basis object to a dynamic mrs_data object. — basis2dyn_mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Value
diff --git a/docs/reference/basis2mrs_data.html b/docs/reference/basis2mrs_data.html
index d712d28f..dd0f65d9 100644
--- a/docs/reference/basis2mrs_data.html
+++ b/docs/reference/basis2mrs_data.html
@@ -1,7 +1,5 @@
-Convert a basis object to an mrs_data object - where basis signals are spread
-across the dynamic dimension. — basis2mrs_data • Spectroscopy Analysis Tools (spant) Convert a basis object to an mrs_data object - where basis signals are spread across the dynamic dimension. — basis2mrs_data • Spectroscopy Analysis Tools (spant) Generate a spline basis, slightly adapted from : "Splines, knots, and
-penalties", Eilers 2010. — bbase • Spectroscopy Analysis Tools (spant) Baseline correction using the ALS method. — bc_als • Spectroscopy Analysis Tools (spant) Baseline correction using the ALS method. — bc_als • Spectroscopy Analysis Tools (spant) Remove a constant baseline offset based on a reference spectral region. — bc_constant • Spectroscopy Analysis Tools (spant) Remove a constant baseline offset based on a reference spectral region. — bc_constant • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/bc_gauss.html b/docs/reference/bc_gauss.html
index 265fce5e..29fee72a 100644
--- a/docs/reference/bc_gauss.html
+++ b/docs/reference/bc_gauss.html
@@ -1,5 +1,5 @@
-Apply and subtract a Gaussian smoother in the spectral domain. — bc_gauss • Spectroscopy Analysis Tools (spant) Apply and subtract a Gaussian smoother in the spectral domain. — bc_gauss • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/bc_poly.html b/docs/reference/bc_poly.html
index e4f74fea..50b824de 100644
--- a/docs/reference/bc_poly.html
+++ b/docs/reference/bc_poly.html
@@ -1,5 +1,5 @@
-Fit and subtract a polynomial to each spectrum in a dataset. — bc_poly • Spectroscopy Analysis Tools (spant) Fit and subtract a polynomial to each spectrum in a dataset. — bc_poly • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/bc_spline.html b/docs/reference/bc_spline.html
index 09d7fc51..33239c4a 100644
--- a/docs/reference/bc_spline.html
+++ b/docs/reference/bc_spline.html
@@ -1,5 +1,5 @@
-Fit and subtract a smoothing spline to each spectrum in a dataset. — bc_spline • Spectroscopy Analysis Tools (spant) Fit and subtract a smoothing spline to each spectrum in a dataset. — bc_spline • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/beta2lw.html b/docs/reference/beta2lw.html
index 331a5c0b..d6afbc92 100644
--- a/docs/reference/beta2lw.html
+++ b/docs/reference/beta2lw.html
@@ -1,7 +1,5 @@
-Covert a beta value in the time-domain to an equivalent linewidth in Hz:
-x * exp(-i * t * t * beta). — beta2lw • Spectroscopy Analysis Tools (spant) Covert a beta value in the time-domain to an equivalent linewidth in Hz: x * exp(-i * t * t * beta). — beta2lw • Spectroscopy Analysis Tools (spant) Bin equally spaced spectral regions. — bin_spec • Spectroscopy Analysis Tools (spant) Bin equally spaced spectral regions. — bin_spec • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/calc_coil_noise_cor.html b/docs/reference/calc_coil_noise_cor.html
index beeab373..935cf09f 100644
--- a/docs/reference/calc_coil_noise_cor.html
+++ b/docs/reference/calc_coil_noise_cor.html
@@ -1,5 +1,5 @@
-Calculate the noise correlation between coil elements. — calc_coil_noise_cor • Spectroscopy Analysis Tools (spant) Calculate the noise correlation between coil elements. — calc_coil_noise_cor • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/calc_coil_noise_sd.html b/docs/reference/calc_coil_noise_sd.html
index 2a788fc7..d5f47a93 100644
--- a/docs/reference/calc_coil_noise_sd.html
+++ b/docs/reference/calc_coil_noise_sd.html
@@ -1,5 +1,5 @@
-Calculate the noise standard deviation for each coil element. — calc_coil_noise_sd • Spectroscopy Analysis Tools (spant) Calculate the noise standard deviation for each coil element. — calc_coil_noise_sd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/calc_design_efficiency.html b/docs/reference/calc_design_efficiency.html
index 0fc73261..2975440c 100644
--- a/docs/reference/calc_design_efficiency.html
+++ b/docs/reference/calc_design_efficiency.html
@@ -1,5 +1,5 @@
-Calculate the efficiency of a regressor data frame. — calc_design_efficiency • Spectroscopy Analysis Tools (spant) Calculate the efficiency of a regressor data frame. — calc_design_efficiency • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/calc_ed_from_lambda.html b/docs/reference/calc_ed_from_lambda.html
index 56237859..7962e054 100644
--- a/docs/reference/calc_ed_from_lambda.html
+++ b/docs/reference/calc_ed_from_lambda.html
@@ -1,5 +1,5 @@
-Calculate the effective dimensions of a spline smoother from lambda. — calc_ed_from_lambda • Spectroscopy Analysis Tools (spant) Calculate the effective dimensions of a spline smoother from lambda. — calc_ed_from_lambda • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/calc_peak_info_vec.html b/docs/reference/calc_peak_info_vec.html
index 79914d1f..03813eb8 100644
--- a/docs/reference/calc_peak_info_vec.html
+++ b/docs/reference/calc_peak_info_vec.html
@@ -1,5 +1,5 @@
-Calculate the FWHM of a peak from a vector of intensity values. — calc_peak_info_vec • Spectroscopy Analysis Tools (spant) Calculate the FWHM of a peak from a vector of intensity values. — calc_peak_info_vec • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/calc_sd_poly.html b/docs/reference/calc_sd_poly.html
index 737d68c7..c2f6d1eb 100644
--- a/docs/reference/calc_sd_poly.html
+++ b/docs/reference/calc_sd_poly.html
@@ -1,7 +1,5 @@
-Perform a polynomial fit, subtract and return the standard deviation of the
-residuals. — calc_sd_poly • Spectroscopy Analysis Tools (spant) Perform a polynomial fit, subtract and return the standard deviation of the residuals. — calc_sd_poly • Spectroscopy Analysis Tools (spant) Calculate the sum of squares differences between two mrs_data objects. — calc_spec_diff • Spectroscopy Analysis Tools (spant) Calculate the sum of squares differences between two mrs_data objects. — calc_spec_diff • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/calc_spec_snr.html b/docs/reference/calc_spec_snr.html
index 702fc62d..972912a0 100644
--- a/docs/reference/calc_spec_snr.html
+++ b/docs/reference/calc_spec_snr.html
@@ -1,5 +1,5 @@
-Calculate the spectral SNR. — calc_spec_snr • Spectroscopy Analysis Tools (spant) Calculate the spectral SNR. — calc_spec_snr • Spectroscopy Analysis Tools (spant) Check LCModel can be run — check_lcm • Spectroscopy Analysis Tools (spant) Check LCModel can be run — check_lcm • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -94,7 +94,7 @@ Check LCModel can be run
diff --git a/docs/reference/check_tqn.html b/docs/reference/check_tqn.html
index 7cdb1d18..4bfd1977 100644
--- a/docs/reference/check_tqn.html
+++ b/docs/reference/check_tqn.html
@@ -1,5 +1,5 @@
-Check the TARQUIN binary can be run — check_tqn • Spectroscopy Analysis Tools (spant) Check the TARQUIN binary can be run — check_tqn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -94,7 +94,7 @@ Check the TARQUIN binary can be run
diff --git a/docs/reference/circ_mask.html b/docs/reference/circ_mask.html
index 462f90f1..4634256d 100644
--- a/docs/reference/circ_mask.html
+++ b/docs/reference/circ_mask.html
@@ -1,5 +1,5 @@
-Create a logical circular mask spanning the full extent of an n x n matrix. — circ_mask • Spectroscopy Analysis Tools (spant) Create a logical circular mask spanning the full extent of an n x n matrix. — circ_mask • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/coherence_filter.html b/docs/reference/coherence_filter.html
index 61141857..852d1489 100644
--- a/docs/reference/coherence_filter.html
+++ b/docs/reference/coherence_filter.html
@@ -1,5 +1,5 @@
-Zero all coherence orders other than the one supplied as an argument. — coherence_filter • Spectroscopy Analysis Tools (spant) Zero all coherence orders other than the one supplied as an argument. — coherence_filter • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/collapse_to_dyns.html b/docs/reference/collapse_to_dyns.html
index f4dc6b97..7668cb08 100644
--- a/docs/reference/collapse_to_dyns.html
+++ b/docs/reference/collapse_to_dyns.html
@@ -1,5 +1,5 @@
-Collapse MRS data by concatenating spectra along the dynamic dimension. — collapse_to_dyns • Spectroscopy Analysis Tools (spant) Collapse MRS data by concatenating spectra along the dynamic dimension. — collapse_to_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -117,7 +117,7 @@ Value
diff --git a/docs/reference/comb_coils.html b/docs/reference/comb_coils.html
index 2f1cd561..9253b058 100644
--- a/docs/reference/comb_coils.html
+++ b/docs/reference/comb_coils.html
@@ -1,5 +1,5 @@
-Combine coil data based on the first data point of a reference signal. — comb_coils • Spectroscopy Analysis Tools (spant) Combine coil data based on the first data point of a reference signal. — comb_coils • Spectroscopy Analysis Tools (spant) Combine MRSI coil data using the GLS method presented by An et al JMRI 37:1445-1450 (2013). — comb_coils_mrsi_gls • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Combine MRSI coil data using the GLS method presented by An et al JMRI 37:1445-1450 (2013).
+ Source: R/mrs_data_proc.R
+ comb_coils_mrsi_gls.Rd
+
+
+
+ Combine MRSI coil data using the GLS method presented by An et al
+JMRI 37:1445-1450 (2013).
+
+
+
+ comb_coils_mrsi_gls(metab, noise_pts = 30, noise_mrs = NULL)
+
+
+
+ Arguments
+ - metab
+MRSI data containing metabolite data.
- noise_pts
+number of points from the end of the FIDs to use for noise
+covariance estimation.
- noise_mrs
+MRS data containing noise information for each coil.
+
+ Value
+
+
+coil combined MRSI data.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/comb_coils_svs_gls.html b/docs/reference/comb_coils_svs_gls.html
new file mode 100644
index 00000000..05b14d6d
--- /dev/null
+++ b/docs/reference/comb_coils_svs_gls.html
@@ -0,0 +1,145 @@
+
+Combine SVS coil data using the GLS method presented by An et al JMRI 37:1445-1450 (2013). — comb_coils_svs_gls • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Combine SVS coil data using the GLS method presented by An et al JMRI 37:1445-1450 (2013).
+ Source: R/mrs_data_proc.R
+ comb_coils_svs_gls.Rd
+
+
+
+ Combine SVS coil data using the GLS method presented by An et al
+JMRI 37:1445-1450 (2013).
+
+
+
+ comb_coils_svs_gls(
+ metab,
+ ref = NULL,
+ noise_pts = 256,
+ noise_mrs = NULL,
+ use_mean_sens = TRUE
+)
+
+
+
+ Arguments
+ - metab
+MRS data containing metabolite data.
- ref
+MRS data containing reference data (optional).
- noise_pts
+number of points from the end of the FIDs to use for noise
+covariance estimation.
- noise_mrs
+MRS data containing noise information for each coil.
- use_mean_sens
+use the dynamic mean to estimate coil sensitivities.
+
+ Value
+
+
+coil combined MRS data.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/comb_fit_list_fit_tables.html b/docs/reference/comb_fit_list_fit_tables.html
index e88c513a..098dea6e 100644
--- a/docs/reference/comb_fit_list_fit_tables.html
+++ b/docs/reference/comb_fit_list_fit_tables.html
@@ -1,5 +1,5 @@
-Combine all fitting data points from a list of fits into a single data frame. — comb_fit_list_fit_tables • Spectroscopy Analysis Tools (spant) Combine all fitting data points from a list of fits into a single data frame. — comb_fit_list_fit_tables • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -137,7 +137,7 @@ Value
diff --git a/docs/reference/comb_fit_list_result_tables.html b/docs/reference/comb_fit_list_result_tables.html
index 9a9cd20f..82008f85 100644
--- a/docs/reference/comb_fit_list_result_tables.html
+++ b/docs/reference/comb_fit_list_result_tables.html
@@ -1,5 +1,5 @@
-Combine the fit result tables from a list of fit results. — comb_fit_list_result_tables • Spectroscopy Analysis Tools (spant) Combine the fit result tables from a list of fit results. — comb_fit_list_result_tables • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -117,7 +117,7 @@ Value
diff --git a/docs/reference/comb_fit_tables.html b/docs/reference/comb_fit_tables.html
index 52315125..5ab0b533 100644
--- a/docs/reference/comb_fit_tables.html
+++ b/docs/reference/comb_fit_tables.html
@@ -1,5 +1,5 @@
-Combine all fitting data points into a single data frame. — comb_fit_tables • Spectroscopy Analysis Tools (spant) Combine all fitting data points into a single data frame. — comb_fit_tables • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -116,7 +116,7 @@ Value
diff --git a/docs/reference/comb_metab_ref.html b/docs/reference/comb_metab_ref.html
index 40474562..ac6d5555 100644
--- a/docs/reference/comb_metab_ref.html
+++ b/docs/reference/comb_metab_ref.html
@@ -1,5 +1,5 @@
-Combine a reference and metabolite mrs_data object. — comb_metab_ref • Spectroscopy Analysis Tools (spant) Combine a reference and metabolite mrs_data object. — comb_metab_ref • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/conv_mrs.html b/docs/reference/conv_mrs.html
index 3c349299..298e9810 100644
--- a/docs/reference/conv_mrs.html
+++ b/docs/reference/conv_mrs.html
@@ -1,5 +1,5 @@
-Convolve two MRS data objects. — conv_mrs • Spectroscopy Analysis Tools (spant) Convolve two MRS data objects. — conv_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/crop_basis.html b/docs/reference/crop_basis.html
index 25adfcc2..8193c2fe 100644
--- a/docs/reference/crop_basis.html
+++ b/docs/reference/crop_basis.html
@@ -1,5 +1,5 @@
-Crop basis_set object based on a frequency range. — crop_basis • Spectroscopy Analysis Tools (spant) Crop basis_set object based on a frequency range. — crop_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -116,7 +116,7 @@ Value
diff --git a/docs/reference/crop_spec.html b/docs/reference/crop_spec.html
index bac28c4b..be5e2e87 100644
--- a/docs/reference/crop_spec.html
+++ b/docs/reference/crop_spec.html
@@ -1,5 +1,5 @@
-Crop mrs_data object based on a frequency range. — crop_spec • Spectroscopy Analysis Tools (spant) Crop mrs_data object based on a frequency range. — crop_spec • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -116,7 +116,7 @@ Value
diff --git a/docs/reference/crop_td_pts.html b/docs/reference/crop_td_pts.html
index c9c4a213..c810fa4b 100644
--- a/docs/reference/crop_td_pts.html
+++ b/docs/reference/crop_td_pts.html
@@ -1,5 +1,5 @@
-Crop mrs_data object data points in the time-domain. — crop_td_pts • Spectroscopy Analysis Tools (spant) Crop mrs_data object data points in the time-domain. — crop_td_pts • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/crop_td_pts_end.html b/docs/reference/crop_td_pts_end.html
index 3560fee2..45fd251f 100644
--- a/docs/reference/crop_td_pts_end.html
+++ b/docs/reference/crop_td_pts_end.html
@@ -1,5 +1,5 @@
-Crop mrs_data object data points at the end of the FID. — crop_td_pts_end • Spectroscopy Analysis Tools (spant) Crop mrs_data object data points at the end of the FID. — crop_td_pts_end • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/crop_td_pts_pot.html b/docs/reference/crop_td_pts_pot.html
index d6c77479..4e2c39de 100644
--- a/docs/reference/crop_td_pts_pot.html
+++ b/docs/reference/crop_td_pts_pot.html
@@ -1,9 +1,5 @@
-Crop mrs_data object data points in the time-domain rounding down to
-the next smallest power of two (pot). Data that already has a pot length will
-not be changed. — crop_td_pts_pot • Spectroscopy Analysis Tools (spant) Crop mrs_data object data points in the time-domain rounding down to the next smallest power of two (pot). Data that already has a pot length will not be changed. — crop_td_pts_pot • Spectroscopy Analysis Tools (spant) Crop an MRSI dataset in the x-y direction — crop_xy • Spectroscopy Analysis Tools (spant) Crop an MRSI dataset in the x-y direction — crop_xy • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/crossprod_3d.html b/docs/reference/crossprod_3d.html
index 417852cd..eaf22eac 100644
--- a/docs/reference/crossprod_3d.html
+++ b/docs/reference/crossprod_3d.html
@@ -1,7 +1,5 @@
-Compute the vector cross product between vectors x and y. Adapted from
-http://stackoverflow.com/questions/15162741/what-is-rs-crossproduct-function — crossprod_3d • Spectroscopy Analysis Tools (spant) Compute the vector cross product between vectors x and y. Adapted from http://stackoverflow.com/questions/15162741/what-is-rs-crossproduct-function — crossprod_3d • Spectroscopy Analysis Tools (spant) Decimate an MRS signal to half the original sampling frequency by filtering
-in the frequency domain before down sampling. — decimate_mrs_fd • Spectroscopy Analysis Tools (spant) Decimate an MRS signal to half the original sampling frequency by filtering in the frequency domain before down sampling. — decimate_mrs_fd • Spectroscopy Analysis Tools (spant) Decimate an MRS signal by filtering in the time domain before downsampling. — decimate_mrs_td • Spectroscopy Analysis Tools (spant) Decimate an MRS signal by filtering in the time domain before downsampling. — decimate_mrs_td • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -118,7 +118,7 @@ Value
diff --git a/docs/reference/deconv_mrs.html b/docs/reference/deconv_mrs.html
index 1640eb61..61ad2631 100644
--- a/docs/reference/deconv_mrs.html
+++ b/docs/reference/deconv_mrs.html
@@ -1,5 +1,5 @@
-Deconvolve two MRS data objects. — deconv_mrs • Spectroscopy Analysis Tools (spant) Deconvolve two MRS data objects. — deconv_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/def_N.html b/docs/reference/def_N.html
index 1b8c28e2..204d145b 100644
--- a/docs/reference/def_N.html
+++ b/docs/reference/def_N.html
@@ -1,5 +1,5 @@
-Return the default number of data points in the spectral dimension. — def_N • Spectroscopy Analysis Tools (spant) Return the default number of data points in the spectral dimension. — def_N • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Value
diff --git a/docs/reference/def_acq_paras.html b/docs/reference/def_acq_paras.html
index e5dfddab..b06e4d22 100644
--- a/docs/reference/def_acq_paras.html
+++ b/docs/reference/def_acq_paras.html
@@ -1,7 +1,5 @@
-Return (and optionally modify using the input arguments) a list of the
-default acquisition parameters. — def_acq_paras • Spectroscopy Analysis Tools (spant) Return (and optionally modify using the input arguments) a list of the default acquisition parameters. — def_acq_paras • Spectroscopy Analysis Tools (spant) Return the default sampling frequency in Hz. — def_fs • Spectroscopy Analysis Tools (spant) Return the default sampling frequency in Hz. — def_fs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Value
diff --git a/docs/reference/def_ft.html b/docs/reference/def_ft.html
index 715f0c1f..cb7a33fb 100644
--- a/docs/reference/def_ft.html
+++ b/docs/reference/def_ft.html
@@ -1,5 +1,5 @@
-Return the default transmitter frequency in Hz. — def_ft • Spectroscopy Analysis Tools (spant) Return the default transmitter frequency in Hz. — def_ft • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Value
diff --git a/docs/reference/def_nuc.html b/docs/reference/def_nuc.html
index cfffaa97..addd88b8 100644
--- a/docs/reference/def_nuc.html
+++ b/docs/reference/def_nuc.html
@@ -1,5 +1,5 @@
-Return the default nucleus. — def_nuc • Spectroscopy Analysis Tools (spant) Return the default nucleus. — def_nuc • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Value
diff --git a/docs/reference/def_ref.html b/docs/reference/def_ref.html
index 1aed7ccf..0ff90af1 100644
--- a/docs/reference/def_ref.html
+++ b/docs/reference/def_ref.html
@@ -1,5 +1,5 @@
-Return the default reference value for ppm scale. — def_ref • Spectroscopy Analysis Tools (spant) Return the default reference value for ppm scale. — def_ref • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Value
diff --git a/docs/reference/dicom_reader.html b/docs/reference/dicom_reader.html
index f27d6e7f..0d19c93c 100644
--- a/docs/reference/dicom_reader.html
+++ b/docs/reference/dicom_reader.html
@@ -1,5 +1,5 @@
-A very simple DICOM reader. — dicom_reader • Spectroscopy Analysis Tools (spant) A very simple DICOM reader. — dicom_reader • Spectroscopy Analysis Tools (spant) Apply the diff operator to an MRS dataset in the FID/spectral dimension. — diff_mrs • Spectroscopy Analysis Tools (spant) Apply the diff operator to an MRS dataset in the FID/spectral dimension. — diff_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/downsample_mrs_fd.html b/docs/reference/downsample_mrs_fd.html
index 9974daa5..abb34365 100644
--- a/docs/reference/downsample_mrs_fd.html
+++ b/docs/reference/downsample_mrs_fd.html
@@ -1,5 +1,5 @@
-Downsample an MRS signal by a factor of 2 using an FFT "brick-wall" filter. — downsample_mrs_fd • Spectroscopy Analysis Tools (spant) Downsample an MRS signal by a factor of 2 using an FFT "brick-wall" filter. — downsample_mrs_fd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/downsample_mrs_td.html b/docs/reference/downsample_mrs_td.html
index 1a131574..c8464ac5 100644
--- a/docs/reference/downsample_mrs_td.html
+++ b/docs/reference/downsample_mrs_td.html
@@ -1,9 +1,5 @@
-Downsample an MRS signal by a factor of 2 by removing every other data point
-in the time-domain. Note, signals outside the new sampling frequency will be
-aliased. — downsample_mrs_td • Spectroscopy Analysis Tools (spant) Downsample an MRS signal by a factor of 2 by removing every other data point in the time-domain. Note, signals outside the new sampling frequency will be aliased. — downsample_mrs_td • Spectroscopy Analysis Tools (spant) Return a time scale vector of acquisition times for a dynamic MRS scan. The
-first temporal scan is assigned a value of 0. — dyn_acq_times • Spectroscopy Analysis Tools (spant) Return a time scale vector of acquisition times for a dynamic MRS scan. The first temporal scan is assigned a value of 0. — dyn_acq_times • Spectroscopy Analysis Tools (spant) Eddy current correction. — ecc • Spectroscopy Analysis Tools (spant) Eddy current correction. — ecc • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -120,7 +120,7 @@ Details
diff --git a/docs/reference/elliptical_mask.html b/docs/reference/elliptical_mask.html
index 9736c7c1..0e8f2c72 100644
--- a/docs/reference/elliptical_mask.html
+++ b/docs/reference/elliptical_mask.html
@@ -1,5 +1,5 @@
-Create an elliptical mask stored as a matrix of logical values. — elliptical_mask • Spectroscopy Analysis Tools (spant) Create an elliptical mask stored as a matrix of logical values. — elliptical_mask • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -130,7 +130,7 @@ Value
diff --git a/docs/reference/est_noise_sd.html b/docs/reference/est_noise_sd.html
index d0bcbc47..287ec04c 100644
--- a/docs/reference/est_noise_sd.html
+++ b/docs/reference/est_noise_sd.html
@@ -1,7 +1,5 @@
-Estimate the standard deviation of the noise from a segment of an mrs_data
-object. — est_noise_sd • Spectroscopy Analysis Tools (spant) Estimate the standard deviation of the noise from a segment of an mrs_data object. — est_noise_sd • Spectroscopy Analysis Tools (spant) Transform frequency-domain data to the time-domain. — fd2td • Spectroscopy Analysis Tools (spant) Transform frequency-domain data to the time-domain. — fd2td • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/fd_conv_filt.html b/docs/reference/fd_conv_filt.html
index d419e680..daf83ea8 100644
--- a/docs/reference/fd_conv_filt.html
+++ b/docs/reference/fd_conv_filt.html
@@ -1,5 +1,5 @@
-Frequency-domain convolution based filter. — fd_conv_filt • Spectroscopy Analysis Tools (spant) Frequency-domain convolution based filter. — fd_conv_filt • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -108,7 +108,7 @@ Arguments
diff --git a/docs/reference/fd_gauss_smo.html b/docs/reference/fd_gauss_smo.html
index 43fbb24b..0e6f1a96 100644
--- a/docs/reference/fd_gauss_smo.html
+++ b/docs/reference/fd_gauss_smo.html
@@ -1,5 +1,5 @@
-Apply a Gaussian smoother in the spectral domain. — fd_gauss_smo • Spectroscopy Analysis Tools (spant) Apply a Gaussian smoother in the spectral domain. — fd_gauss_smo • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/find_bids_mrs.html b/docs/reference/find_bids_mrs.html
index 81ef7726..ec9106b3 100644
--- a/docs/reference/find_bids_mrs.html
+++ b/docs/reference/find_bids_mrs.html
@@ -1,5 +1,5 @@
-Search for MRS data files in a BIDS filesystem structure. — find_bids_mrs • Spectroscopy Analysis Tools (spant) Search for MRS data files in a BIDS filesystem structure. — find_bids_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -78,7 +78,7 @@ Search for MRS data files in a BIDS filesystem structure.
- find_bids_mrs(path)
+ find_bids_mrs(path, output_full_path = FALSE)
@@ -86,6 +86,10 @@ Arguments
- path
path to the directory containing the BIDS structure.
- output_full_path
+output the full normalised data paths.
Value
@@ -106,7 +110,7 @@ Value
diff --git a/docs/reference/find_mrs_files.html b/docs/reference/find_mrs_files.html
index aa88618b..675c6ef0 100644
--- a/docs/reference/find_mrs_files.html
+++ b/docs/reference/find_mrs_files.html
@@ -1,5 +1,5 @@
-Find valid MRS data files recursively from a directory path. — find_mrs_files • Spectroscopy Analysis Tools (spant) Find valid MRS data files recursively from a directory path. — find_mrs_files • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/fit_amps.html b/docs/reference/fit_amps.html
index 2190b708..af27c9c7 100644
--- a/docs/reference/fit_amps.html
+++ b/docs/reference/fit_amps.html
@@ -1,5 +1,5 @@
-Extract the fit amplitudes from an object of class fit_result. — fit_amps • Spectroscopy Analysis Tools (spant) Extract the fit amplitudes from an object of class fit_result. — fit_amps • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -124,7 +124,7 @@ Value
diff --git a/docs/reference/fit_diags.html b/docs/reference/fit_diags.html
index 9f940ff1..b7ce449b 100644
--- a/docs/reference/fit_diags.html
+++ b/docs/reference/fit_diags.html
@@ -1,5 +1,5 @@
-Calculate diagnostic information for object of class fit_result. — fit_diags • Spectroscopy Analysis Tools (spant) Calculate diagnostic information for object of class fit_result. — fit_diags • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/fit_mrs.html b/docs/reference/fit_mrs.html
index 9eb523df..e088a98f 100644
--- a/docs/reference/fit_mrs.html
+++ b/docs/reference/fit_mrs.html
@@ -1,5 +1,5 @@
-Perform a fit based analysis of MRS data. — fit_mrs • Spectroscopy Analysis Tools (spant) Perform a fit based analysis of MRS data. — fit_mrs • Spectroscopy Analysis Tools (spant) Write fit results table to a csv file. — fit_res2csv • Spectroscopy Analysis Tools (spant) Write fit results table to a csv file. — fit_res2csv • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -108,7 +108,7 @@ Arguments
diff --git a/docs/reference/fit_t1_ti_array.html b/docs/reference/fit_t1_ti_array.html
index 5360fbc3..c8e26e48 100644
--- a/docs/reference/fit_t1_ti_array.html
+++ b/docs/reference/fit_t1_ti_array.html
@@ -1,5 +1,5 @@
-Fit a T1 recovery curve, from multiple TIs, to a set of amplitudes. — fit_t1_ti_array • Spectroscopy Analysis Tools (spant) Fit a T1 recovery curve, from multiple TIs, to a set of amplitudes. — fit_t1_ti_array • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -136,7 +136,7 @@ Value
diff --git a/docs/reference/fit_t1_tr_array.html b/docs/reference/fit_t1_tr_array.html
index 42d6961a..0a1f6cf3 100644
--- a/docs/reference/fit_t1_tr_array.html
+++ b/docs/reference/fit_t1_tr_array.html
@@ -1,5 +1,5 @@
-Fit a T1 recovery curve, from multiple TRs, to a set of amplitudes. — fit_t1_tr_array • Spectroscopy Analysis Tools (spant) Fit a T1 recovery curve, from multiple TRs, to a set of amplitudes. — fit_t1_tr_array • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -136,7 +136,7 @@ Value
diff --git a/docs/reference/fit_t2_te_array.html b/docs/reference/fit_t2_te_array.html
index abfc708c..75983e35 100644
--- a/docs/reference/fit_t2_te_array.html
+++ b/docs/reference/fit_t2_te_array.html
@@ -1,5 +1,5 @@
-Fit a T2 relaxation curve, from multiple TEs, to a set of amplitudes. — fit_t2_te_array • Spectroscopy Analysis Tools (spant) Fit a T2 relaxation curve, from multiple TEs, to a set of amplitudes. — fit_t2_te_array • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -136,7 +136,7 @@ Value
diff --git a/docs/reference/fp_phase.html b/docs/reference/fp_phase.html
index 55b65a21..5053cca5 100644
--- a/docs/reference/fp_phase.html
+++ b/docs/reference/fp_phase.html
@@ -1,5 +1,5 @@
-Return the phase of the first data point in the time-domain. — fp_phase • Spectroscopy Analysis Tools (spant) Return the phase of the first data point in the time-domain. — fp_phase • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/fp_phase_correct.html b/docs/reference/fp_phase_correct.html
index 8f847ebf..8859b25b 100644
--- a/docs/reference/fp_phase_correct.html
+++ b/docs/reference/fp_phase_correct.html
@@ -1,7 +1,5 @@
-Perform a zeroth order phase correction based on the phase of the first data
-point in the time-domain. — fp_phase_correct • Spectroscopy Analysis Tools (spant) Perform a zeroth order phase correction based on the phase of the first data point in the time-domain. — fp_phase_correct • Spectroscopy Analysis Tools (spant) Scale the first time-domain data point in an mrs_data object. — fp_scale • Spectroscopy Analysis Tools (spant) Scale the first time-domain data point in an mrs_data object. — fp_scale • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/fs.html b/docs/reference/fs.html
index 9e576eef..cd022581 100644
--- a/docs/reference/fs.html
+++ b/docs/reference/fs.html
@@ -1,5 +1,5 @@
-Return the sampling frequency in Hz of an MRS dataset. — fs • Spectroscopy Analysis Tools (spant) Return the sampling frequency in Hz of an MRS dataset. — fs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/ft_dyns.html b/docs/reference/ft_dyns.html
index de5e96a4..b8838eba 100644
--- a/docs/reference/ft_dyns.html
+++ b/docs/reference/ft_dyns.html
@@ -1,5 +1,5 @@
-Apply the Fourier transform over the dynamic dimension. — ft_dyns • Spectroscopy Analysis Tools (spant) Apply the Fourier transform over the dynamic dimension. — ft_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -119,7 +119,7 @@ Value
diff --git a/docs/reference/ft_shift.html b/docs/reference/ft_shift.html
index 7b55740b..a91d15c4 100644
--- a/docs/reference/ft_shift.html
+++ b/docs/reference/ft_shift.html
@@ -1,5 +1,5 @@
-Perform a fft and ffshift on a vector. — ft_shift • Spectroscopy Analysis Tools (spant) Perform a fft and ffshift on a vector. — ft_shift • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/ft_shift_mat.html b/docs/reference/ft_shift_mat.html
index 7009d0b9..46b6e787 100644
--- a/docs/reference/ft_shift_mat.html
+++ b/docs/reference/ft_shift_mat.html
@@ -1,7 +1,5 @@
-Perform a fft and fftshift on a matrix with each column replaced by its
-shifted fft. — ft_shift_mat • Spectroscopy Analysis Tools (spant) Perform a fft and fftshift on a matrix with each column replaced by its shifted fft. — ft_shift_mat • Spectroscopy Analysis Tools (spant) Create a two dimensional Gaussian window function stored as a matrix. — gausswin_2d • Spectroscopy Analysis Tools (spant) Create a two dimensional Gaussian window function stored as a matrix. — gausswin_2d • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -130,7 +130,7 @@ Value
diff --git a/docs/reference/gen_F.html b/docs/reference/gen_F.html
index 0eee85ab..2bdbe201 100644
--- a/docs/reference/gen_F.html
+++ b/docs/reference/gen_F.html
@@ -1,5 +1,5 @@
-Generate the F product operator. — gen_F • Spectroscopy Analysis Tools (spant) Generate the F product operator. — gen_F • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/gen_F_xy.html b/docs/reference/gen_F_xy.html
index 67c141e0..34e0242c 100644
--- a/docs/reference/gen_F_xy.html
+++ b/docs/reference/gen_F_xy.html
@@ -1,5 +1,5 @@
-Generate the Fxy product operator with a specified phase. — gen_F_xy • Spectroscopy Analysis Tools (spant) Generate the Fxy product operator with a specified phase. — gen_F_xy • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/gen_I.html b/docs/reference/gen_I.html
index 546e31e0..3b071790 100644
--- a/docs/reference/gen_I.html
+++ b/docs/reference/gen_I.html
@@ -1,5 +1,5 @@
-Generate the I product operator for a single spin. — gen_I • Spectroscopy Analysis Tools (spant) Generate the I product operator for a single spin. — gen_I • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/gen_baseline_reg.html b/docs/reference/gen_baseline_reg.html
index 499cd905..6c061185 100644
--- a/docs/reference/gen_baseline_reg.html
+++ b/docs/reference/gen_baseline_reg.html
@@ -1,5 +1,5 @@
-Generate baseline regressor. — gen_baseline_reg • Spectroscopy Analysis Tools (spant) Generate baseline regressor. — gen_baseline_reg • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -78,7 +78,7 @@ Generate baseline regressor.
- gen_baseline_reg(mrs_data)
+ gen_baseline_reg(mrs_data = NULL, tr = NULL, Ndyns = NULL, Ntrans = NULL)
@@ -86,6 +86,19 @@ Arguments
- mrs_data
mrs_data object for timing information.
- tr
+repetition time.
- Ndyns
+number of dynamic scans stored, potentially less than Ntrans
+if block averaging has been performed.
- Ntrans
+number of dynamic scans acquired.
Value
@@ -106,7 +119,7 @@ Value
diff --git a/docs/reference/gen_bold_reg.html b/docs/reference/gen_bold_reg.html
index 56bf47b9..e8755630 100644
--- a/docs/reference/gen_bold_reg.html
+++ b/docs/reference/gen_bold_reg.html
@@ -1,5 +1,5 @@
-Generate BOLD regressors. — gen_bold_reg • Spectroscopy Analysis Tools (spant) Generate BOLD regressors. — gen_bold_reg • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -83,6 +83,9 @@ Generate BOLD regressors.
duration = NULL,
trial_type = NULL,
mrs_data = NULL,
+ tr = NULL,
+ Ndyns = NULL,
+ Ntrans = NULL,
match_tr = TRUE,
dt = 0.1,
normalise = FALSE
@@ -107,6 +110,19 @@ Arguments
mrs_data object for timing information.
tr
+repetition time.
Ndyns
+number of dynamic scans stored, potentially less than Ntrans
+if block averaging has been performed.
Ntrans
+number of dynamic scans acquired.
match_tr
match the output to the input mrs_data.
Value
diff --git a/docs/reference/gen_conv_reg.html b/docs/reference/gen_conv_reg.html
index e94d6114..2a62bfc6 100644
--- a/docs/reference/gen_conv_reg.html
+++ b/docs/reference/gen_conv_reg.html
@@ -1,7 +1,5 @@
-Generate regressors by convolving a specified response function with a
-stimulus. — gen_conv_reg • Spectroscopy Analysis Tools (spant) Generate regressors by convolving a specified response function with a stimulus. — gen_conv_reg • Spectroscopy Analysis Tools (spant) Expand a regressor matrix for a group analysis. — gen_group_reg • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+
+
+ Expand a regressor matrix for a group analysis.
+
+
+
+ gen_group_reg(regressor_df, n)
+
+
+
+ Arguments
+ - regressor_df
+input regressor data frame.
- n
+number of datasets n the group.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/gen_impulse_reg.html b/docs/reference/gen_impulse_reg.html
index a900c805..b31ec7ff 100644
--- a/docs/reference/gen_impulse_reg.html
+++ b/docs/reference/gen_impulse_reg.html
@@ -1,5 +1,5 @@
-Generate impulse regressors. — gen_impulse_reg • Spectroscopy Analysis Tools (spant) Generate impulse regressors. — gen_impulse_reg • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -78,7 +78,14 @@ Generate impulse regressors.
- gen_impulse_reg(onset, trial_type = NULL, mrs_data = NULL)
+ gen_impulse_reg(
+ onset,
+ trial_type = NULL,
+ mrs_data = NULL,
+ tr = NULL,
+ Ndyns = NULL,
+ Ntrans = NULL
+)
@@ -94,6 +101,19 @@ Arguments
mrs_data
mrs_data object for timing information.
tr
+repetition time.
Ndyns
+number of dynamic scans stored, potentially less than Ntrans
+if block averaging has been performed.
Ntrans
+number of dynamic scans acquired.
Value
@@ -114,7 +134,7 @@ Value
diff --git a/docs/reference/gen_poly_reg.html b/docs/reference/gen_poly_reg.html
index 44c2aee5..e90af45c 100644
--- a/docs/reference/gen_poly_reg.html
+++ b/docs/reference/gen_poly_reg.html
@@ -1,5 +1,5 @@
-Generate polynomial regressors. — gen_poly_reg • Spectroscopy Analysis Tools (spant) Generate polynomial regressors. — gen_poly_reg • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -78,17 +78,30 @@ Generate polynomial regressors.
- gen_poly_reg(mrs_data, degree)
+ gen_poly_reg(degree, mrs_data = NULL, tr = NULL, Ndyns = NULL, Ntrans = NULL)
Arguments
- - mrs_data
+ - degree
+the degree of the polynomial.
- mrs_data
mrs_data object for timing information.
- degree
-the degree of the polynomial.
- tr
+repetition time.
- Ndyns
+number of dynamic scans stored, potentially less than Ntrans
+if block averaging has been performed.
- Ntrans
+number of dynamic scans acquired.
@@ -110,7 +123,7 @@ Value
diff --git a/docs/reference/gen_trap_reg.html b/docs/reference/gen_trap_reg.html
index 6c3d083a..d624f730 100644
--- a/docs/reference/gen_trap_reg.html
+++ b/docs/reference/gen_trap_reg.html
@@ -1,5 +1,5 @@
-Generate trapezoidal regressors. — gen_trap_reg • Spectroscopy Analysis Tools (spant) Generate trapezoidal regressors. — gen_trap_reg • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -83,6 +83,9 @@ Generate trapezoidal regressors.
duration,
trial_type = NULL,
mrs_data = NULL,
+ tr = NULL,
+ Ndyns = NULL,
+ Ntrans = NULL,
rise_t = 0,
fall_t = 0,
exp_fall = FALSE,
@@ -112,6 +115,19 @@ Arguments
mrs_data object for timing information.
tr
+repetition time.
Ndyns
+number of dynamic scans stored, potentially less than Ntrans
+if block averaging has been performed.
Ntrans
+number of dynamic scans acquired.
rise_t
time to reach a plateau from baseline in seconds.
Value
diff --git a/docs/reference/get_1h_brain_basis_names.html b/docs/reference/get_1h_brain_basis_names.html
index a8496ee7..0f940926 100644
--- a/docs/reference/get_1h_brain_basis_names.html
+++ b/docs/reference/get_1h_brain_basis_names.html
@@ -1,7 +1,5 @@
-Return a character vector of common 1H molecules found in healthy human
-brain. — get_1h_brain_basis_names • Spectroscopy Analysis Tools (spant) Return a character vector of common 1H molecules found in healthy human brain. — get_1h_brain_basis_names • Spectroscopy Analysis Tools (spant) Return a list of mol_parameter objects suitable for 1H brain MRS
-analyses. — get_1h_brain_basis_paras • Spectroscopy Analysis Tools (spant) Return a list of mol_parameter objects suitable for 1H brain MRS analyses. — get_1h_brain_basis_paras • Spectroscopy Analysis Tools (spant) Return a list of mol_parameter objects suitable for 1H brain MRS
-analyses. — get_1h_brain_basis_paras_v1 • Spectroscopy Analysis Tools (spant) Return a list of mol_parameter objects suitable for 1H brain MRS analyses. — get_1h_brain_basis_paras_v1 • Spectroscopy Analysis Tools (spant) Return a list of mol_parameter objects suitable for 1H brain MRS
-analyses. — get_1h_brain_basis_paras_v2 • Spectroscopy Analysis Tools (spant) Return a list of mol_parameter objects suitable for 1H brain MRS analyses. — get_1h_brain_basis_paras_v2 • Spectroscopy Analysis Tools (spant) Return a list of mol_parameter objects suitable for 1H brain MRS
-analyses. — get_1h_brain_basis_paras_v3 • Spectroscopy Analysis Tools (spant) Return a list of mol_parameter objects suitable for 1H brain MRS analyses. — get_1h_brain_basis_paras_v3 • Spectroscopy Analysis Tools (spant) Return a character vector of molecules included in the GE BRAINO phantom. — get_1h_braino_basis_names • Spectroscopy Analysis Tools (spant) Return a character vector of molecules included in the GE BRAINO phantom. — get_1h_braino_basis_names • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Value
diff --git a/docs/reference/get_1h_spectre_basis_names.html b/docs/reference/get_1h_spectre_basis_names.html
index 14f088ac..1a559f2e 100644
--- a/docs/reference/get_1h_spectre_basis_names.html
+++ b/docs/reference/get_1h_spectre_basis_names.html
@@ -1,7 +1,5 @@
-Return a character vector of molecules included in the Gold Star Phantoms
-SPECTRE phantom. — get_1h_spectre_basis_names • Spectroscopy Analysis Tools (spant) Return a character vector of molecules included in the Gold Star Phantoms SPECTRE phantom. — get_1h_spectre_basis_names • Spectroscopy Analysis Tools (spant) Get the point spread function (PSF) for a 2D phase encoded MRSI scan. — get_2d_psf • Spectroscopy Analysis Tools (spant) Get the point spread function (PSF) for a 2D phase encoded MRSI scan. — get_2d_psf • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -129,7 +129,7 @@ Value
diff --git a/docs/reference/get_acq_paras.html b/docs/reference/get_acq_paras.html
index 5bb919aa..3050cfff 100644
--- a/docs/reference/get_acq_paras.html
+++ b/docs/reference/get_acq_paras.html
@@ -1,5 +1,5 @@
-Return acquisition parameters from a MRS data object. — get_acq_paras • Spectroscopy Analysis Tools (spant) Return acquisition parameters from a MRS data object. — get_acq_paras • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/get_basis_subset.html b/docs/reference/get_basis_subset.html
index b7c1b5ed..08340cca 100644
--- a/docs/reference/get_basis_subset.html
+++ b/docs/reference/get_basis_subset.html
@@ -1,5 +1,5 @@
-Return a subset of the input basis. — get_basis_subset • Spectroscopy Analysis Tools (spant) Return a subset of the input basis. — get_basis_subset • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Value
diff --git a/docs/reference/get_dyns.html b/docs/reference/get_dyns.html
index d4376131..f9ef2c85 100644
--- a/docs/reference/get_dyns.html
+++ b/docs/reference/get_dyns.html
@@ -1,5 +1,5 @@
-Extract a subset of dynamic scans. — get_dyns • Spectroscopy Analysis Tools (spant) Extract a subset of dynamic scans. — get_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/get_even_dyns.html b/docs/reference/get_even_dyns.html
index 85fac0a6..8869a5aa 100644
--- a/docs/reference/get_even_dyns.html
+++ b/docs/reference/get_even_dyns.html
@@ -1,5 +1,5 @@
-Return even numbered dynamic scans starting from 1 (2,4,6...). — get_even_dyns • Spectroscopy Analysis Tools (spant) Return even numbered dynamic scans starting from 1 (2,4,6...). — get_even_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/get_fh_dyns.html b/docs/reference/get_fh_dyns.html
index 80d45928..e040408f 100644
--- a/docs/reference/get_fh_dyns.html
+++ b/docs/reference/get_fh_dyns.html
@@ -1,5 +1,5 @@
-Return the first half of a dynamic series. — get_fh_dyns • Spectroscopy Analysis Tools (spant) Return the first half of a dynamic series. — get_fh_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/get_fit_map.html b/docs/reference/get_fit_map.html
index 9584babd..0a20e465 100644
--- a/docs/reference/get_fit_map.html
+++ b/docs/reference/get_fit_map.html
@@ -1,5 +1,5 @@
-Get a data array from a fit result. — get_fit_map • Spectroscopy Analysis Tools (spant) Get a data array from a fit result. — get_fit_map • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/get_fp.html b/docs/reference/get_fp.html
index cce9f222..f6a7c7e3 100644
--- a/docs/reference/get_fp.html
+++ b/docs/reference/get_fp.html
@@ -1,5 +1,5 @@
-Return the first time-domain data point. — get_fp • Spectroscopy Analysis Tools (spant) Return the first time-domain data point. — get_fp • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/get_guassian_pulse.html b/docs/reference/get_guassian_pulse.html
index 739ef620..a6b1117c 100644
--- a/docs/reference/get_guassian_pulse.html
+++ b/docs/reference/get_guassian_pulse.html
@@ -1,5 +1,5 @@
-Generate a gaussian pulse shape. — get_guassian_pulse • Spectroscopy Analysis Tools (spant) Generate a gaussian pulse shape. — get_guassian_pulse • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -108,7 +108,7 @@ Arguments
diff --git a/docs/reference/get_head_dyns.html b/docs/reference/get_head_dyns.html
index 075c37b7..b3eea046 100644
--- a/docs/reference/get_head_dyns.html
+++ b/docs/reference/get_head_dyns.html
@@ -1,5 +1,5 @@
-Return the first scans of a dynamic series. — get_head_dyns • Spectroscopy Analysis Tools (spant) Return the first scans of a dynamic series. — get_head_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/get_lcm_cmd.html b/docs/reference/get_lcm_cmd.html
index 84ae0186..df411eaf 100644
--- a/docs/reference/get_lcm_cmd.html
+++ b/docs/reference/get_lcm_cmd.html
@@ -1,5 +1,5 @@
-Print the command to run the LCModel command-line program. — get_lcm_cmd • Spectroscopy Analysis Tools (spant) Print the command to run the LCModel command-line program. — get_lcm_cmd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -94,7 +94,7 @@ Print the command to run the LCModel command-line program.
diff --git a/docs/reference/get_metab.html b/docs/reference/get_metab.html
index 8c345609..e4777661 100644
--- a/docs/reference/get_metab.html
+++ b/docs/reference/get_metab.html
@@ -1,5 +1,5 @@
-Extract the metabolite component from an mrs_data object. — get_metab • Spectroscopy Analysis Tools (spant) Extract the metabolite component from an mrs_data object. — get_metab • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/get_mol_names.html b/docs/reference/get_mol_names.html
index ac6a75b5..44c0460f 100644
--- a/docs/reference/get_mol_names.html
+++ b/docs/reference/get_mol_names.html
@@ -1,7 +1,5 @@
-Return a character array of names that may be used with the
-get_mol_paras function. — get_mol_names • Spectroscopy Analysis Tools (spant) Return a character array of names that may be used with the get_mol_paras function. — get_mol_names • Spectroscopy Analysis Tools (spant) Get a mol_parameters object for a named molecule. — get_mol_paras • Spectroscopy Analysis Tools (spant) Get a mol_parameters object for a named molecule. — get_mol_paras • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/get_mrs_affine.html b/docs/reference/get_mrs_affine.html
index ae0672bd..1f4c519f 100644
--- a/docs/reference/get_mrs_affine.html
+++ b/docs/reference/get_mrs_affine.html
@@ -1,5 +1,5 @@
-Generate an affine for nifti generation. — get_mrs_affine • Spectroscopy Analysis Tools (spant) Generate an affine for nifti generation. — get_mrs_affine • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -118,7 +118,7 @@ Value
diff --git a/docs/reference/get_mrsi2d_seg.html b/docs/reference/get_mrsi2d_seg.html
index c8d981cd..99e56c11 100644
--- a/docs/reference/get_mrsi2d_seg.html
+++ b/docs/reference/get_mrsi2d_seg.html
@@ -1,5 +1,5 @@
-Calculate the partial volume estimates for each voxel in a 2D MRSI dataset. — get_mrsi2d_seg • Spectroscopy Analysis Tools (spant) Calculate the partial volume estimates for each voxel in a 2D MRSI dataset. — get_mrsi2d_seg • Spectroscopy Analysis Tools (spant) Generate a MRSI VOI from an mrs_data object. — get_mrsi_voi • Spectroscopy Analysis Tools (spant) Generate a MRSI VOI from an mrs_data object. — get_mrsi_voi • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -119,7 +119,7 @@ Value
diff --git a/docs/reference/get_mrsi_voxel.html b/docs/reference/get_mrsi_voxel.html
index c4255416..9f082f05 100644
--- a/docs/reference/get_mrsi_voxel.html
+++ b/docs/reference/get_mrsi_voxel.html
@@ -1,5 +1,5 @@
-Generate a MRSI voxel from an mrs_data object. — get_mrsi_voxel • Spectroscopy Analysis Tools (spant) Generate a MRSI voxel from an mrs_data object. — get_mrsi_voxel • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/get_mrsi_voxel_xy_psf.html b/docs/reference/get_mrsi_voxel_xy_psf.html
index 04c90780..1af5dfd5 100644
--- a/docs/reference/get_mrsi_voxel_xy_psf.html
+++ b/docs/reference/get_mrsi_voxel_xy_psf.html
@@ -1,5 +1,5 @@
-Generate a MRSI voxel PSF from an mrs_data object. — get_mrsi_voxel_xy_psf • Spectroscopy Analysis Tools (spant) Generate a MRSI voxel PSF from an mrs_data object. — get_mrsi_voxel_xy_psf • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/get_odd_dyns.html b/docs/reference/get_odd_dyns.html
index d016c241..498c924f 100644
--- a/docs/reference/get_odd_dyns.html
+++ b/docs/reference/get_odd_dyns.html
@@ -1,5 +1,5 @@
-Return odd numbered dynamic scans starting from 1 (1,3,5...). — get_odd_dyns • Spectroscopy Analysis Tools (spant) Return odd numbered dynamic scans starting from 1 (1,3,5...). — get_odd_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/get_ref.html b/docs/reference/get_ref.html
index d8234a92..9cf13eab 100644
--- a/docs/reference/get_ref.html
+++ b/docs/reference/get_ref.html
@@ -1,5 +1,5 @@
-Extract the reference component from an mrs_data object. — get_ref • Spectroscopy Analysis Tools (spant) Extract the reference component from an mrs_data object. — get_ref • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/get_seg_ind.html b/docs/reference/get_seg_ind.html
index e97e51ac..68eaa5f1 100644
--- a/docs/reference/get_seg_ind.html
+++ b/docs/reference/get_seg_ind.html
@@ -1,5 +1,5 @@
-Get the indices of data points lying between two values (end > x > start). — get_seg_ind • Spectroscopy Analysis Tools (spant) Get the indices of data points lying between two values (end > x > start). — get_seg_ind • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/get_sh_dyns.html b/docs/reference/get_sh_dyns.html
index 932c4247..8ea1d7be 100644
--- a/docs/reference/get_sh_dyns.html
+++ b/docs/reference/get_sh_dyns.html
@@ -1,5 +1,5 @@
-Return the second half of a dynamic series. — get_sh_dyns • Spectroscopy Analysis Tools (spant) Return the second half of a dynamic series. — get_sh_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/get_slice.html b/docs/reference/get_slice.html
index e8b9fa7e..1fb729cc 100644
--- a/docs/reference/get_slice.html
+++ b/docs/reference/get_slice.html
@@ -1,5 +1,5 @@
-Return a single slice from a larger MRSI dataset. — get_slice • Spectroscopy Analysis Tools (spant) Return a single slice from a larger MRSI dataset. — get_slice • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/get_spin_num.html b/docs/reference/get_spin_num.html
index 021d4e60..acff1245 100644
--- a/docs/reference/get_spin_num.html
+++ b/docs/reference/get_spin_num.html
@@ -1,5 +1,5 @@
-Return the spin number for a given nucleus. — get_spin_num • Spectroscopy Analysis Tools (spant) Return the spin number for a given nucleus. — get_spin_num • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/get_subset.html b/docs/reference/get_subset.html
index 34df3128..ecab116c 100644
--- a/docs/reference/get_subset.html
+++ b/docs/reference/get_subset.html
@@ -1,5 +1,5 @@
-Extract a subset of MRS data. — get_subset • Spectroscopy Analysis Tools (spant) Extract a subset of MRS data. — get_subset • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -144,7 +144,7 @@ Value
diff --git a/docs/reference/get_svs_voi.html b/docs/reference/get_svs_voi.html
index 54de4821..97437d5d 100644
--- a/docs/reference/get_svs_voi.html
+++ b/docs/reference/get_svs_voi.html
@@ -1,5 +1,5 @@
-Generate a SVS acquisition volume from an mrs_data object. — get_svs_voi • Spectroscopy Analysis Tools (spant) Generate a SVS acquisition volume from an mrs_data object. — get_svs_voi • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/get_tail_dyns.html b/docs/reference/get_tail_dyns.html
index cace1556..cee1cec3 100644
--- a/docs/reference/get_tail_dyns.html
+++ b/docs/reference/get_tail_dyns.html
@@ -1,5 +1,5 @@
-Return the last scans of a dynamic series. — get_tail_dyns • Spectroscopy Analysis Tools (spant) Return the last scans of a dynamic series. — get_tail_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/get_td_amp.html b/docs/reference/get_td_amp.html
index ad9f3f71..5e2b5814 100644
--- a/docs/reference/get_td_amp.html
+++ b/docs/reference/get_td_amp.html
@@ -1,7 +1,5 @@
-Return an array of amplitudes derived from fitting the initial points in the
-time domain and extrapolating back to t=0. — get_td_amp • Spectroscopy Analysis Tools (spant) Return an array of amplitudes derived from fitting the initial points in the time domain and extrapolating back to t=0. — get_td_amp • Spectroscopy Analysis Tools (spant) Print the command to run the TARQUIN command-line program. — get_tqn_cmd • Spectroscopy Analysis Tools (spant) Print the command to run the TARQUIN command-line program. — get_tqn_cmd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -94,7 +94,7 @@ Print the command to run the TARQUIN command-line program.
diff --git a/docs/reference/get_uncoupled_mol.html b/docs/reference/get_uncoupled_mol.html
index 0747cc21..5fd5cb69 100644
--- a/docs/reference/get_uncoupled_mol.html
+++ b/docs/reference/get_uncoupled_mol.html
@@ -1,7 +1,5 @@
-Generate a mol_parameters object for a simple spin system with one
-resonance. — get_uncoupled_mol • Spectroscopy Analysis Tools (spant) Generate a mol_parameters object for a simple spin system with one resonance. — get_uncoupled_mol • Spectroscopy Analysis Tools (spant) Calculate the centre of gravity for an image containing 0 and 1's. — get_voi_cog • Spectroscopy Analysis Tools (spant) Calculate the centre of gravity for an image containing 0 and 1's. — get_voi_cog • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/get_voi_seg.html b/docs/reference/get_voi_seg.html
index 9f0f7f44..261f5aa2 100644
--- a/docs/reference/get_voi_seg.html
+++ b/docs/reference/get_voi_seg.html
@@ -1,5 +1,5 @@
-Return the white matter, gray matter and CSF composition of a volume. — get_voi_seg • Spectroscopy Analysis Tools (spant) Return the white matter, gray matter and CSF composition of a volume. — get_voi_seg • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/get_voi_seg_psf.html b/docs/reference/get_voi_seg_psf.html
index 2e632a30..7982a0a4 100644
--- a/docs/reference/get_voi_seg_psf.html
+++ b/docs/reference/get_voi_seg_psf.html
@@ -1,5 +1,5 @@
-Return the white matter, gray matter and CSF composition of a volume. — get_voi_seg_psf • Spectroscopy Analysis Tools (spant) Return the white matter, gray matter and CSF composition of a volume. — get_voi_seg_psf • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/get_voxel.html b/docs/reference/get_voxel.html
index cb474e6c..93a4b392 100644
--- a/docs/reference/get_voxel.html
+++ b/docs/reference/get_voxel.html
@@ -1,5 +1,5 @@
-Return a single voxel from a larger mrs dataset. — get_voxel • Spectroscopy Analysis Tools (spant) Return a single voxel from a larger mrs dataset. — get_voxel • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -126,7 +126,7 @@ Value
diff --git a/docs/reference/glm_spec.html b/docs/reference/glm_spec.html
index 20459117..e767ecbf 100644
--- a/docs/reference/glm_spec.html
+++ b/docs/reference/glm_spec.html
@@ -1,5 +1,5 @@
-Perform a GLM analysis of dynamic MRS data in the spectral domain. — glm_spec • Spectroscopy Analysis Tools (spant) Perform a GLM analysis of dynamic MRS data in the spectral domain. — glm_spec • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -78,7 +78,7 @@ Perform a GLM analysis of dynamic MRS data in the spectral domain.
- glm_spec(mrs_data, regressor_df)
+ glm_spec(mrs_data, regressor_df, full_output = FALSE)
@@ -91,6 +91,10 @@ Arguments
a data frame containing temporal regressors to be applied
to each spectral datapoint.
full_output
+append mrs_data and regressor_df to the output list.
Value
@@ -111,7 +115,7 @@ Value
diff --git a/docs/reference/glm_spec_fmrs_fl.html b/docs/reference/glm_spec_fmrs_fl.html
new file mode 100644
index 00000000..30584e18
--- /dev/null
+++ b/docs/reference/glm_spec_fmrs_fl.html
@@ -0,0 +1,149 @@
+
+Perform first-level spectral GLM analysis of an fMRS dataset. — glm_spec_fmrs_fl • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Perform first-level spectral GLM analysis of an fMRS dataset.
+ Source: R/fmrs.R
+ glm_spec_fmrs_fl.Rd
+
+
+
+ Perform first-level spectral GLM analysis of an fMRS dataset.
+
+
+
+
+
+
+
+ Arguments
+ - regressor_df
+a data frame containing temporal regressors to be applied
+to each spectral datapoint.
- analysis_dir
+directory containing preprocessed data generated by
+the preproc_svs_dataset function.
- exclude_labels
+vector of labels of scans to exclude, eg poor quality
+data.
- labels
+labels to describe each data set.
- xlim
+spectral range to include in the analysis.
- vline
+vertical lines to add to the plot.
- return_results
+function will return key outputs, defaults to FALSE.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/glm_spec_fmrs_group.html b/docs/reference/glm_spec_fmrs_group.html
new file mode 100644
index 00000000..527478e5
--- /dev/null
+++ b/docs/reference/glm_spec_fmrs_group.html
@@ -0,0 +1,134 @@
+
+Perform group-level spectral GLM analysis of an fMRS dataset. — glm_spec_fmrs_group • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Perform group-level spectral GLM analysis of an fMRS dataset.
+ Source: R/fmrs.R
+ glm_spec_fmrs_group.Rd
+
+
+
+ Perform group-level spectral GLM analysis of an fMRS dataset.
+
+
+
+ glm_spec_fmrs_group(
+ regressor_df,
+ analysis_dir = "spant_analysis",
+ exclude_labels = NULL,
+ labels = NULL
+)
+
+
+
+ Arguments
+ - regressor_df
+a data frame containing temporal regressors to be applied
+to each spectral datapoint.
- analysis_dir
+directory containing preprocessed data generated by
+the preproc_svs_dataset function.
- exclude_labels
+vector of labels of scans to exclude, eg poor quality
+data.
- labels
+labels to describe each data set.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/glm_spec_group_linhyp.html b/docs/reference/glm_spec_group_linhyp.html
new file mode 100644
index 00000000..747860d9
--- /dev/null
+++ b/docs/reference/glm_spec_group_linhyp.html
@@ -0,0 +1,119 @@
+
+Test a group-level spectral GLM linear hypothesis. — glm_spec_group_linhyp • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Test a group-level spectral GLM linear hypothesis.
+ Source: R/fmrs.R
+ glm_spec_group_linhyp.Rd
+
+
+
+ Test a group-level spectral GLM linear hypothesis.
+
+
+
+ glm_spec_group_linhyp(hmat, analysis_dir = "spant_analysis")
+
+
+
+ Arguments
+ - hmat
+linear hypothesis matrix.
- analysis_dir
+directory containing preprocessed data generated by
+the preproc_svs_dataset function.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/grid_shift_xy.html b/docs/reference/grid_shift_xy.html
index 592fa3ec..d0e05b1d 100644
--- a/docs/reference/grid_shift_xy.html
+++ b/docs/reference/grid_shift_xy.html
@@ -1,5 +1,5 @@
-Grid shift MRSI data in the x/y dimension. — grid_shift_xy • Spectroscopy Analysis Tools (spant) Grid shift MRSI data in the x/y dimension. — grid_shift_xy • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/gridplot.html b/docs/reference/gridplot.html
index ca385d91..54e40afe 100644
--- a/docs/reference/gridplot.html
+++ b/docs/reference/gridplot.html
@@ -1,5 +1,5 @@
-Arrange spectral plots in a grid. — gridplot • Spectroscopy Analysis Tools (spant) Arrange spectral plots in a grid. — gridplot • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/gridplot.mrs_data.html b/docs/reference/gridplot.mrs_data.html
index 1f4d09b5..8d68edae 100644
--- a/docs/reference/gridplot.mrs_data.html
+++ b/docs/reference/gridplot.mrs_data.html
@@ -1,5 +1,5 @@
-Arrange spectral plots in a grid. — gridplot.mrs_data • Spectroscopy Analysis Tools (spant) Arrange spectral plots in a grid. — gridplot.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -139,7 +139,7 @@ Arguments
diff --git a/docs/reference/hsvd.html b/docs/reference/hsvd.html
index 25734f49..41c28be8 100644
--- a/docs/reference/hsvd.html
+++ b/docs/reference/hsvd.html
@@ -1,5 +1,5 @@
-HSVD of an mrs_data object. — hsvd • Spectroscopy Analysis Tools (spant) HSVD of an mrs_data object. — hsvd • Spectroscopy Analysis Tools (spant) HSVD based signal filter. — hsvd_filt • Spectroscopy Analysis Tools (spant) HSVD based signal filter. — hsvd_filt • Spectroscopy Analysis Tools (spant) HSVD of a complex vector. — hsvd_vec • Spectroscopy Analysis Tools (spant) HSVD of a complex vector. — hsvd_vec • Spectroscopy Analysis Tools (spant) Return the frequency scale of an MRS dataset in Hz. — hz • Spectroscopy Analysis Tools (spant) Return the frequency scale of an MRS dataset in Hz. — hz • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/ift_shift.html b/docs/reference/ift_shift.html
index 9fba4a24..168b58dd 100644
--- a/docs/reference/ift_shift.html
+++ b/docs/reference/ift_shift.html
@@ -1,5 +1,5 @@
-Perform an iffshift and ifft on a vector. — ift_shift • Spectroscopy Analysis Tools (spant) Perform an iffshift and ifft on a vector. — ift_shift • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/ift_shift_mat.html b/docs/reference/ift_shift_mat.html
index 1a7c85ca..22a75c11 100644
--- a/docs/reference/ift_shift_mat.html
+++ b/docs/reference/ift_shift_mat.html
@@ -1,7 +1,5 @@
-Perform an ifft and ifftshift on a matrix with each column replaced by its
-shifted ifft. — ift_shift_mat • Spectroscopy Analysis Tools (spant) Perform an ifft and ifftshift on a matrix with each column replaced by its shifted ifft. — ift_shift_mat • Spectroscopy Analysis Tools (spant) Image plot method for objects of class mrs_data. — image.mrs_data • Spectroscopy Analysis Tools (spant) Image plot method for objects of class mrs_data. — image.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -92,8 +92,12 @@ Image plot method for objects of class mrs_data.
coil = 1,
restore_def_par = TRUE,
y_ticks = NULL,
- vline = NULL,
hline = NULL,
+ hline_lty = 2,
+ hline_col = "white",
+ vline = NULL,
+ vline_lty = 2,
+ vline_col = "white",
legend = FALSE,
...
)
@@ -154,12 +158,28 @@ Arguments
tick marks.
+hline
+add a horizontal line at the specified value.
hline_lty
+linetype for the horizontal line.
hline_col
+colour for the horizontal line.
vline
-draw a vertical line at the value of vline.
add a vertical line at the specified value.
hline
-draw a horizontal line at the value of hline.
vline_lty
+linetype for the vertical line.
vline_col
+colour for the vertical line.
legend
@@ -184,7 +204,7 @@ Arguments
diff --git a/docs/reference/img2kspace_xy.html b/docs/reference/img2kspace_xy.html
index db04668f..4b47cc32 100644
--- a/docs/reference/img2kspace_xy.html
+++ b/docs/reference/img2kspace_xy.html
@@ -1,5 +1,5 @@
-Transform 2D MRSI data to k-space in the x-y direction. — img2kspace_xy • Spectroscopy Analysis Tools (spant) Transform 2D MRSI data to k-space in the x-y direction. — img2kspace_xy • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/index.html b/docs/reference/index.html
index 1ef7cafd..689c02a5 100644
--- a/docs/reference/index.html
+++ b/docs/reference/index.html
@@ -1,5 +1,5 @@
-Function reference • Spectroscopy Analysis Tools (spant) Function reference • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -90,8 +90,7 @@ All functions
- Complex rounding function taken from complexplus package to reduce the number
-of spant dependencies.
Complex rounding function taken from complexplus package to reduce the number of spant dependencies.
@@ -139,8 +138,7 @@ All functions
- Return a list of options for an ABfit analysis to maintain comparability with
-analyses performed with version 1.9.0 (and earlier) of spant.
Return a list of options for an ABfit analysis to maintain comparability with analyses performed with version 1.9.0 (and earlier) of spant.
@@ -168,13 +166,11 @@ All functions
- Append MRS data across the coil dimension, assumes they matched across the
-other dimensions.
Append MRS data across the coil dimension, assumes they matched across the other dimensions.
- Append MRS data across the dynamic dimension, assumes they matched across the
-other dimensions.
Append MRS data across the dynamic dimension, assumes they matched across the other dimensions.
@@ -194,14 +190,11 @@ All functions
- Convert a 7 dimensional array in into a mrs_data object. The array dimensions
-should be ordered as : dummy, X, Y, Z, dynamic, coil, FID.
Convert a 7 dimensional array in into a mrs_data object. The array dimensions should be ordered as : dummy, X, Y, Z, dynamic, coil, FID.
- Perform zeroth-order phase correction based on the minimisation of the
-squared difference between the real and magnitude components of the
-spectrum.
Perform zeroth-order phase correction based on the minimisation of the squared difference between the real and magnitude components of the spectrum.
@@ -213,13 +206,11 @@ All functions
- Convert a basis object to an mrs_data object - where basis signals are spread
-across the dynamic dimension.
Convert a basis object to an mrs_data object - where basis signals are spread across the dynamic dimension.
- Generate a spline basis, slightly adapted from : "Splines, knots, and
-penalties", Eilers 2010.
Generate a spline basis, slightly adapted from : "Splines, knots, and penalties", Eilers 2010.
@@ -243,8 +234,7 @@ All functions
- Covert a beta value in the time-domain to an equivalent linewidth in Hz:
-x * exp(-i * t * t * beta).
Covert a beta value in the time-domain to an equivalent linewidth in Hz: x * exp(-i * t * t * beta).
@@ -272,8 +262,7 @@ All functions
- Perform a polynomial fit, subtract and return the standard deviation of the
-residuals.
Perform a polynomial fit, subtract and return the standard deviation of the residuals.
@@ -306,6 +295,14 @@ All functions comb_coils()
Combine coil data based on the first data point of a reference signal.
+
+
+ Combine MRSI coil data using the GLS method presented by An et al JMRI 37:1445-1450 (2013).
+
+
+ Combine SVS coil data using the GLS method presented by An et al JMRI 37:1445-1450 (2013).
@@ -345,9 +342,7 @@ All functions
- Crop mrs_data object data points in the time-domain rounding down to
-the next smallest power of two (pot). Data that already has a pot length will
-not be changed.
Crop mrs_data object data points in the time-domain rounding down to the next smallest power of two (pot). Data that already has a pot length will not be changed.
@@ -355,13 +350,11 @@ All functions
- Compute the vector cross product between vectors x and y. Adapted from
-http://stackoverflow.com/questions/15162741/what-is-rs-crossproduct-function
Compute the vector cross product between vectors x and y. Adapted from http://stackoverflow.com/questions/15162741/what-is-rs-crossproduct-function
- Decimate an MRS signal to half the original sampling frequency by filtering
-in the frequency domain before down sampling.
Decimate an MRS signal to half the original sampling frequency by filtering in the frequency domain before down sampling.
@@ -377,8 +370,7 @@ All functions
- Return (and optionally modify using the input arguments) a list of the
-default acquisition parameters.
Return (and optionally modify using the input arguments) a list of the default acquisition parameters.
@@ -410,14 +402,11 @@ All functions
- Downsample an MRS signal by a factor of 2 by removing every other data point
-in the time-domain. Note, signals outside the new sampling frequency will be
-aliased.
Downsample an MRS signal by a factor of 2 by removing every other data point in the time-domain. Note, signals outside the new sampling frequency will be aliased.
- Return a time scale vector of acquisition times for a dynamic MRS scan. The
-first temporal scan is assigned a value of 0.
Return a time scale vector of acquisition times for a dynamic MRS scan. The first temporal scan is assigned a value of 0.
@@ -429,8 +418,7 @@ All functions
- Estimate the standard deviation of the noise from a segment of an mrs_data
-object.
Estimate the standard deviation of the noise from a segment of an mrs_data object.
@@ -486,8 +474,7 @@ All functions
- Perform a zeroth order phase correction based on the phase of the first data
-point in the time-domain.
Perform a zeroth order phase correction based on the phase of the first data point in the time-domain.
@@ -507,8 +494,7 @@ All functions
- Perform a fft and fftshift on a matrix with each column replaced by its
-shifted fft.
Perform a fft and fftshift on a matrix with each column replaced by its shifted fft.
@@ -536,8 +522,11 @@ All functions
- Generate regressors by convolving a specified response function with a
-stimulus.
Generate regressors by convolving a specified response function with a stimulus.
+
+
+ Expand a regressor matrix for a group analysis.
@@ -553,28 +542,23 @@ All functions
- Return a character vector of common 1H molecules found in healthy human
-brain.
Return a character vector of common 1H molecules found in healthy human brain.
- Return a list of mol_parameter objects suitable for 1H brain MRS
-analyses.
Return a list of mol_parameter objects suitable for 1H brain MRS analyses.
- Return a list of mol_parameter objects suitable for 1H brain MRS
-analyses.
Return a list of mol_parameter objects suitable for 1H brain MRS analyses.
- Return a list of mol_parameter objects suitable for 1H brain MRS
-analyses.
Return a list of mol_parameter objects suitable for 1H brain MRS analyses.
- Return a list of mol_parameter objects suitable for 1H brain MRS
-analyses.
Return a list of mol_parameter objects suitable for 1H brain MRS analyses.
@@ -582,8 +566,7 @@ All functions
- Return a character vector of molecules included in the Gold Star Phantoms
-SPECTRE phantom.
Return a character vector of molecules included in the Gold Star Phantoms SPECTRE phantom.
@@ -635,8 +618,7 @@ All functions
- Return a character array of names that may be used with the
-get_mol_paras function.
Return a character array of names that may be used with the get_mol_paras function.
@@ -700,8 +682,7 @@ All functions
- Return an array of amplitudes derived from fitting the initial points in the
-time domain and extrapolating back to t=0.
Return an array of amplitudes derived from fitting the initial points in the time domain and extrapolating back to t=0.
@@ -709,8 +690,7 @@ All functions
- Generate a mol_parameters object for a simple spin system with one
-resonance.
Generate a mol_parameters object for a simple spin system with one resonance.
@@ -731,6 +711,18 @@ All functions glm_spec()
Perform a GLM analysis of dynamic MRS data in the spectral domain.
+
+
+ Perform first-level spectral GLM analysis of an fMRS dataset.
+
+
+ Perform group-level spectral GLM analysis of an fMRS dataset.
+
+
+ Test a group-level spectral GLM linear hypothesis.
@@ -766,8 +758,7 @@ All functions
- Perform an ifft and ifftshift on a matrix with each column replaced by its
-shifted ifft.
Perform an ifft and ifftshift on a matrix with each column replaced by its shifted ifft.
@@ -799,8 +790,7 @@ All functions
- Check if the chemical shift dimension of an MRS data object is in the
-frequency domain.
Check if the chemical shift dimension of an MRS data object is in the frequency domain.
@@ -820,18 +810,15 @@ All functions
- Covert a linewidth in Hz to an equivalent alpha value in the time-domain ie:
-x * exp(-t * alpha).
Covert a linewidth in Hz to an equivalent alpha value in the time-domain ie: x * exp(-t * alpha).
- Covert a linewidth in Hz to an equivalent beta value in the time-domain ie:
-x * exp(-t * t * beta).
Covert a linewidth in Hz to an equivalent beta value in the time-domain ie: x * exp(-t * t * beta).
- Make a basis-set object from a directory containing LCModel formatted RAW
-files.
Make a basis-set object from a directory containing LCModel formatted RAW files.
@@ -851,8 +838,7 @@ All functions
- Mask the voxels outside an elliptical region spanning the MRSI dataset in the
-x-y plane.
Mask the voxels outside an elliptical region spanning the MRSI dataset in the x-y plane.
@@ -860,13 +846,11 @@ All functions
- Convert a matrix (with spectral points in the column dimension and dynamics
-in the row dimensions) into a mrs_data object.
Convert a matrix (with spectral points in the column dimension and dynamics in the row dimensions) into a mrs_data object.
- Matrix exponential function taken from complexplus package to reduce the
-number of spant dependencies.
Matrix exponential function taken from complexplus package to reduce the number of spant dependencies.
@@ -914,31 +898,31 @@ All functions
- Convert an mrs_data object to basis object - where basis signals are spread
-across the dynamic dimension in the MRS data.
Convert an mrs_data object to basis object - where basis signals are spread across the dynamic dimension in the MRS data.
+
+
+ Create a BIDS file structure from a vector of MRS data paths or list of mrs_data objects.
- Convert mrs_data object to a matrix, with spectral points in the column
-dimension and dynamics in the row dimension.
Convert mrs_data object to a matrix, with spectral points in the column dimension and dynamics in the row dimension.
-
+
- Convert mrs_data object to a vector.
Convert mrs_data object to a matrix, with spectral points in the column dimension and dynamics in the row dimension.
-
+
- Create a BIDS directory and file structure from a list of mrs_data objects.
Convert mrs_data object to a vector.
- Perform a fftshift on a matrix, with each column replaced by its shifted
-result.
Perform a fftshift on a matrix, with each column replaced by its shifted result.
- Perform an ifftshift on a matrix, with each column replaced by its shifted
-result.
Perform an ifftshift on a matrix, with each column replaced by its shifted result.
@@ -946,9 +930,7 @@ All functions
- Flip the x data dimension order of a nifti image. This corresponds to
-flipping MRI data in the left-right direction, assuming the data in save in
-neurological format (can check with fslorient program).
Flip the x data dimension order of a nifti image. This corresponds to flipping MRI data in the left-right direction, assuming the data in save in neurological format (can check with fslorient program).
@@ -964,8 +946,7 @@ All functions
- Search for the highest peak in a spectral region and return the frequency,
-height and FWHM.
Search for the highest peak in a spectral region and return the frequency, height and FWHM.
@@ -974,6 +955,10 @@ All functions phase()
Apply phasing parameters to MRS data.
+
+
+ Corrected zero order phase and chemical shift offset in 1H MRS data from the brain.
@@ -1005,8 +990,7 @@ All functions
- Plot an interactive slice map from a data array where voxels can be selected
-to display a corresponding spectrum.
Plot an interactive slice map from a data array where voxels can be selected to display a corresponding spectrum.
@@ -1026,8 +1010,15 @@ All functions
- Save function results to file and load on subsequent calls to avoid repeat
-computation.
Save function results to file and load on subsequent calls to avoid repeat computation.
+
+
+ Preprocess and perform quality assessment of a single SVS data set.
+
+
+ Preprocess and perform quality assessment of one or more SVS data sets.
@@ -1055,15 +1046,11 @@ All functions
- Read a directory containing Siemens MRS IMA files and combine along the coil
-dimension. Note that the coil ID is inferred from the sorted file name and
-should be checked when consistency is required between two directories.
Read a directory containing Siemens MRS IMA files and combine along the coil dimension. Note that the coil ID is inferred from the sorted file name and should be checked when consistency is required between two directories.
- Read a directory containing Siemens MRS IMA files and combine along the
-dynamic dimension. Note that the coil ID is inferred from the sorted file
-name and should be checked when consistency is required.
Read a directory containing Siemens MRS IMA files and combine along the dynamic dimension. Note that the coil ID is inferred from the sorted file name and should be checked when consistency is required.
@@ -1103,13 +1090,11 @@ All functions
- Reconstruct complex time-domain data from the real part of frequency-domain
-data.
Reconstruct complex time-domain data from the real part of frequency-domain data.
- Reconstruct complex time-domain data from the real part of frequency-domain
-data.
Reconstruct complex time-domain data from the real part of frequency-domain data.
@@ -1141,8 +1126,7 @@ All functions
- Resample a VOI to match a target image space using nearest-neighbour
-interpolation.
Resample a VOI to match a target image space using nearest-neighbour interpolation.
@@ -1158,23 +1142,19 @@ All functions
- Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water).
Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / kg of tissue water).
- Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water).
Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / kg of tissue water).
- Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / Litre of tissue).
Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / Litre of tissue).
- Convert default LCM/TARQUIN concentration scaling to molal units with partial
-volume correction.
Convert default LCM/TARQUIN concentration scaling to molal units with partial volume correction.
@@ -1222,8 +1202,7 @@ All functions
- MEGA-PRESS sequence with ideal localisation pulses and Gaussian shaped
-editing pulse.
MEGA-PRESS sequence with ideal localisation pulses and Gaussian shaped editing pulse.
@@ -1251,13 +1230,11 @@ All functions
- STEAM sequence with ideal pulses and coherence order filtering to simulate
-gradient crushers.
STEAM sequence with ideal pulses and coherence order filtering to simulate gradient crushers.
- STEAM sequence with ideal pulses using the z-rotation gradient simulation
-method described by Young et al JMR 140, 146-152 (1999).
STEAM sequence with ideal pulses using the z-rotation gradient simulation method described by Young et al JMR 140, 146-152 (1999).
@@ -1293,8 +1270,7 @@ All functions
- Set the number of time-domain data points, truncating or zero-filling as
-appropriate.
Set the number of time-domain data points, truncating or zero-filling as appropriate.
@@ -1318,18 +1294,15 @@ All functions
- Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS
-sequence. Note, ideal pulses are assumed.
Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS sequence. Note, ideal pulses are assumed.
- Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS
-sequence. Note, ideal pulses are assumed.
Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS sequence. Note, ideal pulses are assumed.
- Simulate a macromolecular and lipid basis-set suitable for 1H brain MRS
-analysis.
Simulate a macromolecular and lipid basis-set suitable for 1H brain MRS analysis.
@@ -1353,8 +1326,7 @@ All functions
- Simulate an ideal pulse excitation profile by smoothing a top-hat function
-with a Gaussian.
Simulate an ideal pulse excitation profile by smoothing a top-hat function with a Gaussian.
@@ -1374,17 +1346,19 @@ All functions
- Simulate and fit some spectra with ABfit for benchmarking purposes. Basic
-timing and performance metrics will be printed.
Simulate and fit some spectra with ABfit for benchmarking purposes. Basic timing and performance metrics will be printed.
Example MEGA-PRESS data with significant B0 drift.
+
+
+ Simulate an example fMRS dataset for a block design fMRS experiment and export a BIDS structure.
- Simulate a typical metabolite basis set for benchmarking. Timing metrics will
-be printed on completion.
Simulate a typical metabolite basis set for benchmarking. Timing metrics will be printed on completion.
@@ -1400,8 +1374,7 @@ All functions
- Convert SPM style segmentation files to a single categorical image where
-the numerical values map as: 0) Other, 1) CSF, 2) GM and 3) WM.
Convert SPM style segmentation files to a single categorical image where the numerical values map as: 0) Other, 1) CSF, 2) GM and 3) WM.
@@ -1413,8 +1386,7 @@ All functions
- Plot the fitting results of an object of class fit_result with
-individual basis set components shown.
Plot the fitting results of an object of class fit_result with individual basis set components shown.
@@ -1459,6 +1431,10 @@ All functions svs_1h_brain_batch_analysis()
Batch interface to the standard SVS 1H brain analysis pipeline.
+
+
+ Perform a t-test on spectral data points.
@@ -1518,8 +1494,7 @@ All functions
- Fade a spectrum to zero by frequency domain multiplication with a tanh
-function. Note this operation distorts data points at the end of the FID.
Fade a spectrum to zero by frequency domain multiplication with a tanh function. Note this operation distorts data points at the end of the FID.
@@ -1549,7 +1524,7 @@ All functions
diff --git a/docs/reference/int_spec.html b/docs/reference/int_spec.html
index c7060fe7..783325a8 100644
--- a/docs/reference/int_spec.html
+++ b/docs/reference/int_spec.html
@@ -1,5 +1,5 @@
-Integrate a spectral region. — int_spec • Spectroscopy Analysis Tools (spant) Integrate a spectral region. — int_spec • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -118,7 +118,7 @@ Value
diff --git a/docs/reference/interleave_dyns.html b/docs/reference/interleave_dyns.html
index effe5543..441eff27 100644
--- a/docs/reference/interleave_dyns.html
+++ b/docs/reference/interleave_dyns.html
@@ -1,5 +1,5 @@
-Interleave the first and second half of a dynamic series. — interleave_dyns • Spectroscopy Analysis Tools (spant) Interleave the first and second half of a dynamic series. — interleave_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/inv_even_dyns.html b/docs/reference/inv_even_dyns.html
index 9f9d4fff..dcb781dc 100644
--- a/docs/reference/inv_even_dyns.html
+++ b/docs/reference/inv_even_dyns.html
@@ -1,5 +1,5 @@
-Invert even numbered dynamic scans starting from 1 (2,4,6...). — inv_even_dyns • Spectroscopy Analysis Tools (spant) Invert even numbered dynamic scans starting from 1 (2,4,6...). — inv_even_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/inv_odd_dyns.html b/docs/reference/inv_odd_dyns.html
index 26212e2b..78d64660 100644
--- a/docs/reference/inv_odd_dyns.html
+++ b/docs/reference/inv_odd_dyns.html
@@ -1,5 +1,5 @@
-Invert odd numbered dynamic scans starting from 1 (1,3,5...). — inv_odd_dyns • Spectroscopy Analysis Tools (spant) Invert odd numbered dynamic scans starting from 1 (1,3,5...). — inv_odd_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/is.def.html b/docs/reference/is.def.html
index f196ffd0..a67b9eba 100644
--- a/docs/reference/is.def.html
+++ b/docs/reference/is.def.html
@@ -1,5 +1,5 @@
-Check if an object is defined, which is the same as being not NULL. — is.def • Spectroscopy Analysis Tools (spant) Check if an object is defined, which is the same as being not NULL. — is.def • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/is_fd.html b/docs/reference/is_fd.html
index 3b0ca165..18a193aa 100644
--- a/docs/reference/is_fd.html
+++ b/docs/reference/is_fd.html
@@ -1,7 +1,5 @@
-Check if the chemical shift dimension of an MRS data object is in the
-frequency domain. — is_fd • Spectroscopy Analysis Tools (spant) Check if the chemical shift dimension of an MRS data object is in the frequency domain. — is_fd • Spectroscopy Analysis Tools (spant) Transform 2D MRSI data from k-space to image space in the x-y direction. — kspace2img_xy • Spectroscopy Analysis Tools (spant) Transform 2D MRSI data from k-space to image space in the x-y direction. — kspace2img_xy • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/l2_reg.html b/docs/reference/l2_reg.html
index 3d781d80..21aa9849 100644
--- a/docs/reference/l2_reg.html
+++ b/docs/reference/l2_reg.html
@@ -1,5 +1,5 @@
-Perform l2 regularisation artefact suppression. — l2_reg • Spectroscopy Analysis Tools (spant) Perform l2 regularisation artefact suppression. — l2_reg • Spectroscopy Analysis Tools (spant) Apply line-broadening (apodisation) to MRS data or basis object. — lb • Spectroscopy Analysis Tools (spant) Apply line-broadening (apodisation) to MRS data or basis object. — lb • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -123,7 +123,7 @@ Value
diff --git a/docs/reference/lofdc.html b/docs/reference/lofdc.html
index 5419b1ec..31347a25 100644
--- a/docs/reference/lofdc.html
+++ b/docs/reference/lofdc.html
@@ -1,5 +1,5 @@
-Correct linear frequency drift. — lofdc • Spectroscopy Analysis Tools (spant) Correct linear frequency drift. — lofdc • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -138,7 +138,7 @@ Value
diff --git a/docs/reference/lw2alpha.html b/docs/reference/lw2alpha.html
index b83db682..25da229b 100644
--- a/docs/reference/lw2alpha.html
+++ b/docs/reference/lw2alpha.html
@@ -1,7 +1,5 @@
-Covert a linewidth in Hz to an equivalent alpha value in the time-domain ie:
-x * exp(-t * alpha). — lw2alpha • Spectroscopy Analysis Tools (spant) Covert a linewidth in Hz to an equivalent alpha value in the time-domain ie: x * exp(-t * alpha). — lw2alpha • Spectroscopy Analysis Tools (spant) Covert a linewidth in Hz to an equivalent beta value in the time-domain ie:
-x * exp(-t * t * beta). — lw2beta • Spectroscopy Analysis Tools (spant) Covert a linewidth in Hz to an equivalent beta value in the time-domain ie: x * exp(-t * t * beta). — lw2beta • Spectroscopy Analysis Tools (spant) Make a basis-set object from a directory containing LCModel formatted RAW
-files. — make_basis_from_raw • Spectroscopy Analysis Tools (spant) Make a basis-set object from a directory containing LCModel formatted RAW files. — make_basis_from_raw • Spectroscopy Analysis Tools (spant) Mask an MRS dataset in the dynamic dimension. — mask_dyns • Spectroscopy Analysis Tools (spant) Mask an MRS dataset in the dynamic dimension. — mask_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/mask_fit_res.html b/docs/reference/mask_fit_res.html
index 97baaa3f..ebd91a99 100644
--- a/docs/reference/mask_fit_res.html
+++ b/docs/reference/mask_fit_res.html
@@ -1,5 +1,5 @@
-Mask fit result spectra depending on a vector of bool values. — mask_fit_res • Spectroscopy Analysis Tools (spant) Mask fit result spectra depending on a vector of bool values. — mask_fit_res • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -116,7 +116,7 @@ Value
diff --git a/docs/reference/mask_xy.html b/docs/reference/mask_xy.html
index 11bb577c..b0d38619 100644
--- a/docs/reference/mask_xy.html
+++ b/docs/reference/mask_xy.html
@@ -1,5 +1,5 @@
-Mask an MRSI dataset in the x-y direction — mask_xy • Spectroscopy Analysis Tools (spant) Mask an MRSI dataset in the x-y direction — mask_xy • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/mask_xy_corners.html b/docs/reference/mask_xy_corners.html
index 09b16cd2..2d13839d 100644
--- a/docs/reference/mask_xy_corners.html
+++ b/docs/reference/mask_xy_corners.html
@@ -1,5 +1,5 @@
-Mask the four corners of an MRSI dataset in the x-y plane. — mask_xy_corners • Spectroscopy Analysis Tools (spant) Mask the four corners of an MRSI dataset in the x-y plane. — mask_xy_corners • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/mask_xy_ellipse.html b/docs/reference/mask_xy_ellipse.html
index 1d8b02e4..e2e749ef 100644
--- a/docs/reference/mask_xy_ellipse.html
+++ b/docs/reference/mask_xy_ellipse.html
@@ -1,7 +1,5 @@
-Mask the voxels outside an elliptical region spanning the MRSI dataset in the
-x-y plane. — mask_xy_ellipse • Spectroscopy Analysis Tools (spant) Mask the voxels outside an elliptical region spanning the MRSI dataset in the x-y plane. — mask_xy_ellipse • Spectroscopy Analysis Tools (spant) Mask a 2D MRSI dataset in the x-y dimension. — mask_xy_mat • Spectroscopy Analysis Tools (spant) Mask a 2D MRSI dataset in the x-y dimension. — mask_xy_mat • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Value
diff --git a/docs/reference/mat2mrs_data.html b/docs/reference/mat2mrs_data.html
index 2e2895f3..ae55665f 100644
--- a/docs/reference/mat2mrs_data.html
+++ b/docs/reference/mat2mrs_data.html
@@ -1,7 +1,5 @@
-Convert a matrix (with spectral points in the column dimension and dynamics
-in the row dimensions) into a mrs_data object. — mat2mrs_data • Spectroscopy Analysis Tools (spant) Convert a matrix (with spectral points in the column dimension and dynamics in the row dimensions) into a mrs_data object. — mat2mrs_data • Spectroscopy Analysis Tools (spant) Matrix exponential function taken from complexplus package to reduce the
-number of spant dependencies. — matexp • Spectroscopy Analysis Tools (spant) Matrix exponential function taken from complexplus package to reduce the number of spant dependencies. — matexp • Spectroscopy Analysis Tools (spant) Apply the max operator to an MRS dataset. — max_mrs • Spectroscopy Analysis Tools (spant) Apply the max operator to an MRS dataset. — max_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/max_mrs_interp.html b/docs/reference/max_mrs_interp.html
index e4474764..52e63f3e 100644
--- a/docs/reference/max_mrs_interp.html
+++ b/docs/reference/max_mrs_interp.html
@@ -1,5 +1,5 @@
-Apply the max operator to an interpolated MRS dataset. — max_mrs_interp • Spectroscopy Analysis Tools (spant) Apply the max operator to an interpolated MRS dataset. — max_mrs_interp • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/mean.list.html b/docs/reference/mean.list.html
index b8eb3463..048306fd 100644
--- a/docs/reference/mean.list.html
+++ b/docs/reference/mean.list.html
@@ -1,5 +1,5 @@
-Calculate the mean spectrum from an mrs_data object. — mean.list • Spectroscopy Analysis Tools (spant) Calculate the mean spectrum from an mrs_data object. — mean.list • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/mean.mrs_data.html b/docs/reference/mean.mrs_data.html
index 5531a28d..79515014 100644
--- a/docs/reference/mean.mrs_data.html
+++ b/docs/reference/mean.mrs_data.html
@@ -1,5 +1,5 @@
-Calculate the mean spectrum from an mrs_data object. — mean.mrs_data • Spectroscopy Analysis Tools (spant) Calculate the mean spectrum from an mrs_data object. — mean.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/mean_dyn_blocks.html b/docs/reference/mean_dyn_blocks.html
index 10467098..4c042448 100644
--- a/docs/reference/mean_dyn_blocks.html
+++ b/docs/reference/mean_dyn_blocks.html
@@ -1,5 +1,5 @@
-Calculate the mean of adjacent dynamic scans. — mean_dyn_blocks • Spectroscopy Analysis Tools (spant) Calculate the mean of adjacent dynamic scans. — mean_dyn_blocks • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/mean_dyn_pairs.html b/docs/reference/mean_dyn_pairs.html
index 63e909ea..1a241126 100644
--- a/docs/reference/mean_dyn_pairs.html
+++ b/docs/reference/mean_dyn_pairs.html
@@ -1,5 +1,5 @@
-Calculate the pairwise means across a dynamic data set. — mean_dyn_pairs • Spectroscopy Analysis Tools (spant) Calculate the pairwise means across a dynamic data set. — mean_dyn_pairs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/mean_dyns.html b/docs/reference/mean_dyns.html
index 73fdbfa7..0daa27df 100644
--- a/docs/reference/mean_dyns.html
+++ b/docs/reference/mean_dyns.html
@@ -1,5 +1,5 @@
-Calculate the mean dynamic data. — mean_dyns • Spectroscopy Analysis Tools (spant) Calculate the mean dynamic data. — mean_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/mean_mrs_list.html b/docs/reference/mean_mrs_list.html
index 808b6c50..10d842c0 100644
--- a/docs/reference/mean_mrs_list.html
+++ b/docs/reference/mean_mrs_list.html
@@ -1,5 +1,5 @@
-Return the mean of a list of mrs_data objects. — mean_mrs_list • Spectroscopy Analysis Tools (spant) Return the mean of a list of mrs_data objects. — mean_mrs_list • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/mean_vec_blocks.html b/docs/reference/mean_vec_blocks.html
index 8fc92eaa..dd78b122 100644
--- a/docs/reference/mean_vec_blocks.html
+++ b/docs/reference/mean_vec_blocks.html
@@ -1,5 +1,5 @@
-Calculate the mean of adjacent blocks in a vector. — mean_vec_blocks • Spectroscopy Analysis Tools (spant) Calculate the mean of adjacent blocks in a vector. — mean_vec_blocks • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/median_dyns.html b/docs/reference/median_dyns.html
index 1039d4b5..9a085b10 100644
--- a/docs/reference/median_dyns.html
+++ b/docs/reference/median_dyns.html
@@ -1,5 +1,5 @@
-Calculate the median dynamic data. — median_dyns • Spectroscopy Analysis Tools (spant) Calculate the median dynamic data. — median_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/mod_td.html b/docs/reference/mod_td.html
index 76ad0a40..141ef09e 100644
--- a/docs/reference/mod_td.html
+++ b/docs/reference/mod_td.html
@@ -1,5 +1,5 @@
-Apply the Modulus operator to the time-domain MRS signal. — mod_td • Spectroscopy Analysis Tools (spant) Apply the Modulus operator to the time-domain MRS signal. — mod_td • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/mrs_data2basis.html b/docs/reference/mrs_data2basis.html
index 62f7d749..11797b91 100644
--- a/docs/reference/mrs_data2basis.html
+++ b/docs/reference/mrs_data2basis.html
@@ -1,7 +1,5 @@
-Convert an mrs_data object to basis object - where basis signals are spread
-across the dynamic dimension in the MRS data. — mrs_data2basis • Spectroscopy Analysis Tools (spant) Convert an mrs_data object to basis object - where basis signals are spread across the dynamic dimension in the MRS data. — mrs_data2basis • Spectroscopy Analysis Tools (spant) Create a BIDS file structure from a vector of MRS data paths or list of mrs_data objects. — mrs_data2bids • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Create a BIDS file structure from a vector of MRS data paths or list of mrs_data objects.
+ Source: R/fmrs.R
+ mrs_data2bids.Rd
+
+
+
+ Create a BIDS file structure from a vector of MRS data paths or list of
+mrs_data objects.
+
+
+
+ mrs_data2bids(
+ mrs_data,
+ output_dir,
+ suffix = NULL,
+ sub = NULL,
+ ses = NULL,
+ task = NULL,
+ acq = NULL,
+ nuc = NULL,
+ voi = NULL,
+ rec = NULL,
+ run = NULL,
+ echo = NULL,
+ inv = NULL,
+ skip_existing = TRUE
+)
+
+
+
+ Arguments
+ - mrs_data
+vector of MRS data paths or list of mrs_data objects.
- output_dir
+the base directory to create the BIDS structure.
- suffix
+optional vector of file suffixes. Default behaviour is to
+automatically determine these from the input data, however it is recommended
+that they are specified to allow more efficient skipping of existing data.
- sub
+optional vector of subject labels. If not specified, these will be
+automatically generated as a series of increasing zero-padded integer values
+corresponding to the mrs_data input indices.
- ses
+optional vector of session labels.
- task
+optional vector of task labels.
- acq
+optional vector of acquisition labels.
- nuc
+optional vector of nucleus labels.
- voi
+optional vector of volume of interest labels.
- rec
+optional vector of reconstruction labels.
- run
+optional vector of run indices.
- echo
+optional vector of echo time indices.
- inv
+optional vector of inversion indices.
- skip_existing
+skip any data files that have already been converted.
+Defaults to TRUE, set to FALSE to force an overwrite of any existing data
+files.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/mrs_data2mat.html b/docs/reference/mrs_data2mat.html
index cf5ff28c..9e47688a 100644
--- a/docs/reference/mrs_data2mat.html
+++ b/docs/reference/mrs_data2mat.html
@@ -1,7 +1,5 @@
-Convert mrs_data object to a matrix, with spectral points in the column
-dimension and dynamics in the row dimension. — mrs_data2mat • Spectroscopy Analysis Tools (spant) Convert mrs_data object to a matrix, with spectral points in the column dimension and dynamics in the row dimension. — mrs_data2mat • Spectroscopy Analysis Tools (spant) Convert mrs_data object to a matrix, with spectral points in the column dimension and dynamics in the row dimension. — mrs_data2spec_mat • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Convert mrs_data object to a matrix, with spectral points in the column dimension and dynamics in the row dimension.
+ Source: R/mrs_data_proc.R
+ mrs_data2spec_mat.Rd
+
+
+
+ Convert mrs_data object to a matrix, with spectral points in the column
+dimension and dynamics in the row dimension.
+
+
+
+ mrs_data2spec_mat(mrs_data, collapse = TRUE)
+
+
+
+ Arguments
+ - mrs_data
+MRS data object or list of MRS data objects.
- collapse
+collapse all other dimensions along the dynamic dimension, eg
+a 16x16 MRSI grid would be first collapsed across 256 dynamic scans.
+
+ Value
+
+
+MRS data matrix.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/mrs_data2vec.html b/docs/reference/mrs_data2vec.html
index fb172d68..a1fd654d 100644
--- a/docs/reference/mrs_data2vec.html
+++ b/docs/reference/mrs_data2vec.html
@@ -1,5 +1,5 @@
-Convert mrs_data object to a vector. — mrs_data2vec • Spectroscopy Analysis Tools (spant) Convert mrs_data object to a vector. — mrs_data2vec • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -126,7 +126,7 @@ Value
diff --git a/docs/reference/mvfftshift.html b/docs/reference/mvfftshift.html
index 92b0841b..976b3410 100644
--- a/docs/reference/mvfftshift.html
+++ b/docs/reference/mvfftshift.html
@@ -1,7 +1,5 @@
-Perform a fftshift on a matrix, with each column replaced by its shifted
-result. — mvfftshift • Spectroscopy Analysis Tools (spant) Perform a fftshift on a matrix, with each column replaced by its shifted result. — mvfftshift • Spectroscopy Analysis Tools (spant) Perform an ifftshift on a matrix, with each column replaced by its shifted
-result. — mvifftshift • Spectroscopy Analysis Tools (spant) Perform an ifftshift on a matrix, with each column replaced by its shifted result. — mvifftshift • Spectroscopy Analysis Tools (spant) Print fit coordinates from a single index. — n2coord • Spectroscopy Analysis Tools (spant) Print fit coordinates from a single index. — n2coord • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/nifti_flip_lr.html b/docs/reference/nifti_flip_lr.html
index 730abe3c..19860b3c 100644
--- a/docs/reference/nifti_flip_lr.html
+++ b/docs/reference/nifti_flip_lr.html
@@ -1,9 +1,5 @@
-Flip the x data dimension order of a nifti image. This corresponds to
-flipping MRI data in the left-right direction, assuming the data in save in
-neurological format (can check with fslorient program). — nifti_flip_lr • Spectroscopy Analysis Tools (spant) Flip the x data dimension order of a nifti image. This corresponds to flipping MRI data in the left-right direction, assuming the data in save in neurological format (can check with fslorient program). — nifti_flip_lr • Spectroscopy Analysis Tools (spant) Export a one-page pdf of a single fit result — one_page_pdf • Spectroscopy Analysis Tools (spant) Export a one-page pdf of a single fit result — one_page_pdf • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -108,7 +108,7 @@ Arguments
diff --git a/docs/reference/ortho3.html b/docs/reference/ortho3.html
index 13ade97d..5d7dd2fd 100644
--- a/docs/reference/ortho3.html
+++ b/docs/reference/ortho3.html
@@ -1,5 +1,5 @@
-Display an orthographic projection plot of a nifti object. — ortho3 • Spectroscopy Analysis Tools (spant) Display an orthographic projection plot of a nifti object. — ortho3 • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -172,7 +172,7 @@ Arguments
diff --git a/docs/reference/ortho3_inter.html b/docs/reference/ortho3_inter.html
index 090cc5e5..15948899 100644
--- a/docs/reference/ortho3_inter.html
+++ b/docs/reference/ortho3_inter.html
@@ -1,5 +1,5 @@
-Display an interactive orthographic projection plot of a nifti object. — ortho3_inter • Spectroscopy Analysis Tools (spant) Display an interactive orthographic projection plot of a nifti object. — ortho3_inter • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -132,7 +132,7 @@ Arguments
diff --git a/docs/reference/peak_info.html b/docs/reference/peak_info.html
index 09058bd8..41c8ffaf 100644
--- a/docs/reference/peak_info.html
+++ b/docs/reference/peak_info.html
@@ -1,7 +1,5 @@
-Search for the highest peak in a spectral region and return the frequency,
-height and FWHM. — peak_info • Spectroscopy Analysis Tools (spant) Search for the highest peak in a spectral region and return the frequency, height and FWHM. — peak_info • Spectroscopy Analysis Tools (spant) Papoulis-Gerchberg (PG) algorithm method for k-space extrapolation. — pg_extrap_xy • Spectroscopy Analysis Tools (spant) Papoulis-Gerchberg (PG) algorithm method for k-space extrapolation. — pg_extrap_xy • Spectroscopy Analysis Tools (spant) Apply phasing parameters to MRS data. — phase • Spectroscopy Analysis Tools (spant) Apply phasing parameters to MRS data. — phase • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/phase_ref_1h_brain.html b/docs/reference/phase_ref_1h_brain.html
new file mode 100644
index 00000000..8707a74a
--- /dev/null
+++ b/docs/reference/phase_ref_1h_brain.html
@@ -0,0 +1,131 @@
+
+Corrected zero order phase and chemical shift offset in 1H MRS data from the brain. — phase_ref_1h_brain • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Corrected zero order phase and chemical shift offset in 1H MRS data from the brain.
+ Source: R/rats.R
+ phase_ref_1h_brain.Rd
+
+
+
+ Corrected zero order phase and chemical shift offset in 1H MRS data from the
+brain.
+
+
+
+ phase_ref_1h_brain(mrs_data, mean_ref = FALSE, ret_corr_only = TRUE)
+
+
+
+ Arguments
+ - mrs_data
+MRS data to be corrected.
- mean_ref
+apply the phase and offset of the mean spectrum to all
+others. Default is FALSE.
- ret_corr_only
+return the corrected data only.
+
+ Value
+
+
+corrected MRS data.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/plot.fit_result.html b/docs/reference/plot.fit_result.html
index e54d3bc1..836a53ee 100644
--- a/docs/reference/plot.fit_result.html
+++ b/docs/reference/plot.fit_result.html
@@ -1,5 +1,5 @@
-Plot the fitting results of an object of class fit_result. — plot.fit_result • Spectroscopy Analysis Tools (spant) Plot the fitting results of an object of class fit_result. — plot.fit_result • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -207,7 +207,7 @@ Arguments
diff --git a/docs/reference/plot.mrs_data.html b/docs/reference/plot.mrs_data.html
index fabcc35b..bb2ec651 100644
--- a/docs/reference/plot.mrs_data.html
+++ b/docs/reference/plot.mrs_data.html
@@ -1,5 +1,5 @@
-Plotting method for objects of class mrs_data. — plot.mrs_data • Spectroscopy Analysis Tools (spant) Plotting method for objects of class mrs_data. — plot.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -287,7 +287,7 @@ Arguments
diff --git a/docs/reference/plot_bc.html b/docs/reference/plot_bc.html
index 4f8309b4..b48142cc 100644
--- a/docs/reference/plot_bc.html
+++ b/docs/reference/plot_bc.html
@@ -1,5 +1,5 @@
-Convenience function to plot a baseline estimate with the original data. — plot_bc • Spectroscopy Analysis Tools (spant) Convenience function to plot a baseline estimate with the original data. — plot_bc • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -108,7 +108,7 @@ Arguments
diff --git a/docs/reference/plot_reg.html b/docs/reference/plot_reg.html
index ae1acbe7..2addb2f6 100644
--- a/docs/reference/plot_reg.html
+++ b/docs/reference/plot_reg.html
@@ -1,5 +1,5 @@
-Plot regressors as an image. — plot_reg • Spectroscopy Analysis Tools (spant) Plot regressors as an image. — plot_reg • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/plot_slice_fit.html b/docs/reference/plot_slice_fit.html
index fbc7b560..57f1af8a 100644
--- a/docs/reference/plot_slice_fit.html
+++ b/docs/reference/plot_slice_fit.html
@@ -1,5 +1,5 @@
-Plot a 2D slice from an MRSI fit result object. — plot_slice_fit • Spectroscopy Analysis Tools (spant) Plot a 2D slice from an MRSI fit result object. — plot_slice_fit • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -129,7 +129,7 @@ Arguments
diff --git a/docs/reference/plot_slice_fit_inter.html b/docs/reference/plot_slice_fit_inter.html
index 4eed104a..da105a7d 100644
--- a/docs/reference/plot_slice_fit_inter.html
+++ b/docs/reference/plot_slice_fit_inter.html
@@ -1,5 +1,5 @@
-Plot a 2D slice from an MRSI fit result object. — plot_slice_fit_inter • Spectroscopy Analysis Tools (spant) Plot a 2D slice from an MRSI fit result object. — plot_slice_fit_inter • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -134,7 +134,7 @@ Arguments
diff --git a/docs/reference/plot_slice_map.html b/docs/reference/plot_slice_map.html
index 553e9ac8..ffb2a134 100644
--- a/docs/reference/plot_slice_map.html
+++ b/docs/reference/plot_slice_map.html
@@ -1,5 +1,5 @@
-Plot a slice from a 7 dimensional array. — plot_slice_map • Spectroscopy Analysis Tools (spant) Plot a slice from a 7 dimensional array. — plot_slice_map • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -153,7 +153,7 @@ Arguments
diff --git a/docs/reference/plot_slice_map_inter.html b/docs/reference/plot_slice_map_inter.html
index 40d33b42..90968f66 100644
--- a/docs/reference/plot_slice_map_inter.html
+++ b/docs/reference/plot_slice_map_inter.html
@@ -1,7 +1,5 @@
-Plot an interactive slice map from a data array where voxels can be selected
-to display a corresponding spectrum. — plot_slice_map_inter • Spectroscopy Analysis Tools (spant) Plot an interactive slice map from a data array where voxels can be selected to display a corresponding spectrum. — plot_slice_map_inter • Spectroscopy Analysis Tools (spant) Plot the spectral standard deviation. — plot_spec_sd • Spectroscopy Analysis Tools (spant) Plot the spectral standard deviation. — plot_spec_sd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Arguments
diff --git a/docs/reference/plot_voi_overlay.html b/docs/reference/plot_voi_overlay.html
index 9a782e88..bbbbf35e 100644
--- a/docs/reference/plot_voi_overlay.html
+++ b/docs/reference/plot_voi_overlay.html
@@ -1,5 +1,5 @@
-Plot a volume as an image overlay. — plot_voi_overlay • Spectroscopy Analysis Tools (spant) Plot a volume as an image overlay. — plot_voi_overlay • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -116,7 +116,7 @@ Arguments
diff --git a/docs/reference/plot_voi_overlay_seg.html b/docs/reference/plot_voi_overlay_seg.html
index 3d4e74ff..0e800ff2 100644
--- a/docs/reference/plot_voi_overlay_seg.html
+++ b/docs/reference/plot_voi_overlay_seg.html
@@ -1,5 +1,5 @@
-Plot a volume as an overlay on a segmented brain volume. — plot_voi_overlay_seg • Spectroscopy Analysis Tools (spant) Plot a volume as an overlay on a segmented brain volume. — plot_voi_overlay_seg • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Arguments
diff --git a/docs/reference/ppm.html b/docs/reference/ppm.html
index c352327a..ee4696e2 100644
--- a/docs/reference/ppm.html
+++ b/docs/reference/ppm.html
@@ -1,5 +1,5 @@
-Return the ppm scale of an MRS dataset or fit result. — ppm • Spectroscopy Analysis Tools (spant) Return the ppm scale of an MRS dataset or fit result. — ppm • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -132,7 +132,7 @@ Value
diff --git a/docs/reference/precomp.html b/docs/reference/precomp.html
index 822d7336..df3d2c6c 100644
--- a/docs/reference/precomp.html
+++ b/docs/reference/precomp.html
@@ -1,7 +1,5 @@
-Save function results to file and load on subsequent calls to avoid repeat
-computation. — precomp • Spectroscopy Analysis Tools (spant) Save function results to file and load on subsequent calls to avoid repeat computation. — precomp • Spectroscopy Analysis Tools (spant) Preprocess and perform quality assessment of a single SVS data set. — preproc_svs • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Preprocess and perform quality assessment of a single SVS data set.
+ Source: R/fmrs.R
+ preproc_svs.Rd
+
+
+
+ Preprocess and perform quality assessment of a single SVS data set.
+
+
+
+ preproc_svs(path, label = NULL, output_dir = NULL, ref_inds = NULL)
+
+
+
+ Arguments
+ - path
+path to the fMRS data file or IMA directory.
- label
+a label to describe the data set.
- output_dir
+output directory.
- ref_inds
+a vector of 1-based indices for any water reference dynamic
+scans.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/preproc_svs_dataset.html b/docs/reference/preproc_svs_dataset.html
new file mode 100644
index 00000000..07c3a29b
--- /dev/null
+++ b/docs/reference/preproc_svs_dataset.html
@@ -0,0 +1,148 @@
+
+Preprocess and perform quality assessment of one or more SVS data sets. — preproc_svs_dataset • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Preprocess and perform quality assessment of one or more SVS data sets.
+ Source: R/fmrs.R
+ preproc_svs_dataset.Rd
+
+
+
+ Preprocess and perform quality assessment of one or more SVS data sets.
+
+
+
+ preproc_svs_dataset(
+ paths,
+ labels = NULL,
+ output_dir = "spant_analysis",
+ exclude_labels = NULL,
+ overwrite = FALSE,
+ ref_inds = NULL,
+ return_results = FALSE
+)
+
+
+
+ Arguments
+ - paths
+paths to the fMRS data file or IMA directory.
- labels
+labels to describe each data set.
- output_dir
+output directory.
- exclude_labels
+vector of labels of scans to exclude, eg poor quality
+data.
- overwrite
+overwrite saved results, defaults to FALSE.
- ref_inds
+a vector of 1-based indices for any water reference dynamic
+scans.
- return_results
+function will return key outputs, defaults to FALSE.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/print.fit_result.html b/docs/reference/print.fit_result.html
index 297f28dc..5f434e57 100644
--- a/docs/reference/print.fit_result.html
+++ b/docs/reference/print.fit_result.html
@@ -1,5 +1,5 @@
-Print a summary of an object of class fit_result. — print.fit_result • Spectroscopy Analysis Tools (spant) Print a summary of an object of class fit_result. — print.fit_result • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -105,7 +105,7 @@ Arguments
diff --git a/docs/reference/print.mrs_data.html b/docs/reference/print.mrs_data.html
index 51199017..e1561eb2 100644
--- a/docs/reference/print.mrs_data.html
+++ b/docs/reference/print.mrs_data.html
@@ -1,5 +1,5 @@
-Print a summary of mrs_data parameters. — print.mrs_data • Spectroscopy Analysis Tools (spant) Print a summary of mrs_data parameters. — print.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -109,7 +109,7 @@ Arguments
diff --git a/docs/reference/qn_states.html b/docs/reference/qn_states.html
index 0f42f2f9..d7aa6715 100644
--- a/docs/reference/qn_states.html
+++ b/docs/reference/qn_states.html
@@ -1,5 +1,5 @@
-Get the quantum coherence matrix for a spin system. — qn_states • Spectroscopy Analysis Tools (spant) Get the quantum coherence matrix for a spin system. — qn_states • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/rats.html b/docs/reference/rats.html
index 5a39a396..93585e08 100644
--- a/docs/reference/rats.html
+++ b/docs/reference/rats.html
@@ -1,5 +1,5 @@
-Robust Alignment to a Target Spectrum (RATS). — rats • Spectroscopy Analysis Tools (spant) Robust Alignment to a Target Spectrum (RATS). — rats • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -207,7 +207,7 @@ Value
diff --git a/docs/reference/re_weighting.html b/docs/reference/re_weighting.html
index d21caf21..8b0b070a 100644
--- a/docs/reference/re_weighting.html
+++ b/docs/reference/re_weighting.html
@@ -1,5 +1,5 @@
-Apply a weighting to the FID to enhance spectral resolution. — re_weighting • Spectroscopy Analysis Tools (spant) Apply a weighting to the FID to enhance spectral resolution. — re_weighting • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/read_basis.html b/docs/reference/read_basis.html
index da9b94af..eb6f8557 100644
--- a/docs/reference/read_basis.html
+++ b/docs/reference/read_basis.html
@@ -1,5 +1,5 @@
-Read a basis file in LCModel .basis format. — read_basis • Spectroscopy Analysis Tools (spant) Read a basis file in LCModel .basis format. — read_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/read_ima_coil_dir.html b/docs/reference/read_ima_coil_dir.html
index 28c02de0..4f073cd8 100644
--- a/docs/reference/read_ima_coil_dir.html
+++ b/docs/reference/read_ima_coil_dir.html
@@ -1,9 +1,5 @@
-Read a directory containing Siemens MRS IMA files and combine along the coil
-dimension. Note that the coil ID is inferred from the sorted file name and
-should be checked when consistency is required between two directories. — read_ima_coil_dir • Spectroscopy Analysis Tools (spant) Read a directory containing Siemens MRS IMA files and combine along the coil dimension. Note that the coil ID is inferred from the sorted file name and should be checked when consistency is required between two directories. — read_ima_coil_dir • Spectroscopy Analysis Tools (spant) Read a directory containing Siemens MRS IMA files and combine along the
-dynamic dimension. Note that the coil ID is inferred from the sorted file
-name and should be checked when consistency is required. — read_ima_dyn_dir • Spectroscopy Analysis Tools (spant) Read a directory containing Siemens MRS IMA files and combine along the dynamic dimension. Note that the coil ID is inferred from the sorted file name and should be checked when consistency is required. — read_ima_dyn_dir • Spectroscopy Analysis Tools (spant) Read an LCModel formatted coord file containing fit information. — read_lcm_coord • Spectroscopy Analysis Tools (spant) Read an LCModel formatted coord file containing fit information. — read_lcm_coord • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -107,7 +107,7 @@ Value
diff --git a/docs/reference/read_mrs.html b/docs/reference/read_mrs.html
index 3ac2a36b..2cf36b20 100644
--- a/docs/reference/read_mrs.html
+++ b/docs/reference/read_mrs.html
@@ -1,5 +1,5 @@
-Read MRS data from a file. — read_mrs • Spectroscopy Analysis Tools (spant) Read MRS data from a file. — read_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -88,7 +88,8 @@ Read MRS data from a file.
full_fid = FALSE,
omit_svs_ref_scans = TRUE,
verbose = FALSE,
- extra = NULL
+ extra = NULL,
+ fid_filt_dist = NULL
)
@@ -140,6 +141,13 @@ Arguments
an optional data frame to provide additional variables for use
in subsequent analysis steps, eg id or grouping variables.
fid_filt_dist
+indicate if the data has a distorted FID due to a
+brick-wall filter being used to downsample the data. Default is to auto
+detect this from the data, but TRUE or FALSE options can be given to override
+detection.
Value
@@ -183,7 +191,7 @@ Examples
diff --git a/docs/reference/read_mrs_tqn.html b/docs/reference/read_mrs_tqn.html
index 5766362f..84bdaf3a 100644
--- a/docs/reference/read_mrs_tqn.html
+++ b/docs/reference/read_mrs_tqn.html
@@ -1,5 +1,5 @@
-Read MRS data using the TARQUIN software package. — read_mrs_tqn • Spectroscopy Analysis Tools (spant) Read MRS data using the TARQUIN software package. — read_mrs_tqn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -131,7 +131,7 @@ Examples
diff --git a/docs/reference/read_pulse_ascii.html b/docs/reference/read_pulse_ascii.html
index c9e0d43c..ab11c9cc 100644
--- a/docs/reference/read_pulse_ascii.html
+++ b/docs/reference/read_pulse_ascii.html
@@ -1,5 +1,5 @@
-Read an ASCII formatted pulse file. — read_pulse_ascii • Spectroscopy Analysis Tools (spant) Read an ASCII formatted pulse file. — read_pulse_ascii • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/read_pulse_bruker.html b/docs/reference/read_pulse_bruker.html
index c92bf76a..dbe9073b 100644
--- a/docs/reference/read_pulse_bruker.html
+++ b/docs/reference/read_pulse_bruker.html
@@ -1,5 +1,5 @@
-Read a Bruker formatted pulse file — read_pulse_bruker • Spectroscopy Analysis Tools (spant) Read a Bruker formatted pulse file — read_pulse_bruker • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/read_pulse_pta.html b/docs/reference/read_pulse_pta.html
index 72e1b6d4..a0fac3c3 100644
--- a/docs/reference/read_pulse_pta.html
+++ b/docs/reference/read_pulse_pta.html
@@ -1,5 +1,5 @@
-Read a .pta formatted pulse file compatible with Siemens PulseTool. — read_pulse_pta • Spectroscopy Analysis Tools (spant) Read a .pta formatted pulse file compatible with Siemens PulseTool. — read_pulse_pta • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/read_siemens_txt_hdr.html b/docs/reference/read_siemens_txt_hdr.html
index 23fb8c70..3a17d87c 100644
--- a/docs/reference/read_siemens_txt_hdr.html
+++ b/docs/reference/read_siemens_txt_hdr.html
@@ -1,5 +1,5 @@
-Read the text format header found in Siemens IMA and TWIX data files. — read_siemens_txt_hdr • Spectroscopy Analysis Tools (spant) Read the text format header found in Siemens IMA and TWIX data files. — read_siemens_txt_hdr • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -78,7 +78,7 @@ Read the text format header found in Siemens IMA and TWIX data files.
- read_siemens_txt_hdr(input, version = "vd", verbose, offset = 0)
+ read_siemens_txt_hdr(input, version = "vd", verbose = FALSE, offset = 0)
@@ -118,7 +118,7 @@ Value
diff --git a/docs/reference/read_tqn_fit.html b/docs/reference/read_tqn_fit.html
index 4da6c25e..a1630420 100644
--- a/docs/reference/read_tqn_fit.html
+++ b/docs/reference/read_tqn_fit.html
@@ -1,5 +1,5 @@
-Reader for csv fit results generated by TARQUIN. — read_tqn_fit • Spectroscopy Analysis Tools (spant) Reader for csv fit results generated by TARQUIN. — read_tqn_fit • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -113,7 +113,7 @@ Examples
diff --git a/docs/reference/read_tqn_result.html b/docs/reference/read_tqn_result.html
index 36659714..68a3e98c 100644
--- a/docs/reference/read_tqn_result.html
+++ b/docs/reference/read_tqn_result.html
@@ -1,5 +1,5 @@
-Reader for csv results generated by TARQUIN. — read_tqn_result • Spectroscopy Analysis Tools (spant) Reader for csv results generated by TARQUIN. — read_tqn_result • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -117,7 +117,7 @@ Examples
diff --git a/docs/reference/recon_imag.html b/docs/reference/recon_imag.html
index d2a72225..5bc3b1eb 100644
--- a/docs/reference/recon_imag.html
+++ b/docs/reference/recon_imag.html
@@ -1,7 +1,5 @@
-Reconstruct complex time-domain data from the real part of frequency-domain
-data. — recon_imag • Spectroscopy Analysis Tools (spant) Reconstruct complex time-domain data from the real part of frequency-domain data. — recon_imag • Spectroscopy Analysis Tools (spant) Reconstruct complex time-domain data from the real part of frequency-domain
-data. — recon_imag_vec • Spectroscopy Analysis Tools (spant) Reconstruct complex time-domain data from the real part of frequency-domain data. — recon_imag_vec • Spectroscopy Analysis Tools (spant) Reconstruct 2D MRSI data from a twix file loaded with read_mrs. — recon_twix_2d_mrsi • Spectroscopy Analysis Tools (spant) Reconstruct 2D MRSI data from a twix file loaded with read_mrs. — recon_twix_2d_mrsi • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/rectangular_mask.html b/docs/reference/rectangular_mask.html
index a2117283..6e469bc9 100644
--- a/docs/reference/rectangular_mask.html
+++ b/docs/reference/rectangular_mask.html
@@ -1,5 +1,5 @@
-Create a rectangular mask stored as a matrix of logical values. — rectangular_mask • Spectroscopy Analysis Tools (spant) Create a rectangular mask stored as a matrix of logical values. — rectangular_mask • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -130,7 +130,7 @@ Value
diff --git a/docs/reference/reexports.html b/docs/reference/reexports.html
index 694a75d1..a59e8379 100644
--- a/docs/reference/reexports.html
+++ b/docs/reference/reexports.html
@@ -1,5 +1,5 @@
-Objects exported from other packages — reexports • Spectroscopy Analysis Tools (spant) Objects exported from other packages — reexports • Spectroscopy Analysis Tools (spant)
Spectroscopy Analysis Tools (spant)
- 2.21.0
+ 2.22.0
@@ -103,7 +103,7 @@ Objects exported from other packages
diff --git a/docs/reference/rep_array_dim.html b/docs/reference/rep_array_dim.html
index b9c49b4a..48c0a5ed 100644
--- a/docs/reference/rep_array_dim.html
+++ b/docs/reference/rep_array_dim.html
@@ -1,5 +1,5 @@
-Repeat an array over a given dimension. — rep_array_dim • Spectroscopy Analysis Tools (spant) Repeat an array over a given dimension. — rep_array_dim • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/rep_dyn.html b/docs/reference/rep_dyn.html
index 6bbfb0ef..89a4bb9b 100644
--- a/docs/reference/rep_dyn.html
+++ b/docs/reference/rep_dyn.html
@@ -1,5 +1,5 @@
-Replicate a scan in the dynamic dimension. — rep_dyn • Spectroscopy Analysis Tools (spant) Replicate a scan in the dynamic dimension. — rep_dyn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/rep_mrs.html b/docs/reference/rep_mrs.html
index 67730b5c..becb8f00 100644
--- a/docs/reference/rep_mrs.html
+++ b/docs/reference/rep_mrs.html
@@ -1,5 +1,5 @@
-Replicate a scan over a given dimension. — rep_mrs • Spectroscopy Analysis Tools (spant) Replicate a scan over a given dimension. — rep_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -138,7 +138,7 @@ Value
diff --git a/docs/reference/resample_basis.html b/docs/reference/resample_basis.html
index b0f2ab17..c7a6222a 100644
--- a/docs/reference/resample_basis.html
+++ b/docs/reference/resample_basis.html
@@ -1,5 +1,5 @@
-Resample a basis-set to match a mrs_data acquisition. — resample_basis • Spectroscopy Analysis Tools (spant) Resample a basis-set to match a mrs_data acquisition. — resample_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -116,7 +116,7 @@ Value
diff --git a/docs/reference/resample_img.html b/docs/reference/resample_img.html
index f1e7beaf..b0cc8f71 100644
--- a/docs/reference/resample_img.html
+++ b/docs/reference/resample_img.html
@@ -1,5 +1,5 @@
-Resample an image to match a target image space. — resample_img • Spectroscopy Analysis Tools (spant) Resample an image to match a target image space. — resample_img • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/resample_voi.html b/docs/reference/resample_voi.html
index 8fbfa836..a29ab096 100644
--- a/docs/reference/resample_voi.html
+++ b/docs/reference/resample_voi.html
@@ -1,7 +1,5 @@
-Resample a VOI to match a target image space using nearest-neighbour
-interpolation. — resample_voi • Spectroscopy Analysis Tools (spant) Resample a VOI to match a target image space using nearest-neighbour interpolation. — resample_voi • Spectroscopy Analysis Tools (spant) Reslice a nifti object to match the orientation of mrs data. — reslice_to_mrs • Spectroscopy Analysis Tools (spant) Reslice a nifti object to match the orientation of mrs data. — reslice_to_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/reson_table2mrs_data.html b/docs/reference/reson_table2mrs_data.html
index d75579ee..c5a2167a 100644
--- a/docs/reference/reson_table2mrs_data.html
+++ b/docs/reference/reson_table2mrs_data.html
@@ -1,5 +1,5 @@
-Generate mrs_data from a table of single Lorentzian resonances. — reson_table2mrs_data • Spectroscopy Analysis Tools (spant) Generate mrs_data from a table of single Lorentzian resonances. — reson_table2mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -119,7 +119,7 @@ Value
diff --git a/docs/reference/rm_dyns.html b/docs/reference/rm_dyns.html
index 5d5ef692..573e1f51 100644
--- a/docs/reference/rm_dyns.html
+++ b/docs/reference/rm_dyns.html
@@ -1,5 +1,5 @@
-Remove a subset of dynamic scans. — rm_dyns • Spectroscopy Analysis Tools (spant) Remove a subset of dynamic scans. — rm_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/scale_amp_molal.html b/docs/reference/scale_amp_molal.html
index aaeee1f2..7acb8cb0 100644
--- a/docs/reference/scale_amp_molal.html
+++ b/docs/reference/scale_amp_molal.html
@@ -1,7 +1,5 @@
-Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water). — scale_amp_molal • Spectroscopy Analysis Tools (spant) Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / kg of tissue water). — scale_amp_molal • Spectroscopy Analysis Tools (spant)
Spectroscopy Analysis Tools (spant)
- 2.21.0
+ 2.22.0
@@ -76,8 +74,7 @@
- Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water).
+ Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / kg of tissue water).
Source: R/amp_scaling.R
scale_amp_molal.Rd
@@ -163,7 +160,7 @@ Value
diff --git a/docs/reference/scale_amp_molal_pvc.html b/docs/reference/scale_amp_molal_pvc.html
index 962d6afc..4d194abd 100644
--- a/docs/reference/scale_amp_molal_pvc.html
+++ b/docs/reference/scale_amp_molal_pvc.html
@@ -1,7 +1,5 @@
-Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water). — scale_amp_molal_pvc • Spectroscopy Analysis Tools (spant)
@@ -75,8 +73,7 @@
- Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water).
+ Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / kg of tissue water).
Source: R/amp_scaling.R
scale_amp_molal_pvc.Rd
@@ -141,7 +138,7 @@ Value
diff --git a/docs/reference/scale_amp_molar.html b/docs/reference/scale_amp_molar.html
index 02358d91..dc87a338 100644
--- a/docs/reference/scale_amp_molar.html
+++ b/docs/reference/scale_amp_molar.html
@@ -1,7 +1,5 @@
-Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / Litre of tissue). — scale_amp_molar • Spectroscopy Analysis Tools (spant) Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / Litre of tissue). — scale_amp_molar • Spectroscopy Analysis Tools (spant) Convert default LCM/TARQUIN concentration scaling to molal units with partial
-volume correction. — scale_amp_molar2molal_pvc • Spectroscopy Analysis Tools (spant) Convert default LCM/TARQUIN concentration scaling to molal units with partial volume correction. — scale_amp_molar2molal_pvc • Spectroscopy Analysis Tools (spant) Scale fitted amplitudes to a ratio of signal amplitude. — scale_amp_ratio • Spectroscopy Analysis Tools (spant) Scale fitted amplitudes to a ratio of signal amplitude. — scale_amp_ratio • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -116,7 +116,7 @@ Value
diff --git a/docs/reference/scale_amp_ratio_value.html b/docs/reference/scale_amp_ratio_value.html
index 2036837a..6af8ac51 100644
--- a/docs/reference/scale_amp_ratio_value.html
+++ b/docs/reference/scale_amp_ratio_value.html
@@ -1,5 +1,5 @@
-Scale fitted amplitudes to a ratio of signal amplitude. — scale_amp_ratio_value • Spectroscopy Analysis Tools (spant) Scale fitted amplitudes to a ratio of signal amplitude. — scale_amp_ratio_value • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/scale_amp_water_ratio.html b/docs/reference/scale_amp_water_ratio.html
index 5b25e884..35a76b00 100644
--- a/docs/reference/scale_amp_water_ratio.html
+++ b/docs/reference/scale_amp_water_ratio.html
@@ -1,5 +1,5 @@
-Scale metabolite amplitudes as a ratio to the unsuppressed water amplitude. — scale_amp_water_ratio • Spectroscopy Analysis Tools (spant) Scale metabolite amplitudes as a ratio to the unsuppressed water amplitude. — scale_amp_water_ratio • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/scale_basis_amp.html b/docs/reference/scale_basis_amp.html
index 9401c3f1..5a58b5e5 100644
--- a/docs/reference/scale_basis_amp.html
+++ b/docs/reference/scale_basis_amp.html
@@ -1,5 +1,5 @@
-Scale a basis object by a scalar. — scale_basis_amp • Spectroscopy Analysis Tools (spant) Scale a basis object by a scalar. — scale_basis_amp • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/scale_basis_from_singlet.html b/docs/reference/scale_basis_from_singlet.html
index 0d542bc8..c9a19e77 100644
--- a/docs/reference/scale_basis_from_singlet.html
+++ b/docs/reference/scale_basis_from_singlet.html
@@ -1,5 +1,5 @@
-Scale a basis-set to be consistent with spant assumptions for water scaling. — scale_basis_from_singlet • Spectroscopy Analysis Tools (spant) Scale a basis-set to be consistent with spant assumptions for water scaling. — scale_basis_from_singlet • Spectroscopy Analysis Tools (spant)
Spectroscopy Analysis Tools (spant)
- 2.21.0
+ 2.22.0
@@ -127,7 +127,7 @@ Value
diff --git a/docs/reference/scale_mrs_amp.html b/docs/reference/scale_mrs_amp.html
index b5501a0d..990f058a 100644
--- a/docs/reference/scale_mrs_amp.html
+++ b/docs/reference/scale_mrs_amp.html
@@ -1,5 +1,5 @@
-Scale an mrs_data object by a scalar or vector or amplitudes. — scale_mrs_amp • Spectroscopy Analysis Tools (spant) Scale an mrs_data object by a scalar or vector or amplitudes. — scale_mrs_amp • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/scale_spec.html b/docs/reference/scale_spec.html
index 4f6ea835..6b3ddba4 100644
--- a/docs/reference/scale_spec.html
+++ b/docs/reference/scale_spec.html
@@ -1,5 +1,5 @@
-Scale mrs_data to a spectral region. — scale_spec • Spectroscopy Analysis Tools (spant) Scale mrs_data to a spectral region. — scale_spec • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -141,7 +141,7 @@ Value
diff --git a/docs/reference/sd.html b/docs/reference/sd.html
index ea1eec9f..3ae4dfd4 100644
--- a/docs/reference/sd.html
+++ b/docs/reference/sd.html
@@ -1,5 +1,5 @@
-Calculate the standard deviation spectrum from an mrs_data object. — sd • Spectroscopy Analysis Tools (spant) Calculate the standard deviation spectrum from an mrs_data object. — sd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/sd.mrs_data.html b/docs/reference/sd.mrs_data.html
index 3f92a49f..13bdda85 100644
--- a/docs/reference/sd.mrs_data.html
+++ b/docs/reference/sd.mrs_data.html
@@ -1,5 +1,5 @@
-Calculate the standard deviation spectrum from an mrs_data object. — sd.mrs_data • Spectroscopy Analysis Tools (spant) Calculate the standard deviation spectrum from an mrs_data object. — sd.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/seconds.html b/docs/reference/seconds.html
index b34d6627..467ee17f 100644
--- a/docs/reference/seconds.html
+++ b/docs/reference/seconds.html
@@ -1,5 +1,5 @@
-Return a time scale vector to match the FID of an MRS data object. — seconds • Spectroscopy Analysis Tools (spant) Return a time scale vector to match the FID of an MRS data object. — seconds • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/seq_cpmg_ideal.html b/docs/reference/seq_cpmg_ideal.html
index 547e96ab..45727c86 100644
--- a/docs/reference/seq_cpmg_ideal.html
+++ b/docs/reference/seq_cpmg_ideal.html
@@ -1,5 +1,5 @@
-CPMG style sequence with ideal pulses. — seq_cpmg_ideal • Spectroscopy Analysis Tools (spant) CPMG style sequence with ideal pulses. — seq_cpmg_ideal • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/seq_mega_press_ideal.html b/docs/reference/seq_mega_press_ideal.html
index 0769b8b4..a9cd7fa0 100644
--- a/docs/reference/seq_mega_press_ideal.html
+++ b/docs/reference/seq_mega_press_ideal.html
@@ -1,7 +1,5 @@
-MEGA-PRESS sequence with ideal localisation pulses and Gaussian shaped
-editing pulse. — seq_mega_press_ideal • Spectroscopy Analysis Tools (spant) MEGA-PRESS sequence with ideal localisation pulses and Gaussian shaped editing pulse. — seq_mega_press_ideal • Spectroscopy Analysis Tools (spant) PRESS sequence with shaped refocusing pulses. — seq_press_2d_shaped • Spectroscopy Analysis Tools (spant) PRESS sequence with shaped refocusing pulses. — seq_press_2d_shaped • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -165,7 +165,7 @@ Value
diff --git a/docs/reference/seq_press_ideal.html b/docs/reference/seq_press_ideal.html
index 8c976856..72c3af3d 100644
--- a/docs/reference/seq_press_ideal.html
+++ b/docs/reference/seq_press_ideal.html
@@ -1,5 +1,5 @@
-PRESS sequence with ideal pulses. — seq_press_ideal • Spectroscopy Analysis Tools (spant) PRESS sequence with ideal pulses. — seq_press_ideal • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/seq_pulse_acquire.html b/docs/reference/seq_pulse_acquire.html
index 4a88fc64..ad80571e 100644
--- a/docs/reference/seq_pulse_acquire.html
+++ b/docs/reference/seq_pulse_acquire.html
@@ -1,5 +1,5 @@
-Simple pulse and acquire sequence with ideal pulses. — seq_pulse_acquire • Spectroscopy Analysis Tools (spant) Simple pulse and acquire sequence with ideal pulses. — seq_pulse_acquire • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/seq_slaser_ideal.html b/docs/reference/seq_slaser_ideal.html
index 74688f4d..eb83e8e3 100644
--- a/docs/reference/seq_slaser_ideal.html
+++ b/docs/reference/seq_slaser_ideal.html
@@ -1,5 +1,5 @@
-sLASER sequence with ideal pulses. — seq_slaser_ideal • Spectroscopy Analysis Tools (spant) sLASER sequence with ideal pulses. — seq_slaser_ideal • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -126,7 +126,7 @@ Value
diff --git a/docs/reference/seq_spin_echo_ideal.html b/docs/reference/seq_spin_echo_ideal.html
index e23271de..4248716f 100644
--- a/docs/reference/seq_spin_echo_ideal.html
+++ b/docs/reference/seq_spin_echo_ideal.html
@@ -1,5 +1,5 @@
-Spin echo sequence with ideal pulses. — seq_spin_echo_ideal • Spectroscopy Analysis Tools (spant) Spin echo sequence with ideal pulses. — seq_spin_echo_ideal • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/seq_steam_ideal.html b/docs/reference/seq_steam_ideal.html
index a60685a8..1c8115d7 100644
--- a/docs/reference/seq_steam_ideal.html
+++ b/docs/reference/seq_steam_ideal.html
@@ -1,5 +1,5 @@
-STEAM sequence with ideal pulses. — seq_steam_ideal • Spectroscopy Analysis Tools (spant) STEAM sequence with ideal pulses. — seq_steam_ideal • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -128,7 +128,7 @@ Value
diff --git a/docs/reference/seq_steam_ideal_cof.html b/docs/reference/seq_steam_ideal_cof.html
index 8f225740..cba7af91 100644
--- a/docs/reference/seq_steam_ideal_cof.html
+++ b/docs/reference/seq_steam_ideal_cof.html
@@ -1,7 +1,5 @@
-STEAM sequence with ideal pulses and coherence order filtering to simulate
-gradient crushers. — seq_steam_ideal_cof • Spectroscopy Analysis Tools (spant) STEAM sequence with ideal pulses and coherence order filtering to simulate gradient crushers. — seq_steam_ideal_cof • Spectroscopy Analysis Tools (spant) STEAM sequence with ideal pulses using the z-rotation gradient simulation
-method described by Young et al JMR 140, 146-152 (1999). — seq_steam_ideal_young • Spectroscopy Analysis Tools (spant) STEAM sequence with ideal pulses using the z-rotation gradient simulation method described by Young et al JMR 140, 146-152 (1999). — seq_steam_ideal_young • Spectroscopy Analysis Tools (spant) Set the number of transients for an mrs_data object. — set_Ntrans • Spectroscopy Analysis Tools (spant) Set the number of transients for an mrs_data object. — set_Ntrans • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/set_def_acq_paras.html b/docs/reference/set_def_acq_paras.html
index 3e1b4004..cc2ada9c 100644
--- a/docs/reference/set_def_acq_paras.html
+++ b/docs/reference/set_def_acq_paras.html
@@ -1,5 +1,5 @@
-Set the default acquisition parameters. — set_def_acq_paras • Spectroscopy Analysis Tools (spant) Set the default acquisition parameters. — set_def_acq_paras • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Arguments
diff --git a/docs/reference/set_lcm_cmd.html b/docs/reference/set_lcm_cmd.html
index 2056ed01..42bb2f24 100644
--- a/docs/reference/set_lcm_cmd.html
+++ b/docs/reference/set_lcm_cmd.html
@@ -1,5 +1,5 @@
-Set the command to run the LCModel command-line program. — set_lcm_cmd • Spectroscopy Analysis Tools (spant) Set the command to run the LCModel command-line program. — set_lcm_cmd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/set_lw.html b/docs/reference/set_lw.html
index b64ec851..bb176c62 100644
--- a/docs/reference/set_lw.html
+++ b/docs/reference/set_lw.html
@@ -1,5 +1,5 @@
-Apply line-broadening to an mrs_data object to achieve a specified linewidth. — set_lw • Spectroscopy Analysis Tools (spant) Apply line-broadening to an mrs_data object to achieve a specified linewidth. — set_lw • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -123,7 +123,7 @@ Value
diff --git a/docs/reference/set_mask_xy_mat.html b/docs/reference/set_mask_xy_mat.html
index 49dc5d4e..52c4b617 100644
--- a/docs/reference/set_mask_xy_mat.html
+++ b/docs/reference/set_mask_xy_mat.html
@@ -1,5 +1,5 @@
-Set the masked voxels in a 2D MRSI dataset to given spectrum. — set_mask_xy_mat • Spectroscopy Analysis Tools (spant) Set the masked voxels in a 2D MRSI dataset to given spectrum. — set_mask_xy_mat • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Value
diff --git a/docs/reference/set_precomp_mode.html b/docs/reference/set_precomp_mode.html
index f44bd5d3..47c28e3b 100644
--- a/docs/reference/set_precomp_mode.html
+++ b/docs/reference/set_precomp_mode.html
@@ -1,5 +1,5 @@
-Set the precompute mode. — set_precomp_mode • Spectroscopy Analysis Tools (spant) Set the precompute mode. — set_precomp_mode • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/set_precomp_verbose.html b/docs/reference/set_precomp_verbose.html
index 1453a231..9c613505 100644
--- a/docs/reference/set_precomp_verbose.html
+++ b/docs/reference/set_precomp_verbose.html
@@ -1,5 +1,5 @@
-Set the verbosity of the precompute function. — set_precomp_verbose • Spectroscopy Analysis Tools (spant) Set the verbosity of the precompute function. — set_precomp_verbose • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/set_ref.html b/docs/reference/set_ref.html
index 8953fa50..5436dfa2 100644
--- a/docs/reference/set_ref.html
+++ b/docs/reference/set_ref.html
@@ -1,5 +1,5 @@
-Set the ppm reference value (eg ppm value at 0Hz). — set_ref • Spectroscopy Analysis Tools (spant) Set the ppm reference value (eg ppm value at 0Hz). — set_ref • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/set_td_pts.html b/docs/reference/set_td_pts.html
index 8a80d42a..586459ff 100644
--- a/docs/reference/set_td_pts.html
+++ b/docs/reference/set_td_pts.html
@@ -1,7 +1,5 @@
-Set the number of time-domain data points, truncating or zero-filling as
-appropriate. — set_td_pts • Spectroscopy Analysis Tools (spant) Set the number of time-domain data points, truncating or zero-filling as appropriate. — set_td_pts • Spectroscopy Analysis Tools (spant) Set the command to run the TARQUIN command-line program. — set_tqn_cmd • Spectroscopy Analysis Tools (spant) Set the command to run the TARQUIN command-line program. — set_tqn_cmd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/set_tr.html b/docs/reference/set_tr.html
index b2109ab0..65c9df5f 100644
--- a/docs/reference/set_tr.html
+++ b/docs/reference/set_tr.html
@@ -1,5 +1,5 @@
-Set the repetition time of an MRS dataset. — set_tr • Spectroscopy Analysis Tools (spant) Set the repetition time of an MRS dataset. — set_tr • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/shift.html b/docs/reference/shift.html
index ab0fe724..034591d0 100644
--- a/docs/reference/shift.html
+++ b/docs/reference/shift.html
@@ -1,5 +1,5 @@
-Apply a frequency shift to MRS data. — shift • Spectroscopy Analysis Tools (spant) Apply a frequency shift to MRS data. — shift • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/shift_basis.html b/docs/reference/shift_basis.html
index 2884be19..f55a65e0 100644
--- a/docs/reference/shift_basis.html
+++ b/docs/reference/shift_basis.html
@@ -1,5 +1,5 @@
-Apply frequency shifts to basis set signals. — shift_basis • Spectroscopy Analysis Tools (spant) Apply frequency shifts to basis set signals. — shift_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Value
diff --git a/docs/reference/sim_basis.html b/docs/reference/sim_basis.html
index c7838c46..bb5fefc6 100644
--- a/docs/reference/sim_basis.html
+++ b/docs/reference/sim_basis.html
@@ -1,5 +1,5 @@
-Simulate a basis set object. — sim_basis • Spectroscopy Analysis Tools (spant) Simulate a basis set object. — sim_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -136,7 +136,7 @@ Value
diff --git a/docs/reference/sim_basis_1h_brain.html b/docs/reference/sim_basis_1h_brain.html
index 62ed7389..f71ffa0b 100644
--- a/docs/reference/sim_basis_1h_brain.html
+++ b/docs/reference/sim_basis_1h_brain.html
@@ -1,7 +1,5 @@
-Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS
-sequence. Note, ideal pulses are assumed. — sim_basis_1h_brain • Spectroscopy Analysis Tools (spant) Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS sequence. Note, ideal pulses are assumed. — sim_basis_1h_brain • Spectroscopy Analysis Tools (spant) Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS
-sequence. Note, ideal pulses are assumed. — sim_basis_1h_brain_press • Spectroscopy Analysis Tools (spant) Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS sequence. Note, ideal pulses are assumed. — sim_basis_1h_brain_press • Spectroscopy Analysis Tools (spant) Simulate a macromolecular and lipid basis-set suitable for 1H brain MRS
-analysis. — sim_basis_mm_lip_lcm • Spectroscopy Analysis Tools (spant) Simulate a macromolecular and lipid basis-set suitable for 1H brain MRS analysis. — sim_basis_mm_lip_lcm • Spectroscopy Analysis Tools (spant) Simulate a basis file using TARQUIN. — sim_basis_tqn • Spectroscopy Analysis Tools (spant) Simulate a basis file using TARQUIN. — sim_basis_tqn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -129,7 +129,7 @@ Examples
diff --git a/docs/reference/sim_brain_1h.html b/docs/reference/sim_brain_1h.html
index 2044cf1a..717ee289 100644
--- a/docs/reference/sim_brain_1h.html
+++ b/docs/reference/sim_brain_1h.html
@@ -1,5 +1,5 @@
-Simulate MRS data with a similar appearance to normal brain (by default). — sim_brain_1h • Spectroscopy Analysis Tools (spant) Simulate MRS data with a similar appearance to normal brain (by default). — sim_brain_1h • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -159,7 +159,7 @@ Value
diff --git a/docs/reference/sim_mol.html b/docs/reference/sim_mol.html
index 23bcef50..77f76a50 100644
--- a/docs/reference/sim_mol.html
+++ b/docs/reference/sim_mol.html
@@ -1,5 +1,5 @@
-Simulate a mol_parameter object. — sim_mol • Spectroscopy Analysis Tools (spant) Simulate a mol_parameter object. — sim_mol • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -143,7 +143,7 @@ Value
diff --git a/docs/reference/sim_noise.html b/docs/reference/sim_noise.html
index 23875f79..a71477d4 100644
--- a/docs/reference/sim_noise.html
+++ b/docs/reference/sim_noise.html
@@ -1,5 +1,5 @@
-Simulate an mrs_data object containing simulated Gaussian noise. — sim_noise • Spectroscopy Analysis Tools (spant) Simulate an mrs_data object containing simulated Gaussian noise. — sim_noise • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -84,6 +84,7 @@ Simulate an mrs_data object containing simulated Gaussian noise.
ft = def_ft(),
N = def_N(),
ref = def_ref(),
+ nuc = def_nuc(),
dyns = 1,
fd = TRUE
)
@@ -111,6 +112,10 @@ Arguments
reference value for ppm scale.
nuc
+resonant nucleus.
dyns
number of dynamic scans to generate.
Value
diff --git a/docs/reference/sim_resonances.html b/docs/reference/sim_resonances.html
index 19e9a8a4..d4f8d7c0 100644
--- a/docs/reference/sim_resonances.html
+++ b/docs/reference/sim_resonances.html
@@ -1,5 +1,5 @@
-Simulate a MRS data object containing a set of simulated resonances. — sim_resonances • Spectroscopy Analysis Tools (spant) Simulate a MRS data object containing a set of simulated resonances. — sim_resonances • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -161,7 +161,7 @@ Examples
diff --git a/docs/reference/sim_th_excit_profile.html b/docs/reference/sim_th_excit_profile.html
index 5535c5ef..e781cab1 100644
--- a/docs/reference/sim_th_excit_profile.html
+++ b/docs/reference/sim_th_excit_profile.html
@@ -1,7 +1,5 @@
-Simulate an ideal pulse excitation profile by smoothing a top-hat function
-with a Gaussian. — sim_th_excit_profile • Spectroscopy Analysis Tools (spant) Simulate an ideal pulse excitation profile by smoothing a top-hat function with a Gaussian. — sim_th_excit_profile • Spectroscopy Analysis Tools (spant) Simulate an mrs_data object containing complex zero valued samples. — sim_zero • Spectroscopy Analysis Tools (spant) Simulate an mrs_data object containing complex zero valued samples. — sim_zero • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -78,7 +78,14 @@ Simulate an mrs_data object containing complex zero valued samples.
-
+
@@ -99,6 +106,10 @@ Arguments
reference value for ppm scale.
nuc
+resonant nucleus.
dyns
number of dynamic scans to generate.
Value
diff --git a/docs/reference/smooth_dyns.html b/docs/reference/smooth_dyns.html
index 4cc8da50..accf3a51 100644
--- a/docs/reference/smooth_dyns.html
+++ b/docs/reference/smooth_dyns.html
@@ -1,5 +1,5 @@
-Smooth data across the dynamic dimension with a Gaussian kernel. — smooth_dyns • Spectroscopy Analysis Tools (spant) Smooth data across the dynamic dimension with a Gaussian kernel. — smooth_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/sort_basis.html b/docs/reference/sort_basis.html
index 6a676ea2..d25cc006 100644
--- a/docs/reference/sort_basis.html
+++ b/docs/reference/sort_basis.html
@@ -1,5 +1,5 @@
-Sort the basis-set elements alphabetically. — sort_basis • Spectroscopy Analysis Tools (spant) Sort the basis-set elements alphabetically. — sort_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/spant-package.html b/docs/reference/spant-package.html
index b3dd8e21..90f19ec3 100644
--- a/docs/reference/spant-package.html
+++ b/docs/reference/spant-package.html
@@ -1,5 +1,5 @@
-spant: spectroscopy analysis tools. — spant-package • Spectroscopy Analysis Tools (spant) spant: spectroscopy analysis tools. — spant-package • Spectroscopy Analysis Tools (spant) Simulate and fit some spectra with ABfit for benchmarking purposes. Basic
-timing and performance metrics will be printed. — spant_abfit_benchmark • Spectroscopy Analysis Tools (spant) Simulate and fit some spectra with ABfit for benchmarking purposes. Basic timing and performance metrics will be printed. — spant_abfit_benchmark • Spectroscopy Analysis Tools (spant) Example MEGA-PRESS data with significant B0 drift. — spant_mpress_drift • Spectroscopy Analysis Tools (spant) Example MEGA-PRESS data with significant B0 drift. — spant_mpress_drift • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -83,7 +83,7 @@ Example MEGA-PRESS data with significant B0 drift.
Format
- An object of class mrs_data of length 13.
+ An object of class mrs_data of dimension 1 x 1 x 1 x 1 x 40 x 1 x 1024.
@@ -98,7 +98,7 @@ Format
diff --git a/docs/reference/spant_sim_fmrs_dataset.html b/docs/reference/spant_sim_fmrs_dataset.html
new file mode 100644
index 00000000..00e48b56
--- /dev/null
+++ b/docs/reference/spant_sim_fmrs_dataset.html
@@ -0,0 +1,117 @@
+
+Simulate an example fMRS dataset for a block design fMRS experiment and export a BIDS structure. — spant_sim_fmrs_dataset • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Simulate an example fMRS dataset for a block design fMRS experiment and export a BIDS structure.
+ Source: R/fmrs.R
+ spant_sim_fmrs_dataset.Rd
+
+
+
+ Simulate an example fMRS dataset for a block design fMRS experiment and
+export a BIDS structure.
+
+
+
+ spant_sim_fmrs_dataset(output_dir = NULL)
+
+
+
+ Arguments
+ - output_dir
+output directory for the BIDS data. Defaults to :
+"HOME/sim_fmrs_dataset/data".
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/spant_simulation_benchmark.html b/docs/reference/spant_simulation_benchmark.html
index 32daa8bf..d8cc6841 100644
--- a/docs/reference/spant_simulation_benchmark.html
+++ b/docs/reference/spant_simulation_benchmark.html
@@ -1,7 +1,5 @@
-Simulate a typical metabolite basis set for benchmarking. Timing metrics will
-be printed on completion. — spant_simulation_benchmark • Spectroscopy Analysis Tools (spant) Simulate a typical metabolite basis set for benchmarking. Timing metrics will be printed on completion. — spant_simulation_benchmark • Spectroscopy Analysis Tools (spant) Decompose an mrs_data object into white and gray matter spectra. — spec_decomp • Spectroscopy Analysis Tools (spant) Perform a mathematical operation on a spectral region. — spec_op • Spectroscopy Analysis Tools (spant) Perform a mathematical operation on a spectral region. — spec_op • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -98,8 +98,8 @@ Arguments
operator
-can be "sum" (default), "mean", "l2", "max", "min" or
-"max-min".
can be "sum" (default), "mean", "l2", "max", "max_cplx,
+"min" or "max-min".
freq_scale
@@ -129,7 +129,7 @@ Value
diff --git a/docs/reference/spin_sys.html b/docs/reference/spin_sys.html
index 853423a4..1eaa9e76 100644
--- a/docs/reference/spin_sys.html
+++ b/docs/reference/spin_sys.html
@@ -1,5 +1,5 @@
-Create a spin system object for pulse sequence simulation. — spin_sys • Spectroscopy Analysis Tools (spant) Create a spin system object for pulse sequence simulation. — spin_sys • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/spm_pve2categorical.html b/docs/reference/spm_pve2categorical.html
index 23a1bad9..70f10729 100644
--- a/docs/reference/spm_pve2categorical.html
+++ b/docs/reference/spm_pve2categorical.html
@@ -1,7 +1,5 @@
-Convert SPM style segmentation files to a single categorical image where
-the numerical values map as: 0) Other, 1) CSF, 2) GM and 3) WM. — spm_pve2categorical • Spectroscopy Analysis Tools (spant) Convert SPM style segmentation files to a single categorical image where the numerical values map as: 0) Other, 1) CSF, 2) GM and 3) WM. — spm_pve2categorical • Spectroscopy Analysis Tools (spant) Signal space projection method for lipid suppression. — ssp • Spectroscopy Analysis Tools (spant) Signal space projection method for lipid suppression. — ssp • Spectroscopy Analysis Tools (spant) Plot the fitting results of an object of class fit_result with
-individual basis set components shown. — stackplot.fit_result • Spectroscopy Analysis Tools (spant) Plot the fitting results of an object of class fit_result with individual basis set components shown. — stackplot.fit_result • Spectroscopy Analysis Tools (spant) Produce a plot with multiple traces. — stackplot • Spectroscopy Analysis Tools (spant) Produce a plot with multiple traces. — stackplot • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/stackplot.mrs_data.html b/docs/reference/stackplot.mrs_data.html
index 17ff5648..64eea445 100644
--- a/docs/reference/stackplot.mrs_data.html
+++ b/docs/reference/stackplot.mrs_data.html
@@ -1,5 +1,5 @@
-Stackplot plotting method for objects of class mrs_data. — stackplot.mrs_data • Spectroscopy Analysis Tools (spant) Stackplot plotting method for objects of class mrs_data. — stackplot.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -255,7 +255,7 @@ Arguments
diff --git a/docs/reference/sub_first_dyn.html b/docs/reference/sub_first_dyn.html
index dbd7f831..493b7242 100644
--- a/docs/reference/sub_first_dyn.html
+++ b/docs/reference/sub_first_dyn.html
@@ -1,5 +1,5 @@
-Subtract the first dynamic spectrum from a dynamic series. — sub_first_dyn • Spectroscopy Analysis Tools (spant) Subtract the first dynamic spectrum from a dynamic series. — sub_first_dyn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/sub_mean_dyns.html b/docs/reference/sub_mean_dyns.html
index 6e3bb2df..221bd0c1 100644
--- a/docs/reference/sub_mean_dyns.html
+++ b/docs/reference/sub_mean_dyns.html
@@ -1,5 +1,5 @@
-Subtract the mean dynamic spectrum from a dynamic series. — sub_mean_dyns • Spectroscopy Analysis Tools (spant) Subtract the mean dynamic spectrum from a dynamic series. — sub_mean_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/sub_median_dyns.html b/docs/reference/sub_median_dyns.html
index 134c495d..1e834f14 100644
--- a/docs/reference/sub_median_dyns.html
+++ b/docs/reference/sub_median_dyns.html
@@ -1,5 +1,5 @@
-Subtract the median dynamic spectrum from a dynamic series. — sub_median_dyns • Spectroscopy Analysis Tools (spant) Subtract the median dynamic spectrum from a dynamic series. — sub_median_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/sum_coils.html b/docs/reference/sum_coils.html
index 7bf559f2..e1ab3cc0 100644
--- a/docs/reference/sum_coils.html
+++ b/docs/reference/sum_coils.html
@@ -1,5 +1,5 @@
-Calculate the sum across receiver coil elements. — sum_coils • Spectroscopy Analysis Tools (spant) Calculate the sum across receiver coil elements. — sum_coils • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/sum_dyns.html b/docs/reference/sum_dyns.html
index a0be19d3..bbda2ffc 100644
--- a/docs/reference/sum_dyns.html
+++ b/docs/reference/sum_dyns.html
@@ -1,5 +1,5 @@
-Calculate the sum of data dynamics. — sum_dyns • Spectroscopy Analysis Tools (spant) Calculate the sum of data dynamics. — sum_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/sum_mrs.html b/docs/reference/sum_mrs.html
index a22f215b..3cc3ab9e 100644
--- a/docs/reference/sum_mrs.html
+++ b/docs/reference/sum_mrs.html
@@ -1,5 +1,5 @@
-Sum two mrs_data objects. — sum_mrs • Spectroscopy Analysis Tools (spant) Sum two mrs_data objects. — sum_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Value
diff --git a/docs/reference/sum_mrs_list.html b/docs/reference/sum_mrs_list.html
index f4e09aea..c3584348 100644
--- a/docs/reference/sum_mrs_list.html
+++ b/docs/reference/sum_mrs_list.html
@@ -1,5 +1,5 @@
-Return the sum of a list of mrs_data objects. — sum_mrs_list • Spectroscopy Analysis Tools (spant) Return the sum of a list of mrs_data objects. — sum_mrs_list • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/svs_1h_brain_analysis.html b/docs/reference/svs_1h_brain_analysis.html
index 8ce514db..dff0ef7d 100644
--- a/docs/reference/svs_1h_brain_analysis.html
+++ b/docs/reference/svs_1h_brain_analysis.html
@@ -1,5 +1,5 @@
-Standard SVS 1H brain analysis pipeline. — svs_1h_brain_analysis • Spectroscopy Analysis Tools (spant) Standard SVS 1H brain analysis pipeline. — svs_1h_brain_analysis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -199,7 +199,7 @@ Value
diff --git a/docs/reference/svs_1h_brain_analysis_dev.html b/docs/reference/svs_1h_brain_analysis_dev.html
index d70a14d3..d71bfea2 100644
--- a/docs/reference/svs_1h_brain_analysis_dev.html
+++ b/docs/reference/svs_1h_brain_analysis_dev.html
@@ -1,5 +1,5 @@
-Standard SVS 1H brain analysis pipeline. — svs_1h_brain_analysis_dev • Spectroscopy Analysis Tools (spant) Standard SVS 1H brain analysis pipeline. — svs_1h_brain_analysis_dev • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -193,7 +193,7 @@ Examples
diff --git a/docs/reference/svs_1h_brain_batch_analysis.html b/docs/reference/svs_1h_brain_batch_analysis.html
index 5631e8cc..15f7223e 100644
--- a/docs/reference/svs_1h_brain_batch_analysis.html
+++ b/docs/reference/svs_1h_brain_batch_analysis.html
@@ -1,5 +1,5 @@
-Batch interface to the standard SVS 1H brain analysis pipeline. — svs_1h_brain_batch_analysis • Spectroscopy Analysis Tools (spant) Batch interface to the standard SVS 1H brain analysis pipeline. — svs_1h_brain_batch_analysis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -144,7 +144,7 @@ Value
diff --git a/docs/reference/t_test_spec.html b/docs/reference/t_test_spec.html
new file mode 100644
index 00000000..56a7ea1b
--- /dev/null
+++ b/docs/reference/t_test_spec.html
@@ -0,0 +1,124 @@
+
+Perform a t-test on spectral data points. — t_test_spec • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+
+
+ Perform a t-test on spectral data points.
+
+
+
+ t_test_spec(mrs_data, group)
+
+
+
+ Arguments
+ - mrs_data
+an mrs_data object with spectra in the dynamic dimension.
- group
+vector describing the group membership of each dynamic spectrum.
+
+ Value
+
+
+a list of statistical results.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/td2fd.html b/docs/reference/td2fd.html
index 6748a6a8..f31ed524 100644
--- a/docs/reference/td2fd.html
+++ b/docs/reference/td2fd.html
@@ -1,5 +1,5 @@
-Transform time-domain data to the frequency-domain. — td2fd • Spectroscopy Analysis Tools (spant) Transform time-domain data to the frequency-domain. — td2fd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/td_conv_filt.html b/docs/reference/td_conv_filt.html
index a9f340c3..106b9b00 100644
--- a/docs/reference/td_conv_filt.html
+++ b/docs/reference/td_conv_filt.html
@@ -1,5 +1,5 @@
-Time-domain convolution based filter. — td_conv_filt • Spectroscopy Analysis Tools (spant) Time-domain convolution based filter. — td_conv_filt • Spectroscopy Analysis Tools (spant) Time-domain spectral registration. — tdsr • Spectroscopy Analysis Tools (spant) Time-domain spectral registration. — tdsr • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -121,7 +121,7 @@ Value
diff --git a/docs/reference/te.html b/docs/reference/te.html
index 010361b1..4a65711d 100644
--- a/docs/reference/te.html
+++ b/docs/reference/te.html
@@ -1,5 +1,5 @@
-Return the echo time of an MRS dataset. — te • Spectroscopy Analysis Tools (spant) Return the echo time of an MRS dataset. — te • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/tr.html b/docs/reference/tr.html
index 0c0bd63b..2e749e02 100644
--- a/docs/reference/tr.html
+++ b/docs/reference/tr.html
@@ -1,5 +1,5 @@
-Return the repetition time of an MRS dataset. — tr • Spectroscopy Analysis Tools (spant) Return the repetition time of an MRS dataset. — tr • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/varpro_3_para_opts.html b/docs/reference/varpro_3_para_opts.html
index c2270a16..52d7cd84 100644
--- a/docs/reference/varpro_3_para_opts.html
+++ b/docs/reference/varpro_3_para_opts.html
@@ -1,5 +1,5 @@
-Return a list of options for VARPRO based fitting with 3 free parameters. — varpro_3_para_opts • Spectroscopy Analysis Tools (spant) Return a list of options for VARPRO based fitting with 3 free parameters. — varpro_3_para_opts • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -141,7 +141,7 @@ Value
diff --git a/docs/reference/varpro_basic_opts.html b/docs/reference/varpro_basic_opts.html
index 32c86d22..c5104891 100644
--- a/docs/reference/varpro_basic_opts.html
+++ b/docs/reference/varpro_basic_opts.html
@@ -1,5 +1,5 @@
-Return a list of options for a basic VARPRO analysis. — varpro_basic_opts • Spectroscopy Analysis Tools (spant) Return a list of options for a basic VARPRO analysis. — varpro_basic_opts • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -118,7 +118,7 @@ Value
diff --git a/docs/reference/varpro_opts.html b/docs/reference/varpro_opts.html
index 2aabf11d..6332f730 100644
--- a/docs/reference/varpro_opts.html
+++ b/docs/reference/varpro_opts.html
@@ -1,5 +1,5 @@
-Return a list of options for VARPRO based fitting. — varpro_opts • Spectroscopy Analysis Tools (spant) Return a list of options for VARPRO based fitting. — varpro_opts • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -177,7 +177,7 @@ Examples
diff --git a/docs/reference/vec2mrs_data.html b/docs/reference/vec2mrs_data.html
index 0cccd73b..f0d58bf0 100644
--- a/docs/reference/vec2mrs_data.html
+++ b/docs/reference/vec2mrs_data.html
@@ -1,5 +1,5 @@
-Convert a vector into a mrs_data object. — vec2mrs_data • Spectroscopy Analysis Tools (spant) Convert a vector into a mrs_data object. — vec2mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -80,10 +80,11 @@ Convert a vector into a mrs_data object.
vec2mrs_data(
vec,
- fs = def_fs(),
- ft = def_ft(),
- ref = def_ref(),
- nuc = def_nuc(),
+ mrs_data = NULL,
+ fs = NULL,
+ ft = NULL,
+ ref = NULL,
+ nuc = NULL,
dyns = 1,
fd = FALSE
)
@@ -95,6 +96,10 @@ Arguments
the data vector.
mrs_data
+example data to copy acquisition parameters from.
fs
sampling frequency in Hz.
Arguments
fd
-flag to indicate if the matrix is in the frequency domain (logical).
flag to indicate if the vector is in the frequency domain (logical).
Value
diff --git a/docs/reference/write_basis.html b/docs/reference/write_basis.html
index b6e27cbd..94c5e021 100644
--- a/docs/reference/write_basis.html
+++ b/docs/reference/write_basis.html
@@ -1,5 +1,5 @@
-Write a basis object to an LCModel .basis formatted file. — write_basis • Spectroscopy Analysis Tools (spant) Write a basis object to an LCModel .basis formatted file. — write_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -108,7 +108,7 @@ Arguments
diff --git a/docs/reference/write_basis_tqn.html b/docs/reference/write_basis_tqn.html
index 6aa51c1d..116c73ec 100644
--- a/docs/reference/write_basis_tqn.html
+++ b/docs/reference/write_basis_tqn.html
@@ -1,5 +1,5 @@
-Generate a basis file using TARQUIN. — write_basis_tqn • Spectroscopy Analysis Tools (spant) Generate a basis file using TARQUIN. — write_basis_tqn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Examples
diff --git a/docs/reference/write_mrs.html b/docs/reference/write_mrs.html
index fff25f15..124b9dc4 100644
--- a/docs/reference/write_mrs.html
+++ b/docs/reference/write_mrs.html
@@ -1,5 +1,5 @@
-Write MRS data object to file. — write_mrs • Spectroscopy Analysis Tools (spant) Write MRS data object to file. — write_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Arguments
diff --git a/docs/reference/write_mrs_nifti.html b/docs/reference/write_mrs_nifti.html
index f4bf1921..bd3ed4b7 100644
--- a/docs/reference/write_mrs_nifti.html
+++ b/docs/reference/write_mrs_nifti.html
@@ -1,5 +1,5 @@
-Write MRS data object to file in NIFTI format. — write_mrs_nifti • Spectroscopy Analysis Tools (spant) Write MRS data object to file in NIFTI format. — write_mrs_nifti • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/write_pulse_ascii.html b/docs/reference/write_pulse_ascii.html
index 067ae086..221f8ebb 100644
--- a/docs/reference/write_pulse_ascii.html
+++ b/docs/reference/write_pulse_ascii.html
@@ -1,5 +1,5 @@
-Write an ASCII formatted pulse file. — write_pulse_ascii • Spectroscopy Analysis Tools (spant) Write an ASCII formatted pulse file. — write_pulse_ascii • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/zero_fade_spec.html b/docs/reference/zero_fade_spec.html
index c703745c..c8b572c3 100644
--- a/docs/reference/zero_fade_spec.html
+++ b/docs/reference/zero_fade_spec.html
@@ -1,7 +1,5 @@
-Fade a spectrum to zero by frequency domain multiplication with a tanh
-function. Note this operation distorts data points at the end of the FID. — zero_fade_spec • Spectroscopy Analysis Tools (spant) Fade a spectrum to zero by frequency domain multiplication with a tanh function. Note this operation distorts data points at the end of the FID. — zero_fade_spec • Spectroscopy Analysis Tools (spant) Zero all coherences including and above a given order. — zero_higher_orders • Spectroscopy Analysis Tools (spant) Zero all coherences including and above a given order. — zero_higher_orders • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Value
diff --git a/docs/reference/zero_td_pts_end.html b/docs/reference/zero_td_pts_end.html
index 8c1123c8..71d24ebb 100644
--- a/docs/reference/zero_td_pts_end.html
+++ b/docs/reference/zero_td_pts_end.html
@@ -1,5 +1,5 @@
-Set mrs_data object data points at the end of the FID to zero. — zero_td_pts_end • Spectroscopy Analysis Tools (spant) Set mrs_data object data points at the end of the FID to zero. — zero_td_pts_end • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/zf.html b/docs/reference/zf.html
index 85e2013c..baf50256 100644
--- a/docs/reference/zf.html
+++ b/docs/reference/zf.html
@@ -1,5 +1,5 @@
-Zero-fill MRS data in the time domain. — zf • Spectroscopy Analysis Tools (spant) Zero-fill MRS data in the time domain. — zf • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -125,7 +125,7 @@ Value
diff --git a/docs/reference/zf_xy.html b/docs/reference/zf_xy.html
index ebca3999..c4104a74 100644
--- a/docs/reference/zf_xy.html
+++ b/docs/reference/zf_xy.html
@@ -1,5 +1,5 @@
-Zero-fill MRSI data in the k-space x-y direction. — zf_xy • Spectroscopy Analysis Tools (spant) Zero-fill MRSI data in the k-space x-y direction. — zf_xy • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -113,7 +113,7 @@ Value
diff --git a/docs/sitemap.xml b/docs/sitemap.xml
index e2139f71..4c39f515 100644
--- a/docs/sitemap.xml
+++ b/docs/sitemap.xml
@@ -216,6 +216,12 @@
https://martin3141.github.io/spant/reference/comb_coils_fp_pc.html
+
+ https://martin3141.github.io/spant/reference/comb_coils_mrsi_gls.html
+
+
+ https://martin3141.github.io/spant/reference/comb_coils_svs_gls.html
+
https://martin3141.github.io/spant/reference/comb_csv_results.html
@@ -411,6 +417,9 @@
https://martin3141.github.io/spant/reference/gen_conv_reg.html
+
+ https://martin3141.github.io/spant/reference/gen_group_reg.html
+
https://martin3141.github.io/spant/reference/gen_impulse_reg.html
@@ -555,6 +564,15 @@
https://martin3141.github.io/spant/reference/glm_spec.html
+
+ https://martin3141.github.io/spant/reference/glm_spec_fmrs_fl.html
+
+
+ https://martin3141.github.io/spant/reference/glm_spec_fmrs_group.html
+
+
+ https://martin3141.github.io/spant/reference/glm_spec_group_linhyp.html
+
https://martin3141.github.io/spant/reference/grid_shift_xy.html
@@ -690,9 +708,15 @@
https://martin3141.github.io/spant/reference/mrs_data2basis.html
+
+ https://martin3141.github.io/spant/reference/mrs_data2bids.html
+
https://martin3141.github.io/spant/reference/mrs_data2mat.html
+
+ https://martin3141.github.io/spant/reference/mrs_data2spec_mat.html
+
https://martin3141.github.io/spant/reference/mrs_data2vec.html
@@ -741,6 +765,9 @@
https://martin3141.github.io/spant/reference/phase.html
+
+ https://martin3141.github.io/spant/reference/phase_ref_1h_brain.html
+
https://martin3141.github.io/spant/reference/plot.fit_result.html
@@ -780,6 +807,12 @@
https://martin3141.github.io/spant/reference/precomp.html
+
+ https://martin3141.github.io/spant/reference/preproc_svs.html
+
+
+ https://martin3141.github.io/spant/reference/preproc_svs_dataset.html
+
https://martin3141.github.io/spant/reference/print.fit_result.html
@@ -1050,6 +1083,9 @@
https://martin3141.github.io/spant/reference/spant_mpress_drift.html
+
+ https://martin3141.github.io/spant/reference/spant_sim_fmrs_dataset.html
+
https://martin3141.github.io/spant/reference/spant_simulation_benchmark.html
@@ -1107,6 +1143,9 @@
https://martin3141.github.io/spant/reference/svs_1h_brain_batch_analysis.html
+
+ https://martin3141.github.io/spant/reference/t_test_spec.html
+
https://martin3141.github.io/spant/reference/td2fd.html
spant 2.21.0
+spant 2.22.0
+- Added find_bids_mrs and mrs_data2bids helper functions. +
- Improved handling of CMRR semi-LASER SVS water reference scans. +
- Added functions for GLS coil combination. +
spant 2.21.02024-05-30
- Fixed compiler warnings for Fortran code.
- Added glm_spec function.
- Added add_noise_spec_snr function. @@ -584,7 +590,7 @@
spant 0.1.02
offset in number of data points from the end of the FID to +zero-fill. Default is NULL and will automatically set this to 50 points when +the FID distortion flag is set for the mrs_data.
Value
@@ -372,7 +379,7 @@Examples
add_noise_spec_snr(mrs_data, target_snr, sig_region = c(4, 0.5))add_noise_spec_snr(
+ mrs_data,
+ target_snr,
+ sig_region = c(4, 0.5),
+ ref_data = NULL
+)Arguments
spectral limits to search for the strongest spectral data point.
measure the signal from the first scan in this reference data +and apply the same target noise level to mrs_data.
Value
@@ -117,7 +127,7 @@Value
must be "hamming" or "gaussian".
must be "hamming", "hanning" or "gaussian".
+
+
+
+
+
+
+
+
+
+
+ Combine MRSI coil data using the GLS method presented by An et al JMRI 37:1445-1450 (2013).
+ Source:R/mrs_data_proc.R
+ comb_coils_mrsi_gls.Rd
+
+
+ Combine MRSI coil data using the GLS method presented by An et al +JMRI 37:1445-1450 (2013).
+
+
+
+
+ comb_coils_mrsi_gls(metab, noise_pts = 30, noise_mrs = NULL)
+
+ Arguments
+- metab +
MRSI data containing metabolite data.
+
+
+- noise_pts +
number of points from the end of the FIDs to use for noise +covariance estimation.
+
+
+- noise_mrs +
MRS data containing noise information for each coil.
+
+
+
+
+ Value
+ + +coil combined MRSI data.
+
+
+
+
+
+
+
+
+
+
+
+ Combine SVS coil data using the GLS method presented by An et al JMRI 37:1445-1450 (2013).
+ Source:R/mrs_data_proc.R
+ comb_coils_svs_gls.Rd
+
+
+ Combine SVS coil data using the GLS method presented by An et al +JMRI 37:1445-1450 (2013).
+
+
+
+
+ comb_coils_svs_gls(
+ metab,
+ ref = NULL,
+ noise_pts = 256,
+ noise_mrs = NULL,
+ use_mean_sens = TRUE
+)
+
+ Arguments
+- metab +
MRS data containing metabolite data.
+
+
+- ref +
MRS data containing reference data (optional).
+
+
+- noise_pts +
number of points from the end of the FIDs to use for noise +covariance estimation.
+
+
+- noise_mrs +
MRS data containing noise information for each coil.
+
+
+- use_mean_sens +
use the dynamic mean to estimate coil sensitivities.
+
+
+
+
+ Value
+ + +coil combined MRS data.
+find_bids_mrs(path)find_bids_mrs(path, output_full_path = FALSE)Arguments
- path
path to the directory containing the BIDS structure.
+
+- output_full_path +
output the full normalised data paths.
+
Value
@@ -106,7 +110,7 @@Value
gen_baseline_reg(mrs_data)gen_baseline_reg(mrs_data = NULL, tr = NULL, Ndyns = NULL, Ntrans = NULL)Arguments
- mrs_data
mrs_data object for timing information.
+
+- tr +
repetition time.
+
+
+- Ndyns +
number of dynamic scans stored, potentially less than Ntrans +if block averaging has been performed.
+
+
+- Ntrans +
number of dynamic scans acquired.
+
Value
@@ -106,7 +119,7 @@Value
mrs_data object for timing information.
repetition time.
number of dynamic scans stored, potentially less than Ntrans +if block averaging has been performed.
number of dynamic scans acquired.
match the output to the input mrs_data.
+
+
+
+
+
+
+
+
+
+
+
+ Expand a regressor matrix for a group analysis.
+
+
+
+
+ gen_group_reg(regressor_df, n)
+
+
+ Arguments
+- regressor_df +
input regressor data frame.
+
+
+- n +
number of datasets n the group.
+
+
gen_impulse_reg(onset, trial_type = NULL, mrs_data = NULL)gen_impulse_reg(
+ onset,
+ trial_type = NULL,
+ mrs_data = NULL,
+ tr = NULL,
+ Ndyns = NULL,
+ Ntrans = NULL
+)Arguments
mrs_data object for timing information.
repetition time.
number of dynamic scans stored, potentially less than Ntrans +if block averaging has been performed.
number of dynamic scans acquired.
Value
@@ -114,7 +134,7 @@Value
gen_poly_reg(mrs_data, degree)gen_poly_reg(degree, mrs_data = NULL, tr = NULL, Ndyns = NULL, Ntrans = NULL)Arguments
-- mrs_data +
- degree +
the degree of the polynomial.
+
+
+- mrs_data
mrs_data object for timing information.
-- degree -
the degree of the polynomial.
+- tr +
repetition time.
+
+
+- Ndyns +
number of dynamic scans stored, potentially less than Ntrans +if block averaging has been performed.
+
+
+- Ntrans +
number of dynamic scans acquired.
Value
mrs_data object for timing information.
repetition time.
number of dynamic scans stored, potentially less than Ntrans +if block averaging has been performed.
number of dynamic scans acquired.
time to reach a plateau from baseline in seconds.
glm_spec(mrs_data, regressor_df)glm_spec(mrs_data, regressor_df, full_output = FALSE)Arguments
a data frame containing temporal regressors to be applied to each spectral datapoint.
append mrs_data and regressor_df to the output list.
Value
@@ -111,7 +115,7 @@Value
+
+
+
+
+
+
+
+
+
+
+ Perform first-level spectral GLM analysis of an fMRS dataset.
+ Source:R/fmrs.R
+ glm_spec_fmrs_fl.Rd
+
+
+ Perform first-level spectral GLM analysis of an fMRS dataset.
+
+
+
+
+
+
+
+ Arguments
+- regressor_df +
a data frame containing temporal regressors to be applied +to each spectral datapoint.
+
+
+- analysis_dir +
directory containing preprocessed data generated by +the preproc_svs_dataset function.
+
+
+- exclude_labels +
vector of labels of scans to exclude, eg poor quality +data.
+
+
+- labels +
labels to describe each data set.
+
+
+- xlim +
spectral range to include in the analysis.
+
+
+- vline +
vertical lines to add to the plot.
+
+
+- return_results +
function will return key outputs, defaults to FALSE.
+
+
+
+
+
+
+
+
+
+
+
+
+ Perform group-level spectral GLM analysis of an fMRS dataset.
+ Source:R/fmrs.R
+ glm_spec_fmrs_group.Rd
+
+
+ Perform group-level spectral GLM analysis of an fMRS dataset.
+
+
+
+
+ glm_spec_fmrs_group(
+ regressor_df,
+ analysis_dir = "spant_analysis",
+ exclude_labels = NULL,
+ labels = NULL
+)
+
+
+ Arguments
+- regressor_df +
a data frame containing temporal regressors to be applied +to each spectral datapoint.
+
+
+- analysis_dir +
directory containing preprocessed data generated by +the preproc_svs_dataset function.
+
+
+- exclude_labels +
vector of labels of scans to exclude, eg poor quality +data.
+
+
+- labels +
labels to describe each data set.
+
+
+
+
+
+
+
+
+
+
+
+
+ Test a group-level spectral GLM linear hypothesis.
+ Source:R/fmrs.R
+ glm_spec_group_linhyp.Rd
+
+
+ Test a group-level spectral GLM linear hypothesis.
+
+
+
+
+ glm_spec_group_linhyp(hmat, analysis_dir = "spant_analysis")
+
+
+ Arguments
+- hmat +
linear hypothesis matrix.
+
+
+- analysis_dir +
directory containing preprocessed data generated by +the preproc_svs_dataset function.
+
+
add a horizontal line at the specified value.
linetype for the horizontal line.
colour for the horizontal line.
draw a vertical line at the value of vline.
add a vertical line at the specified value.
draw a horizontal line at the value of hline.
linetype for the vertical line.
colour for the vertical line.
Complex rounding function taken from complexplus package to reduce the number -of spant dependencies.
Complex rounding function taken from complexplus package to reduce the number of spant dependencies.
All functions
- Return a list of options for an ABfit analysis to maintain comparability with
-analyses performed with version 1.9.0 (and earlier) of spant.
Return a list of options for an ABfit analysis to maintain comparability with analyses performed with version 1.9.0 (and earlier) of spant.
@@ -168,13 +166,11 @@ All functions
- Append MRS data across the coil dimension, assumes they matched across the
-other dimensions.
Append MRS data across the coil dimension, assumes they matched across the other dimensions.
- Append MRS data across the dynamic dimension, assumes they matched across the
-other dimensions.
Append MRS data across the dynamic dimension, assumes they matched across the other dimensions.
@@ -194,14 +190,11 @@ All functions
- Convert a 7 dimensional array in into a mrs_data object. The array dimensions
-should be ordered as : dummy, X, Y, Z, dynamic, coil, FID.
Convert a 7 dimensional array in into a mrs_data object. The array dimensions should be ordered as : dummy, X, Y, Z, dynamic, coil, FID.
- Perform zeroth-order phase correction based on the minimisation of the
-squared difference between the real and magnitude components of the
-spectrum.
Perform zeroth-order phase correction based on the minimisation of the squared difference between the real and magnitude components of the spectrum.
@@ -213,13 +206,11 @@ All functions
- Convert a basis object to an mrs_data object - where basis signals are spread
-across the dynamic dimension.
Convert a basis object to an mrs_data object - where basis signals are spread across the dynamic dimension.
- Generate a spline basis, slightly adapted from : "Splines, knots, and
-penalties", Eilers 2010.
Generate a spline basis, slightly adapted from : "Splines, knots, and penalties", Eilers 2010.
@@ -243,8 +234,7 @@ All functions
- Covert a beta value in the time-domain to an equivalent linewidth in Hz:
-x * exp(-i * t * t * beta).
Covert a beta value in the time-domain to an equivalent linewidth in Hz: x * exp(-i * t * t * beta).
@@ -272,8 +262,7 @@ All functions
- Perform a polynomial fit, subtract and return the standard deviation of the
-residuals.
Perform a polynomial fit, subtract and return the standard deviation of the residuals.
@@ -306,6 +295,14 @@ All functions comb_coils()
Combine coil data based on the first data point of a reference signal.
+
+
+ Combine MRSI coil data using the GLS method presented by An et al JMRI 37:1445-1450 (2013).
+
+
+ Combine SVS coil data using the GLS method presented by An et al JMRI 37:1445-1450 (2013).
@@ -345,9 +342,7 @@ All functions
- Crop mrs_data object data points in the time-domain rounding down to
-the next smallest power of two (pot). Data that already has a pot length will
-not be changed.
Crop mrs_data object data points in the time-domain rounding down to the next smallest power of two (pot). Data that already has a pot length will not be changed.
@@ -355,13 +350,11 @@ All functions
- Compute the vector cross product between vectors x and y. Adapted from
-http://stackoverflow.com/questions/15162741/what-is-rs-crossproduct-function
Compute the vector cross product between vectors x and y. Adapted from http://stackoverflow.com/questions/15162741/what-is-rs-crossproduct-function
- Decimate an MRS signal to half the original sampling frequency by filtering
-in the frequency domain before down sampling.
Decimate an MRS signal to half the original sampling frequency by filtering in the frequency domain before down sampling.
@@ -377,8 +370,7 @@ All functions
- Return (and optionally modify using the input arguments) a list of the
-default acquisition parameters.
Return (and optionally modify using the input arguments) a list of the default acquisition parameters.
@@ -410,14 +402,11 @@ All functions
- Downsample an MRS signal by a factor of 2 by removing every other data point
-in the time-domain. Note, signals outside the new sampling frequency will be
-aliased.
Downsample an MRS signal by a factor of 2 by removing every other data point in the time-domain. Note, signals outside the new sampling frequency will be aliased.
- Return a time scale vector of acquisition times for a dynamic MRS scan. The
-first temporal scan is assigned a value of 0.
Return a time scale vector of acquisition times for a dynamic MRS scan. The first temporal scan is assigned a value of 0.
@@ -429,8 +418,7 @@ All functions
- Estimate the standard deviation of the noise from a segment of an mrs_data
-object.
Estimate the standard deviation of the noise from a segment of an mrs_data object.
@@ -486,8 +474,7 @@ All functions
- Perform a zeroth order phase correction based on the phase of the first data
-point in the time-domain.
Perform a zeroth order phase correction based on the phase of the first data point in the time-domain.
@@ -507,8 +494,7 @@ All functions
- Perform a fft and fftshift on a matrix with each column replaced by its
-shifted fft.
Perform a fft and fftshift on a matrix with each column replaced by its shifted fft.
@@ -536,8 +522,11 @@ All functions
- Generate regressors by convolving a specified response function with a
-stimulus.
Generate regressors by convolving a specified response function with a stimulus.
+
+
+ Expand a regressor matrix for a group analysis.
@@ -553,28 +542,23 @@ All functions
- Return a character vector of common 1H molecules found in healthy human
-brain.
Return a character vector of common 1H molecules found in healthy human brain.
- Return a list of mol_parameter objects suitable for 1H brain MRS
-analyses.
Return a list of mol_parameter objects suitable for 1H brain MRS analyses.
- Return a list of mol_parameter objects suitable for 1H brain MRS
-analyses.
Return a list of mol_parameter objects suitable for 1H brain MRS analyses.
- Return a list of mol_parameter objects suitable for 1H brain MRS
-analyses.
Return a list of mol_parameter objects suitable for 1H brain MRS analyses.
- Return a list of mol_parameter objects suitable for 1H brain MRS
-analyses.
Return a list of mol_parameter objects suitable for 1H brain MRS analyses.
@@ -582,8 +566,7 @@ All functions
- Return a character vector of molecules included in the Gold Star Phantoms
-SPECTRE phantom.
Return a character vector of molecules included in the Gold Star Phantoms SPECTRE phantom.
@@ -635,8 +618,7 @@ All functions
- Return a character array of names that may be used with the
-get_mol_paras function.
Return a character array of names that may be used with the get_mol_paras function.
@@ -700,8 +682,7 @@ All functions
- Return an array of amplitudes derived from fitting the initial points in the
-time domain and extrapolating back to t=0.
Return an array of amplitudes derived from fitting the initial points in the time domain and extrapolating back to t=0.
@@ -709,8 +690,7 @@ All functions
- Generate a mol_parameters object for a simple spin system with one
-resonance.
Generate a mol_parameters object for a simple spin system with one resonance.
@@ -731,6 +711,18 @@ All functions glm_spec()
Perform a GLM analysis of dynamic MRS data in the spectral domain.
+
+
+ Perform first-level spectral GLM analysis of an fMRS dataset.
+
+
+ Perform group-level spectral GLM analysis of an fMRS dataset.
+
+
+ Test a group-level spectral GLM linear hypothesis.
@@ -766,8 +758,7 @@ All functions
- Perform an ifft and ifftshift on a matrix with each column replaced by its
-shifted ifft.
Perform an ifft and ifftshift on a matrix with each column replaced by its shifted ifft.
@@ -799,8 +790,7 @@ All functions
- Check if the chemical shift dimension of an MRS data object is in the
-frequency domain.
Check if the chemical shift dimension of an MRS data object is in the frequency domain.
@@ -820,18 +810,15 @@ All functions
- Covert a linewidth in Hz to an equivalent alpha value in the time-domain ie:
-x * exp(-t * alpha).
Covert a linewidth in Hz to an equivalent alpha value in the time-domain ie: x * exp(-t * alpha).
- Covert a linewidth in Hz to an equivalent beta value in the time-domain ie:
-x * exp(-t * t * beta).
Covert a linewidth in Hz to an equivalent beta value in the time-domain ie: x * exp(-t * t * beta).
- Make a basis-set object from a directory containing LCModel formatted RAW
-files.
Make a basis-set object from a directory containing LCModel formatted RAW files.
@@ -851,8 +838,7 @@ All functions
- Mask the voxels outside an elliptical region spanning the MRSI dataset in the
-x-y plane.
Mask the voxels outside an elliptical region spanning the MRSI dataset in the x-y plane.
@@ -860,13 +846,11 @@ All functions
- Convert a matrix (with spectral points in the column dimension and dynamics
-in the row dimensions) into a mrs_data object.
Convert a matrix (with spectral points in the column dimension and dynamics in the row dimensions) into a mrs_data object.
- Matrix exponential function taken from complexplus package to reduce the
-number of spant dependencies.
Matrix exponential function taken from complexplus package to reduce the number of spant dependencies.
@@ -914,31 +898,31 @@ All functions
- Convert an mrs_data object to basis object - where basis signals are spread
-across the dynamic dimension in the MRS data.
Convert an mrs_data object to basis object - where basis signals are spread across the dynamic dimension in the MRS data.
+
+
+ Create a BIDS file structure from a vector of MRS data paths or list of mrs_data objects.
- Convert mrs_data object to a matrix, with spectral points in the column
-dimension and dynamics in the row dimension.
Convert mrs_data object to a matrix, with spectral points in the column dimension and dynamics in the row dimension.
-
+
- Convert mrs_data object to a vector.
Convert mrs_data object to a matrix, with spectral points in the column dimension and dynamics in the row dimension.
-
+
- Create a BIDS directory and file structure from a list of mrs_data objects.
Convert mrs_data object to a vector.
- Perform a fftshift on a matrix, with each column replaced by its shifted
-result.
Perform a fftshift on a matrix, with each column replaced by its shifted result.
- Perform an ifftshift on a matrix, with each column replaced by its shifted
-result.
Perform an ifftshift on a matrix, with each column replaced by its shifted result.
@@ -946,9 +930,7 @@ All functions
- Flip the x data dimension order of a nifti image. This corresponds to
-flipping MRI data in the left-right direction, assuming the data in save in
-neurological format (can check with fslorient program).
Flip the x data dimension order of a nifti image. This corresponds to flipping MRI data in the left-right direction, assuming the data in save in neurological format (can check with fslorient program).
@@ -964,8 +946,7 @@ All functions
- Search for the highest peak in a spectral region and return the frequency,
-height and FWHM.
Search for the highest peak in a spectral region and return the frequency, height and FWHM.
@@ -974,6 +955,10 @@ All functions phase()
Apply phasing parameters to MRS data.
+
+
+ Corrected zero order phase and chemical shift offset in 1H MRS data from the brain.
@@ -1005,8 +990,7 @@ All functions
- Plot an interactive slice map from a data array where voxels can be selected
-to display a corresponding spectrum.
Plot an interactive slice map from a data array where voxels can be selected to display a corresponding spectrum.
@@ -1026,8 +1010,15 @@ All functions
- Save function results to file and load on subsequent calls to avoid repeat
-computation.
Save function results to file and load on subsequent calls to avoid repeat computation.
+
+
+ Preprocess and perform quality assessment of a single SVS data set.
+
+
+ Preprocess and perform quality assessment of one or more SVS data sets.
@@ -1055,15 +1046,11 @@ All functions
- Read a directory containing Siemens MRS IMA files and combine along the coil
-dimension. Note that the coil ID is inferred from the sorted file name and
-should be checked when consistency is required between two directories.
Read a directory containing Siemens MRS IMA files and combine along the coil dimension. Note that the coil ID is inferred from the sorted file name and should be checked when consistency is required between two directories.
- Read a directory containing Siemens MRS IMA files and combine along the
-dynamic dimension. Note that the coil ID is inferred from the sorted file
-name and should be checked when consistency is required.
Read a directory containing Siemens MRS IMA files and combine along the dynamic dimension. Note that the coil ID is inferred from the sorted file name and should be checked when consistency is required.
@@ -1103,13 +1090,11 @@ All functions
- Reconstruct complex time-domain data from the real part of frequency-domain
-data.
Reconstruct complex time-domain data from the real part of frequency-domain data.
- Reconstruct complex time-domain data from the real part of frequency-domain
-data.
Reconstruct complex time-domain data from the real part of frequency-domain data.
@@ -1141,8 +1126,7 @@ All functions
- Resample a VOI to match a target image space using nearest-neighbour
-interpolation.
Resample a VOI to match a target image space using nearest-neighbour interpolation.
@@ -1158,23 +1142,19 @@ All functions
- Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water).
Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / kg of tissue water).
- Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water).
Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / kg of tissue water).
- Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / Litre of tissue).
Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / Litre of tissue).
- Convert default LCM/TARQUIN concentration scaling to molal units with partial
-volume correction.
Convert default LCM/TARQUIN concentration scaling to molal units with partial volume correction.
@@ -1222,8 +1202,7 @@ All functions
- MEGA-PRESS sequence with ideal localisation pulses and Gaussian shaped
-editing pulse.
MEGA-PRESS sequence with ideal localisation pulses and Gaussian shaped editing pulse.
@@ -1251,13 +1230,11 @@ All functions
- STEAM sequence with ideal pulses and coherence order filtering to simulate
-gradient crushers.
STEAM sequence with ideal pulses and coherence order filtering to simulate gradient crushers.
- STEAM sequence with ideal pulses using the z-rotation gradient simulation
-method described by Young et al JMR 140, 146-152 (1999).
STEAM sequence with ideal pulses using the z-rotation gradient simulation method described by Young et al JMR 140, 146-152 (1999).
@@ -1293,8 +1270,7 @@ All functions
- Set the number of time-domain data points, truncating or zero-filling as
-appropriate.
Set the number of time-domain data points, truncating or zero-filling as appropriate.
@@ -1318,18 +1294,15 @@ All functions
- Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS
-sequence. Note, ideal pulses are assumed.
Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS sequence. Note, ideal pulses are assumed.
- Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS
-sequence. Note, ideal pulses are assumed.
Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS sequence. Note, ideal pulses are assumed.
- Simulate a macromolecular and lipid basis-set suitable for 1H brain MRS
-analysis.
Simulate a macromolecular and lipid basis-set suitable for 1H brain MRS analysis.
@@ -1353,8 +1326,7 @@ All functions
- Simulate an ideal pulse excitation profile by smoothing a top-hat function
-with a Gaussian.
Simulate an ideal pulse excitation profile by smoothing a top-hat function with a Gaussian.
@@ -1374,17 +1346,19 @@ All functions
- Simulate and fit some spectra with ABfit for benchmarking purposes. Basic
-timing and performance metrics will be printed.
Simulate and fit some spectra with ABfit for benchmarking purposes. Basic timing and performance metrics will be printed.
Example MEGA-PRESS data with significant B0 drift.
+
+
+ Simulate an example fMRS dataset for a block design fMRS experiment and export a BIDS structure.
- Simulate a typical metabolite basis set for benchmarking. Timing metrics will
-be printed on completion.
Simulate a typical metabolite basis set for benchmarking. Timing metrics will be printed on completion.
@@ -1400,8 +1374,7 @@ All functions
- Convert SPM style segmentation files to a single categorical image where
-the numerical values map as: 0) Other, 1) CSF, 2) GM and 3) WM.
Convert SPM style segmentation files to a single categorical image where the numerical values map as: 0) Other, 1) CSF, 2) GM and 3) WM.
@@ -1413,8 +1386,7 @@ All functions
- Plot the fitting results of an object of class fit_result with
-individual basis set components shown.
Plot the fitting results of an object of class fit_result with individual basis set components shown.
@@ -1459,6 +1431,10 @@ All functions svs_1h_brain_batch_analysis()
Batch interface to the standard SVS 1H brain analysis pipeline.
+
+
+ Perform a t-test on spectral data points.
@@ -1518,8 +1494,7 @@ All functions
- Fade a spectrum to zero by frequency domain multiplication with a tanh
-function. Note this operation distorts data points at the end of the FID.
Fade a spectrum to zero by frequency domain multiplication with a tanh function. Note this operation distorts data points at the end of the FID.
@@ -1549,7 +1524,7 @@ All functions
diff --git a/docs/reference/int_spec.html b/docs/reference/int_spec.html
index c7060fe7..783325a8 100644
--- a/docs/reference/int_spec.html
+++ b/docs/reference/int_spec.html
@@ -1,5 +1,5 @@
-Integrate a spectral region. — int_spec • Spectroscopy Analysis Tools (spant) Integrate a spectral region. — int_spec • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -118,7 +118,7 @@ Value
diff --git a/docs/reference/interleave_dyns.html b/docs/reference/interleave_dyns.html
index effe5543..441eff27 100644
--- a/docs/reference/interleave_dyns.html
+++ b/docs/reference/interleave_dyns.html
@@ -1,5 +1,5 @@
-Interleave the first and second half of a dynamic series. — interleave_dyns • Spectroscopy Analysis Tools (spant) Interleave the first and second half of a dynamic series. — interleave_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/inv_even_dyns.html b/docs/reference/inv_even_dyns.html
index 9f9d4fff..dcb781dc 100644
--- a/docs/reference/inv_even_dyns.html
+++ b/docs/reference/inv_even_dyns.html
@@ -1,5 +1,5 @@
-Invert even numbered dynamic scans starting from 1 (2,4,6...). — inv_even_dyns • Spectroscopy Analysis Tools (spant) Invert even numbered dynamic scans starting from 1 (2,4,6...). — inv_even_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/inv_odd_dyns.html b/docs/reference/inv_odd_dyns.html
index 26212e2b..78d64660 100644
--- a/docs/reference/inv_odd_dyns.html
+++ b/docs/reference/inv_odd_dyns.html
@@ -1,5 +1,5 @@
-Invert odd numbered dynamic scans starting from 1 (1,3,5...). — inv_odd_dyns • Spectroscopy Analysis Tools (spant) Invert odd numbered dynamic scans starting from 1 (1,3,5...). — inv_odd_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/is.def.html b/docs/reference/is.def.html
index f196ffd0..a67b9eba 100644
--- a/docs/reference/is.def.html
+++ b/docs/reference/is.def.html
@@ -1,5 +1,5 @@
-Check if an object is defined, which is the same as being not NULL. — is.def • Spectroscopy Analysis Tools (spant) Check if an object is defined, which is the same as being not NULL. — is.def • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/is_fd.html b/docs/reference/is_fd.html
index 3b0ca165..18a193aa 100644
--- a/docs/reference/is_fd.html
+++ b/docs/reference/is_fd.html
@@ -1,7 +1,5 @@
-Check if the chemical shift dimension of an MRS data object is in the
-frequency domain. — is_fd • Spectroscopy Analysis Tools (spant) Check if the chemical shift dimension of an MRS data object is in the frequency domain. — is_fd • Spectroscopy Analysis Tools (spant) Transform 2D MRSI data from k-space to image space in the x-y direction. — kspace2img_xy • Spectroscopy Analysis Tools (spant) Transform 2D MRSI data from k-space to image space in the x-y direction. — kspace2img_xy • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/l2_reg.html b/docs/reference/l2_reg.html
index 3d781d80..21aa9849 100644
--- a/docs/reference/l2_reg.html
+++ b/docs/reference/l2_reg.html
@@ -1,5 +1,5 @@
-Perform l2 regularisation artefact suppression. — l2_reg • Spectroscopy Analysis Tools (spant) Perform l2 regularisation artefact suppression. — l2_reg • Spectroscopy Analysis Tools (spant) Apply line-broadening (apodisation) to MRS data or basis object. — lb • Spectroscopy Analysis Tools (spant) Apply line-broadening (apodisation) to MRS data or basis object. — lb • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -123,7 +123,7 @@ Value
diff --git a/docs/reference/lofdc.html b/docs/reference/lofdc.html
index 5419b1ec..31347a25 100644
--- a/docs/reference/lofdc.html
+++ b/docs/reference/lofdc.html
@@ -1,5 +1,5 @@
-Correct linear frequency drift. — lofdc • Spectroscopy Analysis Tools (spant) Correct linear frequency drift. — lofdc • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -138,7 +138,7 @@ Value
diff --git a/docs/reference/lw2alpha.html b/docs/reference/lw2alpha.html
index b83db682..25da229b 100644
--- a/docs/reference/lw2alpha.html
+++ b/docs/reference/lw2alpha.html
@@ -1,7 +1,5 @@
-Covert a linewidth in Hz to an equivalent alpha value in the time-domain ie:
-x * exp(-t * alpha). — lw2alpha • Spectroscopy Analysis Tools (spant) Covert a linewidth in Hz to an equivalent alpha value in the time-domain ie: x * exp(-t * alpha). — lw2alpha • Spectroscopy Analysis Tools (spant) Covert a linewidth in Hz to an equivalent beta value in the time-domain ie:
-x * exp(-t * t * beta). — lw2beta • Spectroscopy Analysis Tools (spant) Covert a linewidth in Hz to an equivalent beta value in the time-domain ie: x * exp(-t * t * beta). — lw2beta • Spectroscopy Analysis Tools (spant) Make a basis-set object from a directory containing LCModel formatted RAW
-files. — make_basis_from_raw • Spectroscopy Analysis Tools (spant) Make a basis-set object from a directory containing LCModel formatted RAW files. — make_basis_from_raw • Spectroscopy Analysis Tools (spant) Mask an MRS dataset in the dynamic dimension. — mask_dyns • Spectroscopy Analysis Tools (spant) Mask an MRS dataset in the dynamic dimension. — mask_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/mask_fit_res.html b/docs/reference/mask_fit_res.html
index 97baaa3f..ebd91a99 100644
--- a/docs/reference/mask_fit_res.html
+++ b/docs/reference/mask_fit_res.html
@@ -1,5 +1,5 @@
-Mask fit result spectra depending on a vector of bool values. — mask_fit_res • Spectroscopy Analysis Tools (spant) Mask fit result spectra depending on a vector of bool values. — mask_fit_res • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -116,7 +116,7 @@ Value
diff --git a/docs/reference/mask_xy.html b/docs/reference/mask_xy.html
index 11bb577c..b0d38619 100644
--- a/docs/reference/mask_xy.html
+++ b/docs/reference/mask_xy.html
@@ -1,5 +1,5 @@
-Mask an MRSI dataset in the x-y direction — mask_xy • Spectroscopy Analysis Tools (spant) Mask an MRSI dataset in the x-y direction — mask_xy • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/mask_xy_corners.html b/docs/reference/mask_xy_corners.html
index 09b16cd2..2d13839d 100644
--- a/docs/reference/mask_xy_corners.html
+++ b/docs/reference/mask_xy_corners.html
@@ -1,5 +1,5 @@
-Mask the four corners of an MRSI dataset in the x-y plane. — mask_xy_corners • Spectroscopy Analysis Tools (spant) Mask the four corners of an MRSI dataset in the x-y plane. — mask_xy_corners • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/mask_xy_ellipse.html b/docs/reference/mask_xy_ellipse.html
index 1d8b02e4..e2e749ef 100644
--- a/docs/reference/mask_xy_ellipse.html
+++ b/docs/reference/mask_xy_ellipse.html
@@ -1,7 +1,5 @@
-Mask the voxels outside an elliptical region spanning the MRSI dataset in the
-x-y plane. — mask_xy_ellipse • Spectroscopy Analysis Tools (spant) Mask the voxels outside an elliptical region spanning the MRSI dataset in the x-y plane. — mask_xy_ellipse • Spectroscopy Analysis Tools (spant) Mask a 2D MRSI dataset in the x-y dimension. — mask_xy_mat • Spectroscopy Analysis Tools (spant) Mask a 2D MRSI dataset in the x-y dimension. — mask_xy_mat • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Value
diff --git a/docs/reference/mat2mrs_data.html b/docs/reference/mat2mrs_data.html
index 2e2895f3..ae55665f 100644
--- a/docs/reference/mat2mrs_data.html
+++ b/docs/reference/mat2mrs_data.html
@@ -1,7 +1,5 @@
-Convert a matrix (with spectral points in the column dimension and dynamics
-in the row dimensions) into a mrs_data object. — mat2mrs_data • Spectroscopy Analysis Tools (spant) Convert a matrix (with spectral points in the column dimension and dynamics in the row dimensions) into a mrs_data object. — mat2mrs_data • Spectroscopy Analysis Tools (spant) Matrix exponential function taken from complexplus package to reduce the
-number of spant dependencies. — matexp • Spectroscopy Analysis Tools (spant) Matrix exponential function taken from complexplus package to reduce the number of spant dependencies. — matexp • Spectroscopy Analysis Tools (spant) Apply the max operator to an MRS dataset. — max_mrs • Spectroscopy Analysis Tools (spant) Apply the max operator to an MRS dataset. — max_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/max_mrs_interp.html b/docs/reference/max_mrs_interp.html
index e4474764..52e63f3e 100644
--- a/docs/reference/max_mrs_interp.html
+++ b/docs/reference/max_mrs_interp.html
@@ -1,5 +1,5 @@
-Apply the max operator to an interpolated MRS dataset. — max_mrs_interp • Spectroscopy Analysis Tools (spant) Apply the max operator to an interpolated MRS dataset. — max_mrs_interp • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/mean.list.html b/docs/reference/mean.list.html
index b8eb3463..048306fd 100644
--- a/docs/reference/mean.list.html
+++ b/docs/reference/mean.list.html
@@ -1,5 +1,5 @@
-Calculate the mean spectrum from an mrs_data object. — mean.list • Spectroscopy Analysis Tools (spant) Calculate the mean spectrum from an mrs_data object. — mean.list • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/mean.mrs_data.html b/docs/reference/mean.mrs_data.html
index 5531a28d..79515014 100644
--- a/docs/reference/mean.mrs_data.html
+++ b/docs/reference/mean.mrs_data.html
@@ -1,5 +1,5 @@
-Calculate the mean spectrum from an mrs_data object. — mean.mrs_data • Spectroscopy Analysis Tools (spant) Calculate the mean spectrum from an mrs_data object. — mean.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/mean_dyn_blocks.html b/docs/reference/mean_dyn_blocks.html
index 10467098..4c042448 100644
--- a/docs/reference/mean_dyn_blocks.html
+++ b/docs/reference/mean_dyn_blocks.html
@@ -1,5 +1,5 @@
-Calculate the mean of adjacent dynamic scans. — mean_dyn_blocks • Spectroscopy Analysis Tools (spant) Calculate the mean of adjacent dynamic scans. — mean_dyn_blocks • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/mean_dyn_pairs.html b/docs/reference/mean_dyn_pairs.html
index 63e909ea..1a241126 100644
--- a/docs/reference/mean_dyn_pairs.html
+++ b/docs/reference/mean_dyn_pairs.html
@@ -1,5 +1,5 @@
-Calculate the pairwise means across a dynamic data set. — mean_dyn_pairs • Spectroscopy Analysis Tools (spant) Calculate the pairwise means across a dynamic data set. — mean_dyn_pairs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/mean_dyns.html b/docs/reference/mean_dyns.html
index 73fdbfa7..0daa27df 100644
--- a/docs/reference/mean_dyns.html
+++ b/docs/reference/mean_dyns.html
@@ -1,5 +1,5 @@
-Calculate the mean dynamic data. — mean_dyns • Spectroscopy Analysis Tools (spant) Calculate the mean dynamic data. — mean_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/mean_mrs_list.html b/docs/reference/mean_mrs_list.html
index 808b6c50..10d842c0 100644
--- a/docs/reference/mean_mrs_list.html
+++ b/docs/reference/mean_mrs_list.html
@@ -1,5 +1,5 @@
-Return the mean of a list of mrs_data objects. — mean_mrs_list • Spectroscopy Analysis Tools (spant) Return the mean of a list of mrs_data objects. — mean_mrs_list • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/mean_vec_blocks.html b/docs/reference/mean_vec_blocks.html
index 8fc92eaa..dd78b122 100644
--- a/docs/reference/mean_vec_blocks.html
+++ b/docs/reference/mean_vec_blocks.html
@@ -1,5 +1,5 @@
-Calculate the mean of adjacent blocks in a vector. — mean_vec_blocks • Spectroscopy Analysis Tools (spant) Calculate the mean of adjacent blocks in a vector. — mean_vec_blocks • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/median_dyns.html b/docs/reference/median_dyns.html
index 1039d4b5..9a085b10 100644
--- a/docs/reference/median_dyns.html
+++ b/docs/reference/median_dyns.html
@@ -1,5 +1,5 @@
-Calculate the median dynamic data. — median_dyns • Spectroscopy Analysis Tools (spant) Calculate the median dynamic data. — median_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/mod_td.html b/docs/reference/mod_td.html
index 76ad0a40..141ef09e 100644
--- a/docs/reference/mod_td.html
+++ b/docs/reference/mod_td.html
@@ -1,5 +1,5 @@
-Apply the Modulus operator to the time-domain MRS signal. — mod_td • Spectroscopy Analysis Tools (spant) Apply the Modulus operator to the time-domain MRS signal. — mod_td • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/mrs_data2basis.html b/docs/reference/mrs_data2basis.html
index 62f7d749..11797b91 100644
--- a/docs/reference/mrs_data2basis.html
+++ b/docs/reference/mrs_data2basis.html
@@ -1,7 +1,5 @@
-Convert an mrs_data object to basis object - where basis signals are spread
-across the dynamic dimension in the MRS data. — mrs_data2basis • Spectroscopy Analysis Tools (spant) Convert an mrs_data object to basis object - where basis signals are spread across the dynamic dimension in the MRS data. — mrs_data2basis • Spectroscopy Analysis Tools (spant) Create a BIDS file structure from a vector of MRS data paths or list of mrs_data objects. — mrs_data2bids • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Create a BIDS file structure from a vector of MRS data paths or list of mrs_data objects.
+ Source: R/fmrs.R
+ mrs_data2bids.Rd
+
+
+
+ Create a BIDS file structure from a vector of MRS data paths or list of
+mrs_data objects.
+
+
+
+ mrs_data2bids(
+ mrs_data,
+ output_dir,
+ suffix = NULL,
+ sub = NULL,
+ ses = NULL,
+ task = NULL,
+ acq = NULL,
+ nuc = NULL,
+ voi = NULL,
+ rec = NULL,
+ run = NULL,
+ echo = NULL,
+ inv = NULL,
+ skip_existing = TRUE
+)
+
+
+
+ Arguments
+ - mrs_data
+vector of MRS data paths or list of mrs_data objects.
- output_dir
+the base directory to create the BIDS structure.
- suffix
+optional vector of file suffixes. Default behaviour is to
+automatically determine these from the input data, however it is recommended
+that they are specified to allow more efficient skipping of existing data.
- sub
+optional vector of subject labels. If not specified, these will be
+automatically generated as a series of increasing zero-padded integer values
+corresponding to the mrs_data input indices.
- ses
+optional vector of session labels.
- task
+optional vector of task labels.
- acq
+optional vector of acquisition labels.
- nuc
+optional vector of nucleus labels.
- voi
+optional vector of volume of interest labels.
- rec
+optional vector of reconstruction labels.
- run
+optional vector of run indices.
- echo
+optional vector of echo time indices.
- inv
+optional vector of inversion indices.
- skip_existing
+skip any data files that have already been converted.
+Defaults to TRUE, set to FALSE to force an overwrite of any existing data
+files.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/mrs_data2mat.html b/docs/reference/mrs_data2mat.html
index cf5ff28c..9e47688a 100644
--- a/docs/reference/mrs_data2mat.html
+++ b/docs/reference/mrs_data2mat.html
@@ -1,7 +1,5 @@
-Convert mrs_data object to a matrix, with spectral points in the column
-dimension and dynamics in the row dimension. — mrs_data2mat • Spectroscopy Analysis Tools (spant) Convert mrs_data object to a matrix, with spectral points in the column dimension and dynamics in the row dimension. — mrs_data2mat • Spectroscopy Analysis Tools (spant) Convert mrs_data object to a matrix, with spectral points in the column dimension and dynamics in the row dimension. — mrs_data2spec_mat • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Convert mrs_data object to a matrix, with spectral points in the column dimension and dynamics in the row dimension.
+ Source: R/mrs_data_proc.R
+ mrs_data2spec_mat.Rd
+
+
+
+ Convert mrs_data object to a matrix, with spectral points in the column
+dimension and dynamics in the row dimension.
+
+
+
+ mrs_data2spec_mat(mrs_data, collapse = TRUE)
+
+
+
+ Arguments
+ - mrs_data
+MRS data object or list of MRS data objects.
- collapse
+collapse all other dimensions along the dynamic dimension, eg
+a 16x16 MRSI grid would be first collapsed across 256 dynamic scans.
+
+ Value
+
+
+MRS data matrix.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/mrs_data2vec.html b/docs/reference/mrs_data2vec.html
index fb172d68..a1fd654d 100644
--- a/docs/reference/mrs_data2vec.html
+++ b/docs/reference/mrs_data2vec.html
@@ -1,5 +1,5 @@
-Convert mrs_data object to a vector. — mrs_data2vec • Spectroscopy Analysis Tools (spant) Convert mrs_data object to a vector. — mrs_data2vec • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -126,7 +126,7 @@ Value
diff --git a/docs/reference/mvfftshift.html b/docs/reference/mvfftshift.html
index 92b0841b..976b3410 100644
--- a/docs/reference/mvfftshift.html
+++ b/docs/reference/mvfftshift.html
@@ -1,7 +1,5 @@
-Perform a fftshift on a matrix, with each column replaced by its shifted
-result. — mvfftshift • Spectroscopy Analysis Tools (spant) Perform a fftshift on a matrix, with each column replaced by its shifted result. — mvfftshift • Spectroscopy Analysis Tools (spant) Perform an ifftshift on a matrix, with each column replaced by its shifted
-result. — mvifftshift • Spectroscopy Analysis Tools (spant) Perform an ifftshift on a matrix, with each column replaced by its shifted result. — mvifftshift • Spectroscopy Analysis Tools (spant) Print fit coordinates from a single index. — n2coord • Spectroscopy Analysis Tools (spant) Print fit coordinates from a single index. — n2coord • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/nifti_flip_lr.html b/docs/reference/nifti_flip_lr.html
index 730abe3c..19860b3c 100644
--- a/docs/reference/nifti_flip_lr.html
+++ b/docs/reference/nifti_flip_lr.html
@@ -1,9 +1,5 @@
-Flip the x data dimension order of a nifti image. This corresponds to
-flipping MRI data in the left-right direction, assuming the data in save in
-neurological format (can check with fslorient program). — nifti_flip_lr • Spectroscopy Analysis Tools (spant) Flip the x data dimension order of a nifti image. This corresponds to flipping MRI data in the left-right direction, assuming the data in save in neurological format (can check with fslorient program). — nifti_flip_lr • Spectroscopy Analysis Tools (spant) Export a one-page pdf of a single fit result — one_page_pdf • Spectroscopy Analysis Tools (spant) Export a one-page pdf of a single fit result — one_page_pdf • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -108,7 +108,7 @@ Arguments
diff --git a/docs/reference/ortho3.html b/docs/reference/ortho3.html
index 13ade97d..5d7dd2fd 100644
--- a/docs/reference/ortho3.html
+++ b/docs/reference/ortho3.html
@@ -1,5 +1,5 @@
-Display an orthographic projection plot of a nifti object. — ortho3 • Spectroscopy Analysis Tools (spant) Display an orthographic projection plot of a nifti object. — ortho3 • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -172,7 +172,7 @@ Arguments
diff --git a/docs/reference/ortho3_inter.html b/docs/reference/ortho3_inter.html
index 090cc5e5..15948899 100644
--- a/docs/reference/ortho3_inter.html
+++ b/docs/reference/ortho3_inter.html
@@ -1,5 +1,5 @@
-Display an interactive orthographic projection plot of a nifti object. — ortho3_inter • Spectroscopy Analysis Tools (spant) Display an interactive orthographic projection plot of a nifti object. — ortho3_inter • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -132,7 +132,7 @@ Arguments
diff --git a/docs/reference/peak_info.html b/docs/reference/peak_info.html
index 09058bd8..41c8ffaf 100644
--- a/docs/reference/peak_info.html
+++ b/docs/reference/peak_info.html
@@ -1,7 +1,5 @@
-Search for the highest peak in a spectral region and return the frequency,
-height and FWHM. — peak_info • Spectroscopy Analysis Tools (spant) Search for the highest peak in a spectral region and return the frequency, height and FWHM. — peak_info • Spectroscopy Analysis Tools (spant) Papoulis-Gerchberg (PG) algorithm method for k-space extrapolation. — pg_extrap_xy • Spectroscopy Analysis Tools (spant) Papoulis-Gerchberg (PG) algorithm method for k-space extrapolation. — pg_extrap_xy • Spectroscopy Analysis Tools (spant) Apply phasing parameters to MRS data. — phase • Spectroscopy Analysis Tools (spant) Apply phasing parameters to MRS data. — phase • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/phase_ref_1h_brain.html b/docs/reference/phase_ref_1h_brain.html
new file mode 100644
index 00000000..8707a74a
--- /dev/null
+++ b/docs/reference/phase_ref_1h_brain.html
@@ -0,0 +1,131 @@
+
+Corrected zero order phase and chemical shift offset in 1H MRS data from the brain. — phase_ref_1h_brain • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Corrected zero order phase and chemical shift offset in 1H MRS data from the brain.
+ Source: R/rats.R
+ phase_ref_1h_brain.Rd
+
+
+
+ Corrected zero order phase and chemical shift offset in 1H MRS data from the
+brain.
+
+
+
+ phase_ref_1h_brain(mrs_data, mean_ref = FALSE, ret_corr_only = TRUE)
+
+
+
+ Arguments
+ - mrs_data
+MRS data to be corrected.
- mean_ref
+apply the phase and offset of the mean spectrum to all
+others. Default is FALSE.
- ret_corr_only
+return the corrected data only.
+
+ Value
+
+
+corrected MRS data.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/plot.fit_result.html b/docs/reference/plot.fit_result.html
index e54d3bc1..836a53ee 100644
--- a/docs/reference/plot.fit_result.html
+++ b/docs/reference/plot.fit_result.html
@@ -1,5 +1,5 @@
-Plot the fitting results of an object of class fit_result. — plot.fit_result • Spectroscopy Analysis Tools (spant) Plot the fitting results of an object of class fit_result. — plot.fit_result • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -207,7 +207,7 @@ Arguments
diff --git a/docs/reference/plot.mrs_data.html b/docs/reference/plot.mrs_data.html
index fabcc35b..bb2ec651 100644
--- a/docs/reference/plot.mrs_data.html
+++ b/docs/reference/plot.mrs_data.html
@@ -1,5 +1,5 @@
-Plotting method for objects of class mrs_data. — plot.mrs_data • Spectroscopy Analysis Tools (spant) Plotting method for objects of class mrs_data. — plot.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -287,7 +287,7 @@ Arguments
diff --git a/docs/reference/plot_bc.html b/docs/reference/plot_bc.html
index 4f8309b4..b48142cc 100644
--- a/docs/reference/plot_bc.html
+++ b/docs/reference/plot_bc.html
@@ -1,5 +1,5 @@
-Convenience function to plot a baseline estimate with the original data. — plot_bc • Spectroscopy Analysis Tools (spant) Convenience function to plot a baseline estimate with the original data. — plot_bc • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -108,7 +108,7 @@ Arguments
diff --git a/docs/reference/plot_reg.html b/docs/reference/plot_reg.html
index ae1acbe7..2addb2f6 100644
--- a/docs/reference/plot_reg.html
+++ b/docs/reference/plot_reg.html
@@ -1,5 +1,5 @@
-Plot regressors as an image. — plot_reg • Spectroscopy Analysis Tools (spant) Plot regressors as an image. — plot_reg • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/plot_slice_fit.html b/docs/reference/plot_slice_fit.html
index fbc7b560..57f1af8a 100644
--- a/docs/reference/plot_slice_fit.html
+++ b/docs/reference/plot_slice_fit.html
@@ -1,5 +1,5 @@
-Plot a 2D slice from an MRSI fit result object. — plot_slice_fit • Spectroscopy Analysis Tools (spant) Plot a 2D slice from an MRSI fit result object. — plot_slice_fit • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -129,7 +129,7 @@ Arguments
diff --git a/docs/reference/plot_slice_fit_inter.html b/docs/reference/plot_slice_fit_inter.html
index 4eed104a..da105a7d 100644
--- a/docs/reference/plot_slice_fit_inter.html
+++ b/docs/reference/plot_slice_fit_inter.html
@@ -1,5 +1,5 @@
-Plot a 2D slice from an MRSI fit result object. — plot_slice_fit_inter • Spectroscopy Analysis Tools (spant) Plot a 2D slice from an MRSI fit result object. — plot_slice_fit_inter • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -134,7 +134,7 @@ Arguments
diff --git a/docs/reference/plot_slice_map.html b/docs/reference/plot_slice_map.html
index 553e9ac8..ffb2a134 100644
--- a/docs/reference/plot_slice_map.html
+++ b/docs/reference/plot_slice_map.html
@@ -1,5 +1,5 @@
-Plot a slice from a 7 dimensional array. — plot_slice_map • Spectroscopy Analysis Tools (spant) Plot a slice from a 7 dimensional array. — plot_slice_map • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -153,7 +153,7 @@ Arguments
diff --git a/docs/reference/plot_slice_map_inter.html b/docs/reference/plot_slice_map_inter.html
index 40d33b42..90968f66 100644
--- a/docs/reference/plot_slice_map_inter.html
+++ b/docs/reference/plot_slice_map_inter.html
@@ -1,7 +1,5 @@
-Plot an interactive slice map from a data array where voxels can be selected
-to display a corresponding spectrum. — plot_slice_map_inter • Spectroscopy Analysis Tools (spant) Plot an interactive slice map from a data array where voxels can be selected to display a corresponding spectrum. — plot_slice_map_inter • Spectroscopy Analysis Tools (spant) Plot the spectral standard deviation. — plot_spec_sd • Spectroscopy Analysis Tools (spant) Plot the spectral standard deviation. — plot_spec_sd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Arguments
diff --git a/docs/reference/plot_voi_overlay.html b/docs/reference/plot_voi_overlay.html
index 9a782e88..bbbbf35e 100644
--- a/docs/reference/plot_voi_overlay.html
+++ b/docs/reference/plot_voi_overlay.html
@@ -1,5 +1,5 @@
-Plot a volume as an image overlay. — plot_voi_overlay • Spectroscopy Analysis Tools (spant) Plot a volume as an image overlay. — plot_voi_overlay • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -116,7 +116,7 @@ Arguments
diff --git a/docs/reference/plot_voi_overlay_seg.html b/docs/reference/plot_voi_overlay_seg.html
index 3d4e74ff..0e800ff2 100644
--- a/docs/reference/plot_voi_overlay_seg.html
+++ b/docs/reference/plot_voi_overlay_seg.html
@@ -1,5 +1,5 @@
-Plot a volume as an overlay on a segmented brain volume. — plot_voi_overlay_seg • Spectroscopy Analysis Tools (spant) Plot a volume as an overlay on a segmented brain volume. — plot_voi_overlay_seg • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Arguments
diff --git a/docs/reference/ppm.html b/docs/reference/ppm.html
index c352327a..ee4696e2 100644
--- a/docs/reference/ppm.html
+++ b/docs/reference/ppm.html
@@ -1,5 +1,5 @@
-Return the ppm scale of an MRS dataset or fit result. — ppm • Spectroscopy Analysis Tools (spant) Return the ppm scale of an MRS dataset or fit result. — ppm • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -132,7 +132,7 @@ Value
diff --git a/docs/reference/precomp.html b/docs/reference/precomp.html
index 822d7336..df3d2c6c 100644
--- a/docs/reference/precomp.html
+++ b/docs/reference/precomp.html
@@ -1,7 +1,5 @@
-Save function results to file and load on subsequent calls to avoid repeat
-computation. — precomp • Spectroscopy Analysis Tools (spant) Save function results to file and load on subsequent calls to avoid repeat computation. — precomp • Spectroscopy Analysis Tools (spant) Preprocess and perform quality assessment of a single SVS data set. — preproc_svs • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Preprocess and perform quality assessment of a single SVS data set.
+ Source: R/fmrs.R
+ preproc_svs.Rd
+
+
+
+ Preprocess and perform quality assessment of a single SVS data set.
+
+
+
+ preproc_svs(path, label = NULL, output_dir = NULL, ref_inds = NULL)
+
+
+
+ Arguments
+ - path
+path to the fMRS data file or IMA directory.
- label
+a label to describe the data set.
- output_dir
+output directory.
- ref_inds
+a vector of 1-based indices for any water reference dynamic
+scans.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/preproc_svs_dataset.html b/docs/reference/preproc_svs_dataset.html
new file mode 100644
index 00000000..07c3a29b
--- /dev/null
+++ b/docs/reference/preproc_svs_dataset.html
@@ -0,0 +1,148 @@
+
+Preprocess and perform quality assessment of one or more SVS data sets. — preproc_svs_dataset • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Preprocess and perform quality assessment of one or more SVS data sets.
+ Source: R/fmrs.R
+ preproc_svs_dataset.Rd
+
+
+
+ Preprocess and perform quality assessment of one or more SVS data sets.
+
+
+
+ preproc_svs_dataset(
+ paths,
+ labels = NULL,
+ output_dir = "spant_analysis",
+ exclude_labels = NULL,
+ overwrite = FALSE,
+ ref_inds = NULL,
+ return_results = FALSE
+)
+
+
+
+ Arguments
+ - paths
+paths to the fMRS data file or IMA directory.
- labels
+labels to describe each data set.
- output_dir
+output directory.
- exclude_labels
+vector of labels of scans to exclude, eg poor quality
+data.
- overwrite
+overwrite saved results, defaults to FALSE.
- ref_inds
+a vector of 1-based indices for any water reference dynamic
+scans.
- return_results
+function will return key outputs, defaults to FALSE.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/print.fit_result.html b/docs/reference/print.fit_result.html
index 297f28dc..5f434e57 100644
--- a/docs/reference/print.fit_result.html
+++ b/docs/reference/print.fit_result.html
@@ -1,5 +1,5 @@
-Print a summary of an object of class fit_result. — print.fit_result • Spectroscopy Analysis Tools (spant) Print a summary of an object of class fit_result. — print.fit_result • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -105,7 +105,7 @@ Arguments
diff --git a/docs/reference/print.mrs_data.html b/docs/reference/print.mrs_data.html
index 51199017..e1561eb2 100644
--- a/docs/reference/print.mrs_data.html
+++ b/docs/reference/print.mrs_data.html
@@ -1,5 +1,5 @@
-Print a summary of mrs_data parameters. — print.mrs_data • Spectroscopy Analysis Tools (spant) Print a summary of mrs_data parameters. — print.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -109,7 +109,7 @@ Arguments
diff --git a/docs/reference/qn_states.html b/docs/reference/qn_states.html
index 0f42f2f9..d7aa6715 100644
--- a/docs/reference/qn_states.html
+++ b/docs/reference/qn_states.html
@@ -1,5 +1,5 @@
-Get the quantum coherence matrix for a spin system. — qn_states • Spectroscopy Analysis Tools (spant) Get the quantum coherence matrix for a spin system. — qn_states • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/rats.html b/docs/reference/rats.html
index 5a39a396..93585e08 100644
--- a/docs/reference/rats.html
+++ b/docs/reference/rats.html
@@ -1,5 +1,5 @@
-Robust Alignment to a Target Spectrum (RATS). — rats • Spectroscopy Analysis Tools (spant) Robust Alignment to a Target Spectrum (RATS). — rats • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -207,7 +207,7 @@ Value
diff --git a/docs/reference/re_weighting.html b/docs/reference/re_weighting.html
index d21caf21..8b0b070a 100644
--- a/docs/reference/re_weighting.html
+++ b/docs/reference/re_weighting.html
@@ -1,5 +1,5 @@
-Apply a weighting to the FID to enhance spectral resolution. — re_weighting • Spectroscopy Analysis Tools (spant) Apply a weighting to the FID to enhance spectral resolution. — re_weighting • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/read_basis.html b/docs/reference/read_basis.html
index da9b94af..eb6f8557 100644
--- a/docs/reference/read_basis.html
+++ b/docs/reference/read_basis.html
@@ -1,5 +1,5 @@
-Read a basis file in LCModel .basis format. — read_basis • Spectroscopy Analysis Tools (spant) Read a basis file in LCModel .basis format. — read_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/read_ima_coil_dir.html b/docs/reference/read_ima_coil_dir.html
index 28c02de0..4f073cd8 100644
--- a/docs/reference/read_ima_coil_dir.html
+++ b/docs/reference/read_ima_coil_dir.html
@@ -1,9 +1,5 @@
-Read a directory containing Siemens MRS IMA files and combine along the coil
-dimension. Note that the coil ID is inferred from the sorted file name and
-should be checked when consistency is required between two directories. — read_ima_coil_dir • Spectroscopy Analysis Tools (spant) Read a directory containing Siemens MRS IMA files and combine along the coil dimension. Note that the coil ID is inferred from the sorted file name and should be checked when consistency is required between two directories. — read_ima_coil_dir • Spectroscopy Analysis Tools (spant) Read a directory containing Siemens MRS IMA files and combine along the
-dynamic dimension. Note that the coil ID is inferred from the sorted file
-name and should be checked when consistency is required. — read_ima_dyn_dir • Spectroscopy Analysis Tools (spant) Read a directory containing Siemens MRS IMA files and combine along the dynamic dimension. Note that the coil ID is inferred from the sorted file name and should be checked when consistency is required. — read_ima_dyn_dir • Spectroscopy Analysis Tools (spant) Read an LCModel formatted coord file containing fit information. — read_lcm_coord • Spectroscopy Analysis Tools (spant) Read an LCModel formatted coord file containing fit information. — read_lcm_coord • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -107,7 +107,7 @@ Value
diff --git a/docs/reference/read_mrs.html b/docs/reference/read_mrs.html
index 3ac2a36b..2cf36b20 100644
--- a/docs/reference/read_mrs.html
+++ b/docs/reference/read_mrs.html
@@ -1,5 +1,5 @@
-Read MRS data from a file. — read_mrs • Spectroscopy Analysis Tools (spant) Read MRS data from a file. — read_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -88,7 +88,8 @@ Read MRS data from a file.
full_fid = FALSE,
omit_svs_ref_scans = TRUE,
verbose = FALSE,
- extra = NULL
+ extra = NULL,
+ fid_filt_dist = NULL
)
@@ -140,6 +141,13 @@ Arguments
an optional data frame to provide additional variables for use
in subsequent analysis steps, eg id or grouping variables.
fid_filt_dist
+indicate if the data has a distorted FID due to a
+brick-wall filter being used to downsample the data. Default is to auto
+detect this from the data, but TRUE or FALSE options can be given to override
+detection.
Value
@@ -183,7 +191,7 @@ Examples
diff --git a/docs/reference/read_mrs_tqn.html b/docs/reference/read_mrs_tqn.html
index 5766362f..84bdaf3a 100644
--- a/docs/reference/read_mrs_tqn.html
+++ b/docs/reference/read_mrs_tqn.html
@@ -1,5 +1,5 @@
-Read MRS data using the TARQUIN software package. — read_mrs_tqn • Spectroscopy Analysis Tools (spant) Read MRS data using the TARQUIN software package. — read_mrs_tqn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -131,7 +131,7 @@ Examples
diff --git a/docs/reference/read_pulse_ascii.html b/docs/reference/read_pulse_ascii.html
index c9e0d43c..ab11c9cc 100644
--- a/docs/reference/read_pulse_ascii.html
+++ b/docs/reference/read_pulse_ascii.html
@@ -1,5 +1,5 @@
-Read an ASCII formatted pulse file. — read_pulse_ascii • Spectroscopy Analysis Tools (spant) Read an ASCII formatted pulse file. — read_pulse_ascii • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/read_pulse_bruker.html b/docs/reference/read_pulse_bruker.html
index c92bf76a..dbe9073b 100644
--- a/docs/reference/read_pulse_bruker.html
+++ b/docs/reference/read_pulse_bruker.html
@@ -1,5 +1,5 @@
-Read a Bruker formatted pulse file — read_pulse_bruker • Spectroscopy Analysis Tools (spant) Read a Bruker formatted pulse file — read_pulse_bruker • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/read_pulse_pta.html b/docs/reference/read_pulse_pta.html
index 72e1b6d4..a0fac3c3 100644
--- a/docs/reference/read_pulse_pta.html
+++ b/docs/reference/read_pulse_pta.html
@@ -1,5 +1,5 @@
-Read a .pta formatted pulse file compatible with Siemens PulseTool. — read_pulse_pta • Spectroscopy Analysis Tools (spant) Read a .pta formatted pulse file compatible with Siemens PulseTool. — read_pulse_pta • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/read_siemens_txt_hdr.html b/docs/reference/read_siemens_txt_hdr.html
index 23fb8c70..3a17d87c 100644
--- a/docs/reference/read_siemens_txt_hdr.html
+++ b/docs/reference/read_siemens_txt_hdr.html
@@ -1,5 +1,5 @@
-Read the text format header found in Siemens IMA and TWIX data files. — read_siemens_txt_hdr • Spectroscopy Analysis Tools (spant) Read the text format header found in Siemens IMA and TWIX data files. — read_siemens_txt_hdr • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -78,7 +78,7 @@ Read the text format header found in Siemens IMA and TWIX data files.
- read_siemens_txt_hdr(input, version = "vd", verbose, offset = 0)
+ read_siemens_txt_hdr(input, version = "vd", verbose = FALSE, offset = 0)
@@ -118,7 +118,7 @@ Value
diff --git a/docs/reference/read_tqn_fit.html b/docs/reference/read_tqn_fit.html
index 4da6c25e..a1630420 100644
--- a/docs/reference/read_tqn_fit.html
+++ b/docs/reference/read_tqn_fit.html
@@ -1,5 +1,5 @@
-Reader for csv fit results generated by TARQUIN. — read_tqn_fit • Spectroscopy Analysis Tools (spant) Reader for csv fit results generated by TARQUIN. — read_tqn_fit • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -113,7 +113,7 @@ Examples
diff --git a/docs/reference/read_tqn_result.html b/docs/reference/read_tqn_result.html
index 36659714..68a3e98c 100644
--- a/docs/reference/read_tqn_result.html
+++ b/docs/reference/read_tqn_result.html
@@ -1,5 +1,5 @@
-Reader for csv results generated by TARQUIN. — read_tqn_result • Spectroscopy Analysis Tools (spant) Reader for csv results generated by TARQUIN. — read_tqn_result • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -117,7 +117,7 @@ Examples
diff --git a/docs/reference/recon_imag.html b/docs/reference/recon_imag.html
index d2a72225..5bc3b1eb 100644
--- a/docs/reference/recon_imag.html
+++ b/docs/reference/recon_imag.html
@@ -1,7 +1,5 @@
-Reconstruct complex time-domain data from the real part of frequency-domain
-data. — recon_imag • Spectroscopy Analysis Tools (spant) Reconstruct complex time-domain data from the real part of frequency-domain data. — recon_imag • Spectroscopy Analysis Tools (spant) Reconstruct complex time-domain data from the real part of frequency-domain
-data. — recon_imag_vec • Spectroscopy Analysis Tools (spant) Reconstruct complex time-domain data from the real part of frequency-domain data. — recon_imag_vec • Spectroscopy Analysis Tools (spant) Reconstruct 2D MRSI data from a twix file loaded with read_mrs. — recon_twix_2d_mrsi • Spectroscopy Analysis Tools (spant) Reconstruct 2D MRSI data from a twix file loaded with read_mrs. — recon_twix_2d_mrsi • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/rectangular_mask.html b/docs/reference/rectangular_mask.html
index a2117283..6e469bc9 100644
--- a/docs/reference/rectangular_mask.html
+++ b/docs/reference/rectangular_mask.html
@@ -1,5 +1,5 @@
-Create a rectangular mask stored as a matrix of logical values. — rectangular_mask • Spectroscopy Analysis Tools (spant) Create a rectangular mask stored as a matrix of logical values. — rectangular_mask • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -130,7 +130,7 @@ Value
diff --git a/docs/reference/reexports.html b/docs/reference/reexports.html
index 694a75d1..a59e8379 100644
--- a/docs/reference/reexports.html
+++ b/docs/reference/reexports.html
@@ -1,5 +1,5 @@
-Objects exported from other packages — reexports • Spectroscopy Analysis Tools (spant) Objects exported from other packages — reexports • Spectroscopy Analysis Tools (spant)
Spectroscopy Analysis Tools (spant)
- 2.21.0
+ 2.22.0
@@ -103,7 +103,7 @@ Objects exported from other packages
diff --git a/docs/reference/rep_array_dim.html b/docs/reference/rep_array_dim.html
index b9c49b4a..48c0a5ed 100644
--- a/docs/reference/rep_array_dim.html
+++ b/docs/reference/rep_array_dim.html
@@ -1,5 +1,5 @@
-Repeat an array over a given dimension. — rep_array_dim • Spectroscopy Analysis Tools (spant) Repeat an array over a given dimension. — rep_array_dim • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/rep_dyn.html b/docs/reference/rep_dyn.html
index 6bbfb0ef..89a4bb9b 100644
--- a/docs/reference/rep_dyn.html
+++ b/docs/reference/rep_dyn.html
@@ -1,5 +1,5 @@
-Replicate a scan in the dynamic dimension. — rep_dyn • Spectroscopy Analysis Tools (spant) Replicate a scan in the dynamic dimension. — rep_dyn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/rep_mrs.html b/docs/reference/rep_mrs.html
index 67730b5c..becb8f00 100644
--- a/docs/reference/rep_mrs.html
+++ b/docs/reference/rep_mrs.html
@@ -1,5 +1,5 @@
-Replicate a scan over a given dimension. — rep_mrs • Spectroscopy Analysis Tools (spant) Replicate a scan over a given dimension. — rep_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -138,7 +138,7 @@ Value
diff --git a/docs/reference/resample_basis.html b/docs/reference/resample_basis.html
index b0f2ab17..c7a6222a 100644
--- a/docs/reference/resample_basis.html
+++ b/docs/reference/resample_basis.html
@@ -1,5 +1,5 @@
-Resample a basis-set to match a mrs_data acquisition. — resample_basis • Spectroscopy Analysis Tools (spant) Resample a basis-set to match a mrs_data acquisition. — resample_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -116,7 +116,7 @@ Value
diff --git a/docs/reference/resample_img.html b/docs/reference/resample_img.html
index f1e7beaf..b0cc8f71 100644
--- a/docs/reference/resample_img.html
+++ b/docs/reference/resample_img.html
@@ -1,5 +1,5 @@
-Resample an image to match a target image space. — resample_img • Spectroscopy Analysis Tools (spant) Resample an image to match a target image space. — resample_img • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/resample_voi.html b/docs/reference/resample_voi.html
index 8fbfa836..a29ab096 100644
--- a/docs/reference/resample_voi.html
+++ b/docs/reference/resample_voi.html
@@ -1,7 +1,5 @@
-Resample a VOI to match a target image space using nearest-neighbour
-interpolation. — resample_voi • Spectroscopy Analysis Tools (spant) Resample a VOI to match a target image space using nearest-neighbour interpolation. — resample_voi • Spectroscopy Analysis Tools (spant) Reslice a nifti object to match the orientation of mrs data. — reslice_to_mrs • Spectroscopy Analysis Tools (spant) Reslice a nifti object to match the orientation of mrs data. — reslice_to_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/reson_table2mrs_data.html b/docs/reference/reson_table2mrs_data.html
index d75579ee..c5a2167a 100644
--- a/docs/reference/reson_table2mrs_data.html
+++ b/docs/reference/reson_table2mrs_data.html
@@ -1,5 +1,5 @@
-Generate mrs_data from a table of single Lorentzian resonances. — reson_table2mrs_data • Spectroscopy Analysis Tools (spant) Generate mrs_data from a table of single Lorentzian resonances. — reson_table2mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -119,7 +119,7 @@ Value
diff --git a/docs/reference/rm_dyns.html b/docs/reference/rm_dyns.html
index 5d5ef692..573e1f51 100644
--- a/docs/reference/rm_dyns.html
+++ b/docs/reference/rm_dyns.html
@@ -1,5 +1,5 @@
-Remove a subset of dynamic scans. — rm_dyns • Spectroscopy Analysis Tools (spant) Remove a subset of dynamic scans. — rm_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/scale_amp_molal.html b/docs/reference/scale_amp_molal.html
index aaeee1f2..7acb8cb0 100644
--- a/docs/reference/scale_amp_molal.html
+++ b/docs/reference/scale_amp_molal.html
@@ -1,7 +1,5 @@
-Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water). — scale_amp_molal • Spectroscopy Analysis Tools (spant) Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / kg of tissue water). — scale_amp_molal • Spectroscopy Analysis Tools (spant)
Spectroscopy Analysis Tools (spant)
- 2.21.0
+ 2.22.0
@@ -76,8 +74,7 @@
- Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water).
+ Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / kg of tissue water).
Source: R/amp_scaling.R
scale_amp_molal.Rd
@@ -163,7 +160,7 @@ Value
diff --git a/docs/reference/scale_amp_molal_pvc.html b/docs/reference/scale_amp_molal_pvc.html
index 962d6afc..4d194abd 100644
--- a/docs/reference/scale_amp_molal_pvc.html
+++ b/docs/reference/scale_amp_molal_pvc.html
@@ -1,7 +1,5 @@
-Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water). — scale_amp_molal_pvc • Spectroscopy Analysis Tools (spant)
@@ -75,8 +73,7 @@
- Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water).
+ Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / kg of tissue water).
Source: R/amp_scaling.R
scale_amp_molal_pvc.Rd
@@ -141,7 +138,7 @@ Value
diff --git a/docs/reference/scale_amp_molar.html b/docs/reference/scale_amp_molar.html
index 02358d91..dc87a338 100644
--- a/docs/reference/scale_amp_molar.html
+++ b/docs/reference/scale_amp_molar.html
@@ -1,7 +1,5 @@
-Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / Litre of tissue). — scale_amp_molar • Spectroscopy Analysis Tools (spant) Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / Litre of tissue). — scale_amp_molar • Spectroscopy Analysis Tools (spant) Convert default LCM/TARQUIN concentration scaling to molal units with partial
-volume correction. — scale_amp_molar2molal_pvc • Spectroscopy Analysis Tools (spant) Convert default LCM/TARQUIN concentration scaling to molal units with partial volume correction. — scale_amp_molar2molal_pvc • Spectroscopy Analysis Tools (spant) Scale fitted amplitudes to a ratio of signal amplitude. — scale_amp_ratio • Spectroscopy Analysis Tools (spant) Scale fitted amplitudes to a ratio of signal amplitude. — scale_amp_ratio • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -116,7 +116,7 @@ Value
diff --git a/docs/reference/scale_amp_ratio_value.html b/docs/reference/scale_amp_ratio_value.html
index 2036837a..6af8ac51 100644
--- a/docs/reference/scale_amp_ratio_value.html
+++ b/docs/reference/scale_amp_ratio_value.html
@@ -1,5 +1,5 @@
-Scale fitted amplitudes to a ratio of signal amplitude. — scale_amp_ratio_value • Spectroscopy Analysis Tools (spant) Scale fitted amplitudes to a ratio of signal amplitude. — scale_amp_ratio_value • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/scale_amp_water_ratio.html b/docs/reference/scale_amp_water_ratio.html
index 5b25e884..35a76b00 100644
--- a/docs/reference/scale_amp_water_ratio.html
+++ b/docs/reference/scale_amp_water_ratio.html
@@ -1,5 +1,5 @@
-Scale metabolite amplitudes as a ratio to the unsuppressed water amplitude. — scale_amp_water_ratio • Spectroscopy Analysis Tools (spant) Scale metabolite amplitudes as a ratio to the unsuppressed water amplitude. — scale_amp_water_ratio • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/scale_basis_amp.html b/docs/reference/scale_basis_amp.html
index 9401c3f1..5a58b5e5 100644
--- a/docs/reference/scale_basis_amp.html
+++ b/docs/reference/scale_basis_amp.html
@@ -1,5 +1,5 @@
-Scale a basis object by a scalar. — scale_basis_amp • Spectroscopy Analysis Tools (spant) Scale a basis object by a scalar. — scale_basis_amp • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/scale_basis_from_singlet.html b/docs/reference/scale_basis_from_singlet.html
index 0d542bc8..c9a19e77 100644
--- a/docs/reference/scale_basis_from_singlet.html
+++ b/docs/reference/scale_basis_from_singlet.html
@@ -1,5 +1,5 @@
-Scale a basis-set to be consistent with spant assumptions for water scaling. — scale_basis_from_singlet • Spectroscopy Analysis Tools (spant) Scale a basis-set to be consistent with spant assumptions for water scaling. — scale_basis_from_singlet • Spectroscopy Analysis Tools (spant)
Spectroscopy Analysis Tools (spant)
- 2.21.0
+ 2.22.0
@@ -127,7 +127,7 @@ Value
diff --git a/docs/reference/scale_mrs_amp.html b/docs/reference/scale_mrs_amp.html
index b5501a0d..990f058a 100644
--- a/docs/reference/scale_mrs_amp.html
+++ b/docs/reference/scale_mrs_amp.html
@@ -1,5 +1,5 @@
-Scale an mrs_data object by a scalar or vector or amplitudes. — scale_mrs_amp • Spectroscopy Analysis Tools (spant) Scale an mrs_data object by a scalar or vector or amplitudes. — scale_mrs_amp • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/scale_spec.html b/docs/reference/scale_spec.html
index 4f6ea835..6b3ddba4 100644
--- a/docs/reference/scale_spec.html
+++ b/docs/reference/scale_spec.html
@@ -1,5 +1,5 @@
-Scale mrs_data to a spectral region. — scale_spec • Spectroscopy Analysis Tools (spant) Scale mrs_data to a spectral region. — scale_spec • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -141,7 +141,7 @@ Value
diff --git a/docs/reference/sd.html b/docs/reference/sd.html
index ea1eec9f..3ae4dfd4 100644
--- a/docs/reference/sd.html
+++ b/docs/reference/sd.html
@@ -1,5 +1,5 @@
-Calculate the standard deviation spectrum from an mrs_data object. — sd • Spectroscopy Analysis Tools (spant) Calculate the standard deviation spectrum from an mrs_data object. — sd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/sd.mrs_data.html b/docs/reference/sd.mrs_data.html
index 3f92a49f..13bdda85 100644
--- a/docs/reference/sd.mrs_data.html
+++ b/docs/reference/sd.mrs_data.html
@@ -1,5 +1,5 @@
-Calculate the standard deviation spectrum from an mrs_data object. — sd.mrs_data • Spectroscopy Analysis Tools (spant) Calculate the standard deviation spectrum from an mrs_data object. — sd.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/seconds.html b/docs/reference/seconds.html
index b34d6627..467ee17f 100644
--- a/docs/reference/seconds.html
+++ b/docs/reference/seconds.html
@@ -1,5 +1,5 @@
-Return a time scale vector to match the FID of an MRS data object. — seconds • Spectroscopy Analysis Tools (spant) Return a time scale vector to match the FID of an MRS data object. — seconds • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/seq_cpmg_ideal.html b/docs/reference/seq_cpmg_ideal.html
index 547e96ab..45727c86 100644
--- a/docs/reference/seq_cpmg_ideal.html
+++ b/docs/reference/seq_cpmg_ideal.html
@@ -1,5 +1,5 @@
-CPMG style sequence with ideal pulses. — seq_cpmg_ideal • Spectroscopy Analysis Tools (spant) CPMG style sequence with ideal pulses. — seq_cpmg_ideal • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/seq_mega_press_ideal.html b/docs/reference/seq_mega_press_ideal.html
index 0769b8b4..a9cd7fa0 100644
--- a/docs/reference/seq_mega_press_ideal.html
+++ b/docs/reference/seq_mega_press_ideal.html
@@ -1,7 +1,5 @@
-MEGA-PRESS sequence with ideal localisation pulses and Gaussian shaped
-editing pulse. — seq_mega_press_ideal • Spectroscopy Analysis Tools (spant) MEGA-PRESS sequence with ideal localisation pulses and Gaussian shaped editing pulse. — seq_mega_press_ideal • Spectroscopy Analysis Tools (spant) PRESS sequence with shaped refocusing pulses. — seq_press_2d_shaped • Spectroscopy Analysis Tools (spant) PRESS sequence with shaped refocusing pulses. — seq_press_2d_shaped • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -165,7 +165,7 @@ Value
diff --git a/docs/reference/seq_press_ideal.html b/docs/reference/seq_press_ideal.html
index 8c976856..72c3af3d 100644
--- a/docs/reference/seq_press_ideal.html
+++ b/docs/reference/seq_press_ideal.html
@@ -1,5 +1,5 @@
-PRESS sequence with ideal pulses. — seq_press_ideal • Spectroscopy Analysis Tools (spant) PRESS sequence with ideal pulses. — seq_press_ideal • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/seq_pulse_acquire.html b/docs/reference/seq_pulse_acquire.html
index 4a88fc64..ad80571e 100644
--- a/docs/reference/seq_pulse_acquire.html
+++ b/docs/reference/seq_pulse_acquire.html
@@ -1,5 +1,5 @@
-Simple pulse and acquire sequence with ideal pulses. — seq_pulse_acquire • Spectroscopy Analysis Tools (spant) Simple pulse and acquire sequence with ideal pulses. — seq_pulse_acquire • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/seq_slaser_ideal.html b/docs/reference/seq_slaser_ideal.html
index 74688f4d..eb83e8e3 100644
--- a/docs/reference/seq_slaser_ideal.html
+++ b/docs/reference/seq_slaser_ideal.html
@@ -1,5 +1,5 @@
-sLASER sequence with ideal pulses. — seq_slaser_ideal • Spectroscopy Analysis Tools (spant) sLASER sequence with ideal pulses. — seq_slaser_ideal • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -126,7 +126,7 @@ Value
diff --git a/docs/reference/seq_spin_echo_ideal.html b/docs/reference/seq_spin_echo_ideal.html
index e23271de..4248716f 100644
--- a/docs/reference/seq_spin_echo_ideal.html
+++ b/docs/reference/seq_spin_echo_ideal.html
@@ -1,5 +1,5 @@
-Spin echo sequence with ideal pulses. — seq_spin_echo_ideal • Spectroscopy Analysis Tools (spant) Spin echo sequence with ideal pulses. — seq_spin_echo_ideal • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/seq_steam_ideal.html b/docs/reference/seq_steam_ideal.html
index a60685a8..1c8115d7 100644
--- a/docs/reference/seq_steam_ideal.html
+++ b/docs/reference/seq_steam_ideal.html
@@ -1,5 +1,5 @@
-STEAM sequence with ideal pulses. — seq_steam_ideal • Spectroscopy Analysis Tools (spant) STEAM sequence with ideal pulses. — seq_steam_ideal • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -128,7 +128,7 @@ Value
diff --git a/docs/reference/seq_steam_ideal_cof.html b/docs/reference/seq_steam_ideal_cof.html
index 8f225740..cba7af91 100644
--- a/docs/reference/seq_steam_ideal_cof.html
+++ b/docs/reference/seq_steam_ideal_cof.html
@@ -1,7 +1,5 @@
-STEAM sequence with ideal pulses and coherence order filtering to simulate
-gradient crushers. — seq_steam_ideal_cof • Spectroscopy Analysis Tools (spant) STEAM sequence with ideal pulses and coherence order filtering to simulate gradient crushers. — seq_steam_ideal_cof • Spectroscopy Analysis Tools (spant) STEAM sequence with ideal pulses using the z-rotation gradient simulation
-method described by Young et al JMR 140, 146-152 (1999). — seq_steam_ideal_young • Spectroscopy Analysis Tools (spant) STEAM sequence with ideal pulses using the z-rotation gradient simulation method described by Young et al JMR 140, 146-152 (1999). — seq_steam_ideal_young • Spectroscopy Analysis Tools (spant) Set the number of transients for an mrs_data object. — set_Ntrans • Spectroscopy Analysis Tools (spant) Set the number of transients for an mrs_data object. — set_Ntrans • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/set_def_acq_paras.html b/docs/reference/set_def_acq_paras.html
index 3e1b4004..cc2ada9c 100644
--- a/docs/reference/set_def_acq_paras.html
+++ b/docs/reference/set_def_acq_paras.html
@@ -1,5 +1,5 @@
-Set the default acquisition parameters. — set_def_acq_paras • Spectroscopy Analysis Tools (spant) Set the default acquisition parameters. — set_def_acq_paras • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Arguments
diff --git a/docs/reference/set_lcm_cmd.html b/docs/reference/set_lcm_cmd.html
index 2056ed01..42bb2f24 100644
--- a/docs/reference/set_lcm_cmd.html
+++ b/docs/reference/set_lcm_cmd.html
@@ -1,5 +1,5 @@
-Set the command to run the LCModel command-line program. — set_lcm_cmd • Spectroscopy Analysis Tools (spant) Set the command to run the LCModel command-line program. — set_lcm_cmd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/set_lw.html b/docs/reference/set_lw.html
index b64ec851..bb176c62 100644
--- a/docs/reference/set_lw.html
+++ b/docs/reference/set_lw.html
@@ -1,5 +1,5 @@
-Apply line-broadening to an mrs_data object to achieve a specified linewidth. — set_lw • Spectroscopy Analysis Tools (spant) Apply line-broadening to an mrs_data object to achieve a specified linewidth. — set_lw • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -123,7 +123,7 @@ Value
diff --git a/docs/reference/set_mask_xy_mat.html b/docs/reference/set_mask_xy_mat.html
index 49dc5d4e..52c4b617 100644
--- a/docs/reference/set_mask_xy_mat.html
+++ b/docs/reference/set_mask_xy_mat.html
@@ -1,5 +1,5 @@
-Set the masked voxels in a 2D MRSI dataset to given spectrum. — set_mask_xy_mat • Spectroscopy Analysis Tools (spant) Set the masked voxels in a 2D MRSI dataset to given spectrum. — set_mask_xy_mat • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Value
diff --git a/docs/reference/set_precomp_mode.html b/docs/reference/set_precomp_mode.html
index f44bd5d3..47c28e3b 100644
--- a/docs/reference/set_precomp_mode.html
+++ b/docs/reference/set_precomp_mode.html
@@ -1,5 +1,5 @@
-Set the precompute mode. — set_precomp_mode • Spectroscopy Analysis Tools (spant) Set the precompute mode. — set_precomp_mode • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/set_precomp_verbose.html b/docs/reference/set_precomp_verbose.html
index 1453a231..9c613505 100644
--- a/docs/reference/set_precomp_verbose.html
+++ b/docs/reference/set_precomp_verbose.html
@@ -1,5 +1,5 @@
-Set the verbosity of the precompute function. — set_precomp_verbose • Spectroscopy Analysis Tools (spant) Set the verbosity of the precompute function. — set_precomp_verbose • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/set_ref.html b/docs/reference/set_ref.html
index 8953fa50..5436dfa2 100644
--- a/docs/reference/set_ref.html
+++ b/docs/reference/set_ref.html
@@ -1,5 +1,5 @@
-Set the ppm reference value (eg ppm value at 0Hz). — set_ref • Spectroscopy Analysis Tools (spant) Set the ppm reference value (eg ppm value at 0Hz). — set_ref • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/set_td_pts.html b/docs/reference/set_td_pts.html
index 8a80d42a..586459ff 100644
--- a/docs/reference/set_td_pts.html
+++ b/docs/reference/set_td_pts.html
@@ -1,7 +1,5 @@
-Set the number of time-domain data points, truncating or zero-filling as
-appropriate. — set_td_pts • Spectroscopy Analysis Tools (spant) Set the number of time-domain data points, truncating or zero-filling as appropriate. — set_td_pts • Spectroscopy Analysis Tools (spant) Set the command to run the TARQUIN command-line program. — set_tqn_cmd • Spectroscopy Analysis Tools (spant) Set the command to run the TARQUIN command-line program. — set_tqn_cmd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/set_tr.html b/docs/reference/set_tr.html
index b2109ab0..65c9df5f 100644
--- a/docs/reference/set_tr.html
+++ b/docs/reference/set_tr.html
@@ -1,5 +1,5 @@
-Set the repetition time of an MRS dataset. — set_tr • Spectroscopy Analysis Tools (spant) Set the repetition time of an MRS dataset. — set_tr • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/shift.html b/docs/reference/shift.html
index ab0fe724..034591d0 100644
--- a/docs/reference/shift.html
+++ b/docs/reference/shift.html
@@ -1,5 +1,5 @@
-Apply a frequency shift to MRS data. — shift • Spectroscopy Analysis Tools (spant) Apply a frequency shift to MRS data. — shift • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/shift_basis.html b/docs/reference/shift_basis.html
index 2884be19..f55a65e0 100644
--- a/docs/reference/shift_basis.html
+++ b/docs/reference/shift_basis.html
@@ -1,5 +1,5 @@
-Apply frequency shifts to basis set signals. — shift_basis • Spectroscopy Analysis Tools (spant) Apply frequency shifts to basis set signals. — shift_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Value
diff --git a/docs/reference/sim_basis.html b/docs/reference/sim_basis.html
index c7838c46..bb5fefc6 100644
--- a/docs/reference/sim_basis.html
+++ b/docs/reference/sim_basis.html
@@ -1,5 +1,5 @@
-Simulate a basis set object. — sim_basis • Spectroscopy Analysis Tools (spant) Simulate a basis set object. — sim_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -136,7 +136,7 @@ Value
diff --git a/docs/reference/sim_basis_1h_brain.html b/docs/reference/sim_basis_1h_brain.html
index 62ed7389..f71ffa0b 100644
--- a/docs/reference/sim_basis_1h_brain.html
+++ b/docs/reference/sim_basis_1h_brain.html
@@ -1,7 +1,5 @@
-Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS
-sequence. Note, ideal pulses are assumed. — sim_basis_1h_brain • Spectroscopy Analysis Tools (spant) Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS sequence. Note, ideal pulses are assumed. — sim_basis_1h_brain • Spectroscopy Analysis Tools (spant) Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS
-sequence. Note, ideal pulses are assumed. — sim_basis_1h_brain_press • Spectroscopy Analysis Tools (spant) Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS sequence. Note, ideal pulses are assumed. — sim_basis_1h_brain_press • Spectroscopy Analysis Tools (spant) Simulate a macromolecular and lipid basis-set suitable for 1H brain MRS
-analysis. — sim_basis_mm_lip_lcm • Spectroscopy Analysis Tools (spant) Simulate a macromolecular and lipid basis-set suitable for 1H brain MRS analysis. — sim_basis_mm_lip_lcm • Spectroscopy Analysis Tools (spant) Simulate a basis file using TARQUIN. — sim_basis_tqn • Spectroscopy Analysis Tools (spant) Simulate a basis file using TARQUIN. — sim_basis_tqn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -129,7 +129,7 @@ Examples
diff --git a/docs/reference/sim_brain_1h.html b/docs/reference/sim_brain_1h.html
index 2044cf1a..717ee289 100644
--- a/docs/reference/sim_brain_1h.html
+++ b/docs/reference/sim_brain_1h.html
@@ -1,5 +1,5 @@
-Simulate MRS data with a similar appearance to normal brain (by default). — sim_brain_1h • Spectroscopy Analysis Tools (spant) Simulate MRS data with a similar appearance to normal brain (by default). — sim_brain_1h • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -159,7 +159,7 @@ Value
diff --git a/docs/reference/sim_mol.html b/docs/reference/sim_mol.html
index 23bcef50..77f76a50 100644
--- a/docs/reference/sim_mol.html
+++ b/docs/reference/sim_mol.html
@@ -1,5 +1,5 @@
-Simulate a mol_parameter object. — sim_mol • Spectroscopy Analysis Tools (spant) Simulate a mol_parameter object. — sim_mol • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -143,7 +143,7 @@ Value
diff --git a/docs/reference/sim_noise.html b/docs/reference/sim_noise.html
index 23875f79..a71477d4 100644
--- a/docs/reference/sim_noise.html
+++ b/docs/reference/sim_noise.html
@@ -1,5 +1,5 @@
-Simulate an mrs_data object containing simulated Gaussian noise. — sim_noise • Spectroscopy Analysis Tools (spant) Simulate an mrs_data object containing simulated Gaussian noise. — sim_noise • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -84,6 +84,7 @@ Simulate an mrs_data object containing simulated Gaussian noise.
ft = def_ft(),
N = def_N(),
ref = def_ref(),
+ nuc = def_nuc(),
dyns = 1,
fd = TRUE
)
@@ -111,6 +112,10 @@ Arguments
reference value for ppm scale.
nuc
+resonant nucleus.
dyns
number of dynamic scans to generate.
Value
diff --git a/docs/reference/sim_resonances.html b/docs/reference/sim_resonances.html
index 19e9a8a4..d4f8d7c0 100644
--- a/docs/reference/sim_resonances.html
+++ b/docs/reference/sim_resonances.html
@@ -1,5 +1,5 @@
-Simulate a MRS data object containing a set of simulated resonances. — sim_resonances • Spectroscopy Analysis Tools (spant) Simulate a MRS data object containing a set of simulated resonances. — sim_resonances • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -161,7 +161,7 @@ Examples
diff --git a/docs/reference/sim_th_excit_profile.html b/docs/reference/sim_th_excit_profile.html
index 5535c5ef..e781cab1 100644
--- a/docs/reference/sim_th_excit_profile.html
+++ b/docs/reference/sim_th_excit_profile.html
@@ -1,7 +1,5 @@
-Simulate an ideal pulse excitation profile by smoothing a top-hat function
-with a Gaussian. — sim_th_excit_profile • Spectroscopy Analysis Tools (spant) Simulate an ideal pulse excitation profile by smoothing a top-hat function with a Gaussian. — sim_th_excit_profile • Spectroscopy Analysis Tools (spant) Simulate an mrs_data object containing complex zero valued samples. — sim_zero • Spectroscopy Analysis Tools (spant) Simulate an mrs_data object containing complex zero valued samples. — sim_zero • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -78,7 +78,14 @@ Simulate an mrs_data object containing complex zero valued samples.
-
+
@@ -99,6 +106,10 @@ Arguments
reference value for ppm scale.
nuc
+resonant nucleus.
dyns
number of dynamic scans to generate.
Value
diff --git a/docs/reference/smooth_dyns.html b/docs/reference/smooth_dyns.html
index 4cc8da50..accf3a51 100644
--- a/docs/reference/smooth_dyns.html
+++ b/docs/reference/smooth_dyns.html
@@ -1,5 +1,5 @@
-Smooth data across the dynamic dimension with a Gaussian kernel. — smooth_dyns • Spectroscopy Analysis Tools (spant) Smooth data across the dynamic dimension with a Gaussian kernel. — smooth_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/sort_basis.html b/docs/reference/sort_basis.html
index 6a676ea2..d25cc006 100644
--- a/docs/reference/sort_basis.html
+++ b/docs/reference/sort_basis.html
@@ -1,5 +1,5 @@
-Sort the basis-set elements alphabetically. — sort_basis • Spectroscopy Analysis Tools (spant) Sort the basis-set elements alphabetically. — sort_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/spant-package.html b/docs/reference/spant-package.html
index b3dd8e21..90f19ec3 100644
--- a/docs/reference/spant-package.html
+++ b/docs/reference/spant-package.html
@@ -1,5 +1,5 @@
-spant: spectroscopy analysis tools. — spant-package • Spectroscopy Analysis Tools (spant) spant: spectroscopy analysis tools. — spant-package • Spectroscopy Analysis Tools (spant) Simulate and fit some spectra with ABfit for benchmarking purposes. Basic
-timing and performance metrics will be printed. — spant_abfit_benchmark • Spectroscopy Analysis Tools (spant) Simulate and fit some spectra with ABfit for benchmarking purposes. Basic timing and performance metrics will be printed. — spant_abfit_benchmark • Spectroscopy Analysis Tools (spant) Example MEGA-PRESS data with significant B0 drift. — spant_mpress_drift • Spectroscopy Analysis Tools (spant) Example MEGA-PRESS data with significant B0 drift. — spant_mpress_drift • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -83,7 +83,7 @@ Example MEGA-PRESS data with significant B0 drift.
Format
- An object of class mrs_data of length 13.
+ An object of class mrs_data of dimension 1 x 1 x 1 x 1 x 40 x 1 x 1024.
@@ -98,7 +98,7 @@ Format
diff --git a/docs/reference/spant_sim_fmrs_dataset.html b/docs/reference/spant_sim_fmrs_dataset.html
new file mode 100644
index 00000000..00e48b56
--- /dev/null
+++ b/docs/reference/spant_sim_fmrs_dataset.html
@@ -0,0 +1,117 @@
+
+Simulate an example fMRS dataset for a block design fMRS experiment and export a BIDS structure. — spant_sim_fmrs_dataset • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Simulate an example fMRS dataset for a block design fMRS experiment and export a BIDS structure.
+ Source: R/fmrs.R
+ spant_sim_fmrs_dataset.Rd
+
+
+
+ Simulate an example fMRS dataset for a block design fMRS experiment and
+export a BIDS structure.
+
+
+
+ spant_sim_fmrs_dataset(output_dir = NULL)
+
+
+
+ Arguments
+ - output_dir
+output directory for the BIDS data. Defaults to :
+"HOME/sim_fmrs_dataset/data".
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/spant_simulation_benchmark.html b/docs/reference/spant_simulation_benchmark.html
index 32daa8bf..d8cc6841 100644
--- a/docs/reference/spant_simulation_benchmark.html
+++ b/docs/reference/spant_simulation_benchmark.html
@@ -1,7 +1,5 @@
-Simulate a typical metabolite basis set for benchmarking. Timing metrics will
-be printed on completion. — spant_simulation_benchmark • Spectroscopy Analysis Tools (spant) Simulate a typical metabolite basis set for benchmarking. Timing metrics will be printed on completion. — spant_simulation_benchmark • Spectroscopy Analysis Tools (spant) Decompose an mrs_data object into white and gray matter spectra. — spec_decomp • Spectroscopy Analysis Tools (spant) Perform a mathematical operation on a spectral region. — spec_op • Spectroscopy Analysis Tools (spant) Perform a mathematical operation on a spectral region. — spec_op • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -98,8 +98,8 @@ Arguments
operator
-can be "sum" (default), "mean", "l2", "max", "min" or
-"max-min".
can be "sum" (default), "mean", "l2", "max", "max_cplx,
+"min" or "max-min".
freq_scale
@@ -129,7 +129,7 @@ Value
diff --git a/docs/reference/spin_sys.html b/docs/reference/spin_sys.html
index 853423a4..1eaa9e76 100644
--- a/docs/reference/spin_sys.html
+++ b/docs/reference/spin_sys.html
@@ -1,5 +1,5 @@
-Create a spin system object for pulse sequence simulation. — spin_sys • Spectroscopy Analysis Tools (spant) Create a spin system object for pulse sequence simulation. — spin_sys • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/spm_pve2categorical.html b/docs/reference/spm_pve2categorical.html
index 23a1bad9..70f10729 100644
--- a/docs/reference/spm_pve2categorical.html
+++ b/docs/reference/spm_pve2categorical.html
@@ -1,7 +1,5 @@
-Convert SPM style segmentation files to a single categorical image where
-the numerical values map as: 0) Other, 1) CSF, 2) GM and 3) WM. — spm_pve2categorical • Spectroscopy Analysis Tools (spant) Convert SPM style segmentation files to a single categorical image where the numerical values map as: 0) Other, 1) CSF, 2) GM and 3) WM. — spm_pve2categorical • Spectroscopy Analysis Tools (spant) Signal space projection method for lipid suppression. — ssp • Spectroscopy Analysis Tools (spant) Signal space projection method for lipid suppression. — ssp • Spectroscopy Analysis Tools (spant) Plot the fitting results of an object of class fit_result with
-individual basis set components shown. — stackplot.fit_result • Spectroscopy Analysis Tools (spant) Plot the fitting results of an object of class fit_result with individual basis set components shown. — stackplot.fit_result • Spectroscopy Analysis Tools (spant) Produce a plot with multiple traces. — stackplot • Spectroscopy Analysis Tools (spant) Produce a plot with multiple traces. — stackplot • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/stackplot.mrs_data.html b/docs/reference/stackplot.mrs_data.html
index 17ff5648..64eea445 100644
--- a/docs/reference/stackplot.mrs_data.html
+++ b/docs/reference/stackplot.mrs_data.html
@@ -1,5 +1,5 @@
-Stackplot plotting method for objects of class mrs_data. — stackplot.mrs_data • Spectroscopy Analysis Tools (spant) Stackplot plotting method for objects of class mrs_data. — stackplot.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -255,7 +255,7 @@ Arguments
diff --git a/docs/reference/sub_first_dyn.html b/docs/reference/sub_first_dyn.html
index dbd7f831..493b7242 100644
--- a/docs/reference/sub_first_dyn.html
+++ b/docs/reference/sub_first_dyn.html
@@ -1,5 +1,5 @@
-Subtract the first dynamic spectrum from a dynamic series. — sub_first_dyn • Spectroscopy Analysis Tools (spant) Subtract the first dynamic spectrum from a dynamic series. — sub_first_dyn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/sub_mean_dyns.html b/docs/reference/sub_mean_dyns.html
index 6e3bb2df..221bd0c1 100644
--- a/docs/reference/sub_mean_dyns.html
+++ b/docs/reference/sub_mean_dyns.html
@@ -1,5 +1,5 @@
-Subtract the mean dynamic spectrum from a dynamic series. — sub_mean_dyns • Spectroscopy Analysis Tools (spant) Subtract the mean dynamic spectrum from a dynamic series. — sub_mean_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/sub_median_dyns.html b/docs/reference/sub_median_dyns.html
index 134c495d..1e834f14 100644
--- a/docs/reference/sub_median_dyns.html
+++ b/docs/reference/sub_median_dyns.html
@@ -1,5 +1,5 @@
-Subtract the median dynamic spectrum from a dynamic series. — sub_median_dyns • Spectroscopy Analysis Tools (spant) Subtract the median dynamic spectrum from a dynamic series. — sub_median_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/sum_coils.html b/docs/reference/sum_coils.html
index 7bf559f2..e1ab3cc0 100644
--- a/docs/reference/sum_coils.html
+++ b/docs/reference/sum_coils.html
@@ -1,5 +1,5 @@
-Calculate the sum across receiver coil elements. — sum_coils • Spectroscopy Analysis Tools (spant) Calculate the sum across receiver coil elements. — sum_coils • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/sum_dyns.html b/docs/reference/sum_dyns.html
index a0be19d3..bbda2ffc 100644
--- a/docs/reference/sum_dyns.html
+++ b/docs/reference/sum_dyns.html
@@ -1,5 +1,5 @@
-Calculate the sum of data dynamics. — sum_dyns • Spectroscopy Analysis Tools (spant) Calculate the sum of data dynamics. — sum_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/sum_mrs.html b/docs/reference/sum_mrs.html
index a22f215b..3cc3ab9e 100644
--- a/docs/reference/sum_mrs.html
+++ b/docs/reference/sum_mrs.html
@@ -1,5 +1,5 @@
-Sum two mrs_data objects. — sum_mrs • Spectroscopy Analysis Tools (spant) Sum two mrs_data objects. — sum_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Value
diff --git a/docs/reference/sum_mrs_list.html b/docs/reference/sum_mrs_list.html
index f4e09aea..c3584348 100644
--- a/docs/reference/sum_mrs_list.html
+++ b/docs/reference/sum_mrs_list.html
@@ -1,5 +1,5 @@
-Return the sum of a list of mrs_data objects. — sum_mrs_list • Spectroscopy Analysis Tools (spant) Return the sum of a list of mrs_data objects. — sum_mrs_list • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/svs_1h_brain_analysis.html b/docs/reference/svs_1h_brain_analysis.html
index 8ce514db..dff0ef7d 100644
--- a/docs/reference/svs_1h_brain_analysis.html
+++ b/docs/reference/svs_1h_brain_analysis.html
@@ -1,5 +1,5 @@
-Standard SVS 1H brain analysis pipeline. — svs_1h_brain_analysis • Spectroscopy Analysis Tools (spant) Standard SVS 1H brain analysis pipeline. — svs_1h_brain_analysis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -199,7 +199,7 @@ Value
diff --git a/docs/reference/svs_1h_brain_analysis_dev.html b/docs/reference/svs_1h_brain_analysis_dev.html
index d70a14d3..d71bfea2 100644
--- a/docs/reference/svs_1h_brain_analysis_dev.html
+++ b/docs/reference/svs_1h_brain_analysis_dev.html
@@ -1,5 +1,5 @@
-Standard SVS 1H brain analysis pipeline. — svs_1h_brain_analysis_dev • Spectroscopy Analysis Tools (spant) Standard SVS 1H brain analysis pipeline. — svs_1h_brain_analysis_dev • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -193,7 +193,7 @@ Examples
diff --git a/docs/reference/svs_1h_brain_batch_analysis.html b/docs/reference/svs_1h_brain_batch_analysis.html
index 5631e8cc..15f7223e 100644
--- a/docs/reference/svs_1h_brain_batch_analysis.html
+++ b/docs/reference/svs_1h_brain_batch_analysis.html
@@ -1,5 +1,5 @@
-Batch interface to the standard SVS 1H brain analysis pipeline. — svs_1h_brain_batch_analysis • Spectroscopy Analysis Tools (spant) Batch interface to the standard SVS 1H brain analysis pipeline. — svs_1h_brain_batch_analysis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -144,7 +144,7 @@ Value
diff --git a/docs/reference/t_test_spec.html b/docs/reference/t_test_spec.html
new file mode 100644
index 00000000..56a7ea1b
--- /dev/null
+++ b/docs/reference/t_test_spec.html
@@ -0,0 +1,124 @@
+
+Perform a t-test on spectral data points. — t_test_spec • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+
+
+ Perform a t-test on spectral data points.
+
+
+
+ t_test_spec(mrs_data, group)
+
+
+
+ Arguments
+ - mrs_data
+an mrs_data object with spectra in the dynamic dimension.
- group
+vector describing the group membership of each dynamic spectrum.
+
+ Value
+
+
+a list of statistical results.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/td2fd.html b/docs/reference/td2fd.html
index 6748a6a8..f31ed524 100644
--- a/docs/reference/td2fd.html
+++ b/docs/reference/td2fd.html
@@ -1,5 +1,5 @@
-Transform time-domain data to the frequency-domain. — td2fd • Spectroscopy Analysis Tools (spant) Transform time-domain data to the frequency-domain. — td2fd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/td_conv_filt.html b/docs/reference/td_conv_filt.html
index a9f340c3..106b9b00 100644
--- a/docs/reference/td_conv_filt.html
+++ b/docs/reference/td_conv_filt.html
@@ -1,5 +1,5 @@
-Time-domain convolution based filter. — td_conv_filt • Spectroscopy Analysis Tools (spant) Time-domain convolution based filter. — td_conv_filt • Spectroscopy Analysis Tools (spant) Time-domain spectral registration. — tdsr • Spectroscopy Analysis Tools (spant) Time-domain spectral registration. — tdsr • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -121,7 +121,7 @@ Value
diff --git a/docs/reference/te.html b/docs/reference/te.html
index 010361b1..4a65711d 100644
--- a/docs/reference/te.html
+++ b/docs/reference/te.html
@@ -1,5 +1,5 @@
-Return the echo time of an MRS dataset. — te • Spectroscopy Analysis Tools (spant) Return the echo time of an MRS dataset. — te • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/tr.html b/docs/reference/tr.html
index 0c0bd63b..2e749e02 100644
--- a/docs/reference/tr.html
+++ b/docs/reference/tr.html
@@ -1,5 +1,5 @@
-Return the repetition time of an MRS dataset. — tr • Spectroscopy Analysis Tools (spant) Return the repetition time of an MRS dataset. — tr • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/varpro_3_para_opts.html b/docs/reference/varpro_3_para_opts.html
index c2270a16..52d7cd84 100644
--- a/docs/reference/varpro_3_para_opts.html
+++ b/docs/reference/varpro_3_para_opts.html
@@ -1,5 +1,5 @@
-Return a list of options for VARPRO based fitting with 3 free parameters. — varpro_3_para_opts • Spectroscopy Analysis Tools (spant) Return a list of options for VARPRO based fitting with 3 free parameters. — varpro_3_para_opts • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -141,7 +141,7 @@ Value
diff --git a/docs/reference/varpro_basic_opts.html b/docs/reference/varpro_basic_opts.html
index 32c86d22..c5104891 100644
--- a/docs/reference/varpro_basic_opts.html
+++ b/docs/reference/varpro_basic_opts.html
@@ -1,5 +1,5 @@
-Return a list of options for a basic VARPRO analysis. — varpro_basic_opts • Spectroscopy Analysis Tools (spant) Return a list of options for a basic VARPRO analysis. — varpro_basic_opts • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -118,7 +118,7 @@ Value
diff --git a/docs/reference/varpro_opts.html b/docs/reference/varpro_opts.html
index 2aabf11d..6332f730 100644
--- a/docs/reference/varpro_opts.html
+++ b/docs/reference/varpro_opts.html
@@ -1,5 +1,5 @@
-Return a list of options for VARPRO based fitting. — varpro_opts • Spectroscopy Analysis Tools (spant) Return a list of options for VARPRO based fitting. — varpro_opts • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -177,7 +177,7 @@ Examples
diff --git a/docs/reference/vec2mrs_data.html b/docs/reference/vec2mrs_data.html
index 0cccd73b..f0d58bf0 100644
--- a/docs/reference/vec2mrs_data.html
+++ b/docs/reference/vec2mrs_data.html
@@ -1,5 +1,5 @@
-Convert a vector into a mrs_data object. — vec2mrs_data • Spectroscopy Analysis Tools (spant) Convert a vector into a mrs_data object. — vec2mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -80,10 +80,11 @@ Convert a vector into a mrs_data object.
vec2mrs_data(
vec,
- fs = def_fs(),
- ft = def_ft(),
- ref = def_ref(),
- nuc = def_nuc(),
+ mrs_data = NULL,
+ fs = NULL,
+ ft = NULL,
+ ref = NULL,
+ nuc = NULL,
dyns = 1,
fd = FALSE
)
@@ -95,6 +96,10 @@ Arguments
the data vector.
mrs_data
+example data to copy acquisition parameters from.
fs
sampling frequency in Hz.
Arguments
fd
-flag to indicate if the matrix is in the frequency domain (logical).
flag to indicate if the vector is in the frequency domain (logical).
Value
diff --git a/docs/reference/write_basis.html b/docs/reference/write_basis.html
index b6e27cbd..94c5e021 100644
--- a/docs/reference/write_basis.html
+++ b/docs/reference/write_basis.html
@@ -1,5 +1,5 @@
-Write a basis object to an LCModel .basis formatted file. — write_basis • Spectroscopy Analysis Tools (spant) Write a basis object to an LCModel .basis formatted file. — write_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -108,7 +108,7 @@ Arguments
diff --git a/docs/reference/write_basis_tqn.html b/docs/reference/write_basis_tqn.html
index 6aa51c1d..116c73ec 100644
--- a/docs/reference/write_basis_tqn.html
+++ b/docs/reference/write_basis_tqn.html
@@ -1,5 +1,5 @@
-Generate a basis file using TARQUIN. — write_basis_tqn • Spectroscopy Analysis Tools (spant) Generate a basis file using TARQUIN. — write_basis_tqn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Examples
diff --git a/docs/reference/write_mrs.html b/docs/reference/write_mrs.html
index fff25f15..124b9dc4 100644
--- a/docs/reference/write_mrs.html
+++ b/docs/reference/write_mrs.html
@@ -1,5 +1,5 @@
-Write MRS data object to file. — write_mrs • Spectroscopy Analysis Tools (spant) Write MRS data object to file. — write_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Arguments
diff --git a/docs/reference/write_mrs_nifti.html b/docs/reference/write_mrs_nifti.html
index f4bf1921..bd3ed4b7 100644
--- a/docs/reference/write_mrs_nifti.html
+++ b/docs/reference/write_mrs_nifti.html
@@ -1,5 +1,5 @@
-Write MRS data object to file in NIFTI format. — write_mrs_nifti • Spectroscopy Analysis Tools (spant) Write MRS data object to file in NIFTI format. — write_mrs_nifti • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/write_pulse_ascii.html b/docs/reference/write_pulse_ascii.html
index 067ae086..221f8ebb 100644
--- a/docs/reference/write_pulse_ascii.html
+++ b/docs/reference/write_pulse_ascii.html
@@ -1,5 +1,5 @@
-Write an ASCII formatted pulse file. — write_pulse_ascii • Spectroscopy Analysis Tools (spant) Write an ASCII formatted pulse file. — write_pulse_ascii • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/zero_fade_spec.html b/docs/reference/zero_fade_spec.html
index c703745c..c8b572c3 100644
--- a/docs/reference/zero_fade_spec.html
+++ b/docs/reference/zero_fade_spec.html
@@ -1,7 +1,5 @@
-Fade a spectrum to zero by frequency domain multiplication with a tanh
-function. Note this operation distorts data points at the end of the FID. — zero_fade_spec • Spectroscopy Analysis Tools (spant) Fade a spectrum to zero by frequency domain multiplication with a tanh function. Note this operation distorts data points at the end of the FID. — zero_fade_spec • Spectroscopy Analysis Tools (spant) Zero all coherences including and above a given order. — zero_higher_orders • Spectroscopy Analysis Tools (spant) Zero all coherences including and above a given order. — zero_higher_orders • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Value
diff --git a/docs/reference/zero_td_pts_end.html b/docs/reference/zero_td_pts_end.html
index 8c1123c8..71d24ebb 100644
--- a/docs/reference/zero_td_pts_end.html
+++ b/docs/reference/zero_td_pts_end.html
@@ -1,5 +1,5 @@
-Set mrs_data object data points at the end of the FID to zero. — zero_td_pts_end • Spectroscopy Analysis Tools (spant) Set mrs_data object data points at the end of the FID to zero. — zero_td_pts_end • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/zf.html b/docs/reference/zf.html
index 85e2013c..baf50256 100644
--- a/docs/reference/zf.html
+++ b/docs/reference/zf.html
@@ -1,5 +1,5 @@
-Zero-fill MRS data in the time domain. — zf • Spectroscopy Analysis Tools (spant) Zero-fill MRS data in the time domain. — zf • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -125,7 +125,7 @@ Value
diff --git a/docs/reference/zf_xy.html b/docs/reference/zf_xy.html
index ebca3999..c4104a74 100644
--- a/docs/reference/zf_xy.html
+++ b/docs/reference/zf_xy.html
@@ -1,5 +1,5 @@
-Zero-fill MRSI data in the k-space x-y direction. — zf_xy • Spectroscopy Analysis Tools (spant) Zero-fill MRSI data in the k-space x-y direction. — zf_xy • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -113,7 +113,7 @@ Value
diff --git a/docs/sitemap.xml b/docs/sitemap.xml
index e2139f71..4c39f515 100644
--- a/docs/sitemap.xml
+++ b/docs/sitemap.xml
@@ -216,6 +216,12 @@
https://martin3141.github.io/spant/reference/comb_coils_fp_pc.html
+
+ https://martin3141.github.io/spant/reference/comb_coils_mrsi_gls.html
+
+
+ https://martin3141.github.io/spant/reference/comb_coils_svs_gls.html
+
https://martin3141.github.io/spant/reference/comb_csv_results.html
@@ -411,6 +417,9 @@
https://martin3141.github.io/spant/reference/gen_conv_reg.html
+
+ https://martin3141.github.io/spant/reference/gen_group_reg.html
+
https://martin3141.github.io/spant/reference/gen_impulse_reg.html
@@ -555,6 +564,15 @@
https://martin3141.github.io/spant/reference/glm_spec.html
+
+ https://martin3141.github.io/spant/reference/glm_spec_fmrs_fl.html
+
+
+ https://martin3141.github.io/spant/reference/glm_spec_fmrs_group.html
+
+
+ https://martin3141.github.io/spant/reference/glm_spec_group_linhyp.html
+
https://martin3141.github.io/spant/reference/grid_shift_xy.html
@@ -690,9 +708,15 @@
https://martin3141.github.io/spant/reference/mrs_data2basis.html
+
+ https://martin3141.github.io/spant/reference/mrs_data2bids.html
+
https://martin3141.github.io/spant/reference/mrs_data2mat.html
+
+ https://martin3141.github.io/spant/reference/mrs_data2spec_mat.html
+
https://martin3141.github.io/spant/reference/mrs_data2vec.html
@@ -741,6 +765,9 @@
https://martin3141.github.io/spant/reference/phase.html
+
+ https://martin3141.github.io/spant/reference/phase_ref_1h_brain.html
+
https://martin3141.github.io/spant/reference/plot.fit_result.html
@@ -780,6 +807,12 @@
https://martin3141.github.io/spant/reference/precomp.html
+
+ https://martin3141.github.io/spant/reference/preproc_svs.html
+
+
+ https://martin3141.github.io/spant/reference/preproc_svs_dataset.html
+
https://martin3141.github.io/spant/reference/print.fit_result.html
@@ -1050,6 +1083,9 @@
https://martin3141.github.io/spant/reference/spant_mpress_drift.html
+
+ https://martin3141.github.io/spant/reference/spant_sim_fmrs_dataset.html
+
https://martin3141.github.io/spant/reference/spant_simulation_benchmark.html
@@ -1107,6 +1143,9 @@
https://martin3141.github.io/spant/reference/svs_1h_brain_batch_analysis.html
+
+ https://martin3141.github.io/spant/reference/t_test_spec.html
+
https://martin3141.github.io/spant/reference/td2fd.html
Return a list of options for an ABfit analysis to maintain comparability with -analyses performed with version 1.9.0 (and earlier) of spant.
Return a list of options for an ABfit analysis to maintain comparability with analyses performed with version 1.9.0 (and earlier) of spant.
All functions
- Append MRS data across the coil dimension, assumes they matched across the
-other dimensions.
Append MRS data across the coil dimension, assumes they matched across the other dimensions.
- Append MRS data across the dynamic dimension, assumes they matched across the
-other dimensions.
Append MRS data across the dynamic dimension, assumes they matched across the other dimensions.
@@ -194,14 +190,11 @@ All functions
- Convert a 7 dimensional array in into a mrs_data object. The array dimensions
-should be ordered as : dummy, X, Y, Z, dynamic, coil, FID.
Convert a 7 dimensional array in into a mrs_data object. The array dimensions should be ordered as : dummy, X, Y, Z, dynamic, coil, FID.
- Perform zeroth-order phase correction based on the minimisation of the
-squared difference between the real and magnitude components of the
-spectrum.
Perform zeroth-order phase correction based on the minimisation of the squared difference between the real and magnitude components of the spectrum.
@@ -213,13 +206,11 @@ All functions
- Convert a basis object to an mrs_data object - where basis signals are spread
-across the dynamic dimension.
Convert a basis object to an mrs_data object - where basis signals are spread across the dynamic dimension.
- Generate a spline basis, slightly adapted from : "Splines, knots, and
-penalties", Eilers 2010.
Generate a spline basis, slightly adapted from : "Splines, knots, and penalties", Eilers 2010.
@@ -243,8 +234,7 @@ All functions
- Covert a beta value in the time-domain to an equivalent linewidth in Hz:
-x * exp(-i * t * t * beta).
Covert a beta value in the time-domain to an equivalent linewidth in Hz: x * exp(-i * t * t * beta).
@@ -272,8 +262,7 @@ All functions
- Perform a polynomial fit, subtract and return the standard deviation of the
-residuals.
Perform a polynomial fit, subtract and return the standard deviation of the residuals.
@@ -306,6 +295,14 @@ All functions comb_coils()
Combine coil data based on the first data point of a reference signal.
+
+
+ Combine MRSI coil data using the GLS method presented by An et al JMRI 37:1445-1450 (2013).
+
+
+ Combine SVS coil data using the GLS method presented by An et al JMRI 37:1445-1450 (2013).
@@ -345,9 +342,7 @@ All functions
- Crop mrs_data object data points in the time-domain rounding down to
-the next smallest power of two (pot). Data that already has a pot length will
-not be changed.
Crop mrs_data object data points in the time-domain rounding down to the next smallest power of two (pot). Data that already has a pot length will not be changed.
@@ -355,13 +350,11 @@ All functions
- Compute the vector cross product between vectors x and y. Adapted from
-http://stackoverflow.com/questions/15162741/what-is-rs-crossproduct-function
Compute the vector cross product between vectors x and y. Adapted from http://stackoverflow.com/questions/15162741/what-is-rs-crossproduct-function
- Decimate an MRS signal to half the original sampling frequency by filtering
-in the frequency domain before down sampling.
Decimate an MRS signal to half the original sampling frequency by filtering in the frequency domain before down sampling.
@@ -377,8 +370,7 @@ All functions
- Return (and optionally modify using the input arguments) a list of the
-default acquisition parameters.
Return (and optionally modify using the input arguments) a list of the default acquisition parameters.
@@ -410,14 +402,11 @@ All functions
- Downsample an MRS signal by a factor of 2 by removing every other data point
-in the time-domain. Note, signals outside the new sampling frequency will be
-aliased.
Downsample an MRS signal by a factor of 2 by removing every other data point in the time-domain. Note, signals outside the new sampling frequency will be aliased.
- Return a time scale vector of acquisition times for a dynamic MRS scan. The
-first temporal scan is assigned a value of 0.
Return a time scale vector of acquisition times for a dynamic MRS scan. The first temporal scan is assigned a value of 0.
@@ -429,8 +418,7 @@ All functions
- Estimate the standard deviation of the noise from a segment of an mrs_data
-object.
Estimate the standard deviation of the noise from a segment of an mrs_data object.
@@ -486,8 +474,7 @@ All functions
- Perform a zeroth order phase correction based on the phase of the first data
-point in the time-domain.
Perform a zeroth order phase correction based on the phase of the first data point in the time-domain.
@@ -507,8 +494,7 @@ All functions
- Perform a fft and fftshift on a matrix with each column replaced by its
-shifted fft.
Perform a fft and fftshift on a matrix with each column replaced by its shifted fft.
@@ -536,8 +522,11 @@ All functions
- Generate regressors by convolving a specified response function with a
-stimulus.
Generate regressors by convolving a specified response function with a stimulus.
+
+
+ Expand a regressor matrix for a group analysis.
@@ -553,28 +542,23 @@ All functions
- Return a character vector of common 1H molecules found in healthy human
-brain.
Return a character vector of common 1H molecules found in healthy human brain.
- Return a list of mol_parameter objects suitable for 1H brain MRS
-analyses.
Return a list of mol_parameter objects suitable for 1H brain MRS analyses.
- Return a list of mol_parameter objects suitable for 1H brain MRS
-analyses.
Return a list of mol_parameter objects suitable for 1H brain MRS analyses.
- Return a list of mol_parameter objects suitable for 1H brain MRS
-analyses.
Return a list of mol_parameter objects suitable for 1H brain MRS analyses.
- Return a list of mol_parameter objects suitable for 1H brain MRS
-analyses.
Return a list of mol_parameter objects suitable for 1H brain MRS analyses.
@@ -582,8 +566,7 @@ All functions
- Return a character vector of molecules included in the Gold Star Phantoms
-SPECTRE phantom.
Return a character vector of molecules included in the Gold Star Phantoms SPECTRE phantom.
@@ -635,8 +618,7 @@ All functions
- Return a character array of names that may be used with the
-get_mol_paras function.
Return a character array of names that may be used with the get_mol_paras function.
@@ -700,8 +682,7 @@ All functions
- Return an array of amplitudes derived from fitting the initial points in the
-time domain and extrapolating back to t=0.
Return an array of amplitudes derived from fitting the initial points in the time domain and extrapolating back to t=0.
@@ -709,8 +690,7 @@ All functions
- Generate a mol_parameters object for a simple spin system with one
-resonance.
Generate a mol_parameters object for a simple spin system with one resonance.
@@ -731,6 +711,18 @@ All functions glm_spec()
Perform a GLM analysis of dynamic MRS data in the spectral domain.
+
+
+ Perform first-level spectral GLM analysis of an fMRS dataset.
+
+
+ Perform group-level spectral GLM analysis of an fMRS dataset.
+
+
+ Test a group-level spectral GLM linear hypothesis.
@@ -766,8 +758,7 @@ All functions
- Perform an ifft and ifftshift on a matrix with each column replaced by its
-shifted ifft.
Perform an ifft and ifftshift on a matrix with each column replaced by its shifted ifft.
@@ -799,8 +790,7 @@ All functions
- Check if the chemical shift dimension of an MRS data object is in the
-frequency domain.
Check if the chemical shift dimension of an MRS data object is in the frequency domain.
@@ -820,18 +810,15 @@ All functions
- Covert a linewidth in Hz to an equivalent alpha value in the time-domain ie:
-x * exp(-t * alpha).
Covert a linewidth in Hz to an equivalent alpha value in the time-domain ie: x * exp(-t * alpha).
- Covert a linewidth in Hz to an equivalent beta value in the time-domain ie:
-x * exp(-t * t * beta).
Covert a linewidth in Hz to an equivalent beta value in the time-domain ie: x * exp(-t * t * beta).
- Make a basis-set object from a directory containing LCModel formatted RAW
-files.
Make a basis-set object from a directory containing LCModel formatted RAW files.
@@ -851,8 +838,7 @@ All functions
- Mask the voxels outside an elliptical region spanning the MRSI dataset in the
-x-y plane.
Mask the voxels outside an elliptical region spanning the MRSI dataset in the x-y plane.
@@ -860,13 +846,11 @@ All functions
- Convert a matrix (with spectral points in the column dimension and dynamics
-in the row dimensions) into a mrs_data object.
Convert a matrix (with spectral points in the column dimension and dynamics in the row dimensions) into a mrs_data object.
- Matrix exponential function taken from complexplus package to reduce the
-number of spant dependencies.
Matrix exponential function taken from complexplus package to reduce the number of spant dependencies.
@@ -914,31 +898,31 @@ All functions
- Convert an mrs_data object to basis object - where basis signals are spread
-across the dynamic dimension in the MRS data.
Convert an mrs_data object to basis object - where basis signals are spread across the dynamic dimension in the MRS data.
+
+
+ Create a BIDS file structure from a vector of MRS data paths or list of mrs_data objects.
- Convert mrs_data object to a matrix, with spectral points in the column
-dimension and dynamics in the row dimension.
Convert mrs_data object to a matrix, with spectral points in the column dimension and dynamics in the row dimension.
-
+
- Convert mrs_data object to a vector.
Convert mrs_data object to a matrix, with spectral points in the column dimension and dynamics in the row dimension.
-
+
- Create a BIDS directory and file structure from a list of mrs_data objects.
Convert mrs_data object to a vector.
- Perform a fftshift on a matrix, with each column replaced by its shifted
-result.
Perform a fftshift on a matrix, with each column replaced by its shifted result.
- Perform an ifftshift on a matrix, with each column replaced by its shifted
-result.
Perform an ifftshift on a matrix, with each column replaced by its shifted result.
@@ -946,9 +930,7 @@ All functions
- Flip the x data dimension order of a nifti image. This corresponds to
-flipping MRI data in the left-right direction, assuming the data in save in
-neurological format (can check with fslorient program).
Flip the x data dimension order of a nifti image. This corresponds to flipping MRI data in the left-right direction, assuming the data in save in neurological format (can check with fslorient program).
@@ -964,8 +946,7 @@ All functions
- Search for the highest peak in a spectral region and return the frequency,
-height and FWHM.
Search for the highest peak in a spectral region and return the frequency, height and FWHM.
@@ -974,6 +955,10 @@ All functions phase()
Apply phasing parameters to MRS data.
+
+
+ Corrected zero order phase and chemical shift offset in 1H MRS data from the brain.
@@ -1005,8 +990,7 @@ All functions
- Plot an interactive slice map from a data array where voxels can be selected
-to display a corresponding spectrum.
Plot an interactive slice map from a data array where voxels can be selected to display a corresponding spectrum.
@@ -1026,8 +1010,15 @@ All functions
- Save function results to file and load on subsequent calls to avoid repeat
-computation.
Save function results to file and load on subsequent calls to avoid repeat computation.
+
+
+ Preprocess and perform quality assessment of a single SVS data set.
+
+
+ Preprocess and perform quality assessment of one or more SVS data sets.
@@ -1055,15 +1046,11 @@ All functions
- Read a directory containing Siemens MRS IMA files and combine along the coil
-dimension. Note that the coil ID is inferred from the sorted file name and
-should be checked when consistency is required between two directories.
Read a directory containing Siemens MRS IMA files and combine along the coil dimension. Note that the coil ID is inferred from the sorted file name and should be checked when consistency is required between two directories.
- Read a directory containing Siemens MRS IMA files and combine along the
-dynamic dimension. Note that the coil ID is inferred from the sorted file
-name and should be checked when consistency is required.
Read a directory containing Siemens MRS IMA files and combine along the dynamic dimension. Note that the coil ID is inferred from the sorted file name and should be checked when consistency is required.
@@ -1103,13 +1090,11 @@ All functions
- Reconstruct complex time-domain data from the real part of frequency-domain
-data.
Reconstruct complex time-domain data from the real part of frequency-domain data.
- Reconstruct complex time-domain data from the real part of frequency-domain
-data.
Reconstruct complex time-domain data from the real part of frequency-domain data.
@@ -1141,8 +1126,7 @@ All functions
- Resample a VOI to match a target image space using nearest-neighbour
-interpolation.
Resample a VOI to match a target image space using nearest-neighbour interpolation.
@@ -1158,23 +1142,19 @@ All functions
- Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water).
Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / kg of tissue water).
- Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water).
Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / kg of tissue water).
- Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / Litre of tissue).
Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / Litre of tissue).
- Convert default LCM/TARQUIN concentration scaling to molal units with partial
-volume correction.
Convert default LCM/TARQUIN concentration scaling to molal units with partial volume correction.
@@ -1222,8 +1202,7 @@ All functions
- MEGA-PRESS sequence with ideal localisation pulses and Gaussian shaped
-editing pulse.
MEGA-PRESS sequence with ideal localisation pulses and Gaussian shaped editing pulse.
@@ -1251,13 +1230,11 @@ All functions
- STEAM sequence with ideal pulses and coherence order filtering to simulate
-gradient crushers.
STEAM sequence with ideal pulses and coherence order filtering to simulate gradient crushers.
- STEAM sequence with ideal pulses using the z-rotation gradient simulation
-method described by Young et al JMR 140, 146-152 (1999).
STEAM sequence with ideal pulses using the z-rotation gradient simulation method described by Young et al JMR 140, 146-152 (1999).
@@ -1293,8 +1270,7 @@ All functions
- Set the number of time-domain data points, truncating or zero-filling as
-appropriate.
Set the number of time-domain data points, truncating or zero-filling as appropriate.
@@ -1318,18 +1294,15 @@ All functions
- Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS
-sequence. Note, ideal pulses are assumed.
Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS sequence. Note, ideal pulses are assumed.
- Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS
-sequence. Note, ideal pulses are assumed.
Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS sequence. Note, ideal pulses are assumed.
- Simulate a macromolecular and lipid basis-set suitable for 1H brain MRS
-analysis.
Simulate a macromolecular and lipid basis-set suitable for 1H brain MRS analysis.
@@ -1353,8 +1326,7 @@ All functions
- Simulate an ideal pulse excitation profile by smoothing a top-hat function
-with a Gaussian.
Simulate an ideal pulse excitation profile by smoothing a top-hat function with a Gaussian.
@@ -1374,17 +1346,19 @@ All functions
- Simulate and fit some spectra with ABfit for benchmarking purposes. Basic
-timing and performance metrics will be printed.
Simulate and fit some spectra with ABfit for benchmarking purposes. Basic timing and performance metrics will be printed.
Example MEGA-PRESS data with significant B0 drift.
+
+
+ Simulate an example fMRS dataset for a block design fMRS experiment and export a BIDS structure.
- Simulate a typical metabolite basis set for benchmarking. Timing metrics will
-be printed on completion.
Simulate a typical metabolite basis set for benchmarking. Timing metrics will be printed on completion.
@@ -1400,8 +1374,7 @@ All functions
- Convert SPM style segmentation files to a single categorical image where
-the numerical values map as: 0) Other, 1) CSF, 2) GM and 3) WM.
Convert SPM style segmentation files to a single categorical image where the numerical values map as: 0) Other, 1) CSF, 2) GM and 3) WM.
@@ -1413,8 +1386,7 @@ All functions
- Plot the fitting results of an object of class fit_result with
-individual basis set components shown.
Plot the fitting results of an object of class fit_result with individual basis set components shown.
@@ -1459,6 +1431,10 @@ All functions svs_1h_brain_batch_analysis()
Batch interface to the standard SVS 1H brain analysis pipeline.
+
+
+ Perform a t-test on spectral data points.
@@ -1518,8 +1494,7 @@ All functions
- Fade a spectrum to zero by frequency domain multiplication with a tanh
-function. Note this operation distorts data points at the end of the FID.
Fade a spectrum to zero by frequency domain multiplication with a tanh function. Note this operation distorts data points at the end of the FID.
@@ -1549,7 +1524,7 @@ All functions
diff --git a/docs/reference/int_spec.html b/docs/reference/int_spec.html
index c7060fe7..783325a8 100644
--- a/docs/reference/int_spec.html
+++ b/docs/reference/int_spec.html
@@ -1,5 +1,5 @@
-Integrate a spectral region. — int_spec • Spectroscopy Analysis Tools (spant) Integrate a spectral region. — int_spec • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -118,7 +118,7 @@ Value
diff --git a/docs/reference/interleave_dyns.html b/docs/reference/interleave_dyns.html
index effe5543..441eff27 100644
--- a/docs/reference/interleave_dyns.html
+++ b/docs/reference/interleave_dyns.html
@@ -1,5 +1,5 @@
-Interleave the first and second half of a dynamic series. — interleave_dyns • Spectroscopy Analysis Tools (spant) Interleave the first and second half of a dynamic series. — interleave_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/inv_even_dyns.html b/docs/reference/inv_even_dyns.html
index 9f9d4fff..dcb781dc 100644
--- a/docs/reference/inv_even_dyns.html
+++ b/docs/reference/inv_even_dyns.html
@@ -1,5 +1,5 @@
-Invert even numbered dynamic scans starting from 1 (2,4,6...). — inv_even_dyns • Spectroscopy Analysis Tools (spant) Invert even numbered dynamic scans starting from 1 (2,4,6...). — inv_even_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/inv_odd_dyns.html b/docs/reference/inv_odd_dyns.html
index 26212e2b..78d64660 100644
--- a/docs/reference/inv_odd_dyns.html
+++ b/docs/reference/inv_odd_dyns.html
@@ -1,5 +1,5 @@
-Invert odd numbered dynamic scans starting from 1 (1,3,5...). — inv_odd_dyns • Spectroscopy Analysis Tools (spant) Invert odd numbered dynamic scans starting from 1 (1,3,5...). — inv_odd_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/is.def.html b/docs/reference/is.def.html
index f196ffd0..a67b9eba 100644
--- a/docs/reference/is.def.html
+++ b/docs/reference/is.def.html
@@ -1,5 +1,5 @@
-Check if an object is defined, which is the same as being not NULL. — is.def • Spectroscopy Analysis Tools (spant) Check if an object is defined, which is the same as being not NULL. — is.def • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/is_fd.html b/docs/reference/is_fd.html
index 3b0ca165..18a193aa 100644
--- a/docs/reference/is_fd.html
+++ b/docs/reference/is_fd.html
@@ -1,7 +1,5 @@
-Check if the chemical shift dimension of an MRS data object is in the
-frequency domain. — is_fd • Spectroscopy Analysis Tools (spant) Check if the chemical shift dimension of an MRS data object is in the frequency domain. — is_fd • Spectroscopy Analysis Tools (spant) Transform 2D MRSI data from k-space to image space in the x-y direction. — kspace2img_xy • Spectroscopy Analysis Tools (spant) Transform 2D MRSI data from k-space to image space in the x-y direction. — kspace2img_xy • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/l2_reg.html b/docs/reference/l2_reg.html
index 3d781d80..21aa9849 100644
--- a/docs/reference/l2_reg.html
+++ b/docs/reference/l2_reg.html
@@ -1,5 +1,5 @@
-Perform l2 regularisation artefact suppression. — l2_reg • Spectroscopy Analysis Tools (spant) Perform l2 regularisation artefact suppression. — l2_reg • Spectroscopy Analysis Tools (spant) Apply line-broadening (apodisation) to MRS data or basis object. — lb • Spectroscopy Analysis Tools (spant) Apply line-broadening (apodisation) to MRS data or basis object. — lb • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -123,7 +123,7 @@ Value
diff --git a/docs/reference/lofdc.html b/docs/reference/lofdc.html
index 5419b1ec..31347a25 100644
--- a/docs/reference/lofdc.html
+++ b/docs/reference/lofdc.html
@@ -1,5 +1,5 @@
-Correct linear frequency drift. — lofdc • Spectroscopy Analysis Tools (spant) Correct linear frequency drift. — lofdc • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -138,7 +138,7 @@ Value
diff --git a/docs/reference/lw2alpha.html b/docs/reference/lw2alpha.html
index b83db682..25da229b 100644
--- a/docs/reference/lw2alpha.html
+++ b/docs/reference/lw2alpha.html
@@ -1,7 +1,5 @@
-Covert a linewidth in Hz to an equivalent alpha value in the time-domain ie:
-x * exp(-t * alpha). — lw2alpha • Spectroscopy Analysis Tools (spant) Covert a linewidth in Hz to an equivalent alpha value in the time-domain ie: x * exp(-t * alpha). — lw2alpha • Spectroscopy Analysis Tools (spant) Covert a linewidth in Hz to an equivalent beta value in the time-domain ie:
-x * exp(-t * t * beta). — lw2beta • Spectroscopy Analysis Tools (spant) Covert a linewidth in Hz to an equivalent beta value in the time-domain ie: x * exp(-t * t * beta). — lw2beta • Spectroscopy Analysis Tools (spant) Make a basis-set object from a directory containing LCModel formatted RAW
-files. — make_basis_from_raw • Spectroscopy Analysis Tools (spant) Make a basis-set object from a directory containing LCModel formatted RAW files. — make_basis_from_raw • Spectroscopy Analysis Tools (spant) Mask an MRS dataset in the dynamic dimension. — mask_dyns • Spectroscopy Analysis Tools (spant) Mask an MRS dataset in the dynamic dimension. — mask_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/mask_fit_res.html b/docs/reference/mask_fit_res.html
index 97baaa3f..ebd91a99 100644
--- a/docs/reference/mask_fit_res.html
+++ b/docs/reference/mask_fit_res.html
@@ -1,5 +1,5 @@
-Mask fit result spectra depending on a vector of bool values. — mask_fit_res • Spectroscopy Analysis Tools (spant) Mask fit result spectra depending on a vector of bool values. — mask_fit_res • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -116,7 +116,7 @@ Value
diff --git a/docs/reference/mask_xy.html b/docs/reference/mask_xy.html
index 11bb577c..b0d38619 100644
--- a/docs/reference/mask_xy.html
+++ b/docs/reference/mask_xy.html
@@ -1,5 +1,5 @@
-Mask an MRSI dataset in the x-y direction — mask_xy • Spectroscopy Analysis Tools (spant) Mask an MRSI dataset in the x-y direction — mask_xy • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/mask_xy_corners.html b/docs/reference/mask_xy_corners.html
index 09b16cd2..2d13839d 100644
--- a/docs/reference/mask_xy_corners.html
+++ b/docs/reference/mask_xy_corners.html
@@ -1,5 +1,5 @@
-Mask the four corners of an MRSI dataset in the x-y plane. — mask_xy_corners • Spectroscopy Analysis Tools (spant) Mask the four corners of an MRSI dataset in the x-y plane. — mask_xy_corners • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/mask_xy_ellipse.html b/docs/reference/mask_xy_ellipse.html
index 1d8b02e4..e2e749ef 100644
--- a/docs/reference/mask_xy_ellipse.html
+++ b/docs/reference/mask_xy_ellipse.html
@@ -1,7 +1,5 @@
-Mask the voxels outside an elliptical region spanning the MRSI dataset in the
-x-y plane. — mask_xy_ellipse • Spectroscopy Analysis Tools (spant) Mask the voxels outside an elliptical region spanning the MRSI dataset in the x-y plane. — mask_xy_ellipse • Spectroscopy Analysis Tools (spant) Mask a 2D MRSI dataset in the x-y dimension. — mask_xy_mat • Spectroscopy Analysis Tools (spant) Mask a 2D MRSI dataset in the x-y dimension. — mask_xy_mat • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Value
diff --git a/docs/reference/mat2mrs_data.html b/docs/reference/mat2mrs_data.html
index 2e2895f3..ae55665f 100644
--- a/docs/reference/mat2mrs_data.html
+++ b/docs/reference/mat2mrs_data.html
@@ -1,7 +1,5 @@
-Convert a matrix (with spectral points in the column dimension and dynamics
-in the row dimensions) into a mrs_data object. — mat2mrs_data • Spectroscopy Analysis Tools (spant) Convert a matrix (with spectral points in the column dimension and dynamics in the row dimensions) into a mrs_data object. — mat2mrs_data • Spectroscopy Analysis Tools (spant) Matrix exponential function taken from complexplus package to reduce the
-number of spant dependencies. — matexp • Spectroscopy Analysis Tools (spant) Matrix exponential function taken from complexplus package to reduce the number of spant dependencies. — matexp • Spectroscopy Analysis Tools (spant) Apply the max operator to an MRS dataset. — max_mrs • Spectroscopy Analysis Tools (spant) Apply the max operator to an MRS dataset. — max_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/max_mrs_interp.html b/docs/reference/max_mrs_interp.html
index e4474764..52e63f3e 100644
--- a/docs/reference/max_mrs_interp.html
+++ b/docs/reference/max_mrs_interp.html
@@ -1,5 +1,5 @@
-Apply the max operator to an interpolated MRS dataset. — max_mrs_interp • Spectroscopy Analysis Tools (spant) Apply the max operator to an interpolated MRS dataset. — max_mrs_interp • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/mean.list.html b/docs/reference/mean.list.html
index b8eb3463..048306fd 100644
--- a/docs/reference/mean.list.html
+++ b/docs/reference/mean.list.html
@@ -1,5 +1,5 @@
-Calculate the mean spectrum from an mrs_data object. — mean.list • Spectroscopy Analysis Tools (spant) Calculate the mean spectrum from an mrs_data object. — mean.list • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/mean.mrs_data.html b/docs/reference/mean.mrs_data.html
index 5531a28d..79515014 100644
--- a/docs/reference/mean.mrs_data.html
+++ b/docs/reference/mean.mrs_data.html
@@ -1,5 +1,5 @@
-Calculate the mean spectrum from an mrs_data object. — mean.mrs_data • Spectroscopy Analysis Tools (spant) Calculate the mean spectrum from an mrs_data object. — mean.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/mean_dyn_blocks.html b/docs/reference/mean_dyn_blocks.html
index 10467098..4c042448 100644
--- a/docs/reference/mean_dyn_blocks.html
+++ b/docs/reference/mean_dyn_blocks.html
@@ -1,5 +1,5 @@
-Calculate the mean of adjacent dynamic scans. — mean_dyn_blocks • Spectroscopy Analysis Tools (spant) Calculate the mean of adjacent dynamic scans. — mean_dyn_blocks • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/mean_dyn_pairs.html b/docs/reference/mean_dyn_pairs.html
index 63e909ea..1a241126 100644
--- a/docs/reference/mean_dyn_pairs.html
+++ b/docs/reference/mean_dyn_pairs.html
@@ -1,5 +1,5 @@
-Calculate the pairwise means across a dynamic data set. — mean_dyn_pairs • Spectroscopy Analysis Tools (spant) Calculate the pairwise means across a dynamic data set. — mean_dyn_pairs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/mean_dyns.html b/docs/reference/mean_dyns.html
index 73fdbfa7..0daa27df 100644
--- a/docs/reference/mean_dyns.html
+++ b/docs/reference/mean_dyns.html
@@ -1,5 +1,5 @@
-Calculate the mean dynamic data. — mean_dyns • Spectroscopy Analysis Tools (spant) Calculate the mean dynamic data. — mean_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/mean_mrs_list.html b/docs/reference/mean_mrs_list.html
index 808b6c50..10d842c0 100644
--- a/docs/reference/mean_mrs_list.html
+++ b/docs/reference/mean_mrs_list.html
@@ -1,5 +1,5 @@
-Return the mean of a list of mrs_data objects. — mean_mrs_list • Spectroscopy Analysis Tools (spant) Return the mean of a list of mrs_data objects. — mean_mrs_list • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/mean_vec_blocks.html b/docs/reference/mean_vec_blocks.html
index 8fc92eaa..dd78b122 100644
--- a/docs/reference/mean_vec_blocks.html
+++ b/docs/reference/mean_vec_blocks.html
@@ -1,5 +1,5 @@
-Calculate the mean of adjacent blocks in a vector. — mean_vec_blocks • Spectroscopy Analysis Tools (spant) Calculate the mean of adjacent blocks in a vector. — mean_vec_blocks • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/median_dyns.html b/docs/reference/median_dyns.html
index 1039d4b5..9a085b10 100644
--- a/docs/reference/median_dyns.html
+++ b/docs/reference/median_dyns.html
@@ -1,5 +1,5 @@
-Calculate the median dynamic data. — median_dyns • Spectroscopy Analysis Tools (spant) Calculate the median dynamic data. — median_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/mod_td.html b/docs/reference/mod_td.html
index 76ad0a40..141ef09e 100644
--- a/docs/reference/mod_td.html
+++ b/docs/reference/mod_td.html
@@ -1,5 +1,5 @@
-Apply the Modulus operator to the time-domain MRS signal. — mod_td • Spectroscopy Analysis Tools (spant) Apply the Modulus operator to the time-domain MRS signal. — mod_td • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/mrs_data2basis.html b/docs/reference/mrs_data2basis.html
index 62f7d749..11797b91 100644
--- a/docs/reference/mrs_data2basis.html
+++ b/docs/reference/mrs_data2basis.html
@@ -1,7 +1,5 @@
-Convert an mrs_data object to basis object - where basis signals are spread
-across the dynamic dimension in the MRS data. — mrs_data2basis • Spectroscopy Analysis Tools (spant) Convert an mrs_data object to basis object - where basis signals are spread across the dynamic dimension in the MRS data. — mrs_data2basis • Spectroscopy Analysis Tools (spant) Create a BIDS file structure from a vector of MRS data paths or list of mrs_data objects. — mrs_data2bids • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Create a BIDS file structure from a vector of MRS data paths or list of mrs_data objects.
+ Source: R/fmrs.R
+ mrs_data2bids.Rd
+
+
+
+ Create a BIDS file structure from a vector of MRS data paths or list of
+mrs_data objects.
+
+
+
+ mrs_data2bids(
+ mrs_data,
+ output_dir,
+ suffix = NULL,
+ sub = NULL,
+ ses = NULL,
+ task = NULL,
+ acq = NULL,
+ nuc = NULL,
+ voi = NULL,
+ rec = NULL,
+ run = NULL,
+ echo = NULL,
+ inv = NULL,
+ skip_existing = TRUE
+)
+
+
+
+ Arguments
+ - mrs_data
+vector of MRS data paths or list of mrs_data objects.
- output_dir
+the base directory to create the BIDS structure.
- suffix
+optional vector of file suffixes. Default behaviour is to
+automatically determine these from the input data, however it is recommended
+that they are specified to allow more efficient skipping of existing data.
- sub
+optional vector of subject labels. If not specified, these will be
+automatically generated as a series of increasing zero-padded integer values
+corresponding to the mrs_data input indices.
- ses
+optional vector of session labels.
- task
+optional vector of task labels.
- acq
+optional vector of acquisition labels.
- nuc
+optional vector of nucleus labels.
- voi
+optional vector of volume of interest labels.
- rec
+optional vector of reconstruction labels.
- run
+optional vector of run indices.
- echo
+optional vector of echo time indices.
- inv
+optional vector of inversion indices.
- skip_existing
+skip any data files that have already been converted.
+Defaults to TRUE, set to FALSE to force an overwrite of any existing data
+files.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/mrs_data2mat.html b/docs/reference/mrs_data2mat.html
index cf5ff28c..9e47688a 100644
--- a/docs/reference/mrs_data2mat.html
+++ b/docs/reference/mrs_data2mat.html
@@ -1,7 +1,5 @@
-Convert mrs_data object to a matrix, with spectral points in the column
-dimension and dynamics in the row dimension. — mrs_data2mat • Spectroscopy Analysis Tools (spant) Convert mrs_data object to a matrix, with spectral points in the column dimension and dynamics in the row dimension. — mrs_data2mat • Spectroscopy Analysis Tools (spant) Convert mrs_data object to a matrix, with spectral points in the column dimension and dynamics in the row dimension. — mrs_data2spec_mat • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Convert mrs_data object to a matrix, with spectral points in the column dimension and dynamics in the row dimension.
+ Source: R/mrs_data_proc.R
+ mrs_data2spec_mat.Rd
+
+
+
+ Convert mrs_data object to a matrix, with spectral points in the column
+dimension and dynamics in the row dimension.
+
+
+
+ mrs_data2spec_mat(mrs_data, collapse = TRUE)
+
+
+
+ Arguments
+ - mrs_data
+MRS data object or list of MRS data objects.
- collapse
+collapse all other dimensions along the dynamic dimension, eg
+a 16x16 MRSI grid would be first collapsed across 256 dynamic scans.
+
+ Value
+
+
+MRS data matrix.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/mrs_data2vec.html b/docs/reference/mrs_data2vec.html
index fb172d68..a1fd654d 100644
--- a/docs/reference/mrs_data2vec.html
+++ b/docs/reference/mrs_data2vec.html
@@ -1,5 +1,5 @@
-Convert mrs_data object to a vector. — mrs_data2vec • Spectroscopy Analysis Tools (spant) Convert mrs_data object to a vector. — mrs_data2vec • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -126,7 +126,7 @@ Value
diff --git a/docs/reference/mvfftshift.html b/docs/reference/mvfftshift.html
index 92b0841b..976b3410 100644
--- a/docs/reference/mvfftshift.html
+++ b/docs/reference/mvfftshift.html
@@ -1,7 +1,5 @@
-Perform a fftshift on a matrix, with each column replaced by its shifted
-result. — mvfftshift • Spectroscopy Analysis Tools (spant) Perform a fftshift on a matrix, with each column replaced by its shifted result. — mvfftshift • Spectroscopy Analysis Tools (spant) Perform an ifftshift on a matrix, with each column replaced by its shifted
-result. — mvifftshift • Spectroscopy Analysis Tools (spant) Perform an ifftshift on a matrix, with each column replaced by its shifted result. — mvifftshift • Spectroscopy Analysis Tools (spant) Print fit coordinates from a single index. — n2coord • Spectroscopy Analysis Tools (spant) Print fit coordinates from a single index. — n2coord • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/nifti_flip_lr.html b/docs/reference/nifti_flip_lr.html
index 730abe3c..19860b3c 100644
--- a/docs/reference/nifti_flip_lr.html
+++ b/docs/reference/nifti_flip_lr.html
@@ -1,9 +1,5 @@
-Flip the x data dimension order of a nifti image. This corresponds to
-flipping MRI data in the left-right direction, assuming the data in save in
-neurological format (can check with fslorient program). — nifti_flip_lr • Spectroscopy Analysis Tools (spant) Flip the x data dimension order of a nifti image. This corresponds to flipping MRI data in the left-right direction, assuming the data in save in neurological format (can check with fslorient program). — nifti_flip_lr • Spectroscopy Analysis Tools (spant) Export a one-page pdf of a single fit result — one_page_pdf • Spectroscopy Analysis Tools (spant) Export a one-page pdf of a single fit result — one_page_pdf • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -108,7 +108,7 @@ Arguments
diff --git a/docs/reference/ortho3.html b/docs/reference/ortho3.html
index 13ade97d..5d7dd2fd 100644
--- a/docs/reference/ortho3.html
+++ b/docs/reference/ortho3.html
@@ -1,5 +1,5 @@
-Display an orthographic projection plot of a nifti object. — ortho3 • Spectroscopy Analysis Tools (spant) Display an orthographic projection plot of a nifti object. — ortho3 • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -172,7 +172,7 @@ Arguments
diff --git a/docs/reference/ortho3_inter.html b/docs/reference/ortho3_inter.html
index 090cc5e5..15948899 100644
--- a/docs/reference/ortho3_inter.html
+++ b/docs/reference/ortho3_inter.html
@@ -1,5 +1,5 @@
-Display an interactive orthographic projection plot of a nifti object. — ortho3_inter • Spectroscopy Analysis Tools (spant) Display an interactive orthographic projection plot of a nifti object. — ortho3_inter • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -132,7 +132,7 @@ Arguments
diff --git a/docs/reference/peak_info.html b/docs/reference/peak_info.html
index 09058bd8..41c8ffaf 100644
--- a/docs/reference/peak_info.html
+++ b/docs/reference/peak_info.html
@@ -1,7 +1,5 @@
-Search for the highest peak in a spectral region and return the frequency,
-height and FWHM. — peak_info • Spectroscopy Analysis Tools (spant) Search for the highest peak in a spectral region and return the frequency, height and FWHM. — peak_info • Spectroscopy Analysis Tools (spant) Papoulis-Gerchberg (PG) algorithm method for k-space extrapolation. — pg_extrap_xy • Spectroscopy Analysis Tools (spant) Papoulis-Gerchberg (PG) algorithm method for k-space extrapolation. — pg_extrap_xy • Spectroscopy Analysis Tools (spant) Apply phasing parameters to MRS data. — phase • Spectroscopy Analysis Tools (spant) Apply phasing parameters to MRS data. — phase • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/phase_ref_1h_brain.html b/docs/reference/phase_ref_1h_brain.html
new file mode 100644
index 00000000..8707a74a
--- /dev/null
+++ b/docs/reference/phase_ref_1h_brain.html
@@ -0,0 +1,131 @@
+
+Corrected zero order phase and chemical shift offset in 1H MRS data from the brain. — phase_ref_1h_brain • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Corrected zero order phase and chemical shift offset in 1H MRS data from the brain.
+ Source: R/rats.R
+ phase_ref_1h_brain.Rd
+
+
+
+ Corrected zero order phase and chemical shift offset in 1H MRS data from the
+brain.
+
+
+
+ phase_ref_1h_brain(mrs_data, mean_ref = FALSE, ret_corr_only = TRUE)
+
+
+
+ Arguments
+ - mrs_data
+MRS data to be corrected.
- mean_ref
+apply the phase and offset of the mean spectrum to all
+others. Default is FALSE.
- ret_corr_only
+return the corrected data only.
+
+ Value
+
+
+corrected MRS data.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/plot.fit_result.html b/docs/reference/plot.fit_result.html
index e54d3bc1..836a53ee 100644
--- a/docs/reference/plot.fit_result.html
+++ b/docs/reference/plot.fit_result.html
@@ -1,5 +1,5 @@
-Plot the fitting results of an object of class fit_result. — plot.fit_result • Spectroscopy Analysis Tools (spant) Plot the fitting results of an object of class fit_result. — plot.fit_result • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -207,7 +207,7 @@ Arguments
diff --git a/docs/reference/plot.mrs_data.html b/docs/reference/plot.mrs_data.html
index fabcc35b..bb2ec651 100644
--- a/docs/reference/plot.mrs_data.html
+++ b/docs/reference/plot.mrs_data.html
@@ -1,5 +1,5 @@
-Plotting method for objects of class mrs_data. — plot.mrs_data • Spectroscopy Analysis Tools (spant) Plotting method for objects of class mrs_data. — plot.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -287,7 +287,7 @@ Arguments
diff --git a/docs/reference/plot_bc.html b/docs/reference/plot_bc.html
index 4f8309b4..b48142cc 100644
--- a/docs/reference/plot_bc.html
+++ b/docs/reference/plot_bc.html
@@ -1,5 +1,5 @@
-Convenience function to plot a baseline estimate with the original data. — plot_bc • Spectroscopy Analysis Tools (spant) Convenience function to plot a baseline estimate with the original data. — plot_bc • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -108,7 +108,7 @@ Arguments
diff --git a/docs/reference/plot_reg.html b/docs/reference/plot_reg.html
index ae1acbe7..2addb2f6 100644
--- a/docs/reference/plot_reg.html
+++ b/docs/reference/plot_reg.html
@@ -1,5 +1,5 @@
-Plot regressors as an image. — plot_reg • Spectroscopy Analysis Tools (spant) Plot regressors as an image. — plot_reg • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/plot_slice_fit.html b/docs/reference/plot_slice_fit.html
index fbc7b560..57f1af8a 100644
--- a/docs/reference/plot_slice_fit.html
+++ b/docs/reference/plot_slice_fit.html
@@ -1,5 +1,5 @@
-Plot a 2D slice from an MRSI fit result object. — plot_slice_fit • Spectroscopy Analysis Tools (spant) Plot a 2D slice from an MRSI fit result object. — plot_slice_fit • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -129,7 +129,7 @@ Arguments
diff --git a/docs/reference/plot_slice_fit_inter.html b/docs/reference/plot_slice_fit_inter.html
index 4eed104a..da105a7d 100644
--- a/docs/reference/plot_slice_fit_inter.html
+++ b/docs/reference/plot_slice_fit_inter.html
@@ -1,5 +1,5 @@
-Plot a 2D slice from an MRSI fit result object. — plot_slice_fit_inter • Spectroscopy Analysis Tools (spant) Plot a 2D slice from an MRSI fit result object. — plot_slice_fit_inter • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -134,7 +134,7 @@ Arguments
diff --git a/docs/reference/plot_slice_map.html b/docs/reference/plot_slice_map.html
index 553e9ac8..ffb2a134 100644
--- a/docs/reference/plot_slice_map.html
+++ b/docs/reference/plot_slice_map.html
@@ -1,5 +1,5 @@
-Plot a slice from a 7 dimensional array. — plot_slice_map • Spectroscopy Analysis Tools (spant) Plot a slice from a 7 dimensional array. — plot_slice_map • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -153,7 +153,7 @@ Arguments
diff --git a/docs/reference/plot_slice_map_inter.html b/docs/reference/plot_slice_map_inter.html
index 40d33b42..90968f66 100644
--- a/docs/reference/plot_slice_map_inter.html
+++ b/docs/reference/plot_slice_map_inter.html
@@ -1,7 +1,5 @@
-Plot an interactive slice map from a data array where voxels can be selected
-to display a corresponding spectrum. — plot_slice_map_inter • Spectroscopy Analysis Tools (spant) Plot an interactive slice map from a data array where voxels can be selected to display a corresponding spectrum. — plot_slice_map_inter • Spectroscopy Analysis Tools (spant) Plot the spectral standard deviation. — plot_spec_sd • Spectroscopy Analysis Tools (spant) Plot the spectral standard deviation. — plot_spec_sd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Arguments
diff --git a/docs/reference/plot_voi_overlay.html b/docs/reference/plot_voi_overlay.html
index 9a782e88..bbbbf35e 100644
--- a/docs/reference/plot_voi_overlay.html
+++ b/docs/reference/plot_voi_overlay.html
@@ -1,5 +1,5 @@
-Plot a volume as an image overlay. — plot_voi_overlay • Spectroscopy Analysis Tools (spant) Plot a volume as an image overlay. — plot_voi_overlay • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -116,7 +116,7 @@ Arguments
diff --git a/docs/reference/plot_voi_overlay_seg.html b/docs/reference/plot_voi_overlay_seg.html
index 3d4e74ff..0e800ff2 100644
--- a/docs/reference/plot_voi_overlay_seg.html
+++ b/docs/reference/plot_voi_overlay_seg.html
@@ -1,5 +1,5 @@
-Plot a volume as an overlay on a segmented brain volume. — plot_voi_overlay_seg • Spectroscopy Analysis Tools (spant) Plot a volume as an overlay on a segmented brain volume. — plot_voi_overlay_seg • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Arguments
diff --git a/docs/reference/ppm.html b/docs/reference/ppm.html
index c352327a..ee4696e2 100644
--- a/docs/reference/ppm.html
+++ b/docs/reference/ppm.html
@@ -1,5 +1,5 @@
-Return the ppm scale of an MRS dataset or fit result. — ppm • Spectroscopy Analysis Tools (spant) Return the ppm scale of an MRS dataset or fit result. — ppm • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -132,7 +132,7 @@ Value
diff --git a/docs/reference/precomp.html b/docs/reference/precomp.html
index 822d7336..df3d2c6c 100644
--- a/docs/reference/precomp.html
+++ b/docs/reference/precomp.html
@@ -1,7 +1,5 @@
-Save function results to file and load on subsequent calls to avoid repeat
-computation. — precomp • Spectroscopy Analysis Tools (spant) Save function results to file and load on subsequent calls to avoid repeat computation. — precomp • Spectroscopy Analysis Tools (spant) Preprocess and perform quality assessment of a single SVS data set. — preproc_svs • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Preprocess and perform quality assessment of a single SVS data set.
+ Source: R/fmrs.R
+ preproc_svs.Rd
+
+
+
+ Preprocess and perform quality assessment of a single SVS data set.
+
+
+
+ preproc_svs(path, label = NULL, output_dir = NULL, ref_inds = NULL)
+
+
+
+ Arguments
+ - path
+path to the fMRS data file or IMA directory.
- label
+a label to describe the data set.
- output_dir
+output directory.
- ref_inds
+a vector of 1-based indices for any water reference dynamic
+scans.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/preproc_svs_dataset.html b/docs/reference/preproc_svs_dataset.html
new file mode 100644
index 00000000..07c3a29b
--- /dev/null
+++ b/docs/reference/preproc_svs_dataset.html
@@ -0,0 +1,148 @@
+
+Preprocess and perform quality assessment of one or more SVS data sets. — preproc_svs_dataset • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Preprocess and perform quality assessment of one or more SVS data sets.
+ Source: R/fmrs.R
+ preproc_svs_dataset.Rd
+
+
+
+ Preprocess and perform quality assessment of one or more SVS data sets.
+
+
+
+ preproc_svs_dataset(
+ paths,
+ labels = NULL,
+ output_dir = "spant_analysis",
+ exclude_labels = NULL,
+ overwrite = FALSE,
+ ref_inds = NULL,
+ return_results = FALSE
+)
+
+
+
+ Arguments
+ - paths
+paths to the fMRS data file or IMA directory.
- labels
+labels to describe each data set.
- output_dir
+output directory.
- exclude_labels
+vector of labels of scans to exclude, eg poor quality
+data.
- overwrite
+overwrite saved results, defaults to FALSE.
- ref_inds
+a vector of 1-based indices for any water reference dynamic
+scans.
- return_results
+function will return key outputs, defaults to FALSE.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/print.fit_result.html b/docs/reference/print.fit_result.html
index 297f28dc..5f434e57 100644
--- a/docs/reference/print.fit_result.html
+++ b/docs/reference/print.fit_result.html
@@ -1,5 +1,5 @@
-Print a summary of an object of class fit_result. — print.fit_result • Spectroscopy Analysis Tools (spant) Print a summary of an object of class fit_result. — print.fit_result • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -105,7 +105,7 @@ Arguments
diff --git a/docs/reference/print.mrs_data.html b/docs/reference/print.mrs_data.html
index 51199017..e1561eb2 100644
--- a/docs/reference/print.mrs_data.html
+++ b/docs/reference/print.mrs_data.html
@@ -1,5 +1,5 @@
-Print a summary of mrs_data parameters. — print.mrs_data • Spectroscopy Analysis Tools (spant) Print a summary of mrs_data parameters. — print.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -109,7 +109,7 @@ Arguments
diff --git a/docs/reference/qn_states.html b/docs/reference/qn_states.html
index 0f42f2f9..d7aa6715 100644
--- a/docs/reference/qn_states.html
+++ b/docs/reference/qn_states.html
@@ -1,5 +1,5 @@
-Get the quantum coherence matrix for a spin system. — qn_states • Spectroscopy Analysis Tools (spant) Get the quantum coherence matrix for a spin system. — qn_states • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/rats.html b/docs/reference/rats.html
index 5a39a396..93585e08 100644
--- a/docs/reference/rats.html
+++ b/docs/reference/rats.html
@@ -1,5 +1,5 @@
-Robust Alignment to a Target Spectrum (RATS). — rats • Spectroscopy Analysis Tools (spant) Robust Alignment to a Target Spectrum (RATS). — rats • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -207,7 +207,7 @@ Value
diff --git a/docs/reference/re_weighting.html b/docs/reference/re_weighting.html
index d21caf21..8b0b070a 100644
--- a/docs/reference/re_weighting.html
+++ b/docs/reference/re_weighting.html
@@ -1,5 +1,5 @@
-Apply a weighting to the FID to enhance spectral resolution. — re_weighting • Spectroscopy Analysis Tools (spant) Apply a weighting to the FID to enhance spectral resolution. — re_weighting • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/read_basis.html b/docs/reference/read_basis.html
index da9b94af..eb6f8557 100644
--- a/docs/reference/read_basis.html
+++ b/docs/reference/read_basis.html
@@ -1,5 +1,5 @@
-Read a basis file in LCModel .basis format. — read_basis • Spectroscopy Analysis Tools (spant) Read a basis file in LCModel .basis format. — read_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/read_ima_coil_dir.html b/docs/reference/read_ima_coil_dir.html
index 28c02de0..4f073cd8 100644
--- a/docs/reference/read_ima_coil_dir.html
+++ b/docs/reference/read_ima_coil_dir.html
@@ -1,9 +1,5 @@
-Read a directory containing Siemens MRS IMA files and combine along the coil
-dimension. Note that the coil ID is inferred from the sorted file name and
-should be checked when consistency is required between two directories. — read_ima_coil_dir • Spectroscopy Analysis Tools (spant) Read a directory containing Siemens MRS IMA files and combine along the coil dimension. Note that the coil ID is inferred from the sorted file name and should be checked when consistency is required between two directories. — read_ima_coil_dir • Spectroscopy Analysis Tools (spant) Read a directory containing Siemens MRS IMA files and combine along the
-dynamic dimension. Note that the coil ID is inferred from the sorted file
-name and should be checked when consistency is required. — read_ima_dyn_dir • Spectroscopy Analysis Tools (spant) Read a directory containing Siemens MRS IMA files and combine along the dynamic dimension. Note that the coil ID is inferred from the sorted file name and should be checked when consistency is required. — read_ima_dyn_dir • Spectroscopy Analysis Tools (spant) Read an LCModel formatted coord file containing fit information. — read_lcm_coord • Spectroscopy Analysis Tools (spant) Read an LCModel formatted coord file containing fit information. — read_lcm_coord • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -107,7 +107,7 @@ Value
diff --git a/docs/reference/read_mrs.html b/docs/reference/read_mrs.html
index 3ac2a36b..2cf36b20 100644
--- a/docs/reference/read_mrs.html
+++ b/docs/reference/read_mrs.html
@@ -1,5 +1,5 @@
-Read MRS data from a file. — read_mrs • Spectroscopy Analysis Tools (spant) Read MRS data from a file. — read_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -88,7 +88,8 @@ Read MRS data from a file.
full_fid = FALSE,
omit_svs_ref_scans = TRUE,
verbose = FALSE,
- extra = NULL
+ extra = NULL,
+ fid_filt_dist = NULL
)
@@ -140,6 +141,13 @@ Arguments
an optional data frame to provide additional variables for use
in subsequent analysis steps, eg id or grouping variables.
fid_filt_dist
+indicate if the data has a distorted FID due to a
+brick-wall filter being used to downsample the data. Default is to auto
+detect this from the data, but TRUE or FALSE options can be given to override
+detection.
Value
@@ -183,7 +191,7 @@ Examples
diff --git a/docs/reference/read_mrs_tqn.html b/docs/reference/read_mrs_tqn.html
index 5766362f..84bdaf3a 100644
--- a/docs/reference/read_mrs_tqn.html
+++ b/docs/reference/read_mrs_tqn.html
@@ -1,5 +1,5 @@
-Read MRS data using the TARQUIN software package. — read_mrs_tqn • Spectroscopy Analysis Tools (spant) Read MRS data using the TARQUIN software package. — read_mrs_tqn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -131,7 +131,7 @@ Examples
diff --git a/docs/reference/read_pulse_ascii.html b/docs/reference/read_pulse_ascii.html
index c9e0d43c..ab11c9cc 100644
--- a/docs/reference/read_pulse_ascii.html
+++ b/docs/reference/read_pulse_ascii.html
@@ -1,5 +1,5 @@
-Read an ASCII formatted pulse file. — read_pulse_ascii • Spectroscopy Analysis Tools (spant) Read an ASCII formatted pulse file. — read_pulse_ascii • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/read_pulse_bruker.html b/docs/reference/read_pulse_bruker.html
index c92bf76a..dbe9073b 100644
--- a/docs/reference/read_pulse_bruker.html
+++ b/docs/reference/read_pulse_bruker.html
@@ -1,5 +1,5 @@
-Read a Bruker formatted pulse file — read_pulse_bruker • Spectroscopy Analysis Tools (spant) Read a Bruker formatted pulse file — read_pulse_bruker • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/read_pulse_pta.html b/docs/reference/read_pulse_pta.html
index 72e1b6d4..a0fac3c3 100644
--- a/docs/reference/read_pulse_pta.html
+++ b/docs/reference/read_pulse_pta.html
@@ -1,5 +1,5 @@
-Read a .pta formatted pulse file compatible with Siemens PulseTool. — read_pulse_pta • Spectroscopy Analysis Tools (spant) Read a .pta formatted pulse file compatible with Siemens PulseTool. — read_pulse_pta • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/read_siemens_txt_hdr.html b/docs/reference/read_siemens_txt_hdr.html
index 23fb8c70..3a17d87c 100644
--- a/docs/reference/read_siemens_txt_hdr.html
+++ b/docs/reference/read_siemens_txt_hdr.html
@@ -1,5 +1,5 @@
-Read the text format header found in Siemens IMA and TWIX data files. — read_siemens_txt_hdr • Spectroscopy Analysis Tools (spant) Read the text format header found in Siemens IMA and TWIX data files. — read_siemens_txt_hdr • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -78,7 +78,7 @@ Read the text format header found in Siemens IMA and TWIX data files.
- read_siemens_txt_hdr(input, version = "vd", verbose, offset = 0)
+ read_siemens_txt_hdr(input, version = "vd", verbose = FALSE, offset = 0)
@@ -118,7 +118,7 @@ Value
diff --git a/docs/reference/read_tqn_fit.html b/docs/reference/read_tqn_fit.html
index 4da6c25e..a1630420 100644
--- a/docs/reference/read_tqn_fit.html
+++ b/docs/reference/read_tqn_fit.html
@@ -1,5 +1,5 @@
-Reader for csv fit results generated by TARQUIN. — read_tqn_fit • Spectroscopy Analysis Tools (spant) Reader for csv fit results generated by TARQUIN. — read_tqn_fit • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -113,7 +113,7 @@ Examples
diff --git a/docs/reference/read_tqn_result.html b/docs/reference/read_tqn_result.html
index 36659714..68a3e98c 100644
--- a/docs/reference/read_tqn_result.html
+++ b/docs/reference/read_tqn_result.html
@@ -1,5 +1,5 @@
-Reader for csv results generated by TARQUIN. — read_tqn_result • Spectroscopy Analysis Tools (spant) Reader for csv results generated by TARQUIN. — read_tqn_result • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -117,7 +117,7 @@ Examples
diff --git a/docs/reference/recon_imag.html b/docs/reference/recon_imag.html
index d2a72225..5bc3b1eb 100644
--- a/docs/reference/recon_imag.html
+++ b/docs/reference/recon_imag.html
@@ -1,7 +1,5 @@
-Reconstruct complex time-domain data from the real part of frequency-domain
-data. — recon_imag • Spectroscopy Analysis Tools (spant) Reconstruct complex time-domain data from the real part of frequency-domain data. — recon_imag • Spectroscopy Analysis Tools (spant) Reconstruct complex time-domain data from the real part of frequency-domain
-data. — recon_imag_vec • Spectroscopy Analysis Tools (spant) Reconstruct complex time-domain data from the real part of frequency-domain data. — recon_imag_vec • Spectroscopy Analysis Tools (spant) Reconstruct 2D MRSI data from a twix file loaded with read_mrs. — recon_twix_2d_mrsi • Spectroscopy Analysis Tools (spant) Reconstruct 2D MRSI data from a twix file loaded with read_mrs. — recon_twix_2d_mrsi • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/rectangular_mask.html b/docs/reference/rectangular_mask.html
index a2117283..6e469bc9 100644
--- a/docs/reference/rectangular_mask.html
+++ b/docs/reference/rectangular_mask.html
@@ -1,5 +1,5 @@
-Create a rectangular mask stored as a matrix of logical values. — rectangular_mask • Spectroscopy Analysis Tools (spant) Create a rectangular mask stored as a matrix of logical values. — rectangular_mask • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -130,7 +130,7 @@ Value
diff --git a/docs/reference/reexports.html b/docs/reference/reexports.html
index 694a75d1..a59e8379 100644
--- a/docs/reference/reexports.html
+++ b/docs/reference/reexports.html
@@ -1,5 +1,5 @@
-Objects exported from other packages — reexports • Spectroscopy Analysis Tools (spant) Objects exported from other packages — reexports • Spectroscopy Analysis Tools (spant)
Spectroscopy Analysis Tools (spant)
- 2.21.0
+ 2.22.0
@@ -103,7 +103,7 @@ Objects exported from other packages
diff --git a/docs/reference/rep_array_dim.html b/docs/reference/rep_array_dim.html
index b9c49b4a..48c0a5ed 100644
--- a/docs/reference/rep_array_dim.html
+++ b/docs/reference/rep_array_dim.html
@@ -1,5 +1,5 @@
-Repeat an array over a given dimension. — rep_array_dim • Spectroscopy Analysis Tools (spant) Repeat an array over a given dimension. — rep_array_dim • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/rep_dyn.html b/docs/reference/rep_dyn.html
index 6bbfb0ef..89a4bb9b 100644
--- a/docs/reference/rep_dyn.html
+++ b/docs/reference/rep_dyn.html
@@ -1,5 +1,5 @@
-Replicate a scan in the dynamic dimension. — rep_dyn • Spectroscopy Analysis Tools (spant) Replicate a scan in the dynamic dimension. — rep_dyn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/rep_mrs.html b/docs/reference/rep_mrs.html
index 67730b5c..becb8f00 100644
--- a/docs/reference/rep_mrs.html
+++ b/docs/reference/rep_mrs.html
@@ -1,5 +1,5 @@
-Replicate a scan over a given dimension. — rep_mrs • Spectroscopy Analysis Tools (spant) Replicate a scan over a given dimension. — rep_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -138,7 +138,7 @@ Value
diff --git a/docs/reference/resample_basis.html b/docs/reference/resample_basis.html
index b0f2ab17..c7a6222a 100644
--- a/docs/reference/resample_basis.html
+++ b/docs/reference/resample_basis.html
@@ -1,5 +1,5 @@
-Resample a basis-set to match a mrs_data acquisition. — resample_basis • Spectroscopy Analysis Tools (spant) Resample a basis-set to match a mrs_data acquisition. — resample_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -116,7 +116,7 @@ Value
diff --git a/docs/reference/resample_img.html b/docs/reference/resample_img.html
index f1e7beaf..b0cc8f71 100644
--- a/docs/reference/resample_img.html
+++ b/docs/reference/resample_img.html
@@ -1,5 +1,5 @@
-Resample an image to match a target image space. — resample_img • Spectroscopy Analysis Tools (spant) Resample an image to match a target image space. — resample_img • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/resample_voi.html b/docs/reference/resample_voi.html
index 8fbfa836..a29ab096 100644
--- a/docs/reference/resample_voi.html
+++ b/docs/reference/resample_voi.html
@@ -1,7 +1,5 @@
-Resample a VOI to match a target image space using nearest-neighbour
-interpolation. — resample_voi • Spectroscopy Analysis Tools (spant) Resample a VOI to match a target image space using nearest-neighbour interpolation. — resample_voi • Spectroscopy Analysis Tools (spant) Reslice a nifti object to match the orientation of mrs data. — reslice_to_mrs • Spectroscopy Analysis Tools (spant) Reslice a nifti object to match the orientation of mrs data. — reslice_to_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/reson_table2mrs_data.html b/docs/reference/reson_table2mrs_data.html
index d75579ee..c5a2167a 100644
--- a/docs/reference/reson_table2mrs_data.html
+++ b/docs/reference/reson_table2mrs_data.html
@@ -1,5 +1,5 @@
-Generate mrs_data from a table of single Lorentzian resonances. — reson_table2mrs_data • Spectroscopy Analysis Tools (spant) Generate mrs_data from a table of single Lorentzian resonances. — reson_table2mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -119,7 +119,7 @@ Value
diff --git a/docs/reference/rm_dyns.html b/docs/reference/rm_dyns.html
index 5d5ef692..573e1f51 100644
--- a/docs/reference/rm_dyns.html
+++ b/docs/reference/rm_dyns.html
@@ -1,5 +1,5 @@
-Remove a subset of dynamic scans. — rm_dyns • Spectroscopy Analysis Tools (spant) Remove a subset of dynamic scans. — rm_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/scale_amp_molal.html b/docs/reference/scale_amp_molal.html
index aaeee1f2..7acb8cb0 100644
--- a/docs/reference/scale_amp_molal.html
+++ b/docs/reference/scale_amp_molal.html
@@ -1,7 +1,5 @@
-Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water). — scale_amp_molal • Spectroscopy Analysis Tools (spant) Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / kg of tissue water). — scale_amp_molal • Spectroscopy Analysis Tools (spant)
Spectroscopy Analysis Tools (spant)
- 2.21.0
+ 2.22.0
@@ -76,8 +74,7 @@
- Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water).
+ Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / kg of tissue water).
Source: R/amp_scaling.R
scale_amp_molal.Rd
@@ -163,7 +160,7 @@ Value
diff --git a/docs/reference/scale_amp_molal_pvc.html b/docs/reference/scale_amp_molal_pvc.html
index 962d6afc..4d194abd 100644
--- a/docs/reference/scale_amp_molal_pvc.html
+++ b/docs/reference/scale_amp_molal_pvc.html
@@ -1,7 +1,5 @@
-Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water). — scale_amp_molal_pvc • Spectroscopy Analysis Tools (spant)
@@ -75,8 +73,7 @@
- Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water).
+ Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / kg of tissue water).
Source: R/amp_scaling.R
scale_amp_molal_pvc.Rd
@@ -141,7 +138,7 @@ Value
diff --git a/docs/reference/scale_amp_molar.html b/docs/reference/scale_amp_molar.html
index 02358d91..dc87a338 100644
--- a/docs/reference/scale_amp_molar.html
+++ b/docs/reference/scale_amp_molar.html
@@ -1,7 +1,5 @@
-Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / Litre of tissue). — scale_amp_molar • Spectroscopy Analysis Tools (spant) Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / Litre of tissue). — scale_amp_molar • Spectroscopy Analysis Tools (spant) Convert default LCM/TARQUIN concentration scaling to molal units with partial
-volume correction. — scale_amp_molar2molal_pvc • Spectroscopy Analysis Tools (spant) Convert default LCM/TARQUIN concentration scaling to molal units with partial volume correction. — scale_amp_molar2molal_pvc • Spectroscopy Analysis Tools (spant) Scale fitted amplitudes to a ratio of signal amplitude. — scale_amp_ratio • Spectroscopy Analysis Tools (spant) Scale fitted amplitudes to a ratio of signal amplitude. — scale_amp_ratio • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -116,7 +116,7 @@ Value
diff --git a/docs/reference/scale_amp_ratio_value.html b/docs/reference/scale_amp_ratio_value.html
index 2036837a..6af8ac51 100644
--- a/docs/reference/scale_amp_ratio_value.html
+++ b/docs/reference/scale_amp_ratio_value.html
@@ -1,5 +1,5 @@
-Scale fitted amplitudes to a ratio of signal amplitude. — scale_amp_ratio_value • Spectroscopy Analysis Tools (spant) Scale fitted amplitudes to a ratio of signal amplitude. — scale_amp_ratio_value • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/scale_amp_water_ratio.html b/docs/reference/scale_amp_water_ratio.html
index 5b25e884..35a76b00 100644
--- a/docs/reference/scale_amp_water_ratio.html
+++ b/docs/reference/scale_amp_water_ratio.html
@@ -1,5 +1,5 @@
-Scale metabolite amplitudes as a ratio to the unsuppressed water amplitude. — scale_amp_water_ratio • Spectroscopy Analysis Tools (spant) Scale metabolite amplitudes as a ratio to the unsuppressed water amplitude. — scale_amp_water_ratio • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/scale_basis_amp.html b/docs/reference/scale_basis_amp.html
index 9401c3f1..5a58b5e5 100644
--- a/docs/reference/scale_basis_amp.html
+++ b/docs/reference/scale_basis_amp.html
@@ -1,5 +1,5 @@
-Scale a basis object by a scalar. — scale_basis_amp • Spectroscopy Analysis Tools (spant) Scale a basis object by a scalar. — scale_basis_amp • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/scale_basis_from_singlet.html b/docs/reference/scale_basis_from_singlet.html
index 0d542bc8..c9a19e77 100644
--- a/docs/reference/scale_basis_from_singlet.html
+++ b/docs/reference/scale_basis_from_singlet.html
@@ -1,5 +1,5 @@
-Scale a basis-set to be consistent with spant assumptions for water scaling. — scale_basis_from_singlet • Spectroscopy Analysis Tools (spant) Scale a basis-set to be consistent with spant assumptions for water scaling. — scale_basis_from_singlet • Spectroscopy Analysis Tools (spant)
Spectroscopy Analysis Tools (spant)
- 2.21.0
+ 2.22.0
@@ -127,7 +127,7 @@ Value
diff --git a/docs/reference/scale_mrs_amp.html b/docs/reference/scale_mrs_amp.html
index b5501a0d..990f058a 100644
--- a/docs/reference/scale_mrs_amp.html
+++ b/docs/reference/scale_mrs_amp.html
@@ -1,5 +1,5 @@
-Scale an mrs_data object by a scalar or vector or amplitudes. — scale_mrs_amp • Spectroscopy Analysis Tools (spant) Scale an mrs_data object by a scalar or vector or amplitudes. — scale_mrs_amp • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/scale_spec.html b/docs/reference/scale_spec.html
index 4f6ea835..6b3ddba4 100644
--- a/docs/reference/scale_spec.html
+++ b/docs/reference/scale_spec.html
@@ -1,5 +1,5 @@
-Scale mrs_data to a spectral region. — scale_spec • Spectroscopy Analysis Tools (spant) Scale mrs_data to a spectral region. — scale_spec • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -141,7 +141,7 @@ Value
diff --git a/docs/reference/sd.html b/docs/reference/sd.html
index ea1eec9f..3ae4dfd4 100644
--- a/docs/reference/sd.html
+++ b/docs/reference/sd.html
@@ -1,5 +1,5 @@
-Calculate the standard deviation spectrum from an mrs_data object. — sd • Spectroscopy Analysis Tools (spant) Calculate the standard deviation spectrum from an mrs_data object. — sd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/sd.mrs_data.html b/docs/reference/sd.mrs_data.html
index 3f92a49f..13bdda85 100644
--- a/docs/reference/sd.mrs_data.html
+++ b/docs/reference/sd.mrs_data.html
@@ -1,5 +1,5 @@
-Calculate the standard deviation spectrum from an mrs_data object. — sd.mrs_data • Spectroscopy Analysis Tools (spant) Calculate the standard deviation spectrum from an mrs_data object. — sd.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/seconds.html b/docs/reference/seconds.html
index b34d6627..467ee17f 100644
--- a/docs/reference/seconds.html
+++ b/docs/reference/seconds.html
@@ -1,5 +1,5 @@
-Return a time scale vector to match the FID of an MRS data object. — seconds • Spectroscopy Analysis Tools (spant) Return a time scale vector to match the FID of an MRS data object. — seconds • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/seq_cpmg_ideal.html b/docs/reference/seq_cpmg_ideal.html
index 547e96ab..45727c86 100644
--- a/docs/reference/seq_cpmg_ideal.html
+++ b/docs/reference/seq_cpmg_ideal.html
@@ -1,5 +1,5 @@
-CPMG style sequence with ideal pulses. — seq_cpmg_ideal • Spectroscopy Analysis Tools (spant) CPMG style sequence with ideal pulses. — seq_cpmg_ideal • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/seq_mega_press_ideal.html b/docs/reference/seq_mega_press_ideal.html
index 0769b8b4..a9cd7fa0 100644
--- a/docs/reference/seq_mega_press_ideal.html
+++ b/docs/reference/seq_mega_press_ideal.html
@@ -1,7 +1,5 @@
-MEGA-PRESS sequence with ideal localisation pulses and Gaussian shaped
-editing pulse. — seq_mega_press_ideal • Spectroscopy Analysis Tools (spant) MEGA-PRESS sequence with ideal localisation pulses and Gaussian shaped editing pulse. — seq_mega_press_ideal • Spectroscopy Analysis Tools (spant) PRESS sequence with shaped refocusing pulses. — seq_press_2d_shaped • Spectroscopy Analysis Tools (spant) PRESS sequence with shaped refocusing pulses. — seq_press_2d_shaped • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -165,7 +165,7 @@ Value
diff --git a/docs/reference/seq_press_ideal.html b/docs/reference/seq_press_ideal.html
index 8c976856..72c3af3d 100644
--- a/docs/reference/seq_press_ideal.html
+++ b/docs/reference/seq_press_ideal.html
@@ -1,5 +1,5 @@
-PRESS sequence with ideal pulses. — seq_press_ideal • Spectroscopy Analysis Tools (spant) PRESS sequence with ideal pulses. — seq_press_ideal • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/seq_pulse_acquire.html b/docs/reference/seq_pulse_acquire.html
index 4a88fc64..ad80571e 100644
--- a/docs/reference/seq_pulse_acquire.html
+++ b/docs/reference/seq_pulse_acquire.html
@@ -1,5 +1,5 @@
-Simple pulse and acquire sequence with ideal pulses. — seq_pulse_acquire • Spectroscopy Analysis Tools (spant) Simple pulse and acquire sequence with ideal pulses. — seq_pulse_acquire • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/seq_slaser_ideal.html b/docs/reference/seq_slaser_ideal.html
index 74688f4d..eb83e8e3 100644
--- a/docs/reference/seq_slaser_ideal.html
+++ b/docs/reference/seq_slaser_ideal.html
@@ -1,5 +1,5 @@
-sLASER sequence with ideal pulses. — seq_slaser_ideal • Spectroscopy Analysis Tools (spant) sLASER sequence with ideal pulses. — seq_slaser_ideal • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -126,7 +126,7 @@ Value
diff --git a/docs/reference/seq_spin_echo_ideal.html b/docs/reference/seq_spin_echo_ideal.html
index e23271de..4248716f 100644
--- a/docs/reference/seq_spin_echo_ideal.html
+++ b/docs/reference/seq_spin_echo_ideal.html
@@ -1,5 +1,5 @@
-Spin echo sequence with ideal pulses. — seq_spin_echo_ideal • Spectroscopy Analysis Tools (spant) Spin echo sequence with ideal pulses. — seq_spin_echo_ideal • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/seq_steam_ideal.html b/docs/reference/seq_steam_ideal.html
index a60685a8..1c8115d7 100644
--- a/docs/reference/seq_steam_ideal.html
+++ b/docs/reference/seq_steam_ideal.html
@@ -1,5 +1,5 @@
-STEAM sequence with ideal pulses. — seq_steam_ideal • Spectroscopy Analysis Tools (spant) STEAM sequence with ideal pulses. — seq_steam_ideal • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -128,7 +128,7 @@ Value
diff --git a/docs/reference/seq_steam_ideal_cof.html b/docs/reference/seq_steam_ideal_cof.html
index 8f225740..cba7af91 100644
--- a/docs/reference/seq_steam_ideal_cof.html
+++ b/docs/reference/seq_steam_ideal_cof.html
@@ -1,7 +1,5 @@
-STEAM sequence with ideal pulses and coherence order filtering to simulate
-gradient crushers. — seq_steam_ideal_cof • Spectroscopy Analysis Tools (spant) STEAM sequence with ideal pulses and coherence order filtering to simulate gradient crushers. — seq_steam_ideal_cof • Spectroscopy Analysis Tools (spant) STEAM sequence with ideal pulses using the z-rotation gradient simulation
-method described by Young et al JMR 140, 146-152 (1999). — seq_steam_ideal_young • Spectroscopy Analysis Tools (spant) STEAM sequence with ideal pulses using the z-rotation gradient simulation method described by Young et al JMR 140, 146-152 (1999). — seq_steam_ideal_young • Spectroscopy Analysis Tools (spant) Set the number of transients for an mrs_data object. — set_Ntrans • Spectroscopy Analysis Tools (spant) Set the number of transients for an mrs_data object. — set_Ntrans • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/set_def_acq_paras.html b/docs/reference/set_def_acq_paras.html
index 3e1b4004..cc2ada9c 100644
--- a/docs/reference/set_def_acq_paras.html
+++ b/docs/reference/set_def_acq_paras.html
@@ -1,5 +1,5 @@
-Set the default acquisition parameters. — set_def_acq_paras • Spectroscopy Analysis Tools (spant) Set the default acquisition parameters. — set_def_acq_paras • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Arguments
diff --git a/docs/reference/set_lcm_cmd.html b/docs/reference/set_lcm_cmd.html
index 2056ed01..42bb2f24 100644
--- a/docs/reference/set_lcm_cmd.html
+++ b/docs/reference/set_lcm_cmd.html
@@ -1,5 +1,5 @@
-Set the command to run the LCModel command-line program. — set_lcm_cmd • Spectroscopy Analysis Tools (spant) Set the command to run the LCModel command-line program. — set_lcm_cmd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/set_lw.html b/docs/reference/set_lw.html
index b64ec851..bb176c62 100644
--- a/docs/reference/set_lw.html
+++ b/docs/reference/set_lw.html
@@ -1,5 +1,5 @@
-Apply line-broadening to an mrs_data object to achieve a specified linewidth. — set_lw • Spectroscopy Analysis Tools (spant) Apply line-broadening to an mrs_data object to achieve a specified linewidth. — set_lw • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -123,7 +123,7 @@ Value
diff --git a/docs/reference/set_mask_xy_mat.html b/docs/reference/set_mask_xy_mat.html
index 49dc5d4e..52c4b617 100644
--- a/docs/reference/set_mask_xy_mat.html
+++ b/docs/reference/set_mask_xy_mat.html
@@ -1,5 +1,5 @@
-Set the masked voxels in a 2D MRSI dataset to given spectrum. — set_mask_xy_mat • Spectroscopy Analysis Tools (spant) Set the masked voxels in a 2D MRSI dataset to given spectrum. — set_mask_xy_mat • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Value
diff --git a/docs/reference/set_precomp_mode.html b/docs/reference/set_precomp_mode.html
index f44bd5d3..47c28e3b 100644
--- a/docs/reference/set_precomp_mode.html
+++ b/docs/reference/set_precomp_mode.html
@@ -1,5 +1,5 @@
-Set the precompute mode. — set_precomp_mode • Spectroscopy Analysis Tools (spant) Set the precompute mode. — set_precomp_mode • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/set_precomp_verbose.html b/docs/reference/set_precomp_verbose.html
index 1453a231..9c613505 100644
--- a/docs/reference/set_precomp_verbose.html
+++ b/docs/reference/set_precomp_verbose.html
@@ -1,5 +1,5 @@
-Set the verbosity of the precompute function. — set_precomp_verbose • Spectroscopy Analysis Tools (spant) Set the verbosity of the precompute function. — set_precomp_verbose • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/set_ref.html b/docs/reference/set_ref.html
index 8953fa50..5436dfa2 100644
--- a/docs/reference/set_ref.html
+++ b/docs/reference/set_ref.html
@@ -1,5 +1,5 @@
-Set the ppm reference value (eg ppm value at 0Hz). — set_ref • Spectroscopy Analysis Tools (spant) Set the ppm reference value (eg ppm value at 0Hz). — set_ref • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/set_td_pts.html b/docs/reference/set_td_pts.html
index 8a80d42a..586459ff 100644
--- a/docs/reference/set_td_pts.html
+++ b/docs/reference/set_td_pts.html
@@ -1,7 +1,5 @@
-Set the number of time-domain data points, truncating or zero-filling as
-appropriate. — set_td_pts • Spectroscopy Analysis Tools (spant) Set the number of time-domain data points, truncating or zero-filling as appropriate. — set_td_pts • Spectroscopy Analysis Tools (spant) Set the command to run the TARQUIN command-line program. — set_tqn_cmd • Spectroscopy Analysis Tools (spant) Set the command to run the TARQUIN command-line program. — set_tqn_cmd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/set_tr.html b/docs/reference/set_tr.html
index b2109ab0..65c9df5f 100644
--- a/docs/reference/set_tr.html
+++ b/docs/reference/set_tr.html
@@ -1,5 +1,5 @@
-Set the repetition time of an MRS dataset. — set_tr • Spectroscopy Analysis Tools (spant) Set the repetition time of an MRS dataset. — set_tr • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/shift.html b/docs/reference/shift.html
index ab0fe724..034591d0 100644
--- a/docs/reference/shift.html
+++ b/docs/reference/shift.html
@@ -1,5 +1,5 @@
-Apply a frequency shift to MRS data. — shift • Spectroscopy Analysis Tools (spant) Apply a frequency shift to MRS data. — shift • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/shift_basis.html b/docs/reference/shift_basis.html
index 2884be19..f55a65e0 100644
--- a/docs/reference/shift_basis.html
+++ b/docs/reference/shift_basis.html
@@ -1,5 +1,5 @@
-Apply frequency shifts to basis set signals. — shift_basis • Spectroscopy Analysis Tools (spant) Apply frequency shifts to basis set signals. — shift_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Value
diff --git a/docs/reference/sim_basis.html b/docs/reference/sim_basis.html
index c7838c46..bb5fefc6 100644
--- a/docs/reference/sim_basis.html
+++ b/docs/reference/sim_basis.html
@@ -1,5 +1,5 @@
-Simulate a basis set object. — sim_basis • Spectroscopy Analysis Tools (spant) Simulate a basis set object. — sim_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -136,7 +136,7 @@ Value
diff --git a/docs/reference/sim_basis_1h_brain.html b/docs/reference/sim_basis_1h_brain.html
index 62ed7389..f71ffa0b 100644
--- a/docs/reference/sim_basis_1h_brain.html
+++ b/docs/reference/sim_basis_1h_brain.html
@@ -1,7 +1,5 @@
-Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS
-sequence. Note, ideal pulses are assumed. — sim_basis_1h_brain • Spectroscopy Analysis Tools (spant) Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS sequence. Note, ideal pulses are assumed. — sim_basis_1h_brain • Spectroscopy Analysis Tools (spant) Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS
-sequence. Note, ideal pulses are assumed. — sim_basis_1h_brain_press • Spectroscopy Analysis Tools (spant) Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS sequence. Note, ideal pulses are assumed. — sim_basis_1h_brain_press • Spectroscopy Analysis Tools (spant) Simulate a macromolecular and lipid basis-set suitable for 1H brain MRS
-analysis. — sim_basis_mm_lip_lcm • Spectroscopy Analysis Tools (spant) Simulate a macromolecular and lipid basis-set suitable for 1H brain MRS analysis. — sim_basis_mm_lip_lcm • Spectroscopy Analysis Tools (spant) Simulate a basis file using TARQUIN. — sim_basis_tqn • Spectroscopy Analysis Tools (spant) Simulate a basis file using TARQUIN. — sim_basis_tqn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -129,7 +129,7 @@ Examples
diff --git a/docs/reference/sim_brain_1h.html b/docs/reference/sim_brain_1h.html
index 2044cf1a..717ee289 100644
--- a/docs/reference/sim_brain_1h.html
+++ b/docs/reference/sim_brain_1h.html
@@ -1,5 +1,5 @@
-Simulate MRS data with a similar appearance to normal brain (by default). — sim_brain_1h • Spectroscopy Analysis Tools (spant) Simulate MRS data with a similar appearance to normal brain (by default). — sim_brain_1h • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -159,7 +159,7 @@ Value
diff --git a/docs/reference/sim_mol.html b/docs/reference/sim_mol.html
index 23bcef50..77f76a50 100644
--- a/docs/reference/sim_mol.html
+++ b/docs/reference/sim_mol.html
@@ -1,5 +1,5 @@
-Simulate a mol_parameter object. — sim_mol • Spectroscopy Analysis Tools (spant) Simulate a mol_parameter object. — sim_mol • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -143,7 +143,7 @@ Value
diff --git a/docs/reference/sim_noise.html b/docs/reference/sim_noise.html
index 23875f79..a71477d4 100644
--- a/docs/reference/sim_noise.html
+++ b/docs/reference/sim_noise.html
@@ -1,5 +1,5 @@
-Simulate an mrs_data object containing simulated Gaussian noise. — sim_noise • Spectroscopy Analysis Tools (spant) Simulate an mrs_data object containing simulated Gaussian noise. — sim_noise • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -84,6 +84,7 @@ Simulate an mrs_data object containing simulated Gaussian noise.
ft = def_ft(),
N = def_N(),
ref = def_ref(),
+ nuc = def_nuc(),
dyns = 1,
fd = TRUE
)
@@ -111,6 +112,10 @@ Arguments
reference value for ppm scale.
nuc
+resonant nucleus.
dyns
number of dynamic scans to generate.
Value
diff --git a/docs/reference/sim_resonances.html b/docs/reference/sim_resonances.html
index 19e9a8a4..d4f8d7c0 100644
--- a/docs/reference/sim_resonances.html
+++ b/docs/reference/sim_resonances.html
@@ -1,5 +1,5 @@
-Simulate a MRS data object containing a set of simulated resonances. — sim_resonances • Spectroscopy Analysis Tools (spant) Simulate a MRS data object containing a set of simulated resonances. — sim_resonances • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -161,7 +161,7 @@ Examples
diff --git a/docs/reference/sim_th_excit_profile.html b/docs/reference/sim_th_excit_profile.html
index 5535c5ef..e781cab1 100644
--- a/docs/reference/sim_th_excit_profile.html
+++ b/docs/reference/sim_th_excit_profile.html
@@ -1,7 +1,5 @@
-Simulate an ideal pulse excitation profile by smoothing a top-hat function
-with a Gaussian. — sim_th_excit_profile • Spectroscopy Analysis Tools (spant) Simulate an ideal pulse excitation profile by smoothing a top-hat function with a Gaussian. — sim_th_excit_profile • Spectroscopy Analysis Tools (spant) Simulate an mrs_data object containing complex zero valued samples. — sim_zero • Spectroscopy Analysis Tools (spant) Simulate an mrs_data object containing complex zero valued samples. — sim_zero • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -78,7 +78,14 @@ Simulate an mrs_data object containing complex zero valued samples.
-
+
@@ -99,6 +106,10 @@ Arguments
reference value for ppm scale.
nuc
+resonant nucleus.
dyns
number of dynamic scans to generate.
Value
diff --git a/docs/reference/smooth_dyns.html b/docs/reference/smooth_dyns.html
index 4cc8da50..accf3a51 100644
--- a/docs/reference/smooth_dyns.html
+++ b/docs/reference/smooth_dyns.html
@@ -1,5 +1,5 @@
-Smooth data across the dynamic dimension with a Gaussian kernel. — smooth_dyns • Spectroscopy Analysis Tools (spant) Smooth data across the dynamic dimension with a Gaussian kernel. — smooth_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/sort_basis.html b/docs/reference/sort_basis.html
index 6a676ea2..d25cc006 100644
--- a/docs/reference/sort_basis.html
+++ b/docs/reference/sort_basis.html
@@ -1,5 +1,5 @@
-Sort the basis-set elements alphabetically. — sort_basis • Spectroscopy Analysis Tools (spant) Sort the basis-set elements alphabetically. — sort_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/spant-package.html b/docs/reference/spant-package.html
index b3dd8e21..90f19ec3 100644
--- a/docs/reference/spant-package.html
+++ b/docs/reference/spant-package.html
@@ -1,5 +1,5 @@
-spant: spectroscopy analysis tools. — spant-package • Spectroscopy Analysis Tools (spant) spant: spectroscopy analysis tools. — spant-package • Spectroscopy Analysis Tools (spant) Simulate and fit some spectra with ABfit for benchmarking purposes. Basic
-timing and performance metrics will be printed. — spant_abfit_benchmark • Spectroscopy Analysis Tools (spant) Simulate and fit some spectra with ABfit for benchmarking purposes. Basic timing and performance metrics will be printed. — spant_abfit_benchmark • Spectroscopy Analysis Tools (spant) Example MEGA-PRESS data with significant B0 drift. — spant_mpress_drift • Spectroscopy Analysis Tools (spant) Example MEGA-PRESS data with significant B0 drift. — spant_mpress_drift • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -83,7 +83,7 @@ Example MEGA-PRESS data with significant B0 drift.
Format
- An object of class mrs_data of length 13.
+ An object of class mrs_data of dimension 1 x 1 x 1 x 1 x 40 x 1 x 1024.
@@ -98,7 +98,7 @@ Format
diff --git a/docs/reference/spant_sim_fmrs_dataset.html b/docs/reference/spant_sim_fmrs_dataset.html
new file mode 100644
index 00000000..00e48b56
--- /dev/null
+++ b/docs/reference/spant_sim_fmrs_dataset.html
@@ -0,0 +1,117 @@
+
+Simulate an example fMRS dataset for a block design fMRS experiment and export a BIDS structure. — spant_sim_fmrs_dataset • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Simulate an example fMRS dataset for a block design fMRS experiment and export a BIDS structure.
+ Source: R/fmrs.R
+ spant_sim_fmrs_dataset.Rd
+
+
+
+ Simulate an example fMRS dataset for a block design fMRS experiment and
+export a BIDS structure.
+
+
+
+ spant_sim_fmrs_dataset(output_dir = NULL)
+
+
+
+ Arguments
+ - output_dir
+output directory for the BIDS data. Defaults to :
+"HOME/sim_fmrs_dataset/data".
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/spant_simulation_benchmark.html b/docs/reference/spant_simulation_benchmark.html
index 32daa8bf..d8cc6841 100644
--- a/docs/reference/spant_simulation_benchmark.html
+++ b/docs/reference/spant_simulation_benchmark.html
@@ -1,7 +1,5 @@
-Simulate a typical metabolite basis set for benchmarking. Timing metrics will
-be printed on completion. — spant_simulation_benchmark • Spectroscopy Analysis Tools (spant) Simulate a typical metabolite basis set for benchmarking. Timing metrics will be printed on completion. — spant_simulation_benchmark • Spectroscopy Analysis Tools (spant) Decompose an mrs_data object into white and gray matter spectra. — spec_decomp • Spectroscopy Analysis Tools (spant) Perform a mathematical operation on a spectral region. — spec_op • Spectroscopy Analysis Tools (spant) Perform a mathematical operation on a spectral region. — spec_op • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -98,8 +98,8 @@ Arguments
operator
-can be "sum" (default), "mean", "l2", "max", "min" or
-"max-min".
can be "sum" (default), "mean", "l2", "max", "max_cplx,
+"min" or "max-min".
freq_scale
@@ -129,7 +129,7 @@ Value
diff --git a/docs/reference/spin_sys.html b/docs/reference/spin_sys.html
index 853423a4..1eaa9e76 100644
--- a/docs/reference/spin_sys.html
+++ b/docs/reference/spin_sys.html
@@ -1,5 +1,5 @@
-Create a spin system object for pulse sequence simulation. — spin_sys • Spectroscopy Analysis Tools (spant) Create a spin system object for pulse sequence simulation. — spin_sys • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/spm_pve2categorical.html b/docs/reference/spm_pve2categorical.html
index 23a1bad9..70f10729 100644
--- a/docs/reference/spm_pve2categorical.html
+++ b/docs/reference/spm_pve2categorical.html
@@ -1,7 +1,5 @@
-Convert SPM style segmentation files to a single categorical image where
-the numerical values map as: 0) Other, 1) CSF, 2) GM and 3) WM. — spm_pve2categorical • Spectroscopy Analysis Tools (spant) Convert SPM style segmentation files to a single categorical image where the numerical values map as: 0) Other, 1) CSF, 2) GM and 3) WM. — spm_pve2categorical • Spectroscopy Analysis Tools (spant) Signal space projection method for lipid suppression. — ssp • Spectroscopy Analysis Tools (spant) Signal space projection method for lipid suppression. — ssp • Spectroscopy Analysis Tools (spant) Plot the fitting results of an object of class fit_result with
-individual basis set components shown. — stackplot.fit_result • Spectroscopy Analysis Tools (spant) Plot the fitting results of an object of class fit_result with individual basis set components shown. — stackplot.fit_result • Spectroscopy Analysis Tools (spant) Produce a plot with multiple traces. — stackplot • Spectroscopy Analysis Tools (spant) Produce a plot with multiple traces. — stackplot • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/stackplot.mrs_data.html b/docs/reference/stackplot.mrs_data.html
index 17ff5648..64eea445 100644
--- a/docs/reference/stackplot.mrs_data.html
+++ b/docs/reference/stackplot.mrs_data.html
@@ -1,5 +1,5 @@
-Stackplot plotting method for objects of class mrs_data. — stackplot.mrs_data • Spectroscopy Analysis Tools (spant) Stackplot plotting method for objects of class mrs_data. — stackplot.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -255,7 +255,7 @@ Arguments
diff --git a/docs/reference/sub_first_dyn.html b/docs/reference/sub_first_dyn.html
index dbd7f831..493b7242 100644
--- a/docs/reference/sub_first_dyn.html
+++ b/docs/reference/sub_first_dyn.html
@@ -1,5 +1,5 @@
-Subtract the first dynamic spectrum from a dynamic series. — sub_first_dyn • Spectroscopy Analysis Tools (spant) Subtract the first dynamic spectrum from a dynamic series. — sub_first_dyn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/sub_mean_dyns.html b/docs/reference/sub_mean_dyns.html
index 6e3bb2df..221bd0c1 100644
--- a/docs/reference/sub_mean_dyns.html
+++ b/docs/reference/sub_mean_dyns.html
@@ -1,5 +1,5 @@
-Subtract the mean dynamic spectrum from a dynamic series. — sub_mean_dyns • Spectroscopy Analysis Tools (spant) Subtract the mean dynamic spectrum from a dynamic series. — sub_mean_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/sub_median_dyns.html b/docs/reference/sub_median_dyns.html
index 134c495d..1e834f14 100644
--- a/docs/reference/sub_median_dyns.html
+++ b/docs/reference/sub_median_dyns.html
@@ -1,5 +1,5 @@
-Subtract the median dynamic spectrum from a dynamic series. — sub_median_dyns • Spectroscopy Analysis Tools (spant) Subtract the median dynamic spectrum from a dynamic series. — sub_median_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/sum_coils.html b/docs/reference/sum_coils.html
index 7bf559f2..e1ab3cc0 100644
--- a/docs/reference/sum_coils.html
+++ b/docs/reference/sum_coils.html
@@ -1,5 +1,5 @@
-Calculate the sum across receiver coil elements. — sum_coils • Spectroscopy Analysis Tools (spant) Calculate the sum across receiver coil elements. — sum_coils • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/sum_dyns.html b/docs/reference/sum_dyns.html
index a0be19d3..bbda2ffc 100644
--- a/docs/reference/sum_dyns.html
+++ b/docs/reference/sum_dyns.html
@@ -1,5 +1,5 @@
-Calculate the sum of data dynamics. — sum_dyns • Spectroscopy Analysis Tools (spant) Calculate the sum of data dynamics. — sum_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/sum_mrs.html b/docs/reference/sum_mrs.html
index a22f215b..3cc3ab9e 100644
--- a/docs/reference/sum_mrs.html
+++ b/docs/reference/sum_mrs.html
@@ -1,5 +1,5 @@
-Sum two mrs_data objects. — sum_mrs • Spectroscopy Analysis Tools (spant) Sum two mrs_data objects. — sum_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Value
diff --git a/docs/reference/sum_mrs_list.html b/docs/reference/sum_mrs_list.html
index f4e09aea..c3584348 100644
--- a/docs/reference/sum_mrs_list.html
+++ b/docs/reference/sum_mrs_list.html
@@ -1,5 +1,5 @@
-Return the sum of a list of mrs_data objects. — sum_mrs_list • Spectroscopy Analysis Tools (spant) Return the sum of a list of mrs_data objects. — sum_mrs_list • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/svs_1h_brain_analysis.html b/docs/reference/svs_1h_brain_analysis.html
index 8ce514db..dff0ef7d 100644
--- a/docs/reference/svs_1h_brain_analysis.html
+++ b/docs/reference/svs_1h_brain_analysis.html
@@ -1,5 +1,5 @@
-Standard SVS 1H brain analysis pipeline. — svs_1h_brain_analysis • Spectroscopy Analysis Tools (spant) Standard SVS 1H brain analysis pipeline. — svs_1h_brain_analysis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -199,7 +199,7 @@ Value
diff --git a/docs/reference/svs_1h_brain_analysis_dev.html b/docs/reference/svs_1h_brain_analysis_dev.html
index d70a14d3..d71bfea2 100644
--- a/docs/reference/svs_1h_brain_analysis_dev.html
+++ b/docs/reference/svs_1h_brain_analysis_dev.html
@@ -1,5 +1,5 @@
-Standard SVS 1H brain analysis pipeline. — svs_1h_brain_analysis_dev • Spectroscopy Analysis Tools (spant) Standard SVS 1H brain analysis pipeline. — svs_1h_brain_analysis_dev • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -193,7 +193,7 @@ Examples
diff --git a/docs/reference/svs_1h_brain_batch_analysis.html b/docs/reference/svs_1h_brain_batch_analysis.html
index 5631e8cc..15f7223e 100644
--- a/docs/reference/svs_1h_brain_batch_analysis.html
+++ b/docs/reference/svs_1h_brain_batch_analysis.html
@@ -1,5 +1,5 @@
-Batch interface to the standard SVS 1H brain analysis pipeline. — svs_1h_brain_batch_analysis • Spectroscopy Analysis Tools (spant) Batch interface to the standard SVS 1H brain analysis pipeline. — svs_1h_brain_batch_analysis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -144,7 +144,7 @@ Value
diff --git a/docs/reference/t_test_spec.html b/docs/reference/t_test_spec.html
new file mode 100644
index 00000000..56a7ea1b
--- /dev/null
+++ b/docs/reference/t_test_spec.html
@@ -0,0 +1,124 @@
+
+Perform a t-test on spectral data points. — t_test_spec • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+
+
+ Perform a t-test on spectral data points.
+
+
+
+ t_test_spec(mrs_data, group)
+
+
+
+ Arguments
+ - mrs_data
+an mrs_data object with spectra in the dynamic dimension.
- group
+vector describing the group membership of each dynamic spectrum.
+
+ Value
+
+
+a list of statistical results.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/td2fd.html b/docs/reference/td2fd.html
index 6748a6a8..f31ed524 100644
--- a/docs/reference/td2fd.html
+++ b/docs/reference/td2fd.html
@@ -1,5 +1,5 @@
-Transform time-domain data to the frequency-domain. — td2fd • Spectroscopy Analysis Tools (spant) Transform time-domain data to the frequency-domain. — td2fd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/td_conv_filt.html b/docs/reference/td_conv_filt.html
index a9f340c3..106b9b00 100644
--- a/docs/reference/td_conv_filt.html
+++ b/docs/reference/td_conv_filt.html
@@ -1,5 +1,5 @@
-Time-domain convolution based filter. — td_conv_filt • Spectroscopy Analysis Tools (spant) Time-domain convolution based filter. — td_conv_filt • Spectroscopy Analysis Tools (spant) Time-domain spectral registration. — tdsr • Spectroscopy Analysis Tools (spant) Time-domain spectral registration. — tdsr • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -121,7 +121,7 @@ Value
diff --git a/docs/reference/te.html b/docs/reference/te.html
index 010361b1..4a65711d 100644
--- a/docs/reference/te.html
+++ b/docs/reference/te.html
@@ -1,5 +1,5 @@
-Return the echo time of an MRS dataset. — te • Spectroscopy Analysis Tools (spant) Return the echo time of an MRS dataset. — te • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/tr.html b/docs/reference/tr.html
index 0c0bd63b..2e749e02 100644
--- a/docs/reference/tr.html
+++ b/docs/reference/tr.html
@@ -1,5 +1,5 @@
-Return the repetition time of an MRS dataset. — tr • Spectroscopy Analysis Tools (spant) Return the repetition time of an MRS dataset. — tr • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/varpro_3_para_opts.html b/docs/reference/varpro_3_para_opts.html
index c2270a16..52d7cd84 100644
--- a/docs/reference/varpro_3_para_opts.html
+++ b/docs/reference/varpro_3_para_opts.html
@@ -1,5 +1,5 @@
-Return a list of options for VARPRO based fitting with 3 free parameters. — varpro_3_para_opts • Spectroscopy Analysis Tools (spant) Return a list of options for VARPRO based fitting with 3 free parameters. — varpro_3_para_opts • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -141,7 +141,7 @@ Value
diff --git a/docs/reference/varpro_basic_opts.html b/docs/reference/varpro_basic_opts.html
index 32c86d22..c5104891 100644
--- a/docs/reference/varpro_basic_opts.html
+++ b/docs/reference/varpro_basic_opts.html
@@ -1,5 +1,5 @@
-Return a list of options for a basic VARPRO analysis. — varpro_basic_opts • Spectroscopy Analysis Tools (spant) Return a list of options for a basic VARPRO analysis. — varpro_basic_opts • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -118,7 +118,7 @@ Value
diff --git a/docs/reference/varpro_opts.html b/docs/reference/varpro_opts.html
index 2aabf11d..6332f730 100644
--- a/docs/reference/varpro_opts.html
+++ b/docs/reference/varpro_opts.html
@@ -1,5 +1,5 @@
-Return a list of options for VARPRO based fitting. — varpro_opts • Spectroscopy Analysis Tools (spant) Return a list of options for VARPRO based fitting. — varpro_opts • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -177,7 +177,7 @@ Examples
diff --git a/docs/reference/vec2mrs_data.html b/docs/reference/vec2mrs_data.html
index 0cccd73b..f0d58bf0 100644
--- a/docs/reference/vec2mrs_data.html
+++ b/docs/reference/vec2mrs_data.html
@@ -1,5 +1,5 @@
-Convert a vector into a mrs_data object. — vec2mrs_data • Spectroscopy Analysis Tools (spant) Convert a vector into a mrs_data object. — vec2mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -80,10 +80,11 @@ Convert a vector into a mrs_data object.
vec2mrs_data(
vec,
- fs = def_fs(),
- ft = def_ft(),
- ref = def_ref(),
- nuc = def_nuc(),
+ mrs_data = NULL,
+ fs = NULL,
+ ft = NULL,
+ ref = NULL,
+ nuc = NULL,
dyns = 1,
fd = FALSE
)
@@ -95,6 +96,10 @@ Arguments
the data vector.
mrs_data
+example data to copy acquisition parameters from.
fs
sampling frequency in Hz.
Arguments
fd
-flag to indicate if the matrix is in the frequency domain (logical).
flag to indicate if the vector is in the frequency domain (logical).
Value
diff --git a/docs/reference/write_basis.html b/docs/reference/write_basis.html
index b6e27cbd..94c5e021 100644
--- a/docs/reference/write_basis.html
+++ b/docs/reference/write_basis.html
@@ -1,5 +1,5 @@
-Write a basis object to an LCModel .basis formatted file. — write_basis • Spectroscopy Analysis Tools (spant) Write a basis object to an LCModel .basis formatted file. — write_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -108,7 +108,7 @@ Arguments
diff --git a/docs/reference/write_basis_tqn.html b/docs/reference/write_basis_tqn.html
index 6aa51c1d..116c73ec 100644
--- a/docs/reference/write_basis_tqn.html
+++ b/docs/reference/write_basis_tqn.html
@@ -1,5 +1,5 @@
-Generate a basis file using TARQUIN. — write_basis_tqn • Spectroscopy Analysis Tools (spant) Generate a basis file using TARQUIN. — write_basis_tqn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Examples
diff --git a/docs/reference/write_mrs.html b/docs/reference/write_mrs.html
index fff25f15..124b9dc4 100644
--- a/docs/reference/write_mrs.html
+++ b/docs/reference/write_mrs.html
@@ -1,5 +1,5 @@
-Write MRS data object to file. — write_mrs • Spectroscopy Analysis Tools (spant) Write MRS data object to file. — write_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Arguments
diff --git a/docs/reference/write_mrs_nifti.html b/docs/reference/write_mrs_nifti.html
index f4bf1921..bd3ed4b7 100644
--- a/docs/reference/write_mrs_nifti.html
+++ b/docs/reference/write_mrs_nifti.html
@@ -1,5 +1,5 @@
-Write MRS data object to file in NIFTI format. — write_mrs_nifti • Spectroscopy Analysis Tools (spant) Write MRS data object to file in NIFTI format. — write_mrs_nifti • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/write_pulse_ascii.html b/docs/reference/write_pulse_ascii.html
index 067ae086..221f8ebb 100644
--- a/docs/reference/write_pulse_ascii.html
+++ b/docs/reference/write_pulse_ascii.html
@@ -1,5 +1,5 @@
-Write an ASCII formatted pulse file. — write_pulse_ascii • Spectroscopy Analysis Tools (spant) Write an ASCII formatted pulse file. — write_pulse_ascii • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/zero_fade_spec.html b/docs/reference/zero_fade_spec.html
index c703745c..c8b572c3 100644
--- a/docs/reference/zero_fade_spec.html
+++ b/docs/reference/zero_fade_spec.html
@@ -1,7 +1,5 @@
-Fade a spectrum to zero by frequency domain multiplication with a tanh
-function. Note this operation distorts data points at the end of the FID. — zero_fade_spec • Spectroscopy Analysis Tools (spant) Fade a spectrum to zero by frequency domain multiplication with a tanh function. Note this operation distorts data points at the end of the FID. — zero_fade_spec • Spectroscopy Analysis Tools (spant) Zero all coherences including and above a given order. — zero_higher_orders • Spectroscopy Analysis Tools (spant) Zero all coherences including and above a given order. — zero_higher_orders • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Value
diff --git a/docs/reference/zero_td_pts_end.html b/docs/reference/zero_td_pts_end.html
index 8c1123c8..71d24ebb 100644
--- a/docs/reference/zero_td_pts_end.html
+++ b/docs/reference/zero_td_pts_end.html
@@ -1,5 +1,5 @@
-Set mrs_data object data points at the end of the FID to zero. — zero_td_pts_end • Spectroscopy Analysis Tools (spant) Set mrs_data object data points at the end of the FID to zero. — zero_td_pts_end • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/zf.html b/docs/reference/zf.html
index 85e2013c..baf50256 100644
--- a/docs/reference/zf.html
+++ b/docs/reference/zf.html
@@ -1,5 +1,5 @@
-Zero-fill MRS data in the time domain. — zf • Spectroscopy Analysis Tools (spant) Zero-fill MRS data in the time domain. — zf • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -125,7 +125,7 @@ Value
diff --git a/docs/reference/zf_xy.html b/docs/reference/zf_xy.html
index ebca3999..c4104a74 100644
--- a/docs/reference/zf_xy.html
+++ b/docs/reference/zf_xy.html
@@ -1,5 +1,5 @@
-Zero-fill MRSI data in the k-space x-y direction. — zf_xy • Spectroscopy Analysis Tools (spant) Zero-fill MRSI data in the k-space x-y direction. — zf_xy • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -113,7 +113,7 @@ Value
diff --git a/docs/sitemap.xml b/docs/sitemap.xml
index e2139f71..4c39f515 100644
--- a/docs/sitemap.xml
+++ b/docs/sitemap.xml
@@ -216,6 +216,12 @@
https://martin3141.github.io/spant/reference/comb_coils_fp_pc.html
+
+ https://martin3141.github.io/spant/reference/comb_coils_mrsi_gls.html
+
+
+ https://martin3141.github.io/spant/reference/comb_coils_svs_gls.html
+
https://martin3141.github.io/spant/reference/comb_csv_results.html
@@ -411,6 +417,9 @@
https://martin3141.github.io/spant/reference/gen_conv_reg.html
+
+ https://martin3141.github.io/spant/reference/gen_group_reg.html
+
https://martin3141.github.io/spant/reference/gen_impulse_reg.html
@@ -555,6 +564,15 @@
https://martin3141.github.io/spant/reference/glm_spec.html
+
+ https://martin3141.github.io/spant/reference/glm_spec_fmrs_fl.html
+
+
+ https://martin3141.github.io/spant/reference/glm_spec_fmrs_group.html
+
+
+ https://martin3141.github.io/spant/reference/glm_spec_group_linhyp.html
+
https://martin3141.github.io/spant/reference/grid_shift_xy.html
@@ -690,9 +708,15 @@
https://martin3141.github.io/spant/reference/mrs_data2basis.html
+
+ https://martin3141.github.io/spant/reference/mrs_data2bids.html
+
https://martin3141.github.io/spant/reference/mrs_data2mat.html
+
+ https://martin3141.github.io/spant/reference/mrs_data2spec_mat.html
+
https://martin3141.github.io/spant/reference/mrs_data2vec.html
@@ -741,6 +765,9 @@
https://martin3141.github.io/spant/reference/phase.html
+
+ https://martin3141.github.io/spant/reference/phase_ref_1h_brain.html
+
https://martin3141.github.io/spant/reference/plot.fit_result.html
@@ -780,6 +807,12 @@
https://martin3141.github.io/spant/reference/precomp.html
+
+ https://martin3141.github.io/spant/reference/preproc_svs.html
+
+
+ https://martin3141.github.io/spant/reference/preproc_svs_dataset.html
+
https://martin3141.github.io/spant/reference/print.fit_result.html
@@ -1050,6 +1083,9 @@
https://martin3141.github.io/spant/reference/spant_mpress_drift.html
+
+ https://martin3141.github.io/spant/reference/spant_sim_fmrs_dataset.html
+
https://martin3141.github.io/spant/reference/spant_simulation_benchmark.html
@@ -1107,6 +1143,9 @@
https://martin3141.github.io/spant/reference/svs_1h_brain_batch_analysis.html
+
+ https://martin3141.github.io/spant/reference/t_test_spec.html
+
https://martin3141.github.io/spant/reference/td2fd.html
Append MRS data across the coil dimension, assumes they matched across the -other dimensions.
Append MRS data across the coil dimension, assumes they matched across the other dimensions.
Append MRS data across the dynamic dimension, assumes they matched across the -other dimensions.
Append MRS data across the dynamic dimension, assumes they matched across the other dimensions.
All functions
- Convert a 7 dimensional array in into a mrs_data object. The array dimensions
-should be ordered as : dummy, X, Y, Z, dynamic, coil, FID.
Convert a 7 dimensional array in into a mrs_data object. The array dimensions should be ordered as : dummy, X, Y, Z, dynamic, coil, FID.
- Perform zeroth-order phase correction based on the minimisation of the
-squared difference between the real and magnitude components of the
-spectrum.
Perform zeroth-order phase correction based on the minimisation of the squared difference between the real and magnitude components of the spectrum.
@@ -213,13 +206,11 @@ All functions
- Convert a basis object to an mrs_data object - where basis signals are spread
-across the dynamic dimension.
Convert a basis object to an mrs_data object - where basis signals are spread across the dynamic dimension.
- Generate a spline basis, slightly adapted from : "Splines, knots, and
-penalties", Eilers 2010.
Generate a spline basis, slightly adapted from : "Splines, knots, and penalties", Eilers 2010.
@@ -243,8 +234,7 @@ All functions
- Covert a beta value in the time-domain to an equivalent linewidth in Hz:
-x * exp(-i * t * t * beta).
Covert a beta value in the time-domain to an equivalent linewidth in Hz: x * exp(-i * t * t * beta).
@@ -272,8 +262,7 @@ All functions
- Perform a polynomial fit, subtract and return the standard deviation of the
-residuals.
Perform a polynomial fit, subtract and return the standard deviation of the residuals.
@@ -306,6 +295,14 @@ All functions comb_coils()
Combine coil data based on the first data point of a reference signal.
+
+
+ Combine MRSI coil data using the GLS method presented by An et al JMRI 37:1445-1450 (2013).
+
+
+ Combine SVS coil data using the GLS method presented by An et al JMRI 37:1445-1450 (2013).
@@ -345,9 +342,7 @@ All functions
- Crop mrs_data object data points in the time-domain rounding down to
-the next smallest power of two (pot). Data that already has a pot length will
-not be changed.
Crop mrs_data object data points in the time-domain rounding down to the next smallest power of two (pot). Data that already has a pot length will not be changed.
@@ -355,13 +350,11 @@ All functions
- Compute the vector cross product between vectors x and y. Adapted from
-http://stackoverflow.com/questions/15162741/what-is-rs-crossproduct-function
Compute the vector cross product between vectors x and y. Adapted from http://stackoverflow.com/questions/15162741/what-is-rs-crossproduct-function
- Decimate an MRS signal to half the original sampling frequency by filtering
-in the frequency domain before down sampling.
Decimate an MRS signal to half the original sampling frequency by filtering in the frequency domain before down sampling.
@@ -377,8 +370,7 @@ All functions
- Return (and optionally modify using the input arguments) a list of the
-default acquisition parameters.
Return (and optionally modify using the input arguments) a list of the default acquisition parameters.
@@ -410,14 +402,11 @@ All functions
- Downsample an MRS signal by a factor of 2 by removing every other data point
-in the time-domain. Note, signals outside the new sampling frequency will be
-aliased.
Downsample an MRS signal by a factor of 2 by removing every other data point in the time-domain. Note, signals outside the new sampling frequency will be aliased.
- Return a time scale vector of acquisition times for a dynamic MRS scan. The
-first temporal scan is assigned a value of 0.
Return a time scale vector of acquisition times for a dynamic MRS scan. The first temporal scan is assigned a value of 0.
@@ -429,8 +418,7 @@ All functions
- Estimate the standard deviation of the noise from a segment of an mrs_data
-object.
Estimate the standard deviation of the noise from a segment of an mrs_data object.
@@ -486,8 +474,7 @@ All functions
- Perform a zeroth order phase correction based on the phase of the first data
-point in the time-domain.
Perform a zeroth order phase correction based on the phase of the first data point in the time-domain.
@@ -507,8 +494,7 @@ All functions
- Perform a fft and fftshift on a matrix with each column replaced by its
-shifted fft.
Perform a fft and fftshift on a matrix with each column replaced by its shifted fft.
@@ -536,8 +522,11 @@ All functions
- Generate regressors by convolving a specified response function with a
-stimulus.
Generate regressors by convolving a specified response function with a stimulus.
+
+
+ Expand a regressor matrix for a group analysis.
@@ -553,28 +542,23 @@ All functions
- Return a character vector of common 1H molecules found in healthy human
-brain.
Return a character vector of common 1H molecules found in healthy human brain.
- Return a list of mol_parameter objects suitable for 1H brain MRS
-analyses.
Return a list of mol_parameter objects suitable for 1H brain MRS analyses.
- Return a list of mol_parameter objects suitable for 1H brain MRS
-analyses.
Return a list of mol_parameter objects suitable for 1H brain MRS analyses.
- Return a list of mol_parameter objects suitable for 1H brain MRS
-analyses.
Return a list of mol_parameter objects suitable for 1H brain MRS analyses.
- Return a list of mol_parameter objects suitable for 1H brain MRS
-analyses.
Return a list of mol_parameter objects suitable for 1H brain MRS analyses.
@@ -582,8 +566,7 @@ All functions
- Return a character vector of molecules included in the Gold Star Phantoms
-SPECTRE phantom.
Return a character vector of molecules included in the Gold Star Phantoms SPECTRE phantom.
@@ -635,8 +618,7 @@ All functions
- Return a character array of names that may be used with the
-get_mol_paras function.
Return a character array of names that may be used with the get_mol_paras function.
@@ -700,8 +682,7 @@ All functions
- Return an array of amplitudes derived from fitting the initial points in the
-time domain and extrapolating back to t=0.
Return an array of amplitudes derived from fitting the initial points in the time domain and extrapolating back to t=0.
@@ -709,8 +690,7 @@ All functions
- Generate a mol_parameters object for a simple spin system with one
-resonance.
Generate a mol_parameters object for a simple spin system with one resonance.
@@ -731,6 +711,18 @@ All functions glm_spec()
Perform a GLM analysis of dynamic MRS data in the spectral domain.
+
+
+ Perform first-level spectral GLM analysis of an fMRS dataset.
+
+
+ Perform group-level spectral GLM analysis of an fMRS dataset.
+
+
+ Test a group-level spectral GLM linear hypothesis.
@@ -766,8 +758,7 @@ All functions
- Perform an ifft and ifftshift on a matrix with each column replaced by its
-shifted ifft.
Perform an ifft and ifftshift on a matrix with each column replaced by its shifted ifft.
@@ -799,8 +790,7 @@ All functions
- Check if the chemical shift dimension of an MRS data object is in the
-frequency domain.
Check if the chemical shift dimension of an MRS data object is in the frequency domain.
@@ -820,18 +810,15 @@ All functions
- Covert a linewidth in Hz to an equivalent alpha value in the time-domain ie:
-x * exp(-t * alpha).
Covert a linewidth in Hz to an equivalent alpha value in the time-domain ie: x * exp(-t * alpha).
- Covert a linewidth in Hz to an equivalent beta value in the time-domain ie:
-x * exp(-t * t * beta).
Covert a linewidth in Hz to an equivalent beta value in the time-domain ie: x * exp(-t * t * beta).
- Make a basis-set object from a directory containing LCModel formatted RAW
-files.
Make a basis-set object from a directory containing LCModel formatted RAW files.
@@ -851,8 +838,7 @@ All functions
- Mask the voxels outside an elliptical region spanning the MRSI dataset in the
-x-y plane.
Mask the voxels outside an elliptical region spanning the MRSI dataset in the x-y plane.
@@ -860,13 +846,11 @@ All functions
- Convert a matrix (with spectral points in the column dimension and dynamics
-in the row dimensions) into a mrs_data object.
Convert a matrix (with spectral points in the column dimension and dynamics in the row dimensions) into a mrs_data object.
- Matrix exponential function taken from complexplus package to reduce the
-number of spant dependencies.
Matrix exponential function taken from complexplus package to reduce the number of spant dependencies.
@@ -914,31 +898,31 @@ All functions
- Convert an mrs_data object to basis object - where basis signals are spread
-across the dynamic dimension in the MRS data.
Convert an mrs_data object to basis object - where basis signals are spread across the dynamic dimension in the MRS data.
+
+
+ Create a BIDS file structure from a vector of MRS data paths or list of mrs_data objects.
- Convert mrs_data object to a matrix, with spectral points in the column
-dimension and dynamics in the row dimension.
Convert mrs_data object to a matrix, with spectral points in the column dimension and dynamics in the row dimension.
-
+
- Convert mrs_data object to a vector.
Convert mrs_data object to a matrix, with spectral points in the column dimension and dynamics in the row dimension.
-
+
- Create a BIDS directory and file structure from a list of mrs_data objects.
Convert mrs_data object to a vector.
- Perform a fftshift on a matrix, with each column replaced by its shifted
-result.
Perform a fftshift on a matrix, with each column replaced by its shifted result.
- Perform an ifftshift on a matrix, with each column replaced by its shifted
-result.
Perform an ifftshift on a matrix, with each column replaced by its shifted result.
@@ -946,9 +930,7 @@ All functions
- Flip the x data dimension order of a nifti image. This corresponds to
-flipping MRI data in the left-right direction, assuming the data in save in
-neurological format (can check with fslorient program).
Flip the x data dimension order of a nifti image. This corresponds to flipping MRI data in the left-right direction, assuming the data in save in neurological format (can check with fslorient program).
@@ -964,8 +946,7 @@ All functions
- Search for the highest peak in a spectral region and return the frequency,
-height and FWHM.
Search for the highest peak in a spectral region and return the frequency, height and FWHM.
@@ -974,6 +955,10 @@ All functions phase()
Apply phasing parameters to MRS data.
+
+
+ Corrected zero order phase and chemical shift offset in 1H MRS data from the brain.
@@ -1005,8 +990,7 @@ All functions
- Plot an interactive slice map from a data array where voxels can be selected
-to display a corresponding spectrum.
Plot an interactive slice map from a data array where voxels can be selected to display a corresponding spectrum.
@@ -1026,8 +1010,15 @@ All functions
- Save function results to file and load on subsequent calls to avoid repeat
-computation.
Save function results to file and load on subsequent calls to avoid repeat computation.
+
+
+ Preprocess and perform quality assessment of a single SVS data set.
+
+
+ Preprocess and perform quality assessment of one or more SVS data sets.
@@ -1055,15 +1046,11 @@ All functions
- Read a directory containing Siemens MRS IMA files and combine along the coil
-dimension. Note that the coil ID is inferred from the sorted file name and
-should be checked when consistency is required between two directories.
Read a directory containing Siemens MRS IMA files and combine along the coil dimension. Note that the coil ID is inferred from the sorted file name and should be checked when consistency is required between two directories.
- Read a directory containing Siemens MRS IMA files and combine along the
-dynamic dimension. Note that the coil ID is inferred from the sorted file
-name and should be checked when consistency is required.
Read a directory containing Siemens MRS IMA files and combine along the dynamic dimension. Note that the coil ID is inferred from the sorted file name and should be checked when consistency is required.
@@ -1103,13 +1090,11 @@ All functions
- Reconstruct complex time-domain data from the real part of frequency-domain
-data.
Reconstruct complex time-domain data from the real part of frequency-domain data.
- Reconstruct complex time-domain data from the real part of frequency-domain
-data.
Reconstruct complex time-domain data from the real part of frequency-domain data.
@@ -1141,8 +1126,7 @@ All functions
- Resample a VOI to match a target image space using nearest-neighbour
-interpolation.
Resample a VOI to match a target image space using nearest-neighbour interpolation.
@@ -1158,23 +1142,19 @@ All functions
- Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water).
Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / kg of tissue water).
- Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water).
Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / kg of tissue water).
- Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / Litre of tissue).
Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / Litre of tissue).
- Convert default LCM/TARQUIN concentration scaling to molal units with partial
-volume correction.
Convert default LCM/TARQUIN concentration scaling to molal units with partial volume correction.
@@ -1222,8 +1202,7 @@ All functions
- MEGA-PRESS sequence with ideal localisation pulses and Gaussian shaped
-editing pulse.
MEGA-PRESS sequence with ideal localisation pulses and Gaussian shaped editing pulse.
@@ -1251,13 +1230,11 @@ All functions
- STEAM sequence with ideal pulses and coherence order filtering to simulate
-gradient crushers.
STEAM sequence with ideal pulses and coherence order filtering to simulate gradient crushers.
- STEAM sequence with ideal pulses using the z-rotation gradient simulation
-method described by Young et al JMR 140, 146-152 (1999).
STEAM sequence with ideal pulses using the z-rotation gradient simulation method described by Young et al JMR 140, 146-152 (1999).
@@ -1293,8 +1270,7 @@ All functions
- Set the number of time-domain data points, truncating or zero-filling as
-appropriate.
Set the number of time-domain data points, truncating or zero-filling as appropriate.
@@ -1318,18 +1294,15 @@ All functions
- Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS
-sequence. Note, ideal pulses are assumed.
Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS sequence. Note, ideal pulses are assumed.
- Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS
-sequence. Note, ideal pulses are assumed.
Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS sequence. Note, ideal pulses are assumed.
- Simulate a macromolecular and lipid basis-set suitable for 1H brain MRS
-analysis.
Simulate a macromolecular and lipid basis-set suitable for 1H brain MRS analysis.
@@ -1353,8 +1326,7 @@ All functions
- Simulate an ideal pulse excitation profile by smoothing a top-hat function
-with a Gaussian.
Simulate an ideal pulse excitation profile by smoothing a top-hat function with a Gaussian.
@@ -1374,17 +1346,19 @@ All functions
- Simulate and fit some spectra with ABfit for benchmarking purposes. Basic
-timing and performance metrics will be printed.
Simulate and fit some spectra with ABfit for benchmarking purposes. Basic timing and performance metrics will be printed.
Example MEGA-PRESS data with significant B0 drift.
+
+
+ Simulate an example fMRS dataset for a block design fMRS experiment and export a BIDS structure.
- Simulate a typical metabolite basis set for benchmarking. Timing metrics will
-be printed on completion.
Simulate a typical metabolite basis set for benchmarking. Timing metrics will be printed on completion.
@@ -1400,8 +1374,7 @@ All functions
- Convert SPM style segmentation files to a single categorical image where
-the numerical values map as: 0) Other, 1) CSF, 2) GM and 3) WM.
Convert SPM style segmentation files to a single categorical image where the numerical values map as: 0) Other, 1) CSF, 2) GM and 3) WM.
@@ -1413,8 +1386,7 @@ All functions
- Plot the fitting results of an object of class fit_result with
-individual basis set components shown.
Plot the fitting results of an object of class fit_result with individual basis set components shown.
@@ -1459,6 +1431,10 @@ All functions svs_1h_brain_batch_analysis()
Batch interface to the standard SVS 1H brain analysis pipeline.
+
+
+ Perform a t-test on spectral data points.
@@ -1518,8 +1494,7 @@ All functions
- Fade a spectrum to zero by frequency domain multiplication with a tanh
-function. Note this operation distorts data points at the end of the FID.
Fade a spectrum to zero by frequency domain multiplication with a tanh function. Note this operation distorts data points at the end of the FID.
@@ -1549,7 +1524,7 @@ All functions
diff --git a/docs/reference/int_spec.html b/docs/reference/int_spec.html
index c7060fe7..783325a8 100644
--- a/docs/reference/int_spec.html
+++ b/docs/reference/int_spec.html
@@ -1,5 +1,5 @@
-Integrate a spectral region. — int_spec • Spectroscopy Analysis Tools (spant) Integrate a spectral region. — int_spec • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -118,7 +118,7 @@ Value
diff --git a/docs/reference/interleave_dyns.html b/docs/reference/interleave_dyns.html
index effe5543..441eff27 100644
--- a/docs/reference/interleave_dyns.html
+++ b/docs/reference/interleave_dyns.html
@@ -1,5 +1,5 @@
-Interleave the first and second half of a dynamic series. — interleave_dyns • Spectroscopy Analysis Tools (spant) Interleave the first and second half of a dynamic series. — interleave_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/inv_even_dyns.html b/docs/reference/inv_even_dyns.html
index 9f9d4fff..dcb781dc 100644
--- a/docs/reference/inv_even_dyns.html
+++ b/docs/reference/inv_even_dyns.html
@@ -1,5 +1,5 @@
-Invert even numbered dynamic scans starting from 1 (2,4,6...). — inv_even_dyns • Spectroscopy Analysis Tools (spant) Invert even numbered dynamic scans starting from 1 (2,4,6...). — inv_even_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/inv_odd_dyns.html b/docs/reference/inv_odd_dyns.html
index 26212e2b..78d64660 100644
--- a/docs/reference/inv_odd_dyns.html
+++ b/docs/reference/inv_odd_dyns.html
@@ -1,5 +1,5 @@
-Invert odd numbered dynamic scans starting from 1 (1,3,5...). — inv_odd_dyns • Spectroscopy Analysis Tools (spant) Invert odd numbered dynamic scans starting from 1 (1,3,5...). — inv_odd_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/is.def.html b/docs/reference/is.def.html
index f196ffd0..a67b9eba 100644
--- a/docs/reference/is.def.html
+++ b/docs/reference/is.def.html
@@ -1,5 +1,5 @@
-Check if an object is defined, which is the same as being not NULL. — is.def • Spectroscopy Analysis Tools (spant) Check if an object is defined, which is the same as being not NULL. — is.def • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/is_fd.html b/docs/reference/is_fd.html
index 3b0ca165..18a193aa 100644
--- a/docs/reference/is_fd.html
+++ b/docs/reference/is_fd.html
@@ -1,7 +1,5 @@
-Check if the chemical shift dimension of an MRS data object is in the
-frequency domain. — is_fd • Spectroscopy Analysis Tools (spant) Check if the chemical shift dimension of an MRS data object is in the frequency domain. — is_fd • Spectroscopy Analysis Tools (spant) Transform 2D MRSI data from k-space to image space in the x-y direction. — kspace2img_xy • Spectroscopy Analysis Tools (spant) Transform 2D MRSI data from k-space to image space in the x-y direction. — kspace2img_xy • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/l2_reg.html b/docs/reference/l2_reg.html
index 3d781d80..21aa9849 100644
--- a/docs/reference/l2_reg.html
+++ b/docs/reference/l2_reg.html
@@ -1,5 +1,5 @@
-Perform l2 regularisation artefact suppression. — l2_reg • Spectroscopy Analysis Tools (spant) Perform l2 regularisation artefact suppression. — l2_reg • Spectroscopy Analysis Tools (spant) Apply line-broadening (apodisation) to MRS data or basis object. — lb • Spectroscopy Analysis Tools (spant) Apply line-broadening (apodisation) to MRS data or basis object. — lb • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -123,7 +123,7 @@ Value
diff --git a/docs/reference/lofdc.html b/docs/reference/lofdc.html
index 5419b1ec..31347a25 100644
--- a/docs/reference/lofdc.html
+++ b/docs/reference/lofdc.html
@@ -1,5 +1,5 @@
-Correct linear frequency drift. — lofdc • Spectroscopy Analysis Tools (spant) Correct linear frequency drift. — lofdc • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -138,7 +138,7 @@ Value
diff --git a/docs/reference/lw2alpha.html b/docs/reference/lw2alpha.html
index b83db682..25da229b 100644
--- a/docs/reference/lw2alpha.html
+++ b/docs/reference/lw2alpha.html
@@ -1,7 +1,5 @@
-Covert a linewidth in Hz to an equivalent alpha value in the time-domain ie:
-x * exp(-t * alpha). — lw2alpha • Spectroscopy Analysis Tools (spant) Covert a linewidth in Hz to an equivalent alpha value in the time-domain ie: x * exp(-t * alpha). — lw2alpha • Spectroscopy Analysis Tools (spant) Covert a linewidth in Hz to an equivalent beta value in the time-domain ie:
-x * exp(-t * t * beta). — lw2beta • Spectroscopy Analysis Tools (spant) Covert a linewidth in Hz to an equivalent beta value in the time-domain ie: x * exp(-t * t * beta). — lw2beta • Spectroscopy Analysis Tools (spant) Make a basis-set object from a directory containing LCModel formatted RAW
-files. — make_basis_from_raw • Spectroscopy Analysis Tools (spant) Make a basis-set object from a directory containing LCModel formatted RAW files. — make_basis_from_raw • Spectroscopy Analysis Tools (spant) Mask an MRS dataset in the dynamic dimension. — mask_dyns • Spectroscopy Analysis Tools (spant) Mask an MRS dataset in the dynamic dimension. — mask_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/mask_fit_res.html b/docs/reference/mask_fit_res.html
index 97baaa3f..ebd91a99 100644
--- a/docs/reference/mask_fit_res.html
+++ b/docs/reference/mask_fit_res.html
@@ -1,5 +1,5 @@
-Mask fit result spectra depending on a vector of bool values. — mask_fit_res • Spectroscopy Analysis Tools (spant) Mask fit result spectra depending on a vector of bool values. — mask_fit_res • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -116,7 +116,7 @@ Value
diff --git a/docs/reference/mask_xy.html b/docs/reference/mask_xy.html
index 11bb577c..b0d38619 100644
--- a/docs/reference/mask_xy.html
+++ b/docs/reference/mask_xy.html
@@ -1,5 +1,5 @@
-Mask an MRSI dataset in the x-y direction — mask_xy • Spectroscopy Analysis Tools (spant) Mask an MRSI dataset in the x-y direction — mask_xy • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/mask_xy_corners.html b/docs/reference/mask_xy_corners.html
index 09b16cd2..2d13839d 100644
--- a/docs/reference/mask_xy_corners.html
+++ b/docs/reference/mask_xy_corners.html
@@ -1,5 +1,5 @@
-Mask the four corners of an MRSI dataset in the x-y plane. — mask_xy_corners • Spectroscopy Analysis Tools (spant) Mask the four corners of an MRSI dataset in the x-y plane. — mask_xy_corners • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/mask_xy_ellipse.html b/docs/reference/mask_xy_ellipse.html
index 1d8b02e4..e2e749ef 100644
--- a/docs/reference/mask_xy_ellipse.html
+++ b/docs/reference/mask_xy_ellipse.html
@@ -1,7 +1,5 @@
-Mask the voxels outside an elliptical region spanning the MRSI dataset in the
-x-y plane. — mask_xy_ellipse • Spectroscopy Analysis Tools (spant) Mask the voxels outside an elliptical region spanning the MRSI dataset in the x-y plane. — mask_xy_ellipse • Spectroscopy Analysis Tools (spant) Mask a 2D MRSI dataset in the x-y dimension. — mask_xy_mat • Spectroscopy Analysis Tools (spant) Mask a 2D MRSI dataset in the x-y dimension. — mask_xy_mat • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Value
diff --git a/docs/reference/mat2mrs_data.html b/docs/reference/mat2mrs_data.html
index 2e2895f3..ae55665f 100644
--- a/docs/reference/mat2mrs_data.html
+++ b/docs/reference/mat2mrs_data.html
@@ -1,7 +1,5 @@
-Convert a matrix (with spectral points in the column dimension and dynamics
-in the row dimensions) into a mrs_data object. — mat2mrs_data • Spectroscopy Analysis Tools (spant) Convert a matrix (with spectral points in the column dimension and dynamics in the row dimensions) into a mrs_data object. — mat2mrs_data • Spectroscopy Analysis Tools (spant) Matrix exponential function taken from complexplus package to reduce the
-number of spant dependencies. — matexp • Spectroscopy Analysis Tools (spant) Matrix exponential function taken from complexplus package to reduce the number of spant dependencies. — matexp • Spectroscopy Analysis Tools (spant) Apply the max operator to an MRS dataset. — max_mrs • Spectroscopy Analysis Tools (spant) Apply the max operator to an MRS dataset. — max_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/max_mrs_interp.html b/docs/reference/max_mrs_interp.html
index e4474764..52e63f3e 100644
--- a/docs/reference/max_mrs_interp.html
+++ b/docs/reference/max_mrs_interp.html
@@ -1,5 +1,5 @@
-Apply the max operator to an interpolated MRS dataset. — max_mrs_interp • Spectroscopy Analysis Tools (spant) Apply the max operator to an interpolated MRS dataset. — max_mrs_interp • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/mean.list.html b/docs/reference/mean.list.html
index b8eb3463..048306fd 100644
--- a/docs/reference/mean.list.html
+++ b/docs/reference/mean.list.html
@@ -1,5 +1,5 @@
-Calculate the mean spectrum from an mrs_data object. — mean.list • Spectroscopy Analysis Tools (spant) Calculate the mean spectrum from an mrs_data object. — mean.list • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/mean.mrs_data.html b/docs/reference/mean.mrs_data.html
index 5531a28d..79515014 100644
--- a/docs/reference/mean.mrs_data.html
+++ b/docs/reference/mean.mrs_data.html
@@ -1,5 +1,5 @@
-Calculate the mean spectrum from an mrs_data object. — mean.mrs_data • Spectroscopy Analysis Tools (spant) Calculate the mean spectrum from an mrs_data object. — mean.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/mean_dyn_blocks.html b/docs/reference/mean_dyn_blocks.html
index 10467098..4c042448 100644
--- a/docs/reference/mean_dyn_blocks.html
+++ b/docs/reference/mean_dyn_blocks.html
@@ -1,5 +1,5 @@
-Calculate the mean of adjacent dynamic scans. — mean_dyn_blocks • Spectroscopy Analysis Tools (spant) Calculate the mean of adjacent dynamic scans. — mean_dyn_blocks • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/mean_dyn_pairs.html b/docs/reference/mean_dyn_pairs.html
index 63e909ea..1a241126 100644
--- a/docs/reference/mean_dyn_pairs.html
+++ b/docs/reference/mean_dyn_pairs.html
@@ -1,5 +1,5 @@
-Calculate the pairwise means across a dynamic data set. — mean_dyn_pairs • Spectroscopy Analysis Tools (spant) Calculate the pairwise means across a dynamic data set. — mean_dyn_pairs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/mean_dyns.html b/docs/reference/mean_dyns.html
index 73fdbfa7..0daa27df 100644
--- a/docs/reference/mean_dyns.html
+++ b/docs/reference/mean_dyns.html
@@ -1,5 +1,5 @@
-Calculate the mean dynamic data. — mean_dyns • Spectroscopy Analysis Tools (spant) Calculate the mean dynamic data. — mean_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/mean_mrs_list.html b/docs/reference/mean_mrs_list.html
index 808b6c50..10d842c0 100644
--- a/docs/reference/mean_mrs_list.html
+++ b/docs/reference/mean_mrs_list.html
@@ -1,5 +1,5 @@
-Return the mean of a list of mrs_data objects. — mean_mrs_list • Spectroscopy Analysis Tools (spant) Return the mean of a list of mrs_data objects. — mean_mrs_list • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/mean_vec_blocks.html b/docs/reference/mean_vec_blocks.html
index 8fc92eaa..dd78b122 100644
--- a/docs/reference/mean_vec_blocks.html
+++ b/docs/reference/mean_vec_blocks.html
@@ -1,5 +1,5 @@
-Calculate the mean of adjacent blocks in a vector. — mean_vec_blocks • Spectroscopy Analysis Tools (spant) Calculate the mean of adjacent blocks in a vector. — mean_vec_blocks • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/median_dyns.html b/docs/reference/median_dyns.html
index 1039d4b5..9a085b10 100644
--- a/docs/reference/median_dyns.html
+++ b/docs/reference/median_dyns.html
@@ -1,5 +1,5 @@
-Calculate the median dynamic data. — median_dyns • Spectroscopy Analysis Tools (spant) Calculate the median dynamic data. — median_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/mod_td.html b/docs/reference/mod_td.html
index 76ad0a40..141ef09e 100644
--- a/docs/reference/mod_td.html
+++ b/docs/reference/mod_td.html
@@ -1,5 +1,5 @@
-Apply the Modulus operator to the time-domain MRS signal. — mod_td • Spectroscopy Analysis Tools (spant) Apply the Modulus operator to the time-domain MRS signal. — mod_td • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/mrs_data2basis.html b/docs/reference/mrs_data2basis.html
index 62f7d749..11797b91 100644
--- a/docs/reference/mrs_data2basis.html
+++ b/docs/reference/mrs_data2basis.html
@@ -1,7 +1,5 @@
-Convert an mrs_data object to basis object - where basis signals are spread
-across the dynamic dimension in the MRS data. — mrs_data2basis • Spectroscopy Analysis Tools (spant) Convert an mrs_data object to basis object - where basis signals are spread across the dynamic dimension in the MRS data. — mrs_data2basis • Spectroscopy Analysis Tools (spant) Create a BIDS file structure from a vector of MRS data paths or list of mrs_data objects. — mrs_data2bids • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Create a BIDS file structure from a vector of MRS data paths or list of mrs_data objects.
+ Source: R/fmrs.R
+ mrs_data2bids.Rd
+
+
+
+ Create a BIDS file structure from a vector of MRS data paths or list of
+mrs_data objects.
+
+
+
+ mrs_data2bids(
+ mrs_data,
+ output_dir,
+ suffix = NULL,
+ sub = NULL,
+ ses = NULL,
+ task = NULL,
+ acq = NULL,
+ nuc = NULL,
+ voi = NULL,
+ rec = NULL,
+ run = NULL,
+ echo = NULL,
+ inv = NULL,
+ skip_existing = TRUE
+)
+
+
+
+ Arguments
+ - mrs_data
+vector of MRS data paths or list of mrs_data objects.
- output_dir
+the base directory to create the BIDS structure.
- suffix
+optional vector of file suffixes. Default behaviour is to
+automatically determine these from the input data, however it is recommended
+that they are specified to allow more efficient skipping of existing data.
- sub
+optional vector of subject labels. If not specified, these will be
+automatically generated as a series of increasing zero-padded integer values
+corresponding to the mrs_data input indices.
- ses
+optional vector of session labels.
- task
+optional vector of task labels.
- acq
+optional vector of acquisition labels.
- nuc
+optional vector of nucleus labels.
- voi
+optional vector of volume of interest labels.
- rec
+optional vector of reconstruction labels.
- run
+optional vector of run indices.
- echo
+optional vector of echo time indices.
- inv
+optional vector of inversion indices.
- skip_existing
+skip any data files that have already been converted.
+Defaults to TRUE, set to FALSE to force an overwrite of any existing data
+files.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/mrs_data2mat.html b/docs/reference/mrs_data2mat.html
index cf5ff28c..9e47688a 100644
--- a/docs/reference/mrs_data2mat.html
+++ b/docs/reference/mrs_data2mat.html
@@ -1,7 +1,5 @@
-Convert mrs_data object to a matrix, with spectral points in the column
-dimension and dynamics in the row dimension. — mrs_data2mat • Spectroscopy Analysis Tools (spant) Convert mrs_data object to a matrix, with spectral points in the column dimension and dynamics in the row dimension. — mrs_data2mat • Spectroscopy Analysis Tools (spant) Convert mrs_data object to a matrix, with spectral points in the column dimension and dynamics in the row dimension. — mrs_data2spec_mat • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Convert mrs_data object to a matrix, with spectral points in the column dimension and dynamics in the row dimension.
+ Source: R/mrs_data_proc.R
+ mrs_data2spec_mat.Rd
+
+
+
+ Convert mrs_data object to a matrix, with spectral points in the column
+dimension and dynamics in the row dimension.
+
+
+
+ mrs_data2spec_mat(mrs_data, collapse = TRUE)
+
+
+
+ Arguments
+ - mrs_data
+MRS data object or list of MRS data objects.
- collapse
+collapse all other dimensions along the dynamic dimension, eg
+a 16x16 MRSI grid would be first collapsed across 256 dynamic scans.
+
+ Value
+
+
+MRS data matrix.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/mrs_data2vec.html b/docs/reference/mrs_data2vec.html
index fb172d68..a1fd654d 100644
--- a/docs/reference/mrs_data2vec.html
+++ b/docs/reference/mrs_data2vec.html
@@ -1,5 +1,5 @@
-Convert mrs_data object to a vector. — mrs_data2vec • Spectroscopy Analysis Tools (spant) Convert mrs_data object to a vector. — mrs_data2vec • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -126,7 +126,7 @@ Value
diff --git a/docs/reference/mvfftshift.html b/docs/reference/mvfftshift.html
index 92b0841b..976b3410 100644
--- a/docs/reference/mvfftshift.html
+++ b/docs/reference/mvfftshift.html
@@ -1,7 +1,5 @@
-Perform a fftshift on a matrix, with each column replaced by its shifted
-result. — mvfftshift • Spectroscopy Analysis Tools (spant) Perform a fftshift on a matrix, with each column replaced by its shifted result. — mvfftshift • Spectroscopy Analysis Tools (spant) Perform an ifftshift on a matrix, with each column replaced by its shifted
-result. — mvifftshift • Spectroscopy Analysis Tools (spant) Perform an ifftshift on a matrix, with each column replaced by its shifted result. — mvifftshift • Spectroscopy Analysis Tools (spant) Print fit coordinates from a single index. — n2coord • Spectroscopy Analysis Tools (spant) Print fit coordinates from a single index. — n2coord • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/nifti_flip_lr.html b/docs/reference/nifti_flip_lr.html
index 730abe3c..19860b3c 100644
--- a/docs/reference/nifti_flip_lr.html
+++ b/docs/reference/nifti_flip_lr.html
@@ -1,9 +1,5 @@
-Flip the x data dimension order of a nifti image. This corresponds to
-flipping MRI data in the left-right direction, assuming the data in save in
-neurological format (can check with fslorient program). — nifti_flip_lr • Spectroscopy Analysis Tools (spant) Flip the x data dimension order of a nifti image. This corresponds to flipping MRI data in the left-right direction, assuming the data in save in neurological format (can check with fslorient program). — nifti_flip_lr • Spectroscopy Analysis Tools (spant) Export a one-page pdf of a single fit result — one_page_pdf • Spectroscopy Analysis Tools (spant) Export a one-page pdf of a single fit result — one_page_pdf • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -108,7 +108,7 @@ Arguments
diff --git a/docs/reference/ortho3.html b/docs/reference/ortho3.html
index 13ade97d..5d7dd2fd 100644
--- a/docs/reference/ortho3.html
+++ b/docs/reference/ortho3.html
@@ -1,5 +1,5 @@
-Display an orthographic projection plot of a nifti object. — ortho3 • Spectroscopy Analysis Tools (spant) Display an orthographic projection plot of a nifti object. — ortho3 • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -172,7 +172,7 @@ Arguments
diff --git a/docs/reference/ortho3_inter.html b/docs/reference/ortho3_inter.html
index 090cc5e5..15948899 100644
--- a/docs/reference/ortho3_inter.html
+++ b/docs/reference/ortho3_inter.html
@@ -1,5 +1,5 @@
-Display an interactive orthographic projection plot of a nifti object. — ortho3_inter • Spectroscopy Analysis Tools (spant) Display an interactive orthographic projection plot of a nifti object. — ortho3_inter • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -132,7 +132,7 @@ Arguments
diff --git a/docs/reference/peak_info.html b/docs/reference/peak_info.html
index 09058bd8..41c8ffaf 100644
--- a/docs/reference/peak_info.html
+++ b/docs/reference/peak_info.html
@@ -1,7 +1,5 @@
-Search for the highest peak in a spectral region and return the frequency,
-height and FWHM. — peak_info • Spectroscopy Analysis Tools (spant) Search for the highest peak in a spectral region and return the frequency, height and FWHM. — peak_info • Spectroscopy Analysis Tools (spant) Papoulis-Gerchberg (PG) algorithm method for k-space extrapolation. — pg_extrap_xy • Spectroscopy Analysis Tools (spant) Papoulis-Gerchberg (PG) algorithm method for k-space extrapolation. — pg_extrap_xy • Spectroscopy Analysis Tools (spant) Apply phasing parameters to MRS data. — phase • Spectroscopy Analysis Tools (spant) Apply phasing parameters to MRS data. — phase • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/phase_ref_1h_brain.html b/docs/reference/phase_ref_1h_brain.html
new file mode 100644
index 00000000..8707a74a
--- /dev/null
+++ b/docs/reference/phase_ref_1h_brain.html
@@ -0,0 +1,131 @@
+
+Corrected zero order phase and chemical shift offset in 1H MRS data from the brain. — phase_ref_1h_brain • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Corrected zero order phase and chemical shift offset in 1H MRS data from the brain.
+ Source: R/rats.R
+ phase_ref_1h_brain.Rd
+
+
+
+ Corrected zero order phase and chemical shift offset in 1H MRS data from the
+brain.
+
+
+
+ phase_ref_1h_brain(mrs_data, mean_ref = FALSE, ret_corr_only = TRUE)
+
+
+
+ Arguments
+ - mrs_data
+MRS data to be corrected.
- mean_ref
+apply the phase and offset of the mean spectrum to all
+others. Default is FALSE.
- ret_corr_only
+return the corrected data only.
+
+ Value
+
+
+corrected MRS data.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/plot.fit_result.html b/docs/reference/plot.fit_result.html
index e54d3bc1..836a53ee 100644
--- a/docs/reference/plot.fit_result.html
+++ b/docs/reference/plot.fit_result.html
@@ -1,5 +1,5 @@
-Plot the fitting results of an object of class fit_result. — plot.fit_result • Spectroscopy Analysis Tools (spant) Plot the fitting results of an object of class fit_result. — plot.fit_result • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -207,7 +207,7 @@ Arguments
diff --git a/docs/reference/plot.mrs_data.html b/docs/reference/plot.mrs_data.html
index fabcc35b..bb2ec651 100644
--- a/docs/reference/plot.mrs_data.html
+++ b/docs/reference/plot.mrs_data.html
@@ -1,5 +1,5 @@
-Plotting method for objects of class mrs_data. — plot.mrs_data • Spectroscopy Analysis Tools (spant) Plotting method for objects of class mrs_data. — plot.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -287,7 +287,7 @@ Arguments
diff --git a/docs/reference/plot_bc.html b/docs/reference/plot_bc.html
index 4f8309b4..b48142cc 100644
--- a/docs/reference/plot_bc.html
+++ b/docs/reference/plot_bc.html
@@ -1,5 +1,5 @@
-Convenience function to plot a baseline estimate with the original data. — plot_bc • Spectroscopy Analysis Tools (spant) Convenience function to plot a baseline estimate with the original data. — plot_bc • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -108,7 +108,7 @@ Arguments
diff --git a/docs/reference/plot_reg.html b/docs/reference/plot_reg.html
index ae1acbe7..2addb2f6 100644
--- a/docs/reference/plot_reg.html
+++ b/docs/reference/plot_reg.html
@@ -1,5 +1,5 @@
-Plot regressors as an image. — plot_reg • Spectroscopy Analysis Tools (spant) Plot regressors as an image. — plot_reg • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/plot_slice_fit.html b/docs/reference/plot_slice_fit.html
index fbc7b560..57f1af8a 100644
--- a/docs/reference/plot_slice_fit.html
+++ b/docs/reference/plot_slice_fit.html
@@ -1,5 +1,5 @@
-Plot a 2D slice from an MRSI fit result object. — plot_slice_fit • Spectroscopy Analysis Tools (spant) Plot a 2D slice from an MRSI fit result object. — plot_slice_fit • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -129,7 +129,7 @@ Arguments
diff --git a/docs/reference/plot_slice_fit_inter.html b/docs/reference/plot_slice_fit_inter.html
index 4eed104a..da105a7d 100644
--- a/docs/reference/plot_slice_fit_inter.html
+++ b/docs/reference/plot_slice_fit_inter.html
@@ -1,5 +1,5 @@
-Plot a 2D slice from an MRSI fit result object. — plot_slice_fit_inter • Spectroscopy Analysis Tools (spant) Plot a 2D slice from an MRSI fit result object. — plot_slice_fit_inter • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -134,7 +134,7 @@ Arguments
diff --git a/docs/reference/plot_slice_map.html b/docs/reference/plot_slice_map.html
index 553e9ac8..ffb2a134 100644
--- a/docs/reference/plot_slice_map.html
+++ b/docs/reference/plot_slice_map.html
@@ -1,5 +1,5 @@
-Plot a slice from a 7 dimensional array. — plot_slice_map • Spectroscopy Analysis Tools (spant) Plot a slice from a 7 dimensional array. — plot_slice_map • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -153,7 +153,7 @@ Arguments
diff --git a/docs/reference/plot_slice_map_inter.html b/docs/reference/plot_slice_map_inter.html
index 40d33b42..90968f66 100644
--- a/docs/reference/plot_slice_map_inter.html
+++ b/docs/reference/plot_slice_map_inter.html
@@ -1,7 +1,5 @@
-Plot an interactive slice map from a data array where voxels can be selected
-to display a corresponding spectrum. — plot_slice_map_inter • Spectroscopy Analysis Tools (spant) Plot an interactive slice map from a data array where voxels can be selected to display a corresponding spectrum. — plot_slice_map_inter • Spectroscopy Analysis Tools (spant) Plot the spectral standard deviation. — plot_spec_sd • Spectroscopy Analysis Tools (spant) Plot the spectral standard deviation. — plot_spec_sd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Arguments
diff --git a/docs/reference/plot_voi_overlay.html b/docs/reference/plot_voi_overlay.html
index 9a782e88..bbbbf35e 100644
--- a/docs/reference/plot_voi_overlay.html
+++ b/docs/reference/plot_voi_overlay.html
@@ -1,5 +1,5 @@
-Plot a volume as an image overlay. — plot_voi_overlay • Spectroscopy Analysis Tools (spant) Plot a volume as an image overlay. — plot_voi_overlay • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -116,7 +116,7 @@ Arguments
diff --git a/docs/reference/plot_voi_overlay_seg.html b/docs/reference/plot_voi_overlay_seg.html
index 3d4e74ff..0e800ff2 100644
--- a/docs/reference/plot_voi_overlay_seg.html
+++ b/docs/reference/plot_voi_overlay_seg.html
@@ -1,5 +1,5 @@
-Plot a volume as an overlay on a segmented brain volume. — plot_voi_overlay_seg • Spectroscopy Analysis Tools (spant) Plot a volume as an overlay on a segmented brain volume. — plot_voi_overlay_seg • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Arguments
diff --git a/docs/reference/ppm.html b/docs/reference/ppm.html
index c352327a..ee4696e2 100644
--- a/docs/reference/ppm.html
+++ b/docs/reference/ppm.html
@@ -1,5 +1,5 @@
-Return the ppm scale of an MRS dataset or fit result. — ppm • Spectroscopy Analysis Tools (spant) Return the ppm scale of an MRS dataset or fit result. — ppm • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -132,7 +132,7 @@ Value
diff --git a/docs/reference/precomp.html b/docs/reference/precomp.html
index 822d7336..df3d2c6c 100644
--- a/docs/reference/precomp.html
+++ b/docs/reference/precomp.html
@@ -1,7 +1,5 @@
-Save function results to file and load on subsequent calls to avoid repeat
-computation. — precomp • Spectroscopy Analysis Tools (spant) Save function results to file and load on subsequent calls to avoid repeat computation. — precomp • Spectroscopy Analysis Tools (spant) Preprocess and perform quality assessment of a single SVS data set. — preproc_svs • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Preprocess and perform quality assessment of a single SVS data set.
+ Source: R/fmrs.R
+ preproc_svs.Rd
+
+
+
+ Preprocess and perform quality assessment of a single SVS data set.
+
+
+
+ preproc_svs(path, label = NULL, output_dir = NULL, ref_inds = NULL)
+
+
+
+ Arguments
+ - path
+path to the fMRS data file or IMA directory.
- label
+a label to describe the data set.
- output_dir
+output directory.
- ref_inds
+a vector of 1-based indices for any water reference dynamic
+scans.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/preproc_svs_dataset.html b/docs/reference/preproc_svs_dataset.html
new file mode 100644
index 00000000..07c3a29b
--- /dev/null
+++ b/docs/reference/preproc_svs_dataset.html
@@ -0,0 +1,148 @@
+
+Preprocess and perform quality assessment of one or more SVS data sets. — preproc_svs_dataset • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Preprocess and perform quality assessment of one or more SVS data sets.
+ Source: R/fmrs.R
+ preproc_svs_dataset.Rd
+
+
+
+ Preprocess and perform quality assessment of one or more SVS data sets.
+
+
+
+ preproc_svs_dataset(
+ paths,
+ labels = NULL,
+ output_dir = "spant_analysis",
+ exclude_labels = NULL,
+ overwrite = FALSE,
+ ref_inds = NULL,
+ return_results = FALSE
+)
+
+
+
+ Arguments
+ - paths
+paths to the fMRS data file or IMA directory.
- labels
+labels to describe each data set.
- output_dir
+output directory.
- exclude_labels
+vector of labels of scans to exclude, eg poor quality
+data.
- overwrite
+overwrite saved results, defaults to FALSE.
- ref_inds
+a vector of 1-based indices for any water reference dynamic
+scans.
- return_results
+function will return key outputs, defaults to FALSE.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/print.fit_result.html b/docs/reference/print.fit_result.html
index 297f28dc..5f434e57 100644
--- a/docs/reference/print.fit_result.html
+++ b/docs/reference/print.fit_result.html
@@ -1,5 +1,5 @@
-Print a summary of an object of class fit_result. — print.fit_result • Spectroscopy Analysis Tools (spant) Print a summary of an object of class fit_result. — print.fit_result • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -105,7 +105,7 @@ Arguments
diff --git a/docs/reference/print.mrs_data.html b/docs/reference/print.mrs_data.html
index 51199017..e1561eb2 100644
--- a/docs/reference/print.mrs_data.html
+++ b/docs/reference/print.mrs_data.html
@@ -1,5 +1,5 @@
-Print a summary of mrs_data parameters. — print.mrs_data • Spectroscopy Analysis Tools (spant) Print a summary of mrs_data parameters. — print.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -109,7 +109,7 @@ Arguments
diff --git a/docs/reference/qn_states.html b/docs/reference/qn_states.html
index 0f42f2f9..d7aa6715 100644
--- a/docs/reference/qn_states.html
+++ b/docs/reference/qn_states.html
@@ -1,5 +1,5 @@
-Get the quantum coherence matrix for a spin system. — qn_states • Spectroscopy Analysis Tools (spant) Get the quantum coherence matrix for a spin system. — qn_states • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/rats.html b/docs/reference/rats.html
index 5a39a396..93585e08 100644
--- a/docs/reference/rats.html
+++ b/docs/reference/rats.html
@@ -1,5 +1,5 @@
-Robust Alignment to a Target Spectrum (RATS). — rats • Spectroscopy Analysis Tools (spant) Robust Alignment to a Target Spectrum (RATS). — rats • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -207,7 +207,7 @@ Value
diff --git a/docs/reference/re_weighting.html b/docs/reference/re_weighting.html
index d21caf21..8b0b070a 100644
--- a/docs/reference/re_weighting.html
+++ b/docs/reference/re_weighting.html
@@ -1,5 +1,5 @@
-Apply a weighting to the FID to enhance spectral resolution. — re_weighting • Spectroscopy Analysis Tools (spant) Apply a weighting to the FID to enhance spectral resolution. — re_weighting • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/read_basis.html b/docs/reference/read_basis.html
index da9b94af..eb6f8557 100644
--- a/docs/reference/read_basis.html
+++ b/docs/reference/read_basis.html
@@ -1,5 +1,5 @@
-Read a basis file in LCModel .basis format. — read_basis • Spectroscopy Analysis Tools (spant) Read a basis file in LCModel .basis format. — read_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/read_ima_coil_dir.html b/docs/reference/read_ima_coil_dir.html
index 28c02de0..4f073cd8 100644
--- a/docs/reference/read_ima_coil_dir.html
+++ b/docs/reference/read_ima_coil_dir.html
@@ -1,9 +1,5 @@
-Read a directory containing Siemens MRS IMA files and combine along the coil
-dimension. Note that the coil ID is inferred from the sorted file name and
-should be checked when consistency is required between two directories. — read_ima_coil_dir • Spectroscopy Analysis Tools (spant) Read a directory containing Siemens MRS IMA files and combine along the coil dimension. Note that the coil ID is inferred from the sorted file name and should be checked when consistency is required between two directories. — read_ima_coil_dir • Spectroscopy Analysis Tools (spant) Read a directory containing Siemens MRS IMA files and combine along the
-dynamic dimension. Note that the coil ID is inferred from the sorted file
-name and should be checked when consistency is required. — read_ima_dyn_dir • Spectroscopy Analysis Tools (spant) Read a directory containing Siemens MRS IMA files and combine along the dynamic dimension. Note that the coil ID is inferred from the sorted file name and should be checked when consistency is required. — read_ima_dyn_dir • Spectroscopy Analysis Tools (spant) Read an LCModel formatted coord file containing fit information. — read_lcm_coord • Spectroscopy Analysis Tools (spant) Read an LCModel formatted coord file containing fit information. — read_lcm_coord • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -107,7 +107,7 @@ Value
diff --git a/docs/reference/read_mrs.html b/docs/reference/read_mrs.html
index 3ac2a36b..2cf36b20 100644
--- a/docs/reference/read_mrs.html
+++ b/docs/reference/read_mrs.html
@@ -1,5 +1,5 @@
-Read MRS data from a file. — read_mrs • Spectroscopy Analysis Tools (spant) Read MRS data from a file. — read_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -88,7 +88,8 @@ Read MRS data from a file.
full_fid = FALSE,
omit_svs_ref_scans = TRUE,
verbose = FALSE,
- extra = NULL
+ extra = NULL,
+ fid_filt_dist = NULL
)
@@ -140,6 +141,13 @@ Arguments
an optional data frame to provide additional variables for use
in subsequent analysis steps, eg id or grouping variables.
fid_filt_dist
+indicate if the data has a distorted FID due to a
+brick-wall filter being used to downsample the data. Default is to auto
+detect this from the data, but TRUE or FALSE options can be given to override
+detection.
Value
@@ -183,7 +191,7 @@ Examples
diff --git a/docs/reference/read_mrs_tqn.html b/docs/reference/read_mrs_tqn.html
index 5766362f..84bdaf3a 100644
--- a/docs/reference/read_mrs_tqn.html
+++ b/docs/reference/read_mrs_tqn.html
@@ -1,5 +1,5 @@
-Read MRS data using the TARQUIN software package. — read_mrs_tqn • Spectroscopy Analysis Tools (spant) Read MRS data using the TARQUIN software package. — read_mrs_tqn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -131,7 +131,7 @@ Examples
diff --git a/docs/reference/read_pulse_ascii.html b/docs/reference/read_pulse_ascii.html
index c9e0d43c..ab11c9cc 100644
--- a/docs/reference/read_pulse_ascii.html
+++ b/docs/reference/read_pulse_ascii.html
@@ -1,5 +1,5 @@
-Read an ASCII formatted pulse file. — read_pulse_ascii • Spectroscopy Analysis Tools (spant) Read an ASCII formatted pulse file. — read_pulse_ascii • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/read_pulse_bruker.html b/docs/reference/read_pulse_bruker.html
index c92bf76a..dbe9073b 100644
--- a/docs/reference/read_pulse_bruker.html
+++ b/docs/reference/read_pulse_bruker.html
@@ -1,5 +1,5 @@
-Read a Bruker formatted pulse file — read_pulse_bruker • Spectroscopy Analysis Tools (spant) Read a Bruker formatted pulse file — read_pulse_bruker • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/read_pulse_pta.html b/docs/reference/read_pulse_pta.html
index 72e1b6d4..a0fac3c3 100644
--- a/docs/reference/read_pulse_pta.html
+++ b/docs/reference/read_pulse_pta.html
@@ -1,5 +1,5 @@
-Read a .pta formatted pulse file compatible with Siemens PulseTool. — read_pulse_pta • Spectroscopy Analysis Tools (spant) Read a .pta formatted pulse file compatible with Siemens PulseTool. — read_pulse_pta • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/read_siemens_txt_hdr.html b/docs/reference/read_siemens_txt_hdr.html
index 23fb8c70..3a17d87c 100644
--- a/docs/reference/read_siemens_txt_hdr.html
+++ b/docs/reference/read_siemens_txt_hdr.html
@@ -1,5 +1,5 @@
-Read the text format header found in Siemens IMA and TWIX data files. — read_siemens_txt_hdr • Spectroscopy Analysis Tools (spant) Read the text format header found in Siemens IMA and TWIX data files. — read_siemens_txt_hdr • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -78,7 +78,7 @@ Read the text format header found in Siemens IMA and TWIX data files.
- read_siemens_txt_hdr(input, version = "vd", verbose, offset = 0)
+ read_siemens_txt_hdr(input, version = "vd", verbose = FALSE, offset = 0)
@@ -118,7 +118,7 @@ Value
diff --git a/docs/reference/read_tqn_fit.html b/docs/reference/read_tqn_fit.html
index 4da6c25e..a1630420 100644
--- a/docs/reference/read_tqn_fit.html
+++ b/docs/reference/read_tqn_fit.html
@@ -1,5 +1,5 @@
-Reader for csv fit results generated by TARQUIN. — read_tqn_fit • Spectroscopy Analysis Tools (spant) Reader for csv fit results generated by TARQUIN. — read_tqn_fit • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -113,7 +113,7 @@ Examples
diff --git a/docs/reference/read_tqn_result.html b/docs/reference/read_tqn_result.html
index 36659714..68a3e98c 100644
--- a/docs/reference/read_tqn_result.html
+++ b/docs/reference/read_tqn_result.html
@@ -1,5 +1,5 @@
-Reader for csv results generated by TARQUIN. — read_tqn_result • Spectroscopy Analysis Tools (spant) Reader for csv results generated by TARQUIN. — read_tqn_result • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -117,7 +117,7 @@ Examples
diff --git a/docs/reference/recon_imag.html b/docs/reference/recon_imag.html
index d2a72225..5bc3b1eb 100644
--- a/docs/reference/recon_imag.html
+++ b/docs/reference/recon_imag.html
@@ -1,7 +1,5 @@
-Reconstruct complex time-domain data from the real part of frequency-domain
-data. — recon_imag • Spectroscopy Analysis Tools (spant) Reconstruct complex time-domain data from the real part of frequency-domain data. — recon_imag • Spectroscopy Analysis Tools (spant) Reconstruct complex time-domain data from the real part of frequency-domain
-data. — recon_imag_vec • Spectroscopy Analysis Tools (spant) Reconstruct complex time-domain data from the real part of frequency-domain data. — recon_imag_vec • Spectroscopy Analysis Tools (spant) Reconstruct 2D MRSI data from a twix file loaded with read_mrs. — recon_twix_2d_mrsi • Spectroscopy Analysis Tools (spant) Reconstruct 2D MRSI data from a twix file loaded with read_mrs. — recon_twix_2d_mrsi • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/rectangular_mask.html b/docs/reference/rectangular_mask.html
index a2117283..6e469bc9 100644
--- a/docs/reference/rectangular_mask.html
+++ b/docs/reference/rectangular_mask.html
@@ -1,5 +1,5 @@
-Create a rectangular mask stored as a matrix of logical values. — rectangular_mask • Spectroscopy Analysis Tools (spant) Create a rectangular mask stored as a matrix of logical values. — rectangular_mask • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -130,7 +130,7 @@ Value
diff --git a/docs/reference/reexports.html b/docs/reference/reexports.html
index 694a75d1..a59e8379 100644
--- a/docs/reference/reexports.html
+++ b/docs/reference/reexports.html
@@ -1,5 +1,5 @@
-Objects exported from other packages — reexports • Spectroscopy Analysis Tools (spant) Objects exported from other packages — reexports • Spectroscopy Analysis Tools (spant)
Spectroscopy Analysis Tools (spant)
- 2.21.0
+ 2.22.0
@@ -103,7 +103,7 @@ Objects exported from other packages
diff --git a/docs/reference/rep_array_dim.html b/docs/reference/rep_array_dim.html
index b9c49b4a..48c0a5ed 100644
--- a/docs/reference/rep_array_dim.html
+++ b/docs/reference/rep_array_dim.html
@@ -1,5 +1,5 @@
-Repeat an array over a given dimension. — rep_array_dim • Spectroscopy Analysis Tools (spant) Repeat an array over a given dimension. — rep_array_dim • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/rep_dyn.html b/docs/reference/rep_dyn.html
index 6bbfb0ef..89a4bb9b 100644
--- a/docs/reference/rep_dyn.html
+++ b/docs/reference/rep_dyn.html
@@ -1,5 +1,5 @@
-Replicate a scan in the dynamic dimension. — rep_dyn • Spectroscopy Analysis Tools (spant) Replicate a scan in the dynamic dimension. — rep_dyn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/rep_mrs.html b/docs/reference/rep_mrs.html
index 67730b5c..becb8f00 100644
--- a/docs/reference/rep_mrs.html
+++ b/docs/reference/rep_mrs.html
@@ -1,5 +1,5 @@
-Replicate a scan over a given dimension. — rep_mrs • Spectroscopy Analysis Tools (spant) Replicate a scan over a given dimension. — rep_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -138,7 +138,7 @@ Value
diff --git a/docs/reference/resample_basis.html b/docs/reference/resample_basis.html
index b0f2ab17..c7a6222a 100644
--- a/docs/reference/resample_basis.html
+++ b/docs/reference/resample_basis.html
@@ -1,5 +1,5 @@
-Resample a basis-set to match a mrs_data acquisition. — resample_basis • Spectroscopy Analysis Tools (spant) Resample a basis-set to match a mrs_data acquisition. — resample_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -116,7 +116,7 @@ Value
diff --git a/docs/reference/resample_img.html b/docs/reference/resample_img.html
index f1e7beaf..b0cc8f71 100644
--- a/docs/reference/resample_img.html
+++ b/docs/reference/resample_img.html
@@ -1,5 +1,5 @@
-Resample an image to match a target image space. — resample_img • Spectroscopy Analysis Tools (spant) Resample an image to match a target image space. — resample_img • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/resample_voi.html b/docs/reference/resample_voi.html
index 8fbfa836..a29ab096 100644
--- a/docs/reference/resample_voi.html
+++ b/docs/reference/resample_voi.html
@@ -1,7 +1,5 @@
-Resample a VOI to match a target image space using nearest-neighbour
-interpolation. — resample_voi • Spectroscopy Analysis Tools (spant) Resample a VOI to match a target image space using nearest-neighbour interpolation. — resample_voi • Spectroscopy Analysis Tools (spant) Reslice a nifti object to match the orientation of mrs data. — reslice_to_mrs • Spectroscopy Analysis Tools (spant) Reslice a nifti object to match the orientation of mrs data. — reslice_to_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/reson_table2mrs_data.html b/docs/reference/reson_table2mrs_data.html
index d75579ee..c5a2167a 100644
--- a/docs/reference/reson_table2mrs_data.html
+++ b/docs/reference/reson_table2mrs_data.html
@@ -1,5 +1,5 @@
-Generate mrs_data from a table of single Lorentzian resonances. — reson_table2mrs_data • Spectroscopy Analysis Tools (spant) Generate mrs_data from a table of single Lorentzian resonances. — reson_table2mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -119,7 +119,7 @@ Value
diff --git a/docs/reference/rm_dyns.html b/docs/reference/rm_dyns.html
index 5d5ef692..573e1f51 100644
--- a/docs/reference/rm_dyns.html
+++ b/docs/reference/rm_dyns.html
@@ -1,5 +1,5 @@
-Remove a subset of dynamic scans. — rm_dyns • Spectroscopy Analysis Tools (spant) Remove a subset of dynamic scans. — rm_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/scale_amp_molal.html b/docs/reference/scale_amp_molal.html
index aaeee1f2..7acb8cb0 100644
--- a/docs/reference/scale_amp_molal.html
+++ b/docs/reference/scale_amp_molal.html
@@ -1,7 +1,5 @@
-Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water). — scale_amp_molal • Spectroscopy Analysis Tools (spant) Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / kg of tissue water). — scale_amp_molal • Spectroscopy Analysis Tools (spant)
Spectroscopy Analysis Tools (spant)
- 2.21.0
+ 2.22.0
@@ -76,8 +74,7 @@
- Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water).
+ Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / kg of tissue water).
Source: R/amp_scaling.R
scale_amp_molal.Rd
@@ -163,7 +160,7 @@ Value
diff --git a/docs/reference/scale_amp_molal_pvc.html b/docs/reference/scale_amp_molal_pvc.html
index 962d6afc..4d194abd 100644
--- a/docs/reference/scale_amp_molal_pvc.html
+++ b/docs/reference/scale_amp_molal_pvc.html
@@ -1,7 +1,5 @@
-Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water). — scale_amp_molal_pvc • Spectroscopy Analysis Tools (spant)
@@ -75,8 +73,7 @@
- Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water).
+ Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / kg of tissue water).
Source: R/amp_scaling.R
scale_amp_molal_pvc.Rd
@@ -141,7 +138,7 @@ Value
diff --git a/docs/reference/scale_amp_molar.html b/docs/reference/scale_amp_molar.html
index 02358d91..dc87a338 100644
--- a/docs/reference/scale_amp_molar.html
+++ b/docs/reference/scale_amp_molar.html
@@ -1,7 +1,5 @@
-Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / Litre of tissue). — scale_amp_molar • Spectroscopy Analysis Tools (spant) Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / Litre of tissue). — scale_amp_molar • Spectroscopy Analysis Tools (spant) Convert default LCM/TARQUIN concentration scaling to molal units with partial
-volume correction. — scale_amp_molar2molal_pvc • Spectroscopy Analysis Tools (spant) Convert default LCM/TARQUIN concentration scaling to molal units with partial volume correction. — scale_amp_molar2molal_pvc • Spectroscopy Analysis Tools (spant) Scale fitted amplitudes to a ratio of signal amplitude. — scale_amp_ratio • Spectroscopy Analysis Tools (spant) Scale fitted amplitudes to a ratio of signal amplitude. — scale_amp_ratio • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -116,7 +116,7 @@ Value
diff --git a/docs/reference/scale_amp_ratio_value.html b/docs/reference/scale_amp_ratio_value.html
index 2036837a..6af8ac51 100644
--- a/docs/reference/scale_amp_ratio_value.html
+++ b/docs/reference/scale_amp_ratio_value.html
@@ -1,5 +1,5 @@
-Scale fitted amplitudes to a ratio of signal amplitude. — scale_amp_ratio_value • Spectroscopy Analysis Tools (spant) Scale fitted amplitudes to a ratio of signal amplitude. — scale_amp_ratio_value • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/scale_amp_water_ratio.html b/docs/reference/scale_amp_water_ratio.html
index 5b25e884..35a76b00 100644
--- a/docs/reference/scale_amp_water_ratio.html
+++ b/docs/reference/scale_amp_water_ratio.html
@@ -1,5 +1,5 @@
-Scale metabolite amplitudes as a ratio to the unsuppressed water amplitude. — scale_amp_water_ratio • Spectroscopy Analysis Tools (spant) Scale metabolite amplitudes as a ratio to the unsuppressed water amplitude. — scale_amp_water_ratio • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/scale_basis_amp.html b/docs/reference/scale_basis_amp.html
index 9401c3f1..5a58b5e5 100644
--- a/docs/reference/scale_basis_amp.html
+++ b/docs/reference/scale_basis_amp.html
@@ -1,5 +1,5 @@
-Scale a basis object by a scalar. — scale_basis_amp • Spectroscopy Analysis Tools (spant) Scale a basis object by a scalar. — scale_basis_amp • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/scale_basis_from_singlet.html b/docs/reference/scale_basis_from_singlet.html
index 0d542bc8..c9a19e77 100644
--- a/docs/reference/scale_basis_from_singlet.html
+++ b/docs/reference/scale_basis_from_singlet.html
@@ -1,5 +1,5 @@
-Scale a basis-set to be consistent with spant assumptions for water scaling. — scale_basis_from_singlet • Spectroscopy Analysis Tools (spant) Scale a basis-set to be consistent with spant assumptions for water scaling. — scale_basis_from_singlet • Spectroscopy Analysis Tools (spant)
Spectroscopy Analysis Tools (spant)
- 2.21.0
+ 2.22.0
@@ -127,7 +127,7 @@ Value
diff --git a/docs/reference/scale_mrs_amp.html b/docs/reference/scale_mrs_amp.html
index b5501a0d..990f058a 100644
--- a/docs/reference/scale_mrs_amp.html
+++ b/docs/reference/scale_mrs_amp.html
@@ -1,5 +1,5 @@
-Scale an mrs_data object by a scalar or vector or amplitudes. — scale_mrs_amp • Spectroscopy Analysis Tools (spant) Scale an mrs_data object by a scalar or vector or amplitudes. — scale_mrs_amp • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/scale_spec.html b/docs/reference/scale_spec.html
index 4f6ea835..6b3ddba4 100644
--- a/docs/reference/scale_spec.html
+++ b/docs/reference/scale_spec.html
@@ -1,5 +1,5 @@
-Scale mrs_data to a spectral region. — scale_spec • Spectroscopy Analysis Tools (spant) Scale mrs_data to a spectral region. — scale_spec • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -141,7 +141,7 @@ Value
diff --git a/docs/reference/sd.html b/docs/reference/sd.html
index ea1eec9f..3ae4dfd4 100644
--- a/docs/reference/sd.html
+++ b/docs/reference/sd.html
@@ -1,5 +1,5 @@
-Calculate the standard deviation spectrum from an mrs_data object. — sd • Spectroscopy Analysis Tools (spant) Calculate the standard deviation spectrum from an mrs_data object. — sd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/sd.mrs_data.html b/docs/reference/sd.mrs_data.html
index 3f92a49f..13bdda85 100644
--- a/docs/reference/sd.mrs_data.html
+++ b/docs/reference/sd.mrs_data.html
@@ -1,5 +1,5 @@
-Calculate the standard deviation spectrum from an mrs_data object. — sd.mrs_data • Spectroscopy Analysis Tools (spant) Calculate the standard deviation spectrum from an mrs_data object. — sd.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/seconds.html b/docs/reference/seconds.html
index b34d6627..467ee17f 100644
--- a/docs/reference/seconds.html
+++ b/docs/reference/seconds.html
@@ -1,5 +1,5 @@
-Return a time scale vector to match the FID of an MRS data object. — seconds • Spectroscopy Analysis Tools (spant) Return a time scale vector to match the FID of an MRS data object. — seconds • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/seq_cpmg_ideal.html b/docs/reference/seq_cpmg_ideal.html
index 547e96ab..45727c86 100644
--- a/docs/reference/seq_cpmg_ideal.html
+++ b/docs/reference/seq_cpmg_ideal.html
@@ -1,5 +1,5 @@
-CPMG style sequence with ideal pulses. — seq_cpmg_ideal • Spectroscopy Analysis Tools (spant) CPMG style sequence with ideal pulses. — seq_cpmg_ideal • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/seq_mega_press_ideal.html b/docs/reference/seq_mega_press_ideal.html
index 0769b8b4..a9cd7fa0 100644
--- a/docs/reference/seq_mega_press_ideal.html
+++ b/docs/reference/seq_mega_press_ideal.html
@@ -1,7 +1,5 @@
-MEGA-PRESS sequence with ideal localisation pulses and Gaussian shaped
-editing pulse. — seq_mega_press_ideal • Spectroscopy Analysis Tools (spant) MEGA-PRESS sequence with ideal localisation pulses and Gaussian shaped editing pulse. — seq_mega_press_ideal • Spectroscopy Analysis Tools (spant) PRESS sequence with shaped refocusing pulses. — seq_press_2d_shaped • Spectroscopy Analysis Tools (spant) PRESS sequence with shaped refocusing pulses. — seq_press_2d_shaped • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -165,7 +165,7 @@ Value
diff --git a/docs/reference/seq_press_ideal.html b/docs/reference/seq_press_ideal.html
index 8c976856..72c3af3d 100644
--- a/docs/reference/seq_press_ideal.html
+++ b/docs/reference/seq_press_ideal.html
@@ -1,5 +1,5 @@
-PRESS sequence with ideal pulses. — seq_press_ideal • Spectroscopy Analysis Tools (spant) PRESS sequence with ideal pulses. — seq_press_ideal • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/seq_pulse_acquire.html b/docs/reference/seq_pulse_acquire.html
index 4a88fc64..ad80571e 100644
--- a/docs/reference/seq_pulse_acquire.html
+++ b/docs/reference/seq_pulse_acquire.html
@@ -1,5 +1,5 @@
-Simple pulse and acquire sequence with ideal pulses. — seq_pulse_acquire • Spectroscopy Analysis Tools (spant) Simple pulse and acquire sequence with ideal pulses. — seq_pulse_acquire • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/seq_slaser_ideal.html b/docs/reference/seq_slaser_ideal.html
index 74688f4d..eb83e8e3 100644
--- a/docs/reference/seq_slaser_ideal.html
+++ b/docs/reference/seq_slaser_ideal.html
@@ -1,5 +1,5 @@
-sLASER sequence with ideal pulses. — seq_slaser_ideal • Spectroscopy Analysis Tools (spant) sLASER sequence with ideal pulses. — seq_slaser_ideal • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -126,7 +126,7 @@ Value
diff --git a/docs/reference/seq_spin_echo_ideal.html b/docs/reference/seq_spin_echo_ideal.html
index e23271de..4248716f 100644
--- a/docs/reference/seq_spin_echo_ideal.html
+++ b/docs/reference/seq_spin_echo_ideal.html
@@ -1,5 +1,5 @@
-Spin echo sequence with ideal pulses. — seq_spin_echo_ideal • Spectroscopy Analysis Tools (spant) Spin echo sequence with ideal pulses. — seq_spin_echo_ideal • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/seq_steam_ideal.html b/docs/reference/seq_steam_ideal.html
index a60685a8..1c8115d7 100644
--- a/docs/reference/seq_steam_ideal.html
+++ b/docs/reference/seq_steam_ideal.html
@@ -1,5 +1,5 @@
-STEAM sequence with ideal pulses. — seq_steam_ideal • Spectroscopy Analysis Tools (spant) STEAM sequence with ideal pulses. — seq_steam_ideal • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -128,7 +128,7 @@ Value
diff --git a/docs/reference/seq_steam_ideal_cof.html b/docs/reference/seq_steam_ideal_cof.html
index 8f225740..cba7af91 100644
--- a/docs/reference/seq_steam_ideal_cof.html
+++ b/docs/reference/seq_steam_ideal_cof.html
@@ -1,7 +1,5 @@
-STEAM sequence with ideal pulses and coherence order filtering to simulate
-gradient crushers. — seq_steam_ideal_cof • Spectroscopy Analysis Tools (spant) STEAM sequence with ideal pulses and coherence order filtering to simulate gradient crushers. — seq_steam_ideal_cof • Spectroscopy Analysis Tools (spant) STEAM sequence with ideal pulses using the z-rotation gradient simulation
-method described by Young et al JMR 140, 146-152 (1999). — seq_steam_ideal_young • Spectroscopy Analysis Tools (spant) STEAM sequence with ideal pulses using the z-rotation gradient simulation method described by Young et al JMR 140, 146-152 (1999). — seq_steam_ideal_young • Spectroscopy Analysis Tools (spant) Set the number of transients for an mrs_data object. — set_Ntrans • Spectroscopy Analysis Tools (spant) Set the number of transients for an mrs_data object. — set_Ntrans • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/set_def_acq_paras.html b/docs/reference/set_def_acq_paras.html
index 3e1b4004..cc2ada9c 100644
--- a/docs/reference/set_def_acq_paras.html
+++ b/docs/reference/set_def_acq_paras.html
@@ -1,5 +1,5 @@
-Set the default acquisition parameters. — set_def_acq_paras • Spectroscopy Analysis Tools (spant) Set the default acquisition parameters. — set_def_acq_paras • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Arguments
diff --git a/docs/reference/set_lcm_cmd.html b/docs/reference/set_lcm_cmd.html
index 2056ed01..42bb2f24 100644
--- a/docs/reference/set_lcm_cmd.html
+++ b/docs/reference/set_lcm_cmd.html
@@ -1,5 +1,5 @@
-Set the command to run the LCModel command-line program. — set_lcm_cmd • Spectroscopy Analysis Tools (spant) Set the command to run the LCModel command-line program. — set_lcm_cmd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/set_lw.html b/docs/reference/set_lw.html
index b64ec851..bb176c62 100644
--- a/docs/reference/set_lw.html
+++ b/docs/reference/set_lw.html
@@ -1,5 +1,5 @@
-Apply line-broadening to an mrs_data object to achieve a specified linewidth. — set_lw • Spectroscopy Analysis Tools (spant) Apply line-broadening to an mrs_data object to achieve a specified linewidth. — set_lw • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -123,7 +123,7 @@ Value
diff --git a/docs/reference/set_mask_xy_mat.html b/docs/reference/set_mask_xy_mat.html
index 49dc5d4e..52c4b617 100644
--- a/docs/reference/set_mask_xy_mat.html
+++ b/docs/reference/set_mask_xy_mat.html
@@ -1,5 +1,5 @@
-Set the masked voxels in a 2D MRSI dataset to given spectrum. — set_mask_xy_mat • Spectroscopy Analysis Tools (spant) Set the masked voxels in a 2D MRSI dataset to given spectrum. — set_mask_xy_mat • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Value
diff --git a/docs/reference/set_precomp_mode.html b/docs/reference/set_precomp_mode.html
index f44bd5d3..47c28e3b 100644
--- a/docs/reference/set_precomp_mode.html
+++ b/docs/reference/set_precomp_mode.html
@@ -1,5 +1,5 @@
-Set the precompute mode. — set_precomp_mode • Spectroscopy Analysis Tools (spant) Set the precompute mode. — set_precomp_mode • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/set_precomp_verbose.html b/docs/reference/set_precomp_verbose.html
index 1453a231..9c613505 100644
--- a/docs/reference/set_precomp_verbose.html
+++ b/docs/reference/set_precomp_verbose.html
@@ -1,5 +1,5 @@
-Set the verbosity of the precompute function. — set_precomp_verbose • Spectroscopy Analysis Tools (spant) Set the verbosity of the precompute function. — set_precomp_verbose • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/set_ref.html b/docs/reference/set_ref.html
index 8953fa50..5436dfa2 100644
--- a/docs/reference/set_ref.html
+++ b/docs/reference/set_ref.html
@@ -1,5 +1,5 @@
-Set the ppm reference value (eg ppm value at 0Hz). — set_ref • Spectroscopy Analysis Tools (spant) Set the ppm reference value (eg ppm value at 0Hz). — set_ref • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/set_td_pts.html b/docs/reference/set_td_pts.html
index 8a80d42a..586459ff 100644
--- a/docs/reference/set_td_pts.html
+++ b/docs/reference/set_td_pts.html
@@ -1,7 +1,5 @@
-Set the number of time-domain data points, truncating or zero-filling as
-appropriate. — set_td_pts • Spectroscopy Analysis Tools (spant) Set the number of time-domain data points, truncating or zero-filling as appropriate. — set_td_pts • Spectroscopy Analysis Tools (spant) Set the command to run the TARQUIN command-line program. — set_tqn_cmd • Spectroscopy Analysis Tools (spant) Set the command to run the TARQUIN command-line program. — set_tqn_cmd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/set_tr.html b/docs/reference/set_tr.html
index b2109ab0..65c9df5f 100644
--- a/docs/reference/set_tr.html
+++ b/docs/reference/set_tr.html
@@ -1,5 +1,5 @@
-Set the repetition time of an MRS dataset. — set_tr • Spectroscopy Analysis Tools (spant) Set the repetition time of an MRS dataset. — set_tr • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/shift.html b/docs/reference/shift.html
index ab0fe724..034591d0 100644
--- a/docs/reference/shift.html
+++ b/docs/reference/shift.html
@@ -1,5 +1,5 @@
-Apply a frequency shift to MRS data. — shift • Spectroscopy Analysis Tools (spant) Apply a frequency shift to MRS data. — shift • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/shift_basis.html b/docs/reference/shift_basis.html
index 2884be19..f55a65e0 100644
--- a/docs/reference/shift_basis.html
+++ b/docs/reference/shift_basis.html
@@ -1,5 +1,5 @@
-Apply frequency shifts to basis set signals. — shift_basis • Spectroscopy Analysis Tools (spant) Apply frequency shifts to basis set signals. — shift_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Value
diff --git a/docs/reference/sim_basis.html b/docs/reference/sim_basis.html
index c7838c46..bb5fefc6 100644
--- a/docs/reference/sim_basis.html
+++ b/docs/reference/sim_basis.html
@@ -1,5 +1,5 @@
-Simulate a basis set object. — sim_basis • Spectroscopy Analysis Tools (spant) Simulate a basis set object. — sim_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -136,7 +136,7 @@ Value
diff --git a/docs/reference/sim_basis_1h_brain.html b/docs/reference/sim_basis_1h_brain.html
index 62ed7389..f71ffa0b 100644
--- a/docs/reference/sim_basis_1h_brain.html
+++ b/docs/reference/sim_basis_1h_brain.html
@@ -1,7 +1,5 @@
-Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS
-sequence. Note, ideal pulses are assumed. — sim_basis_1h_brain • Spectroscopy Analysis Tools (spant) Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS sequence. Note, ideal pulses are assumed. — sim_basis_1h_brain • Spectroscopy Analysis Tools (spant) Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS
-sequence. Note, ideal pulses are assumed. — sim_basis_1h_brain_press • Spectroscopy Analysis Tools (spant) Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS sequence. Note, ideal pulses are assumed. — sim_basis_1h_brain_press • Spectroscopy Analysis Tools (spant) Simulate a macromolecular and lipid basis-set suitable for 1H brain MRS
-analysis. — sim_basis_mm_lip_lcm • Spectroscopy Analysis Tools (spant) Simulate a macromolecular and lipid basis-set suitable for 1H brain MRS analysis. — sim_basis_mm_lip_lcm • Spectroscopy Analysis Tools (spant) Simulate a basis file using TARQUIN. — sim_basis_tqn • Spectroscopy Analysis Tools (spant) Simulate a basis file using TARQUIN. — sim_basis_tqn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -129,7 +129,7 @@ Examples
diff --git a/docs/reference/sim_brain_1h.html b/docs/reference/sim_brain_1h.html
index 2044cf1a..717ee289 100644
--- a/docs/reference/sim_brain_1h.html
+++ b/docs/reference/sim_brain_1h.html
@@ -1,5 +1,5 @@
-Simulate MRS data with a similar appearance to normal brain (by default). — sim_brain_1h • Spectroscopy Analysis Tools (spant) Simulate MRS data with a similar appearance to normal brain (by default). — sim_brain_1h • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -159,7 +159,7 @@ Value
diff --git a/docs/reference/sim_mol.html b/docs/reference/sim_mol.html
index 23bcef50..77f76a50 100644
--- a/docs/reference/sim_mol.html
+++ b/docs/reference/sim_mol.html
@@ -1,5 +1,5 @@
-Simulate a mol_parameter object. — sim_mol • Spectroscopy Analysis Tools (spant) Simulate a mol_parameter object. — sim_mol • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -143,7 +143,7 @@ Value
diff --git a/docs/reference/sim_noise.html b/docs/reference/sim_noise.html
index 23875f79..a71477d4 100644
--- a/docs/reference/sim_noise.html
+++ b/docs/reference/sim_noise.html
@@ -1,5 +1,5 @@
-Simulate an mrs_data object containing simulated Gaussian noise. — sim_noise • Spectroscopy Analysis Tools (spant) Simulate an mrs_data object containing simulated Gaussian noise. — sim_noise • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -84,6 +84,7 @@ Simulate an mrs_data object containing simulated Gaussian noise.
ft = def_ft(),
N = def_N(),
ref = def_ref(),
+ nuc = def_nuc(),
dyns = 1,
fd = TRUE
)
@@ -111,6 +112,10 @@ Arguments
reference value for ppm scale.
nuc
+resonant nucleus.
dyns
number of dynamic scans to generate.
Value
diff --git a/docs/reference/sim_resonances.html b/docs/reference/sim_resonances.html
index 19e9a8a4..d4f8d7c0 100644
--- a/docs/reference/sim_resonances.html
+++ b/docs/reference/sim_resonances.html
@@ -1,5 +1,5 @@
-Simulate a MRS data object containing a set of simulated resonances. — sim_resonances • Spectroscopy Analysis Tools (spant) Simulate a MRS data object containing a set of simulated resonances. — sim_resonances • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -161,7 +161,7 @@ Examples
diff --git a/docs/reference/sim_th_excit_profile.html b/docs/reference/sim_th_excit_profile.html
index 5535c5ef..e781cab1 100644
--- a/docs/reference/sim_th_excit_profile.html
+++ b/docs/reference/sim_th_excit_profile.html
@@ -1,7 +1,5 @@
-Simulate an ideal pulse excitation profile by smoothing a top-hat function
-with a Gaussian. — sim_th_excit_profile • Spectroscopy Analysis Tools (spant) Simulate an ideal pulse excitation profile by smoothing a top-hat function with a Gaussian. — sim_th_excit_profile • Spectroscopy Analysis Tools (spant) Simulate an mrs_data object containing complex zero valued samples. — sim_zero • Spectroscopy Analysis Tools (spant) Simulate an mrs_data object containing complex zero valued samples. — sim_zero • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -78,7 +78,14 @@ Simulate an mrs_data object containing complex zero valued samples.
-
+
@@ -99,6 +106,10 @@ Arguments
reference value for ppm scale.
nuc
+resonant nucleus.
dyns
number of dynamic scans to generate.
Value
diff --git a/docs/reference/smooth_dyns.html b/docs/reference/smooth_dyns.html
index 4cc8da50..accf3a51 100644
--- a/docs/reference/smooth_dyns.html
+++ b/docs/reference/smooth_dyns.html
@@ -1,5 +1,5 @@
-Smooth data across the dynamic dimension with a Gaussian kernel. — smooth_dyns • Spectroscopy Analysis Tools (spant) Smooth data across the dynamic dimension with a Gaussian kernel. — smooth_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/sort_basis.html b/docs/reference/sort_basis.html
index 6a676ea2..d25cc006 100644
--- a/docs/reference/sort_basis.html
+++ b/docs/reference/sort_basis.html
@@ -1,5 +1,5 @@
-Sort the basis-set elements alphabetically. — sort_basis • Spectroscopy Analysis Tools (spant) Sort the basis-set elements alphabetically. — sort_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/spant-package.html b/docs/reference/spant-package.html
index b3dd8e21..90f19ec3 100644
--- a/docs/reference/spant-package.html
+++ b/docs/reference/spant-package.html
@@ -1,5 +1,5 @@
-spant: spectroscopy analysis tools. — spant-package • Spectroscopy Analysis Tools (spant) spant: spectroscopy analysis tools. — spant-package • Spectroscopy Analysis Tools (spant) Simulate and fit some spectra with ABfit for benchmarking purposes. Basic
-timing and performance metrics will be printed. — spant_abfit_benchmark • Spectroscopy Analysis Tools (spant) Simulate and fit some spectra with ABfit for benchmarking purposes. Basic timing and performance metrics will be printed. — spant_abfit_benchmark • Spectroscopy Analysis Tools (spant) Example MEGA-PRESS data with significant B0 drift. — spant_mpress_drift • Spectroscopy Analysis Tools (spant) Example MEGA-PRESS data with significant B0 drift. — spant_mpress_drift • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -83,7 +83,7 @@ Example MEGA-PRESS data with significant B0 drift.
Format
- An object of class mrs_data of length 13.
+ An object of class mrs_data of dimension 1 x 1 x 1 x 1 x 40 x 1 x 1024.
@@ -98,7 +98,7 @@ Format
diff --git a/docs/reference/spant_sim_fmrs_dataset.html b/docs/reference/spant_sim_fmrs_dataset.html
new file mode 100644
index 00000000..00e48b56
--- /dev/null
+++ b/docs/reference/spant_sim_fmrs_dataset.html
@@ -0,0 +1,117 @@
+
+Simulate an example fMRS dataset for a block design fMRS experiment and export a BIDS structure. — spant_sim_fmrs_dataset • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Simulate an example fMRS dataset for a block design fMRS experiment and export a BIDS structure.
+ Source: R/fmrs.R
+ spant_sim_fmrs_dataset.Rd
+
+
+
+ Simulate an example fMRS dataset for a block design fMRS experiment and
+export a BIDS structure.
+
+
+
+ spant_sim_fmrs_dataset(output_dir = NULL)
+
+
+
+ Arguments
+ - output_dir
+output directory for the BIDS data. Defaults to :
+"HOME/sim_fmrs_dataset/data".
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/spant_simulation_benchmark.html b/docs/reference/spant_simulation_benchmark.html
index 32daa8bf..d8cc6841 100644
--- a/docs/reference/spant_simulation_benchmark.html
+++ b/docs/reference/spant_simulation_benchmark.html
@@ -1,7 +1,5 @@
-Simulate a typical metabolite basis set for benchmarking. Timing metrics will
-be printed on completion. — spant_simulation_benchmark • Spectroscopy Analysis Tools (spant) Simulate a typical metabolite basis set for benchmarking. Timing metrics will be printed on completion. — spant_simulation_benchmark • Spectroscopy Analysis Tools (spant) Decompose an mrs_data object into white and gray matter spectra. — spec_decomp • Spectroscopy Analysis Tools (spant) Perform a mathematical operation on a spectral region. — spec_op • Spectroscopy Analysis Tools (spant) Perform a mathematical operation on a spectral region. — spec_op • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -98,8 +98,8 @@ Arguments
operator
-can be "sum" (default), "mean", "l2", "max", "min" or
-"max-min".
can be "sum" (default), "mean", "l2", "max", "max_cplx,
+"min" or "max-min".
freq_scale
@@ -129,7 +129,7 @@ Value
diff --git a/docs/reference/spin_sys.html b/docs/reference/spin_sys.html
index 853423a4..1eaa9e76 100644
--- a/docs/reference/spin_sys.html
+++ b/docs/reference/spin_sys.html
@@ -1,5 +1,5 @@
-Create a spin system object for pulse sequence simulation. — spin_sys • Spectroscopy Analysis Tools (spant) Create a spin system object for pulse sequence simulation. — spin_sys • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/spm_pve2categorical.html b/docs/reference/spm_pve2categorical.html
index 23a1bad9..70f10729 100644
--- a/docs/reference/spm_pve2categorical.html
+++ b/docs/reference/spm_pve2categorical.html
@@ -1,7 +1,5 @@
-Convert SPM style segmentation files to a single categorical image where
-the numerical values map as: 0) Other, 1) CSF, 2) GM and 3) WM. — spm_pve2categorical • Spectroscopy Analysis Tools (spant) Convert SPM style segmentation files to a single categorical image where the numerical values map as: 0) Other, 1) CSF, 2) GM and 3) WM. — spm_pve2categorical • Spectroscopy Analysis Tools (spant) Signal space projection method for lipid suppression. — ssp • Spectroscopy Analysis Tools (spant) Signal space projection method for lipid suppression. — ssp • Spectroscopy Analysis Tools (spant) Plot the fitting results of an object of class fit_result with
-individual basis set components shown. — stackplot.fit_result • Spectroscopy Analysis Tools (spant) Plot the fitting results of an object of class fit_result with individual basis set components shown. — stackplot.fit_result • Spectroscopy Analysis Tools (spant) Produce a plot with multiple traces. — stackplot • Spectroscopy Analysis Tools (spant) Produce a plot with multiple traces. — stackplot • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/stackplot.mrs_data.html b/docs/reference/stackplot.mrs_data.html
index 17ff5648..64eea445 100644
--- a/docs/reference/stackplot.mrs_data.html
+++ b/docs/reference/stackplot.mrs_data.html
@@ -1,5 +1,5 @@
-Stackplot plotting method for objects of class mrs_data. — stackplot.mrs_data • Spectroscopy Analysis Tools (spant) Stackplot plotting method for objects of class mrs_data. — stackplot.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -255,7 +255,7 @@ Arguments
diff --git a/docs/reference/sub_first_dyn.html b/docs/reference/sub_first_dyn.html
index dbd7f831..493b7242 100644
--- a/docs/reference/sub_first_dyn.html
+++ b/docs/reference/sub_first_dyn.html
@@ -1,5 +1,5 @@
-Subtract the first dynamic spectrum from a dynamic series. — sub_first_dyn • Spectroscopy Analysis Tools (spant) Subtract the first dynamic spectrum from a dynamic series. — sub_first_dyn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/sub_mean_dyns.html b/docs/reference/sub_mean_dyns.html
index 6e3bb2df..221bd0c1 100644
--- a/docs/reference/sub_mean_dyns.html
+++ b/docs/reference/sub_mean_dyns.html
@@ -1,5 +1,5 @@
-Subtract the mean dynamic spectrum from a dynamic series. — sub_mean_dyns • Spectroscopy Analysis Tools (spant) Subtract the mean dynamic spectrum from a dynamic series. — sub_mean_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/sub_median_dyns.html b/docs/reference/sub_median_dyns.html
index 134c495d..1e834f14 100644
--- a/docs/reference/sub_median_dyns.html
+++ b/docs/reference/sub_median_dyns.html
@@ -1,5 +1,5 @@
-Subtract the median dynamic spectrum from a dynamic series. — sub_median_dyns • Spectroscopy Analysis Tools (spant) Subtract the median dynamic spectrum from a dynamic series. — sub_median_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/sum_coils.html b/docs/reference/sum_coils.html
index 7bf559f2..e1ab3cc0 100644
--- a/docs/reference/sum_coils.html
+++ b/docs/reference/sum_coils.html
@@ -1,5 +1,5 @@
-Calculate the sum across receiver coil elements. — sum_coils • Spectroscopy Analysis Tools (spant) Calculate the sum across receiver coil elements. — sum_coils • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/sum_dyns.html b/docs/reference/sum_dyns.html
index a0be19d3..bbda2ffc 100644
--- a/docs/reference/sum_dyns.html
+++ b/docs/reference/sum_dyns.html
@@ -1,5 +1,5 @@
-Calculate the sum of data dynamics. — sum_dyns • Spectroscopy Analysis Tools (spant) Calculate the sum of data dynamics. — sum_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/sum_mrs.html b/docs/reference/sum_mrs.html
index a22f215b..3cc3ab9e 100644
--- a/docs/reference/sum_mrs.html
+++ b/docs/reference/sum_mrs.html
@@ -1,5 +1,5 @@
-Sum two mrs_data objects. — sum_mrs • Spectroscopy Analysis Tools (spant) Sum two mrs_data objects. — sum_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Value
diff --git a/docs/reference/sum_mrs_list.html b/docs/reference/sum_mrs_list.html
index f4e09aea..c3584348 100644
--- a/docs/reference/sum_mrs_list.html
+++ b/docs/reference/sum_mrs_list.html
@@ -1,5 +1,5 @@
-Return the sum of a list of mrs_data objects. — sum_mrs_list • Spectroscopy Analysis Tools (spant) Return the sum of a list of mrs_data objects. — sum_mrs_list • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/svs_1h_brain_analysis.html b/docs/reference/svs_1h_brain_analysis.html
index 8ce514db..dff0ef7d 100644
--- a/docs/reference/svs_1h_brain_analysis.html
+++ b/docs/reference/svs_1h_brain_analysis.html
@@ -1,5 +1,5 @@
-Standard SVS 1H brain analysis pipeline. — svs_1h_brain_analysis • Spectroscopy Analysis Tools (spant) Standard SVS 1H brain analysis pipeline. — svs_1h_brain_analysis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -199,7 +199,7 @@ Value
diff --git a/docs/reference/svs_1h_brain_analysis_dev.html b/docs/reference/svs_1h_brain_analysis_dev.html
index d70a14d3..d71bfea2 100644
--- a/docs/reference/svs_1h_brain_analysis_dev.html
+++ b/docs/reference/svs_1h_brain_analysis_dev.html
@@ -1,5 +1,5 @@
-Standard SVS 1H brain analysis pipeline. — svs_1h_brain_analysis_dev • Spectroscopy Analysis Tools (spant) Standard SVS 1H brain analysis pipeline. — svs_1h_brain_analysis_dev • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -193,7 +193,7 @@ Examples
diff --git a/docs/reference/svs_1h_brain_batch_analysis.html b/docs/reference/svs_1h_brain_batch_analysis.html
index 5631e8cc..15f7223e 100644
--- a/docs/reference/svs_1h_brain_batch_analysis.html
+++ b/docs/reference/svs_1h_brain_batch_analysis.html
@@ -1,5 +1,5 @@
-Batch interface to the standard SVS 1H brain analysis pipeline. — svs_1h_brain_batch_analysis • Spectroscopy Analysis Tools (spant) Batch interface to the standard SVS 1H brain analysis pipeline. — svs_1h_brain_batch_analysis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -144,7 +144,7 @@ Value
diff --git a/docs/reference/t_test_spec.html b/docs/reference/t_test_spec.html
new file mode 100644
index 00000000..56a7ea1b
--- /dev/null
+++ b/docs/reference/t_test_spec.html
@@ -0,0 +1,124 @@
+
+Perform a t-test on spectral data points. — t_test_spec • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+
+
+ Perform a t-test on spectral data points.
+
+
+
+ t_test_spec(mrs_data, group)
+
+
+
+ Arguments
+ - mrs_data
+an mrs_data object with spectra in the dynamic dimension.
- group
+vector describing the group membership of each dynamic spectrum.
+
+ Value
+
+
+a list of statistical results.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/td2fd.html b/docs/reference/td2fd.html
index 6748a6a8..f31ed524 100644
--- a/docs/reference/td2fd.html
+++ b/docs/reference/td2fd.html
@@ -1,5 +1,5 @@
-Transform time-domain data to the frequency-domain. — td2fd • Spectroscopy Analysis Tools (spant) Transform time-domain data to the frequency-domain. — td2fd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/td_conv_filt.html b/docs/reference/td_conv_filt.html
index a9f340c3..106b9b00 100644
--- a/docs/reference/td_conv_filt.html
+++ b/docs/reference/td_conv_filt.html
@@ -1,5 +1,5 @@
-Time-domain convolution based filter. — td_conv_filt • Spectroscopy Analysis Tools (spant) Time-domain convolution based filter. — td_conv_filt • Spectroscopy Analysis Tools (spant) Time-domain spectral registration. — tdsr • Spectroscopy Analysis Tools (spant) Time-domain spectral registration. — tdsr • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -121,7 +121,7 @@ Value
diff --git a/docs/reference/te.html b/docs/reference/te.html
index 010361b1..4a65711d 100644
--- a/docs/reference/te.html
+++ b/docs/reference/te.html
@@ -1,5 +1,5 @@
-Return the echo time of an MRS dataset. — te • Spectroscopy Analysis Tools (spant) Return the echo time of an MRS dataset. — te • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/tr.html b/docs/reference/tr.html
index 0c0bd63b..2e749e02 100644
--- a/docs/reference/tr.html
+++ b/docs/reference/tr.html
@@ -1,5 +1,5 @@
-Return the repetition time of an MRS dataset. — tr • Spectroscopy Analysis Tools (spant) Return the repetition time of an MRS dataset. — tr • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/varpro_3_para_opts.html b/docs/reference/varpro_3_para_opts.html
index c2270a16..52d7cd84 100644
--- a/docs/reference/varpro_3_para_opts.html
+++ b/docs/reference/varpro_3_para_opts.html
@@ -1,5 +1,5 @@
-Return a list of options for VARPRO based fitting with 3 free parameters. — varpro_3_para_opts • Spectroscopy Analysis Tools (spant) Return a list of options for VARPRO based fitting with 3 free parameters. — varpro_3_para_opts • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -141,7 +141,7 @@ Value
diff --git a/docs/reference/varpro_basic_opts.html b/docs/reference/varpro_basic_opts.html
index 32c86d22..c5104891 100644
--- a/docs/reference/varpro_basic_opts.html
+++ b/docs/reference/varpro_basic_opts.html
@@ -1,5 +1,5 @@
-Return a list of options for a basic VARPRO analysis. — varpro_basic_opts • Spectroscopy Analysis Tools (spant) Return a list of options for a basic VARPRO analysis. — varpro_basic_opts • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -118,7 +118,7 @@ Value
diff --git a/docs/reference/varpro_opts.html b/docs/reference/varpro_opts.html
index 2aabf11d..6332f730 100644
--- a/docs/reference/varpro_opts.html
+++ b/docs/reference/varpro_opts.html
@@ -1,5 +1,5 @@
-Return a list of options for VARPRO based fitting. — varpro_opts • Spectroscopy Analysis Tools (spant) Return a list of options for VARPRO based fitting. — varpro_opts • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -177,7 +177,7 @@ Examples
diff --git a/docs/reference/vec2mrs_data.html b/docs/reference/vec2mrs_data.html
index 0cccd73b..f0d58bf0 100644
--- a/docs/reference/vec2mrs_data.html
+++ b/docs/reference/vec2mrs_data.html
@@ -1,5 +1,5 @@
-Convert a vector into a mrs_data object. — vec2mrs_data • Spectroscopy Analysis Tools (spant) Convert a vector into a mrs_data object. — vec2mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -80,10 +80,11 @@ Convert a vector into a mrs_data object.
vec2mrs_data(
vec,
- fs = def_fs(),
- ft = def_ft(),
- ref = def_ref(),
- nuc = def_nuc(),
+ mrs_data = NULL,
+ fs = NULL,
+ ft = NULL,
+ ref = NULL,
+ nuc = NULL,
dyns = 1,
fd = FALSE
)
@@ -95,6 +96,10 @@ Arguments
the data vector.
mrs_data
+example data to copy acquisition parameters from.
fs
sampling frequency in Hz.
Arguments
fd
-flag to indicate if the matrix is in the frequency domain (logical).
flag to indicate if the vector is in the frequency domain (logical).
Value
diff --git a/docs/reference/write_basis.html b/docs/reference/write_basis.html
index b6e27cbd..94c5e021 100644
--- a/docs/reference/write_basis.html
+++ b/docs/reference/write_basis.html
@@ -1,5 +1,5 @@
-Write a basis object to an LCModel .basis formatted file. — write_basis • Spectroscopy Analysis Tools (spant) Write a basis object to an LCModel .basis formatted file. — write_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -108,7 +108,7 @@ Arguments
diff --git a/docs/reference/write_basis_tqn.html b/docs/reference/write_basis_tqn.html
index 6aa51c1d..116c73ec 100644
--- a/docs/reference/write_basis_tqn.html
+++ b/docs/reference/write_basis_tqn.html
@@ -1,5 +1,5 @@
-Generate a basis file using TARQUIN. — write_basis_tqn • Spectroscopy Analysis Tools (spant) Generate a basis file using TARQUIN. — write_basis_tqn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Examples
diff --git a/docs/reference/write_mrs.html b/docs/reference/write_mrs.html
index fff25f15..124b9dc4 100644
--- a/docs/reference/write_mrs.html
+++ b/docs/reference/write_mrs.html
@@ -1,5 +1,5 @@
-Write MRS data object to file. — write_mrs • Spectroscopy Analysis Tools (spant) Write MRS data object to file. — write_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Arguments
diff --git a/docs/reference/write_mrs_nifti.html b/docs/reference/write_mrs_nifti.html
index f4bf1921..bd3ed4b7 100644
--- a/docs/reference/write_mrs_nifti.html
+++ b/docs/reference/write_mrs_nifti.html
@@ -1,5 +1,5 @@
-Write MRS data object to file in NIFTI format. — write_mrs_nifti • Spectroscopy Analysis Tools (spant) Write MRS data object to file in NIFTI format. — write_mrs_nifti • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/write_pulse_ascii.html b/docs/reference/write_pulse_ascii.html
index 067ae086..221f8ebb 100644
--- a/docs/reference/write_pulse_ascii.html
+++ b/docs/reference/write_pulse_ascii.html
@@ -1,5 +1,5 @@
-Write an ASCII formatted pulse file. — write_pulse_ascii • Spectroscopy Analysis Tools (spant) Write an ASCII formatted pulse file. — write_pulse_ascii • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/zero_fade_spec.html b/docs/reference/zero_fade_spec.html
index c703745c..c8b572c3 100644
--- a/docs/reference/zero_fade_spec.html
+++ b/docs/reference/zero_fade_spec.html
@@ -1,7 +1,5 @@
-Fade a spectrum to zero by frequency domain multiplication with a tanh
-function. Note this operation distorts data points at the end of the FID. — zero_fade_spec • Spectroscopy Analysis Tools (spant) Fade a spectrum to zero by frequency domain multiplication with a tanh function. Note this operation distorts data points at the end of the FID. — zero_fade_spec • Spectroscopy Analysis Tools (spant) Zero all coherences including and above a given order. — zero_higher_orders • Spectroscopy Analysis Tools (spant) Zero all coherences including and above a given order. — zero_higher_orders • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Value
diff --git a/docs/reference/zero_td_pts_end.html b/docs/reference/zero_td_pts_end.html
index 8c1123c8..71d24ebb 100644
--- a/docs/reference/zero_td_pts_end.html
+++ b/docs/reference/zero_td_pts_end.html
@@ -1,5 +1,5 @@
-Set mrs_data object data points at the end of the FID to zero. — zero_td_pts_end • Spectroscopy Analysis Tools (spant) Set mrs_data object data points at the end of the FID to zero. — zero_td_pts_end • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/zf.html b/docs/reference/zf.html
index 85e2013c..baf50256 100644
--- a/docs/reference/zf.html
+++ b/docs/reference/zf.html
@@ -1,5 +1,5 @@
-Zero-fill MRS data in the time domain. — zf • Spectroscopy Analysis Tools (spant) Zero-fill MRS data in the time domain. — zf • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -125,7 +125,7 @@ Value
diff --git a/docs/reference/zf_xy.html b/docs/reference/zf_xy.html
index ebca3999..c4104a74 100644
--- a/docs/reference/zf_xy.html
+++ b/docs/reference/zf_xy.html
@@ -1,5 +1,5 @@
-Zero-fill MRSI data in the k-space x-y direction. — zf_xy • Spectroscopy Analysis Tools (spant) Zero-fill MRSI data in the k-space x-y direction. — zf_xy • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -113,7 +113,7 @@ Value
diff --git a/docs/sitemap.xml b/docs/sitemap.xml
index e2139f71..4c39f515 100644
--- a/docs/sitemap.xml
+++ b/docs/sitemap.xml
@@ -216,6 +216,12 @@
https://martin3141.github.io/spant/reference/comb_coils_fp_pc.html
+
+ https://martin3141.github.io/spant/reference/comb_coils_mrsi_gls.html
+
+
+ https://martin3141.github.io/spant/reference/comb_coils_svs_gls.html
+
https://martin3141.github.io/spant/reference/comb_csv_results.html
@@ -411,6 +417,9 @@
https://martin3141.github.io/spant/reference/gen_conv_reg.html
+
+ https://martin3141.github.io/spant/reference/gen_group_reg.html
+
https://martin3141.github.io/spant/reference/gen_impulse_reg.html
@@ -555,6 +564,15 @@
https://martin3141.github.io/spant/reference/glm_spec.html
+
+ https://martin3141.github.io/spant/reference/glm_spec_fmrs_fl.html
+
+
+ https://martin3141.github.io/spant/reference/glm_spec_fmrs_group.html
+
+
+ https://martin3141.github.io/spant/reference/glm_spec_group_linhyp.html
+
https://martin3141.github.io/spant/reference/grid_shift_xy.html
@@ -690,9 +708,15 @@
https://martin3141.github.io/spant/reference/mrs_data2basis.html
+
+ https://martin3141.github.io/spant/reference/mrs_data2bids.html
+
https://martin3141.github.io/spant/reference/mrs_data2mat.html
+
+ https://martin3141.github.io/spant/reference/mrs_data2spec_mat.html
+
https://martin3141.github.io/spant/reference/mrs_data2vec.html
@@ -741,6 +765,9 @@
https://martin3141.github.io/spant/reference/phase.html
+
+ https://martin3141.github.io/spant/reference/phase_ref_1h_brain.html
+
https://martin3141.github.io/spant/reference/plot.fit_result.html
@@ -780,6 +807,12 @@
https://martin3141.github.io/spant/reference/precomp.html
+
+ https://martin3141.github.io/spant/reference/preproc_svs.html
+
+
+ https://martin3141.github.io/spant/reference/preproc_svs_dataset.html
+
https://martin3141.github.io/spant/reference/print.fit_result.html
@@ -1050,6 +1083,9 @@
https://martin3141.github.io/spant/reference/spant_mpress_drift.html
+
+ https://martin3141.github.io/spant/reference/spant_sim_fmrs_dataset.html
+
https://martin3141.github.io/spant/reference/spant_simulation_benchmark.html
@@ -1107,6 +1143,9 @@
https://martin3141.github.io/spant/reference/svs_1h_brain_batch_analysis.html
+
+ https://martin3141.github.io/spant/reference/t_test_spec.html
+
https://martin3141.github.io/spant/reference/td2fd.html
Convert a 7 dimensional array in into a mrs_data object. The array dimensions -should be ordered as : dummy, X, Y, Z, dynamic, coil, FID.
Convert a 7 dimensional array in into a mrs_data object. The array dimensions should be ordered as : dummy, X, Y, Z, dynamic, coil, FID.
Perform zeroth-order phase correction based on the minimisation of the -squared difference between the real and magnitude components of the -spectrum.
Perform zeroth-order phase correction based on the minimisation of the squared difference between the real and magnitude components of the spectrum.
All functions
- Convert a basis object to an mrs_data object - where basis signals are spread
-across the dynamic dimension.
Convert a basis object to an mrs_data object - where basis signals are spread across the dynamic dimension.
- Generate a spline basis, slightly adapted from : "Splines, knots, and
-penalties", Eilers 2010.
Generate a spline basis, slightly adapted from : "Splines, knots, and penalties", Eilers 2010.
@@ -243,8 +234,7 @@ All functions
- Covert a beta value in the time-domain to an equivalent linewidth in Hz:
-x * exp(-i * t * t * beta).
Covert a beta value in the time-domain to an equivalent linewidth in Hz: x * exp(-i * t * t * beta).
@@ -272,8 +262,7 @@ All functions
- Perform a polynomial fit, subtract and return the standard deviation of the
-residuals.
Perform a polynomial fit, subtract and return the standard deviation of the residuals.
@@ -306,6 +295,14 @@ All functions comb_coils()
Combine coil data based on the first data point of a reference signal.
+
+
+ Combine MRSI coil data using the GLS method presented by An et al JMRI 37:1445-1450 (2013).
+
+
+ Combine SVS coil data using the GLS method presented by An et al JMRI 37:1445-1450 (2013).
@@ -345,9 +342,7 @@ All functions
- Crop mrs_data object data points in the time-domain rounding down to
-the next smallest power of two (pot). Data that already has a pot length will
-not be changed.
Crop mrs_data object data points in the time-domain rounding down to the next smallest power of two (pot). Data that already has a pot length will not be changed.
@@ -355,13 +350,11 @@ All functions
- Compute the vector cross product between vectors x and y. Adapted from
-http://stackoverflow.com/questions/15162741/what-is-rs-crossproduct-function
Compute the vector cross product between vectors x and y. Adapted from http://stackoverflow.com/questions/15162741/what-is-rs-crossproduct-function
- Decimate an MRS signal to half the original sampling frequency by filtering
-in the frequency domain before down sampling.
Decimate an MRS signal to half the original sampling frequency by filtering in the frequency domain before down sampling.
@@ -377,8 +370,7 @@ All functions
- Return (and optionally modify using the input arguments) a list of the
-default acquisition parameters.
Return (and optionally modify using the input arguments) a list of the default acquisition parameters.
@@ -410,14 +402,11 @@ All functions
- Downsample an MRS signal by a factor of 2 by removing every other data point
-in the time-domain. Note, signals outside the new sampling frequency will be
-aliased.
Downsample an MRS signal by a factor of 2 by removing every other data point in the time-domain. Note, signals outside the new sampling frequency will be aliased.
- Return a time scale vector of acquisition times for a dynamic MRS scan. The
-first temporal scan is assigned a value of 0.
Return a time scale vector of acquisition times for a dynamic MRS scan. The first temporal scan is assigned a value of 0.
@@ -429,8 +418,7 @@ All functions
- Estimate the standard deviation of the noise from a segment of an mrs_data
-object.
Estimate the standard deviation of the noise from a segment of an mrs_data object.
@@ -486,8 +474,7 @@ All functions
- Perform a zeroth order phase correction based on the phase of the first data
-point in the time-domain.
Perform a zeroth order phase correction based on the phase of the first data point in the time-domain.
@@ -507,8 +494,7 @@ All functions
- Perform a fft and fftshift on a matrix with each column replaced by its
-shifted fft.
Perform a fft and fftshift on a matrix with each column replaced by its shifted fft.
@@ -536,8 +522,11 @@ All functions
- Generate regressors by convolving a specified response function with a
-stimulus.
Generate regressors by convolving a specified response function with a stimulus.
+
+
+ Expand a regressor matrix for a group analysis.
@@ -553,28 +542,23 @@ All functions
- Return a character vector of common 1H molecules found in healthy human
-brain.
Return a character vector of common 1H molecules found in healthy human brain.
- Return a list of mol_parameter objects suitable for 1H brain MRS
-analyses.
Return a list of mol_parameter objects suitable for 1H brain MRS analyses.
- Return a list of mol_parameter objects suitable for 1H brain MRS
-analyses.
Return a list of mol_parameter objects suitable for 1H brain MRS analyses.
- Return a list of mol_parameter objects suitable for 1H brain MRS
-analyses.
Return a list of mol_parameter objects suitable for 1H brain MRS analyses.
- Return a list of mol_parameter objects suitable for 1H brain MRS
-analyses.
Return a list of mol_parameter objects suitable for 1H brain MRS analyses.
@@ -582,8 +566,7 @@ All functions
- Return a character vector of molecules included in the Gold Star Phantoms
-SPECTRE phantom.
Return a character vector of molecules included in the Gold Star Phantoms SPECTRE phantom.
@@ -635,8 +618,7 @@ All functions
- Return a character array of names that may be used with the
-get_mol_paras function.
Return a character array of names that may be used with the get_mol_paras function.
@@ -700,8 +682,7 @@ All functions
- Return an array of amplitudes derived from fitting the initial points in the
-time domain and extrapolating back to t=0.
Return an array of amplitudes derived from fitting the initial points in the time domain and extrapolating back to t=0.
@@ -709,8 +690,7 @@ All functions
- Generate a mol_parameters object for a simple spin system with one
-resonance.
Generate a mol_parameters object for a simple spin system with one resonance.
@@ -731,6 +711,18 @@ All functions glm_spec()
Perform a GLM analysis of dynamic MRS data in the spectral domain.
+
+
+ Perform first-level spectral GLM analysis of an fMRS dataset.
+
+
+ Perform group-level spectral GLM analysis of an fMRS dataset.
+
+
+ Test a group-level spectral GLM linear hypothesis.
@@ -766,8 +758,7 @@ All functions
- Perform an ifft and ifftshift on a matrix with each column replaced by its
-shifted ifft.
Perform an ifft and ifftshift on a matrix with each column replaced by its shifted ifft.
@@ -799,8 +790,7 @@ All functions
- Check if the chemical shift dimension of an MRS data object is in the
-frequency domain.
Check if the chemical shift dimension of an MRS data object is in the frequency domain.
@@ -820,18 +810,15 @@ All functions
- Covert a linewidth in Hz to an equivalent alpha value in the time-domain ie:
-x * exp(-t * alpha).
Covert a linewidth in Hz to an equivalent alpha value in the time-domain ie: x * exp(-t * alpha).
- Covert a linewidth in Hz to an equivalent beta value in the time-domain ie:
-x * exp(-t * t * beta).
Covert a linewidth in Hz to an equivalent beta value in the time-domain ie: x * exp(-t * t * beta).
- Make a basis-set object from a directory containing LCModel formatted RAW
-files.
Make a basis-set object from a directory containing LCModel formatted RAW files.
@@ -851,8 +838,7 @@ All functions
- Mask the voxels outside an elliptical region spanning the MRSI dataset in the
-x-y plane.
Mask the voxels outside an elliptical region spanning the MRSI dataset in the x-y plane.
@@ -860,13 +846,11 @@ All functions
- Convert a matrix (with spectral points in the column dimension and dynamics
-in the row dimensions) into a mrs_data object.
Convert a matrix (with spectral points in the column dimension and dynamics in the row dimensions) into a mrs_data object.
- Matrix exponential function taken from complexplus package to reduce the
-number of spant dependencies.
Matrix exponential function taken from complexplus package to reduce the number of spant dependencies.
@@ -914,31 +898,31 @@ All functions
- Convert an mrs_data object to basis object - where basis signals are spread
-across the dynamic dimension in the MRS data.
Convert an mrs_data object to basis object - where basis signals are spread across the dynamic dimension in the MRS data.
+
+
+ Create a BIDS file structure from a vector of MRS data paths or list of mrs_data objects.
- Convert mrs_data object to a matrix, with spectral points in the column
-dimension and dynamics in the row dimension.
Convert mrs_data object to a matrix, with spectral points in the column dimension and dynamics in the row dimension.
-
+
- Convert mrs_data object to a vector.
Convert mrs_data object to a matrix, with spectral points in the column dimension and dynamics in the row dimension.
-
+
- Create a BIDS directory and file structure from a list of mrs_data objects.
Convert mrs_data object to a vector.
- Perform a fftshift on a matrix, with each column replaced by its shifted
-result.
Perform a fftshift on a matrix, with each column replaced by its shifted result.
- Perform an ifftshift on a matrix, with each column replaced by its shifted
-result.
Perform an ifftshift on a matrix, with each column replaced by its shifted result.
@@ -946,9 +930,7 @@ All functions
- Flip the x data dimension order of a nifti image. This corresponds to
-flipping MRI data in the left-right direction, assuming the data in save in
-neurological format (can check with fslorient program).
Flip the x data dimension order of a nifti image. This corresponds to flipping MRI data in the left-right direction, assuming the data in save in neurological format (can check with fslorient program).
@@ -964,8 +946,7 @@ All functions
- Search for the highest peak in a spectral region and return the frequency,
-height and FWHM.
Search for the highest peak in a spectral region and return the frequency, height and FWHM.
@@ -974,6 +955,10 @@ All functions phase()
Apply phasing parameters to MRS data.
+
+
+ Corrected zero order phase and chemical shift offset in 1H MRS data from the brain.
@@ -1005,8 +990,7 @@ All functions
- Plot an interactive slice map from a data array where voxels can be selected
-to display a corresponding spectrum.
Plot an interactive slice map from a data array where voxels can be selected to display a corresponding spectrum.
@@ -1026,8 +1010,15 @@ All functions
- Save function results to file and load on subsequent calls to avoid repeat
-computation.
Save function results to file and load on subsequent calls to avoid repeat computation.
+
+
+ Preprocess and perform quality assessment of a single SVS data set.
+
+
+ Preprocess and perform quality assessment of one or more SVS data sets.
@@ -1055,15 +1046,11 @@ All functions
- Read a directory containing Siemens MRS IMA files and combine along the coil
-dimension. Note that the coil ID is inferred from the sorted file name and
-should be checked when consistency is required between two directories.
Read a directory containing Siemens MRS IMA files and combine along the coil dimension. Note that the coil ID is inferred from the sorted file name and should be checked when consistency is required between two directories.
- Read a directory containing Siemens MRS IMA files and combine along the
-dynamic dimension. Note that the coil ID is inferred from the sorted file
-name and should be checked when consistency is required.
Read a directory containing Siemens MRS IMA files and combine along the dynamic dimension. Note that the coil ID is inferred from the sorted file name and should be checked when consistency is required.
@@ -1103,13 +1090,11 @@ All functions
- Reconstruct complex time-domain data from the real part of frequency-domain
-data.
Reconstruct complex time-domain data from the real part of frequency-domain data.
- Reconstruct complex time-domain data from the real part of frequency-domain
-data.
Reconstruct complex time-domain data from the real part of frequency-domain data.
@@ -1141,8 +1126,7 @@ All functions
- Resample a VOI to match a target image space using nearest-neighbour
-interpolation.
Resample a VOI to match a target image space using nearest-neighbour interpolation.
@@ -1158,23 +1142,19 @@ All functions
- Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water).
Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / kg of tissue water).
- Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water).
Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / kg of tissue water).
- Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / Litre of tissue).
Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / Litre of tissue).
- Convert default LCM/TARQUIN concentration scaling to molal units with partial
-volume correction.
Convert default LCM/TARQUIN concentration scaling to molal units with partial volume correction.
@@ -1222,8 +1202,7 @@ All functions
- MEGA-PRESS sequence with ideal localisation pulses and Gaussian shaped
-editing pulse.
MEGA-PRESS sequence with ideal localisation pulses and Gaussian shaped editing pulse.
@@ -1251,13 +1230,11 @@ All functions
- STEAM sequence with ideal pulses and coherence order filtering to simulate
-gradient crushers.
STEAM sequence with ideal pulses and coherence order filtering to simulate gradient crushers.
- STEAM sequence with ideal pulses using the z-rotation gradient simulation
-method described by Young et al JMR 140, 146-152 (1999).
STEAM sequence with ideal pulses using the z-rotation gradient simulation method described by Young et al JMR 140, 146-152 (1999).
@@ -1293,8 +1270,7 @@ All functions
- Set the number of time-domain data points, truncating or zero-filling as
-appropriate.
Set the number of time-domain data points, truncating or zero-filling as appropriate.
@@ -1318,18 +1294,15 @@ All functions
- Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS
-sequence. Note, ideal pulses are assumed.
Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS sequence. Note, ideal pulses are assumed.
- Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS
-sequence. Note, ideal pulses are assumed.
Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS sequence. Note, ideal pulses are assumed.
- Simulate a macromolecular and lipid basis-set suitable for 1H brain MRS
-analysis.
Simulate a macromolecular and lipid basis-set suitable for 1H brain MRS analysis.
@@ -1353,8 +1326,7 @@ All functions
- Simulate an ideal pulse excitation profile by smoothing a top-hat function
-with a Gaussian.
Simulate an ideal pulse excitation profile by smoothing a top-hat function with a Gaussian.
@@ -1374,17 +1346,19 @@ All functions
- Simulate and fit some spectra with ABfit for benchmarking purposes. Basic
-timing and performance metrics will be printed.
Simulate and fit some spectra with ABfit for benchmarking purposes. Basic timing and performance metrics will be printed.
Example MEGA-PRESS data with significant B0 drift.
+
+
+ Simulate an example fMRS dataset for a block design fMRS experiment and export a BIDS structure.
- Simulate a typical metabolite basis set for benchmarking. Timing metrics will
-be printed on completion.
Simulate a typical metabolite basis set for benchmarking. Timing metrics will be printed on completion.
@@ -1400,8 +1374,7 @@ All functions
- Convert SPM style segmentation files to a single categorical image where
-the numerical values map as: 0) Other, 1) CSF, 2) GM and 3) WM.
Convert SPM style segmentation files to a single categorical image where the numerical values map as: 0) Other, 1) CSF, 2) GM and 3) WM.
@@ -1413,8 +1386,7 @@ All functions
- Plot the fitting results of an object of class fit_result with
-individual basis set components shown.
Plot the fitting results of an object of class fit_result with individual basis set components shown.
@@ -1459,6 +1431,10 @@ All functions svs_1h_brain_batch_analysis()
Batch interface to the standard SVS 1H brain analysis pipeline.
+
+
+ Perform a t-test on spectral data points.
@@ -1518,8 +1494,7 @@ All functions
- Fade a spectrum to zero by frequency domain multiplication with a tanh
-function. Note this operation distorts data points at the end of the FID.
Fade a spectrum to zero by frequency domain multiplication with a tanh function. Note this operation distorts data points at the end of the FID.
@@ -1549,7 +1524,7 @@ All functions
diff --git a/docs/reference/int_spec.html b/docs/reference/int_spec.html
index c7060fe7..783325a8 100644
--- a/docs/reference/int_spec.html
+++ b/docs/reference/int_spec.html
@@ -1,5 +1,5 @@
-Integrate a spectral region. — int_spec • Spectroscopy Analysis Tools (spant) Integrate a spectral region. — int_spec • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -118,7 +118,7 @@ Value
diff --git a/docs/reference/interleave_dyns.html b/docs/reference/interleave_dyns.html
index effe5543..441eff27 100644
--- a/docs/reference/interleave_dyns.html
+++ b/docs/reference/interleave_dyns.html
@@ -1,5 +1,5 @@
-Interleave the first and second half of a dynamic series. — interleave_dyns • Spectroscopy Analysis Tools (spant) Interleave the first and second half of a dynamic series. — interleave_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/inv_even_dyns.html b/docs/reference/inv_even_dyns.html
index 9f9d4fff..dcb781dc 100644
--- a/docs/reference/inv_even_dyns.html
+++ b/docs/reference/inv_even_dyns.html
@@ -1,5 +1,5 @@
-Invert even numbered dynamic scans starting from 1 (2,4,6...). — inv_even_dyns • Spectroscopy Analysis Tools (spant) Invert even numbered dynamic scans starting from 1 (2,4,6...). — inv_even_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/inv_odd_dyns.html b/docs/reference/inv_odd_dyns.html
index 26212e2b..78d64660 100644
--- a/docs/reference/inv_odd_dyns.html
+++ b/docs/reference/inv_odd_dyns.html
@@ -1,5 +1,5 @@
-Invert odd numbered dynamic scans starting from 1 (1,3,5...). — inv_odd_dyns • Spectroscopy Analysis Tools (spant) Invert odd numbered dynamic scans starting from 1 (1,3,5...). — inv_odd_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/is.def.html b/docs/reference/is.def.html
index f196ffd0..a67b9eba 100644
--- a/docs/reference/is.def.html
+++ b/docs/reference/is.def.html
@@ -1,5 +1,5 @@
-Check if an object is defined, which is the same as being not NULL. — is.def • Spectroscopy Analysis Tools (spant) Check if an object is defined, which is the same as being not NULL. — is.def • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/is_fd.html b/docs/reference/is_fd.html
index 3b0ca165..18a193aa 100644
--- a/docs/reference/is_fd.html
+++ b/docs/reference/is_fd.html
@@ -1,7 +1,5 @@
-Check if the chemical shift dimension of an MRS data object is in the
-frequency domain. — is_fd • Spectroscopy Analysis Tools (spant) Check if the chemical shift dimension of an MRS data object is in the frequency domain. — is_fd • Spectroscopy Analysis Tools (spant) Transform 2D MRSI data from k-space to image space in the x-y direction. — kspace2img_xy • Spectroscopy Analysis Tools (spant) Transform 2D MRSI data from k-space to image space in the x-y direction. — kspace2img_xy • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/l2_reg.html b/docs/reference/l2_reg.html
index 3d781d80..21aa9849 100644
--- a/docs/reference/l2_reg.html
+++ b/docs/reference/l2_reg.html
@@ -1,5 +1,5 @@
-Perform l2 regularisation artefact suppression. — l2_reg • Spectroscopy Analysis Tools (spant) Perform l2 regularisation artefact suppression. — l2_reg • Spectroscopy Analysis Tools (spant) Apply line-broadening (apodisation) to MRS data or basis object. — lb • Spectroscopy Analysis Tools (spant) Apply line-broadening (apodisation) to MRS data or basis object. — lb • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -123,7 +123,7 @@ Value
diff --git a/docs/reference/lofdc.html b/docs/reference/lofdc.html
index 5419b1ec..31347a25 100644
--- a/docs/reference/lofdc.html
+++ b/docs/reference/lofdc.html
@@ -1,5 +1,5 @@
-Correct linear frequency drift. — lofdc • Spectroscopy Analysis Tools (spant) Correct linear frequency drift. — lofdc • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -138,7 +138,7 @@ Value
diff --git a/docs/reference/lw2alpha.html b/docs/reference/lw2alpha.html
index b83db682..25da229b 100644
--- a/docs/reference/lw2alpha.html
+++ b/docs/reference/lw2alpha.html
@@ -1,7 +1,5 @@
-Covert a linewidth in Hz to an equivalent alpha value in the time-domain ie:
-x * exp(-t * alpha). — lw2alpha • Spectroscopy Analysis Tools (spant) Covert a linewidth in Hz to an equivalent alpha value in the time-domain ie: x * exp(-t * alpha). — lw2alpha • Spectroscopy Analysis Tools (spant) Covert a linewidth in Hz to an equivalent beta value in the time-domain ie:
-x * exp(-t * t * beta). — lw2beta • Spectroscopy Analysis Tools (spant) Covert a linewidth in Hz to an equivalent beta value in the time-domain ie: x * exp(-t * t * beta). — lw2beta • Spectroscopy Analysis Tools (spant) Make a basis-set object from a directory containing LCModel formatted RAW
-files. — make_basis_from_raw • Spectroscopy Analysis Tools (spant) Make a basis-set object from a directory containing LCModel formatted RAW files. — make_basis_from_raw • Spectroscopy Analysis Tools (spant) Mask an MRS dataset in the dynamic dimension. — mask_dyns • Spectroscopy Analysis Tools (spant) Mask an MRS dataset in the dynamic dimension. — mask_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/mask_fit_res.html b/docs/reference/mask_fit_res.html
index 97baaa3f..ebd91a99 100644
--- a/docs/reference/mask_fit_res.html
+++ b/docs/reference/mask_fit_res.html
@@ -1,5 +1,5 @@
-Mask fit result spectra depending on a vector of bool values. — mask_fit_res • Spectroscopy Analysis Tools (spant) Mask fit result spectra depending on a vector of bool values. — mask_fit_res • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -116,7 +116,7 @@ Value
diff --git a/docs/reference/mask_xy.html b/docs/reference/mask_xy.html
index 11bb577c..b0d38619 100644
--- a/docs/reference/mask_xy.html
+++ b/docs/reference/mask_xy.html
@@ -1,5 +1,5 @@
-Mask an MRSI dataset in the x-y direction — mask_xy • Spectroscopy Analysis Tools (spant) Mask an MRSI dataset in the x-y direction — mask_xy • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/mask_xy_corners.html b/docs/reference/mask_xy_corners.html
index 09b16cd2..2d13839d 100644
--- a/docs/reference/mask_xy_corners.html
+++ b/docs/reference/mask_xy_corners.html
@@ -1,5 +1,5 @@
-Mask the four corners of an MRSI dataset in the x-y plane. — mask_xy_corners • Spectroscopy Analysis Tools (spant) Mask the four corners of an MRSI dataset in the x-y plane. — mask_xy_corners • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/mask_xy_ellipse.html b/docs/reference/mask_xy_ellipse.html
index 1d8b02e4..e2e749ef 100644
--- a/docs/reference/mask_xy_ellipse.html
+++ b/docs/reference/mask_xy_ellipse.html
@@ -1,7 +1,5 @@
-Mask the voxels outside an elliptical region spanning the MRSI dataset in the
-x-y plane. — mask_xy_ellipse • Spectroscopy Analysis Tools (spant) Mask the voxels outside an elliptical region spanning the MRSI dataset in the x-y plane. — mask_xy_ellipse • Spectroscopy Analysis Tools (spant) Mask a 2D MRSI dataset in the x-y dimension. — mask_xy_mat • Spectroscopy Analysis Tools (spant) Mask a 2D MRSI dataset in the x-y dimension. — mask_xy_mat • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Value
diff --git a/docs/reference/mat2mrs_data.html b/docs/reference/mat2mrs_data.html
index 2e2895f3..ae55665f 100644
--- a/docs/reference/mat2mrs_data.html
+++ b/docs/reference/mat2mrs_data.html
@@ -1,7 +1,5 @@
-Convert a matrix (with spectral points in the column dimension and dynamics
-in the row dimensions) into a mrs_data object. — mat2mrs_data • Spectroscopy Analysis Tools (spant) Convert a matrix (with spectral points in the column dimension and dynamics in the row dimensions) into a mrs_data object. — mat2mrs_data • Spectroscopy Analysis Tools (spant) Matrix exponential function taken from complexplus package to reduce the
-number of spant dependencies. — matexp • Spectroscopy Analysis Tools (spant) Matrix exponential function taken from complexplus package to reduce the number of spant dependencies. — matexp • Spectroscopy Analysis Tools (spant) Apply the max operator to an MRS dataset. — max_mrs • Spectroscopy Analysis Tools (spant) Apply the max operator to an MRS dataset. — max_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/max_mrs_interp.html b/docs/reference/max_mrs_interp.html
index e4474764..52e63f3e 100644
--- a/docs/reference/max_mrs_interp.html
+++ b/docs/reference/max_mrs_interp.html
@@ -1,5 +1,5 @@
-Apply the max operator to an interpolated MRS dataset. — max_mrs_interp • Spectroscopy Analysis Tools (spant) Apply the max operator to an interpolated MRS dataset. — max_mrs_interp • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/mean.list.html b/docs/reference/mean.list.html
index b8eb3463..048306fd 100644
--- a/docs/reference/mean.list.html
+++ b/docs/reference/mean.list.html
@@ -1,5 +1,5 @@
-Calculate the mean spectrum from an mrs_data object. — mean.list • Spectroscopy Analysis Tools (spant) Calculate the mean spectrum from an mrs_data object. — mean.list • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/mean.mrs_data.html b/docs/reference/mean.mrs_data.html
index 5531a28d..79515014 100644
--- a/docs/reference/mean.mrs_data.html
+++ b/docs/reference/mean.mrs_data.html
@@ -1,5 +1,5 @@
-Calculate the mean spectrum from an mrs_data object. — mean.mrs_data • Spectroscopy Analysis Tools (spant) Calculate the mean spectrum from an mrs_data object. — mean.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/mean_dyn_blocks.html b/docs/reference/mean_dyn_blocks.html
index 10467098..4c042448 100644
--- a/docs/reference/mean_dyn_blocks.html
+++ b/docs/reference/mean_dyn_blocks.html
@@ -1,5 +1,5 @@
-Calculate the mean of adjacent dynamic scans. — mean_dyn_blocks • Spectroscopy Analysis Tools (spant) Calculate the mean of adjacent dynamic scans. — mean_dyn_blocks • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/mean_dyn_pairs.html b/docs/reference/mean_dyn_pairs.html
index 63e909ea..1a241126 100644
--- a/docs/reference/mean_dyn_pairs.html
+++ b/docs/reference/mean_dyn_pairs.html
@@ -1,5 +1,5 @@
-Calculate the pairwise means across a dynamic data set. — mean_dyn_pairs • Spectroscopy Analysis Tools (spant) Calculate the pairwise means across a dynamic data set. — mean_dyn_pairs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/mean_dyns.html b/docs/reference/mean_dyns.html
index 73fdbfa7..0daa27df 100644
--- a/docs/reference/mean_dyns.html
+++ b/docs/reference/mean_dyns.html
@@ -1,5 +1,5 @@
-Calculate the mean dynamic data. — mean_dyns • Spectroscopy Analysis Tools (spant) Calculate the mean dynamic data. — mean_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/mean_mrs_list.html b/docs/reference/mean_mrs_list.html
index 808b6c50..10d842c0 100644
--- a/docs/reference/mean_mrs_list.html
+++ b/docs/reference/mean_mrs_list.html
@@ -1,5 +1,5 @@
-Return the mean of a list of mrs_data objects. — mean_mrs_list • Spectroscopy Analysis Tools (spant) Return the mean of a list of mrs_data objects. — mean_mrs_list • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/mean_vec_blocks.html b/docs/reference/mean_vec_blocks.html
index 8fc92eaa..dd78b122 100644
--- a/docs/reference/mean_vec_blocks.html
+++ b/docs/reference/mean_vec_blocks.html
@@ -1,5 +1,5 @@
-Calculate the mean of adjacent blocks in a vector. — mean_vec_blocks • Spectroscopy Analysis Tools (spant) Calculate the mean of adjacent blocks in a vector. — mean_vec_blocks • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/median_dyns.html b/docs/reference/median_dyns.html
index 1039d4b5..9a085b10 100644
--- a/docs/reference/median_dyns.html
+++ b/docs/reference/median_dyns.html
@@ -1,5 +1,5 @@
-Calculate the median dynamic data. — median_dyns • Spectroscopy Analysis Tools (spant) Calculate the median dynamic data. — median_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/mod_td.html b/docs/reference/mod_td.html
index 76ad0a40..141ef09e 100644
--- a/docs/reference/mod_td.html
+++ b/docs/reference/mod_td.html
@@ -1,5 +1,5 @@
-Apply the Modulus operator to the time-domain MRS signal. — mod_td • Spectroscopy Analysis Tools (spant) Apply the Modulus operator to the time-domain MRS signal. — mod_td • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/mrs_data2basis.html b/docs/reference/mrs_data2basis.html
index 62f7d749..11797b91 100644
--- a/docs/reference/mrs_data2basis.html
+++ b/docs/reference/mrs_data2basis.html
@@ -1,7 +1,5 @@
-Convert an mrs_data object to basis object - where basis signals are spread
-across the dynamic dimension in the MRS data. — mrs_data2basis • Spectroscopy Analysis Tools (spant) Convert an mrs_data object to basis object - where basis signals are spread across the dynamic dimension in the MRS data. — mrs_data2basis • Spectroscopy Analysis Tools (spant) Create a BIDS file structure from a vector of MRS data paths or list of mrs_data objects. — mrs_data2bids • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Create a BIDS file structure from a vector of MRS data paths or list of mrs_data objects.
+ Source: R/fmrs.R
+ mrs_data2bids.Rd
+
+
+
+ Create a BIDS file structure from a vector of MRS data paths or list of
+mrs_data objects.
+
+
+
+ mrs_data2bids(
+ mrs_data,
+ output_dir,
+ suffix = NULL,
+ sub = NULL,
+ ses = NULL,
+ task = NULL,
+ acq = NULL,
+ nuc = NULL,
+ voi = NULL,
+ rec = NULL,
+ run = NULL,
+ echo = NULL,
+ inv = NULL,
+ skip_existing = TRUE
+)
+
+
+
+ Arguments
+ - mrs_data
+vector of MRS data paths or list of mrs_data objects.
- output_dir
+the base directory to create the BIDS structure.
- suffix
+optional vector of file suffixes. Default behaviour is to
+automatically determine these from the input data, however it is recommended
+that they are specified to allow more efficient skipping of existing data.
- sub
+optional vector of subject labels. If not specified, these will be
+automatically generated as a series of increasing zero-padded integer values
+corresponding to the mrs_data input indices.
- ses
+optional vector of session labels.
- task
+optional vector of task labels.
- acq
+optional vector of acquisition labels.
- nuc
+optional vector of nucleus labels.
- voi
+optional vector of volume of interest labels.
- rec
+optional vector of reconstruction labels.
- run
+optional vector of run indices.
- echo
+optional vector of echo time indices.
- inv
+optional vector of inversion indices.
- skip_existing
+skip any data files that have already been converted.
+Defaults to TRUE, set to FALSE to force an overwrite of any existing data
+files.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/mrs_data2mat.html b/docs/reference/mrs_data2mat.html
index cf5ff28c..9e47688a 100644
--- a/docs/reference/mrs_data2mat.html
+++ b/docs/reference/mrs_data2mat.html
@@ -1,7 +1,5 @@
-Convert mrs_data object to a matrix, with spectral points in the column
-dimension and dynamics in the row dimension. — mrs_data2mat • Spectroscopy Analysis Tools (spant) Convert mrs_data object to a matrix, with spectral points in the column dimension and dynamics in the row dimension. — mrs_data2mat • Spectroscopy Analysis Tools (spant) Convert mrs_data object to a matrix, with spectral points in the column dimension and dynamics in the row dimension. — mrs_data2spec_mat • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Convert mrs_data object to a matrix, with spectral points in the column dimension and dynamics in the row dimension.
+ Source: R/mrs_data_proc.R
+ mrs_data2spec_mat.Rd
+
+
+
+ Convert mrs_data object to a matrix, with spectral points in the column
+dimension and dynamics in the row dimension.
+
+
+
+ mrs_data2spec_mat(mrs_data, collapse = TRUE)
+
+
+
+ Arguments
+ - mrs_data
+MRS data object or list of MRS data objects.
- collapse
+collapse all other dimensions along the dynamic dimension, eg
+a 16x16 MRSI grid would be first collapsed across 256 dynamic scans.
+
+ Value
+
+
+MRS data matrix.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/mrs_data2vec.html b/docs/reference/mrs_data2vec.html
index fb172d68..a1fd654d 100644
--- a/docs/reference/mrs_data2vec.html
+++ b/docs/reference/mrs_data2vec.html
@@ -1,5 +1,5 @@
-Convert mrs_data object to a vector. — mrs_data2vec • Spectroscopy Analysis Tools (spant) Convert mrs_data object to a vector. — mrs_data2vec • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -126,7 +126,7 @@ Value
diff --git a/docs/reference/mvfftshift.html b/docs/reference/mvfftshift.html
index 92b0841b..976b3410 100644
--- a/docs/reference/mvfftshift.html
+++ b/docs/reference/mvfftshift.html
@@ -1,7 +1,5 @@
-Perform a fftshift on a matrix, with each column replaced by its shifted
-result. — mvfftshift • Spectroscopy Analysis Tools (spant) Perform a fftshift on a matrix, with each column replaced by its shifted result. — mvfftshift • Spectroscopy Analysis Tools (spant) Perform an ifftshift on a matrix, with each column replaced by its shifted
-result. — mvifftshift • Spectroscopy Analysis Tools (spant) Perform an ifftshift on a matrix, with each column replaced by its shifted result. — mvifftshift • Spectroscopy Analysis Tools (spant) Print fit coordinates from a single index. — n2coord • Spectroscopy Analysis Tools (spant) Print fit coordinates from a single index. — n2coord • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/nifti_flip_lr.html b/docs/reference/nifti_flip_lr.html
index 730abe3c..19860b3c 100644
--- a/docs/reference/nifti_flip_lr.html
+++ b/docs/reference/nifti_flip_lr.html
@@ -1,9 +1,5 @@
-Flip the x data dimension order of a nifti image. This corresponds to
-flipping MRI data in the left-right direction, assuming the data in save in
-neurological format (can check with fslorient program). — nifti_flip_lr • Spectroscopy Analysis Tools (spant) Flip the x data dimension order of a nifti image. This corresponds to flipping MRI data in the left-right direction, assuming the data in save in neurological format (can check with fslorient program). — nifti_flip_lr • Spectroscopy Analysis Tools (spant) Export a one-page pdf of a single fit result — one_page_pdf • Spectroscopy Analysis Tools (spant) Export a one-page pdf of a single fit result — one_page_pdf • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -108,7 +108,7 @@ Arguments
diff --git a/docs/reference/ortho3.html b/docs/reference/ortho3.html
index 13ade97d..5d7dd2fd 100644
--- a/docs/reference/ortho3.html
+++ b/docs/reference/ortho3.html
@@ -1,5 +1,5 @@
-Display an orthographic projection plot of a nifti object. — ortho3 • Spectroscopy Analysis Tools (spant) Display an orthographic projection plot of a nifti object. — ortho3 • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -172,7 +172,7 @@ Arguments
diff --git a/docs/reference/ortho3_inter.html b/docs/reference/ortho3_inter.html
index 090cc5e5..15948899 100644
--- a/docs/reference/ortho3_inter.html
+++ b/docs/reference/ortho3_inter.html
@@ -1,5 +1,5 @@
-Display an interactive orthographic projection plot of a nifti object. — ortho3_inter • Spectroscopy Analysis Tools (spant) Display an interactive orthographic projection plot of a nifti object. — ortho3_inter • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -132,7 +132,7 @@ Arguments
diff --git a/docs/reference/peak_info.html b/docs/reference/peak_info.html
index 09058bd8..41c8ffaf 100644
--- a/docs/reference/peak_info.html
+++ b/docs/reference/peak_info.html
@@ -1,7 +1,5 @@
-Search for the highest peak in a spectral region and return the frequency,
-height and FWHM. — peak_info • Spectroscopy Analysis Tools (spant) Search for the highest peak in a spectral region and return the frequency, height and FWHM. — peak_info • Spectroscopy Analysis Tools (spant) Papoulis-Gerchberg (PG) algorithm method for k-space extrapolation. — pg_extrap_xy • Spectroscopy Analysis Tools (spant) Papoulis-Gerchberg (PG) algorithm method for k-space extrapolation. — pg_extrap_xy • Spectroscopy Analysis Tools (spant) Apply phasing parameters to MRS data. — phase • Spectroscopy Analysis Tools (spant) Apply phasing parameters to MRS data. — phase • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/phase_ref_1h_brain.html b/docs/reference/phase_ref_1h_brain.html
new file mode 100644
index 00000000..8707a74a
--- /dev/null
+++ b/docs/reference/phase_ref_1h_brain.html
@@ -0,0 +1,131 @@
+
+Corrected zero order phase and chemical shift offset in 1H MRS data from the brain. — phase_ref_1h_brain • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Corrected zero order phase and chemical shift offset in 1H MRS data from the brain.
+ Source: R/rats.R
+ phase_ref_1h_brain.Rd
+
+
+
+ Corrected zero order phase and chemical shift offset in 1H MRS data from the
+brain.
+
+
+
+ phase_ref_1h_brain(mrs_data, mean_ref = FALSE, ret_corr_only = TRUE)
+
+
+
+ Arguments
+ - mrs_data
+MRS data to be corrected.
- mean_ref
+apply the phase and offset of the mean spectrum to all
+others. Default is FALSE.
- ret_corr_only
+return the corrected data only.
+
+ Value
+
+
+corrected MRS data.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/plot.fit_result.html b/docs/reference/plot.fit_result.html
index e54d3bc1..836a53ee 100644
--- a/docs/reference/plot.fit_result.html
+++ b/docs/reference/plot.fit_result.html
@@ -1,5 +1,5 @@
-Plot the fitting results of an object of class fit_result. — plot.fit_result • Spectroscopy Analysis Tools (spant) Plot the fitting results of an object of class fit_result. — plot.fit_result • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -207,7 +207,7 @@ Arguments
diff --git a/docs/reference/plot.mrs_data.html b/docs/reference/plot.mrs_data.html
index fabcc35b..bb2ec651 100644
--- a/docs/reference/plot.mrs_data.html
+++ b/docs/reference/plot.mrs_data.html
@@ -1,5 +1,5 @@
-Plotting method for objects of class mrs_data. — plot.mrs_data • Spectroscopy Analysis Tools (spant) Plotting method for objects of class mrs_data. — plot.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -287,7 +287,7 @@ Arguments
diff --git a/docs/reference/plot_bc.html b/docs/reference/plot_bc.html
index 4f8309b4..b48142cc 100644
--- a/docs/reference/plot_bc.html
+++ b/docs/reference/plot_bc.html
@@ -1,5 +1,5 @@
-Convenience function to plot a baseline estimate with the original data. — plot_bc • Spectroscopy Analysis Tools (spant) Convenience function to plot a baseline estimate with the original data. — plot_bc • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -108,7 +108,7 @@ Arguments
diff --git a/docs/reference/plot_reg.html b/docs/reference/plot_reg.html
index ae1acbe7..2addb2f6 100644
--- a/docs/reference/plot_reg.html
+++ b/docs/reference/plot_reg.html
@@ -1,5 +1,5 @@
-Plot regressors as an image. — plot_reg • Spectroscopy Analysis Tools (spant) Plot regressors as an image. — plot_reg • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/plot_slice_fit.html b/docs/reference/plot_slice_fit.html
index fbc7b560..57f1af8a 100644
--- a/docs/reference/plot_slice_fit.html
+++ b/docs/reference/plot_slice_fit.html
@@ -1,5 +1,5 @@
-Plot a 2D slice from an MRSI fit result object. — plot_slice_fit • Spectroscopy Analysis Tools (spant) Plot a 2D slice from an MRSI fit result object. — plot_slice_fit • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -129,7 +129,7 @@ Arguments
diff --git a/docs/reference/plot_slice_fit_inter.html b/docs/reference/plot_slice_fit_inter.html
index 4eed104a..da105a7d 100644
--- a/docs/reference/plot_slice_fit_inter.html
+++ b/docs/reference/plot_slice_fit_inter.html
@@ -1,5 +1,5 @@
-Plot a 2D slice from an MRSI fit result object. — plot_slice_fit_inter • Spectroscopy Analysis Tools (spant) Plot a 2D slice from an MRSI fit result object. — plot_slice_fit_inter • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -134,7 +134,7 @@ Arguments
diff --git a/docs/reference/plot_slice_map.html b/docs/reference/plot_slice_map.html
index 553e9ac8..ffb2a134 100644
--- a/docs/reference/plot_slice_map.html
+++ b/docs/reference/plot_slice_map.html
@@ -1,5 +1,5 @@
-Plot a slice from a 7 dimensional array. — plot_slice_map • Spectroscopy Analysis Tools (spant) Plot a slice from a 7 dimensional array. — plot_slice_map • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -153,7 +153,7 @@ Arguments
diff --git a/docs/reference/plot_slice_map_inter.html b/docs/reference/plot_slice_map_inter.html
index 40d33b42..90968f66 100644
--- a/docs/reference/plot_slice_map_inter.html
+++ b/docs/reference/plot_slice_map_inter.html
@@ -1,7 +1,5 @@
-Plot an interactive slice map from a data array where voxels can be selected
-to display a corresponding spectrum. — plot_slice_map_inter • Spectroscopy Analysis Tools (spant) Plot an interactive slice map from a data array where voxels can be selected to display a corresponding spectrum. — plot_slice_map_inter • Spectroscopy Analysis Tools (spant) Plot the spectral standard deviation. — plot_spec_sd • Spectroscopy Analysis Tools (spant) Plot the spectral standard deviation. — plot_spec_sd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Arguments
diff --git a/docs/reference/plot_voi_overlay.html b/docs/reference/plot_voi_overlay.html
index 9a782e88..bbbbf35e 100644
--- a/docs/reference/plot_voi_overlay.html
+++ b/docs/reference/plot_voi_overlay.html
@@ -1,5 +1,5 @@
-Plot a volume as an image overlay. — plot_voi_overlay • Spectroscopy Analysis Tools (spant) Plot a volume as an image overlay. — plot_voi_overlay • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -116,7 +116,7 @@ Arguments
diff --git a/docs/reference/plot_voi_overlay_seg.html b/docs/reference/plot_voi_overlay_seg.html
index 3d4e74ff..0e800ff2 100644
--- a/docs/reference/plot_voi_overlay_seg.html
+++ b/docs/reference/plot_voi_overlay_seg.html
@@ -1,5 +1,5 @@
-Plot a volume as an overlay on a segmented brain volume. — plot_voi_overlay_seg • Spectroscopy Analysis Tools (spant) Plot a volume as an overlay on a segmented brain volume. — plot_voi_overlay_seg • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Arguments
diff --git a/docs/reference/ppm.html b/docs/reference/ppm.html
index c352327a..ee4696e2 100644
--- a/docs/reference/ppm.html
+++ b/docs/reference/ppm.html
@@ -1,5 +1,5 @@
-Return the ppm scale of an MRS dataset or fit result. — ppm • Spectroscopy Analysis Tools (spant) Return the ppm scale of an MRS dataset or fit result. — ppm • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -132,7 +132,7 @@ Value
diff --git a/docs/reference/precomp.html b/docs/reference/precomp.html
index 822d7336..df3d2c6c 100644
--- a/docs/reference/precomp.html
+++ b/docs/reference/precomp.html
@@ -1,7 +1,5 @@
-Save function results to file and load on subsequent calls to avoid repeat
-computation. — precomp • Spectroscopy Analysis Tools (spant) Save function results to file and load on subsequent calls to avoid repeat computation. — precomp • Spectroscopy Analysis Tools (spant) Preprocess and perform quality assessment of a single SVS data set. — preproc_svs • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Preprocess and perform quality assessment of a single SVS data set.
+ Source: R/fmrs.R
+ preproc_svs.Rd
+
+
+
+ Preprocess and perform quality assessment of a single SVS data set.
+
+
+
+ preproc_svs(path, label = NULL, output_dir = NULL, ref_inds = NULL)
+
+
+
+ Arguments
+ - path
+path to the fMRS data file or IMA directory.
- label
+a label to describe the data set.
- output_dir
+output directory.
- ref_inds
+a vector of 1-based indices for any water reference dynamic
+scans.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/preproc_svs_dataset.html b/docs/reference/preproc_svs_dataset.html
new file mode 100644
index 00000000..07c3a29b
--- /dev/null
+++ b/docs/reference/preproc_svs_dataset.html
@@ -0,0 +1,148 @@
+
+Preprocess and perform quality assessment of one or more SVS data sets. — preproc_svs_dataset • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Preprocess and perform quality assessment of one or more SVS data sets.
+ Source: R/fmrs.R
+ preproc_svs_dataset.Rd
+
+
+
+ Preprocess and perform quality assessment of one or more SVS data sets.
+
+
+
+ preproc_svs_dataset(
+ paths,
+ labels = NULL,
+ output_dir = "spant_analysis",
+ exclude_labels = NULL,
+ overwrite = FALSE,
+ ref_inds = NULL,
+ return_results = FALSE
+)
+
+
+
+ Arguments
+ - paths
+paths to the fMRS data file or IMA directory.
- labels
+labels to describe each data set.
- output_dir
+output directory.
- exclude_labels
+vector of labels of scans to exclude, eg poor quality
+data.
- overwrite
+overwrite saved results, defaults to FALSE.
- ref_inds
+a vector of 1-based indices for any water reference dynamic
+scans.
- return_results
+function will return key outputs, defaults to FALSE.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/print.fit_result.html b/docs/reference/print.fit_result.html
index 297f28dc..5f434e57 100644
--- a/docs/reference/print.fit_result.html
+++ b/docs/reference/print.fit_result.html
@@ -1,5 +1,5 @@
-Print a summary of an object of class fit_result. — print.fit_result • Spectroscopy Analysis Tools (spant) Print a summary of an object of class fit_result. — print.fit_result • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -105,7 +105,7 @@ Arguments
diff --git a/docs/reference/print.mrs_data.html b/docs/reference/print.mrs_data.html
index 51199017..e1561eb2 100644
--- a/docs/reference/print.mrs_data.html
+++ b/docs/reference/print.mrs_data.html
@@ -1,5 +1,5 @@
-Print a summary of mrs_data parameters. — print.mrs_data • Spectroscopy Analysis Tools (spant) Print a summary of mrs_data parameters. — print.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -109,7 +109,7 @@ Arguments
diff --git a/docs/reference/qn_states.html b/docs/reference/qn_states.html
index 0f42f2f9..d7aa6715 100644
--- a/docs/reference/qn_states.html
+++ b/docs/reference/qn_states.html
@@ -1,5 +1,5 @@
-Get the quantum coherence matrix for a spin system. — qn_states • Spectroscopy Analysis Tools (spant) Get the quantum coherence matrix for a spin system. — qn_states • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/rats.html b/docs/reference/rats.html
index 5a39a396..93585e08 100644
--- a/docs/reference/rats.html
+++ b/docs/reference/rats.html
@@ -1,5 +1,5 @@
-Robust Alignment to a Target Spectrum (RATS). — rats • Spectroscopy Analysis Tools (spant) Robust Alignment to a Target Spectrum (RATS). — rats • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -207,7 +207,7 @@ Value
diff --git a/docs/reference/re_weighting.html b/docs/reference/re_weighting.html
index d21caf21..8b0b070a 100644
--- a/docs/reference/re_weighting.html
+++ b/docs/reference/re_weighting.html
@@ -1,5 +1,5 @@
-Apply a weighting to the FID to enhance spectral resolution. — re_weighting • Spectroscopy Analysis Tools (spant) Apply a weighting to the FID to enhance spectral resolution. — re_weighting • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/read_basis.html b/docs/reference/read_basis.html
index da9b94af..eb6f8557 100644
--- a/docs/reference/read_basis.html
+++ b/docs/reference/read_basis.html
@@ -1,5 +1,5 @@
-Read a basis file in LCModel .basis format. — read_basis • Spectroscopy Analysis Tools (spant) Read a basis file in LCModel .basis format. — read_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/read_ima_coil_dir.html b/docs/reference/read_ima_coil_dir.html
index 28c02de0..4f073cd8 100644
--- a/docs/reference/read_ima_coil_dir.html
+++ b/docs/reference/read_ima_coil_dir.html
@@ -1,9 +1,5 @@
-Read a directory containing Siemens MRS IMA files and combine along the coil
-dimension. Note that the coil ID is inferred from the sorted file name and
-should be checked when consistency is required between two directories. — read_ima_coil_dir • Spectroscopy Analysis Tools (spant) Read a directory containing Siemens MRS IMA files and combine along the coil dimension. Note that the coil ID is inferred from the sorted file name and should be checked when consistency is required between two directories. — read_ima_coil_dir • Spectroscopy Analysis Tools (spant) Read a directory containing Siemens MRS IMA files and combine along the
-dynamic dimension. Note that the coil ID is inferred from the sorted file
-name and should be checked when consistency is required. — read_ima_dyn_dir • Spectroscopy Analysis Tools (spant) Read a directory containing Siemens MRS IMA files and combine along the dynamic dimension. Note that the coil ID is inferred from the sorted file name and should be checked when consistency is required. — read_ima_dyn_dir • Spectroscopy Analysis Tools (spant) Read an LCModel formatted coord file containing fit information. — read_lcm_coord • Spectroscopy Analysis Tools (spant) Read an LCModel formatted coord file containing fit information. — read_lcm_coord • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -107,7 +107,7 @@ Value
diff --git a/docs/reference/read_mrs.html b/docs/reference/read_mrs.html
index 3ac2a36b..2cf36b20 100644
--- a/docs/reference/read_mrs.html
+++ b/docs/reference/read_mrs.html
@@ -1,5 +1,5 @@
-Read MRS data from a file. — read_mrs • Spectroscopy Analysis Tools (spant) Read MRS data from a file. — read_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -88,7 +88,8 @@ Read MRS data from a file.
full_fid = FALSE,
omit_svs_ref_scans = TRUE,
verbose = FALSE,
- extra = NULL
+ extra = NULL,
+ fid_filt_dist = NULL
)
@@ -140,6 +141,13 @@ Arguments
an optional data frame to provide additional variables for use
in subsequent analysis steps, eg id or grouping variables.
fid_filt_dist
+indicate if the data has a distorted FID due to a
+brick-wall filter being used to downsample the data. Default is to auto
+detect this from the data, but TRUE or FALSE options can be given to override
+detection.
Value
@@ -183,7 +191,7 @@ Examples
diff --git a/docs/reference/read_mrs_tqn.html b/docs/reference/read_mrs_tqn.html
index 5766362f..84bdaf3a 100644
--- a/docs/reference/read_mrs_tqn.html
+++ b/docs/reference/read_mrs_tqn.html
@@ -1,5 +1,5 @@
-Read MRS data using the TARQUIN software package. — read_mrs_tqn • Spectroscopy Analysis Tools (spant) Read MRS data using the TARQUIN software package. — read_mrs_tqn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -131,7 +131,7 @@ Examples
diff --git a/docs/reference/read_pulse_ascii.html b/docs/reference/read_pulse_ascii.html
index c9e0d43c..ab11c9cc 100644
--- a/docs/reference/read_pulse_ascii.html
+++ b/docs/reference/read_pulse_ascii.html
@@ -1,5 +1,5 @@
-Read an ASCII formatted pulse file. — read_pulse_ascii • Spectroscopy Analysis Tools (spant) Read an ASCII formatted pulse file. — read_pulse_ascii • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/read_pulse_bruker.html b/docs/reference/read_pulse_bruker.html
index c92bf76a..dbe9073b 100644
--- a/docs/reference/read_pulse_bruker.html
+++ b/docs/reference/read_pulse_bruker.html
@@ -1,5 +1,5 @@
-Read a Bruker formatted pulse file — read_pulse_bruker • Spectroscopy Analysis Tools (spant) Read a Bruker formatted pulse file — read_pulse_bruker • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/read_pulse_pta.html b/docs/reference/read_pulse_pta.html
index 72e1b6d4..a0fac3c3 100644
--- a/docs/reference/read_pulse_pta.html
+++ b/docs/reference/read_pulse_pta.html
@@ -1,5 +1,5 @@
-Read a .pta formatted pulse file compatible with Siemens PulseTool. — read_pulse_pta • Spectroscopy Analysis Tools (spant) Read a .pta formatted pulse file compatible with Siemens PulseTool. — read_pulse_pta • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/read_siemens_txt_hdr.html b/docs/reference/read_siemens_txt_hdr.html
index 23fb8c70..3a17d87c 100644
--- a/docs/reference/read_siemens_txt_hdr.html
+++ b/docs/reference/read_siemens_txt_hdr.html
@@ -1,5 +1,5 @@
-Read the text format header found in Siemens IMA and TWIX data files. — read_siemens_txt_hdr • Spectroscopy Analysis Tools (spant) Read the text format header found in Siemens IMA and TWIX data files. — read_siemens_txt_hdr • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -78,7 +78,7 @@ Read the text format header found in Siemens IMA and TWIX data files.
- read_siemens_txt_hdr(input, version = "vd", verbose, offset = 0)
+ read_siemens_txt_hdr(input, version = "vd", verbose = FALSE, offset = 0)
@@ -118,7 +118,7 @@ Value
diff --git a/docs/reference/read_tqn_fit.html b/docs/reference/read_tqn_fit.html
index 4da6c25e..a1630420 100644
--- a/docs/reference/read_tqn_fit.html
+++ b/docs/reference/read_tqn_fit.html
@@ -1,5 +1,5 @@
-Reader for csv fit results generated by TARQUIN. — read_tqn_fit • Spectroscopy Analysis Tools (spant) Reader for csv fit results generated by TARQUIN. — read_tqn_fit • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -113,7 +113,7 @@ Examples
diff --git a/docs/reference/read_tqn_result.html b/docs/reference/read_tqn_result.html
index 36659714..68a3e98c 100644
--- a/docs/reference/read_tqn_result.html
+++ b/docs/reference/read_tqn_result.html
@@ -1,5 +1,5 @@
-Reader for csv results generated by TARQUIN. — read_tqn_result • Spectroscopy Analysis Tools (spant) Reader for csv results generated by TARQUIN. — read_tqn_result • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -117,7 +117,7 @@ Examples
diff --git a/docs/reference/recon_imag.html b/docs/reference/recon_imag.html
index d2a72225..5bc3b1eb 100644
--- a/docs/reference/recon_imag.html
+++ b/docs/reference/recon_imag.html
@@ -1,7 +1,5 @@
-Reconstruct complex time-domain data from the real part of frequency-domain
-data. — recon_imag • Spectroscopy Analysis Tools (spant) Reconstruct complex time-domain data from the real part of frequency-domain data. — recon_imag • Spectroscopy Analysis Tools (spant) Reconstruct complex time-domain data from the real part of frequency-domain
-data. — recon_imag_vec • Spectroscopy Analysis Tools (spant) Reconstruct complex time-domain data from the real part of frequency-domain data. — recon_imag_vec • Spectroscopy Analysis Tools (spant) Reconstruct 2D MRSI data from a twix file loaded with read_mrs. — recon_twix_2d_mrsi • Spectroscopy Analysis Tools (spant) Reconstruct 2D MRSI data from a twix file loaded with read_mrs. — recon_twix_2d_mrsi • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/rectangular_mask.html b/docs/reference/rectangular_mask.html
index a2117283..6e469bc9 100644
--- a/docs/reference/rectangular_mask.html
+++ b/docs/reference/rectangular_mask.html
@@ -1,5 +1,5 @@
-Create a rectangular mask stored as a matrix of logical values. — rectangular_mask • Spectroscopy Analysis Tools (spant) Create a rectangular mask stored as a matrix of logical values. — rectangular_mask • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -130,7 +130,7 @@ Value
diff --git a/docs/reference/reexports.html b/docs/reference/reexports.html
index 694a75d1..a59e8379 100644
--- a/docs/reference/reexports.html
+++ b/docs/reference/reexports.html
@@ -1,5 +1,5 @@
-Objects exported from other packages — reexports • Spectroscopy Analysis Tools (spant) Objects exported from other packages — reexports • Spectroscopy Analysis Tools (spant)
Spectroscopy Analysis Tools (spant)
- 2.21.0
+ 2.22.0
@@ -103,7 +103,7 @@ Objects exported from other packages
diff --git a/docs/reference/rep_array_dim.html b/docs/reference/rep_array_dim.html
index b9c49b4a..48c0a5ed 100644
--- a/docs/reference/rep_array_dim.html
+++ b/docs/reference/rep_array_dim.html
@@ -1,5 +1,5 @@
-Repeat an array over a given dimension. — rep_array_dim • Spectroscopy Analysis Tools (spant) Repeat an array over a given dimension. — rep_array_dim • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/rep_dyn.html b/docs/reference/rep_dyn.html
index 6bbfb0ef..89a4bb9b 100644
--- a/docs/reference/rep_dyn.html
+++ b/docs/reference/rep_dyn.html
@@ -1,5 +1,5 @@
-Replicate a scan in the dynamic dimension. — rep_dyn • Spectroscopy Analysis Tools (spant) Replicate a scan in the dynamic dimension. — rep_dyn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/rep_mrs.html b/docs/reference/rep_mrs.html
index 67730b5c..becb8f00 100644
--- a/docs/reference/rep_mrs.html
+++ b/docs/reference/rep_mrs.html
@@ -1,5 +1,5 @@
-Replicate a scan over a given dimension. — rep_mrs • Spectroscopy Analysis Tools (spant) Replicate a scan over a given dimension. — rep_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -138,7 +138,7 @@ Value
diff --git a/docs/reference/resample_basis.html b/docs/reference/resample_basis.html
index b0f2ab17..c7a6222a 100644
--- a/docs/reference/resample_basis.html
+++ b/docs/reference/resample_basis.html
@@ -1,5 +1,5 @@
-Resample a basis-set to match a mrs_data acquisition. — resample_basis • Spectroscopy Analysis Tools (spant) Resample a basis-set to match a mrs_data acquisition. — resample_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -116,7 +116,7 @@ Value
diff --git a/docs/reference/resample_img.html b/docs/reference/resample_img.html
index f1e7beaf..b0cc8f71 100644
--- a/docs/reference/resample_img.html
+++ b/docs/reference/resample_img.html
@@ -1,5 +1,5 @@
-Resample an image to match a target image space. — resample_img • Spectroscopy Analysis Tools (spant) Resample an image to match a target image space. — resample_img • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/resample_voi.html b/docs/reference/resample_voi.html
index 8fbfa836..a29ab096 100644
--- a/docs/reference/resample_voi.html
+++ b/docs/reference/resample_voi.html
@@ -1,7 +1,5 @@
-Resample a VOI to match a target image space using nearest-neighbour
-interpolation. — resample_voi • Spectroscopy Analysis Tools (spant) Resample a VOI to match a target image space using nearest-neighbour interpolation. — resample_voi • Spectroscopy Analysis Tools (spant) Reslice a nifti object to match the orientation of mrs data. — reslice_to_mrs • Spectroscopy Analysis Tools (spant) Reslice a nifti object to match the orientation of mrs data. — reslice_to_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/reson_table2mrs_data.html b/docs/reference/reson_table2mrs_data.html
index d75579ee..c5a2167a 100644
--- a/docs/reference/reson_table2mrs_data.html
+++ b/docs/reference/reson_table2mrs_data.html
@@ -1,5 +1,5 @@
-Generate mrs_data from a table of single Lorentzian resonances. — reson_table2mrs_data • Spectroscopy Analysis Tools (spant) Generate mrs_data from a table of single Lorentzian resonances. — reson_table2mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -119,7 +119,7 @@ Value
diff --git a/docs/reference/rm_dyns.html b/docs/reference/rm_dyns.html
index 5d5ef692..573e1f51 100644
--- a/docs/reference/rm_dyns.html
+++ b/docs/reference/rm_dyns.html
@@ -1,5 +1,5 @@
-Remove a subset of dynamic scans. — rm_dyns • Spectroscopy Analysis Tools (spant) Remove a subset of dynamic scans. — rm_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/scale_amp_molal.html b/docs/reference/scale_amp_molal.html
index aaeee1f2..7acb8cb0 100644
--- a/docs/reference/scale_amp_molal.html
+++ b/docs/reference/scale_amp_molal.html
@@ -1,7 +1,5 @@
-Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water). — scale_amp_molal • Spectroscopy Analysis Tools (spant) Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / kg of tissue water). — scale_amp_molal • Spectroscopy Analysis Tools (spant)
Spectroscopy Analysis Tools (spant)
- 2.21.0
+ 2.22.0
@@ -76,8 +74,7 @@
- Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water).
+ Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / kg of tissue water).
Source: R/amp_scaling.R
scale_amp_molal.Rd
@@ -163,7 +160,7 @@ Value
diff --git a/docs/reference/scale_amp_molal_pvc.html b/docs/reference/scale_amp_molal_pvc.html
index 962d6afc..4d194abd 100644
--- a/docs/reference/scale_amp_molal_pvc.html
+++ b/docs/reference/scale_amp_molal_pvc.html
@@ -1,7 +1,5 @@
-Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water). — scale_amp_molal_pvc • Spectroscopy Analysis Tools (spant)
@@ -75,8 +73,7 @@
- Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water).
+ Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / kg of tissue water).
Source: R/amp_scaling.R
scale_amp_molal_pvc.Rd
@@ -141,7 +138,7 @@ Value
diff --git a/docs/reference/scale_amp_molar.html b/docs/reference/scale_amp_molar.html
index 02358d91..dc87a338 100644
--- a/docs/reference/scale_amp_molar.html
+++ b/docs/reference/scale_amp_molar.html
@@ -1,7 +1,5 @@
-Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / Litre of tissue). — scale_amp_molar • Spectroscopy Analysis Tools (spant) Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / Litre of tissue). — scale_amp_molar • Spectroscopy Analysis Tools (spant) Convert default LCM/TARQUIN concentration scaling to molal units with partial
-volume correction. — scale_amp_molar2molal_pvc • Spectroscopy Analysis Tools (spant) Convert default LCM/TARQUIN concentration scaling to molal units with partial volume correction. — scale_amp_molar2molal_pvc • Spectroscopy Analysis Tools (spant) Scale fitted amplitudes to a ratio of signal amplitude. — scale_amp_ratio • Spectroscopy Analysis Tools (spant) Scale fitted amplitudes to a ratio of signal amplitude. — scale_amp_ratio • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -116,7 +116,7 @@ Value
diff --git a/docs/reference/scale_amp_ratio_value.html b/docs/reference/scale_amp_ratio_value.html
index 2036837a..6af8ac51 100644
--- a/docs/reference/scale_amp_ratio_value.html
+++ b/docs/reference/scale_amp_ratio_value.html
@@ -1,5 +1,5 @@
-Scale fitted amplitudes to a ratio of signal amplitude. — scale_amp_ratio_value • Spectroscopy Analysis Tools (spant) Scale fitted amplitudes to a ratio of signal amplitude. — scale_amp_ratio_value • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/scale_amp_water_ratio.html b/docs/reference/scale_amp_water_ratio.html
index 5b25e884..35a76b00 100644
--- a/docs/reference/scale_amp_water_ratio.html
+++ b/docs/reference/scale_amp_water_ratio.html
@@ -1,5 +1,5 @@
-Scale metabolite amplitudes as a ratio to the unsuppressed water amplitude. — scale_amp_water_ratio • Spectroscopy Analysis Tools (spant) Scale metabolite amplitudes as a ratio to the unsuppressed water amplitude. — scale_amp_water_ratio • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/scale_basis_amp.html b/docs/reference/scale_basis_amp.html
index 9401c3f1..5a58b5e5 100644
--- a/docs/reference/scale_basis_amp.html
+++ b/docs/reference/scale_basis_amp.html
@@ -1,5 +1,5 @@
-Scale a basis object by a scalar. — scale_basis_amp • Spectroscopy Analysis Tools (spant) Scale a basis object by a scalar. — scale_basis_amp • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/scale_basis_from_singlet.html b/docs/reference/scale_basis_from_singlet.html
index 0d542bc8..c9a19e77 100644
--- a/docs/reference/scale_basis_from_singlet.html
+++ b/docs/reference/scale_basis_from_singlet.html
@@ -1,5 +1,5 @@
-Scale a basis-set to be consistent with spant assumptions for water scaling. — scale_basis_from_singlet • Spectroscopy Analysis Tools (spant) Scale a basis-set to be consistent with spant assumptions for water scaling. — scale_basis_from_singlet • Spectroscopy Analysis Tools (spant)
Spectroscopy Analysis Tools (spant)
- 2.21.0
+ 2.22.0
@@ -127,7 +127,7 @@ Value
diff --git a/docs/reference/scale_mrs_amp.html b/docs/reference/scale_mrs_amp.html
index b5501a0d..990f058a 100644
--- a/docs/reference/scale_mrs_amp.html
+++ b/docs/reference/scale_mrs_amp.html
@@ -1,5 +1,5 @@
-Scale an mrs_data object by a scalar or vector or amplitudes. — scale_mrs_amp • Spectroscopy Analysis Tools (spant) Scale an mrs_data object by a scalar or vector or amplitudes. — scale_mrs_amp • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/scale_spec.html b/docs/reference/scale_spec.html
index 4f6ea835..6b3ddba4 100644
--- a/docs/reference/scale_spec.html
+++ b/docs/reference/scale_spec.html
@@ -1,5 +1,5 @@
-Scale mrs_data to a spectral region. — scale_spec • Spectroscopy Analysis Tools (spant) Scale mrs_data to a spectral region. — scale_spec • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -141,7 +141,7 @@ Value
diff --git a/docs/reference/sd.html b/docs/reference/sd.html
index ea1eec9f..3ae4dfd4 100644
--- a/docs/reference/sd.html
+++ b/docs/reference/sd.html
@@ -1,5 +1,5 @@
-Calculate the standard deviation spectrum from an mrs_data object. — sd • Spectroscopy Analysis Tools (spant) Calculate the standard deviation spectrum from an mrs_data object. — sd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/sd.mrs_data.html b/docs/reference/sd.mrs_data.html
index 3f92a49f..13bdda85 100644
--- a/docs/reference/sd.mrs_data.html
+++ b/docs/reference/sd.mrs_data.html
@@ -1,5 +1,5 @@
-Calculate the standard deviation spectrum from an mrs_data object. — sd.mrs_data • Spectroscopy Analysis Tools (spant) Calculate the standard deviation spectrum from an mrs_data object. — sd.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/seconds.html b/docs/reference/seconds.html
index b34d6627..467ee17f 100644
--- a/docs/reference/seconds.html
+++ b/docs/reference/seconds.html
@@ -1,5 +1,5 @@
-Return a time scale vector to match the FID of an MRS data object. — seconds • Spectroscopy Analysis Tools (spant) Return a time scale vector to match the FID of an MRS data object. — seconds • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/seq_cpmg_ideal.html b/docs/reference/seq_cpmg_ideal.html
index 547e96ab..45727c86 100644
--- a/docs/reference/seq_cpmg_ideal.html
+++ b/docs/reference/seq_cpmg_ideal.html
@@ -1,5 +1,5 @@
-CPMG style sequence with ideal pulses. — seq_cpmg_ideal • Spectroscopy Analysis Tools (spant) CPMG style sequence with ideal pulses. — seq_cpmg_ideal • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/seq_mega_press_ideal.html b/docs/reference/seq_mega_press_ideal.html
index 0769b8b4..a9cd7fa0 100644
--- a/docs/reference/seq_mega_press_ideal.html
+++ b/docs/reference/seq_mega_press_ideal.html
@@ -1,7 +1,5 @@
-MEGA-PRESS sequence with ideal localisation pulses and Gaussian shaped
-editing pulse. — seq_mega_press_ideal • Spectroscopy Analysis Tools (spant) MEGA-PRESS sequence with ideal localisation pulses and Gaussian shaped editing pulse. — seq_mega_press_ideal • Spectroscopy Analysis Tools (spant) PRESS sequence with shaped refocusing pulses. — seq_press_2d_shaped • Spectroscopy Analysis Tools (spant) PRESS sequence with shaped refocusing pulses. — seq_press_2d_shaped • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -165,7 +165,7 @@ Value
diff --git a/docs/reference/seq_press_ideal.html b/docs/reference/seq_press_ideal.html
index 8c976856..72c3af3d 100644
--- a/docs/reference/seq_press_ideal.html
+++ b/docs/reference/seq_press_ideal.html
@@ -1,5 +1,5 @@
-PRESS sequence with ideal pulses. — seq_press_ideal • Spectroscopy Analysis Tools (spant) PRESS sequence with ideal pulses. — seq_press_ideal • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/seq_pulse_acquire.html b/docs/reference/seq_pulse_acquire.html
index 4a88fc64..ad80571e 100644
--- a/docs/reference/seq_pulse_acquire.html
+++ b/docs/reference/seq_pulse_acquire.html
@@ -1,5 +1,5 @@
-Simple pulse and acquire sequence with ideal pulses. — seq_pulse_acquire • Spectroscopy Analysis Tools (spant) Simple pulse and acquire sequence with ideal pulses. — seq_pulse_acquire • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/seq_slaser_ideal.html b/docs/reference/seq_slaser_ideal.html
index 74688f4d..eb83e8e3 100644
--- a/docs/reference/seq_slaser_ideal.html
+++ b/docs/reference/seq_slaser_ideal.html
@@ -1,5 +1,5 @@
-sLASER sequence with ideal pulses. — seq_slaser_ideal • Spectroscopy Analysis Tools (spant) sLASER sequence with ideal pulses. — seq_slaser_ideal • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -126,7 +126,7 @@ Value
diff --git a/docs/reference/seq_spin_echo_ideal.html b/docs/reference/seq_spin_echo_ideal.html
index e23271de..4248716f 100644
--- a/docs/reference/seq_spin_echo_ideal.html
+++ b/docs/reference/seq_spin_echo_ideal.html
@@ -1,5 +1,5 @@
-Spin echo sequence with ideal pulses. — seq_spin_echo_ideal • Spectroscopy Analysis Tools (spant) Spin echo sequence with ideal pulses. — seq_spin_echo_ideal • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/seq_steam_ideal.html b/docs/reference/seq_steam_ideal.html
index a60685a8..1c8115d7 100644
--- a/docs/reference/seq_steam_ideal.html
+++ b/docs/reference/seq_steam_ideal.html
@@ -1,5 +1,5 @@
-STEAM sequence with ideal pulses. — seq_steam_ideal • Spectroscopy Analysis Tools (spant) STEAM sequence with ideal pulses. — seq_steam_ideal • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -128,7 +128,7 @@ Value
diff --git a/docs/reference/seq_steam_ideal_cof.html b/docs/reference/seq_steam_ideal_cof.html
index 8f225740..cba7af91 100644
--- a/docs/reference/seq_steam_ideal_cof.html
+++ b/docs/reference/seq_steam_ideal_cof.html
@@ -1,7 +1,5 @@
-STEAM sequence with ideal pulses and coherence order filtering to simulate
-gradient crushers. — seq_steam_ideal_cof • Spectroscopy Analysis Tools (spant) STEAM sequence with ideal pulses and coherence order filtering to simulate gradient crushers. — seq_steam_ideal_cof • Spectroscopy Analysis Tools (spant) STEAM sequence with ideal pulses using the z-rotation gradient simulation
-method described by Young et al JMR 140, 146-152 (1999). — seq_steam_ideal_young • Spectroscopy Analysis Tools (spant) STEAM sequence with ideal pulses using the z-rotation gradient simulation method described by Young et al JMR 140, 146-152 (1999). — seq_steam_ideal_young • Spectroscopy Analysis Tools (spant) Set the number of transients for an mrs_data object. — set_Ntrans • Spectroscopy Analysis Tools (spant) Set the number of transients for an mrs_data object. — set_Ntrans • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/set_def_acq_paras.html b/docs/reference/set_def_acq_paras.html
index 3e1b4004..cc2ada9c 100644
--- a/docs/reference/set_def_acq_paras.html
+++ b/docs/reference/set_def_acq_paras.html
@@ -1,5 +1,5 @@
-Set the default acquisition parameters. — set_def_acq_paras • Spectroscopy Analysis Tools (spant) Set the default acquisition parameters. — set_def_acq_paras • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Arguments
diff --git a/docs/reference/set_lcm_cmd.html b/docs/reference/set_lcm_cmd.html
index 2056ed01..42bb2f24 100644
--- a/docs/reference/set_lcm_cmd.html
+++ b/docs/reference/set_lcm_cmd.html
@@ -1,5 +1,5 @@
-Set the command to run the LCModel command-line program. — set_lcm_cmd • Spectroscopy Analysis Tools (spant) Set the command to run the LCModel command-line program. — set_lcm_cmd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/set_lw.html b/docs/reference/set_lw.html
index b64ec851..bb176c62 100644
--- a/docs/reference/set_lw.html
+++ b/docs/reference/set_lw.html
@@ -1,5 +1,5 @@
-Apply line-broadening to an mrs_data object to achieve a specified linewidth. — set_lw • Spectroscopy Analysis Tools (spant) Apply line-broadening to an mrs_data object to achieve a specified linewidth. — set_lw • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -123,7 +123,7 @@ Value
diff --git a/docs/reference/set_mask_xy_mat.html b/docs/reference/set_mask_xy_mat.html
index 49dc5d4e..52c4b617 100644
--- a/docs/reference/set_mask_xy_mat.html
+++ b/docs/reference/set_mask_xy_mat.html
@@ -1,5 +1,5 @@
-Set the masked voxels in a 2D MRSI dataset to given spectrum. — set_mask_xy_mat • Spectroscopy Analysis Tools (spant) Set the masked voxels in a 2D MRSI dataset to given spectrum. — set_mask_xy_mat • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Value
diff --git a/docs/reference/set_precomp_mode.html b/docs/reference/set_precomp_mode.html
index f44bd5d3..47c28e3b 100644
--- a/docs/reference/set_precomp_mode.html
+++ b/docs/reference/set_precomp_mode.html
@@ -1,5 +1,5 @@
-Set the precompute mode. — set_precomp_mode • Spectroscopy Analysis Tools (spant) Set the precompute mode. — set_precomp_mode • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/set_precomp_verbose.html b/docs/reference/set_precomp_verbose.html
index 1453a231..9c613505 100644
--- a/docs/reference/set_precomp_verbose.html
+++ b/docs/reference/set_precomp_verbose.html
@@ -1,5 +1,5 @@
-Set the verbosity of the precompute function. — set_precomp_verbose • Spectroscopy Analysis Tools (spant) Set the verbosity of the precompute function. — set_precomp_verbose • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/set_ref.html b/docs/reference/set_ref.html
index 8953fa50..5436dfa2 100644
--- a/docs/reference/set_ref.html
+++ b/docs/reference/set_ref.html
@@ -1,5 +1,5 @@
-Set the ppm reference value (eg ppm value at 0Hz). — set_ref • Spectroscopy Analysis Tools (spant) Set the ppm reference value (eg ppm value at 0Hz). — set_ref • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/set_td_pts.html b/docs/reference/set_td_pts.html
index 8a80d42a..586459ff 100644
--- a/docs/reference/set_td_pts.html
+++ b/docs/reference/set_td_pts.html
@@ -1,7 +1,5 @@
-Set the number of time-domain data points, truncating or zero-filling as
-appropriate. — set_td_pts • Spectroscopy Analysis Tools (spant) Set the number of time-domain data points, truncating or zero-filling as appropriate. — set_td_pts • Spectroscopy Analysis Tools (spant) Set the command to run the TARQUIN command-line program. — set_tqn_cmd • Spectroscopy Analysis Tools (spant) Set the command to run the TARQUIN command-line program. — set_tqn_cmd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/set_tr.html b/docs/reference/set_tr.html
index b2109ab0..65c9df5f 100644
--- a/docs/reference/set_tr.html
+++ b/docs/reference/set_tr.html
@@ -1,5 +1,5 @@
-Set the repetition time of an MRS dataset. — set_tr • Spectroscopy Analysis Tools (spant) Set the repetition time of an MRS dataset. — set_tr • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/shift.html b/docs/reference/shift.html
index ab0fe724..034591d0 100644
--- a/docs/reference/shift.html
+++ b/docs/reference/shift.html
@@ -1,5 +1,5 @@
-Apply a frequency shift to MRS data. — shift • Spectroscopy Analysis Tools (spant) Apply a frequency shift to MRS data. — shift • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/shift_basis.html b/docs/reference/shift_basis.html
index 2884be19..f55a65e0 100644
--- a/docs/reference/shift_basis.html
+++ b/docs/reference/shift_basis.html
@@ -1,5 +1,5 @@
-Apply frequency shifts to basis set signals. — shift_basis • Spectroscopy Analysis Tools (spant) Apply frequency shifts to basis set signals. — shift_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Value
diff --git a/docs/reference/sim_basis.html b/docs/reference/sim_basis.html
index c7838c46..bb5fefc6 100644
--- a/docs/reference/sim_basis.html
+++ b/docs/reference/sim_basis.html
@@ -1,5 +1,5 @@
-Simulate a basis set object. — sim_basis • Spectroscopy Analysis Tools (spant) Simulate a basis set object. — sim_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -136,7 +136,7 @@ Value
diff --git a/docs/reference/sim_basis_1h_brain.html b/docs/reference/sim_basis_1h_brain.html
index 62ed7389..f71ffa0b 100644
--- a/docs/reference/sim_basis_1h_brain.html
+++ b/docs/reference/sim_basis_1h_brain.html
@@ -1,7 +1,5 @@
-Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS
-sequence. Note, ideal pulses are assumed. — sim_basis_1h_brain • Spectroscopy Analysis Tools (spant) Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS sequence. Note, ideal pulses are assumed. — sim_basis_1h_brain • Spectroscopy Analysis Tools (spant) Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS
-sequence. Note, ideal pulses are assumed. — sim_basis_1h_brain_press • Spectroscopy Analysis Tools (spant) Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS sequence. Note, ideal pulses are assumed. — sim_basis_1h_brain_press • Spectroscopy Analysis Tools (spant) Simulate a macromolecular and lipid basis-set suitable for 1H brain MRS
-analysis. — sim_basis_mm_lip_lcm • Spectroscopy Analysis Tools (spant) Simulate a macromolecular and lipid basis-set suitable for 1H brain MRS analysis. — sim_basis_mm_lip_lcm • Spectroscopy Analysis Tools (spant) Simulate a basis file using TARQUIN. — sim_basis_tqn • Spectroscopy Analysis Tools (spant) Simulate a basis file using TARQUIN. — sim_basis_tqn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -129,7 +129,7 @@ Examples
diff --git a/docs/reference/sim_brain_1h.html b/docs/reference/sim_brain_1h.html
index 2044cf1a..717ee289 100644
--- a/docs/reference/sim_brain_1h.html
+++ b/docs/reference/sim_brain_1h.html
@@ -1,5 +1,5 @@
-Simulate MRS data with a similar appearance to normal brain (by default). — sim_brain_1h • Spectroscopy Analysis Tools (spant) Simulate MRS data with a similar appearance to normal brain (by default). — sim_brain_1h • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -159,7 +159,7 @@ Value
diff --git a/docs/reference/sim_mol.html b/docs/reference/sim_mol.html
index 23bcef50..77f76a50 100644
--- a/docs/reference/sim_mol.html
+++ b/docs/reference/sim_mol.html
@@ -1,5 +1,5 @@
-Simulate a mol_parameter object. — sim_mol • Spectroscopy Analysis Tools (spant) Simulate a mol_parameter object. — sim_mol • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -143,7 +143,7 @@ Value
diff --git a/docs/reference/sim_noise.html b/docs/reference/sim_noise.html
index 23875f79..a71477d4 100644
--- a/docs/reference/sim_noise.html
+++ b/docs/reference/sim_noise.html
@@ -1,5 +1,5 @@
-Simulate an mrs_data object containing simulated Gaussian noise. — sim_noise • Spectroscopy Analysis Tools (spant) Simulate an mrs_data object containing simulated Gaussian noise. — sim_noise • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -84,6 +84,7 @@ Simulate an mrs_data object containing simulated Gaussian noise.
ft = def_ft(),
N = def_N(),
ref = def_ref(),
+ nuc = def_nuc(),
dyns = 1,
fd = TRUE
)
@@ -111,6 +112,10 @@ Arguments
reference value for ppm scale.
nuc
+resonant nucleus.
dyns
number of dynamic scans to generate.
Value
diff --git a/docs/reference/sim_resonances.html b/docs/reference/sim_resonances.html
index 19e9a8a4..d4f8d7c0 100644
--- a/docs/reference/sim_resonances.html
+++ b/docs/reference/sim_resonances.html
@@ -1,5 +1,5 @@
-Simulate a MRS data object containing a set of simulated resonances. — sim_resonances • Spectroscopy Analysis Tools (spant) Simulate a MRS data object containing a set of simulated resonances. — sim_resonances • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -161,7 +161,7 @@ Examples
diff --git a/docs/reference/sim_th_excit_profile.html b/docs/reference/sim_th_excit_profile.html
index 5535c5ef..e781cab1 100644
--- a/docs/reference/sim_th_excit_profile.html
+++ b/docs/reference/sim_th_excit_profile.html
@@ -1,7 +1,5 @@
-Simulate an ideal pulse excitation profile by smoothing a top-hat function
-with a Gaussian. — sim_th_excit_profile • Spectroscopy Analysis Tools (spant) Simulate an ideal pulse excitation profile by smoothing a top-hat function with a Gaussian. — sim_th_excit_profile • Spectroscopy Analysis Tools (spant) Simulate an mrs_data object containing complex zero valued samples. — sim_zero • Spectroscopy Analysis Tools (spant) Simulate an mrs_data object containing complex zero valued samples. — sim_zero • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -78,7 +78,14 @@ Simulate an mrs_data object containing complex zero valued samples.
-
+
@@ -99,6 +106,10 @@ Arguments
reference value for ppm scale.
nuc
+resonant nucleus.
dyns
number of dynamic scans to generate.
Value
diff --git a/docs/reference/smooth_dyns.html b/docs/reference/smooth_dyns.html
index 4cc8da50..accf3a51 100644
--- a/docs/reference/smooth_dyns.html
+++ b/docs/reference/smooth_dyns.html
@@ -1,5 +1,5 @@
-Smooth data across the dynamic dimension with a Gaussian kernel. — smooth_dyns • Spectroscopy Analysis Tools (spant) Smooth data across the dynamic dimension with a Gaussian kernel. — smooth_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/sort_basis.html b/docs/reference/sort_basis.html
index 6a676ea2..d25cc006 100644
--- a/docs/reference/sort_basis.html
+++ b/docs/reference/sort_basis.html
@@ -1,5 +1,5 @@
-Sort the basis-set elements alphabetically. — sort_basis • Spectroscopy Analysis Tools (spant) Sort the basis-set elements alphabetically. — sort_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/spant-package.html b/docs/reference/spant-package.html
index b3dd8e21..90f19ec3 100644
--- a/docs/reference/spant-package.html
+++ b/docs/reference/spant-package.html
@@ -1,5 +1,5 @@
-spant: spectroscopy analysis tools. — spant-package • Spectroscopy Analysis Tools (spant) spant: spectroscopy analysis tools. — spant-package • Spectroscopy Analysis Tools (spant) Simulate and fit some spectra with ABfit for benchmarking purposes. Basic
-timing and performance metrics will be printed. — spant_abfit_benchmark • Spectroscopy Analysis Tools (spant) Simulate and fit some spectra with ABfit for benchmarking purposes. Basic timing and performance metrics will be printed. — spant_abfit_benchmark • Spectroscopy Analysis Tools (spant) Example MEGA-PRESS data with significant B0 drift. — spant_mpress_drift • Spectroscopy Analysis Tools (spant) Example MEGA-PRESS data with significant B0 drift. — spant_mpress_drift • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -83,7 +83,7 @@ Example MEGA-PRESS data with significant B0 drift.
Format
- An object of class mrs_data of length 13.
+ An object of class mrs_data of dimension 1 x 1 x 1 x 1 x 40 x 1 x 1024.
@@ -98,7 +98,7 @@ Format
diff --git a/docs/reference/spant_sim_fmrs_dataset.html b/docs/reference/spant_sim_fmrs_dataset.html
new file mode 100644
index 00000000..00e48b56
--- /dev/null
+++ b/docs/reference/spant_sim_fmrs_dataset.html
@@ -0,0 +1,117 @@
+
+Simulate an example fMRS dataset for a block design fMRS experiment and export a BIDS structure. — spant_sim_fmrs_dataset • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Simulate an example fMRS dataset for a block design fMRS experiment and export a BIDS structure.
+ Source: R/fmrs.R
+ spant_sim_fmrs_dataset.Rd
+
+
+
+ Simulate an example fMRS dataset for a block design fMRS experiment and
+export a BIDS structure.
+
+
+
+ spant_sim_fmrs_dataset(output_dir = NULL)
+
+
+
+ Arguments
+ - output_dir
+output directory for the BIDS data. Defaults to :
+"HOME/sim_fmrs_dataset/data".
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/spant_simulation_benchmark.html b/docs/reference/spant_simulation_benchmark.html
index 32daa8bf..d8cc6841 100644
--- a/docs/reference/spant_simulation_benchmark.html
+++ b/docs/reference/spant_simulation_benchmark.html
@@ -1,7 +1,5 @@
-Simulate a typical metabolite basis set for benchmarking. Timing metrics will
-be printed on completion. — spant_simulation_benchmark • Spectroscopy Analysis Tools (spant) Simulate a typical metabolite basis set for benchmarking. Timing metrics will be printed on completion. — spant_simulation_benchmark • Spectroscopy Analysis Tools (spant) Decompose an mrs_data object into white and gray matter spectra. — spec_decomp • Spectroscopy Analysis Tools (spant) Perform a mathematical operation on a spectral region. — spec_op • Spectroscopy Analysis Tools (spant) Perform a mathematical operation on a spectral region. — spec_op • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -98,8 +98,8 @@ Arguments
operator
-can be "sum" (default), "mean", "l2", "max", "min" or
-"max-min".
can be "sum" (default), "mean", "l2", "max", "max_cplx,
+"min" or "max-min".
freq_scale
@@ -129,7 +129,7 @@ Value
diff --git a/docs/reference/spin_sys.html b/docs/reference/spin_sys.html
index 853423a4..1eaa9e76 100644
--- a/docs/reference/spin_sys.html
+++ b/docs/reference/spin_sys.html
@@ -1,5 +1,5 @@
-Create a spin system object for pulse sequence simulation. — spin_sys • Spectroscopy Analysis Tools (spant) Create a spin system object for pulse sequence simulation. — spin_sys • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/spm_pve2categorical.html b/docs/reference/spm_pve2categorical.html
index 23a1bad9..70f10729 100644
--- a/docs/reference/spm_pve2categorical.html
+++ b/docs/reference/spm_pve2categorical.html
@@ -1,7 +1,5 @@
-Convert SPM style segmentation files to a single categorical image where
-the numerical values map as: 0) Other, 1) CSF, 2) GM and 3) WM. — spm_pve2categorical • Spectroscopy Analysis Tools (spant) Convert SPM style segmentation files to a single categorical image where the numerical values map as: 0) Other, 1) CSF, 2) GM and 3) WM. — spm_pve2categorical • Spectroscopy Analysis Tools (spant) Signal space projection method for lipid suppression. — ssp • Spectroscopy Analysis Tools (spant) Signal space projection method for lipid suppression. — ssp • Spectroscopy Analysis Tools (spant) Plot the fitting results of an object of class fit_result with
-individual basis set components shown. — stackplot.fit_result • Spectroscopy Analysis Tools (spant) Plot the fitting results of an object of class fit_result with individual basis set components shown. — stackplot.fit_result • Spectroscopy Analysis Tools (spant) Produce a plot with multiple traces. — stackplot • Spectroscopy Analysis Tools (spant) Produce a plot with multiple traces. — stackplot • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/stackplot.mrs_data.html b/docs/reference/stackplot.mrs_data.html
index 17ff5648..64eea445 100644
--- a/docs/reference/stackplot.mrs_data.html
+++ b/docs/reference/stackplot.mrs_data.html
@@ -1,5 +1,5 @@
-Stackplot plotting method for objects of class mrs_data. — stackplot.mrs_data • Spectroscopy Analysis Tools (spant) Stackplot plotting method for objects of class mrs_data. — stackplot.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -255,7 +255,7 @@ Arguments
diff --git a/docs/reference/sub_first_dyn.html b/docs/reference/sub_first_dyn.html
index dbd7f831..493b7242 100644
--- a/docs/reference/sub_first_dyn.html
+++ b/docs/reference/sub_first_dyn.html
@@ -1,5 +1,5 @@
-Subtract the first dynamic spectrum from a dynamic series. — sub_first_dyn • Spectroscopy Analysis Tools (spant) Subtract the first dynamic spectrum from a dynamic series. — sub_first_dyn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/sub_mean_dyns.html b/docs/reference/sub_mean_dyns.html
index 6e3bb2df..221bd0c1 100644
--- a/docs/reference/sub_mean_dyns.html
+++ b/docs/reference/sub_mean_dyns.html
@@ -1,5 +1,5 @@
-Subtract the mean dynamic spectrum from a dynamic series. — sub_mean_dyns • Spectroscopy Analysis Tools (spant) Subtract the mean dynamic spectrum from a dynamic series. — sub_mean_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/sub_median_dyns.html b/docs/reference/sub_median_dyns.html
index 134c495d..1e834f14 100644
--- a/docs/reference/sub_median_dyns.html
+++ b/docs/reference/sub_median_dyns.html
@@ -1,5 +1,5 @@
-Subtract the median dynamic spectrum from a dynamic series. — sub_median_dyns • Spectroscopy Analysis Tools (spant) Subtract the median dynamic spectrum from a dynamic series. — sub_median_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/sum_coils.html b/docs/reference/sum_coils.html
index 7bf559f2..e1ab3cc0 100644
--- a/docs/reference/sum_coils.html
+++ b/docs/reference/sum_coils.html
@@ -1,5 +1,5 @@
-Calculate the sum across receiver coil elements. — sum_coils • Spectroscopy Analysis Tools (spant) Calculate the sum across receiver coil elements. — sum_coils • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/sum_dyns.html b/docs/reference/sum_dyns.html
index a0be19d3..bbda2ffc 100644
--- a/docs/reference/sum_dyns.html
+++ b/docs/reference/sum_dyns.html
@@ -1,5 +1,5 @@
-Calculate the sum of data dynamics. — sum_dyns • Spectroscopy Analysis Tools (spant) Calculate the sum of data dynamics. — sum_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/sum_mrs.html b/docs/reference/sum_mrs.html
index a22f215b..3cc3ab9e 100644
--- a/docs/reference/sum_mrs.html
+++ b/docs/reference/sum_mrs.html
@@ -1,5 +1,5 @@
-Sum two mrs_data objects. — sum_mrs • Spectroscopy Analysis Tools (spant) Sum two mrs_data objects. — sum_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Value
diff --git a/docs/reference/sum_mrs_list.html b/docs/reference/sum_mrs_list.html
index f4e09aea..c3584348 100644
--- a/docs/reference/sum_mrs_list.html
+++ b/docs/reference/sum_mrs_list.html
@@ -1,5 +1,5 @@
-Return the sum of a list of mrs_data objects. — sum_mrs_list • Spectroscopy Analysis Tools (spant) Return the sum of a list of mrs_data objects. — sum_mrs_list • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/svs_1h_brain_analysis.html b/docs/reference/svs_1h_brain_analysis.html
index 8ce514db..dff0ef7d 100644
--- a/docs/reference/svs_1h_brain_analysis.html
+++ b/docs/reference/svs_1h_brain_analysis.html
@@ -1,5 +1,5 @@
-Standard SVS 1H brain analysis pipeline. — svs_1h_brain_analysis • Spectroscopy Analysis Tools (spant) Standard SVS 1H brain analysis pipeline. — svs_1h_brain_analysis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -199,7 +199,7 @@ Value
diff --git a/docs/reference/svs_1h_brain_analysis_dev.html b/docs/reference/svs_1h_brain_analysis_dev.html
index d70a14d3..d71bfea2 100644
--- a/docs/reference/svs_1h_brain_analysis_dev.html
+++ b/docs/reference/svs_1h_brain_analysis_dev.html
@@ -1,5 +1,5 @@
-Standard SVS 1H brain analysis pipeline. — svs_1h_brain_analysis_dev • Spectroscopy Analysis Tools (spant) Standard SVS 1H brain analysis pipeline. — svs_1h_brain_analysis_dev • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -193,7 +193,7 @@ Examples
diff --git a/docs/reference/svs_1h_brain_batch_analysis.html b/docs/reference/svs_1h_brain_batch_analysis.html
index 5631e8cc..15f7223e 100644
--- a/docs/reference/svs_1h_brain_batch_analysis.html
+++ b/docs/reference/svs_1h_brain_batch_analysis.html
@@ -1,5 +1,5 @@
-Batch interface to the standard SVS 1H brain analysis pipeline. — svs_1h_brain_batch_analysis • Spectroscopy Analysis Tools (spant) Batch interface to the standard SVS 1H brain analysis pipeline. — svs_1h_brain_batch_analysis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -144,7 +144,7 @@ Value
diff --git a/docs/reference/t_test_spec.html b/docs/reference/t_test_spec.html
new file mode 100644
index 00000000..56a7ea1b
--- /dev/null
+++ b/docs/reference/t_test_spec.html
@@ -0,0 +1,124 @@
+
+Perform a t-test on spectral data points. — t_test_spec • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+
+
+ Perform a t-test on spectral data points.
+
+
+
+ t_test_spec(mrs_data, group)
+
+
+
+ Arguments
+ - mrs_data
+an mrs_data object with spectra in the dynamic dimension.
- group
+vector describing the group membership of each dynamic spectrum.
+
+ Value
+
+
+a list of statistical results.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/td2fd.html b/docs/reference/td2fd.html
index 6748a6a8..f31ed524 100644
--- a/docs/reference/td2fd.html
+++ b/docs/reference/td2fd.html
@@ -1,5 +1,5 @@
-Transform time-domain data to the frequency-domain. — td2fd • Spectroscopy Analysis Tools (spant) Transform time-domain data to the frequency-domain. — td2fd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/td_conv_filt.html b/docs/reference/td_conv_filt.html
index a9f340c3..106b9b00 100644
--- a/docs/reference/td_conv_filt.html
+++ b/docs/reference/td_conv_filt.html
@@ -1,5 +1,5 @@
-Time-domain convolution based filter. — td_conv_filt • Spectroscopy Analysis Tools (spant) Time-domain convolution based filter. — td_conv_filt • Spectroscopy Analysis Tools (spant) Time-domain spectral registration. — tdsr • Spectroscopy Analysis Tools (spant) Time-domain spectral registration. — tdsr • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -121,7 +121,7 @@ Value
diff --git a/docs/reference/te.html b/docs/reference/te.html
index 010361b1..4a65711d 100644
--- a/docs/reference/te.html
+++ b/docs/reference/te.html
@@ -1,5 +1,5 @@
-Return the echo time of an MRS dataset. — te • Spectroscopy Analysis Tools (spant) Return the echo time of an MRS dataset. — te • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/tr.html b/docs/reference/tr.html
index 0c0bd63b..2e749e02 100644
--- a/docs/reference/tr.html
+++ b/docs/reference/tr.html
@@ -1,5 +1,5 @@
-Return the repetition time of an MRS dataset. — tr • Spectroscopy Analysis Tools (spant) Return the repetition time of an MRS dataset. — tr • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/varpro_3_para_opts.html b/docs/reference/varpro_3_para_opts.html
index c2270a16..52d7cd84 100644
--- a/docs/reference/varpro_3_para_opts.html
+++ b/docs/reference/varpro_3_para_opts.html
@@ -1,5 +1,5 @@
-Return a list of options for VARPRO based fitting with 3 free parameters. — varpro_3_para_opts • Spectroscopy Analysis Tools (spant) Return a list of options for VARPRO based fitting with 3 free parameters. — varpro_3_para_opts • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -141,7 +141,7 @@ Value
diff --git a/docs/reference/varpro_basic_opts.html b/docs/reference/varpro_basic_opts.html
index 32c86d22..c5104891 100644
--- a/docs/reference/varpro_basic_opts.html
+++ b/docs/reference/varpro_basic_opts.html
@@ -1,5 +1,5 @@
-Return a list of options for a basic VARPRO analysis. — varpro_basic_opts • Spectroscopy Analysis Tools (spant) Return a list of options for a basic VARPRO analysis. — varpro_basic_opts • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -118,7 +118,7 @@ Value
diff --git a/docs/reference/varpro_opts.html b/docs/reference/varpro_opts.html
index 2aabf11d..6332f730 100644
--- a/docs/reference/varpro_opts.html
+++ b/docs/reference/varpro_opts.html
@@ -1,5 +1,5 @@
-Return a list of options for VARPRO based fitting. — varpro_opts • Spectroscopy Analysis Tools (spant) Return a list of options for VARPRO based fitting. — varpro_opts • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -177,7 +177,7 @@ Examples
diff --git a/docs/reference/vec2mrs_data.html b/docs/reference/vec2mrs_data.html
index 0cccd73b..f0d58bf0 100644
--- a/docs/reference/vec2mrs_data.html
+++ b/docs/reference/vec2mrs_data.html
@@ -1,5 +1,5 @@
-Convert a vector into a mrs_data object. — vec2mrs_data • Spectroscopy Analysis Tools (spant) Convert a vector into a mrs_data object. — vec2mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -80,10 +80,11 @@ Convert a vector into a mrs_data object.
vec2mrs_data(
vec,
- fs = def_fs(),
- ft = def_ft(),
- ref = def_ref(),
- nuc = def_nuc(),
+ mrs_data = NULL,
+ fs = NULL,
+ ft = NULL,
+ ref = NULL,
+ nuc = NULL,
dyns = 1,
fd = FALSE
)
@@ -95,6 +96,10 @@ Arguments
the data vector.
mrs_data
+example data to copy acquisition parameters from.
fs
sampling frequency in Hz.
Arguments
fd
-flag to indicate if the matrix is in the frequency domain (logical).
flag to indicate if the vector is in the frequency domain (logical).
Value
diff --git a/docs/reference/write_basis.html b/docs/reference/write_basis.html
index b6e27cbd..94c5e021 100644
--- a/docs/reference/write_basis.html
+++ b/docs/reference/write_basis.html
@@ -1,5 +1,5 @@
-Write a basis object to an LCModel .basis formatted file. — write_basis • Spectroscopy Analysis Tools (spant) Write a basis object to an LCModel .basis formatted file. — write_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -108,7 +108,7 @@ Arguments
diff --git a/docs/reference/write_basis_tqn.html b/docs/reference/write_basis_tqn.html
index 6aa51c1d..116c73ec 100644
--- a/docs/reference/write_basis_tqn.html
+++ b/docs/reference/write_basis_tqn.html
@@ -1,5 +1,5 @@
-Generate a basis file using TARQUIN. — write_basis_tqn • Spectroscopy Analysis Tools (spant) Generate a basis file using TARQUIN. — write_basis_tqn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Examples
diff --git a/docs/reference/write_mrs.html b/docs/reference/write_mrs.html
index fff25f15..124b9dc4 100644
--- a/docs/reference/write_mrs.html
+++ b/docs/reference/write_mrs.html
@@ -1,5 +1,5 @@
-Write MRS data object to file. — write_mrs • Spectroscopy Analysis Tools (spant) Write MRS data object to file. — write_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Arguments
diff --git a/docs/reference/write_mrs_nifti.html b/docs/reference/write_mrs_nifti.html
index f4bf1921..bd3ed4b7 100644
--- a/docs/reference/write_mrs_nifti.html
+++ b/docs/reference/write_mrs_nifti.html
@@ -1,5 +1,5 @@
-Write MRS data object to file in NIFTI format. — write_mrs_nifti • Spectroscopy Analysis Tools (spant) Write MRS data object to file in NIFTI format. — write_mrs_nifti • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/write_pulse_ascii.html b/docs/reference/write_pulse_ascii.html
index 067ae086..221f8ebb 100644
--- a/docs/reference/write_pulse_ascii.html
+++ b/docs/reference/write_pulse_ascii.html
@@ -1,5 +1,5 @@
-Write an ASCII formatted pulse file. — write_pulse_ascii • Spectroscopy Analysis Tools (spant) Write an ASCII formatted pulse file. — write_pulse_ascii • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/zero_fade_spec.html b/docs/reference/zero_fade_spec.html
index c703745c..c8b572c3 100644
--- a/docs/reference/zero_fade_spec.html
+++ b/docs/reference/zero_fade_spec.html
@@ -1,7 +1,5 @@
-Fade a spectrum to zero by frequency domain multiplication with a tanh
-function. Note this operation distorts data points at the end of the FID. — zero_fade_spec • Spectroscopy Analysis Tools (spant) Fade a spectrum to zero by frequency domain multiplication with a tanh function. Note this operation distorts data points at the end of the FID. — zero_fade_spec • Spectroscopy Analysis Tools (spant) Zero all coherences including and above a given order. — zero_higher_orders • Spectroscopy Analysis Tools (spant) Zero all coherences including and above a given order. — zero_higher_orders • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Value
diff --git a/docs/reference/zero_td_pts_end.html b/docs/reference/zero_td_pts_end.html
index 8c1123c8..71d24ebb 100644
--- a/docs/reference/zero_td_pts_end.html
+++ b/docs/reference/zero_td_pts_end.html
@@ -1,5 +1,5 @@
-Set mrs_data object data points at the end of the FID to zero. — zero_td_pts_end • Spectroscopy Analysis Tools (spant) Set mrs_data object data points at the end of the FID to zero. — zero_td_pts_end • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/zf.html b/docs/reference/zf.html
index 85e2013c..baf50256 100644
--- a/docs/reference/zf.html
+++ b/docs/reference/zf.html
@@ -1,5 +1,5 @@
-Zero-fill MRS data in the time domain. — zf • Spectroscopy Analysis Tools (spant) Zero-fill MRS data in the time domain. — zf • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -125,7 +125,7 @@ Value
diff --git a/docs/reference/zf_xy.html b/docs/reference/zf_xy.html
index ebca3999..c4104a74 100644
--- a/docs/reference/zf_xy.html
+++ b/docs/reference/zf_xy.html
@@ -1,5 +1,5 @@
-Zero-fill MRSI data in the k-space x-y direction. — zf_xy • Spectroscopy Analysis Tools (spant) Zero-fill MRSI data in the k-space x-y direction. — zf_xy • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -113,7 +113,7 @@ Value
diff --git a/docs/sitemap.xml b/docs/sitemap.xml
index e2139f71..4c39f515 100644
--- a/docs/sitemap.xml
+++ b/docs/sitemap.xml
@@ -216,6 +216,12 @@
https://martin3141.github.io/spant/reference/comb_coils_fp_pc.html
+
+ https://martin3141.github.io/spant/reference/comb_coils_mrsi_gls.html
+
+
+ https://martin3141.github.io/spant/reference/comb_coils_svs_gls.html
+
https://martin3141.github.io/spant/reference/comb_csv_results.html
@@ -411,6 +417,9 @@
https://martin3141.github.io/spant/reference/gen_conv_reg.html
+
+ https://martin3141.github.io/spant/reference/gen_group_reg.html
+
https://martin3141.github.io/spant/reference/gen_impulse_reg.html
@@ -555,6 +564,15 @@
https://martin3141.github.io/spant/reference/glm_spec.html
+
+ https://martin3141.github.io/spant/reference/glm_spec_fmrs_fl.html
+
+
+ https://martin3141.github.io/spant/reference/glm_spec_fmrs_group.html
+
+
+ https://martin3141.github.io/spant/reference/glm_spec_group_linhyp.html
+
https://martin3141.github.io/spant/reference/grid_shift_xy.html
@@ -690,9 +708,15 @@
https://martin3141.github.io/spant/reference/mrs_data2basis.html
+
+ https://martin3141.github.io/spant/reference/mrs_data2bids.html
+
https://martin3141.github.io/spant/reference/mrs_data2mat.html
+
+ https://martin3141.github.io/spant/reference/mrs_data2spec_mat.html
+
https://martin3141.github.io/spant/reference/mrs_data2vec.html
@@ -741,6 +765,9 @@
https://martin3141.github.io/spant/reference/phase.html
+
+ https://martin3141.github.io/spant/reference/phase_ref_1h_brain.html
+
https://martin3141.github.io/spant/reference/plot.fit_result.html
@@ -780,6 +807,12 @@
https://martin3141.github.io/spant/reference/precomp.html
+
+ https://martin3141.github.io/spant/reference/preproc_svs.html
+
+
+ https://martin3141.github.io/spant/reference/preproc_svs_dataset.html
+
https://martin3141.github.io/spant/reference/print.fit_result.html
@@ -1050,6 +1083,9 @@
https://martin3141.github.io/spant/reference/spant_mpress_drift.html
+
+ https://martin3141.github.io/spant/reference/spant_sim_fmrs_dataset.html
+
https://martin3141.github.io/spant/reference/spant_simulation_benchmark.html
@@ -1107,6 +1143,9 @@
https://martin3141.github.io/spant/reference/svs_1h_brain_batch_analysis.html
+
+ https://martin3141.github.io/spant/reference/t_test_spec.html
+
https://martin3141.github.io/spant/reference/td2fd.html
Convert a basis object to an mrs_data object - where basis signals are spread -across the dynamic dimension.
Convert a basis object to an mrs_data object - where basis signals are spread across the dynamic dimension.
Generate a spline basis, slightly adapted from : "Splines, knots, and -penalties", Eilers 2010.
Generate a spline basis, slightly adapted from : "Splines, knots, and penalties", Eilers 2010.
All functions
- Covert a beta value in the time-domain to an equivalent linewidth in Hz:
-x * exp(-i * t * t * beta).
Covert a beta value in the time-domain to an equivalent linewidth in Hz: x * exp(-i * t * t * beta).
@@ -272,8 +262,7 @@ All functions
- Perform a polynomial fit, subtract and return the standard deviation of the
-residuals.
Perform a polynomial fit, subtract and return the standard deviation of the residuals.
@@ -306,6 +295,14 @@ All functions comb_coils()
Combine coil data based on the first data point of a reference signal.
+
+
+ Combine MRSI coil data using the GLS method presented by An et al JMRI 37:1445-1450 (2013).
+
+
+ Combine SVS coil data using the GLS method presented by An et al JMRI 37:1445-1450 (2013).
@@ -345,9 +342,7 @@ All functions
- Crop mrs_data object data points in the time-domain rounding down to
-the next smallest power of two (pot). Data that already has a pot length will
-not be changed.
Crop mrs_data object data points in the time-domain rounding down to the next smallest power of two (pot). Data that already has a pot length will not be changed.
@@ -355,13 +350,11 @@ All functions
- Compute the vector cross product between vectors x and y. Adapted from
-http://stackoverflow.com/questions/15162741/what-is-rs-crossproduct-function
Compute the vector cross product between vectors x and y. Adapted from http://stackoverflow.com/questions/15162741/what-is-rs-crossproduct-function
- Decimate an MRS signal to half the original sampling frequency by filtering
-in the frequency domain before down sampling.
Decimate an MRS signal to half the original sampling frequency by filtering in the frequency domain before down sampling.
@@ -377,8 +370,7 @@ All functions
- Return (and optionally modify using the input arguments) a list of the
-default acquisition parameters.
Return (and optionally modify using the input arguments) a list of the default acquisition parameters.
@@ -410,14 +402,11 @@ All functions
- Downsample an MRS signal by a factor of 2 by removing every other data point
-in the time-domain. Note, signals outside the new sampling frequency will be
-aliased.
Downsample an MRS signal by a factor of 2 by removing every other data point in the time-domain. Note, signals outside the new sampling frequency will be aliased.
- Return a time scale vector of acquisition times for a dynamic MRS scan. The
-first temporal scan is assigned a value of 0.
Return a time scale vector of acquisition times for a dynamic MRS scan. The first temporal scan is assigned a value of 0.
@@ -429,8 +418,7 @@ All functions
- Estimate the standard deviation of the noise from a segment of an mrs_data
-object.
Estimate the standard deviation of the noise from a segment of an mrs_data object.
@@ -486,8 +474,7 @@ All functions
- Perform a zeroth order phase correction based on the phase of the first data
-point in the time-domain.
Perform a zeroth order phase correction based on the phase of the first data point in the time-domain.
@@ -507,8 +494,7 @@ All functions
- Perform a fft and fftshift on a matrix with each column replaced by its
-shifted fft.
Perform a fft and fftshift on a matrix with each column replaced by its shifted fft.
@@ -536,8 +522,11 @@ All functions
- Generate regressors by convolving a specified response function with a
-stimulus.
Generate regressors by convolving a specified response function with a stimulus.
+
+
+ Expand a regressor matrix for a group analysis.
@@ -553,28 +542,23 @@ All functions
- Return a character vector of common 1H molecules found in healthy human
-brain.
Return a character vector of common 1H molecules found in healthy human brain.
- Return a list of mol_parameter objects suitable for 1H brain MRS
-analyses.
Return a list of mol_parameter objects suitable for 1H brain MRS analyses.
- Return a list of mol_parameter objects suitable for 1H brain MRS
-analyses.
Return a list of mol_parameter objects suitable for 1H brain MRS analyses.
- Return a list of mol_parameter objects suitable for 1H brain MRS
-analyses.
Return a list of mol_parameter objects suitable for 1H brain MRS analyses.
- Return a list of mol_parameter objects suitable for 1H brain MRS
-analyses.
Return a list of mol_parameter objects suitable for 1H brain MRS analyses.
@@ -582,8 +566,7 @@ All functions
- Return a character vector of molecules included in the Gold Star Phantoms
-SPECTRE phantom.
Return a character vector of molecules included in the Gold Star Phantoms SPECTRE phantom.
@@ -635,8 +618,7 @@ All functions
- Return a character array of names that may be used with the
-get_mol_paras function.
Return a character array of names that may be used with the get_mol_paras function.
@@ -700,8 +682,7 @@ All functions
- Return an array of amplitudes derived from fitting the initial points in the
-time domain and extrapolating back to t=0.
Return an array of amplitudes derived from fitting the initial points in the time domain and extrapolating back to t=0.
@@ -709,8 +690,7 @@ All functions
- Generate a mol_parameters object for a simple spin system with one
-resonance.
Generate a mol_parameters object for a simple spin system with one resonance.
@@ -731,6 +711,18 @@ All functions glm_spec()
Perform a GLM analysis of dynamic MRS data in the spectral domain.
+
+
+ Perform first-level spectral GLM analysis of an fMRS dataset.
+
+
+ Perform group-level spectral GLM analysis of an fMRS dataset.
+
+
+ Test a group-level spectral GLM linear hypothesis.
@@ -766,8 +758,7 @@ All functions
- Perform an ifft and ifftshift on a matrix with each column replaced by its
-shifted ifft.
Perform an ifft and ifftshift on a matrix with each column replaced by its shifted ifft.
@@ -799,8 +790,7 @@ All functions
- Check if the chemical shift dimension of an MRS data object is in the
-frequency domain.
Check if the chemical shift dimension of an MRS data object is in the frequency domain.
@@ -820,18 +810,15 @@ All functions
- Covert a linewidth in Hz to an equivalent alpha value in the time-domain ie:
-x * exp(-t * alpha).
Covert a linewidth in Hz to an equivalent alpha value in the time-domain ie: x * exp(-t * alpha).
- Covert a linewidth in Hz to an equivalent beta value in the time-domain ie:
-x * exp(-t * t * beta).
Covert a linewidth in Hz to an equivalent beta value in the time-domain ie: x * exp(-t * t * beta).
- Make a basis-set object from a directory containing LCModel formatted RAW
-files.
Make a basis-set object from a directory containing LCModel formatted RAW files.
@@ -851,8 +838,7 @@ All functions
- Mask the voxels outside an elliptical region spanning the MRSI dataset in the
-x-y plane.
Mask the voxels outside an elliptical region spanning the MRSI dataset in the x-y plane.
@@ -860,13 +846,11 @@ All functions
- Convert a matrix (with spectral points in the column dimension and dynamics
-in the row dimensions) into a mrs_data object.
Convert a matrix (with spectral points in the column dimension and dynamics in the row dimensions) into a mrs_data object.
- Matrix exponential function taken from complexplus package to reduce the
-number of spant dependencies.
Matrix exponential function taken from complexplus package to reduce the number of spant dependencies.
@@ -914,31 +898,31 @@ All functions
- Convert an mrs_data object to basis object - where basis signals are spread
-across the dynamic dimension in the MRS data.
Convert an mrs_data object to basis object - where basis signals are spread across the dynamic dimension in the MRS data.
+
+
+ Create a BIDS file structure from a vector of MRS data paths or list of mrs_data objects.
- Convert mrs_data object to a matrix, with spectral points in the column
-dimension and dynamics in the row dimension.
Convert mrs_data object to a matrix, with spectral points in the column dimension and dynamics in the row dimension.
-
+
- Convert mrs_data object to a vector.
Convert mrs_data object to a matrix, with spectral points in the column dimension and dynamics in the row dimension.
-
+
- Create a BIDS directory and file structure from a list of mrs_data objects.
Convert mrs_data object to a vector.
- Perform a fftshift on a matrix, with each column replaced by its shifted
-result.
Perform a fftshift on a matrix, with each column replaced by its shifted result.
- Perform an ifftshift on a matrix, with each column replaced by its shifted
-result.
Perform an ifftshift on a matrix, with each column replaced by its shifted result.
@@ -946,9 +930,7 @@ All functions
- Flip the x data dimension order of a nifti image. This corresponds to
-flipping MRI data in the left-right direction, assuming the data in save in
-neurological format (can check with fslorient program).
Flip the x data dimension order of a nifti image. This corresponds to flipping MRI data in the left-right direction, assuming the data in save in neurological format (can check with fslorient program).
@@ -964,8 +946,7 @@ All functions
- Search for the highest peak in a spectral region and return the frequency,
-height and FWHM.
Search for the highest peak in a spectral region and return the frequency, height and FWHM.
@@ -974,6 +955,10 @@ All functions phase()
Apply phasing parameters to MRS data.
+
+
+ Corrected zero order phase and chemical shift offset in 1H MRS data from the brain.
@@ -1005,8 +990,7 @@ All functions
- Plot an interactive slice map from a data array where voxels can be selected
-to display a corresponding spectrum.
Plot an interactive slice map from a data array where voxels can be selected to display a corresponding spectrum.
@@ -1026,8 +1010,15 @@ All functions
- Save function results to file and load on subsequent calls to avoid repeat
-computation.
Save function results to file and load on subsequent calls to avoid repeat computation.
+
+
+ Preprocess and perform quality assessment of a single SVS data set.
+
+
+ Preprocess and perform quality assessment of one or more SVS data sets.
@@ -1055,15 +1046,11 @@ All functions
- Read a directory containing Siemens MRS IMA files and combine along the coil
-dimension. Note that the coil ID is inferred from the sorted file name and
-should be checked when consistency is required between two directories.
Read a directory containing Siemens MRS IMA files and combine along the coil dimension. Note that the coil ID is inferred from the sorted file name and should be checked when consistency is required between two directories.
- Read a directory containing Siemens MRS IMA files and combine along the
-dynamic dimension. Note that the coil ID is inferred from the sorted file
-name and should be checked when consistency is required.
Read a directory containing Siemens MRS IMA files and combine along the dynamic dimension. Note that the coil ID is inferred from the sorted file name and should be checked when consistency is required.
@@ -1103,13 +1090,11 @@ All functions
- Reconstruct complex time-domain data from the real part of frequency-domain
-data.
Reconstruct complex time-domain data from the real part of frequency-domain data.
- Reconstruct complex time-domain data from the real part of frequency-domain
-data.
Reconstruct complex time-domain data from the real part of frequency-domain data.
@@ -1141,8 +1126,7 @@ All functions
- Resample a VOI to match a target image space using nearest-neighbour
-interpolation.
Resample a VOI to match a target image space using nearest-neighbour interpolation.
@@ -1158,23 +1142,19 @@ All functions
- Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water).
Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / kg of tissue water).
- Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water).
Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / kg of tissue water).
- Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / Litre of tissue).
Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / Litre of tissue).
- Convert default LCM/TARQUIN concentration scaling to molal units with partial
-volume correction.
Convert default LCM/TARQUIN concentration scaling to molal units with partial volume correction.
@@ -1222,8 +1202,7 @@ All functions
- MEGA-PRESS sequence with ideal localisation pulses and Gaussian shaped
-editing pulse.
MEGA-PRESS sequence with ideal localisation pulses and Gaussian shaped editing pulse.
@@ -1251,13 +1230,11 @@ All functions
- STEAM sequence with ideal pulses and coherence order filtering to simulate
-gradient crushers.
STEAM sequence with ideal pulses and coherence order filtering to simulate gradient crushers.
- STEAM sequence with ideal pulses using the z-rotation gradient simulation
-method described by Young et al JMR 140, 146-152 (1999).
STEAM sequence with ideal pulses using the z-rotation gradient simulation method described by Young et al JMR 140, 146-152 (1999).
@@ -1293,8 +1270,7 @@ All functions
- Set the number of time-domain data points, truncating or zero-filling as
-appropriate.
Set the number of time-domain data points, truncating or zero-filling as appropriate.
@@ -1318,18 +1294,15 @@ All functions
- Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS
-sequence. Note, ideal pulses are assumed.
Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS sequence. Note, ideal pulses are assumed.
- Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS
-sequence. Note, ideal pulses are assumed.
Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS sequence. Note, ideal pulses are assumed.
- Simulate a macromolecular and lipid basis-set suitable for 1H brain MRS
-analysis.
Simulate a macromolecular and lipid basis-set suitable for 1H brain MRS analysis.
@@ -1353,8 +1326,7 @@ All functions
- Simulate an ideal pulse excitation profile by smoothing a top-hat function
-with a Gaussian.
Simulate an ideal pulse excitation profile by smoothing a top-hat function with a Gaussian.
@@ -1374,17 +1346,19 @@ All functions
- Simulate and fit some spectra with ABfit for benchmarking purposes. Basic
-timing and performance metrics will be printed.
Simulate and fit some spectra with ABfit for benchmarking purposes. Basic timing and performance metrics will be printed.
Example MEGA-PRESS data with significant B0 drift.
+
+
+ Simulate an example fMRS dataset for a block design fMRS experiment and export a BIDS structure.
- Simulate a typical metabolite basis set for benchmarking. Timing metrics will
-be printed on completion.
Simulate a typical metabolite basis set for benchmarking. Timing metrics will be printed on completion.
@@ -1400,8 +1374,7 @@ All functions
- Convert SPM style segmentation files to a single categorical image where
-the numerical values map as: 0) Other, 1) CSF, 2) GM and 3) WM.
Convert SPM style segmentation files to a single categorical image where the numerical values map as: 0) Other, 1) CSF, 2) GM and 3) WM.
@@ -1413,8 +1386,7 @@ All functions
- Plot the fitting results of an object of class fit_result with
-individual basis set components shown.
Plot the fitting results of an object of class fit_result with individual basis set components shown.
@@ -1459,6 +1431,10 @@ All functions svs_1h_brain_batch_analysis()
Batch interface to the standard SVS 1H brain analysis pipeline.
+
+
+ Perform a t-test on spectral data points.
@@ -1518,8 +1494,7 @@ All functions
- Fade a spectrum to zero by frequency domain multiplication with a tanh
-function. Note this operation distorts data points at the end of the FID.
Fade a spectrum to zero by frequency domain multiplication with a tanh function. Note this operation distorts data points at the end of the FID.
@@ -1549,7 +1524,7 @@ All functions
diff --git a/docs/reference/int_spec.html b/docs/reference/int_spec.html
index c7060fe7..783325a8 100644
--- a/docs/reference/int_spec.html
+++ b/docs/reference/int_spec.html
@@ -1,5 +1,5 @@
-Integrate a spectral region. — int_spec • Spectroscopy Analysis Tools (spant) Integrate a spectral region. — int_spec • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -118,7 +118,7 @@ Value
diff --git a/docs/reference/interleave_dyns.html b/docs/reference/interleave_dyns.html
index effe5543..441eff27 100644
--- a/docs/reference/interleave_dyns.html
+++ b/docs/reference/interleave_dyns.html
@@ -1,5 +1,5 @@
-Interleave the first and second half of a dynamic series. — interleave_dyns • Spectroscopy Analysis Tools (spant) Interleave the first and second half of a dynamic series. — interleave_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/inv_even_dyns.html b/docs/reference/inv_even_dyns.html
index 9f9d4fff..dcb781dc 100644
--- a/docs/reference/inv_even_dyns.html
+++ b/docs/reference/inv_even_dyns.html
@@ -1,5 +1,5 @@
-Invert even numbered dynamic scans starting from 1 (2,4,6...). — inv_even_dyns • Spectroscopy Analysis Tools (spant) Invert even numbered dynamic scans starting from 1 (2,4,6...). — inv_even_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/inv_odd_dyns.html b/docs/reference/inv_odd_dyns.html
index 26212e2b..78d64660 100644
--- a/docs/reference/inv_odd_dyns.html
+++ b/docs/reference/inv_odd_dyns.html
@@ -1,5 +1,5 @@
-Invert odd numbered dynamic scans starting from 1 (1,3,5...). — inv_odd_dyns • Spectroscopy Analysis Tools (spant) Invert odd numbered dynamic scans starting from 1 (1,3,5...). — inv_odd_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/is.def.html b/docs/reference/is.def.html
index f196ffd0..a67b9eba 100644
--- a/docs/reference/is.def.html
+++ b/docs/reference/is.def.html
@@ -1,5 +1,5 @@
-Check if an object is defined, which is the same as being not NULL. — is.def • Spectroscopy Analysis Tools (spant) Check if an object is defined, which is the same as being not NULL. — is.def • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/is_fd.html b/docs/reference/is_fd.html
index 3b0ca165..18a193aa 100644
--- a/docs/reference/is_fd.html
+++ b/docs/reference/is_fd.html
@@ -1,7 +1,5 @@
-Check if the chemical shift dimension of an MRS data object is in the
-frequency domain. — is_fd • Spectroscopy Analysis Tools (spant) Check if the chemical shift dimension of an MRS data object is in the frequency domain. — is_fd • Spectroscopy Analysis Tools (spant) Transform 2D MRSI data from k-space to image space in the x-y direction. — kspace2img_xy • Spectroscopy Analysis Tools (spant) Transform 2D MRSI data from k-space to image space in the x-y direction. — kspace2img_xy • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/l2_reg.html b/docs/reference/l2_reg.html
index 3d781d80..21aa9849 100644
--- a/docs/reference/l2_reg.html
+++ b/docs/reference/l2_reg.html
@@ -1,5 +1,5 @@
-Perform l2 regularisation artefact suppression. — l2_reg • Spectroscopy Analysis Tools (spant) Perform l2 regularisation artefact suppression. — l2_reg • Spectroscopy Analysis Tools (spant) Apply line-broadening (apodisation) to MRS data or basis object. — lb • Spectroscopy Analysis Tools (spant) Apply line-broadening (apodisation) to MRS data or basis object. — lb • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -123,7 +123,7 @@ Value
diff --git a/docs/reference/lofdc.html b/docs/reference/lofdc.html
index 5419b1ec..31347a25 100644
--- a/docs/reference/lofdc.html
+++ b/docs/reference/lofdc.html
@@ -1,5 +1,5 @@
-Correct linear frequency drift. — lofdc • Spectroscopy Analysis Tools (spant) Correct linear frequency drift. — lofdc • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -138,7 +138,7 @@ Value
diff --git a/docs/reference/lw2alpha.html b/docs/reference/lw2alpha.html
index b83db682..25da229b 100644
--- a/docs/reference/lw2alpha.html
+++ b/docs/reference/lw2alpha.html
@@ -1,7 +1,5 @@
-Covert a linewidth in Hz to an equivalent alpha value in the time-domain ie:
-x * exp(-t * alpha). — lw2alpha • Spectroscopy Analysis Tools (spant) Covert a linewidth in Hz to an equivalent alpha value in the time-domain ie: x * exp(-t * alpha). — lw2alpha • Spectroscopy Analysis Tools (spant) Covert a linewidth in Hz to an equivalent beta value in the time-domain ie:
-x * exp(-t * t * beta). — lw2beta • Spectroscopy Analysis Tools (spant) Covert a linewidth in Hz to an equivalent beta value in the time-domain ie: x * exp(-t * t * beta). — lw2beta • Spectroscopy Analysis Tools (spant) Make a basis-set object from a directory containing LCModel formatted RAW
-files. — make_basis_from_raw • Spectroscopy Analysis Tools (spant) Make a basis-set object from a directory containing LCModel formatted RAW files. — make_basis_from_raw • Spectroscopy Analysis Tools (spant) Mask an MRS dataset in the dynamic dimension. — mask_dyns • Spectroscopy Analysis Tools (spant) Mask an MRS dataset in the dynamic dimension. — mask_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/mask_fit_res.html b/docs/reference/mask_fit_res.html
index 97baaa3f..ebd91a99 100644
--- a/docs/reference/mask_fit_res.html
+++ b/docs/reference/mask_fit_res.html
@@ -1,5 +1,5 @@
-Mask fit result spectra depending on a vector of bool values. — mask_fit_res • Spectroscopy Analysis Tools (spant) Mask fit result spectra depending on a vector of bool values. — mask_fit_res • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -116,7 +116,7 @@ Value
diff --git a/docs/reference/mask_xy.html b/docs/reference/mask_xy.html
index 11bb577c..b0d38619 100644
--- a/docs/reference/mask_xy.html
+++ b/docs/reference/mask_xy.html
@@ -1,5 +1,5 @@
-Mask an MRSI dataset in the x-y direction — mask_xy • Spectroscopy Analysis Tools (spant) Mask an MRSI dataset in the x-y direction — mask_xy • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/mask_xy_corners.html b/docs/reference/mask_xy_corners.html
index 09b16cd2..2d13839d 100644
--- a/docs/reference/mask_xy_corners.html
+++ b/docs/reference/mask_xy_corners.html
@@ -1,5 +1,5 @@
-Mask the four corners of an MRSI dataset in the x-y plane. — mask_xy_corners • Spectroscopy Analysis Tools (spant) Mask the four corners of an MRSI dataset in the x-y plane. — mask_xy_corners • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/mask_xy_ellipse.html b/docs/reference/mask_xy_ellipse.html
index 1d8b02e4..e2e749ef 100644
--- a/docs/reference/mask_xy_ellipse.html
+++ b/docs/reference/mask_xy_ellipse.html
@@ -1,7 +1,5 @@
-Mask the voxels outside an elliptical region spanning the MRSI dataset in the
-x-y plane. — mask_xy_ellipse • Spectroscopy Analysis Tools (spant) Mask the voxels outside an elliptical region spanning the MRSI dataset in the x-y plane. — mask_xy_ellipse • Spectroscopy Analysis Tools (spant) Mask a 2D MRSI dataset in the x-y dimension. — mask_xy_mat • Spectroscopy Analysis Tools (spant) Mask a 2D MRSI dataset in the x-y dimension. — mask_xy_mat • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Value
diff --git a/docs/reference/mat2mrs_data.html b/docs/reference/mat2mrs_data.html
index 2e2895f3..ae55665f 100644
--- a/docs/reference/mat2mrs_data.html
+++ b/docs/reference/mat2mrs_data.html
@@ -1,7 +1,5 @@
-Convert a matrix (with spectral points in the column dimension and dynamics
-in the row dimensions) into a mrs_data object. — mat2mrs_data • Spectroscopy Analysis Tools (spant) Convert a matrix (with spectral points in the column dimension and dynamics in the row dimensions) into a mrs_data object. — mat2mrs_data • Spectroscopy Analysis Tools (spant) Matrix exponential function taken from complexplus package to reduce the
-number of spant dependencies. — matexp • Spectroscopy Analysis Tools (spant) Matrix exponential function taken from complexplus package to reduce the number of spant dependencies. — matexp • Spectroscopy Analysis Tools (spant) Apply the max operator to an MRS dataset. — max_mrs • Spectroscopy Analysis Tools (spant) Apply the max operator to an MRS dataset. — max_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/max_mrs_interp.html b/docs/reference/max_mrs_interp.html
index e4474764..52e63f3e 100644
--- a/docs/reference/max_mrs_interp.html
+++ b/docs/reference/max_mrs_interp.html
@@ -1,5 +1,5 @@
-Apply the max operator to an interpolated MRS dataset. — max_mrs_interp • Spectroscopy Analysis Tools (spant) Apply the max operator to an interpolated MRS dataset. — max_mrs_interp • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/mean.list.html b/docs/reference/mean.list.html
index b8eb3463..048306fd 100644
--- a/docs/reference/mean.list.html
+++ b/docs/reference/mean.list.html
@@ -1,5 +1,5 @@
-Calculate the mean spectrum from an mrs_data object. — mean.list • Spectroscopy Analysis Tools (spant) Calculate the mean spectrum from an mrs_data object. — mean.list • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/mean.mrs_data.html b/docs/reference/mean.mrs_data.html
index 5531a28d..79515014 100644
--- a/docs/reference/mean.mrs_data.html
+++ b/docs/reference/mean.mrs_data.html
@@ -1,5 +1,5 @@
-Calculate the mean spectrum from an mrs_data object. — mean.mrs_data • Spectroscopy Analysis Tools (spant) Calculate the mean spectrum from an mrs_data object. — mean.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/mean_dyn_blocks.html b/docs/reference/mean_dyn_blocks.html
index 10467098..4c042448 100644
--- a/docs/reference/mean_dyn_blocks.html
+++ b/docs/reference/mean_dyn_blocks.html
@@ -1,5 +1,5 @@
-Calculate the mean of adjacent dynamic scans. — mean_dyn_blocks • Spectroscopy Analysis Tools (spant) Calculate the mean of adjacent dynamic scans. — mean_dyn_blocks • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/mean_dyn_pairs.html b/docs/reference/mean_dyn_pairs.html
index 63e909ea..1a241126 100644
--- a/docs/reference/mean_dyn_pairs.html
+++ b/docs/reference/mean_dyn_pairs.html
@@ -1,5 +1,5 @@
-Calculate the pairwise means across a dynamic data set. — mean_dyn_pairs • Spectroscopy Analysis Tools (spant) Calculate the pairwise means across a dynamic data set. — mean_dyn_pairs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/mean_dyns.html b/docs/reference/mean_dyns.html
index 73fdbfa7..0daa27df 100644
--- a/docs/reference/mean_dyns.html
+++ b/docs/reference/mean_dyns.html
@@ -1,5 +1,5 @@
-Calculate the mean dynamic data. — mean_dyns • Spectroscopy Analysis Tools (spant) Calculate the mean dynamic data. — mean_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/mean_mrs_list.html b/docs/reference/mean_mrs_list.html
index 808b6c50..10d842c0 100644
--- a/docs/reference/mean_mrs_list.html
+++ b/docs/reference/mean_mrs_list.html
@@ -1,5 +1,5 @@
-Return the mean of a list of mrs_data objects. — mean_mrs_list • Spectroscopy Analysis Tools (spant) Return the mean of a list of mrs_data objects. — mean_mrs_list • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/mean_vec_blocks.html b/docs/reference/mean_vec_blocks.html
index 8fc92eaa..dd78b122 100644
--- a/docs/reference/mean_vec_blocks.html
+++ b/docs/reference/mean_vec_blocks.html
@@ -1,5 +1,5 @@
-Calculate the mean of adjacent blocks in a vector. — mean_vec_blocks • Spectroscopy Analysis Tools (spant) Calculate the mean of adjacent blocks in a vector. — mean_vec_blocks • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/median_dyns.html b/docs/reference/median_dyns.html
index 1039d4b5..9a085b10 100644
--- a/docs/reference/median_dyns.html
+++ b/docs/reference/median_dyns.html
@@ -1,5 +1,5 @@
-Calculate the median dynamic data. — median_dyns • Spectroscopy Analysis Tools (spant) Calculate the median dynamic data. — median_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/mod_td.html b/docs/reference/mod_td.html
index 76ad0a40..141ef09e 100644
--- a/docs/reference/mod_td.html
+++ b/docs/reference/mod_td.html
@@ -1,5 +1,5 @@
-Apply the Modulus operator to the time-domain MRS signal. — mod_td • Spectroscopy Analysis Tools (spant) Apply the Modulus operator to the time-domain MRS signal. — mod_td • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/mrs_data2basis.html b/docs/reference/mrs_data2basis.html
index 62f7d749..11797b91 100644
--- a/docs/reference/mrs_data2basis.html
+++ b/docs/reference/mrs_data2basis.html
@@ -1,7 +1,5 @@
-Convert an mrs_data object to basis object - where basis signals are spread
-across the dynamic dimension in the MRS data. — mrs_data2basis • Spectroscopy Analysis Tools (spant) Convert an mrs_data object to basis object - where basis signals are spread across the dynamic dimension in the MRS data. — mrs_data2basis • Spectroscopy Analysis Tools (spant) Create a BIDS file structure from a vector of MRS data paths or list of mrs_data objects. — mrs_data2bids • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Create a BIDS file structure from a vector of MRS data paths or list of mrs_data objects.
+ Source: R/fmrs.R
+ mrs_data2bids.Rd
+
+
+
+ Create a BIDS file structure from a vector of MRS data paths or list of
+mrs_data objects.
+
+
+
+ mrs_data2bids(
+ mrs_data,
+ output_dir,
+ suffix = NULL,
+ sub = NULL,
+ ses = NULL,
+ task = NULL,
+ acq = NULL,
+ nuc = NULL,
+ voi = NULL,
+ rec = NULL,
+ run = NULL,
+ echo = NULL,
+ inv = NULL,
+ skip_existing = TRUE
+)
+
+
+
+ Arguments
+ - mrs_data
+vector of MRS data paths or list of mrs_data objects.
- output_dir
+the base directory to create the BIDS structure.
- suffix
+optional vector of file suffixes. Default behaviour is to
+automatically determine these from the input data, however it is recommended
+that they are specified to allow more efficient skipping of existing data.
- sub
+optional vector of subject labels. If not specified, these will be
+automatically generated as a series of increasing zero-padded integer values
+corresponding to the mrs_data input indices.
- ses
+optional vector of session labels.
- task
+optional vector of task labels.
- acq
+optional vector of acquisition labels.
- nuc
+optional vector of nucleus labels.
- voi
+optional vector of volume of interest labels.
- rec
+optional vector of reconstruction labels.
- run
+optional vector of run indices.
- echo
+optional vector of echo time indices.
- inv
+optional vector of inversion indices.
- skip_existing
+skip any data files that have already been converted.
+Defaults to TRUE, set to FALSE to force an overwrite of any existing data
+files.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/mrs_data2mat.html b/docs/reference/mrs_data2mat.html
index cf5ff28c..9e47688a 100644
--- a/docs/reference/mrs_data2mat.html
+++ b/docs/reference/mrs_data2mat.html
@@ -1,7 +1,5 @@
-Convert mrs_data object to a matrix, with spectral points in the column
-dimension and dynamics in the row dimension. — mrs_data2mat • Spectroscopy Analysis Tools (spant) Convert mrs_data object to a matrix, with spectral points in the column dimension and dynamics in the row dimension. — mrs_data2mat • Spectroscopy Analysis Tools (spant) Convert mrs_data object to a matrix, with spectral points in the column dimension and dynamics in the row dimension. — mrs_data2spec_mat • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Convert mrs_data object to a matrix, with spectral points in the column dimension and dynamics in the row dimension.
+ Source: R/mrs_data_proc.R
+ mrs_data2spec_mat.Rd
+
+
+
+ Convert mrs_data object to a matrix, with spectral points in the column
+dimension and dynamics in the row dimension.
+
+
+
+ mrs_data2spec_mat(mrs_data, collapse = TRUE)
+
+
+
+ Arguments
+ - mrs_data
+MRS data object or list of MRS data objects.
- collapse
+collapse all other dimensions along the dynamic dimension, eg
+a 16x16 MRSI grid would be first collapsed across 256 dynamic scans.
+
+ Value
+
+
+MRS data matrix.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/mrs_data2vec.html b/docs/reference/mrs_data2vec.html
index fb172d68..a1fd654d 100644
--- a/docs/reference/mrs_data2vec.html
+++ b/docs/reference/mrs_data2vec.html
@@ -1,5 +1,5 @@
-Convert mrs_data object to a vector. — mrs_data2vec • Spectroscopy Analysis Tools (spant) Convert mrs_data object to a vector. — mrs_data2vec • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -126,7 +126,7 @@ Value
diff --git a/docs/reference/mvfftshift.html b/docs/reference/mvfftshift.html
index 92b0841b..976b3410 100644
--- a/docs/reference/mvfftshift.html
+++ b/docs/reference/mvfftshift.html
@@ -1,7 +1,5 @@
-Perform a fftshift on a matrix, with each column replaced by its shifted
-result. — mvfftshift • Spectroscopy Analysis Tools (spant) Perform a fftshift on a matrix, with each column replaced by its shifted result. — mvfftshift • Spectroscopy Analysis Tools (spant) Perform an ifftshift on a matrix, with each column replaced by its shifted
-result. — mvifftshift • Spectroscopy Analysis Tools (spant) Perform an ifftshift on a matrix, with each column replaced by its shifted result. — mvifftshift • Spectroscopy Analysis Tools (spant) Print fit coordinates from a single index. — n2coord • Spectroscopy Analysis Tools (spant) Print fit coordinates from a single index. — n2coord • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/nifti_flip_lr.html b/docs/reference/nifti_flip_lr.html
index 730abe3c..19860b3c 100644
--- a/docs/reference/nifti_flip_lr.html
+++ b/docs/reference/nifti_flip_lr.html
@@ -1,9 +1,5 @@
-Flip the x data dimension order of a nifti image. This corresponds to
-flipping MRI data in the left-right direction, assuming the data in save in
-neurological format (can check with fslorient program). — nifti_flip_lr • Spectroscopy Analysis Tools (spant) Flip the x data dimension order of a nifti image. This corresponds to flipping MRI data in the left-right direction, assuming the data in save in neurological format (can check with fslorient program). — nifti_flip_lr • Spectroscopy Analysis Tools (spant) Export a one-page pdf of a single fit result — one_page_pdf • Spectroscopy Analysis Tools (spant) Export a one-page pdf of a single fit result — one_page_pdf • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -108,7 +108,7 @@ Arguments
diff --git a/docs/reference/ortho3.html b/docs/reference/ortho3.html
index 13ade97d..5d7dd2fd 100644
--- a/docs/reference/ortho3.html
+++ b/docs/reference/ortho3.html
@@ -1,5 +1,5 @@
-Display an orthographic projection plot of a nifti object. — ortho3 • Spectroscopy Analysis Tools (spant) Display an orthographic projection plot of a nifti object. — ortho3 • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -172,7 +172,7 @@ Arguments
diff --git a/docs/reference/ortho3_inter.html b/docs/reference/ortho3_inter.html
index 090cc5e5..15948899 100644
--- a/docs/reference/ortho3_inter.html
+++ b/docs/reference/ortho3_inter.html
@@ -1,5 +1,5 @@
-Display an interactive orthographic projection plot of a nifti object. — ortho3_inter • Spectroscopy Analysis Tools (spant) Display an interactive orthographic projection plot of a nifti object. — ortho3_inter • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -132,7 +132,7 @@ Arguments
diff --git a/docs/reference/peak_info.html b/docs/reference/peak_info.html
index 09058bd8..41c8ffaf 100644
--- a/docs/reference/peak_info.html
+++ b/docs/reference/peak_info.html
@@ -1,7 +1,5 @@
-Search for the highest peak in a spectral region and return the frequency,
-height and FWHM. — peak_info • Spectroscopy Analysis Tools (spant) Search for the highest peak in a spectral region and return the frequency, height and FWHM. — peak_info • Spectroscopy Analysis Tools (spant) Papoulis-Gerchberg (PG) algorithm method for k-space extrapolation. — pg_extrap_xy • Spectroscopy Analysis Tools (spant) Papoulis-Gerchberg (PG) algorithm method for k-space extrapolation. — pg_extrap_xy • Spectroscopy Analysis Tools (spant) Apply phasing parameters to MRS data. — phase • Spectroscopy Analysis Tools (spant) Apply phasing parameters to MRS data. — phase • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/phase_ref_1h_brain.html b/docs/reference/phase_ref_1h_brain.html
new file mode 100644
index 00000000..8707a74a
--- /dev/null
+++ b/docs/reference/phase_ref_1h_brain.html
@@ -0,0 +1,131 @@
+
+Corrected zero order phase and chemical shift offset in 1H MRS data from the brain. — phase_ref_1h_brain • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Corrected zero order phase and chemical shift offset in 1H MRS data from the brain.
+ Source: R/rats.R
+ phase_ref_1h_brain.Rd
+
+
+
+ Corrected zero order phase and chemical shift offset in 1H MRS data from the
+brain.
+
+
+
+ phase_ref_1h_brain(mrs_data, mean_ref = FALSE, ret_corr_only = TRUE)
+
+
+
+ Arguments
+ - mrs_data
+MRS data to be corrected.
- mean_ref
+apply the phase and offset of the mean spectrum to all
+others. Default is FALSE.
- ret_corr_only
+return the corrected data only.
+
+ Value
+
+
+corrected MRS data.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/plot.fit_result.html b/docs/reference/plot.fit_result.html
index e54d3bc1..836a53ee 100644
--- a/docs/reference/plot.fit_result.html
+++ b/docs/reference/plot.fit_result.html
@@ -1,5 +1,5 @@
-Plot the fitting results of an object of class fit_result. — plot.fit_result • Spectroscopy Analysis Tools (spant) Plot the fitting results of an object of class fit_result. — plot.fit_result • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -207,7 +207,7 @@ Arguments
diff --git a/docs/reference/plot.mrs_data.html b/docs/reference/plot.mrs_data.html
index fabcc35b..bb2ec651 100644
--- a/docs/reference/plot.mrs_data.html
+++ b/docs/reference/plot.mrs_data.html
@@ -1,5 +1,5 @@
-Plotting method for objects of class mrs_data. — plot.mrs_data • Spectroscopy Analysis Tools (spant) Plotting method for objects of class mrs_data. — plot.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -287,7 +287,7 @@ Arguments
diff --git a/docs/reference/plot_bc.html b/docs/reference/plot_bc.html
index 4f8309b4..b48142cc 100644
--- a/docs/reference/plot_bc.html
+++ b/docs/reference/plot_bc.html
@@ -1,5 +1,5 @@
-Convenience function to plot a baseline estimate with the original data. — plot_bc • Spectroscopy Analysis Tools (spant) Convenience function to plot a baseline estimate with the original data. — plot_bc • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -108,7 +108,7 @@ Arguments
diff --git a/docs/reference/plot_reg.html b/docs/reference/plot_reg.html
index ae1acbe7..2addb2f6 100644
--- a/docs/reference/plot_reg.html
+++ b/docs/reference/plot_reg.html
@@ -1,5 +1,5 @@
-Plot regressors as an image. — plot_reg • Spectroscopy Analysis Tools (spant) Plot regressors as an image. — plot_reg • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/plot_slice_fit.html b/docs/reference/plot_slice_fit.html
index fbc7b560..57f1af8a 100644
--- a/docs/reference/plot_slice_fit.html
+++ b/docs/reference/plot_slice_fit.html
@@ -1,5 +1,5 @@
-Plot a 2D slice from an MRSI fit result object. — plot_slice_fit • Spectroscopy Analysis Tools (spant) Plot a 2D slice from an MRSI fit result object. — plot_slice_fit • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -129,7 +129,7 @@ Arguments
diff --git a/docs/reference/plot_slice_fit_inter.html b/docs/reference/plot_slice_fit_inter.html
index 4eed104a..da105a7d 100644
--- a/docs/reference/plot_slice_fit_inter.html
+++ b/docs/reference/plot_slice_fit_inter.html
@@ -1,5 +1,5 @@
-Plot a 2D slice from an MRSI fit result object. — plot_slice_fit_inter • Spectroscopy Analysis Tools (spant) Plot a 2D slice from an MRSI fit result object. — plot_slice_fit_inter • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -134,7 +134,7 @@ Arguments
diff --git a/docs/reference/plot_slice_map.html b/docs/reference/plot_slice_map.html
index 553e9ac8..ffb2a134 100644
--- a/docs/reference/plot_slice_map.html
+++ b/docs/reference/plot_slice_map.html
@@ -1,5 +1,5 @@
-Plot a slice from a 7 dimensional array. — plot_slice_map • Spectroscopy Analysis Tools (spant) Plot a slice from a 7 dimensional array. — plot_slice_map • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -153,7 +153,7 @@ Arguments
diff --git a/docs/reference/plot_slice_map_inter.html b/docs/reference/plot_slice_map_inter.html
index 40d33b42..90968f66 100644
--- a/docs/reference/plot_slice_map_inter.html
+++ b/docs/reference/plot_slice_map_inter.html
@@ -1,7 +1,5 @@
-Plot an interactive slice map from a data array where voxels can be selected
-to display a corresponding spectrum. — plot_slice_map_inter • Spectroscopy Analysis Tools (spant) Plot an interactive slice map from a data array where voxels can be selected to display a corresponding spectrum. — plot_slice_map_inter • Spectroscopy Analysis Tools (spant) Plot the spectral standard deviation. — plot_spec_sd • Spectroscopy Analysis Tools (spant) Plot the spectral standard deviation. — plot_spec_sd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Arguments
diff --git a/docs/reference/plot_voi_overlay.html b/docs/reference/plot_voi_overlay.html
index 9a782e88..bbbbf35e 100644
--- a/docs/reference/plot_voi_overlay.html
+++ b/docs/reference/plot_voi_overlay.html
@@ -1,5 +1,5 @@
-Plot a volume as an image overlay. — plot_voi_overlay • Spectroscopy Analysis Tools (spant) Plot a volume as an image overlay. — plot_voi_overlay • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -116,7 +116,7 @@ Arguments
diff --git a/docs/reference/plot_voi_overlay_seg.html b/docs/reference/plot_voi_overlay_seg.html
index 3d4e74ff..0e800ff2 100644
--- a/docs/reference/plot_voi_overlay_seg.html
+++ b/docs/reference/plot_voi_overlay_seg.html
@@ -1,5 +1,5 @@
-Plot a volume as an overlay on a segmented brain volume. — plot_voi_overlay_seg • Spectroscopy Analysis Tools (spant) Plot a volume as an overlay on a segmented brain volume. — plot_voi_overlay_seg • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Arguments
diff --git a/docs/reference/ppm.html b/docs/reference/ppm.html
index c352327a..ee4696e2 100644
--- a/docs/reference/ppm.html
+++ b/docs/reference/ppm.html
@@ -1,5 +1,5 @@
-Return the ppm scale of an MRS dataset or fit result. — ppm • Spectroscopy Analysis Tools (spant) Return the ppm scale of an MRS dataset or fit result. — ppm • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -132,7 +132,7 @@ Value
diff --git a/docs/reference/precomp.html b/docs/reference/precomp.html
index 822d7336..df3d2c6c 100644
--- a/docs/reference/precomp.html
+++ b/docs/reference/precomp.html
@@ -1,7 +1,5 @@
-Save function results to file and load on subsequent calls to avoid repeat
-computation. — precomp • Spectroscopy Analysis Tools (spant) Save function results to file and load on subsequent calls to avoid repeat computation. — precomp • Spectroscopy Analysis Tools (spant) Preprocess and perform quality assessment of a single SVS data set. — preproc_svs • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Preprocess and perform quality assessment of a single SVS data set.
+ Source: R/fmrs.R
+ preproc_svs.Rd
+
+
+
+ Preprocess and perform quality assessment of a single SVS data set.
+
+
+
+ preproc_svs(path, label = NULL, output_dir = NULL, ref_inds = NULL)
+
+
+
+ Arguments
+ - path
+path to the fMRS data file or IMA directory.
- label
+a label to describe the data set.
- output_dir
+output directory.
- ref_inds
+a vector of 1-based indices for any water reference dynamic
+scans.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/preproc_svs_dataset.html b/docs/reference/preproc_svs_dataset.html
new file mode 100644
index 00000000..07c3a29b
--- /dev/null
+++ b/docs/reference/preproc_svs_dataset.html
@@ -0,0 +1,148 @@
+
+Preprocess and perform quality assessment of one or more SVS data sets. — preproc_svs_dataset • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Preprocess and perform quality assessment of one or more SVS data sets.
+ Source: R/fmrs.R
+ preproc_svs_dataset.Rd
+
+
+
+ Preprocess and perform quality assessment of one or more SVS data sets.
+
+
+
+ preproc_svs_dataset(
+ paths,
+ labels = NULL,
+ output_dir = "spant_analysis",
+ exclude_labels = NULL,
+ overwrite = FALSE,
+ ref_inds = NULL,
+ return_results = FALSE
+)
+
+
+
+ Arguments
+ - paths
+paths to the fMRS data file or IMA directory.
- labels
+labels to describe each data set.
- output_dir
+output directory.
- exclude_labels
+vector of labels of scans to exclude, eg poor quality
+data.
- overwrite
+overwrite saved results, defaults to FALSE.
- ref_inds
+a vector of 1-based indices for any water reference dynamic
+scans.
- return_results
+function will return key outputs, defaults to FALSE.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/print.fit_result.html b/docs/reference/print.fit_result.html
index 297f28dc..5f434e57 100644
--- a/docs/reference/print.fit_result.html
+++ b/docs/reference/print.fit_result.html
@@ -1,5 +1,5 @@
-Print a summary of an object of class fit_result. — print.fit_result • Spectroscopy Analysis Tools (spant) Print a summary of an object of class fit_result. — print.fit_result • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -105,7 +105,7 @@ Arguments
diff --git a/docs/reference/print.mrs_data.html b/docs/reference/print.mrs_data.html
index 51199017..e1561eb2 100644
--- a/docs/reference/print.mrs_data.html
+++ b/docs/reference/print.mrs_data.html
@@ -1,5 +1,5 @@
-Print a summary of mrs_data parameters. — print.mrs_data • Spectroscopy Analysis Tools (spant) Print a summary of mrs_data parameters. — print.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -109,7 +109,7 @@ Arguments
diff --git a/docs/reference/qn_states.html b/docs/reference/qn_states.html
index 0f42f2f9..d7aa6715 100644
--- a/docs/reference/qn_states.html
+++ b/docs/reference/qn_states.html
@@ -1,5 +1,5 @@
-Get the quantum coherence matrix for a spin system. — qn_states • Spectroscopy Analysis Tools (spant) Get the quantum coherence matrix for a spin system. — qn_states • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/rats.html b/docs/reference/rats.html
index 5a39a396..93585e08 100644
--- a/docs/reference/rats.html
+++ b/docs/reference/rats.html
@@ -1,5 +1,5 @@
-Robust Alignment to a Target Spectrum (RATS). — rats • Spectroscopy Analysis Tools (spant) Robust Alignment to a Target Spectrum (RATS). — rats • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -207,7 +207,7 @@ Value
diff --git a/docs/reference/re_weighting.html b/docs/reference/re_weighting.html
index d21caf21..8b0b070a 100644
--- a/docs/reference/re_weighting.html
+++ b/docs/reference/re_weighting.html
@@ -1,5 +1,5 @@
-Apply a weighting to the FID to enhance spectral resolution. — re_weighting • Spectroscopy Analysis Tools (spant) Apply a weighting to the FID to enhance spectral resolution. — re_weighting • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/read_basis.html b/docs/reference/read_basis.html
index da9b94af..eb6f8557 100644
--- a/docs/reference/read_basis.html
+++ b/docs/reference/read_basis.html
@@ -1,5 +1,5 @@
-Read a basis file in LCModel .basis format. — read_basis • Spectroscopy Analysis Tools (spant) Read a basis file in LCModel .basis format. — read_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/read_ima_coil_dir.html b/docs/reference/read_ima_coil_dir.html
index 28c02de0..4f073cd8 100644
--- a/docs/reference/read_ima_coil_dir.html
+++ b/docs/reference/read_ima_coil_dir.html
@@ -1,9 +1,5 @@
-Read a directory containing Siemens MRS IMA files and combine along the coil
-dimension. Note that the coil ID is inferred from the sorted file name and
-should be checked when consistency is required between two directories. — read_ima_coil_dir • Spectroscopy Analysis Tools (spant) Read a directory containing Siemens MRS IMA files and combine along the coil dimension. Note that the coil ID is inferred from the sorted file name and should be checked when consistency is required between two directories. — read_ima_coil_dir • Spectroscopy Analysis Tools (spant) Read a directory containing Siemens MRS IMA files and combine along the
-dynamic dimension. Note that the coil ID is inferred from the sorted file
-name and should be checked when consistency is required. — read_ima_dyn_dir • Spectroscopy Analysis Tools (spant) Read a directory containing Siemens MRS IMA files and combine along the dynamic dimension. Note that the coil ID is inferred from the sorted file name and should be checked when consistency is required. — read_ima_dyn_dir • Spectroscopy Analysis Tools (spant) Read an LCModel formatted coord file containing fit information. — read_lcm_coord • Spectroscopy Analysis Tools (spant) Read an LCModel formatted coord file containing fit information. — read_lcm_coord • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -107,7 +107,7 @@ Value
diff --git a/docs/reference/read_mrs.html b/docs/reference/read_mrs.html
index 3ac2a36b..2cf36b20 100644
--- a/docs/reference/read_mrs.html
+++ b/docs/reference/read_mrs.html
@@ -1,5 +1,5 @@
-Read MRS data from a file. — read_mrs • Spectroscopy Analysis Tools (spant) Read MRS data from a file. — read_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -88,7 +88,8 @@ Read MRS data from a file.
full_fid = FALSE,
omit_svs_ref_scans = TRUE,
verbose = FALSE,
- extra = NULL
+ extra = NULL,
+ fid_filt_dist = NULL
)
@@ -140,6 +141,13 @@ Arguments
an optional data frame to provide additional variables for use
in subsequent analysis steps, eg id or grouping variables.
fid_filt_dist
+indicate if the data has a distorted FID due to a
+brick-wall filter being used to downsample the data. Default is to auto
+detect this from the data, but TRUE or FALSE options can be given to override
+detection.
Value
@@ -183,7 +191,7 @@ Examples
diff --git a/docs/reference/read_mrs_tqn.html b/docs/reference/read_mrs_tqn.html
index 5766362f..84bdaf3a 100644
--- a/docs/reference/read_mrs_tqn.html
+++ b/docs/reference/read_mrs_tqn.html
@@ -1,5 +1,5 @@
-Read MRS data using the TARQUIN software package. — read_mrs_tqn • Spectroscopy Analysis Tools (spant) Read MRS data using the TARQUIN software package. — read_mrs_tqn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -131,7 +131,7 @@ Examples
diff --git a/docs/reference/read_pulse_ascii.html b/docs/reference/read_pulse_ascii.html
index c9e0d43c..ab11c9cc 100644
--- a/docs/reference/read_pulse_ascii.html
+++ b/docs/reference/read_pulse_ascii.html
@@ -1,5 +1,5 @@
-Read an ASCII formatted pulse file. — read_pulse_ascii • Spectroscopy Analysis Tools (spant) Read an ASCII formatted pulse file. — read_pulse_ascii • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/read_pulse_bruker.html b/docs/reference/read_pulse_bruker.html
index c92bf76a..dbe9073b 100644
--- a/docs/reference/read_pulse_bruker.html
+++ b/docs/reference/read_pulse_bruker.html
@@ -1,5 +1,5 @@
-Read a Bruker formatted pulse file — read_pulse_bruker • Spectroscopy Analysis Tools (spant) Read a Bruker formatted pulse file — read_pulse_bruker • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/read_pulse_pta.html b/docs/reference/read_pulse_pta.html
index 72e1b6d4..a0fac3c3 100644
--- a/docs/reference/read_pulse_pta.html
+++ b/docs/reference/read_pulse_pta.html
@@ -1,5 +1,5 @@
-Read a .pta formatted pulse file compatible with Siemens PulseTool. — read_pulse_pta • Spectroscopy Analysis Tools (spant) Read a .pta formatted pulse file compatible with Siemens PulseTool. — read_pulse_pta • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/read_siemens_txt_hdr.html b/docs/reference/read_siemens_txt_hdr.html
index 23fb8c70..3a17d87c 100644
--- a/docs/reference/read_siemens_txt_hdr.html
+++ b/docs/reference/read_siemens_txt_hdr.html
@@ -1,5 +1,5 @@
-Read the text format header found in Siemens IMA and TWIX data files. — read_siemens_txt_hdr • Spectroscopy Analysis Tools (spant) Read the text format header found in Siemens IMA and TWIX data files. — read_siemens_txt_hdr • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -78,7 +78,7 @@ Read the text format header found in Siemens IMA and TWIX data files.
- read_siemens_txt_hdr(input, version = "vd", verbose, offset = 0)
+ read_siemens_txt_hdr(input, version = "vd", verbose = FALSE, offset = 0)
@@ -118,7 +118,7 @@ Value
diff --git a/docs/reference/read_tqn_fit.html b/docs/reference/read_tqn_fit.html
index 4da6c25e..a1630420 100644
--- a/docs/reference/read_tqn_fit.html
+++ b/docs/reference/read_tqn_fit.html
@@ -1,5 +1,5 @@
-Reader for csv fit results generated by TARQUIN. — read_tqn_fit • Spectroscopy Analysis Tools (spant) Reader for csv fit results generated by TARQUIN. — read_tqn_fit • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -113,7 +113,7 @@ Examples
diff --git a/docs/reference/read_tqn_result.html b/docs/reference/read_tqn_result.html
index 36659714..68a3e98c 100644
--- a/docs/reference/read_tqn_result.html
+++ b/docs/reference/read_tqn_result.html
@@ -1,5 +1,5 @@
-Reader for csv results generated by TARQUIN. — read_tqn_result • Spectroscopy Analysis Tools (spant) Reader for csv results generated by TARQUIN. — read_tqn_result • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -117,7 +117,7 @@ Examples
diff --git a/docs/reference/recon_imag.html b/docs/reference/recon_imag.html
index d2a72225..5bc3b1eb 100644
--- a/docs/reference/recon_imag.html
+++ b/docs/reference/recon_imag.html
@@ -1,7 +1,5 @@
-Reconstruct complex time-domain data from the real part of frequency-domain
-data. — recon_imag • Spectroscopy Analysis Tools (spant) Reconstruct complex time-domain data from the real part of frequency-domain data. — recon_imag • Spectroscopy Analysis Tools (spant) Reconstruct complex time-domain data from the real part of frequency-domain
-data. — recon_imag_vec • Spectroscopy Analysis Tools (spant) Reconstruct complex time-domain data from the real part of frequency-domain data. — recon_imag_vec • Spectroscopy Analysis Tools (spant) Reconstruct 2D MRSI data from a twix file loaded with read_mrs. — recon_twix_2d_mrsi • Spectroscopy Analysis Tools (spant) Reconstruct 2D MRSI data from a twix file loaded with read_mrs. — recon_twix_2d_mrsi • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/rectangular_mask.html b/docs/reference/rectangular_mask.html
index a2117283..6e469bc9 100644
--- a/docs/reference/rectangular_mask.html
+++ b/docs/reference/rectangular_mask.html
@@ -1,5 +1,5 @@
-Create a rectangular mask stored as a matrix of logical values. — rectangular_mask • Spectroscopy Analysis Tools (spant) Create a rectangular mask stored as a matrix of logical values. — rectangular_mask • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -130,7 +130,7 @@ Value
diff --git a/docs/reference/reexports.html b/docs/reference/reexports.html
index 694a75d1..a59e8379 100644
--- a/docs/reference/reexports.html
+++ b/docs/reference/reexports.html
@@ -1,5 +1,5 @@
-Objects exported from other packages — reexports • Spectroscopy Analysis Tools (spant) Objects exported from other packages — reexports • Spectroscopy Analysis Tools (spant)
Spectroscopy Analysis Tools (spant)
- 2.21.0
+ 2.22.0
@@ -103,7 +103,7 @@ Objects exported from other packages
diff --git a/docs/reference/rep_array_dim.html b/docs/reference/rep_array_dim.html
index b9c49b4a..48c0a5ed 100644
--- a/docs/reference/rep_array_dim.html
+++ b/docs/reference/rep_array_dim.html
@@ -1,5 +1,5 @@
-Repeat an array over a given dimension. — rep_array_dim • Spectroscopy Analysis Tools (spant) Repeat an array over a given dimension. — rep_array_dim • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/rep_dyn.html b/docs/reference/rep_dyn.html
index 6bbfb0ef..89a4bb9b 100644
--- a/docs/reference/rep_dyn.html
+++ b/docs/reference/rep_dyn.html
@@ -1,5 +1,5 @@
-Replicate a scan in the dynamic dimension. — rep_dyn • Spectroscopy Analysis Tools (spant) Replicate a scan in the dynamic dimension. — rep_dyn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/rep_mrs.html b/docs/reference/rep_mrs.html
index 67730b5c..becb8f00 100644
--- a/docs/reference/rep_mrs.html
+++ b/docs/reference/rep_mrs.html
@@ -1,5 +1,5 @@
-Replicate a scan over a given dimension. — rep_mrs • Spectroscopy Analysis Tools (spant) Replicate a scan over a given dimension. — rep_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -138,7 +138,7 @@ Value
diff --git a/docs/reference/resample_basis.html b/docs/reference/resample_basis.html
index b0f2ab17..c7a6222a 100644
--- a/docs/reference/resample_basis.html
+++ b/docs/reference/resample_basis.html
@@ -1,5 +1,5 @@
-Resample a basis-set to match a mrs_data acquisition. — resample_basis • Spectroscopy Analysis Tools (spant) Resample a basis-set to match a mrs_data acquisition. — resample_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -116,7 +116,7 @@ Value
diff --git a/docs/reference/resample_img.html b/docs/reference/resample_img.html
index f1e7beaf..b0cc8f71 100644
--- a/docs/reference/resample_img.html
+++ b/docs/reference/resample_img.html
@@ -1,5 +1,5 @@
-Resample an image to match a target image space. — resample_img • Spectroscopy Analysis Tools (spant) Resample an image to match a target image space. — resample_img • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/resample_voi.html b/docs/reference/resample_voi.html
index 8fbfa836..a29ab096 100644
--- a/docs/reference/resample_voi.html
+++ b/docs/reference/resample_voi.html
@@ -1,7 +1,5 @@
-Resample a VOI to match a target image space using nearest-neighbour
-interpolation. — resample_voi • Spectroscopy Analysis Tools (spant) Resample a VOI to match a target image space using nearest-neighbour interpolation. — resample_voi • Spectroscopy Analysis Tools (spant) Reslice a nifti object to match the orientation of mrs data. — reslice_to_mrs • Spectroscopy Analysis Tools (spant) Reslice a nifti object to match the orientation of mrs data. — reslice_to_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/reson_table2mrs_data.html b/docs/reference/reson_table2mrs_data.html
index d75579ee..c5a2167a 100644
--- a/docs/reference/reson_table2mrs_data.html
+++ b/docs/reference/reson_table2mrs_data.html
@@ -1,5 +1,5 @@
-Generate mrs_data from a table of single Lorentzian resonances. — reson_table2mrs_data • Spectroscopy Analysis Tools (spant) Generate mrs_data from a table of single Lorentzian resonances. — reson_table2mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -119,7 +119,7 @@ Value
diff --git a/docs/reference/rm_dyns.html b/docs/reference/rm_dyns.html
index 5d5ef692..573e1f51 100644
--- a/docs/reference/rm_dyns.html
+++ b/docs/reference/rm_dyns.html
@@ -1,5 +1,5 @@
-Remove a subset of dynamic scans. — rm_dyns • Spectroscopy Analysis Tools (spant) Remove a subset of dynamic scans. — rm_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/scale_amp_molal.html b/docs/reference/scale_amp_molal.html
index aaeee1f2..7acb8cb0 100644
--- a/docs/reference/scale_amp_molal.html
+++ b/docs/reference/scale_amp_molal.html
@@ -1,7 +1,5 @@
-Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water). — scale_amp_molal • Spectroscopy Analysis Tools (spant) Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / kg of tissue water). — scale_amp_molal • Spectroscopy Analysis Tools (spant)
Spectroscopy Analysis Tools (spant)
- 2.21.0
+ 2.22.0
@@ -76,8 +74,7 @@
- Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water).
+ Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / kg of tissue water).
Source: R/amp_scaling.R
scale_amp_molal.Rd
@@ -163,7 +160,7 @@ Value
diff --git a/docs/reference/scale_amp_molal_pvc.html b/docs/reference/scale_amp_molal_pvc.html
index 962d6afc..4d194abd 100644
--- a/docs/reference/scale_amp_molal_pvc.html
+++ b/docs/reference/scale_amp_molal_pvc.html
@@ -1,7 +1,5 @@
-Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water). — scale_amp_molal_pvc • Spectroscopy Analysis Tools (spant)
@@ -75,8 +73,7 @@
- Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water).
+ Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / kg of tissue water).
Source: R/amp_scaling.R
scale_amp_molal_pvc.Rd
@@ -141,7 +138,7 @@ Value
diff --git a/docs/reference/scale_amp_molar.html b/docs/reference/scale_amp_molar.html
index 02358d91..dc87a338 100644
--- a/docs/reference/scale_amp_molar.html
+++ b/docs/reference/scale_amp_molar.html
@@ -1,7 +1,5 @@
-Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / Litre of tissue). — scale_amp_molar • Spectroscopy Analysis Tools (spant) Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / Litre of tissue). — scale_amp_molar • Spectroscopy Analysis Tools (spant) Convert default LCM/TARQUIN concentration scaling to molal units with partial
-volume correction. — scale_amp_molar2molal_pvc • Spectroscopy Analysis Tools (spant) Convert default LCM/TARQUIN concentration scaling to molal units with partial volume correction. — scale_amp_molar2molal_pvc • Spectroscopy Analysis Tools (spant) Scale fitted amplitudes to a ratio of signal amplitude. — scale_amp_ratio • Spectroscopy Analysis Tools (spant) Scale fitted amplitudes to a ratio of signal amplitude. — scale_amp_ratio • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -116,7 +116,7 @@ Value
diff --git a/docs/reference/scale_amp_ratio_value.html b/docs/reference/scale_amp_ratio_value.html
index 2036837a..6af8ac51 100644
--- a/docs/reference/scale_amp_ratio_value.html
+++ b/docs/reference/scale_amp_ratio_value.html
@@ -1,5 +1,5 @@
-Scale fitted amplitudes to a ratio of signal amplitude. — scale_amp_ratio_value • Spectroscopy Analysis Tools (spant) Scale fitted amplitudes to a ratio of signal amplitude. — scale_amp_ratio_value • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/scale_amp_water_ratio.html b/docs/reference/scale_amp_water_ratio.html
index 5b25e884..35a76b00 100644
--- a/docs/reference/scale_amp_water_ratio.html
+++ b/docs/reference/scale_amp_water_ratio.html
@@ -1,5 +1,5 @@
-Scale metabolite amplitudes as a ratio to the unsuppressed water amplitude. — scale_amp_water_ratio • Spectroscopy Analysis Tools (spant) Scale metabolite amplitudes as a ratio to the unsuppressed water amplitude. — scale_amp_water_ratio • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/scale_basis_amp.html b/docs/reference/scale_basis_amp.html
index 9401c3f1..5a58b5e5 100644
--- a/docs/reference/scale_basis_amp.html
+++ b/docs/reference/scale_basis_amp.html
@@ -1,5 +1,5 @@
-Scale a basis object by a scalar. — scale_basis_amp • Spectroscopy Analysis Tools (spant) Scale a basis object by a scalar. — scale_basis_amp • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/scale_basis_from_singlet.html b/docs/reference/scale_basis_from_singlet.html
index 0d542bc8..c9a19e77 100644
--- a/docs/reference/scale_basis_from_singlet.html
+++ b/docs/reference/scale_basis_from_singlet.html
@@ -1,5 +1,5 @@
-Scale a basis-set to be consistent with spant assumptions for water scaling. — scale_basis_from_singlet • Spectroscopy Analysis Tools (spant) Scale a basis-set to be consistent with spant assumptions for water scaling. — scale_basis_from_singlet • Spectroscopy Analysis Tools (spant)
Spectroscopy Analysis Tools (spant)
- 2.21.0
+ 2.22.0
@@ -127,7 +127,7 @@ Value
diff --git a/docs/reference/scale_mrs_amp.html b/docs/reference/scale_mrs_amp.html
index b5501a0d..990f058a 100644
--- a/docs/reference/scale_mrs_amp.html
+++ b/docs/reference/scale_mrs_amp.html
@@ -1,5 +1,5 @@
-Scale an mrs_data object by a scalar or vector or amplitudes. — scale_mrs_amp • Spectroscopy Analysis Tools (spant) Scale an mrs_data object by a scalar or vector or amplitudes. — scale_mrs_amp • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/scale_spec.html b/docs/reference/scale_spec.html
index 4f6ea835..6b3ddba4 100644
--- a/docs/reference/scale_spec.html
+++ b/docs/reference/scale_spec.html
@@ -1,5 +1,5 @@
-Scale mrs_data to a spectral region. — scale_spec • Spectroscopy Analysis Tools (spant) Scale mrs_data to a spectral region. — scale_spec • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -141,7 +141,7 @@ Value
diff --git a/docs/reference/sd.html b/docs/reference/sd.html
index ea1eec9f..3ae4dfd4 100644
--- a/docs/reference/sd.html
+++ b/docs/reference/sd.html
@@ -1,5 +1,5 @@
-Calculate the standard deviation spectrum from an mrs_data object. — sd • Spectroscopy Analysis Tools (spant) Calculate the standard deviation spectrum from an mrs_data object. — sd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/sd.mrs_data.html b/docs/reference/sd.mrs_data.html
index 3f92a49f..13bdda85 100644
--- a/docs/reference/sd.mrs_data.html
+++ b/docs/reference/sd.mrs_data.html
@@ -1,5 +1,5 @@
-Calculate the standard deviation spectrum from an mrs_data object. — sd.mrs_data • Spectroscopy Analysis Tools (spant) Calculate the standard deviation spectrum from an mrs_data object. — sd.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/seconds.html b/docs/reference/seconds.html
index b34d6627..467ee17f 100644
--- a/docs/reference/seconds.html
+++ b/docs/reference/seconds.html
@@ -1,5 +1,5 @@
-Return a time scale vector to match the FID of an MRS data object. — seconds • Spectroscopy Analysis Tools (spant) Return a time scale vector to match the FID of an MRS data object. — seconds • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/seq_cpmg_ideal.html b/docs/reference/seq_cpmg_ideal.html
index 547e96ab..45727c86 100644
--- a/docs/reference/seq_cpmg_ideal.html
+++ b/docs/reference/seq_cpmg_ideal.html
@@ -1,5 +1,5 @@
-CPMG style sequence with ideal pulses. — seq_cpmg_ideal • Spectroscopy Analysis Tools (spant) CPMG style sequence with ideal pulses. — seq_cpmg_ideal • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/seq_mega_press_ideal.html b/docs/reference/seq_mega_press_ideal.html
index 0769b8b4..a9cd7fa0 100644
--- a/docs/reference/seq_mega_press_ideal.html
+++ b/docs/reference/seq_mega_press_ideal.html
@@ -1,7 +1,5 @@
-MEGA-PRESS sequence with ideal localisation pulses and Gaussian shaped
-editing pulse. — seq_mega_press_ideal • Spectroscopy Analysis Tools (spant) MEGA-PRESS sequence with ideal localisation pulses and Gaussian shaped editing pulse. — seq_mega_press_ideal • Spectroscopy Analysis Tools (spant) PRESS sequence with shaped refocusing pulses. — seq_press_2d_shaped • Spectroscopy Analysis Tools (spant) PRESS sequence with shaped refocusing pulses. — seq_press_2d_shaped • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -165,7 +165,7 @@ Value
diff --git a/docs/reference/seq_press_ideal.html b/docs/reference/seq_press_ideal.html
index 8c976856..72c3af3d 100644
--- a/docs/reference/seq_press_ideal.html
+++ b/docs/reference/seq_press_ideal.html
@@ -1,5 +1,5 @@
-PRESS sequence with ideal pulses. — seq_press_ideal • Spectroscopy Analysis Tools (spant) PRESS sequence with ideal pulses. — seq_press_ideal • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/seq_pulse_acquire.html b/docs/reference/seq_pulse_acquire.html
index 4a88fc64..ad80571e 100644
--- a/docs/reference/seq_pulse_acquire.html
+++ b/docs/reference/seq_pulse_acquire.html
@@ -1,5 +1,5 @@
-Simple pulse and acquire sequence with ideal pulses. — seq_pulse_acquire • Spectroscopy Analysis Tools (spant) Simple pulse and acquire sequence with ideal pulses. — seq_pulse_acquire • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/seq_slaser_ideal.html b/docs/reference/seq_slaser_ideal.html
index 74688f4d..eb83e8e3 100644
--- a/docs/reference/seq_slaser_ideal.html
+++ b/docs/reference/seq_slaser_ideal.html
@@ -1,5 +1,5 @@
-sLASER sequence with ideal pulses. — seq_slaser_ideal • Spectroscopy Analysis Tools (spant) sLASER sequence with ideal pulses. — seq_slaser_ideal • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -126,7 +126,7 @@ Value
diff --git a/docs/reference/seq_spin_echo_ideal.html b/docs/reference/seq_spin_echo_ideal.html
index e23271de..4248716f 100644
--- a/docs/reference/seq_spin_echo_ideal.html
+++ b/docs/reference/seq_spin_echo_ideal.html
@@ -1,5 +1,5 @@
-Spin echo sequence with ideal pulses. — seq_spin_echo_ideal • Spectroscopy Analysis Tools (spant) Spin echo sequence with ideal pulses. — seq_spin_echo_ideal • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/seq_steam_ideal.html b/docs/reference/seq_steam_ideal.html
index a60685a8..1c8115d7 100644
--- a/docs/reference/seq_steam_ideal.html
+++ b/docs/reference/seq_steam_ideal.html
@@ -1,5 +1,5 @@
-STEAM sequence with ideal pulses. — seq_steam_ideal • Spectroscopy Analysis Tools (spant) STEAM sequence with ideal pulses. — seq_steam_ideal • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -128,7 +128,7 @@ Value
diff --git a/docs/reference/seq_steam_ideal_cof.html b/docs/reference/seq_steam_ideal_cof.html
index 8f225740..cba7af91 100644
--- a/docs/reference/seq_steam_ideal_cof.html
+++ b/docs/reference/seq_steam_ideal_cof.html
@@ -1,7 +1,5 @@
-STEAM sequence with ideal pulses and coherence order filtering to simulate
-gradient crushers. — seq_steam_ideal_cof • Spectroscopy Analysis Tools (spant) STEAM sequence with ideal pulses and coherence order filtering to simulate gradient crushers. — seq_steam_ideal_cof • Spectroscopy Analysis Tools (spant) STEAM sequence with ideal pulses using the z-rotation gradient simulation
-method described by Young et al JMR 140, 146-152 (1999). — seq_steam_ideal_young • Spectroscopy Analysis Tools (spant) STEAM sequence with ideal pulses using the z-rotation gradient simulation method described by Young et al JMR 140, 146-152 (1999). — seq_steam_ideal_young • Spectroscopy Analysis Tools (spant) Set the number of transients for an mrs_data object. — set_Ntrans • Spectroscopy Analysis Tools (spant) Set the number of transients for an mrs_data object. — set_Ntrans • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/set_def_acq_paras.html b/docs/reference/set_def_acq_paras.html
index 3e1b4004..cc2ada9c 100644
--- a/docs/reference/set_def_acq_paras.html
+++ b/docs/reference/set_def_acq_paras.html
@@ -1,5 +1,5 @@
-Set the default acquisition parameters. — set_def_acq_paras • Spectroscopy Analysis Tools (spant) Set the default acquisition parameters. — set_def_acq_paras • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Arguments
diff --git a/docs/reference/set_lcm_cmd.html b/docs/reference/set_lcm_cmd.html
index 2056ed01..42bb2f24 100644
--- a/docs/reference/set_lcm_cmd.html
+++ b/docs/reference/set_lcm_cmd.html
@@ -1,5 +1,5 @@
-Set the command to run the LCModel command-line program. — set_lcm_cmd • Spectroscopy Analysis Tools (spant) Set the command to run the LCModel command-line program. — set_lcm_cmd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/set_lw.html b/docs/reference/set_lw.html
index b64ec851..bb176c62 100644
--- a/docs/reference/set_lw.html
+++ b/docs/reference/set_lw.html
@@ -1,5 +1,5 @@
-Apply line-broadening to an mrs_data object to achieve a specified linewidth. — set_lw • Spectroscopy Analysis Tools (spant) Apply line-broadening to an mrs_data object to achieve a specified linewidth. — set_lw • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -123,7 +123,7 @@ Value
diff --git a/docs/reference/set_mask_xy_mat.html b/docs/reference/set_mask_xy_mat.html
index 49dc5d4e..52c4b617 100644
--- a/docs/reference/set_mask_xy_mat.html
+++ b/docs/reference/set_mask_xy_mat.html
@@ -1,5 +1,5 @@
-Set the masked voxels in a 2D MRSI dataset to given spectrum. — set_mask_xy_mat • Spectroscopy Analysis Tools (spant) Set the masked voxels in a 2D MRSI dataset to given spectrum. — set_mask_xy_mat • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Value
diff --git a/docs/reference/set_precomp_mode.html b/docs/reference/set_precomp_mode.html
index f44bd5d3..47c28e3b 100644
--- a/docs/reference/set_precomp_mode.html
+++ b/docs/reference/set_precomp_mode.html
@@ -1,5 +1,5 @@
-Set the precompute mode. — set_precomp_mode • Spectroscopy Analysis Tools (spant) Set the precompute mode. — set_precomp_mode • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/set_precomp_verbose.html b/docs/reference/set_precomp_verbose.html
index 1453a231..9c613505 100644
--- a/docs/reference/set_precomp_verbose.html
+++ b/docs/reference/set_precomp_verbose.html
@@ -1,5 +1,5 @@
-Set the verbosity of the precompute function. — set_precomp_verbose • Spectroscopy Analysis Tools (spant) Set the verbosity of the precompute function. — set_precomp_verbose • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/set_ref.html b/docs/reference/set_ref.html
index 8953fa50..5436dfa2 100644
--- a/docs/reference/set_ref.html
+++ b/docs/reference/set_ref.html
@@ -1,5 +1,5 @@
-Set the ppm reference value (eg ppm value at 0Hz). — set_ref • Spectroscopy Analysis Tools (spant) Set the ppm reference value (eg ppm value at 0Hz). — set_ref • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/set_td_pts.html b/docs/reference/set_td_pts.html
index 8a80d42a..586459ff 100644
--- a/docs/reference/set_td_pts.html
+++ b/docs/reference/set_td_pts.html
@@ -1,7 +1,5 @@
-Set the number of time-domain data points, truncating or zero-filling as
-appropriate. — set_td_pts • Spectroscopy Analysis Tools (spant) Set the number of time-domain data points, truncating or zero-filling as appropriate. — set_td_pts • Spectroscopy Analysis Tools (spant) Set the command to run the TARQUIN command-line program. — set_tqn_cmd • Spectroscopy Analysis Tools (spant) Set the command to run the TARQUIN command-line program. — set_tqn_cmd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/set_tr.html b/docs/reference/set_tr.html
index b2109ab0..65c9df5f 100644
--- a/docs/reference/set_tr.html
+++ b/docs/reference/set_tr.html
@@ -1,5 +1,5 @@
-Set the repetition time of an MRS dataset. — set_tr • Spectroscopy Analysis Tools (spant) Set the repetition time of an MRS dataset. — set_tr • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/shift.html b/docs/reference/shift.html
index ab0fe724..034591d0 100644
--- a/docs/reference/shift.html
+++ b/docs/reference/shift.html
@@ -1,5 +1,5 @@
-Apply a frequency shift to MRS data. — shift • Spectroscopy Analysis Tools (spant) Apply a frequency shift to MRS data. — shift • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/shift_basis.html b/docs/reference/shift_basis.html
index 2884be19..f55a65e0 100644
--- a/docs/reference/shift_basis.html
+++ b/docs/reference/shift_basis.html
@@ -1,5 +1,5 @@
-Apply frequency shifts to basis set signals. — shift_basis • Spectroscopy Analysis Tools (spant) Apply frequency shifts to basis set signals. — shift_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Value
diff --git a/docs/reference/sim_basis.html b/docs/reference/sim_basis.html
index c7838c46..bb5fefc6 100644
--- a/docs/reference/sim_basis.html
+++ b/docs/reference/sim_basis.html
@@ -1,5 +1,5 @@
-Simulate a basis set object. — sim_basis • Spectroscopy Analysis Tools (spant) Simulate a basis set object. — sim_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -136,7 +136,7 @@ Value
diff --git a/docs/reference/sim_basis_1h_brain.html b/docs/reference/sim_basis_1h_brain.html
index 62ed7389..f71ffa0b 100644
--- a/docs/reference/sim_basis_1h_brain.html
+++ b/docs/reference/sim_basis_1h_brain.html
@@ -1,7 +1,5 @@
-Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS
-sequence. Note, ideal pulses are assumed. — sim_basis_1h_brain • Spectroscopy Analysis Tools (spant) Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS sequence. Note, ideal pulses are assumed. — sim_basis_1h_brain • Spectroscopy Analysis Tools (spant) Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS
-sequence. Note, ideal pulses are assumed. — sim_basis_1h_brain_press • Spectroscopy Analysis Tools (spant) Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS sequence. Note, ideal pulses are assumed. — sim_basis_1h_brain_press • Spectroscopy Analysis Tools (spant) Simulate a macromolecular and lipid basis-set suitable for 1H brain MRS
-analysis. — sim_basis_mm_lip_lcm • Spectroscopy Analysis Tools (spant) Simulate a macromolecular and lipid basis-set suitable for 1H brain MRS analysis. — sim_basis_mm_lip_lcm • Spectroscopy Analysis Tools (spant) Simulate a basis file using TARQUIN. — sim_basis_tqn • Spectroscopy Analysis Tools (spant) Simulate a basis file using TARQUIN. — sim_basis_tqn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -129,7 +129,7 @@ Examples
diff --git a/docs/reference/sim_brain_1h.html b/docs/reference/sim_brain_1h.html
index 2044cf1a..717ee289 100644
--- a/docs/reference/sim_brain_1h.html
+++ b/docs/reference/sim_brain_1h.html
@@ -1,5 +1,5 @@
-Simulate MRS data with a similar appearance to normal brain (by default). — sim_brain_1h • Spectroscopy Analysis Tools (spant) Simulate MRS data with a similar appearance to normal brain (by default). — sim_brain_1h • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -159,7 +159,7 @@ Value
diff --git a/docs/reference/sim_mol.html b/docs/reference/sim_mol.html
index 23bcef50..77f76a50 100644
--- a/docs/reference/sim_mol.html
+++ b/docs/reference/sim_mol.html
@@ -1,5 +1,5 @@
-Simulate a mol_parameter object. — sim_mol • Spectroscopy Analysis Tools (spant) Simulate a mol_parameter object. — sim_mol • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -143,7 +143,7 @@ Value
diff --git a/docs/reference/sim_noise.html b/docs/reference/sim_noise.html
index 23875f79..a71477d4 100644
--- a/docs/reference/sim_noise.html
+++ b/docs/reference/sim_noise.html
@@ -1,5 +1,5 @@
-Simulate an mrs_data object containing simulated Gaussian noise. — sim_noise • Spectroscopy Analysis Tools (spant) Simulate an mrs_data object containing simulated Gaussian noise. — sim_noise • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -84,6 +84,7 @@ Simulate an mrs_data object containing simulated Gaussian noise.
ft = def_ft(),
N = def_N(),
ref = def_ref(),
+ nuc = def_nuc(),
dyns = 1,
fd = TRUE
)
@@ -111,6 +112,10 @@ Arguments
reference value for ppm scale.
nuc
+resonant nucleus.
dyns
number of dynamic scans to generate.
Value
diff --git a/docs/reference/sim_resonances.html b/docs/reference/sim_resonances.html
index 19e9a8a4..d4f8d7c0 100644
--- a/docs/reference/sim_resonances.html
+++ b/docs/reference/sim_resonances.html
@@ -1,5 +1,5 @@
-Simulate a MRS data object containing a set of simulated resonances. — sim_resonances • Spectroscopy Analysis Tools (spant) Simulate a MRS data object containing a set of simulated resonances. — sim_resonances • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -161,7 +161,7 @@ Examples
diff --git a/docs/reference/sim_th_excit_profile.html b/docs/reference/sim_th_excit_profile.html
index 5535c5ef..e781cab1 100644
--- a/docs/reference/sim_th_excit_profile.html
+++ b/docs/reference/sim_th_excit_profile.html
@@ -1,7 +1,5 @@
-Simulate an ideal pulse excitation profile by smoothing a top-hat function
-with a Gaussian. — sim_th_excit_profile • Spectroscopy Analysis Tools (spant) Simulate an ideal pulse excitation profile by smoothing a top-hat function with a Gaussian. — sim_th_excit_profile • Spectroscopy Analysis Tools (spant) Simulate an mrs_data object containing complex zero valued samples. — sim_zero • Spectroscopy Analysis Tools (spant) Simulate an mrs_data object containing complex zero valued samples. — sim_zero • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -78,7 +78,14 @@ Simulate an mrs_data object containing complex zero valued samples.
-
+
@@ -99,6 +106,10 @@ Arguments
reference value for ppm scale.
nuc
+resonant nucleus.
dyns
number of dynamic scans to generate.
Value
diff --git a/docs/reference/smooth_dyns.html b/docs/reference/smooth_dyns.html
index 4cc8da50..accf3a51 100644
--- a/docs/reference/smooth_dyns.html
+++ b/docs/reference/smooth_dyns.html
@@ -1,5 +1,5 @@
-Smooth data across the dynamic dimension with a Gaussian kernel. — smooth_dyns • Spectroscopy Analysis Tools (spant) Smooth data across the dynamic dimension with a Gaussian kernel. — smooth_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/sort_basis.html b/docs/reference/sort_basis.html
index 6a676ea2..d25cc006 100644
--- a/docs/reference/sort_basis.html
+++ b/docs/reference/sort_basis.html
@@ -1,5 +1,5 @@
-Sort the basis-set elements alphabetically. — sort_basis • Spectroscopy Analysis Tools (spant) Sort the basis-set elements alphabetically. — sort_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/spant-package.html b/docs/reference/spant-package.html
index b3dd8e21..90f19ec3 100644
--- a/docs/reference/spant-package.html
+++ b/docs/reference/spant-package.html
@@ -1,5 +1,5 @@
-spant: spectroscopy analysis tools. — spant-package • Spectroscopy Analysis Tools (spant) spant: spectroscopy analysis tools. — spant-package • Spectroscopy Analysis Tools (spant) Simulate and fit some spectra with ABfit for benchmarking purposes. Basic
-timing and performance metrics will be printed. — spant_abfit_benchmark • Spectroscopy Analysis Tools (spant) Simulate and fit some spectra with ABfit for benchmarking purposes. Basic timing and performance metrics will be printed. — spant_abfit_benchmark • Spectroscopy Analysis Tools (spant) Example MEGA-PRESS data with significant B0 drift. — spant_mpress_drift • Spectroscopy Analysis Tools (spant) Example MEGA-PRESS data with significant B0 drift. — spant_mpress_drift • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -83,7 +83,7 @@ Example MEGA-PRESS data with significant B0 drift.
Format
- An object of class mrs_data of length 13.
+ An object of class mrs_data of dimension 1 x 1 x 1 x 1 x 40 x 1 x 1024.
@@ -98,7 +98,7 @@ Format
diff --git a/docs/reference/spant_sim_fmrs_dataset.html b/docs/reference/spant_sim_fmrs_dataset.html
new file mode 100644
index 00000000..00e48b56
--- /dev/null
+++ b/docs/reference/spant_sim_fmrs_dataset.html
@@ -0,0 +1,117 @@
+
+Simulate an example fMRS dataset for a block design fMRS experiment and export a BIDS structure. — spant_sim_fmrs_dataset • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Simulate an example fMRS dataset for a block design fMRS experiment and export a BIDS structure.
+ Source: R/fmrs.R
+ spant_sim_fmrs_dataset.Rd
+
+
+
+ Simulate an example fMRS dataset for a block design fMRS experiment and
+export a BIDS structure.
+
+
+
+ spant_sim_fmrs_dataset(output_dir = NULL)
+
+
+
+ Arguments
+ - output_dir
+output directory for the BIDS data. Defaults to :
+"HOME/sim_fmrs_dataset/data".
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/spant_simulation_benchmark.html b/docs/reference/spant_simulation_benchmark.html
index 32daa8bf..d8cc6841 100644
--- a/docs/reference/spant_simulation_benchmark.html
+++ b/docs/reference/spant_simulation_benchmark.html
@@ -1,7 +1,5 @@
-Simulate a typical metabolite basis set for benchmarking. Timing metrics will
-be printed on completion. — spant_simulation_benchmark • Spectroscopy Analysis Tools (spant) Simulate a typical metabolite basis set for benchmarking. Timing metrics will be printed on completion. — spant_simulation_benchmark • Spectroscopy Analysis Tools (spant) Decompose an mrs_data object into white and gray matter spectra. — spec_decomp • Spectroscopy Analysis Tools (spant) Perform a mathematical operation on a spectral region. — spec_op • Spectroscopy Analysis Tools (spant) Perform a mathematical operation on a spectral region. — spec_op • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -98,8 +98,8 @@ Arguments
operator
-can be "sum" (default), "mean", "l2", "max", "min" or
-"max-min".
can be "sum" (default), "mean", "l2", "max", "max_cplx,
+"min" or "max-min".
freq_scale
@@ -129,7 +129,7 @@ Value
diff --git a/docs/reference/spin_sys.html b/docs/reference/spin_sys.html
index 853423a4..1eaa9e76 100644
--- a/docs/reference/spin_sys.html
+++ b/docs/reference/spin_sys.html
@@ -1,5 +1,5 @@
-Create a spin system object for pulse sequence simulation. — spin_sys • Spectroscopy Analysis Tools (spant) Create a spin system object for pulse sequence simulation. — spin_sys • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/spm_pve2categorical.html b/docs/reference/spm_pve2categorical.html
index 23a1bad9..70f10729 100644
--- a/docs/reference/spm_pve2categorical.html
+++ b/docs/reference/spm_pve2categorical.html
@@ -1,7 +1,5 @@
-Convert SPM style segmentation files to a single categorical image where
-the numerical values map as: 0) Other, 1) CSF, 2) GM and 3) WM. — spm_pve2categorical • Spectroscopy Analysis Tools (spant) Convert SPM style segmentation files to a single categorical image where the numerical values map as: 0) Other, 1) CSF, 2) GM and 3) WM. — spm_pve2categorical • Spectroscopy Analysis Tools (spant) Signal space projection method for lipid suppression. — ssp • Spectroscopy Analysis Tools (spant) Signal space projection method for lipid suppression. — ssp • Spectroscopy Analysis Tools (spant) Plot the fitting results of an object of class fit_result with
-individual basis set components shown. — stackplot.fit_result • Spectroscopy Analysis Tools (spant) Plot the fitting results of an object of class fit_result with individual basis set components shown. — stackplot.fit_result • Spectroscopy Analysis Tools (spant) Produce a plot with multiple traces. — stackplot • Spectroscopy Analysis Tools (spant) Produce a plot with multiple traces. — stackplot • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/stackplot.mrs_data.html b/docs/reference/stackplot.mrs_data.html
index 17ff5648..64eea445 100644
--- a/docs/reference/stackplot.mrs_data.html
+++ b/docs/reference/stackplot.mrs_data.html
@@ -1,5 +1,5 @@
-Stackplot plotting method for objects of class mrs_data. — stackplot.mrs_data • Spectroscopy Analysis Tools (spant) Stackplot plotting method for objects of class mrs_data. — stackplot.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -255,7 +255,7 @@ Arguments
diff --git a/docs/reference/sub_first_dyn.html b/docs/reference/sub_first_dyn.html
index dbd7f831..493b7242 100644
--- a/docs/reference/sub_first_dyn.html
+++ b/docs/reference/sub_first_dyn.html
@@ -1,5 +1,5 @@
-Subtract the first dynamic spectrum from a dynamic series. — sub_first_dyn • Spectroscopy Analysis Tools (spant) Subtract the first dynamic spectrum from a dynamic series. — sub_first_dyn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/sub_mean_dyns.html b/docs/reference/sub_mean_dyns.html
index 6e3bb2df..221bd0c1 100644
--- a/docs/reference/sub_mean_dyns.html
+++ b/docs/reference/sub_mean_dyns.html
@@ -1,5 +1,5 @@
-Subtract the mean dynamic spectrum from a dynamic series. — sub_mean_dyns • Spectroscopy Analysis Tools (spant) Subtract the mean dynamic spectrum from a dynamic series. — sub_mean_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/sub_median_dyns.html b/docs/reference/sub_median_dyns.html
index 134c495d..1e834f14 100644
--- a/docs/reference/sub_median_dyns.html
+++ b/docs/reference/sub_median_dyns.html
@@ -1,5 +1,5 @@
-Subtract the median dynamic spectrum from a dynamic series. — sub_median_dyns • Spectroscopy Analysis Tools (spant) Subtract the median dynamic spectrum from a dynamic series. — sub_median_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/sum_coils.html b/docs/reference/sum_coils.html
index 7bf559f2..e1ab3cc0 100644
--- a/docs/reference/sum_coils.html
+++ b/docs/reference/sum_coils.html
@@ -1,5 +1,5 @@
-Calculate the sum across receiver coil elements. — sum_coils • Spectroscopy Analysis Tools (spant) Calculate the sum across receiver coil elements. — sum_coils • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/sum_dyns.html b/docs/reference/sum_dyns.html
index a0be19d3..bbda2ffc 100644
--- a/docs/reference/sum_dyns.html
+++ b/docs/reference/sum_dyns.html
@@ -1,5 +1,5 @@
-Calculate the sum of data dynamics. — sum_dyns • Spectroscopy Analysis Tools (spant) Calculate the sum of data dynamics. — sum_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/sum_mrs.html b/docs/reference/sum_mrs.html
index a22f215b..3cc3ab9e 100644
--- a/docs/reference/sum_mrs.html
+++ b/docs/reference/sum_mrs.html
@@ -1,5 +1,5 @@
-Sum two mrs_data objects. — sum_mrs • Spectroscopy Analysis Tools (spant) Sum two mrs_data objects. — sum_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Value
diff --git a/docs/reference/sum_mrs_list.html b/docs/reference/sum_mrs_list.html
index f4e09aea..c3584348 100644
--- a/docs/reference/sum_mrs_list.html
+++ b/docs/reference/sum_mrs_list.html
@@ -1,5 +1,5 @@
-Return the sum of a list of mrs_data objects. — sum_mrs_list • Spectroscopy Analysis Tools (spant) Return the sum of a list of mrs_data objects. — sum_mrs_list • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/svs_1h_brain_analysis.html b/docs/reference/svs_1h_brain_analysis.html
index 8ce514db..dff0ef7d 100644
--- a/docs/reference/svs_1h_brain_analysis.html
+++ b/docs/reference/svs_1h_brain_analysis.html
@@ -1,5 +1,5 @@
-Standard SVS 1H brain analysis pipeline. — svs_1h_brain_analysis • Spectroscopy Analysis Tools (spant) Standard SVS 1H brain analysis pipeline. — svs_1h_brain_analysis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -199,7 +199,7 @@ Value
diff --git a/docs/reference/svs_1h_brain_analysis_dev.html b/docs/reference/svs_1h_brain_analysis_dev.html
index d70a14d3..d71bfea2 100644
--- a/docs/reference/svs_1h_brain_analysis_dev.html
+++ b/docs/reference/svs_1h_brain_analysis_dev.html
@@ -1,5 +1,5 @@
-Standard SVS 1H brain analysis pipeline. — svs_1h_brain_analysis_dev • Spectroscopy Analysis Tools (spant) Standard SVS 1H brain analysis pipeline. — svs_1h_brain_analysis_dev • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -193,7 +193,7 @@ Examples
diff --git a/docs/reference/svs_1h_brain_batch_analysis.html b/docs/reference/svs_1h_brain_batch_analysis.html
index 5631e8cc..15f7223e 100644
--- a/docs/reference/svs_1h_brain_batch_analysis.html
+++ b/docs/reference/svs_1h_brain_batch_analysis.html
@@ -1,5 +1,5 @@
-Batch interface to the standard SVS 1H brain analysis pipeline. — svs_1h_brain_batch_analysis • Spectroscopy Analysis Tools (spant) Batch interface to the standard SVS 1H brain analysis pipeline. — svs_1h_brain_batch_analysis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -144,7 +144,7 @@ Value
diff --git a/docs/reference/t_test_spec.html b/docs/reference/t_test_spec.html
new file mode 100644
index 00000000..56a7ea1b
--- /dev/null
+++ b/docs/reference/t_test_spec.html
@@ -0,0 +1,124 @@
+
+Perform a t-test on spectral data points. — t_test_spec • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+
+
+ Perform a t-test on spectral data points.
+
+
+
+ t_test_spec(mrs_data, group)
+
+
+
+ Arguments
+ - mrs_data
+an mrs_data object with spectra in the dynamic dimension.
- group
+vector describing the group membership of each dynamic spectrum.
+
+ Value
+
+
+a list of statistical results.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/td2fd.html b/docs/reference/td2fd.html
index 6748a6a8..f31ed524 100644
--- a/docs/reference/td2fd.html
+++ b/docs/reference/td2fd.html
@@ -1,5 +1,5 @@
-Transform time-domain data to the frequency-domain. — td2fd • Spectroscopy Analysis Tools (spant) Transform time-domain data to the frequency-domain. — td2fd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/td_conv_filt.html b/docs/reference/td_conv_filt.html
index a9f340c3..106b9b00 100644
--- a/docs/reference/td_conv_filt.html
+++ b/docs/reference/td_conv_filt.html
@@ -1,5 +1,5 @@
-Time-domain convolution based filter. — td_conv_filt • Spectroscopy Analysis Tools (spant) Time-domain convolution based filter. — td_conv_filt • Spectroscopy Analysis Tools (spant) Time-domain spectral registration. — tdsr • Spectroscopy Analysis Tools (spant) Time-domain spectral registration. — tdsr • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -121,7 +121,7 @@ Value
diff --git a/docs/reference/te.html b/docs/reference/te.html
index 010361b1..4a65711d 100644
--- a/docs/reference/te.html
+++ b/docs/reference/te.html
@@ -1,5 +1,5 @@
-Return the echo time of an MRS dataset. — te • Spectroscopy Analysis Tools (spant) Return the echo time of an MRS dataset. — te • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/tr.html b/docs/reference/tr.html
index 0c0bd63b..2e749e02 100644
--- a/docs/reference/tr.html
+++ b/docs/reference/tr.html
@@ -1,5 +1,5 @@
-Return the repetition time of an MRS dataset. — tr • Spectroscopy Analysis Tools (spant) Return the repetition time of an MRS dataset. — tr • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/varpro_3_para_opts.html b/docs/reference/varpro_3_para_opts.html
index c2270a16..52d7cd84 100644
--- a/docs/reference/varpro_3_para_opts.html
+++ b/docs/reference/varpro_3_para_opts.html
@@ -1,5 +1,5 @@
-Return a list of options for VARPRO based fitting with 3 free parameters. — varpro_3_para_opts • Spectroscopy Analysis Tools (spant) Return a list of options for VARPRO based fitting with 3 free parameters. — varpro_3_para_opts • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -141,7 +141,7 @@ Value
diff --git a/docs/reference/varpro_basic_opts.html b/docs/reference/varpro_basic_opts.html
index 32c86d22..c5104891 100644
--- a/docs/reference/varpro_basic_opts.html
+++ b/docs/reference/varpro_basic_opts.html
@@ -1,5 +1,5 @@
-Return a list of options for a basic VARPRO analysis. — varpro_basic_opts • Spectroscopy Analysis Tools (spant) Return a list of options for a basic VARPRO analysis. — varpro_basic_opts • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -118,7 +118,7 @@ Value
diff --git a/docs/reference/varpro_opts.html b/docs/reference/varpro_opts.html
index 2aabf11d..6332f730 100644
--- a/docs/reference/varpro_opts.html
+++ b/docs/reference/varpro_opts.html
@@ -1,5 +1,5 @@
-Return a list of options for VARPRO based fitting. — varpro_opts • Spectroscopy Analysis Tools (spant) Return a list of options for VARPRO based fitting. — varpro_opts • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -177,7 +177,7 @@ Examples
diff --git a/docs/reference/vec2mrs_data.html b/docs/reference/vec2mrs_data.html
index 0cccd73b..f0d58bf0 100644
--- a/docs/reference/vec2mrs_data.html
+++ b/docs/reference/vec2mrs_data.html
@@ -1,5 +1,5 @@
-Convert a vector into a mrs_data object. — vec2mrs_data • Spectroscopy Analysis Tools (spant) Convert a vector into a mrs_data object. — vec2mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -80,10 +80,11 @@ Convert a vector into a mrs_data object.
vec2mrs_data(
vec,
- fs = def_fs(),
- ft = def_ft(),
- ref = def_ref(),
- nuc = def_nuc(),
+ mrs_data = NULL,
+ fs = NULL,
+ ft = NULL,
+ ref = NULL,
+ nuc = NULL,
dyns = 1,
fd = FALSE
)
@@ -95,6 +96,10 @@ Arguments
the data vector.
mrs_data
+example data to copy acquisition parameters from.
fs
sampling frequency in Hz.
Arguments
fd
-flag to indicate if the matrix is in the frequency domain (logical).
flag to indicate if the vector is in the frequency domain (logical).
Value
diff --git a/docs/reference/write_basis.html b/docs/reference/write_basis.html
index b6e27cbd..94c5e021 100644
--- a/docs/reference/write_basis.html
+++ b/docs/reference/write_basis.html
@@ -1,5 +1,5 @@
-Write a basis object to an LCModel .basis formatted file. — write_basis • Spectroscopy Analysis Tools (spant) Write a basis object to an LCModel .basis formatted file. — write_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -108,7 +108,7 @@ Arguments
diff --git a/docs/reference/write_basis_tqn.html b/docs/reference/write_basis_tqn.html
index 6aa51c1d..116c73ec 100644
--- a/docs/reference/write_basis_tqn.html
+++ b/docs/reference/write_basis_tqn.html
@@ -1,5 +1,5 @@
-Generate a basis file using TARQUIN. — write_basis_tqn • Spectroscopy Analysis Tools (spant) Generate a basis file using TARQUIN. — write_basis_tqn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Examples
diff --git a/docs/reference/write_mrs.html b/docs/reference/write_mrs.html
index fff25f15..124b9dc4 100644
--- a/docs/reference/write_mrs.html
+++ b/docs/reference/write_mrs.html
@@ -1,5 +1,5 @@
-Write MRS data object to file. — write_mrs • Spectroscopy Analysis Tools (spant) Write MRS data object to file. — write_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Arguments
diff --git a/docs/reference/write_mrs_nifti.html b/docs/reference/write_mrs_nifti.html
index f4bf1921..bd3ed4b7 100644
--- a/docs/reference/write_mrs_nifti.html
+++ b/docs/reference/write_mrs_nifti.html
@@ -1,5 +1,5 @@
-Write MRS data object to file in NIFTI format. — write_mrs_nifti • Spectroscopy Analysis Tools (spant) Write MRS data object to file in NIFTI format. — write_mrs_nifti • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/write_pulse_ascii.html b/docs/reference/write_pulse_ascii.html
index 067ae086..221f8ebb 100644
--- a/docs/reference/write_pulse_ascii.html
+++ b/docs/reference/write_pulse_ascii.html
@@ -1,5 +1,5 @@
-Write an ASCII formatted pulse file. — write_pulse_ascii • Spectroscopy Analysis Tools (spant) Write an ASCII formatted pulse file. — write_pulse_ascii • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/zero_fade_spec.html b/docs/reference/zero_fade_spec.html
index c703745c..c8b572c3 100644
--- a/docs/reference/zero_fade_spec.html
+++ b/docs/reference/zero_fade_spec.html
@@ -1,7 +1,5 @@
-Fade a spectrum to zero by frequency domain multiplication with a tanh
-function. Note this operation distorts data points at the end of the FID. — zero_fade_spec • Spectroscopy Analysis Tools (spant) Fade a spectrum to zero by frequency domain multiplication with a tanh function. Note this operation distorts data points at the end of the FID. — zero_fade_spec • Spectroscopy Analysis Tools (spant) Zero all coherences including and above a given order. — zero_higher_orders • Spectroscopy Analysis Tools (spant) Zero all coherences including and above a given order. — zero_higher_orders • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Value
diff --git a/docs/reference/zero_td_pts_end.html b/docs/reference/zero_td_pts_end.html
index 8c1123c8..71d24ebb 100644
--- a/docs/reference/zero_td_pts_end.html
+++ b/docs/reference/zero_td_pts_end.html
@@ -1,5 +1,5 @@
-Set mrs_data object data points at the end of the FID to zero. — zero_td_pts_end • Spectroscopy Analysis Tools (spant) Set mrs_data object data points at the end of the FID to zero. — zero_td_pts_end • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/zf.html b/docs/reference/zf.html
index 85e2013c..baf50256 100644
--- a/docs/reference/zf.html
+++ b/docs/reference/zf.html
@@ -1,5 +1,5 @@
-Zero-fill MRS data in the time domain. — zf • Spectroscopy Analysis Tools (spant) Zero-fill MRS data in the time domain. — zf • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -125,7 +125,7 @@ Value
diff --git a/docs/reference/zf_xy.html b/docs/reference/zf_xy.html
index ebca3999..c4104a74 100644
--- a/docs/reference/zf_xy.html
+++ b/docs/reference/zf_xy.html
@@ -1,5 +1,5 @@
-Zero-fill MRSI data in the k-space x-y direction. — zf_xy • Spectroscopy Analysis Tools (spant) Zero-fill MRSI data in the k-space x-y direction. — zf_xy • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -113,7 +113,7 @@ Value
diff --git a/docs/sitemap.xml b/docs/sitemap.xml
index e2139f71..4c39f515 100644
--- a/docs/sitemap.xml
+++ b/docs/sitemap.xml
@@ -216,6 +216,12 @@
https://martin3141.github.io/spant/reference/comb_coils_fp_pc.html
+
+ https://martin3141.github.io/spant/reference/comb_coils_mrsi_gls.html
+
+
+ https://martin3141.github.io/spant/reference/comb_coils_svs_gls.html
+
https://martin3141.github.io/spant/reference/comb_csv_results.html
@@ -411,6 +417,9 @@
https://martin3141.github.io/spant/reference/gen_conv_reg.html
+
+ https://martin3141.github.io/spant/reference/gen_group_reg.html
+
https://martin3141.github.io/spant/reference/gen_impulse_reg.html
@@ -555,6 +564,15 @@
https://martin3141.github.io/spant/reference/glm_spec.html
+
+ https://martin3141.github.io/spant/reference/glm_spec_fmrs_fl.html
+
+
+ https://martin3141.github.io/spant/reference/glm_spec_fmrs_group.html
+
+
+ https://martin3141.github.io/spant/reference/glm_spec_group_linhyp.html
+
https://martin3141.github.io/spant/reference/grid_shift_xy.html
@@ -690,9 +708,15 @@
https://martin3141.github.io/spant/reference/mrs_data2basis.html
+
+ https://martin3141.github.io/spant/reference/mrs_data2bids.html
+
https://martin3141.github.io/spant/reference/mrs_data2mat.html
+
+ https://martin3141.github.io/spant/reference/mrs_data2spec_mat.html
+
https://martin3141.github.io/spant/reference/mrs_data2vec.html
@@ -741,6 +765,9 @@
https://martin3141.github.io/spant/reference/phase.html
+
+ https://martin3141.github.io/spant/reference/phase_ref_1h_brain.html
+
https://martin3141.github.io/spant/reference/plot.fit_result.html
@@ -780,6 +807,12 @@
https://martin3141.github.io/spant/reference/precomp.html
+
+ https://martin3141.github.io/spant/reference/preproc_svs.html
+
+
+ https://martin3141.github.io/spant/reference/preproc_svs_dataset.html
+
https://martin3141.github.io/spant/reference/print.fit_result.html
@@ -1050,6 +1083,9 @@
https://martin3141.github.io/spant/reference/spant_mpress_drift.html
+
+ https://martin3141.github.io/spant/reference/spant_sim_fmrs_dataset.html
+
https://martin3141.github.io/spant/reference/spant_simulation_benchmark.html
@@ -1107,6 +1143,9 @@
https://martin3141.github.io/spant/reference/svs_1h_brain_batch_analysis.html
+
+ https://martin3141.github.io/spant/reference/t_test_spec.html
+
https://martin3141.github.io/spant/reference/td2fd.html
Covert a beta value in the time-domain to an equivalent linewidth in Hz: -x * exp(-i * t * t * beta).
Covert a beta value in the time-domain to an equivalent linewidth in Hz: x * exp(-i * t * t * beta).
All functions
- Perform a polynomial fit, subtract and return the standard deviation of the
-residuals.
Perform a polynomial fit, subtract and return the standard deviation of the residuals.
@@ -306,6 +295,14 @@ All functions comb_coils()
Combine coil data based on the first data point of a reference signal.
+
+
+ Combine MRSI coil data using the GLS method presented by An et al JMRI 37:1445-1450 (2013).
+
+
+ Combine SVS coil data using the GLS method presented by An et al JMRI 37:1445-1450 (2013).
@@ -345,9 +342,7 @@ All functions
- Crop mrs_data object data points in the time-domain rounding down to
-the next smallest power of two (pot). Data that already has a pot length will
-not be changed.
Crop mrs_data object data points in the time-domain rounding down to the next smallest power of two (pot). Data that already has a pot length will not be changed.
@@ -355,13 +350,11 @@ All functions
- Compute the vector cross product between vectors x and y. Adapted from
-http://stackoverflow.com/questions/15162741/what-is-rs-crossproduct-function
Compute the vector cross product between vectors x and y. Adapted from http://stackoverflow.com/questions/15162741/what-is-rs-crossproduct-function
- Decimate an MRS signal to half the original sampling frequency by filtering
-in the frequency domain before down sampling.
Decimate an MRS signal to half the original sampling frequency by filtering in the frequency domain before down sampling.
@@ -377,8 +370,7 @@ All functions
- Return (and optionally modify using the input arguments) a list of the
-default acquisition parameters.
Return (and optionally modify using the input arguments) a list of the default acquisition parameters.
@@ -410,14 +402,11 @@ All functions
- Downsample an MRS signal by a factor of 2 by removing every other data point
-in the time-domain. Note, signals outside the new sampling frequency will be
-aliased.
Downsample an MRS signal by a factor of 2 by removing every other data point in the time-domain. Note, signals outside the new sampling frequency will be aliased.
- Return a time scale vector of acquisition times for a dynamic MRS scan. The
-first temporal scan is assigned a value of 0.
Return a time scale vector of acquisition times for a dynamic MRS scan. The first temporal scan is assigned a value of 0.
@@ -429,8 +418,7 @@ All functions
- Estimate the standard deviation of the noise from a segment of an mrs_data
-object.
Estimate the standard deviation of the noise from a segment of an mrs_data object.
@@ -486,8 +474,7 @@ All functions
- Perform a zeroth order phase correction based on the phase of the first data
-point in the time-domain.
Perform a zeroth order phase correction based on the phase of the first data point in the time-domain.
@@ -507,8 +494,7 @@ All functions
- Perform a fft and fftshift on a matrix with each column replaced by its
-shifted fft.
Perform a fft and fftshift on a matrix with each column replaced by its shifted fft.
@@ -536,8 +522,11 @@ All functions
- Generate regressors by convolving a specified response function with a
-stimulus.
Generate regressors by convolving a specified response function with a stimulus.
+
+
+ Expand a regressor matrix for a group analysis.
@@ -553,28 +542,23 @@ All functions
- Return a character vector of common 1H molecules found in healthy human
-brain.
Return a character vector of common 1H molecules found in healthy human brain.
- Return a list of mol_parameter objects suitable for 1H brain MRS
-analyses.
Return a list of mol_parameter objects suitable for 1H brain MRS analyses.
- Return a list of mol_parameter objects suitable for 1H brain MRS
-analyses.
Return a list of mol_parameter objects suitable for 1H brain MRS analyses.
- Return a list of mol_parameter objects suitable for 1H brain MRS
-analyses.
Return a list of mol_parameter objects suitable for 1H brain MRS analyses.
- Return a list of mol_parameter objects suitable for 1H brain MRS
-analyses.
Return a list of mol_parameter objects suitable for 1H brain MRS analyses.
@@ -582,8 +566,7 @@ All functions
- Return a character vector of molecules included in the Gold Star Phantoms
-SPECTRE phantom.
Return a character vector of molecules included in the Gold Star Phantoms SPECTRE phantom.
@@ -635,8 +618,7 @@ All functions
- Return a character array of names that may be used with the
-get_mol_paras function.
Return a character array of names that may be used with the get_mol_paras function.
@@ -700,8 +682,7 @@ All functions
- Return an array of amplitudes derived from fitting the initial points in the
-time domain and extrapolating back to t=0.
Return an array of amplitudes derived from fitting the initial points in the time domain and extrapolating back to t=0.
@@ -709,8 +690,7 @@ All functions
- Generate a mol_parameters object for a simple spin system with one
-resonance.
Generate a mol_parameters object for a simple spin system with one resonance.
@@ -731,6 +711,18 @@ All functions glm_spec()
Perform a GLM analysis of dynamic MRS data in the spectral domain.
+
+
+ Perform first-level spectral GLM analysis of an fMRS dataset.
+
+
+ Perform group-level spectral GLM analysis of an fMRS dataset.
+
+
+ Test a group-level spectral GLM linear hypothesis.
@@ -766,8 +758,7 @@ All functions
- Perform an ifft and ifftshift on a matrix with each column replaced by its
-shifted ifft.
Perform an ifft and ifftshift on a matrix with each column replaced by its shifted ifft.
@@ -799,8 +790,7 @@ All functions
- Check if the chemical shift dimension of an MRS data object is in the
-frequency domain.
Check if the chemical shift dimension of an MRS data object is in the frequency domain.
@@ -820,18 +810,15 @@ All functions
- Covert a linewidth in Hz to an equivalent alpha value in the time-domain ie:
-x * exp(-t * alpha).
Covert a linewidth in Hz to an equivalent alpha value in the time-domain ie: x * exp(-t * alpha).
- Covert a linewidth in Hz to an equivalent beta value in the time-domain ie:
-x * exp(-t * t * beta).
Covert a linewidth in Hz to an equivalent beta value in the time-domain ie: x * exp(-t * t * beta).
- Make a basis-set object from a directory containing LCModel formatted RAW
-files.
Make a basis-set object from a directory containing LCModel formatted RAW files.
@@ -851,8 +838,7 @@ All functions
- Mask the voxels outside an elliptical region spanning the MRSI dataset in the
-x-y plane.
Mask the voxels outside an elliptical region spanning the MRSI dataset in the x-y plane.
@@ -860,13 +846,11 @@ All functions
- Convert a matrix (with spectral points in the column dimension and dynamics
-in the row dimensions) into a mrs_data object.
Convert a matrix (with spectral points in the column dimension and dynamics in the row dimensions) into a mrs_data object.
- Matrix exponential function taken from complexplus package to reduce the
-number of spant dependencies.
Matrix exponential function taken from complexplus package to reduce the number of spant dependencies.
@@ -914,31 +898,31 @@ All functions
- Convert an mrs_data object to basis object - where basis signals are spread
-across the dynamic dimension in the MRS data.
Convert an mrs_data object to basis object - where basis signals are spread across the dynamic dimension in the MRS data.
+
+
+ Create a BIDS file structure from a vector of MRS data paths or list of mrs_data objects.
- Convert mrs_data object to a matrix, with spectral points in the column
-dimension and dynamics in the row dimension.
Convert mrs_data object to a matrix, with spectral points in the column dimension and dynamics in the row dimension.
-
+
- Convert mrs_data object to a vector.
Convert mrs_data object to a matrix, with spectral points in the column dimension and dynamics in the row dimension.
-
+
- Create a BIDS directory and file structure from a list of mrs_data objects.
Convert mrs_data object to a vector.
- Perform a fftshift on a matrix, with each column replaced by its shifted
-result.
Perform a fftshift on a matrix, with each column replaced by its shifted result.
- Perform an ifftshift on a matrix, with each column replaced by its shifted
-result.
Perform an ifftshift on a matrix, with each column replaced by its shifted result.
@@ -946,9 +930,7 @@ All functions
- Flip the x data dimension order of a nifti image. This corresponds to
-flipping MRI data in the left-right direction, assuming the data in save in
-neurological format (can check with fslorient program).
Flip the x data dimension order of a nifti image. This corresponds to flipping MRI data in the left-right direction, assuming the data in save in neurological format (can check with fslorient program).
@@ -964,8 +946,7 @@ All functions
- Search for the highest peak in a spectral region and return the frequency,
-height and FWHM.
Search for the highest peak in a spectral region and return the frequency, height and FWHM.
@@ -974,6 +955,10 @@ All functions phase()
Apply phasing parameters to MRS data.
+
+
+ Corrected zero order phase and chemical shift offset in 1H MRS data from the brain.
@@ -1005,8 +990,7 @@ All functions
- Plot an interactive slice map from a data array where voxels can be selected
-to display a corresponding spectrum.
Plot an interactive slice map from a data array where voxels can be selected to display a corresponding spectrum.
@@ -1026,8 +1010,15 @@ All functions
- Save function results to file and load on subsequent calls to avoid repeat
-computation.
Save function results to file and load on subsequent calls to avoid repeat computation.
+
+
+ Preprocess and perform quality assessment of a single SVS data set.
+
+
+ Preprocess and perform quality assessment of one or more SVS data sets.
@@ -1055,15 +1046,11 @@ All functions
- Read a directory containing Siemens MRS IMA files and combine along the coil
-dimension. Note that the coil ID is inferred from the sorted file name and
-should be checked when consistency is required between two directories.
Read a directory containing Siemens MRS IMA files and combine along the coil dimension. Note that the coil ID is inferred from the sorted file name and should be checked when consistency is required between two directories.
- Read a directory containing Siemens MRS IMA files and combine along the
-dynamic dimension. Note that the coil ID is inferred from the sorted file
-name and should be checked when consistency is required.
Read a directory containing Siemens MRS IMA files and combine along the dynamic dimension. Note that the coil ID is inferred from the sorted file name and should be checked when consistency is required.
@@ -1103,13 +1090,11 @@ All functions
- Reconstruct complex time-domain data from the real part of frequency-domain
-data.
Reconstruct complex time-domain data from the real part of frequency-domain data.
- Reconstruct complex time-domain data from the real part of frequency-domain
-data.
Reconstruct complex time-domain data from the real part of frequency-domain data.
@@ -1141,8 +1126,7 @@ All functions
- Resample a VOI to match a target image space using nearest-neighbour
-interpolation.
Resample a VOI to match a target image space using nearest-neighbour interpolation.
@@ -1158,23 +1142,19 @@ All functions
- Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water).
Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / kg of tissue water).
- Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water).
Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / kg of tissue water).
- Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / Litre of tissue).
Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / Litre of tissue).
- Convert default LCM/TARQUIN concentration scaling to molal units with partial
-volume correction.
Convert default LCM/TARQUIN concentration scaling to molal units with partial volume correction.
@@ -1222,8 +1202,7 @@ All functions
- MEGA-PRESS sequence with ideal localisation pulses and Gaussian shaped
-editing pulse.
MEGA-PRESS sequence with ideal localisation pulses and Gaussian shaped editing pulse.
@@ -1251,13 +1230,11 @@ All functions
- STEAM sequence with ideal pulses and coherence order filtering to simulate
-gradient crushers.
STEAM sequence with ideal pulses and coherence order filtering to simulate gradient crushers.
- STEAM sequence with ideal pulses using the z-rotation gradient simulation
-method described by Young et al JMR 140, 146-152 (1999).
STEAM sequence with ideal pulses using the z-rotation gradient simulation method described by Young et al JMR 140, 146-152 (1999).
@@ -1293,8 +1270,7 @@ All functions
- Set the number of time-domain data points, truncating or zero-filling as
-appropriate.
Set the number of time-domain data points, truncating or zero-filling as appropriate.
@@ -1318,18 +1294,15 @@ All functions
- Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS
-sequence. Note, ideal pulses are assumed.
Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS sequence. Note, ideal pulses are assumed.
- Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS
-sequence. Note, ideal pulses are assumed.
Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS sequence. Note, ideal pulses are assumed.
- Simulate a macromolecular and lipid basis-set suitable for 1H brain MRS
-analysis.
Simulate a macromolecular and lipid basis-set suitable for 1H brain MRS analysis.
@@ -1353,8 +1326,7 @@ All functions
- Simulate an ideal pulse excitation profile by smoothing a top-hat function
-with a Gaussian.
Simulate an ideal pulse excitation profile by smoothing a top-hat function with a Gaussian.
@@ -1374,17 +1346,19 @@ All functions
- Simulate and fit some spectra with ABfit for benchmarking purposes. Basic
-timing and performance metrics will be printed.
Simulate and fit some spectra with ABfit for benchmarking purposes. Basic timing and performance metrics will be printed.
Example MEGA-PRESS data with significant B0 drift.
+
+
+ Simulate an example fMRS dataset for a block design fMRS experiment and export a BIDS structure.
- Simulate a typical metabolite basis set for benchmarking. Timing metrics will
-be printed on completion.
Simulate a typical metabolite basis set for benchmarking. Timing metrics will be printed on completion.
@@ -1400,8 +1374,7 @@ All functions
- Convert SPM style segmentation files to a single categorical image where
-the numerical values map as: 0) Other, 1) CSF, 2) GM and 3) WM.
Convert SPM style segmentation files to a single categorical image where the numerical values map as: 0) Other, 1) CSF, 2) GM and 3) WM.
@@ -1413,8 +1386,7 @@ All functions
- Plot the fitting results of an object of class fit_result with
-individual basis set components shown.
Plot the fitting results of an object of class fit_result with individual basis set components shown.
@@ -1459,6 +1431,10 @@ All functions svs_1h_brain_batch_analysis()
Batch interface to the standard SVS 1H brain analysis pipeline.
+
+
+ Perform a t-test on spectral data points.
@@ -1518,8 +1494,7 @@ All functions
- Fade a spectrum to zero by frequency domain multiplication with a tanh
-function. Note this operation distorts data points at the end of the FID.
Fade a spectrum to zero by frequency domain multiplication with a tanh function. Note this operation distorts data points at the end of the FID.
@@ -1549,7 +1524,7 @@ All functions
diff --git a/docs/reference/int_spec.html b/docs/reference/int_spec.html
index c7060fe7..783325a8 100644
--- a/docs/reference/int_spec.html
+++ b/docs/reference/int_spec.html
@@ -1,5 +1,5 @@
-Integrate a spectral region. — int_spec • Spectroscopy Analysis Tools (spant) Integrate a spectral region. — int_spec • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -118,7 +118,7 @@ Value
diff --git a/docs/reference/interleave_dyns.html b/docs/reference/interleave_dyns.html
index effe5543..441eff27 100644
--- a/docs/reference/interleave_dyns.html
+++ b/docs/reference/interleave_dyns.html
@@ -1,5 +1,5 @@
-Interleave the first and second half of a dynamic series. — interleave_dyns • Spectroscopy Analysis Tools (spant) Interleave the first and second half of a dynamic series. — interleave_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/inv_even_dyns.html b/docs/reference/inv_even_dyns.html
index 9f9d4fff..dcb781dc 100644
--- a/docs/reference/inv_even_dyns.html
+++ b/docs/reference/inv_even_dyns.html
@@ -1,5 +1,5 @@
-Invert even numbered dynamic scans starting from 1 (2,4,6...). — inv_even_dyns • Spectroscopy Analysis Tools (spant) Invert even numbered dynamic scans starting from 1 (2,4,6...). — inv_even_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/inv_odd_dyns.html b/docs/reference/inv_odd_dyns.html
index 26212e2b..78d64660 100644
--- a/docs/reference/inv_odd_dyns.html
+++ b/docs/reference/inv_odd_dyns.html
@@ -1,5 +1,5 @@
-Invert odd numbered dynamic scans starting from 1 (1,3,5...). — inv_odd_dyns • Spectroscopy Analysis Tools (spant) Invert odd numbered dynamic scans starting from 1 (1,3,5...). — inv_odd_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/is.def.html b/docs/reference/is.def.html
index f196ffd0..a67b9eba 100644
--- a/docs/reference/is.def.html
+++ b/docs/reference/is.def.html
@@ -1,5 +1,5 @@
-Check if an object is defined, which is the same as being not NULL. — is.def • Spectroscopy Analysis Tools (spant) Check if an object is defined, which is the same as being not NULL. — is.def • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/is_fd.html b/docs/reference/is_fd.html
index 3b0ca165..18a193aa 100644
--- a/docs/reference/is_fd.html
+++ b/docs/reference/is_fd.html
@@ -1,7 +1,5 @@
-Check if the chemical shift dimension of an MRS data object is in the
-frequency domain. — is_fd • Spectroscopy Analysis Tools (spant) Check if the chemical shift dimension of an MRS data object is in the frequency domain. — is_fd • Spectroscopy Analysis Tools (spant) Transform 2D MRSI data from k-space to image space in the x-y direction. — kspace2img_xy • Spectroscopy Analysis Tools (spant) Transform 2D MRSI data from k-space to image space in the x-y direction. — kspace2img_xy • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/l2_reg.html b/docs/reference/l2_reg.html
index 3d781d80..21aa9849 100644
--- a/docs/reference/l2_reg.html
+++ b/docs/reference/l2_reg.html
@@ -1,5 +1,5 @@
-Perform l2 regularisation artefact suppression. — l2_reg • Spectroscopy Analysis Tools (spant) Perform l2 regularisation artefact suppression. — l2_reg • Spectroscopy Analysis Tools (spant) Apply line-broadening (apodisation) to MRS data or basis object. — lb • Spectroscopy Analysis Tools (spant) Apply line-broadening (apodisation) to MRS data or basis object. — lb • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -123,7 +123,7 @@ Value
diff --git a/docs/reference/lofdc.html b/docs/reference/lofdc.html
index 5419b1ec..31347a25 100644
--- a/docs/reference/lofdc.html
+++ b/docs/reference/lofdc.html
@@ -1,5 +1,5 @@
-Correct linear frequency drift. — lofdc • Spectroscopy Analysis Tools (spant) Correct linear frequency drift. — lofdc • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -138,7 +138,7 @@ Value
diff --git a/docs/reference/lw2alpha.html b/docs/reference/lw2alpha.html
index b83db682..25da229b 100644
--- a/docs/reference/lw2alpha.html
+++ b/docs/reference/lw2alpha.html
@@ -1,7 +1,5 @@
-Covert a linewidth in Hz to an equivalent alpha value in the time-domain ie:
-x * exp(-t * alpha). — lw2alpha • Spectroscopy Analysis Tools (spant) Covert a linewidth in Hz to an equivalent alpha value in the time-domain ie: x * exp(-t * alpha). — lw2alpha • Spectroscopy Analysis Tools (spant) Covert a linewidth in Hz to an equivalent beta value in the time-domain ie:
-x * exp(-t * t * beta). — lw2beta • Spectroscopy Analysis Tools (spant) Covert a linewidth in Hz to an equivalent beta value in the time-domain ie: x * exp(-t * t * beta). — lw2beta • Spectroscopy Analysis Tools (spant) Make a basis-set object from a directory containing LCModel formatted RAW
-files. — make_basis_from_raw • Spectroscopy Analysis Tools (spant) Make a basis-set object from a directory containing LCModel formatted RAW files. — make_basis_from_raw • Spectroscopy Analysis Tools (spant) Mask an MRS dataset in the dynamic dimension. — mask_dyns • Spectroscopy Analysis Tools (spant) Mask an MRS dataset in the dynamic dimension. — mask_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/mask_fit_res.html b/docs/reference/mask_fit_res.html
index 97baaa3f..ebd91a99 100644
--- a/docs/reference/mask_fit_res.html
+++ b/docs/reference/mask_fit_res.html
@@ -1,5 +1,5 @@
-Mask fit result spectra depending on a vector of bool values. — mask_fit_res • Spectroscopy Analysis Tools (spant) Mask fit result spectra depending on a vector of bool values. — mask_fit_res • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -116,7 +116,7 @@ Value
diff --git a/docs/reference/mask_xy.html b/docs/reference/mask_xy.html
index 11bb577c..b0d38619 100644
--- a/docs/reference/mask_xy.html
+++ b/docs/reference/mask_xy.html
@@ -1,5 +1,5 @@
-Mask an MRSI dataset in the x-y direction — mask_xy • Spectroscopy Analysis Tools (spant) Mask an MRSI dataset in the x-y direction — mask_xy • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/mask_xy_corners.html b/docs/reference/mask_xy_corners.html
index 09b16cd2..2d13839d 100644
--- a/docs/reference/mask_xy_corners.html
+++ b/docs/reference/mask_xy_corners.html
@@ -1,5 +1,5 @@
-Mask the four corners of an MRSI dataset in the x-y plane. — mask_xy_corners • Spectroscopy Analysis Tools (spant) Mask the four corners of an MRSI dataset in the x-y plane. — mask_xy_corners • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/mask_xy_ellipse.html b/docs/reference/mask_xy_ellipse.html
index 1d8b02e4..e2e749ef 100644
--- a/docs/reference/mask_xy_ellipse.html
+++ b/docs/reference/mask_xy_ellipse.html
@@ -1,7 +1,5 @@
-Mask the voxels outside an elliptical region spanning the MRSI dataset in the
-x-y plane. — mask_xy_ellipse • Spectroscopy Analysis Tools (spant) Mask the voxels outside an elliptical region spanning the MRSI dataset in the x-y plane. — mask_xy_ellipse • Spectroscopy Analysis Tools (spant) Mask a 2D MRSI dataset in the x-y dimension. — mask_xy_mat • Spectroscopy Analysis Tools (spant) Mask a 2D MRSI dataset in the x-y dimension. — mask_xy_mat • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Value
diff --git a/docs/reference/mat2mrs_data.html b/docs/reference/mat2mrs_data.html
index 2e2895f3..ae55665f 100644
--- a/docs/reference/mat2mrs_data.html
+++ b/docs/reference/mat2mrs_data.html
@@ -1,7 +1,5 @@
-Convert a matrix (with spectral points in the column dimension and dynamics
-in the row dimensions) into a mrs_data object. — mat2mrs_data • Spectroscopy Analysis Tools (spant) Convert a matrix (with spectral points in the column dimension and dynamics in the row dimensions) into a mrs_data object. — mat2mrs_data • Spectroscopy Analysis Tools (spant) Matrix exponential function taken from complexplus package to reduce the
-number of spant dependencies. — matexp • Spectroscopy Analysis Tools (spant) Matrix exponential function taken from complexplus package to reduce the number of spant dependencies. — matexp • Spectroscopy Analysis Tools (spant) Apply the max operator to an MRS dataset. — max_mrs • Spectroscopy Analysis Tools (spant) Apply the max operator to an MRS dataset. — max_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/max_mrs_interp.html b/docs/reference/max_mrs_interp.html
index e4474764..52e63f3e 100644
--- a/docs/reference/max_mrs_interp.html
+++ b/docs/reference/max_mrs_interp.html
@@ -1,5 +1,5 @@
-Apply the max operator to an interpolated MRS dataset. — max_mrs_interp • Spectroscopy Analysis Tools (spant) Apply the max operator to an interpolated MRS dataset. — max_mrs_interp • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/mean.list.html b/docs/reference/mean.list.html
index b8eb3463..048306fd 100644
--- a/docs/reference/mean.list.html
+++ b/docs/reference/mean.list.html
@@ -1,5 +1,5 @@
-Calculate the mean spectrum from an mrs_data object. — mean.list • Spectroscopy Analysis Tools (spant) Calculate the mean spectrum from an mrs_data object. — mean.list • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/mean.mrs_data.html b/docs/reference/mean.mrs_data.html
index 5531a28d..79515014 100644
--- a/docs/reference/mean.mrs_data.html
+++ b/docs/reference/mean.mrs_data.html
@@ -1,5 +1,5 @@
-Calculate the mean spectrum from an mrs_data object. — mean.mrs_data • Spectroscopy Analysis Tools (spant) Calculate the mean spectrum from an mrs_data object. — mean.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/mean_dyn_blocks.html b/docs/reference/mean_dyn_blocks.html
index 10467098..4c042448 100644
--- a/docs/reference/mean_dyn_blocks.html
+++ b/docs/reference/mean_dyn_blocks.html
@@ -1,5 +1,5 @@
-Calculate the mean of adjacent dynamic scans. — mean_dyn_blocks • Spectroscopy Analysis Tools (spant) Calculate the mean of adjacent dynamic scans. — mean_dyn_blocks • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/mean_dyn_pairs.html b/docs/reference/mean_dyn_pairs.html
index 63e909ea..1a241126 100644
--- a/docs/reference/mean_dyn_pairs.html
+++ b/docs/reference/mean_dyn_pairs.html
@@ -1,5 +1,5 @@
-Calculate the pairwise means across a dynamic data set. — mean_dyn_pairs • Spectroscopy Analysis Tools (spant) Calculate the pairwise means across a dynamic data set. — mean_dyn_pairs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/mean_dyns.html b/docs/reference/mean_dyns.html
index 73fdbfa7..0daa27df 100644
--- a/docs/reference/mean_dyns.html
+++ b/docs/reference/mean_dyns.html
@@ -1,5 +1,5 @@
-Calculate the mean dynamic data. — mean_dyns • Spectroscopy Analysis Tools (spant) Calculate the mean dynamic data. — mean_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/mean_mrs_list.html b/docs/reference/mean_mrs_list.html
index 808b6c50..10d842c0 100644
--- a/docs/reference/mean_mrs_list.html
+++ b/docs/reference/mean_mrs_list.html
@@ -1,5 +1,5 @@
-Return the mean of a list of mrs_data objects. — mean_mrs_list • Spectroscopy Analysis Tools (spant) Return the mean of a list of mrs_data objects. — mean_mrs_list • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/mean_vec_blocks.html b/docs/reference/mean_vec_blocks.html
index 8fc92eaa..dd78b122 100644
--- a/docs/reference/mean_vec_blocks.html
+++ b/docs/reference/mean_vec_blocks.html
@@ -1,5 +1,5 @@
-Calculate the mean of adjacent blocks in a vector. — mean_vec_blocks • Spectroscopy Analysis Tools (spant) Calculate the mean of adjacent blocks in a vector. — mean_vec_blocks • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/median_dyns.html b/docs/reference/median_dyns.html
index 1039d4b5..9a085b10 100644
--- a/docs/reference/median_dyns.html
+++ b/docs/reference/median_dyns.html
@@ -1,5 +1,5 @@
-Calculate the median dynamic data. — median_dyns • Spectroscopy Analysis Tools (spant) Calculate the median dynamic data. — median_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/mod_td.html b/docs/reference/mod_td.html
index 76ad0a40..141ef09e 100644
--- a/docs/reference/mod_td.html
+++ b/docs/reference/mod_td.html
@@ -1,5 +1,5 @@
-Apply the Modulus operator to the time-domain MRS signal. — mod_td • Spectroscopy Analysis Tools (spant) Apply the Modulus operator to the time-domain MRS signal. — mod_td • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/mrs_data2basis.html b/docs/reference/mrs_data2basis.html
index 62f7d749..11797b91 100644
--- a/docs/reference/mrs_data2basis.html
+++ b/docs/reference/mrs_data2basis.html
@@ -1,7 +1,5 @@
-Convert an mrs_data object to basis object - where basis signals are spread
-across the dynamic dimension in the MRS data. — mrs_data2basis • Spectroscopy Analysis Tools (spant) Convert an mrs_data object to basis object - where basis signals are spread across the dynamic dimension in the MRS data. — mrs_data2basis • Spectroscopy Analysis Tools (spant) Create a BIDS file structure from a vector of MRS data paths or list of mrs_data objects. — mrs_data2bids • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Create a BIDS file structure from a vector of MRS data paths or list of mrs_data objects.
+ Source: R/fmrs.R
+ mrs_data2bids.Rd
+
+
+
+ Create a BIDS file structure from a vector of MRS data paths or list of
+mrs_data objects.
+
+
+
+ mrs_data2bids(
+ mrs_data,
+ output_dir,
+ suffix = NULL,
+ sub = NULL,
+ ses = NULL,
+ task = NULL,
+ acq = NULL,
+ nuc = NULL,
+ voi = NULL,
+ rec = NULL,
+ run = NULL,
+ echo = NULL,
+ inv = NULL,
+ skip_existing = TRUE
+)
+
+
+
+ Arguments
+ - mrs_data
+vector of MRS data paths or list of mrs_data objects.
- output_dir
+the base directory to create the BIDS structure.
- suffix
+optional vector of file suffixes. Default behaviour is to
+automatically determine these from the input data, however it is recommended
+that they are specified to allow more efficient skipping of existing data.
- sub
+optional vector of subject labels. If not specified, these will be
+automatically generated as a series of increasing zero-padded integer values
+corresponding to the mrs_data input indices.
- ses
+optional vector of session labels.
- task
+optional vector of task labels.
- acq
+optional vector of acquisition labels.
- nuc
+optional vector of nucleus labels.
- voi
+optional vector of volume of interest labels.
- rec
+optional vector of reconstruction labels.
- run
+optional vector of run indices.
- echo
+optional vector of echo time indices.
- inv
+optional vector of inversion indices.
- skip_existing
+skip any data files that have already been converted.
+Defaults to TRUE, set to FALSE to force an overwrite of any existing data
+files.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/mrs_data2mat.html b/docs/reference/mrs_data2mat.html
index cf5ff28c..9e47688a 100644
--- a/docs/reference/mrs_data2mat.html
+++ b/docs/reference/mrs_data2mat.html
@@ -1,7 +1,5 @@
-Convert mrs_data object to a matrix, with spectral points in the column
-dimension and dynamics in the row dimension. — mrs_data2mat • Spectroscopy Analysis Tools (spant) Convert mrs_data object to a matrix, with spectral points in the column dimension and dynamics in the row dimension. — mrs_data2mat • Spectroscopy Analysis Tools (spant) Convert mrs_data object to a matrix, with spectral points in the column dimension and dynamics in the row dimension. — mrs_data2spec_mat • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Convert mrs_data object to a matrix, with spectral points in the column dimension and dynamics in the row dimension.
+ Source: R/mrs_data_proc.R
+ mrs_data2spec_mat.Rd
+
+
+
+ Convert mrs_data object to a matrix, with spectral points in the column
+dimension and dynamics in the row dimension.
+
+
+
+ mrs_data2spec_mat(mrs_data, collapse = TRUE)
+
+
+
+ Arguments
+ - mrs_data
+MRS data object or list of MRS data objects.
- collapse
+collapse all other dimensions along the dynamic dimension, eg
+a 16x16 MRSI grid would be first collapsed across 256 dynamic scans.
+
+ Value
+
+
+MRS data matrix.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/mrs_data2vec.html b/docs/reference/mrs_data2vec.html
index fb172d68..a1fd654d 100644
--- a/docs/reference/mrs_data2vec.html
+++ b/docs/reference/mrs_data2vec.html
@@ -1,5 +1,5 @@
-Convert mrs_data object to a vector. — mrs_data2vec • Spectroscopy Analysis Tools (spant) Convert mrs_data object to a vector. — mrs_data2vec • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -126,7 +126,7 @@ Value
diff --git a/docs/reference/mvfftshift.html b/docs/reference/mvfftshift.html
index 92b0841b..976b3410 100644
--- a/docs/reference/mvfftshift.html
+++ b/docs/reference/mvfftshift.html
@@ -1,7 +1,5 @@
-Perform a fftshift on a matrix, with each column replaced by its shifted
-result. — mvfftshift • Spectroscopy Analysis Tools (spant) Perform a fftshift on a matrix, with each column replaced by its shifted result. — mvfftshift • Spectroscopy Analysis Tools (spant) Perform an ifftshift on a matrix, with each column replaced by its shifted
-result. — mvifftshift • Spectroscopy Analysis Tools (spant) Perform an ifftshift on a matrix, with each column replaced by its shifted result. — mvifftshift • Spectroscopy Analysis Tools (spant) Print fit coordinates from a single index. — n2coord • Spectroscopy Analysis Tools (spant) Print fit coordinates from a single index. — n2coord • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/nifti_flip_lr.html b/docs/reference/nifti_flip_lr.html
index 730abe3c..19860b3c 100644
--- a/docs/reference/nifti_flip_lr.html
+++ b/docs/reference/nifti_flip_lr.html
@@ -1,9 +1,5 @@
-Flip the x data dimension order of a nifti image. This corresponds to
-flipping MRI data in the left-right direction, assuming the data in save in
-neurological format (can check with fslorient program). — nifti_flip_lr • Spectroscopy Analysis Tools (spant) Flip the x data dimension order of a nifti image. This corresponds to flipping MRI data in the left-right direction, assuming the data in save in neurological format (can check with fslorient program). — nifti_flip_lr • Spectroscopy Analysis Tools (spant) Export a one-page pdf of a single fit result — one_page_pdf • Spectroscopy Analysis Tools (spant) Export a one-page pdf of a single fit result — one_page_pdf • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -108,7 +108,7 @@ Arguments
diff --git a/docs/reference/ortho3.html b/docs/reference/ortho3.html
index 13ade97d..5d7dd2fd 100644
--- a/docs/reference/ortho3.html
+++ b/docs/reference/ortho3.html
@@ -1,5 +1,5 @@
-Display an orthographic projection plot of a nifti object. — ortho3 • Spectroscopy Analysis Tools (spant) Display an orthographic projection plot of a nifti object. — ortho3 • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -172,7 +172,7 @@ Arguments
diff --git a/docs/reference/ortho3_inter.html b/docs/reference/ortho3_inter.html
index 090cc5e5..15948899 100644
--- a/docs/reference/ortho3_inter.html
+++ b/docs/reference/ortho3_inter.html
@@ -1,5 +1,5 @@
-Display an interactive orthographic projection plot of a nifti object. — ortho3_inter • Spectroscopy Analysis Tools (spant) Display an interactive orthographic projection plot of a nifti object. — ortho3_inter • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -132,7 +132,7 @@ Arguments
diff --git a/docs/reference/peak_info.html b/docs/reference/peak_info.html
index 09058bd8..41c8ffaf 100644
--- a/docs/reference/peak_info.html
+++ b/docs/reference/peak_info.html
@@ -1,7 +1,5 @@
-Search for the highest peak in a spectral region and return the frequency,
-height and FWHM. — peak_info • Spectroscopy Analysis Tools (spant) Search for the highest peak in a spectral region and return the frequency, height and FWHM. — peak_info • Spectroscopy Analysis Tools (spant) Papoulis-Gerchberg (PG) algorithm method for k-space extrapolation. — pg_extrap_xy • Spectroscopy Analysis Tools (spant) Papoulis-Gerchberg (PG) algorithm method for k-space extrapolation. — pg_extrap_xy • Spectroscopy Analysis Tools (spant) Apply phasing parameters to MRS data. — phase • Spectroscopy Analysis Tools (spant) Apply phasing parameters to MRS data. — phase • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/phase_ref_1h_brain.html b/docs/reference/phase_ref_1h_brain.html
new file mode 100644
index 00000000..8707a74a
--- /dev/null
+++ b/docs/reference/phase_ref_1h_brain.html
@@ -0,0 +1,131 @@
+
+Corrected zero order phase and chemical shift offset in 1H MRS data from the brain. — phase_ref_1h_brain • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Corrected zero order phase and chemical shift offset in 1H MRS data from the brain.
+ Source: R/rats.R
+ phase_ref_1h_brain.Rd
+
+
+
+ Corrected zero order phase and chemical shift offset in 1H MRS data from the
+brain.
+
+
+
+ phase_ref_1h_brain(mrs_data, mean_ref = FALSE, ret_corr_only = TRUE)
+
+
+
+ Arguments
+ - mrs_data
+MRS data to be corrected.
- mean_ref
+apply the phase and offset of the mean spectrum to all
+others. Default is FALSE.
- ret_corr_only
+return the corrected data only.
+
+ Value
+
+
+corrected MRS data.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/plot.fit_result.html b/docs/reference/plot.fit_result.html
index e54d3bc1..836a53ee 100644
--- a/docs/reference/plot.fit_result.html
+++ b/docs/reference/plot.fit_result.html
@@ -1,5 +1,5 @@
-Plot the fitting results of an object of class fit_result. — plot.fit_result • Spectroscopy Analysis Tools (spant) Plot the fitting results of an object of class fit_result. — plot.fit_result • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -207,7 +207,7 @@ Arguments
diff --git a/docs/reference/plot.mrs_data.html b/docs/reference/plot.mrs_data.html
index fabcc35b..bb2ec651 100644
--- a/docs/reference/plot.mrs_data.html
+++ b/docs/reference/plot.mrs_data.html
@@ -1,5 +1,5 @@
-Plotting method for objects of class mrs_data. — plot.mrs_data • Spectroscopy Analysis Tools (spant) Plotting method for objects of class mrs_data. — plot.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -287,7 +287,7 @@ Arguments
diff --git a/docs/reference/plot_bc.html b/docs/reference/plot_bc.html
index 4f8309b4..b48142cc 100644
--- a/docs/reference/plot_bc.html
+++ b/docs/reference/plot_bc.html
@@ -1,5 +1,5 @@
-Convenience function to plot a baseline estimate with the original data. — plot_bc • Spectroscopy Analysis Tools (spant) Convenience function to plot a baseline estimate with the original data. — plot_bc • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -108,7 +108,7 @@ Arguments
diff --git a/docs/reference/plot_reg.html b/docs/reference/plot_reg.html
index ae1acbe7..2addb2f6 100644
--- a/docs/reference/plot_reg.html
+++ b/docs/reference/plot_reg.html
@@ -1,5 +1,5 @@
-Plot regressors as an image. — plot_reg • Spectroscopy Analysis Tools (spant) Plot regressors as an image. — plot_reg • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/plot_slice_fit.html b/docs/reference/plot_slice_fit.html
index fbc7b560..57f1af8a 100644
--- a/docs/reference/plot_slice_fit.html
+++ b/docs/reference/plot_slice_fit.html
@@ -1,5 +1,5 @@
-Plot a 2D slice from an MRSI fit result object. — plot_slice_fit • Spectroscopy Analysis Tools (spant) Plot a 2D slice from an MRSI fit result object. — plot_slice_fit • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -129,7 +129,7 @@ Arguments
diff --git a/docs/reference/plot_slice_fit_inter.html b/docs/reference/plot_slice_fit_inter.html
index 4eed104a..da105a7d 100644
--- a/docs/reference/plot_slice_fit_inter.html
+++ b/docs/reference/plot_slice_fit_inter.html
@@ -1,5 +1,5 @@
-Plot a 2D slice from an MRSI fit result object. — plot_slice_fit_inter • Spectroscopy Analysis Tools (spant) Plot a 2D slice from an MRSI fit result object. — plot_slice_fit_inter • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -134,7 +134,7 @@ Arguments
diff --git a/docs/reference/plot_slice_map.html b/docs/reference/plot_slice_map.html
index 553e9ac8..ffb2a134 100644
--- a/docs/reference/plot_slice_map.html
+++ b/docs/reference/plot_slice_map.html
@@ -1,5 +1,5 @@
-Plot a slice from a 7 dimensional array. — plot_slice_map • Spectroscopy Analysis Tools (spant) Plot a slice from a 7 dimensional array. — plot_slice_map • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -153,7 +153,7 @@ Arguments
diff --git a/docs/reference/plot_slice_map_inter.html b/docs/reference/plot_slice_map_inter.html
index 40d33b42..90968f66 100644
--- a/docs/reference/plot_slice_map_inter.html
+++ b/docs/reference/plot_slice_map_inter.html
@@ -1,7 +1,5 @@
-Plot an interactive slice map from a data array where voxels can be selected
-to display a corresponding spectrum. — plot_slice_map_inter • Spectroscopy Analysis Tools (spant) Plot an interactive slice map from a data array where voxels can be selected to display a corresponding spectrum. — plot_slice_map_inter • Spectroscopy Analysis Tools (spant) Plot the spectral standard deviation. — plot_spec_sd • Spectroscopy Analysis Tools (spant) Plot the spectral standard deviation. — plot_spec_sd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Arguments
diff --git a/docs/reference/plot_voi_overlay.html b/docs/reference/plot_voi_overlay.html
index 9a782e88..bbbbf35e 100644
--- a/docs/reference/plot_voi_overlay.html
+++ b/docs/reference/plot_voi_overlay.html
@@ -1,5 +1,5 @@
-Plot a volume as an image overlay. — plot_voi_overlay • Spectroscopy Analysis Tools (spant) Plot a volume as an image overlay. — plot_voi_overlay • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -116,7 +116,7 @@ Arguments
diff --git a/docs/reference/plot_voi_overlay_seg.html b/docs/reference/plot_voi_overlay_seg.html
index 3d4e74ff..0e800ff2 100644
--- a/docs/reference/plot_voi_overlay_seg.html
+++ b/docs/reference/plot_voi_overlay_seg.html
@@ -1,5 +1,5 @@
-Plot a volume as an overlay on a segmented brain volume. — plot_voi_overlay_seg • Spectroscopy Analysis Tools (spant) Plot a volume as an overlay on a segmented brain volume. — plot_voi_overlay_seg • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Arguments
diff --git a/docs/reference/ppm.html b/docs/reference/ppm.html
index c352327a..ee4696e2 100644
--- a/docs/reference/ppm.html
+++ b/docs/reference/ppm.html
@@ -1,5 +1,5 @@
-Return the ppm scale of an MRS dataset or fit result. — ppm • Spectroscopy Analysis Tools (spant) Return the ppm scale of an MRS dataset or fit result. — ppm • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -132,7 +132,7 @@ Value
diff --git a/docs/reference/precomp.html b/docs/reference/precomp.html
index 822d7336..df3d2c6c 100644
--- a/docs/reference/precomp.html
+++ b/docs/reference/precomp.html
@@ -1,7 +1,5 @@
-Save function results to file and load on subsequent calls to avoid repeat
-computation. — precomp • Spectroscopy Analysis Tools (spant) Save function results to file and load on subsequent calls to avoid repeat computation. — precomp • Spectroscopy Analysis Tools (spant) Preprocess and perform quality assessment of a single SVS data set. — preproc_svs • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Preprocess and perform quality assessment of a single SVS data set.
+ Source: R/fmrs.R
+ preproc_svs.Rd
+
+
+
+ Preprocess and perform quality assessment of a single SVS data set.
+
+
+
+ preproc_svs(path, label = NULL, output_dir = NULL, ref_inds = NULL)
+
+
+
+ Arguments
+ - path
+path to the fMRS data file or IMA directory.
- label
+a label to describe the data set.
- output_dir
+output directory.
- ref_inds
+a vector of 1-based indices for any water reference dynamic
+scans.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/preproc_svs_dataset.html b/docs/reference/preproc_svs_dataset.html
new file mode 100644
index 00000000..07c3a29b
--- /dev/null
+++ b/docs/reference/preproc_svs_dataset.html
@@ -0,0 +1,148 @@
+
+Preprocess and perform quality assessment of one or more SVS data sets. — preproc_svs_dataset • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Preprocess and perform quality assessment of one or more SVS data sets.
+ Source: R/fmrs.R
+ preproc_svs_dataset.Rd
+
+
+
+ Preprocess and perform quality assessment of one or more SVS data sets.
+
+
+
+ preproc_svs_dataset(
+ paths,
+ labels = NULL,
+ output_dir = "spant_analysis",
+ exclude_labels = NULL,
+ overwrite = FALSE,
+ ref_inds = NULL,
+ return_results = FALSE
+)
+
+
+
+ Arguments
+ - paths
+paths to the fMRS data file or IMA directory.
- labels
+labels to describe each data set.
- output_dir
+output directory.
- exclude_labels
+vector of labels of scans to exclude, eg poor quality
+data.
- overwrite
+overwrite saved results, defaults to FALSE.
- ref_inds
+a vector of 1-based indices for any water reference dynamic
+scans.
- return_results
+function will return key outputs, defaults to FALSE.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/print.fit_result.html b/docs/reference/print.fit_result.html
index 297f28dc..5f434e57 100644
--- a/docs/reference/print.fit_result.html
+++ b/docs/reference/print.fit_result.html
@@ -1,5 +1,5 @@
-Print a summary of an object of class fit_result. — print.fit_result • Spectroscopy Analysis Tools (spant) Print a summary of an object of class fit_result. — print.fit_result • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -105,7 +105,7 @@ Arguments
diff --git a/docs/reference/print.mrs_data.html b/docs/reference/print.mrs_data.html
index 51199017..e1561eb2 100644
--- a/docs/reference/print.mrs_data.html
+++ b/docs/reference/print.mrs_data.html
@@ -1,5 +1,5 @@
-Print a summary of mrs_data parameters. — print.mrs_data • Spectroscopy Analysis Tools (spant) Print a summary of mrs_data parameters. — print.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -109,7 +109,7 @@ Arguments
diff --git a/docs/reference/qn_states.html b/docs/reference/qn_states.html
index 0f42f2f9..d7aa6715 100644
--- a/docs/reference/qn_states.html
+++ b/docs/reference/qn_states.html
@@ -1,5 +1,5 @@
-Get the quantum coherence matrix for a spin system. — qn_states • Spectroscopy Analysis Tools (spant) Get the quantum coherence matrix for a spin system. — qn_states • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/rats.html b/docs/reference/rats.html
index 5a39a396..93585e08 100644
--- a/docs/reference/rats.html
+++ b/docs/reference/rats.html
@@ -1,5 +1,5 @@
-Robust Alignment to a Target Spectrum (RATS). — rats • Spectroscopy Analysis Tools (spant) Robust Alignment to a Target Spectrum (RATS). — rats • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -207,7 +207,7 @@ Value
diff --git a/docs/reference/re_weighting.html b/docs/reference/re_weighting.html
index d21caf21..8b0b070a 100644
--- a/docs/reference/re_weighting.html
+++ b/docs/reference/re_weighting.html
@@ -1,5 +1,5 @@
-Apply a weighting to the FID to enhance spectral resolution. — re_weighting • Spectroscopy Analysis Tools (spant) Apply a weighting to the FID to enhance spectral resolution. — re_weighting • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/read_basis.html b/docs/reference/read_basis.html
index da9b94af..eb6f8557 100644
--- a/docs/reference/read_basis.html
+++ b/docs/reference/read_basis.html
@@ -1,5 +1,5 @@
-Read a basis file in LCModel .basis format. — read_basis • Spectroscopy Analysis Tools (spant) Read a basis file in LCModel .basis format. — read_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/read_ima_coil_dir.html b/docs/reference/read_ima_coil_dir.html
index 28c02de0..4f073cd8 100644
--- a/docs/reference/read_ima_coil_dir.html
+++ b/docs/reference/read_ima_coil_dir.html
@@ -1,9 +1,5 @@
-Read a directory containing Siemens MRS IMA files and combine along the coil
-dimension. Note that the coil ID is inferred from the sorted file name and
-should be checked when consistency is required between two directories. — read_ima_coil_dir • Spectroscopy Analysis Tools (spant) Read a directory containing Siemens MRS IMA files and combine along the coil dimension. Note that the coil ID is inferred from the sorted file name and should be checked when consistency is required between two directories. — read_ima_coil_dir • Spectroscopy Analysis Tools (spant) Read a directory containing Siemens MRS IMA files and combine along the
-dynamic dimension. Note that the coil ID is inferred from the sorted file
-name and should be checked when consistency is required. — read_ima_dyn_dir • Spectroscopy Analysis Tools (spant) Read a directory containing Siemens MRS IMA files and combine along the dynamic dimension. Note that the coil ID is inferred from the sorted file name and should be checked when consistency is required. — read_ima_dyn_dir • Spectroscopy Analysis Tools (spant) Read an LCModel formatted coord file containing fit information. — read_lcm_coord • Spectroscopy Analysis Tools (spant) Read an LCModel formatted coord file containing fit information. — read_lcm_coord • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -107,7 +107,7 @@ Value
diff --git a/docs/reference/read_mrs.html b/docs/reference/read_mrs.html
index 3ac2a36b..2cf36b20 100644
--- a/docs/reference/read_mrs.html
+++ b/docs/reference/read_mrs.html
@@ -1,5 +1,5 @@
-Read MRS data from a file. — read_mrs • Spectroscopy Analysis Tools (spant) Read MRS data from a file. — read_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -88,7 +88,8 @@ Read MRS data from a file.
full_fid = FALSE,
omit_svs_ref_scans = TRUE,
verbose = FALSE,
- extra = NULL
+ extra = NULL,
+ fid_filt_dist = NULL
)
@@ -140,6 +141,13 @@ Arguments
an optional data frame to provide additional variables for use
in subsequent analysis steps, eg id or grouping variables.
fid_filt_dist
+indicate if the data has a distorted FID due to a
+brick-wall filter being used to downsample the data. Default is to auto
+detect this from the data, but TRUE or FALSE options can be given to override
+detection.
Value
@@ -183,7 +191,7 @@ Examples
diff --git a/docs/reference/read_mrs_tqn.html b/docs/reference/read_mrs_tqn.html
index 5766362f..84bdaf3a 100644
--- a/docs/reference/read_mrs_tqn.html
+++ b/docs/reference/read_mrs_tqn.html
@@ -1,5 +1,5 @@
-Read MRS data using the TARQUIN software package. — read_mrs_tqn • Spectroscopy Analysis Tools (spant) Read MRS data using the TARQUIN software package. — read_mrs_tqn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -131,7 +131,7 @@ Examples
diff --git a/docs/reference/read_pulse_ascii.html b/docs/reference/read_pulse_ascii.html
index c9e0d43c..ab11c9cc 100644
--- a/docs/reference/read_pulse_ascii.html
+++ b/docs/reference/read_pulse_ascii.html
@@ -1,5 +1,5 @@
-Read an ASCII formatted pulse file. — read_pulse_ascii • Spectroscopy Analysis Tools (spant) Read an ASCII formatted pulse file. — read_pulse_ascii • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/read_pulse_bruker.html b/docs/reference/read_pulse_bruker.html
index c92bf76a..dbe9073b 100644
--- a/docs/reference/read_pulse_bruker.html
+++ b/docs/reference/read_pulse_bruker.html
@@ -1,5 +1,5 @@
-Read a Bruker formatted pulse file — read_pulse_bruker • Spectroscopy Analysis Tools (spant) Read a Bruker formatted pulse file — read_pulse_bruker • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/read_pulse_pta.html b/docs/reference/read_pulse_pta.html
index 72e1b6d4..a0fac3c3 100644
--- a/docs/reference/read_pulse_pta.html
+++ b/docs/reference/read_pulse_pta.html
@@ -1,5 +1,5 @@
-Read a .pta formatted pulse file compatible with Siemens PulseTool. — read_pulse_pta • Spectroscopy Analysis Tools (spant) Read a .pta formatted pulse file compatible with Siemens PulseTool. — read_pulse_pta • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/read_siemens_txt_hdr.html b/docs/reference/read_siemens_txt_hdr.html
index 23fb8c70..3a17d87c 100644
--- a/docs/reference/read_siemens_txt_hdr.html
+++ b/docs/reference/read_siemens_txt_hdr.html
@@ -1,5 +1,5 @@
-Read the text format header found in Siemens IMA and TWIX data files. — read_siemens_txt_hdr • Spectroscopy Analysis Tools (spant) Read the text format header found in Siemens IMA and TWIX data files. — read_siemens_txt_hdr • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -78,7 +78,7 @@ Read the text format header found in Siemens IMA and TWIX data files.
- read_siemens_txt_hdr(input, version = "vd", verbose, offset = 0)
+ read_siemens_txt_hdr(input, version = "vd", verbose = FALSE, offset = 0)
@@ -118,7 +118,7 @@ Value
diff --git a/docs/reference/read_tqn_fit.html b/docs/reference/read_tqn_fit.html
index 4da6c25e..a1630420 100644
--- a/docs/reference/read_tqn_fit.html
+++ b/docs/reference/read_tqn_fit.html
@@ -1,5 +1,5 @@
-Reader for csv fit results generated by TARQUIN. — read_tqn_fit • Spectroscopy Analysis Tools (spant) Reader for csv fit results generated by TARQUIN. — read_tqn_fit • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -113,7 +113,7 @@ Examples
diff --git a/docs/reference/read_tqn_result.html b/docs/reference/read_tqn_result.html
index 36659714..68a3e98c 100644
--- a/docs/reference/read_tqn_result.html
+++ b/docs/reference/read_tqn_result.html
@@ -1,5 +1,5 @@
-Reader for csv results generated by TARQUIN. — read_tqn_result • Spectroscopy Analysis Tools (spant) Reader for csv results generated by TARQUIN. — read_tqn_result • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -117,7 +117,7 @@ Examples
diff --git a/docs/reference/recon_imag.html b/docs/reference/recon_imag.html
index d2a72225..5bc3b1eb 100644
--- a/docs/reference/recon_imag.html
+++ b/docs/reference/recon_imag.html
@@ -1,7 +1,5 @@
-Reconstruct complex time-domain data from the real part of frequency-domain
-data. — recon_imag • Spectroscopy Analysis Tools (spant) Reconstruct complex time-domain data from the real part of frequency-domain data. — recon_imag • Spectroscopy Analysis Tools (spant) Reconstruct complex time-domain data from the real part of frequency-domain
-data. — recon_imag_vec • Spectroscopy Analysis Tools (spant) Reconstruct complex time-domain data from the real part of frequency-domain data. — recon_imag_vec • Spectroscopy Analysis Tools (spant) Reconstruct 2D MRSI data from a twix file loaded with read_mrs. — recon_twix_2d_mrsi • Spectroscopy Analysis Tools (spant) Reconstruct 2D MRSI data from a twix file loaded with read_mrs. — recon_twix_2d_mrsi • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/rectangular_mask.html b/docs/reference/rectangular_mask.html
index a2117283..6e469bc9 100644
--- a/docs/reference/rectangular_mask.html
+++ b/docs/reference/rectangular_mask.html
@@ -1,5 +1,5 @@
-Create a rectangular mask stored as a matrix of logical values. — rectangular_mask • Spectroscopy Analysis Tools (spant) Create a rectangular mask stored as a matrix of logical values. — rectangular_mask • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -130,7 +130,7 @@ Value
diff --git a/docs/reference/reexports.html b/docs/reference/reexports.html
index 694a75d1..a59e8379 100644
--- a/docs/reference/reexports.html
+++ b/docs/reference/reexports.html
@@ -1,5 +1,5 @@
-Objects exported from other packages — reexports • Spectroscopy Analysis Tools (spant) Objects exported from other packages — reexports • Spectroscopy Analysis Tools (spant)
Spectroscopy Analysis Tools (spant)
- 2.21.0
+ 2.22.0
@@ -103,7 +103,7 @@ Objects exported from other packages
diff --git a/docs/reference/rep_array_dim.html b/docs/reference/rep_array_dim.html
index b9c49b4a..48c0a5ed 100644
--- a/docs/reference/rep_array_dim.html
+++ b/docs/reference/rep_array_dim.html
@@ -1,5 +1,5 @@
-Repeat an array over a given dimension. — rep_array_dim • Spectroscopy Analysis Tools (spant) Repeat an array over a given dimension. — rep_array_dim • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/rep_dyn.html b/docs/reference/rep_dyn.html
index 6bbfb0ef..89a4bb9b 100644
--- a/docs/reference/rep_dyn.html
+++ b/docs/reference/rep_dyn.html
@@ -1,5 +1,5 @@
-Replicate a scan in the dynamic dimension. — rep_dyn • Spectroscopy Analysis Tools (spant) Replicate a scan in the dynamic dimension. — rep_dyn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/rep_mrs.html b/docs/reference/rep_mrs.html
index 67730b5c..becb8f00 100644
--- a/docs/reference/rep_mrs.html
+++ b/docs/reference/rep_mrs.html
@@ -1,5 +1,5 @@
-Replicate a scan over a given dimension. — rep_mrs • Spectroscopy Analysis Tools (spant) Replicate a scan over a given dimension. — rep_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -138,7 +138,7 @@ Value
diff --git a/docs/reference/resample_basis.html b/docs/reference/resample_basis.html
index b0f2ab17..c7a6222a 100644
--- a/docs/reference/resample_basis.html
+++ b/docs/reference/resample_basis.html
@@ -1,5 +1,5 @@
-Resample a basis-set to match a mrs_data acquisition. — resample_basis • Spectroscopy Analysis Tools (spant) Resample a basis-set to match a mrs_data acquisition. — resample_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -116,7 +116,7 @@ Value
diff --git a/docs/reference/resample_img.html b/docs/reference/resample_img.html
index f1e7beaf..b0cc8f71 100644
--- a/docs/reference/resample_img.html
+++ b/docs/reference/resample_img.html
@@ -1,5 +1,5 @@
-Resample an image to match a target image space. — resample_img • Spectroscopy Analysis Tools (spant) Resample an image to match a target image space. — resample_img • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/resample_voi.html b/docs/reference/resample_voi.html
index 8fbfa836..a29ab096 100644
--- a/docs/reference/resample_voi.html
+++ b/docs/reference/resample_voi.html
@@ -1,7 +1,5 @@
-Resample a VOI to match a target image space using nearest-neighbour
-interpolation. — resample_voi • Spectroscopy Analysis Tools (spant) Resample a VOI to match a target image space using nearest-neighbour interpolation. — resample_voi • Spectroscopy Analysis Tools (spant) Reslice a nifti object to match the orientation of mrs data. — reslice_to_mrs • Spectroscopy Analysis Tools (spant) Reslice a nifti object to match the orientation of mrs data. — reslice_to_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/reson_table2mrs_data.html b/docs/reference/reson_table2mrs_data.html
index d75579ee..c5a2167a 100644
--- a/docs/reference/reson_table2mrs_data.html
+++ b/docs/reference/reson_table2mrs_data.html
@@ -1,5 +1,5 @@
-Generate mrs_data from a table of single Lorentzian resonances. — reson_table2mrs_data • Spectroscopy Analysis Tools (spant) Generate mrs_data from a table of single Lorentzian resonances. — reson_table2mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -119,7 +119,7 @@ Value
diff --git a/docs/reference/rm_dyns.html b/docs/reference/rm_dyns.html
index 5d5ef692..573e1f51 100644
--- a/docs/reference/rm_dyns.html
+++ b/docs/reference/rm_dyns.html
@@ -1,5 +1,5 @@
-Remove a subset of dynamic scans. — rm_dyns • Spectroscopy Analysis Tools (spant) Remove a subset of dynamic scans. — rm_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/scale_amp_molal.html b/docs/reference/scale_amp_molal.html
index aaeee1f2..7acb8cb0 100644
--- a/docs/reference/scale_amp_molal.html
+++ b/docs/reference/scale_amp_molal.html
@@ -1,7 +1,5 @@
-Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water). — scale_amp_molal • Spectroscopy Analysis Tools (spant) Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / kg of tissue water). — scale_amp_molal • Spectroscopy Analysis Tools (spant)
Spectroscopy Analysis Tools (spant)
- 2.21.0
+ 2.22.0
@@ -76,8 +74,7 @@
- Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water).
+ Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / kg of tissue water).
Source: R/amp_scaling.R
scale_amp_molal.Rd
@@ -163,7 +160,7 @@ Value
diff --git a/docs/reference/scale_amp_molal_pvc.html b/docs/reference/scale_amp_molal_pvc.html
index 962d6afc..4d194abd 100644
--- a/docs/reference/scale_amp_molal_pvc.html
+++ b/docs/reference/scale_amp_molal_pvc.html
@@ -1,7 +1,5 @@
-Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water). — scale_amp_molal_pvc • Spectroscopy Analysis Tools (spant)
@@ -75,8 +73,7 @@
- Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water).
+ Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / kg of tissue water).
Source: R/amp_scaling.R
scale_amp_molal_pvc.Rd
@@ -141,7 +138,7 @@ Value
diff --git a/docs/reference/scale_amp_molar.html b/docs/reference/scale_amp_molar.html
index 02358d91..dc87a338 100644
--- a/docs/reference/scale_amp_molar.html
+++ b/docs/reference/scale_amp_molar.html
@@ -1,7 +1,5 @@
-Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / Litre of tissue). — scale_amp_molar • Spectroscopy Analysis Tools (spant) Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / Litre of tissue). — scale_amp_molar • Spectroscopy Analysis Tools (spant) Convert default LCM/TARQUIN concentration scaling to molal units with partial
-volume correction. — scale_amp_molar2molal_pvc • Spectroscopy Analysis Tools (spant) Convert default LCM/TARQUIN concentration scaling to molal units with partial volume correction. — scale_amp_molar2molal_pvc • Spectroscopy Analysis Tools (spant) Scale fitted amplitudes to a ratio of signal amplitude. — scale_amp_ratio • Spectroscopy Analysis Tools (spant) Scale fitted amplitudes to a ratio of signal amplitude. — scale_amp_ratio • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -116,7 +116,7 @@ Value
diff --git a/docs/reference/scale_amp_ratio_value.html b/docs/reference/scale_amp_ratio_value.html
index 2036837a..6af8ac51 100644
--- a/docs/reference/scale_amp_ratio_value.html
+++ b/docs/reference/scale_amp_ratio_value.html
@@ -1,5 +1,5 @@
-Scale fitted amplitudes to a ratio of signal amplitude. — scale_amp_ratio_value • Spectroscopy Analysis Tools (spant) Scale fitted amplitudes to a ratio of signal amplitude. — scale_amp_ratio_value • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/scale_amp_water_ratio.html b/docs/reference/scale_amp_water_ratio.html
index 5b25e884..35a76b00 100644
--- a/docs/reference/scale_amp_water_ratio.html
+++ b/docs/reference/scale_amp_water_ratio.html
@@ -1,5 +1,5 @@
-Scale metabolite amplitudes as a ratio to the unsuppressed water amplitude. — scale_amp_water_ratio • Spectroscopy Analysis Tools (spant) Scale metabolite amplitudes as a ratio to the unsuppressed water amplitude. — scale_amp_water_ratio • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/scale_basis_amp.html b/docs/reference/scale_basis_amp.html
index 9401c3f1..5a58b5e5 100644
--- a/docs/reference/scale_basis_amp.html
+++ b/docs/reference/scale_basis_amp.html
@@ -1,5 +1,5 @@
-Scale a basis object by a scalar. — scale_basis_amp • Spectroscopy Analysis Tools (spant) Scale a basis object by a scalar. — scale_basis_amp • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/scale_basis_from_singlet.html b/docs/reference/scale_basis_from_singlet.html
index 0d542bc8..c9a19e77 100644
--- a/docs/reference/scale_basis_from_singlet.html
+++ b/docs/reference/scale_basis_from_singlet.html
@@ -1,5 +1,5 @@
-Scale a basis-set to be consistent with spant assumptions for water scaling. — scale_basis_from_singlet • Spectroscopy Analysis Tools (spant) Scale a basis-set to be consistent with spant assumptions for water scaling. — scale_basis_from_singlet • Spectroscopy Analysis Tools (spant)
Spectroscopy Analysis Tools (spant)
- 2.21.0
+ 2.22.0
@@ -127,7 +127,7 @@ Value
diff --git a/docs/reference/scale_mrs_amp.html b/docs/reference/scale_mrs_amp.html
index b5501a0d..990f058a 100644
--- a/docs/reference/scale_mrs_amp.html
+++ b/docs/reference/scale_mrs_amp.html
@@ -1,5 +1,5 @@
-Scale an mrs_data object by a scalar or vector or amplitudes. — scale_mrs_amp • Spectroscopy Analysis Tools (spant) Scale an mrs_data object by a scalar or vector or amplitudes. — scale_mrs_amp • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/scale_spec.html b/docs/reference/scale_spec.html
index 4f6ea835..6b3ddba4 100644
--- a/docs/reference/scale_spec.html
+++ b/docs/reference/scale_spec.html
@@ -1,5 +1,5 @@
-Scale mrs_data to a spectral region. — scale_spec • Spectroscopy Analysis Tools (spant) Scale mrs_data to a spectral region. — scale_spec • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -141,7 +141,7 @@ Value
diff --git a/docs/reference/sd.html b/docs/reference/sd.html
index ea1eec9f..3ae4dfd4 100644
--- a/docs/reference/sd.html
+++ b/docs/reference/sd.html
@@ -1,5 +1,5 @@
-Calculate the standard deviation spectrum from an mrs_data object. — sd • Spectroscopy Analysis Tools (spant) Calculate the standard deviation spectrum from an mrs_data object. — sd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/sd.mrs_data.html b/docs/reference/sd.mrs_data.html
index 3f92a49f..13bdda85 100644
--- a/docs/reference/sd.mrs_data.html
+++ b/docs/reference/sd.mrs_data.html
@@ -1,5 +1,5 @@
-Calculate the standard deviation spectrum from an mrs_data object. — sd.mrs_data • Spectroscopy Analysis Tools (spant) Calculate the standard deviation spectrum from an mrs_data object. — sd.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/seconds.html b/docs/reference/seconds.html
index b34d6627..467ee17f 100644
--- a/docs/reference/seconds.html
+++ b/docs/reference/seconds.html
@@ -1,5 +1,5 @@
-Return a time scale vector to match the FID of an MRS data object. — seconds • Spectroscopy Analysis Tools (spant) Return a time scale vector to match the FID of an MRS data object. — seconds • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/seq_cpmg_ideal.html b/docs/reference/seq_cpmg_ideal.html
index 547e96ab..45727c86 100644
--- a/docs/reference/seq_cpmg_ideal.html
+++ b/docs/reference/seq_cpmg_ideal.html
@@ -1,5 +1,5 @@
-CPMG style sequence with ideal pulses. — seq_cpmg_ideal • Spectroscopy Analysis Tools (spant) CPMG style sequence with ideal pulses. — seq_cpmg_ideal • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/seq_mega_press_ideal.html b/docs/reference/seq_mega_press_ideal.html
index 0769b8b4..a9cd7fa0 100644
--- a/docs/reference/seq_mega_press_ideal.html
+++ b/docs/reference/seq_mega_press_ideal.html
@@ -1,7 +1,5 @@
-MEGA-PRESS sequence with ideal localisation pulses and Gaussian shaped
-editing pulse. — seq_mega_press_ideal • Spectroscopy Analysis Tools (spant) MEGA-PRESS sequence with ideal localisation pulses and Gaussian shaped editing pulse. — seq_mega_press_ideal • Spectroscopy Analysis Tools (spant) PRESS sequence with shaped refocusing pulses. — seq_press_2d_shaped • Spectroscopy Analysis Tools (spant) PRESS sequence with shaped refocusing pulses. — seq_press_2d_shaped • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -165,7 +165,7 @@ Value
diff --git a/docs/reference/seq_press_ideal.html b/docs/reference/seq_press_ideal.html
index 8c976856..72c3af3d 100644
--- a/docs/reference/seq_press_ideal.html
+++ b/docs/reference/seq_press_ideal.html
@@ -1,5 +1,5 @@
-PRESS sequence with ideal pulses. — seq_press_ideal • Spectroscopy Analysis Tools (spant) PRESS sequence with ideal pulses. — seq_press_ideal • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/seq_pulse_acquire.html b/docs/reference/seq_pulse_acquire.html
index 4a88fc64..ad80571e 100644
--- a/docs/reference/seq_pulse_acquire.html
+++ b/docs/reference/seq_pulse_acquire.html
@@ -1,5 +1,5 @@
-Simple pulse and acquire sequence with ideal pulses. — seq_pulse_acquire • Spectroscopy Analysis Tools (spant) Simple pulse and acquire sequence with ideal pulses. — seq_pulse_acquire • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/seq_slaser_ideal.html b/docs/reference/seq_slaser_ideal.html
index 74688f4d..eb83e8e3 100644
--- a/docs/reference/seq_slaser_ideal.html
+++ b/docs/reference/seq_slaser_ideal.html
@@ -1,5 +1,5 @@
-sLASER sequence with ideal pulses. — seq_slaser_ideal • Spectroscopy Analysis Tools (spant) sLASER sequence with ideal pulses. — seq_slaser_ideal • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -126,7 +126,7 @@ Value
diff --git a/docs/reference/seq_spin_echo_ideal.html b/docs/reference/seq_spin_echo_ideal.html
index e23271de..4248716f 100644
--- a/docs/reference/seq_spin_echo_ideal.html
+++ b/docs/reference/seq_spin_echo_ideal.html
@@ -1,5 +1,5 @@
-Spin echo sequence with ideal pulses. — seq_spin_echo_ideal • Spectroscopy Analysis Tools (spant) Spin echo sequence with ideal pulses. — seq_spin_echo_ideal • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/seq_steam_ideal.html b/docs/reference/seq_steam_ideal.html
index a60685a8..1c8115d7 100644
--- a/docs/reference/seq_steam_ideal.html
+++ b/docs/reference/seq_steam_ideal.html
@@ -1,5 +1,5 @@
-STEAM sequence with ideal pulses. — seq_steam_ideal • Spectroscopy Analysis Tools (spant) STEAM sequence with ideal pulses. — seq_steam_ideal • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -128,7 +128,7 @@ Value
diff --git a/docs/reference/seq_steam_ideal_cof.html b/docs/reference/seq_steam_ideal_cof.html
index 8f225740..cba7af91 100644
--- a/docs/reference/seq_steam_ideal_cof.html
+++ b/docs/reference/seq_steam_ideal_cof.html
@@ -1,7 +1,5 @@
-STEAM sequence with ideal pulses and coherence order filtering to simulate
-gradient crushers. — seq_steam_ideal_cof • Spectroscopy Analysis Tools (spant) STEAM sequence with ideal pulses and coherence order filtering to simulate gradient crushers. — seq_steam_ideal_cof • Spectroscopy Analysis Tools (spant) STEAM sequence with ideal pulses using the z-rotation gradient simulation
-method described by Young et al JMR 140, 146-152 (1999). — seq_steam_ideal_young • Spectroscopy Analysis Tools (spant) STEAM sequence with ideal pulses using the z-rotation gradient simulation method described by Young et al JMR 140, 146-152 (1999). — seq_steam_ideal_young • Spectroscopy Analysis Tools (spant) Set the number of transients for an mrs_data object. — set_Ntrans • Spectroscopy Analysis Tools (spant) Set the number of transients for an mrs_data object. — set_Ntrans • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/set_def_acq_paras.html b/docs/reference/set_def_acq_paras.html
index 3e1b4004..cc2ada9c 100644
--- a/docs/reference/set_def_acq_paras.html
+++ b/docs/reference/set_def_acq_paras.html
@@ -1,5 +1,5 @@
-Set the default acquisition parameters. — set_def_acq_paras • Spectroscopy Analysis Tools (spant) Set the default acquisition parameters. — set_def_acq_paras • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Arguments
diff --git a/docs/reference/set_lcm_cmd.html b/docs/reference/set_lcm_cmd.html
index 2056ed01..42bb2f24 100644
--- a/docs/reference/set_lcm_cmd.html
+++ b/docs/reference/set_lcm_cmd.html
@@ -1,5 +1,5 @@
-Set the command to run the LCModel command-line program. — set_lcm_cmd • Spectroscopy Analysis Tools (spant) Set the command to run the LCModel command-line program. — set_lcm_cmd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/set_lw.html b/docs/reference/set_lw.html
index b64ec851..bb176c62 100644
--- a/docs/reference/set_lw.html
+++ b/docs/reference/set_lw.html
@@ -1,5 +1,5 @@
-Apply line-broadening to an mrs_data object to achieve a specified linewidth. — set_lw • Spectroscopy Analysis Tools (spant) Apply line-broadening to an mrs_data object to achieve a specified linewidth. — set_lw • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -123,7 +123,7 @@ Value
diff --git a/docs/reference/set_mask_xy_mat.html b/docs/reference/set_mask_xy_mat.html
index 49dc5d4e..52c4b617 100644
--- a/docs/reference/set_mask_xy_mat.html
+++ b/docs/reference/set_mask_xy_mat.html
@@ -1,5 +1,5 @@
-Set the masked voxels in a 2D MRSI dataset to given spectrum. — set_mask_xy_mat • Spectroscopy Analysis Tools (spant) Set the masked voxels in a 2D MRSI dataset to given spectrum. — set_mask_xy_mat • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Value
diff --git a/docs/reference/set_precomp_mode.html b/docs/reference/set_precomp_mode.html
index f44bd5d3..47c28e3b 100644
--- a/docs/reference/set_precomp_mode.html
+++ b/docs/reference/set_precomp_mode.html
@@ -1,5 +1,5 @@
-Set the precompute mode. — set_precomp_mode • Spectroscopy Analysis Tools (spant) Set the precompute mode. — set_precomp_mode • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/set_precomp_verbose.html b/docs/reference/set_precomp_verbose.html
index 1453a231..9c613505 100644
--- a/docs/reference/set_precomp_verbose.html
+++ b/docs/reference/set_precomp_verbose.html
@@ -1,5 +1,5 @@
-Set the verbosity of the precompute function. — set_precomp_verbose • Spectroscopy Analysis Tools (spant) Set the verbosity of the precompute function. — set_precomp_verbose • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/set_ref.html b/docs/reference/set_ref.html
index 8953fa50..5436dfa2 100644
--- a/docs/reference/set_ref.html
+++ b/docs/reference/set_ref.html
@@ -1,5 +1,5 @@
-Set the ppm reference value (eg ppm value at 0Hz). — set_ref • Spectroscopy Analysis Tools (spant) Set the ppm reference value (eg ppm value at 0Hz). — set_ref • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/set_td_pts.html b/docs/reference/set_td_pts.html
index 8a80d42a..586459ff 100644
--- a/docs/reference/set_td_pts.html
+++ b/docs/reference/set_td_pts.html
@@ -1,7 +1,5 @@
-Set the number of time-domain data points, truncating or zero-filling as
-appropriate. — set_td_pts • Spectroscopy Analysis Tools (spant) Set the number of time-domain data points, truncating or zero-filling as appropriate. — set_td_pts • Spectroscopy Analysis Tools (spant) Set the command to run the TARQUIN command-line program. — set_tqn_cmd • Spectroscopy Analysis Tools (spant) Set the command to run the TARQUIN command-line program. — set_tqn_cmd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/set_tr.html b/docs/reference/set_tr.html
index b2109ab0..65c9df5f 100644
--- a/docs/reference/set_tr.html
+++ b/docs/reference/set_tr.html
@@ -1,5 +1,5 @@
-Set the repetition time of an MRS dataset. — set_tr • Spectroscopy Analysis Tools (spant) Set the repetition time of an MRS dataset. — set_tr • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/shift.html b/docs/reference/shift.html
index ab0fe724..034591d0 100644
--- a/docs/reference/shift.html
+++ b/docs/reference/shift.html
@@ -1,5 +1,5 @@
-Apply a frequency shift to MRS data. — shift • Spectroscopy Analysis Tools (spant) Apply a frequency shift to MRS data. — shift • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/shift_basis.html b/docs/reference/shift_basis.html
index 2884be19..f55a65e0 100644
--- a/docs/reference/shift_basis.html
+++ b/docs/reference/shift_basis.html
@@ -1,5 +1,5 @@
-Apply frequency shifts to basis set signals. — shift_basis • Spectroscopy Analysis Tools (spant) Apply frequency shifts to basis set signals. — shift_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Value
diff --git a/docs/reference/sim_basis.html b/docs/reference/sim_basis.html
index c7838c46..bb5fefc6 100644
--- a/docs/reference/sim_basis.html
+++ b/docs/reference/sim_basis.html
@@ -1,5 +1,5 @@
-Simulate a basis set object. — sim_basis • Spectroscopy Analysis Tools (spant) Simulate a basis set object. — sim_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -136,7 +136,7 @@ Value
diff --git a/docs/reference/sim_basis_1h_brain.html b/docs/reference/sim_basis_1h_brain.html
index 62ed7389..f71ffa0b 100644
--- a/docs/reference/sim_basis_1h_brain.html
+++ b/docs/reference/sim_basis_1h_brain.html
@@ -1,7 +1,5 @@
-Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS
-sequence. Note, ideal pulses are assumed. — sim_basis_1h_brain • Spectroscopy Analysis Tools (spant) Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS sequence. Note, ideal pulses are assumed. — sim_basis_1h_brain • Spectroscopy Analysis Tools (spant) Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS
-sequence. Note, ideal pulses are assumed. — sim_basis_1h_brain_press • Spectroscopy Analysis Tools (spant) Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS sequence. Note, ideal pulses are assumed. — sim_basis_1h_brain_press • Spectroscopy Analysis Tools (spant) Simulate a macromolecular and lipid basis-set suitable for 1H brain MRS
-analysis. — sim_basis_mm_lip_lcm • Spectroscopy Analysis Tools (spant) Simulate a macromolecular and lipid basis-set suitable for 1H brain MRS analysis. — sim_basis_mm_lip_lcm • Spectroscopy Analysis Tools (spant) Simulate a basis file using TARQUIN. — sim_basis_tqn • Spectroscopy Analysis Tools (spant) Simulate a basis file using TARQUIN. — sim_basis_tqn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -129,7 +129,7 @@ Examples
diff --git a/docs/reference/sim_brain_1h.html b/docs/reference/sim_brain_1h.html
index 2044cf1a..717ee289 100644
--- a/docs/reference/sim_brain_1h.html
+++ b/docs/reference/sim_brain_1h.html
@@ -1,5 +1,5 @@
-Simulate MRS data with a similar appearance to normal brain (by default). — sim_brain_1h • Spectroscopy Analysis Tools (spant) Simulate MRS data with a similar appearance to normal brain (by default). — sim_brain_1h • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -159,7 +159,7 @@ Value
diff --git a/docs/reference/sim_mol.html b/docs/reference/sim_mol.html
index 23bcef50..77f76a50 100644
--- a/docs/reference/sim_mol.html
+++ b/docs/reference/sim_mol.html
@@ -1,5 +1,5 @@
-Simulate a mol_parameter object. — sim_mol • Spectroscopy Analysis Tools (spant) Simulate a mol_parameter object. — sim_mol • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -143,7 +143,7 @@ Value
diff --git a/docs/reference/sim_noise.html b/docs/reference/sim_noise.html
index 23875f79..a71477d4 100644
--- a/docs/reference/sim_noise.html
+++ b/docs/reference/sim_noise.html
@@ -1,5 +1,5 @@
-Simulate an mrs_data object containing simulated Gaussian noise. — sim_noise • Spectroscopy Analysis Tools (spant) Simulate an mrs_data object containing simulated Gaussian noise. — sim_noise • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -84,6 +84,7 @@ Simulate an mrs_data object containing simulated Gaussian noise.
ft = def_ft(),
N = def_N(),
ref = def_ref(),
+ nuc = def_nuc(),
dyns = 1,
fd = TRUE
)
@@ -111,6 +112,10 @@ Arguments
reference value for ppm scale.
nuc
+resonant nucleus.
dyns
number of dynamic scans to generate.
Value
diff --git a/docs/reference/sim_resonances.html b/docs/reference/sim_resonances.html
index 19e9a8a4..d4f8d7c0 100644
--- a/docs/reference/sim_resonances.html
+++ b/docs/reference/sim_resonances.html
@@ -1,5 +1,5 @@
-Simulate a MRS data object containing a set of simulated resonances. — sim_resonances • Spectroscopy Analysis Tools (spant) Simulate a MRS data object containing a set of simulated resonances. — sim_resonances • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -161,7 +161,7 @@ Examples
diff --git a/docs/reference/sim_th_excit_profile.html b/docs/reference/sim_th_excit_profile.html
index 5535c5ef..e781cab1 100644
--- a/docs/reference/sim_th_excit_profile.html
+++ b/docs/reference/sim_th_excit_profile.html
@@ -1,7 +1,5 @@
-Simulate an ideal pulse excitation profile by smoothing a top-hat function
-with a Gaussian. — sim_th_excit_profile • Spectroscopy Analysis Tools (spant) Simulate an ideal pulse excitation profile by smoothing a top-hat function with a Gaussian. — sim_th_excit_profile • Spectroscopy Analysis Tools (spant) Simulate an mrs_data object containing complex zero valued samples. — sim_zero • Spectroscopy Analysis Tools (spant) Simulate an mrs_data object containing complex zero valued samples. — sim_zero • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -78,7 +78,14 @@ Simulate an mrs_data object containing complex zero valued samples.
-
+
@@ -99,6 +106,10 @@ Arguments
reference value for ppm scale.
nuc
+resonant nucleus.
dyns
number of dynamic scans to generate.
Value
diff --git a/docs/reference/smooth_dyns.html b/docs/reference/smooth_dyns.html
index 4cc8da50..accf3a51 100644
--- a/docs/reference/smooth_dyns.html
+++ b/docs/reference/smooth_dyns.html
@@ -1,5 +1,5 @@
-Smooth data across the dynamic dimension with a Gaussian kernel. — smooth_dyns • Spectroscopy Analysis Tools (spant) Smooth data across the dynamic dimension with a Gaussian kernel. — smooth_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/sort_basis.html b/docs/reference/sort_basis.html
index 6a676ea2..d25cc006 100644
--- a/docs/reference/sort_basis.html
+++ b/docs/reference/sort_basis.html
@@ -1,5 +1,5 @@
-Sort the basis-set elements alphabetically. — sort_basis • Spectroscopy Analysis Tools (spant) Sort the basis-set elements alphabetically. — sort_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/spant-package.html b/docs/reference/spant-package.html
index b3dd8e21..90f19ec3 100644
--- a/docs/reference/spant-package.html
+++ b/docs/reference/spant-package.html
@@ -1,5 +1,5 @@
-spant: spectroscopy analysis tools. — spant-package • Spectroscopy Analysis Tools (spant) spant: spectroscopy analysis tools. — spant-package • Spectroscopy Analysis Tools (spant) Simulate and fit some spectra with ABfit for benchmarking purposes. Basic
-timing and performance metrics will be printed. — spant_abfit_benchmark • Spectroscopy Analysis Tools (spant) Simulate and fit some spectra with ABfit for benchmarking purposes. Basic timing and performance metrics will be printed. — spant_abfit_benchmark • Spectroscopy Analysis Tools (spant) Example MEGA-PRESS data with significant B0 drift. — spant_mpress_drift • Spectroscopy Analysis Tools (spant) Example MEGA-PRESS data with significant B0 drift. — spant_mpress_drift • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -83,7 +83,7 @@ Example MEGA-PRESS data with significant B0 drift.
Format
- An object of class mrs_data of length 13.
+ An object of class mrs_data of dimension 1 x 1 x 1 x 1 x 40 x 1 x 1024.
@@ -98,7 +98,7 @@ Format
diff --git a/docs/reference/spant_sim_fmrs_dataset.html b/docs/reference/spant_sim_fmrs_dataset.html
new file mode 100644
index 00000000..00e48b56
--- /dev/null
+++ b/docs/reference/spant_sim_fmrs_dataset.html
@@ -0,0 +1,117 @@
+
+Simulate an example fMRS dataset for a block design fMRS experiment and export a BIDS structure. — spant_sim_fmrs_dataset • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Simulate an example fMRS dataset for a block design fMRS experiment and export a BIDS structure.
+ Source: R/fmrs.R
+ spant_sim_fmrs_dataset.Rd
+
+
+
+ Simulate an example fMRS dataset for a block design fMRS experiment and
+export a BIDS structure.
+
+
+
+ spant_sim_fmrs_dataset(output_dir = NULL)
+
+
+
+ Arguments
+ - output_dir
+output directory for the BIDS data. Defaults to :
+"HOME/sim_fmrs_dataset/data".
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/spant_simulation_benchmark.html b/docs/reference/spant_simulation_benchmark.html
index 32daa8bf..d8cc6841 100644
--- a/docs/reference/spant_simulation_benchmark.html
+++ b/docs/reference/spant_simulation_benchmark.html
@@ -1,7 +1,5 @@
-Simulate a typical metabolite basis set for benchmarking. Timing metrics will
-be printed on completion. — spant_simulation_benchmark • Spectroscopy Analysis Tools (spant) Simulate a typical metabolite basis set for benchmarking. Timing metrics will be printed on completion. — spant_simulation_benchmark • Spectroscopy Analysis Tools (spant) Decompose an mrs_data object into white and gray matter spectra. — spec_decomp • Spectroscopy Analysis Tools (spant) Perform a mathematical operation on a spectral region. — spec_op • Spectroscopy Analysis Tools (spant) Perform a mathematical operation on a spectral region. — spec_op • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -98,8 +98,8 @@ Arguments
operator
-can be "sum" (default), "mean", "l2", "max", "min" or
-"max-min".
can be "sum" (default), "mean", "l2", "max", "max_cplx,
+"min" or "max-min".
freq_scale
@@ -129,7 +129,7 @@ Value
diff --git a/docs/reference/spin_sys.html b/docs/reference/spin_sys.html
index 853423a4..1eaa9e76 100644
--- a/docs/reference/spin_sys.html
+++ b/docs/reference/spin_sys.html
@@ -1,5 +1,5 @@
-Create a spin system object for pulse sequence simulation. — spin_sys • Spectroscopy Analysis Tools (spant) Create a spin system object for pulse sequence simulation. — spin_sys • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/spm_pve2categorical.html b/docs/reference/spm_pve2categorical.html
index 23a1bad9..70f10729 100644
--- a/docs/reference/spm_pve2categorical.html
+++ b/docs/reference/spm_pve2categorical.html
@@ -1,7 +1,5 @@
-Convert SPM style segmentation files to a single categorical image where
-the numerical values map as: 0) Other, 1) CSF, 2) GM and 3) WM. — spm_pve2categorical • Spectroscopy Analysis Tools (spant) Convert SPM style segmentation files to a single categorical image where the numerical values map as: 0) Other, 1) CSF, 2) GM and 3) WM. — spm_pve2categorical • Spectroscopy Analysis Tools (spant) Signal space projection method for lipid suppression. — ssp • Spectroscopy Analysis Tools (spant) Signal space projection method for lipid suppression. — ssp • Spectroscopy Analysis Tools (spant) Plot the fitting results of an object of class fit_result with
-individual basis set components shown. — stackplot.fit_result • Spectroscopy Analysis Tools (spant) Plot the fitting results of an object of class fit_result with individual basis set components shown. — stackplot.fit_result • Spectroscopy Analysis Tools (spant) Produce a plot with multiple traces. — stackplot • Spectroscopy Analysis Tools (spant) Produce a plot with multiple traces. — stackplot • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/stackplot.mrs_data.html b/docs/reference/stackplot.mrs_data.html
index 17ff5648..64eea445 100644
--- a/docs/reference/stackplot.mrs_data.html
+++ b/docs/reference/stackplot.mrs_data.html
@@ -1,5 +1,5 @@
-Stackplot plotting method for objects of class mrs_data. — stackplot.mrs_data • Spectroscopy Analysis Tools (spant) Stackplot plotting method for objects of class mrs_data. — stackplot.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -255,7 +255,7 @@ Arguments
diff --git a/docs/reference/sub_first_dyn.html b/docs/reference/sub_first_dyn.html
index dbd7f831..493b7242 100644
--- a/docs/reference/sub_first_dyn.html
+++ b/docs/reference/sub_first_dyn.html
@@ -1,5 +1,5 @@
-Subtract the first dynamic spectrum from a dynamic series. — sub_first_dyn • Spectroscopy Analysis Tools (spant) Subtract the first dynamic spectrum from a dynamic series. — sub_first_dyn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/sub_mean_dyns.html b/docs/reference/sub_mean_dyns.html
index 6e3bb2df..221bd0c1 100644
--- a/docs/reference/sub_mean_dyns.html
+++ b/docs/reference/sub_mean_dyns.html
@@ -1,5 +1,5 @@
-Subtract the mean dynamic spectrum from a dynamic series. — sub_mean_dyns • Spectroscopy Analysis Tools (spant) Subtract the mean dynamic spectrum from a dynamic series. — sub_mean_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/sub_median_dyns.html b/docs/reference/sub_median_dyns.html
index 134c495d..1e834f14 100644
--- a/docs/reference/sub_median_dyns.html
+++ b/docs/reference/sub_median_dyns.html
@@ -1,5 +1,5 @@
-Subtract the median dynamic spectrum from a dynamic series. — sub_median_dyns • Spectroscopy Analysis Tools (spant) Subtract the median dynamic spectrum from a dynamic series. — sub_median_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/sum_coils.html b/docs/reference/sum_coils.html
index 7bf559f2..e1ab3cc0 100644
--- a/docs/reference/sum_coils.html
+++ b/docs/reference/sum_coils.html
@@ -1,5 +1,5 @@
-Calculate the sum across receiver coil elements. — sum_coils • Spectroscopy Analysis Tools (spant) Calculate the sum across receiver coil elements. — sum_coils • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/sum_dyns.html b/docs/reference/sum_dyns.html
index a0be19d3..bbda2ffc 100644
--- a/docs/reference/sum_dyns.html
+++ b/docs/reference/sum_dyns.html
@@ -1,5 +1,5 @@
-Calculate the sum of data dynamics. — sum_dyns • Spectroscopy Analysis Tools (spant) Calculate the sum of data dynamics. — sum_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/sum_mrs.html b/docs/reference/sum_mrs.html
index a22f215b..3cc3ab9e 100644
--- a/docs/reference/sum_mrs.html
+++ b/docs/reference/sum_mrs.html
@@ -1,5 +1,5 @@
-Sum two mrs_data objects. — sum_mrs • Spectroscopy Analysis Tools (spant) Sum two mrs_data objects. — sum_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Value
diff --git a/docs/reference/sum_mrs_list.html b/docs/reference/sum_mrs_list.html
index f4e09aea..c3584348 100644
--- a/docs/reference/sum_mrs_list.html
+++ b/docs/reference/sum_mrs_list.html
@@ -1,5 +1,5 @@
-Return the sum of a list of mrs_data objects. — sum_mrs_list • Spectroscopy Analysis Tools (spant) Return the sum of a list of mrs_data objects. — sum_mrs_list • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/svs_1h_brain_analysis.html b/docs/reference/svs_1h_brain_analysis.html
index 8ce514db..dff0ef7d 100644
--- a/docs/reference/svs_1h_brain_analysis.html
+++ b/docs/reference/svs_1h_brain_analysis.html
@@ -1,5 +1,5 @@
-Standard SVS 1H brain analysis pipeline. — svs_1h_brain_analysis • Spectroscopy Analysis Tools (spant) Standard SVS 1H brain analysis pipeline. — svs_1h_brain_analysis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -199,7 +199,7 @@ Value
diff --git a/docs/reference/svs_1h_brain_analysis_dev.html b/docs/reference/svs_1h_brain_analysis_dev.html
index d70a14d3..d71bfea2 100644
--- a/docs/reference/svs_1h_brain_analysis_dev.html
+++ b/docs/reference/svs_1h_brain_analysis_dev.html
@@ -1,5 +1,5 @@
-Standard SVS 1H brain analysis pipeline. — svs_1h_brain_analysis_dev • Spectroscopy Analysis Tools (spant) Standard SVS 1H brain analysis pipeline. — svs_1h_brain_analysis_dev • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -193,7 +193,7 @@ Examples
diff --git a/docs/reference/svs_1h_brain_batch_analysis.html b/docs/reference/svs_1h_brain_batch_analysis.html
index 5631e8cc..15f7223e 100644
--- a/docs/reference/svs_1h_brain_batch_analysis.html
+++ b/docs/reference/svs_1h_brain_batch_analysis.html
@@ -1,5 +1,5 @@
-Batch interface to the standard SVS 1H brain analysis pipeline. — svs_1h_brain_batch_analysis • Spectroscopy Analysis Tools (spant) Batch interface to the standard SVS 1H brain analysis pipeline. — svs_1h_brain_batch_analysis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -144,7 +144,7 @@ Value
diff --git a/docs/reference/t_test_spec.html b/docs/reference/t_test_spec.html
new file mode 100644
index 00000000..56a7ea1b
--- /dev/null
+++ b/docs/reference/t_test_spec.html
@@ -0,0 +1,124 @@
+
+Perform a t-test on spectral data points. — t_test_spec • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+
+
+ Perform a t-test on spectral data points.
+
+
+
+ t_test_spec(mrs_data, group)
+
+
+
+ Arguments
+ - mrs_data
+an mrs_data object with spectra in the dynamic dimension.
- group
+vector describing the group membership of each dynamic spectrum.
+
+ Value
+
+
+a list of statistical results.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/td2fd.html b/docs/reference/td2fd.html
index 6748a6a8..f31ed524 100644
--- a/docs/reference/td2fd.html
+++ b/docs/reference/td2fd.html
@@ -1,5 +1,5 @@
-Transform time-domain data to the frequency-domain. — td2fd • Spectroscopy Analysis Tools (spant) Transform time-domain data to the frequency-domain. — td2fd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/td_conv_filt.html b/docs/reference/td_conv_filt.html
index a9f340c3..106b9b00 100644
--- a/docs/reference/td_conv_filt.html
+++ b/docs/reference/td_conv_filt.html
@@ -1,5 +1,5 @@
-Time-domain convolution based filter. — td_conv_filt • Spectroscopy Analysis Tools (spant) Time-domain convolution based filter. — td_conv_filt • Spectroscopy Analysis Tools (spant) Time-domain spectral registration. — tdsr • Spectroscopy Analysis Tools (spant) Time-domain spectral registration. — tdsr • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -121,7 +121,7 @@ Value
diff --git a/docs/reference/te.html b/docs/reference/te.html
index 010361b1..4a65711d 100644
--- a/docs/reference/te.html
+++ b/docs/reference/te.html
@@ -1,5 +1,5 @@
-Return the echo time of an MRS dataset. — te • Spectroscopy Analysis Tools (spant) Return the echo time of an MRS dataset. — te • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/tr.html b/docs/reference/tr.html
index 0c0bd63b..2e749e02 100644
--- a/docs/reference/tr.html
+++ b/docs/reference/tr.html
@@ -1,5 +1,5 @@
-Return the repetition time of an MRS dataset. — tr • Spectroscopy Analysis Tools (spant) Return the repetition time of an MRS dataset. — tr • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/varpro_3_para_opts.html b/docs/reference/varpro_3_para_opts.html
index c2270a16..52d7cd84 100644
--- a/docs/reference/varpro_3_para_opts.html
+++ b/docs/reference/varpro_3_para_opts.html
@@ -1,5 +1,5 @@
-Return a list of options for VARPRO based fitting with 3 free parameters. — varpro_3_para_opts • Spectroscopy Analysis Tools (spant) Return a list of options for VARPRO based fitting with 3 free parameters. — varpro_3_para_opts • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -141,7 +141,7 @@ Value
diff --git a/docs/reference/varpro_basic_opts.html b/docs/reference/varpro_basic_opts.html
index 32c86d22..c5104891 100644
--- a/docs/reference/varpro_basic_opts.html
+++ b/docs/reference/varpro_basic_opts.html
@@ -1,5 +1,5 @@
-Return a list of options for a basic VARPRO analysis. — varpro_basic_opts • Spectroscopy Analysis Tools (spant) Return a list of options for a basic VARPRO analysis. — varpro_basic_opts • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -118,7 +118,7 @@ Value
diff --git a/docs/reference/varpro_opts.html b/docs/reference/varpro_opts.html
index 2aabf11d..6332f730 100644
--- a/docs/reference/varpro_opts.html
+++ b/docs/reference/varpro_opts.html
@@ -1,5 +1,5 @@
-Return a list of options for VARPRO based fitting. — varpro_opts • Spectroscopy Analysis Tools (spant) Return a list of options for VARPRO based fitting. — varpro_opts • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -177,7 +177,7 @@ Examples
diff --git a/docs/reference/vec2mrs_data.html b/docs/reference/vec2mrs_data.html
index 0cccd73b..f0d58bf0 100644
--- a/docs/reference/vec2mrs_data.html
+++ b/docs/reference/vec2mrs_data.html
@@ -1,5 +1,5 @@
-Convert a vector into a mrs_data object. — vec2mrs_data • Spectroscopy Analysis Tools (spant) Convert a vector into a mrs_data object. — vec2mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -80,10 +80,11 @@ Convert a vector into a mrs_data object.
vec2mrs_data(
vec,
- fs = def_fs(),
- ft = def_ft(),
- ref = def_ref(),
- nuc = def_nuc(),
+ mrs_data = NULL,
+ fs = NULL,
+ ft = NULL,
+ ref = NULL,
+ nuc = NULL,
dyns = 1,
fd = FALSE
)
@@ -95,6 +96,10 @@ Arguments
the data vector.
mrs_data
+example data to copy acquisition parameters from.
fs
sampling frequency in Hz.
Arguments
fd
-flag to indicate if the matrix is in the frequency domain (logical).
flag to indicate if the vector is in the frequency domain (logical).
Value
diff --git a/docs/reference/write_basis.html b/docs/reference/write_basis.html
index b6e27cbd..94c5e021 100644
--- a/docs/reference/write_basis.html
+++ b/docs/reference/write_basis.html
@@ -1,5 +1,5 @@
-Write a basis object to an LCModel .basis formatted file. — write_basis • Spectroscopy Analysis Tools (spant) Write a basis object to an LCModel .basis formatted file. — write_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -108,7 +108,7 @@ Arguments
diff --git a/docs/reference/write_basis_tqn.html b/docs/reference/write_basis_tqn.html
index 6aa51c1d..116c73ec 100644
--- a/docs/reference/write_basis_tqn.html
+++ b/docs/reference/write_basis_tqn.html
@@ -1,5 +1,5 @@
-Generate a basis file using TARQUIN. — write_basis_tqn • Spectroscopy Analysis Tools (spant) Generate a basis file using TARQUIN. — write_basis_tqn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Examples
diff --git a/docs/reference/write_mrs.html b/docs/reference/write_mrs.html
index fff25f15..124b9dc4 100644
--- a/docs/reference/write_mrs.html
+++ b/docs/reference/write_mrs.html
@@ -1,5 +1,5 @@
-Write MRS data object to file. — write_mrs • Spectroscopy Analysis Tools (spant) Write MRS data object to file. — write_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Arguments
diff --git a/docs/reference/write_mrs_nifti.html b/docs/reference/write_mrs_nifti.html
index f4bf1921..bd3ed4b7 100644
--- a/docs/reference/write_mrs_nifti.html
+++ b/docs/reference/write_mrs_nifti.html
@@ -1,5 +1,5 @@
-Write MRS data object to file in NIFTI format. — write_mrs_nifti • Spectroscopy Analysis Tools (spant) Write MRS data object to file in NIFTI format. — write_mrs_nifti • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/write_pulse_ascii.html b/docs/reference/write_pulse_ascii.html
index 067ae086..221f8ebb 100644
--- a/docs/reference/write_pulse_ascii.html
+++ b/docs/reference/write_pulse_ascii.html
@@ -1,5 +1,5 @@
-Write an ASCII formatted pulse file. — write_pulse_ascii • Spectroscopy Analysis Tools (spant) Write an ASCII formatted pulse file. — write_pulse_ascii • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/zero_fade_spec.html b/docs/reference/zero_fade_spec.html
index c703745c..c8b572c3 100644
--- a/docs/reference/zero_fade_spec.html
+++ b/docs/reference/zero_fade_spec.html
@@ -1,7 +1,5 @@
-Fade a spectrum to zero by frequency domain multiplication with a tanh
-function. Note this operation distorts data points at the end of the FID. — zero_fade_spec • Spectroscopy Analysis Tools (spant) Fade a spectrum to zero by frequency domain multiplication with a tanh function. Note this operation distorts data points at the end of the FID. — zero_fade_spec • Spectroscopy Analysis Tools (spant) Zero all coherences including and above a given order. — zero_higher_orders • Spectroscopy Analysis Tools (spant) Zero all coherences including and above a given order. — zero_higher_orders • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Value
diff --git a/docs/reference/zero_td_pts_end.html b/docs/reference/zero_td_pts_end.html
index 8c1123c8..71d24ebb 100644
--- a/docs/reference/zero_td_pts_end.html
+++ b/docs/reference/zero_td_pts_end.html
@@ -1,5 +1,5 @@
-Set mrs_data object data points at the end of the FID to zero. — zero_td_pts_end • Spectroscopy Analysis Tools (spant) Set mrs_data object data points at the end of the FID to zero. — zero_td_pts_end • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/zf.html b/docs/reference/zf.html
index 85e2013c..baf50256 100644
--- a/docs/reference/zf.html
+++ b/docs/reference/zf.html
@@ -1,5 +1,5 @@
-Zero-fill MRS data in the time domain. — zf • Spectroscopy Analysis Tools (spant) Zero-fill MRS data in the time domain. — zf • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -125,7 +125,7 @@ Value
diff --git a/docs/reference/zf_xy.html b/docs/reference/zf_xy.html
index ebca3999..c4104a74 100644
--- a/docs/reference/zf_xy.html
+++ b/docs/reference/zf_xy.html
@@ -1,5 +1,5 @@
-Zero-fill MRSI data in the k-space x-y direction. — zf_xy • Spectroscopy Analysis Tools (spant) Zero-fill MRSI data in the k-space x-y direction. — zf_xy • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -113,7 +113,7 @@ Value
diff --git a/docs/sitemap.xml b/docs/sitemap.xml
index e2139f71..4c39f515 100644
--- a/docs/sitemap.xml
+++ b/docs/sitemap.xml
@@ -216,6 +216,12 @@
https://martin3141.github.io/spant/reference/comb_coils_fp_pc.html
+
+ https://martin3141.github.io/spant/reference/comb_coils_mrsi_gls.html
+
+
+ https://martin3141.github.io/spant/reference/comb_coils_svs_gls.html
+
https://martin3141.github.io/spant/reference/comb_csv_results.html
@@ -411,6 +417,9 @@
https://martin3141.github.io/spant/reference/gen_conv_reg.html
+
+ https://martin3141.github.io/spant/reference/gen_group_reg.html
+
https://martin3141.github.io/spant/reference/gen_impulse_reg.html
@@ -555,6 +564,15 @@
https://martin3141.github.io/spant/reference/glm_spec.html
+
+ https://martin3141.github.io/spant/reference/glm_spec_fmrs_fl.html
+
+
+ https://martin3141.github.io/spant/reference/glm_spec_fmrs_group.html
+
+
+ https://martin3141.github.io/spant/reference/glm_spec_group_linhyp.html
+
https://martin3141.github.io/spant/reference/grid_shift_xy.html
@@ -690,9 +708,15 @@
https://martin3141.github.io/spant/reference/mrs_data2basis.html
+
+ https://martin3141.github.io/spant/reference/mrs_data2bids.html
+
https://martin3141.github.io/spant/reference/mrs_data2mat.html
+
+ https://martin3141.github.io/spant/reference/mrs_data2spec_mat.html
+
https://martin3141.github.io/spant/reference/mrs_data2vec.html
@@ -741,6 +765,9 @@
https://martin3141.github.io/spant/reference/phase.html
+
+ https://martin3141.github.io/spant/reference/phase_ref_1h_brain.html
+
https://martin3141.github.io/spant/reference/plot.fit_result.html
@@ -780,6 +807,12 @@
https://martin3141.github.io/spant/reference/precomp.html
+
+ https://martin3141.github.io/spant/reference/preproc_svs.html
+
+
+ https://martin3141.github.io/spant/reference/preproc_svs_dataset.html
+
https://martin3141.github.io/spant/reference/print.fit_result.html
@@ -1050,6 +1083,9 @@
https://martin3141.github.io/spant/reference/spant_mpress_drift.html
+
+ https://martin3141.github.io/spant/reference/spant_sim_fmrs_dataset.html
+
https://martin3141.github.io/spant/reference/spant_simulation_benchmark.html
@@ -1107,6 +1143,9 @@
https://martin3141.github.io/spant/reference/svs_1h_brain_batch_analysis.html
+
+ https://martin3141.github.io/spant/reference/t_test_spec.html
+
https://martin3141.github.io/spant/reference/td2fd.html
Perform a polynomial fit, subtract and return the standard deviation of the -residuals.
Perform a polynomial fit, subtract and return the standard deviation of the residuals.
All functions comb_coils()
Combine coil data based on the first data point of a reference signal.
Combine coil data based on the first data point of a reference signal.
Combine MRSI coil data using the GLS method presented by An et al JMRI 37:1445-1450 (2013).
Combine SVS coil data using the GLS method presented by An et al JMRI 37:1445-1450 (2013).
All functions
- Crop mrs_data object data points in the time-domain rounding down to
-the next smallest power of two (pot). Data that already has a pot length will
-not be changed.
Crop mrs_data object data points in the time-domain rounding down to the next smallest power of two (pot). Data that already has a pot length will not be changed.
@@ -355,13 +350,11 @@ All functions
- Compute the vector cross product between vectors x and y. Adapted from
-http://stackoverflow.com/questions/15162741/what-is-rs-crossproduct-function
Compute the vector cross product between vectors x and y. Adapted from http://stackoverflow.com/questions/15162741/what-is-rs-crossproduct-function
- Decimate an MRS signal to half the original sampling frequency by filtering
-in the frequency domain before down sampling.
Decimate an MRS signal to half the original sampling frequency by filtering in the frequency domain before down sampling.
@@ -377,8 +370,7 @@ All functions
- Return (and optionally modify using the input arguments) a list of the
-default acquisition parameters.
Return (and optionally modify using the input arguments) a list of the default acquisition parameters.
@@ -410,14 +402,11 @@ All functions
- Downsample an MRS signal by a factor of 2 by removing every other data point
-in the time-domain. Note, signals outside the new sampling frequency will be
-aliased.
Downsample an MRS signal by a factor of 2 by removing every other data point in the time-domain. Note, signals outside the new sampling frequency will be aliased.
- Return a time scale vector of acquisition times for a dynamic MRS scan. The
-first temporal scan is assigned a value of 0.
Return a time scale vector of acquisition times for a dynamic MRS scan. The first temporal scan is assigned a value of 0.
@@ -429,8 +418,7 @@ All functions
- Estimate the standard deviation of the noise from a segment of an mrs_data
-object.
Estimate the standard deviation of the noise from a segment of an mrs_data object.
@@ -486,8 +474,7 @@ All functions
- Perform a zeroth order phase correction based on the phase of the first data
-point in the time-domain.
Perform a zeroth order phase correction based on the phase of the first data point in the time-domain.
@@ -507,8 +494,7 @@ All functions
- Perform a fft and fftshift on a matrix with each column replaced by its
-shifted fft.
Perform a fft and fftshift on a matrix with each column replaced by its shifted fft.
@@ -536,8 +522,11 @@ All functions
- Generate regressors by convolving a specified response function with a
-stimulus.
Generate regressors by convolving a specified response function with a stimulus.
+
+
+ Expand a regressor matrix for a group analysis.
@@ -553,28 +542,23 @@ All functions
- Return a character vector of common 1H molecules found in healthy human
-brain.
Return a character vector of common 1H molecules found in healthy human brain.
- Return a list of mol_parameter objects suitable for 1H brain MRS
-analyses.
Return a list of mol_parameter objects suitable for 1H brain MRS analyses.
- Return a list of mol_parameter objects suitable for 1H brain MRS
-analyses.
Return a list of mol_parameter objects suitable for 1H brain MRS analyses.
- Return a list of mol_parameter objects suitable for 1H brain MRS
-analyses.
Return a list of mol_parameter objects suitable for 1H brain MRS analyses.
- Return a list of mol_parameter objects suitable for 1H brain MRS
-analyses.
Return a list of mol_parameter objects suitable for 1H brain MRS analyses.
@@ -582,8 +566,7 @@ All functions
- Return a character vector of molecules included in the Gold Star Phantoms
-SPECTRE phantom.
Return a character vector of molecules included in the Gold Star Phantoms SPECTRE phantom.
@@ -635,8 +618,7 @@ All functions
- Return a character array of names that may be used with the
-get_mol_paras function.
Return a character array of names that may be used with the get_mol_paras function.
@@ -700,8 +682,7 @@ All functions
- Return an array of amplitudes derived from fitting the initial points in the
-time domain and extrapolating back to t=0.
Return an array of amplitudes derived from fitting the initial points in the time domain and extrapolating back to t=0.
@@ -709,8 +690,7 @@ All functions
- Generate a mol_parameters object for a simple spin system with one
-resonance.
Generate a mol_parameters object for a simple spin system with one resonance.
@@ -731,6 +711,18 @@ All functions glm_spec()
Perform a GLM analysis of dynamic MRS data in the spectral domain.
+
+
+ Perform first-level spectral GLM analysis of an fMRS dataset.
+
+
+ Perform group-level spectral GLM analysis of an fMRS dataset.
+
+
+ Test a group-level spectral GLM linear hypothesis.
@@ -766,8 +758,7 @@ All functions
- Perform an ifft and ifftshift on a matrix with each column replaced by its
-shifted ifft.
Perform an ifft and ifftshift on a matrix with each column replaced by its shifted ifft.
@@ -799,8 +790,7 @@ All functions
- Check if the chemical shift dimension of an MRS data object is in the
-frequency domain.
Check if the chemical shift dimension of an MRS data object is in the frequency domain.
@@ -820,18 +810,15 @@ All functions
- Covert a linewidth in Hz to an equivalent alpha value in the time-domain ie:
-x * exp(-t * alpha).
Covert a linewidth in Hz to an equivalent alpha value in the time-domain ie: x * exp(-t * alpha).
- Covert a linewidth in Hz to an equivalent beta value in the time-domain ie:
-x * exp(-t * t * beta).
Covert a linewidth in Hz to an equivalent beta value in the time-domain ie: x * exp(-t * t * beta).
- Make a basis-set object from a directory containing LCModel formatted RAW
-files.
Make a basis-set object from a directory containing LCModel formatted RAW files.
@@ -851,8 +838,7 @@ All functions
- Mask the voxels outside an elliptical region spanning the MRSI dataset in the
-x-y plane.
Mask the voxels outside an elliptical region spanning the MRSI dataset in the x-y plane.
@@ -860,13 +846,11 @@ All functions
- Convert a matrix (with spectral points in the column dimension and dynamics
-in the row dimensions) into a mrs_data object.
Convert a matrix (with spectral points in the column dimension and dynamics in the row dimensions) into a mrs_data object.
- Matrix exponential function taken from complexplus package to reduce the
-number of spant dependencies.
Matrix exponential function taken from complexplus package to reduce the number of spant dependencies.
@@ -914,31 +898,31 @@ All functions
- Convert an mrs_data object to basis object - where basis signals are spread
-across the dynamic dimension in the MRS data.
Convert an mrs_data object to basis object - where basis signals are spread across the dynamic dimension in the MRS data.
+
+
+ Create a BIDS file structure from a vector of MRS data paths or list of mrs_data objects.
- Convert mrs_data object to a matrix, with spectral points in the column
-dimension and dynamics in the row dimension.
Convert mrs_data object to a matrix, with spectral points in the column dimension and dynamics in the row dimension.
-
+
- Convert mrs_data object to a vector.
Convert mrs_data object to a matrix, with spectral points in the column dimension and dynamics in the row dimension.
-
+
- Create a BIDS directory and file structure from a list of mrs_data objects.
Convert mrs_data object to a vector.
- Perform a fftshift on a matrix, with each column replaced by its shifted
-result.
Perform a fftshift on a matrix, with each column replaced by its shifted result.
- Perform an ifftshift on a matrix, with each column replaced by its shifted
-result.
Perform an ifftshift on a matrix, with each column replaced by its shifted result.
@@ -946,9 +930,7 @@ All functions
- Flip the x data dimension order of a nifti image. This corresponds to
-flipping MRI data in the left-right direction, assuming the data in save in
-neurological format (can check with fslorient program).
Flip the x data dimension order of a nifti image. This corresponds to flipping MRI data in the left-right direction, assuming the data in save in neurological format (can check with fslorient program).
@@ -964,8 +946,7 @@ All functions
- Search for the highest peak in a spectral region and return the frequency,
-height and FWHM.
Search for the highest peak in a spectral region and return the frequency, height and FWHM.
@@ -974,6 +955,10 @@ All functions phase()
Apply phasing parameters to MRS data.
+
+
+ Corrected zero order phase and chemical shift offset in 1H MRS data from the brain.
@@ -1005,8 +990,7 @@ All functions
- Plot an interactive slice map from a data array where voxels can be selected
-to display a corresponding spectrum.
Plot an interactive slice map from a data array where voxels can be selected to display a corresponding spectrum.
@@ -1026,8 +1010,15 @@ All functions
- Save function results to file and load on subsequent calls to avoid repeat
-computation.
Save function results to file and load on subsequent calls to avoid repeat computation.
+
+
+ Preprocess and perform quality assessment of a single SVS data set.
+
+
+ Preprocess and perform quality assessment of one or more SVS data sets.
@@ -1055,15 +1046,11 @@ All functions
- Read a directory containing Siemens MRS IMA files and combine along the coil
-dimension. Note that the coil ID is inferred from the sorted file name and
-should be checked when consistency is required between two directories.
Read a directory containing Siemens MRS IMA files and combine along the coil dimension. Note that the coil ID is inferred from the sorted file name and should be checked when consistency is required between two directories.
- Read a directory containing Siemens MRS IMA files and combine along the
-dynamic dimension. Note that the coil ID is inferred from the sorted file
-name and should be checked when consistency is required.
Read a directory containing Siemens MRS IMA files and combine along the dynamic dimension. Note that the coil ID is inferred from the sorted file name and should be checked when consistency is required.
@@ -1103,13 +1090,11 @@ All functions
- Reconstruct complex time-domain data from the real part of frequency-domain
-data.
Reconstruct complex time-domain data from the real part of frequency-domain data.
- Reconstruct complex time-domain data from the real part of frequency-domain
-data.
Reconstruct complex time-domain data from the real part of frequency-domain data.
@@ -1141,8 +1126,7 @@ All functions
- Resample a VOI to match a target image space using nearest-neighbour
-interpolation.
Resample a VOI to match a target image space using nearest-neighbour interpolation.
@@ -1158,23 +1142,19 @@ All functions
- Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water).
Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / kg of tissue water).
- Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water).
Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / kg of tissue water).
- Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / Litre of tissue).
Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / Litre of tissue).
- Convert default LCM/TARQUIN concentration scaling to molal units with partial
-volume correction.
Convert default LCM/TARQUIN concentration scaling to molal units with partial volume correction.
@@ -1222,8 +1202,7 @@ All functions
- MEGA-PRESS sequence with ideal localisation pulses and Gaussian shaped
-editing pulse.
MEGA-PRESS sequence with ideal localisation pulses and Gaussian shaped editing pulse.
@@ -1251,13 +1230,11 @@ All functions
- STEAM sequence with ideal pulses and coherence order filtering to simulate
-gradient crushers.
STEAM sequence with ideal pulses and coherence order filtering to simulate gradient crushers.
- STEAM sequence with ideal pulses using the z-rotation gradient simulation
-method described by Young et al JMR 140, 146-152 (1999).
STEAM sequence with ideal pulses using the z-rotation gradient simulation method described by Young et al JMR 140, 146-152 (1999).
@@ -1293,8 +1270,7 @@ All functions
- Set the number of time-domain data points, truncating or zero-filling as
-appropriate.
Set the number of time-domain data points, truncating or zero-filling as appropriate.
@@ -1318,18 +1294,15 @@ All functions
- Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS
-sequence. Note, ideal pulses are assumed.
Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS sequence. Note, ideal pulses are assumed.
- Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS
-sequence. Note, ideal pulses are assumed.
Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS sequence. Note, ideal pulses are assumed.
- Simulate a macromolecular and lipid basis-set suitable for 1H brain MRS
-analysis.
Simulate a macromolecular and lipid basis-set suitable for 1H brain MRS analysis.
@@ -1353,8 +1326,7 @@ All functions
- Simulate an ideal pulse excitation profile by smoothing a top-hat function
-with a Gaussian.
Simulate an ideal pulse excitation profile by smoothing a top-hat function with a Gaussian.
@@ -1374,17 +1346,19 @@ All functions
- Simulate and fit some spectra with ABfit for benchmarking purposes. Basic
-timing and performance metrics will be printed.
Simulate and fit some spectra with ABfit for benchmarking purposes. Basic timing and performance metrics will be printed.
Example MEGA-PRESS data with significant B0 drift.
+
+
+ Simulate an example fMRS dataset for a block design fMRS experiment and export a BIDS structure.
- Simulate a typical metabolite basis set for benchmarking. Timing metrics will
-be printed on completion.
Simulate a typical metabolite basis set for benchmarking. Timing metrics will be printed on completion.
@@ -1400,8 +1374,7 @@ All functions
- Convert SPM style segmentation files to a single categorical image where
-the numerical values map as: 0) Other, 1) CSF, 2) GM and 3) WM.
Convert SPM style segmentation files to a single categorical image where the numerical values map as: 0) Other, 1) CSF, 2) GM and 3) WM.
@@ -1413,8 +1386,7 @@ All functions
- Plot the fitting results of an object of class fit_result with
-individual basis set components shown.
Plot the fitting results of an object of class fit_result with individual basis set components shown.
@@ -1459,6 +1431,10 @@ All functions svs_1h_brain_batch_analysis()
Batch interface to the standard SVS 1H brain analysis pipeline.
+
+
+ Perform a t-test on spectral data points.
@@ -1518,8 +1494,7 @@ All functions
- Fade a spectrum to zero by frequency domain multiplication with a tanh
-function. Note this operation distorts data points at the end of the FID.
Fade a spectrum to zero by frequency domain multiplication with a tanh function. Note this operation distorts data points at the end of the FID.
@@ -1549,7 +1524,7 @@ All functions
diff --git a/docs/reference/int_spec.html b/docs/reference/int_spec.html
index c7060fe7..783325a8 100644
--- a/docs/reference/int_spec.html
+++ b/docs/reference/int_spec.html
@@ -1,5 +1,5 @@
-Integrate a spectral region. — int_spec • Spectroscopy Analysis Tools (spant) Integrate a spectral region. — int_spec • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -118,7 +118,7 @@ Value
diff --git a/docs/reference/interleave_dyns.html b/docs/reference/interleave_dyns.html
index effe5543..441eff27 100644
--- a/docs/reference/interleave_dyns.html
+++ b/docs/reference/interleave_dyns.html
@@ -1,5 +1,5 @@
-Interleave the first and second half of a dynamic series. — interleave_dyns • Spectroscopy Analysis Tools (spant) Interleave the first and second half of a dynamic series. — interleave_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/inv_even_dyns.html b/docs/reference/inv_even_dyns.html
index 9f9d4fff..dcb781dc 100644
--- a/docs/reference/inv_even_dyns.html
+++ b/docs/reference/inv_even_dyns.html
@@ -1,5 +1,5 @@
-Invert even numbered dynamic scans starting from 1 (2,4,6...). — inv_even_dyns • Spectroscopy Analysis Tools (spant) Invert even numbered dynamic scans starting from 1 (2,4,6...). — inv_even_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/inv_odd_dyns.html b/docs/reference/inv_odd_dyns.html
index 26212e2b..78d64660 100644
--- a/docs/reference/inv_odd_dyns.html
+++ b/docs/reference/inv_odd_dyns.html
@@ -1,5 +1,5 @@
-Invert odd numbered dynamic scans starting from 1 (1,3,5...). — inv_odd_dyns • Spectroscopy Analysis Tools (spant) Invert odd numbered dynamic scans starting from 1 (1,3,5...). — inv_odd_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/is.def.html b/docs/reference/is.def.html
index f196ffd0..a67b9eba 100644
--- a/docs/reference/is.def.html
+++ b/docs/reference/is.def.html
@@ -1,5 +1,5 @@
-Check if an object is defined, which is the same as being not NULL. — is.def • Spectroscopy Analysis Tools (spant) Check if an object is defined, which is the same as being not NULL. — is.def • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/is_fd.html b/docs/reference/is_fd.html
index 3b0ca165..18a193aa 100644
--- a/docs/reference/is_fd.html
+++ b/docs/reference/is_fd.html
@@ -1,7 +1,5 @@
-Check if the chemical shift dimension of an MRS data object is in the
-frequency domain. — is_fd • Spectroscopy Analysis Tools (spant) Check if the chemical shift dimension of an MRS data object is in the frequency domain. — is_fd • Spectroscopy Analysis Tools (spant) Transform 2D MRSI data from k-space to image space in the x-y direction. — kspace2img_xy • Spectroscopy Analysis Tools (spant) Transform 2D MRSI data from k-space to image space in the x-y direction. — kspace2img_xy • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/l2_reg.html b/docs/reference/l2_reg.html
index 3d781d80..21aa9849 100644
--- a/docs/reference/l2_reg.html
+++ b/docs/reference/l2_reg.html
@@ -1,5 +1,5 @@
-Perform l2 regularisation artefact suppression. — l2_reg • Spectroscopy Analysis Tools (spant) Perform l2 regularisation artefact suppression. — l2_reg • Spectroscopy Analysis Tools (spant) Apply line-broadening (apodisation) to MRS data or basis object. — lb • Spectroscopy Analysis Tools (spant) Apply line-broadening (apodisation) to MRS data or basis object. — lb • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -123,7 +123,7 @@ Value
diff --git a/docs/reference/lofdc.html b/docs/reference/lofdc.html
index 5419b1ec..31347a25 100644
--- a/docs/reference/lofdc.html
+++ b/docs/reference/lofdc.html
@@ -1,5 +1,5 @@
-Correct linear frequency drift. — lofdc • Spectroscopy Analysis Tools (spant) Correct linear frequency drift. — lofdc • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -138,7 +138,7 @@ Value
diff --git a/docs/reference/lw2alpha.html b/docs/reference/lw2alpha.html
index b83db682..25da229b 100644
--- a/docs/reference/lw2alpha.html
+++ b/docs/reference/lw2alpha.html
@@ -1,7 +1,5 @@
-Covert a linewidth in Hz to an equivalent alpha value in the time-domain ie:
-x * exp(-t * alpha). — lw2alpha • Spectroscopy Analysis Tools (spant) Covert a linewidth in Hz to an equivalent alpha value in the time-domain ie: x * exp(-t * alpha). — lw2alpha • Spectroscopy Analysis Tools (spant) Covert a linewidth in Hz to an equivalent beta value in the time-domain ie:
-x * exp(-t * t * beta). — lw2beta • Spectroscopy Analysis Tools (spant) Covert a linewidth in Hz to an equivalent beta value in the time-domain ie: x * exp(-t * t * beta). — lw2beta • Spectroscopy Analysis Tools (spant) Make a basis-set object from a directory containing LCModel formatted RAW
-files. — make_basis_from_raw • Spectroscopy Analysis Tools (spant) Make a basis-set object from a directory containing LCModel formatted RAW files. — make_basis_from_raw • Spectroscopy Analysis Tools (spant) Mask an MRS dataset in the dynamic dimension. — mask_dyns • Spectroscopy Analysis Tools (spant) Mask an MRS dataset in the dynamic dimension. — mask_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/mask_fit_res.html b/docs/reference/mask_fit_res.html
index 97baaa3f..ebd91a99 100644
--- a/docs/reference/mask_fit_res.html
+++ b/docs/reference/mask_fit_res.html
@@ -1,5 +1,5 @@
-Mask fit result spectra depending on a vector of bool values. — mask_fit_res • Spectroscopy Analysis Tools (spant) Mask fit result spectra depending on a vector of bool values. — mask_fit_res • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -116,7 +116,7 @@ Value
diff --git a/docs/reference/mask_xy.html b/docs/reference/mask_xy.html
index 11bb577c..b0d38619 100644
--- a/docs/reference/mask_xy.html
+++ b/docs/reference/mask_xy.html
@@ -1,5 +1,5 @@
-Mask an MRSI dataset in the x-y direction — mask_xy • Spectroscopy Analysis Tools (spant) Mask an MRSI dataset in the x-y direction — mask_xy • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/mask_xy_corners.html b/docs/reference/mask_xy_corners.html
index 09b16cd2..2d13839d 100644
--- a/docs/reference/mask_xy_corners.html
+++ b/docs/reference/mask_xy_corners.html
@@ -1,5 +1,5 @@
-Mask the four corners of an MRSI dataset in the x-y plane. — mask_xy_corners • Spectroscopy Analysis Tools (spant) Mask the four corners of an MRSI dataset in the x-y plane. — mask_xy_corners • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/mask_xy_ellipse.html b/docs/reference/mask_xy_ellipse.html
index 1d8b02e4..e2e749ef 100644
--- a/docs/reference/mask_xy_ellipse.html
+++ b/docs/reference/mask_xy_ellipse.html
@@ -1,7 +1,5 @@
-Mask the voxels outside an elliptical region spanning the MRSI dataset in the
-x-y plane. — mask_xy_ellipse • Spectroscopy Analysis Tools (spant) Mask the voxels outside an elliptical region spanning the MRSI dataset in the x-y plane. — mask_xy_ellipse • Spectroscopy Analysis Tools (spant) Mask a 2D MRSI dataset in the x-y dimension. — mask_xy_mat • Spectroscopy Analysis Tools (spant) Mask a 2D MRSI dataset in the x-y dimension. — mask_xy_mat • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Value
diff --git a/docs/reference/mat2mrs_data.html b/docs/reference/mat2mrs_data.html
index 2e2895f3..ae55665f 100644
--- a/docs/reference/mat2mrs_data.html
+++ b/docs/reference/mat2mrs_data.html
@@ -1,7 +1,5 @@
-Convert a matrix (with spectral points in the column dimension and dynamics
-in the row dimensions) into a mrs_data object. — mat2mrs_data • Spectroscopy Analysis Tools (spant) Convert a matrix (with spectral points in the column dimension and dynamics in the row dimensions) into a mrs_data object. — mat2mrs_data • Spectroscopy Analysis Tools (spant) Matrix exponential function taken from complexplus package to reduce the
-number of spant dependencies. — matexp • Spectroscopy Analysis Tools (spant) Matrix exponential function taken from complexplus package to reduce the number of spant dependencies. — matexp • Spectroscopy Analysis Tools (spant) Apply the max operator to an MRS dataset. — max_mrs • Spectroscopy Analysis Tools (spant) Apply the max operator to an MRS dataset. — max_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/max_mrs_interp.html b/docs/reference/max_mrs_interp.html
index e4474764..52e63f3e 100644
--- a/docs/reference/max_mrs_interp.html
+++ b/docs/reference/max_mrs_interp.html
@@ -1,5 +1,5 @@
-Apply the max operator to an interpolated MRS dataset. — max_mrs_interp • Spectroscopy Analysis Tools (spant) Apply the max operator to an interpolated MRS dataset. — max_mrs_interp • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/mean.list.html b/docs/reference/mean.list.html
index b8eb3463..048306fd 100644
--- a/docs/reference/mean.list.html
+++ b/docs/reference/mean.list.html
@@ -1,5 +1,5 @@
-Calculate the mean spectrum from an mrs_data object. — mean.list • Spectroscopy Analysis Tools (spant) Calculate the mean spectrum from an mrs_data object. — mean.list • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/mean.mrs_data.html b/docs/reference/mean.mrs_data.html
index 5531a28d..79515014 100644
--- a/docs/reference/mean.mrs_data.html
+++ b/docs/reference/mean.mrs_data.html
@@ -1,5 +1,5 @@
-Calculate the mean spectrum from an mrs_data object. — mean.mrs_data • Spectroscopy Analysis Tools (spant) Calculate the mean spectrum from an mrs_data object. — mean.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/mean_dyn_blocks.html b/docs/reference/mean_dyn_blocks.html
index 10467098..4c042448 100644
--- a/docs/reference/mean_dyn_blocks.html
+++ b/docs/reference/mean_dyn_blocks.html
@@ -1,5 +1,5 @@
-Calculate the mean of adjacent dynamic scans. — mean_dyn_blocks • Spectroscopy Analysis Tools (spant) Calculate the mean of adjacent dynamic scans. — mean_dyn_blocks • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/mean_dyn_pairs.html b/docs/reference/mean_dyn_pairs.html
index 63e909ea..1a241126 100644
--- a/docs/reference/mean_dyn_pairs.html
+++ b/docs/reference/mean_dyn_pairs.html
@@ -1,5 +1,5 @@
-Calculate the pairwise means across a dynamic data set. — mean_dyn_pairs • Spectroscopy Analysis Tools (spant) Calculate the pairwise means across a dynamic data set. — mean_dyn_pairs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/mean_dyns.html b/docs/reference/mean_dyns.html
index 73fdbfa7..0daa27df 100644
--- a/docs/reference/mean_dyns.html
+++ b/docs/reference/mean_dyns.html
@@ -1,5 +1,5 @@
-Calculate the mean dynamic data. — mean_dyns • Spectroscopy Analysis Tools (spant) Calculate the mean dynamic data. — mean_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/mean_mrs_list.html b/docs/reference/mean_mrs_list.html
index 808b6c50..10d842c0 100644
--- a/docs/reference/mean_mrs_list.html
+++ b/docs/reference/mean_mrs_list.html
@@ -1,5 +1,5 @@
-Return the mean of a list of mrs_data objects. — mean_mrs_list • Spectroscopy Analysis Tools (spant) Return the mean of a list of mrs_data objects. — mean_mrs_list • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/mean_vec_blocks.html b/docs/reference/mean_vec_blocks.html
index 8fc92eaa..dd78b122 100644
--- a/docs/reference/mean_vec_blocks.html
+++ b/docs/reference/mean_vec_blocks.html
@@ -1,5 +1,5 @@
-Calculate the mean of adjacent blocks in a vector. — mean_vec_blocks • Spectroscopy Analysis Tools (spant) Calculate the mean of adjacent blocks in a vector. — mean_vec_blocks • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/median_dyns.html b/docs/reference/median_dyns.html
index 1039d4b5..9a085b10 100644
--- a/docs/reference/median_dyns.html
+++ b/docs/reference/median_dyns.html
@@ -1,5 +1,5 @@
-Calculate the median dynamic data. — median_dyns • Spectroscopy Analysis Tools (spant) Calculate the median dynamic data. — median_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/mod_td.html b/docs/reference/mod_td.html
index 76ad0a40..141ef09e 100644
--- a/docs/reference/mod_td.html
+++ b/docs/reference/mod_td.html
@@ -1,5 +1,5 @@
-Apply the Modulus operator to the time-domain MRS signal. — mod_td • Spectroscopy Analysis Tools (spant) Apply the Modulus operator to the time-domain MRS signal. — mod_td • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/mrs_data2basis.html b/docs/reference/mrs_data2basis.html
index 62f7d749..11797b91 100644
--- a/docs/reference/mrs_data2basis.html
+++ b/docs/reference/mrs_data2basis.html
@@ -1,7 +1,5 @@
-Convert an mrs_data object to basis object - where basis signals are spread
-across the dynamic dimension in the MRS data. — mrs_data2basis • Spectroscopy Analysis Tools (spant) Convert an mrs_data object to basis object - where basis signals are spread across the dynamic dimension in the MRS data. — mrs_data2basis • Spectroscopy Analysis Tools (spant) Create a BIDS file structure from a vector of MRS data paths or list of mrs_data objects. — mrs_data2bids • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Create a BIDS file structure from a vector of MRS data paths or list of mrs_data objects.
+ Source: R/fmrs.R
+ mrs_data2bids.Rd
+
+
+
+ Create a BIDS file structure from a vector of MRS data paths or list of
+mrs_data objects.
+
+
+
+ mrs_data2bids(
+ mrs_data,
+ output_dir,
+ suffix = NULL,
+ sub = NULL,
+ ses = NULL,
+ task = NULL,
+ acq = NULL,
+ nuc = NULL,
+ voi = NULL,
+ rec = NULL,
+ run = NULL,
+ echo = NULL,
+ inv = NULL,
+ skip_existing = TRUE
+)
+
+
+
+ Arguments
+ - mrs_data
+vector of MRS data paths or list of mrs_data objects.
- output_dir
+the base directory to create the BIDS structure.
- suffix
+optional vector of file suffixes. Default behaviour is to
+automatically determine these from the input data, however it is recommended
+that they are specified to allow more efficient skipping of existing data.
- sub
+optional vector of subject labels. If not specified, these will be
+automatically generated as a series of increasing zero-padded integer values
+corresponding to the mrs_data input indices.
- ses
+optional vector of session labels.
- task
+optional vector of task labels.
- acq
+optional vector of acquisition labels.
- nuc
+optional vector of nucleus labels.
- voi
+optional vector of volume of interest labels.
- rec
+optional vector of reconstruction labels.
- run
+optional vector of run indices.
- echo
+optional vector of echo time indices.
- inv
+optional vector of inversion indices.
- skip_existing
+skip any data files that have already been converted.
+Defaults to TRUE, set to FALSE to force an overwrite of any existing data
+files.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/mrs_data2mat.html b/docs/reference/mrs_data2mat.html
index cf5ff28c..9e47688a 100644
--- a/docs/reference/mrs_data2mat.html
+++ b/docs/reference/mrs_data2mat.html
@@ -1,7 +1,5 @@
-Convert mrs_data object to a matrix, with spectral points in the column
-dimension and dynamics in the row dimension. — mrs_data2mat • Spectroscopy Analysis Tools (spant) Convert mrs_data object to a matrix, with spectral points in the column dimension and dynamics in the row dimension. — mrs_data2mat • Spectroscopy Analysis Tools (spant) Convert mrs_data object to a matrix, with spectral points in the column dimension and dynamics in the row dimension. — mrs_data2spec_mat • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Convert mrs_data object to a matrix, with spectral points in the column dimension and dynamics in the row dimension.
+ Source: R/mrs_data_proc.R
+ mrs_data2spec_mat.Rd
+
+
+
+ Convert mrs_data object to a matrix, with spectral points in the column
+dimension and dynamics in the row dimension.
+
+
+
+ mrs_data2spec_mat(mrs_data, collapse = TRUE)
+
+
+
+ Arguments
+ - mrs_data
+MRS data object or list of MRS data objects.
- collapse
+collapse all other dimensions along the dynamic dimension, eg
+a 16x16 MRSI grid would be first collapsed across 256 dynamic scans.
+
+ Value
+
+
+MRS data matrix.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/mrs_data2vec.html b/docs/reference/mrs_data2vec.html
index fb172d68..a1fd654d 100644
--- a/docs/reference/mrs_data2vec.html
+++ b/docs/reference/mrs_data2vec.html
@@ -1,5 +1,5 @@
-Convert mrs_data object to a vector. — mrs_data2vec • Spectroscopy Analysis Tools (spant) Convert mrs_data object to a vector. — mrs_data2vec • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -126,7 +126,7 @@ Value
diff --git a/docs/reference/mvfftshift.html b/docs/reference/mvfftshift.html
index 92b0841b..976b3410 100644
--- a/docs/reference/mvfftshift.html
+++ b/docs/reference/mvfftshift.html
@@ -1,7 +1,5 @@
-Perform a fftshift on a matrix, with each column replaced by its shifted
-result. — mvfftshift • Spectroscopy Analysis Tools (spant) Perform a fftshift on a matrix, with each column replaced by its shifted result. — mvfftshift • Spectroscopy Analysis Tools (spant) Perform an ifftshift on a matrix, with each column replaced by its shifted
-result. — mvifftshift • Spectroscopy Analysis Tools (spant) Perform an ifftshift on a matrix, with each column replaced by its shifted result. — mvifftshift • Spectroscopy Analysis Tools (spant) Print fit coordinates from a single index. — n2coord • Spectroscopy Analysis Tools (spant) Print fit coordinates from a single index. — n2coord • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/nifti_flip_lr.html b/docs/reference/nifti_flip_lr.html
index 730abe3c..19860b3c 100644
--- a/docs/reference/nifti_flip_lr.html
+++ b/docs/reference/nifti_flip_lr.html
@@ -1,9 +1,5 @@
-Flip the x data dimension order of a nifti image. This corresponds to
-flipping MRI data in the left-right direction, assuming the data in save in
-neurological format (can check with fslorient program). — nifti_flip_lr • Spectroscopy Analysis Tools (spant) Flip the x data dimension order of a nifti image. This corresponds to flipping MRI data in the left-right direction, assuming the data in save in neurological format (can check with fslorient program). — nifti_flip_lr • Spectroscopy Analysis Tools (spant) Export a one-page pdf of a single fit result — one_page_pdf • Spectroscopy Analysis Tools (spant) Export a one-page pdf of a single fit result — one_page_pdf • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -108,7 +108,7 @@ Arguments
diff --git a/docs/reference/ortho3.html b/docs/reference/ortho3.html
index 13ade97d..5d7dd2fd 100644
--- a/docs/reference/ortho3.html
+++ b/docs/reference/ortho3.html
@@ -1,5 +1,5 @@
-Display an orthographic projection plot of a nifti object. — ortho3 • Spectroscopy Analysis Tools (spant) Display an orthographic projection plot of a nifti object. — ortho3 • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -172,7 +172,7 @@ Arguments
diff --git a/docs/reference/ortho3_inter.html b/docs/reference/ortho3_inter.html
index 090cc5e5..15948899 100644
--- a/docs/reference/ortho3_inter.html
+++ b/docs/reference/ortho3_inter.html
@@ -1,5 +1,5 @@
-Display an interactive orthographic projection plot of a nifti object. — ortho3_inter • Spectroscopy Analysis Tools (spant) Display an interactive orthographic projection plot of a nifti object. — ortho3_inter • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -132,7 +132,7 @@ Arguments
diff --git a/docs/reference/peak_info.html b/docs/reference/peak_info.html
index 09058bd8..41c8ffaf 100644
--- a/docs/reference/peak_info.html
+++ b/docs/reference/peak_info.html
@@ -1,7 +1,5 @@
-Search for the highest peak in a spectral region and return the frequency,
-height and FWHM. — peak_info • Spectroscopy Analysis Tools (spant) Search for the highest peak in a spectral region and return the frequency, height and FWHM. — peak_info • Spectroscopy Analysis Tools (spant) Papoulis-Gerchberg (PG) algorithm method for k-space extrapolation. — pg_extrap_xy • Spectroscopy Analysis Tools (spant) Papoulis-Gerchberg (PG) algorithm method for k-space extrapolation. — pg_extrap_xy • Spectroscopy Analysis Tools (spant) Apply phasing parameters to MRS data. — phase • Spectroscopy Analysis Tools (spant) Apply phasing parameters to MRS data. — phase • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/phase_ref_1h_brain.html b/docs/reference/phase_ref_1h_brain.html
new file mode 100644
index 00000000..8707a74a
--- /dev/null
+++ b/docs/reference/phase_ref_1h_brain.html
@@ -0,0 +1,131 @@
+
+Corrected zero order phase and chemical shift offset in 1H MRS data from the brain. — phase_ref_1h_brain • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Corrected zero order phase and chemical shift offset in 1H MRS data from the brain.
+ Source: R/rats.R
+ phase_ref_1h_brain.Rd
+
+
+
+ Corrected zero order phase and chemical shift offset in 1H MRS data from the
+brain.
+
+
+
+ phase_ref_1h_brain(mrs_data, mean_ref = FALSE, ret_corr_only = TRUE)
+
+
+
+ Arguments
+ - mrs_data
+MRS data to be corrected.
- mean_ref
+apply the phase and offset of the mean spectrum to all
+others. Default is FALSE.
- ret_corr_only
+return the corrected data only.
+
+ Value
+
+
+corrected MRS data.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/plot.fit_result.html b/docs/reference/plot.fit_result.html
index e54d3bc1..836a53ee 100644
--- a/docs/reference/plot.fit_result.html
+++ b/docs/reference/plot.fit_result.html
@@ -1,5 +1,5 @@
-Plot the fitting results of an object of class fit_result. — plot.fit_result • Spectroscopy Analysis Tools (spant) Plot the fitting results of an object of class fit_result. — plot.fit_result • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -207,7 +207,7 @@ Arguments
diff --git a/docs/reference/plot.mrs_data.html b/docs/reference/plot.mrs_data.html
index fabcc35b..bb2ec651 100644
--- a/docs/reference/plot.mrs_data.html
+++ b/docs/reference/plot.mrs_data.html
@@ -1,5 +1,5 @@
-Plotting method for objects of class mrs_data. — plot.mrs_data • Spectroscopy Analysis Tools (spant) Plotting method for objects of class mrs_data. — plot.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -287,7 +287,7 @@ Arguments
diff --git a/docs/reference/plot_bc.html b/docs/reference/plot_bc.html
index 4f8309b4..b48142cc 100644
--- a/docs/reference/plot_bc.html
+++ b/docs/reference/plot_bc.html
@@ -1,5 +1,5 @@
-Convenience function to plot a baseline estimate with the original data. — plot_bc • Spectroscopy Analysis Tools (spant) Convenience function to plot a baseline estimate with the original data. — plot_bc • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -108,7 +108,7 @@ Arguments
diff --git a/docs/reference/plot_reg.html b/docs/reference/plot_reg.html
index ae1acbe7..2addb2f6 100644
--- a/docs/reference/plot_reg.html
+++ b/docs/reference/plot_reg.html
@@ -1,5 +1,5 @@
-Plot regressors as an image. — plot_reg • Spectroscopy Analysis Tools (spant) Plot regressors as an image. — plot_reg • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/plot_slice_fit.html b/docs/reference/plot_slice_fit.html
index fbc7b560..57f1af8a 100644
--- a/docs/reference/plot_slice_fit.html
+++ b/docs/reference/plot_slice_fit.html
@@ -1,5 +1,5 @@
-Plot a 2D slice from an MRSI fit result object. — plot_slice_fit • Spectroscopy Analysis Tools (spant) Plot a 2D slice from an MRSI fit result object. — plot_slice_fit • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -129,7 +129,7 @@ Arguments
diff --git a/docs/reference/plot_slice_fit_inter.html b/docs/reference/plot_slice_fit_inter.html
index 4eed104a..da105a7d 100644
--- a/docs/reference/plot_slice_fit_inter.html
+++ b/docs/reference/plot_slice_fit_inter.html
@@ -1,5 +1,5 @@
-Plot a 2D slice from an MRSI fit result object. — plot_slice_fit_inter • Spectroscopy Analysis Tools (spant) Plot a 2D slice from an MRSI fit result object. — plot_slice_fit_inter • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -134,7 +134,7 @@ Arguments
diff --git a/docs/reference/plot_slice_map.html b/docs/reference/plot_slice_map.html
index 553e9ac8..ffb2a134 100644
--- a/docs/reference/plot_slice_map.html
+++ b/docs/reference/plot_slice_map.html
@@ -1,5 +1,5 @@
-Plot a slice from a 7 dimensional array. — plot_slice_map • Spectroscopy Analysis Tools (spant) Plot a slice from a 7 dimensional array. — plot_slice_map • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -153,7 +153,7 @@ Arguments
diff --git a/docs/reference/plot_slice_map_inter.html b/docs/reference/plot_slice_map_inter.html
index 40d33b42..90968f66 100644
--- a/docs/reference/plot_slice_map_inter.html
+++ b/docs/reference/plot_slice_map_inter.html
@@ -1,7 +1,5 @@
-Plot an interactive slice map from a data array where voxels can be selected
-to display a corresponding spectrum. — plot_slice_map_inter • Spectroscopy Analysis Tools (spant) Plot an interactive slice map from a data array where voxels can be selected to display a corresponding spectrum. — plot_slice_map_inter • Spectroscopy Analysis Tools (spant) Plot the spectral standard deviation. — plot_spec_sd • Spectroscopy Analysis Tools (spant) Plot the spectral standard deviation. — plot_spec_sd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Arguments
diff --git a/docs/reference/plot_voi_overlay.html b/docs/reference/plot_voi_overlay.html
index 9a782e88..bbbbf35e 100644
--- a/docs/reference/plot_voi_overlay.html
+++ b/docs/reference/plot_voi_overlay.html
@@ -1,5 +1,5 @@
-Plot a volume as an image overlay. — plot_voi_overlay • Spectroscopy Analysis Tools (spant) Plot a volume as an image overlay. — plot_voi_overlay • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -116,7 +116,7 @@ Arguments
diff --git a/docs/reference/plot_voi_overlay_seg.html b/docs/reference/plot_voi_overlay_seg.html
index 3d4e74ff..0e800ff2 100644
--- a/docs/reference/plot_voi_overlay_seg.html
+++ b/docs/reference/plot_voi_overlay_seg.html
@@ -1,5 +1,5 @@
-Plot a volume as an overlay on a segmented brain volume. — plot_voi_overlay_seg • Spectroscopy Analysis Tools (spant) Plot a volume as an overlay on a segmented brain volume. — plot_voi_overlay_seg • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Arguments
diff --git a/docs/reference/ppm.html b/docs/reference/ppm.html
index c352327a..ee4696e2 100644
--- a/docs/reference/ppm.html
+++ b/docs/reference/ppm.html
@@ -1,5 +1,5 @@
-Return the ppm scale of an MRS dataset or fit result. — ppm • Spectroscopy Analysis Tools (spant) Return the ppm scale of an MRS dataset or fit result. — ppm • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -132,7 +132,7 @@ Value
diff --git a/docs/reference/precomp.html b/docs/reference/precomp.html
index 822d7336..df3d2c6c 100644
--- a/docs/reference/precomp.html
+++ b/docs/reference/precomp.html
@@ -1,7 +1,5 @@
-Save function results to file and load on subsequent calls to avoid repeat
-computation. — precomp • Spectroscopy Analysis Tools (spant) Save function results to file and load on subsequent calls to avoid repeat computation. — precomp • Spectroscopy Analysis Tools (spant) Preprocess and perform quality assessment of a single SVS data set. — preproc_svs • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Preprocess and perform quality assessment of a single SVS data set.
+ Source: R/fmrs.R
+ preproc_svs.Rd
+
+
+
+ Preprocess and perform quality assessment of a single SVS data set.
+
+
+
+ preproc_svs(path, label = NULL, output_dir = NULL, ref_inds = NULL)
+
+
+
+ Arguments
+ - path
+path to the fMRS data file or IMA directory.
- label
+a label to describe the data set.
- output_dir
+output directory.
- ref_inds
+a vector of 1-based indices for any water reference dynamic
+scans.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/preproc_svs_dataset.html b/docs/reference/preproc_svs_dataset.html
new file mode 100644
index 00000000..07c3a29b
--- /dev/null
+++ b/docs/reference/preproc_svs_dataset.html
@@ -0,0 +1,148 @@
+
+Preprocess and perform quality assessment of one or more SVS data sets. — preproc_svs_dataset • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Preprocess and perform quality assessment of one or more SVS data sets.
+ Source: R/fmrs.R
+ preproc_svs_dataset.Rd
+
+
+
+ Preprocess and perform quality assessment of one or more SVS data sets.
+
+
+
+ preproc_svs_dataset(
+ paths,
+ labels = NULL,
+ output_dir = "spant_analysis",
+ exclude_labels = NULL,
+ overwrite = FALSE,
+ ref_inds = NULL,
+ return_results = FALSE
+)
+
+
+
+ Arguments
+ - paths
+paths to the fMRS data file or IMA directory.
- labels
+labels to describe each data set.
- output_dir
+output directory.
- exclude_labels
+vector of labels of scans to exclude, eg poor quality
+data.
- overwrite
+overwrite saved results, defaults to FALSE.
- ref_inds
+a vector of 1-based indices for any water reference dynamic
+scans.
- return_results
+function will return key outputs, defaults to FALSE.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/print.fit_result.html b/docs/reference/print.fit_result.html
index 297f28dc..5f434e57 100644
--- a/docs/reference/print.fit_result.html
+++ b/docs/reference/print.fit_result.html
@@ -1,5 +1,5 @@
-Print a summary of an object of class fit_result. — print.fit_result • Spectroscopy Analysis Tools (spant) Print a summary of an object of class fit_result. — print.fit_result • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -105,7 +105,7 @@ Arguments
diff --git a/docs/reference/print.mrs_data.html b/docs/reference/print.mrs_data.html
index 51199017..e1561eb2 100644
--- a/docs/reference/print.mrs_data.html
+++ b/docs/reference/print.mrs_data.html
@@ -1,5 +1,5 @@
-Print a summary of mrs_data parameters. — print.mrs_data • Spectroscopy Analysis Tools (spant) Print a summary of mrs_data parameters. — print.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -109,7 +109,7 @@ Arguments
diff --git a/docs/reference/qn_states.html b/docs/reference/qn_states.html
index 0f42f2f9..d7aa6715 100644
--- a/docs/reference/qn_states.html
+++ b/docs/reference/qn_states.html
@@ -1,5 +1,5 @@
-Get the quantum coherence matrix for a spin system. — qn_states • Spectroscopy Analysis Tools (spant) Get the quantum coherence matrix for a spin system. — qn_states • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/rats.html b/docs/reference/rats.html
index 5a39a396..93585e08 100644
--- a/docs/reference/rats.html
+++ b/docs/reference/rats.html
@@ -1,5 +1,5 @@
-Robust Alignment to a Target Spectrum (RATS). — rats • Spectroscopy Analysis Tools (spant) Robust Alignment to a Target Spectrum (RATS). — rats • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -207,7 +207,7 @@ Value
diff --git a/docs/reference/re_weighting.html b/docs/reference/re_weighting.html
index d21caf21..8b0b070a 100644
--- a/docs/reference/re_weighting.html
+++ b/docs/reference/re_weighting.html
@@ -1,5 +1,5 @@
-Apply a weighting to the FID to enhance spectral resolution. — re_weighting • Spectroscopy Analysis Tools (spant) Apply a weighting to the FID to enhance spectral resolution. — re_weighting • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/read_basis.html b/docs/reference/read_basis.html
index da9b94af..eb6f8557 100644
--- a/docs/reference/read_basis.html
+++ b/docs/reference/read_basis.html
@@ -1,5 +1,5 @@
-Read a basis file in LCModel .basis format. — read_basis • Spectroscopy Analysis Tools (spant) Read a basis file in LCModel .basis format. — read_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/read_ima_coil_dir.html b/docs/reference/read_ima_coil_dir.html
index 28c02de0..4f073cd8 100644
--- a/docs/reference/read_ima_coil_dir.html
+++ b/docs/reference/read_ima_coil_dir.html
@@ -1,9 +1,5 @@
-Read a directory containing Siemens MRS IMA files and combine along the coil
-dimension. Note that the coil ID is inferred from the sorted file name and
-should be checked when consistency is required between two directories. — read_ima_coil_dir • Spectroscopy Analysis Tools (spant) Read a directory containing Siemens MRS IMA files and combine along the coil dimension. Note that the coil ID is inferred from the sorted file name and should be checked when consistency is required between two directories. — read_ima_coil_dir • Spectroscopy Analysis Tools (spant) Read a directory containing Siemens MRS IMA files and combine along the
-dynamic dimension. Note that the coil ID is inferred from the sorted file
-name and should be checked when consistency is required. — read_ima_dyn_dir • Spectroscopy Analysis Tools (spant) Read a directory containing Siemens MRS IMA files and combine along the dynamic dimension. Note that the coil ID is inferred from the sorted file name and should be checked when consistency is required. — read_ima_dyn_dir • Spectroscopy Analysis Tools (spant) Read an LCModel formatted coord file containing fit information. — read_lcm_coord • Spectroscopy Analysis Tools (spant) Read an LCModel formatted coord file containing fit information. — read_lcm_coord • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -107,7 +107,7 @@ Value
diff --git a/docs/reference/read_mrs.html b/docs/reference/read_mrs.html
index 3ac2a36b..2cf36b20 100644
--- a/docs/reference/read_mrs.html
+++ b/docs/reference/read_mrs.html
@@ -1,5 +1,5 @@
-Read MRS data from a file. — read_mrs • Spectroscopy Analysis Tools (spant) Read MRS data from a file. — read_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -88,7 +88,8 @@ Read MRS data from a file.
full_fid = FALSE,
omit_svs_ref_scans = TRUE,
verbose = FALSE,
- extra = NULL
+ extra = NULL,
+ fid_filt_dist = NULL
)
@@ -140,6 +141,13 @@ Arguments
an optional data frame to provide additional variables for use
in subsequent analysis steps, eg id or grouping variables.
fid_filt_dist
+indicate if the data has a distorted FID due to a
+brick-wall filter being used to downsample the data. Default is to auto
+detect this from the data, but TRUE or FALSE options can be given to override
+detection.
Value
@@ -183,7 +191,7 @@ Examples
diff --git a/docs/reference/read_mrs_tqn.html b/docs/reference/read_mrs_tqn.html
index 5766362f..84bdaf3a 100644
--- a/docs/reference/read_mrs_tqn.html
+++ b/docs/reference/read_mrs_tqn.html
@@ -1,5 +1,5 @@
-Read MRS data using the TARQUIN software package. — read_mrs_tqn • Spectroscopy Analysis Tools (spant) Read MRS data using the TARQUIN software package. — read_mrs_tqn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -131,7 +131,7 @@ Examples
diff --git a/docs/reference/read_pulse_ascii.html b/docs/reference/read_pulse_ascii.html
index c9e0d43c..ab11c9cc 100644
--- a/docs/reference/read_pulse_ascii.html
+++ b/docs/reference/read_pulse_ascii.html
@@ -1,5 +1,5 @@
-Read an ASCII formatted pulse file. — read_pulse_ascii • Spectroscopy Analysis Tools (spant) Read an ASCII formatted pulse file. — read_pulse_ascii • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/read_pulse_bruker.html b/docs/reference/read_pulse_bruker.html
index c92bf76a..dbe9073b 100644
--- a/docs/reference/read_pulse_bruker.html
+++ b/docs/reference/read_pulse_bruker.html
@@ -1,5 +1,5 @@
-Read a Bruker formatted pulse file — read_pulse_bruker • Spectroscopy Analysis Tools (spant) Read a Bruker formatted pulse file — read_pulse_bruker • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/read_pulse_pta.html b/docs/reference/read_pulse_pta.html
index 72e1b6d4..a0fac3c3 100644
--- a/docs/reference/read_pulse_pta.html
+++ b/docs/reference/read_pulse_pta.html
@@ -1,5 +1,5 @@
-Read a .pta formatted pulse file compatible with Siemens PulseTool. — read_pulse_pta • Spectroscopy Analysis Tools (spant) Read a .pta formatted pulse file compatible with Siemens PulseTool. — read_pulse_pta • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/read_siemens_txt_hdr.html b/docs/reference/read_siemens_txt_hdr.html
index 23fb8c70..3a17d87c 100644
--- a/docs/reference/read_siemens_txt_hdr.html
+++ b/docs/reference/read_siemens_txt_hdr.html
@@ -1,5 +1,5 @@
-Read the text format header found in Siemens IMA and TWIX data files. — read_siemens_txt_hdr • Spectroscopy Analysis Tools (spant) Read the text format header found in Siemens IMA and TWIX data files. — read_siemens_txt_hdr • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -78,7 +78,7 @@ Read the text format header found in Siemens IMA and TWIX data files.
- read_siemens_txt_hdr(input, version = "vd", verbose, offset = 0)
+ read_siemens_txt_hdr(input, version = "vd", verbose = FALSE, offset = 0)
@@ -118,7 +118,7 @@ Value
diff --git a/docs/reference/read_tqn_fit.html b/docs/reference/read_tqn_fit.html
index 4da6c25e..a1630420 100644
--- a/docs/reference/read_tqn_fit.html
+++ b/docs/reference/read_tqn_fit.html
@@ -1,5 +1,5 @@
-Reader for csv fit results generated by TARQUIN. — read_tqn_fit • Spectroscopy Analysis Tools (spant) Reader for csv fit results generated by TARQUIN. — read_tqn_fit • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -113,7 +113,7 @@ Examples
diff --git a/docs/reference/read_tqn_result.html b/docs/reference/read_tqn_result.html
index 36659714..68a3e98c 100644
--- a/docs/reference/read_tqn_result.html
+++ b/docs/reference/read_tqn_result.html
@@ -1,5 +1,5 @@
-Reader for csv results generated by TARQUIN. — read_tqn_result • Spectroscopy Analysis Tools (spant) Reader for csv results generated by TARQUIN. — read_tqn_result • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -117,7 +117,7 @@ Examples
diff --git a/docs/reference/recon_imag.html b/docs/reference/recon_imag.html
index d2a72225..5bc3b1eb 100644
--- a/docs/reference/recon_imag.html
+++ b/docs/reference/recon_imag.html
@@ -1,7 +1,5 @@
-Reconstruct complex time-domain data from the real part of frequency-domain
-data. — recon_imag • Spectroscopy Analysis Tools (spant) Reconstruct complex time-domain data from the real part of frequency-domain data. — recon_imag • Spectroscopy Analysis Tools (spant) Reconstruct complex time-domain data from the real part of frequency-domain
-data. — recon_imag_vec • Spectroscopy Analysis Tools (spant) Reconstruct complex time-domain data from the real part of frequency-domain data. — recon_imag_vec • Spectroscopy Analysis Tools (spant) Reconstruct 2D MRSI data from a twix file loaded with read_mrs. — recon_twix_2d_mrsi • Spectroscopy Analysis Tools (spant) Reconstruct 2D MRSI data from a twix file loaded with read_mrs. — recon_twix_2d_mrsi • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/rectangular_mask.html b/docs/reference/rectangular_mask.html
index a2117283..6e469bc9 100644
--- a/docs/reference/rectangular_mask.html
+++ b/docs/reference/rectangular_mask.html
@@ -1,5 +1,5 @@
-Create a rectangular mask stored as a matrix of logical values. — rectangular_mask • Spectroscopy Analysis Tools (spant) Create a rectangular mask stored as a matrix of logical values. — rectangular_mask • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -130,7 +130,7 @@ Value
diff --git a/docs/reference/reexports.html b/docs/reference/reexports.html
index 694a75d1..a59e8379 100644
--- a/docs/reference/reexports.html
+++ b/docs/reference/reexports.html
@@ -1,5 +1,5 @@
-Objects exported from other packages — reexports • Spectroscopy Analysis Tools (spant) Objects exported from other packages — reexports • Spectroscopy Analysis Tools (spant)
Spectroscopy Analysis Tools (spant)
- 2.21.0
+ 2.22.0
@@ -103,7 +103,7 @@ Objects exported from other packages
diff --git a/docs/reference/rep_array_dim.html b/docs/reference/rep_array_dim.html
index b9c49b4a..48c0a5ed 100644
--- a/docs/reference/rep_array_dim.html
+++ b/docs/reference/rep_array_dim.html
@@ -1,5 +1,5 @@
-Repeat an array over a given dimension. — rep_array_dim • Spectroscopy Analysis Tools (spant) Repeat an array over a given dimension. — rep_array_dim • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/rep_dyn.html b/docs/reference/rep_dyn.html
index 6bbfb0ef..89a4bb9b 100644
--- a/docs/reference/rep_dyn.html
+++ b/docs/reference/rep_dyn.html
@@ -1,5 +1,5 @@
-Replicate a scan in the dynamic dimension. — rep_dyn • Spectroscopy Analysis Tools (spant) Replicate a scan in the dynamic dimension. — rep_dyn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/rep_mrs.html b/docs/reference/rep_mrs.html
index 67730b5c..becb8f00 100644
--- a/docs/reference/rep_mrs.html
+++ b/docs/reference/rep_mrs.html
@@ -1,5 +1,5 @@
-Replicate a scan over a given dimension. — rep_mrs • Spectroscopy Analysis Tools (spant) Replicate a scan over a given dimension. — rep_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -138,7 +138,7 @@ Value
diff --git a/docs/reference/resample_basis.html b/docs/reference/resample_basis.html
index b0f2ab17..c7a6222a 100644
--- a/docs/reference/resample_basis.html
+++ b/docs/reference/resample_basis.html
@@ -1,5 +1,5 @@
-Resample a basis-set to match a mrs_data acquisition. — resample_basis • Spectroscopy Analysis Tools (spant) Resample a basis-set to match a mrs_data acquisition. — resample_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -116,7 +116,7 @@ Value
diff --git a/docs/reference/resample_img.html b/docs/reference/resample_img.html
index f1e7beaf..b0cc8f71 100644
--- a/docs/reference/resample_img.html
+++ b/docs/reference/resample_img.html
@@ -1,5 +1,5 @@
-Resample an image to match a target image space. — resample_img • Spectroscopy Analysis Tools (spant) Resample an image to match a target image space. — resample_img • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/resample_voi.html b/docs/reference/resample_voi.html
index 8fbfa836..a29ab096 100644
--- a/docs/reference/resample_voi.html
+++ b/docs/reference/resample_voi.html
@@ -1,7 +1,5 @@
-Resample a VOI to match a target image space using nearest-neighbour
-interpolation. — resample_voi • Spectroscopy Analysis Tools (spant) Resample a VOI to match a target image space using nearest-neighbour interpolation. — resample_voi • Spectroscopy Analysis Tools (spant) Reslice a nifti object to match the orientation of mrs data. — reslice_to_mrs • Spectroscopy Analysis Tools (spant) Reslice a nifti object to match the orientation of mrs data. — reslice_to_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/reson_table2mrs_data.html b/docs/reference/reson_table2mrs_data.html
index d75579ee..c5a2167a 100644
--- a/docs/reference/reson_table2mrs_data.html
+++ b/docs/reference/reson_table2mrs_data.html
@@ -1,5 +1,5 @@
-Generate mrs_data from a table of single Lorentzian resonances. — reson_table2mrs_data • Spectroscopy Analysis Tools (spant) Generate mrs_data from a table of single Lorentzian resonances. — reson_table2mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -119,7 +119,7 @@ Value
diff --git a/docs/reference/rm_dyns.html b/docs/reference/rm_dyns.html
index 5d5ef692..573e1f51 100644
--- a/docs/reference/rm_dyns.html
+++ b/docs/reference/rm_dyns.html
@@ -1,5 +1,5 @@
-Remove a subset of dynamic scans. — rm_dyns • Spectroscopy Analysis Tools (spant) Remove a subset of dynamic scans. — rm_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/scale_amp_molal.html b/docs/reference/scale_amp_molal.html
index aaeee1f2..7acb8cb0 100644
--- a/docs/reference/scale_amp_molal.html
+++ b/docs/reference/scale_amp_molal.html
@@ -1,7 +1,5 @@
-Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water). — scale_amp_molal • Spectroscopy Analysis Tools (spant) Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / kg of tissue water). — scale_amp_molal • Spectroscopy Analysis Tools (spant)
Spectroscopy Analysis Tools (spant)
- 2.21.0
+ 2.22.0
@@ -76,8 +74,7 @@
- Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water).
+ Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / kg of tissue water).
Source: R/amp_scaling.R
scale_amp_molal.Rd
@@ -163,7 +160,7 @@ Value
diff --git a/docs/reference/scale_amp_molal_pvc.html b/docs/reference/scale_amp_molal_pvc.html
index 962d6afc..4d194abd 100644
--- a/docs/reference/scale_amp_molal_pvc.html
+++ b/docs/reference/scale_amp_molal_pvc.html
@@ -1,7 +1,5 @@
-Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water). — scale_amp_molal_pvc • Spectroscopy Analysis Tools (spant)
@@ -75,8 +73,7 @@
- Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water).
+ Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / kg of tissue water).
Source: R/amp_scaling.R
scale_amp_molal_pvc.Rd
@@ -141,7 +138,7 @@ Value
diff --git a/docs/reference/scale_amp_molar.html b/docs/reference/scale_amp_molar.html
index 02358d91..dc87a338 100644
--- a/docs/reference/scale_amp_molar.html
+++ b/docs/reference/scale_amp_molar.html
@@ -1,7 +1,5 @@
-Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / Litre of tissue). — scale_amp_molar • Spectroscopy Analysis Tools (spant) Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / Litre of tissue). — scale_amp_molar • Spectroscopy Analysis Tools (spant) Convert default LCM/TARQUIN concentration scaling to molal units with partial
-volume correction. — scale_amp_molar2molal_pvc • Spectroscopy Analysis Tools (spant) Convert default LCM/TARQUIN concentration scaling to molal units with partial volume correction. — scale_amp_molar2molal_pvc • Spectroscopy Analysis Tools (spant) Scale fitted amplitudes to a ratio of signal amplitude. — scale_amp_ratio • Spectroscopy Analysis Tools (spant) Scale fitted amplitudes to a ratio of signal amplitude. — scale_amp_ratio • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -116,7 +116,7 @@ Value
diff --git a/docs/reference/scale_amp_ratio_value.html b/docs/reference/scale_amp_ratio_value.html
index 2036837a..6af8ac51 100644
--- a/docs/reference/scale_amp_ratio_value.html
+++ b/docs/reference/scale_amp_ratio_value.html
@@ -1,5 +1,5 @@
-Scale fitted amplitudes to a ratio of signal amplitude. — scale_amp_ratio_value • Spectroscopy Analysis Tools (spant) Scale fitted amplitudes to a ratio of signal amplitude. — scale_amp_ratio_value • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/scale_amp_water_ratio.html b/docs/reference/scale_amp_water_ratio.html
index 5b25e884..35a76b00 100644
--- a/docs/reference/scale_amp_water_ratio.html
+++ b/docs/reference/scale_amp_water_ratio.html
@@ -1,5 +1,5 @@
-Scale metabolite amplitudes as a ratio to the unsuppressed water amplitude. — scale_amp_water_ratio • Spectroscopy Analysis Tools (spant) Scale metabolite amplitudes as a ratio to the unsuppressed water amplitude. — scale_amp_water_ratio • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/scale_basis_amp.html b/docs/reference/scale_basis_amp.html
index 9401c3f1..5a58b5e5 100644
--- a/docs/reference/scale_basis_amp.html
+++ b/docs/reference/scale_basis_amp.html
@@ -1,5 +1,5 @@
-Scale a basis object by a scalar. — scale_basis_amp • Spectroscopy Analysis Tools (spant) Scale a basis object by a scalar. — scale_basis_amp • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/scale_basis_from_singlet.html b/docs/reference/scale_basis_from_singlet.html
index 0d542bc8..c9a19e77 100644
--- a/docs/reference/scale_basis_from_singlet.html
+++ b/docs/reference/scale_basis_from_singlet.html
@@ -1,5 +1,5 @@
-Scale a basis-set to be consistent with spant assumptions for water scaling. — scale_basis_from_singlet • Spectroscopy Analysis Tools (spant) Scale a basis-set to be consistent with spant assumptions for water scaling. — scale_basis_from_singlet • Spectroscopy Analysis Tools (spant)
Spectroscopy Analysis Tools (spant)
- 2.21.0
+ 2.22.0
@@ -127,7 +127,7 @@ Value
diff --git a/docs/reference/scale_mrs_amp.html b/docs/reference/scale_mrs_amp.html
index b5501a0d..990f058a 100644
--- a/docs/reference/scale_mrs_amp.html
+++ b/docs/reference/scale_mrs_amp.html
@@ -1,5 +1,5 @@
-Scale an mrs_data object by a scalar or vector or amplitudes. — scale_mrs_amp • Spectroscopy Analysis Tools (spant) Scale an mrs_data object by a scalar or vector or amplitudes. — scale_mrs_amp • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/scale_spec.html b/docs/reference/scale_spec.html
index 4f6ea835..6b3ddba4 100644
--- a/docs/reference/scale_spec.html
+++ b/docs/reference/scale_spec.html
@@ -1,5 +1,5 @@
-Scale mrs_data to a spectral region. — scale_spec • Spectroscopy Analysis Tools (spant) Scale mrs_data to a spectral region. — scale_spec • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -141,7 +141,7 @@ Value
diff --git a/docs/reference/sd.html b/docs/reference/sd.html
index ea1eec9f..3ae4dfd4 100644
--- a/docs/reference/sd.html
+++ b/docs/reference/sd.html
@@ -1,5 +1,5 @@
-Calculate the standard deviation spectrum from an mrs_data object. — sd • Spectroscopy Analysis Tools (spant) Calculate the standard deviation spectrum from an mrs_data object. — sd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/sd.mrs_data.html b/docs/reference/sd.mrs_data.html
index 3f92a49f..13bdda85 100644
--- a/docs/reference/sd.mrs_data.html
+++ b/docs/reference/sd.mrs_data.html
@@ -1,5 +1,5 @@
-Calculate the standard deviation spectrum from an mrs_data object. — sd.mrs_data • Spectroscopy Analysis Tools (spant) Calculate the standard deviation spectrum from an mrs_data object. — sd.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/seconds.html b/docs/reference/seconds.html
index b34d6627..467ee17f 100644
--- a/docs/reference/seconds.html
+++ b/docs/reference/seconds.html
@@ -1,5 +1,5 @@
-Return a time scale vector to match the FID of an MRS data object. — seconds • Spectroscopy Analysis Tools (spant) Return a time scale vector to match the FID of an MRS data object. — seconds • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/seq_cpmg_ideal.html b/docs/reference/seq_cpmg_ideal.html
index 547e96ab..45727c86 100644
--- a/docs/reference/seq_cpmg_ideal.html
+++ b/docs/reference/seq_cpmg_ideal.html
@@ -1,5 +1,5 @@
-CPMG style sequence with ideal pulses. — seq_cpmg_ideal • Spectroscopy Analysis Tools (spant) CPMG style sequence with ideal pulses. — seq_cpmg_ideal • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/seq_mega_press_ideal.html b/docs/reference/seq_mega_press_ideal.html
index 0769b8b4..a9cd7fa0 100644
--- a/docs/reference/seq_mega_press_ideal.html
+++ b/docs/reference/seq_mega_press_ideal.html
@@ -1,7 +1,5 @@
-MEGA-PRESS sequence with ideal localisation pulses and Gaussian shaped
-editing pulse. — seq_mega_press_ideal • Spectroscopy Analysis Tools (spant) MEGA-PRESS sequence with ideal localisation pulses and Gaussian shaped editing pulse. — seq_mega_press_ideal • Spectroscopy Analysis Tools (spant) PRESS sequence with shaped refocusing pulses. — seq_press_2d_shaped • Spectroscopy Analysis Tools (spant) PRESS sequence with shaped refocusing pulses. — seq_press_2d_shaped • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -165,7 +165,7 @@ Value
diff --git a/docs/reference/seq_press_ideal.html b/docs/reference/seq_press_ideal.html
index 8c976856..72c3af3d 100644
--- a/docs/reference/seq_press_ideal.html
+++ b/docs/reference/seq_press_ideal.html
@@ -1,5 +1,5 @@
-PRESS sequence with ideal pulses. — seq_press_ideal • Spectroscopy Analysis Tools (spant) PRESS sequence with ideal pulses. — seq_press_ideal • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/seq_pulse_acquire.html b/docs/reference/seq_pulse_acquire.html
index 4a88fc64..ad80571e 100644
--- a/docs/reference/seq_pulse_acquire.html
+++ b/docs/reference/seq_pulse_acquire.html
@@ -1,5 +1,5 @@
-Simple pulse and acquire sequence with ideal pulses. — seq_pulse_acquire • Spectroscopy Analysis Tools (spant) Simple pulse and acquire sequence with ideal pulses. — seq_pulse_acquire • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/seq_slaser_ideal.html b/docs/reference/seq_slaser_ideal.html
index 74688f4d..eb83e8e3 100644
--- a/docs/reference/seq_slaser_ideal.html
+++ b/docs/reference/seq_slaser_ideal.html
@@ -1,5 +1,5 @@
-sLASER sequence with ideal pulses. — seq_slaser_ideal • Spectroscopy Analysis Tools (spant) sLASER sequence with ideal pulses. — seq_slaser_ideal • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -126,7 +126,7 @@ Value
diff --git a/docs/reference/seq_spin_echo_ideal.html b/docs/reference/seq_spin_echo_ideal.html
index e23271de..4248716f 100644
--- a/docs/reference/seq_spin_echo_ideal.html
+++ b/docs/reference/seq_spin_echo_ideal.html
@@ -1,5 +1,5 @@
-Spin echo sequence with ideal pulses. — seq_spin_echo_ideal • Spectroscopy Analysis Tools (spant) Spin echo sequence with ideal pulses. — seq_spin_echo_ideal • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/seq_steam_ideal.html b/docs/reference/seq_steam_ideal.html
index a60685a8..1c8115d7 100644
--- a/docs/reference/seq_steam_ideal.html
+++ b/docs/reference/seq_steam_ideal.html
@@ -1,5 +1,5 @@
-STEAM sequence with ideal pulses. — seq_steam_ideal • Spectroscopy Analysis Tools (spant) STEAM sequence with ideal pulses. — seq_steam_ideal • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -128,7 +128,7 @@ Value
diff --git a/docs/reference/seq_steam_ideal_cof.html b/docs/reference/seq_steam_ideal_cof.html
index 8f225740..cba7af91 100644
--- a/docs/reference/seq_steam_ideal_cof.html
+++ b/docs/reference/seq_steam_ideal_cof.html
@@ -1,7 +1,5 @@
-STEAM sequence with ideal pulses and coherence order filtering to simulate
-gradient crushers. — seq_steam_ideal_cof • Spectroscopy Analysis Tools (spant) STEAM sequence with ideal pulses and coherence order filtering to simulate gradient crushers. — seq_steam_ideal_cof • Spectroscopy Analysis Tools (spant) STEAM sequence with ideal pulses using the z-rotation gradient simulation
-method described by Young et al JMR 140, 146-152 (1999). — seq_steam_ideal_young • Spectroscopy Analysis Tools (spant) STEAM sequence with ideal pulses using the z-rotation gradient simulation method described by Young et al JMR 140, 146-152 (1999). — seq_steam_ideal_young • Spectroscopy Analysis Tools (spant) Set the number of transients for an mrs_data object. — set_Ntrans • Spectroscopy Analysis Tools (spant) Set the number of transients for an mrs_data object. — set_Ntrans • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/set_def_acq_paras.html b/docs/reference/set_def_acq_paras.html
index 3e1b4004..cc2ada9c 100644
--- a/docs/reference/set_def_acq_paras.html
+++ b/docs/reference/set_def_acq_paras.html
@@ -1,5 +1,5 @@
-Set the default acquisition parameters. — set_def_acq_paras • Spectroscopy Analysis Tools (spant) Set the default acquisition parameters. — set_def_acq_paras • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Arguments
diff --git a/docs/reference/set_lcm_cmd.html b/docs/reference/set_lcm_cmd.html
index 2056ed01..42bb2f24 100644
--- a/docs/reference/set_lcm_cmd.html
+++ b/docs/reference/set_lcm_cmd.html
@@ -1,5 +1,5 @@
-Set the command to run the LCModel command-line program. — set_lcm_cmd • Spectroscopy Analysis Tools (spant) Set the command to run the LCModel command-line program. — set_lcm_cmd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/set_lw.html b/docs/reference/set_lw.html
index b64ec851..bb176c62 100644
--- a/docs/reference/set_lw.html
+++ b/docs/reference/set_lw.html
@@ -1,5 +1,5 @@
-Apply line-broadening to an mrs_data object to achieve a specified linewidth. — set_lw • Spectroscopy Analysis Tools (spant) Apply line-broadening to an mrs_data object to achieve a specified linewidth. — set_lw • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -123,7 +123,7 @@ Value
diff --git a/docs/reference/set_mask_xy_mat.html b/docs/reference/set_mask_xy_mat.html
index 49dc5d4e..52c4b617 100644
--- a/docs/reference/set_mask_xy_mat.html
+++ b/docs/reference/set_mask_xy_mat.html
@@ -1,5 +1,5 @@
-Set the masked voxels in a 2D MRSI dataset to given spectrum. — set_mask_xy_mat • Spectroscopy Analysis Tools (spant) Set the masked voxels in a 2D MRSI dataset to given spectrum. — set_mask_xy_mat • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Value
diff --git a/docs/reference/set_precomp_mode.html b/docs/reference/set_precomp_mode.html
index f44bd5d3..47c28e3b 100644
--- a/docs/reference/set_precomp_mode.html
+++ b/docs/reference/set_precomp_mode.html
@@ -1,5 +1,5 @@
-Set the precompute mode. — set_precomp_mode • Spectroscopy Analysis Tools (spant) Set the precompute mode. — set_precomp_mode • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/set_precomp_verbose.html b/docs/reference/set_precomp_verbose.html
index 1453a231..9c613505 100644
--- a/docs/reference/set_precomp_verbose.html
+++ b/docs/reference/set_precomp_verbose.html
@@ -1,5 +1,5 @@
-Set the verbosity of the precompute function. — set_precomp_verbose • Spectroscopy Analysis Tools (spant) Set the verbosity of the precompute function. — set_precomp_verbose • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/set_ref.html b/docs/reference/set_ref.html
index 8953fa50..5436dfa2 100644
--- a/docs/reference/set_ref.html
+++ b/docs/reference/set_ref.html
@@ -1,5 +1,5 @@
-Set the ppm reference value (eg ppm value at 0Hz). — set_ref • Spectroscopy Analysis Tools (spant) Set the ppm reference value (eg ppm value at 0Hz). — set_ref • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/set_td_pts.html b/docs/reference/set_td_pts.html
index 8a80d42a..586459ff 100644
--- a/docs/reference/set_td_pts.html
+++ b/docs/reference/set_td_pts.html
@@ -1,7 +1,5 @@
-Set the number of time-domain data points, truncating or zero-filling as
-appropriate. — set_td_pts • Spectroscopy Analysis Tools (spant) Set the number of time-domain data points, truncating or zero-filling as appropriate. — set_td_pts • Spectroscopy Analysis Tools (spant) Set the command to run the TARQUIN command-line program. — set_tqn_cmd • Spectroscopy Analysis Tools (spant) Set the command to run the TARQUIN command-line program. — set_tqn_cmd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/set_tr.html b/docs/reference/set_tr.html
index b2109ab0..65c9df5f 100644
--- a/docs/reference/set_tr.html
+++ b/docs/reference/set_tr.html
@@ -1,5 +1,5 @@
-Set the repetition time of an MRS dataset. — set_tr • Spectroscopy Analysis Tools (spant) Set the repetition time of an MRS dataset. — set_tr • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/shift.html b/docs/reference/shift.html
index ab0fe724..034591d0 100644
--- a/docs/reference/shift.html
+++ b/docs/reference/shift.html
@@ -1,5 +1,5 @@
-Apply a frequency shift to MRS data. — shift • Spectroscopy Analysis Tools (spant) Apply a frequency shift to MRS data. — shift • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/shift_basis.html b/docs/reference/shift_basis.html
index 2884be19..f55a65e0 100644
--- a/docs/reference/shift_basis.html
+++ b/docs/reference/shift_basis.html
@@ -1,5 +1,5 @@
-Apply frequency shifts to basis set signals. — shift_basis • Spectroscopy Analysis Tools (spant) Apply frequency shifts to basis set signals. — shift_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Value
diff --git a/docs/reference/sim_basis.html b/docs/reference/sim_basis.html
index c7838c46..bb5fefc6 100644
--- a/docs/reference/sim_basis.html
+++ b/docs/reference/sim_basis.html
@@ -1,5 +1,5 @@
-Simulate a basis set object. — sim_basis • Spectroscopy Analysis Tools (spant) Simulate a basis set object. — sim_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -136,7 +136,7 @@ Value
diff --git a/docs/reference/sim_basis_1h_brain.html b/docs/reference/sim_basis_1h_brain.html
index 62ed7389..f71ffa0b 100644
--- a/docs/reference/sim_basis_1h_brain.html
+++ b/docs/reference/sim_basis_1h_brain.html
@@ -1,7 +1,5 @@
-Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS
-sequence. Note, ideal pulses are assumed. — sim_basis_1h_brain • Spectroscopy Analysis Tools (spant) Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS sequence. Note, ideal pulses are assumed. — sim_basis_1h_brain • Spectroscopy Analysis Tools (spant) Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS
-sequence. Note, ideal pulses are assumed. — sim_basis_1h_brain_press • Spectroscopy Analysis Tools (spant) Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS sequence. Note, ideal pulses are assumed. — sim_basis_1h_brain_press • Spectroscopy Analysis Tools (spant) Simulate a macromolecular and lipid basis-set suitable for 1H brain MRS
-analysis. — sim_basis_mm_lip_lcm • Spectroscopy Analysis Tools (spant) Simulate a macromolecular and lipid basis-set suitable for 1H brain MRS analysis. — sim_basis_mm_lip_lcm • Spectroscopy Analysis Tools (spant) Simulate a basis file using TARQUIN. — sim_basis_tqn • Spectroscopy Analysis Tools (spant) Simulate a basis file using TARQUIN. — sim_basis_tqn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -129,7 +129,7 @@ Examples
diff --git a/docs/reference/sim_brain_1h.html b/docs/reference/sim_brain_1h.html
index 2044cf1a..717ee289 100644
--- a/docs/reference/sim_brain_1h.html
+++ b/docs/reference/sim_brain_1h.html
@@ -1,5 +1,5 @@
-Simulate MRS data with a similar appearance to normal brain (by default). — sim_brain_1h • Spectroscopy Analysis Tools (spant) Simulate MRS data with a similar appearance to normal brain (by default). — sim_brain_1h • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -159,7 +159,7 @@ Value
diff --git a/docs/reference/sim_mol.html b/docs/reference/sim_mol.html
index 23bcef50..77f76a50 100644
--- a/docs/reference/sim_mol.html
+++ b/docs/reference/sim_mol.html
@@ -1,5 +1,5 @@
-Simulate a mol_parameter object. — sim_mol • Spectroscopy Analysis Tools (spant) Simulate a mol_parameter object. — sim_mol • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -143,7 +143,7 @@ Value
diff --git a/docs/reference/sim_noise.html b/docs/reference/sim_noise.html
index 23875f79..a71477d4 100644
--- a/docs/reference/sim_noise.html
+++ b/docs/reference/sim_noise.html
@@ -1,5 +1,5 @@
-Simulate an mrs_data object containing simulated Gaussian noise. — sim_noise • Spectroscopy Analysis Tools (spant) Simulate an mrs_data object containing simulated Gaussian noise. — sim_noise • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -84,6 +84,7 @@ Simulate an mrs_data object containing simulated Gaussian noise.
ft = def_ft(),
N = def_N(),
ref = def_ref(),
+ nuc = def_nuc(),
dyns = 1,
fd = TRUE
)
@@ -111,6 +112,10 @@ Arguments
reference value for ppm scale.
nuc
+resonant nucleus.
dyns
number of dynamic scans to generate.
Value
diff --git a/docs/reference/sim_resonances.html b/docs/reference/sim_resonances.html
index 19e9a8a4..d4f8d7c0 100644
--- a/docs/reference/sim_resonances.html
+++ b/docs/reference/sim_resonances.html
@@ -1,5 +1,5 @@
-Simulate a MRS data object containing a set of simulated resonances. — sim_resonances • Spectroscopy Analysis Tools (spant) Simulate a MRS data object containing a set of simulated resonances. — sim_resonances • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -161,7 +161,7 @@ Examples
diff --git a/docs/reference/sim_th_excit_profile.html b/docs/reference/sim_th_excit_profile.html
index 5535c5ef..e781cab1 100644
--- a/docs/reference/sim_th_excit_profile.html
+++ b/docs/reference/sim_th_excit_profile.html
@@ -1,7 +1,5 @@
-Simulate an ideal pulse excitation profile by smoothing a top-hat function
-with a Gaussian. — sim_th_excit_profile • Spectroscopy Analysis Tools (spant) Simulate an ideal pulse excitation profile by smoothing a top-hat function with a Gaussian. — sim_th_excit_profile • Spectroscopy Analysis Tools (spant) Simulate an mrs_data object containing complex zero valued samples. — sim_zero • Spectroscopy Analysis Tools (spant) Simulate an mrs_data object containing complex zero valued samples. — sim_zero • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -78,7 +78,14 @@ Simulate an mrs_data object containing complex zero valued samples.
-
+
@@ -99,6 +106,10 @@ Arguments
reference value for ppm scale.
nuc
+resonant nucleus.
dyns
number of dynamic scans to generate.
Value
diff --git a/docs/reference/smooth_dyns.html b/docs/reference/smooth_dyns.html
index 4cc8da50..accf3a51 100644
--- a/docs/reference/smooth_dyns.html
+++ b/docs/reference/smooth_dyns.html
@@ -1,5 +1,5 @@
-Smooth data across the dynamic dimension with a Gaussian kernel. — smooth_dyns • Spectroscopy Analysis Tools (spant) Smooth data across the dynamic dimension with a Gaussian kernel. — smooth_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/sort_basis.html b/docs/reference/sort_basis.html
index 6a676ea2..d25cc006 100644
--- a/docs/reference/sort_basis.html
+++ b/docs/reference/sort_basis.html
@@ -1,5 +1,5 @@
-Sort the basis-set elements alphabetically. — sort_basis • Spectroscopy Analysis Tools (spant) Sort the basis-set elements alphabetically. — sort_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/spant-package.html b/docs/reference/spant-package.html
index b3dd8e21..90f19ec3 100644
--- a/docs/reference/spant-package.html
+++ b/docs/reference/spant-package.html
@@ -1,5 +1,5 @@
-spant: spectroscopy analysis tools. — spant-package • Spectroscopy Analysis Tools (spant) spant: spectroscopy analysis tools. — spant-package • Spectroscopy Analysis Tools (spant) Simulate and fit some spectra with ABfit for benchmarking purposes. Basic
-timing and performance metrics will be printed. — spant_abfit_benchmark • Spectroscopy Analysis Tools (spant) Simulate and fit some spectra with ABfit for benchmarking purposes. Basic timing and performance metrics will be printed. — spant_abfit_benchmark • Spectroscopy Analysis Tools (spant) Example MEGA-PRESS data with significant B0 drift. — spant_mpress_drift • Spectroscopy Analysis Tools (spant) Example MEGA-PRESS data with significant B0 drift. — spant_mpress_drift • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -83,7 +83,7 @@ Example MEGA-PRESS data with significant B0 drift.
Format
- An object of class mrs_data of length 13.
+ An object of class mrs_data of dimension 1 x 1 x 1 x 1 x 40 x 1 x 1024.
@@ -98,7 +98,7 @@ Format
diff --git a/docs/reference/spant_sim_fmrs_dataset.html b/docs/reference/spant_sim_fmrs_dataset.html
new file mode 100644
index 00000000..00e48b56
--- /dev/null
+++ b/docs/reference/spant_sim_fmrs_dataset.html
@@ -0,0 +1,117 @@
+
+Simulate an example fMRS dataset for a block design fMRS experiment and export a BIDS structure. — spant_sim_fmrs_dataset • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Simulate an example fMRS dataset for a block design fMRS experiment and export a BIDS structure.
+ Source: R/fmrs.R
+ spant_sim_fmrs_dataset.Rd
+
+
+
+ Simulate an example fMRS dataset for a block design fMRS experiment and
+export a BIDS structure.
+
+
+
+ spant_sim_fmrs_dataset(output_dir = NULL)
+
+
+
+ Arguments
+ - output_dir
+output directory for the BIDS data. Defaults to :
+"HOME/sim_fmrs_dataset/data".
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/spant_simulation_benchmark.html b/docs/reference/spant_simulation_benchmark.html
index 32daa8bf..d8cc6841 100644
--- a/docs/reference/spant_simulation_benchmark.html
+++ b/docs/reference/spant_simulation_benchmark.html
@@ -1,7 +1,5 @@
-Simulate a typical metabolite basis set for benchmarking. Timing metrics will
-be printed on completion. — spant_simulation_benchmark • Spectroscopy Analysis Tools (spant) Simulate a typical metabolite basis set for benchmarking. Timing metrics will be printed on completion. — spant_simulation_benchmark • Spectroscopy Analysis Tools (spant) Decompose an mrs_data object into white and gray matter spectra. — spec_decomp • Spectroscopy Analysis Tools (spant) Perform a mathematical operation on a spectral region. — spec_op • Spectroscopy Analysis Tools (spant) Perform a mathematical operation on a spectral region. — spec_op • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -98,8 +98,8 @@ Arguments
operator
-can be "sum" (default), "mean", "l2", "max", "min" or
-"max-min".
can be "sum" (default), "mean", "l2", "max", "max_cplx,
+"min" or "max-min".
freq_scale
@@ -129,7 +129,7 @@ Value
diff --git a/docs/reference/spin_sys.html b/docs/reference/spin_sys.html
index 853423a4..1eaa9e76 100644
--- a/docs/reference/spin_sys.html
+++ b/docs/reference/spin_sys.html
@@ -1,5 +1,5 @@
-Create a spin system object for pulse sequence simulation. — spin_sys • Spectroscopy Analysis Tools (spant) Create a spin system object for pulse sequence simulation. — spin_sys • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/spm_pve2categorical.html b/docs/reference/spm_pve2categorical.html
index 23a1bad9..70f10729 100644
--- a/docs/reference/spm_pve2categorical.html
+++ b/docs/reference/spm_pve2categorical.html
@@ -1,7 +1,5 @@
-Convert SPM style segmentation files to a single categorical image where
-the numerical values map as: 0) Other, 1) CSF, 2) GM and 3) WM. — spm_pve2categorical • Spectroscopy Analysis Tools (spant) Convert SPM style segmentation files to a single categorical image where the numerical values map as: 0) Other, 1) CSF, 2) GM and 3) WM. — spm_pve2categorical • Spectroscopy Analysis Tools (spant) Signal space projection method for lipid suppression. — ssp • Spectroscopy Analysis Tools (spant) Signal space projection method for lipid suppression. — ssp • Spectroscopy Analysis Tools (spant) Plot the fitting results of an object of class fit_result with
-individual basis set components shown. — stackplot.fit_result • Spectroscopy Analysis Tools (spant) Plot the fitting results of an object of class fit_result with individual basis set components shown. — stackplot.fit_result • Spectroscopy Analysis Tools (spant) Produce a plot with multiple traces. — stackplot • Spectroscopy Analysis Tools (spant) Produce a plot with multiple traces. — stackplot • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/stackplot.mrs_data.html b/docs/reference/stackplot.mrs_data.html
index 17ff5648..64eea445 100644
--- a/docs/reference/stackplot.mrs_data.html
+++ b/docs/reference/stackplot.mrs_data.html
@@ -1,5 +1,5 @@
-Stackplot plotting method for objects of class mrs_data. — stackplot.mrs_data • Spectroscopy Analysis Tools (spant) Stackplot plotting method for objects of class mrs_data. — stackplot.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -255,7 +255,7 @@ Arguments
diff --git a/docs/reference/sub_first_dyn.html b/docs/reference/sub_first_dyn.html
index dbd7f831..493b7242 100644
--- a/docs/reference/sub_first_dyn.html
+++ b/docs/reference/sub_first_dyn.html
@@ -1,5 +1,5 @@
-Subtract the first dynamic spectrum from a dynamic series. — sub_first_dyn • Spectroscopy Analysis Tools (spant) Subtract the first dynamic spectrum from a dynamic series. — sub_first_dyn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/sub_mean_dyns.html b/docs/reference/sub_mean_dyns.html
index 6e3bb2df..221bd0c1 100644
--- a/docs/reference/sub_mean_dyns.html
+++ b/docs/reference/sub_mean_dyns.html
@@ -1,5 +1,5 @@
-Subtract the mean dynamic spectrum from a dynamic series. — sub_mean_dyns • Spectroscopy Analysis Tools (spant) Subtract the mean dynamic spectrum from a dynamic series. — sub_mean_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/sub_median_dyns.html b/docs/reference/sub_median_dyns.html
index 134c495d..1e834f14 100644
--- a/docs/reference/sub_median_dyns.html
+++ b/docs/reference/sub_median_dyns.html
@@ -1,5 +1,5 @@
-Subtract the median dynamic spectrum from a dynamic series. — sub_median_dyns • Spectroscopy Analysis Tools (spant) Subtract the median dynamic spectrum from a dynamic series. — sub_median_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/sum_coils.html b/docs/reference/sum_coils.html
index 7bf559f2..e1ab3cc0 100644
--- a/docs/reference/sum_coils.html
+++ b/docs/reference/sum_coils.html
@@ -1,5 +1,5 @@
-Calculate the sum across receiver coil elements. — sum_coils • Spectroscopy Analysis Tools (spant) Calculate the sum across receiver coil elements. — sum_coils • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/sum_dyns.html b/docs/reference/sum_dyns.html
index a0be19d3..bbda2ffc 100644
--- a/docs/reference/sum_dyns.html
+++ b/docs/reference/sum_dyns.html
@@ -1,5 +1,5 @@
-Calculate the sum of data dynamics. — sum_dyns • Spectroscopy Analysis Tools (spant) Calculate the sum of data dynamics. — sum_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/sum_mrs.html b/docs/reference/sum_mrs.html
index a22f215b..3cc3ab9e 100644
--- a/docs/reference/sum_mrs.html
+++ b/docs/reference/sum_mrs.html
@@ -1,5 +1,5 @@
-Sum two mrs_data objects. — sum_mrs • Spectroscopy Analysis Tools (spant) Sum two mrs_data objects. — sum_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Value
diff --git a/docs/reference/sum_mrs_list.html b/docs/reference/sum_mrs_list.html
index f4e09aea..c3584348 100644
--- a/docs/reference/sum_mrs_list.html
+++ b/docs/reference/sum_mrs_list.html
@@ -1,5 +1,5 @@
-Return the sum of a list of mrs_data objects. — sum_mrs_list • Spectroscopy Analysis Tools (spant) Return the sum of a list of mrs_data objects. — sum_mrs_list • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/svs_1h_brain_analysis.html b/docs/reference/svs_1h_brain_analysis.html
index 8ce514db..dff0ef7d 100644
--- a/docs/reference/svs_1h_brain_analysis.html
+++ b/docs/reference/svs_1h_brain_analysis.html
@@ -1,5 +1,5 @@
-Standard SVS 1H brain analysis pipeline. — svs_1h_brain_analysis • Spectroscopy Analysis Tools (spant) Standard SVS 1H brain analysis pipeline. — svs_1h_brain_analysis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -199,7 +199,7 @@ Value
diff --git a/docs/reference/svs_1h_brain_analysis_dev.html b/docs/reference/svs_1h_brain_analysis_dev.html
index d70a14d3..d71bfea2 100644
--- a/docs/reference/svs_1h_brain_analysis_dev.html
+++ b/docs/reference/svs_1h_brain_analysis_dev.html
@@ -1,5 +1,5 @@
-Standard SVS 1H brain analysis pipeline. — svs_1h_brain_analysis_dev • Spectroscopy Analysis Tools (spant) Standard SVS 1H brain analysis pipeline. — svs_1h_brain_analysis_dev • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -193,7 +193,7 @@ Examples
diff --git a/docs/reference/svs_1h_brain_batch_analysis.html b/docs/reference/svs_1h_brain_batch_analysis.html
index 5631e8cc..15f7223e 100644
--- a/docs/reference/svs_1h_brain_batch_analysis.html
+++ b/docs/reference/svs_1h_brain_batch_analysis.html
@@ -1,5 +1,5 @@
-Batch interface to the standard SVS 1H brain analysis pipeline. — svs_1h_brain_batch_analysis • Spectroscopy Analysis Tools (spant) Batch interface to the standard SVS 1H brain analysis pipeline. — svs_1h_brain_batch_analysis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -144,7 +144,7 @@ Value
diff --git a/docs/reference/t_test_spec.html b/docs/reference/t_test_spec.html
new file mode 100644
index 00000000..56a7ea1b
--- /dev/null
+++ b/docs/reference/t_test_spec.html
@@ -0,0 +1,124 @@
+
+Perform a t-test on spectral data points. — t_test_spec • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+
+
+ Perform a t-test on spectral data points.
+
+
+
+ t_test_spec(mrs_data, group)
+
+
+
+ Arguments
+ - mrs_data
+an mrs_data object with spectra in the dynamic dimension.
- group
+vector describing the group membership of each dynamic spectrum.
+
+ Value
+
+
+a list of statistical results.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/td2fd.html b/docs/reference/td2fd.html
index 6748a6a8..f31ed524 100644
--- a/docs/reference/td2fd.html
+++ b/docs/reference/td2fd.html
@@ -1,5 +1,5 @@
-Transform time-domain data to the frequency-domain. — td2fd • Spectroscopy Analysis Tools (spant) Transform time-domain data to the frequency-domain. — td2fd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/td_conv_filt.html b/docs/reference/td_conv_filt.html
index a9f340c3..106b9b00 100644
--- a/docs/reference/td_conv_filt.html
+++ b/docs/reference/td_conv_filt.html
@@ -1,5 +1,5 @@
-Time-domain convolution based filter. — td_conv_filt • Spectroscopy Analysis Tools (spant) Time-domain convolution based filter. — td_conv_filt • Spectroscopy Analysis Tools (spant) Time-domain spectral registration. — tdsr • Spectroscopy Analysis Tools (spant) Time-domain spectral registration. — tdsr • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -121,7 +121,7 @@ Value
diff --git a/docs/reference/te.html b/docs/reference/te.html
index 010361b1..4a65711d 100644
--- a/docs/reference/te.html
+++ b/docs/reference/te.html
@@ -1,5 +1,5 @@
-Return the echo time of an MRS dataset. — te • Spectroscopy Analysis Tools (spant) Return the echo time of an MRS dataset. — te • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/tr.html b/docs/reference/tr.html
index 0c0bd63b..2e749e02 100644
--- a/docs/reference/tr.html
+++ b/docs/reference/tr.html
@@ -1,5 +1,5 @@
-Return the repetition time of an MRS dataset. — tr • Spectroscopy Analysis Tools (spant) Return the repetition time of an MRS dataset. — tr • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/varpro_3_para_opts.html b/docs/reference/varpro_3_para_opts.html
index c2270a16..52d7cd84 100644
--- a/docs/reference/varpro_3_para_opts.html
+++ b/docs/reference/varpro_3_para_opts.html
@@ -1,5 +1,5 @@
-Return a list of options for VARPRO based fitting with 3 free parameters. — varpro_3_para_opts • Spectroscopy Analysis Tools (spant) Return a list of options for VARPRO based fitting with 3 free parameters. — varpro_3_para_opts • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -141,7 +141,7 @@ Value
diff --git a/docs/reference/varpro_basic_opts.html b/docs/reference/varpro_basic_opts.html
index 32c86d22..c5104891 100644
--- a/docs/reference/varpro_basic_opts.html
+++ b/docs/reference/varpro_basic_opts.html
@@ -1,5 +1,5 @@
-Return a list of options for a basic VARPRO analysis. — varpro_basic_opts • Spectroscopy Analysis Tools (spant) Return a list of options for a basic VARPRO analysis. — varpro_basic_opts • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -118,7 +118,7 @@ Value
diff --git a/docs/reference/varpro_opts.html b/docs/reference/varpro_opts.html
index 2aabf11d..6332f730 100644
--- a/docs/reference/varpro_opts.html
+++ b/docs/reference/varpro_opts.html
@@ -1,5 +1,5 @@
-Return a list of options for VARPRO based fitting. — varpro_opts • Spectroscopy Analysis Tools (spant) Return a list of options for VARPRO based fitting. — varpro_opts • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -177,7 +177,7 @@ Examples
diff --git a/docs/reference/vec2mrs_data.html b/docs/reference/vec2mrs_data.html
index 0cccd73b..f0d58bf0 100644
--- a/docs/reference/vec2mrs_data.html
+++ b/docs/reference/vec2mrs_data.html
@@ -1,5 +1,5 @@
-Convert a vector into a mrs_data object. — vec2mrs_data • Spectroscopy Analysis Tools (spant) Convert a vector into a mrs_data object. — vec2mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -80,10 +80,11 @@ Convert a vector into a mrs_data object.
vec2mrs_data(
vec,
- fs = def_fs(),
- ft = def_ft(),
- ref = def_ref(),
- nuc = def_nuc(),
+ mrs_data = NULL,
+ fs = NULL,
+ ft = NULL,
+ ref = NULL,
+ nuc = NULL,
dyns = 1,
fd = FALSE
)
@@ -95,6 +96,10 @@ Arguments
the data vector.
mrs_data
+example data to copy acquisition parameters from.
fs
sampling frequency in Hz.
Arguments
fd
-flag to indicate if the matrix is in the frequency domain (logical).
flag to indicate if the vector is in the frequency domain (logical).
Value
diff --git a/docs/reference/write_basis.html b/docs/reference/write_basis.html
index b6e27cbd..94c5e021 100644
--- a/docs/reference/write_basis.html
+++ b/docs/reference/write_basis.html
@@ -1,5 +1,5 @@
-Write a basis object to an LCModel .basis formatted file. — write_basis • Spectroscopy Analysis Tools (spant) Write a basis object to an LCModel .basis formatted file. — write_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -108,7 +108,7 @@ Arguments
diff --git a/docs/reference/write_basis_tqn.html b/docs/reference/write_basis_tqn.html
index 6aa51c1d..116c73ec 100644
--- a/docs/reference/write_basis_tqn.html
+++ b/docs/reference/write_basis_tqn.html
@@ -1,5 +1,5 @@
-Generate a basis file using TARQUIN. — write_basis_tqn • Spectroscopy Analysis Tools (spant) Generate a basis file using TARQUIN. — write_basis_tqn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Examples
diff --git a/docs/reference/write_mrs.html b/docs/reference/write_mrs.html
index fff25f15..124b9dc4 100644
--- a/docs/reference/write_mrs.html
+++ b/docs/reference/write_mrs.html
@@ -1,5 +1,5 @@
-Write MRS data object to file. — write_mrs • Spectroscopy Analysis Tools (spant) Write MRS data object to file. — write_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Arguments
diff --git a/docs/reference/write_mrs_nifti.html b/docs/reference/write_mrs_nifti.html
index f4bf1921..bd3ed4b7 100644
--- a/docs/reference/write_mrs_nifti.html
+++ b/docs/reference/write_mrs_nifti.html
@@ -1,5 +1,5 @@
-Write MRS data object to file in NIFTI format. — write_mrs_nifti • Spectroscopy Analysis Tools (spant) Write MRS data object to file in NIFTI format. — write_mrs_nifti • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/write_pulse_ascii.html b/docs/reference/write_pulse_ascii.html
index 067ae086..221f8ebb 100644
--- a/docs/reference/write_pulse_ascii.html
+++ b/docs/reference/write_pulse_ascii.html
@@ -1,5 +1,5 @@
-Write an ASCII formatted pulse file. — write_pulse_ascii • Spectroscopy Analysis Tools (spant) Write an ASCII formatted pulse file. — write_pulse_ascii • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/zero_fade_spec.html b/docs/reference/zero_fade_spec.html
index c703745c..c8b572c3 100644
--- a/docs/reference/zero_fade_spec.html
+++ b/docs/reference/zero_fade_spec.html
@@ -1,7 +1,5 @@
-Fade a spectrum to zero by frequency domain multiplication with a tanh
-function. Note this operation distorts data points at the end of the FID. — zero_fade_spec • Spectroscopy Analysis Tools (spant) Fade a spectrum to zero by frequency domain multiplication with a tanh function. Note this operation distorts data points at the end of the FID. — zero_fade_spec • Spectroscopy Analysis Tools (spant) Zero all coherences including and above a given order. — zero_higher_orders • Spectroscopy Analysis Tools (spant) Zero all coherences including and above a given order. — zero_higher_orders • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Value
diff --git a/docs/reference/zero_td_pts_end.html b/docs/reference/zero_td_pts_end.html
index 8c1123c8..71d24ebb 100644
--- a/docs/reference/zero_td_pts_end.html
+++ b/docs/reference/zero_td_pts_end.html
@@ -1,5 +1,5 @@
-Set mrs_data object data points at the end of the FID to zero. — zero_td_pts_end • Spectroscopy Analysis Tools (spant) Set mrs_data object data points at the end of the FID to zero. — zero_td_pts_end • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/zf.html b/docs/reference/zf.html
index 85e2013c..baf50256 100644
--- a/docs/reference/zf.html
+++ b/docs/reference/zf.html
@@ -1,5 +1,5 @@
-Zero-fill MRS data in the time domain. — zf • Spectroscopy Analysis Tools (spant) Zero-fill MRS data in the time domain. — zf • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -125,7 +125,7 @@ Value
diff --git a/docs/reference/zf_xy.html b/docs/reference/zf_xy.html
index ebca3999..c4104a74 100644
--- a/docs/reference/zf_xy.html
+++ b/docs/reference/zf_xy.html
@@ -1,5 +1,5 @@
-Zero-fill MRSI data in the k-space x-y direction. — zf_xy • Spectroscopy Analysis Tools (spant) Zero-fill MRSI data in the k-space x-y direction. — zf_xy • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -113,7 +113,7 @@ Value
diff --git a/docs/sitemap.xml b/docs/sitemap.xml
index e2139f71..4c39f515 100644
--- a/docs/sitemap.xml
+++ b/docs/sitemap.xml
@@ -216,6 +216,12 @@
https://martin3141.github.io/spant/reference/comb_coils_fp_pc.html
+
+ https://martin3141.github.io/spant/reference/comb_coils_mrsi_gls.html
+
+
+ https://martin3141.github.io/spant/reference/comb_coils_svs_gls.html
+
https://martin3141.github.io/spant/reference/comb_csv_results.html
@@ -411,6 +417,9 @@
https://martin3141.github.io/spant/reference/gen_conv_reg.html
+
+ https://martin3141.github.io/spant/reference/gen_group_reg.html
+
https://martin3141.github.io/spant/reference/gen_impulse_reg.html
@@ -555,6 +564,15 @@
https://martin3141.github.io/spant/reference/glm_spec.html
+
+ https://martin3141.github.io/spant/reference/glm_spec_fmrs_fl.html
+
+
+ https://martin3141.github.io/spant/reference/glm_spec_fmrs_group.html
+
+
+ https://martin3141.github.io/spant/reference/glm_spec_group_linhyp.html
+
https://martin3141.github.io/spant/reference/grid_shift_xy.html
@@ -690,9 +708,15 @@
https://martin3141.github.io/spant/reference/mrs_data2basis.html
+
+ https://martin3141.github.io/spant/reference/mrs_data2bids.html
+
https://martin3141.github.io/spant/reference/mrs_data2mat.html
+
+ https://martin3141.github.io/spant/reference/mrs_data2spec_mat.html
+
https://martin3141.github.io/spant/reference/mrs_data2vec.html
@@ -741,6 +765,9 @@
https://martin3141.github.io/spant/reference/phase.html
+
+ https://martin3141.github.io/spant/reference/phase_ref_1h_brain.html
+
https://martin3141.github.io/spant/reference/plot.fit_result.html
@@ -780,6 +807,12 @@
https://martin3141.github.io/spant/reference/precomp.html
+
+ https://martin3141.github.io/spant/reference/preproc_svs.html
+
+
+ https://martin3141.github.io/spant/reference/preproc_svs_dataset.html
+
https://martin3141.github.io/spant/reference/print.fit_result.html
@@ -1050,6 +1083,9 @@
https://martin3141.github.io/spant/reference/spant_mpress_drift.html
+
+ https://martin3141.github.io/spant/reference/spant_sim_fmrs_dataset.html
+
https://martin3141.github.io/spant/reference/spant_simulation_benchmark.html
@@ -1107,6 +1143,9 @@
https://martin3141.github.io/spant/reference/svs_1h_brain_batch_analysis.html
+
+ https://martin3141.github.io/spant/reference/t_test_spec.html
+
https://martin3141.github.io/spant/reference/td2fd.html
Crop mrs_data object data points in the time-domain rounding down to
-the next smallest power of two (pot). Data that already has a pot length will
-not be changed.
Crop mrs_data object data points in the time-domain rounding down to the next smallest power of two (pot). Data that already has a pot length will not be changed.
All functions
- Compute the vector cross product between vectors x and y. Adapted from
-http://stackoverflow.com/questions/15162741/what-is-rs-crossproduct-function
Compute the vector cross product between vectors x and y. Adapted from http://stackoverflow.com/questions/15162741/what-is-rs-crossproduct-function
- Decimate an MRS signal to half the original sampling frequency by filtering
-in the frequency domain before down sampling.
Decimate an MRS signal to half the original sampling frequency by filtering in the frequency domain before down sampling.
@@ -377,8 +370,7 @@ All functions
- Return (and optionally modify using the input arguments) a list of the
-default acquisition parameters.
Return (and optionally modify using the input arguments) a list of the default acquisition parameters.
@@ -410,14 +402,11 @@ All functions
- Downsample an MRS signal by a factor of 2 by removing every other data point
-in the time-domain. Note, signals outside the new sampling frequency will be
-aliased.
Downsample an MRS signal by a factor of 2 by removing every other data point in the time-domain. Note, signals outside the new sampling frequency will be aliased.
- Return a time scale vector of acquisition times for a dynamic MRS scan. The
-first temporal scan is assigned a value of 0.
Return a time scale vector of acquisition times for a dynamic MRS scan. The first temporal scan is assigned a value of 0.
@@ -429,8 +418,7 @@ All functions
- Estimate the standard deviation of the noise from a segment of an mrs_data
-object.
Estimate the standard deviation of the noise from a segment of an mrs_data object.
@@ -486,8 +474,7 @@ All functions
- Perform a zeroth order phase correction based on the phase of the first data
-point in the time-domain.
Perform a zeroth order phase correction based on the phase of the first data point in the time-domain.
@@ -507,8 +494,7 @@ All functions
- Perform a fft and fftshift on a matrix with each column replaced by its
-shifted fft.
Perform a fft and fftshift on a matrix with each column replaced by its shifted fft.
@@ -536,8 +522,11 @@ All functions
- Generate regressors by convolving a specified response function with a
-stimulus.
Generate regressors by convolving a specified response function with a stimulus.
+
+
+ Expand a regressor matrix for a group analysis.
@@ -553,28 +542,23 @@ All functions
- Return a character vector of common 1H molecules found in healthy human
-brain.
Return a character vector of common 1H molecules found in healthy human brain.
- Return a list of mol_parameter objects suitable for 1H brain MRS
-analyses.
Return a list of mol_parameter objects suitable for 1H brain MRS analyses.
- Return a list of mol_parameter objects suitable for 1H brain MRS
-analyses.
Return a list of mol_parameter objects suitable for 1H brain MRS analyses.
- Return a list of mol_parameter objects suitable for 1H brain MRS
-analyses.
Return a list of mol_parameter objects suitable for 1H brain MRS analyses.
- Return a list of mol_parameter objects suitable for 1H brain MRS
-analyses.
Return a list of mol_parameter objects suitable for 1H brain MRS analyses.
@@ -582,8 +566,7 @@ All functions
- Return a character vector of molecules included in the Gold Star Phantoms
-SPECTRE phantom.
Return a character vector of molecules included in the Gold Star Phantoms SPECTRE phantom.
@@ -635,8 +618,7 @@ All functions
- Return a character array of names that may be used with the
-get_mol_paras function.
Return a character array of names that may be used with the get_mol_paras function.
@@ -700,8 +682,7 @@ All functions
- Return an array of amplitudes derived from fitting the initial points in the
-time domain and extrapolating back to t=0.
Return an array of amplitudes derived from fitting the initial points in the time domain and extrapolating back to t=0.
@@ -709,8 +690,7 @@ All functions
- Generate a mol_parameters object for a simple spin system with one
-resonance.
Generate a mol_parameters object for a simple spin system with one resonance.
@@ -731,6 +711,18 @@ All functions glm_spec()
Perform a GLM analysis of dynamic MRS data in the spectral domain.
+
+
+ Perform first-level spectral GLM analysis of an fMRS dataset.
+
+
+ Perform group-level spectral GLM analysis of an fMRS dataset.
+
+
+ Test a group-level spectral GLM linear hypothesis.
@@ -766,8 +758,7 @@ All functions
- Perform an ifft and ifftshift on a matrix with each column replaced by its
-shifted ifft.
Perform an ifft and ifftshift on a matrix with each column replaced by its shifted ifft.
@@ -799,8 +790,7 @@ All functions
- Check if the chemical shift dimension of an MRS data object is in the
-frequency domain.
Check if the chemical shift dimension of an MRS data object is in the frequency domain.
@@ -820,18 +810,15 @@ All functions
- Covert a linewidth in Hz to an equivalent alpha value in the time-domain ie:
-x * exp(-t * alpha).
Covert a linewidth in Hz to an equivalent alpha value in the time-domain ie: x * exp(-t * alpha).
- Covert a linewidth in Hz to an equivalent beta value in the time-domain ie:
-x * exp(-t * t * beta).
Covert a linewidth in Hz to an equivalent beta value in the time-domain ie: x * exp(-t * t * beta).
- Make a basis-set object from a directory containing LCModel formatted RAW
-files.
Make a basis-set object from a directory containing LCModel formatted RAW files.
@@ -851,8 +838,7 @@ All functions
- Mask the voxels outside an elliptical region spanning the MRSI dataset in the
-x-y plane.
Mask the voxels outside an elliptical region spanning the MRSI dataset in the x-y plane.
@@ -860,13 +846,11 @@ All functions
- Convert a matrix (with spectral points in the column dimension and dynamics
-in the row dimensions) into a mrs_data object.
Convert a matrix (with spectral points in the column dimension and dynamics in the row dimensions) into a mrs_data object.
- Matrix exponential function taken from complexplus package to reduce the
-number of spant dependencies.
Matrix exponential function taken from complexplus package to reduce the number of spant dependencies.
@@ -914,31 +898,31 @@ All functions
- Convert an mrs_data object to basis object - where basis signals are spread
-across the dynamic dimension in the MRS data.
Convert an mrs_data object to basis object - where basis signals are spread across the dynamic dimension in the MRS data.
+
+
+ Create a BIDS file structure from a vector of MRS data paths or list of mrs_data objects.
- Convert mrs_data object to a matrix, with spectral points in the column
-dimension and dynamics in the row dimension.
Convert mrs_data object to a matrix, with spectral points in the column dimension and dynamics in the row dimension.
-
+
- Convert mrs_data object to a vector.
Convert mrs_data object to a matrix, with spectral points in the column dimension and dynamics in the row dimension.
-
+
- Create a BIDS directory and file structure from a list of mrs_data objects.
Convert mrs_data object to a vector.
- Perform a fftshift on a matrix, with each column replaced by its shifted
-result.
Perform a fftshift on a matrix, with each column replaced by its shifted result.
- Perform an ifftshift on a matrix, with each column replaced by its shifted
-result.
Perform an ifftshift on a matrix, with each column replaced by its shifted result.
@@ -946,9 +930,7 @@ All functions
- Flip the x data dimension order of a nifti image. This corresponds to
-flipping MRI data in the left-right direction, assuming the data in save in
-neurological format (can check with fslorient program).
Flip the x data dimension order of a nifti image. This corresponds to flipping MRI data in the left-right direction, assuming the data in save in neurological format (can check with fslorient program).
@@ -964,8 +946,7 @@ All functions
- Search for the highest peak in a spectral region and return the frequency,
-height and FWHM.
Search for the highest peak in a spectral region and return the frequency, height and FWHM.
@@ -974,6 +955,10 @@ All functions phase()
Apply phasing parameters to MRS data.
+
+
+ Corrected zero order phase and chemical shift offset in 1H MRS data from the brain.
@@ -1005,8 +990,7 @@ All functions
- Plot an interactive slice map from a data array where voxels can be selected
-to display a corresponding spectrum.
Plot an interactive slice map from a data array where voxels can be selected to display a corresponding spectrum.
@@ -1026,8 +1010,15 @@ All functions
- Save function results to file and load on subsequent calls to avoid repeat
-computation.
Save function results to file and load on subsequent calls to avoid repeat computation.
+
+
+ Preprocess and perform quality assessment of a single SVS data set.
+
+
+ Preprocess and perform quality assessment of one or more SVS data sets.
@@ -1055,15 +1046,11 @@ All functions
- Read a directory containing Siemens MRS IMA files and combine along the coil
-dimension. Note that the coil ID is inferred from the sorted file name and
-should be checked when consistency is required between two directories.
Read a directory containing Siemens MRS IMA files and combine along the coil dimension. Note that the coil ID is inferred from the sorted file name and should be checked when consistency is required between two directories.
- Read a directory containing Siemens MRS IMA files and combine along the
-dynamic dimension. Note that the coil ID is inferred from the sorted file
-name and should be checked when consistency is required.
Read a directory containing Siemens MRS IMA files and combine along the dynamic dimension. Note that the coil ID is inferred from the sorted file name and should be checked when consistency is required.
@@ -1103,13 +1090,11 @@ All functions
- Reconstruct complex time-domain data from the real part of frequency-domain
-data.
Reconstruct complex time-domain data from the real part of frequency-domain data.
- Reconstruct complex time-domain data from the real part of frequency-domain
-data.
Reconstruct complex time-domain data from the real part of frequency-domain data.
@@ -1141,8 +1126,7 @@ All functions
- Resample a VOI to match a target image space using nearest-neighbour
-interpolation.
Resample a VOI to match a target image space using nearest-neighbour interpolation.
@@ -1158,23 +1142,19 @@ All functions
- Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water).
Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / kg of tissue water).
- Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water).
Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / kg of tissue water).
- Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / Litre of tissue).
Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / Litre of tissue).
- Convert default LCM/TARQUIN concentration scaling to molal units with partial
-volume correction.
Convert default LCM/TARQUIN concentration scaling to molal units with partial volume correction.
@@ -1222,8 +1202,7 @@ All functions
- MEGA-PRESS sequence with ideal localisation pulses and Gaussian shaped
-editing pulse.
MEGA-PRESS sequence with ideal localisation pulses and Gaussian shaped editing pulse.
@@ -1251,13 +1230,11 @@ All functions
- STEAM sequence with ideal pulses and coherence order filtering to simulate
-gradient crushers.
STEAM sequence with ideal pulses and coherence order filtering to simulate gradient crushers.
- STEAM sequence with ideal pulses using the z-rotation gradient simulation
-method described by Young et al JMR 140, 146-152 (1999).
STEAM sequence with ideal pulses using the z-rotation gradient simulation method described by Young et al JMR 140, 146-152 (1999).
@@ -1293,8 +1270,7 @@ All functions
- Set the number of time-domain data points, truncating or zero-filling as
-appropriate.
Set the number of time-domain data points, truncating or zero-filling as appropriate.
@@ -1318,18 +1294,15 @@ All functions
- Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS
-sequence. Note, ideal pulses are assumed.
Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS sequence. Note, ideal pulses are assumed.
- Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS
-sequence. Note, ideal pulses are assumed.
Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS sequence. Note, ideal pulses are assumed.
- Simulate a macromolecular and lipid basis-set suitable for 1H brain MRS
-analysis.
Simulate a macromolecular and lipid basis-set suitable for 1H brain MRS analysis.
@@ -1353,8 +1326,7 @@ All functions
- Simulate an ideal pulse excitation profile by smoothing a top-hat function
-with a Gaussian.
Simulate an ideal pulse excitation profile by smoothing a top-hat function with a Gaussian.
@@ -1374,17 +1346,19 @@ All functions
- Simulate and fit some spectra with ABfit for benchmarking purposes. Basic
-timing and performance metrics will be printed.
Simulate and fit some spectra with ABfit for benchmarking purposes. Basic timing and performance metrics will be printed.
Example MEGA-PRESS data with significant B0 drift.
+
+
+ Simulate an example fMRS dataset for a block design fMRS experiment and export a BIDS structure.
- Simulate a typical metabolite basis set for benchmarking. Timing metrics will
-be printed on completion.
Simulate a typical metabolite basis set for benchmarking. Timing metrics will be printed on completion.
@@ -1400,8 +1374,7 @@ All functions
- Convert SPM style segmentation files to a single categorical image where
-the numerical values map as: 0) Other, 1) CSF, 2) GM and 3) WM.
Convert SPM style segmentation files to a single categorical image where the numerical values map as: 0) Other, 1) CSF, 2) GM and 3) WM.
@@ -1413,8 +1386,7 @@ All functions
- Plot the fitting results of an object of class fit_result with
-individual basis set components shown.
Plot the fitting results of an object of class fit_result with individual basis set components shown.
@@ -1459,6 +1431,10 @@ All functions svs_1h_brain_batch_analysis()
Batch interface to the standard SVS 1H brain analysis pipeline.
+
+
+ Perform a t-test on spectral data points.
@@ -1518,8 +1494,7 @@ All functions
- Fade a spectrum to zero by frequency domain multiplication with a tanh
-function. Note this operation distorts data points at the end of the FID.
Fade a spectrum to zero by frequency domain multiplication with a tanh function. Note this operation distorts data points at the end of the FID.
@@ -1549,7 +1524,7 @@ All functions
diff --git a/docs/reference/int_spec.html b/docs/reference/int_spec.html
index c7060fe7..783325a8 100644
--- a/docs/reference/int_spec.html
+++ b/docs/reference/int_spec.html
@@ -1,5 +1,5 @@
-Integrate a spectral region. — int_spec • Spectroscopy Analysis Tools (spant) Integrate a spectral region. — int_spec • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -118,7 +118,7 @@ Value
diff --git a/docs/reference/interleave_dyns.html b/docs/reference/interleave_dyns.html
index effe5543..441eff27 100644
--- a/docs/reference/interleave_dyns.html
+++ b/docs/reference/interleave_dyns.html
@@ -1,5 +1,5 @@
-Interleave the first and second half of a dynamic series. — interleave_dyns • Spectroscopy Analysis Tools (spant) Interleave the first and second half of a dynamic series. — interleave_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/inv_even_dyns.html b/docs/reference/inv_even_dyns.html
index 9f9d4fff..dcb781dc 100644
--- a/docs/reference/inv_even_dyns.html
+++ b/docs/reference/inv_even_dyns.html
@@ -1,5 +1,5 @@
-Invert even numbered dynamic scans starting from 1 (2,4,6...). — inv_even_dyns • Spectroscopy Analysis Tools (spant) Invert even numbered dynamic scans starting from 1 (2,4,6...). — inv_even_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/inv_odd_dyns.html b/docs/reference/inv_odd_dyns.html
index 26212e2b..78d64660 100644
--- a/docs/reference/inv_odd_dyns.html
+++ b/docs/reference/inv_odd_dyns.html
@@ -1,5 +1,5 @@
-Invert odd numbered dynamic scans starting from 1 (1,3,5...). — inv_odd_dyns • Spectroscopy Analysis Tools (spant) Invert odd numbered dynamic scans starting from 1 (1,3,5...). — inv_odd_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/is.def.html b/docs/reference/is.def.html
index f196ffd0..a67b9eba 100644
--- a/docs/reference/is.def.html
+++ b/docs/reference/is.def.html
@@ -1,5 +1,5 @@
-Check if an object is defined, which is the same as being not NULL. — is.def • Spectroscopy Analysis Tools (spant) Check if an object is defined, which is the same as being not NULL. — is.def • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/is_fd.html b/docs/reference/is_fd.html
index 3b0ca165..18a193aa 100644
--- a/docs/reference/is_fd.html
+++ b/docs/reference/is_fd.html
@@ -1,7 +1,5 @@
-Check if the chemical shift dimension of an MRS data object is in the
-frequency domain. — is_fd • Spectroscopy Analysis Tools (spant) Check if the chemical shift dimension of an MRS data object is in the frequency domain. — is_fd • Spectroscopy Analysis Tools (spant) Transform 2D MRSI data from k-space to image space in the x-y direction. — kspace2img_xy • Spectroscopy Analysis Tools (spant) Transform 2D MRSI data from k-space to image space in the x-y direction. — kspace2img_xy • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/l2_reg.html b/docs/reference/l2_reg.html
index 3d781d80..21aa9849 100644
--- a/docs/reference/l2_reg.html
+++ b/docs/reference/l2_reg.html
@@ -1,5 +1,5 @@
-Perform l2 regularisation artefact suppression. — l2_reg • Spectroscopy Analysis Tools (spant) Perform l2 regularisation artefact suppression. — l2_reg • Spectroscopy Analysis Tools (spant) Apply line-broadening (apodisation) to MRS data or basis object. — lb • Spectroscopy Analysis Tools (spant) Apply line-broadening (apodisation) to MRS data or basis object. — lb • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -123,7 +123,7 @@ Value
diff --git a/docs/reference/lofdc.html b/docs/reference/lofdc.html
index 5419b1ec..31347a25 100644
--- a/docs/reference/lofdc.html
+++ b/docs/reference/lofdc.html
@@ -1,5 +1,5 @@
-Correct linear frequency drift. — lofdc • Spectroscopy Analysis Tools (spant) Correct linear frequency drift. — lofdc • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -138,7 +138,7 @@ Value
diff --git a/docs/reference/lw2alpha.html b/docs/reference/lw2alpha.html
index b83db682..25da229b 100644
--- a/docs/reference/lw2alpha.html
+++ b/docs/reference/lw2alpha.html
@@ -1,7 +1,5 @@
-Covert a linewidth in Hz to an equivalent alpha value in the time-domain ie:
-x * exp(-t * alpha). — lw2alpha • Spectroscopy Analysis Tools (spant) Covert a linewidth in Hz to an equivalent alpha value in the time-domain ie: x * exp(-t * alpha). — lw2alpha • Spectroscopy Analysis Tools (spant) Covert a linewidth in Hz to an equivalent beta value in the time-domain ie:
-x * exp(-t * t * beta). — lw2beta • Spectroscopy Analysis Tools (spant) Covert a linewidth in Hz to an equivalent beta value in the time-domain ie: x * exp(-t * t * beta). — lw2beta • Spectroscopy Analysis Tools (spant) Make a basis-set object from a directory containing LCModel formatted RAW
-files. — make_basis_from_raw • Spectroscopy Analysis Tools (spant) Make a basis-set object from a directory containing LCModel formatted RAW files. — make_basis_from_raw • Spectroscopy Analysis Tools (spant) Mask an MRS dataset in the dynamic dimension. — mask_dyns • Spectroscopy Analysis Tools (spant) Mask an MRS dataset in the dynamic dimension. — mask_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/mask_fit_res.html b/docs/reference/mask_fit_res.html
index 97baaa3f..ebd91a99 100644
--- a/docs/reference/mask_fit_res.html
+++ b/docs/reference/mask_fit_res.html
@@ -1,5 +1,5 @@
-Mask fit result spectra depending on a vector of bool values. — mask_fit_res • Spectroscopy Analysis Tools (spant) Mask fit result spectra depending on a vector of bool values. — mask_fit_res • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -116,7 +116,7 @@ Value
diff --git a/docs/reference/mask_xy.html b/docs/reference/mask_xy.html
index 11bb577c..b0d38619 100644
--- a/docs/reference/mask_xy.html
+++ b/docs/reference/mask_xy.html
@@ -1,5 +1,5 @@
-Mask an MRSI dataset in the x-y direction — mask_xy • Spectroscopy Analysis Tools (spant) Mask an MRSI dataset in the x-y direction — mask_xy • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/mask_xy_corners.html b/docs/reference/mask_xy_corners.html
index 09b16cd2..2d13839d 100644
--- a/docs/reference/mask_xy_corners.html
+++ b/docs/reference/mask_xy_corners.html
@@ -1,5 +1,5 @@
-Mask the four corners of an MRSI dataset in the x-y plane. — mask_xy_corners • Spectroscopy Analysis Tools (spant) Mask the four corners of an MRSI dataset in the x-y plane. — mask_xy_corners • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/mask_xy_ellipse.html b/docs/reference/mask_xy_ellipse.html
index 1d8b02e4..e2e749ef 100644
--- a/docs/reference/mask_xy_ellipse.html
+++ b/docs/reference/mask_xy_ellipse.html
@@ -1,7 +1,5 @@
-Mask the voxels outside an elliptical region spanning the MRSI dataset in the
-x-y plane. — mask_xy_ellipse • Spectroscopy Analysis Tools (spant) Mask the voxels outside an elliptical region spanning the MRSI dataset in the x-y plane. — mask_xy_ellipse • Spectroscopy Analysis Tools (spant) Mask a 2D MRSI dataset in the x-y dimension. — mask_xy_mat • Spectroscopy Analysis Tools (spant) Mask a 2D MRSI dataset in the x-y dimension. — mask_xy_mat • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Value
diff --git a/docs/reference/mat2mrs_data.html b/docs/reference/mat2mrs_data.html
index 2e2895f3..ae55665f 100644
--- a/docs/reference/mat2mrs_data.html
+++ b/docs/reference/mat2mrs_data.html
@@ -1,7 +1,5 @@
-Convert a matrix (with spectral points in the column dimension and dynamics
-in the row dimensions) into a mrs_data object. — mat2mrs_data • Spectroscopy Analysis Tools (spant) Convert a matrix (with spectral points in the column dimension and dynamics in the row dimensions) into a mrs_data object. — mat2mrs_data • Spectroscopy Analysis Tools (spant) Matrix exponential function taken from complexplus package to reduce the
-number of spant dependencies. — matexp • Spectroscopy Analysis Tools (spant) Matrix exponential function taken from complexplus package to reduce the number of spant dependencies. — matexp • Spectroscopy Analysis Tools (spant) Apply the max operator to an MRS dataset. — max_mrs • Spectroscopy Analysis Tools (spant) Apply the max operator to an MRS dataset. — max_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/max_mrs_interp.html b/docs/reference/max_mrs_interp.html
index e4474764..52e63f3e 100644
--- a/docs/reference/max_mrs_interp.html
+++ b/docs/reference/max_mrs_interp.html
@@ -1,5 +1,5 @@
-Apply the max operator to an interpolated MRS dataset. — max_mrs_interp • Spectroscopy Analysis Tools (spant) Apply the max operator to an interpolated MRS dataset. — max_mrs_interp • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/mean.list.html b/docs/reference/mean.list.html
index b8eb3463..048306fd 100644
--- a/docs/reference/mean.list.html
+++ b/docs/reference/mean.list.html
@@ -1,5 +1,5 @@
-Calculate the mean spectrum from an mrs_data object. — mean.list • Spectroscopy Analysis Tools (spant) Calculate the mean spectrum from an mrs_data object. — mean.list • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/mean.mrs_data.html b/docs/reference/mean.mrs_data.html
index 5531a28d..79515014 100644
--- a/docs/reference/mean.mrs_data.html
+++ b/docs/reference/mean.mrs_data.html
@@ -1,5 +1,5 @@
-Calculate the mean spectrum from an mrs_data object. — mean.mrs_data • Spectroscopy Analysis Tools (spant) Calculate the mean spectrum from an mrs_data object. — mean.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/mean_dyn_blocks.html b/docs/reference/mean_dyn_blocks.html
index 10467098..4c042448 100644
--- a/docs/reference/mean_dyn_blocks.html
+++ b/docs/reference/mean_dyn_blocks.html
@@ -1,5 +1,5 @@
-Calculate the mean of adjacent dynamic scans. — mean_dyn_blocks • Spectroscopy Analysis Tools (spant) Calculate the mean of adjacent dynamic scans. — mean_dyn_blocks • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/mean_dyn_pairs.html b/docs/reference/mean_dyn_pairs.html
index 63e909ea..1a241126 100644
--- a/docs/reference/mean_dyn_pairs.html
+++ b/docs/reference/mean_dyn_pairs.html
@@ -1,5 +1,5 @@
-Calculate the pairwise means across a dynamic data set. — mean_dyn_pairs • Spectroscopy Analysis Tools (spant) Calculate the pairwise means across a dynamic data set. — mean_dyn_pairs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/mean_dyns.html b/docs/reference/mean_dyns.html
index 73fdbfa7..0daa27df 100644
--- a/docs/reference/mean_dyns.html
+++ b/docs/reference/mean_dyns.html
@@ -1,5 +1,5 @@
-Calculate the mean dynamic data. — mean_dyns • Spectroscopy Analysis Tools (spant) Calculate the mean dynamic data. — mean_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/mean_mrs_list.html b/docs/reference/mean_mrs_list.html
index 808b6c50..10d842c0 100644
--- a/docs/reference/mean_mrs_list.html
+++ b/docs/reference/mean_mrs_list.html
@@ -1,5 +1,5 @@
-Return the mean of a list of mrs_data objects. — mean_mrs_list • Spectroscopy Analysis Tools (spant) Return the mean of a list of mrs_data objects. — mean_mrs_list • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/mean_vec_blocks.html b/docs/reference/mean_vec_blocks.html
index 8fc92eaa..dd78b122 100644
--- a/docs/reference/mean_vec_blocks.html
+++ b/docs/reference/mean_vec_blocks.html
@@ -1,5 +1,5 @@
-Calculate the mean of adjacent blocks in a vector. — mean_vec_blocks • Spectroscopy Analysis Tools (spant) Calculate the mean of adjacent blocks in a vector. — mean_vec_blocks • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/median_dyns.html b/docs/reference/median_dyns.html
index 1039d4b5..9a085b10 100644
--- a/docs/reference/median_dyns.html
+++ b/docs/reference/median_dyns.html
@@ -1,5 +1,5 @@
-Calculate the median dynamic data. — median_dyns • Spectroscopy Analysis Tools (spant) Calculate the median dynamic data. — median_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/mod_td.html b/docs/reference/mod_td.html
index 76ad0a40..141ef09e 100644
--- a/docs/reference/mod_td.html
+++ b/docs/reference/mod_td.html
@@ -1,5 +1,5 @@
-Apply the Modulus operator to the time-domain MRS signal. — mod_td • Spectroscopy Analysis Tools (spant) Apply the Modulus operator to the time-domain MRS signal. — mod_td • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/mrs_data2basis.html b/docs/reference/mrs_data2basis.html
index 62f7d749..11797b91 100644
--- a/docs/reference/mrs_data2basis.html
+++ b/docs/reference/mrs_data2basis.html
@@ -1,7 +1,5 @@
-Convert an mrs_data object to basis object - where basis signals are spread
-across the dynamic dimension in the MRS data. — mrs_data2basis • Spectroscopy Analysis Tools (spant) Convert an mrs_data object to basis object - where basis signals are spread across the dynamic dimension in the MRS data. — mrs_data2basis • Spectroscopy Analysis Tools (spant) Create a BIDS file structure from a vector of MRS data paths or list of mrs_data objects. — mrs_data2bids • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Create a BIDS file structure from a vector of MRS data paths or list of mrs_data objects.
+ Source: R/fmrs.R
+ mrs_data2bids.Rd
+
+
+
+ Create a BIDS file structure from a vector of MRS data paths or list of
+mrs_data objects.
+
+
+
+ mrs_data2bids(
+ mrs_data,
+ output_dir,
+ suffix = NULL,
+ sub = NULL,
+ ses = NULL,
+ task = NULL,
+ acq = NULL,
+ nuc = NULL,
+ voi = NULL,
+ rec = NULL,
+ run = NULL,
+ echo = NULL,
+ inv = NULL,
+ skip_existing = TRUE
+)
+
+
+
+ Arguments
+ - mrs_data
+vector of MRS data paths or list of mrs_data objects.
- output_dir
+the base directory to create the BIDS structure.
- suffix
+optional vector of file suffixes. Default behaviour is to
+automatically determine these from the input data, however it is recommended
+that they are specified to allow more efficient skipping of existing data.
- sub
+optional vector of subject labels. If not specified, these will be
+automatically generated as a series of increasing zero-padded integer values
+corresponding to the mrs_data input indices.
- ses
+optional vector of session labels.
- task
+optional vector of task labels.
- acq
+optional vector of acquisition labels.
- nuc
+optional vector of nucleus labels.
- voi
+optional vector of volume of interest labels.
- rec
+optional vector of reconstruction labels.
- run
+optional vector of run indices.
- echo
+optional vector of echo time indices.
- inv
+optional vector of inversion indices.
- skip_existing
+skip any data files that have already been converted.
+Defaults to TRUE, set to FALSE to force an overwrite of any existing data
+files.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/mrs_data2mat.html b/docs/reference/mrs_data2mat.html
index cf5ff28c..9e47688a 100644
--- a/docs/reference/mrs_data2mat.html
+++ b/docs/reference/mrs_data2mat.html
@@ -1,7 +1,5 @@
-Convert mrs_data object to a matrix, with spectral points in the column
-dimension and dynamics in the row dimension. — mrs_data2mat • Spectroscopy Analysis Tools (spant) Convert mrs_data object to a matrix, with spectral points in the column dimension and dynamics in the row dimension. — mrs_data2mat • Spectroscopy Analysis Tools (spant) Convert mrs_data object to a matrix, with spectral points in the column dimension and dynamics in the row dimension. — mrs_data2spec_mat • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Convert mrs_data object to a matrix, with spectral points in the column dimension and dynamics in the row dimension.
+ Source: R/mrs_data_proc.R
+ mrs_data2spec_mat.Rd
+
+
+
+ Convert mrs_data object to a matrix, with spectral points in the column
+dimension and dynamics in the row dimension.
+
+
+
+ mrs_data2spec_mat(mrs_data, collapse = TRUE)
+
+
+
+ Arguments
+ - mrs_data
+MRS data object or list of MRS data objects.
- collapse
+collapse all other dimensions along the dynamic dimension, eg
+a 16x16 MRSI grid would be first collapsed across 256 dynamic scans.
+
+ Value
+
+
+MRS data matrix.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/mrs_data2vec.html b/docs/reference/mrs_data2vec.html
index fb172d68..a1fd654d 100644
--- a/docs/reference/mrs_data2vec.html
+++ b/docs/reference/mrs_data2vec.html
@@ -1,5 +1,5 @@
-Convert mrs_data object to a vector. — mrs_data2vec • Spectroscopy Analysis Tools (spant) Convert mrs_data object to a vector. — mrs_data2vec • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -126,7 +126,7 @@ Value
diff --git a/docs/reference/mvfftshift.html b/docs/reference/mvfftshift.html
index 92b0841b..976b3410 100644
--- a/docs/reference/mvfftshift.html
+++ b/docs/reference/mvfftshift.html
@@ -1,7 +1,5 @@
-Perform a fftshift on a matrix, with each column replaced by its shifted
-result. — mvfftshift • Spectroscopy Analysis Tools (spant) Perform a fftshift on a matrix, with each column replaced by its shifted result. — mvfftshift • Spectroscopy Analysis Tools (spant) Perform an ifftshift on a matrix, with each column replaced by its shifted
-result. — mvifftshift • Spectroscopy Analysis Tools (spant) Perform an ifftshift on a matrix, with each column replaced by its shifted result. — mvifftshift • Spectroscopy Analysis Tools (spant) Print fit coordinates from a single index. — n2coord • Spectroscopy Analysis Tools (spant) Print fit coordinates from a single index. — n2coord • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/nifti_flip_lr.html b/docs/reference/nifti_flip_lr.html
index 730abe3c..19860b3c 100644
--- a/docs/reference/nifti_flip_lr.html
+++ b/docs/reference/nifti_flip_lr.html
@@ -1,9 +1,5 @@
-Flip the x data dimension order of a nifti image. This corresponds to
-flipping MRI data in the left-right direction, assuming the data in save in
-neurological format (can check with fslorient program). — nifti_flip_lr • Spectroscopy Analysis Tools (spant) Flip the x data dimension order of a nifti image. This corresponds to flipping MRI data in the left-right direction, assuming the data in save in neurological format (can check with fslorient program). — nifti_flip_lr • Spectroscopy Analysis Tools (spant) Export a one-page pdf of a single fit result — one_page_pdf • Spectroscopy Analysis Tools (spant) Export a one-page pdf of a single fit result — one_page_pdf • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -108,7 +108,7 @@ Arguments
diff --git a/docs/reference/ortho3.html b/docs/reference/ortho3.html
index 13ade97d..5d7dd2fd 100644
--- a/docs/reference/ortho3.html
+++ b/docs/reference/ortho3.html
@@ -1,5 +1,5 @@
-Display an orthographic projection plot of a nifti object. — ortho3 • Spectroscopy Analysis Tools (spant) Display an orthographic projection plot of a nifti object. — ortho3 • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -172,7 +172,7 @@ Arguments
diff --git a/docs/reference/ortho3_inter.html b/docs/reference/ortho3_inter.html
index 090cc5e5..15948899 100644
--- a/docs/reference/ortho3_inter.html
+++ b/docs/reference/ortho3_inter.html
@@ -1,5 +1,5 @@
-Display an interactive orthographic projection plot of a nifti object. — ortho3_inter • Spectroscopy Analysis Tools (spant) Display an interactive orthographic projection plot of a nifti object. — ortho3_inter • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -132,7 +132,7 @@ Arguments
diff --git a/docs/reference/peak_info.html b/docs/reference/peak_info.html
index 09058bd8..41c8ffaf 100644
--- a/docs/reference/peak_info.html
+++ b/docs/reference/peak_info.html
@@ -1,7 +1,5 @@
-Search for the highest peak in a spectral region and return the frequency,
-height and FWHM. — peak_info • Spectroscopy Analysis Tools (spant) Search for the highest peak in a spectral region and return the frequency, height and FWHM. — peak_info • Spectroscopy Analysis Tools (spant) Papoulis-Gerchberg (PG) algorithm method for k-space extrapolation. — pg_extrap_xy • Spectroscopy Analysis Tools (spant) Papoulis-Gerchberg (PG) algorithm method for k-space extrapolation. — pg_extrap_xy • Spectroscopy Analysis Tools (spant) Apply phasing parameters to MRS data. — phase • Spectroscopy Analysis Tools (spant) Apply phasing parameters to MRS data. — phase • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/phase_ref_1h_brain.html b/docs/reference/phase_ref_1h_brain.html
new file mode 100644
index 00000000..8707a74a
--- /dev/null
+++ b/docs/reference/phase_ref_1h_brain.html
@@ -0,0 +1,131 @@
+
+Corrected zero order phase and chemical shift offset in 1H MRS data from the brain. — phase_ref_1h_brain • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Corrected zero order phase and chemical shift offset in 1H MRS data from the brain.
+ Source: R/rats.R
+ phase_ref_1h_brain.Rd
+
+
+
+ Corrected zero order phase and chemical shift offset in 1H MRS data from the
+brain.
+
+
+
+ phase_ref_1h_brain(mrs_data, mean_ref = FALSE, ret_corr_only = TRUE)
+
+
+
+ Arguments
+ - mrs_data
+MRS data to be corrected.
- mean_ref
+apply the phase and offset of the mean spectrum to all
+others. Default is FALSE.
- ret_corr_only
+return the corrected data only.
+
+ Value
+
+
+corrected MRS data.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/plot.fit_result.html b/docs/reference/plot.fit_result.html
index e54d3bc1..836a53ee 100644
--- a/docs/reference/plot.fit_result.html
+++ b/docs/reference/plot.fit_result.html
@@ -1,5 +1,5 @@
-Plot the fitting results of an object of class fit_result. — plot.fit_result • Spectroscopy Analysis Tools (spant) Plot the fitting results of an object of class fit_result. — plot.fit_result • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -207,7 +207,7 @@ Arguments
diff --git a/docs/reference/plot.mrs_data.html b/docs/reference/plot.mrs_data.html
index fabcc35b..bb2ec651 100644
--- a/docs/reference/plot.mrs_data.html
+++ b/docs/reference/plot.mrs_data.html
@@ -1,5 +1,5 @@
-Plotting method for objects of class mrs_data. — plot.mrs_data • Spectroscopy Analysis Tools (spant) Plotting method for objects of class mrs_data. — plot.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -287,7 +287,7 @@ Arguments
diff --git a/docs/reference/plot_bc.html b/docs/reference/plot_bc.html
index 4f8309b4..b48142cc 100644
--- a/docs/reference/plot_bc.html
+++ b/docs/reference/plot_bc.html
@@ -1,5 +1,5 @@
-Convenience function to plot a baseline estimate with the original data. — plot_bc • Spectroscopy Analysis Tools (spant) Convenience function to plot a baseline estimate with the original data. — plot_bc • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -108,7 +108,7 @@ Arguments
diff --git a/docs/reference/plot_reg.html b/docs/reference/plot_reg.html
index ae1acbe7..2addb2f6 100644
--- a/docs/reference/plot_reg.html
+++ b/docs/reference/plot_reg.html
@@ -1,5 +1,5 @@
-Plot regressors as an image. — plot_reg • Spectroscopy Analysis Tools (spant) Plot regressors as an image. — plot_reg • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/plot_slice_fit.html b/docs/reference/plot_slice_fit.html
index fbc7b560..57f1af8a 100644
--- a/docs/reference/plot_slice_fit.html
+++ b/docs/reference/plot_slice_fit.html
@@ -1,5 +1,5 @@
-Plot a 2D slice from an MRSI fit result object. — plot_slice_fit • Spectroscopy Analysis Tools (spant) Plot a 2D slice from an MRSI fit result object. — plot_slice_fit • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -129,7 +129,7 @@ Arguments
diff --git a/docs/reference/plot_slice_fit_inter.html b/docs/reference/plot_slice_fit_inter.html
index 4eed104a..da105a7d 100644
--- a/docs/reference/plot_slice_fit_inter.html
+++ b/docs/reference/plot_slice_fit_inter.html
@@ -1,5 +1,5 @@
-Plot a 2D slice from an MRSI fit result object. — plot_slice_fit_inter • Spectroscopy Analysis Tools (spant) Plot a 2D slice from an MRSI fit result object. — plot_slice_fit_inter • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -134,7 +134,7 @@ Arguments
diff --git a/docs/reference/plot_slice_map.html b/docs/reference/plot_slice_map.html
index 553e9ac8..ffb2a134 100644
--- a/docs/reference/plot_slice_map.html
+++ b/docs/reference/plot_slice_map.html
@@ -1,5 +1,5 @@
-Plot a slice from a 7 dimensional array. — plot_slice_map • Spectroscopy Analysis Tools (spant) Plot a slice from a 7 dimensional array. — plot_slice_map • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -153,7 +153,7 @@ Arguments
diff --git a/docs/reference/plot_slice_map_inter.html b/docs/reference/plot_slice_map_inter.html
index 40d33b42..90968f66 100644
--- a/docs/reference/plot_slice_map_inter.html
+++ b/docs/reference/plot_slice_map_inter.html
@@ -1,7 +1,5 @@
-Plot an interactive slice map from a data array where voxels can be selected
-to display a corresponding spectrum. — plot_slice_map_inter • Spectroscopy Analysis Tools (spant) Plot an interactive slice map from a data array where voxels can be selected to display a corresponding spectrum. — plot_slice_map_inter • Spectroscopy Analysis Tools (spant) Plot the spectral standard deviation. — plot_spec_sd • Spectroscopy Analysis Tools (spant) Plot the spectral standard deviation. — plot_spec_sd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Arguments
diff --git a/docs/reference/plot_voi_overlay.html b/docs/reference/plot_voi_overlay.html
index 9a782e88..bbbbf35e 100644
--- a/docs/reference/plot_voi_overlay.html
+++ b/docs/reference/plot_voi_overlay.html
@@ -1,5 +1,5 @@
-Plot a volume as an image overlay. — plot_voi_overlay • Spectroscopy Analysis Tools (spant) Plot a volume as an image overlay. — plot_voi_overlay • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -116,7 +116,7 @@ Arguments
diff --git a/docs/reference/plot_voi_overlay_seg.html b/docs/reference/plot_voi_overlay_seg.html
index 3d4e74ff..0e800ff2 100644
--- a/docs/reference/plot_voi_overlay_seg.html
+++ b/docs/reference/plot_voi_overlay_seg.html
@@ -1,5 +1,5 @@
-Plot a volume as an overlay on a segmented brain volume. — plot_voi_overlay_seg • Spectroscopy Analysis Tools (spant) Plot a volume as an overlay on a segmented brain volume. — plot_voi_overlay_seg • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Arguments
diff --git a/docs/reference/ppm.html b/docs/reference/ppm.html
index c352327a..ee4696e2 100644
--- a/docs/reference/ppm.html
+++ b/docs/reference/ppm.html
@@ -1,5 +1,5 @@
-Return the ppm scale of an MRS dataset or fit result. — ppm • Spectroscopy Analysis Tools (spant) Return the ppm scale of an MRS dataset or fit result. — ppm • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -132,7 +132,7 @@ Value
diff --git a/docs/reference/precomp.html b/docs/reference/precomp.html
index 822d7336..df3d2c6c 100644
--- a/docs/reference/precomp.html
+++ b/docs/reference/precomp.html
@@ -1,7 +1,5 @@
-Save function results to file and load on subsequent calls to avoid repeat
-computation. — precomp • Spectroscopy Analysis Tools (spant) Save function results to file and load on subsequent calls to avoid repeat computation. — precomp • Spectroscopy Analysis Tools (spant) Preprocess and perform quality assessment of a single SVS data set. — preproc_svs • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Preprocess and perform quality assessment of a single SVS data set.
+ Source: R/fmrs.R
+ preproc_svs.Rd
+
+
+
+ Preprocess and perform quality assessment of a single SVS data set.
+
+
+
+ preproc_svs(path, label = NULL, output_dir = NULL, ref_inds = NULL)
+
+
+
+ Arguments
+ - path
+path to the fMRS data file or IMA directory.
- label
+a label to describe the data set.
- output_dir
+output directory.
- ref_inds
+a vector of 1-based indices for any water reference dynamic
+scans.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/preproc_svs_dataset.html b/docs/reference/preproc_svs_dataset.html
new file mode 100644
index 00000000..07c3a29b
--- /dev/null
+++ b/docs/reference/preproc_svs_dataset.html
@@ -0,0 +1,148 @@
+
+Preprocess and perform quality assessment of one or more SVS data sets. — preproc_svs_dataset • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Preprocess and perform quality assessment of one or more SVS data sets.
+ Source: R/fmrs.R
+ preproc_svs_dataset.Rd
+
+
+
+ Preprocess and perform quality assessment of one or more SVS data sets.
+
+
+
+ preproc_svs_dataset(
+ paths,
+ labels = NULL,
+ output_dir = "spant_analysis",
+ exclude_labels = NULL,
+ overwrite = FALSE,
+ ref_inds = NULL,
+ return_results = FALSE
+)
+
+
+
+ Arguments
+ - paths
+paths to the fMRS data file or IMA directory.
- labels
+labels to describe each data set.
- output_dir
+output directory.
- exclude_labels
+vector of labels of scans to exclude, eg poor quality
+data.
- overwrite
+overwrite saved results, defaults to FALSE.
- ref_inds
+a vector of 1-based indices for any water reference dynamic
+scans.
- return_results
+function will return key outputs, defaults to FALSE.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/print.fit_result.html b/docs/reference/print.fit_result.html
index 297f28dc..5f434e57 100644
--- a/docs/reference/print.fit_result.html
+++ b/docs/reference/print.fit_result.html
@@ -1,5 +1,5 @@
-Print a summary of an object of class fit_result. — print.fit_result • Spectroscopy Analysis Tools (spant) Print a summary of an object of class fit_result. — print.fit_result • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -105,7 +105,7 @@ Arguments
diff --git a/docs/reference/print.mrs_data.html b/docs/reference/print.mrs_data.html
index 51199017..e1561eb2 100644
--- a/docs/reference/print.mrs_data.html
+++ b/docs/reference/print.mrs_data.html
@@ -1,5 +1,5 @@
-Print a summary of mrs_data parameters. — print.mrs_data • Spectroscopy Analysis Tools (spant) Print a summary of mrs_data parameters. — print.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -109,7 +109,7 @@ Arguments
diff --git a/docs/reference/qn_states.html b/docs/reference/qn_states.html
index 0f42f2f9..d7aa6715 100644
--- a/docs/reference/qn_states.html
+++ b/docs/reference/qn_states.html
@@ -1,5 +1,5 @@
-Get the quantum coherence matrix for a spin system. — qn_states • Spectroscopy Analysis Tools (spant) Get the quantum coherence matrix for a spin system. — qn_states • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/rats.html b/docs/reference/rats.html
index 5a39a396..93585e08 100644
--- a/docs/reference/rats.html
+++ b/docs/reference/rats.html
@@ -1,5 +1,5 @@
-Robust Alignment to a Target Spectrum (RATS). — rats • Spectroscopy Analysis Tools (spant) Robust Alignment to a Target Spectrum (RATS). — rats • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -207,7 +207,7 @@ Value
diff --git a/docs/reference/re_weighting.html b/docs/reference/re_weighting.html
index d21caf21..8b0b070a 100644
--- a/docs/reference/re_weighting.html
+++ b/docs/reference/re_weighting.html
@@ -1,5 +1,5 @@
-Apply a weighting to the FID to enhance spectral resolution. — re_weighting • Spectroscopy Analysis Tools (spant) Apply a weighting to the FID to enhance spectral resolution. — re_weighting • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/read_basis.html b/docs/reference/read_basis.html
index da9b94af..eb6f8557 100644
--- a/docs/reference/read_basis.html
+++ b/docs/reference/read_basis.html
@@ -1,5 +1,5 @@
-Read a basis file in LCModel .basis format. — read_basis • Spectroscopy Analysis Tools (spant) Read a basis file in LCModel .basis format. — read_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/read_ima_coil_dir.html b/docs/reference/read_ima_coil_dir.html
index 28c02de0..4f073cd8 100644
--- a/docs/reference/read_ima_coil_dir.html
+++ b/docs/reference/read_ima_coil_dir.html
@@ -1,9 +1,5 @@
-Read a directory containing Siemens MRS IMA files and combine along the coil
-dimension. Note that the coil ID is inferred from the sorted file name and
-should be checked when consistency is required between two directories. — read_ima_coil_dir • Spectroscopy Analysis Tools (spant) Read a directory containing Siemens MRS IMA files and combine along the coil dimension. Note that the coil ID is inferred from the sorted file name and should be checked when consistency is required between two directories. — read_ima_coil_dir • Spectroscopy Analysis Tools (spant) Read a directory containing Siemens MRS IMA files and combine along the
-dynamic dimension. Note that the coil ID is inferred from the sorted file
-name and should be checked when consistency is required. — read_ima_dyn_dir • Spectroscopy Analysis Tools (spant) Read a directory containing Siemens MRS IMA files and combine along the dynamic dimension. Note that the coil ID is inferred from the sorted file name and should be checked when consistency is required. — read_ima_dyn_dir • Spectroscopy Analysis Tools (spant) Read an LCModel formatted coord file containing fit information. — read_lcm_coord • Spectroscopy Analysis Tools (spant) Read an LCModel formatted coord file containing fit information. — read_lcm_coord • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -107,7 +107,7 @@ Value
diff --git a/docs/reference/read_mrs.html b/docs/reference/read_mrs.html
index 3ac2a36b..2cf36b20 100644
--- a/docs/reference/read_mrs.html
+++ b/docs/reference/read_mrs.html
@@ -1,5 +1,5 @@
-Read MRS data from a file. — read_mrs • Spectroscopy Analysis Tools (spant) Read MRS data from a file. — read_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -88,7 +88,8 @@ Read MRS data from a file.
full_fid = FALSE,
omit_svs_ref_scans = TRUE,
verbose = FALSE,
- extra = NULL
+ extra = NULL,
+ fid_filt_dist = NULL
)
@@ -140,6 +141,13 @@ Arguments
an optional data frame to provide additional variables for use
in subsequent analysis steps, eg id or grouping variables.
fid_filt_dist
+indicate if the data has a distorted FID due to a
+brick-wall filter being used to downsample the data. Default is to auto
+detect this from the data, but TRUE or FALSE options can be given to override
+detection.
Value
@@ -183,7 +191,7 @@ Examples
diff --git a/docs/reference/read_mrs_tqn.html b/docs/reference/read_mrs_tqn.html
index 5766362f..84bdaf3a 100644
--- a/docs/reference/read_mrs_tqn.html
+++ b/docs/reference/read_mrs_tqn.html
@@ -1,5 +1,5 @@
-Read MRS data using the TARQUIN software package. — read_mrs_tqn • Spectroscopy Analysis Tools (spant) Read MRS data using the TARQUIN software package. — read_mrs_tqn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -131,7 +131,7 @@ Examples
diff --git a/docs/reference/read_pulse_ascii.html b/docs/reference/read_pulse_ascii.html
index c9e0d43c..ab11c9cc 100644
--- a/docs/reference/read_pulse_ascii.html
+++ b/docs/reference/read_pulse_ascii.html
@@ -1,5 +1,5 @@
-Read an ASCII formatted pulse file. — read_pulse_ascii • Spectroscopy Analysis Tools (spant) Read an ASCII formatted pulse file. — read_pulse_ascii • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/read_pulse_bruker.html b/docs/reference/read_pulse_bruker.html
index c92bf76a..dbe9073b 100644
--- a/docs/reference/read_pulse_bruker.html
+++ b/docs/reference/read_pulse_bruker.html
@@ -1,5 +1,5 @@
-Read a Bruker formatted pulse file — read_pulse_bruker • Spectroscopy Analysis Tools (spant) Read a Bruker formatted pulse file — read_pulse_bruker • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/read_pulse_pta.html b/docs/reference/read_pulse_pta.html
index 72e1b6d4..a0fac3c3 100644
--- a/docs/reference/read_pulse_pta.html
+++ b/docs/reference/read_pulse_pta.html
@@ -1,5 +1,5 @@
-Read a .pta formatted pulse file compatible with Siemens PulseTool. — read_pulse_pta • Spectroscopy Analysis Tools (spant) Read a .pta formatted pulse file compatible with Siemens PulseTool. — read_pulse_pta • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/read_siemens_txt_hdr.html b/docs/reference/read_siemens_txt_hdr.html
index 23fb8c70..3a17d87c 100644
--- a/docs/reference/read_siemens_txt_hdr.html
+++ b/docs/reference/read_siemens_txt_hdr.html
@@ -1,5 +1,5 @@
-Read the text format header found in Siemens IMA and TWIX data files. — read_siemens_txt_hdr • Spectroscopy Analysis Tools (spant) Read the text format header found in Siemens IMA and TWIX data files. — read_siemens_txt_hdr • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -78,7 +78,7 @@ Read the text format header found in Siemens IMA and TWIX data files.
- read_siemens_txt_hdr(input, version = "vd", verbose, offset = 0)
+ read_siemens_txt_hdr(input, version = "vd", verbose = FALSE, offset = 0)
@@ -118,7 +118,7 @@ Value
diff --git a/docs/reference/read_tqn_fit.html b/docs/reference/read_tqn_fit.html
index 4da6c25e..a1630420 100644
--- a/docs/reference/read_tqn_fit.html
+++ b/docs/reference/read_tqn_fit.html
@@ -1,5 +1,5 @@
-Reader for csv fit results generated by TARQUIN. — read_tqn_fit • Spectroscopy Analysis Tools (spant) Reader for csv fit results generated by TARQUIN. — read_tqn_fit • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -113,7 +113,7 @@ Examples
diff --git a/docs/reference/read_tqn_result.html b/docs/reference/read_tqn_result.html
index 36659714..68a3e98c 100644
--- a/docs/reference/read_tqn_result.html
+++ b/docs/reference/read_tqn_result.html
@@ -1,5 +1,5 @@
-Reader for csv results generated by TARQUIN. — read_tqn_result • Spectroscopy Analysis Tools (spant) Reader for csv results generated by TARQUIN. — read_tqn_result • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -117,7 +117,7 @@ Examples
diff --git a/docs/reference/recon_imag.html b/docs/reference/recon_imag.html
index d2a72225..5bc3b1eb 100644
--- a/docs/reference/recon_imag.html
+++ b/docs/reference/recon_imag.html
@@ -1,7 +1,5 @@
-Reconstruct complex time-domain data from the real part of frequency-domain
-data. — recon_imag • Spectroscopy Analysis Tools (spant) Reconstruct complex time-domain data from the real part of frequency-domain data. — recon_imag • Spectroscopy Analysis Tools (spant) Reconstruct complex time-domain data from the real part of frequency-domain
-data. — recon_imag_vec • Spectroscopy Analysis Tools (spant) Reconstruct complex time-domain data from the real part of frequency-domain data. — recon_imag_vec • Spectroscopy Analysis Tools (spant) Reconstruct 2D MRSI data from a twix file loaded with read_mrs. — recon_twix_2d_mrsi • Spectroscopy Analysis Tools (spant) Reconstruct 2D MRSI data from a twix file loaded with read_mrs. — recon_twix_2d_mrsi • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/rectangular_mask.html b/docs/reference/rectangular_mask.html
index a2117283..6e469bc9 100644
--- a/docs/reference/rectangular_mask.html
+++ b/docs/reference/rectangular_mask.html
@@ -1,5 +1,5 @@
-Create a rectangular mask stored as a matrix of logical values. — rectangular_mask • Spectroscopy Analysis Tools (spant) Create a rectangular mask stored as a matrix of logical values. — rectangular_mask • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -130,7 +130,7 @@ Value
diff --git a/docs/reference/reexports.html b/docs/reference/reexports.html
index 694a75d1..a59e8379 100644
--- a/docs/reference/reexports.html
+++ b/docs/reference/reexports.html
@@ -1,5 +1,5 @@
-Objects exported from other packages — reexports • Spectroscopy Analysis Tools (spant) Objects exported from other packages — reexports • Spectroscopy Analysis Tools (spant)
Spectroscopy Analysis Tools (spant)
- 2.21.0
+ 2.22.0
@@ -103,7 +103,7 @@ Objects exported from other packages
diff --git a/docs/reference/rep_array_dim.html b/docs/reference/rep_array_dim.html
index b9c49b4a..48c0a5ed 100644
--- a/docs/reference/rep_array_dim.html
+++ b/docs/reference/rep_array_dim.html
@@ -1,5 +1,5 @@
-Repeat an array over a given dimension. — rep_array_dim • Spectroscopy Analysis Tools (spant) Repeat an array over a given dimension. — rep_array_dim • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/rep_dyn.html b/docs/reference/rep_dyn.html
index 6bbfb0ef..89a4bb9b 100644
--- a/docs/reference/rep_dyn.html
+++ b/docs/reference/rep_dyn.html
@@ -1,5 +1,5 @@
-Replicate a scan in the dynamic dimension. — rep_dyn • Spectroscopy Analysis Tools (spant) Replicate a scan in the dynamic dimension. — rep_dyn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/rep_mrs.html b/docs/reference/rep_mrs.html
index 67730b5c..becb8f00 100644
--- a/docs/reference/rep_mrs.html
+++ b/docs/reference/rep_mrs.html
@@ -1,5 +1,5 @@
-Replicate a scan over a given dimension. — rep_mrs • Spectroscopy Analysis Tools (spant) Replicate a scan over a given dimension. — rep_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -138,7 +138,7 @@ Value
diff --git a/docs/reference/resample_basis.html b/docs/reference/resample_basis.html
index b0f2ab17..c7a6222a 100644
--- a/docs/reference/resample_basis.html
+++ b/docs/reference/resample_basis.html
@@ -1,5 +1,5 @@
-Resample a basis-set to match a mrs_data acquisition. — resample_basis • Spectroscopy Analysis Tools (spant) Resample a basis-set to match a mrs_data acquisition. — resample_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -116,7 +116,7 @@ Value
diff --git a/docs/reference/resample_img.html b/docs/reference/resample_img.html
index f1e7beaf..b0cc8f71 100644
--- a/docs/reference/resample_img.html
+++ b/docs/reference/resample_img.html
@@ -1,5 +1,5 @@
-Resample an image to match a target image space. — resample_img • Spectroscopy Analysis Tools (spant) Resample an image to match a target image space. — resample_img • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/resample_voi.html b/docs/reference/resample_voi.html
index 8fbfa836..a29ab096 100644
--- a/docs/reference/resample_voi.html
+++ b/docs/reference/resample_voi.html
@@ -1,7 +1,5 @@
-Resample a VOI to match a target image space using nearest-neighbour
-interpolation. — resample_voi • Spectroscopy Analysis Tools (spant) Resample a VOI to match a target image space using nearest-neighbour interpolation. — resample_voi • Spectroscopy Analysis Tools (spant) Reslice a nifti object to match the orientation of mrs data. — reslice_to_mrs • Spectroscopy Analysis Tools (spant) Reslice a nifti object to match the orientation of mrs data. — reslice_to_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/reson_table2mrs_data.html b/docs/reference/reson_table2mrs_data.html
index d75579ee..c5a2167a 100644
--- a/docs/reference/reson_table2mrs_data.html
+++ b/docs/reference/reson_table2mrs_data.html
@@ -1,5 +1,5 @@
-Generate mrs_data from a table of single Lorentzian resonances. — reson_table2mrs_data • Spectroscopy Analysis Tools (spant) Generate mrs_data from a table of single Lorentzian resonances. — reson_table2mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -119,7 +119,7 @@ Value
diff --git a/docs/reference/rm_dyns.html b/docs/reference/rm_dyns.html
index 5d5ef692..573e1f51 100644
--- a/docs/reference/rm_dyns.html
+++ b/docs/reference/rm_dyns.html
@@ -1,5 +1,5 @@
-Remove a subset of dynamic scans. — rm_dyns • Spectroscopy Analysis Tools (spant) Remove a subset of dynamic scans. — rm_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/scale_amp_molal.html b/docs/reference/scale_amp_molal.html
index aaeee1f2..7acb8cb0 100644
--- a/docs/reference/scale_amp_molal.html
+++ b/docs/reference/scale_amp_molal.html
@@ -1,7 +1,5 @@
-Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water). — scale_amp_molal • Spectroscopy Analysis Tools (spant) Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / kg of tissue water). — scale_amp_molal • Spectroscopy Analysis Tools (spant)
Spectroscopy Analysis Tools (spant)
- 2.21.0
+ 2.22.0
@@ -76,8 +74,7 @@
- Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water).
+ Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / kg of tissue water).
Source: R/amp_scaling.R
scale_amp_molal.Rd
@@ -163,7 +160,7 @@ Value
diff --git a/docs/reference/scale_amp_molal_pvc.html b/docs/reference/scale_amp_molal_pvc.html
index 962d6afc..4d194abd 100644
--- a/docs/reference/scale_amp_molal_pvc.html
+++ b/docs/reference/scale_amp_molal_pvc.html
@@ -1,7 +1,5 @@
-Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water). — scale_amp_molal_pvc • Spectroscopy Analysis Tools (spant)
@@ -75,8 +73,7 @@
- Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water).
+ Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / kg of tissue water).
Source: R/amp_scaling.R
scale_amp_molal_pvc.Rd
@@ -141,7 +138,7 @@ Value
diff --git a/docs/reference/scale_amp_molar.html b/docs/reference/scale_amp_molar.html
index 02358d91..dc87a338 100644
--- a/docs/reference/scale_amp_molar.html
+++ b/docs/reference/scale_amp_molar.html
@@ -1,7 +1,5 @@
-Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / Litre of tissue). — scale_amp_molar • Spectroscopy Analysis Tools (spant) Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / Litre of tissue). — scale_amp_molar • Spectroscopy Analysis Tools (spant) Convert default LCM/TARQUIN concentration scaling to molal units with partial
-volume correction. — scale_amp_molar2molal_pvc • Spectroscopy Analysis Tools (spant) Convert default LCM/TARQUIN concentration scaling to molal units with partial volume correction. — scale_amp_molar2molal_pvc • Spectroscopy Analysis Tools (spant) Scale fitted amplitudes to a ratio of signal amplitude. — scale_amp_ratio • Spectroscopy Analysis Tools (spant) Scale fitted amplitudes to a ratio of signal amplitude. — scale_amp_ratio • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -116,7 +116,7 @@ Value
diff --git a/docs/reference/scale_amp_ratio_value.html b/docs/reference/scale_amp_ratio_value.html
index 2036837a..6af8ac51 100644
--- a/docs/reference/scale_amp_ratio_value.html
+++ b/docs/reference/scale_amp_ratio_value.html
@@ -1,5 +1,5 @@
-Scale fitted amplitudes to a ratio of signal amplitude. — scale_amp_ratio_value • Spectroscopy Analysis Tools (spant) Scale fitted amplitudes to a ratio of signal amplitude. — scale_amp_ratio_value • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/scale_amp_water_ratio.html b/docs/reference/scale_amp_water_ratio.html
index 5b25e884..35a76b00 100644
--- a/docs/reference/scale_amp_water_ratio.html
+++ b/docs/reference/scale_amp_water_ratio.html
@@ -1,5 +1,5 @@
-Scale metabolite amplitudes as a ratio to the unsuppressed water amplitude. — scale_amp_water_ratio • Spectroscopy Analysis Tools (spant) Scale metabolite amplitudes as a ratio to the unsuppressed water amplitude. — scale_amp_water_ratio • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/scale_basis_amp.html b/docs/reference/scale_basis_amp.html
index 9401c3f1..5a58b5e5 100644
--- a/docs/reference/scale_basis_amp.html
+++ b/docs/reference/scale_basis_amp.html
@@ -1,5 +1,5 @@
-Scale a basis object by a scalar. — scale_basis_amp • Spectroscopy Analysis Tools (spant) Scale a basis object by a scalar. — scale_basis_amp • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/scale_basis_from_singlet.html b/docs/reference/scale_basis_from_singlet.html
index 0d542bc8..c9a19e77 100644
--- a/docs/reference/scale_basis_from_singlet.html
+++ b/docs/reference/scale_basis_from_singlet.html
@@ -1,5 +1,5 @@
-Scale a basis-set to be consistent with spant assumptions for water scaling. — scale_basis_from_singlet • Spectroscopy Analysis Tools (spant) Scale a basis-set to be consistent with spant assumptions for water scaling. — scale_basis_from_singlet • Spectroscopy Analysis Tools (spant)
Spectroscopy Analysis Tools (spant)
- 2.21.0
+ 2.22.0
@@ -127,7 +127,7 @@ Value
diff --git a/docs/reference/scale_mrs_amp.html b/docs/reference/scale_mrs_amp.html
index b5501a0d..990f058a 100644
--- a/docs/reference/scale_mrs_amp.html
+++ b/docs/reference/scale_mrs_amp.html
@@ -1,5 +1,5 @@
-Scale an mrs_data object by a scalar or vector or amplitudes. — scale_mrs_amp • Spectroscopy Analysis Tools (spant) Scale an mrs_data object by a scalar or vector or amplitudes. — scale_mrs_amp • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/scale_spec.html b/docs/reference/scale_spec.html
index 4f6ea835..6b3ddba4 100644
--- a/docs/reference/scale_spec.html
+++ b/docs/reference/scale_spec.html
@@ -1,5 +1,5 @@
-Scale mrs_data to a spectral region. — scale_spec • Spectroscopy Analysis Tools (spant) Scale mrs_data to a spectral region. — scale_spec • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -141,7 +141,7 @@ Value
diff --git a/docs/reference/sd.html b/docs/reference/sd.html
index ea1eec9f..3ae4dfd4 100644
--- a/docs/reference/sd.html
+++ b/docs/reference/sd.html
@@ -1,5 +1,5 @@
-Calculate the standard deviation spectrum from an mrs_data object. — sd • Spectroscopy Analysis Tools (spant) Calculate the standard deviation spectrum from an mrs_data object. — sd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/sd.mrs_data.html b/docs/reference/sd.mrs_data.html
index 3f92a49f..13bdda85 100644
--- a/docs/reference/sd.mrs_data.html
+++ b/docs/reference/sd.mrs_data.html
@@ -1,5 +1,5 @@
-Calculate the standard deviation spectrum from an mrs_data object. — sd.mrs_data • Spectroscopy Analysis Tools (spant) Calculate the standard deviation spectrum from an mrs_data object. — sd.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/seconds.html b/docs/reference/seconds.html
index b34d6627..467ee17f 100644
--- a/docs/reference/seconds.html
+++ b/docs/reference/seconds.html
@@ -1,5 +1,5 @@
-Return a time scale vector to match the FID of an MRS data object. — seconds • Spectroscopy Analysis Tools (spant) Return a time scale vector to match the FID of an MRS data object. — seconds • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/seq_cpmg_ideal.html b/docs/reference/seq_cpmg_ideal.html
index 547e96ab..45727c86 100644
--- a/docs/reference/seq_cpmg_ideal.html
+++ b/docs/reference/seq_cpmg_ideal.html
@@ -1,5 +1,5 @@
-CPMG style sequence with ideal pulses. — seq_cpmg_ideal • Spectroscopy Analysis Tools (spant) CPMG style sequence with ideal pulses. — seq_cpmg_ideal • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/seq_mega_press_ideal.html b/docs/reference/seq_mega_press_ideal.html
index 0769b8b4..a9cd7fa0 100644
--- a/docs/reference/seq_mega_press_ideal.html
+++ b/docs/reference/seq_mega_press_ideal.html
@@ -1,7 +1,5 @@
-MEGA-PRESS sequence with ideal localisation pulses and Gaussian shaped
-editing pulse. — seq_mega_press_ideal • Spectroscopy Analysis Tools (spant) MEGA-PRESS sequence with ideal localisation pulses and Gaussian shaped editing pulse. — seq_mega_press_ideal • Spectroscopy Analysis Tools (spant) PRESS sequence with shaped refocusing pulses. — seq_press_2d_shaped • Spectroscopy Analysis Tools (spant) PRESS sequence with shaped refocusing pulses. — seq_press_2d_shaped • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -165,7 +165,7 @@ Value
diff --git a/docs/reference/seq_press_ideal.html b/docs/reference/seq_press_ideal.html
index 8c976856..72c3af3d 100644
--- a/docs/reference/seq_press_ideal.html
+++ b/docs/reference/seq_press_ideal.html
@@ -1,5 +1,5 @@
-PRESS sequence with ideal pulses. — seq_press_ideal • Spectroscopy Analysis Tools (spant) PRESS sequence with ideal pulses. — seq_press_ideal • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/seq_pulse_acquire.html b/docs/reference/seq_pulse_acquire.html
index 4a88fc64..ad80571e 100644
--- a/docs/reference/seq_pulse_acquire.html
+++ b/docs/reference/seq_pulse_acquire.html
@@ -1,5 +1,5 @@
-Simple pulse and acquire sequence with ideal pulses. — seq_pulse_acquire • Spectroscopy Analysis Tools (spant) Simple pulse and acquire sequence with ideal pulses. — seq_pulse_acquire • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/seq_slaser_ideal.html b/docs/reference/seq_slaser_ideal.html
index 74688f4d..eb83e8e3 100644
--- a/docs/reference/seq_slaser_ideal.html
+++ b/docs/reference/seq_slaser_ideal.html
@@ -1,5 +1,5 @@
-sLASER sequence with ideal pulses. — seq_slaser_ideal • Spectroscopy Analysis Tools (spant) sLASER sequence with ideal pulses. — seq_slaser_ideal • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -126,7 +126,7 @@ Value
diff --git a/docs/reference/seq_spin_echo_ideal.html b/docs/reference/seq_spin_echo_ideal.html
index e23271de..4248716f 100644
--- a/docs/reference/seq_spin_echo_ideal.html
+++ b/docs/reference/seq_spin_echo_ideal.html
@@ -1,5 +1,5 @@
-Spin echo sequence with ideal pulses. — seq_spin_echo_ideal • Spectroscopy Analysis Tools (spant) Spin echo sequence with ideal pulses. — seq_spin_echo_ideal • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/seq_steam_ideal.html b/docs/reference/seq_steam_ideal.html
index a60685a8..1c8115d7 100644
--- a/docs/reference/seq_steam_ideal.html
+++ b/docs/reference/seq_steam_ideal.html
@@ -1,5 +1,5 @@
-STEAM sequence with ideal pulses. — seq_steam_ideal • Spectroscopy Analysis Tools (spant) STEAM sequence with ideal pulses. — seq_steam_ideal • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -128,7 +128,7 @@ Value
diff --git a/docs/reference/seq_steam_ideal_cof.html b/docs/reference/seq_steam_ideal_cof.html
index 8f225740..cba7af91 100644
--- a/docs/reference/seq_steam_ideal_cof.html
+++ b/docs/reference/seq_steam_ideal_cof.html
@@ -1,7 +1,5 @@
-STEAM sequence with ideal pulses and coherence order filtering to simulate
-gradient crushers. — seq_steam_ideal_cof • Spectroscopy Analysis Tools (spant) STEAM sequence with ideal pulses and coherence order filtering to simulate gradient crushers. — seq_steam_ideal_cof • Spectroscopy Analysis Tools (spant) STEAM sequence with ideal pulses using the z-rotation gradient simulation
-method described by Young et al JMR 140, 146-152 (1999). — seq_steam_ideal_young • Spectroscopy Analysis Tools (spant) STEAM sequence with ideal pulses using the z-rotation gradient simulation method described by Young et al JMR 140, 146-152 (1999). — seq_steam_ideal_young • Spectroscopy Analysis Tools (spant) Set the number of transients for an mrs_data object. — set_Ntrans • Spectroscopy Analysis Tools (spant) Set the number of transients for an mrs_data object. — set_Ntrans • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/set_def_acq_paras.html b/docs/reference/set_def_acq_paras.html
index 3e1b4004..cc2ada9c 100644
--- a/docs/reference/set_def_acq_paras.html
+++ b/docs/reference/set_def_acq_paras.html
@@ -1,5 +1,5 @@
-Set the default acquisition parameters. — set_def_acq_paras • Spectroscopy Analysis Tools (spant) Set the default acquisition parameters. — set_def_acq_paras • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Arguments
diff --git a/docs/reference/set_lcm_cmd.html b/docs/reference/set_lcm_cmd.html
index 2056ed01..42bb2f24 100644
--- a/docs/reference/set_lcm_cmd.html
+++ b/docs/reference/set_lcm_cmd.html
@@ -1,5 +1,5 @@
-Set the command to run the LCModel command-line program. — set_lcm_cmd • Spectroscopy Analysis Tools (spant) Set the command to run the LCModel command-line program. — set_lcm_cmd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/set_lw.html b/docs/reference/set_lw.html
index b64ec851..bb176c62 100644
--- a/docs/reference/set_lw.html
+++ b/docs/reference/set_lw.html
@@ -1,5 +1,5 @@
-Apply line-broadening to an mrs_data object to achieve a specified linewidth. — set_lw • Spectroscopy Analysis Tools (spant) Apply line-broadening to an mrs_data object to achieve a specified linewidth. — set_lw • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -123,7 +123,7 @@ Value
diff --git a/docs/reference/set_mask_xy_mat.html b/docs/reference/set_mask_xy_mat.html
index 49dc5d4e..52c4b617 100644
--- a/docs/reference/set_mask_xy_mat.html
+++ b/docs/reference/set_mask_xy_mat.html
@@ -1,5 +1,5 @@
-Set the masked voxels in a 2D MRSI dataset to given spectrum. — set_mask_xy_mat • Spectroscopy Analysis Tools (spant) Set the masked voxels in a 2D MRSI dataset to given spectrum. — set_mask_xy_mat • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Value
diff --git a/docs/reference/set_precomp_mode.html b/docs/reference/set_precomp_mode.html
index f44bd5d3..47c28e3b 100644
--- a/docs/reference/set_precomp_mode.html
+++ b/docs/reference/set_precomp_mode.html
@@ -1,5 +1,5 @@
-Set the precompute mode. — set_precomp_mode • Spectroscopy Analysis Tools (spant) Set the precompute mode. — set_precomp_mode • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/set_precomp_verbose.html b/docs/reference/set_precomp_verbose.html
index 1453a231..9c613505 100644
--- a/docs/reference/set_precomp_verbose.html
+++ b/docs/reference/set_precomp_verbose.html
@@ -1,5 +1,5 @@
-Set the verbosity of the precompute function. — set_precomp_verbose • Spectroscopy Analysis Tools (spant) Set the verbosity of the precompute function. — set_precomp_verbose • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/set_ref.html b/docs/reference/set_ref.html
index 8953fa50..5436dfa2 100644
--- a/docs/reference/set_ref.html
+++ b/docs/reference/set_ref.html
@@ -1,5 +1,5 @@
-Set the ppm reference value (eg ppm value at 0Hz). — set_ref • Spectroscopy Analysis Tools (spant) Set the ppm reference value (eg ppm value at 0Hz). — set_ref • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/set_td_pts.html b/docs/reference/set_td_pts.html
index 8a80d42a..586459ff 100644
--- a/docs/reference/set_td_pts.html
+++ b/docs/reference/set_td_pts.html
@@ -1,7 +1,5 @@
-Set the number of time-domain data points, truncating or zero-filling as
-appropriate. — set_td_pts • Spectroscopy Analysis Tools (spant) Set the number of time-domain data points, truncating or zero-filling as appropriate. — set_td_pts • Spectroscopy Analysis Tools (spant) Set the command to run the TARQUIN command-line program. — set_tqn_cmd • Spectroscopy Analysis Tools (spant) Set the command to run the TARQUIN command-line program. — set_tqn_cmd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/set_tr.html b/docs/reference/set_tr.html
index b2109ab0..65c9df5f 100644
--- a/docs/reference/set_tr.html
+++ b/docs/reference/set_tr.html
@@ -1,5 +1,5 @@
-Set the repetition time of an MRS dataset. — set_tr • Spectroscopy Analysis Tools (spant) Set the repetition time of an MRS dataset. — set_tr • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/shift.html b/docs/reference/shift.html
index ab0fe724..034591d0 100644
--- a/docs/reference/shift.html
+++ b/docs/reference/shift.html
@@ -1,5 +1,5 @@
-Apply a frequency shift to MRS data. — shift • Spectroscopy Analysis Tools (spant) Apply a frequency shift to MRS data. — shift • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/shift_basis.html b/docs/reference/shift_basis.html
index 2884be19..f55a65e0 100644
--- a/docs/reference/shift_basis.html
+++ b/docs/reference/shift_basis.html
@@ -1,5 +1,5 @@
-Apply frequency shifts to basis set signals. — shift_basis • Spectroscopy Analysis Tools (spant) Apply frequency shifts to basis set signals. — shift_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Value
diff --git a/docs/reference/sim_basis.html b/docs/reference/sim_basis.html
index c7838c46..bb5fefc6 100644
--- a/docs/reference/sim_basis.html
+++ b/docs/reference/sim_basis.html
@@ -1,5 +1,5 @@
-Simulate a basis set object. — sim_basis • Spectroscopy Analysis Tools (spant) Simulate a basis set object. — sim_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -136,7 +136,7 @@ Value
diff --git a/docs/reference/sim_basis_1h_brain.html b/docs/reference/sim_basis_1h_brain.html
index 62ed7389..f71ffa0b 100644
--- a/docs/reference/sim_basis_1h_brain.html
+++ b/docs/reference/sim_basis_1h_brain.html
@@ -1,7 +1,5 @@
-Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS
-sequence. Note, ideal pulses are assumed. — sim_basis_1h_brain • Spectroscopy Analysis Tools (spant) Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS sequence. Note, ideal pulses are assumed. — sim_basis_1h_brain • Spectroscopy Analysis Tools (spant) Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS
-sequence. Note, ideal pulses are assumed. — sim_basis_1h_brain_press • Spectroscopy Analysis Tools (spant) Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS sequence. Note, ideal pulses are assumed. — sim_basis_1h_brain_press • Spectroscopy Analysis Tools (spant) Simulate a macromolecular and lipid basis-set suitable for 1H brain MRS
-analysis. — sim_basis_mm_lip_lcm • Spectroscopy Analysis Tools (spant) Simulate a macromolecular and lipid basis-set suitable for 1H brain MRS analysis. — sim_basis_mm_lip_lcm • Spectroscopy Analysis Tools (spant) Simulate a basis file using TARQUIN. — sim_basis_tqn • Spectroscopy Analysis Tools (spant) Simulate a basis file using TARQUIN. — sim_basis_tqn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -129,7 +129,7 @@ Examples
diff --git a/docs/reference/sim_brain_1h.html b/docs/reference/sim_brain_1h.html
index 2044cf1a..717ee289 100644
--- a/docs/reference/sim_brain_1h.html
+++ b/docs/reference/sim_brain_1h.html
@@ -1,5 +1,5 @@
-Simulate MRS data with a similar appearance to normal brain (by default). — sim_brain_1h • Spectroscopy Analysis Tools (spant) Simulate MRS data with a similar appearance to normal brain (by default). — sim_brain_1h • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -159,7 +159,7 @@ Value
diff --git a/docs/reference/sim_mol.html b/docs/reference/sim_mol.html
index 23bcef50..77f76a50 100644
--- a/docs/reference/sim_mol.html
+++ b/docs/reference/sim_mol.html
@@ -1,5 +1,5 @@
-Simulate a mol_parameter object. — sim_mol • Spectroscopy Analysis Tools (spant) Simulate a mol_parameter object. — sim_mol • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -143,7 +143,7 @@ Value
diff --git a/docs/reference/sim_noise.html b/docs/reference/sim_noise.html
index 23875f79..a71477d4 100644
--- a/docs/reference/sim_noise.html
+++ b/docs/reference/sim_noise.html
@@ -1,5 +1,5 @@
-Simulate an mrs_data object containing simulated Gaussian noise. — sim_noise • Spectroscopy Analysis Tools (spant) Simulate an mrs_data object containing simulated Gaussian noise. — sim_noise • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -84,6 +84,7 @@ Simulate an mrs_data object containing simulated Gaussian noise.
ft = def_ft(),
N = def_N(),
ref = def_ref(),
+ nuc = def_nuc(),
dyns = 1,
fd = TRUE
)
@@ -111,6 +112,10 @@ Arguments
reference value for ppm scale.
nuc
+resonant nucleus.
dyns
number of dynamic scans to generate.
Value
diff --git a/docs/reference/sim_resonances.html b/docs/reference/sim_resonances.html
index 19e9a8a4..d4f8d7c0 100644
--- a/docs/reference/sim_resonances.html
+++ b/docs/reference/sim_resonances.html
@@ -1,5 +1,5 @@
-Simulate a MRS data object containing a set of simulated resonances. — sim_resonances • Spectroscopy Analysis Tools (spant) Simulate a MRS data object containing a set of simulated resonances. — sim_resonances • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -161,7 +161,7 @@ Examples
diff --git a/docs/reference/sim_th_excit_profile.html b/docs/reference/sim_th_excit_profile.html
index 5535c5ef..e781cab1 100644
--- a/docs/reference/sim_th_excit_profile.html
+++ b/docs/reference/sim_th_excit_profile.html
@@ -1,7 +1,5 @@
-Simulate an ideal pulse excitation profile by smoothing a top-hat function
-with a Gaussian. — sim_th_excit_profile • Spectroscopy Analysis Tools (spant) Simulate an ideal pulse excitation profile by smoothing a top-hat function with a Gaussian. — sim_th_excit_profile • Spectroscopy Analysis Tools (spant) Simulate an mrs_data object containing complex zero valued samples. — sim_zero • Spectroscopy Analysis Tools (spant) Simulate an mrs_data object containing complex zero valued samples. — sim_zero • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -78,7 +78,14 @@ Simulate an mrs_data object containing complex zero valued samples.
-
+
@@ -99,6 +106,10 @@ Arguments
reference value for ppm scale.
nuc
+resonant nucleus.
dyns
number of dynamic scans to generate.
Value
diff --git a/docs/reference/smooth_dyns.html b/docs/reference/smooth_dyns.html
index 4cc8da50..accf3a51 100644
--- a/docs/reference/smooth_dyns.html
+++ b/docs/reference/smooth_dyns.html
@@ -1,5 +1,5 @@
-Smooth data across the dynamic dimension with a Gaussian kernel. — smooth_dyns • Spectroscopy Analysis Tools (spant) Smooth data across the dynamic dimension with a Gaussian kernel. — smooth_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/sort_basis.html b/docs/reference/sort_basis.html
index 6a676ea2..d25cc006 100644
--- a/docs/reference/sort_basis.html
+++ b/docs/reference/sort_basis.html
@@ -1,5 +1,5 @@
-Sort the basis-set elements alphabetically. — sort_basis • Spectroscopy Analysis Tools (spant) Sort the basis-set elements alphabetically. — sort_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/spant-package.html b/docs/reference/spant-package.html
index b3dd8e21..90f19ec3 100644
--- a/docs/reference/spant-package.html
+++ b/docs/reference/spant-package.html
@@ -1,5 +1,5 @@
-spant: spectroscopy analysis tools. — spant-package • Spectroscopy Analysis Tools (spant) spant: spectroscopy analysis tools. — spant-package • Spectroscopy Analysis Tools (spant) Simulate and fit some spectra with ABfit for benchmarking purposes. Basic
-timing and performance metrics will be printed. — spant_abfit_benchmark • Spectroscopy Analysis Tools (spant) Simulate and fit some spectra with ABfit for benchmarking purposes. Basic timing and performance metrics will be printed. — spant_abfit_benchmark • Spectroscopy Analysis Tools (spant) Example MEGA-PRESS data with significant B0 drift. — spant_mpress_drift • Spectroscopy Analysis Tools (spant) Example MEGA-PRESS data with significant B0 drift. — spant_mpress_drift • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -83,7 +83,7 @@ Example MEGA-PRESS data with significant B0 drift.
Format
- An object of class mrs_data of length 13.
+ An object of class mrs_data of dimension 1 x 1 x 1 x 1 x 40 x 1 x 1024.
@@ -98,7 +98,7 @@ Format
diff --git a/docs/reference/spant_sim_fmrs_dataset.html b/docs/reference/spant_sim_fmrs_dataset.html
new file mode 100644
index 00000000..00e48b56
--- /dev/null
+++ b/docs/reference/spant_sim_fmrs_dataset.html
@@ -0,0 +1,117 @@
+
+Simulate an example fMRS dataset for a block design fMRS experiment and export a BIDS structure. — spant_sim_fmrs_dataset • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Simulate an example fMRS dataset for a block design fMRS experiment and export a BIDS structure.
+ Source: R/fmrs.R
+ spant_sim_fmrs_dataset.Rd
+
+
+
+ Simulate an example fMRS dataset for a block design fMRS experiment and
+export a BIDS structure.
+
+
+
+ spant_sim_fmrs_dataset(output_dir = NULL)
+
+
+
+ Arguments
+ - output_dir
+output directory for the BIDS data. Defaults to :
+"HOME/sim_fmrs_dataset/data".
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/spant_simulation_benchmark.html b/docs/reference/spant_simulation_benchmark.html
index 32daa8bf..d8cc6841 100644
--- a/docs/reference/spant_simulation_benchmark.html
+++ b/docs/reference/spant_simulation_benchmark.html
@@ -1,7 +1,5 @@
-Simulate a typical metabolite basis set for benchmarking. Timing metrics will
-be printed on completion. — spant_simulation_benchmark • Spectroscopy Analysis Tools (spant) Simulate a typical metabolite basis set for benchmarking. Timing metrics will be printed on completion. — spant_simulation_benchmark • Spectroscopy Analysis Tools (spant) Decompose an mrs_data object into white and gray matter spectra. — spec_decomp • Spectroscopy Analysis Tools (spant) Perform a mathematical operation on a spectral region. — spec_op • Spectroscopy Analysis Tools (spant) Perform a mathematical operation on a spectral region. — spec_op • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -98,8 +98,8 @@ Arguments
operator
-can be "sum" (default), "mean", "l2", "max", "min" or
-"max-min".
can be "sum" (default), "mean", "l2", "max", "max_cplx,
+"min" or "max-min".
freq_scale
@@ -129,7 +129,7 @@ Value
diff --git a/docs/reference/spin_sys.html b/docs/reference/spin_sys.html
index 853423a4..1eaa9e76 100644
--- a/docs/reference/spin_sys.html
+++ b/docs/reference/spin_sys.html
@@ -1,5 +1,5 @@
-Create a spin system object for pulse sequence simulation. — spin_sys • Spectroscopy Analysis Tools (spant) Create a spin system object for pulse sequence simulation. — spin_sys • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/spm_pve2categorical.html b/docs/reference/spm_pve2categorical.html
index 23a1bad9..70f10729 100644
--- a/docs/reference/spm_pve2categorical.html
+++ b/docs/reference/spm_pve2categorical.html
@@ -1,7 +1,5 @@
-Convert SPM style segmentation files to a single categorical image where
-the numerical values map as: 0) Other, 1) CSF, 2) GM and 3) WM. — spm_pve2categorical • Spectroscopy Analysis Tools (spant) Convert SPM style segmentation files to a single categorical image where the numerical values map as: 0) Other, 1) CSF, 2) GM and 3) WM. — spm_pve2categorical • Spectroscopy Analysis Tools (spant) Signal space projection method for lipid suppression. — ssp • Spectroscopy Analysis Tools (spant) Signal space projection method for lipid suppression. — ssp • Spectroscopy Analysis Tools (spant) Plot the fitting results of an object of class fit_result with
-individual basis set components shown. — stackplot.fit_result • Spectroscopy Analysis Tools (spant) Plot the fitting results of an object of class fit_result with individual basis set components shown. — stackplot.fit_result • Spectroscopy Analysis Tools (spant) Produce a plot with multiple traces. — stackplot • Spectroscopy Analysis Tools (spant) Produce a plot with multiple traces. — stackplot • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/stackplot.mrs_data.html b/docs/reference/stackplot.mrs_data.html
index 17ff5648..64eea445 100644
--- a/docs/reference/stackplot.mrs_data.html
+++ b/docs/reference/stackplot.mrs_data.html
@@ -1,5 +1,5 @@
-Stackplot plotting method for objects of class mrs_data. — stackplot.mrs_data • Spectroscopy Analysis Tools (spant) Stackplot plotting method for objects of class mrs_data. — stackplot.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -255,7 +255,7 @@ Arguments
diff --git a/docs/reference/sub_first_dyn.html b/docs/reference/sub_first_dyn.html
index dbd7f831..493b7242 100644
--- a/docs/reference/sub_first_dyn.html
+++ b/docs/reference/sub_first_dyn.html
@@ -1,5 +1,5 @@
-Subtract the first dynamic spectrum from a dynamic series. — sub_first_dyn • Spectroscopy Analysis Tools (spant) Subtract the first dynamic spectrum from a dynamic series. — sub_first_dyn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/sub_mean_dyns.html b/docs/reference/sub_mean_dyns.html
index 6e3bb2df..221bd0c1 100644
--- a/docs/reference/sub_mean_dyns.html
+++ b/docs/reference/sub_mean_dyns.html
@@ -1,5 +1,5 @@
-Subtract the mean dynamic spectrum from a dynamic series. — sub_mean_dyns • Spectroscopy Analysis Tools (spant) Subtract the mean dynamic spectrum from a dynamic series. — sub_mean_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/sub_median_dyns.html b/docs/reference/sub_median_dyns.html
index 134c495d..1e834f14 100644
--- a/docs/reference/sub_median_dyns.html
+++ b/docs/reference/sub_median_dyns.html
@@ -1,5 +1,5 @@
-Subtract the median dynamic spectrum from a dynamic series. — sub_median_dyns • Spectroscopy Analysis Tools (spant) Subtract the median dynamic spectrum from a dynamic series. — sub_median_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/sum_coils.html b/docs/reference/sum_coils.html
index 7bf559f2..e1ab3cc0 100644
--- a/docs/reference/sum_coils.html
+++ b/docs/reference/sum_coils.html
@@ -1,5 +1,5 @@
-Calculate the sum across receiver coil elements. — sum_coils • Spectroscopy Analysis Tools (spant) Calculate the sum across receiver coil elements. — sum_coils • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/sum_dyns.html b/docs/reference/sum_dyns.html
index a0be19d3..bbda2ffc 100644
--- a/docs/reference/sum_dyns.html
+++ b/docs/reference/sum_dyns.html
@@ -1,5 +1,5 @@
-Calculate the sum of data dynamics. — sum_dyns • Spectroscopy Analysis Tools (spant) Calculate the sum of data dynamics. — sum_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/sum_mrs.html b/docs/reference/sum_mrs.html
index a22f215b..3cc3ab9e 100644
--- a/docs/reference/sum_mrs.html
+++ b/docs/reference/sum_mrs.html
@@ -1,5 +1,5 @@
-Sum two mrs_data objects. — sum_mrs • Spectroscopy Analysis Tools (spant) Sum two mrs_data objects. — sum_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Value
diff --git a/docs/reference/sum_mrs_list.html b/docs/reference/sum_mrs_list.html
index f4e09aea..c3584348 100644
--- a/docs/reference/sum_mrs_list.html
+++ b/docs/reference/sum_mrs_list.html
@@ -1,5 +1,5 @@
-Return the sum of a list of mrs_data objects. — sum_mrs_list • Spectroscopy Analysis Tools (spant) Return the sum of a list of mrs_data objects. — sum_mrs_list • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/svs_1h_brain_analysis.html b/docs/reference/svs_1h_brain_analysis.html
index 8ce514db..dff0ef7d 100644
--- a/docs/reference/svs_1h_brain_analysis.html
+++ b/docs/reference/svs_1h_brain_analysis.html
@@ -1,5 +1,5 @@
-Standard SVS 1H brain analysis pipeline. — svs_1h_brain_analysis • Spectroscopy Analysis Tools (spant) Standard SVS 1H brain analysis pipeline. — svs_1h_brain_analysis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -199,7 +199,7 @@ Value
diff --git a/docs/reference/svs_1h_brain_analysis_dev.html b/docs/reference/svs_1h_brain_analysis_dev.html
index d70a14d3..d71bfea2 100644
--- a/docs/reference/svs_1h_brain_analysis_dev.html
+++ b/docs/reference/svs_1h_brain_analysis_dev.html
@@ -1,5 +1,5 @@
-Standard SVS 1H brain analysis pipeline. — svs_1h_brain_analysis_dev • Spectroscopy Analysis Tools (spant) Standard SVS 1H brain analysis pipeline. — svs_1h_brain_analysis_dev • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -193,7 +193,7 @@ Examples
diff --git a/docs/reference/svs_1h_brain_batch_analysis.html b/docs/reference/svs_1h_brain_batch_analysis.html
index 5631e8cc..15f7223e 100644
--- a/docs/reference/svs_1h_brain_batch_analysis.html
+++ b/docs/reference/svs_1h_brain_batch_analysis.html
@@ -1,5 +1,5 @@
-Batch interface to the standard SVS 1H brain analysis pipeline. — svs_1h_brain_batch_analysis • Spectroscopy Analysis Tools (spant) Batch interface to the standard SVS 1H brain analysis pipeline. — svs_1h_brain_batch_analysis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -144,7 +144,7 @@ Value
diff --git a/docs/reference/t_test_spec.html b/docs/reference/t_test_spec.html
new file mode 100644
index 00000000..56a7ea1b
--- /dev/null
+++ b/docs/reference/t_test_spec.html
@@ -0,0 +1,124 @@
+
+Perform a t-test on spectral data points. — t_test_spec • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+
+
+ Perform a t-test on spectral data points.
+
+
+
+ t_test_spec(mrs_data, group)
+
+
+
+ Arguments
+ - mrs_data
+an mrs_data object with spectra in the dynamic dimension.
- group
+vector describing the group membership of each dynamic spectrum.
+
+ Value
+
+
+a list of statistical results.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/td2fd.html b/docs/reference/td2fd.html
index 6748a6a8..f31ed524 100644
--- a/docs/reference/td2fd.html
+++ b/docs/reference/td2fd.html
@@ -1,5 +1,5 @@
-Transform time-domain data to the frequency-domain. — td2fd • Spectroscopy Analysis Tools (spant) Transform time-domain data to the frequency-domain. — td2fd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/td_conv_filt.html b/docs/reference/td_conv_filt.html
index a9f340c3..106b9b00 100644
--- a/docs/reference/td_conv_filt.html
+++ b/docs/reference/td_conv_filt.html
@@ -1,5 +1,5 @@
-Time-domain convolution based filter. — td_conv_filt • Spectroscopy Analysis Tools (spant) Time-domain convolution based filter. — td_conv_filt • Spectroscopy Analysis Tools (spant) Time-domain spectral registration. — tdsr • Spectroscopy Analysis Tools (spant) Time-domain spectral registration. — tdsr • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -121,7 +121,7 @@ Value
diff --git a/docs/reference/te.html b/docs/reference/te.html
index 010361b1..4a65711d 100644
--- a/docs/reference/te.html
+++ b/docs/reference/te.html
@@ -1,5 +1,5 @@
-Return the echo time of an MRS dataset. — te • Spectroscopy Analysis Tools (spant) Return the echo time of an MRS dataset. — te • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/tr.html b/docs/reference/tr.html
index 0c0bd63b..2e749e02 100644
--- a/docs/reference/tr.html
+++ b/docs/reference/tr.html
@@ -1,5 +1,5 @@
-Return the repetition time of an MRS dataset. — tr • Spectroscopy Analysis Tools (spant) Return the repetition time of an MRS dataset. — tr • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/varpro_3_para_opts.html b/docs/reference/varpro_3_para_opts.html
index c2270a16..52d7cd84 100644
--- a/docs/reference/varpro_3_para_opts.html
+++ b/docs/reference/varpro_3_para_opts.html
@@ -1,5 +1,5 @@
-Return a list of options for VARPRO based fitting with 3 free parameters. — varpro_3_para_opts • Spectroscopy Analysis Tools (spant) Return a list of options for VARPRO based fitting with 3 free parameters. — varpro_3_para_opts • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -141,7 +141,7 @@ Value
diff --git a/docs/reference/varpro_basic_opts.html b/docs/reference/varpro_basic_opts.html
index 32c86d22..c5104891 100644
--- a/docs/reference/varpro_basic_opts.html
+++ b/docs/reference/varpro_basic_opts.html
@@ -1,5 +1,5 @@
-Return a list of options for a basic VARPRO analysis. — varpro_basic_opts • Spectroscopy Analysis Tools (spant) Return a list of options for a basic VARPRO analysis. — varpro_basic_opts • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -118,7 +118,7 @@ Value
diff --git a/docs/reference/varpro_opts.html b/docs/reference/varpro_opts.html
index 2aabf11d..6332f730 100644
--- a/docs/reference/varpro_opts.html
+++ b/docs/reference/varpro_opts.html
@@ -1,5 +1,5 @@
-Return a list of options for VARPRO based fitting. — varpro_opts • Spectroscopy Analysis Tools (spant) Return a list of options for VARPRO based fitting. — varpro_opts • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -177,7 +177,7 @@ Examples
diff --git a/docs/reference/vec2mrs_data.html b/docs/reference/vec2mrs_data.html
index 0cccd73b..f0d58bf0 100644
--- a/docs/reference/vec2mrs_data.html
+++ b/docs/reference/vec2mrs_data.html
@@ -1,5 +1,5 @@
-Convert a vector into a mrs_data object. — vec2mrs_data • Spectroscopy Analysis Tools (spant) Convert a vector into a mrs_data object. — vec2mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -80,10 +80,11 @@ Convert a vector into a mrs_data object.
vec2mrs_data(
vec,
- fs = def_fs(),
- ft = def_ft(),
- ref = def_ref(),
- nuc = def_nuc(),
+ mrs_data = NULL,
+ fs = NULL,
+ ft = NULL,
+ ref = NULL,
+ nuc = NULL,
dyns = 1,
fd = FALSE
)
@@ -95,6 +96,10 @@ Arguments
the data vector.
mrs_data
+example data to copy acquisition parameters from.
fs
sampling frequency in Hz.
Arguments
fd
-flag to indicate if the matrix is in the frequency domain (logical).
flag to indicate if the vector is in the frequency domain (logical).
Value
diff --git a/docs/reference/write_basis.html b/docs/reference/write_basis.html
index b6e27cbd..94c5e021 100644
--- a/docs/reference/write_basis.html
+++ b/docs/reference/write_basis.html
@@ -1,5 +1,5 @@
-Write a basis object to an LCModel .basis formatted file. — write_basis • Spectroscopy Analysis Tools (spant) Write a basis object to an LCModel .basis formatted file. — write_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -108,7 +108,7 @@ Arguments
diff --git a/docs/reference/write_basis_tqn.html b/docs/reference/write_basis_tqn.html
index 6aa51c1d..116c73ec 100644
--- a/docs/reference/write_basis_tqn.html
+++ b/docs/reference/write_basis_tqn.html
@@ -1,5 +1,5 @@
-Generate a basis file using TARQUIN. — write_basis_tqn • Spectroscopy Analysis Tools (spant) Generate a basis file using TARQUIN. — write_basis_tqn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Examples
diff --git a/docs/reference/write_mrs.html b/docs/reference/write_mrs.html
index fff25f15..124b9dc4 100644
--- a/docs/reference/write_mrs.html
+++ b/docs/reference/write_mrs.html
@@ -1,5 +1,5 @@
-Write MRS data object to file. — write_mrs • Spectroscopy Analysis Tools (spant) Write MRS data object to file. — write_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Arguments
diff --git a/docs/reference/write_mrs_nifti.html b/docs/reference/write_mrs_nifti.html
index f4bf1921..bd3ed4b7 100644
--- a/docs/reference/write_mrs_nifti.html
+++ b/docs/reference/write_mrs_nifti.html
@@ -1,5 +1,5 @@
-Write MRS data object to file in NIFTI format. — write_mrs_nifti • Spectroscopy Analysis Tools (spant) Write MRS data object to file in NIFTI format. — write_mrs_nifti • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/write_pulse_ascii.html b/docs/reference/write_pulse_ascii.html
index 067ae086..221f8ebb 100644
--- a/docs/reference/write_pulse_ascii.html
+++ b/docs/reference/write_pulse_ascii.html
@@ -1,5 +1,5 @@
-Write an ASCII formatted pulse file. — write_pulse_ascii • Spectroscopy Analysis Tools (spant) Write an ASCII formatted pulse file. — write_pulse_ascii • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/zero_fade_spec.html b/docs/reference/zero_fade_spec.html
index c703745c..c8b572c3 100644
--- a/docs/reference/zero_fade_spec.html
+++ b/docs/reference/zero_fade_spec.html
@@ -1,7 +1,5 @@
-Fade a spectrum to zero by frequency domain multiplication with a tanh
-function. Note this operation distorts data points at the end of the FID. — zero_fade_spec • Spectroscopy Analysis Tools (spant) Fade a spectrum to zero by frequency domain multiplication with a tanh function. Note this operation distorts data points at the end of the FID. — zero_fade_spec • Spectroscopy Analysis Tools (spant) Zero all coherences including and above a given order. — zero_higher_orders • Spectroscopy Analysis Tools (spant) Zero all coherences including and above a given order. — zero_higher_orders • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Value
diff --git a/docs/reference/zero_td_pts_end.html b/docs/reference/zero_td_pts_end.html
index 8c1123c8..71d24ebb 100644
--- a/docs/reference/zero_td_pts_end.html
+++ b/docs/reference/zero_td_pts_end.html
@@ -1,5 +1,5 @@
-Set mrs_data object data points at the end of the FID to zero. — zero_td_pts_end • Spectroscopy Analysis Tools (spant) Set mrs_data object data points at the end of the FID to zero. — zero_td_pts_end • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/zf.html b/docs/reference/zf.html
index 85e2013c..baf50256 100644
--- a/docs/reference/zf.html
+++ b/docs/reference/zf.html
@@ -1,5 +1,5 @@
-Zero-fill MRS data in the time domain. — zf • Spectroscopy Analysis Tools (spant) Zero-fill MRS data in the time domain. — zf • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -125,7 +125,7 @@ Value
diff --git a/docs/reference/zf_xy.html b/docs/reference/zf_xy.html
index ebca3999..c4104a74 100644
--- a/docs/reference/zf_xy.html
+++ b/docs/reference/zf_xy.html
@@ -1,5 +1,5 @@
-Zero-fill MRSI data in the k-space x-y direction. — zf_xy • Spectroscopy Analysis Tools (spant) Zero-fill MRSI data in the k-space x-y direction. — zf_xy • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -113,7 +113,7 @@ Value
diff --git a/docs/sitemap.xml b/docs/sitemap.xml
index e2139f71..4c39f515 100644
--- a/docs/sitemap.xml
+++ b/docs/sitemap.xml
@@ -216,6 +216,12 @@
https://martin3141.github.io/spant/reference/comb_coils_fp_pc.html
+
+ https://martin3141.github.io/spant/reference/comb_coils_mrsi_gls.html
+
+
+ https://martin3141.github.io/spant/reference/comb_coils_svs_gls.html
+
https://martin3141.github.io/spant/reference/comb_csv_results.html
@@ -411,6 +417,9 @@
https://martin3141.github.io/spant/reference/gen_conv_reg.html
+
+ https://martin3141.github.io/spant/reference/gen_group_reg.html
+
https://martin3141.github.io/spant/reference/gen_impulse_reg.html
@@ -555,6 +564,15 @@
https://martin3141.github.io/spant/reference/glm_spec.html
+
+ https://martin3141.github.io/spant/reference/glm_spec_fmrs_fl.html
+
+
+ https://martin3141.github.io/spant/reference/glm_spec_fmrs_group.html
+
+
+ https://martin3141.github.io/spant/reference/glm_spec_group_linhyp.html
+
https://martin3141.github.io/spant/reference/grid_shift_xy.html
@@ -690,9 +708,15 @@
https://martin3141.github.io/spant/reference/mrs_data2basis.html
+
+ https://martin3141.github.io/spant/reference/mrs_data2bids.html
+
https://martin3141.github.io/spant/reference/mrs_data2mat.html
+
+ https://martin3141.github.io/spant/reference/mrs_data2spec_mat.html
+
https://martin3141.github.io/spant/reference/mrs_data2vec.html
@@ -741,6 +765,9 @@
https://martin3141.github.io/spant/reference/phase.html
+
+ https://martin3141.github.io/spant/reference/phase_ref_1h_brain.html
+
https://martin3141.github.io/spant/reference/plot.fit_result.html
@@ -780,6 +807,12 @@
https://martin3141.github.io/spant/reference/precomp.html
+
+ https://martin3141.github.io/spant/reference/preproc_svs.html
+
+
+ https://martin3141.github.io/spant/reference/preproc_svs_dataset.html
+
https://martin3141.github.io/spant/reference/print.fit_result.html
@@ -1050,6 +1083,9 @@
https://martin3141.github.io/spant/reference/spant_mpress_drift.html
+
+ https://martin3141.github.io/spant/reference/spant_sim_fmrs_dataset.html
+
https://martin3141.github.io/spant/reference/spant_simulation_benchmark.html
@@ -1107,6 +1143,9 @@
https://martin3141.github.io/spant/reference/svs_1h_brain_batch_analysis.html
+
+ https://martin3141.github.io/spant/reference/t_test_spec.html
+
https://martin3141.github.io/spant/reference/td2fd.html
Compute the vector cross product between vectors x and y. Adapted from -http://stackoverflow.com/questions/15162741/what-is-rs-crossproduct-function
Compute the vector cross product between vectors x and y. Adapted from http://stackoverflow.com/questions/15162741/what-is-rs-crossproduct-function
Decimate an MRS signal to half the original sampling frequency by filtering -in the frequency domain before down sampling.
Decimate an MRS signal to half the original sampling frequency by filtering in the frequency domain before down sampling.
All functions
- Return (and optionally modify using the input arguments) a list of the
-default acquisition parameters.
Return (and optionally modify using the input arguments) a list of the default acquisition parameters.
@@ -410,14 +402,11 @@ All functions
- Downsample an MRS signal by a factor of 2 by removing every other data point
-in the time-domain. Note, signals outside the new sampling frequency will be
-aliased.
Downsample an MRS signal by a factor of 2 by removing every other data point in the time-domain. Note, signals outside the new sampling frequency will be aliased.
- Return a time scale vector of acquisition times for a dynamic MRS scan. The
-first temporal scan is assigned a value of 0.
Return a time scale vector of acquisition times for a dynamic MRS scan. The first temporal scan is assigned a value of 0.
@@ -429,8 +418,7 @@ All functions
- Estimate the standard deviation of the noise from a segment of an mrs_data
-object.
Estimate the standard deviation of the noise from a segment of an mrs_data object.
@@ -486,8 +474,7 @@ All functions
- Perform a zeroth order phase correction based on the phase of the first data
-point in the time-domain.
Perform a zeroth order phase correction based on the phase of the first data point in the time-domain.
@@ -507,8 +494,7 @@ All functions
- Perform a fft and fftshift on a matrix with each column replaced by its
-shifted fft.
Perform a fft and fftshift on a matrix with each column replaced by its shifted fft.
@@ -536,8 +522,11 @@ All functions
- Generate regressors by convolving a specified response function with a
-stimulus.
Generate regressors by convolving a specified response function with a stimulus.
+
+
+ Expand a regressor matrix for a group analysis.
@@ -553,28 +542,23 @@ All functions
- Return a character vector of common 1H molecules found in healthy human
-brain.
Return a character vector of common 1H molecules found in healthy human brain.
- Return a list of mol_parameter objects suitable for 1H brain MRS
-analyses.
Return a list of mol_parameter objects suitable for 1H brain MRS analyses.
- Return a list of mol_parameter objects suitable for 1H brain MRS
-analyses.
Return a list of mol_parameter objects suitable for 1H brain MRS analyses.
- Return a list of mol_parameter objects suitable for 1H brain MRS
-analyses.
Return a list of mol_parameter objects suitable for 1H brain MRS analyses.
- Return a list of mol_parameter objects suitable for 1H brain MRS
-analyses.
Return a list of mol_parameter objects suitable for 1H brain MRS analyses.
@@ -582,8 +566,7 @@ All functions
- Return a character vector of molecules included in the Gold Star Phantoms
-SPECTRE phantom.
Return a character vector of molecules included in the Gold Star Phantoms SPECTRE phantom.
@@ -635,8 +618,7 @@ All functions
- Return a character array of names that may be used with the
-get_mol_paras function.
Return a character array of names that may be used with the get_mol_paras function.
@@ -700,8 +682,7 @@ All functions
- Return an array of amplitudes derived from fitting the initial points in the
-time domain and extrapolating back to t=0.
Return an array of amplitudes derived from fitting the initial points in the time domain and extrapolating back to t=0.
@@ -709,8 +690,7 @@ All functions
- Generate a mol_parameters object for a simple spin system with one
-resonance.
Generate a mol_parameters object for a simple spin system with one resonance.
@@ -731,6 +711,18 @@ All functions glm_spec()
Perform a GLM analysis of dynamic MRS data in the spectral domain.
+
+
+ Perform first-level spectral GLM analysis of an fMRS dataset.
+
+
+ Perform group-level spectral GLM analysis of an fMRS dataset.
+
+
+ Test a group-level spectral GLM linear hypothesis.
@@ -766,8 +758,7 @@ All functions
- Perform an ifft and ifftshift on a matrix with each column replaced by its
-shifted ifft.
Perform an ifft and ifftshift on a matrix with each column replaced by its shifted ifft.
@@ -799,8 +790,7 @@ All functions
- Check if the chemical shift dimension of an MRS data object is in the
-frequency domain.
Check if the chemical shift dimension of an MRS data object is in the frequency domain.
@@ -820,18 +810,15 @@ All functions
- Covert a linewidth in Hz to an equivalent alpha value in the time-domain ie:
-x * exp(-t * alpha).
Covert a linewidth in Hz to an equivalent alpha value in the time-domain ie: x * exp(-t * alpha).
- Covert a linewidth in Hz to an equivalent beta value in the time-domain ie:
-x * exp(-t * t * beta).
Covert a linewidth in Hz to an equivalent beta value in the time-domain ie: x * exp(-t * t * beta).
- Make a basis-set object from a directory containing LCModel formatted RAW
-files.
Make a basis-set object from a directory containing LCModel formatted RAW files.
@@ -851,8 +838,7 @@ All functions
- Mask the voxels outside an elliptical region spanning the MRSI dataset in the
-x-y plane.
Mask the voxels outside an elliptical region spanning the MRSI dataset in the x-y plane.
@@ -860,13 +846,11 @@ All functions
- Convert a matrix (with spectral points in the column dimension and dynamics
-in the row dimensions) into a mrs_data object.
Convert a matrix (with spectral points in the column dimension and dynamics in the row dimensions) into a mrs_data object.
- Matrix exponential function taken from complexplus package to reduce the
-number of spant dependencies.
Matrix exponential function taken from complexplus package to reduce the number of spant dependencies.
@@ -914,31 +898,31 @@ All functions
- Convert an mrs_data object to basis object - where basis signals are spread
-across the dynamic dimension in the MRS data.
Convert an mrs_data object to basis object - where basis signals are spread across the dynamic dimension in the MRS data.
+
+
+ Create a BIDS file structure from a vector of MRS data paths or list of mrs_data objects.
- Convert mrs_data object to a matrix, with spectral points in the column
-dimension and dynamics in the row dimension.
Convert mrs_data object to a matrix, with spectral points in the column dimension and dynamics in the row dimension.
-
+
- Convert mrs_data object to a vector.
Convert mrs_data object to a matrix, with spectral points in the column dimension and dynamics in the row dimension.
-
+
- Create a BIDS directory and file structure from a list of mrs_data objects.
Convert mrs_data object to a vector.
- Perform a fftshift on a matrix, with each column replaced by its shifted
-result.
Perform a fftshift on a matrix, with each column replaced by its shifted result.
- Perform an ifftshift on a matrix, with each column replaced by its shifted
-result.
Perform an ifftshift on a matrix, with each column replaced by its shifted result.
@@ -946,9 +930,7 @@ All functions
- Flip the x data dimension order of a nifti image. This corresponds to
-flipping MRI data in the left-right direction, assuming the data in save in
-neurological format (can check with fslorient program).
Flip the x data dimension order of a nifti image. This corresponds to flipping MRI data in the left-right direction, assuming the data in save in neurological format (can check with fslorient program).
@@ -964,8 +946,7 @@ All functions
- Search for the highest peak in a spectral region and return the frequency,
-height and FWHM.
Search for the highest peak in a spectral region and return the frequency, height and FWHM.
@@ -974,6 +955,10 @@ All functions phase()
Apply phasing parameters to MRS data.
+
+
+ Corrected zero order phase and chemical shift offset in 1H MRS data from the brain.
@@ -1005,8 +990,7 @@ All functions
- Plot an interactive slice map from a data array where voxels can be selected
-to display a corresponding spectrum.
Plot an interactive slice map from a data array where voxels can be selected to display a corresponding spectrum.
@@ -1026,8 +1010,15 @@ All functions
- Save function results to file and load on subsequent calls to avoid repeat
-computation.
Save function results to file and load on subsequent calls to avoid repeat computation.
+
+
+ Preprocess and perform quality assessment of a single SVS data set.
+
+
+ Preprocess and perform quality assessment of one or more SVS data sets.
@@ -1055,15 +1046,11 @@ All functions
- Read a directory containing Siemens MRS IMA files and combine along the coil
-dimension. Note that the coil ID is inferred from the sorted file name and
-should be checked when consistency is required between two directories.
Read a directory containing Siemens MRS IMA files and combine along the coil dimension. Note that the coil ID is inferred from the sorted file name and should be checked when consistency is required between two directories.
- Read a directory containing Siemens MRS IMA files and combine along the
-dynamic dimension. Note that the coil ID is inferred from the sorted file
-name and should be checked when consistency is required.
Read a directory containing Siemens MRS IMA files and combine along the dynamic dimension. Note that the coil ID is inferred from the sorted file name and should be checked when consistency is required.
@@ -1103,13 +1090,11 @@ All functions
- Reconstruct complex time-domain data from the real part of frequency-domain
-data.
Reconstruct complex time-domain data from the real part of frequency-domain data.
- Reconstruct complex time-domain data from the real part of frequency-domain
-data.
Reconstruct complex time-domain data from the real part of frequency-domain data.
@@ -1141,8 +1126,7 @@ All functions
- Resample a VOI to match a target image space using nearest-neighbour
-interpolation.
Resample a VOI to match a target image space using nearest-neighbour interpolation.
@@ -1158,23 +1142,19 @@ All functions
- Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water).
Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / kg of tissue water).
- Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water).
Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / kg of tissue water).
- Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / Litre of tissue).
Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / Litre of tissue).
- Convert default LCM/TARQUIN concentration scaling to molal units with partial
-volume correction.
Convert default LCM/TARQUIN concentration scaling to molal units with partial volume correction.
@@ -1222,8 +1202,7 @@ All functions
- MEGA-PRESS sequence with ideal localisation pulses and Gaussian shaped
-editing pulse.
MEGA-PRESS sequence with ideal localisation pulses and Gaussian shaped editing pulse.
@@ -1251,13 +1230,11 @@ All functions
- STEAM sequence with ideal pulses and coherence order filtering to simulate
-gradient crushers.
STEAM sequence with ideal pulses and coherence order filtering to simulate gradient crushers.
- STEAM sequence with ideal pulses using the z-rotation gradient simulation
-method described by Young et al JMR 140, 146-152 (1999).
STEAM sequence with ideal pulses using the z-rotation gradient simulation method described by Young et al JMR 140, 146-152 (1999).
@@ -1293,8 +1270,7 @@ All functions
- Set the number of time-domain data points, truncating or zero-filling as
-appropriate.
Set the number of time-domain data points, truncating or zero-filling as appropriate.
@@ -1318,18 +1294,15 @@ All functions
- Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS
-sequence. Note, ideal pulses are assumed.
Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS sequence. Note, ideal pulses are assumed.
- Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS
-sequence. Note, ideal pulses are assumed.
Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS sequence. Note, ideal pulses are assumed.
- Simulate a macromolecular and lipid basis-set suitable for 1H brain MRS
-analysis.
Simulate a macromolecular and lipid basis-set suitable for 1H brain MRS analysis.
@@ -1353,8 +1326,7 @@ All functions
- Simulate an ideal pulse excitation profile by smoothing a top-hat function
-with a Gaussian.
Simulate an ideal pulse excitation profile by smoothing a top-hat function with a Gaussian.
@@ -1374,17 +1346,19 @@ All functions
- Simulate and fit some spectra with ABfit for benchmarking purposes. Basic
-timing and performance metrics will be printed.
Simulate and fit some spectra with ABfit for benchmarking purposes. Basic timing and performance metrics will be printed.
Example MEGA-PRESS data with significant B0 drift.
+
+
+ Simulate an example fMRS dataset for a block design fMRS experiment and export a BIDS structure.
- Simulate a typical metabolite basis set for benchmarking. Timing metrics will
-be printed on completion.
Simulate a typical metabolite basis set for benchmarking. Timing metrics will be printed on completion.
@@ -1400,8 +1374,7 @@ All functions
- Convert SPM style segmentation files to a single categorical image where
-the numerical values map as: 0) Other, 1) CSF, 2) GM and 3) WM.
Convert SPM style segmentation files to a single categorical image where the numerical values map as: 0) Other, 1) CSF, 2) GM and 3) WM.
@@ -1413,8 +1386,7 @@ All functions
- Plot the fitting results of an object of class fit_result with
-individual basis set components shown.
Plot the fitting results of an object of class fit_result with individual basis set components shown.
@@ -1459,6 +1431,10 @@ All functions svs_1h_brain_batch_analysis()
Batch interface to the standard SVS 1H brain analysis pipeline.
+
+
+ Perform a t-test on spectral data points.
@@ -1518,8 +1494,7 @@ All functions
- Fade a spectrum to zero by frequency domain multiplication with a tanh
-function. Note this operation distorts data points at the end of the FID.
Fade a spectrum to zero by frequency domain multiplication with a tanh function. Note this operation distorts data points at the end of the FID.
@@ -1549,7 +1524,7 @@ All functions
diff --git a/docs/reference/int_spec.html b/docs/reference/int_spec.html
index c7060fe7..783325a8 100644
--- a/docs/reference/int_spec.html
+++ b/docs/reference/int_spec.html
@@ -1,5 +1,5 @@
-Integrate a spectral region. — int_spec • Spectroscopy Analysis Tools (spant) Integrate a spectral region. — int_spec • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -118,7 +118,7 @@ Value
diff --git a/docs/reference/interleave_dyns.html b/docs/reference/interleave_dyns.html
index effe5543..441eff27 100644
--- a/docs/reference/interleave_dyns.html
+++ b/docs/reference/interleave_dyns.html
@@ -1,5 +1,5 @@
-Interleave the first and second half of a dynamic series. — interleave_dyns • Spectroscopy Analysis Tools (spant) Interleave the first and second half of a dynamic series. — interleave_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/inv_even_dyns.html b/docs/reference/inv_even_dyns.html
index 9f9d4fff..dcb781dc 100644
--- a/docs/reference/inv_even_dyns.html
+++ b/docs/reference/inv_even_dyns.html
@@ -1,5 +1,5 @@
-Invert even numbered dynamic scans starting from 1 (2,4,6...). — inv_even_dyns • Spectroscopy Analysis Tools (spant) Invert even numbered dynamic scans starting from 1 (2,4,6...). — inv_even_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/inv_odd_dyns.html b/docs/reference/inv_odd_dyns.html
index 26212e2b..78d64660 100644
--- a/docs/reference/inv_odd_dyns.html
+++ b/docs/reference/inv_odd_dyns.html
@@ -1,5 +1,5 @@
-Invert odd numbered dynamic scans starting from 1 (1,3,5...). — inv_odd_dyns • Spectroscopy Analysis Tools (spant) Invert odd numbered dynamic scans starting from 1 (1,3,5...). — inv_odd_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/is.def.html b/docs/reference/is.def.html
index f196ffd0..a67b9eba 100644
--- a/docs/reference/is.def.html
+++ b/docs/reference/is.def.html
@@ -1,5 +1,5 @@
-Check if an object is defined, which is the same as being not NULL. — is.def • Spectroscopy Analysis Tools (spant) Check if an object is defined, which is the same as being not NULL. — is.def • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/is_fd.html b/docs/reference/is_fd.html
index 3b0ca165..18a193aa 100644
--- a/docs/reference/is_fd.html
+++ b/docs/reference/is_fd.html
@@ -1,7 +1,5 @@
-Check if the chemical shift dimension of an MRS data object is in the
-frequency domain. — is_fd • Spectroscopy Analysis Tools (spant) Check if the chemical shift dimension of an MRS data object is in the frequency domain. — is_fd • Spectroscopy Analysis Tools (spant) Transform 2D MRSI data from k-space to image space in the x-y direction. — kspace2img_xy • Spectroscopy Analysis Tools (spant) Transform 2D MRSI data from k-space to image space in the x-y direction. — kspace2img_xy • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/l2_reg.html b/docs/reference/l2_reg.html
index 3d781d80..21aa9849 100644
--- a/docs/reference/l2_reg.html
+++ b/docs/reference/l2_reg.html
@@ -1,5 +1,5 @@
-Perform l2 regularisation artefact suppression. — l2_reg • Spectroscopy Analysis Tools (spant) Perform l2 regularisation artefact suppression. — l2_reg • Spectroscopy Analysis Tools (spant) Apply line-broadening (apodisation) to MRS data or basis object. — lb • Spectroscopy Analysis Tools (spant) Apply line-broadening (apodisation) to MRS data or basis object. — lb • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -123,7 +123,7 @@ Value
diff --git a/docs/reference/lofdc.html b/docs/reference/lofdc.html
index 5419b1ec..31347a25 100644
--- a/docs/reference/lofdc.html
+++ b/docs/reference/lofdc.html
@@ -1,5 +1,5 @@
-Correct linear frequency drift. — lofdc • Spectroscopy Analysis Tools (spant) Correct linear frequency drift. — lofdc • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -138,7 +138,7 @@ Value
diff --git a/docs/reference/lw2alpha.html b/docs/reference/lw2alpha.html
index b83db682..25da229b 100644
--- a/docs/reference/lw2alpha.html
+++ b/docs/reference/lw2alpha.html
@@ -1,7 +1,5 @@
-Covert a linewidth in Hz to an equivalent alpha value in the time-domain ie:
-x * exp(-t * alpha). — lw2alpha • Spectroscopy Analysis Tools (spant) Covert a linewidth in Hz to an equivalent alpha value in the time-domain ie: x * exp(-t * alpha). — lw2alpha • Spectroscopy Analysis Tools (spant) Covert a linewidth in Hz to an equivalent beta value in the time-domain ie:
-x * exp(-t * t * beta). — lw2beta • Spectroscopy Analysis Tools (spant) Covert a linewidth in Hz to an equivalent beta value in the time-domain ie: x * exp(-t * t * beta). — lw2beta • Spectroscopy Analysis Tools (spant) Make a basis-set object from a directory containing LCModel formatted RAW
-files. — make_basis_from_raw • Spectroscopy Analysis Tools (spant) Make a basis-set object from a directory containing LCModel formatted RAW files. — make_basis_from_raw • Spectroscopy Analysis Tools (spant) Mask an MRS dataset in the dynamic dimension. — mask_dyns • Spectroscopy Analysis Tools (spant) Mask an MRS dataset in the dynamic dimension. — mask_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/mask_fit_res.html b/docs/reference/mask_fit_res.html
index 97baaa3f..ebd91a99 100644
--- a/docs/reference/mask_fit_res.html
+++ b/docs/reference/mask_fit_res.html
@@ -1,5 +1,5 @@
-Mask fit result spectra depending on a vector of bool values. — mask_fit_res • Spectroscopy Analysis Tools (spant) Mask fit result spectra depending on a vector of bool values. — mask_fit_res • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -116,7 +116,7 @@ Value
diff --git a/docs/reference/mask_xy.html b/docs/reference/mask_xy.html
index 11bb577c..b0d38619 100644
--- a/docs/reference/mask_xy.html
+++ b/docs/reference/mask_xy.html
@@ -1,5 +1,5 @@
-Mask an MRSI dataset in the x-y direction — mask_xy • Spectroscopy Analysis Tools (spant) Mask an MRSI dataset in the x-y direction — mask_xy • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/mask_xy_corners.html b/docs/reference/mask_xy_corners.html
index 09b16cd2..2d13839d 100644
--- a/docs/reference/mask_xy_corners.html
+++ b/docs/reference/mask_xy_corners.html
@@ -1,5 +1,5 @@
-Mask the four corners of an MRSI dataset in the x-y plane. — mask_xy_corners • Spectroscopy Analysis Tools (spant) Mask the four corners of an MRSI dataset in the x-y plane. — mask_xy_corners • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/mask_xy_ellipse.html b/docs/reference/mask_xy_ellipse.html
index 1d8b02e4..e2e749ef 100644
--- a/docs/reference/mask_xy_ellipse.html
+++ b/docs/reference/mask_xy_ellipse.html
@@ -1,7 +1,5 @@
-Mask the voxels outside an elliptical region spanning the MRSI dataset in the
-x-y plane. — mask_xy_ellipse • Spectroscopy Analysis Tools (spant) Mask the voxels outside an elliptical region spanning the MRSI dataset in the x-y plane. — mask_xy_ellipse • Spectroscopy Analysis Tools (spant) Mask a 2D MRSI dataset in the x-y dimension. — mask_xy_mat • Spectroscopy Analysis Tools (spant) Mask a 2D MRSI dataset in the x-y dimension. — mask_xy_mat • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Value
diff --git a/docs/reference/mat2mrs_data.html b/docs/reference/mat2mrs_data.html
index 2e2895f3..ae55665f 100644
--- a/docs/reference/mat2mrs_data.html
+++ b/docs/reference/mat2mrs_data.html
@@ -1,7 +1,5 @@
-Convert a matrix (with spectral points in the column dimension and dynamics
-in the row dimensions) into a mrs_data object. — mat2mrs_data • Spectroscopy Analysis Tools (spant) Convert a matrix (with spectral points in the column dimension and dynamics in the row dimensions) into a mrs_data object. — mat2mrs_data • Spectroscopy Analysis Tools (spant) Matrix exponential function taken from complexplus package to reduce the
-number of spant dependencies. — matexp • Spectroscopy Analysis Tools (spant) Matrix exponential function taken from complexplus package to reduce the number of spant dependencies. — matexp • Spectroscopy Analysis Tools (spant) Apply the max operator to an MRS dataset. — max_mrs • Spectroscopy Analysis Tools (spant) Apply the max operator to an MRS dataset. — max_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/max_mrs_interp.html b/docs/reference/max_mrs_interp.html
index e4474764..52e63f3e 100644
--- a/docs/reference/max_mrs_interp.html
+++ b/docs/reference/max_mrs_interp.html
@@ -1,5 +1,5 @@
-Apply the max operator to an interpolated MRS dataset. — max_mrs_interp • Spectroscopy Analysis Tools (spant) Apply the max operator to an interpolated MRS dataset. — max_mrs_interp • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/mean.list.html b/docs/reference/mean.list.html
index b8eb3463..048306fd 100644
--- a/docs/reference/mean.list.html
+++ b/docs/reference/mean.list.html
@@ -1,5 +1,5 @@
-Calculate the mean spectrum from an mrs_data object. — mean.list • Spectroscopy Analysis Tools (spant) Calculate the mean spectrum from an mrs_data object. — mean.list • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/mean.mrs_data.html b/docs/reference/mean.mrs_data.html
index 5531a28d..79515014 100644
--- a/docs/reference/mean.mrs_data.html
+++ b/docs/reference/mean.mrs_data.html
@@ -1,5 +1,5 @@
-Calculate the mean spectrum from an mrs_data object. — mean.mrs_data • Spectroscopy Analysis Tools (spant) Calculate the mean spectrum from an mrs_data object. — mean.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/mean_dyn_blocks.html b/docs/reference/mean_dyn_blocks.html
index 10467098..4c042448 100644
--- a/docs/reference/mean_dyn_blocks.html
+++ b/docs/reference/mean_dyn_blocks.html
@@ -1,5 +1,5 @@
-Calculate the mean of adjacent dynamic scans. — mean_dyn_blocks • Spectroscopy Analysis Tools (spant) Calculate the mean of adjacent dynamic scans. — mean_dyn_blocks • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/mean_dyn_pairs.html b/docs/reference/mean_dyn_pairs.html
index 63e909ea..1a241126 100644
--- a/docs/reference/mean_dyn_pairs.html
+++ b/docs/reference/mean_dyn_pairs.html
@@ -1,5 +1,5 @@
-Calculate the pairwise means across a dynamic data set. — mean_dyn_pairs • Spectroscopy Analysis Tools (spant) Calculate the pairwise means across a dynamic data set. — mean_dyn_pairs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/mean_dyns.html b/docs/reference/mean_dyns.html
index 73fdbfa7..0daa27df 100644
--- a/docs/reference/mean_dyns.html
+++ b/docs/reference/mean_dyns.html
@@ -1,5 +1,5 @@
-Calculate the mean dynamic data. — mean_dyns • Spectroscopy Analysis Tools (spant) Calculate the mean dynamic data. — mean_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/mean_mrs_list.html b/docs/reference/mean_mrs_list.html
index 808b6c50..10d842c0 100644
--- a/docs/reference/mean_mrs_list.html
+++ b/docs/reference/mean_mrs_list.html
@@ -1,5 +1,5 @@
-Return the mean of a list of mrs_data objects. — mean_mrs_list • Spectroscopy Analysis Tools (spant) Return the mean of a list of mrs_data objects. — mean_mrs_list • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/mean_vec_blocks.html b/docs/reference/mean_vec_blocks.html
index 8fc92eaa..dd78b122 100644
--- a/docs/reference/mean_vec_blocks.html
+++ b/docs/reference/mean_vec_blocks.html
@@ -1,5 +1,5 @@
-Calculate the mean of adjacent blocks in a vector. — mean_vec_blocks • Spectroscopy Analysis Tools (spant) Calculate the mean of adjacent blocks in a vector. — mean_vec_blocks • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/median_dyns.html b/docs/reference/median_dyns.html
index 1039d4b5..9a085b10 100644
--- a/docs/reference/median_dyns.html
+++ b/docs/reference/median_dyns.html
@@ -1,5 +1,5 @@
-Calculate the median dynamic data. — median_dyns • Spectroscopy Analysis Tools (spant) Calculate the median dynamic data. — median_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/mod_td.html b/docs/reference/mod_td.html
index 76ad0a40..141ef09e 100644
--- a/docs/reference/mod_td.html
+++ b/docs/reference/mod_td.html
@@ -1,5 +1,5 @@
-Apply the Modulus operator to the time-domain MRS signal. — mod_td • Spectroscopy Analysis Tools (spant) Apply the Modulus operator to the time-domain MRS signal. — mod_td • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/mrs_data2basis.html b/docs/reference/mrs_data2basis.html
index 62f7d749..11797b91 100644
--- a/docs/reference/mrs_data2basis.html
+++ b/docs/reference/mrs_data2basis.html
@@ -1,7 +1,5 @@
-Convert an mrs_data object to basis object - where basis signals are spread
-across the dynamic dimension in the MRS data. — mrs_data2basis • Spectroscopy Analysis Tools (spant) Convert an mrs_data object to basis object - where basis signals are spread across the dynamic dimension in the MRS data. — mrs_data2basis • Spectroscopy Analysis Tools (spant) Create a BIDS file structure from a vector of MRS data paths or list of mrs_data objects. — mrs_data2bids • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Create a BIDS file structure from a vector of MRS data paths or list of mrs_data objects.
+ Source: R/fmrs.R
+ mrs_data2bids.Rd
+
+
+
+ Create a BIDS file structure from a vector of MRS data paths or list of
+mrs_data objects.
+
+
+
+ mrs_data2bids(
+ mrs_data,
+ output_dir,
+ suffix = NULL,
+ sub = NULL,
+ ses = NULL,
+ task = NULL,
+ acq = NULL,
+ nuc = NULL,
+ voi = NULL,
+ rec = NULL,
+ run = NULL,
+ echo = NULL,
+ inv = NULL,
+ skip_existing = TRUE
+)
+
+
+
+ Arguments
+ - mrs_data
+vector of MRS data paths or list of mrs_data objects.
- output_dir
+the base directory to create the BIDS structure.
- suffix
+optional vector of file suffixes. Default behaviour is to
+automatically determine these from the input data, however it is recommended
+that they are specified to allow more efficient skipping of existing data.
- sub
+optional vector of subject labels. If not specified, these will be
+automatically generated as a series of increasing zero-padded integer values
+corresponding to the mrs_data input indices.
- ses
+optional vector of session labels.
- task
+optional vector of task labels.
- acq
+optional vector of acquisition labels.
- nuc
+optional vector of nucleus labels.
- voi
+optional vector of volume of interest labels.
- rec
+optional vector of reconstruction labels.
- run
+optional vector of run indices.
- echo
+optional vector of echo time indices.
- inv
+optional vector of inversion indices.
- skip_existing
+skip any data files that have already been converted.
+Defaults to TRUE, set to FALSE to force an overwrite of any existing data
+files.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/mrs_data2mat.html b/docs/reference/mrs_data2mat.html
index cf5ff28c..9e47688a 100644
--- a/docs/reference/mrs_data2mat.html
+++ b/docs/reference/mrs_data2mat.html
@@ -1,7 +1,5 @@
-Convert mrs_data object to a matrix, with spectral points in the column
-dimension and dynamics in the row dimension. — mrs_data2mat • Spectroscopy Analysis Tools (spant) Convert mrs_data object to a matrix, with spectral points in the column dimension and dynamics in the row dimension. — mrs_data2mat • Spectroscopy Analysis Tools (spant) Convert mrs_data object to a matrix, with spectral points in the column dimension and dynamics in the row dimension. — mrs_data2spec_mat • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Convert mrs_data object to a matrix, with spectral points in the column dimension and dynamics in the row dimension.
+ Source: R/mrs_data_proc.R
+ mrs_data2spec_mat.Rd
+
+
+
+ Convert mrs_data object to a matrix, with spectral points in the column
+dimension and dynamics in the row dimension.
+
+
+
+ mrs_data2spec_mat(mrs_data, collapse = TRUE)
+
+
+
+ Arguments
+ - mrs_data
+MRS data object or list of MRS data objects.
- collapse
+collapse all other dimensions along the dynamic dimension, eg
+a 16x16 MRSI grid would be first collapsed across 256 dynamic scans.
+
+ Value
+
+
+MRS data matrix.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/mrs_data2vec.html b/docs/reference/mrs_data2vec.html
index fb172d68..a1fd654d 100644
--- a/docs/reference/mrs_data2vec.html
+++ b/docs/reference/mrs_data2vec.html
@@ -1,5 +1,5 @@
-Convert mrs_data object to a vector. — mrs_data2vec • Spectroscopy Analysis Tools (spant) Convert mrs_data object to a vector. — mrs_data2vec • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -126,7 +126,7 @@ Value
diff --git a/docs/reference/mvfftshift.html b/docs/reference/mvfftshift.html
index 92b0841b..976b3410 100644
--- a/docs/reference/mvfftshift.html
+++ b/docs/reference/mvfftshift.html
@@ -1,7 +1,5 @@
-Perform a fftshift on a matrix, with each column replaced by its shifted
-result. — mvfftshift • Spectroscopy Analysis Tools (spant) Perform a fftshift on a matrix, with each column replaced by its shifted result. — mvfftshift • Spectroscopy Analysis Tools (spant) Perform an ifftshift on a matrix, with each column replaced by its shifted
-result. — mvifftshift • Spectroscopy Analysis Tools (spant) Perform an ifftshift on a matrix, with each column replaced by its shifted result. — mvifftshift • Spectroscopy Analysis Tools (spant) Print fit coordinates from a single index. — n2coord • Spectroscopy Analysis Tools (spant) Print fit coordinates from a single index. — n2coord • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/nifti_flip_lr.html b/docs/reference/nifti_flip_lr.html
index 730abe3c..19860b3c 100644
--- a/docs/reference/nifti_flip_lr.html
+++ b/docs/reference/nifti_flip_lr.html
@@ -1,9 +1,5 @@
-Flip the x data dimension order of a nifti image. This corresponds to
-flipping MRI data in the left-right direction, assuming the data in save in
-neurological format (can check with fslorient program). — nifti_flip_lr • Spectroscopy Analysis Tools (spant) Flip the x data dimension order of a nifti image. This corresponds to flipping MRI data in the left-right direction, assuming the data in save in neurological format (can check with fslorient program). — nifti_flip_lr • Spectroscopy Analysis Tools (spant) Export a one-page pdf of a single fit result — one_page_pdf • Spectroscopy Analysis Tools (spant) Export a one-page pdf of a single fit result — one_page_pdf • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -108,7 +108,7 @@ Arguments
diff --git a/docs/reference/ortho3.html b/docs/reference/ortho3.html
index 13ade97d..5d7dd2fd 100644
--- a/docs/reference/ortho3.html
+++ b/docs/reference/ortho3.html
@@ -1,5 +1,5 @@
-Display an orthographic projection plot of a nifti object. — ortho3 • Spectroscopy Analysis Tools (spant) Display an orthographic projection plot of a nifti object. — ortho3 • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -172,7 +172,7 @@ Arguments
diff --git a/docs/reference/ortho3_inter.html b/docs/reference/ortho3_inter.html
index 090cc5e5..15948899 100644
--- a/docs/reference/ortho3_inter.html
+++ b/docs/reference/ortho3_inter.html
@@ -1,5 +1,5 @@
-Display an interactive orthographic projection plot of a nifti object. — ortho3_inter • Spectroscopy Analysis Tools (spant) Display an interactive orthographic projection plot of a nifti object. — ortho3_inter • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -132,7 +132,7 @@ Arguments
diff --git a/docs/reference/peak_info.html b/docs/reference/peak_info.html
index 09058bd8..41c8ffaf 100644
--- a/docs/reference/peak_info.html
+++ b/docs/reference/peak_info.html
@@ -1,7 +1,5 @@
-Search for the highest peak in a spectral region and return the frequency,
-height and FWHM. — peak_info • Spectroscopy Analysis Tools (spant) Search for the highest peak in a spectral region and return the frequency, height and FWHM. — peak_info • Spectroscopy Analysis Tools (spant) Papoulis-Gerchberg (PG) algorithm method for k-space extrapolation. — pg_extrap_xy • Spectroscopy Analysis Tools (spant) Papoulis-Gerchberg (PG) algorithm method for k-space extrapolation. — pg_extrap_xy • Spectroscopy Analysis Tools (spant) Apply phasing parameters to MRS data. — phase • Spectroscopy Analysis Tools (spant) Apply phasing parameters to MRS data. — phase • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/phase_ref_1h_brain.html b/docs/reference/phase_ref_1h_brain.html
new file mode 100644
index 00000000..8707a74a
--- /dev/null
+++ b/docs/reference/phase_ref_1h_brain.html
@@ -0,0 +1,131 @@
+
+Corrected zero order phase and chemical shift offset in 1H MRS data from the brain. — phase_ref_1h_brain • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Corrected zero order phase and chemical shift offset in 1H MRS data from the brain.
+ Source: R/rats.R
+ phase_ref_1h_brain.Rd
+
+
+
+ Corrected zero order phase and chemical shift offset in 1H MRS data from the
+brain.
+
+
+
+ phase_ref_1h_brain(mrs_data, mean_ref = FALSE, ret_corr_only = TRUE)
+
+
+
+ Arguments
+ - mrs_data
+MRS data to be corrected.
- mean_ref
+apply the phase and offset of the mean spectrum to all
+others. Default is FALSE.
- ret_corr_only
+return the corrected data only.
+
+ Value
+
+
+corrected MRS data.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/plot.fit_result.html b/docs/reference/plot.fit_result.html
index e54d3bc1..836a53ee 100644
--- a/docs/reference/plot.fit_result.html
+++ b/docs/reference/plot.fit_result.html
@@ -1,5 +1,5 @@
-Plot the fitting results of an object of class fit_result. — plot.fit_result • Spectroscopy Analysis Tools (spant) Plot the fitting results of an object of class fit_result. — plot.fit_result • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -207,7 +207,7 @@ Arguments
diff --git a/docs/reference/plot.mrs_data.html b/docs/reference/plot.mrs_data.html
index fabcc35b..bb2ec651 100644
--- a/docs/reference/plot.mrs_data.html
+++ b/docs/reference/plot.mrs_data.html
@@ -1,5 +1,5 @@
-Plotting method for objects of class mrs_data. — plot.mrs_data • Spectroscopy Analysis Tools (spant) Plotting method for objects of class mrs_data. — plot.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -287,7 +287,7 @@ Arguments
diff --git a/docs/reference/plot_bc.html b/docs/reference/plot_bc.html
index 4f8309b4..b48142cc 100644
--- a/docs/reference/plot_bc.html
+++ b/docs/reference/plot_bc.html
@@ -1,5 +1,5 @@
-Convenience function to plot a baseline estimate with the original data. — plot_bc • Spectroscopy Analysis Tools (spant) Convenience function to plot a baseline estimate with the original data. — plot_bc • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -108,7 +108,7 @@ Arguments
diff --git a/docs/reference/plot_reg.html b/docs/reference/plot_reg.html
index ae1acbe7..2addb2f6 100644
--- a/docs/reference/plot_reg.html
+++ b/docs/reference/plot_reg.html
@@ -1,5 +1,5 @@
-Plot regressors as an image. — plot_reg • Spectroscopy Analysis Tools (spant) Plot regressors as an image. — plot_reg • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/plot_slice_fit.html b/docs/reference/plot_slice_fit.html
index fbc7b560..57f1af8a 100644
--- a/docs/reference/plot_slice_fit.html
+++ b/docs/reference/plot_slice_fit.html
@@ -1,5 +1,5 @@
-Plot a 2D slice from an MRSI fit result object. — plot_slice_fit • Spectroscopy Analysis Tools (spant) Plot a 2D slice from an MRSI fit result object. — plot_slice_fit • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -129,7 +129,7 @@ Arguments
diff --git a/docs/reference/plot_slice_fit_inter.html b/docs/reference/plot_slice_fit_inter.html
index 4eed104a..da105a7d 100644
--- a/docs/reference/plot_slice_fit_inter.html
+++ b/docs/reference/plot_slice_fit_inter.html
@@ -1,5 +1,5 @@
-Plot a 2D slice from an MRSI fit result object. — plot_slice_fit_inter • Spectroscopy Analysis Tools (spant) Plot a 2D slice from an MRSI fit result object. — plot_slice_fit_inter • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -134,7 +134,7 @@ Arguments
diff --git a/docs/reference/plot_slice_map.html b/docs/reference/plot_slice_map.html
index 553e9ac8..ffb2a134 100644
--- a/docs/reference/plot_slice_map.html
+++ b/docs/reference/plot_slice_map.html
@@ -1,5 +1,5 @@
-Plot a slice from a 7 dimensional array. — plot_slice_map • Spectroscopy Analysis Tools (spant) Plot a slice from a 7 dimensional array. — plot_slice_map • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -153,7 +153,7 @@ Arguments
diff --git a/docs/reference/plot_slice_map_inter.html b/docs/reference/plot_slice_map_inter.html
index 40d33b42..90968f66 100644
--- a/docs/reference/plot_slice_map_inter.html
+++ b/docs/reference/plot_slice_map_inter.html
@@ -1,7 +1,5 @@
-Plot an interactive slice map from a data array where voxels can be selected
-to display a corresponding spectrum. — plot_slice_map_inter • Spectroscopy Analysis Tools (spant) Plot an interactive slice map from a data array where voxels can be selected to display a corresponding spectrum. — plot_slice_map_inter • Spectroscopy Analysis Tools (spant) Plot the spectral standard deviation. — plot_spec_sd • Spectroscopy Analysis Tools (spant) Plot the spectral standard deviation. — plot_spec_sd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Arguments
diff --git a/docs/reference/plot_voi_overlay.html b/docs/reference/plot_voi_overlay.html
index 9a782e88..bbbbf35e 100644
--- a/docs/reference/plot_voi_overlay.html
+++ b/docs/reference/plot_voi_overlay.html
@@ -1,5 +1,5 @@
-Plot a volume as an image overlay. — plot_voi_overlay • Spectroscopy Analysis Tools (spant) Plot a volume as an image overlay. — plot_voi_overlay • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -116,7 +116,7 @@ Arguments
diff --git a/docs/reference/plot_voi_overlay_seg.html b/docs/reference/plot_voi_overlay_seg.html
index 3d4e74ff..0e800ff2 100644
--- a/docs/reference/plot_voi_overlay_seg.html
+++ b/docs/reference/plot_voi_overlay_seg.html
@@ -1,5 +1,5 @@
-Plot a volume as an overlay on a segmented brain volume. — plot_voi_overlay_seg • Spectroscopy Analysis Tools (spant) Plot a volume as an overlay on a segmented brain volume. — plot_voi_overlay_seg • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Arguments
diff --git a/docs/reference/ppm.html b/docs/reference/ppm.html
index c352327a..ee4696e2 100644
--- a/docs/reference/ppm.html
+++ b/docs/reference/ppm.html
@@ -1,5 +1,5 @@
-Return the ppm scale of an MRS dataset or fit result. — ppm • Spectroscopy Analysis Tools (spant) Return the ppm scale of an MRS dataset or fit result. — ppm • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -132,7 +132,7 @@ Value
diff --git a/docs/reference/precomp.html b/docs/reference/precomp.html
index 822d7336..df3d2c6c 100644
--- a/docs/reference/precomp.html
+++ b/docs/reference/precomp.html
@@ -1,7 +1,5 @@
-Save function results to file and load on subsequent calls to avoid repeat
-computation. — precomp • Spectroscopy Analysis Tools (spant) Save function results to file and load on subsequent calls to avoid repeat computation. — precomp • Spectroscopy Analysis Tools (spant) Preprocess and perform quality assessment of a single SVS data set. — preproc_svs • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Preprocess and perform quality assessment of a single SVS data set.
+ Source: R/fmrs.R
+ preproc_svs.Rd
+
+
+
+ Preprocess and perform quality assessment of a single SVS data set.
+
+
+
+ preproc_svs(path, label = NULL, output_dir = NULL, ref_inds = NULL)
+
+
+
+ Arguments
+ - path
+path to the fMRS data file or IMA directory.
- label
+a label to describe the data set.
- output_dir
+output directory.
- ref_inds
+a vector of 1-based indices for any water reference dynamic
+scans.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/preproc_svs_dataset.html b/docs/reference/preproc_svs_dataset.html
new file mode 100644
index 00000000..07c3a29b
--- /dev/null
+++ b/docs/reference/preproc_svs_dataset.html
@@ -0,0 +1,148 @@
+
+Preprocess and perform quality assessment of one or more SVS data sets. — preproc_svs_dataset • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Preprocess and perform quality assessment of one or more SVS data sets.
+ Source: R/fmrs.R
+ preproc_svs_dataset.Rd
+
+
+
+ Preprocess and perform quality assessment of one or more SVS data sets.
+
+
+
+ preproc_svs_dataset(
+ paths,
+ labels = NULL,
+ output_dir = "spant_analysis",
+ exclude_labels = NULL,
+ overwrite = FALSE,
+ ref_inds = NULL,
+ return_results = FALSE
+)
+
+
+
+ Arguments
+ - paths
+paths to the fMRS data file or IMA directory.
- labels
+labels to describe each data set.
- output_dir
+output directory.
- exclude_labels
+vector of labels of scans to exclude, eg poor quality
+data.
- overwrite
+overwrite saved results, defaults to FALSE.
- ref_inds
+a vector of 1-based indices for any water reference dynamic
+scans.
- return_results
+function will return key outputs, defaults to FALSE.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/print.fit_result.html b/docs/reference/print.fit_result.html
index 297f28dc..5f434e57 100644
--- a/docs/reference/print.fit_result.html
+++ b/docs/reference/print.fit_result.html
@@ -1,5 +1,5 @@
-Print a summary of an object of class fit_result. — print.fit_result • Spectroscopy Analysis Tools (spant) Print a summary of an object of class fit_result. — print.fit_result • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -105,7 +105,7 @@ Arguments
diff --git a/docs/reference/print.mrs_data.html b/docs/reference/print.mrs_data.html
index 51199017..e1561eb2 100644
--- a/docs/reference/print.mrs_data.html
+++ b/docs/reference/print.mrs_data.html
@@ -1,5 +1,5 @@
-Print a summary of mrs_data parameters. — print.mrs_data • Spectroscopy Analysis Tools (spant) Print a summary of mrs_data parameters. — print.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -109,7 +109,7 @@ Arguments
diff --git a/docs/reference/qn_states.html b/docs/reference/qn_states.html
index 0f42f2f9..d7aa6715 100644
--- a/docs/reference/qn_states.html
+++ b/docs/reference/qn_states.html
@@ -1,5 +1,5 @@
-Get the quantum coherence matrix for a spin system. — qn_states • Spectroscopy Analysis Tools (spant) Get the quantum coherence matrix for a spin system. — qn_states • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/rats.html b/docs/reference/rats.html
index 5a39a396..93585e08 100644
--- a/docs/reference/rats.html
+++ b/docs/reference/rats.html
@@ -1,5 +1,5 @@
-Robust Alignment to a Target Spectrum (RATS). — rats • Spectroscopy Analysis Tools (spant) Robust Alignment to a Target Spectrum (RATS). — rats • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -207,7 +207,7 @@ Value
diff --git a/docs/reference/re_weighting.html b/docs/reference/re_weighting.html
index d21caf21..8b0b070a 100644
--- a/docs/reference/re_weighting.html
+++ b/docs/reference/re_weighting.html
@@ -1,5 +1,5 @@
-Apply a weighting to the FID to enhance spectral resolution. — re_weighting • Spectroscopy Analysis Tools (spant) Apply a weighting to the FID to enhance spectral resolution. — re_weighting • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/read_basis.html b/docs/reference/read_basis.html
index da9b94af..eb6f8557 100644
--- a/docs/reference/read_basis.html
+++ b/docs/reference/read_basis.html
@@ -1,5 +1,5 @@
-Read a basis file in LCModel .basis format. — read_basis • Spectroscopy Analysis Tools (spant) Read a basis file in LCModel .basis format. — read_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/read_ima_coil_dir.html b/docs/reference/read_ima_coil_dir.html
index 28c02de0..4f073cd8 100644
--- a/docs/reference/read_ima_coil_dir.html
+++ b/docs/reference/read_ima_coil_dir.html
@@ -1,9 +1,5 @@
-Read a directory containing Siemens MRS IMA files and combine along the coil
-dimension. Note that the coil ID is inferred from the sorted file name and
-should be checked when consistency is required between two directories. — read_ima_coil_dir • Spectroscopy Analysis Tools (spant) Read a directory containing Siemens MRS IMA files and combine along the coil dimension. Note that the coil ID is inferred from the sorted file name and should be checked when consistency is required between two directories. — read_ima_coil_dir • Spectroscopy Analysis Tools (spant) Read a directory containing Siemens MRS IMA files and combine along the
-dynamic dimension. Note that the coil ID is inferred from the sorted file
-name and should be checked when consistency is required. — read_ima_dyn_dir • Spectroscopy Analysis Tools (spant) Read a directory containing Siemens MRS IMA files and combine along the dynamic dimension. Note that the coil ID is inferred from the sorted file name and should be checked when consistency is required. — read_ima_dyn_dir • Spectroscopy Analysis Tools (spant) Read an LCModel formatted coord file containing fit information. — read_lcm_coord • Spectroscopy Analysis Tools (spant) Read an LCModel formatted coord file containing fit information. — read_lcm_coord • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -107,7 +107,7 @@ Value
diff --git a/docs/reference/read_mrs.html b/docs/reference/read_mrs.html
index 3ac2a36b..2cf36b20 100644
--- a/docs/reference/read_mrs.html
+++ b/docs/reference/read_mrs.html
@@ -1,5 +1,5 @@
-Read MRS data from a file. — read_mrs • Spectroscopy Analysis Tools (spant) Read MRS data from a file. — read_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -88,7 +88,8 @@ Read MRS data from a file.
full_fid = FALSE,
omit_svs_ref_scans = TRUE,
verbose = FALSE,
- extra = NULL
+ extra = NULL,
+ fid_filt_dist = NULL
)
@@ -140,6 +141,13 @@ Arguments
an optional data frame to provide additional variables for use
in subsequent analysis steps, eg id or grouping variables.
fid_filt_dist
+indicate if the data has a distorted FID due to a
+brick-wall filter being used to downsample the data. Default is to auto
+detect this from the data, but TRUE or FALSE options can be given to override
+detection.
Value
@@ -183,7 +191,7 @@ Examples
diff --git a/docs/reference/read_mrs_tqn.html b/docs/reference/read_mrs_tqn.html
index 5766362f..84bdaf3a 100644
--- a/docs/reference/read_mrs_tqn.html
+++ b/docs/reference/read_mrs_tqn.html
@@ -1,5 +1,5 @@
-Read MRS data using the TARQUIN software package. — read_mrs_tqn • Spectroscopy Analysis Tools (spant) Read MRS data using the TARQUIN software package. — read_mrs_tqn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -131,7 +131,7 @@ Examples
diff --git a/docs/reference/read_pulse_ascii.html b/docs/reference/read_pulse_ascii.html
index c9e0d43c..ab11c9cc 100644
--- a/docs/reference/read_pulse_ascii.html
+++ b/docs/reference/read_pulse_ascii.html
@@ -1,5 +1,5 @@
-Read an ASCII formatted pulse file. — read_pulse_ascii • Spectroscopy Analysis Tools (spant) Read an ASCII formatted pulse file. — read_pulse_ascii • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/read_pulse_bruker.html b/docs/reference/read_pulse_bruker.html
index c92bf76a..dbe9073b 100644
--- a/docs/reference/read_pulse_bruker.html
+++ b/docs/reference/read_pulse_bruker.html
@@ -1,5 +1,5 @@
-Read a Bruker formatted pulse file — read_pulse_bruker • Spectroscopy Analysis Tools (spant) Read a Bruker formatted pulse file — read_pulse_bruker • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/read_pulse_pta.html b/docs/reference/read_pulse_pta.html
index 72e1b6d4..a0fac3c3 100644
--- a/docs/reference/read_pulse_pta.html
+++ b/docs/reference/read_pulse_pta.html
@@ -1,5 +1,5 @@
-Read a .pta formatted pulse file compatible with Siemens PulseTool. — read_pulse_pta • Spectroscopy Analysis Tools (spant) Read a .pta formatted pulse file compatible with Siemens PulseTool. — read_pulse_pta • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/read_siemens_txt_hdr.html b/docs/reference/read_siemens_txt_hdr.html
index 23fb8c70..3a17d87c 100644
--- a/docs/reference/read_siemens_txt_hdr.html
+++ b/docs/reference/read_siemens_txt_hdr.html
@@ -1,5 +1,5 @@
-Read the text format header found in Siemens IMA and TWIX data files. — read_siemens_txt_hdr • Spectroscopy Analysis Tools (spant) Read the text format header found in Siemens IMA and TWIX data files. — read_siemens_txt_hdr • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -78,7 +78,7 @@ Read the text format header found in Siemens IMA and TWIX data files.
- read_siemens_txt_hdr(input, version = "vd", verbose, offset = 0)
+ read_siemens_txt_hdr(input, version = "vd", verbose = FALSE, offset = 0)
@@ -118,7 +118,7 @@ Value
diff --git a/docs/reference/read_tqn_fit.html b/docs/reference/read_tqn_fit.html
index 4da6c25e..a1630420 100644
--- a/docs/reference/read_tqn_fit.html
+++ b/docs/reference/read_tqn_fit.html
@@ -1,5 +1,5 @@
-Reader for csv fit results generated by TARQUIN. — read_tqn_fit • Spectroscopy Analysis Tools (spant) Reader for csv fit results generated by TARQUIN. — read_tqn_fit • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -113,7 +113,7 @@ Examples
diff --git a/docs/reference/read_tqn_result.html b/docs/reference/read_tqn_result.html
index 36659714..68a3e98c 100644
--- a/docs/reference/read_tqn_result.html
+++ b/docs/reference/read_tqn_result.html
@@ -1,5 +1,5 @@
-Reader for csv results generated by TARQUIN. — read_tqn_result • Spectroscopy Analysis Tools (spant) Reader for csv results generated by TARQUIN. — read_tqn_result • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -117,7 +117,7 @@ Examples
diff --git a/docs/reference/recon_imag.html b/docs/reference/recon_imag.html
index d2a72225..5bc3b1eb 100644
--- a/docs/reference/recon_imag.html
+++ b/docs/reference/recon_imag.html
@@ -1,7 +1,5 @@
-Reconstruct complex time-domain data from the real part of frequency-domain
-data. — recon_imag • Spectroscopy Analysis Tools (spant) Reconstruct complex time-domain data from the real part of frequency-domain data. — recon_imag • Spectroscopy Analysis Tools (spant) Reconstruct complex time-domain data from the real part of frequency-domain
-data. — recon_imag_vec • Spectroscopy Analysis Tools (spant) Reconstruct complex time-domain data from the real part of frequency-domain data. — recon_imag_vec • Spectroscopy Analysis Tools (spant) Reconstruct 2D MRSI data from a twix file loaded with read_mrs. — recon_twix_2d_mrsi • Spectroscopy Analysis Tools (spant) Reconstruct 2D MRSI data from a twix file loaded with read_mrs. — recon_twix_2d_mrsi • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/rectangular_mask.html b/docs/reference/rectangular_mask.html
index a2117283..6e469bc9 100644
--- a/docs/reference/rectangular_mask.html
+++ b/docs/reference/rectangular_mask.html
@@ -1,5 +1,5 @@
-Create a rectangular mask stored as a matrix of logical values. — rectangular_mask • Spectroscopy Analysis Tools (spant) Create a rectangular mask stored as a matrix of logical values. — rectangular_mask • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -130,7 +130,7 @@ Value
diff --git a/docs/reference/reexports.html b/docs/reference/reexports.html
index 694a75d1..a59e8379 100644
--- a/docs/reference/reexports.html
+++ b/docs/reference/reexports.html
@@ -1,5 +1,5 @@
-Objects exported from other packages — reexports • Spectroscopy Analysis Tools (spant) Objects exported from other packages — reexports • Spectroscopy Analysis Tools (spant)
Spectroscopy Analysis Tools (spant)
- 2.21.0
+ 2.22.0
@@ -103,7 +103,7 @@ Objects exported from other packages
diff --git a/docs/reference/rep_array_dim.html b/docs/reference/rep_array_dim.html
index b9c49b4a..48c0a5ed 100644
--- a/docs/reference/rep_array_dim.html
+++ b/docs/reference/rep_array_dim.html
@@ -1,5 +1,5 @@
-Repeat an array over a given dimension. — rep_array_dim • Spectroscopy Analysis Tools (spant) Repeat an array over a given dimension. — rep_array_dim • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/rep_dyn.html b/docs/reference/rep_dyn.html
index 6bbfb0ef..89a4bb9b 100644
--- a/docs/reference/rep_dyn.html
+++ b/docs/reference/rep_dyn.html
@@ -1,5 +1,5 @@
-Replicate a scan in the dynamic dimension. — rep_dyn • Spectroscopy Analysis Tools (spant) Replicate a scan in the dynamic dimension. — rep_dyn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/rep_mrs.html b/docs/reference/rep_mrs.html
index 67730b5c..becb8f00 100644
--- a/docs/reference/rep_mrs.html
+++ b/docs/reference/rep_mrs.html
@@ -1,5 +1,5 @@
-Replicate a scan over a given dimension. — rep_mrs • Spectroscopy Analysis Tools (spant) Replicate a scan over a given dimension. — rep_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -138,7 +138,7 @@ Value
diff --git a/docs/reference/resample_basis.html b/docs/reference/resample_basis.html
index b0f2ab17..c7a6222a 100644
--- a/docs/reference/resample_basis.html
+++ b/docs/reference/resample_basis.html
@@ -1,5 +1,5 @@
-Resample a basis-set to match a mrs_data acquisition. — resample_basis • Spectroscopy Analysis Tools (spant) Resample a basis-set to match a mrs_data acquisition. — resample_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -116,7 +116,7 @@ Value
diff --git a/docs/reference/resample_img.html b/docs/reference/resample_img.html
index f1e7beaf..b0cc8f71 100644
--- a/docs/reference/resample_img.html
+++ b/docs/reference/resample_img.html
@@ -1,5 +1,5 @@
-Resample an image to match a target image space. — resample_img • Spectroscopy Analysis Tools (spant) Resample an image to match a target image space. — resample_img • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/resample_voi.html b/docs/reference/resample_voi.html
index 8fbfa836..a29ab096 100644
--- a/docs/reference/resample_voi.html
+++ b/docs/reference/resample_voi.html
@@ -1,7 +1,5 @@
-Resample a VOI to match a target image space using nearest-neighbour
-interpolation. — resample_voi • Spectroscopy Analysis Tools (spant) Resample a VOI to match a target image space using nearest-neighbour interpolation. — resample_voi • Spectroscopy Analysis Tools (spant) Reslice a nifti object to match the orientation of mrs data. — reslice_to_mrs • Spectroscopy Analysis Tools (spant) Reslice a nifti object to match the orientation of mrs data. — reslice_to_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/reson_table2mrs_data.html b/docs/reference/reson_table2mrs_data.html
index d75579ee..c5a2167a 100644
--- a/docs/reference/reson_table2mrs_data.html
+++ b/docs/reference/reson_table2mrs_data.html
@@ -1,5 +1,5 @@
-Generate mrs_data from a table of single Lorentzian resonances. — reson_table2mrs_data • Spectroscopy Analysis Tools (spant) Generate mrs_data from a table of single Lorentzian resonances. — reson_table2mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -119,7 +119,7 @@ Value
diff --git a/docs/reference/rm_dyns.html b/docs/reference/rm_dyns.html
index 5d5ef692..573e1f51 100644
--- a/docs/reference/rm_dyns.html
+++ b/docs/reference/rm_dyns.html
@@ -1,5 +1,5 @@
-Remove a subset of dynamic scans. — rm_dyns • Spectroscopy Analysis Tools (spant) Remove a subset of dynamic scans. — rm_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/scale_amp_molal.html b/docs/reference/scale_amp_molal.html
index aaeee1f2..7acb8cb0 100644
--- a/docs/reference/scale_amp_molal.html
+++ b/docs/reference/scale_amp_molal.html
@@ -1,7 +1,5 @@
-Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water). — scale_amp_molal • Spectroscopy Analysis Tools (spant) Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / kg of tissue water). — scale_amp_molal • Spectroscopy Analysis Tools (spant)
Spectroscopy Analysis Tools (spant)
- 2.21.0
+ 2.22.0
@@ -76,8 +74,7 @@
- Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water).
+ Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / kg of tissue water).
Source: R/amp_scaling.R
scale_amp_molal.Rd
@@ -163,7 +160,7 @@ Value
diff --git a/docs/reference/scale_amp_molal_pvc.html b/docs/reference/scale_amp_molal_pvc.html
index 962d6afc..4d194abd 100644
--- a/docs/reference/scale_amp_molal_pvc.html
+++ b/docs/reference/scale_amp_molal_pvc.html
@@ -1,7 +1,5 @@
-Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water). — scale_amp_molal_pvc • Spectroscopy Analysis Tools (spant)
@@ -75,8 +73,7 @@
- Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water).
+ Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / kg of tissue water).
Source: R/amp_scaling.R
scale_amp_molal_pvc.Rd
@@ -141,7 +138,7 @@ Value
diff --git a/docs/reference/scale_amp_molar.html b/docs/reference/scale_amp_molar.html
index 02358d91..dc87a338 100644
--- a/docs/reference/scale_amp_molar.html
+++ b/docs/reference/scale_amp_molar.html
@@ -1,7 +1,5 @@
-Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / Litre of tissue). — scale_amp_molar • Spectroscopy Analysis Tools (spant) Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / Litre of tissue). — scale_amp_molar • Spectroscopy Analysis Tools (spant) Convert default LCM/TARQUIN concentration scaling to molal units with partial
-volume correction. — scale_amp_molar2molal_pvc • Spectroscopy Analysis Tools (spant) Convert default LCM/TARQUIN concentration scaling to molal units with partial volume correction. — scale_amp_molar2molal_pvc • Spectroscopy Analysis Tools (spant) Scale fitted amplitudes to a ratio of signal amplitude. — scale_amp_ratio • Spectroscopy Analysis Tools (spant) Scale fitted amplitudes to a ratio of signal amplitude. — scale_amp_ratio • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -116,7 +116,7 @@ Value
diff --git a/docs/reference/scale_amp_ratio_value.html b/docs/reference/scale_amp_ratio_value.html
index 2036837a..6af8ac51 100644
--- a/docs/reference/scale_amp_ratio_value.html
+++ b/docs/reference/scale_amp_ratio_value.html
@@ -1,5 +1,5 @@
-Scale fitted amplitudes to a ratio of signal amplitude. — scale_amp_ratio_value • Spectroscopy Analysis Tools (spant) Scale fitted amplitudes to a ratio of signal amplitude. — scale_amp_ratio_value • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/scale_amp_water_ratio.html b/docs/reference/scale_amp_water_ratio.html
index 5b25e884..35a76b00 100644
--- a/docs/reference/scale_amp_water_ratio.html
+++ b/docs/reference/scale_amp_water_ratio.html
@@ -1,5 +1,5 @@
-Scale metabolite amplitudes as a ratio to the unsuppressed water amplitude. — scale_amp_water_ratio • Spectroscopy Analysis Tools (spant) Scale metabolite amplitudes as a ratio to the unsuppressed water amplitude. — scale_amp_water_ratio • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/scale_basis_amp.html b/docs/reference/scale_basis_amp.html
index 9401c3f1..5a58b5e5 100644
--- a/docs/reference/scale_basis_amp.html
+++ b/docs/reference/scale_basis_amp.html
@@ -1,5 +1,5 @@
-Scale a basis object by a scalar. — scale_basis_amp • Spectroscopy Analysis Tools (spant) Scale a basis object by a scalar. — scale_basis_amp • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/scale_basis_from_singlet.html b/docs/reference/scale_basis_from_singlet.html
index 0d542bc8..c9a19e77 100644
--- a/docs/reference/scale_basis_from_singlet.html
+++ b/docs/reference/scale_basis_from_singlet.html
@@ -1,5 +1,5 @@
-Scale a basis-set to be consistent with spant assumptions for water scaling. — scale_basis_from_singlet • Spectroscopy Analysis Tools (spant) Scale a basis-set to be consistent with spant assumptions for water scaling. — scale_basis_from_singlet • Spectroscopy Analysis Tools (spant)
Spectroscopy Analysis Tools (spant)
- 2.21.0
+ 2.22.0
@@ -127,7 +127,7 @@ Value
diff --git a/docs/reference/scale_mrs_amp.html b/docs/reference/scale_mrs_amp.html
index b5501a0d..990f058a 100644
--- a/docs/reference/scale_mrs_amp.html
+++ b/docs/reference/scale_mrs_amp.html
@@ -1,5 +1,5 @@
-Scale an mrs_data object by a scalar or vector or amplitudes. — scale_mrs_amp • Spectroscopy Analysis Tools (spant) Scale an mrs_data object by a scalar or vector or amplitudes. — scale_mrs_amp • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/scale_spec.html b/docs/reference/scale_spec.html
index 4f6ea835..6b3ddba4 100644
--- a/docs/reference/scale_spec.html
+++ b/docs/reference/scale_spec.html
@@ -1,5 +1,5 @@
-Scale mrs_data to a spectral region. — scale_spec • Spectroscopy Analysis Tools (spant) Scale mrs_data to a spectral region. — scale_spec • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -141,7 +141,7 @@ Value
diff --git a/docs/reference/sd.html b/docs/reference/sd.html
index ea1eec9f..3ae4dfd4 100644
--- a/docs/reference/sd.html
+++ b/docs/reference/sd.html
@@ -1,5 +1,5 @@
-Calculate the standard deviation spectrum from an mrs_data object. — sd • Spectroscopy Analysis Tools (spant) Calculate the standard deviation spectrum from an mrs_data object. — sd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/sd.mrs_data.html b/docs/reference/sd.mrs_data.html
index 3f92a49f..13bdda85 100644
--- a/docs/reference/sd.mrs_data.html
+++ b/docs/reference/sd.mrs_data.html
@@ -1,5 +1,5 @@
-Calculate the standard deviation spectrum from an mrs_data object. — sd.mrs_data • Spectroscopy Analysis Tools (spant) Calculate the standard deviation spectrum from an mrs_data object. — sd.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/seconds.html b/docs/reference/seconds.html
index b34d6627..467ee17f 100644
--- a/docs/reference/seconds.html
+++ b/docs/reference/seconds.html
@@ -1,5 +1,5 @@
-Return a time scale vector to match the FID of an MRS data object. — seconds • Spectroscopy Analysis Tools (spant) Return a time scale vector to match the FID of an MRS data object. — seconds • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/seq_cpmg_ideal.html b/docs/reference/seq_cpmg_ideal.html
index 547e96ab..45727c86 100644
--- a/docs/reference/seq_cpmg_ideal.html
+++ b/docs/reference/seq_cpmg_ideal.html
@@ -1,5 +1,5 @@
-CPMG style sequence with ideal pulses. — seq_cpmg_ideal • Spectroscopy Analysis Tools (spant) CPMG style sequence with ideal pulses. — seq_cpmg_ideal • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/seq_mega_press_ideal.html b/docs/reference/seq_mega_press_ideal.html
index 0769b8b4..a9cd7fa0 100644
--- a/docs/reference/seq_mega_press_ideal.html
+++ b/docs/reference/seq_mega_press_ideal.html
@@ -1,7 +1,5 @@
-MEGA-PRESS sequence with ideal localisation pulses and Gaussian shaped
-editing pulse. — seq_mega_press_ideal • Spectroscopy Analysis Tools (spant) MEGA-PRESS sequence with ideal localisation pulses and Gaussian shaped editing pulse. — seq_mega_press_ideal • Spectroscopy Analysis Tools (spant) PRESS sequence with shaped refocusing pulses. — seq_press_2d_shaped • Spectroscopy Analysis Tools (spant) PRESS sequence with shaped refocusing pulses. — seq_press_2d_shaped • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -165,7 +165,7 @@ Value
diff --git a/docs/reference/seq_press_ideal.html b/docs/reference/seq_press_ideal.html
index 8c976856..72c3af3d 100644
--- a/docs/reference/seq_press_ideal.html
+++ b/docs/reference/seq_press_ideal.html
@@ -1,5 +1,5 @@
-PRESS sequence with ideal pulses. — seq_press_ideal • Spectroscopy Analysis Tools (spant) PRESS sequence with ideal pulses. — seq_press_ideal • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/seq_pulse_acquire.html b/docs/reference/seq_pulse_acquire.html
index 4a88fc64..ad80571e 100644
--- a/docs/reference/seq_pulse_acquire.html
+++ b/docs/reference/seq_pulse_acquire.html
@@ -1,5 +1,5 @@
-Simple pulse and acquire sequence with ideal pulses. — seq_pulse_acquire • Spectroscopy Analysis Tools (spant) Simple pulse and acquire sequence with ideal pulses. — seq_pulse_acquire • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/seq_slaser_ideal.html b/docs/reference/seq_slaser_ideal.html
index 74688f4d..eb83e8e3 100644
--- a/docs/reference/seq_slaser_ideal.html
+++ b/docs/reference/seq_slaser_ideal.html
@@ -1,5 +1,5 @@
-sLASER sequence with ideal pulses. — seq_slaser_ideal • Spectroscopy Analysis Tools (spant) sLASER sequence with ideal pulses. — seq_slaser_ideal • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -126,7 +126,7 @@ Value
diff --git a/docs/reference/seq_spin_echo_ideal.html b/docs/reference/seq_spin_echo_ideal.html
index e23271de..4248716f 100644
--- a/docs/reference/seq_spin_echo_ideal.html
+++ b/docs/reference/seq_spin_echo_ideal.html
@@ -1,5 +1,5 @@
-Spin echo sequence with ideal pulses. — seq_spin_echo_ideal • Spectroscopy Analysis Tools (spant) Spin echo sequence with ideal pulses. — seq_spin_echo_ideal • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/seq_steam_ideal.html b/docs/reference/seq_steam_ideal.html
index a60685a8..1c8115d7 100644
--- a/docs/reference/seq_steam_ideal.html
+++ b/docs/reference/seq_steam_ideal.html
@@ -1,5 +1,5 @@
-STEAM sequence with ideal pulses. — seq_steam_ideal • Spectroscopy Analysis Tools (spant) STEAM sequence with ideal pulses. — seq_steam_ideal • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -128,7 +128,7 @@ Value
diff --git a/docs/reference/seq_steam_ideal_cof.html b/docs/reference/seq_steam_ideal_cof.html
index 8f225740..cba7af91 100644
--- a/docs/reference/seq_steam_ideal_cof.html
+++ b/docs/reference/seq_steam_ideal_cof.html
@@ -1,7 +1,5 @@
-STEAM sequence with ideal pulses and coherence order filtering to simulate
-gradient crushers. — seq_steam_ideal_cof • Spectroscopy Analysis Tools (spant) STEAM sequence with ideal pulses and coherence order filtering to simulate gradient crushers. — seq_steam_ideal_cof • Spectroscopy Analysis Tools (spant) STEAM sequence with ideal pulses using the z-rotation gradient simulation
-method described by Young et al JMR 140, 146-152 (1999). — seq_steam_ideal_young • Spectroscopy Analysis Tools (spant) STEAM sequence with ideal pulses using the z-rotation gradient simulation method described by Young et al JMR 140, 146-152 (1999). — seq_steam_ideal_young • Spectroscopy Analysis Tools (spant) Set the number of transients for an mrs_data object. — set_Ntrans • Spectroscopy Analysis Tools (spant) Set the number of transients for an mrs_data object. — set_Ntrans • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/set_def_acq_paras.html b/docs/reference/set_def_acq_paras.html
index 3e1b4004..cc2ada9c 100644
--- a/docs/reference/set_def_acq_paras.html
+++ b/docs/reference/set_def_acq_paras.html
@@ -1,5 +1,5 @@
-Set the default acquisition parameters. — set_def_acq_paras • Spectroscopy Analysis Tools (spant) Set the default acquisition parameters. — set_def_acq_paras • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Arguments
diff --git a/docs/reference/set_lcm_cmd.html b/docs/reference/set_lcm_cmd.html
index 2056ed01..42bb2f24 100644
--- a/docs/reference/set_lcm_cmd.html
+++ b/docs/reference/set_lcm_cmd.html
@@ -1,5 +1,5 @@
-Set the command to run the LCModel command-line program. — set_lcm_cmd • Spectroscopy Analysis Tools (spant) Set the command to run the LCModel command-line program. — set_lcm_cmd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/set_lw.html b/docs/reference/set_lw.html
index b64ec851..bb176c62 100644
--- a/docs/reference/set_lw.html
+++ b/docs/reference/set_lw.html
@@ -1,5 +1,5 @@
-Apply line-broadening to an mrs_data object to achieve a specified linewidth. — set_lw • Spectroscopy Analysis Tools (spant) Apply line-broadening to an mrs_data object to achieve a specified linewidth. — set_lw • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -123,7 +123,7 @@ Value
diff --git a/docs/reference/set_mask_xy_mat.html b/docs/reference/set_mask_xy_mat.html
index 49dc5d4e..52c4b617 100644
--- a/docs/reference/set_mask_xy_mat.html
+++ b/docs/reference/set_mask_xy_mat.html
@@ -1,5 +1,5 @@
-Set the masked voxels in a 2D MRSI dataset to given spectrum. — set_mask_xy_mat • Spectroscopy Analysis Tools (spant) Set the masked voxels in a 2D MRSI dataset to given spectrum. — set_mask_xy_mat • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Value
diff --git a/docs/reference/set_precomp_mode.html b/docs/reference/set_precomp_mode.html
index f44bd5d3..47c28e3b 100644
--- a/docs/reference/set_precomp_mode.html
+++ b/docs/reference/set_precomp_mode.html
@@ -1,5 +1,5 @@
-Set the precompute mode. — set_precomp_mode • Spectroscopy Analysis Tools (spant) Set the precompute mode. — set_precomp_mode • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/set_precomp_verbose.html b/docs/reference/set_precomp_verbose.html
index 1453a231..9c613505 100644
--- a/docs/reference/set_precomp_verbose.html
+++ b/docs/reference/set_precomp_verbose.html
@@ -1,5 +1,5 @@
-Set the verbosity of the precompute function. — set_precomp_verbose • Spectroscopy Analysis Tools (spant) Set the verbosity of the precompute function. — set_precomp_verbose • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/set_ref.html b/docs/reference/set_ref.html
index 8953fa50..5436dfa2 100644
--- a/docs/reference/set_ref.html
+++ b/docs/reference/set_ref.html
@@ -1,5 +1,5 @@
-Set the ppm reference value (eg ppm value at 0Hz). — set_ref • Spectroscopy Analysis Tools (spant) Set the ppm reference value (eg ppm value at 0Hz). — set_ref • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/set_td_pts.html b/docs/reference/set_td_pts.html
index 8a80d42a..586459ff 100644
--- a/docs/reference/set_td_pts.html
+++ b/docs/reference/set_td_pts.html
@@ -1,7 +1,5 @@
-Set the number of time-domain data points, truncating or zero-filling as
-appropriate. — set_td_pts • Spectroscopy Analysis Tools (spant) Set the number of time-domain data points, truncating or zero-filling as appropriate. — set_td_pts • Spectroscopy Analysis Tools (spant) Set the command to run the TARQUIN command-line program. — set_tqn_cmd • Spectroscopy Analysis Tools (spant) Set the command to run the TARQUIN command-line program. — set_tqn_cmd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/set_tr.html b/docs/reference/set_tr.html
index b2109ab0..65c9df5f 100644
--- a/docs/reference/set_tr.html
+++ b/docs/reference/set_tr.html
@@ -1,5 +1,5 @@
-Set the repetition time of an MRS dataset. — set_tr • Spectroscopy Analysis Tools (spant) Set the repetition time of an MRS dataset. — set_tr • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/shift.html b/docs/reference/shift.html
index ab0fe724..034591d0 100644
--- a/docs/reference/shift.html
+++ b/docs/reference/shift.html
@@ -1,5 +1,5 @@
-Apply a frequency shift to MRS data. — shift • Spectroscopy Analysis Tools (spant) Apply a frequency shift to MRS data. — shift • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/shift_basis.html b/docs/reference/shift_basis.html
index 2884be19..f55a65e0 100644
--- a/docs/reference/shift_basis.html
+++ b/docs/reference/shift_basis.html
@@ -1,5 +1,5 @@
-Apply frequency shifts to basis set signals. — shift_basis • Spectroscopy Analysis Tools (spant) Apply frequency shifts to basis set signals. — shift_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Value
diff --git a/docs/reference/sim_basis.html b/docs/reference/sim_basis.html
index c7838c46..bb5fefc6 100644
--- a/docs/reference/sim_basis.html
+++ b/docs/reference/sim_basis.html
@@ -1,5 +1,5 @@
-Simulate a basis set object. — sim_basis • Spectroscopy Analysis Tools (spant) Simulate a basis set object. — sim_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -136,7 +136,7 @@ Value
diff --git a/docs/reference/sim_basis_1h_brain.html b/docs/reference/sim_basis_1h_brain.html
index 62ed7389..f71ffa0b 100644
--- a/docs/reference/sim_basis_1h_brain.html
+++ b/docs/reference/sim_basis_1h_brain.html
@@ -1,7 +1,5 @@
-Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS
-sequence. Note, ideal pulses are assumed. — sim_basis_1h_brain • Spectroscopy Analysis Tools (spant) Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS sequence. Note, ideal pulses are assumed. — sim_basis_1h_brain • Spectroscopy Analysis Tools (spant) Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS
-sequence. Note, ideal pulses are assumed. — sim_basis_1h_brain_press • Spectroscopy Analysis Tools (spant) Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS sequence. Note, ideal pulses are assumed. — sim_basis_1h_brain_press • Spectroscopy Analysis Tools (spant) Simulate a macromolecular and lipid basis-set suitable for 1H brain MRS
-analysis. — sim_basis_mm_lip_lcm • Spectroscopy Analysis Tools (spant) Simulate a macromolecular and lipid basis-set suitable for 1H brain MRS analysis. — sim_basis_mm_lip_lcm • Spectroscopy Analysis Tools (spant) Simulate a basis file using TARQUIN. — sim_basis_tqn • Spectroscopy Analysis Tools (spant) Simulate a basis file using TARQUIN. — sim_basis_tqn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -129,7 +129,7 @@ Examples
diff --git a/docs/reference/sim_brain_1h.html b/docs/reference/sim_brain_1h.html
index 2044cf1a..717ee289 100644
--- a/docs/reference/sim_brain_1h.html
+++ b/docs/reference/sim_brain_1h.html
@@ -1,5 +1,5 @@
-Simulate MRS data with a similar appearance to normal brain (by default). — sim_brain_1h • Spectroscopy Analysis Tools (spant) Simulate MRS data with a similar appearance to normal brain (by default). — sim_brain_1h • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -159,7 +159,7 @@ Value
diff --git a/docs/reference/sim_mol.html b/docs/reference/sim_mol.html
index 23bcef50..77f76a50 100644
--- a/docs/reference/sim_mol.html
+++ b/docs/reference/sim_mol.html
@@ -1,5 +1,5 @@
-Simulate a mol_parameter object. — sim_mol • Spectroscopy Analysis Tools (spant) Simulate a mol_parameter object. — sim_mol • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -143,7 +143,7 @@ Value
diff --git a/docs/reference/sim_noise.html b/docs/reference/sim_noise.html
index 23875f79..a71477d4 100644
--- a/docs/reference/sim_noise.html
+++ b/docs/reference/sim_noise.html
@@ -1,5 +1,5 @@
-Simulate an mrs_data object containing simulated Gaussian noise. — sim_noise • Spectroscopy Analysis Tools (spant) Simulate an mrs_data object containing simulated Gaussian noise. — sim_noise • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -84,6 +84,7 @@ Simulate an mrs_data object containing simulated Gaussian noise.
ft = def_ft(),
N = def_N(),
ref = def_ref(),
+ nuc = def_nuc(),
dyns = 1,
fd = TRUE
)
@@ -111,6 +112,10 @@ Arguments
reference value for ppm scale.
nuc
+resonant nucleus.
dyns
number of dynamic scans to generate.
Value
diff --git a/docs/reference/sim_resonances.html b/docs/reference/sim_resonances.html
index 19e9a8a4..d4f8d7c0 100644
--- a/docs/reference/sim_resonances.html
+++ b/docs/reference/sim_resonances.html
@@ -1,5 +1,5 @@
-Simulate a MRS data object containing a set of simulated resonances. — sim_resonances • Spectroscopy Analysis Tools (spant) Simulate a MRS data object containing a set of simulated resonances. — sim_resonances • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -161,7 +161,7 @@ Examples
diff --git a/docs/reference/sim_th_excit_profile.html b/docs/reference/sim_th_excit_profile.html
index 5535c5ef..e781cab1 100644
--- a/docs/reference/sim_th_excit_profile.html
+++ b/docs/reference/sim_th_excit_profile.html
@@ -1,7 +1,5 @@
-Simulate an ideal pulse excitation profile by smoothing a top-hat function
-with a Gaussian. — sim_th_excit_profile • Spectroscopy Analysis Tools (spant) Simulate an ideal pulse excitation profile by smoothing a top-hat function with a Gaussian. — sim_th_excit_profile • Spectroscopy Analysis Tools (spant) Simulate an mrs_data object containing complex zero valued samples. — sim_zero • Spectroscopy Analysis Tools (spant) Simulate an mrs_data object containing complex zero valued samples. — sim_zero • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -78,7 +78,14 @@ Simulate an mrs_data object containing complex zero valued samples.
-
+
@@ -99,6 +106,10 @@ Arguments
reference value for ppm scale.
nuc
+resonant nucleus.
dyns
number of dynamic scans to generate.
Value
diff --git a/docs/reference/smooth_dyns.html b/docs/reference/smooth_dyns.html
index 4cc8da50..accf3a51 100644
--- a/docs/reference/smooth_dyns.html
+++ b/docs/reference/smooth_dyns.html
@@ -1,5 +1,5 @@
-Smooth data across the dynamic dimension with a Gaussian kernel. — smooth_dyns • Spectroscopy Analysis Tools (spant) Smooth data across the dynamic dimension with a Gaussian kernel. — smooth_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/sort_basis.html b/docs/reference/sort_basis.html
index 6a676ea2..d25cc006 100644
--- a/docs/reference/sort_basis.html
+++ b/docs/reference/sort_basis.html
@@ -1,5 +1,5 @@
-Sort the basis-set elements alphabetically. — sort_basis • Spectroscopy Analysis Tools (spant) Sort the basis-set elements alphabetically. — sort_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/spant-package.html b/docs/reference/spant-package.html
index b3dd8e21..90f19ec3 100644
--- a/docs/reference/spant-package.html
+++ b/docs/reference/spant-package.html
@@ -1,5 +1,5 @@
-spant: spectroscopy analysis tools. — spant-package • Spectroscopy Analysis Tools (spant) spant: spectroscopy analysis tools. — spant-package • Spectroscopy Analysis Tools (spant) Simulate and fit some spectra with ABfit for benchmarking purposes. Basic
-timing and performance metrics will be printed. — spant_abfit_benchmark • Spectroscopy Analysis Tools (spant) Simulate and fit some spectra with ABfit for benchmarking purposes. Basic timing and performance metrics will be printed. — spant_abfit_benchmark • Spectroscopy Analysis Tools (spant) Example MEGA-PRESS data with significant B0 drift. — spant_mpress_drift • Spectroscopy Analysis Tools (spant) Example MEGA-PRESS data with significant B0 drift. — spant_mpress_drift • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -83,7 +83,7 @@ Example MEGA-PRESS data with significant B0 drift.
Format
- An object of class mrs_data of length 13.
+ An object of class mrs_data of dimension 1 x 1 x 1 x 1 x 40 x 1 x 1024.
@@ -98,7 +98,7 @@ Format
diff --git a/docs/reference/spant_sim_fmrs_dataset.html b/docs/reference/spant_sim_fmrs_dataset.html
new file mode 100644
index 00000000..00e48b56
--- /dev/null
+++ b/docs/reference/spant_sim_fmrs_dataset.html
@@ -0,0 +1,117 @@
+
+Simulate an example fMRS dataset for a block design fMRS experiment and export a BIDS structure. — spant_sim_fmrs_dataset • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Simulate an example fMRS dataset for a block design fMRS experiment and export a BIDS structure.
+ Source: R/fmrs.R
+ spant_sim_fmrs_dataset.Rd
+
+
+
+ Simulate an example fMRS dataset for a block design fMRS experiment and
+export a BIDS structure.
+
+
+
+ spant_sim_fmrs_dataset(output_dir = NULL)
+
+
+
+ Arguments
+ - output_dir
+output directory for the BIDS data. Defaults to :
+"HOME/sim_fmrs_dataset/data".
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/spant_simulation_benchmark.html b/docs/reference/spant_simulation_benchmark.html
index 32daa8bf..d8cc6841 100644
--- a/docs/reference/spant_simulation_benchmark.html
+++ b/docs/reference/spant_simulation_benchmark.html
@@ -1,7 +1,5 @@
-Simulate a typical metabolite basis set for benchmarking. Timing metrics will
-be printed on completion. — spant_simulation_benchmark • Spectroscopy Analysis Tools (spant) Simulate a typical metabolite basis set for benchmarking. Timing metrics will be printed on completion. — spant_simulation_benchmark • Spectroscopy Analysis Tools (spant) Decompose an mrs_data object into white and gray matter spectra. — spec_decomp • Spectroscopy Analysis Tools (spant) Perform a mathematical operation on a spectral region. — spec_op • Spectroscopy Analysis Tools (spant) Perform a mathematical operation on a spectral region. — spec_op • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -98,8 +98,8 @@ Arguments
operator
-can be "sum" (default), "mean", "l2", "max", "min" or
-"max-min".
can be "sum" (default), "mean", "l2", "max", "max_cplx,
+"min" or "max-min".
freq_scale
@@ -129,7 +129,7 @@ Value
diff --git a/docs/reference/spin_sys.html b/docs/reference/spin_sys.html
index 853423a4..1eaa9e76 100644
--- a/docs/reference/spin_sys.html
+++ b/docs/reference/spin_sys.html
@@ -1,5 +1,5 @@
-Create a spin system object for pulse sequence simulation. — spin_sys • Spectroscopy Analysis Tools (spant) Create a spin system object for pulse sequence simulation. — spin_sys • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/spm_pve2categorical.html b/docs/reference/spm_pve2categorical.html
index 23a1bad9..70f10729 100644
--- a/docs/reference/spm_pve2categorical.html
+++ b/docs/reference/spm_pve2categorical.html
@@ -1,7 +1,5 @@
-Convert SPM style segmentation files to a single categorical image where
-the numerical values map as: 0) Other, 1) CSF, 2) GM and 3) WM. — spm_pve2categorical • Spectroscopy Analysis Tools (spant) Convert SPM style segmentation files to a single categorical image where the numerical values map as: 0) Other, 1) CSF, 2) GM and 3) WM. — spm_pve2categorical • Spectroscopy Analysis Tools (spant) Signal space projection method for lipid suppression. — ssp • Spectroscopy Analysis Tools (spant) Signal space projection method for lipid suppression. — ssp • Spectroscopy Analysis Tools (spant) Plot the fitting results of an object of class fit_result with
-individual basis set components shown. — stackplot.fit_result • Spectroscopy Analysis Tools (spant) Plot the fitting results of an object of class fit_result with individual basis set components shown. — stackplot.fit_result • Spectroscopy Analysis Tools (spant) Produce a plot with multiple traces. — stackplot • Spectroscopy Analysis Tools (spant) Produce a plot with multiple traces. — stackplot • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/stackplot.mrs_data.html b/docs/reference/stackplot.mrs_data.html
index 17ff5648..64eea445 100644
--- a/docs/reference/stackplot.mrs_data.html
+++ b/docs/reference/stackplot.mrs_data.html
@@ -1,5 +1,5 @@
-Stackplot plotting method for objects of class mrs_data. — stackplot.mrs_data • Spectroscopy Analysis Tools (spant) Stackplot plotting method for objects of class mrs_data. — stackplot.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -255,7 +255,7 @@ Arguments
diff --git a/docs/reference/sub_first_dyn.html b/docs/reference/sub_first_dyn.html
index dbd7f831..493b7242 100644
--- a/docs/reference/sub_first_dyn.html
+++ b/docs/reference/sub_first_dyn.html
@@ -1,5 +1,5 @@
-Subtract the first dynamic spectrum from a dynamic series. — sub_first_dyn • Spectroscopy Analysis Tools (spant) Subtract the first dynamic spectrum from a dynamic series. — sub_first_dyn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/sub_mean_dyns.html b/docs/reference/sub_mean_dyns.html
index 6e3bb2df..221bd0c1 100644
--- a/docs/reference/sub_mean_dyns.html
+++ b/docs/reference/sub_mean_dyns.html
@@ -1,5 +1,5 @@
-Subtract the mean dynamic spectrum from a dynamic series. — sub_mean_dyns • Spectroscopy Analysis Tools (spant) Subtract the mean dynamic spectrum from a dynamic series. — sub_mean_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/sub_median_dyns.html b/docs/reference/sub_median_dyns.html
index 134c495d..1e834f14 100644
--- a/docs/reference/sub_median_dyns.html
+++ b/docs/reference/sub_median_dyns.html
@@ -1,5 +1,5 @@
-Subtract the median dynamic spectrum from a dynamic series. — sub_median_dyns • Spectroscopy Analysis Tools (spant) Subtract the median dynamic spectrum from a dynamic series. — sub_median_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/sum_coils.html b/docs/reference/sum_coils.html
index 7bf559f2..e1ab3cc0 100644
--- a/docs/reference/sum_coils.html
+++ b/docs/reference/sum_coils.html
@@ -1,5 +1,5 @@
-Calculate the sum across receiver coil elements. — sum_coils • Spectroscopy Analysis Tools (spant) Calculate the sum across receiver coil elements. — sum_coils • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/sum_dyns.html b/docs/reference/sum_dyns.html
index a0be19d3..bbda2ffc 100644
--- a/docs/reference/sum_dyns.html
+++ b/docs/reference/sum_dyns.html
@@ -1,5 +1,5 @@
-Calculate the sum of data dynamics. — sum_dyns • Spectroscopy Analysis Tools (spant) Calculate the sum of data dynamics. — sum_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/sum_mrs.html b/docs/reference/sum_mrs.html
index a22f215b..3cc3ab9e 100644
--- a/docs/reference/sum_mrs.html
+++ b/docs/reference/sum_mrs.html
@@ -1,5 +1,5 @@
-Sum two mrs_data objects. — sum_mrs • Spectroscopy Analysis Tools (spant) Sum two mrs_data objects. — sum_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Value
diff --git a/docs/reference/sum_mrs_list.html b/docs/reference/sum_mrs_list.html
index f4e09aea..c3584348 100644
--- a/docs/reference/sum_mrs_list.html
+++ b/docs/reference/sum_mrs_list.html
@@ -1,5 +1,5 @@
-Return the sum of a list of mrs_data objects. — sum_mrs_list • Spectroscopy Analysis Tools (spant) Return the sum of a list of mrs_data objects. — sum_mrs_list • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/svs_1h_brain_analysis.html b/docs/reference/svs_1h_brain_analysis.html
index 8ce514db..dff0ef7d 100644
--- a/docs/reference/svs_1h_brain_analysis.html
+++ b/docs/reference/svs_1h_brain_analysis.html
@@ -1,5 +1,5 @@
-Standard SVS 1H brain analysis pipeline. — svs_1h_brain_analysis • Spectroscopy Analysis Tools (spant) Standard SVS 1H brain analysis pipeline. — svs_1h_brain_analysis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -199,7 +199,7 @@ Value
diff --git a/docs/reference/svs_1h_brain_analysis_dev.html b/docs/reference/svs_1h_brain_analysis_dev.html
index d70a14d3..d71bfea2 100644
--- a/docs/reference/svs_1h_brain_analysis_dev.html
+++ b/docs/reference/svs_1h_brain_analysis_dev.html
@@ -1,5 +1,5 @@
-Standard SVS 1H brain analysis pipeline. — svs_1h_brain_analysis_dev • Spectroscopy Analysis Tools (spant) Standard SVS 1H brain analysis pipeline. — svs_1h_brain_analysis_dev • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -193,7 +193,7 @@ Examples
diff --git a/docs/reference/svs_1h_brain_batch_analysis.html b/docs/reference/svs_1h_brain_batch_analysis.html
index 5631e8cc..15f7223e 100644
--- a/docs/reference/svs_1h_brain_batch_analysis.html
+++ b/docs/reference/svs_1h_brain_batch_analysis.html
@@ -1,5 +1,5 @@
-Batch interface to the standard SVS 1H brain analysis pipeline. — svs_1h_brain_batch_analysis • Spectroscopy Analysis Tools (spant) Batch interface to the standard SVS 1H brain analysis pipeline. — svs_1h_brain_batch_analysis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -144,7 +144,7 @@ Value
diff --git a/docs/reference/t_test_spec.html b/docs/reference/t_test_spec.html
new file mode 100644
index 00000000..56a7ea1b
--- /dev/null
+++ b/docs/reference/t_test_spec.html
@@ -0,0 +1,124 @@
+
+Perform a t-test on spectral data points. — t_test_spec • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+
+
+ Perform a t-test on spectral data points.
+
+
+
+ t_test_spec(mrs_data, group)
+
+
+
+ Arguments
+ - mrs_data
+an mrs_data object with spectra in the dynamic dimension.
- group
+vector describing the group membership of each dynamic spectrum.
+
+ Value
+
+
+a list of statistical results.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/td2fd.html b/docs/reference/td2fd.html
index 6748a6a8..f31ed524 100644
--- a/docs/reference/td2fd.html
+++ b/docs/reference/td2fd.html
@@ -1,5 +1,5 @@
-Transform time-domain data to the frequency-domain. — td2fd • Spectroscopy Analysis Tools (spant) Transform time-domain data to the frequency-domain. — td2fd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/td_conv_filt.html b/docs/reference/td_conv_filt.html
index a9f340c3..106b9b00 100644
--- a/docs/reference/td_conv_filt.html
+++ b/docs/reference/td_conv_filt.html
@@ -1,5 +1,5 @@
-Time-domain convolution based filter. — td_conv_filt • Spectroscopy Analysis Tools (spant) Time-domain convolution based filter. — td_conv_filt • Spectroscopy Analysis Tools (spant) Time-domain spectral registration. — tdsr • Spectroscopy Analysis Tools (spant) Time-domain spectral registration. — tdsr • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -121,7 +121,7 @@ Value
diff --git a/docs/reference/te.html b/docs/reference/te.html
index 010361b1..4a65711d 100644
--- a/docs/reference/te.html
+++ b/docs/reference/te.html
@@ -1,5 +1,5 @@
-Return the echo time of an MRS dataset. — te • Spectroscopy Analysis Tools (spant) Return the echo time of an MRS dataset. — te • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/tr.html b/docs/reference/tr.html
index 0c0bd63b..2e749e02 100644
--- a/docs/reference/tr.html
+++ b/docs/reference/tr.html
@@ -1,5 +1,5 @@
-Return the repetition time of an MRS dataset. — tr • Spectroscopy Analysis Tools (spant) Return the repetition time of an MRS dataset. — tr • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/varpro_3_para_opts.html b/docs/reference/varpro_3_para_opts.html
index c2270a16..52d7cd84 100644
--- a/docs/reference/varpro_3_para_opts.html
+++ b/docs/reference/varpro_3_para_opts.html
@@ -1,5 +1,5 @@
-Return a list of options for VARPRO based fitting with 3 free parameters. — varpro_3_para_opts • Spectroscopy Analysis Tools (spant) Return a list of options for VARPRO based fitting with 3 free parameters. — varpro_3_para_opts • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -141,7 +141,7 @@ Value
diff --git a/docs/reference/varpro_basic_opts.html b/docs/reference/varpro_basic_opts.html
index 32c86d22..c5104891 100644
--- a/docs/reference/varpro_basic_opts.html
+++ b/docs/reference/varpro_basic_opts.html
@@ -1,5 +1,5 @@
-Return a list of options for a basic VARPRO analysis. — varpro_basic_opts • Spectroscopy Analysis Tools (spant) Return a list of options for a basic VARPRO analysis. — varpro_basic_opts • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -118,7 +118,7 @@ Value
diff --git a/docs/reference/varpro_opts.html b/docs/reference/varpro_opts.html
index 2aabf11d..6332f730 100644
--- a/docs/reference/varpro_opts.html
+++ b/docs/reference/varpro_opts.html
@@ -1,5 +1,5 @@
-Return a list of options for VARPRO based fitting. — varpro_opts • Spectroscopy Analysis Tools (spant) Return a list of options for VARPRO based fitting. — varpro_opts • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -177,7 +177,7 @@ Examples
diff --git a/docs/reference/vec2mrs_data.html b/docs/reference/vec2mrs_data.html
index 0cccd73b..f0d58bf0 100644
--- a/docs/reference/vec2mrs_data.html
+++ b/docs/reference/vec2mrs_data.html
@@ -1,5 +1,5 @@
-Convert a vector into a mrs_data object. — vec2mrs_data • Spectroscopy Analysis Tools (spant) Convert a vector into a mrs_data object. — vec2mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -80,10 +80,11 @@ Convert a vector into a mrs_data object.
vec2mrs_data(
vec,
- fs = def_fs(),
- ft = def_ft(),
- ref = def_ref(),
- nuc = def_nuc(),
+ mrs_data = NULL,
+ fs = NULL,
+ ft = NULL,
+ ref = NULL,
+ nuc = NULL,
dyns = 1,
fd = FALSE
)
@@ -95,6 +96,10 @@ Arguments
the data vector.
mrs_data
+example data to copy acquisition parameters from.
fs
sampling frequency in Hz.
Arguments
fd
-flag to indicate if the matrix is in the frequency domain (logical).
flag to indicate if the vector is in the frequency domain (logical).
Value
diff --git a/docs/reference/write_basis.html b/docs/reference/write_basis.html
index b6e27cbd..94c5e021 100644
--- a/docs/reference/write_basis.html
+++ b/docs/reference/write_basis.html
@@ -1,5 +1,5 @@
-Write a basis object to an LCModel .basis formatted file. — write_basis • Spectroscopy Analysis Tools (spant) Write a basis object to an LCModel .basis formatted file. — write_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -108,7 +108,7 @@ Arguments
diff --git a/docs/reference/write_basis_tqn.html b/docs/reference/write_basis_tqn.html
index 6aa51c1d..116c73ec 100644
--- a/docs/reference/write_basis_tqn.html
+++ b/docs/reference/write_basis_tqn.html
@@ -1,5 +1,5 @@
-Generate a basis file using TARQUIN. — write_basis_tqn • Spectroscopy Analysis Tools (spant) Generate a basis file using TARQUIN. — write_basis_tqn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Examples
diff --git a/docs/reference/write_mrs.html b/docs/reference/write_mrs.html
index fff25f15..124b9dc4 100644
--- a/docs/reference/write_mrs.html
+++ b/docs/reference/write_mrs.html
@@ -1,5 +1,5 @@
-Write MRS data object to file. — write_mrs • Spectroscopy Analysis Tools (spant) Write MRS data object to file. — write_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Arguments
diff --git a/docs/reference/write_mrs_nifti.html b/docs/reference/write_mrs_nifti.html
index f4bf1921..bd3ed4b7 100644
--- a/docs/reference/write_mrs_nifti.html
+++ b/docs/reference/write_mrs_nifti.html
@@ -1,5 +1,5 @@
-Write MRS data object to file in NIFTI format. — write_mrs_nifti • Spectroscopy Analysis Tools (spant) Write MRS data object to file in NIFTI format. — write_mrs_nifti • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/write_pulse_ascii.html b/docs/reference/write_pulse_ascii.html
index 067ae086..221f8ebb 100644
--- a/docs/reference/write_pulse_ascii.html
+++ b/docs/reference/write_pulse_ascii.html
@@ -1,5 +1,5 @@
-Write an ASCII formatted pulse file. — write_pulse_ascii • Spectroscopy Analysis Tools (spant) Write an ASCII formatted pulse file. — write_pulse_ascii • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/zero_fade_spec.html b/docs/reference/zero_fade_spec.html
index c703745c..c8b572c3 100644
--- a/docs/reference/zero_fade_spec.html
+++ b/docs/reference/zero_fade_spec.html
@@ -1,7 +1,5 @@
-Fade a spectrum to zero by frequency domain multiplication with a tanh
-function. Note this operation distorts data points at the end of the FID. — zero_fade_spec • Spectroscopy Analysis Tools (spant) Fade a spectrum to zero by frequency domain multiplication with a tanh function. Note this operation distorts data points at the end of the FID. — zero_fade_spec • Spectroscopy Analysis Tools (spant) Zero all coherences including and above a given order. — zero_higher_orders • Spectroscopy Analysis Tools (spant) Zero all coherences including and above a given order. — zero_higher_orders • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Value
diff --git a/docs/reference/zero_td_pts_end.html b/docs/reference/zero_td_pts_end.html
index 8c1123c8..71d24ebb 100644
--- a/docs/reference/zero_td_pts_end.html
+++ b/docs/reference/zero_td_pts_end.html
@@ -1,5 +1,5 @@
-Set mrs_data object data points at the end of the FID to zero. — zero_td_pts_end • Spectroscopy Analysis Tools (spant) Set mrs_data object data points at the end of the FID to zero. — zero_td_pts_end • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/zf.html b/docs/reference/zf.html
index 85e2013c..baf50256 100644
--- a/docs/reference/zf.html
+++ b/docs/reference/zf.html
@@ -1,5 +1,5 @@
-Zero-fill MRS data in the time domain. — zf • Spectroscopy Analysis Tools (spant) Zero-fill MRS data in the time domain. — zf • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -125,7 +125,7 @@ Value
diff --git a/docs/reference/zf_xy.html b/docs/reference/zf_xy.html
index ebca3999..c4104a74 100644
--- a/docs/reference/zf_xy.html
+++ b/docs/reference/zf_xy.html
@@ -1,5 +1,5 @@
-Zero-fill MRSI data in the k-space x-y direction. — zf_xy • Spectroscopy Analysis Tools (spant) Zero-fill MRSI data in the k-space x-y direction. — zf_xy • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -113,7 +113,7 @@ Value
diff --git a/docs/sitemap.xml b/docs/sitemap.xml
index e2139f71..4c39f515 100644
--- a/docs/sitemap.xml
+++ b/docs/sitemap.xml
@@ -216,6 +216,12 @@
https://martin3141.github.io/spant/reference/comb_coils_fp_pc.html
+
+ https://martin3141.github.io/spant/reference/comb_coils_mrsi_gls.html
+
+
+ https://martin3141.github.io/spant/reference/comb_coils_svs_gls.html
+
https://martin3141.github.io/spant/reference/comb_csv_results.html
@@ -411,6 +417,9 @@
https://martin3141.github.io/spant/reference/gen_conv_reg.html
+
+ https://martin3141.github.io/spant/reference/gen_group_reg.html
+
https://martin3141.github.io/spant/reference/gen_impulse_reg.html
@@ -555,6 +564,15 @@
https://martin3141.github.io/spant/reference/glm_spec.html
+
+ https://martin3141.github.io/spant/reference/glm_spec_fmrs_fl.html
+
+
+ https://martin3141.github.io/spant/reference/glm_spec_fmrs_group.html
+
+
+ https://martin3141.github.io/spant/reference/glm_spec_group_linhyp.html
+
https://martin3141.github.io/spant/reference/grid_shift_xy.html
@@ -690,9 +708,15 @@
https://martin3141.github.io/spant/reference/mrs_data2basis.html
+
+ https://martin3141.github.io/spant/reference/mrs_data2bids.html
+
https://martin3141.github.io/spant/reference/mrs_data2mat.html
+
+ https://martin3141.github.io/spant/reference/mrs_data2spec_mat.html
+
https://martin3141.github.io/spant/reference/mrs_data2vec.html
@@ -741,6 +765,9 @@
https://martin3141.github.io/spant/reference/phase.html
+
+ https://martin3141.github.io/spant/reference/phase_ref_1h_brain.html
+
https://martin3141.github.io/spant/reference/plot.fit_result.html
@@ -780,6 +807,12 @@
https://martin3141.github.io/spant/reference/precomp.html
+
+ https://martin3141.github.io/spant/reference/preproc_svs.html
+
+
+ https://martin3141.github.io/spant/reference/preproc_svs_dataset.html
+
https://martin3141.github.io/spant/reference/print.fit_result.html
@@ -1050,6 +1083,9 @@
https://martin3141.github.io/spant/reference/spant_mpress_drift.html
+
+ https://martin3141.github.io/spant/reference/spant_sim_fmrs_dataset.html
+
https://martin3141.github.io/spant/reference/spant_simulation_benchmark.html
@@ -1107,6 +1143,9 @@
https://martin3141.github.io/spant/reference/svs_1h_brain_batch_analysis.html
+
+ https://martin3141.github.io/spant/reference/t_test_spec.html
+
https://martin3141.github.io/spant/reference/td2fd.html
Return (and optionally modify using the input arguments) a list of the -default acquisition parameters.
Return (and optionally modify using the input arguments) a list of the default acquisition parameters.
All functions
- Downsample an MRS signal by a factor of 2 by removing every other data point
-in the time-domain. Note, signals outside the new sampling frequency will be
-aliased.
Downsample an MRS signal by a factor of 2 by removing every other data point in the time-domain. Note, signals outside the new sampling frequency will be aliased.
- Return a time scale vector of acquisition times for a dynamic MRS scan. The
-first temporal scan is assigned a value of 0.
Return a time scale vector of acquisition times for a dynamic MRS scan. The first temporal scan is assigned a value of 0.
@@ -429,8 +418,7 @@ All functions
- Estimate the standard deviation of the noise from a segment of an mrs_data
-object.
Estimate the standard deviation of the noise from a segment of an mrs_data object.
@@ -486,8 +474,7 @@ All functions
- Perform a zeroth order phase correction based on the phase of the first data
-point in the time-domain.
Perform a zeroth order phase correction based on the phase of the first data point in the time-domain.
@@ -507,8 +494,7 @@ All functions
- Perform a fft and fftshift on a matrix with each column replaced by its
-shifted fft.
Perform a fft and fftshift on a matrix with each column replaced by its shifted fft.
@@ -536,8 +522,11 @@ All functions
- Generate regressors by convolving a specified response function with a
-stimulus.
Generate regressors by convolving a specified response function with a stimulus.
+
+
+ Expand a regressor matrix for a group analysis.
@@ -553,28 +542,23 @@ All functions
- Return a character vector of common 1H molecules found in healthy human
-brain.
Return a character vector of common 1H molecules found in healthy human brain.
- Return a list of mol_parameter objects suitable for 1H brain MRS
-analyses.
Return a list of mol_parameter objects suitable for 1H brain MRS analyses.
- Return a list of mol_parameter objects suitable for 1H brain MRS
-analyses.
Return a list of mol_parameter objects suitable for 1H brain MRS analyses.
- Return a list of mol_parameter objects suitable for 1H brain MRS
-analyses.
Return a list of mol_parameter objects suitable for 1H brain MRS analyses.
- Return a list of mol_parameter objects suitable for 1H brain MRS
-analyses.
Return a list of mol_parameter objects suitable for 1H brain MRS analyses.
@@ -582,8 +566,7 @@ All functions
- Return a character vector of molecules included in the Gold Star Phantoms
-SPECTRE phantom.
Return a character vector of molecules included in the Gold Star Phantoms SPECTRE phantom.
@@ -635,8 +618,7 @@ All functions
- Return a character array of names that may be used with the
-get_mol_paras function.
Return a character array of names that may be used with the get_mol_paras function.
@@ -700,8 +682,7 @@ All functions
- Return an array of amplitudes derived from fitting the initial points in the
-time domain and extrapolating back to t=0.
Return an array of amplitudes derived from fitting the initial points in the time domain and extrapolating back to t=0.
@@ -709,8 +690,7 @@ All functions
- Generate a mol_parameters object for a simple spin system with one
-resonance.
Generate a mol_parameters object for a simple spin system with one resonance.
@@ -731,6 +711,18 @@ All functions glm_spec()
Perform a GLM analysis of dynamic MRS data in the spectral domain.
+
+
+ Perform first-level spectral GLM analysis of an fMRS dataset.
+
+
+ Perform group-level spectral GLM analysis of an fMRS dataset.
+
+
+ Test a group-level spectral GLM linear hypothesis.
@@ -766,8 +758,7 @@ All functions
- Perform an ifft and ifftshift on a matrix with each column replaced by its
-shifted ifft.
Perform an ifft and ifftshift on a matrix with each column replaced by its shifted ifft.
@@ -799,8 +790,7 @@ All functions
- Check if the chemical shift dimension of an MRS data object is in the
-frequency domain.
Check if the chemical shift dimension of an MRS data object is in the frequency domain.
@@ -820,18 +810,15 @@ All functions
- Covert a linewidth in Hz to an equivalent alpha value in the time-domain ie:
-x * exp(-t * alpha).
Covert a linewidth in Hz to an equivalent alpha value in the time-domain ie: x * exp(-t * alpha).
- Covert a linewidth in Hz to an equivalent beta value in the time-domain ie:
-x * exp(-t * t * beta).
Covert a linewidth in Hz to an equivalent beta value in the time-domain ie: x * exp(-t * t * beta).
- Make a basis-set object from a directory containing LCModel formatted RAW
-files.
Make a basis-set object from a directory containing LCModel formatted RAW files.
@@ -851,8 +838,7 @@ All functions
- Mask the voxels outside an elliptical region spanning the MRSI dataset in the
-x-y plane.
Mask the voxels outside an elliptical region spanning the MRSI dataset in the x-y plane.
@@ -860,13 +846,11 @@ All functions
- Convert a matrix (with spectral points in the column dimension and dynamics
-in the row dimensions) into a mrs_data object.
Convert a matrix (with spectral points in the column dimension and dynamics in the row dimensions) into a mrs_data object.
- Matrix exponential function taken from complexplus package to reduce the
-number of spant dependencies.
Matrix exponential function taken from complexplus package to reduce the number of spant dependencies.
@@ -914,31 +898,31 @@ All functions
- Convert an mrs_data object to basis object - where basis signals are spread
-across the dynamic dimension in the MRS data.
Convert an mrs_data object to basis object - where basis signals are spread across the dynamic dimension in the MRS data.
+
+
+ Create a BIDS file structure from a vector of MRS data paths or list of mrs_data objects.
- Convert mrs_data object to a matrix, with spectral points in the column
-dimension and dynamics in the row dimension.
Convert mrs_data object to a matrix, with spectral points in the column dimension and dynamics in the row dimension.
-
+
- Convert mrs_data object to a vector.
Convert mrs_data object to a matrix, with spectral points in the column dimension and dynamics in the row dimension.
-
+
- Create a BIDS directory and file structure from a list of mrs_data objects.
Convert mrs_data object to a vector.
- Perform a fftshift on a matrix, with each column replaced by its shifted
-result.
Perform a fftshift on a matrix, with each column replaced by its shifted result.
- Perform an ifftshift on a matrix, with each column replaced by its shifted
-result.
Perform an ifftshift on a matrix, with each column replaced by its shifted result.
@@ -946,9 +930,7 @@ All functions
- Flip the x data dimension order of a nifti image. This corresponds to
-flipping MRI data in the left-right direction, assuming the data in save in
-neurological format (can check with fslorient program).
Flip the x data dimension order of a nifti image. This corresponds to flipping MRI data in the left-right direction, assuming the data in save in neurological format (can check with fslorient program).
@@ -964,8 +946,7 @@ All functions
- Search for the highest peak in a spectral region and return the frequency,
-height and FWHM.
Search for the highest peak in a spectral region and return the frequency, height and FWHM.
@@ -974,6 +955,10 @@ All functions phase()
Apply phasing parameters to MRS data.
+
+
+ Corrected zero order phase and chemical shift offset in 1H MRS data from the brain.
@@ -1005,8 +990,7 @@ All functions
- Plot an interactive slice map from a data array where voxels can be selected
-to display a corresponding spectrum.
Plot an interactive slice map from a data array where voxels can be selected to display a corresponding spectrum.
@@ -1026,8 +1010,15 @@ All functions
- Save function results to file and load on subsequent calls to avoid repeat
-computation.
Save function results to file and load on subsequent calls to avoid repeat computation.
+
+
+ Preprocess and perform quality assessment of a single SVS data set.
+
+
+ Preprocess and perform quality assessment of one or more SVS data sets.
@@ -1055,15 +1046,11 @@ All functions
- Read a directory containing Siemens MRS IMA files and combine along the coil
-dimension. Note that the coil ID is inferred from the sorted file name and
-should be checked when consistency is required between two directories.
Read a directory containing Siemens MRS IMA files and combine along the coil dimension. Note that the coil ID is inferred from the sorted file name and should be checked when consistency is required between two directories.
- Read a directory containing Siemens MRS IMA files and combine along the
-dynamic dimension. Note that the coil ID is inferred from the sorted file
-name and should be checked when consistency is required.
Read a directory containing Siemens MRS IMA files and combine along the dynamic dimension. Note that the coil ID is inferred from the sorted file name and should be checked when consistency is required.
@@ -1103,13 +1090,11 @@ All functions
- Reconstruct complex time-domain data from the real part of frequency-domain
-data.
Reconstruct complex time-domain data from the real part of frequency-domain data.
- Reconstruct complex time-domain data from the real part of frequency-domain
-data.
Reconstruct complex time-domain data from the real part of frequency-domain data.
@@ -1141,8 +1126,7 @@ All functions
- Resample a VOI to match a target image space using nearest-neighbour
-interpolation.
Resample a VOI to match a target image space using nearest-neighbour interpolation.
@@ -1158,23 +1142,19 @@ All functions
- Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water).
Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / kg of tissue water).
- Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water).
Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / kg of tissue water).
- Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / Litre of tissue).
Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / Litre of tissue).
- Convert default LCM/TARQUIN concentration scaling to molal units with partial
-volume correction.
Convert default LCM/TARQUIN concentration scaling to molal units with partial volume correction.
@@ -1222,8 +1202,7 @@ All functions
- MEGA-PRESS sequence with ideal localisation pulses and Gaussian shaped
-editing pulse.
MEGA-PRESS sequence with ideal localisation pulses and Gaussian shaped editing pulse.
@@ -1251,13 +1230,11 @@ All functions
- STEAM sequence with ideal pulses and coherence order filtering to simulate
-gradient crushers.
STEAM sequence with ideal pulses and coherence order filtering to simulate gradient crushers.
- STEAM sequence with ideal pulses using the z-rotation gradient simulation
-method described by Young et al JMR 140, 146-152 (1999).
STEAM sequence with ideal pulses using the z-rotation gradient simulation method described by Young et al JMR 140, 146-152 (1999).
@@ -1293,8 +1270,7 @@ All functions
- Set the number of time-domain data points, truncating or zero-filling as
-appropriate.
Set the number of time-domain data points, truncating or zero-filling as appropriate.
@@ -1318,18 +1294,15 @@ All functions
- Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS
-sequence. Note, ideal pulses are assumed.
Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS sequence. Note, ideal pulses are assumed.
- Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS
-sequence. Note, ideal pulses are assumed.
Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS sequence. Note, ideal pulses are assumed.
- Simulate a macromolecular and lipid basis-set suitable for 1H brain MRS
-analysis.
Simulate a macromolecular and lipid basis-set suitable for 1H brain MRS analysis.
@@ -1353,8 +1326,7 @@ All functions
- Simulate an ideal pulse excitation profile by smoothing a top-hat function
-with a Gaussian.
Simulate an ideal pulse excitation profile by smoothing a top-hat function with a Gaussian.
@@ -1374,17 +1346,19 @@ All functions
- Simulate and fit some spectra with ABfit for benchmarking purposes. Basic
-timing and performance metrics will be printed.
Simulate and fit some spectra with ABfit for benchmarking purposes. Basic timing and performance metrics will be printed.
Example MEGA-PRESS data with significant B0 drift.
+
+
+ Simulate an example fMRS dataset for a block design fMRS experiment and export a BIDS structure.
- Simulate a typical metabolite basis set for benchmarking. Timing metrics will
-be printed on completion.
Simulate a typical metabolite basis set for benchmarking. Timing metrics will be printed on completion.
@@ -1400,8 +1374,7 @@ All functions
- Convert SPM style segmentation files to a single categorical image where
-the numerical values map as: 0) Other, 1) CSF, 2) GM and 3) WM.
Convert SPM style segmentation files to a single categorical image where the numerical values map as: 0) Other, 1) CSF, 2) GM and 3) WM.
@@ -1413,8 +1386,7 @@ All functions
- Plot the fitting results of an object of class fit_result with
-individual basis set components shown.
Plot the fitting results of an object of class fit_result with individual basis set components shown.
@@ -1459,6 +1431,10 @@ All functions svs_1h_brain_batch_analysis()
Batch interface to the standard SVS 1H brain analysis pipeline.
+
+
+ Perform a t-test on spectral data points.
@@ -1518,8 +1494,7 @@ All functions
- Fade a spectrum to zero by frequency domain multiplication with a tanh
-function. Note this operation distorts data points at the end of the FID.
Fade a spectrum to zero by frequency domain multiplication with a tanh function. Note this operation distorts data points at the end of the FID.
@@ -1549,7 +1524,7 @@ All functions
diff --git a/docs/reference/int_spec.html b/docs/reference/int_spec.html
index c7060fe7..783325a8 100644
--- a/docs/reference/int_spec.html
+++ b/docs/reference/int_spec.html
@@ -1,5 +1,5 @@
-Integrate a spectral region. — int_spec • Spectroscopy Analysis Tools (spant) Integrate a spectral region. — int_spec • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -118,7 +118,7 @@ Value
diff --git a/docs/reference/interleave_dyns.html b/docs/reference/interleave_dyns.html
index effe5543..441eff27 100644
--- a/docs/reference/interleave_dyns.html
+++ b/docs/reference/interleave_dyns.html
@@ -1,5 +1,5 @@
-Interleave the first and second half of a dynamic series. — interleave_dyns • Spectroscopy Analysis Tools (spant) Interleave the first and second half of a dynamic series. — interleave_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/inv_even_dyns.html b/docs/reference/inv_even_dyns.html
index 9f9d4fff..dcb781dc 100644
--- a/docs/reference/inv_even_dyns.html
+++ b/docs/reference/inv_even_dyns.html
@@ -1,5 +1,5 @@
-Invert even numbered dynamic scans starting from 1 (2,4,6...). — inv_even_dyns • Spectroscopy Analysis Tools (spant) Invert even numbered dynamic scans starting from 1 (2,4,6...). — inv_even_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/inv_odd_dyns.html b/docs/reference/inv_odd_dyns.html
index 26212e2b..78d64660 100644
--- a/docs/reference/inv_odd_dyns.html
+++ b/docs/reference/inv_odd_dyns.html
@@ -1,5 +1,5 @@
-Invert odd numbered dynamic scans starting from 1 (1,3,5...). — inv_odd_dyns • Spectroscopy Analysis Tools (spant) Invert odd numbered dynamic scans starting from 1 (1,3,5...). — inv_odd_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/is.def.html b/docs/reference/is.def.html
index f196ffd0..a67b9eba 100644
--- a/docs/reference/is.def.html
+++ b/docs/reference/is.def.html
@@ -1,5 +1,5 @@
-Check if an object is defined, which is the same as being not NULL. — is.def • Spectroscopy Analysis Tools (spant) Check if an object is defined, which is the same as being not NULL. — is.def • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/is_fd.html b/docs/reference/is_fd.html
index 3b0ca165..18a193aa 100644
--- a/docs/reference/is_fd.html
+++ b/docs/reference/is_fd.html
@@ -1,7 +1,5 @@
-Check if the chemical shift dimension of an MRS data object is in the
-frequency domain. — is_fd • Spectroscopy Analysis Tools (spant) Check if the chemical shift dimension of an MRS data object is in the frequency domain. — is_fd • Spectroscopy Analysis Tools (spant) Transform 2D MRSI data from k-space to image space in the x-y direction. — kspace2img_xy • Spectroscopy Analysis Tools (spant) Transform 2D MRSI data from k-space to image space in the x-y direction. — kspace2img_xy • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/l2_reg.html b/docs/reference/l2_reg.html
index 3d781d80..21aa9849 100644
--- a/docs/reference/l2_reg.html
+++ b/docs/reference/l2_reg.html
@@ -1,5 +1,5 @@
-Perform l2 regularisation artefact suppression. — l2_reg • Spectroscopy Analysis Tools (spant) Perform l2 regularisation artefact suppression. — l2_reg • Spectroscopy Analysis Tools (spant) Apply line-broadening (apodisation) to MRS data or basis object. — lb • Spectroscopy Analysis Tools (spant) Apply line-broadening (apodisation) to MRS data or basis object. — lb • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -123,7 +123,7 @@ Value
diff --git a/docs/reference/lofdc.html b/docs/reference/lofdc.html
index 5419b1ec..31347a25 100644
--- a/docs/reference/lofdc.html
+++ b/docs/reference/lofdc.html
@@ -1,5 +1,5 @@
-Correct linear frequency drift. — lofdc • Spectroscopy Analysis Tools (spant) Correct linear frequency drift. — lofdc • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -138,7 +138,7 @@ Value
diff --git a/docs/reference/lw2alpha.html b/docs/reference/lw2alpha.html
index b83db682..25da229b 100644
--- a/docs/reference/lw2alpha.html
+++ b/docs/reference/lw2alpha.html
@@ -1,7 +1,5 @@
-Covert a linewidth in Hz to an equivalent alpha value in the time-domain ie:
-x * exp(-t * alpha). — lw2alpha • Spectroscopy Analysis Tools (spant) Covert a linewidth in Hz to an equivalent alpha value in the time-domain ie: x * exp(-t * alpha). — lw2alpha • Spectroscopy Analysis Tools (spant) Covert a linewidth in Hz to an equivalent beta value in the time-domain ie:
-x * exp(-t * t * beta). — lw2beta • Spectroscopy Analysis Tools (spant) Covert a linewidth in Hz to an equivalent beta value in the time-domain ie: x * exp(-t * t * beta). — lw2beta • Spectroscopy Analysis Tools (spant) Make a basis-set object from a directory containing LCModel formatted RAW
-files. — make_basis_from_raw • Spectroscopy Analysis Tools (spant) Make a basis-set object from a directory containing LCModel formatted RAW files. — make_basis_from_raw • Spectroscopy Analysis Tools (spant) Mask an MRS dataset in the dynamic dimension. — mask_dyns • Spectroscopy Analysis Tools (spant) Mask an MRS dataset in the dynamic dimension. — mask_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/mask_fit_res.html b/docs/reference/mask_fit_res.html
index 97baaa3f..ebd91a99 100644
--- a/docs/reference/mask_fit_res.html
+++ b/docs/reference/mask_fit_res.html
@@ -1,5 +1,5 @@
-Mask fit result spectra depending on a vector of bool values. — mask_fit_res • Spectroscopy Analysis Tools (spant) Mask fit result spectra depending on a vector of bool values. — mask_fit_res • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -116,7 +116,7 @@ Value
diff --git a/docs/reference/mask_xy.html b/docs/reference/mask_xy.html
index 11bb577c..b0d38619 100644
--- a/docs/reference/mask_xy.html
+++ b/docs/reference/mask_xy.html
@@ -1,5 +1,5 @@
-Mask an MRSI dataset in the x-y direction — mask_xy • Spectroscopy Analysis Tools (spant) Mask an MRSI dataset in the x-y direction — mask_xy • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/mask_xy_corners.html b/docs/reference/mask_xy_corners.html
index 09b16cd2..2d13839d 100644
--- a/docs/reference/mask_xy_corners.html
+++ b/docs/reference/mask_xy_corners.html
@@ -1,5 +1,5 @@
-Mask the four corners of an MRSI dataset in the x-y plane. — mask_xy_corners • Spectroscopy Analysis Tools (spant) Mask the four corners of an MRSI dataset in the x-y plane. — mask_xy_corners • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/mask_xy_ellipse.html b/docs/reference/mask_xy_ellipse.html
index 1d8b02e4..e2e749ef 100644
--- a/docs/reference/mask_xy_ellipse.html
+++ b/docs/reference/mask_xy_ellipse.html
@@ -1,7 +1,5 @@
-Mask the voxels outside an elliptical region spanning the MRSI dataset in the
-x-y plane. — mask_xy_ellipse • Spectroscopy Analysis Tools (spant) Mask the voxels outside an elliptical region spanning the MRSI dataset in the x-y plane. — mask_xy_ellipse • Spectroscopy Analysis Tools (spant) Mask a 2D MRSI dataset in the x-y dimension. — mask_xy_mat • Spectroscopy Analysis Tools (spant) Mask a 2D MRSI dataset in the x-y dimension. — mask_xy_mat • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Value
diff --git a/docs/reference/mat2mrs_data.html b/docs/reference/mat2mrs_data.html
index 2e2895f3..ae55665f 100644
--- a/docs/reference/mat2mrs_data.html
+++ b/docs/reference/mat2mrs_data.html
@@ -1,7 +1,5 @@
-Convert a matrix (with spectral points in the column dimension and dynamics
-in the row dimensions) into a mrs_data object. — mat2mrs_data • Spectroscopy Analysis Tools (spant) Convert a matrix (with spectral points in the column dimension and dynamics in the row dimensions) into a mrs_data object. — mat2mrs_data • Spectroscopy Analysis Tools (spant) Matrix exponential function taken from complexplus package to reduce the
-number of spant dependencies. — matexp • Spectroscopy Analysis Tools (spant) Matrix exponential function taken from complexplus package to reduce the number of spant dependencies. — matexp • Spectroscopy Analysis Tools (spant) Apply the max operator to an MRS dataset. — max_mrs • Spectroscopy Analysis Tools (spant) Apply the max operator to an MRS dataset. — max_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/max_mrs_interp.html b/docs/reference/max_mrs_interp.html
index e4474764..52e63f3e 100644
--- a/docs/reference/max_mrs_interp.html
+++ b/docs/reference/max_mrs_interp.html
@@ -1,5 +1,5 @@
-Apply the max operator to an interpolated MRS dataset. — max_mrs_interp • Spectroscopy Analysis Tools (spant) Apply the max operator to an interpolated MRS dataset. — max_mrs_interp • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/mean.list.html b/docs/reference/mean.list.html
index b8eb3463..048306fd 100644
--- a/docs/reference/mean.list.html
+++ b/docs/reference/mean.list.html
@@ -1,5 +1,5 @@
-Calculate the mean spectrum from an mrs_data object. — mean.list • Spectroscopy Analysis Tools (spant) Calculate the mean spectrum from an mrs_data object. — mean.list • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/mean.mrs_data.html b/docs/reference/mean.mrs_data.html
index 5531a28d..79515014 100644
--- a/docs/reference/mean.mrs_data.html
+++ b/docs/reference/mean.mrs_data.html
@@ -1,5 +1,5 @@
-Calculate the mean spectrum from an mrs_data object. — mean.mrs_data • Spectroscopy Analysis Tools (spant) Calculate the mean spectrum from an mrs_data object. — mean.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/mean_dyn_blocks.html b/docs/reference/mean_dyn_blocks.html
index 10467098..4c042448 100644
--- a/docs/reference/mean_dyn_blocks.html
+++ b/docs/reference/mean_dyn_blocks.html
@@ -1,5 +1,5 @@
-Calculate the mean of adjacent dynamic scans. — mean_dyn_blocks • Spectroscopy Analysis Tools (spant) Calculate the mean of adjacent dynamic scans. — mean_dyn_blocks • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/mean_dyn_pairs.html b/docs/reference/mean_dyn_pairs.html
index 63e909ea..1a241126 100644
--- a/docs/reference/mean_dyn_pairs.html
+++ b/docs/reference/mean_dyn_pairs.html
@@ -1,5 +1,5 @@
-Calculate the pairwise means across a dynamic data set. — mean_dyn_pairs • Spectroscopy Analysis Tools (spant) Calculate the pairwise means across a dynamic data set. — mean_dyn_pairs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/mean_dyns.html b/docs/reference/mean_dyns.html
index 73fdbfa7..0daa27df 100644
--- a/docs/reference/mean_dyns.html
+++ b/docs/reference/mean_dyns.html
@@ -1,5 +1,5 @@
-Calculate the mean dynamic data. — mean_dyns • Spectroscopy Analysis Tools (spant) Calculate the mean dynamic data. — mean_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/mean_mrs_list.html b/docs/reference/mean_mrs_list.html
index 808b6c50..10d842c0 100644
--- a/docs/reference/mean_mrs_list.html
+++ b/docs/reference/mean_mrs_list.html
@@ -1,5 +1,5 @@
-Return the mean of a list of mrs_data objects. — mean_mrs_list • Spectroscopy Analysis Tools (spant) Return the mean of a list of mrs_data objects. — mean_mrs_list • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/mean_vec_blocks.html b/docs/reference/mean_vec_blocks.html
index 8fc92eaa..dd78b122 100644
--- a/docs/reference/mean_vec_blocks.html
+++ b/docs/reference/mean_vec_blocks.html
@@ -1,5 +1,5 @@
-Calculate the mean of adjacent blocks in a vector. — mean_vec_blocks • Spectroscopy Analysis Tools (spant) Calculate the mean of adjacent blocks in a vector. — mean_vec_blocks • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/median_dyns.html b/docs/reference/median_dyns.html
index 1039d4b5..9a085b10 100644
--- a/docs/reference/median_dyns.html
+++ b/docs/reference/median_dyns.html
@@ -1,5 +1,5 @@
-Calculate the median dynamic data. — median_dyns • Spectroscopy Analysis Tools (spant) Calculate the median dynamic data. — median_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/mod_td.html b/docs/reference/mod_td.html
index 76ad0a40..141ef09e 100644
--- a/docs/reference/mod_td.html
+++ b/docs/reference/mod_td.html
@@ -1,5 +1,5 @@
-Apply the Modulus operator to the time-domain MRS signal. — mod_td • Spectroscopy Analysis Tools (spant) Apply the Modulus operator to the time-domain MRS signal. — mod_td • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/mrs_data2basis.html b/docs/reference/mrs_data2basis.html
index 62f7d749..11797b91 100644
--- a/docs/reference/mrs_data2basis.html
+++ b/docs/reference/mrs_data2basis.html
@@ -1,7 +1,5 @@
-Convert an mrs_data object to basis object - where basis signals are spread
-across the dynamic dimension in the MRS data. — mrs_data2basis • Spectroscopy Analysis Tools (spant) Convert an mrs_data object to basis object - where basis signals are spread across the dynamic dimension in the MRS data. — mrs_data2basis • Spectroscopy Analysis Tools (spant) Create a BIDS file structure from a vector of MRS data paths or list of mrs_data objects. — mrs_data2bids • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Create a BIDS file structure from a vector of MRS data paths or list of mrs_data objects.
+ Source: R/fmrs.R
+ mrs_data2bids.Rd
+
+
+
+ Create a BIDS file structure from a vector of MRS data paths or list of
+mrs_data objects.
+
+
+
+ mrs_data2bids(
+ mrs_data,
+ output_dir,
+ suffix = NULL,
+ sub = NULL,
+ ses = NULL,
+ task = NULL,
+ acq = NULL,
+ nuc = NULL,
+ voi = NULL,
+ rec = NULL,
+ run = NULL,
+ echo = NULL,
+ inv = NULL,
+ skip_existing = TRUE
+)
+
+
+
+ Arguments
+ - mrs_data
+vector of MRS data paths or list of mrs_data objects.
- output_dir
+the base directory to create the BIDS structure.
- suffix
+optional vector of file suffixes. Default behaviour is to
+automatically determine these from the input data, however it is recommended
+that they are specified to allow more efficient skipping of existing data.
- sub
+optional vector of subject labels. If not specified, these will be
+automatically generated as a series of increasing zero-padded integer values
+corresponding to the mrs_data input indices.
- ses
+optional vector of session labels.
- task
+optional vector of task labels.
- acq
+optional vector of acquisition labels.
- nuc
+optional vector of nucleus labels.
- voi
+optional vector of volume of interest labels.
- rec
+optional vector of reconstruction labels.
- run
+optional vector of run indices.
- echo
+optional vector of echo time indices.
- inv
+optional vector of inversion indices.
- skip_existing
+skip any data files that have already been converted.
+Defaults to TRUE, set to FALSE to force an overwrite of any existing data
+files.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/mrs_data2mat.html b/docs/reference/mrs_data2mat.html
index cf5ff28c..9e47688a 100644
--- a/docs/reference/mrs_data2mat.html
+++ b/docs/reference/mrs_data2mat.html
@@ -1,7 +1,5 @@
-Convert mrs_data object to a matrix, with spectral points in the column
-dimension and dynamics in the row dimension. — mrs_data2mat • Spectroscopy Analysis Tools (spant) Convert mrs_data object to a matrix, with spectral points in the column dimension and dynamics in the row dimension. — mrs_data2mat • Spectroscopy Analysis Tools (spant) Convert mrs_data object to a matrix, with spectral points in the column dimension and dynamics in the row dimension. — mrs_data2spec_mat • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Convert mrs_data object to a matrix, with spectral points in the column dimension and dynamics in the row dimension.
+ Source: R/mrs_data_proc.R
+ mrs_data2spec_mat.Rd
+
+
+
+ Convert mrs_data object to a matrix, with spectral points in the column
+dimension and dynamics in the row dimension.
+
+
+
+ mrs_data2spec_mat(mrs_data, collapse = TRUE)
+
+
+
+ Arguments
+ - mrs_data
+MRS data object or list of MRS data objects.
- collapse
+collapse all other dimensions along the dynamic dimension, eg
+a 16x16 MRSI grid would be first collapsed across 256 dynamic scans.
+
+ Value
+
+
+MRS data matrix.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/mrs_data2vec.html b/docs/reference/mrs_data2vec.html
index fb172d68..a1fd654d 100644
--- a/docs/reference/mrs_data2vec.html
+++ b/docs/reference/mrs_data2vec.html
@@ -1,5 +1,5 @@
-Convert mrs_data object to a vector. — mrs_data2vec • Spectroscopy Analysis Tools (spant) Convert mrs_data object to a vector. — mrs_data2vec • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -126,7 +126,7 @@ Value
diff --git a/docs/reference/mvfftshift.html b/docs/reference/mvfftshift.html
index 92b0841b..976b3410 100644
--- a/docs/reference/mvfftshift.html
+++ b/docs/reference/mvfftshift.html
@@ -1,7 +1,5 @@
-Perform a fftshift on a matrix, with each column replaced by its shifted
-result. — mvfftshift • Spectroscopy Analysis Tools (spant) Perform a fftshift on a matrix, with each column replaced by its shifted result. — mvfftshift • Spectroscopy Analysis Tools (spant) Perform an ifftshift on a matrix, with each column replaced by its shifted
-result. — mvifftshift • Spectroscopy Analysis Tools (spant) Perform an ifftshift on a matrix, with each column replaced by its shifted result. — mvifftshift • Spectroscopy Analysis Tools (spant) Print fit coordinates from a single index. — n2coord • Spectroscopy Analysis Tools (spant) Print fit coordinates from a single index. — n2coord • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/nifti_flip_lr.html b/docs/reference/nifti_flip_lr.html
index 730abe3c..19860b3c 100644
--- a/docs/reference/nifti_flip_lr.html
+++ b/docs/reference/nifti_flip_lr.html
@@ -1,9 +1,5 @@
-Flip the x data dimension order of a nifti image. This corresponds to
-flipping MRI data in the left-right direction, assuming the data in save in
-neurological format (can check with fslorient program). — nifti_flip_lr • Spectroscopy Analysis Tools (spant) Flip the x data dimension order of a nifti image. This corresponds to flipping MRI data in the left-right direction, assuming the data in save in neurological format (can check with fslorient program). — nifti_flip_lr • Spectroscopy Analysis Tools (spant) Export a one-page pdf of a single fit result — one_page_pdf • Spectroscopy Analysis Tools (spant) Export a one-page pdf of a single fit result — one_page_pdf • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -108,7 +108,7 @@ Arguments
diff --git a/docs/reference/ortho3.html b/docs/reference/ortho3.html
index 13ade97d..5d7dd2fd 100644
--- a/docs/reference/ortho3.html
+++ b/docs/reference/ortho3.html
@@ -1,5 +1,5 @@
-Display an orthographic projection plot of a nifti object. — ortho3 • Spectroscopy Analysis Tools (spant) Display an orthographic projection plot of a nifti object. — ortho3 • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -172,7 +172,7 @@ Arguments
diff --git a/docs/reference/ortho3_inter.html b/docs/reference/ortho3_inter.html
index 090cc5e5..15948899 100644
--- a/docs/reference/ortho3_inter.html
+++ b/docs/reference/ortho3_inter.html
@@ -1,5 +1,5 @@
-Display an interactive orthographic projection plot of a nifti object. — ortho3_inter • Spectroscopy Analysis Tools (spant) Display an interactive orthographic projection plot of a nifti object. — ortho3_inter • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -132,7 +132,7 @@ Arguments
diff --git a/docs/reference/peak_info.html b/docs/reference/peak_info.html
index 09058bd8..41c8ffaf 100644
--- a/docs/reference/peak_info.html
+++ b/docs/reference/peak_info.html
@@ -1,7 +1,5 @@
-Search for the highest peak in a spectral region and return the frequency,
-height and FWHM. — peak_info • Spectroscopy Analysis Tools (spant) Search for the highest peak in a spectral region and return the frequency, height and FWHM. — peak_info • Spectroscopy Analysis Tools (spant) Papoulis-Gerchberg (PG) algorithm method for k-space extrapolation. — pg_extrap_xy • Spectroscopy Analysis Tools (spant) Papoulis-Gerchberg (PG) algorithm method for k-space extrapolation. — pg_extrap_xy • Spectroscopy Analysis Tools (spant) Apply phasing parameters to MRS data. — phase • Spectroscopy Analysis Tools (spant) Apply phasing parameters to MRS data. — phase • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/phase_ref_1h_brain.html b/docs/reference/phase_ref_1h_brain.html
new file mode 100644
index 00000000..8707a74a
--- /dev/null
+++ b/docs/reference/phase_ref_1h_brain.html
@@ -0,0 +1,131 @@
+
+Corrected zero order phase and chemical shift offset in 1H MRS data from the brain. — phase_ref_1h_brain • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Corrected zero order phase and chemical shift offset in 1H MRS data from the brain.
+ Source: R/rats.R
+ phase_ref_1h_brain.Rd
+
+
+
+ Corrected zero order phase and chemical shift offset in 1H MRS data from the
+brain.
+
+
+
+ phase_ref_1h_brain(mrs_data, mean_ref = FALSE, ret_corr_only = TRUE)
+
+
+
+ Arguments
+ - mrs_data
+MRS data to be corrected.
- mean_ref
+apply the phase and offset of the mean spectrum to all
+others. Default is FALSE.
- ret_corr_only
+return the corrected data only.
+
+ Value
+
+
+corrected MRS data.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/plot.fit_result.html b/docs/reference/plot.fit_result.html
index e54d3bc1..836a53ee 100644
--- a/docs/reference/plot.fit_result.html
+++ b/docs/reference/plot.fit_result.html
@@ -1,5 +1,5 @@
-Plot the fitting results of an object of class fit_result. — plot.fit_result • Spectroscopy Analysis Tools (spant) Plot the fitting results of an object of class fit_result. — plot.fit_result • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -207,7 +207,7 @@ Arguments
diff --git a/docs/reference/plot.mrs_data.html b/docs/reference/plot.mrs_data.html
index fabcc35b..bb2ec651 100644
--- a/docs/reference/plot.mrs_data.html
+++ b/docs/reference/plot.mrs_data.html
@@ -1,5 +1,5 @@
-Plotting method for objects of class mrs_data. — plot.mrs_data • Spectroscopy Analysis Tools (spant) Plotting method for objects of class mrs_data. — plot.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -287,7 +287,7 @@ Arguments
diff --git a/docs/reference/plot_bc.html b/docs/reference/plot_bc.html
index 4f8309b4..b48142cc 100644
--- a/docs/reference/plot_bc.html
+++ b/docs/reference/plot_bc.html
@@ -1,5 +1,5 @@
-Convenience function to plot a baseline estimate with the original data. — plot_bc • Spectroscopy Analysis Tools (spant) Convenience function to plot a baseline estimate with the original data. — plot_bc • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -108,7 +108,7 @@ Arguments
diff --git a/docs/reference/plot_reg.html b/docs/reference/plot_reg.html
index ae1acbe7..2addb2f6 100644
--- a/docs/reference/plot_reg.html
+++ b/docs/reference/plot_reg.html
@@ -1,5 +1,5 @@
-Plot regressors as an image. — plot_reg • Spectroscopy Analysis Tools (spant) Plot regressors as an image. — plot_reg • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/plot_slice_fit.html b/docs/reference/plot_slice_fit.html
index fbc7b560..57f1af8a 100644
--- a/docs/reference/plot_slice_fit.html
+++ b/docs/reference/plot_slice_fit.html
@@ -1,5 +1,5 @@
-Plot a 2D slice from an MRSI fit result object. — plot_slice_fit • Spectroscopy Analysis Tools (spant) Plot a 2D slice from an MRSI fit result object. — plot_slice_fit • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -129,7 +129,7 @@ Arguments
diff --git a/docs/reference/plot_slice_fit_inter.html b/docs/reference/plot_slice_fit_inter.html
index 4eed104a..da105a7d 100644
--- a/docs/reference/plot_slice_fit_inter.html
+++ b/docs/reference/plot_slice_fit_inter.html
@@ -1,5 +1,5 @@
-Plot a 2D slice from an MRSI fit result object. — plot_slice_fit_inter • Spectroscopy Analysis Tools (spant) Plot a 2D slice from an MRSI fit result object. — plot_slice_fit_inter • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -134,7 +134,7 @@ Arguments
diff --git a/docs/reference/plot_slice_map.html b/docs/reference/plot_slice_map.html
index 553e9ac8..ffb2a134 100644
--- a/docs/reference/plot_slice_map.html
+++ b/docs/reference/plot_slice_map.html
@@ -1,5 +1,5 @@
-Plot a slice from a 7 dimensional array. — plot_slice_map • Spectroscopy Analysis Tools (spant) Plot a slice from a 7 dimensional array. — plot_slice_map • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -153,7 +153,7 @@ Arguments
diff --git a/docs/reference/plot_slice_map_inter.html b/docs/reference/plot_slice_map_inter.html
index 40d33b42..90968f66 100644
--- a/docs/reference/plot_slice_map_inter.html
+++ b/docs/reference/plot_slice_map_inter.html
@@ -1,7 +1,5 @@
-Plot an interactive slice map from a data array where voxels can be selected
-to display a corresponding spectrum. — plot_slice_map_inter • Spectroscopy Analysis Tools (spant) Plot an interactive slice map from a data array where voxels can be selected to display a corresponding spectrum. — plot_slice_map_inter • Spectroscopy Analysis Tools (spant) Plot the spectral standard deviation. — plot_spec_sd • Spectroscopy Analysis Tools (spant) Plot the spectral standard deviation. — plot_spec_sd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Arguments
diff --git a/docs/reference/plot_voi_overlay.html b/docs/reference/plot_voi_overlay.html
index 9a782e88..bbbbf35e 100644
--- a/docs/reference/plot_voi_overlay.html
+++ b/docs/reference/plot_voi_overlay.html
@@ -1,5 +1,5 @@
-Plot a volume as an image overlay. — plot_voi_overlay • Spectroscopy Analysis Tools (spant) Plot a volume as an image overlay. — plot_voi_overlay • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -116,7 +116,7 @@ Arguments
diff --git a/docs/reference/plot_voi_overlay_seg.html b/docs/reference/plot_voi_overlay_seg.html
index 3d4e74ff..0e800ff2 100644
--- a/docs/reference/plot_voi_overlay_seg.html
+++ b/docs/reference/plot_voi_overlay_seg.html
@@ -1,5 +1,5 @@
-Plot a volume as an overlay on a segmented brain volume. — plot_voi_overlay_seg • Spectroscopy Analysis Tools (spant) Plot a volume as an overlay on a segmented brain volume. — plot_voi_overlay_seg • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Arguments
diff --git a/docs/reference/ppm.html b/docs/reference/ppm.html
index c352327a..ee4696e2 100644
--- a/docs/reference/ppm.html
+++ b/docs/reference/ppm.html
@@ -1,5 +1,5 @@
-Return the ppm scale of an MRS dataset or fit result. — ppm • Spectroscopy Analysis Tools (spant) Return the ppm scale of an MRS dataset or fit result. — ppm • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -132,7 +132,7 @@ Value
diff --git a/docs/reference/precomp.html b/docs/reference/precomp.html
index 822d7336..df3d2c6c 100644
--- a/docs/reference/precomp.html
+++ b/docs/reference/precomp.html
@@ -1,7 +1,5 @@
-Save function results to file and load on subsequent calls to avoid repeat
-computation. — precomp • Spectroscopy Analysis Tools (spant) Save function results to file and load on subsequent calls to avoid repeat computation. — precomp • Spectroscopy Analysis Tools (spant) Preprocess and perform quality assessment of a single SVS data set. — preproc_svs • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Preprocess and perform quality assessment of a single SVS data set.
+ Source: R/fmrs.R
+ preproc_svs.Rd
+
+
+
+ Preprocess and perform quality assessment of a single SVS data set.
+
+
+
+ preproc_svs(path, label = NULL, output_dir = NULL, ref_inds = NULL)
+
+
+
+ Arguments
+ - path
+path to the fMRS data file or IMA directory.
- label
+a label to describe the data set.
- output_dir
+output directory.
- ref_inds
+a vector of 1-based indices for any water reference dynamic
+scans.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/preproc_svs_dataset.html b/docs/reference/preproc_svs_dataset.html
new file mode 100644
index 00000000..07c3a29b
--- /dev/null
+++ b/docs/reference/preproc_svs_dataset.html
@@ -0,0 +1,148 @@
+
+Preprocess and perform quality assessment of one or more SVS data sets. — preproc_svs_dataset • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Preprocess and perform quality assessment of one or more SVS data sets.
+ Source: R/fmrs.R
+ preproc_svs_dataset.Rd
+
+
+
+ Preprocess and perform quality assessment of one or more SVS data sets.
+
+
+
+ preproc_svs_dataset(
+ paths,
+ labels = NULL,
+ output_dir = "spant_analysis",
+ exclude_labels = NULL,
+ overwrite = FALSE,
+ ref_inds = NULL,
+ return_results = FALSE
+)
+
+
+
+ Arguments
+ - paths
+paths to the fMRS data file or IMA directory.
- labels
+labels to describe each data set.
- output_dir
+output directory.
- exclude_labels
+vector of labels of scans to exclude, eg poor quality
+data.
- overwrite
+overwrite saved results, defaults to FALSE.
- ref_inds
+a vector of 1-based indices for any water reference dynamic
+scans.
- return_results
+function will return key outputs, defaults to FALSE.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/print.fit_result.html b/docs/reference/print.fit_result.html
index 297f28dc..5f434e57 100644
--- a/docs/reference/print.fit_result.html
+++ b/docs/reference/print.fit_result.html
@@ -1,5 +1,5 @@
-Print a summary of an object of class fit_result. — print.fit_result • Spectroscopy Analysis Tools (spant) Print a summary of an object of class fit_result. — print.fit_result • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -105,7 +105,7 @@ Arguments
diff --git a/docs/reference/print.mrs_data.html b/docs/reference/print.mrs_data.html
index 51199017..e1561eb2 100644
--- a/docs/reference/print.mrs_data.html
+++ b/docs/reference/print.mrs_data.html
@@ -1,5 +1,5 @@
-Print a summary of mrs_data parameters. — print.mrs_data • Spectroscopy Analysis Tools (spant) Print a summary of mrs_data parameters. — print.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -109,7 +109,7 @@ Arguments
diff --git a/docs/reference/qn_states.html b/docs/reference/qn_states.html
index 0f42f2f9..d7aa6715 100644
--- a/docs/reference/qn_states.html
+++ b/docs/reference/qn_states.html
@@ -1,5 +1,5 @@
-Get the quantum coherence matrix for a spin system. — qn_states • Spectroscopy Analysis Tools (spant) Get the quantum coherence matrix for a spin system. — qn_states • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/rats.html b/docs/reference/rats.html
index 5a39a396..93585e08 100644
--- a/docs/reference/rats.html
+++ b/docs/reference/rats.html
@@ -1,5 +1,5 @@
-Robust Alignment to a Target Spectrum (RATS). — rats • Spectroscopy Analysis Tools (spant) Robust Alignment to a Target Spectrum (RATS). — rats • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -207,7 +207,7 @@ Value
diff --git a/docs/reference/re_weighting.html b/docs/reference/re_weighting.html
index d21caf21..8b0b070a 100644
--- a/docs/reference/re_weighting.html
+++ b/docs/reference/re_weighting.html
@@ -1,5 +1,5 @@
-Apply a weighting to the FID to enhance spectral resolution. — re_weighting • Spectroscopy Analysis Tools (spant) Apply a weighting to the FID to enhance spectral resolution. — re_weighting • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/read_basis.html b/docs/reference/read_basis.html
index da9b94af..eb6f8557 100644
--- a/docs/reference/read_basis.html
+++ b/docs/reference/read_basis.html
@@ -1,5 +1,5 @@
-Read a basis file in LCModel .basis format. — read_basis • Spectroscopy Analysis Tools (spant) Read a basis file in LCModel .basis format. — read_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/read_ima_coil_dir.html b/docs/reference/read_ima_coil_dir.html
index 28c02de0..4f073cd8 100644
--- a/docs/reference/read_ima_coil_dir.html
+++ b/docs/reference/read_ima_coil_dir.html
@@ -1,9 +1,5 @@
-Read a directory containing Siemens MRS IMA files and combine along the coil
-dimension. Note that the coil ID is inferred from the sorted file name and
-should be checked when consistency is required between two directories. — read_ima_coil_dir • Spectroscopy Analysis Tools (spant) Read a directory containing Siemens MRS IMA files and combine along the coil dimension. Note that the coil ID is inferred from the sorted file name and should be checked when consistency is required between two directories. — read_ima_coil_dir • Spectroscopy Analysis Tools (spant) Read a directory containing Siemens MRS IMA files and combine along the
-dynamic dimension. Note that the coil ID is inferred from the sorted file
-name and should be checked when consistency is required. — read_ima_dyn_dir • Spectroscopy Analysis Tools (spant) Read a directory containing Siemens MRS IMA files and combine along the dynamic dimension. Note that the coil ID is inferred from the sorted file name and should be checked when consistency is required. — read_ima_dyn_dir • Spectroscopy Analysis Tools (spant) Read an LCModel formatted coord file containing fit information. — read_lcm_coord • Spectroscopy Analysis Tools (spant) Read an LCModel formatted coord file containing fit information. — read_lcm_coord • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -107,7 +107,7 @@ Value
diff --git a/docs/reference/read_mrs.html b/docs/reference/read_mrs.html
index 3ac2a36b..2cf36b20 100644
--- a/docs/reference/read_mrs.html
+++ b/docs/reference/read_mrs.html
@@ -1,5 +1,5 @@
-Read MRS data from a file. — read_mrs • Spectroscopy Analysis Tools (spant) Read MRS data from a file. — read_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -88,7 +88,8 @@ Read MRS data from a file.
full_fid = FALSE,
omit_svs_ref_scans = TRUE,
verbose = FALSE,
- extra = NULL
+ extra = NULL,
+ fid_filt_dist = NULL
)
@@ -140,6 +141,13 @@ Arguments
an optional data frame to provide additional variables for use
in subsequent analysis steps, eg id or grouping variables.
fid_filt_dist
+indicate if the data has a distorted FID due to a
+brick-wall filter being used to downsample the data. Default is to auto
+detect this from the data, but TRUE or FALSE options can be given to override
+detection.
Value
@@ -183,7 +191,7 @@ Examples
diff --git a/docs/reference/read_mrs_tqn.html b/docs/reference/read_mrs_tqn.html
index 5766362f..84bdaf3a 100644
--- a/docs/reference/read_mrs_tqn.html
+++ b/docs/reference/read_mrs_tqn.html
@@ -1,5 +1,5 @@
-Read MRS data using the TARQUIN software package. — read_mrs_tqn • Spectroscopy Analysis Tools (spant) Read MRS data using the TARQUIN software package. — read_mrs_tqn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -131,7 +131,7 @@ Examples
diff --git a/docs/reference/read_pulse_ascii.html b/docs/reference/read_pulse_ascii.html
index c9e0d43c..ab11c9cc 100644
--- a/docs/reference/read_pulse_ascii.html
+++ b/docs/reference/read_pulse_ascii.html
@@ -1,5 +1,5 @@
-Read an ASCII formatted pulse file. — read_pulse_ascii • Spectroscopy Analysis Tools (spant) Read an ASCII formatted pulse file. — read_pulse_ascii • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/read_pulse_bruker.html b/docs/reference/read_pulse_bruker.html
index c92bf76a..dbe9073b 100644
--- a/docs/reference/read_pulse_bruker.html
+++ b/docs/reference/read_pulse_bruker.html
@@ -1,5 +1,5 @@
-Read a Bruker formatted pulse file — read_pulse_bruker • Spectroscopy Analysis Tools (spant) Read a Bruker formatted pulse file — read_pulse_bruker • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/read_pulse_pta.html b/docs/reference/read_pulse_pta.html
index 72e1b6d4..a0fac3c3 100644
--- a/docs/reference/read_pulse_pta.html
+++ b/docs/reference/read_pulse_pta.html
@@ -1,5 +1,5 @@
-Read a .pta formatted pulse file compatible with Siemens PulseTool. — read_pulse_pta • Spectroscopy Analysis Tools (spant) Read a .pta formatted pulse file compatible with Siemens PulseTool. — read_pulse_pta • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/read_siemens_txt_hdr.html b/docs/reference/read_siemens_txt_hdr.html
index 23fb8c70..3a17d87c 100644
--- a/docs/reference/read_siemens_txt_hdr.html
+++ b/docs/reference/read_siemens_txt_hdr.html
@@ -1,5 +1,5 @@
-Read the text format header found in Siemens IMA and TWIX data files. — read_siemens_txt_hdr • Spectroscopy Analysis Tools (spant) Read the text format header found in Siemens IMA and TWIX data files. — read_siemens_txt_hdr • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -78,7 +78,7 @@ Read the text format header found in Siemens IMA and TWIX data files.
- read_siemens_txt_hdr(input, version = "vd", verbose, offset = 0)
+ read_siemens_txt_hdr(input, version = "vd", verbose = FALSE, offset = 0)
@@ -118,7 +118,7 @@ Value
diff --git a/docs/reference/read_tqn_fit.html b/docs/reference/read_tqn_fit.html
index 4da6c25e..a1630420 100644
--- a/docs/reference/read_tqn_fit.html
+++ b/docs/reference/read_tqn_fit.html
@@ -1,5 +1,5 @@
-Reader for csv fit results generated by TARQUIN. — read_tqn_fit • Spectroscopy Analysis Tools (spant) Reader for csv fit results generated by TARQUIN. — read_tqn_fit • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -113,7 +113,7 @@ Examples
diff --git a/docs/reference/read_tqn_result.html b/docs/reference/read_tqn_result.html
index 36659714..68a3e98c 100644
--- a/docs/reference/read_tqn_result.html
+++ b/docs/reference/read_tqn_result.html
@@ -1,5 +1,5 @@
-Reader for csv results generated by TARQUIN. — read_tqn_result • Spectroscopy Analysis Tools (spant) Reader for csv results generated by TARQUIN. — read_tqn_result • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -117,7 +117,7 @@ Examples
diff --git a/docs/reference/recon_imag.html b/docs/reference/recon_imag.html
index d2a72225..5bc3b1eb 100644
--- a/docs/reference/recon_imag.html
+++ b/docs/reference/recon_imag.html
@@ -1,7 +1,5 @@
-Reconstruct complex time-domain data from the real part of frequency-domain
-data. — recon_imag • Spectroscopy Analysis Tools (spant) Reconstruct complex time-domain data from the real part of frequency-domain data. — recon_imag • Spectroscopy Analysis Tools (spant) Reconstruct complex time-domain data from the real part of frequency-domain
-data. — recon_imag_vec • Spectroscopy Analysis Tools (spant) Reconstruct complex time-domain data from the real part of frequency-domain data. — recon_imag_vec • Spectroscopy Analysis Tools (spant) Reconstruct 2D MRSI data from a twix file loaded with read_mrs. — recon_twix_2d_mrsi • Spectroscopy Analysis Tools (spant) Reconstruct 2D MRSI data from a twix file loaded with read_mrs. — recon_twix_2d_mrsi • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/rectangular_mask.html b/docs/reference/rectangular_mask.html
index a2117283..6e469bc9 100644
--- a/docs/reference/rectangular_mask.html
+++ b/docs/reference/rectangular_mask.html
@@ -1,5 +1,5 @@
-Create a rectangular mask stored as a matrix of logical values. — rectangular_mask • Spectroscopy Analysis Tools (spant) Create a rectangular mask stored as a matrix of logical values. — rectangular_mask • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -130,7 +130,7 @@ Value
diff --git a/docs/reference/reexports.html b/docs/reference/reexports.html
index 694a75d1..a59e8379 100644
--- a/docs/reference/reexports.html
+++ b/docs/reference/reexports.html
@@ -1,5 +1,5 @@
-Objects exported from other packages — reexports • Spectroscopy Analysis Tools (spant) Objects exported from other packages — reexports • Spectroscopy Analysis Tools (spant)
Spectroscopy Analysis Tools (spant)
- 2.21.0
+ 2.22.0
@@ -103,7 +103,7 @@ Objects exported from other packages
diff --git a/docs/reference/rep_array_dim.html b/docs/reference/rep_array_dim.html
index b9c49b4a..48c0a5ed 100644
--- a/docs/reference/rep_array_dim.html
+++ b/docs/reference/rep_array_dim.html
@@ -1,5 +1,5 @@
-Repeat an array over a given dimension. — rep_array_dim • Spectroscopy Analysis Tools (spant) Repeat an array over a given dimension. — rep_array_dim • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/rep_dyn.html b/docs/reference/rep_dyn.html
index 6bbfb0ef..89a4bb9b 100644
--- a/docs/reference/rep_dyn.html
+++ b/docs/reference/rep_dyn.html
@@ -1,5 +1,5 @@
-Replicate a scan in the dynamic dimension. — rep_dyn • Spectroscopy Analysis Tools (spant) Replicate a scan in the dynamic dimension. — rep_dyn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/rep_mrs.html b/docs/reference/rep_mrs.html
index 67730b5c..becb8f00 100644
--- a/docs/reference/rep_mrs.html
+++ b/docs/reference/rep_mrs.html
@@ -1,5 +1,5 @@
-Replicate a scan over a given dimension. — rep_mrs • Spectroscopy Analysis Tools (spant) Replicate a scan over a given dimension. — rep_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -138,7 +138,7 @@ Value
diff --git a/docs/reference/resample_basis.html b/docs/reference/resample_basis.html
index b0f2ab17..c7a6222a 100644
--- a/docs/reference/resample_basis.html
+++ b/docs/reference/resample_basis.html
@@ -1,5 +1,5 @@
-Resample a basis-set to match a mrs_data acquisition. — resample_basis • Spectroscopy Analysis Tools (spant) Resample a basis-set to match a mrs_data acquisition. — resample_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -116,7 +116,7 @@ Value
diff --git a/docs/reference/resample_img.html b/docs/reference/resample_img.html
index f1e7beaf..b0cc8f71 100644
--- a/docs/reference/resample_img.html
+++ b/docs/reference/resample_img.html
@@ -1,5 +1,5 @@
-Resample an image to match a target image space. — resample_img • Spectroscopy Analysis Tools (spant) Resample an image to match a target image space. — resample_img • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/resample_voi.html b/docs/reference/resample_voi.html
index 8fbfa836..a29ab096 100644
--- a/docs/reference/resample_voi.html
+++ b/docs/reference/resample_voi.html
@@ -1,7 +1,5 @@
-Resample a VOI to match a target image space using nearest-neighbour
-interpolation. — resample_voi • Spectroscopy Analysis Tools (spant) Resample a VOI to match a target image space using nearest-neighbour interpolation. — resample_voi • Spectroscopy Analysis Tools (spant) Reslice a nifti object to match the orientation of mrs data. — reslice_to_mrs • Spectroscopy Analysis Tools (spant) Reslice a nifti object to match the orientation of mrs data. — reslice_to_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/reson_table2mrs_data.html b/docs/reference/reson_table2mrs_data.html
index d75579ee..c5a2167a 100644
--- a/docs/reference/reson_table2mrs_data.html
+++ b/docs/reference/reson_table2mrs_data.html
@@ -1,5 +1,5 @@
-Generate mrs_data from a table of single Lorentzian resonances. — reson_table2mrs_data • Spectroscopy Analysis Tools (spant) Generate mrs_data from a table of single Lorentzian resonances. — reson_table2mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -119,7 +119,7 @@ Value
diff --git a/docs/reference/rm_dyns.html b/docs/reference/rm_dyns.html
index 5d5ef692..573e1f51 100644
--- a/docs/reference/rm_dyns.html
+++ b/docs/reference/rm_dyns.html
@@ -1,5 +1,5 @@
-Remove a subset of dynamic scans. — rm_dyns • Spectroscopy Analysis Tools (spant) Remove a subset of dynamic scans. — rm_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/scale_amp_molal.html b/docs/reference/scale_amp_molal.html
index aaeee1f2..7acb8cb0 100644
--- a/docs/reference/scale_amp_molal.html
+++ b/docs/reference/scale_amp_molal.html
@@ -1,7 +1,5 @@
-Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water). — scale_amp_molal • Spectroscopy Analysis Tools (spant) Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / kg of tissue water). — scale_amp_molal • Spectroscopy Analysis Tools (spant)
Spectroscopy Analysis Tools (spant)
- 2.21.0
+ 2.22.0
@@ -76,8 +74,7 @@
- Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water).
+ Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / kg of tissue water).
Source: R/amp_scaling.R
scale_amp_molal.Rd
@@ -163,7 +160,7 @@ Value
diff --git a/docs/reference/scale_amp_molal_pvc.html b/docs/reference/scale_amp_molal_pvc.html
index 962d6afc..4d194abd 100644
--- a/docs/reference/scale_amp_molal_pvc.html
+++ b/docs/reference/scale_amp_molal_pvc.html
@@ -1,7 +1,5 @@
-Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water). — scale_amp_molal_pvc • Spectroscopy Analysis Tools (spant)
@@ -75,8 +73,7 @@
- Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water).
+ Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / kg of tissue water).
Source: R/amp_scaling.R
scale_amp_molal_pvc.Rd
@@ -141,7 +138,7 @@ Value
diff --git a/docs/reference/scale_amp_molar.html b/docs/reference/scale_amp_molar.html
index 02358d91..dc87a338 100644
--- a/docs/reference/scale_amp_molar.html
+++ b/docs/reference/scale_amp_molar.html
@@ -1,7 +1,5 @@
-Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / Litre of tissue). — scale_amp_molar • Spectroscopy Analysis Tools (spant) Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / Litre of tissue). — scale_amp_molar • Spectroscopy Analysis Tools (spant) Convert default LCM/TARQUIN concentration scaling to molal units with partial
-volume correction. — scale_amp_molar2molal_pvc • Spectroscopy Analysis Tools (spant) Convert default LCM/TARQUIN concentration scaling to molal units with partial volume correction. — scale_amp_molar2molal_pvc • Spectroscopy Analysis Tools (spant) Scale fitted amplitudes to a ratio of signal amplitude. — scale_amp_ratio • Spectroscopy Analysis Tools (spant) Scale fitted amplitudes to a ratio of signal amplitude. — scale_amp_ratio • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -116,7 +116,7 @@ Value
diff --git a/docs/reference/scale_amp_ratio_value.html b/docs/reference/scale_amp_ratio_value.html
index 2036837a..6af8ac51 100644
--- a/docs/reference/scale_amp_ratio_value.html
+++ b/docs/reference/scale_amp_ratio_value.html
@@ -1,5 +1,5 @@
-Scale fitted amplitudes to a ratio of signal amplitude. — scale_amp_ratio_value • Spectroscopy Analysis Tools (spant) Scale fitted amplitudes to a ratio of signal amplitude. — scale_amp_ratio_value • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/scale_amp_water_ratio.html b/docs/reference/scale_amp_water_ratio.html
index 5b25e884..35a76b00 100644
--- a/docs/reference/scale_amp_water_ratio.html
+++ b/docs/reference/scale_amp_water_ratio.html
@@ -1,5 +1,5 @@
-Scale metabolite amplitudes as a ratio to the unsuppressed water amplitude. — scale_amp_water_ratio • Spectroscopy Analysis Tools (spant) Scale metabolite amplitudes as a ratio to the unsuppressed water amplitude. — scale_amp_water_ratio • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/scale_basis_amp.html b/docs/reference/scale_basis_amp.html
index 9401c3f1..5a58b5e5 100644
--- a/docs/reference/scale_basis_amp.html
+++ b/docs/reference/scale_basis_amp.html
@@ -1,5 +1,5 @@
-Scale a basis object by a scalar. — scale_basis_amp • Spectroscopy Analysis Tools (spant) Scale a basis object by a scalar. — scale_basis_amp • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/scale_basis_from_singlet.html b/docs/reference/scale_basis_from_singlet.html
index 0d542bc8..c9a19e77 100644
--- a/docs/reference/scale_basis_from_singlet.html
+++ b/docs/reference/scale_basis_from_singlet.html
@@ -1,5 +1,5 @@
-Scale a basis-set to be consistent with spant assumptions for water scaling. — scale_basis_from_singlet • Spectroscopy Analysis Tools (spant) Scale a basis-set to be consistent with spant assumptions for water scaling. — scale_basis_from_singlet • Spectroscopy Analysis Tools (spant)
Spectroscopy Analysis Tools (spant)
- 2.21.0
+ 2.22.0
@@ -127,7 +127,7 @@ Value
diff --git a/docs/reference/scale_mrs_amp.html b/docs/reference/scale_mrs_amp.html
index b5501a0d..990f058a 100644
--- a/docs/reference/scale_mrs_amp.html
+++ b/docs/reference/scale_mrs_amp.html
@@ -1,5 +1,5 @@
-Scale an mrs_data object by a scalar or vector or amplitudes. — scale_mrs_amp • Spectroscopy Analysis Tools (spant) Scale an mrs_data object by a scalar or vector or amplitudes. — scale_mrs_amp • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/scale_spec.html b/docs/reference/scale_spec.html
index 4f6ea835..6b3ddba4 100644
--- a/docs/reference/scale_spec.html
+++ b/docs/reference/scale_spec.html
@@ -1,5 +1,5 @@
-Scale mrs_data to a spectral region. — scale_spec • Spectroscopy Analysis Tools (spant) Scale mrs_data to a spectral region. — scale_spec • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -141,7 +141,7 @@ Value
diff --git a/docs/reference/sd.html b/docs/reference/sd.html
index ea1eec9f..3ae4dfd4 100644
--- a/docs/reference/sd.html
+++ b/docs/reference/sd.html
@@ -1,5 +1,5 @@
-Calculate the standard deviation spectrum from an mrs_data object. — sd • Spectroscopy Analysis Tools (spant) Calculate the standard deviation spectrum from an mrs_data object. — sd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/sd.mrs_data.html b/docs/reference/sd.mrs_data.html
index 3f92a49f..13bdda85 100644
--- a/docs/reference/sd.mrs_data.html
+++ b/docs/reference/sd.mrs_data.html
@@ -1,5 +1,5 @@
-Calculate the standard deviation spectrum from an mrs_data object. — sd.mrs_data • Spectroscopy Analysis Tools (spant) Calculate the standard deviation spectrum from an mrs_data object. — sd.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/seconds.html b/docs/reference/seconds.html
index b34d6627..467ee17f 100644
--- a/docs/reference/seconds.html
+++ b/docs/reference/seconds.html
@@ -1,5 +1,5 @@
-Return a time scale vector to match the FID of an MRS data object. — seconds • Spectroscopy Analysis Tools (spant) Return a time scale vector to match the FID of an MRS data object. — seconds • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/seq_cpmg_ideal.html b/docs/reference/seq_cpmg_ideal.html
index 547e96ab..45727c86 100644
--- a/docs/reference/seq_cpmg_ideal.html
+++ b/docs/reference/seq_cpmg_ideal.html
@@ -1,5 +1,5 @@
-CPMG style sequence with ideal pulses. — seq_cpmg_ideal • Spectroscopy Analysis Tools (spant) CPMG style sequence with ideal pulses. — seq_cpmg_ideal • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/seq_mega_press_ideal.html b/docs/reference/seq_mega_press_ideal.html
index 0769b8b4..a9cd7fa0 100644
--- a/docs/reference/seq_mega_press_ideal.html
+++ b/docs/reference/seq_mega_press_ideal.html
@@ -1,7 +1,5 @@
-MEGA-PRESS sequence with ideal localisation pulses and Gaussian shaped
-editing pulse. — seq_mega_press_ideal • Spectroscopy Analysis Tools (spant) MEGA-PRESS sequence with ideal localisation pulses and Gaussian shaped editing pulse. — seq_mega_press_ideal • Spectroscopy Analysis Tools (spant) PRESS sequence with shaped refocusing pulses. — seq_press_2d_shaped • Spectroscopy Analysis Tools (spant) PRESS sequence with shaped refocusing pulses. — seq_press_2d_shaped • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -165,7 +165,7 @@ Value
diff --git a/docs/reference/seq_press_ideal.html b/docs/reference/seq_press_ideal.html
index 8c976856..72c3af3d 100644
--- a/docs/reference/seq_press_ideal.html
+++ b/docs/reference/seq_press_ideal.html
@@ -1,5 +1,5 @@
-PRESS sequence with ideal pulses. — seq_press_ideal • Spectroscopy Analysis Tools (spant) PRESS sequence with ideal pulses. — seq_press_ideal • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/seq_pulse_acquire.html b/docs/reference/seq_pulse_acquire.html
index 4a88fc64..ad80571e 100644
--- a/docs/reference/seq_pulse_acquire.html
+++ b/docs/reference/seq_pulse_acquire.html
@@ -1,5 +1,5 @@
-Simple pulse and acquire sequence with ideal pulses. — seq_pulse_acquire • Spectroscopy Analysis Tools (spant) Simple pulse and acquire sequence with ideal pulses. — seq_pulse_acquire • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/seq_slaser_ideal.html b/docs/reference/seq_slaser_ideal.html
index 74688f4d..eb83e8e3 100644
--- a/docs/reference/seq_slaser_ideal.html
+++ b/docs/reference/seq_slaser_ideal.html
@@ -1,5 +1,5 @@
-sLASER sequence with ideal pulses. — seq_slaser_ideal • Spectroscopy Analysis Tools (spant) sLASER sequence with ideal pulses. — seq_slaser_ideal • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -126,7 +126,7 @@ Value
diff --git a/docs/reference/seq_spin_echo_ideal.html b/docs/reference/seq_spin_echo_ideal.html
index e23271de..4248716f 100644
--- a/docs/reference/seq_spin_echo_ideal.html
+++ b/docs/reference/seq_spin_echo_ideal.html
@@ -1,5 +1,5 @@
-Spin echo sequence with ideal pulses. — seq_spin_echo_ideal • Spectroscopy Analysis Tools (spant) Spin echo sequence with ideal pulses. — seq_spin_echo_ideal • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/seq_steam_ideal.html b/docs/reference/seq_steam_ideal.html
index a60685a8..1c8115d7 100644
--- a/docs/reference/seq_steam_ideal.html
+++ b/docs/reference/seq_steam_ideal.html
@@ -1,5 +1,5 @@
-STEAM sequence with ideal pulses. — seq_steam_ideal • Spectroscopy Analysis Tools (spant) STEAM sequence with ideal pulses. — seq_steam_ideal • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -128,7 +128,7 @@ Value
diff --git a/docs/reference/seq_steam_ideal_cof.html b/docs/reference/seq_steam_ideal_cof.html
index 8f225740..cba7af91 100644
--- a/docs/reference/seq_steam_ideal_cof.html
+++ b/docs/reference/seq_steam_ideal_cof.html
@@ -1,7 +1,5 @@
-STEAM sequence with ideal pulses and coherence order filtering to simulate
-gradient crushers. — seq_steam_ideal_cof • Spectroscopy Analysis Tools (spant) STEAM sequence with ideal pulses and coherence order filtering to simulate gradient crushers. — seq_steam_ideal_cof • Spectroscopy Analysis Tools (spant) STEAM sequence with ideal pulses using the z-rotation gradient simulation
-method described by Young et al JMR 140, 146-152 (1999). — seq_steam_ideal_young • Spectroscopy Analysis Tools (spant) STEAM sequence with ideal pulses using the z-rotation gradient simulation method described by Young et al JMR 140, 146-152 (1999). — seq_steam_ideal_young • Spectroscopy Analysis Tools (spant) Set the number of transients for an mrs_data object. — set_Ntrans • Spectroscopy Analysis Tools (spant) Set the number of transients for an mrs_data object. — set_Ntrans • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/set_def_acq_paras.html b/docs/reference/set_def_acq_paras.html
index 3e1b4004..cc2ada9c 100644
--- a/docs/reference/set_def_acq_paras.html
+++ b/docs/reference/set_def_acq_paras.html
@@ -1,5 +1,5 @@
-Set the default acquisition parameters. — set_def_acq_paras • Spectroscopy Analysis Tools (spant) Set the default acquisition parameters. — set_def_acq_paras • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Arguments
diff --git a/docs/reference/set_lcm_cmd.html b/docs/reference/set_lcm_cmd.html
index 2056ed01..42bb2f24 100644
--- a/docs/reference/set_lcm_cmd.html
+++ b/docs/reference/set_lcm_cmd.html
@@ -1,5 +1,5 @@
-Set the command to run the LCModel command-line program. — set_lcm_cmd • Spectroscopy Analysis Tools (spant) Set the command to run the LCModel command-line program. — set_lcm_cmd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/set_lw.html b/docs/reference/set_lw.html
index b64ec851..bb176c62 100644
--- a/docs/reference/set_lw.html
+++ b/docs/reference/set_lw.html
@@ -1,5 +1,5 @@
-Apply line-broadening to an mrs_data object to achieve a specified linewidth. — set_lw • Spectroscopy Analysis Tools (spant) Apply line-broadening to an mrs_data object to achieve a specified linewidth. — set_lw • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -123,7 +123,7 @@ Value
diff --git a/docs/reference/set_mask_xy_mat.html b/docs/reference/set_mask_xy_mat.html
index 49dc5d4e..52c4b617 100644
--- a/docs/reference/set_mask_xy_mat.html
+++ b/docs/reference/set_mask_xy_mat.html
@@ -1,5 +1,5 @@
-Set the masked voxels in a 2D MRSI dataset to given spectrum. — set_mask_xy_mat • Spectroscopy Analysis Tools (spant) Set the masked voxels in a 2D MRSI dataset to given spectrum. — set_mask_xy_mat • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Value
diff --git a/docs/reference/set_precomp_mode.html b/docs/reference/set_precomp_mode.html
index f44bd5d3..47c28e3b 100644
--- a/docs/reference/set_precomp_mode.html
+++ b/docs/reference/set_precomp_mode.html
@@ -1,5 +1,5 @@
-Set the precompute mode. — set_precomp_mode • Spectroscopy Analysis Tools (spant) Set the precompute mode. — set_precomp_mode • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/set_precomp_verbose.html b/docs/reference/set_precomp_verbose.html
index 1453a231..9c613505 100644
--- a/docs/reference/set_precomp_verbose.html
+++ b/docs/reference/set_precomp_verbose.html
@@ -1,5 +1,5 @@
-Set the verbosity of the precompute function. — set_precomp_verbose • Spectroscopy Analysis Tools (spant) Set the verbosity of the precompute function. — set_precomp_verbose • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/set_ref.html b/docs/reference/set_ref.html
index 8953fa50..5436dfa2 100644
--- a/docs/reference/set_ref.html
+++ b/docs/reference/set_ref.html
@@ -1,5 +1,5 @@
-Set the ppm reference value (eg ppm value at 0Hz). — set_ref • Spectroscopy Analysis Tools (spant) Set the ppm reference value (eg ppm value at 0Hz). — set_ref • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/set_td_pts.html b/docs/reference/set_td_pts.html
index 8a80d42a..586459ff 100644
--- a/docs/reference/set_td_pts.html
+++ b/docs/reference/set_td_pts.html
@@ -1,7 +1,5 @@
-Set the number of time-domain data points, truncating or zero-filling as
-appropriate. — set_td_pts • Spectroscopy Analysis Tools (spant) Set the number of time-domain data points, truncating or zero-filling as appropriate. — set_td_pts • Spectroscopy Analysis Tools (spant) Set the command to run the TARQUIN command-line program. — set_tqn_cmd • Spectroscopy Analysis Tools (spant) Set the command to run the TARQUIN command-line program. — set_tqn_cmd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/set_tr.html b/docs/reference/set_tr.html
index b2109ab0..65c9df5f 100644
--- a/docs/reference/set_tr.html
+++ b/docs/reference/set_tr.html
@@ -1,5 +1,5 @@
-Set the repetition time of an MRS dataset. — set_tr • Spectroscopy Analysis Tools (spant) Set the repetition time of an MRS dataset. — set_tr • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/shift.html b/docs/reference/shift.html
index ab0fe724..034591d0 100644
--- a/docs/reference/shift.html
+++ b/docs/reference/shift.html
@@ -1,5 +1,5 @@
-Apply a frequency shift to MRS data. — shift • Spectroscopy Analysis Tools (spant) Apply a frequency shift to MRS data. — shift • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/shift_basis.html b/docs/reference/shift_basis.html
index 2884be19..f55a65e0 100644
--- a/docs/reference/shift_basis.html
+++ b/docs/reference/shift_basis.html
@@ -1,5 +1,5 @@
-Apply frequency shifts to basis set signals. — shift_basis • Spectroscopy Analysis Tools (spant) Apply frequency shifts to basis set signals. — shift_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Value
diff --git a/docs/reference/sim_basis.html b/docs/reference/sim_basis.html
index c7838c46..bb5fefc6 100644
--- a/docs/reference/sim_basis.html
+++ b/docs/reference/sim_basis.html
@@ -1,5 +1,5 @@
-Simulate a basis set object. — sim_basis • Spectroscopy Analysis Tools (spant) Simulate a basis set object. — sim_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -136,7 +136,7 @@ Value
diff --git a/docs/reference/sim_basis_1h_brain.html b/docs/reference/sim_basis_1h_brain.html
index 62ed7389..f71ffa0b 100644
--- a/docs/reference/sim_basis_1h_brain.html
+++ b/docs/reference/sim_basis_1h_brain.html
@@ -1,7 +1,5 @@
-Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS
-sequence. Note, ideal pulses are assumed. — sim_basis_1h_brain • Spectroscopy Analysis Tools (spant) Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS sequence. Note, ideal pulses are assumed. — sim_basis_1h_brain • Spectroscopy Analysis Tools (spant) Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS
-sequence. Note, ideal pulses are assumed. — sim_basis_1h_brain_press • Spectroscopy Analysis Tools (spant) Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS sequence. Note, ideal pulses are assumed. — sim_basis_1h_brain_press • Spectroscopy Analysis Tools (spant) Simulate a macromolecular and lipid basis-set suitable for 1H brain MRS
-analysis. — sim_basis_mm_lip_lcm • Spectroscopy Analysis Tools (spant) Simulate a macromolecular and lipid basis-set suitable for 1H brain MRS analysis. — sim_basis_mm_lip_lcm • Spectroscopy Analysis Tools (spant) Simulate a basis file using TARQUIN. — sim_basis_tqn • Spectroscopy Analysis Tools (spant) Simulate a basis file using TARQUIN. — sim_basis_tqn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -129,7 +129,7 @@ Examples
diff --git a/docs/reference/sim_brain_1h.html b/docs/reference/sim_brain_1h.html
index 2044cf1a..717ee289 100644
--- a/docs/reference/sim_brain_1h.html
+++ b/docs/reference/sim_brain_1h.html
@@ -1,5 +1,5 @@
-Simulate MRS data with a similar appearance to normal brain (by default). — sim_brain_1h • Spectroscopy Analysis Tools (spant) Simulate MRS data with a similar appearance to normal brain (by default). — sim_brain_1h • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -159,7 +159,7 @@ Value
diff --git a/docs/reference/sim_mol.html b/docs/reference/sim_mol.html
index 23bcef50..77f76a50 100644
--- a/docs/reference/sim_mol.html
+++ b/docs/reference/sim_mol.html
@@ -1,5 +1,5 @@
-Simulate a mol_parameter object. — sim_mol • Spectroscopy Analysis Tools (spant) Simulate a mol_parameter object. — sim_mol • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -143,7 +143,7 @@ Value
diff --git a/docs/reference/sim_noise.html b/docs/reference/sim_noise.html
index 23875f79..a71477d4 100644
--- a/docs/reference/sim_noise.html
+++ b/docs/reference/sim_noise.html
@@ -1,5 +1,5 @@
-Simulate an mrs_data object containing simulated Gaussian noise. — sim_noise • Spectroscopy Analysis Tools (spant) Simulate an mrs_data object containing simulated Gaussian noise. — sim_noise • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -84,6 +84,7 @@ Simulate an mrs_data object containing simulated Gaussian noise.
ft = def_ft(),
N = def_N(),
ref = def_ref(),
+ nuc = def_nuc(),
dyns = 1,
fd = TRUE
)
@@ -111,6 +112,10 @@ Arguments
reference value for ppm scale.
nuc
+resonant nucleus.
dyns
number of dynamic scans to generate.
Value
diff --git a/docs/reference/sim_resonances.html b/docs/reference/sim_resonances.html
index 19e9a8a4..d4f8d7c0 100644
--- a/docs/reference/sim_resonances.html
+++ b/docs/reference/sim_resonances.html
@@ -1,5 +1,5 @@
-Simulate a MRS data object containing a set of simulated resonances. — sim_resonances • Spectroscopy Analysis Tools (spant) Simulate a MRS data object containing a set of simulated resonances. — sim_resonances • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -161,7 +161,7 @@ Examples
diff --git a/docs/reference/sim_th_excit_profile.html b/docs/reference/sim_th_excit_profile.html
index 5535c5ef..e781cab1 100644
--- a/docs/reference/sim_th_excit_profile.html
+++ b/docs/reference/sim_th_excit_profile.html
@@ -1,7 +1,5 @@
-Simulate an ideal pulse excitation profile by smoothing a top-hat function
-with a Gaussian. — sim_th_excit_profile • Spectroscopy Analysis Tools (spant) Simulate an ideal pulse excitation profile by smoothing a top-hat function with a Gaussian. — sim_th_excit_profile • Spectroscopy Analysis Tools (spant) Simulate an mrs_data object containing complex zero valued samples. — sim_zero • Spectroscopy Analysis Tools (spant) Simulate an mrs_data object containing complex zero valued samples. — sim_zero • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -78,7 +78,14 @@ Simulate an mrs_data object containing complex zero valued samples.
-
+
@@ -99,6 +106,10 @@ Arguments
reference value for ppm scale.
nuc
+resonant nucleus.
dyns
number of dynamic scans to generate.
Value
diff --git a/docs/reference/smooth_dyns.html b/docs/reference/smooth_dyns.html
index 4cc8da50..accf3a51 100644
--- a/docs/reference/smooth_dyns.html
+++ b/docs/reference/smooth_dyns.html
@@ -1,5 +1,5 @@
-Smooth data across the dynamic dimension with a Gaussian kernel. — smooth_dyns • Spectroscopy Analysis Tools (spant) Smooth data across the dynamic dimension with a Gaussian kernel. — smooth_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/sort_basis.html b/docs/reference/sort_basis.html
index 6a676ea2..d25cc006 100644
--- a/docs/reference/sort_basis.html
+++ b/docs/reference/sort_basis.html
@@ -1,5 +1,5 @@
-Sort the basis-set elements alphabetically. — sort_basis • Spectroscopy Analysis Tools (spant) Sort the basis-set elements alphabetically. — sort_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/spant-package.html b/docs/reference/spant-package.html
index b3dd8e21..90f19ec3 100644
--- a/docs/reference/spant-package.html
+++ b/docs/reference/spant-package.html
@@ -1,5 +1,5 @@
-spant: spectroscopy analysis tools. — spant-package • Spectroscopy Analysis Tools (spant) spant: spectroscopy analysis tools. — spant-package • Spectroscopy Analysis Tools (spant) Simulate and fit some spectra with ABfit for benchmarking purposes. Basic
-timing and performance metrics will be printed. — spant_abfit_benchmark • Spectroscopy Analysis Tools (spant) Simulate and fit some spectra with ABfit for benchmarking purposes. Basic timing and performance metrics will be printed. — spant_abfit_benchmark • Spectroscopy Analysis Tools (spant) Example MEGA-PRESS data with significant B0 drift. — spant_mpress_drift • Spectroscopy Analysis Tools (spant) Example MEGA-PRESS data with significant B0 drift. — spant_mpress_drift • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -83,7 +83,7 @@ Example MEGA-PRESS data with significant B0 drift.
Format
- An object of class mrs_data of length 13.
+ An object of class mrs_data of dimension 1 x 1 x 1 x 1 x 40 x 1 x 1024.
@@ -98,7 +98,7 @@ Format
diff --git a/docs/reference/spant_sim_fmrs_dataset.html b/docs/reference/spant_sim_fmrs_dataset.html
new file mode 100644
index 00000000..00e48b56
--- /dev/null
+++ b/docs/reference/spant_sim_fmrs_dataset.html
@@ -0,0 +1,117 @@
+
+Simulate an example fMRS dataset for a block design fMRS experiment and export a BIDS structure. — spant_sim_fmrs_dataset • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Simulate an example fMRS dataset for a block design fMRS experiment and export a BIDS structure.
+ Source: R/fmrs.R
+ spant_sim_fmrs_dataset.Rd
+
+
+
+ Simulate an example fMRS dataset for a block design fMRS experiment and
+export a BIDS structure.
+
+
+
+ spant_sim_fmrs_dataset(output_dir = NULL)
+
+
+
+ Arguments
+ - output_dir
+output directory for the BIDS data. Defaults to :
+"HOME/sim_fmrs_dataset/data".
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/spant_simulation_benchmark.html b/docs/reference/spant_simulation_benchmark.html
index 32daa8bf..d8cc6841 100644
--- a/docs/reference/spant_simulation_benchmark.html
+++ b/docs/reference/spant_simulation_benchmark.html
@@ -1,7 +1,5 @@
-Simulate a typical metabolite basis set for benchmarking. Timing metrics will
-be printed on completion. — spant_simulation_benchmark • Spectroscopy Analysis Tools (spant) Simulate a typical metabolite basis set for benchmarking. Timing metrics will be printed on completion. — spant_simulation_benchmark • Spectroscopy Analysis Tools (spant) Decompose an mrs_data object into white and gray matter spectra. — spec_decomp • Spectroscopy Analysis Tools (spant) Perform a mathematical operation on a spectral region. — spec_op • Spectroscopy Analysis Tools (spant) Perform a mathematical operation on a spectral region. — spec_op • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -98,8 +98,8 @@ Arguments
operator
-can be "sum" (default), "mean", "l2", "max", "min" or
-"max-min".
can be "sum" (default), "mean", "l2", "max", "max_cplx,
+"min" or "max-min".
freq_scale
@@ -129,7 +129,7 @@ Value
diff --git a/docs/reference/spin_sys.html b/docs/reference/spin_sys.html
index 853423a4..1eaa9e76 100644
--- a/docs/reference/spin_sys.html
+++ b/docs/reference/spin_sys.html
@@ -1,5 +1,5 @@
-Create a spin system object for pulse sequence simulation. — spin_sys • Spectroscopy Analysis Tools (spant) Create a spin system object for pulse sequence simulation. — spin_sys • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/spm_pve2categorical.html b/docs/reference/spm_pve2categorical.html
index 23a1bad9..70f10729 100644
--- a/docs/reference/spm_pve2categorical.html
+++ b/docs/reference/spm_pve2categorical.html
@@ -1,7 +1,5 @@
-Convert SPM style segmentation files to a single categorical image where
-the numerical values map as: 0) Other, 1) CSF, 2) GM and 3) WM. — spm_pve2categorical • Spectroscopy Analysis Tools (spant) Convert SPM style segmentation files to a single categorical image where the numerical values map as: 0) Other, 1) CSF, 2) GM and 3) WM. — spm_pve2categorical • Spectroscopy Analysis Tools (spant) Signal space projection method for lipid suppression. — ssp • Spectroscopy Analysis Tools (spant) Signal space projection method for lipid suppression. — ssp • Spectroscopy Analysis Tools (spant) Plot the fitting results of an object of class fit_result with
-individual basis set components shown. — stackplot.fit_result • Spectroscopy Analysis Tools (spant) Plot the fitting results of an object of class fit_result with individual basis set components shown. — stackplot.fit_result • Spectroscopy Analysis Tools (spant) Produce a plot with multiple traces. — stackplot • Spectroscopy Analysis Tools (spant) Produce a plot with multiple traces. — stackplot • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/stackplot.mrs_data.html b/docs/reference/stackplot.mrs_data.html
index 17ff5648..64eea445 100644
--- a/docs/reference/stackplot.mrs_data.html
+++ b/docs/reference/stackplot.mrs_data.html
@@ -1,5 +1,5 @@
-Stackplot plotting method for objects of class mrs_data. — stackplot.mrs_data • Spectroscopy Analysis Tools (spant) Stackplot plotting method for objects of class mrs_data. — stackplot.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -255,7 +255,7 @@ Arguments
diff --git a/docs/reference/sub_first_dyn.html b/docs/reference/sub_first_dyn.html
index dbd7f831..493b7242 100644
--- a/docs/reference/sub_first_dyn.html
+++ b/docs/reference/sub_first_dyn.html
@@ -1,5 +1,5 @@
-Subtract the first dynamic spectrum from a dynamic series. — sub_first_dyn • Spectroscopy Analysis Tools (spant) Subtract the first dynamic spectrum from a dynamic series. — sub_first_dyn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/sub_mean_dyns.html b/docs/reference/sub_mean_dyns.html
index 6e3bb2df..221bd0c1 100644
--- a/docs/reference/sub_mean_dyns.html
+++ b/docs/reference/sub_mean_dyns.html
@@ -1,5 +1,5 @@
-Subtract the mean dynamic spectrum from a dynamic series. — sub_mean_dyns • Spectroscopy Analysis Tools (spant) Subtract the mean dynamic spectrum from a dynamic series. — sub_mean_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/sub_median_dyns.html b/docs/reference/sub_median_dyns.html
index 134c495d..1e834f14 100644
--- a/docs/reference/sub_median_dyns.html
+++ b/docs/reference/sub_median_dyns.html
@@ -1,5 +1,5 @@
-Subtract the median dynamic spectrum from a dynamic series. — sub_median_dyns • Spectroscopy Analysis Tools (spant) Subtract the median dynamic spectrum from a dynamic series. — sub_median_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/sum_coils.html b/docs/reference/sum_coils.html
index 7bf559f2..e1ab3cc0 100644
--- a/docs/reference/sum_coils.html
+++ b/docs/reference/sum_coils.html
@@ -1,5 +1,5 @@
-Calculate the sum across receiver coil elements. — sum_coils • Spectroscopy Analysis Tools (spant) Calculate the sum across receiver coil elements. — sum_coils • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/sum_dyns.html b/docs/reference/sum_dyns.html
index a0be19d3..bbda2ffc 100644
--- a/docs/reference/sum_dyns.html
+++ b/docs/reference/sum_dyns.html
@@ -1,5 +1,5 @@
-Calculate the sum of data dynamics. — sum_dyns • Spectroscopy Analysis Tools (spant) Calculate the sum of data dynamics. — sum_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/sum_mrs.html b/docs/reference/sum_mrs.html
index a22f215b..3cc3ab9e 100644
--- a/docs/reference/sum_mrs.html
+++ b/docs/reference/sum_mrs.html
@@ -1,5 +1,5 @@
-Sum two mrs_data objects. — sum_mrs • Spectroscopy Analysis Tools (spant) Sum two mrs_data objects. — sum_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Value
diff --git a/docs/reference/sum_mrs_list.html b/docs/reference/sum_mrs_list.html
index f4e09aea..c3584348 100644
--- a/docs/reference/sum_mrs_list.html
+++ b/docs/reference/sum_mrs_list.html
@@ -1,5 +1,5 @@
-Return the sum of a list of mrs_data objects. — sum_mrs_list • Spectroscopy Analysis Tools (spant) Return the sum of a list of mrs_data objects. — sum_mrs_list • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/svs_1h_brain_analysis.html b/docs/reference/svs_1h_brain_analysis.html
index 8ce514db..dff0ef7d 100644
--- a/docs/reference/svs_1h_brain_analysis.html
+++ b/docs/reference/svs_1h_brain_analysis.html
@@ -1,5 +1,5 @@
-Standard SVS 1H brain analysis pipeline. — svs_1h_brain_analysis • Spectroscopy Analysis Tools (spant) Standard SVS 1H brain analysis pipeline. — svs_1h_brain_analysis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -199,7 +199,7 @@ Value
diff --git a/docs/reference/svs_1h_brain_analysis_dev.html b/docs/reference/svs_1h_brain_analysis_dev.html
index d70a14d3..d71bfea2 100644
--- a/docs/reference/svs_1h_brain_analysis_dev.html
+++ b/docs/reference/svs_1h_brain_analysis_dev.html
@@ -1,5 +1,5 @@
-Standard SVS 1H brain analysis pipeline. — svs_1h_brain_analysis_dev • Spectroscopy Analysis Tools (spant) Standard SVS 1H brain analysis pipeline. — svs_1h_brain_analysis_dev • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -193,7 +193,7 @@ Examples
diff --git a/docs/reference/svs_1h_brain_batch_analysis.html b/docs/reference/svs_1h_brain_batch_analysis.html
index 5631e8cc..15f7223e 100644
--- a/docs/reference/svs_1h_brain_batch_analysis.html
+++ b/docs/reference/svs_1h_brain_batch_analysis.html
@@ -1,5 +1,5 @@
-Batch interface to the standard SVS 1H brain analysis pipeline. — svs_1h_brain_batch_analysis • Spectroscopy Analysis Tools (spant) Batch interface to the standard SVS 1H brain analysis pipeline. — svs_1h_brain_batch_analysis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -144,7 +144,7 @@ Value
diff --git a/docs/reference/t_test_spec.html b/docs/reference/t_test_spec.html
new file mode 100644
index 00000000..56a7ea1b
--- /dev/null
+++ b/docs/reference/t_test_spec.html
@@ -0,0 +1,124 @@
+
+Perform a t-test on spectral data points. — t_test_spec • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+
+
+ Perform a t-test on spectral data points.
+
+
+
+ t_test_spec(mrs_data, group)
+
+
+
+ Arguments
+ - mrs_data
+an mrs_data object with spectra in the dynamic dimension.
- group
+vector describing the group membership of each dynamic spectrum.
+
+ Value
+
+
+a list of statistical results.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/td2fd.html b/docs/reference/td2fd.html
index 6748a6a8..f31ed524 100644
--- a/docs/reference/td2fd.html
+++ b/docs/reference/td2fd.html
@@ -1,5 +1,5 @@
-Transform time-domain data to the frequency-domain. — td2fd • Spectroscopy Analysis Tools (spant) Transform time-domain data to the frequency-domain. — td2fd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/td_conv_filt.html b/docs/reference/td_conv_filt.html
index a9f340c3..106b9b00 100644
--- a/docs/reference/td_conv_filt.html
+++ b/docs/reference/td_conv_filt.html
@@ -1,5 +1,5 @@
-Time-domain convolution based filter. — td_conv_filt • Spectroscopy Analysis Tools (spant) Time-domain convolution based filter. — td_conv_filt • Spectroscopy Analysis Tools (spant) Time-domain spectral registration. — tdsr • Spectroscopy Analysis Tools (spant) Time-domain spectral registration. — tdsr • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -121,7 +121,7 @@ Value
diff --git a/docs/reference/te.html b/docs/reference/te.html
index 010361b1..4a65711d 100644
--- a/docs/reference/te.html
+++ b/docs/reference/te.html
@@ -1,5 +1,5 @@
-Return the echo time of an MRS dataset. — te • Spectroscopy Analysis Tools (spant) Return the echo time of an MRS dataset. — te • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/tr.html b/docs/reference/tr.html
index 0c0bd63b..2e749e02 100644
--- a/docs/reference/tr.html
+++ b/docs/reference/tr.html
@@ -1,5 +1,5 @@
-Return the repetition time of an MRS dataset. — tr • Spectroscopy Analysis Tools (spant) Return the repetition time of an MRS dataset. — tr • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/varpro_3_para_opts.html b/docs/reference/varpro_3_para_opts.html
index c2270a16..52d7cd84 100644
--- a/docs/reference/varpro_3_para_opts.html
+++ b/docs/reference/varpro_3_para_opts.html
@@ -1,5 +1,5 @@
-Return a list of options for VARPRO based fitting with 3 free parameters. — varpro_3_para_opts • Spectroscopy Analysis Tools (spant) Return a list of options for VARPRO based fitting with 3 free parameters. — varpro_3_para_opts • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -141,7 +141,7 @@ Value
diff --git a/docs/reference/varpro_basic_opts.html b/docs/reference/varpro_basic_opts.html
index 32c86d22..c5104891 100644
--- a/docs/reference/varpro_basic_opts.html
+++ b/docs/reference/varpro_basic_opts.html
@@ -1,5 +1,5 @@
-Return a list of options for a basic VARPRO analysis. — varpro_basic_opts • Spectroscopy Analysis Tools (spant) Return a list of options for a basic VARPRO analysis. — varpro_basic_opts • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -118,7 +118,7 @@ Value
diff --git a/docs/reference/varpro_opts.html b/docs/reference/varpro_opts.html
index 2aabf11d..6332f730 100644
--- a/docs/reference/varpro_opts.html
+++ b/docs/reference/varpro_opts.html
@@ -1,5 +1,5 @@
-Return a list of options for VARPRO based fitting. — varpro_opts • Spectroscopy Analysis Tools (spant) Return a list of options for VARPRO based fitting. — varpro_opts • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -177,7 +177,7 @@ Examples
diff --git a/docs/reference/vec2mrs_data.html b/docs/reference/vec2mrs_data.html
index 0cccd73b..f0d58bf0 100644
--- a/docs/reference/vec2mrs_data.html
+++ b/docs/reference/vec2mrs_data.html
@@ -1,5 +1,5 @@
-Convert a vector into a mrs_data object. — vec2mrs_data • Spectroscopy Analysis Tools (spant) Convert a vector into a mrs_data object. — vec2mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -80,10 +80,11 @@ Convert a vector into a mrs_data object.
vec2mrs_data(
vec,
- fs = def_fs(),
- ft = def_ft(),
- ref = def_ref(),
- nuc = def_nuc(),
+ mrs_data = NULL,
+ fs = NULL,
+ ft = NULL,
+ ref = NULL,
+ nuc = NULL,
dyns = 1,
fd = FALSE
)
@@ -95,6 +96,10 @@ Arguments
the data vector.
mrs_data
+example data to copy acquisition parameters from.
fs
sampling frequency in Hz.
Arguments
fd
-flag to indicate if the matrix is in the frequency domain (logical).
flag to indicate if the vector is in the frequency domain (logical).
Value
diff --git a/docs/reference/write_basis.html b/docs/reference/write_basis.html
index b6e27cbd..94c5e021 100644
--- a/docs/reference/write_basis.html
+++ b/docs/reference/write_basis.html
@@ -1,5 +1,5 @@
-Write a basis object to an LCModel .basis formatted file. — write_basis • Spectroscopy Analysis Tools (spant) Write a basis object to an LCModel .basis formatted file. — write_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -108,7 +108,7 @@ Arguments
diff --git a/docs/reference/write_basis_tqn.html b/docs/reference/write_basis_tqn.html
index 6aa51c1d..116c73ec 100644
--- a/docs/reference/write_basis_tqn.html
+++ b/docs/reference/write_basis_tqn.html
@@ -1,5 +1,5 @@
-Generate a basis file using TARQUIN. — write_basis_tqn • Spectroscopy Analysis Tools (spant) Generate a basis file using TARQUIN. — write_basis_tqn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Examples
diff --git a/docs/reference/write_mrs.html b/docs/reference/write_mrs.html
index fff25f15..124b9dc4 100644
--- a/docs/reference/write_mrs.html
+++ b/docs/reference/write_mrs.html
@@ -1,5 +1,5 @@
-Write MRS data object to file. — write_mrs • Spectroscopy Analysis Tools (spant) Write MRS data object to file. — write_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Arguments
diff --git a/docs/reference/write_mrs_nifti.html b/docs/reference/write_mrs_nifti.html
index f4bf1921..bd3ed4b7 100644
--- a/docs/reference/write_mrs_nifti.html
+++ b/docs/reference/write_mrs_nifti.html
@@ -1,5 +1,5 @@
-Write MRS data object to file in NIFTI format. — write_mrs_nifti • Spectroscopy Analysis Tools (spant) Write MRS data object to file in NIFTI format. — write_mrs_nifti • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/write_pulse_ascii.html b/docs/reference/write_pulse_ascii.html
index 067ae086..221f8ebb 100644
--- a/docs/reference/write_pulse_ascii.html
+++ b/docs/reference/write_pulse_ascii.html
@@ -1,5 +1,5 @@
-Write an ASCII formatted pulse file. — write_pulse_ascii • Spectroscopy Analysis Tools (spant) Write an ASCII formatted pulse file. — write_pulse_ascii • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/zero_fade_spec.html b/docs/reference/zero_fade_spec.html
index c703745c..c8b572c3 100644
--- a/docs/reference/zero_fade_spec.html
+++ b/docs/reference/zero_fade_spec.html
@@ -1,7 +1,5 @@
-Fade a spectrum to zero by frequency domain multiplication with a tanh
-function. Note this operation distorts data points at the end of the FID. — zero_fade_spec • Spectroscopy Analysis Tools (spant) Fade a spectrum to zero by frequency domain multiplication with a tanh function. Note this operation distorts data points at the end of the FID. — zero_fade_spec • Spectroscopy Analysis Tools (spant) Zero all coherences including and above a given order. — zero_higher_orders • Spectroscopy Analysis Tools (spant) Zero all coherences including and above a given order. — zero_higher_orders • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Value
diff --git a/docs/reference/zero_td_pts_end.html b/docs/reference/zero_td_pts_end.html
index 8c1123c8..71d24ebb 100644
--- a/docs/reference/zero_td_pts_end.html
+++ b/docs/reference/zero_td_pts_end.html
@@ -1,5 +1,5 @@
-Set mrs_data object data points at the end of the FID to zero. — zero_td_pts_end • Spectroscopy Analysis Tools (spant) Set mrs_data object data points at the end of the FID to zero. — zero_td_pts_end • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/zf.html b/docs/reference/zf.html
index 85e2013c..baf50256 100644
--- a/docs/reference/zf.html
+++ b/docs/reference/zf.html
@@ -1,5 +1,5 @@
-Zero-fill MRS data in the time domain. — zf • Spectroscopy Analysis Tools (spant) Zero-fill MRS data in the time domain. — zf • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -125,7 +125,7 @@ Value
diff --git a/docs/reference/zf_xy.html b/docs/reference/zf_xy.html
index ebca3999..c4104a74 100644
--- a/docs/reference/zf_xy.html
+++ b/docs/reference/zf_xy.html
@@ -1,5 +1,5 @@
-Zero-fill MRSI data in the k-space x-y direction. — zf_xy • Spectroscopy Analysis Tools (spant) Zero-fill MRSI data in the k-space x-y direction. — zf_xy • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -113,7 +113,7 @@ Value
diff --git a/docs/sitemap.xml b/docs/sitemap.xml
index e2139f71..4c39f515 100644
--- a/docs/sitemap.xml
+++ b/docs/sitemap.xml
@@ -216,6 +216,12 @@
https://martin3141.github.io/spant/reference/comb_coils_fp_pc.html
+
+ https://martin3141.github.io/spant/reference/comb_coils_mrsi_gls.html
+
+
+ https://martin3141.github.io/spant/reference/comb_coils_svs_gls.html
+
https://martin3141.github.io/spant/reference/comb_csv_results.html
@@ -411,6 +417,9 @@
https://martin3141.github.io/spant/reference/gen_conv_reg.html
+
+ https://martin3141.github.io/spant/reference/gen_group_reg.html
+
https://martin3141.github.io/spant/reference/gen_impulse_reg.html
@@ -555,6 +564,15 @@
https://martin3141.github.io/spant/reference/glm_spec.html
+
+ https://martin3141.github.io/spant/reference/glm_spec_fmrs_fl.html
+
+
+ https://martin3141.github.io/spant/reference/glm_spec_fmrs_group.html
+
+
+ https://martin3141.github.io/spant/reference/glm_spec_group_linhyp.html
+
https://martin3141.github.io/spant/reference/grid_shift_xy.html
@@ -690,9 +708,15 @@
https://martin3141.github.io/spant/reference/mrs_data2basis.html
+
+ https://martin3141.github.io/spant/reference/mrs_data2bids.html
+
https://martin3141.github.io/spant/reference/mrs_data2mat.html
+
+ https://martin3141.github.io/spant/reference/mrs_data2spec_mat.html
+
https://martin3141.github.io/spant/reference/mrs_data2vec.html
@@ -741,6 +765,9 @@
https://martin3141.github.io/spant/reference/phase.html
+
+ https://martin3141.github.io/spant/reference/phase_ref_1h_brain.html
+
https://martin3141.github.io/spant/reference/plot.fit_result.html
@@ -780,6 +807,12 @@
https://martin3141.github.io/spant/reference/precomp.html
+
+ https://martin3141.github.io/spant/reference/preproc_svs.html
+
+
+ https://martin3141.github.io/spant/reference/preproc_svs_dataset.html
+
https://martin3141.github.io/spant/reference/print.fit_result.html
@@ -1050,6 +1083,9 @@
https://martin3141.github.io/spant/reference/spant_mpress_drift.html
+
+ https://martin3141.github.io/spant/reference/spant_sim_fmrs_dataset.html
+
https://martin3141.github.io/spant/reference/spant_simulation_benchmark.html
@@ -1107,6 +1143,9 @@
https://martin3141.github.io/spant/reference/svs_1h_brain_batch_analysis.html
+
+ https://martin3141.github.io/spant/reference/t_test_spec.html
+
https://martin3141.github.io/spant/reference/td2fd.html
Downsample an MRS signal by a factor of 2 by removing every other data point -in the time-domain. Note, signals outside the new sampling frequency will be -aliased.
Downsample an MRS signal by a factor of 2 by removing every other data point in the time-domain. Note, signals outside the new sampling frequency will be aliased.
Return a time scale vector of acquisition times for a dynamic MRS scan. The -first temporal scan is assigned a value of 0.
Return a time scale vector of acquisition times for a dynamic MRS scan. The first temporal scan is assigned a value of 0.
All functions
- Estimate the standard deviation of the noise from a segment of an mrs_data
-object.
Estimate the standard deviation of the noise from a segment of an mrs_data object.
@@ -486,8 +474,7 @@ All functions
- Perform a zeroth order phase correction based on the phase of the first data
-point in the time-domain.
Perform a zeroth order phase correction based on the phase of the first data point in the time-domain.
@@ -507,8 +494,7 @@ All functions
- Perform a fft and fftshift on a matrix with each column replaced by its
-shifted fft.
Perform a fft and fftshift on a matrix with each column replaced by its shifted fft.
@@ -536,8 +522,11 @@ All functions
- Generate regressors by convolving a specified response function with a
-stimulus.
Generate regressors by convolving a specified response function with a stimulus.
+
+
+ Expand a regressor matrix for a group analysis.
@@ -553,28 +542,23 @@ All functions
- Return a character vector of common 1H molecules found in healthy human
-brain.
Return a character vector of common 1H molecules found in healthy human brain.
- Return a list of mol_parameter objects suitable for 1H brain MRS
-analyses.
Return a list of mol_parameter objects suitable for 1H brain MRS analyses.
- Return a list of mol_parameter objects suitable for 1H brain MRS
-analyses.
Return a list of mol_parameter objects suitable for 1H brain MRS analyses.
- Return a list of mol_parameter objects suitable for 1H brain MRS
-analyses.
Return a list of mol_parameter objects suitable for 1H brain MRS analyses.
- Return a list of mol_parameter objects suitable for 1H brain MRS
-analyses.
Return a list of mol_parameter objects suitable for 1H brain MRS analyses.
@@ -582,8 +566,7 @@ All functions
- Return a character vector of molecules included in the Gold Star Phantoms
-SPECTRE phantom.
Return a character vector of molecules included in the Gold Star Phantoms SPECTRE phantom.
@@ -635,8 +618,7 @@ All functions
- Return a character array of names that may be used with the
-get_mol_paras function.
Return a character array of names that may be used with the get_mol_paras function.
@@ -700,8 +682,7 @@ All functions
- Return an array of amplitudes derived from fitting the initial points in the
-time domain and extrapolating back to t=0.
Return an array of amplitudes derived from fitting the initial points in the time domain and extrapolating back to t=0.
@@ -709,8 +690,7 @@ All functions
- Generate a mol_parameters object for a simple spin system with one
-resonance.
Generate a mol_parameters object for a simple spin system with one resonance.
@@ -731,6 +711,18 @@ All functions glm_spec()
Perform a GLM analysis of dynamic MRS data in the spectral domain.
+
+
+ Perform first-level spectral GLM analysis of an fMRS dataset.
+
+
+ Perform group-level spectral GLM analysis of an fMRS dataset.
+
+
+ Test a group-level spectral GLM linear hypothesis.
@@ -766,8 +758,7 @@ All functions
- Perform an ifft and ifftshift on a matrix with each column replaced by its
-shifted ifft.
Perform an ifft and ifftshift on a matrix with each column replaced by its shifted ifft.
@@ -799,8 +790,7 @@ All functions
- Check if the chemical shift dimension of an MRS data object is in the
-frequency domain.
Check if the chemical shift dimension of an MRS data object is in the frequency domain.
@@ -820,18 +810,15 @@ All functions
- Covert a linewidth in Hz to an equivalent alpha value in the time-domain ie:
-x * exp(-t * alpha).
Covert a linewidth in Hz to an equivalent alpha value in the time-domain ie: x * exp(-t * alpha).
- Covert a linewidth in Hz to an equivalent beta value in the time-domain ie:
-x * exp(-t * t * beta).
Covert a linewidth in Hz to an equivalent beta value in the time-domain ie: x * exp(-t * t * beta).
- Make a basis-set object from a directory containing LCModel formatted RAW
-files.
Make a basis-set object from a directory containing LCModel formatted RAW files.
@@ -851,8 +838,7 @@ All functions
- Mask the voxels outside an elliptical region spanning the MRSI dataset in the
-x-y plane.
Mask the voxels outside an elliptical region spanning the MRSI dataset in the x-y plane.
@@ -860,13 +846,11 @@ All functions
- Convert a matrix (with spectral points in the column dimension and dynamics
-in the row dimensions) into a mrs_data object.
Convert a matrix (with spectral points in the column dimension and dynamics in the row dimensions) into a mrs_data object.
- Matrix exponential function taken from complexplus package to reduce the
-number of spant dependencies.
Matrix exponential function taken from complexplus package to reduce the number of spant dependencies.
@@ -914,31 +898,31 @@ All functions
- Convert an mrs_data object to basis object - where basis signals are spread
-across the dynamic dimension in the MRS data.
Convert an mrs_data object to basis object - where basis signals are spread across the dynamic dimension in the MRS data.
+
+
+ Create a BIDS file structure from a vector of MRS data paths or list of mrs_data objects.
- Convert mrs_data object to a matrix, with spectral points in the column
-dimension and dynamics in the row dimension.
Convert mrs_data object to a matrix, with spectral points in the column dimension and dynamics in the row dimension.
-
+
- Convert mrs_data object to a vector.
Convert mrs_data object to a matrix, with spectral points in the column dimension and dynamics in the row dimension.
-
+
- Create a BIDS directory and file structure from a list of mrs_data objects.
Convert mrs_data object to a vector.
- Perform a fftshift on a matrix, with each column replaced by its shifted
-result.
Perform a fftshift on a matrix, with each column replaced by its shifted result.
- Perform an ifftshift on a matrix, with each column replaced by its shifted
-result.
Perform an ifftshift on a matrix, with each column replaced by its shifted result.
@@ -946,9 +930,7 @@ All functions
- Flip the x data dimension order of a nifti image. This corresponds to
-flipping MRI data in the left-right direction, assuming the data in save in
-neurological format (can check with fslorient program).
Flip the x data dimension order of a nifti image. This corresponds to flipping MRI data in the left-right direction, assuming the data in save in neurological format (can check with fslorient program).
@@ -964,8 +946,7 @@ All functions
- Search for the highest peak in a spectral region and return the frequency,
-height and FWHM.
Search for the highest peak in a spectral region and return the frequency, height and FWHM.
@@ -974,6 +955,10 @@ All functions phase()
Apply phasing parameters to MRS data.
+
+
+ Corrected zero order phase and chemical shift offset in 1H MRS data from the brain.
@@ -1005,8 +990,7 @@ All functions
- Plot an interactive slice map from a data array where voxels can be selected
-to display a corresponding spectrum.
Plot an interactive slice map from a data array where voxels can be selected to display a corresponding spectrum.
@@ -1026,8 +1010,15 @@ All functions
- Save function results to file and load on subsequent calls to avoid repeat
-computation.
Save function results to file and load on subsequent calls to avoid repeat computation.
+
+
+ Preprocess and perform quality assessment of a single SVS data set.
+
+
+ Preprocess and perform quality assessment of one or more SVS data sets.
@@ -1055,15 +1046,11 @@ All functions
- Read a directory containing Siemens MRS IMA files and combine along the coil
-dimension. Note that the coil ID is inferred from the sorted file name and
-should be checked when consistency is required between two directories.
Read a directory containing Siemens MRS IMA files and combine along the coil dimension. Note that the coil ID is inferred from the sorted file name and should be checked when consistency is required between two directories.
- Read a directory containing Siemens MRS IMA files and combine along the
-dynamic dimension. Note that the coil ID is inferred from the sorted file
-name and should be checked when consistency is required.
Read a directory containing Siemens MRS IMA files and combine along the dynamic dimension. Note that the coil ID is inferred from the sorted file name and should be checked when consistency is required.
@@ -1103,13 +1090,11 @@ All functions
- Reconstruct complex time-domain data from the real part of frequency-domain
-data.
Reconstruct complex time-domain data from the real part of frequency-domain data.
- Reconstruct complex time-domain data from the real part of frequency-domain
-data.
Reconstruct complex time-domain data from the real part of frequency-domain data.
@@ -1141,8 +1126,7 @@ All functions
- Resample a VOI to match a target image space using nearest-neighbour
-interpolation.
Resample a VOI to match a target image space using nearest-neighbour interpolation.
@@ -1158,23 +1142,19 @@ All functions
- Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water).
Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / kg of tissue water).
- Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water).
Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / kg of tissue water).
- Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / Litre of tissue).
Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / Litre of tissue).
- Convert default LCM/TARQUIN concentration scaling to molal units with partial
-volume correction.
Convert default LCM/TARQUIN concentration scaling to molal units with partial volume correction.
@@ -1222,8 +1202,7 @@ All functions
- MEGA-PRESS sequence with ideal localisation pulses and Gaussian shaped
-editing pulse.
MEGA-PRESS sequence with ideal localisation pulses and Gaussian shaped editing pulse.
@@ -1251,13 +1230,11 @@ All functions
- STEAM sequence with ideal pulses and coherence order filtering to simulate
-gradient crushers.
STEAM sequence with ideal pulses and coherence order filtering to simulate gradient crushers.
- STEAM sequence with ideal pulses using the z-rotation gradient simulation
-method described by Young et al JMR 140, 146-152 (1999).
STEAM sequence with ideal pulses using the z-rotation gradient simulation method described by Young et al JMR 140, 146-152 (1999).
@@ -1293,8 +1270,7 @@ All functions
- Set the number of time-domain data points, truncating or zero-filling as
-appropriate.
Set the number of time-domain data points, truncating or zero-filling as appropriate.
@@ -1318,18 +1294,15 @@ All functions
- Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS
-sequence. Note, ideal pulses are assumed.
Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS sequence. Note, ideal pulses are assumed.
- Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS
-sequence. Note, ideal pulses are assumed.
Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS sequence. Note, ideal pulses are assumed.
- Simulate a macromolecular and lipid basis-set suitable for 1H brain MRS
-analysis.
Simulate a macromolecular and lipid basis-set suitable for 1H brain MRS analysis.
@@ -1353,8 +1326,7 @@ All functions
- Simulate an ideal pulse excitation profile by smoothing a top-hat function
-with a Gaussian.
Simulate an ideal pulse excitation profile by smoothing a top-hat function with a Gaussian.
@@ -1374,17 +1346,19 @@ All functions
- Simulate and fit some spectra with ABfit for benchmarking purposes. Basic
-timing and performance metrics will be printed.
Simulate and fit some spectra with ABfit for benchmarking purposes. Basic timing and performance metrics will be printed.
Example MEGA-PRESS data with significant B0 drift.
+
+
+ Simulate an example fMRS dataset for a block design fMRS experiment and export a BIDS structure.
- Simulate a typical metabolite basis set for benchmarking. Timing metrics will
-be printed on completion.
Simulate a typical metabolite basis set for benchmarking. Timing metrics will be printed on completion.
@@ -1400,8 +1374,7 @@ All functions
- Convert SPM style segmentation files to a single categorical image where
-the numerical values map as: 0) Other, 1) CSF, 2) GM and 3) WM.
Convert SPM style segmentation files to a single categorical image where the numerical values map as: 0) Other, 1) CSF, 2) GM and 3) WM.
@@ -1413,8 +1386,7 @@ All functions
- Plot the fitting results of an object of class fit_result with
-individual basis set components shown.
Plot the fitting results of an object of class fit_result with individual basis set components shown.
@@ -1459,6 +1431,10 @@ All functions svs_1h_brain_batch_analysis()
Batch interface to the standard SVS 1H brain analysis pipeline.
+
+
+ Perform a t-test on spectral data points.
@@ -1518,8 +1494,7 @@ All functions
- Fade a spectrum to zero by frequency domain multiplication with a tanh
-function. Note this operation distorts data points at the end of the FID.
Fade a spectrum to zero by frequency domain multiplication with a tanh function. Note this operation distorts data points at the end of the FID.
@@ -1549,7 +1524,7 @@ All functions
diff --git a/docs/reference/int_spec.html b/docs/reference/int_spec.html
index c7060fe7..783325a8 100644
--- a/docs/reference/int_spec.html
+++ b/docs/reference/int_spec.html
@@ -1,5 +1,5 @@
-Integrate a spectral region. — int_spec • Spectroscopy Analysis Tools (spant) Integrate a spectral region. — int_spec • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -118,7 +118,7 @@ Value
diff --git a/docs/reference/interleave_dyns.html b/docs/reference/interleave_dyns.html
index effe5543..441eff27 100644
--- a/docs/reference/interleave_dyns.html
+++ b/docs/reference/interleave_dyns.html
@@ -1,5 +1,5 @@
-Interleave the first and second half of a dynamic series. — interleave_dyns • Spectroscopy Analysis Tools (spant) Interleave the first and second half of a dynamic series. — interleave_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/inv_even_dyns.html b/docs/reference/inv_even_dyns.html
index 9f9d4fff..dcb781dc 100644
--- a/docs/reference/inv_even_dyns.html
+++ b/docs/reference/inv_even_dyns.html
@@ -1,5 +1,5 @@
-Invert even numbered dynamic scans starting from 1 (2,4,6...). — inv_even_dyns • Spectroscopy Analysis Tools (spant) Invert even numbered dynamic scans starting from 1 (2,4,6...). — inv_even_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/inv_odd_dyns.html b/docs/reference/inv_odd_dyns.html
index 26212e2b..78d64660 100644
--- a/docs/reference/inv_odd_dyns.html
+++ b/docs/reference/inv_odd_dyns.html
@@ -1,5 +1,5 @@
-Invert odd numbered dynamic scans starting from 1 (1,3,5...). — inv_odd_dyns • Spectroscopy Analysis Tools (spant) Invert odd numbered dynamic scans starting from 1 (1,3,5...). — inv_odd_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/is.def.html b/docs/reference/is.def.html
index f196ffd0..a67b9eba 100644
--- a/docs/reference/is.def.html
+++ b/docs/reference/is.def.html
@@ -1,5 +1,5 @@
-Check if an object is defined, which is the same as being not NULL. — is.def • Spectroscopy Analysis Tools (spant) Check if an object is defined, which is the same as being not NULL. — is.def • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/is_fd.html b/docs/reference/is_fd.html
index 3b0ca165..18a193aa 100644
--- a/docs/reference/is_fd.html
+++ b/docs/reference/is_fd.html
@@ -1,7 +1,5 @@
-Check if the chemical shift dimension of an MRS data object is in the
-frequency domain. — is_fd • Spectroscopy Analysis Tools (spant) Check if the chemical shift dimension of an MRS data object is in the frequency domain. — is_fd • Spectroscopy Analysis Tools (spant) Transform 2D MRSI data from k-space to image space in the x-y direction. — kspace2img_xy • Spectroscopy Analysis Tools (spant) Transform 2D MRSI data from k-space to image space in the x-y direction. — kspace2img_xy • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/l2_reg.html b/docs/reference/l2_reg.html
index 3d781d80..21aa9849 100644
--- a/docs/reference/l2_reg.html
+++ b/docs/reference/l2_reg.html
@@ -1,5 +1,5 @@
-Perform l2 regularisation artefact suppression. — l2_reg • Spectroscopy Analysis Tools (spant) Perform l2 regularisation artefact suppression. — l2_reg • Spectroscopy Analysis Tools (spant) Apply line-broadening (apodisation) to MRS data or basis object. — lb • Spectroscopy Analysis Tools (spant) Apply line-broadening (apodisation) to MRS data or basis object. — lb • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -123,7 +123,7 @@ Value
diff --git a/docs/reference/lofdc.html b/docs/reference/lofdc.html
index 5419b1ec..31347a25 100644
--- a/docs/reference/lofdc.html
+++ b/docs/reference/lofdc.html
@@ -1,5 +1,5 @@
-Correct linear frequency drift. — lofdc • Spectroscopy Analysis Tools (spant) Correct linear frequency drift. — lofdc • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -138,7 +138,7 @@ Value
diff --git a/docs/reference/lw2alpha.html b/docs/reference/lw2alpha.html
index b83db682..25da229b 100644
--- a/docs/reference/lw2alpha.html
+++ b/docs/reference/lw2alpha.html
@@ -1,7 +1,5 @@
-Covert a linewidth in Hz to an equivalent alpha value in the time-domain ie:
-x * exp(-t * alpha). — lw2alpha • Spectroscopy Analysis Tools (spant) Covert a linewidth in Hz to an equivalent alpha value in the time-domain ie: x * exp(-t * alpha). — lw2alpha • Spectroscopy Analysis Tools (spant) Covert a linewidth in Hz to an equivalent beta value in the time-domain ie:
-x * exp(-t * t * beta). — lw2beta • Spectroscopy Analysis Tools (spant) Covert a linewidth in Hz to an equivalent beta value in the time-domain ie: x * exp(-t * t * beta). — lw2beta • Spectroscopy Analysis Tools (spant) Make a basis-set object from a directory containing LCModel formatted RAW
-files. — make_basis_from_raw • Spectroscopy Analysis Tools (spant) Make a basis-set object from a directory containing LCModel formatted RAW files. — make_basis_from_raw • Spectroscopy Analysis Tools (spant) Mask an MRS dataset in the dynamic dimension. — mask_dyns • Spectroscopy Analysis Tools (spant) Mask an MRS dataset in the dynamic dimension. — mask_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/mask_fit_res.html b/docs/reference/mask_fit_res.html
index 97baaa3f..ebd91a99 100644
--- a/docs/reference/mask_fit_res.html
+++ b/docs/reference/mask_fit_res.html
@@ -1,5 +1,5 @@
-Mask fit result spectra depending on a vector of bool values. — mask_fit_res • Spectroscopy Analysis Tools (spant) Mask fit result spectra depending on a vector of bool values. — mask_fit_res • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -116,7 +116,7 @@ Value
diff --git a/docs/reference/mask_xy.html b/docs/reference/mask_xy.html
index 11bb577c..b0d38619 100644
--- a/docs/reference/mask_xy.html
+++ b/docs/reference/mask_xy.html
@@ -1,5 +1,5 @@
-Mask an MRSI dataset in the x-y direction — mask_xy • Spectroscopy Analysis Tools (spant) Mask an MRSI dataset in the x-y direction — mask_xy • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/mask_xy_corners.html b/docs/reference/mask_xy_corners.html
index 09b16cd2..2d13839d 100644
--- a/docs/reference/mask_xy_corners.html
+++ b/docs/reference/mask_xy_corners.html
@@ -1,5 +1,5 @@
-Mask the four corners of an MRSI dataset in the x-y plane. — mask_xy_corners • Spectroscopy Analysis Tools (spant) Mask the four corners of an MRSI dataset in the x-y plane. — mask_xy_corners • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/mask_xy_ellipse.html b/docs/reference/mask_xy_ellipse.html
index 1d8b02e4..e2e749ef 100644
--- a/docs/reference/mask_xy_ellipse.html
+++ b/docs/reference/mask_xy_ellipse.html
@@ -1,7 +1,5 @@
-Mask the voxels outside an elliptical region spanning the MRSI dataset in the
-x-y plane. — mask_xy_ellipse • Spectroscopy Analysis Tools (spant) Mask the voxels outside an elliptical region spanning the MRSI dataset in the x-y plane. — mask_xy_ellipse • Spectroscopy Analysis Tools (spant) Mask a 2D MRSI dataset in the x-y dimension. — mask_xy_mat • Spectroscopy Analysis Tools (spant) Mask a 2D MRSI dataset in the x-y dimension. — mask_xy_mat • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Value
diff --git a/docs/reference/mat2mrs_data.html b/docs/reference/mat2mrs_data.html
index 2e2895f3..ae55665f 100644
--- a/docs/reference/mat2mrs_data.html
+++ b/docs/reference/mat2mrs_data.html
@@ -1,7 +1,5 @@
-Convert a matrix (with spectral points in the column dimension and dynamics
-in the row dimensions) into a mrs_data object. — mat2mrs_data • Spectroscopy Analysis Tools (spant) Convert a matrix (with spectral points in the column dimension and dynamics in the row dimensions) into a mrs_data object. — mat2mrs_data • Spectroscopy Analysis Tools (spant) Matrix exponential function taken from complexplus package to reduce the
-number of spant dependencies. — matexp • Spectroscopy Analysis Tools (spant) Matrix exponential function taken from complexplus package to reduce the number of spant dependencies. — matexp • Spectroscopy Analysis Tools (spant) Apply the max operator to an MRS dataset. — max_mrs • Spectroscopy Analysis Tools (spant) Apply the max operator to an MRS dataset. — max_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/max_mrs_interp.html b/docs/reference/max_mrs_interp.html
index e4474764..52e63f3e 100644
--- a/docs/reference/max_mrs_interp.html
+++ b/docs/reference/max_mrs_interp.html
@@ -1,5 +1,5 @@
-Apply the max operator to an interpolated MRS dataset. — max_mrs_interp • Spectroscopy Analysis Tools (spant) Apply the max operator to an interpolated MRS dataset. — max_mrs_interp • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/mean.list.html b/docs/reference/mean.list.html
index b8eb3463..048306fd 100644
--- a/docs/reference/mean.list.html
+++ b/docs/reference/mean.list.html
@@ -1,5 +1,5 @@
-Calculate the mean spectrum from an mrs_data object. — mean.list • Spectroscopy Analysis Tools (spant) Calculate the mean spectrum from an mrs_data object. — mean.list • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/mean.mrs_data.html b/docs/reference/mean.mrs_data.html
index 5531a28d..79515014 100644
--- a/docs/reference/mean.mrs_data.html
+++ b/docs/reference/mean.mrs_data.html
@@ -1,5 +1,5 @@
-Calculate the mean spectrum from an mrs_data object. — mean.mrs_data • Spectroscopy Analysis Tools (spant) Calculate the mean spectrum from an mrs_data object. — mean.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/mean_dyn_blocks.html b/docs/reference/mean_dyn_blocks.html
index 10467098..4c042448 100644
--- a/docs/reference/mean_dyn_blocks.html
+++ b/docs/reference/mean_dyn_blocks.html
@@ -1,5 +1,5 @@
-Calculate the mean of adjacent dynamic scans. — mean_dyn_blocks • Spectroscopy Analysis Tools (spant) Calculate the mean of adjacent dynamic scans. — mean_dyn_blocks • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/mean_dyn_pairs.html b/docs/reference/mean_dyn_pairs.html
index 63e909ea..1a241126 100644
--- a/docs/reference/mean_dyn_pairs.html
+++ b/docs/reference/mean_dyn_pairs.html
@@ -1,5 +1,5 @@
-Calculate the pairwise means across a dynamic data set. — mean_dyn_pairs • Spectroscopy Analysis Tools (spant) Calculate the pairwise means across a dynamic data set. — mean_dyn_pairs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/mean_dyns.html b/docs/reference/mean_dyns.html
index 73fdbfa7..0daa27df 100644
--- a/docs/reference/mean_dyns.html
+++ b/docs/reference/mean_dyns.html
@@ -1,5 +1,5 @@
-Calculate the mean dynamic data. — mean_dyns • Spectroscopy Analysis Tools (spant) Calculate the mean dynamic data. — mean_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/mean_mrs_list.html b/docs/reference/mean_mrs_list.html
index 808b6c50..10d842c0 100644
--- a/docs/reference/mean_mrs_list.html
+++ b/docs/reference/mean_mrs_list.html
@@ -1,5 +1,5 @@
-Return the mean of a list of mrs_data objects. — mean_mrs_list • Spectroscopy Analysis Tools (spant) Return the mean of a list of mrs_data objects. — mean_mrs_list • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/mean_vec_blocks.html b/docs/reference/mean_vec_blocks.html
index 8fc92eaa..dd78b122 100644
--- a/docs/reference/mean_vec_blocks.html
+++ b/docs/reference/mean_vec_blocks.html
@@ -1,5 +1,5 @@
-Calculate the mean of adjacent blocks in a vector. — mean_vec_blocks • Spectroscopy Analysis Tools (spant) Calculate the mean of adjacent blocks in a vector. — mean_vec_blocks • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/median_dyns.html b/docs/reference/median_dyns.html
index 1039d4b5..9a085b10 100644
--- a/docs/reference/median_dyns.html
+++ b/docs/reference/median_dyns.html
@@ -1,5 +1,5 @@
-Calculate the median dynamic data. — median_dyns • Spectroscopy Analysis Tools (spant) Calculate the median dynamic data. — median_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/mod_td.html b/docs/reference/mod_td.html
index 76ad0a40..141ef09e 100644
--- a/docs/reference/mod_td.html
+++ b/docs/reference/mod_td.html
@@ -1,5 +1,5 @@
-Apply the Modulus operator to the time-domain MRS signal. — mod_td • Spectroscopy Analysis Tools (spant) Apply the Modulus operator to the time-domain MRS signal. — mod_td • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/mrs_data2basis.html b/docs/reference/mrs_data2basis.html
index 62f7d749..11797b91 100644
--- a/docs/reference/mrs_data2basis.html
+++ b/docs/reference/mrs_data2basis.html
@@ -1,7 +1,5 @@
-Convert an mrs_data object to basis object - where basis signals are spread
-across the dynamic dimension in the MRS data. — mrs_data2basis • Spectroscopy Analysis Tools (spant) Convert an mrs_data object to basis object - where basis signals are spread across the dynamic dimension in the MRS data. — mrs_data2basis • Spectroscopy Analysis Tools (spant) Create a BIDS file structure from a vector of MRS data paths or list of mrs_data objects. — mrs_data2bids • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Create a BIDS file structure from a vector of MRS data paths or list of mrs_data objects.
+ Source: R/fmrs.R
+ mrs_data2bids.Rd
+
+
+
+ Create a BIDS file structure from a vector of MRS data paths or list of
+mrs_data objects.
+
+
+
+ mrs_data2bids(
+ mrs_data,
+ output_dir,
+ suffix = NULL,
+ sub = NULL,
+ ses = NULL,
+ task = NULL,
+ acq = NULL,
+ nuc = NULL,
+ voi = NULL,
+ rec = NULL,
+ run = NULL,
+ echo = NULL,
+ inv = NULL,
+ skip_existing = TRUE
+)
+
+
+
+ Arguments
+ - mrs_data
+vector of MRS data paths or list of mrs_data objects.
- output_dir
+the base directory to create the BIDS structure.
- suffix
+optional vector of file suffixes. Default behaviour is to
+automatically determine these from the input data, however it is recommended
+that they are specified to allow more efficient skipping of existing data.
- sub
+optional vector of subject labels. If not specified, these will be
+automatically generated as a series of increasing zero-padded integer values
+corresponding to the mrs_data input indices.
- ses
+optional vector of session labels.
- task
+optional vector of task labels.
- acq
+optional vector of acquisition labels.
- nuc
+optional vector of nucleus labels.
- voi
+optional vector of volume of interest labels.
- rec
+optional vector of reconstruction labels.
- run
+optional vector of run indices.
- echo
+optional vector of echo time indices.
- inv
+optional vector of inversion indices.
- skip_existing
+skip any data files that have already been converted.
+Defaults to TRUE, set to FALSE to force an overwrite of any existing data
+files.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/mrs_data2mat.html b/docs/reference/mrs_data2mat.html
index cf5ff28c..9e47688a 100644
--- a/docs/reference/mrs_data2mat.html
+++ b/docs/reference/mrs_data2mat.html
@@ -1,7 +1,5 @@
-Convert mrs_data object to a matrix, with spectral points in the column
-dimension and dynamics in the row dimension. — mrs_data2mat • Spectroscopy Analysis Tools (spant) Convert mrs_data object to a matrix, with spectral points in the column dimension and dynamics in the row dimension. — mrs_data2mat • Spectroscopy Analysis Tools (spant) Convert mrs_data object to a matrix, with spectral points in the column dimension and dynamics in the row dimension. — mrs_data2spec_mat • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Convert mrs_data object to a matrix, with spectral points in the column dimension and dynamics in the row dimension.
+ Source: R/mrs_data_proc.R
+ mrs_data2spec_mat.Rd
+
+
+
+ Convert mrs_data object to a matrix, with spectral points in the column
+dimension and dynamics in the row dimension.
+
+
+
+ mrs_data2spec_mat(mrs_data, collapse = TRUE)
+
+
+
+ Arguments
+ - mrs_data
+MRS data object or list of MRS data objects.
- collapse
+collapse all other dimensions along the dynamic dimension, eg
+a 16x16 MRSI grid would be first collapsed across 256 dynamic scans.
+
+ Value
+
+
+MRS data matrix.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/mrs_data2vec.html b/docs/reference/mrs_data2vec.html
index fb172d68..a1fd654d 100644
--- a/docs/reference/mrs_data2vec.html
+++ b/docs/reference/mrs_data2vec.html
@@ -1,5 +1,5 @@
-Convert mrs_data object to a vector. — mrs_data2vec • Spectroscopy Analysis Tools (spant) Convert mrs_data object to a vector. — mrs_data2vec • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -126,7 +126,7 @@ Value
diff --git a/docs/reference/mvfftshift.html b/docs/reference/mvfftshift.html
index 92b0841b..976b3410 100644
--- a/docs/reference/mvfftshift.html
+++ b/docs/reference/mvfftshift.html
@@ -1,7 +1,5 @@
-Perform a fftshift on a matrix, with each column replaced by its shifted
-result. — mvfftshift • Spectroscopy Analysis Tools (spant) Perform a fftshift on a matrix, with each column replaced by its shifted result. — mvfftshift • Spectroscopy Analysis Tools (spant) Perform an ifftshift on a matrix, with each column replaced by its shifted
-result. — mvifftshift • Spectroscopy Analysis Tools (spant) Perform an ifftshift on a matrix, with each column replaced by its shifted result. — mvifftshift • Spectroscopy Analysis Tools (spant) Print fit coordinates from a single index. — n2coord • Spectroscopy Analysis Tools (spant) Print fit coordinates from a single index. — n2coord • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/nifti_flip_lr.html b/docs/reference/nifti_flip_lr.html
index 730abe3c..19860b3c 100644
--- a/docs/reference/nifti_flip_lr.html
+++ b/docs/reference/nifti_flip_lr.html
@@ -1,9 +1,5 @@
-Flip the x data dimension order of a nifti image. This corresponds to
-flipping MRI data in the left-right direction, assuming the data in save in
-neurological format (can check with fslorient program). — nifti_flip_lr • Spectroscopy Analysis Tools (spant) Flip the x data dimension order of a nifti image. This corresponds to flipping MRI data in the left-right direction, assuming the data in save in neurological format (can check with fslorient program). — nifti_flip_lr • Spectroscopy Analysis Tools (spant) Export a one-page pdf of a single fit result — one_page_pdf • Spectroscopy Analysis Tools (spant) Export a one-page pdf of a single fit result — one_page_pdf • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -108,7 +108,7 @@ Arguments
diff --git a/docs/reference/ortho3.html b/docs/reference/ortho3.html
index 13ade97d..5d7dd2fd 100644
--- a/docs/reference/ortho3.html
+++ b/docs/reference/ortho3.html
@@ -1,5 +1,5 @@
-Display an orthographic projection plot of a nifti object. — ortho3 • Spectroscopy Analysis Tools (spant) Display an orthographic projection plot of a nifti object. — ortho3 • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -172,7 +172,7 @@ Arguments
diff --git a/docs/reference/ortho3_inter.html b/docs/reference/ortho3_inter.html
index 090cc5e5..15948899 100644
--- a/docs/reference/ortho3_inter.html
+++ b/docs/reference/ortho3_inter.html
@@ -1,5 +1,5 @@
-Display an interactive orthographic projection plot of a nifti object. — ortho3_inter • Spectroscopy Analysis Tools (spant) Display an interactive orthographic projection plot of a nifti object. — ortho3_inter • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -132,7 +132,7 @@ Arguments
diff --git a/docs/reference/peak_info.html b/docs/reference/peak_info.html
index 09058bd8..41c8ffaf 100644
--- a/docs/reference/peak_info.html
+++ b/docs/reference/peak_info.html
@@ -1,7 +1,5 @@
-Search for the highest peak in a spectral region and return the frequency,
-height and FWHM. — peak_info • Spectroscopy Analysis Tools (spant) Search for the highest peak in a spectral region and return the frequency, height and FWHM. — peak_info • Spectroscopy Analysis Tools (spant) Papoulis-Gerchberg (PG) algorithm method for k-space extrapolation. — pg_extrap_xy • Spectroscopy Analysis Tools (spant) Papoulis-Gerchberg (PG) algorithm method for k-space extrapolation. — pg_extrap_xy • Spectroscopy Analysis Tools (spant) Apply phasing parameters to MRS data. — phase • Spectroscopy Analysis Tools (spant) Apply phasing parameters to MRS data. — phase • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/phase_ref_1h_brain.html b/docs/reference/phase_ref_1h_brain.html
new file mode 100644
index 00000000..8707a74a
--- /dev/null
+++ b/docs/reference/phase_ref_1h_brain.html
@@ -0,0 +1,131 @@
+
+Corrected zero order phase and chemical shift offset in 1H MRS data from the brain. — phase_ref_1h_brain • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Corrected zero order phase and chemical shift offset in 1H MRS data from the brain.
+ Source: R/rats.R
+ phase_ref_1h_brain.Rd
+
+
+
+ Corrected zero order phase and chemical shift offset in 1H MRS data from the
+brain.
+
+
+
+ phase_ref_1h_brain(mrs_data, mean_ref = FALSE, ret_corr_only = TRUE)
+
+
+
+ Arguments
+ - mrs_data
+MRS data to be corrected.
- mean_ref
+apply the phase and offset of the mean spectrum to all
+others. Default is FALSE.
- ret_corr_only
+return the corrected data only.
+
+ Value
+
+
+corrected MRS data.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/plot.fit_result.html b/docs/reference/plot.fit_result.html
index e54d3bc1..836a53ee 100644
--- a/docs/reference/plot.fit_result.html
+++ b/docs/reference/plot.fit_result.html
@@ -1,5 +1,5 @@
-Plot the fitting results of an object of class fit_result. — plot.fit_result • Spectroscopy Analysis Tools (spant) Plot the fitting results of an object of class fit_result. — plot.fit_result • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -207,7 +207,7 @@ Arguments
diff --git a/docs/reference/plot.mrs_data.html b/docs/reference/plot.mrs_data.html
index fabcc35b..bb2ec651 100644
--- a/docs/reference/plot.mrs_data.html
+++ b/docs/reference/plot.mrs_data.html
@@ -1,5 +1,5 @@
-Plotting method for objects of class mrs_data. — plot.mrs_data • Spectroscopy Analysis Tools (spant) Plotting method for objects of class mrs_data. — plot.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -287,7 +287,7 @@ Arguments
diff --git a/docs/reference/plot_bc.html b/docs/reference/plot_bc.html
index 4f8309b4..b48142cc 100644
--- a/docs/reference/plot_bc.html
+++ b/docs/reference/plot_bc.html
@@ -1,5 +1,5 @@
-Convenience function to plot a baseline estimate with the original data. — plot_bc • Spectroscopy Analysis Tools (spant) Convenience function to plot a baseline estimate with the original data. — plot_bc • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -108,7 +108,7 @@ Arguments
diff --git a/docs/reference/plot_reg.html b/docs/reference/plot_reg.html
index ae1acbe7..2addb2f6 100644
--- a/docs/reference/plot_reg.html
+++ b/docs/reference/plot_reg.html
@@ -1,5 +1,5 @@
-Plot regressors as an image. — plot_reg • Spectroscopy Analysis Tools (spant) Plot regressors as an image. — plot_reg • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/plot_slice_fit.html b/docs/reference/plot_slice_fit.html
index fbc7b560..57f1af8a 100644
--- a/docs/reference/plot_slice_fit.html
+++ b/docs/reference/plot_slice_fit.html
@@ -1,5 +1,5 @@
-Plot a 2D slice from an MRSI fit result object. — plot_slice_fit • Spectroscopy Analysis Tools (spant) Plot a 2D slice from an MRSI fit result object. — plot_slice_fit • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -129,7 +129,7 @@ Arguments
diff --git a/docs/reference/plot_slice_fit_inter.html b/docs/reference/plot_slice_fit_inter.html
index 4eed104a..da105a7d 100644
--- a/docs/reference/plot_slice_fit_inter.html
+++ b/docs/reference/plot_slice_fit_inter.html
@@ -1,5 +1,5 @@
-Plot a 2D slice from an MRSI fit result object. — plot_slice_fit_inter • Spectroscopy Analysis Tools (spant) Plot a 2D slice from an MRSI fit result object. — plot_slice_fit_inter • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -134,7 +134,7 @@ Arguments
diff --git a/docs/reference/plot_slice_map.html b/docs/reference/plot_slice_map.html
index 553e9ac8..ffb2a134 100644
--- a/docs/reference/plot_slice_map.html
+++ b/docs/reference/plot_slice_map.html
@@ -1,5 +1,5 @@
-Plot a slice from a 7 dimensional array. — plot_slice_map • Spectroscopy Analysis Tools (spant) Plot a slice from a 7 dimensional array. — plot_slice_map • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -153,7 +153,7 @@ Arguments
diff --git a/docs/reference/plot_slice_map_inter.html b/docs/reference/plot_slice_map_inter.html
index 40d33b42..90968f66 100644
--- a/docs/reference/plot_slice_map_inter.html
+++ b/docs/reference/plot_slice_map_inter.html
@@ -1,7 +1,5 @@
-Plot an interactive slice map from a data array where voxels can be selected
-to display a corresponding spectrum. — plot_slice_map_inter • Spectroscopy Analysis Tools (spant) Plot an interactive slice map from a data array where voxels can be selected to display a corresponding spectrum. — plot_slice_map_inter • Spectroscopy Analysis Tools (spant) Plot the spectral standard deviation. — plot_spec_sd • Spectroscopy Analysis Tools (spant) Plot the spectral standard deviation. — plot_spec_sd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Arguments
diff --git a/docs/reference/plot_voi_overlay.html b/docs/reference/plot_voi_overlay.html
index 9a782e88..bbbbf35e 100644
--- a/docs/reference/plot_voi_overlay.html
+++ b/docs/reference/plot_voi_overlay.html
@@ -1,5 +1,5 @@
-Plot a volume as an image overlay. — plot_voi_overlay • Spectroscopy Analysis Tools (spant) Plot a volume as an image overlay. — plot_voi_overlay • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -116,7 +116,7 @@ Arguments
diff --git a/docs/reference/plot_voi_overlay_seg.html b/docs/reference/plot_voi_overlay_seg.html
index 3d4e74ff..0e800ff2 100644
--- a/docs/reference/plot_voi_overlay_seg.html
+++ b/docs/reference/plot_voi_overlay_seg.html
@@ -1,5 +1,5 @@
-Plot a volume as an overlay on a segmented brain volume. — plot_voi_overlay_seg • Spectroscopy Analysis Tools (spant) Plot a volume as an overlay on a segmented brain volume. — plot_voi_overlay_seg • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Arguments
diff --git a/docs/reference/ppm.html b/docs/reference/ppm.html
index c352327a..ee4696e2 100644
--- a/docs/reference/ppm.html
+++ b/docs/reference/ppm.html
@@ -1,5 +1,5 @@
-Return the ppm scale of an MRS dataset or fit result. — ppm • Spectroscopy Analysis Tools (spant) Return the ppm scale of an MRS dataset or fit result. — ppm • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -132,7 +132,7 @@ Value
diff --git a/docs/reference/precomp.html b/docs/reference/precomp.html
index 822d7336..df3d2c6c 100644
--- a/docs/reference/precomp.html
+++ b/docs/reference/precomp.html
@@ -1,7 +1,5 @@
-Save function results to file and load on subsequent calls to avoid repeat
-computation. — precomp • Spectroscopy Analysis Tools (spant) Save function results to file and load on subsequent calls to avoid repeat computation. — precomp • Spectroscopy Analysis Tools (spant) Preprocess and perform quality assessment of a single SVS data set. — preproc_svs • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Preprocess and perform quality assessment of a single SVS data set.
+ Source: R/fmrs.R
+ preproc_svs.Rd
+
+
+
+ Preprocess and perform quality assessment of a single SVS data set.
+
+
+
+ preproc_svs(path, label = NULL, output_dir = NULL, ref_inds = NULL)
+
+
+
+ Arguments
+ - path
+path to the fMRS data file or IMA directory.
- label
+a label to describe the data set.
- output_dir
+output directory.
- ref_inds
+a vector of 1-based indices for any water reference dynamic
+scans.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/preproc_svs_dataset.html b/docs/reference/preproc_svs_dataset.html
new file mode 100644
index 00000000..07c3a29b
--- /dev/null
+++ b/docs/reference/preproc_svs_dataset.html
@@ -0,0 +1,148 @@
+
+Preprocess and perform quality assessment of one or more SVS data sets. — preproc_svs_dataset • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Preprocess and perform quality assessment of one or more SVS data sets.
+ Source: R/fmrs.R
+ preproc_svs_dataset.Rd
+
+
+
+ Preprocess and perform quality assessment of one or more SVS data sets.
+
+
+
+ preproc_svs_dataset(
+ paths,
+ labels = NULL,
+ output_dir = "spant_analysis",
+ exclude_labels = NULL,
+ overwrite = FALSE,
+ ref_inds = NULL,
+ return_results = FALSE
+)
+
+
+
+ Arguments
+ - paths
+paths to the fMRS data file or IMA directory.
- labels
+labels to describe each data set.
- output_dir
+output directory.
- exclude_labels
+vector of labels of scans to exclude, eg poor quality
+data.
- overwrite
+overwrite saved results, defaults to FALSE.
- ref_inds
+a vector of 1-based indices for any water reference dynamic
+scans.
- return_results
+function will return key outputs, defaults to FALSE.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/print.fit_result.html b/docs/reference/print.fit_result.html
index 297f28dc..5f434e57 100644
--- a/docs/reference/print.fit_result.html
+++ b/docs/reference/print.fit_result.html
@@ -1,5 +1,5 @@
-Print a summary of an object of class fit_result. — print.fit_result • Spectroscopy Analysis Tools (spant) Print a summary of an object of class fit_result. — print.fit_result • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -105,7 +105,7 @@ Arguments
diff --git a/docs/reference/print.mrs_data.html b/docs/reference/print.mrs_data.html
index 51199017..e1561eb2 100644
--- a/docs/reference/print.mrs_data.html
+++ b/docs/reference/print.mrs_data.html
@@ -1,5 +1,5 @@
-Print a summary of mrs_data parameters. — print.mrs_data • Spectroscopy Analysis Tools (spant) Print a summary of mrs_data parameters. — print.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -109,7 +109,7 @@ Arguments
diff --git a/docs/reference/qn_states.html b/docs/reference/qn_states.html
index 0f42f2f9..d7aa6715 100644
--- a/docs/reference/qn_states.html
+++ b/docs/reference/qn_states.html
@@ -1,5 +1,5 @@
-Get the quantum coherence matrix for a spin system. — qn_states • Spectroscopy Analysis Tools (spant) Get the quantum coherence matrix for a spin system. — qn_states • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/rats.html b/docs/reference/rats.html
index 5a39a396..93585e08 100644
--- a/docs/reference/rats.html
+++ b/docs/reference/rats.html
@@ -1,5 +1,5 @@
-Robust Alignment to a Target Spectrum (RATS). — rats • Spectroscopy Analysis Tools (spant) Robust Alignment to a Target Spectrum (RATS). — rats • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -207,7 +207,7 @@ Value
diff --git a/docs/reference/re_weighting.html b/docs/reference/re_weighting.html
index d21caf21..8b0b070a 100644
--- a/docs/reference/re_weighting.html
+++ b/docs/reference/re_weighting.html
@@ -1,5 +1,5 @@
-Apply a weighting to the FID to enhance spectral resolution. — re_weighting • Spectroscopy Analysis Tools (spant) Apply a weighting to the FID to enhance spectral resolution. — re_weighting • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/read_basis.html b/docs/reference/read_basis.html
index da9b94af..eb6f8557 100644
--- a/docs/reference/read_basis.html
+++ b/docs/reference/read_basis.html
@@ -1,5 +1,5 @@
-Read a basis file in LCModel .basis format. — read_basis • Spectroscopy Analysis Tools (spant) Read a basis file in LCModel .basis format. — read_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/read_ima_coil_dir.html b/docs/reference/read_ima_coil_dir.html
index 28c02de0..4f073cd8 100644
--- a/docs/reference/read_ima_coil_dir.html
+++ b/docs/reference/read_ima_coil_dir.html
@@ -1,9 +1,5 @@
-Read a directory containing Siemens MRS IMA files and combine along the coil
-dimension. Note that the coil ID is inferred from the sorted file name and
-should be checked when consistency is required between two directories. — read_ima_coil_dir • Spectroscopy Analysis Tools (spant) Read a directory containing Siemens MRS IMA files and combine along the coil dimension. Note that the coil ID is inferred from the sorted file name and should be checked when consistency is required between two directories. — read_ima_coil_dir • Spectroscopy Analysis Tools (spant) Read a directory containing Siemens MRS IMA files and combine along the
-dynamic dimension. Note that the coil ID is inferred from the sorted file
-name and should be checked when consistency is required. — read_ima_dyn_dir • Spectroscopy Analysis Tools (spant) Read a directory containing Siemens MRS IMA files and combine along the dynamic dimension. Note that the coil ID is inferred from the sorted file name and should be checked when consistency is required. — read_ima_dyn_dir • Spectroscopy Analysis Tools (spant) Read an LCModel formatted coord file containing fit information. — read_lcm_coord • Spectroscopy Analysis Tools (spant) Read an LCModel formatted coord file containing fit information. — read_lcm_coord • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -107,7 +107,7 @@ Value
diff --git a/docs/reference/read_mrs.html b/docs/reference/read_mrs.html
index 3ac2a36b..2cf36b20 100644
--- a/docs/reference/read_mrs.html
+++ b/docs/reference/read_mrs.html
@@ -1,5 +1,5 @@
-Read MRS data from a file. — read_mrs • Spectroscopy Analysis Tools (spant) Read MRS data from a file. — read_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -88,7 +88,8 @@ Read MRS data from a file.
full_fid = FALSE,
omit_svs_ref_scans = TRUE,
verbose = FALSE,
- extra = NULL
+ extra = NULL,
+ fid_filt_dist = NULL
)
@@ -140,6 +141,13 @@ Arguments
an optional data frame to provide additional variables for use
in subsequent analysis steps, eg id or grouping variables.
fid_filt_dist
+indicate if the data has a distorted FID due to a
+brick-wall filter being used to downsample the data. Default is to auto
+detect this from the data, but TRUE or FALSE options can be given to override
+detection.
Value
@@ -183,7 +191,7 @@ Examples
diff --git a/docs/reference/read_mrs_tqn.html b/docs/reference/read_mrs_tqn.html
index 5766362f..84bdaf3a 100644
--- a/docs/reference/read_mrs_tqn.html
+++ b/docs/reference/read_mrs_tqn.html
@@ -1,5 +1,5 @@
-Read MRS data using the TARQUIN software package. — read_mrs_tqn • Spectroscopy Analysis Tools (spant) Read MRS data using the TARQUIN software package. — read_mrs_tqn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -131,7 +131,7 @@ Examples
diff --git a/docs/reference/read_pulse_ascii.html b/docs/reference/read_pulse_ascii.html
index c9e0d43c..ab11c9cc 100644
--- a/docs/reference/read_pulse_ascii.html
+++ b/docs/reference/read_pulse_ascii.html
@@ -1,5 +1,5 @@
-Read an ASCII formatted pulse file. — read_pulse_ascii • Spectroscopy Analysis Tools (spant) Read an ASCII formatted pulse file. — read_pulse_ascii • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/read_pulse_bruker.html b/docs/reference/read_pulse_bruker.html
index c92bf76a..dbe9073b 100644
--- a/docs/reference/read_pulse_bruker.html
+++ b/docs/reference/read_pulse_bruker.html
@@ -1,5 +1,5 @@
-Read a Bruker formatted pulse file — read_pulse_bruker • Spectroscopy Analysis Tools (spant) Read a Bruker formatted pulse file — read_pulse_bruker • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/read_pulse_pta.html b/docs/reference/read_pulse_pta.html
index 72e1b6d4..a0fac3c3 100644
--- a/docs/reference/read_pulse_pta.html
+++ b/docs/reference/read_pulse_pta.html
@@ -1,5 +1,5 @@
-Read a .pta formatted pulse file compatible with Siemens PulseTool. — read_pulse_pta • Spectroscopy Analysis Tools (spant) Read a .pta formatted pulse file compatible with Siemens PulseTool. — read_pulse_pta • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/read_siemens_txt_hdr.html b/docs/reference/read_siemens_txt_hdr.html
index 23fb8c70..3a17d87c 100644
--- a/docs/reference/read_siemens_txt_hdr.html
+++ b/docs/reference/read_siemens_txt_hdr.html
@@ -1,5 +1,5 @@
-Read the text format header found in Siemens IMA and TWIX data files. — read_siemens_txt_hdr • Spectroscopy Analysis Tools (spant) Read the text format header found in Siemens IMA and TWIX data files. — read_siemens_txt_hdr • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -78,7 +78,7 @@ Read the text format header found in Siemens IMA and TWIX data files.
- read_siemens_txt_hdr(input, version = "vd", verbose, offset = 0)
+ read_siemens_txt_hdr(input, version = "vd", verbose = FALSE, offset = 0)
@@ -118,7 +118,7 @@ Value
diff --git a/docs/reference/read_tqn_fit.html b/docs/reference/read_tqn_fit.html
index 4da6c25e..a1630420 100644
--- a/docs/reference/read_tqn_fit.html
+++ b/docs/reference/read_tqn_fit.html
@@ -1,5 +1,5 @@
-Reader for csv fit results generated by TARQUIN. — read_tqn_fit • Spectroscopy Analysis Tools (spant) Reader for csv fit results generated by TARQUIN. — read_tqn_fit • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -113,7 +113,7 @@ Examples
diff --git a/docs/reference/read_tqn_result.html b/docs/reference/read_tqn_result.html
index 36659714..68a3e98c 100644
--- a/docs/reference/read_tqn_result.html
+++ b/docs/reference/read_tqn_result.html
@@ -1,5 +1,5 @@
-Reader for csv results generated by TARQUIN. — read_tqn_result • Spectroscopy Analysis Tools (spant) Reader for csv results generated by TARQUIN. — read_tqn_result • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -117,7 +117,7 @@ Examples
diff --git a/docs/reference/recon_imag.html b/docs/reference/recon_imag.html
index d2a72225..5bc3b1eb 100644
--- a/docs/reference/recon_imag.html
+++ b/docs/reference/recon_imag.html
@@ -1,7 +1,5 @@
-Reconstruct complex time-domain data from the real part of frequency-domain
-data. — recon_imag • Spectroscopy Analysis Tools (spant) Reconstruct complex time-domain data from the real part of frequency-domain data. — recon_imag • Spectroscopy Analysis Tools (spant) Reconstruct complex time-domain data from the real part of frequency-domain
-data. — recon_imag_vec • Spectroscopy Analysis Tools (spant) Reconstruct complex time-domain data from the real part of frequency-domain data. — recon_imag_vec • Spectroscopy Analysis Tools (spant) Reconstruct 2D MRSI data from a twix file loaded with read_mrs. — recon_twix_2d_mrsi • Spectroscopy Analysis Tools (spant) Reconstruct 2D MRSI data from a twix file loaded with read_mrs. — recon_twix_2d_mrsi • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/rectangular_mask.html b/docs/reference/rectangular_mask.html
index a2117283..6e469bc9 100644
--- a/docs/reference/rectangular_mask.html
+++ b/docs/reference/rectangular_mask.html
@@ -1,5 +1,5 @@
-Create a rectangular mask stored as a matrix of logical values. — rectangular_mask • Spectroscopy Analysis Tools (spant) Create a rectangular mask stored as a matrix of logical values. — rectangular_mask • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -130,7 +130,7 @@ Value
diff --git a/docs/reference/reexports.html b/docs/reference/reexports.html
index 694a75d1..a59e8379 100644
--- a/docs/reference/reexports.html
+++ b/docs/reference/reexports.html
@@ -1,5 +1,5 @@
-Objects exported from other packages — reexports • Spectroscopy Analysis Tools (spant) Objects exported from other packages — reexports • Spectroscopy Analysis Tools (spant)
Spectroscopy Analysis Tools (spant)
- 2.21.0
+ 2.22.0
@@ -103,7 +103,7 @@ Objects exported from other packages
diff --git a/docs/reference/rep_array_dim.html b/docs/reference/rep_array_dim.html
index b9c49b4a..48c0a5ed 100644
--- a/docs/reference/rep_array_dim.html
+++ b/docs/reference/rep_array_dim.html
@@ -1,5 +1,5 @@
-Repeat an array over a given dimension. — rep_array_dim • Spectroscopy Analysis Tools (spant) Repeat an array over a given dimension. — rep_array_dim • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/rep_dyn.html b/docs/reference/rep_dyn.html
index 6bbfb0ef..89a4bb9b 100644
--- a/docs/reference/rep_dyn.html
+++ b/docs/reference/rep_dyn.html
@@ -1,5 +1,5 @@
-Replicate a scan in the dynamic dimension. — rep_dyn • Spectroscopy Analysis Tools (spant) Replicate a scan in the dynamic dimension. — rep_dyn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/rep_mrs.html b/docs/reference/rep_mrs.html
index 67730b5c..becb8f00 100644
--- a/docs/reference/rep_mrs.html
+++ b/docs/reference/rep_mrs.html
@@ -1,5 +1,5 @@
-Replicate a scan over a given dimension. — rep_mrs • Spectroscopy Analysis Tools (spant) Replicate a scan over a given dimension. — rep_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -138,7 +138,7 @@ Value
diff --git a/docs/reference/resample_basis.html b/docs/reference/resample_basis.html
index b0f2ab17..c7a6222a 100644
--- a/docs/reference/resample_basis.html
+++ b/docs/reference/resample_basis.html
@@ -1,5 +1,5 @@
-Resample a basis-set to match a mrs_data acquisition. — resample_basis • Spectroscopy Analysis Tools (spant) Resample a basis-set to match a mrs_data acquisition. — resample_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -116,7 +116,7 @@ Value
diff --git a/docs/reference/resample_img.html b/docs/reference/resample_img.html
index f1e7beaf..b0cc8f71 100644
--- a/docs/reference/resample_img.html
+++ b/docs/reference/resample_img.html
@@ -1,5 +1,5 @@
-Resample an image to match a target image space. — resample_img • Spectroscopy Analysis Tools (spant) Resample an image to match a target image space. — resample_img • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/resample_voi.html b/docs/reference/resample_voi.html
index 8fbfa836..a29ab096 100644
--- a/docs/reference/resample_voi.html
+++ b/docs/reference/resample_voi.html
@@ -1,7 +1,5 @@
-Resample a VOI to match a target image space using nearest-neighbour
-interpolation. — resample_voi • Spectroscopy Analysis Tools (spant) Resample a VOI to match a target image space using nearest-neighbour interpolation. — resample_voi • Spectroscopy Analysis Tools (spant) Reslice a nifti object to match the orientation of mrs data. — reslice_to_mrs • Spectroscopy Analysis Tools (spant) Reslice a nifti object to match the orientation of mrs data. — reslice_to_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/reson_table2mrs_data.html b/docs/reference/reson_table2mrs_data.html
index d75579ee..c5a2167a 100644
--- a/docs/reference/reson_table2mrs_data.html
+++ b/docs/reference/reson_table2mrs_data.html
@@ -1,5 +1,5 @@
-Generate mrs_data from a table of single Lorentzian resonances. — reson_table2mrs_data • Spectroscopy Analysis Tools (spant) Generate mrs_data from a table of single Lorentzian resonances. — reson_table2mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -119,7 +119,7 @@ Value
diff --git a/docs/reference/rm_dyns.html b/docs/reference/rm_dyns.html
index 5d5ef692..573e1f51 100644
--- a/docs/reference/rm_dyns.html
+++ b/docs/reference/rm_dyns.html
@@ -1,5 +1,5 @@
-Remove a subset of dynamic scans. — rm_dyns • Spectroscopy Analysis Tools (spant) Remove a subset of dynamic scans. — rm_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/scale_amp_molal.html b/docs/reference/scale_amp_molal.html
index aaeee1f2..7acb8cb0 100644
--- a/docs/reference/scale_amp_molal.html
+++ b/docs/reference/scale_amp_molal.html
@@ -1,7 +1,5 @@
-Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water). — scale_amp_molal • Spectroscopy Analysis Tools (spant) Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / kg of tissue water). — scale_amp_molal • Spectroscopy Analysis Tools (spant)
Spectroscopy Analysis Tools (spant)
- 2.21.0
+ 2.22.0
@@ -76,8 +74,7 @@
- Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water).
+ Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / kg of tissue water).
Source: R/amp_scaling.R
scale_amp_molal.Rd
@@ -163,7 +160,7 @@ Value
diff --git a/docs/reference/scale_amp_molal_pvc.html b/docs/reference/scale_amp_molal_pvc.html
index 962d6afc..4d194abd 100644
--- a/docs/reference/scale_amp_molal_pvc.html
+++ b/docs/reference/scale_amp_molal_pvc.html
@@ -1,7 +1,5 @@
-Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water). — scale_amp_molal_pvc • Spectroscopy Analysis Tools (spant)
@@ -75,8 +73,7 @@
- Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water).
+ Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / kg of tissue water).
Source: R/amp_scaling.R
scale_amp_molal_pvc.Rd
@@ -141,7 +138,7 @@ Value
diff --git a/docs/reference/scale_amp_molar.html b/docs/reference/scale_amp_molar.html
index 02358d91..dc87a338 100644
--- a/docs/reference/scale_amp_molar.html
+++ b/docs/reference/scale_amp_molar.html
@@ -1,7 +1,5 @@
-Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / Litre of tissue). — scale_amp_molar • Spectroscopy Analysis Tools (spant) Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / Litre of tissue). — scale_amp_molar • Spectroscopy Analysis Tools (spant) Convert default LCM/TARQUIN concentration scaling to molal units with partial
-volume correction. — scale_amp_molar2molal_pvc • Spectroscopy Analysis Tools (spant) Convert default LCM/TARQUIN concentration scaling to molal units with partial volume correction. — scale_amp_molar2molal_pvc • Spectroscopy Analysis Tools (spant) Scale fitted amplitudes to a ratio of signal amplitude. — scale_amp_ratio • Spectroscopy Analysis Tools (spant) Scale fitted amplitudes to a ratio of signal amplitude. — scale_amp_ratio • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -116,7 +116,7 @@ Value
diff --git a/docs/reference/scale_amp_ratio_value.html b/docs/reference/scale_amp_ratio_value.html
index 2036837a..6af8ac51 100644
--- a/docs/reference/scale_amp_ratio_value.html
+++ b/docs/reference/scale_amp_ratio_value.html
@@ -1,5 +1,5 @@
-Scale fitted amplitudes to a ratio of signal amplitude. — scale_amp_ratio_value • Spectroscopy Analysis Tools (spant) Scale fitted amplitudes to a ratio of signal amplitude. — scale_amp_ratio_value • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/scale_amp_water_ratio.html b/docs/reference/scale_amp_water_ratio.html
index 5b25e884..35a76b00 100644
--- a/docs/reference/scale_amp_water_ratio.html
+++ b/docs/reference/scale_amp_water_ratio.html
@@ -1,5 +1,5 @@
-Scale metabolite amplitudes as a ratio to the unsuppressed water amplitude. — scale_amp_water_ratio • Spectroscopy Analysis Tools (spant) Scale metabolite amplitudes as a ratio to the unsuppressed water amplitude. — scale_amp_water_ratio • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/scale_basis_amp.html b/docs/reference/scale_basis_amp.html
index 9401c3f1..5a58b5e5 100644
--- a/docs/reference/scale_basis_amp.html
+++ b/docs/reference/scale_basis_amp.html
@@ -1,5 +1,5 @@
-Scale a basis object by a scalar. — scale_basis_amp • Spectroscopy Analysis Tools (spant) Scale a basis object by a scalar. — scale_basis_amp • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/scale_basis_from_singlet.html b/docs/reference/scale_basis_from_singlet.html
index 0d542bc8..c9a19e77 100644
--- a/docs/reference/scale_basis_from_singlet.html
+++ b/docs/reference/scale_basis_from_singlet.html
@@ -1,5 +1,5 @@
-Scale a basis-set to be consistent with spant assumptions for water scaling. — scale_basis_from_singlet • Spectroscopy Analysis Tools (spant) Scale a basis-set to be consistent with spant assumptions for water scaling. — scale_basis_from_singlet • Spectroscopy Analysis Tools (spant)
Spectroscopy Analysis Tools (spant)
- 2.21.0
+ 2.22.0
@@ -127,7 +127,7 @@ Value
diff --git a/docs/reference/scale_mrs_amp.html b/docs/reference/scale_mrs_amp.html
index b5501a0d..990f058a 100644
--- a/docs/reference/scale_mrs_amp.html
+++ b/docs/reference/scale_mrs_amp.html
@@ -1,5 +1,5 @@
-Scale an mrs_data object by a scalar or vector or amplitudes. — scale_mrs_amp • Spectroscopy Analysis Tools (spant) Scale an mrs_data object by a scalar or vector or amplitudes. — scale_mrs_amp • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/scale_spec.html b/docs/reference/scale_spec.html
index 4f6ea835..6b3ddba4 100644
--- a/docs/reference/scale_spec.html
+++ b/docs/reference/scale_spec.html
@@ -1,5 +1,5 @@
-Scale mrs_data to a spectral region. — scale_spec • Spectroscopy Analysis Tools (spant) Scale mrs_data to a spectral region. — scale_spec • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -141,7 +141,7 @@ Value
diff --git a/docs/reference/sd.html b/docs/reference/sd.html
index ea1eec9f..3ae4dfd4 100644
--- a/docs/reference/sd.html
+++ b/docs/reference/sd.html
@@ -1,5 +1,5 @@
-Calculate the standard deviation spectrum from an mrs_data object. — sd • Spectroscopy Analysis Tools (spant) Calculate the standard deviation spectrum from an mrs_data object. — sd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/sd.mrs_data.html b/docs/reference/sd.mrs_data.html
index 3f92a49f..13bdda85 100644
--- a/docs/reference/sd.mrs_data.html
+++ b/docs/reference/sd.mrs_data.html
@@ -1,5 +1,5 @@
-Calculate the standard deviation spectrum from an mrs_data object. — sd.mrs_data • Spectroscopy Analysis Tools (spant) Calculate the standard deviation spectrum from an mrs_data object. — sd.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/seconds.html b/docs/reference/seconds.html
index b34d6627..467ee17f 100644
--- a/docs/reference/seconds.html
+++ b/docs/reference/seconds.html
@@ -1,5 +1,5 @@
-Return a time scale vector to match the FID of an MRS data object. — seconds • Spectroscopy Analysis Tools (spant) Return a time scale vector to match the FID of an MRS data object. — seconds • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/seq_cpmg_ideal.html b/docs/reference/seq_cpmg_ideal.html
index 547e96ab..45727c86 100644
--- a/docs/reference/seq_cpmg_ideal.html
+++ b/docs/reference/seq_cpmg_ideal.html
@@ -1,5 +1,5 @@
-CPMG style sequence with ideal pulses. — seq_cpmg_ideal • Spectroscopy Analysis Tools (spant) CPMG style sequence with ideal pulses. — seq_cpmg_ideal • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/seq_mega_press_ideal.html b/docs/reference/seq_mega_press_ideal.html
index 0769b8b4..a9cd7fa0 100644
--- a/docs/reference/seq_mega_press_ideal.html
+++ b/docs/reference/seq_mega_press_ideal.html
@@ -1,7 +1,5 @@
-MEGA-PRESS sequence with ideal localisation pulses and Gaussian shaped
-editing pulse. — seq_mega_press_ideal • Spectroscopy Analysis Tools (spant) MEGA-PRESS sequence with ideal localisation pulses and Gaussian shaped editing pulse. — seq_mega_press_ideal • Spectroscopy Analysis Tools (spant) PRESS sequence with shaped refocusing pulses. — seq_press_2d_shaped • Spectroscopy Analysis Tools (spant) PRESS sequence with shaped refocusing pulses. — seq_press_2d_shaped • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -165,7 +165,7 @@ Value
diff --git a/docs/reference/seq_press_ideal.html b/docs/reference/seq_press_ideal.html
index 8c976856..72c3af3d 100644
--- a/docs/reference/seq_press_ideal.html
+++ b/docs/reference/seq_press_ideal.html
@@ -1,5 +1,5 @@
-PRESS sequence with ideal pulses. — seq_press_ideal • Spectroscopy Analysis Tools (spant) PRESS sequence with ideal pulses. — seq_press_ideal • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/seq_pulse_acquire.html b/docs/reference/seq_pulse_acquire.html
index 4a88fc64..ad80571e 100644
--- a/docs/reference/seq_pulse_acquire.html
+++ b/docs/reference/seq_pulse_acquire.html
@@ -1,5 +1,5 @@
-Simple pulse and acquire sequence with ideal pulses. — seq_pulse_acquire • Spectroscopy Analysis Tools (spant) Simple pulse and acquire sequence with ideal pulses. — seq_pulse_acquire • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/seq_slaser_ideal.html b/docs/reference/seq_slaser_ideal.html
index 74688f4d..eb83e8e3 100644
--- a/docs/reference/seq_slaser_ideal.html
+++ b/docs/reference/seq_slaser_ideal.html
@@ -1,5 +1,5 @@
-sLASER sequence with ideal pulses. — seq_slaser_ideal • Spectroscopy Analysis Tools (spant) sLASER sequence with ideal pulses. — seq_slaser_ideal • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -126,7 +126,7 @@ Value
diff --git a/docs/reference/seq_spin_echo_ideal.html b/docs/reference/seq_spin_echo_ideal.html
index e23271de..4248716f 100644
--- a/docs/reference/seq_spin_echo_ideal.html
+++ b/docs/reference/seq_spin_echo_ideal.html
@@ -1,5 +1,5 @@
-Spin echo sequence with ideal pulses. — seq_spin_echo_ideal • Spectroscopy Analysis Tools (spant) Spin echo sequence with ideal pulses. — seq_spin_echo_ideal • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/seq_steam_ideal.html b/docs/reference/seq_steam_ideal.html
index a60685a8..1c8115d7 100644
--- a/docs/reference/seq_steam_ideal.html
+++ b/docs/reference/seq_steam_ideal.html
@@ -1,5 +1,5 @@
-STEAM sequence with ideal pulses. — seq_steam_ideal • Spectroscopy Analysis Tools (spant) STEAM sequence with ideal pulses. — seq_steam_ideal • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -128,7 +128,7 @@ Value
diff --git a/docs/reference/seq_steam_ideal_cof.html b/docs/reference/seq_steam_ideal_cof.html
index 8f225740..cba7af91 100644
--- a/docs/reference/seq_steam_ideal_cof.html
+++ b/docs/reference/seq_steam_ideal_cof.html
@@ -1,7 +1,5 @@
-STEAM sequence with ideal pulses and coherence order filtering to simulate
-gradient crushers. — seq_steam_ideal_cof • Spectroscopy Analysis Tools (spant) STEAM sequence with ideal pulses and coherence order filtering to simulate gradient crushers. — seq_steam_ideal_cof • Spectroscopy Analysis Tools (spant) STEAM sequence with ideal pulses using the z-rotation gradient simulation
-method described by Young et al JMR 140, 146-152 (1999). — seq_steam_ideal_young • Spectroscopy Analysis Tools (spant) STEAM sequence with ideal pulses using the z-rotation gradient simulation method described by Young et al JMR 140, 146-152 (1999). — seq_steam_ideal_young • Spectroscopy Analysis Tools (spant) Set the number of transients for an mrs_data object. — set_Ntrans • Spectroscopy Analysis Tools (spant) Set the number of transients for an mrs_data object. — set_Ntrans • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/set_def_acq_paras.html b/docs/reference/set_def_acq_paras.html
index 3e1b4004..cc2ada9c 100644
--- a/docs/reference/set_def_acq_paras.html
+++ b/docs/reference/set_def_acq_paras.html
@@ -1,5 +1,5 @@
-Set the default acquisition parameters. — set_def_acq_paras • Spectroscopy Analysis Tools (spant) Set the default acquisition parameters. — set_def_acq_paras • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Arguments
diff --git a/docs/reference/set_lcm_cmd.html b/docs/reference/set_lcm_cmd.html
index 2056ed01..42bb2f24 100644
--- a/docs/reference/set_lcm_cmd.html
+++ b/docs/reference/set_lcm_cmd.html
@@ -1,5 +1,5 @@
-Set the command to run the LCModel command-line program. — set_lcm_cmd • Spectroscopy Analysis Tools (spant) Set the command to run the LCModel command-line program. — set_lcm_cmd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/set_lw.html b/docs/reference/set_lw.html
index b64ec851..bb176c62 100644
--- a/docs/reference/set_lw.html
+++ b/docs/reference/set_lw.html
@@ -1,5 +1,5 @@
-Apply line-broadening to an mrs_data object to achieve a specified linewidth. — set_lw • Spectroscopy Analysis Tools (spant) Apply line-broadening to an mrs_data object to achieve a specified linewidth. — set_lw • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -123,7 +123,7 @@ Value
diff --git a/docs/reference/set_mask_xy_mat.html b/docs/reference/set_mask_xy_mat.html
index 49dc5d4e..52c4b617 100644
--- a/docs/reference/set_mask_xy_mat.html
+++ b/docs/reference/set_mask_xy_mat.html
@@ -1,5 +1,5 @@
-Set the masked voxels in a 2D MRSI dataset to given spectrum. — set_mask_xy_mat • Spectroscopy Analysis Tools (spant) Set the masked voxels in a 2D MRSI dataset to given spectrum. — set_mask_xy_mat • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Value
diff --git a/docs/reference/set_precomp_mode.html b/docs/reference/set_precomp_mode.html
index f44bd5d3..47c28e3b 100644
--- a/docs/reference/set_precomp_mode.html
+++ b/docs/reference/set_precomp_mode.html
@@ -1,5 +1,5 @@
-Set the precompute mode. — set_precomp_mode • Spectroscopy Analysis Tools (spant) Set the precompute mode. — set_precomp_mode • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/set_precomp_verbose.html b/docs/reference/set_precomp_verbose.html
index 1453a231..9c613505 100644
--- a/docs/reference/set_precomp_verbose.html
+++ b/docs/reference/set_precomp_verbose.html
@@ -1,5 +1,5 @@
-Set the verbosity of the precompute function. — set_precomp_verbose • Spectroscopy Analysis Tools (spant) Set the verbosity of the precompute function. — set_precomp_verbose • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/set_ref.html b/docs/reference/set_ref.html
index 8953fa50..5436dfa2 100644
--- a/docs/reference/set_ref.html
+++ b/docs/reference/set_ref.html
@@ -1,5 +1,5 @@
-Set the ppm reference value (eg ppm value at 0Hz). — set_ref • Spectroscopy Analysis Tools (spant) Set the ppm reference value (eg ppm value at 0Hz). — set_ref • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/set_td_pts.html b/docs/reference/set_td_pts.html
index 8a80d42a..586459ff 100644
--- a/docs/reference/set_td_pts.html
+++ b/docs/reference/set_td_pts.html
@@ -1,7 +1,5 @@
-Set the number of time-domain data points, truncating or zero-filling as
-appropriate. — set_td_pts • Spectroscopy Analysis Tools (spant) Set the number of time-domain data points, truncating or zero-filling as appropriate. — set_td_pts • Spectroscopy Analysis Tools (spant) Set the command to run the TARQUIN command-line program. — set_tqn_cmd • Spectroscopy Analysis Tools (spant) Set the command to run the TARQUIN command-line program. — set_tqn_cmd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/set_tr.html b/docs/reference/set_tr.html
index b2109ab0..65c9df5f 100644
--- a/docs/reference/set_tr.html
+++ b/docs/reference/set_tr.html
@@ -1,5 +1,5 @@
-Set the repetition time of an MRS dataset. — set_tr • Spectroscopy Analysis Tools (spant) Set the repetition time of an MRS dataset. — set_tr • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/shift.html b/docs/reference/shift.html
index ab0fe724..034591d0 100644
--- a/docs/reference/shift.html
+++ b/docs/reference/shift.html
@@ -1,5 +1,5 @@
-Apply a frequency shift to MRS data. — shift • Spectroscopy Analysis Tools (spant) Apply a frequency shift to MRS data. — shift • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/shift_basis.html b/docs/reference/shift_basis.html
index 2884be19..f55a65e0 100644
--- a/docs/reference/shift_basis.html
+++ b/docs/reference/shift_basis.html
@@ -1,5 +1,5 @@
-Apply frequency shifts to basis set signals. — shift_basis • Spectroscopy Analysis Tools (spant) Apply frequency shifts to basis set signals. — shift_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Value
diff --git a/docs/reference/sim_basis.html b/docs/reference/sim_basis.html
index c7838c46..bb5fefc6 100644
--- a/docs/reference/sim_basis.html
+++ b/docs/reference/sim_basis.html
@@ -1,5 +1,5 @@
-Simulate a basis set object. — sim_basis • Spectroscopy Analysis Tools (spant) Simulate a basis set object. — sim_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -136,7 +136,7 @@ Value
diff --git a/docs/reference/sim_basis_1h_brain.html b/docs/reference/sim_basis_1h_brain.html
index 62ed7389..f71ffa0b 100644
--- a/docs/reference/sim_basis_1h_brain.html
+++ b/docs/reference/sim_basis_1h_brain.html
@@ -1,7 +1,5 @@
-Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS
-sequence. Note, ideal pulses are assumed. — sim_basis_1h_brain • Spectroscopy Analysis Tools (spant) Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS sequence. Note, ideal pulses are assumed. — sim_basis_1h_brain • Spectroscopy Analysis Tools (spant) Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS
-sequence. Note, ideal pulses are assumed. — sim_basis_1h_brain_press • Spectroscopy Analysis Tools (spant) Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS sequence. Note, ideal pulses are assumed. — sim_basis_1h_brain_press • Spectroscopy Analysis Tools (spant) Simulate a macromolecular and lipid basis-set suitable for 1H brain MRS
-analysis. — sim_basis_mm_lip_lcm • Spectroscopy Analysis Tools (spant) Simulate a macromolecular and lipid basis-set suitable for 1H brain MRS analysis. — sim_basis_mm_lip_lcm • Spectroscopy Analysis Tools (spant) Simulate a basis file using TARQUIN. — sim_basis_tqn • Spectroscopy Analysis Tools (spant) Simulate a basis file using TARQUIN. — sim_basis_tqn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -129,7 +129,7 @@ Examples
diff --git a/docs/reference/sim_brain_1h.html b/docs/reference/sim_brain_1h.html
index 2044cf1a..717ee289 100644
--- a/docs/reference/sim_brain_1h.html
+++ b/docs/reference/sim_brain_1h.html
@@ -1,5 +1,5 @@
-Simulate MRS data with a similar appearance to normal brain (by default). — sim_brain_1h • Spectroscopy Analysis Tools (spant) Simulate MRS data with a similar appearance to normal brain (by default). — sim_brain_1h • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -159,7 +159,7 @@ Value
diff --git a/docs/reference/sim_mol.html b/docs/reference/sim_mol.html
index 23bcef50..77f76a50 100644
--- a/docs/reference/sim_mol.html
+++ b/docs/reference/sim_mol.html
@@ -1,5 +1,5 @@
-Simulate a mol_parameter object. — sim_mol • Spectroscopy Analysis Tools (spant) Simulate a mol_parameter object. — sim_mol • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -143,7 +143,7 @@ Value
diff --git a/docs/reference/sim_noise.html b/docs/reference/sim_noise.html
index 23875f79..a71477d4 100644
--- a/docs/reference/sim_noise.html
+++ b/docs/reference/sim_noise.html
@@ -1,5 +1,5 @@
-Simulate an mrs_data object containing simulated Gaussian noise. — sim_noise • Spectroscopy Analysis Tools (spant) Simulate an mrs_data object containing simulated Gaussian noise. — sim_noise • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -84,6 +84,7 @@ Simulate an mrs_data object containing simulated Gaussian noise.
ft = def_ft(),
N = def_N(),
ref = def_ref(),
+ nuc = def_nuc(),
dyns = 1,
fd = TRUE
)
@@ -111,6 +112,10 @@ Arguments
reference value for ppm scale.
nuc
+resonant nucleus.
dyns
number of dynamic scans to generate.
Value
diff --git a/docs/reference/sim_resonances.html b/docs/reference/sim_resonances.html
index 19e9a8a4..d4f8d7c0 100644
--- a/docs/reference/sim_resonances.html
+++ b/docs/reference/sim_resonances.html
@@ -1,5 +1,5 @@
-Simulate a MRS data object containing a set of simulated resonances. — sim_resonances • Spectroscopy Analysis Tools (spant) Simulate a MRS data object containing a set of simulated resonances. — sim_resonances • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -161,7 +161,7 @@ Examples
diff --git a/docs/reference/sim_th_excit_profile.html b/docs/reference/sim_th_excit_profile.html
index 5535c5ef..e781cab1 100644
--- a/docs/reference/sim_th_excit_profile.html
+++ b/docs/reference/sim_th_excit_profile.html
@@ -1,7 +1,5 @@
-Simulate an ideal pulse excitation profile by smoothing a top-hat function
-with a Gaussian. — sim_th_excit_profile • Spectroscopy Analysis Tools (spant) Simulate an ideal pulse excitation profile by smoothing a top-hat function with a Gaussian. — sim_th_excit_profile • Spectroscopy Analysis Tools (spant) Simulate an mrs_data object containing complex zero valued samples. — sim_zero • Spectroscopy Analysis Tools (spant) Simulate an mrs_data object containing complex zero valued samples. — sim_zero • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -78,7 +78,14 @@ Simulate an mrs_data object containing complex zero valued samples.
-
+
@@ -99,6 +106,10 @@ Arguments
reference value for ppm scale.
nuc
+resonant nucleus.
dyns
number of dynamic scans to generate.
Value
diff --git a/docs/reference/smooth_dyns.html b/docs/reference/smooth_dyns.html
index 4cc8da50..accf3a51 100644
--- a/docs/reference/smooth_dyns.html
+++ b/docs/reference/smooth_dyns.html
@@ -1,5 +1,5 @@
-Smooth data across the dynamic dimension with a Gaussian kernel. — smooth_dyns • Spectroscopy Analysis Tools (spant) Smooth data across the dynamic dimension with a Gaussian kernel. — smooth_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/sort_basis.html b/docs/reference/sort_basis.html
index 6a676ea2..d25cc006 100644
--- a/docs/reference/sort_basis.html
+++ b/docs/reference/sort_basis.html
@@ -1,5 +1,5 @@
-Sort the basis-set elements alphabetically. — sort_basis • Spectroscopy Analysis Tools (spant) Sort the basis-set elements alphabetically. — sort_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/spant-package.html b/docs/reference/spant-package.html
index b3dd8e21..90f19ec3 100644
--- a/docs/reference/spant-package.html
+++ b/docs/reference/spant-package.html
@@ -1,5 +1,5 @@
-spant: spectroscopy analysis tools. — spant-package • Spectroscopy Analysis Tools (spant) spant: spectroscopy analysis tools. — spant-package • Spectroscopy Analysis Tools (spant) Simulate and fit some spectra with ABfit for benchmarking purposes. Basic
-timing and performance metrics will be printed. — spant_abfit_benchmark • Spectroscopy Analysis Tools (spant) Simulate and fit some spectra with ABfit for benchmarking purposes. Basic timing and performance metrics will be printed. — spant_abfit_benchmark • Spectroscopy Analysis Tools (spant) Example MEGA-PRESS data with significant B0 drift. — spant_mpress_drift • Spectroscopy Analysis Tools (spant) Example MEGA-PRESS data with significant B0 drift. — spant_mpress_drift • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -83,7 +83,7 @@ Example MEGA-PRESS data with significant B0 drift.
Format
- An object of class mrs_data of length 13.
+ An object of class mrs_data of dimension 1 x 1 x 1 x 1 x 40 x 1 x 1024.
@@ -98,7 +98,7 @@ Format
diff --git a/docs/reference/spant_sim_fmrs_dataset.html b/docs/reference/spant_sim_fmrs_dataset.html
new file mode 100644
index 00000000..00e48b56
--- /dev/null
+++ b/docs/reference/spant_sim_fmrs_dataset.html
@@ -0,0 +1,117 @@
+
+Simulate an example fMRS dataset for a block design fMRS experiment and export a BIDS structure. — spant_sim_fmrs_dataset • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Simulate an example fMRS dataset for a block design fMRS experiment and export a BIDS structure.
+ Source: R/fmrs.R
+ spant_sim_fmrs_dataset.Rd
+
+
+
+ Simulate an example fMRS dataset for a block design fMRS experiment and
+export a BIDS structure.
+
+
+
+ spant_sim_fmrs_dataset(output_dir = NULL)
+
+
+
+ Arguments
+ - output_dir
+output directory for the BIDS data. Defaults to :
+"HOME/sim_fmrs_dataset/data".
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/spant_simulation_benchmark.html b/docs/reference/spant_simulation_benchmark.html
index 32daa8bf..d8cc6841 100644
--- a/docs/reference/spant_simulation_benchmark.html
+++ b/docs/reference/spant_simulation_benchmark.html
@@ -1,7 +1,5 @@
-Simulate a typical metabolite basis set for benchmarking. Timing metrics will
-be printed on completion. — spant_simulation_benchmark • Spectroscopy Analysis Tools (spant) Simulate a typical metabolite basis set for benchmarking. Timing metrics will be printed on completion. — spant_simulation_benchmark • Spectroscopy Analysis Tools (spant) Decompose an mrs_data object into white and gray matter spectra. — spec_decomp • Spectroscopy Analysis Tools (spant) Perform a mathematical operation on a spectral region. — spec_op • Spectroscopy Analysis Tools (spant) Perform a mathematical operation on a spectral region. — spec_op • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -98,8 +98,8 @@ Arguments
operator
-can be "sum" (default), "mean", "l2", "max", "min" or
-"max-min".
can be "sum" (default), "mean", "l2", "max", "max_cplx,
+"min" or "max-min".
freq_scale
@@ -129,7 +129,7 @@ Value
diff --git a/docs/reference/spin_sys.html b/docs/reference/spin_sys.html
index 853423a4..1eaa9e76 100644
--- a/docs/reference/spin_sys.html
+++ b/docs/reference/spin_sys.html
@@ -1,5 +1,5 @@
-Create a spin system object for pulse sequence simulation. — spin_sys • Spectroscopy Analysis Tools (spant) Create a spin system object for pulse sequence simulation. — spin_sys • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/spm_pve2categorical.html b/docs/reference/spm_pve2categorical.html
index 23a1bad9..70f10729 100644
--- a/docs/reference/spm_pve2categorical.html
+++ b/docs/reference/spm_pve2categorical.html
@@ -1,7 +1,5 @@
-Convert SPM style segmentation files to a single categorical image where
-the numerical values map as: 0) Other, 1) CSF, 2) GM and 3) WM. — spm_pve2categorical • Spectroscopy Analysis Tools (spant) Convert SPM style segmentation files to a single categorical image where the numerical values map as: 0) Other, 1) CSF, 2) GM and 3) WM. — spm_pve2categorical • Spectroscopy Analysis Tools (spant) Signal space projection method for lipid suppression. — ssp • Spectroscopy Analysis Tools (spant) Signal space projection method for lipid suppression. — ssp • Spectroscopy Analysis Tools (spant) Plot the fitting results of an object of class fit_result with
-individual basis set components shown. — stackplot.fit_result • Spectroscopy Analysis Tools (spant) Plot the fitting results of an object of class fit_result with individual basis set components shown. — stackplot.fit_result • Spectroscopy Analysis Tools (spant) Produce a plot with multiple traces. — stackplot • Spectroscopy Analysis Tools (spant) Produce a plot with multiple traces. — stackplot • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/stackplot.mrs_data.html b/docs/reference/stackplot.mrs_data.html
index 17ff5648..64eea445 100644
--- a/docs/reference/stackplot.mrs_data.html
+++ b/docs/reference/stackplot.mrs_data.html
@@ -1,5 +1,5 @@
-Stackplot plotting method for objects of class mrs_data. — stackplot.mrs_data • Spectroscopy Analysis Tools (spant) Stackplot plotting method for objects of class mrs_data. — stackplot.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -255,7 +255,7 @@ Arguments
diff --git a/docs/reference/sub_first_dyn.html b/docs/reference/sub_first_dyn.html
index dbd7f831..493b7242 100644
--- a/docs/reference/sub_first_dyn.html
+++ b/docs/reference/sub_first_dyn.html
@@ -1,5 +1,5 @@
-Subtract the first dynamic spectrum from a dynamic series. — sub_first_dyn • Spectroscopy Analysis Tools (spant) Subtract the first dynamic spectrum from a dynamic series. — sub_first_dyn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/sub_mean_dyns.html b/docs/reference/sub_mean_dyns.html
index 6e3bb2df..221bd0c1 100644
--- a/docs/reference/sub_mean_dyns.html
+++ b/docs/reference/sub_mean_dyns.html
@@ -1,5 +1,5 @@
-Subtract the mean dynamic spectrum from a dynamic series. — sub_mean_dyns • Spectroscopy Analysis Tools (spant) Subtract the mean dynamic spectrum from a dynamic series. — sub_mean_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/sub_median_dyns.html b/docs/reference/sub_median_dyns.html
index 134c495d..1e834f14 100644
--- a/docs/reference/sub_median_dyns.html
+++ b/docs/reference/sub_median_dyns.html
@@ -1,5 +1,5 @@
-Subtract the median dynamic spectrum from a dynamic series. — sub_median_dyns • Spectroscopy Analysis Tools (spant) Subtract the median dynamic spectrum from a dynamic series. — sub_median_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/sum_coils.html b/docs/reference/sum_coils.html
index 7bf559f2..e1ab3cc0 100644
--- a/docs/reference/sum_coils.html
+++ b/docs/reference/sum_coils.html
@@ -1,5 +1,5 @@
-Calculate the sum across receiver coil elements. — sum_coils • Spectroscopy Analysis Tools (spant) Calculate the sum across receiver coil elements. — sum_coils • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/sum_dyns.html b/docs/reference/sum_dyns.html
index a0be19d3..bbda2ffc 100644
--- a/docs/reference/sum_dyns.html
+++ b/docs/reference/sum_dyns.html
@@ -1,5 +1,5 @@
-Calculate the sum of data dynamics. — sum_dyns • Spectroscopy Analysis Tools (spant) Calculate the sum of data dynamics. — sum_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/sum_mrs.html b/docs/reference/sum_mrs.html
index a22f215b..3cc3ab9e 100644
--- a/docs/reference/sum_mrs.html
+++ b/docs/reference/sum_mrs.html
@@ -1,5 +1,5 @@
-Sum two mrs_data objects. — sum_mrs • Spectroscopy Analysis Tools (spant) Sum two mrs_data objects. — sum_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Value
diff --git a/docs/reference/sum_mrs_list.html b/docs/reference/sum_mrs_list.html
index f4e09aea..c3584348 100644
--- a/docs/reference/sum_mrs_list.html
+++ b/docs/reference/sum_mrs_list.html
@@ -1,5 +1,5 @@
-Return the sum of a list of mrs_data objects. — sum_mrs_list • Spectroscopy Analysis Tools (spant) Return the sum of a list of mrs_data objects. — sum_mrs_list • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/svs_1h_brain_analysis.html b/docs/reference/svs_1h_brain_analysis.html
index 8ce514db..dff0ef7d 100644
--- a/docs/reference/svs_1h_brain_analysis.html
+++ b/docs/reference/svs_1h_brain_analysis.html
@@ -1,5 +1,5 @@
-Standard SVS 1H brain analysis pipeline. — svs_1h_brain_analysis • Spectroscopy Analysis Tools (spant) Standard SVS 1H brain analysis pipeline. — svs_1h_brain_analysis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -199,7 +199,7 @@ Value
diff --git a/docs/reference/svs_1h_brain_analysis_dev.html b/docs/reference/svs_1h_brain_analysis_dev.html
index d70a14d3..d71bfea2 100644
--- a/docs/reference/svs_1h_brain_analysis_dev.html
+++ b/docs/reference/svs_1h_brain_analysis_dev.html
@@ -1,5 +1,5 @@
-Standard SVS 1H brain analysis pipeline. — svs_1h_brain_analysis_dev • Spectroscopy Analysis Tools (spant) Standard SVS 1H brain analysis pipeline. — svs_1h_brain_analysis_dev • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -193,7 +193,7 @@ Examples
diff --git a/docs/reference/svs_1h_brain_batch_analysis.html b/docs/reference/svs_1h_brain_batch_analysis.html
index 5631e8cc..15f7223e 100644
--- a/docs/reference/svs_1h_brain_batch_analysis.html
+++ b/docs/reference/svs_1h_brain_batch_analysis.html
@@ -1,5 +1,5 @@
-Batch interface to the standard SVS 1H brain analysis pipeline. — svs_1h_brain_batch_analysis • Spectroscopy Analysis Tools (spant) Batch interface to the standard SVS 1H brain analysis pipeline. — svs_1h_brain_batch_analysis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -144,7 +144,7 @@ Value
diff --git a/docs/reference/t_test_spec.html b/docs/reference/t_test_spec.html
new file mode 100644
index 00000000..56a7ea1b
--- /dev/null
+++ b/docs/reference/t_test_spec.html
@@ -0,0 +1,124 @@
+
+Perform a t-test on spectral data points. — t_test_spec • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+
+
+ Perform a t-test on spectral data points.
+
+
+
+ t_test_spec(mrs_data, group)
+
+
+
+ Arguments
+ - mrs_data
+an mrs_data object with spectra in the dynamic dimension.
- group
+vector describing the group membership of each dynamic spectrum.
+
+ Value
+
+
+a list of statistical results.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/td2fd.html b/docs/reference/td2fd.html
index 6748a6a8..f31ed524 100644
--- a/docs/reference/td2fd.html
+++ b/docs/reference/td2fd.html
@@ -1,5 +1,5 @@
-Transform time-domain data to the frequency-domain. — td2fd • Spectroscopy Analysis Tools (spant) Transform time-domain data to the frequency-domain. — td2fd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/td_conv_filt.html b/docs/reference/td_conv_filt.html
index a9f340c3..106b9b00 100644
--- a/docs/reference/td_conv_filt.html
+++ b/docs/reference/td_conv_filt.html
@@ -1,5 +1,5 @@
-Time-domain convolution based filter. — td_conv_filt • Spectroscopy Analysis Tools (spant) Time-domain convolution based filter. — td_conv_filt • Spectroscopy Analysis Tools (spant) Time-domain spectral registration. — tdsr • Spectroscopy Analysis Tools (spant) Time-domain spectral registration. — tdsr • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -121,7 +121,7 @@ Value
diff --git a/docs/reference/te.html b/docs/reference/te.html
index 010361b1..4a65711d 100644
--- a/docs/reference/te.html
+++ b/docs/reference/te.html
@@ -1,5 +1,5 @@
-Return the echo time of an MRS dataset. — te • Spectroscopy Analysis Tools (spant) Return the echo time of an MRS dataset. — te • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/tr.html b/docs/reference/tr.html
index 0c0bd63b..2e749e02 100644
--- a/docs/reference/tr.html
+++ b/docs/reference/tr.html
@@ -1,5 +1,5 @@
-Return the repetition time of an MRS dataset. — tr • Spectroscopy Analysis Tools (spant) Return the repetition time of an MRS dataset. — tr • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/varpro_3_para_opts.html b/docs/reference/varpro_3_para_opts.html
index c2270a16..52d7cd84 100644
--- a/docs/reference/varpro_3_para_opts.html
+++ b/docs/reference/varpro_3_para_opts.html
@@ -1,5 +1,5 @@
-Return a list of options for VARPRO based fitting with 3 free parameters. — varpro_3_para_opts • Spectroscopy Analysis Tools (spant) Return a list of options for VARPRO based fitting with 3 free parameters. — varpro_3_para_opts • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -141,7 +141,7 @@ Value
diff --git a/docs/reference/varpro_basic_opts.html b/docs/reference/varpro_basic_opts.html
index 32c86d22..c5104891 100644
--- a/docs/reference/varpro_basic_opts.html
+++ b/docs/reference/varpro_basic_opts.html
@@ -1,5 +1,5 @@
-Return a list of options for a basic VARPRO analysis. — varpro_basic_opts • Spectroscopy Analysis Tools (spant) Return a list of options for a basic VARPRO analysis. — varpro_basic_opts • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -118,7 +118,7 @@ Value
diff --git a/docs/reference/varpro_opts.html b/docs/reference/varpro_opts.html
index 2aabf11d..6332f730 100644
--- a/docs/reference/varpro_opts.html
+++ b/docs/reference/varpro_opts.html
@@ -1,5 +1,5 @@
-Return a list of options for VARPRO based fitting. — varpro_opts • Spectroscopy Analysis Tools (spant) Return a list of options for VARPRO based fitting. — varpro_opts • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -177,7 +177,7 @@ Examples
diff --git a/docs/reference/vec2mrs_data.html b/docs/reference/vec2mrs_data.html
index 0cccd73b..f0d58bf0 100644
--- a/docs/reference/vec2mrs_data.html
+++ b/docs/reference/vec2mrs_data.html
@@ -1,5 +1,5 @@
-Convert a vector into a mrs_data object. — vec2mrs_data • Spectroscopy Analysis Tools (spant) Convert a vector into a mrs_data object. — vec2mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -80,10 +80,11 @@ Convert a vector into a mrs_data object.
vec2mrs_data(
vec,
- fs = def_fs(),
- ft = def_ft(),
- ref = def_ref(),
- nuc = def_nuc(),
+ mrs_data = NULL,
+ fs = NULL,
+ ft = NULL,
+ ref = NULL,
+ nuc = NULL,
dyns = 1,
fd = FALSE
)
@@ -95,6 +96,10 @@ Arguments
the data vector.
mrs_data
+example data to copy acquisition parameters from.
fs
sampling frequency in Hz.
Arguments
fd
-flag to indicate if the matrix is in the frequency domain (logical).
flag to indicate if the vector is in the frequency domain (logical).
Value
diff --git a/docs/reference/write_basis.html b/docs/reference/write_basis.html
index b6e27cbd..94c5e021 100644
--- a/docs/reference/write_basis.html
+++ b/docs/reference/write_basis.html
@@ -1,5 +1,5 @@
-Write a basis object to an LCModel .basis formatted file. — write_basis • Spectroscopy Analysis Tools (spant) Write a basis object to an LCModel .basis formatted file. — write_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -108,7 +108,7 @@ Arguments
diff --git a/docs/reference/write_basis_tqn.html b/docs/reference/write_basis_tqn.html
index 6aa51c1d..116c73ec 100644
--- a/docs/reference/write_basis_tqn.html
+++ b/docs/reference/write_basis_tqn.html
@@ -1,5 +1,5 @@
-Generate a basis file using TARQUIN. — write_basis_tqn • Spectroscopy Analysis Tools (spant) Generate a basis file using TARQUIN. — write_basis_tqn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Examples
diff --git a/docs/reference/write_mrs.html b/docs/reference/write_mrs.html
index fff25f15..124b9dc4 100644
--- a/docs/reference/write_mrs.html
+++ b/docs/reference/write_mrs.html
@@ -1,5 +1,5 @@
-Write MRS data object to file. — write_mrs • Spectroscopy Analysis Tools (spant) Write MRS data object to file. — write_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Arguments
diff --git a/docs/reference/write_mrs_nifti.html b/docs/reference/write_mrs_nifti.html
index f4bf1921..bd3ed4b7 100644
--- a/docs/reference/write_mrs_nifti.html
+++ b/docs/reference/write_mrs_nifti.html
@@ -1,5 +1,5 @@
-Write MRS data object to file in NIFTI format. — write_mrs_nifti • Spectroscopy Analysis Tools (spant) Write MRS data object to file in NIFTI format. — write_mrs_nifti • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/write_pulse_ascii.html b/docs/reference/write_pulse_ascii.html
index 067ae086..221f8ebb 100644
--- a/docs/reference/write_pulse_ascii.html
+++ b/docs/reference/write_pulse_ascii.html
@@ -1,5 +1,5 @@
-Write an ASCII formatted pulse file. — write_pulse_ascii • Spectroscopy Analysis Tools (spant) Write an ASCII formatted pulse file. — write_pulse_ascii • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/zero_fade_spec.html b/docs/reference/zero_fade_spec.html
index c703745c..c8b572c3 100644
--- a/docs/reference/zero_fade_spec.html
+++ b/docs/reference/zero_fade_spec.html
@@ -1,7 +1,5 @@
-Fade a spectrum to zero by frequency domain multiplication with a tanh
-function. Note this operation distorts data points at the end of the FID. — zero_fade_spec • Spectroscopy Analysis Tools (spant) Fade a spectrum to zero by frequency domain multiplication with a tanh function. Note this operation distorts data points at the end of the FID. — zero_fade_spec • Spectroscopy Analysis Tools (spant) Zero all coherences including and above a given order. — zero_higher_orders • Spectroscopy Analysis Tools (spant) Zero all coherences including and above a given order. — zero_higher_orders • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Value
diff --git a/docs/reference/zero_td_pts_end.html b/docs/reference/zero_td_pts_end.html
index 8c1123c8..71d24ebb 100644
--- a/docs/reference/zero_td_pts_end.html
+++ b/docs/reference/zero_td_pts_end.html
@@ -1,5 +1,5 @@
-Set mrs_data object data points at the end of the FID to zero. — zero_td_pts_end • Spectroscopy Analysis Tools (spant) Set mrs_data object data points at the end of the FID to zero. — zero_td_pts_end • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/zf.html b/docs/reference/zf.html
index 85e2013c..baf50256 100644
--- a/docs/reference/zf.html
+++ b/docs/reference/zf.html
@@ -1,5 +1,5 @@
-Zero-fill MRS data in the time domain. — zf • Spectroscopy Analysis Tools (spant) Zero-fill MRS data in the time domain. — zf • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -125,7 +125,7 @@ Value
diff --git a/docs/reference/zf_xy.html b/docs/reference/zf_xy.html
index ebca3999..c4104a74 100644
--- a/docs/reference/zf_xy.html
+++ b/docs/reference/zf_xy.html
@@ -1,5 +1,5 @@
-Zero-fill MRSI data in the k-space x-y direction. — zf_xy • Spectroscopy Analysis Tools (spant) Zero-fill MRSI data in the k-space x-y direction. — zf_xy • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -113,7 +113,7 @@ Value
diff --git a/docs/sitemap.xml b/docs/sitemap.xml
index e2139f71..4c39f515 100644
--- a/docs/sitemap.xml
+++ b/docs/sitemap.xml
@@ -216,6 +216,12 @@
https://martin3141.github.io/spant/reference/comb_coils_fp_pc.html
+
+ https://martin3141.github.io/spant/reference/comb_coils_mrsi_gls.html
+
+
+ https://martin3141.github.io/spant/reference/comb_coils_svs_gls.html
+
https://martin3141.github.io/spant/reference/comb_csv_results.html
@@ -411,6 +417,9 @@
https://martin3141.github.io/spant/reference/gen_conv_reg.html
+
+ https://martin3141.github.io/spant/reference/gen_group_reg.html
+
https://martin3141.github.io/spant/reference/gen_impulse_reg.html
@@ -555,6 +564,15 @@
https://martin3141.github.io/spant/reference/glm_spec.html
+
+ https://martin3141.github.io/spant/reference/glm_spec_fmrs_fl.html
+
+
+ https://martin3141.github.io/spant/reference/glm_spec_fmrs_group.html
+
+
+ https://martin3141.github.io/spant/reference/glm_spec_group_linhyp.html
+
https://martin3141.github.io/spant/reference/grid_shift_xy.html
@@ -690,9 +708,15 @@
https://martin3141.github.io/spant/reference/mrs_data2basis.html
+
+ https://martin3141.github.io/spant/reference/mrs_data2bids.html
+
https://martin3141.github.io/spant/reference/mrs_data2mat.html
+
+ https://martin3141.github.io/spant/reference/mrs_data2spec_mat.html
+
https://martin3141.github.io/spant/reference/mrs_data2vec.html
@@ -741,6 +765,9 @@
https://martin3141.github.io/spant/reference/phase.html
+
+ https://martin3141.github.io/spant/reference/phase_ref_1h_brain.html
+
https://martin3141.github.io/spant/reference/plot.fit_result.html
@@ -780,6 +807,12 @@
https://martin3141.github.io/spant/reference/precomp.html
+
+ https://martin3141.github.io/spant/reference/preproc_svs.html
+
+
+ https://martin3141.github.io/spant/reference/preproc_svs_dataset.html
+
https://martin3141.github.io/spant/reference/print.fit_result.html
@@ -1050,6 +1083,9 @@
https://martin3141.github.io/spant/reference/spant_mpress_drift.html
+
+ https://martin3141.github.io/spant/reference/spant_sim_fmrs_dataset.html
+
https://martin3141.github.io/spant/reference/spant_simulation_benchmark.html
@@ -1107,6 +1143,9 @@
https://martin3141.github.io/spant/reference/svs_1h_brain_batch_analysis.html
+
+ https://martin3141.github.io/spant/reference/t_test_spec.html
+
https://martin3141.github.io/spant/reference/td2fd.html
Estimate the standard deviation of the noise from a segment of an mrs_data -object.
Estimate the standard deviation of the noise from a segment of an mrs_data object.
All functions
- Perform a zeroth order phase correction based on the phase of the first data
-point in the time-domain.
Perform a zeroth order phase correction based on the phase of the first data point in the time-domain.
@@ -507,8 +494,7 @@ All functions
- Perform a fft and fftshift on a matrix with each column replaced by its
-shifted fft.
Perform a fft and fftshift on a matrix with each column replaced by its shifted fft.
@@ -536,8 +522,11 @@ All functions
- Generate regressors by convolving a specified response function with a
-stimulus.
Generate regressors by convolving a specified response function with a stimulus.
+
+
+ Expand a regressor matrix for a group analysis.
@@ -553,28 +542,23 @@ All functions
- Return a character vector of common 1H molecules found in healthy human
-brain.
Return a character vector of common 1H molecules found in healthy human brain.
- Return a list of mol_parameter objects suitable for 1H brain MRS
-analyses.
Return a list of mol_parameter objects suitable for 1H brain MRS analyses.
- Return a list of mol_parameter objects suitable for 1H brain MRS
-analyses.
Return a list of mol_parameter objects suitable for 1H brain MRS analyses.
- Return a list of mol_parameter objects suitable for 1H brain MRS
-analyses.
Return a list of mol_parameter objects suitable for 1H brain MRS analyses.
- Return a list of mol_parameter objects suitable for 1H brain MRS
-analyses.
Return a list of mol_parameter objects suitable for 1H brain MRS analyses.
@@ -582,8 +566,7 @@ All functions
- Return a character vector of molecules included in the Gold Star Phantoms
-SPECTRE phantom.
Return a character vector of molecules included in the Gold Star Phantoms SPECTRE phantom.
@@ -635,8 +618,7 @@ All functions
- Return a character array of names that may be used with the
-get_mol_paras function.
Return a character array of names that may be used with the get_mol_paras function.
@@ -700,8 +682,7 @@ All functions
- Return an array of amplitudes derived from fitting the initial points in the
-time domain and extrapolating back to t=0.
Return an array of amplitudes derived from fitting the initial points in the time domain and extrapolating back to t=0.
@@ -709,8 +690,7 @@ All functions
- Generate a mol_parameters object for a simple spin system with one
-resonance.
Generate a mol_parameters object for a simple spin system with one resonance.
@@ -731,6 +711,18 @@ All functions glm_spec()
Perform a GLM analysis of dynamic MRS data in the spectral domain.
+
+
+ Perform first-level spectral GLM analysis of an fMRS dataset.
+
+
+ Perform group-level spectral GLM analysis of an fMRS dataset.
+
+
+ Test a group-level spectral GLM linear hypothesis.
@@ -766,8 +758,7 @@ All functions
- Perform an ifft and ifftshift on a matrix with each column replaced by its
-shifted ifft.
Perform an ifft and ifftshift on a matrix with each column replaced by its shifted ifft.
@@ -799,8 +790,7 @@ All functions
- Check if the chemical shift dimension of an MRS data object is in the
-frequency domain.
Check if the chemical shift dimension of an MRS data object is in the frequency domain.
@@ -820,18 +810,15 @@ All functions
- Covert a linewidth in Hz to an equivalent alpha value in the time-domain ie:
-x * exp(-t * alpha).
Covert a linewidth in Hz to an equivalent alpha value in the time-domain ie: x * exp(-t * alpha).
- Covert a linewidth in Hz to an equivalent beta value in the time-domain ie:
-x * exp(-t * t * beta).
Covert a linewidth in Hz to an equivalent beta value in the time-domain ie: x * exp(-t * t * beta).
- Make a basis-set object from a directory containing LCModel formatted RAW
-files.
Make a basis-set object from a directory containing LCModel formatted RAW files.
@@ -851,8 +838,7 @@ All functions
- Mask the voxels outside an elliptical region spanning the MRSI dataset in the
-x-y plane.
Mask the voxels outside an elliptical region spanning the MRSI dataset in the x-y plane.
@@ -860,13 +846,11 @@ All functions
- Convert a matrix (with spectral points in the column dimension and dynamics
-in the row dimensions) into a mrs_data object.
Convert a matrix (with spectral points in the column dimension and dynamics in the row dimensions) into a mrs_data object.
- Matrix exponential function taken from complexplus package to reduce the
-number of spant dependencies.
Matrix exponential function taken from complexplus package to reduce the number of spant dependencies.
@@ -914,31 +898,31 @@ All functions
- Convert an mrs_data object to basis object - where basis signals are spread
-across the dynamic dimension in the MRS data.
Convert an mrs_data object to basis object - where basis signals are spread across the dynamic dimension in the MRS data.
+
+
+ Create a BIDS file structure from a vector of MRS data paths or list of mrs_data objects.
- Convert mrs_data object to a matrix, with spectral points in the column
-dimension and dynamics in the row dimension.
Convert mrs_data object to a matrix, with spectral points in the column dimension and dynamics in the row dimension.
-
+
- Convert mrs_data object to a vector.
Convert mrs_data object to a matrix, with spectral points in the column dimension and dynamics in the row dimension.
-
+
- Create a BIDS directory and file structure from a list of mrs_data objects.
Convert mrs_data object to a vector.
- Perform a fftshift on a matrix, with each column replaced by its shifted
-result.
Perform a fftshift on a matrix, with each column replaced by its shifted result.
- Perform an ifftshift on a matrix, with each column replaced by its shifted
-result.
Perform an ifftshift on a matrix, with each column replaced by its shifted result.
@@ -946,9 +930,7 @@ All functions
- Flip the x data dimension order of a nifti image. This corresponds to
-flipping MRI data in the left-right direction, assuming the data in save in
-neurological format (can check with fslorient program).
Flip the x data dimension order of a nifti image. This corresponds to flipping MRI data in the left-right direction, assuming the data in save in neurological format (can check with fslorient program).
@@ -964,8 +946,7 @@ All functions
- Search for the highest peak in a spectral region and return the frequency,
-height and FWHM.
Search for the highest peak in a spectral region and return the frequency, height and FWHM.
@@ -974,6 +955,10 @@ All functions phase()
Apply phasing parameters to MRS data.
+
+
+ Corrected zero order phase and chemical shift offset in 1H MRS data from the brain.
@@ -1005,8 +990,7 @@ All functions
- Plot an interactive slice map from a data array where voxels can be selected
-to display a corresponding spectrum.
Plot an interactive slice map from a data array where voxels can be selected to display a corresponding spectrum.
@@ -1026,8 +1010,15 @@ All functions
- Save function results to file and load on subsequent calls to avoid repeat
-computation.
Save function results to file and load on subsequent calls to avoid repeat computation.
+
+
+ Preprocess and perform quality assessment of a single SVS data set.
+
+
+ Preprocess and perform quality assessment of one or more SVS data sets.
@@ -1055,15 +1046,11 @@ All functions
- Read a directory containing Siemens MRS IMA files and combine along the coil
-dimension. Note that the coil ID is inferred from the sorted file name and
-should be checked when consistency is required between two directories.
Read a directory containing Siemens MRS IMA files and combine along the coil dimension. Note that the coil ID is inferred from the sorted file name and should be checked when consistency is required between two directories.
- Read a directory containing Siemens MRS IMA files and combine along the
-dynamic dimension. Note that the coil ID is inferred from the sorted file
-name and should be checked when consistency is required.
Read a directory containing Siemens MRS IMA files and combine along the dynamic dimension. Note that the coil ID is inferred from the sorted file name and should be checked when consistency is required.
@@ -1103,13 +1090,11 @@ All functions
- Reconstruct complex time-domain data from the real part of frequency-domain
-data.
Reconstruct complex time-domain data from the real part of frequency-domain data.
- Reconstruct complex time-domain data from the real part of frequency-domain
-data.
Reconstruct complex time-domain data from the real part of frequency-domain data.
@@ -1141,8 +1126,7 @@ All functions
- Resample a VOI to match a target image space using nearest-neighbour
-interpolation.
Resample a VOI to match a target image space using nearest-neighbour interpolation.
@@ -1158,23 +1142,19 @@ All functions
- Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water).
Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / kg of tissue water).
- Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water).
Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / kg of tissue water).
- Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / Litre of tissue).
Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / Litre of tissue).
- Convert default LCM/TARQUIN concentration scaling to molal units with partial
-volume correction.
Convert default LCM/TARQUIN concentration scaling to molal units with partial volume correction.
@@ -1222,8 +1202,7 @@ All functions
- MEGA-PRESS sequence with ideal localisation pulses and Gaussian shaped
-editing pulse.
MEGA-PRESS sequence with ideal localisation pulses and Gaussian shaped editing pulse.
@@ -1251,13 +1230,11 @@ All functions
- STEAM sequence with ideal pulses and coherence order filtering to simulate
-gradient crushers.
STEAM sequence with ideal pulses and coherence order filtering to simulate gradient crushers.
- STEAM sequence with ideal pulses using the z-rotation gradient simulation
-method described by Young et al JMR 140, 146-152 (1999).
STEAM sequence with ideal pulses using the z-rotation gradient simulation method described by Young et al JMR 140, 146-152 (1999).
@@ -1293,8 +1270,7 @@ All functions
- Set the number of time-domain data points, truncating or zero-filling as
-appropriate.
Set the number of time-domain data points, truncating or zero-filling as appropriate.
@@ -1318,18 +1294,15 @@ All functions
- Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS
-sequence. Note, ideal pulses are assumed.
Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS sequence. Note, ideal pulses are assumed.
- Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS
-sequence. Note, ideal pulses are assumed.
Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS sequence. Note, ideal pulses are assumed.
- Simulate a macromolecular and lipid basis-set suitable for 1H brain MRS
-analysis.
Simulate a macromolecular and lipid basis-set suitable for 1H brain MRS analysis.
@@ -1353,8 +1326,7 @@ All functions
- Simulate an ideal pulse excitation profile by smoothing a top-hat function
-with a Gaussian.
Simulate an ideal pulse excitation profile by smoothing a top-hat function with a Gaussian.
@@ -1374,17 +1346,19 @@ All functions
- Simulate and fit some spectra with ABfit for benchmarking purposes. Basic
-timing and performance metrics will be printed.
Simulate and fit some spectra with ABfit for benchmarking purposes. Basic timing and performance metrics will be printed.
Example MEGA-PRESS data with significant B0 drift.
+
+
+ Simulate an example fMRS dataset for a block design fMRS experiment and export a BIDS structure.
- Simulate a typical metabolite basis set for benchmarking. Timing metrics will
-be printed on completion.
Simulate a typical metabolite basis set for benchmarking. Timing metrics will be printed on completion.
@@ -1400,8 +1374,7 @@ All functions
- Convert SPM style segmentation files to a single categorical image where
-the numerical values map as: 0) Other, 1) CSF, 2) GM and 3) WM.
Convert SPM style segmentation files to a single categorical image where the numerical values map as: 0) Other, 1) CSF, 2) GM and 3) WM.
@@ -1413,8 +1386,7 @@ All functions
- Plot the fitting results of an object of class fit_result with
-individual basis set components shown.
Plot the fitting results of an object of class fit_result with individual basis set components shown.
@@ -1459,6 +1431,10 @@ All functions svs_1h_brain_batch_analysis()
Batch interface to the standard SVS 1H brain analysis pipeline.
+
+
+ Perform a t-test on spectral data points.
@@ -1518,8 +1494,7 @@ All functions
- Fade a spectrum to zero by frequency domain multiplication with a tanh
-function. Note this operation distorts data points at the end of the FID.
Fade a spectrum to zero by frequency domain multiplication with a tanh function. Note this operation distorts data points at the end of the FID.
@@ -1549,7 +1524,7 @@ All functions
diff --git a/docs/reference/int_spec.html b/docs/reference/int_spec.html
index c7060fe7..783325a8 100644
--- a/docs/reference/int_spec.html
+++ b/docs/reference/int_spec.html
@@ -1,5 +1,5 @@
-Integrate a spectral region. — int_spec • Spectroscopy Analysis Tools (spant) Integrate a spectral region. — int_spec • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -118,7 +118,7 @@ Value
diff --git a/docs/reference/interleave_dyns.html b/docs/reference/interleave_dyns.html
index effe5543..441eff27 100644
--- a/docs/reference/interleave_dyns.html
+++ b/docs/reference/interleave_dyns.html
@@ -1,5 +1,5 @@
-Interleave the first and second half of a dynamic series. — interleave_dyns • Spectroscopy Analysis Tools (spant) Interleave the first and second half of a dynamic series. — interleave_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/inv_even_dyns.html b/docs/reference/inv_even_dyns.html
index 9f9d4fff..dcb781dc 100644
--- a/docs/reference/inv_even_dyns.html
+++ b/docs/reference/inv_even_dyns.html
@@ -1,5 +1,5 @@
-Invert even numbered dynamic scans starting from 1 (2,4,6...). — inv_even_dyns • Spectroscopy Analysis Tools (spant) Invert even numbered dynamic scans starting from 1 (2,4,6...). — inv_even_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/inv_odd_dyns.html b/docs/reference/inv_odd_dyns.html
index 26212e2b..78d64660 100644
--- a/docs/reference/inv_odd_dyns.html
+++ b/docs/reference/inv_odd_dyns.html
@@ -1,5 +1,5 @@
-Invert odd numbered dynamic scans starting from 1 (1,3,5...). — inv_odd_dyns • Spectroscopy Analysis Tools (spant) Invert odd numbered dynamic scans starting from 1 (1,3,5...). — inv_odd_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/is.def.html b/docs/reference/is.def.html
index f196ffd0..a67b9eba 100644
--- a/docs/reference/is.def.html
+++ b/docs/reference/is.def.html
@@ -1,5 +1,5 @@
-Check if an object is defined, which is the same as being not NULL. — is.def • Spectroscopy Analysis Tools (spant) Check if an object is defined, which is the same as being not NULL. — is.def • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/is_fd.html b/docs/reference/is_fd.html
index 3b0ca165..18a193aa 100644
--- a/docs/reference/is_fd.html
+++ b/docs/reference/is_fd.html
@@ -1,7 +1,5 @@
-Check if the chemical shift dimension of an MRS data object is in the
-frequency domain. — is_fd • Spectroscopy Analysis Tools (spant) Check if the chemical shift dimension of an MRS data object is in the frequency domain. — is_fd • Spectroscopy Analysis Tools (spant) Transform 2D MRSI data from k-space to image space in the x-y direction. — kspace2img_xy • Spectroscopy Analysis Tools (spant) Transform 2D MRSI data from k-space to image space in the x-y direction. — kspace2img_xy • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/l2_reg.html b/docs/reference/l2_reg.html
index 3d781d80..21aa9849 100644
--- a/docs/reference/l2_reg.html
+++ b/docs/reference/l2_reg.html
@@ -1,5 +1,5 @@
-Perform l2 regularisation artefact suppression. — l2_reg • Spectroscopy Analysis Tools (spant) Perform l2 regularisation artefact suppression. — l2_reg • Spectroscopy Analysis Tools (spant) Apply line-broadening (apodisation) to MRS data or basis object. — lb • Spectroscopy Analysis Tools (spant) Apply line-broadening (apodisation) to MRS data or basis object. — lb • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -123,7 +123,7 @@ Value
diff --git a/docs/reference/lofdc.html b/docs/reference/lofdc.html
index 5419b1ec..31347a25 100644
--- a/docs/reference/lofdc.html
+++ b/docs/reference/lofdc.html
@@ -1,5 +1,5 @@
-Correct linear frequency drift. — lofdc • Spectroscopy Analysis Tools (spant) Correct linear frequency drift. — lofdc • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -138,7 +138,7 @@ Value
diff --git a/docs/reference/lw2alpha.html b/docs/reference/lw2alpha.html
index b83db682..25da229b 100644
--- a/docs/reference/lw2alpha.html
+++ b/docs/reference/lw2alpha.html
@@ -1,7 +1,5 @@
-Covert a linewidth in Hz to an equivalent alpha value in the time-domain ie:
-x * exp(-t * alpha). — lw2alpha • Spectroscopy Analysis Tools (spant) Covert a linewidth in Hz to an equivalent alpha value in the time-domain ie: x * exp(-t * alpha). — lw2alpha • Spectroscopy Analysis Tools (spant) Covert a linewidth in Hz to an equivalent beta value in the time-domain ie:
-x * exp(-t * t * beta). — lw2beta • Spectroscopy Analysis Tools (spant) Covert a linewidth in Hz to an equivalent beta value in the time-domain ie: x * exp(-t * t * beta). — lw2beta • Spectroscopy Analysis Tools (spant) Make a basis-set object from a directory containing LCModel formatted RAW
-files. — make_basis_from_raw • Spectroscopy Analysis Tools (spant) Make a basis-set object from a directory containing LCModel formatted RAW files. — make_basis_from_raw • Spectroscopy Analysis Tools (spant) Mask an MRS dataset in the dynamic dimension. — mask_dyns • Spectroscopy Analysis Tools (spant) Mask an MRS dataset in the dynamic dimension. — mask_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/mask_fit_res.html b/docs/reference/mask_fit_res.html
index 97baaa3f..ebd91a99 100644
--- a/docs/reference/mask_fit_res.html
+++ b/docs/reference/mask_fit_res.html
@@ -1,5 +1,5 @@
-Mask fit result spectra depending on a vector of bool values. — mask_fit_res • Spectroscopy Analysis Tools (spant) Mask fit result spectra depending on a vector of bool values. — mask_fit_res • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -116,7 +116,7 @@ Value
diff --git a/docs/reference/mask_xy.html b/docs/reference/mask_xy.html
index 11bb577c..b0d38619 100644
--- a/docs/reference/mask_xy.html
+++ b/docs/reference/mask_xy.html
@@ -1,5 +1,5 @@
-Mask an MRSI dataset in the x-y direction — mask_xy • Spectroscopy Analysis Tools (spant) Mask an MRSI dataset in the x-y direction — mask_xy • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/mask_xy_corners.html b/docs/reference/mask_xy_corners.html
index 09b16cd2..2d13839d 100644
--- a/docs/reference/mask_xy_corners.html
+++ b/docs/reference/mask_xy_corners.html
@@ -1,5 +1,5 @@
-Mask the four corners of an MRSI dataset in the x-y plane. — mask_xy_corners • Spectroscopy Analysis Tools (spant) Mask the four corners of an MRSI dataset in the x-y plane. — mask_xy_corners • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/mask_xy_ellipse.html b/docs/reference/mask_xy_ellipse.html
index 1d8b02e4..e2e749ef 100644
--- a/docs/reference/mask_xy_ellipse.html
+++ b/docs/reference/mask_xy_ellipse.html
@@ -1,7 +1,5 @@
-Mask the voxels outside an elliptical region spanning the MRSI dataset in the
-x-y plane. — mask_xy_ellipse • Spectroscopy Analysis Tools (spant) Mask the voxels outside an elliptical region spanning the MRSI dataset in the x-y plane. — mask_xy_ellipse • Spectroscopy Analysis Tools (spant) Mask a 2D MRSI dataset in the x-y dimension. — mask_xy_mat • Spectroscopy Analysis Tools (spant) Mask a 2D MRSI dataset in the x-y dimension. — mask_xy_mat • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Value
diff --git a/docs/reference/mat2mrs_data.html b/docs/reference/mat2mrs_data.html
index 2e2895f3..ae55665f 100644
--- a/docs/reference/mat2mrs_data.html
+++ b/docs/reference/mat2mrs_data.html
@@ -1,7 +1,5 @@
-Convert a matrix (with spectral points in the column dimension and dynamics
-in the row dimensions) into a mrs_data object. — mat2mrs_data • Spectroscopy Analysis Tools (spant) Convert a matrix (with spectral points in the column dimension and dynamics in the row dimensions) into a mrs_data object. — mat2mrs_data • Spectroscopy Analysis Tools (spant) Matrix exponential function taken from complexplus package to reduce the
-number of spant dependencies. — matexp • Spectroscopy Analysis Tools (spant) Matrix exponential function taken from complexplus package to reduce the number of spant dependencies. — matexp • Spectroscopy Analysis Tools (spant) Apply the max operator to an MRS dataset. — max_mrs • Spectroscopy Analysis Tools (spant) Apply the max operator to an MRS dataset. — max_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/max_mrs_interp.html b/docs/reference/max_mrs_interp.html
index e4474764..52e63f3e 100644
--- a/docs/reference/max_mrs_interp.html
+++ b/docs/reference/max_mrs_interp.html
@@ -1,5 +1,5 @@
-Apply the max operator to an interpolated MRS dataset. — max_mrs_interp • Spectroscopy Analysis Tools (spant) Apply the max operator to an interpolated MRS dataset. — max_mrs_interp • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/mean.list.html b/docs/reference/mean.list.html
index b8eb3463..048306fd 100644
--- a/docs/reference/mean.list.html
+++ b/docs/reference/mean.list.html
@@ -1,5 +1,5 @@
-Calculate the mean spectrum from an mrs_data object. — mean.list • Spectroscopy Analysis Tools (spant) Calculate the mean spectrum from an mrs_data object. — mean.list • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/mean.mrs_data.html b/docs/reference/mean.mrs_data.html
index 5531a28d..79515014 100644
--- a/docs/reference/mean.mrs_data.html
+++ b/docs/reference/mean.mrs_data.html
@@ -1,5 +1,5 @@
-Calculate the mean spectrum from an mrs_data object. — mean.mrs_data • Spectroscopy Analysis Tools (spant) Calculate the mean spectrum from an mrs_data object. — mean.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/mean_dyn_blocks.html b/docs/reference/mean_dyn_blocks.html
index 10467098..4c042448 100644
--- a/docs/reference/mean_dyn_blocks.html
+++ b/docs/reference/mean_dyn_blocks.html
@@ -1,5 +1,5 @@
-Calculate the mean of adjacent dynamic scans. — mean_dyn_blocks • Spectroscopy Analysis Tools (spant) Calculate the mean of adjacent dynamic scans. — mean_dyn_blocks • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/mean_dyn_pairs.html b/docs/reference/mean_dyn_pairs.html
index 63e909ea..1a241126 100644
--- a/docs/reference/mean_dyn_pairs.html
+++ b/docs/reference/mean_dyn_pairs.html
@@ -1,5 +1,5 @@
-Calculate the pairwise means across a dynamic data set. — mean_dyn_pairs • Spectroscopy Analysis Tools (spant) Calculate the pairwise means across a dynamic data set. — mean_dyn_pairs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/mean_dyns.html b/docs/reference/mean_dyns.html
index 73fdbfa7..0daa27df 100644
--- a/docs/reference/mean_dyns.html
+++ b/docs/reference/mean_dyns.html
@@ -1,5 +1,5 @@
-Calculate the mean dynamic data. — mean_dyns • Spectroscopy Analysis Tools (spant) Calculate the mean dynamic data. — mean_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/mean_mrs_list.html b/docs/reference/mean_mrs_list.html
index 808b6c50..10d842c0 100644
--- a/docs/reference/mean_mrs_list.html
+++ b/docs/reference/mean_mrs_list.html
@@ -1,5 +1,5 @@
-Return the mean of a list of mrs_data objects. — mean_mrs_list • Spectroscopy Analysis Tools (spant) Return the mean of a list of mrs_data objects. — mean_mrs_list • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/mean_vec_blocks.html b/docs/reference/mean_vec_blocks.html
index 8fc92eaa..dd78b122 100644
--- a/docs/reference/mean_vec_blocks.html
+++ b/docs/reference/mean_vec_blocks.html
@@ -1,5 +1,5 @@
-Calculate the mean of adjacent blocks in a vector. — mean_vec_blocks • Spectroscopy Analysis Tools (spant) Calculate the mean of adjacent blocks in a vector. — mean_vec_blocks • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/median_dyns.html b/docs/reference/median_dyns.html
index 1039d4b5..9a085b10 100644
--- a/docs/reference/median_dyns.html
+++ b/docs/reference/median_dyns.html
@@ -1,5 +1,5 @@
-Calculate the median dynamic data. — median_dyns • Spectroscopy Analysis Tools (spant) Calculate the median dynamic data. — median_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/mod_td.html b/docs/reference/mod_td.html
index 76ad0a40..141ef09e 100644
--- a/docs/reference/mod_td.html
+++ b/docs/reference/mod_td.html
@@ -1,5 +1,5 @@
-Apply the Modulus operator to the time-domain MRS signal. — mod_td • Spectroscopy Analysis Tools (spant) Apply the Modulus operator to the time-domain MRS signal. — mod_td • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/mrs_data2basis.html b/docs/reference/mrs_data2basis.html
index 62f7d749..11797b91 100644
--- a/docs/reference/mrs_data2basis.html
+++ b/docs/reference/mrs_data2basis.html
@@ -1,7 +1,5 @@
-Convert an mrs_data object to basis object - where basis signals are spread
-across the dynamic dimension in the MRS data. — mrs_data2basis • Spectroscopy Analysis Tools (spant) Convert an mrs_data object to basis object - where basis signals are spread across the dynamic dimension in the MRS data. — mrs_data2basis • Spectroscopy Analysis Tools (spant) Create a BIDS file structure from a vector of MRS data paths or list of mrs_data objects. — mrs_data2bids • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Create a BIDS file structure from a vector of MRS data paths or list of mrs_data objects.
+ Source: R/fmrs.R
+ mrs_data2bids.Rd
+
+
+
+ Create a BIDS file structure from a vector of MRS data paths or list of
+mrs_data objects.
+
+
+
+ mrs_data2bids(
+ mrs_data,
+ output_dir,
+ suffix = NULL,
+ sub = NULL,
+ ses = NULL,
+ task = NULL,
+ acq = NULL,
+ nuc = NULL,
+ voi = NULL,
+ rec = NULL,
+ run = NULL,
+ echo = NULL,
+ inv = NULL,
+ skip_existing = TRUE
+)
+
+
+
+ Arguments
+ - mrs_data
+vector of MRS data paths or list of mrs_data objects.
- output_dir
+the base directory to create the BIDS structure.
- suffix
+optional vector of file suffixes. Default behaviour is to
+automatically determine these from the input data, however it is recommended
+that they are specified to allow more efficient skipping of existing data.
- sub
+optional vector of subject labels. If not specified, these will be
+automatically generated as a series of increasing zero-padded integer values
+corresponding to the mrs_data input indices.
- ses
+optional vector of session labels.
- task
+optional vector of task labels.
- acq
+optional vector of acquisition labels.
- nuc
+optional vector of nucleus labels.
- voi
+optional vector of volume of interest labels.
- rec
+optional vector of reconstruction labels.
- run
+optional vector of run indices.
- echo
+optional vector of echo time indices.
- inv
+optional vector of inversion indices.
- skip_existing
+skip any data files that have already been converted.
+Defaults to TRUE, set to FALSE to force an overwrite of any existing data
+files.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/mrs_data2mat.html b/docs/reference/mrs_data2mat.html
index cf5ff28c..9e47688a 100644
--- a/docs/reference/mrs_data2mat.html
+++ b/docs/reference/mrs_data2mat.html
@@ -1,7 +1,5 @@
-Convert mrs_data object to a matrix, with spectral points in the column
-dimension and dynamics in the row dimension. — mrs_data2mat • Spectroscopy Analysis Tools (spant) Convert mrs_data object to a matrix, with spectral points in the column dimension and dynamics in the row dimension. — mrs_data2mat • Spectroscopy Analysis Tools (spant) Convert mrs_data object to a matrix, with spectral points in the column dimension and dynamics in the row dimension. — mrs_data2spec_mat • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Convert mrs_data object to a matrix, with spectral points in the column dimension and dynamics in the row dimension.
+ Source: R/mrs_data_proc.R
+ mrs_data2spec_mat.Rd
+
+
+
+ Convert mrs_data object to a matrix, with spectral points in the column
+dimension and dynamics in the row dimension.
+
+
+
+ mrs_data2spec_mat(mrs_data, collapse = TRUE)
+
+
+
+ Arguments
+ - mrs_data
+MRS data object or list of MRS data objects.
- collapse
+collapse all other dimensions along the dynamic dimension, eg
+a 16x16 MRSI grid would be first collapsed across 256 dynamic scans.
+
+ Value
+
+
+MRS data matrix.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/mrs_data2vec.html b/docs/reference/mrs_data2vec.html
index fb172d68..a1fd654d 100644
--- a/docs/reference/mrs_data2vec.html
+++ b/docs/reference/mrs_data2vec.html
@@ -1,5 +1,5 @@
-Convert mrs_data object to a vector. — mrs_data2vec • Spectroscopy Analysis Tools (spant) Convert mrs_data object to a vector. — mrs_data2vec • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -126,7 +126,7 @@ Value
diff --git a/docs/reference/mvfftshift.html b/docs/reference/mvfftshift.html
index 92b0841b..976b3410 100644
--- a/docs/reference/mvfftshift.html
+++ b/docs/reference/mvfftshift.html
@@ -1,7 +1,5 @@
-Perform a fftshift on a matrix, with each column replaced by its shifted
-result. — mvfftshift • Spectroscopy Analysis Tools (spant) Perform a fftshift on a matrix, with each column replaced by its shifted result. — mvfftshift • Spectroscopy Analysis Tools (spant) Perform an ifftshift on a matrix, with each column replaced by its shifted
-result. — mvifftshift • Spectroscopy Analysis Tools (spant) Perform an ifftshift on a matrix, with each column replaced by its shifted result. — mvifftshift • Spectroscopy Analysis Tools (spant) Print fit coordinates from a single index. — n2coord • Spectroscopy Analysis Tools (spant) Print fit coordinates from a single index. — n2coord • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/nifti_flip_lr.html b/docs/reference/nifti_flip_lr.html
index 730abe3c..19860b3c 100644
--- a/docs/reference/nifti_flip_lr.html
+++ b/docs/reference/nifti_flip_lr.html
@@ -1,9 +1,5 @@
-Flip the x data dimension order of a nifti image. This corresponds to
-flipping MRI data in the left-right direction, assuming the data in save in
-neurological format (can check with fslorient program). — nifti_flip_lr • Spectroscopy Analysis Tools (spant) Flip the x data dimension order of a nifti image. This corresponds to flipping MRI data in the left-right direction, assuming the data in save in neurological format (can check with fslorient program). — nifti_flip_lr • Spectroscopy Analysis Tools (spant) Export a one-page pdf of a single fit result — one_page_pdf • Spectroscopy Analysis Tools (spant) Export a one-page pdf of a single fit result — one_page_pdf • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -108,7 +108,7 @@ Arguments
diff --git a/docs/reference/ortho3.html b/docs/reference/ortho3.html
index 13ade97d..5d7dd2fd 100644
--- a/docs/reference/ortho3.html
+++ b/docs/reference/ortho3.html
@@ -1,5 +1,5 @@
-Display an orthographic projection plot of a nifti object. — ortho3 • Spectroscopy Analysis Tools (spant) Display an orthographic projection plot of a nifti object. — ortho3 • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -172,7 +172,7 @@ Arguments
diff --git a/docs/reference/ortho3_inter.html b/docs/reference/ortho3_inter.html
index 090cc5e5..15948899 100644
--- a/docs/reference/ortho3_inter.html
+++ b/docs/reference/ortho3_inter.html
@@ -1,5 +1,5 @@
-Display an interactive orthographic projection plot of a nifti object. — ortho3_inter • Spectroscopy Analysis Tools (spant) Display an interactive orthographic projection plot of a nifti object. — ortho3_inter • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -132,7 +132,7 @@ Arguments
diff --git a/docs/reference/peak_info.html b/docs/reference/peak_info.html
index 09058bd8..41c8ffaf 100644
--- a/docs/reference/peak_info.html
+++ b/docs/reference/peak_info.html
@@ -1,7 +1,5 @@
-Search for the highest peak in a spectral region and return the frequency,
-height and FWHM. — peak_info • Spectroscopy Analysis Tools (spant) Search for the highest peak in a spectral region and return the frequency, height and FWHM. — peak_info • Spectroscopy Analysis Tools (spant) Papoulis-Gerchberg (PG) algorithm method for k-space extrapolation. — pg_extrap_xy • Spectroscopy Analysis Tools (spant) Papoulis-Gerchberg (PG) algorithm method for k-space extrapolation. — pg_extrap_xy • Spectroscopy Analysis Tools (spant) Apply phasing parameters to MRS data. — phase • Spectroscopy Analysis Tools (spant) Apply phasing parameters to MRS data. — phase • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/phase_ref_1h_brain.html b/docs/reference/phase_ref_1h_brain.html
new file mode 100644
index 00000000..8707a74a
--- /dev/null
+++ b/docs/reference/phase_ref_1h_brain.html
@@ -0,0 +1,131 @@
+
+Corrected zero order phase and chemical shift offset in 1H MRS data from the brain. — phase_ref_1h_brain • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Corrected zero order phase and chemical shift offset in 1H MRS data from the brain.
+ Source: R/rats.R
+ phase_ref_1h_brain.Rd
+
+
+
+ Corrected zero order phase and chemical shift offset in 1H MRS data from the
+brain.
+
+
+
+ phase_ref_1h_brain(mrs_data, mean_ref = FALSE, ret_corr_only = TRUE)
+
+
+
+ Arguments
+ - mrs_data
+MRS data to be corrected.
- mean_ref
+apply the phase and offset of the mean spectrum to all
+others. Default is FALSE.
- ret_corr_only
+return the corrected data only.
+
+ Value
+
+
+corrected MRS data.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/plot.fit_result.html b/docs/reference/plot.fit_result.html
index e54d3bc1..836a53ee 100644
--- a/docs/reference/plot.fit_result.html
+++ b/docs/reference/plot.fit_result.html
@@ -1,5 +1,5 @@
-Plot the fitting results of an object of class fit_result. — plot.fit_result • Spectroscopy Analysis Tools (spant) Plot the fitting results of an object of class fit_result. — plot.fit_result • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -207,7 +207,7 @@ Arguments
diff --git a/docs/reference/plot.mrs_data.html b/docs/reference/plot.mrs_data.html
index fabcc35b..bb2ec651 100644
--- a/docs/reference/plot.mrs_data.html
+++ b/docs/reference/plot.mrs_data.html
@@ -1,5 +1,5 @@
-Plotting method for objects of class mrs_data. — plot.mrs_data • Spectroscopy Analysis Tools (spant) Plotting method for objects of class mrs_data. — plot.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -287,7 +287,7 @@ Arguments
diff --git a/docs/reference/plot_bc.html b/docs/reference/plot_bc.html
index 4f8309b4..b48142cc 100644
--- a/docs/reference/plot_bc.html
+++ b/docs/reference/plot_bc.html
@@ -1,5 +1,5 @@
-Convenience function to plot a baseline estimate with the original data. — plot_bc • Spectroscopy Analysis Tools (spant) Convenience function to plot a baseline estimate with the original data. — plot_bc • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -108,7 +108,7 @@ Arguments
diff --git a/docs/reference/plot_reg.html b/docs/reference/plot_reg.html
index ae1acbe7..2addb2f6 100644
--- a/docs/reference/plot_reg.html
+++ b/docs/reference/plot_reg.html
@@ -1,5 +1,5 @@
-Plot regressors as an image. — plot_reg • Spectroscopy Analysis Tools (spant) Plot regressors as an image. — plot_reg • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/plot_slice_fit.html b/docs/reference/plot_slice_fit.html
index fbc7b560..57f1af8a 100644
--- a/docs/reference/plot_slice_fit.html
+++ b/docs/reference/plot_slice_fit.html
@@ -1,5 +1,5 @@
-Plot a 2D slice from an MRSI fit result object. — plot_slice_fit • Spectroscopy Analysis Tools (spant) Plot a 2D slice from an MRSI fit result object. — plot_slice_fit • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -129,7 +129,7 @@ Arguments
diff --git a/docs/reference/plot_slice_fit_inter.html b/docs/reference/plot_slice_fit_inter.html
index 4eed104a..da105a7d 100644
--- a/docs/reference/plot_slice_fit_inter.html
+++ b/docs/reference/plot_slice_fit_inter.html
@@ -1,5 +1,5 @@
-Plot a 2D slice from an MRSI fit result object. — plot_slice_fit_inter • Spectroscopy Analysis Tools (spant) Plot a 2D slice from an MRSI fit result object. — plot_slice_fit_inter • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -134,7 +134,7 @@ Arguments
diff --git a/docs/reference/plot_slice_map.html b/docs/reference/plot_slice_map.html
index 553e9ac8..ffb2a134 100644
--- a/docs/reference/plot_slice_map.html
+++ b/docs/reference/plot_slice_map.html
@@ -1,5 +1,5 @@
-Plot a slice from a 7 dimensional array. — plot_slice_map • Spectroscopy Analysis Tools (spant) Plot a slice from a 7 dimensional array. — plot_slice_map • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -153,7 +153,7 @@ Arguments
diff --git a/docs/reference/plot_slice_map_inter.html b/docs/reference/plot_slice_map_inter.html
index 40d33b42..90968f66 100644
--- a/docs/reference/plot_slice_map_inter.html
+++ b/docs/reference/plot_slice_map_inter.html
@@ -1,7 +1,5 @@
-Plot an interactive slice map from a data array where voxels can be selected
-to display a corresponding spectrum. — plot_slice_map_inter • Spectroscopy Analysis Tools (spant) Plot an interactive slice map from a data array where voxels can be selected to display a corresponding spectrum. — plot_slice_map_inter • Spectroscopy Analysis Tools (spant) Plot the spectral standard deviation. — plot_spec_sd • Spectroscopy Analysis Tools (spant) Plot the spectral standard deviation. — plot_spec_sd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Arguments
diff --git a/docs/reference/plot_voi_overlay.html b/docs/reference/plot_voi_overlay.html
index 9a782e88..bbbbf35e 100644
--- a/docs/reference/plot_voi_overlay.html
+++ b/docs/reference/plot_voi_overlay.html
@@ -1,5 +1,5 @@
-Plot a volume as an image overlay. — plot_voi_overlay • Spectroscopy Analysis Tools (spant) Plot a volume as an image overlay. — plot_voi_overlay • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -116,7 +116,7 @@ Arguments
diff --git a/docs/reference/plot_voi_overlay_seg.html b/docs/reference/plot_voi_overlay_seg.html
index 3d4e74ff..0e800ff2 100644
--- a/docs/reference/plot_voi_overlay_seg.html
+++ b/docs/reference/plot_voi_overlay_seg.html
@@ -1,5 +1,5 @@
-Plot a volume as an overlay on a segmented brain volume. — plot_voi_overlay_seg • Spectroscopy Analysis Tools (spant) Plot a volume as an overlay on a segmented brain volume. — plot_voi_overlay_seg • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Arguments
diff --git a/docs/reference/ppm.html b/docs/reference/ppm.html
index c352327a..ee4696e2 100644
--- a/docs/reference/ppm.html
+++ b/docs/reference/ppm.html
@@ -1,5 +1,5 @@
-Return the ppm scale of an MRS dataset or fit result. — ppm • Spectroscopy Analysis Tools (spant) Return the ppm scale of an MRS dataset or fit result. — ppm • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -132,7 +132,7 @@ Value
diff --git a/docs/reference/precomp.html b/docs/reference/precomp.html
index 822d7336..df3d2c6c 100644
--- a/docs/reference/precomp.html
+++ b/docs/reference/precomp.html
@@ -1,7 +1,5 @@
-Save function results to file and load on subsequent calls to avoid repeat
-computation. — precomp • Spectroscopy Analysis Tools (spant) Save function results to file and load on subsequent calls to avoid repeat computation. — precomp • Spectroscopy Analysis Tools (spant) Preprocess and perform quality assessment of a single SVS data set. — preproc_svs • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Preprocess and perform quality assessment of a single SVS data set.
+ Source: R/fmrs.R
+ preproc_svs.Rd
+
+
+
+ Preprocess and perform quality assessment of a single SVS data set.
+
+
+
+ preproc_svs(path, label = NULL, output_dir = NULL, ref_inds = NULL)
+
+
+
+ Arguments
+ - path
+path to the fMRS data file or IMA directory.
- label
+a label to describe the data set.
- output_dir
+output directory.
- ref_inds
+a vector of 1-based indices for any water reference dynamic
+scans.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/preproc_svs_dataset.html b/docs/reference/preproc_svs_dataset.html
new file mode 100644
index 00000000..07c3a29b
--- /dev/null
+++ b/docs/reference/preproc_svs_dataset.html
@@ -0,0 +1,148 @@
+
+Preprocess and perform quality assessment of one or more SVS data sets. — preproc_svs_dataset • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Preprocess and perform quality assessment of one or more SVS data sets.
+ Source: R/fmrs.R
+ preproc_svs_dataset.Rd
+
+
+
+ Preprocess and perform quality assessment of one or more SVS data sets.
+
+
+
+ preproc_svs_dataset(
+ paths,
+ labels = NULL,
+ output_dir = "spant_analysis",
+ exclude_labels = NULL,
+ overwrite = FALSE,
+ ref_inds = NULL,
+ return_results = FALSE
+)
+
+
+
+ Arguments
+ - paths
+paths to the fMRS data file or IMA directory.
- labels
+labels to describe each data set.
- output_dir
+output directory.
- exclude_labels
+vector of labels of scans to exclude, eg poor quality
+data.
- overwrite
+overwrite saved results, defaults to FALSE.
- ref_inds
+a vector of 1-based indices for any water reference dynamic
+scans.
- return_results
+function will return key outputs, defaults to FALSE.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/print.fit_result.html b/docs/reference/print.fit_result.html
index 297f28dc..5f434e57 100644
--- a/docs/reference/print.fit_result.html
+++ b/docs/reference/print.fit_result.html
@@ -1,5 +1,5 @@
-Print a summary of an object of class fit_result. — print.fit_result • Spectroscopy Analysis Tools (spant) Print a summary of an object of class fit_result. — print.fit_result • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -105,7 +105,7 @@ Arguments
diff --git a/docs/reference/print.mrs_data.html b/docs/reference/print.mrs_data.html
index 51199017..e1561eb2 100644
--- a/docs/reference/print.mrs_data.html
+++ b/docs/reference/print.mrs_data.html
@@ -1,5 +1,5 @@
-Print a summary of mrs_data parameters. — print.mrs_data • Spectroscopy Analysis Tools (spant) Print a summary of mrs_data parameters. — print.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -109,7 +109,7 @@ Arguments
diff --git a/docs/reference/qn_states.html b/docs/reference/qn_states.html
index 0f42f2f9..d7aa6715 100644
--- a/docs/reference/qn_states.html
+++ b/docs/reference/qn_states.html
@@ -1,5 +1,5 @@
-Get the quantum coherence matrix for a spin system. — qn_states • Spectroscopy Analysis Tools (spant) Get the quantum coherence matrix for a spin system. — qn_states • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/rats.html b/docs/reference/rats.html
index 5a39a396..93585e08 100644
--- a/docs/reference/rats.html
+++ b/docs/reference/rats.html
@@ -1,5 +1,5 @@
-Robust Alignment to a Target Spectrum (RATS). — rats • Spectroscopy Analysis Tools (spant) Robust Alignment to a Target Spectrum (RATS). — rats • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -207,7 +207,7 @@ Value
diff --git a/docs/reference/re_weighting.html b/docs/reference/re_weighting.html
index d21caf21..8b0b070a 100644
--- a/docs/reference/re_weighting.html
+++ b/docs/reference/re_weighting.html
@@ -1,5 +1,5 @@
-Apply a weighting to the FID to enhance spectral resolution. — re_weighting • Spectroscopy Analysis Tools (spant) Apply a weighting to the FID to enhance spectral resolution. — re_weighting • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/read_basis.html b/docs/reference/read_basis.html
index da9b94af..eb6f8557 100644
--- a/docs/reference/read_basis.html
+++ b/docs/reference/read_basis.html
@@ -1,5 +1,5 @@
-Read a basis file in LCModel .basis format. — read_basis • Spectroscopy Analysis Tools (spant) Read a basis file in LCModel .basis format. — read_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/read_ima_coil_dir.html b/docs/reference/read_ima_coil_dir.html
index 28c02de0..4f073cd8 100644
--- a/docs/reference/read_ima_coil_dir.html
+++ b/docs/reference/read_ima_coil_dir.html
@@ -1,9 +1,5 @@
-Read a directory containing Siemens MRS IMA files and combine along the coil
-dimension. Note that the coil ID is inferred from the sorted file name and
-should be checked when consistency is required between two directories. — read_ima_coil_dir • Spectroscopy Analysis Tools (spant) Read a directory containing Siemens MRS IMA files and combine along the coil dimension. Note that the coil ID is inferred from the sorted file name and should be checked when consistency is required between two directories. — read_ima_coil_dir • Spectroscopy Analysis Tools (spant) Read a directory containing Siemens MRS IMA files and combine along the
-dynamic dimension. Note that the coil ID is inferred from the sorted file
-name and should be checked when consistency is required. — read_ima_dyn_dir • Spectroscopy Analysis Tools (spant) Read a directory containing Siemens MRS IMA files and combine along the dynamic dimension. Note that the coil ID is inferred from the sorted file name and should be checked when consistency is required. — read_ima_dyn_dir • Spectroscopy Analysis Tools (spant) Read an LCModel formatted coord file containing fit information. — read_lcm_coord • Spectroscopy Analysis Tools (spant) Read an LCModel formatted coord file containing fit information. — read_lcm_coord • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -107,7 +107,7 @@ Value
diff --git a/docs/reference/read_mrs.html b/docs/reference/read_mrs.html
index 3ac2a36b..2cf36b20 100644
--- a/docs/reference/read_mrs.html
+++ b/docs/reference/read_mrs.html
@@ -1,5 +1,5 @@
-Read MRS data from a file. — read_mrs • Spectroscopy Analysis Tools (spant) Read MRS data from a file. — read_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -88,7 +88,8 @@ Read MRS data from a file.
full_fid = FALSE,
omit_svs_ref_scans = TRUE,
verbose = FALSE,
- extra = NULL
+ extra = NULL,
+ fid_filt_dist = NULL
)
@@ -140,6 +141,13 @@ Arguments
an optional data frame to provide additional variables for use
in subsequent analysis steps, eg id or grouping variables.
fid_filt_dist
+indicate if the data has a distorted FID due to a
+brick-wall filter being used to downsample the data. Default is to auto
+detect this from the data, but TRUE or FALSE options can be given to override
+detection.
Value
@@ -183,7 +191,7 @@ Examples
diff --git a/docs/reference/read_mrs_tqn.html b/docs/reference/read_mrs_tqn.html
index 5766362f..84bdaf3a 100644
--- a/docs/reference/read_mrs_tqn.html
+++ b/docs/reference/read_mrs_tqn.html
@@ -1,5 +1,5 @@
-Read MRS data using the TARQUIN software package. — read_mrs_tqn • Spectroscopy Analysis Tools (spant) Read MRS data using the TARQUIN software package. — read_mrs_tqn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -131,7 +131,7 @@ Examples
diff --git a/docs/reference/read_pulse_ascii.html b/docs/reference/read_pulse_ascii.html
index c9e0d43c..ab11c9cc 100644
--- a/docs/reference/read_pulse_ascii.html
+++ b/docs/reference/read_pulse_ascii.html
@@ -1,5 +1,5 @@
-Read an ASCII formatted pulse file. — read_pulse_ascii • Spectroscopy Analysis Tools (spant) Read an ASCII formatted pulse file. — read_pulse_ascii • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/read_pulse_bruker.html b/docs/reference/read_pulse_bruker.html
index c92bf76a..dbe9073b 100644
--- a/docs/reference/read_pulse_bruker.html
+++ b/docs/reference/read_pulse_bruker.html
@@ -1,5 +1,5 @@
-Read a Bruker formatted pulse file — read_pulse_bruker • Spectroscopy Analysis Tools (spant) Read a Bruker formatted pulse file — read_pulse_bruker • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/read_pulse_pta.html b/docs/reference/read_pulse_pta.html
index 72e1b6d4..a0fac3c3 100644
--- a/docs/reference/read_pulse_pta.html
+++ b/docs/reference/read_pulse_pta.html
@@ -1,5 +1,5 @@
-Read a .pta formatted pulse file compatible with Siemens PulseTool. — read_pulse_pta • Spectroscopy Analysis Tools (spant) Read a .pta formatted pulse file compatible with Siemens PulseTool. — read_pulse_pta • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/read_siemens_txt_hdr.html b/docs/reference/read_siemens_txt_hdr.html
index 23fb8c70..3a17d87c 100644
--- a/docs/reference/read_siemens_txt_hdr.html
+++ b/docs/reference/read_siemens_txt_hdr.html
@@ -1,5 +1,5 @@
-Read the text format header found in Siemens IMA and TWIX data files. — read_siemens_txt_hdr • Spectroscopy Analysis Tools (spant) Read the text format header found in Siemens IMA and TWIX data files. — read_siemens_txt_hdr • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -78,7 +78,7 @@ Read the text format header found in Siemens IMA and TWIX data files.
- read_siemens_txt_hdr(input, version = "vd", verbose, offset = 0)
+ read_siemens_txt_hdr(input, version = "vd", verbose = FALSE, offset = 0)
@@ -118,7 +118,7 @@ Value
diff --git a/docs/reference/read_tqn_fit.html b/docs/reference/read_tqn_fit.html
index 4da6c25e..a1630420 100644
--- a/docs/reference/read_tqn_fit.html
+++ b/docs/reference/read_tqn_fit.html
@@ -1,5 +1,5 @@
-Reader for csv fit results generated by TARQUIN. — read_tqn_fit • Spectroscopy Analysis Tools (spant) Reader for csv fit results generated by TARQUIN. — read_tqn_fit • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -113,7 +113,7 @@ Examples
diff --git a/docs/reference/read_tqn_result.html b/docs/reference/read_tqn_result.html
index 36659714..68a3e98c 100644
--- a/docs/reference/read_tqn_result.html
+++ b/docs/reference/read_tqn_result.html
@@ -1,5 +1,5 @@
-Reader for csv results generated by TARQUIN. — read_tqn_result • Spectroscopy Analysis Tools (spant) Reader for csv results generated by TARQUIN. — read_tqn_result • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -117,7 +117,7 @@ Examples
diff --git a/docs/reference/recon_imag.html b/docs/reference/recon_imag.html
index d2a72225..5bc3b1eb 100644
--- a/docs/reference/recon_imag.html
+++ b/docs/reference/recon_imag.html
@@ -1,7 +1,5 @@
-Reconstruct complex time-domain data from the real part of frequency-domain
-data. — recon_imag • Spectroscopy Analysis Tools (spant) Reconstruct complex time-domain data from the real part of frequency-domain data. — recon_imag • Spectroscopy Analysis Tools (spant) Reconstruct complex time-domain data from the real part of frequency-domain
-data. — recon_imag_vec • Spectroscopy Analysis Tools (spant) Reconstruct complex time-domain data from the real part of frequency-domain data. — recon_imag_vec • Spectroscopy Analysis Tools (spant) Reconstruct 2D MRSI data from a twix file loaded with read_mrs. — recon_twix_2d_mrsi • Spectroscopy Analysis Tools (spant) Reconstruct 2D MRSI data from a twix file loaded with read_mrs. — recon_twix_2d_mrsi • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/rectangular_mask.html b/docs/reference/rectangular_mask.html
index a2117283..6e469bc9 100644
--- a/docs/reference/rectangular_mask.html
+++ b/docs/reference/rectangular_mask.html
@@ -1,5 +1,5 @@
-Create a rectangular mask stored as a matrix of logical values. — rectangular_mask • Spectroscopy Analysis Tools (spant) Create a rectangular mask stored as a matrix of logical values. — rectangular_mask • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -130,7 +130,7 @@ Value
diff --git a/docs/reference/reexports.html b/docs/reference/reexports.html
index 694a75d1..a59e8379 100644
--- a/docs/reference/reexports.html
+++ b/docs/reference/reexports.html
@@ -1,5 +1,5 @@
-Objects exported from other packages — reexports • Spectroscopy Analysis Tools (spant) Objects exported from other packages — reexports • Spectroscopy Analysis Tools (spant)
Spectroscopy Analysis Tools (spant)
- 2.21.0
+ 2.22.0
@@ -103,7 +103,7 @@ Objects exported from other packages
diff --git a/docs/reference/rep_array_dim.html b/docs/reference/rep_array_dim.html
index b9c49b4a..48c0a5ed 100644
--- a/docs/reference/rep_array_dim.html
+++ b/docs/reference/rep_array_dim.html
@@ -1,5 +1,5 @@
-Repeat an array over a given dimension. — rep_array_dim • Spectroscopy Analysis Tools (spant) Repeat an array over a given dimension. — rep_array_dim • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/rep_dyn.html b/docs/reference/rep_dyn.html
index 6bbfb0ef..89a4bb9b 100644
--- a/docs/reference/rep_dyn.html
+++ b/docs/reference/rep_dyn.html
@@ -1,5 +1,5 @@
-Replicate a scan in the dynamic dimension. — rep_dyn • Spectroscopy Analysis Tools (spant) Replicate a scan in the dynamic dimension. — rep_dyn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/rep_mrs.html b/docs/reference/rep_mrs.html
index 67730b5c..becb8f00 100644
--- a/docs/reference/rep_mrs.html
+++ b/docs/reference/rep_mrs.html
@@ -1,5 +1,5 @@
-Replicate a scan over a given dimension. — rep_mrs • Spectroscopy Analysis Tools (spant) Replicate a scan over a given dimension. — rep_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -138,7 +138,7 @@ Value
diff --git a/docs/reference/resample_basis.html b/docs/reference/resample_basis.html
index b0f2ab17..c7a6222a 100644
--- a/docs/reference/resample_basis.html
+++ b/docs/reference/resample_basis.html
@@ -1,5 +1,5 @@
-Resample a basis-set to match a mrs_data acquisition. — resample_basis • Spectroscopy Analysis Tools (spant) Resample a basis-set to match a mrs_data acquisition. — resample_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -116,7 +116,7 @@ Value
diff --git a/docs/reference/resample_img.html b/docs/reference/resample_img.html
index f1e7beaf..b0cc8f71 100644
--- a/docs/reference/resample_img.html
+++ b/docs/reference/resample_img.html
@@ -1,5 +1,5 @@
-Resample an image to match a target image space. — resample_img • Spectroscopy Analysis Tools (spant) Resample an image to match a target image space. — resample_img • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/resample_voi.html b/docs/reference/resample_voi.html
index 8fbfa836..a29ab096 100644
--- a/docs/reference/resample_voi.html
+++ b/docs/reference/resample_voi.html
@@ -1,7 +1,5 @@
-Resample a VOI to match a target image space using nearest-neighbour
-interpolation. — resample_voi • Spectroscopy Analysis Tools (spant) Resample a VOI to match a target image space using nearest-neighbour interpolation. — resample_voi • Spectroscopy Analysis Tools (spant) Reslice a nifti object to match the orientation of mrs data. — reslice_to_mrs • Spectroscopy Analysis Tools (spant) Reslice a nifti object to match the orientation of mrs data. — reslice_to_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/reson_table2mrs_data.html b/docs/reference/reson_table2mrs_data.html
index d75579ee..c5a2167a 100644
--- a/docs/reference/reson_table2mrs_data.html
+++ b/docs/reference/reson_table2mrs_data.html
@@ -1,5 +1,5 @@
-Generate mrs_data from a table of single Lorentzian resonances. — reson_table2mrs_data • Spectroscopy Analysis Tools (spant) Generate mrs_data from a table of single Lorentzian resonances. — reson_table2mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -119,7 +119,7 @@ Value
diff --git a/docs/reference/rm_dyns.html b/docs/reference/rm_dyns.html
index 5d5ef692..573e1f51 100644
--- a/docs/reference/rm_dyns.html
+++ b/docs/reference/rm_dyns.html
@@ -1,5 +1,5 @@
-Remove a subset of dynamic scans. — rm_dyns • Spectroscopy Analysis Tools (spant) Remove a subset of dynamic scans. — rm_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/scale_amp_molal.html b/docs/reference/scale_amp_molal.html
index aaeee1f2..7acb8cb0 100644
--- a/docs/reference/scale_amp_molal.html
+++ b/docs/reference/scale_amp_molal.html
@@ -1,7 +1,5 @@
-Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water). — scale_amp_molal • Spectroscopy Analysis Tools (spant) Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / kg of tissue water). — scale_amp_molal • Spectroscopy Analysis Tools (spant)
Spectroscopy Analysis Tools (spant)
- 2.21.0
+ 2.22.0
@@ -76,8 +74,7 @@
- Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water).
+ Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / kg of tissue water).
Source: R/amp_scaling.R
scale_amp_molal.Rd
@@ -163,7 +160,7 @@ Value
diff --git a/docs/reference/scale_amp_molal_pvc.html b/docs/reference/scale_amp_molal_pvc.html
index 962d6afc..4d194abd 100644
--- a/docs/reference/scale_amp_molal_pvc.html
+++ b/docs/reference/scale_amp_molal_pvc.html
@@ -1,7 +1,5 @@
-Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water). — scale_amp_molal_pvc • Spectroscopy Analysis Tools (spant)
@@ -75,8 +73,7 @@
- Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water).
+ Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / kg of tissue water).
Source: R/amp_scaling.R
scale_amp_molal_pvc.Rd
@@ -141,7 +138,7 @@ Value
diff --git a/docs/reference/scale_amp_molar.html b/docs/reference/scale_amp_molar.html
index 02358d91..dc87a338 100644
--- a/docs/reference/scale_amp_molar.html
+++ b/docs/reference/scale_amp_molar.html
@@ -1,7 +1,5 @@
-Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / Litre of tissue). — scale_amp_molar • Spectroscopy Analysis Tools (spant) Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / Litre of tissue). — scale_amp_molar • Spectroscopy Analysis Tools (spant) Convert default LCM/TARQUIN concentration scaling to molal units with partial
-volume correction. — scale_amp_molar2molal_pvc • Spectroscopy Analysis Tools (spant) Convert default LCM/TARQUIN concentration scaling to molal units with partial volume correction. — scale_amp_molar2molal_pvc • Spectroscopy Analysis Tools (spant) Scale fitted amplitudes to a ratio of signal amplitude. — scale_amp_ratio • Spectroscopy Analysis Tools (spant) Scale fitted amplitudes to a ratio of signal amplitude. — scale_amp_ratio • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -116,7 +116,7 @@ Value
diff --git a/docs/reference/scale_amp_ratio_value.html b/docs/reference/scale_amp_ratio_value.html
index 2036837a..6af8ac51 100644
--- a/docs/reference/scale_amp_ratio_value.html
+++ b/docs/reference/scale_amp_ratio_value.html
@@ -1,5 +1,5 @@
-Scale fitted amplitudes to a ratio of signal amplitude. — scale_amp_ratio_value • Spectroscopy Analysis Tools (spant) Scale fitted amplitudes to a ratio of signal amplitude. — scale_amp_ratio_value • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/scale_amp_water_ratio.html b/docs/reference/scale_amp_water_ratio.html
index 5b25e884..35a76b00 100644
--- a/docs/reference/scale_amp_water_ratio.html
+++ b/docs/reference/scale_amp_water_ratio.html
@@ -1,5 +1,5 @@
-Scale metabolite amplitudes as a ratio to the unsuppressed water amplitude. — scale_amp_water_ratio • Spectroscopy Analysis Tools (spant) Scale metabolite amplitudes as a ratio to the unsuppressed water amplitude. — scale_amp_water_ratio • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/scale_basis_amp.html b/docs/reference/scale_basis_amp.html
index 9401c3f1..5a58b5e5 100644
--- a/docs/reference/scale_basis_amp.html
+++ b/docs/reference/scale_basis_amp.html
@@ -1,5 +1,5 @@
-Scale a basis object by a scalar. — scale_basis_amp • Spectroscopy Analysis Tools (spant) Scale a basis object by a scalar. — scale_basis_amp • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/scale_basis_from_singlet.html b/docs/reference/scale_basis_from_singlet.html
index 0d542bc8..c9a19e77 100644
--- a/docs/reference/scale_basis_from_singlet.html
+++ b/docs/reference/scale_basis_from_singlet.html
@@ -1,5 +1,5 @@
-Scale a basis-set to be consistent with spant assumptions for water scaling. — scale_basis_from_singlet • Spectroscopy Analysis Tools (spant) Scale a basis-set to be consistent with spant assumptions for water scaling. — scale_basis_from_singlet • Spectroscopy Analysis Tools (spant)
Spectroscopy Analysis Tools (spant)
- 2.21.0
+ 2.22.0
@@ -127,7 +127,7 @@ Value
diff --git a/docs/reference/scale_mrs_amp.html b/docs/reference/scale_mrs_amp.html
index b5501a0d..990f058a 100644
--- a/docs/reference/scale_mrs_amp.html
+++ b/docs/reference/scale_mrs_amp.html
@@ -1,5 +1,5 @@
-Scale an mrs_data object by a scalar or vector or amplitudes. — scale_mrs_amp • Spectroscopy Analysis Tools (spant) Scale an mrs_data object by a scalar or vector or amplitudes. — scale_mrs_amp • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/scale_spec.html b/docs/reference/scale_spec.html
index 4f6ea835..6b3ddba4 100644
--- a/docs/reference/scale_spec.html
+++ b/docs/reference/scale_spec.html
@@ -1,5 +1,5 @@
-Scale mrs_data to a spectral region. — scale_spec • Spectroscopy Analysis Tools (spant) Scale mrs_data to a spectral region. — scale_spec • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -141,7 +141,7 @@ Value
diff --git a/docs/reference/sd.html b/docs/reference/sd.html
index ea1eec9f..3ae4dfd4 100644
--- a/docs/reference/sd.html
+++ b/docs/reference/sd.html
@@ -1,5 +1,5 @@
-Calculate the standard deviation spectrum from an mrs_data object. — sd • Spectroscopy Analysis Tools (spant) Calculate the standard deviation spectrum from an mrs_data object. — sd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/sd.mrs_data.html b/docs/reference/sd.mrs_data.html
index 3f92a49f..13bdda85 100644
--- a/docs/reference/sd.mrs_data.html
+++ b/docs/reference/sd.mrs_data.html
@@ -1,5 +1,5 @@
-Calculate the standard deviation spectrum from an mrs_data object. — sd.mrs_data • Spectroscopy Analysis Tools (spant) Calculate the standard deviation spectrum from an mrs_data object. — sd.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/seconds.html b/docs/reference/seconds.html
index b34d6627..467ee17f 100644
--- a/docs/reference/seconds.html
+++ b/docs/reference/seconds.html
@@ -1,5 +1,5 @@
-Return a time scale vector to match the FID of an MRS data object. — seconds • Spectroscopy Analysis Tools (spant) Return a time scale vector to match the FID of an MRS data object. — seconds • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/seq_cpmg_ideal.html b/docs/reference/seq_cpmg_ideal.html
index 547e96ab..45727c86 100644
--- a/docs/reference/seq_cpmg_ideal.html
+++ b/docs/reference/seq_cpmg_ideal.html
@@ -1,5 +1,5 @@
-CPMG style sequence with ideal pulses. — seq_cpmg_ideal • Spectroscopy Analysis Tools (spant) CPMG style sequence with ideal pulses. — seq_cpmg_ideal • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/seq_mega_press_ideal.html b/docs/reference/seq_mega_press_ideal.html
index 0769b8b4..a9cd7fa0 100644
--- a/docs/reference/seq_mega_press_ideal.html
+++ b/docs/reference/seq_mega_press_ideal.html
@@ -1,7 +1,5 @@
-MEGA-PRESS sequence with ideal localisation pulses and Gaussian shaped
-editing pulse. — seq_mega_press_ideal • Spectroscopy Analysis Tools (spant) MEGA-PRESS sequence with ideal localisation pulses and Gaussian shaped editing pulse. — seq_mega_press_ideal • Spectroscopy Analysis Tools (spant) PRESS sequence with shaped refocusing pulses. — seq_press_2d_shaped • Spectroscopy Analysis Tools (spant) PRESS sequence with shaped refocusing pulses. — seq_press_2d_shaped • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -165,7 +165,7 @@ Value
diff --git a/docs/reference/seq_press_ideal.html b/docs/reference/seq_press_ideal.html
index 8c976856..72c3af3d 100644
--- a/docs/reference/seq_press_ideal.html
+++ b/docs/reference/seq_press_ideal.html
@@ -1,5 +1,5 @@
-PRESS sequence with ideal pulses. — seq_press_ideal • Spectroscopy Analysis Tools (spant) PRESS sequence with ideal pulses. — seq_press_ideal • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/seq_pulse_acquire.html b/docs/reference/seq_pulse_acquire.html
index 4a88fc64..ad80571e 100644
--- a/docs/reference/seq_pulse_acquire.html
+++ b/docs/reference/seq_pulse_acquire.html
@@ -1,5 +1,5 @@
-Simple pulse and acquire sequence with ideal pulses. — seq_pulse_acquire • Spectroscopy Analysis Tools (spant) Simple pulse and acquire sequence with ideal pulses. — seq_pulse_acquire • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/seq_slaser_ideal.html b/docs/reference/seq_slaser_ideal.html
index 74688f4d..eb83e8e3 100644
--- a/docs/reference/seq_slaser_ideal.html
+++ b/docs/reference/seq_slaser_ideal.html
@@ -1,5 +1,5 @@
-sLASER sequence with ideal pulses. — seq_slaser_ideal • Spectroscopy Analysis Tools (spant) sLASER sequence with ideal pulses. — seq_slaser_ideal • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -126,7 +126,7 @@ Value
diff --git a/docs/reference/seq_spin_echo_ideal.html b/docs/reference/seq_spin_echo_ideal.html
index e23271de..4248716f 100644
--- a/docs/reference/seq_spin_echo_ideal.html
+++ b/docs/reference/seq_spin_echo_ideal.html
@@ -1,5 +1,5 @@
-Spin echo sequence with ideal pulses. — seq_spin_echo_ideal • Spectroscopy Analysis Tools (spant) Spin echo sequence with ideal pulses. — seq_spin_echo_ideal • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/seq_steam_ideal.html b/docs/reference/seq_steam_ideal.html
index a60685a8..1c8115d7 100644
--- a/docs/reference/seq_steam_ideal.html
+++ b/docs/reference/seq_steam_ideal.html
@@ -1,5 +1,5 @@
-STEAM sequence with ideal pulses. — seq_steam_ideal • Spectroscopy Analysis Tools (spant) STEAM sequence with ideal pulses. — seq_steam_ideal • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -128,7 +128,7 @@ Value
diff --git a/docs/reference/seq_steam_ideal_cof.html b/docs/reference/seq_steam_ideal_cof.html
index 8f225740..cba7af91 100644
--- a/docs/reference/seq_steam_ideal_cof.html
+++ b/docs/reference/seq_steam_ideal_cof.html
@@ -1,7 +1,5 @@
-STEAM sequence with ideal pulses and coherence order filtering to simulate
-gradient crushers. — seq_steam_ideal_cof • Spectroscopy Analysis Tools (spant) STEAM sequence with ideal pulses and coherence order filtering to simulate gradient crushers. — seq_steam_ideal_cof • Spectroscopy Analysis Tools (spant) STEAM sequence with ideal pulses using the z-rotation gradient simulation
-method described by Young et al JMR 140, 146-152 (1999). — seq_steam_ideal_young • Spectroscopy Analysis Tools (spant) STEAM sequence with ideal pulses using the z-rotation gradient simulation method described by Young et al JMR 140, 146-152 (1999). — seq_steam_ideal_young • Spectroscopy Analysis Tools (spant) Set the number of transients for an mrs_data object. — set_Ntrans • Spectroscopy Analysis Tools (spant) Set the number of transients for an mrs_data object. — set_Ntrans • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/set_def_acq_paras.html b/docs/reference/set_def_acq_paras.html
index 3e1b4004..cc2ada9c 100644
--- a/docs/reference/set_def_acq_paras.html
+++ b/docs/reference/set_def_acq_paras.html
@@ -1,5 +1,5 @@
-Set the default acquisition parameters. — set_def_acq_paras • Spectroscopy Analysis Tools (spant) Set the default acquisition parameters. — set_def_acq_paras • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Arguments
diff --git a/docs/reference/set_lcm_cmd.html b/docs/reference/set_lcm_cmd.html
index 2056ed01..42bb2f24 100644
--- a/docs/reference/set_lcm_cmd.html
+++ b/docs/reference/set_lcm_cmd.html
@@ -1,5 +1,5 @@
-Set the command to run the LCModel command-line program. — set_lcm_cmd • Spectroscopy Analysis Tools (spant) Set the command to run the LCModel command-line program. — set_lcm_cmd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/set_lw.html b/docs/reference/set_lw.html
index b64ec851..bb176c62 100644
--- a/docs/reference/set_lw.html
+++ b/docs/reference/set_lw.html
@@ -1,5 +1,5 @@
-Apply line-broadening to an mrs_data object to achieve a specified linewidth. — set_lw • Spectroscopy Analysis Tools (spant) Apply line-broadening to an mrs_data object to achieve a specified linewidth. — set_lw • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -123,7 +123,7 @@ Value
diff --git a/docs/reference/set_mask_xy_mat.html b/docs/reference/set_mask_xy_mat.html
index 49dc5d4e..52c4b617 100644
--- a/docs/reference/set_mask_xy_mat.html
+++ b/docs/reference/set_mask_xy_mat.html
@@ -1,5 +1,5 @@
-Set the masked voxels in a 2D MRSI dataset to given spectrum. — set_mask_xy_mat • Spectroscopy Analysis Tools (spant) Set the masked voxels in a 2D MRSI dataset to given spectrum. — set_mask_xy_mat • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Value
diff --git a/docs/reference/set_precomp_mode.html b/docs/reference/set_precomp_mode.html
index f44bd5d3..47c28e3b 100644
--- a/docs/reference/set_precomp_mode.html
+++ b/docs/reference/set_precomp_mode.html
@@ -1,5 +1,5 @@
-Set the precompute mode. — set_precomp_mode • Spectroscopy Analysis Tools (spant) Set the precompute mode. — set_precomp_mode • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/set_precomp_verbose.html b/docs/reference/set_precomp_verbose.html
index 1453a231..9c613505 100644
--- a/docs/reference/set_precomp_verbose.html
+++ b/docs/reference/set_precomp_verbose.html
@@ -1,5 +1,5 @@
-Set the verbosity of the precompute function. — set_precomp_verbose • Spectroscopy Analysis Tools (spant) Set the verbosity of the precompute function. — set_precomp_verbose • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/set_ref.html b/docs/reference/set_ref.html
index 8953fa50..5436dfa2 100644
--- a/docs/reference/set_ref.html
+++ b/docs/reference/set_ref.html
@@ -1,5 +1,5 @@
-Set the ppm reference value (eg ppm value at 0Hz). — set_ref • Spectroscopy Analysis Tools (spant) Set the ppm reference value (eg ppm value at 0Hz). — set_ref • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/set_td_pts.html b/docs/reference/set_td_pts.html
index 8a80d42a..586459ff 100644
--- a/docs/reference/set_td_pts.html
+++ b/docs/reference/set_td_pts.html
@@ -1,7 +1,5 @@
-Set the number of time-domain data points, truncating or zero-filling as
-appropriate. — set_td_pts • Spectroscopy Analysis Tools (spant) Set the number of time-domain data points, truncating or zero-filling as appropriate. — set_td_pts • Spectroscopy Analysis Tools (spant) Set the command to run the TARQUIN command-line program. — set_tqn_cmd • Spectroscopy Analysis Tools (spant) Set the command to run the TARQUIN command-line program. — set_tqn_cmd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/set_tr.html b/docs/reference/set_tr.html
index b2109ab0..65c9df5f 100644
--- a/docs/reference/set_tr.html
+++ b/docs/reference/set_tr.html
@@ -1,5 +1,5 @@
-Set the repetition time of an MRS dataset. — set_tr • Spectroscopy Analysis Tools (spant) Set the repetition time of an MRS dataset. — set_tr • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/shift.html b/docs/reference/shift.html
index ab0fe724..034591d0 100644
--- a/docs/reference/shift.html
+++ b/docs/reference/shift.html
@@ -1,5 +1,5 @@
-Apply a frequency shift to MRS data. — shift • Spectroscopy Analysis Tools (spant) Apply a frequency shift to MRS data. — shift • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/shift_basis.html b/docs/reference/shift_basis.html
index 2884be19..f55a65e0 100644
--- a/docs/reference/shift_basis.html
+++ b/docs/reference/shift_basis.html
@@ -1,5 +1,5 @@
-Apply frequency shifts to basis set signals. — shift_basis • Spectroscopy Analysis Tools (spant) Apply frequency shifts to basis set signals. — shift_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Value
diff --git a/docs/reference/sim_basis.html b/docs/reference/sim_basis.html
index c7838c46..bb5fefc6 100644
--- a/docs/reference/sim_basis.html
+++ b/docs/reference/sim_basis.html
@@ -1,5 +1,5 @@
-Simulate a basis set object. — sim_basis • Spectroscopy Analysis Tools (spant) Simulate a basis set object. — sim_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -136,7 +136,7 @@ Value
diff --git a/docs/reference/sim_basis_1h_brain.html b/docs/reference/sim_basis_1h_brain.html
index 62ed7389..f71ffa0b 100644
--- a/docs/reference/sim_basis_1h_brain.html
+++ b/docs/reference/sim_basis_1h_brain.html
@@ -1,7 +1,5 @@
-Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS
-sequence. Note, ideal pulses are assumed. — sim_basis_1h_brain • Spectroscopy Analysis Tools (spant) Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS sequence. Note, ideal pulses are assumed. — sim_basis_1h_brain • Spectroscopy Analysis Tools (spant) Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS
-sequence. Note, ideal pulses are assumed. — sim_basis_1h_brain_press • Spectroscopy Analysis Tools (spant) Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS sequence. Note, ideal pulses are assumed. — sim_basis_1h_brain_press • Spectroscopy Analysis Tools (spant) Simulate a macromolecular and lipid basis-set suitable for 1H brain MRS
-analysis. — sim_basis_mm_lip_lcm • Spectroscopy Analysis Tools (spant) Simulate a macromolecular and lipid basis-set suitable for 1H brain MRS analysis. — sim_basis_mm_lip_lcm • Spectroscopy Analysis Tools (spant) Simulate a basis file using TARQUIN. — sim_basis_tqn • Spectroscopy Analysis Tools (spant) Simulate a basis file using TARQUIN. — sim_basis_tqn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -129,7 +129,7 @@ Examples
diff --git a/docs/reference/sim_brain_1h.html b/docs/reference/sim_brain_1h.html
index 2044cf1a..717ee289 100644
--- a/docs/reference/sim_brain_1h.html
+++ b/docs/reference/sim_brain_1h.html
@@ -1,5 +1,5 @@
-Simulate MRS data with a similar appearance to normal brain (by default). — sim_brain_1h • Spectroscopy Analysis Tools (spant) Simulate MRS data with a similar appearance to normal brain (by default). — sim_brain_1h • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -159,7 +159,7 @@ Value
diff --git a/docs/reference/sim_mol.html b/docs/reference/sim_mol.html
index 23bcef50..77f76a50 100644
--- a/docs/reference/sim_mol.html
+++ b/docs/reference/sim_mol.html
@@ -1,5 +1,5 @@
-Simulate a mol_parameter object. — sim_mol • Spectroscopy Analysis Tools (spant) Simulate a mol_parameter object. — sim_mol • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -143,7 +143,7 @@ Value
diff --git a/docs/reference/sim_noise.html b/docs/reference/sim_noise.html
index 23875f79..a71477d4 100644
--- a/docs/reference/sim_noise.html
+++ b/docs/reference/sim_noise.html
@@ -1,5 +1,5 @@
-Simulate an mrs_data object containing simulated Gaussian noise. — sim_noise • Spectroscopy Analysis Tools (spant) Simulate an mrs_data object containing simulated Gaussian noise. — sim_noise • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -84,6 +84,7 @@ Simulate an mrs_data object containing simulated Gaussian noise.
ft = def_ft(),
N = def_N(),
ref = def_ref(),
+ nuc = def_nuc(),
dyns = 1,
fd = TRUE
)
@@ -111,6 +112,10 @@ Arguments
reference value for ppm scale.
nuc
+resonant nucleus.
dyns
number of dynamic scans to generate.
Value
diff --git a/docs/reference/sim_resonances.html b/docs/reference/sim_resonances.html
index 19e9a8a4..d4f8d7c0 100644
--- a/docs/reference/sim_resonances.html
+++ b/docs/reference/sim_resonances.html
@@ -1,5 +1,5 @@
-Simulate a MRS data object containing a set of simulated resonances. — sim_resonances • Spectroscopy Analysis Tools (spant) Simulate a MRS data object containing a set of simulated resonances. — sim_resonances • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -161,7 +161,7 @@ Examples
diff --git a/docs/reference/sim_th_excit_profile.html b/docs/reference/sim_th_excit_profile.html
index 5535c5ef..e781cab1 100644
--- a/docs/reference/sim_th_excit_profile.html
+++ b/docs/reference/sim_th_excit_profile.html
@@ -1,7 +1,5 @@
-Simulate an ideal pulse excitation profile by smoothing a top-hat function
-with a Gaussian. — sim_th_excit_profile • Spectroscopy Analysis Tools (spant) Simulate an ideal pulse excitation profile by smoothing a top-hat function with a Gaussian. — sim_th_excit_profile • Spectroscopy Analysis Tools (spant) Simulate an mrs_data object containing complex zero valued samples. — sim_zero • Spectroscopy Analysis Tools (spant) Simulate an mrs_data object containing complex zero valued samples. — sim_zero • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -78,7 +78,14 @@ Simulate an mrs_data object containing complex zero valued samples.
-
+
@@ -99,6 +106,10 @@ Arguments
reference value for ppm scale.
nuc
+resonant nucleus.
dyns
number of dynamic scans to generate.
Value
diff --git a/docs/reference/smooth_dyns.html b/docs/reference/smooth_dyns.html
index 4cc8da50..accf3a51 100644
--- a/docs/reference/smooth_dyns.html
+++ b/docs/reference/smooth_dyns.html
@@ -1,5 +1,5 @@
-Smooth data across the dynamic dimension with a Gaussian kernel. — smooth_dyns • Spectroscopy Analysis Tools (spant) Smooth data across the dynamic dimension with a Gaussian kernel. — smooth_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/sort_basis.html b/docs/reference/sort_basis.html
index 6a676ea2..d25cc006 100644
--- a/docs/reference/sort_basis.html
+++ b/docs/reference/sort_basis.html
@@ -1,5 +1,5 @@
-Sort the basis-set elements alphabetically. — sort_basis • Spectroscopy Analysis Tools (spant) Sort the basis-set elements alphabetically. — sort_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/spant-package.html b/docs/reference/spant-package.html
index b3dd8e21..90f19ec3 100644
--- a/docs/reference/spant-package.html
+++ b/docs/reference/spant-package.html
@@ -1,5 +1,5 @@
-spant: spectroscopy analysis tools. — spant-package • Spectroscopy Analysis Tools (spant) spant: spectroscopy analysis tools. — spant-package • Spectroscopy Analysis Tools (spant) Simulate and fit some spectra with ABfit for benchmarking purposes. Basic
-timing and performance metrics will be printed. — spant_abfit_benchmark • Spectroscopy Analysis Tools (spant) Simulate and fit some spectra with ABfit for benchmarking purposes. Basic timing and performance metrics will be printed. — spant_abfit_benchmark • Spectroscopy Analysis Tools (spant) Example MEGA-PRESS data with significant B0 drift. — spant_mpress_drift • Spectroscopy Analysis Tools (spant) Example MEGA-PRESS data with significant B0 drift. — spant_mpress_drift • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -83,7 +83,7 @@ Example MEGA-PRESS data with significant B0 drift.
Format
- An object of class mrs_data of length 13.
+ An object of class mrs_data of dimension 1 x 1 x 1 x 1 x 40 x 1 x 1024.
@@ -98,7 +98,7 @@ Format
diff --git a/docs/reference/spant_sim_fmrs_dataset.html b/docs/reference/spant_sim_fmrs_dataset.html
new file mode 100644
index 00000000..00e48b56
--- /dev/null
+++ b/docs/reference/spant_sim_fmrs_dataset.html
@@ -0,0 +1,117 @@
+
+Simulate an example fMRS dataset for a block design fMRS experiment and export a BIDS structure. — spant_sim_fmrs_dataset • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Simulate an example fMRS dataset for a block design fMRS experiment and export a BIDS structure.
+ Source: R/fmrs.R
+ spant_sim_fmrs_dataset.Rd
+
+
+
+ Simulate an example fMRS dataset for a block design fMRS experiment and
+export a BIDS structure.
+
+
+
+ spant_sim_fmrs_dataset(output_dir = NULL)
+
+
+
+ Arguments
+ - output_dir
+output directory for the BIDS data. Defaults to :
+"HOME/sim_fmrs_dataset/data".
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/spant_simulation_benchmark.html b/docs/reference/spant_simulation_benchmark.html
index 32daa8bf..d8cc6841 100644
--- a/docs/reference/spant_simulation_benchmark.html
+++ b/docs/reference/spant_simulation_benchmark.html
@@ -1,7 +1,5 @@
-Simulate a typical metabolite basis set for benchmarking. Timing metrics will
-be printed on completion. — spant_simulation_benchmark • Spectroscopy Analysis Tools (spant) Simulate a typical metabolite basis set for benchmarking. Timing metrics will be printed on completion. — spant_simulation_benchmark • Spectroscopy Analysis Tools (spant) Decompose an mrs_data object into white and gray matter spectra. — spec_decomp • Spectroscopy Analysis Tools (spant) Perform a mathematical operation on a spectral region. — spec_op • Spectroscopy Analysis Tools (spant) Perform a mathematical operation on a spectral region. — spec_op • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -98,8 +98,8 @@ Arguments
operator
-can be "sum" (default), "mean", "l2", "max", "min" or
-"max-min".
can be "sum" (default), "mean", "l2", "max", "max_cplx,
+"min" or "max-min".
freq_scale
@@ -129,7 +129,7 @@ Value
diff --git a/docs/reference/spin_sys.html b/docs/reference/spin_sys.html
index 853423a4..1eaa9e76 100644
--- a/docs/reference/spin_sys.html
+++ b/docs/reference/spin_sys.html
@@ -1,5 +1,5 @@
-Create a spin system object for pulse sequence simulation. — spin_sys • Spectroscopy Analysis Tools (spant) Create a spin system object for pulse sequence simulation. — spin_sys • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/spm_pve2categorical.html b/docs/reference/spm_pve2categorical.html
index 23a1bad9..70f10729 100644
--- a/docs/reference/spm_pve2categorical.html
+++ b/docs/reference/spm_pve2categorical.html
@@ -1,7 +1,5 @@
-Convert SPM style segmentation files to a single categorical image where
-the numerical values map as: 0) Other, 1) CSF, 2) GM and 3) WM. — spm_pve2categorical • Spectroscopy Analysis Tools (spant) Convert SPM style segmentation files to a single categorical image where the numerical values map as: 0) Other, 1) CSF, 2) GM and 3) WM. — spm_pve2categorical • Spectroscopy Analysis Tools (spant) Signal space projection method for lipid suppression. — ssp • Spectroscopy Analysis Tools (spant) Signal space projection method for lipid suppression. — ssp • Spectroscopy Analysis Tools (spant) Plot the fitting results of an object of class fit_result with
-individual basis set components shown. — stackplot.fit_result • Spectroscopy Analysis Tools (spant) Plot the fitting results of an object of class fit_result with individual basis set components shown. — stackplot.fit_result • Spectroscopy Analysis Tools (spant) Produce a plot with multiple traces. — stackplot • Spectroscopy Analysis Tools (spant) Produce a plot with multiple traces. — stackplot • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/stackplot.mrs_data.html b/docs/reference/stackplot.mrs_data.html
index 17ff5648..64eea445 100644
--- a/docs/reference/stackplot.mrs_data.html
+++ b/docs/reference/stackplot.mrs_data.html
@@ -1,5 +1,5 @@
-Stackplot plotting method for objects of class mrs_data. — stackplot.mrs_data • Spectroscopy Analysis Tools (spant) Stackplot plotting method for objects of class mrs_data. — stackplot.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -255,7 +255,7 @@ Arguments
diff --git a/docs/reference/sub_first_dyn.html b/docs/reference/sub_first_dyn.html
index dbd7f831..493b7242 100644
--- a/docs/reference/sub_first_dyn.html
+++ b/docs/reference/sub_first_dyn.html
@@ -1,5 +1,5 @@
-Subtract the first dynamic spectrum from a dynamic series. — sub_first_dyn • Spectroscopy Analysis Tools (spant) Subtract the first dynamic spectrum from a dynamic series. — sub_first_dyn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/sub_mean_dyns.html b/docs/reference/sub_mean_dyns.html
index 6e3bb2df..221bd0c1 100644
--- a/docs/reference/sub_mean_dyns.html
+++ b/docs/reference/sub_mean_dyns.html
@@ -1,5 +1,5 @@
-Subtract the mean dynamic spectrum from a dynamic series. — sub_mean_dyns • Spectroscopy Analysis Tools (spant) Subtract the mean dynamic spectrum from a dynamic series. — sub_mean_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/sub_median_dyns.html b/docs/reference/sub_median_dyns.html
index 134c495d..1e834f14 100644
--- a/docs/reference/sub_median_dyns.html
+++ b/docs/reference/sub_median_dyns.html
@@ -1,5 +1,5 @@
-Subtract the median dynamic spectrum from a dynamic series. — sub_median_dyns • Spectroscopy Analysis Tools (spant) Subtract the median dynamic spectrum from a dynamic series. — sub_median_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/sum_coils.html b/docs/reference/sum_coils.html
index 7bf559f2..e1ab3cc0 100644
--- a/docs/reference/sum_coils.html
+++ b/docs/reference/sum_coils.html
@@ -1,5 +1,5 @@
-Calculate the sum across receiver coil elements. — sum_coils • Spectroscopy Analysis Tools (spant) Calculate the sum across receiver coil elements. — sum_coils • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/sum_dyns.html b/docs/reference/sum_dyns.html
index a0be19d3..bbda2ffc 100644
--- a/docs/reference/sum_dyns.html
+++ b/docs/reference/sum_dyns.html
@@ -1,5 +1,5 @@
-Calculate the sum of data dynamics. — sum_dyns • Spectroscopy Analysis Tools (spant) Calculate the sum of data dynamics. — sum_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/sum_mrs.html b/docs/reference/sum_mrs.html
index a22f215b..3cc3ab9e 100644
--- a/docs/reference/sum_mrs.html
+++ b/docs/reference/sum_mrs.html
@@ -1,5 +1,5 @@
-Sum two mrs_data objects. — sum_mrs • Spectroscopy Analysis Tools (spant) Sum two mrs_data objects. — sum_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Value
diff --git a/docs/reference/sum_mrs_list.html b/docs/reference/sum_mrs_list.html
index f4e09aea..c3584348 100644
--- a/docs/reference/sum_mrs_list.html
+++ b/docs/reference/sum_mrs_list.html
@@ -1,5 +1,5 @@
-Return the sum of a list of mrs_data objects. — sum_mrs_list • Spectroscopy Analysis Tools (spant) Return the sum of a list of mrs_data objects. — sum_mrs_list • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/svs_1h_brain_analysis.html b/docs/reference/svs_1h_brain_analysis.html
index 8ce514db..dff0ef7d 100644
--- a/docs/reference/svs_1h_brain_analysis.html
+++ b/docs/reference/svs_1h_brain_analysis.html
@@ -1,5 +1,5 @@
-Standard SVS 1H brain analysis pipeline. — svs_1h_brain_analysis • Spectroscopy Analysis Tools (spant) Standard SVS 1H brain analysis pipeline. — svs_1h_brain_analysis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -199,7 +199,7 @@ Value
diff --git a/docs/reference/svs_1h_brain_analysis_dev.html b/docs/reference/svs_1h_brain_analysis_dev.html
index d70a14d3..d71bfea2 100644
--- a/docs/reference/svs_1h_brain_analysis_dev.html
+++ b/docs/reference/svs_1h_brain_analysis_dev.html
@@ -1,5 +1,5 @@
-Standard SVS 1H brain analysis pipeline. — svs_1h_brain_analysis_dev • Spectroscopy Analysis Tools (spant) Standard SVS 1H brain analysis pipeline. — svs_1h_brain_analysis_dev • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -193,7 +193,7 @@ Examples
diff --git a/docs/reference/svs_1h_brain_batch_analysis.html b/docs/reference/svs_1h_brain_batch_analysis.html
index 5631e8cc..15f7223e 100644
--- a/docs/reference/svs_1h_brain_batch_analysis.html
+++ b/docs/reference/svs_1h_brain_batch_analysis.html
@@ -1,5 +1,5 @@
-Batch interface to the standard SVS 1H brain analysis pipeline. — svs_1h_brain_batch_analysis • Spectroscopy Analysis Tools (spant) Batch interface to the standard SVS 1H brain analysis pipeline. — svs_1h_brain_batch_analysis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -144,7 +144,7 @@ Value
diff --git a/docs/reference/t_test_spec.html b/docs/reference/t_test_spec.html
new file mode 100644
index 00000000..56a7ea1b
--- /dev/null
+++ b/docs/reference/t_test_spec.html
@@ -0,0 +1,124 @@
+
+Perform a t-test on spectral data points. — t_test_spec • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+
+
+ Perform a t-test on spectral data points.
+
+
+
+ t_test_spec(mrs_data, group)
+
+
+
+ Arguments
+ - mrs_data
+an mrs_data object with spectra in the dynamic dimension.
- group
+vector describing the group membership of each dynamic spectrum.
+
+ Value
+
+
+a list of statistical results.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/td2fd.html b/docs/reference/td2fd.html
index 6748a6a8..f31ed524 100644
--- a/docs/reference/td2fd.html
+++ b/docs/reference/td2fd.html
@@ -1,5 +1,5 @@
-Transform time-domain data to the frequency-domain. — td2fd • Spectroscopy Analysis Tools (spant) Transform time-domain data to the frequency-domain. — td2fd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/td_conv_filt.html b/docs/reference/td_conv_filt.html
index a9f340c3..106b9b00 100644
--- a/docs/reference/td_conv_filt.html
+++ b/docs/reference/td_conv_filt.html
@@ -1,5 +1,5 @@
-Time-domain convolution based filter. — td_conv_filt • Spectroscopy Analysis Tools (spant) Time-domain convolution based filter. — td_conv_filt • Spectroscopy Analysis Tools (spant) Time-domain spectral registration. — tdsr • Spectroscopy Analysis Tools (spant) Time-domain spectral registration. — tdsr • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -121,7 +121,7 @@ Value
diff --git a/docs/reference/te.html b/docs/reference/te.html
index 010361b1..4a65711d 100644
--- a/docs/reference/te.html
+++ b/docs/reference/te.html
@@ -1,5 +1,5 @@
-Return the echo time of an MRS dataset. — te • Spectroscopy Analysis Tools (spant) Return the echo time of an MRS dataset. — te • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/tr.html b/docs/reference/tr.html
index 0c0bd63b..2e749e02 100644
--- a/docs/reference/tr.html
+++ b/docs/reference/tr.html
@@ -1,5 +1,5 @@
-Return the repetition time of an MRS dataset. — tr • Spectroscopy Analysis Tools (spant) Return the repetition time of an MRS dataset. — tr • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/varpro_3_para_opts.html b/docs/reference/varpro_3_para_opts.html
index c2270a16..52d7cd84 100644
--- a/docs/reference/varpro_3_para_opts.html
+++ b/docs/reference/varpro_3_para_opts.html
@@ -1,5 +1,5 @@
-Return a list of options for VARPRO based fitting with 3 free parameters. — varpro_3_para_opts • Spectroscopy Analysis Tools (spant) Return a list of options for VARPRO based fitting with 3 free parameters. — varpro_3_para_opts • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -141,7 +141,7 @@ Value
diff --git a/docs/reference/varpro_basic_opts.html b/docs/reference/varpro_basic_opts.html
index 32c86d22..c5104891 100644
--- a/docs/reference/varpro_basic_opts.html
+++ b/docs/reference/varpro_basic_opts.html
@@ -1,5 +1,5 @@
-Return a list of options for a basic VARPRO analysis. — varpro_basic_opts • Spectroscopy Analysis Tools (spant) Return a list of options for a basic VARPRO analysis. — varpro_basic_opts • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -118,7 +118,7 @@ Value
diff --git a/docs/reference/varpro_opts.html b/docs/reference/varpro_opts.html
index 2aabf11d..6332f730 100644
--- a/docs/reference/varpro_opts.html
+++ b/docs/reference/varpro_opts.html
@@ -1,5 +1,5 @@
-Return a list of options for VARPRO based fitting. — varpro_opts • Spectroscopy Analysis Tools (spant) Return a list of options for VARPRO based fitting. — varpro_opts • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -177,7 +177,7 @@ Examples
diff --git a/docs/reference/vec2mrs_data.html b/docs/reference/vec2mrs_data.html
index 0cccd73b..f0d58bf0 100644
--- a/docs/reference/vec2mrs_data.html
+++ b/docs/reference/vec2mrs_data.html
@@ -1,5 +1,5 @@
-Convert a vector into a mrs_data object. — vec2mrs_data • Spectroscopy Analysis Tools (spant) Convert a vector into a mrs_data object. — vec2mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -80,10 +80,11 @@ Convert a vector into a mrs_data object.
vec2mrs_data(
vec,
- fs = def_fs(),
- ft = def_ft(),
- ref = def_ref(),
- nuc = def_nuc(),
+ mrs_data = NULL,
+ fs = NULL,
+ ft = NULL,
+ ref = NULL,
+ nuc = NULL,
dyns = 1,
fd = FALSE
)
@@ -95,6 +96,10 @@ Arguments
the data vector.
mrs_data
+example data to copy acquisition parameters from.
fs
sampling frequency in Hz.
Arguments
fd
-flag to indicate if the matrix is in the frequency domain (logical).
flag to indicate if the vector is in the frequency domain (logical).
Value
diff --git a/docs/reference/write_basis.html b/docs/reference/write_basis.html
index b6e27cbd..94c5e021 100644
--- a/docs/reference/write_basis.html
+++ b/docs/reference/write_basis.html
@@ -1,5 +1,5 @@
-Write a basis object to an LCModel .basis formatted file. — write_basis • Spectroscopy Analysis Tools (spant) Write a basis object to an LCModel .basis formatted file. — write_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -108,7 +108,7 @@ Arguments
diff --git a/docs/reference/write_basis_tqn.html b/docs/reference/write_basis_tqn.html
index 6aa51c1d..116c73ec 100644
--- a/docs/reference/write_basis_tqn.html
+++ b/docs/reference/write_basis_tqn.html
@@ -1,5 +1,5 @@
-Generate a basis file using TARQUIN. — write_basis_tqn • Spectroscopy Analysis Tools (spant) Generate a basis file using TARQUIN. — write_basis_tqn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Examples
diff --git a/docs/reference/write_mrs.html b/docs/reference/write_mrs.html
index fff25f15..124b9dc4 100644
--- a/docs/reference/write_mrs.html
+++ b/docs/reference/write_mrs.html
@@ -1,5 +1,5 @@
-Write MRS data object to file. — write_mrs • Spectroscopy Analysis Tools (spant) Write MRS data object to file. — write_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Arguments
diff --git a/docs/reference/write_mrs_nifti.html b/docs/reference/write_mrs_nifti.html
index f4bf1921..bd3ed4b7 100644
--- a/docs/reference/write_mrs_nifti.html
+++ b/docs/reference/write_mrs_nifti.html
@@ -1,5 +1,5 @@
-Write MRS data object to file in NIFTI format. — write_mrs_nifti • Spectroscopy Analysis Tools (spant) Write MRS data object to file in NIFTI format. — write_mrs_nifti • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/write_pulse_ascii.html b/docs/reference/write_pulse_ascii.html
index 067ae086..221f8ebb 100644
--- a/docs/reference/write_pulse_ascii.html
+++ b/docs/reference/write_pulse_ascii.html
@@ -1,5 +1,5 @@
-Write an ASCII formatted pulse file. — write_pulse_ascii • Spectroscopy Analysis Tools (spant) Write an ASCII formatted pulse file. — write_pulse_ascii • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/zero_fade_spec.html b/docs/reference/zero_fade_spec.html
index c703745c..c8b572c3 100644
--- a/docs/reference/zero_fade_spec.html
+++ b/docs/reference/zero_fade_spec.html
@@ -1,7 +1,5 @@
-Fade a spectrum to zero by frequency domain multiplication with a tanh
-function. Note this operation distorts data points at the end of the FID. — zero_fade_spec • Spectroscopy Analysis Tools (spant) Fade a spectrum to zero by frequency domain multiplication with a tanh function. Note this operation distorts data points at the end of the FID. — zero_fade_spec • Spectroscopy Analysis Tools (spant) Zero all coherences including and above a given order. — zero_higher_orders • Spectroscopy Analysis Tools (spant) Zero all coherences including and above a given order. — zero_higher_orders • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Value
diff --git a/docs/reference/zero_td_pts_end.html b/docs/reference/zero_td_pts_end.html
index 8c1123c8..71d24ebb 100644
--- a/docs/reference/zero_td_pts_end.html
+++ b/docs/reference/zero_td_pts_end.html
@@ -1,5 +1,5 @@
-Set mrs_data object data points at the end of the FID to zero. — zero_td_pts_end • Spectroscopy Analysis Tools (spant) Set mrs_data object data points at the end of the FID to zero. — zero_td_pts_end • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/zf.html b/docs/reference/zf.html
index 85e2013c..baf50256 100644
--- a/docs/reference/zf.html
+++ b/docs/reference/zf.html
@@ -1,5 +1,5 @@
-Zero-fill MRS data in the time domain. — zf • Spectroscopy Analysis Tools (spant) Zero-fill MRS data in the time domain. — zf • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -125,7 +125,7 @@ Value
diff --git a/docs/reference/zf_xy.html b/docs/reference/zf_xy.html
index ebca3999..c4104a74 100644
--- a/docs/reference/zf_xy.html
+++ b/docs/reference/zf_xy.html
@@ -1,5 +1,5 @@
-Zero-fill MRSI data in the k-space x-y direction. — zf_xy • Spectroscopy Analysis Tools (spant) Zero-fill MRSI data in the k-space x-y direction. — zf_xy • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -113,7 +113,7 @@ Value
diff --git a/docs/sitemap.xml b/docs/sitemap.xml
index e2139f71..4c39f515 100644
--- a/docs/sitemap.xml
+++ b/docs/sitemap.xml
@@ -216,6 +216,12 @@
https://martin3141.github.io/spant/reference/comb_coils_fp_pc.html
+
+ https://martin3141.github.io/spant/reference/comb_coils_mrsi_gls.html
+
+
+ https://martin3141.github.io/spant/reference/comb_coils_svs_gls.html
+
https://martin3141.github.io/spant/reference/comb_csv_results.html
@@ -411,6 +417,9 @@
https://martin3141.github.io/spant/reference/gen_conv_reg.html
+
+ https://martin3141.github.io/spant/reference/gen_group_reg.html
+
https://martin3141.github.io/spant/reference/gen_impulse_reg.html
@@ -555,6 +564,15 @@
https://martin3141.github.io/spant/reference/glm_spec.html
+
+ https://martin3141.github.io/spant/reference/glm_spec_fmrs_fl.html
+
+
+ https://martin3141.github.io/spant/reference/glm_spec_fmrs_group.html
+
+
+ https://martin3141.github.io/spant/reference/glm_spec_group_linhyp.html
+
https://martin3141.github.io/spant/reference/grid_shift_xy.html
@@ -690,9 +708,15 @@
https://martin3141.github.io/spant/reference/mrs_data2basis.html
+
+ https://martin3141.github.io/spant/reference/mrs_data2bids.html
+
https://martin3141.github.io/spant/reference/mrs_data2mat.html
+
+ https://martin3141.github.io/spant/reference/mrs_data2spec_mat.html
+
https://martin3141.github.io/spant/reference/mrs_data2vec.html
@@ -741,6 +765,9 @@
https://martin3141.github.io/spant/reference/phase.html
+
+ https://martin3141.github.io/spant/reference/phase_ref_1h_brain.html
+
https://martin3141.github.io/spant/reference/plot.fit_result.html
@@ -780,6 +807,12 @@
https://martin3141.github.io/spant/reference/precomp.html
+
+ https://martin3141.github.io/spant/reference/preproc_svs.html
+
+
+ https://martin3141.github.io/spant/reference/preproc_svs_dataset.html
+
https://martin3141.github.io/spant/reference/print.fit_result.html
@@ -1050,6 +1083,9 @@
https://martin3141.github.io/spant/reference/spant_mpress_drift.html
+
+ https://martin3141.github.io/spant/reference/spant_sim_fmrs_dataset.html
+
https://martin3141.github.io/spant/reference/spant_simulation_benchmark.html
@@ -1107,6 +1143,9 @@
https://martin3141.github.io/spant/reference/svs_1h_brain_batch_analysis.html
+
+ https://martin3141.github.io/spant/reference/t_test_spec.html
+
https://martin3141.github.io/spant/reference/td2fd.html
Perform a zeroth order phase correction based on the phase of the first data -point in the time-domain.
Perform a zeroth order phase correction based on the phase of the first data point in the time-domain.
All functions
- Perform a fft and fftshift on a matrix with each column replaced by its
-shifted fft.
Perform a fft and fftshift on a matrix with each column replaced by its shifted fft.
@@ -536,8 +522,11 @@ All functions
- Generate regressors by convolving a specified response function with a
-stimulus.
Generate regressors by convolving a specified response function with a stimulus.
+
+
+ Expand a regressor matrix for a group analysis.
@@ -553,28 +542,23 @@ All functions
- Return a character vector of common 1H molecules found in healthy human
-brain.
Return a character vector of common 1H molecules found in healthy human brain.
- Return a list of mol_parameter objects suitable for 1H brain MRS
-analyses.
Return a list of mol_parameter objects suitable for 1H brain MRS analyses.
- Return a list of mol_parameter objects suitable for 1H brain MRS
-analyses.
Return a list of mol_parameter objects suitable for 1H brain MRS analyses.
- Return a list of mol_parameter objects suitable for 1H brain MRS
-analyses.
Return a list of mol_parameter objects suitable for 1H brain MRS analyses.
- Return a list of mol_parameter objects suitable for 1H brain MRS
-analyses.
Return a list of mol_parameter objects suitable for 1H brain MRS analyses.
@@ -582,8 +566,7 @@ All functions
- Return a character vector of molecules included in the Gold Star Phantoms
-SPECTRE phantom.
Return a character vector of molecules included in the Gold Star Phantoms SPECTRE phantom.
@@ -635,8 +618,7 @@ All functions
- Return a character array of names that may be used with the
-get_mol_paras function.
Return a character array of names that may be used with the get_mol_paras function.
@@ -700,8 +682,7 @@ All functions
- Return an array of amplitudes derived from fitting the initial points in the
-time domain and extrapolating back to t=0.
Return an array of amplitudes derived from fitting the initial points in the time domain and extrapolating back to t=0.
@@ -709,8 +690,7 @@ All functions
- Generate a mol_parameters object for a simple spin system with one
-resonance.
Generate a mol_parameters object for a simple spin system with one resonance.
@@ -731,6 +711,18 @@ All functions glm_spec()
Perform a GLM analysis of dynamic MRS data in the spectral domain.
+
+
+ Perform first-level spectral GLM analysis of an fMRS dataset.
+
+
+ Perform group-level spectral GLM analysis of an fMRS dataset.
+
+
+ Test a group-level spectral GLM linear hypothesis.
@@ -766,8 +758,7 @@ All functions
- Perform an ifft and ifftshift on a matrix with each column replaced by its
-shifted ifft.
Perform an ifft and ifftshift on a matrix with each column replaced by its shifted ifft.
@@ -799,8 +790,7 @@ All functions
- Check if the chemical shift dimension of an MRS data object is in the
-frequency domain.
Check if the chemical shift dimension of an MRS data object is in the frequency domain.
@@ -820,18 +810,15 @@ All functions
- Covert a linewidth in Hz to an equivalent alpha value in the time-domain ie:
-x * exp(-t * alpha).
Covert a linewidth in Hz to an equivalent alpha value in the time-domain ie: x * exp(-t * alpha).
- Covert a linewidth in Hz to an equivalent beta value in the time-domain ie:
-x * exp(-t * t * beta).
Covert a linewidth in Hz to an equivalent beta value in the time-domain ie: x * exp(-t * t * beta).
- Make a basis-set object from a directory containing LCModel formatted RAW
-files.
Make a basis-set object from a directory containing LCModel formatted RAW files.
@@ -851,8 +838,7 @@ All functions
- Mask the voxels outside an elliptical region spanning the MRSI dataset in the
-x-y plane.
Mask the voxels outside an elliptical region spanning the MRSI dataset in the x-y plane.
@@ -860,13 +846,11 @@ All functions
- Convert a matrix (with spectral points in the column dimension and dynamics
-in the row dimensions) into a mrs_data object.
Convert a matrix (with spectral points in the column dimension and dynamics in the row dimensions) into a mrs_data object.
- Matrix exponential function taken from complexplus package to reduce the
-number of spant dependencies.
Matrix exponential function taken from complexplus package to reduce the number of spant dependencies.
@@ -914,31 +898,31 @@ All functions
- Convert an mrs_data object to basis object - where basis signals are spread
-across the dynamic dimension in the MRS data.
Convert an mrs_data object to basis object - where basis signals are spread across the dynamic dimension in the MRS data.
+
+
+ Create a BIDS file structure from a vector of MRS data paths or list of mrs_data objects.
- Convert mrs_data object to a matrix, with spectral points in the column
-dimension and dynamics in the row dimension.
Convert mrs_data object to a matrix, with spectral points in the column dimension and dynamics in the row dimension.
-
+
- Convert mrs_data object to a vector.
Convert mrs_data object to a matrix, with spectral points in the column dimension and dynamics in the row dimension.
-
+
- Create a BIDS directory and file structure from a list of mrs_data objects.
Convert mrs_data object to a vector.
- Perform a fftshift on a matrix, with each column replaced by its shifted
-result.
Perform a fftshift on a matrix, with each column replaced by its shifted result.
- Perform an ifftshift on a matrix, with each column replaced by its shifted
-result.
Perform an ifftshift on a matrix, with each column replaced by its shifted result.
@@ -946,9 +930,7 @@ All functions
- Flip the x data dimension order of a nifti image. This corresponds to
-flipping MRI data in the left-right direction, assuming the data in save in
-neurological format (can check with fslorient program).
Flip the x data dimension order of a nifti image. This corresponds to flipping MRI data in the left-right direction, assuming the data in save in neurological format (can check with fslorient program).
@@ -964,8 +946,7 @@ All functions
- Search for the highest peak in a spectral region and return the frequency,
-height and FWHM.
Search for the highest peak in a spectral region and return the frequency, height and FWHM.
@@ -974,6 +955,10 @@ All functions phase()
Apply phasing parameters to MRS data.
+
+
+ Corrected zero order phase and chemical shift offset in 1H MRS data from the brain.
@@ -1005,8 +990,7 @@ All functions
- Plot an interactive slice map from a data array where voxels can be selected
-to display a corresponding spectrum.
Plot an interactive slice map from a data array where voxels can be selected to display a corresponding spectrum.
@@ -1026,8 +1010,15 @@ All functions
- Save function results to file and load on subsequent calls to avoid repeat
-computation.
Save function results to file and load on subsequent calls to avoid repeat computation.
+
+
+ Preprocess and perform quality assessment of a single SVS data set.
+
+
+ Preprocess and perform quality assessment of one or more SVS data sets.
@@ -1055,15 +1046,11 @@ All functions
- Read a directory containing Siemens MRS IMA files and combine along the coil
-dimension. Note that the coil ID is inferred from the sorted file name and
-should be checked when consistency is required between two directories.
Read a directory containing Siemens MRS IMA files and combine along the coil dimension. Note that the coil ID is inferred from the sorted file name and should be checked when consistency is required between two directories.
- Read a directory containing Siemens MRS IMA files and combine along the
-dynamic dimension. Note that the coil ID is inferred from the sorted file
-name and should be checked when consistency is required.
Read a directory containing Siemens MRS IMA files and combine along the dynamic dimension. Note that the coil ID is inferred from the sorted file name and should be checked when consistency is required.
@@ -1103,13 +1090,11 @@ All functions
- Reconstruct complex time-domain data from the real part of frequency-domain
-data.
Reconstruct complex time-domain data from the real part of frequency-domain data.
- Reconstruct complex time-domain data from the real part of frequency-domain
-data.
Reconstruct complex time-domain data from the real part of frequency-domain data.
@@ -1141,8 +1126,7 @@ All functions
- Resample a VOI to match a target image space using nearest-neighbour
-interpolation.
Resample a VOI to match a target image space using nearest-neighbour interpolation.
@@ -1158,23 +1142,19 @@ All functions
- Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water).
Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / kg of tissue water).
- Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water).
Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / kg of tissue water).
- Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / Litre of tissue).
Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / Litre of tissue).
- Convert default LCM/TARQUIN concentration scaling to molal units with partial
-volume correction.
Convert default LCM/TARQUIN concentration scaling to molal units with partial volume correction.
@@ -1222,8 +1202,7 @@ All functions
- MEGA-PRESS sequence with ideal localisation pulses and Gaussian shaped
-editing pulse.
MEGA-PRESS sequence with ideal localisation pulses and Gaussian shaped editing pulse.
@@ -1251,13 +1230,11 @@ All functions
- STEAM sequence with ideal pulses and coherence order filtering to simulate
-gradient crushers.
STEAM sequence with ideal pulses and coherence order filtering to simulate gradient crushers.
- STEAM sequence with ideal pulses using the z-rotation gradient simulation
-method described by Young et al JMR 140, 146-152 (1999).
STEAM sequence with ideal pulses using the z-rotation gradient simulation method described by Young et al JMR 140, 146-152 (1999).
@@ -1293,8 +1270,7 @@ All functions
- Set the number of time-domain data points, truncating or zero-filling as
-appropriate.
Set the number of time-domain data points, truncating or zero-filling as appropriate.
@@ -1318,18 +1294,15 @@ All functions
- Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS
-sequence. Note, ideal pulses are assumed.
Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS sequence. Note, ideal pulses are assumed.
- Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS
-sequence. Note, ideal pulses are assumed.
Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS sequence. Note, ideal pulses are assumed.
- Simulate a macromolecular and lipid basis-set suitable for 1H brain MRS
-analysis.
Simulate a macromolecular and lipid basis-set suitable for 1H brain MRS analysis.
@@ -1353,8 +1326,7 @@ All functions
- Simulate an ideal pulse excitation profile by smoothing a top-hat function
-with a Gaussian.
Simulate an ideal pulse excitation profile by smoothing a top-hat function with a Gaussian.
@@ -1374,17 +1346,19 @@ All functions
- Simulate and fit some spectra with ABfit for benchmarking purposes. Basic
-timing and performance metrics will be printed.
Simulate and fit some spectra with ABfit for benchmarking purposes. Basic timing and performance metrics will be printed.
Example MEGA-PRESS data with significant B0 drift.
+
+
+ Simulate an example fMRS dataset for a block design fMRS experiment and export a BIDS structure.
- Simulate a typical metabolite basis set for benchmarking. Timing metrics will
-be printed on completion.
Simulate a typical metabolite basis set for benchmarking. Timing metrics will be printed on completion.
@@ -1400,8 +1374,7 @@ All functions
- Convert SPM style segmentation files to a single categorical image where
-the numerical values map as: 0) Other, 1) CSF, 2) GM and 3) WM.
Convert SPM style segmentation files to a single categorical image where the numerical values map as: 0) Other, 1) CSF, 2) GM and 3) WM.
@@ -1413,8 +1386,7 @@ All functions
- Plot the fitting results of an object of class fit_result with
-individual basis set components shown.
Plot the fitting results of an object of class fit_result with individual basis set components shown.
@@ -1459,6 +1431,10 @@ All functions svs_1h_brain_batch_analysis()
Batch interface to the standard SVS 1H brain analysis pipeline.
+
+
+ Perform a t-test on spectral data points.
@@ -1518,8 +1494,7 @@ All functions
- Fade a spectrum to zero by frequency domain multiplication with a tanh
-function. Note this operation distorts data points at the end of the FID.
Fade a spectrum to zero by frequency domain multiplication with a tanh function. Note this operation distorts data points at the end of the FID.
@@ -1549,7 +1524,7 @@ All functions
diff --git a/docs/reference/int_spec.html b/docs/reference/int_spec.html
index c7060fe7..783325a8 100644
--- a/docs/reference/int_spec.html
+++ b/docs/reference/int_spec.html
@@ -1,5 +1,5 @@
-Integrate a spectral region. — int_spec • Spectroscopy Analysis Tools (spant) Integrate a spectral region. — int_spec • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -118,7 +118,7 @@ Value
diff --git a/docs/reference/interleave_dyns.html b/docs/reference/interleave_dyns.html
index effe5543..441eff27 100644
--- a/docs/reference/interleave_dyns.html
+++ b/docs/reference/interleave_dyns.html
@@ -1,5 +1,5 @@
-Interleave the first and second half of a dynamic series. — interleave_dyns • Spectroscopy Analysis Tools (spant) Interleave the first and second half of a dynamic series. — interleave_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/inv_even_dyns.html b/docs/reference/inv_even_dyns.html
index 9f9d4fff..dcb781dc 100644
--- a/docs/reference/inv_even_dyns.html
+++ b/docs/reference/inv_even_dyns.html
@@ -1,5 +1,5 @@
-Invert even numbered dynamic scans starting from 1 (2,4,6...). — inv_even_dyns • Spectroscopy Analysis Tools (spant) Invert even numbered dynamic scans starting from 1 (2,4,6...). — inv_even_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/inv_odd_dyns.html b/docs/reference/inv_odd_dyns.html
index 26212e2b..78d64660 100644
--- a/docs/reference/inv_odd_dyns.html
+++ b/docs/reference/inv_odd_dyns.html
@@ -1,5 +1,5 @@
-Invert odd numbered dynamic scans starting from 1 (1,3,5...). — inv_odd_dyns • Spectroscopy Analysis Tools (spant) Invert odd numbered dynamic scans starting from 1 (1,3,5...). — inv_odd_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/is.def.html b/docs/reference/is.def.html
index f196ffd0..a67b9eba 100644
--- a/docs/reference/is.def.html
+++ b/docs/reference/is.def.html
@@ -1,5 +1,5 @@
-Check if an object is defined, which is the same as being not NULL. — is.def • Spectroscopy Analysis Tools (spant) Check if an object is defined, which is the same as being not NULL. — is.def • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/is_fd.html b/docs/reference/is_fd.html
index 3b0ca165..18a193aa 100644
--- a/docs/reference/is_fd.html
+++ b/docs/reference/is_fd.html
@@ -1,7 +1,5 @@
-Check if the chemical shift dimension of an MRS data object is in the
-frequency domain. — is_fd • Spectroscopy Analysis Tools (spant) Check if the chemical shift dimension of an MRS data object is in the frequency domain. — is_fd • Spectroscopy Analysis Tools (spant) Transform 2D MRSI data from k-space to image space in the x-y direction. — kspace2img_xy • Spectroscopy Analysis Tools (spant) Transform 2D MRSI data from k-space to image space in the x-y direction. — kspace2img_xy • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/l2_reg.html b/docs/reference/l2_reg.html
index 3d781d80..21aa9849 100644
--- a/docs/reference/l2_reg.html
+++ b/docs/reference/l2_reg.html
@@ -1,5 +1,5 @@
-Perform l2 regularisation artefact suppression. — l2_reg • Spectroscopy Analysis Tools (spant) Perform l2 regularisation artefact suppression. — l2_reg • Spectroscopy Analysis Tools (spant) Apply line-broadening (apodisation) to MRS data or basis object. — lb • Spectroscopy Analysis Tools (spant) Apply line-broadening (apodisation) to MRS data or basis object. — lb • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -123,7 +123,7 @@ Value
diff --git a/docs/reference/lofdc.html b/docs/reference/lofdc.html
index 5419b1ec..31347a25 100644
--- a/docs/reference/lofdc.html
+++ b/docs/reference/lofdc.html
@@ -1,5 +1,5 @@
-Correct linear frequency drift. — lofdc • Spectroscopy Analysis Tools (spant) Correct linear frequency drift. — lofdc • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -138,7 +138,7 @@ Value
diff --git a/docs/reference/lw2alpha.html b/docs/reference/lw2alpha.html
index b83db682..25da229b 100644
--- a/docs/reference/lw2alpha.html
+++ b/docs/reference/lw2alpha.html
@@ -1,7 +1,5 @@
-Covert a linewidth in Hz to an equivalent alpha value in the time-domain ie:
-x * exp(-t * alpha). — lw2alpha • Spectroscopy Analysis Tools (spant) Covert a linewidth in Hz to an equivalent alpha value in the time-domain ie: x * exp(-t * alpha). — lw2alpha • Spectroscopy Analysis Tools (spant) Covert a linewidth in Hz to an equivalent beta value in the time-domain ie:
-x * exp(-t * t * beta). — lw2beta • Spectroscopy Analysis Tools (spant) Covert a linewidth in Hz to an equivalent beta value in the time-domain ie: x * exp(-t * t * beta). — lw2beta • Spectroscopy Analysis Tools (spant) Make a basis-set object from a directory containing LCModel formatted RAW
-files. — make_basis_from_raw • Spectroscopy Analysis Tools (spant) Make a basis-set object from a directory containing LCModel formatted RAW files. — make_basis_from_raw • Spectroscopy Analysis Tools (spant) Mask an MRS dataset in the dynamic dimension. — mask_dyns • Spectroscopy Analysis Tools (spant) Mask an MRS dataset in the dynamic dimension. — mask_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/mask_fit_res.html b/docs/reference/mask_fit_res.html
index 97baaa3f..ebd91a99 100644
--- a/docs/reference/mask_fit_res.html
+++ b/docs/reference/mask_fit_res.html
@@ -1,5 +1,5 @@
-Mask fit result spectra depending on a vector of bool values. — mask_fit_res • Spectroscopy Analysis Tools (spant) Mask fit result spectra depending on a vector of bool values. — mask_fit_res • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -116,7 +116,7 @@ Value
diff --git a/docs/reference/mask_xy.html b/docs/reference/mask_xy.html
index 11bb577c..b0d38619 100644
--- a/docs/reference/mask_xy.html
+++ b/docs/reference/mask_xy.html
@@ -1,5 +1,5 @@
-Mask an MRSI dataset in the x-y direction — mask_xy • Spectroscopy Analysis Tools (spant) Mask an MRSI dataset in the x-y direction — mask_xy • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/mask_xy_corners.html b/docs/reference/mask_xy_corners.html
index 09b16cd2..2d13839d 100644
--- a/docs/reference/mask_xy_corners.html
+++ b/docs/reference/mask_xy_corners.html
@@ -1,5 +1,5 @@
-Mask the four corners of an MRSI dataset in the x-y plane. — mask_xy_corners • Spectroscopy Analysis Tools (spant) Mask the four corners of an MRSI dataset in the x-y plane. — mask_xy_corners • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/mask_xy_ellipse.html b/docs/reference/mask_xy_ellipse.html
index 1d8b02e4..e2e749ef 100644
--- a/docs/reference/mask_xy_ellipse.html
+++ b/docs/reference/mask_xy_ellipse.html
@@ -1,7 +1,5 @@
-Mask the voxels outside an elliptical region spanning the MRSI dataset in the
-x-y plane. — mask_xy_ellipse • Spectroscopy Analysis Tools (spant) Mask the voxels outside an elliptical region spanning the MRSI dataset in the x-y plane. — mask_xy_ellipse • Spectroscopy Analysis Tools (spant) Mask a 2D MRSI dataset in the x-y dimension. — mask_xy_mat • Spectroscopy Analysis Tools (spant) Mask a 2D MRSI dataset in the x-y dimension. — mask_xy_mat • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Value
diff --git a/docs/reference/mat2mrs_data.html b/docs/reference/mat2mrs_data.html
index 2e2895f3..ae55665f 100644
--- a/docs/reference/mat2mrs_data.html
+++ b/docs/reference/mat2mrs_data.html
@@ -1,7 +1,5 @@
-Convert a matrix (with spectral points in the column dimension and dynamics
-in the row dimensions) into a mrs_data object. — mat2mrs_data • Spectroscopy Analysis Tools (spant) Convert a matrix (with spectral points in the column dimension and dynamics in the row dimensions) into a mrs_data object. — mat2mrs_data • Spectroscopy Analysis Tools (spant) Matrix exponential function taken from complexplus package to reduce the
-number of spant dependencies. — matexp • Spectroscopy Analysis Tools (spant) Matrix exponential function taken from complexplus package to reduce the number of spant dependencies. — matexp • Spectroscopy Analysis Tools (spant) Apply the max operator to an MRS dataset. — max_mrs • Spectroscopy Analysis Tools (spant) Apply the max operator to an MRS dataset. — max_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/max_mrs_interp.html b/docs/reference/max_mrs_interp.html
index e4474764..52e63f3e 100644
--- a/docs/reference/max_mrs_interp.html
+++ b/docs/reference/max_mrs_interp.html
@@ -1,5 +1,5 @@
-Apply the max operator to an interpolated MRS dataset. — max_mrs_interp • Spectroscopy Analysis Tools (spant) Apply the max operator to an interpolated MRS dataset. — max_mrs_interp • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/mean.list.html b/docs/reference/mean.list.html
index b8eb3463..048306fd 100644
--- a/docs/reference/mean.list.html
+++ b/docs/reference/mean.list.html
@@ -1,5 +1,5 @@
-Calculate the mean spectrum from an mrs_data object. — mean.list • Spectroscopy Analysis Tools (spant) Calculate the mean spectrum from an mrs_data object. — mean.list • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/mean.mrs_data.html b/docs/reference/mean.mrs_data.html
index 5531a28d..79515014 100644
--- a/docs/reference/mean.mrs_data.html
+++ b/docs/reference/mean.mrs_data.html
@@ -1,5 +1,5 @@
-Calculate the mean spectrum from an mrs_data object. — mean.mrs_data • Spectroscopy Analysis Tools (spant) Calculate the mean spectrum from an mrs_data object. — mean.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/mean_dyn_blocks.html b/docs/reference/mean_dyn_blocks.html
index 10467098..4c042448 100644
--- a/docs/reference/mean_dyn_blocks.html
+++ b/docs/reference/mean_dyn_blocks.html
@@ -1,5 +1,5 @@
-Calculate the mean of adjacent dynamic scans. — mean_dyn_blocks • Spectroscopy Analysis Tools (spant) Calculate the mean of adjacent dynamic scans. — mean_dyn_blocks • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/mean_dyn_pairs.html b/docs/reference/mean_dyn_pairs.html
index 63e909ea..1a241126 100644
--- a/docs/reference/mean_dyn_pairs.html
+++ b/docs/reference/mean_dyn_pairs.html
@@ -1,5 +1,5 @@
-Calculate the pairwise means across a dynamic data set. — mean_dyn_pairs • Spectroscopy Analysis Tools (spant) Calculate the pairwise means across a dynamic data set. — mean_dyn_pairs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/mean_dyns.html b/docs/reference/mean_dyns.html
index 73fdbfa7..0daa27df 100644
--- a/docs/reference/mean_dyns.html
+++ b/docs/reference/mean_dyns.html
@@ -1,5 +1,5 @@
-Calculate the mean dynamic data. — mean_dyns • Spectroscopy Analysis Tools (spant) Calculate the mean dynamic data. — mean_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/mean_mrs_list.html b/docs/reference/mean_mrs_list.html
index 808b6c50..10d842c0 100644
--- a/docs/reference/mean_mrs_list.html
+++ b/docs/reference/mean_mrs_list.html
@@ -1,5 +1,5 @@
-Return the mean of a list of mrs_data objects. — mean_mrs_list • Spectroscopy Analysis Tools (spant) Return the mean of a list of mrs_data objects. — mean_mrs_list • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/mean_vec_blocks.html b/docs/reference/mean_vec_blocks.html
index 8fc92eaa..dd78b122 100644
--- a/docs/reference/mean_vec_blocks.html
+++ b/docs/reference/mean_vec_blocks.html
@@ -1,5 +1,5 @@
-Calculate the mean of adjacent blocks in a vector. — mean_vec_blocks • Spectroscopy Analysis Tools (spant) Calculate the mean of adjacent blocks in a vector. — mean_vec_blocks • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/median_dyns.html b/docs/reference/median_dyns.html
index 1039d4b5..9a085b10 100644
--- a/docs/reference/median_dyns.html
+++ b/docs/reference/median_dyns.html
@@ -1,5 +1,5 @@
-Calculate the median dynamic data. — median_dyns • Spectroscopy Analysis Tools (spant) Calculate the median dynamic data. — median_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/mod_td.html b/docs/reference/mod_td.html
index 76ad0a40..141ef09e 100644
--- a/docs/reference/mod_td.html
+++ b/docs/reference/mod_td.html
@@ -1,5 +1,5 @@
-Apply the Modulus operator to the time-domain MRS signal. — mod_td • Spectroscopy Analysis Tools (spant) Apply the Modulus operator to the time-domain MRS signal. — mod_td • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/mrs_data2basis.html b/docs/reference/mrs_data2basis.html
index 62f7d749..11797b91 100644
--- a/docs/reference/mrs_data2basis.html
+++ b/docs/reference/mrs_data2basis.html
@@ -1,7 +1,5 @@
-Convert an mrs_data object to basis object - where basis signals are spread
-across the dynamic dimension in the MRS data. — mrs_data2basis • Spectroscopy Analysis Tools (spant) Convert an mrs_data object to basis object - where basis signals are spread across the dynamic dimension in the MRS data. — mrs_data2basis • Spectroscopy Analysis Tools (spant) Create a BIDS file structure from a vector of MRS data paths or list of mrs_data objects. — mrs_data2bids • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Create a BIDS file structure from a vector of MRS data paths or list of mrs_data objects.
+ Source: R/fmrs.R
+ mrs_data2bids.Rd
+
+
+
+ Create a BIDS file structure from a vector of MRS data paths or list of
+mrs_data objects.
+
+
+
+ mrs_data2bids(
+ mrs_data,
+ output_dir,
+ suffix = NULL,
+ sub = NULL,
+ ses = NULL,
+ task = NULL,
+ acq = NULL,
+ nuc = NULL,
+ voi = NULL,
+ rec = NULL,
+ run = NULL,
+ echo = NULL,
+ inv = NULL,
+ skip_existing = TRUE
+)
+
+
+
+ Arguments
+ - mrs_data
+vector of MRS data paths or list of mrs_data objects.
- output_dir
+the base directory to create the BIDS structure.
- suffix
+optional vector of file suffixes. Default behaviour is to
+automatically determine these from the input data, however it is recommended
+that they are specified to allow more efficient skipping of existing data.
- sub
+optional vector of subject labels. If not specified, these will be
+automatically generated as a series of increasing zero-padded integer values
+corresponding to the mrs_data input indices.
- ses
+optional vector of session labels.
- task
+optional vector of task labels.
- acq
+optional vector of acquisition labels.
- nuc
+optional vector of nucleus labels.
- voi
+optional vector of volume of interest labels.
- rec
+optional vector of reconstruction labels.
- run
+optional vector of run indices.
- echo
+optional vector of echo time indices.
- inv
+optional vector of inversion indices.
- skip_existing
+skip any data files that have already been converted.
+Defaults to TRUE, set to FALSE to force an overwrite of any existing data
+files.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/mrs_data2mat.html b/docs/reference/mrs_data2mat.html
index cf5ff28c..9e47688a 100644
--- a/docs/reference/mrs_data2mat.html
+++ b/docs/reference/mrs_data2mat.html
@@ -1,7 +1,5 @@
-Convert mrs_data object to a matrix, with spectral points in the column
-dimension and dynamics in the row dimension. — mrs_data2mat • Spectroscopy Analysis Tools (spant) Convert mrs_data object to a matrix, with spectral points in the column dimension and dynamics in the row dimension. — mrs_data2mat • Spectroscopy Analysis Tools (spant) Convert mrs_data object to a matrix, with spectral points in the column dimension and dynamics in the row dimension. — mrs_data2spec_mat • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Convert mrs_data object to a matrix, with spectral points in the column dimension and dynamics in the row dimension.
+ Source: R/mrs_data_proc.R
+ mrs_data2spec_mat.Rd
+
+
+
+ Convert mrs_data object to a matrix, with spectral points in the column
+dimension and dynamics in the row dimension.
+
+
+
+ mrs_data2spec_mat(mrs_data, collapse = TRUE)
+
+
+
+ Arguments
+ - mrs_data
+MRS data object or list of MRS data objects.
- collapse
+collapse all other dimensions along the dynamic dimension, eg
+a 16x16 MRSI grid would be first collapsed across 256 dynamic scans.
+
+ Value
+
+
+MRS data matrix.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/mrs_data2vec.html b/docs/reference/mrs_data2vec.html
index fb172d68..a1fd654d 100644
--- a/docs/reference/mrs_data2vec.html
+++ b/docs/reference/mrs_data2vec.html
@@ -1,5 +1,5 @@
-Convert mrs_data object to a vector. — mrs_data2vec • Spectroscopy Analysis Tools (spant) Convert mrs_data object to a vector. — mrs_data2vec • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -126,7 +126,7 @@ Value
diff --git a/docs/reference/mvfftshift.html b/docs/reference/mvfftshift.html
index 92b0841b..976b3410 100644
--- a/docs/reference/mvfftshift.html
+++ b/docs/reference/mvfftshift.html
@@ -1,7 +1,5 @@
-Perform a fftshift on a matrix, with each column replaced by its shifted
-result. — mvfftshift • Spectroscopy Analysis Tools (spant) Perform a fftshift on a matrix, with each column replaced by its shifted result. — mvfftshift • Spectroscopy Analysis Tools (spant) Perform an ifftshift on a matrix, with each column replaced by its shifted
-result. — mvifftshift • Spectroscopy Analysis Tools (spant) Perform an ifftshift on a matrix, with each column replaced by its shifted result. — mvifftshift • Spectroscopy Analysis Tools (spant) Print fit coordinates from a single index. — n2coord • Spectroscopy Analysis Tools (spant) Print fit coordinates from a single index. — n2coord • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/nifti_flip_lr.html b/docs/reference/nifti_flip_lr.html
index 730abe3c..19860b3c 100644
--- a/docs/reference/nifti_flip_lr.html
+++ b/docs/reference/nifti_flip_lr.html
@@ -1,9 +1,5 @@
-Flip the x data dimension order of a nifti image. This corresponds to
-flipping MRI data in the left-right direction, assuming the data in save in
-neurological format (can check with fslorient program). — nifti_flip_lr • Spectroscopy Analysis Tools (spant) Flip the x data dimension order of a nifti image. This corresponds to flipping MRI data in the left-right direction, assuming the data in save in neurological format (can check with fslorient program). — nifti_flip_lr • Spectroscopy Analysis Tools (spant) Export a one-page pdf of a single fit result — one_page_pdf • Spectroscopy Analysis Tools (spant) Export a one-page pdf of a single fit result — one_page_pdf • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -108,7 +108,7 @@ Arguments
diff --git a/docs/reference/ortho3.html b/docs/reference/ortho3.html
index 13ade97d..5d7dd2fd 100644
--- a/docs/reference/ortho3.html
+++ b/docs/reference/ortho3.html
@@ -1,5 +1,5 @@
-Display an orthographic projection plot of a nifti object. — ortho3 • Spectroscopy Analysis Tools (spant) Display an orthographic projection plot of a nifti object. — ortho3 • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -172,7 +172,7 @@ Arguments
diff --git a/docs/reference/ortho3_inter.html b/docs/reference/ortho3_inter.html
index 090cc5e5..15948899 100644
--- a/docs/reference/ortho3_inter.html
+++ b/docs/reference/ortho3_inter.html
@@ -1,5 +1,5 @@
-Display an interactive orthographic projection plot of a nifti object. — ortho3_inter • Spectroscopy Analysis Tools (spant) Display an interactive orthographic projection plot of a nifti object. — ortho3_inter • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -132,7 +132,7 @@ Arguments
diff --git a/docs/reference/peak_info.html b/docs/reference/peak_info.html
index 09058bd8..41c8ffaf 100644
--- a/docs/reference/peak_info.html
+++ b/docs/reference/peak_info.html
@@ -1,7 +1,5 @@
-Search for the highest peak in a spectral region and return the frequency,
-height and FWHM. — peak_info • Spectroscopy Analysis Tools (spant) Search for the highest peak in a spectral region and return the frequency, height and FWHM. — peak_info • Spectroscopy Analysis Tools (spant) Papoulis-Gerchberg (PG) algorithm method for k-space extrapolation. — pg_extrap_xy • Spectroscopy Analysis Tools (spant) Papoulis-Gerchberg (PG) algorithm method for k-space extrapolation. — pg_extrap_xy • Spectroscopy Analysis Tools (spant) Apply phasing parameters to MRS data. — phase • Spectroscopy Analysis Tools (spant) Apply phasing parameters to MRS data. — phase • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/phase_ref_1h_brain.html b/docs/reference/phase_ref_1h_brain.html
new file mode 100644
index 00000000..8707a74a
--- /dev/null
+++ b/docs/reference/phase_ref_1h_brain.html
@@ -0,0 +1,131 @@
+
+Corrected zero order phase and chemical shift offset in 1H MRS data from the brain. — phase_ref_1h_brain • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Corrected zero order phase and chemical shift offset in 1H MRS data from the brain.
+ Source: R/rats.R
+ phase_ref_1h_brain.Rd
+
+
+
+ Corrected zero order phase and chemical shift offset in 1H MRS data from the
+brain.
+
+
+
+ phase_ref_1h_brain(mrs_data, mean_ref = FALSE, ret_corr_only = TRUE)
+
+
+
+ Arguments
+ - mrs_data
+MRS data to be corrected.
- mean_ref
+apply the phase and offset of the mean spectrum to all
+others. Default is FALSE.
- ret_corr_only
+return the corrected data only.
+
+ Value
+
+
+corrected MRS data.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/plot.fit_result.html b/docs/reference/plot.fit_result.html
index e54d3bc1..836a53ee 100644
--- a/docs/reference/plot.fit_result.html
+++ b/docs/reference/plot.fit_result.html
@@ -1,5 +1,5 @@
-Plot the fitting results of an object of class fit_result. — plot.fit_result • Spectroscopy Analysis Tools (spant) Plot the fitting results of an object of class fit_result. — plot.fit_result • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -207,7 +207,7 @@ Arguments
diff --git a/docs/reference/plot.mrs_data.html b/docs/reference/plot.mrs_data.html
index fabcc35b..bb2ec651 100644
--- a/docs/reference/plot.mrs_data.html
+++ b/docs/reference/plot.mrs_data.html
@@ -1,5 +1,5 @@
-Plotting method for objects of class mrs_data. — plot.mrs_data • Spectroscopy Analysis Tools (spant) Plotting method for objects of class mrs_data. — plot.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -287,7 +287,7 @@ Arguments
diff --git a/docs/reference/plot_bc.html b/docs/reference/plot_bc.html
index 4f8309b4..b48142cc 100644
--- a/docs/reference/plot_bc.html
+++ b/docs/reference/plot_bc.html
@@ -1,5 +1,5 @@
-Convenience function to plot a baseline estimate with the original data. — plot_bc • Spectroscopy Analysis Tools (spant) Convenience function to plot a baseline estimate with the original data. — plot_bc • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -108,7 +108,7 @@ Arguments
diff --git a/docs/reference/plot_reg.html b/docs/reference/plot_reg.html
index ae1acbe7..2addb2f6 100644
--- a/docs/reference/plot_reg.html
+++ b/docs/reference/plot_reg.html
@@ -1,5 +1,5 @@
-Plot regressors as an image. — plot_reg • Spectroscopy Analysis Tools (spant) Plot regressors as an image. — plot_reg • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/plot_slice_fit.html b/docs/reference/plot_slice_fit.html
index fbc7b560..57f1af8a 100644
--- a/docs/reference/plot_slice_fit.html
+++ b/docs/reference/plot_slice_fit.html
@@ -1,5 +1,5 @@
-Plot a 2D slice from an MRSI fit result object. — plot_slice_fit • Spectroscopy Analysis Tools (spant) Plot a 2D slice from an MRSI fit result object. — plot_slice_fit • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -129,7 +129,7 @@ Arguments
diff --git a/docs/reference/plot_slice_fit_inter.html b/docs/reference/plot_slice_fit_inter.html
index 4eed104a..da105a7d 100644
--- a/docs/reference/plot_slice_fit_inter.html
+++ b/docs/reference/plot_slice_fit_inter.html
@@ -1,5 +1,5 @@
-Plot a 2D slice from an MRSI fit result object. — plot_slice_fit_inter • Spectroscopy Analysis Tools (spant) Plot a 2D slice from an MRSI fit result object. — plot_slice_fit_inter • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -134,7 +134,7 @@ Arguments
diff --git a/docs/reference/plot_slice_map.html b/docs/reference/plot_slice_map.html
index 553e9ac8..ffb2a134 100644
--- a/docs/reference/plot_slice_map.html
+++ b/docs/reference/plot_slice_map.html
@@ -1,5 +1,5 @@
-Plot a slice from a 7 dimensional array. — plot_slice_map • Spectroscopy Analysis Tools (spant) Plot a slice from a 7 dimensional array. — plot_slice_map • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -153,7 +153,7 @@ Arguments
diff --git a/docs/reference/plot_slice_map_inter.html b/docs/reference/plot_slice_map_inter.html
index 40d33b42..90968f66 100644
--- a/docs/reference/plot_slice_map_inter.html
+++ b/docs/reference/plot_slice_map_inter.html
@@ -1,7 +1,5 @@
-Plot an interactive slice map from a data array where voxels can be selected
-to display a corresponding spectrum. — plot_slice_map_inter • Spectroscopy Analysis Tools (spant) Plot an interactive slice map from a data array where voxels can be selected to display a corresponding spectrum. — plot_slice_map_inter • Spectroscopy Analysis Tools (spant) Plot the spectral standard deviation. — plot_spec_sd • Spectroscopy Analysis Tools (spant) Plot the spectral standard deviation. — plot_spec_sd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Arguments
diff --git a/docs/reference/plot_voi_overlay.html b/docs/reference/plot_voi_overlay.html
index 9a782e88..bbbbf35e 100644
--- a/docs/reference/plot_voi_overlay.html
+++ b/docs/reference/plot_voi_overlay.html
@@ -1,5 +1,5 @@
-Plot a volume as an image overlay. — plot_voi_overlay • Spectroscopy Analysis Tools (spant) Plot a volume as an image overlay. — plot_voi_overlay • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -116,7 +116,7 @@ Arguments
diff --git a/docs/reference/plot_voi_overlay_seg.html b/docs/reference/plot_voi_overlay_seg.html
index 3d4e74ff..0e800ff2 100644
--- a/docs/reference/plot_voi_overlay_seg.html
+++ b/docs/reference/plot_voi_overlay_seg.html
@@ -1,5 +1,5 @@
-Plot a volume as an overlay on a segmented brain volume. — plot_voi_overlay_seg • Spectroscopy Analysis Tools (spant) Plot a volume as an overlay on a segmented brain volume. — plot_voi_overlay_seg • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Arguments
diff --git a/docs/reference/ppm.html b/docs/reference/ppm.html
index c352327a..ee4696e2 100644
--- a/docs/reference/ppm.html
+++ b/docs/reference/ppm.html
@@ -1,5 +1,5 @@
-Return the ppm scale of an MRS dataset or fit result. — ppm • Spectroscopy Analysis Tools (spant) Return the ppm scale of an MRS dataset or fit result. — ppm • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -132,7 +132,7 @@ Value
diff --git a/docs/reference/precomp.html b/docs/reference/precomp.html
index 822d7336..df3d2c6c 100644
--- a/docs/reference/precomp.html
+++ b/docs/reference/precomp.html
@@ -1,7 +1,5 @@
-Save function results to file and load on subsequent calls to avoid repeat
-computation. — precomp • Spectroscopy Analysis Tools (spant) Save function results to file and load on subsequent calls to avoid repeat computation. — precomp • Spectroscopy Analysis Tools (spant) Preprocess and perform quality assessment of a single SVS data set. — preproc_svs • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Preprocess and perform quality assessment of a single SVS data set.
+ Source: R/fmrs.R
+ preproc_svs.Rd
+
+
+
+ Preprocess and perform quality assessment of a single SVS data set.
+
+
+
+ preproc_svs(path, label = NULL, output_dir = NULL, ref_inds = NULL)
+
+
+
+ Arguments
+ - path
+path to the fMRS data file or IMA directory.
- label
+a label to describe the data set.
- output_dir
+output directory.
- ref_inds
+a vector of 1-based indices for any water reference dynamic
+scans.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/preproc_svs_dataset.html b/docs/reference/preproc_svs_dataset.html
new file mode 100644
index 00000000..07c3a29b
--- /dev/null
+++ b/docs/reference/preproc_svs_dataset.html
@@ -0,0 +1,148 @@
+
+Preprocess and perform quality assessment of one or more SVS data sets. — preproc_svs_dataset • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Preprocess and perform quality assessment of one or more SVS data sets.
+ Source: R/fmrs.R
+ preproc_svs_dataset.Rd
+
+
+
+ Preprocess and perform quality assessment of one or more SVS data sets.
+
+
+
+ preproc_svs_dataset(
+ paths,
+ labels = NULL,
+ output_dir = "spant_analysis",
+ exclude_labels = NULL,
+ overwrite = FALSE,
+ ref_inds = NULL,
+ return_results = FALSE
+)
+
+
+
+ Arguments
+ - paths
+paths to the fMRS data file or IMA directory.
- labels
+labels to describe each data set.
- output_dir
+output directory.
- exclude_labels
+vector of labels of scans to exclude, eg poor quality
+data.
- overwrite
+overwrite saved results, defaults to FALSE.
- ref_inds
+a vector of 1-based indices for any water reference dynamic
+scans.
- return_results
+function will return key outputs, defaults to FALSE.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/print.fit_result.html b/docs/reference/print.fit_result.html
index 297f28dc..5f434e57 100644
--- a/docs/reference/print.fit_result.html
+++ b/docs/reference/print.fit_result.html
@@ -1,5 +1,5 @@
-Print a summary of an object of class fit_result. — print.fit_result • Spectroscopy Analysis Tools (spant) Print a summary of an object of class fit_result. — print.fit_result • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -105,7 +105,7 @@ Arguments
diff --git a/docs/reference/print.mrs_data.html b/docs/reference/print.mrs_data.html
index 51199017..e1561eb2 100644
--- a/docs/reference/print.mrs_data.html
+++ b/docs/reference/print.mrs_data.html
@@ -1,5 +1,5 @@
-Print a summary of mrs_data parameters. — print.mrs_data • Spectroscopy Analysis Tools (spant) Print a summary of mrs_data parameters. — print.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -109,7 +109,7 @@ Arguments
diff --git a/docs/reference/qn_states.html b/docs/reference/qn_states.html
index 0f42f2f9..d7aa6715 100644
--- a/docs/reference/qn_states.html
+++ b/docs/reference/qn_states.html
@@ -1,5 +1,5 @@
-Get the quantum coherence matrix for a spin system. — qn_states • Spectroscopy Analysis Tools (spant) Get the quantum coherence matrix for a spin system. — qn_states • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/rats.html b/docs/reference/rats.html
index 5a39a396..93585e08 100644
--- a/docs/reference/rats.html
+++ b/docs/reference/rats.html
@@ -1,5 +1,5 @@
-Robust Alignment to a Target Spectrum (RATS). — rats • Spectroscopy Analysis Tools (spant) Robust Alignment to a Target Spectrum (RATS). — rats • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -207,7 +207,7 @@ Value
diff --git a/docs/reference/re_weighting.html b/docs/reference/re_weighting.html
index d21caf21..8b0b070a 100644
--- a/docs/reference/re_weighting.html
+++ b/docs/reference/re_weighting.html
@@ -1,5 +1,5 @@
-Apply a weighting to the FID to enhance spectral resolution. — re_weighting • Spectroscopy Analysis Tools (spant) Apply a weighting to the FID to enhance spectral resolution. — re_weighting • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/read_basis.html b/docs/reference/read_basis.html
index da9b94af..eb6f8557 100644
--- a/docs/reference/read_basis.html
+++ b/docs/reference/read_basis.html
@@ -1,5 +1,5 @@
-Read a basis file in LCModel .basis format. — read_basis • Spectroscopy Analysis Tools (spant) Read a basis file in LCModel .basis format. — read_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/read_ima_coil_dir.html b/docs/reference/read_ima_coil_dir.html
index 28c02de0..4f073cd8 100644
--- a/docs/reference/read_ima_coil_dir.html
+++ b/docs/reference/read_ima_coil_dir.html
@@ -1,9 +1,5 @@
-Read a directory containing Siemens MRS IMA files and combine along the coil
-dimension. Note that the coil ID is inferred from the sorted file name and
-should be checked when consistency is required between two directories. — read_ima_coil_dir • Spectroscopy Analysis Tools (spant) Read a directory containing Siemens MRS IMA files and combine along the coil dimension. Note that the coil ID is inferred from the sorted file name and should be checked when consistency is required between two directories. — read_ima_coil_dir • Spectroscopy Analysis Tools (spant) Read a directory containing Siemens MRS IMA files and combine along the
-dynamic dimension. Note that the coil ID is inferred from the sorted file
-name and should be checked when consistency is required. — read_ima_dyn_dir • Spectroscopy Analysis Tools (spant) Read a directory containing Siemens MRS IMA files and combine along the dynamic dimension. Note that the coil ID is inferred from the sorted file name and should be checked when consistency is required. — read_ima_dyn_dir • Spectroscopy Analysis Tools (spant) Read an LCModel formatted coord file containing fit information. — read_lcm_coord • Spectroscopy Analysis Tools (spant) Read an LCModel formatted coord file containing fit information. — read_lcm_coord • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -107,7 +107,7 @@ Value
diff --git a/docs/reference/read_mrs.html b/docs/reference/read_mrs.html
index 3ac2a36b..2cf36b20 100644
--- a/docs/reference/read_mrs.html
+++ b/docs/reference/read_mrs.html
@@ -1,5 +1,5 @@
-Read MRS data from a file. — read_mrs • Spectroscopy Analysis Tools (spant) Read MRS data from a file. — read_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -88,7 +88,8 @@ Read MRS data from a file.
full_fid = FALSE,
omit_svs_ref_scans = TRUE,
verbose = FALSE,
- extra = NULL
+ extra = NULL,
+ fid_filt_dist = NULL
)
@@ -140,6 +141,13 @@ Arguments
an optional data frame to provide additional variables for use
in subsequent analysis steps, eg id or grouping variables.
fid_filt_dist
+indicate if the data has a distorted FID due to a
+brick-wall filter being used to downsample the data. Default is to auto
+detect this from the data, but TRUE or FALSE options can be given to override
+detection.
Value
@@ -183,7 +191,7 @@ Examples
diff --git a/docs/reference/read_mrs_tqn.html b/docs/reference/read_mrs_tqn.html
index 5766362f..84bdaf3a 100644
--- a/docs/reference/read_mrs_tqn.html
+++ b/docs/reference/read_mrs_tqn.html
@@ -1,5 +1,5 @@
-Read MRS data using the TARQUIN software package. — read_mrs_tqn • Spectroscopy Analysis Tools (spant) Read MRS data using the TARQUIN software package. — read_mrs_tqn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -131,7 +131,7 @@ Examples
diff --git a/docs/reference/read_pulse_ascii.html b/docs/reference/read_pulse_ascii.html
index c9e0d43c..ab11c9cc 100644
--- a/docs/reference/read_pulse_ascii.html
+++ b/docs/reference/read_pulse_ascii.html
@@ -1,5 +1,5 @@
-Read an ASCII formatted pulse file. — read_pulse_ascii • Spectroscopy Analysis Tools (spant) Read an ASCII formatted pulse file. — read_pulse_ascii • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/read_pulse_bruker.html b/docs/reference/read_pulse_bruker.html
index c92bf76a..dbe9073b 100644
--- a/docs/reference/read_pulse_bruker.html
+++ b/docs/reference/read_pulse_bruker.html
@@ -1,5 +1,5 @@
-Read a Bruker formatted pulse file — read_pulse_bruker • Spectroscopy Analysis Tools (spant) Read a Bruker formatted pulse file — read_pulse_bruker • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/read_pulse_pta.html b/docs/reference/read_pulse_pta.html
index 72e1b6d4..a0fac3c3 100644
--- a/docs/reference/read_pulse_pta.html
+++ b/docs/reference/read_pulse_pta.html
@@ -1,5 +1,5 @@
-Read a .pta formatted pulse file compatible with Siemens PulseTool. — read_pulse_pta • Spectroscopy Analysis Tools (spant) Read a .pta formatted pulse file compatible with Siemens PulseTool. — read_pulse_pta • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/read_siemens_txt_hdr.html b/docs/reference/read_siemens_txt_hdr.html
index 23fb8c70..3a17d87c 100644
--- a/docs/reference/read_siemens_txt_hdr.html
+++ b/docs/reference/read_siemens_txt_hdr.html
@@ -1,5 +1,5 @@
-Read the text format header found in Siemens IMA and TWIX data files. — read_siemens_txt_hdr • Spectroscopy Analysis Tools (spant) Read the text format header found in Siemens IMA and TWIX data files. — read_siemens_txt_hdr • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -78,7 +78,7 @@ Read the text format header found in Siemens IMA and TWIX data files.
- read_siemens_txt_hdr(input, version = "vd", verbose, offset = 0)
+ read_siemens_txt_hdr(input, version = "vd", verbose = FALSE, offset = 0)
@@ -118,7 +118,7 @@ Value
diff --git a/docs/reference/read_tqn_fit.html b/docs/reference/read_tqn_fit.html
index 4da6c25e..a1630420 100644
--- a/docs/reference/read_tqn_fit.html
+++ b/docs/reference/read_tqn_fit.html
@@ -1,5 +1,5 @@
-Reader for csv fit results generated by TARQUIN. — read_tqn_fit • Spectroscopy Analysis Tools (spant) Reader for csv fit results generated by TARQUIN. — read_tqn_fit • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -113,7 +113,7 @@ Examples
diff --git a/docs/reference/read_tqn_result.html b/docs/reference/read_tqn_result.html
index 36659714..68a3e98c 100644
--- a/docs/reference/read_tqn_result.html
+++ b/docs/reference/read_tqn_result.html
@@ -1,5 +1,5 @@
-Reader for csv results generated by TARQUIN. — read_tqn_result • Spectroscopy Analysis Tools (spant) Reader for csv results generated by TARQUIN. — read_tqn_result • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -117,7 +117,7 @@ Examples
diff --git a/docs/reference/recon_imag.html b/docs/reference/recon_imag.html
index d2a72225..5bc3b1eb 100644
--- a/docs/reference/recon_imag.html
+++ b/docs/reference/recon_imag.html
@@ -1,7 +1,5 @@
-Reconstruct complex time-domain data from the real part of frequency-domain
-data. — recon_imag • Spectroscopy Analysis Tools (spant) Reconstruct complex time-domain data from the real part of frequency-domain data. — recon_imag • Spectroscopy Analysis Tools (spant) Reconstruct complex time-domain data from the real part of frequency-domain
-data. — recon_imag_vec • Spectroscopy Analysis Tools (spant) Reconstruct complex time-domain data from the real part of frequency-domain data. — recon_imag_vec • Spectroscopy Analysis Tools (spant) Reconstruct 2D MRSI data from a twix file loaded with read_mrs. — recon_twix_2d_mrsi • Spectroscopy Analysis Tools (spant) Reconstruct 2D MRSI data from a twix file loaded with read_mrs. — recon_twix_2d_mrsi • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/rectangular_mask.html b/docs/reference/rectangular_mask.html
index a2117283..6e469bc9 100644
--- a/docs/reference/rectangular_mask.html
+++ b/docs/reference/rectangular_mask.html
@@ -1,5 +1,5 @@
-Create a rectangular mask stored as a matrix of logical values. — rectangular_mask • Spectroscopy Analysis Tools (spant) Create a rectangular mask stored as a matrix of logical values. — rectangular_mask • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -130,7 +130,7 @@ Value
diff --git a/docs/reference/reexports.html b/docs/reference/reexports.html
index 694a75d1..a59e8379 100644
--- a/docs/reference/reexports.html
+++ b/docs/reference/reexports.html
@@ -1,5 +1,5 @@
-Objects exported from other packages — reexports • Spectroscopy Analysis Tools (spant) Objects exported from other packages — reexports • Spectroscopy Analysis Tools (spant)
Spectroscopy Analysis Tools (spant)
- 2.21.0
+ 2.22.0
@@ -103,7 +103,7 @@ Objects exported from other packages
diff --git a/docs/reference/rep_array_dim.html b/docs/reference/rep_array_dim.html
index b9c49b4a..48c0a5ed 100644
--- a/docs/reference/rep_array_dim.html
+++ b/docs/reference/rep_array_dim.html
@@ -1,5 +1,5 @@
-Repeat an array over a given dimension. — rep_array_dim • Spectroscopy Analysis Tools (spant) Repeat an array over a given dimension. — rep_array_dim • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/rep_dyn.html b/docs/reference/rep_dyn.html
index 6bbfb0ef..89a4bb9b 100644
--- a/docs/reference/rep_dyn.html
+++ b/docs/reference/rep_dyn.html
@@ -1,5 +1,5 @@
-Replicate a scan in the dynamic dimension. — rep_dyn • Spectroscopy Analysis Tools (spant) Replicate a scan in the dynamic dimension. — rep_dyn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/rep_mrs.html b/docs/reference/rep_mrs.html
index 67730b5c..becb8f00 100644
--- a/docs/reference/rep_mrs.html
+++ b/docs/reference/rep_mrs.html
@@ -1,5 +1,5 @@
-Replicate a scan over a given dimension. — rep_mrs • Spectroscopy Analysis Tools (spant) Replicate a scan over a given dimension. — rep_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -138,7 +138,7 @@ Value
diff --git a/docs/reference/resample_basis.html b/docs/reference/resample_basis.html
index b0f2ab17..c7a6222a 100644
--- a/docs/reference/resample_basis.html
+++ b/docs/reference/resample_basis.html
@@ -1,5 +1,5 @@
-Resample a basis-set to match a mrs_data acquisition. — resample_basis • Spectroscopy Analysis Tools (spant) Resample a basis-set to match a mrs_data acquisition. — resample_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -116,7 +116,7 @@ Value
diff --git a/docs/reference/resample_img.html b/docs/reference/resample_img.html
index f1e7beaf..b0cc8f71 100644
--- a/docs/reference/resample_img.html
+++ b/docs/reference/resample_img.html
@@ -1,5 +1,5 @@
-Resample an image to match a target image space. — resample_img • Spectroscopy Analysis Tools (spant) Resample an image to match a target image space. — resample_img • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/resample_voi.html b/docs/reference/resample_voi.html
index 8fbfa836..a29ab096 100644
--- a/docs/reference/resample_voi.html
+++ b/docs/reference/resample_voi.html
@@ -1,7 +1,5 @@
-Resample a VOI to match a target image space using nearest-neighbour
-interpolation. — resample_voi • Spectroscopy Analysis Tools (spant) Resample a VOI to match a target image space using nearest-neighbour interpolation. — resample_voi • Spectroscopy Analysis Tools (spant) Reslice a nifti object to match the orientation of mrs data. — reslice_to_mrs • Spectroscopy Analysis Tools (spant) Reslice a nifti object to match the orientation of mrs data. — reslice_to_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/reson_table2mrs_data.html b/docs/reference/reson_table2mrs_data.html
index d75579ee..c5a2167a 100644
--- a/docs/reference/reson_table2mrs_data.html
+++ b/docs/reference/reson_table2mrs_data.html
@@ -1,5 +1,5 @@
-Generate mrs_data from a table of single Lorentzian resonances. — reson_table2mrs_data • Spectroscopy Analysis Tools (spant) Generate mrs_data from a table of single Lorentzian resonances. — reson_table2mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -119,7 +119,7 @@ Value
diff --git a/docs/reference/rm_dyns.html b/docs/reference/rm_dyns.html
index 5d5ef692..573e1f51 100644
--- a/docs/reference/rm_dyns.html
+++ b/docs/reference/rm_dyns.html
@@ -1,5 +1,5 @@
-Remove a subset of dynamic scans. — rm_dyns • Spectroscopy Analysis Tools (spant) Remove a subset of dynamic scans. — rm_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/scale_amp_molal.html b/docs/reference/scale_amp_molal.html
index aaeee1f2..7acb8cb0 100644
--- a/docs/reference/scale_amp_molal.html
+++ b/docs/reference/scale_amp_molal.html
@@ -1,7 +1,5 @@
-Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water). — scale_amp_molal • Spectroscopy Analysis Tools (spant) Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / kg of tissue water). — scale_amp_molal • Spectroscopy Analysis Tools (spant)
Spectroscopy Analysis Tools (spant)
- 2.21.0
+ 2.22.0
@@ -76,8 +74,7 @@
- Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water).
+ Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / kg of tissue water).
Source: R/amp_scaling.R
scale_amp_molal.Rd
@@ -163,7 +160,7 @@ Value
diff --git a/docs/reference/scale_amp_molal_pvc.html b/docs/reference/scale_amp_molal_pvc.html
index 962d6afc..4d194abd 100644
--- a/docs/reference/scale_amp_molal_pvc.html
+++ b/docs/reference/scale_amp_molal_pvc.html
@@ -1,7 +1,5 @@
-Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water). — scale_amp_molal_pvc • Spectroscopy Analysis Tools (spant)
@@ -75,8 +73,7 @@
- Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water).
+ Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / kg of tissue water).
Source: R/amp_scaling.R
scale_amp_molal_pvc.Rd
@@ -141,7 +138,7 @@ Value
diff --git a/docs/reference/scale_amp_molar.html b/docs/reference/scale_amp_molar.html
index 02358d91..dc87a338 100644
--- a/docs/reference/scale_amp_molar.html
+++ b/docs/reference/scale_amp_molar.html
@@ -1,7 +1,5 @@
-Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / Litre of tissue). — scale_amp_molar • Spectroscopy Analysis Tools (spant) Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / Litre of tissue). — scale_amp_molar • Spectroscopy Analysis Tools (spant) Convert default LCM/TARQUIN concentration scaling to molal units with partial
-volume correction. — scale_amp_molar2molal_pvc • Spectroscopy Analysis Tools (spant) Convert default LCM/TARQUIN concentration scaling to molal units with partial volume correction. — scale_amp_molar2molal_pvc • Spectroscopy Analysis Tools (spant) Scale fitted amplitudes to a ratio of signal amplitude. — scale_amp_ratio • Spectroscopy Analysis Tools (spant) Scale fitted amplitudes to a ratio of signal amplitude. — scale_amp_ratio • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -116,7 +116,7 @@ Value
diff --git a/docs/reference/scale_amp_ratio_value.html b/docs/reference/scale_amp_ratio_value.html
index 2036837a..6af8ac51 100644
--- a/docs/reference/scale_amp_ratio_value.html
+++ b/docs/reference/scale_amp_ratio_value.html
@@ -1,5 +1,5 @@
-Scale fitted amplitudes to a ratio of signal amplitude. — scale_amp_ratio_value • Spectroscopy Analysis Tools (spant) Scale fitted amplitudes to a ratio of signal amplitude. — scale_amp_ratio_value • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/scale_amp_water_ratio.html b/docs/reference/scale_amp_water_ratio.html
index 5b25e884..35a76b00 100644
--- a/docs/reference/scale_amp_water_ratio.html
+++ b/docs/reference/scale_amp_water_ratio.html
@@ -1,5 +1,5 @@
-Scale metabolite amplitudes as a ratio to the unsuppressed water amplitude. — scale_amp_water_ratio • Spectroscopy Analysis Tools (spant) Scale metabolite amplitudes as a ratio to the unsuppressed water amplitude. — scale_amp_water_ratio • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/scale_basis_amp.html b/docs/reference/scale_basis_amp.html
index 9401c3f1..5a58b5e5 100644
--- a/docs/reference/scale_basis_amp.html
+++ b/docs/reference/scale_basis_amp.html
@@ -1,5 +1,5 @@
-Scale a basis object by a scalar. — scale_basis_amp • Spectroscopy Analysis Tools (spant) Scale a basis object by a scalar. — scale_basis_amp • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/scale_basis_from_singlet.html b/docs/reference/scale_basis_from_singlet.html
index 0d542bc8..c9a19e77 100644
--- a/docs/reference/scale_basis_from_singlet.html
+++ b/docs/reference/scale_basis_from_singlet.html
@@ -1,5 +1,5 @@
-Scale a basis-set to be consistent with spant assumptions for water scaling. — scale_basis_from_singlet • Spectroscopy Analysis Tools (spant) Scale a basis-set to be consistent with spant assumptions for water scaling. — scale_basis_from_singlet • Spectroscopy Analysis Tools (spant)
Spectroscopy Analysis Tools (spant)
- 2.21.0
+ 2.22.0
@@ -127,7 +127,7 @@ Value
diff --git a/docs/reference/scale_mrs_amp.html b/docs/reference/scale_mrs_amp.html
index b5501a0d..990f058a 100644
--- a/docs/reference/scale_mrs_amp.html
+++ b/docs/reference/scale_mrs_amp.html
@@ -1,5 +1,5 @@
-Scale an mrs_data object by a scalar or vector or amplitudes. — scale_mrs_amp • Spectroscopy Analysis Tools (spant) Scale an mrs_data object by a scalar or vector or amplitudes. — scale_mrs_amp • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/scale_spec.html b/docs/reference/scale_spec.html
index 4f6ea835..6b3ddba4 100644
--- a/docs/reference/scale_spec.html
+++ b/docs/reference/scale_spec.html
@@ -1,5 +1,5 @@
-Scale mrs_data to a spectral region. — scale_spec • Spectroscopy Analysis Tools (spant) Scale mrs_data to a spectral region. — scale_spec • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -141,7 +141,7 @@ Value
diff --git a/docs/reference/sd.html b/docs/reference/sd.html
index ea1eec9f..3ae4dfd4 100644
--- a/docs/reference/sd.html
+++ b/docs/reference/sd.html
@@ -1,5 +1,5 @@
-Calculate the standard deviation spectrum from an mrs_data object. — sd • Spectroscopy Analysis Tools (spant) Calculate the standard deviation spectrum from an mrs_data object. — sd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/sd.mrs_data.html b/docs/reference/sd.mrs_data.html
index 3f92a49f..13bdda85 100644
--- a/docs/reference/sd.mrs_data.html
+++ b/docs/reference/sd.mrs_data.html
@@ -1,5 +1,5 @@
-Calculate the standard deviation spectrum from an mrs_data object. — sd.mrs_data • Spectroscopy Analysis Tools (spant) Calculate the standard deviation spectrum from an mrs_data object. — sd.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/seconds.html b/docs/reference/seconds.html
index b34d6627..467ee17f 100644
--- a/docs/reference/seconds.html
+++ b/docs/reference/seconds.html
@@ -1,5 +1,5 @@
-Return a time scale vector to match the FID of an MRS data object. — seconds • Spectroscopy Analysis Tools (spant) Return a time scale vector to match the FID of an MRS data object. — seconds • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/seq_cpmg_ideal.html b/docs/reference/seq_cpmg_ideal.html
index 547e96ab..45727c86 100644
--- a/docs/reference/seq_cpmg_ideal.html
+++ b/docs/reference/seq_cpmg_ideal.html
@@ -1,5 +1,5 @@
-CPMG style sequence with ideal pulses. — seq_cpmg_ideal • Spectroscopy Analysis Tools (spant) CPMG style sequence with ideal pulses. — seq_cpmg_ideal • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/seq_mega_press_ideal.html b/docs/reference/seq_mega_press_ideal.html
index 0769b8b4..a9cd7fa0 100644
--- a/docs/reference/seq_mega_press_ideal.html
+++ b/docs/reference/seq_mega_press_ideal.html
@@ -1,7 +1,5 @@
-MEGA-PRESS sequence with ideal localisation pulses and Gaussian shaped
-editing pulse. — seq_mega_press_ideal • Spectroscopy Analysis Tools (spant) MEGA-PRESS sequence with ideal localisation pulses and Gaussian shaped editing pulse. — seq_mega_press_ideal • Spectroscopy Analysis Tools (spant) PRESS sequence with shaped refocusing pulses. — seq_press_2d_shaped • Spectroscopy Analysis Tools (spant) PRESS sequence with shaped refocusing pulses. — seq_press_2d_shaped • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -165,7 +165,7 @@ Value
diff --git a/docs/reference/seq_press_ideal.html b/docs/reference/seq_press_ideal.html
index 8c976856..72c3af3d 100644
--- a/docs/reference/seq_press_ideal.html
+++ b/docs/reference/seq_press_ideal.html
@@ -1,5 +1,5 @@
-PRESS sequence with ideal pulses. — seq_press_ideal • Spectroscopy Analysis Tools (spant) PRESS sequence with ideal pulses. — seq_press_ideal • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/seq_pulse_acquire.html b/docs/reference/seq_pulse_acquire.html
index 4a88fc64..ad80571e 100644
--- a/docs/reference/seq_pulse_acquire.html
+++ b/docs/reference/seq_pulse_acquire.html
@@ -1,5 +1,5 @@
-Simple pulse and acquire sequence with ideal pulses. — seq_pulse_acquire • Spectroscopy Analysis Tools (spant) Simple pulse and acquire sequence with ideal pulses. — seq_pulse_acquire • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/seq_slaser_ideal.html b/docs/reference/seq_slaser_ideal.html
index 74688f4d..eb83e8e3 100644
--- a/docs/reference/seq_slaser_ideal.html
+++ b/docs/reference/seq_slaser_ideal.html
@@ -1,5 +1,5 @@
-sLASER sequence with ideal pulses. — seq_slaser_ideal • Spectroscopy Analysis Tools (spant) sLASER sequence with ideal pulses. — seq_slaser_ideal • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -126,7 +126,7 @@ Value
diff --git a/docs/reference/seq_spin_echo_ideal.html b/docs/reference/seq_spin_echo_ideal.html
index e23271de..4248716f 100644
--- a/docs/reference/seq_spin_echo_ideal.html
+++ b/docs/reference/seq_spin_echo_ideal.html
@@ -1,5 +1,5 @@
-Spin echo sequence with ideal pulses. — seq_spin_echo_ideal • Spectroscopy Analysis Tools (spant) Spin echo sequence with ideal pulses. — seq_spin_echo_ideal • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/seq_steam_ideal.html b/docs/reference/seq_steam_ideal.html
index a60685a8..1c8115d7 100644
--- a/docs/reference/seq_steam_ideal.html
+++ b/docs/reference/seq_steam_ideal.html
@@ -1,5 +1,5 @@
-STEAM sequence with ideal pulses. — seq_steam_ideal • Spectroscopy Analysis Tools (spant) STEAM sequence with ideal pulses. — seq_steam_ideal • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -128,7 +128,7 @@ Value
diff --git a/docs/reference/seq_steam_ideal_cof.html b/docs/reference/seq_steam_ideal_cof.html
index 8f225740..cba7af91 100644
--- a/docs/reference/seq_steam_ideal_cof.html
+++ b/docs/reference/seq_steam_ideal_cof.html
@@ -1,7 +1,5 @@
-STEAM sequence with ideal pulses and coherence order filtering to simulate
-gradient crushers. — seq_steam_ideal_cof • Spectroscopy Analysis Tools (spant) STEAM sequence with ideal pulses and coherence order filtering to simulate gradient crushers. — seq_steam_ideal_cof • Spectroscopy Analysis Tools (spant) STEAM sequence with ideal pulses using the z-rotation gradient simulation
-method described by Young et al JMR 140, 146-152 (1999). — seq_steam_ideal_young • Spectroscopy Analysis Tools (spant) STEAM sequence with ideal pulses using the z-rotation gradient simulation method described by Young et al JMR 140, 146-152 (1999). — seq_steam_ideal_young • Spectroscopy Analysis Tools (spant) Set the number of transients for an mrs_data object. — set_Ntrans • Spectroscopy Analysis Tools (spant) Set the number of transients for an mrs_data object. — set_Ntrans • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/set_def_acq_paras.html b/docs/reference/set_def_acq_paras.html
index 3e1b4004..cc2ada9c 100644
--- a/docs/reference/set_def_acq_paras.html
+++ b/docs/reference/set_def_acq_paras.html
@@ -1,5 +1,5 @@
-Set the default acquisition parameters. — set_def_acq_paras • Spectroscopy Analysis Tools (spant) Set the default acquisition parameters. — set_def_acq_paras • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Arguments
diff --git a/docs/reference/set_lcm_cmd.html b/docs/reference/set_lcm_cmd.html
index 2056ed01..42bb2f24 100644
--- a/docs/reference/set_lcm_cmd.html
+++ b/docs/reference/set_lcm_cmd.html
@@ -1,5 +1,5 @@
-Set the command to run the LCModel command-line program. — set_lcm_cmd • Spectroscopy Analysis Tools (spant) Set the command to run the LCModel command-line program. — set_lcm_cmd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/set_lw.html b/docs/reference/set_lw.html
index b64ec851..bb176c62 100644
--- a/docs/reference/set_lw.html
+++ b/docs/reference/set_lw.html
@@ -1,5 +1,5 @@
-Apply line-broadening to an mrs_data object to achieve a specified linewidth. — set_lw • Spectroscopy Analysis Tools (spant) Apply line-broadening to an mrs_data object to achieve a specified linewidth. — set_lw • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -123,7 +123,7 @@ Value
diff --git a/docs/reference/set_mask_xy_mat.html b/docs/reference/set_mask_xy_mat.html
index 49dc5d4e..52c4b617 100644
--- a/docs/reference/set_mask_xy_mat.html
+++ b/docs/reference/set_mask_xy_mat.html
@@ -1,5 +1,5 @@
-Set the masked voxels in a 2D MRSI dataset to given spectrum. — set_mask_xy_mat • Spectroscopy Analysis Tools (spant) Set the masked voxels in a 2D MRSI dataset to given spectrum. — set_mask_xy_mat • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Value
diff --git a/docs/reference/set_precomp_mode.html b/docs/reference/set_precomp_mode.html
index f44bd5d3..47c28e3b 100644
--- a/docs/reference/set_precomp_mode.html
+++ b/docs/reference/set_precomp_mode.html
@@ -1,5 +1,5 @@
-Set the precompute mode. — set_precomp_mode • Spectroscopy Analysis Tools (spant) Set the precompute mode. — set_precomp_mode • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/set_precomp_verbose.html b/docs/reference/set_precomp_verbose.html
index 1453a231..9c613505 100644
--- a/docs/reference/set_precomp_verbose.html
+++ b/docs/reference/set_precomp_verbose.html
@@ -1,5 +1,5 @@
-Set the verbosity of the precompute function. — set_precomp_verbose • Spectroscopy Analysis Tools (spant) Set the verbosity of the precompute function. — set_precomp_verbose • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/set_ref.html b/docs/reference/set_ref.html
index 8953fa50..5436dfa2 100644
--- a/docs/reference/set_ref.html
+++ b/docs/reference/set_ref.html
@@ -1,5 +1,5 @@
-Set the ppm reference value (eg ppm value at 0Hz). — set_ref • Spectroscopy Analysis Tools (spant) Set the ppm reference value (eg ppm value at 0Hz). — set_ref • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/set_td_pts.html b/docs/reference/set_td_pts.html
index 8a80d42a..586459ff 100644
--- a/docs/reference/set_td_pts.html
+++ b/docs/reference/set_td_pts.html
@@ -1,7 +1,5 @@
-Set the number of time-domain data points, truncating or zero-filling as
-appropriate. — set_td_pts • Spectroscopy Analysis Tools (spant) Set the number of time-domain data points, truncating or zero-filling as appropriate. — set_td_pts • Spectroscopy Analysis Tools (spant) Set the command to run the TARQUIN command-line program. — set_tqn_cmd • Spectroscopy Analysis Tools (spant) Set the command to run the TARQUIN command-line program. — set_tqn_cmd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/set_tr.html b/docs/reference/set_tr.html
index b2109ab0..65c9df5f 100644
--- a/docs/reference/set_tr.html
+++ b/docs/reference/set_tr.html
@@ -1,5 +1,5 @@
-Set the repetition time of an MRS dataset. — set_tr • Spectroscopy Analysis Tools (spant) Set the repetition time of an MRS dataset. — set_tr • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/shift.html b/docs/reference/shift.html
index ab0fe724..034591d0 100644
--- a/docs/reference/shift.html
+++ b/docs/reference/shift.html
@@ -1,5 +1,5 @@
-Apply a frequency shift to MRS data. — shift • Spectroscopy Analysis Tools (spant) Apply a frequency shift to MRS data. — shift • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/shift_basis.html b/docs/reference/shift_basis.html
index 2884be19..f55a65e0 100644
--- a/docs/reference/shift_basis.html
+++ b/docs/reference/shift_basis.html
@@ -1,5 +1,5 @@
-Apply frequency shifts to basis set signals. — shift_basis • Spectroscopy Analysis Tools (spant) Apply frequency shifts to basis set signals. — shift_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Value
diff --git a/docs/reference/sim_basis.html b/docs/reference/sim_basis.html
index c7838c46..bb5fefc6 100644
--- a/docs/reference/sim_basis.html
+++ b/docs/reference/sim_basis.html
@@ -1,5 +1,5 @@
-Simulate a basis set object. — sim_basis • Spectroscopy Analysis Tools (spant) Simulate a basis set object. — sim_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -136,7 +136,7 @@ Value
diff --git a/docs/reference/sim_basis_1h_brain.html b/docs/reference/sim_basis_1h_brain.html
index 62ed7389..f71ffa0b 100644
--- a/docs/reference/sim_basis_1h_brain.html
+++ b/docs/reference/sim_basis_1h_brain.html
@@ -1,7 +1,5 @@
-Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS
-sequence. Note, ideal pulses are assumed. — sim_basis_1h_brain • Spectroscopy Analysis Tools (spant) Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS sequence. Note, ideal pulses are assumed. — sim_basis_1h_brain • Spectroscopy Analysis Tools (spant) Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS
-sequence. Note, ideal pulses are assumed. — sim_basis_1h_brain_press • Spectroscopy Analysis Tools (spant) Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS sequence. Note, ideal pulses are assumed. — sim_basis_1h_brain_press • Spectroscopy Analysis Tools (spant) Simulate a macromolecular and lipid basis-set suitable for 1H brain MRS
-analysis. — sim_basis_mm_lip_lcm • Spectroscopy Analysis Tools (spant) Simulate a macromolecular and lipid basis-set suitable for 1H brain MRS analysis. — sim_basis_mm_lip_lcm • Spectroscopy Analysis Tools (spant) Simulate a basis file using TARQUIN. — sim_basis_tqn • Spectroscopy Analysis Tools (spant) Simulate a basis file using TARQUIN. — sim_basis_tqn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -129,7 +129,7 @@ Examples
diff --git a/docs/reference/sim_brain_1h.html b/docs/reference/sim_brain_1h.html
index 2044cf1a..717ee289 100644
--- a/docs/reference/sim_brain_1h.html
+++ b/docs/reference/sim_brain_1h.html
@@ -1,5 +1,5 @@
-Simulate MRS data with a similar appearance to normal brain (by default). — sim_brain_1h • Spectroscopy Analysis Tools (spant) Simulate MRS data with a similar appearance to normal brain (by default). — sim_brain_1h • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -159,7 +159,7 @@ Value
diff --git a/docs/reference/sim_mol.html b/docs/reference/sim_mol.html
index 23bcef50..77f76a50 100644
--- a/docs/reference/sim_mol.html
+++ b/docs/reference/sim_mol.html
@@ -1,5 +1,5 @@
-Simulate a mol_parameter object. — sim_mol • Spectroscopy Analysis Tools (spant) Simulate a mol_parameter object. — sim_mol • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -143,7 +143,7 @@ Value
diff --git a/docs/reference/sim_noise.html b/docs/reference/sim_noise.html
index 23875f79..a71477d4 100644
--- a/docs/reference/sim_noise.html
+++ b/docs/reference/sim_noise.html
@@ -1,5 +1,5 @@
-Simulate an mrs_data object containing simulated Gaussian noise. — sim_noise • Spectroscopy Analysis Tools (spant) Simulate an mrs_data object containing simulated Gaussian noise. — sim_noise • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -84,6 +84,7 @@ Simulate an mrs_data object containing simulated Gaussian noise.
ft = def_ft(),
N = def_N(),
ref = def_ref(),
+ nuc = def_nuc(),
dyns = 1,
fd = TRUE
)
@@ -111,6 +112,10 @@ Arguments
reference value for ppm scale.
nuc
+resonant nucleus.
dyns
number of dynamic scans to generate.
Value
diff --git a/docs/reference/sim_resonances.html b/docs/reference/sim_resonances.html
index 19e9a8a4..d4f8d7c0 100644
--- a/docs/reference/sim_resonances.html
+++ b/docs/reference/sim_resonances.html
@@ -1,5 +1,5 @@
-Simulate a MRS data object containing a set of simulated resonances. — sim_resonances • Spectroscopy Analysis Tools (spant) Simulate a MRS data object containing a set of simulated resonances. — sim_resonances • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -161,7 +161,7 @@ Examples
diff --git a/docs/reference/sim_th_excit_profile.html b/docs/reference/sim_th_excit_profile.html
index 5535c5ef..e781cab1 100644
--- a/docs/reference/sim_th_excit_profile.html
+++ b/docs/reference/sim_th_excit_profile.html
@@ -1,7 +1,5 @@
-Simulate an ideal pulse excitation profile by smoothing a top-hat function
-with a Gaussian. — sim_th_excit_profile • Spectroscopy Analysis Tools (spant) Simulate an ideal pulse excitation profile by smoothing a top-hat function with a Gaussian. — sim_th_excit_profile • Spectroscopy Analysis Tools (spant) Simulate an mrs_data object containing complex zero valued samples. — sim_zero • Spectroscopy Analysis Tools (spant) Simulate an mrs_data object containing complex zero valued samples. — sim_zero • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -78,7 +78,14 @@ Simulate an mrs_data object containing complex zero valued samples.
-
+
@@ -99,6 +106,10 @@ Arguments
reference value for ppm scale.
nuc
+resonant nucleus.
dyns
number of dynamic scans to generate.
Value
diff --git a/docs/reference/smooth_dyns.html b/docs/reference/smooth_dyns.html
index 4cc8da50..accf3a51 100644
--- a/docs/reference/smooth_dyns.html
+++ b/docs/reference/smooth_dyns.html
@@ -1,5 +1,5 @@
-Smooth data across the dynamic dimension with a Gaussian kernel. — smooth_dyns • Spectroscopy Analysis Tools (spant) Smooth data across the dynamic dimension with a Gaussian kernel. — smooth_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/sort_basis.html b/docs/reference/sort_basis.html
index 6a676ea2..d25cc006 100644
--- a/docs/reference/sort_basis.html
+++ b/docs/reference/sort_basis.html
@@ -1,5 +1,5 @@
-Sort the basis-set elements alphabetically. — sort_basis • Spectroscopy Analysis Tools (spant) Sort the basis-set elements alphabetically. — sort_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/spant-package.html b/docs/reference/spant-package.html
index b3dd8e21..90f19ec3 100644
--- a/docs/reference/spant-package.html
+++ b/docs/reference/spant-package.html
@@ -1,5 +1,5 @@
-spant: spectroscopy analysis tools. — spant-package • Spectroscopy Analysis Tools (spant) spant: spectroscopy analysis tools. — spant-package • Spectroscopy Analysis Tools (spant) Simulate and fit some spectra with ABfit for benchmarking purposes. Basic
-timing and performance metrics will be printed. — spant_abfit_benchmark • Spectroscopy Analysis Tools (spant) Simulate and fit some spectra with ABfit for benchmarking purposes. Basic timing and performance metrics will be printed. — spant_abfit_benchmark • Spectroscopy Analysis Tools (spant) Example MEGA-PRESS data with significant B0 drift. — spant_mpress_drift • Spectroscopy Analysis Tools (spant) Example MEGA-PRESS data with significant B0 drift. — spant_mpress_drift • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -83,7 +83,7 @@ Example MEGA-PRESS data with significant B0 drift.
Format
- An object of class mrs_data of length 13.
+ An object of class mrs_data of dimension 1 x 1 x 1 x 1 x 40 x 1 x 1024.
@@ -98,7 +98,7 @@ Format
diff --git a/docs/reference/spant_sim_fmrs_dataset.html b/docs/reference/spant_sim_fmrs_dataset.html
new file mode 100644
index 00000000..00e48b56
--- /dev/null
+++ b/docs/reference/spant_sim_fmrs_dataset.html
@@ -0,0 +1,117 @@
+
+Simulate an example fMRS dataset for a block design fMRS experiment and export a BIDS structure. — spant_sim_fmrs_dataset • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Simulate an example fMRS dataset for a block design fMRS experiment and export a BIDS structure.
+ Source: R/fmrs.R
+ spant_sim_fmrs_dataset.Rd
+
+
+
+ Simulate an example fMRS dataset for a block design fMRS experiment and
+export a BIDS structure.
+
+
+
+ spant_sim_fmrs_dataset(output_dir = NULL)
+
+
+
+ Arguments
+ - output_dir
+output directory for the BIDS data. Defaults to :
+"HOME/sim_fmrs_dataset/data".
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/spant_simulation_benchmark.html b/docs/reference/spant_simulation_benchmark.html
index 32daa8bf..d8cc6841 100644
--- a/docs/reference/spant_simulation_benchmark.html
+++ b/docs/reference/spant_simulation_benchmark.html
@@ -1,7 +1,5 @@
-Simulate a typical metabolite basis set for benchmarking. Timing metrics will
-be printed on completion. — spant_simulation_benchmark • Spectroscopy Analysis Tools (spant) Simulate a typical metabolite basis set for benchmarking. Timing metrics will be printed on completion. — spant_simulation_benchmark • Spectroscopy Analysis Tools (spant) Decompose an mrs_data object into white and gray matter spectra. — spec_decomp • Spectroscopy Analysis Tools (spant) Perform a mathematical operation on a spectral region. — spec_op • Spectroscopy Analysis Tools (spant) Perform a mathematical operation on a spectral region. — spec_op • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -98,8 +98,8 @@ Arguments
operator
-can be "sum" (default), "mean", "l2", "max", "min" or
-"max-min".
can be "sum" (default), "mean", "l2", "max", "max_cplx,
+"min" or "max-min".
freq_scale
@@ -129,7 +129,7 @@ Value
diff --git a/docs/reference/spin_sys.html b/docs/reference/spin_sys.html
index 853423a4..1eaa9e76 100644
--- a/docs/reference/spin_sys.html
+++ b/docs/reference/spin_sys.html
@@ -1,5 +1,5 @@
-Create a spin system object for pulse sequence simulation. — spin_sys • Spectroscopy Analysis Tools (spant) Create a spin system object for pulse sequence simulation. — spin_sys • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/spm_pve2categorical.html b/docs/reference/spm_pve2categorical.html
index 23a1bad9..70f10729 100644
--- a/docs/reference/spm_pve2categorical.html
+++ b/docs/reference/spm_pve2categorical.html
@@ -1,7 +1,5 @@
-Convert SPM style segmentation files to a single categorical image where
-the numerical values map as: 0) Other, 1) CSF, 2) GM and 3) WM. — spm_pve2categorical • Spectroscopy Analysis Tools (spant) Convert SPM style segmentation files to a single categorical image where the numerical values map as: 0) Other, 1) CSF, 2) GM and 3) WM. — spm_pve2categorical • Spectroscopy Analysis Tools (spant) Signal space projection method for lipid suppression. — ssp • Spectroscopy Analysis Tools (spant) Signal space projection method for lipid suppression. — ssp • Spectroscopy Analysis Tools (spant) Plot the fitting results of an object of class fit_result with
-individual basis set components shown. — stackplot.fit_result • Spectroscopy Analysis Tools (spant) Plot the fitting results of an object of class fit_result with individual basis set components shown. — stackplot.fit_result • Spectroscopy Analysis Tools (spant) Produce a plot with multiple traces. — stackplot • Spectroscopy Analysis Tools (spant) Produce a plot with multiple traces. — stackplot • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/stackplot.mrs_data.html b/docs/reference/stackplot.mrs_data.html
index 17ff5648..64eea445 100644
--- a/docs/reference/stackplot.mrs_data.html
+++ b/docs/reference/stackplot.mrs_data.html
@@ -1,5 +1,5 @@
-Stackplot plotting method for objects of class mrs_data. — stackplot.mrs_data • Spectroscopy Analysis Tools (spant) Stackplot plotting method for objects of class mrs_data. — stackplot.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -255,7 +255,7 @@ Arguments
diff --git a/docs/reference/sub_first_dyn.html b/docs/reference/sub_first_dyn.html
index dbd7f831..493b7242 100644
--- a/docs/reference/sub_first_dyn.html
+++ b/docs/reference/sub_first_dyn.html
@@ -1,5 +1,5 @@
-Subtract the first dynamic spectrum from a dynamic series. — sub_first_dyn • Spectroscopy Analysis Tools (spant) Subtract the first dynamic spectrum from a dynamic series. — sub_first_dyn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/sub_mean_dyns.html b/docs/reference/sub_mean_dyns.html
index 6e3bb2df..221bd0c1 100644
--- a/docs/reference/sub_mean_dyns.html
+++ b/docs/reference/sub_mean_dyns.html
@@ -1,5 +1,5 @@
-Subtract the mean dynamic spectrum from a dynamic series. — sub_mean_dyns • Spectroscopy Analysis Tools (spant) Subtract the mean dynamic spectrum from a dynamic series. — sub_mean_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/sub_median_dyns.html b/docs/reference/sub_median_dyns.html
index 134c495d..1e834f14 100644
--- a/docs/reference/sub_median_dyns.html
+++ b/docs/reference/sub_median_dyns.html
@@ -1,5 +1,5 @@
-Subtract the median dynamic spectrum from a dynamic series. — sub_median_dyns • Spectroscopy Analysis Tools (spant) Subtract the median dynamic spectrum from a dynamic series. — sub_median_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/sum_coils.html b/docs/reference/sum_coils.html
index 7bf559f2..e1ab3cc0 100644
--- a/docs/reference/sum_coils.html
+++ b/docs/reference/sum_coils.html
@@ -1,5 +1,5 @@
-Calculate the sum across receiver coil elements. — sum_coils • Spectroscopy Analysis Tools (spant) Calculate the sum across receiver coil elements. — sum_coils • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/sum_dyns.html b/docs/reference/sum_dyns.html
index a0be19d3..bbda2ffc 100644
--- a/docs/reference/sum_dyns.html
+++ b/docs/reference/sum_dyns.html
@@ -1,5 +1,5 @@
-Calculate the sum of data dynamics. — sum_dyns • Spectroscopy Analysis Tools (spant) Calculate the sum of data dynamics. — sum_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/sum_mrs.html b/docs/reference/sum_mrs.html
index a22f215b..3cc3ab9e 100644
--- a/docs/reference/sum_mrs.html
+++ b/docs/reference/sum_mrs.html
@@ -1,5 +1,5 @@
-Sum two mrs_data objects. — sum_mrs • Spectroscopy Analysis Tools (spant) Sum two mrs_data objects. — sum_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Value
diff --git a/docs/reference/sum_mrs_list.html b/docs/reference/sum_mrs_list.html
index f4e09aea..c3584348 100644
--- a/docs/reference/sum_mrs_list.html
+++ b/docs/reference/sum_mrs_list.html
@@ -1,5 +1,5 @@
-Return the sum of a list of mrs_data objects. — sum_mrs_list • Spectroscopy Analysis Tools (spant) Return the sum of a list of mrs_data objects. — sum_mrs_list • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/svs_1h_brain_analysis.html b/docs/reference/svs_1h_brain_analysis.html
index 8ce514db..dff0ef7d 100644
--- a/docs/reference/svs_1h_brain_analysis.html
+++ b/docs/reference/svs_1h_brain_analysis.html
@@ -1,5 +1,5 @@
-Standard SVS 1H brain analysis pipeline. — svs_1h_brain_analysis • Spectroscopy Analysis Tools (spant) Standard SVS 1H brain analysis pipeline. — svs_1h_brain_analysis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -199,7 +199,7 @@ Value
diff --git a/docs/reference/svs_1h_brain_analysis_dev.html b/docs/reference/svs_1h_brain_analysis_dev.html
index d70a14d3..d71bfea2 100644
--- a/docs/reference/svs_1h_brain_analysis_dev.html
+++ b/docs/reference/svs_1h_brain_analysis_dev.html
@@ -1,5 +1,5 @@
-Standard SVS 1H brain analysis pipeline. — svs_1h_brain_analysis_dev • Spectroscopy Analysis Tools (spant) Standard SVS 1H brain analysis pipeline. — svs_1h_brain_analysis_dev • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -193,7 +193,7 @@ Examples
diff --git a/docs/reference/svs_1h_brain_batch_analysis.html b/docs/reference/svs_1h_brain_batch_analysis.html
index 5631e8cc..15f7223e 100644
--- a/docs/reference/svs_1h_brain_batch_analysis.html
+++ b/docs/reference/svs_1h_brain_batch_analysis.html
@@ -1,5 +1,5 @@
-Batch interface to the standard SVS 1H brain analysis pipeline. — svs_1h_brain_batch_analysis • Spectroscopy Analysis Tools (spant) Batch interface to the standard SVS 1H brain analysis pipeline. — svs_1h_brain_batch_analysis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -144,7 +144,7 @@ Value
diff --git a/docs/reference/t_test_spec.html b/docs/reference/t_test_spec.html
new file mode 100644
index 00000000..56a7ea1b
--- /dev/null
+++ b/docs/reference/t_test_spec.html
@@ -0,0 +1,124 @@
+
+Perform a t-test on spectral data points. — t_test_spec • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+
+
+ Perform a t-test on spectral data points.
+
+
+
+ t_test_spec(mrs_data, group)
+
+
+
+ Arguments
+ - mrs_data
+an mrs_data object with spectra in the dynamic dimension.
- group
+vector describing the group membership of each dynamic spectrum.
+
+ Value
+
+
+a list of statistical results.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/td2fd.html b/docs/reference/td2fd.html
index 6748a6a8..f31ed524 100644
--- a/docs/reference/td2fd.html
+++ b/docs/reference/td2fd.html
@@ -1,5 +1,5 @@
-Transform time-domain data to the frequency-domain. — td2fd • Spectroscopy Analysis Tools (spant) Transform time-domain data to the frequency-domain. — td2fd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/td_conv_filt.html b/docs/reference/td_conv_filt.html
index a9f340c3..106b9b00 100644
--- a/docs/reference/td_conv_filt.html
+++ b/docs/reference/td_conv_filt.html
@@ -1,5 +1,5 @@
-Time-domain convolution based filter. — td_conv_filt • Spectroscopy Analysis Tools (spant) Time-domain convolution based filter. — td_conv_filt • Spectroscopy Analysis Tools (spant) Time-domain spectral registration. — tdsr • Spectroscopy Analysis Tools (spant) Time-domain spectral registration. — tdsr • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -121,7 +121,7 @@ Value
diff --git a/docs/reference/te.html b/docs/reference/te.html
index 010361b1..4a65711d 100644
--- a/docs/reference/te.html
+++ b/docs/reference/te.html
@@ -1,5 +1,5 @@
-Return the echo time of an MRS dataset. — te • Spectroscopy Analysis Tools (spant) Return the echo time of an MRS dataset. — te • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/tr.html b/docs/reference/tr.html
index 0c0bd63b..2e749e02 100644
--- a/docs/reference/tr.html
+++ b/docs/reference/tr.html
@@ -1,5 +1,5 @@
-Return the repetition time of an MRS dataset. — tr • Spectroscopy Analysis Tools (spant) Return the repetition time of an MRS dataset. — tr • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/varpro_3_para_opts.html b/docs/reference/varpro_3_para_opts.html
index c2270a16..52d7cd84 100644
--- a/docs/reference/varpro_3_para_opts.html
+++ b/docs/reference/varpro_3_para_opts.html
@@ -1,5 +1,5 @@
-Return a list of options for VARPRO based fitting with 3 free parameters. — varpro_3_para_opts • Spectroscopy Analysis Tools (spant) Return a list of options for VARPRO based fitting with 3 free parameters. — varpro_3_para_opts • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -141,7 +141,7 @@ Value
diff --git a/docs/reference/varpro_basic_opts.html b/docs/reference/varpro_basic_opts.html
index 32c86d22..c5104891 100644
--- a/docs/reference/varpro_basic_opts.html
+++ b/docs/reference/varpro_basic_opts.html
@@ -1,5 +1,5 @@
-Return a list of options for a basic VARPRO analysis. — varpro_basic_opts • Spectroscopy Analysis Tools (spant) Return a list of options for a basic VARPRO analysis. — varpro_basic_opts • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -118,7 +118,7 @@ Value
diff --git a/docs/reference/varpro_opts.html b/docs/reference/varpro_opts.html
index 2aabf11d..6332f730 100644
--- a/docs/reference/varpro_opts.html
+++ b/docs/reference/varpro_opts.html
@@ -1,5 +1,5 @@
-Return a list of options for VARPRO based fitting. — varpro_opts • Spectroscopy Analysis Tools (spant) Return a list of options for VARPRO based fitting. — varpro_opts • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -177,7 +177,7 @@ Examples
diff --git a/docs/reference/vec2mrs_data.html b/docs/reference/vec2mrs_data.html
index 0cccd73b..f0d58bf0 100644
--- a/docs/reference/vec2mrs_data.html
+++ b/docs/reference/vec2mrs_data.html
@@ -1,5 +1,5 @@
-Convert a vector into a mrs_data object. — vec2mrs_data • Spectroscopy Analysis Tools (spant) Convert a vector into a mrs_data object. — vec2mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -80,10 +80,11 @@ Convert a vector into a mrs_data object.
vec2mrs_data(
vec,
- fs = def_fs(),
- ft = def_ft(),
- ref = def_ref(),
- nuc = def_nuc(),
+ mrs_data = NULL,
+ fs = NULL,
+ ft = NULL,
+ ref = NULL,
+ nuc = NULL,
dyns = 1,
fd = FALSE
)
@@ -95,6 +96,10 @@ Arguments
the data vector.
mrs_data
+example data to copy acquisition parameters from.
fs
sampling frequency in Hz.
Arguments
fd
-flag to indicate if the matrix is in the frequency domain (logical).
flag to indicate if the vector is in the frequency domain (logical).
Value
diff --git a/docs/reference/write_basis.html b/docs/reference/write_basis.html
index b6e27cbd..94c5e021 100644
--- a/docs/reference/write_basis.html
+++ b/docs/reference/write_basis.html
@@ -1,5 +1,5 @@
-Write a basis object to an LCModel .basis formatted file. — write_basis • Spectroscopy Analysis Tools (spant) Write a basis object to an LCModel .basis formatted file. — write_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -108,7 +108,7 @@ Arguments
diff --git a/docs/reference/write_basis_tqn.html b/docs/reference/write_basis_tqn.html
index 6aa51c1d..116c73ec 100644
--- a/docs/reference/write_basis_tqn.html
+++ b/docs/reference/write_basis_tqn.html
@@ -1,5 +1,5 @@
-Generate a basis file using TARQUIN. — write_basis_tqn • Spectroscopy Analysis Tools (spant) Generate a basis file using TARQUIN. — write_basis_tqn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Examples
diff --git a/docs/reference/write_mrs.html b/docs/reference/write_mrs.html
index fff25f15..124b9dc4 100644
--- a/docs/reference/write_mrs.html
+++ b/docs/reference/write_mrs.html
@@ -1,5 +1,5 @@
-Write MRS data object to file. — write_mrs • Spectroscopy Analysis Tools (spant) Write MRS data object to file. — write_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Arguments
diff --git a/docs/reference/write_mrs_nifti.html b/docs/reference/write_mrs_nifti.html
index f4bf1921..bd3ed4b7 100644
--- a/docs/reference/write_mrs_nifti.html
+++ b/docs/reference/write_mrs_nifti.html
@@ -1,5 +1,5 @@
-Write MRS data object to file in NIFTI format. — write_mrs_nifti • Spectroscopy Analysis Tools (spant) Write MRS data object to file in NIFTI format. — write_mrs_nifti • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/write_pulse_ascii.html b/docs/reference/write_pulse_ascii.html
index 067ae086..221f8ebb 100644
--- a/docs/reference/write_pulse_ascii.html
+++ b/docs/reference/write_pulse_ascii.html
@@ -1,5 +1,5 @@
-Write an ASCII formatted pulse file. — write_pulse_ascii • Spectroscopy Analysis Tools (spant) Write an ASCII formatted pulse file. — write_pulse_ascii • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/zero_fade_spec.html b/docs/reference/zero_fade_spec.html
index c703745c..c8b572c3 100644
--- a/docs/reference/zero_fade_spec.html
+++ b/docs/reference/zero_fade_spec.html
@@ -1,7 +1,5 @@
-Fade a spectrum to zero by frequency domain multiplication with a tanh
-function. Note this operation distorts data points at the end of the FID. — zero_fade_spec • Spectroscopy Analysis Tools (spant) Fade a spectrum to zero by frequency domain multiplication with a tanh function. Note this operation distorts data points at the end of the FID. — zero_fade_spec • Spectroscopy Analysis Tools (spant) Zero all coherences including and above a given order. — zero_higher_orders • Spectroscopy Analysis Tools (spant) Zero all coherences including and above a given order. — zero_higher_orders • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Value
diff --git a/docs/reference/zero_td_pts_end.html b/docs/reference/zero_td_pts_end.html
index 8c1123c8..71d24ebb 100644
--- a/docs/reference/zero_td_pts_end.html
+++ b/docs/reference/zero_td_pts_end.html
@@ -1,5 +1,5 @@
-Set mrs_data object data points at the end of the FID to zero. — zero_td_pts_end • Spectroscopy Analysis Tools (spant) Set mrs_data object data points at the end of the FID to zero. — zero_td_pts_end • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/zf.html b/docs/reference/zf.html
index 85e2013c..baf50256 100644
--- a/docs/reference/zf.html
+++ b/docs/reference/zf.html
@@ -1,5 +1,5 @@
-Zero-fill MRS data in the time domain. — zf • Spectroscopy Analysis Tools (spant) Zero-fill MRS data in the time domain. — zf • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -125,7 +125,7 @@ Value
diff --git a/docs/reference/zf_xy.html b/docs/reference/zf_xy.html
index ebca3999..c4104a74 100644
--- a/docs/reference/zf_xy.html
+++ b/docs/reference/zf_xy.html
@@ -1,5 +1,5 @@
-Zero-fill MRSI data in the k-space x-y direction. — zf_xy • Spectroscopy Analysis Tools (spant) Zero-fill MRSI data in the k-space x-y direction. — zf_xy • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -113,7 +113,7 @@ Value
diff --git a/docs/sitemap.xml b/docs/sitemap.xml
index e2139f71..4c39f515 100644
--- a/docs/sitemap.xml
+++ b/docs/sitemap.xml
@@ -216,6 +216,12 @@
https://martin3141.github.io/spant/reference/comb_coils_fp_pc.html
+
+ https://martin3141.github.io/spant/reference/comb_coils_mrsi_gls.html
+
+
+ https://martin3141.github.io/spant/reference/comb_coils_svs_gls.html
+
https://martin3141.github.io/spant/reference/comb_csv_results.html
@@ -411,6 +417,9 @@
https://martin3141.github.io/spant/reference/gen_conv_reg.html
+
+ https://martin3141.github.io/spant/reference/gen_group_reg.html
+
https://martin3141.github.io/spant/reference/gen_impulse_reg.html
@@ -555,6 +564,15 @@
https://martin3141.github.io/spant/reference/glm_spec.html
+
+ https://martin3141.github.io/spant/reference/glm_spec_fmrs_fl.html
+
+
+ https://martin3141.github.io/spant/reference/glm_spec_fmrs_group.html
+
+
+ https://martin3141.github.io/spant/reference/glm_spec_group_linhyp.html
+
https://martin3141.github.io/spant/reference/grid_shift_xy.html
@@ -690,9 +708,15 @@
https://martin3141.github.io/spant/reference/mrs_data2basis.html
+
+ https://martin3141.github.io/spant/reference/mrs_data2bids.html
+
https://martin3141.github.io/spant/reference/mrs_data2mat.html
+
+ https://martin3141.github.io/spant/reference/mrs_data2spec_mat.html
+
https://martin3141.github.io/spant/reference/mrs_data2vec.html
@@ -741,6 +765,9 @@
https://martin3141.github.io/spant/reference/phase.html
+
+ https://martin3141.github.io/spant/reference/phase_ref_1h_brain.html
+
https://martin3141.github.io/spant/reference/plot.fit_result.html
@@ -780,6 +807,12 @@
https://martin3141.github.io/spant/reference/precomp.html
+
+ https://martin3141.github.io/spant/reference/preproc_svs.html
+
+
+ https://martin3141.github.io/spant/reference/preproc_svs_dataset.html
+
https://martin3141.github.io/spant/reference/print.fit_result.html
@@ -1050,6 +1083,9 @@
https://martin3141.github.io/spant/reference/spant_mpress_drift.html
+
+ https://martin3141.github.io/spant/reference/spant_sim_fmrs_dataset.html
+
https://martin3141.github.io/spant/reference/spant_simulation_benchmark.html
@@ -1107,6 +1143,9 @@
https://martin3141.github.io/spant/reference/svs_1h_brain_batch_analysis.html
+
+ https://martin3141.github.io/spant/reference/t_test_spec.html
+
https://martin3141.github.io/spant/reference/td2fd.html
Perform a fft and fftshift on a matrix with each column replaced by its -shifted fft.
Perform a fft and fftshift on a matrix with each column replaced by its shifted fft.
All functions
- Generate regressors by convolving a specified response function with a
-stimulus.
Generate regressors by convolving a specified response function with a stimulus.
+
+
+ Expand a regressor matrix for a group analysis.
@@ -553,28 +542,23 @@ All functions
- Return a character vector of common 1H molecules found in healthy human
-brain.
Return a character vector of common 1H molecules found in healthy human brain.
- Return a list of mol_parameter objects suitable for 1H brain MRS
-analyses.
Return a list of mol_parameter objects suitable for 1H brain MRS analyses.
- Return a list of mol_parameter objects suitable for 1H brain MRS
-analyses.
Return a list of mol_parameter objects suitable for 1H brain MRS analyses.
- Return a list of mol_parameter objects suitable for 1H brain MRS
-analyses.
Return a list of mol_parameter objects suitable for 1H brain MRS analyses.
- Return a list of mol_parameter objects suitable for 1H brain MRS
-analyses.
Return a list of mol_parameter objects suitable for 1H brain MRS analyses.
@@ -582,8 +566,7 @@ All functions
- Return a character vector of molecules included in the Gold Star Phantoms
-SPECTRE phantom.
Return a character vector of molecules included in the Gold Star Phantoms SPECTRE phantom.
@@ -635,8 +618,7 @@ All functions
- Return a character array of names that may be used with the
-get_mol_paras function.
Return a character array of names that may be used with the get_mol_paras function.
@@ -700,8 +682,7 @@ All functions
- Return an array of amplitudes derived from fitting the initial points in the
-time domain and extrapolating back to t=0.
Return an array of amplitudes derived from fitting the initial points in the time domain and extrapolating back to t=0.
@@ -709,8 +690,7 @@ All functions
- Generate a mol_parameters object for a simple spin system with one
-resonance.
Generate a mol_parameters object for a simple spin system with one resonance.
@@ -731,6 +711,18 @@ All functions glm_spec()
Perform a GLM analysis of dynamic MRS data in the spectral domain.
+
+
+ Perform first-level spectral GLM analysis of an fMRS dataset.
+
+
+ Perform group-level spectral GLM analysis of an fMRS dataset.
+
+
+ Test a group-level spectral GLM linear hypothesis.
@@ -766,8 +758,7 @@ All functions
- Perform an ifft and ifftshift on a matrix with each column replaced by its
-shifted ifft.
Perform an ifft and ifftshift on a matrix with each column replaced by its shifted ifft.
@@ -799,8 +790,7 @@ All functions
- Check if the chemical shift dimension of an MRS data object is in the
-frequency domain.
Check if the chemical shift dimension of an MRS data object is in the frequency domain.
@@ -820,18 +810,15 @@ All functions
- Covert a linewidth in Hz to an equivalent alpha value in the time-domain ie:
-x * exp(-t * alpha).
Covert a linewidth in Hz to an equivalent alpha value in the time-domain ie: x * exp(-t * alpha).
- Covert a linewidth in Hz to an equivalent beta value in the time-domain ie:
-x * exp(-t * t * beta).
Covert a linewidth in Hz to an equivalent beta value in the time-domain ie: x * exp(-t * t * beta).
- Make a basis-set object from a directory containing LCModel formatted RAW
-files.
Make a basis-set object from a directory containing LCModel formatted RAW files.
@@ -851,8 +838,7 @@ All functions
- Mask the voxels outside an elliptical region spanning the MRSI dataset in the
-x-y plane.
Mask the voxels outside an elliptical region spanning the MRSI dataset in the x-y plane.
@@ -860,13 +846,11 @@ All functions
- Convert a matrix (with spectral points in the column dimension and dynamics
-in the row dimensions) into a mrs_data object.
Convert a matrix (with spectral points in the column dimension and dynamics in the row dimensions) into a mrs_data object.
- Matrix exponential function taken from complexplus package to reduce the
-number of spant dependencies.
Matrix exponential function taken from complexplus package to reduce the number of spant dependencies.
@@ -914,31 +898,31 @@ All functions
- Convert an mrs_data object to basis object - where basis signals are spread
-across the dynamic dimension in the MRS data.
Convert an mrs_data object to basis object - where basis signals are spread across the dynamic dimension in the MRS data.
+
+
+ Create a BIDS file structure from a vector of MRS data paths or list of mrs_data objects.
- Convert mrs_data object to a matrix, with spectral points in the column
-dimension and dynamics in the row dimension.
Convert mrs_data object to a matrix, with spectral points in the column dimension and dynamics in the row dimension.
-
+
- Convert mrs_data object to a vector.
Convert mrs_data object to a matrix, with spectral points in the column dimension and dynamics in the row dimension.
-
+
- Create a BIDS directory and file structure from a list of mrs_data objects.
Convert mrs_data object to a vector.
- Perform a fftshift on a matrix, with each column replaced by its shifted
-result.
Perform a fftshift on a matrix, with each column replaced by its shifted result.
- Perform an ifftshift on a matrix, with each column replaced by its shifted
-result.
Perform an ifftshift on a matrix, with each column replaced by its shifted result.
@@ -946,9 +930,7 @@ All functions
- Flip the x data dimension order of a nifti image. This corresponds to
-flipping MRI data in the left-right direction, assuming the data in save in
-neurological format (can check with fslorient program).
Flip the x data dimension order of a nifti image. This corresponds to flipping MRI data in the left-right direction, assuming the data in save in neurological format (can check with fslorient program).
@@ -964,8 +946,7 @@ All functions
- Search for the highest peak in a spectral region and return the frequency,
-height and FWHM.
Search for the highest peak in a spectral region and return the frequency, height and FWHM.
@@ -974,6 +955,10 @@ All functions phase()
Apply phasing parameters to MRS data.
+
+
+ Corrected zero order phase and chemical shift offset in 1H MRS data from the brain.
@@ -1005,8 +990,7 @@ All functions
- Plot an interactive slice map from a data array where voxels can be selected
-to display a corresponding spectrum.
Plot an interactive slice map from a data array where voxels can be selected to display a corresponding spectrum.
@@ -1026,8 +1010,15 @@ All functions
- Save function results to file and load on subsequent calls to avoid repeat
-computation.
Save function results to file and load on subsequent calls to avoid repeat computation.
+
+
+ Preprocess and perform quality assessment of a single SVS data set.
+
+
+ Preprocess and perform quality assessment of one or more SVS data sets.
@@ -1055,15 +1046,11 @@ All functions
- Read a directory containing Siemens MRS IMA files and combine along the coil
-dimension. Note that the coil ID is inferred from the sorted file name and
-should be checked when consistency is required between two directories.
Read a directory containing Siemens MRS IMA files and combine along the coil dimension. Note that the coil ID is inferred from the sorted file name and should be checked when consistency is required between two directories.
- Read a directory containing Siemens MRS IMA files and combine along the
-dynamic dimension. Note that the coil ID is inferred from the sorted file
-name and should be checked when consistency is required.
Read a directory containing Siemens MRS IMA files and combine along the dynamic dimension. Note that the coil ID is inferred from the sorted file name and should be checked when consistency is required.
@@ -1103,13 +1090,11 @@ All functions
- Reconstruct complex time-domain data from the real part of frequency-domain
-data.
Reconstruct complex time-domain data from the real part of frequency-domain data.
- Reconstruct complex time-domain data from the real part of frequency-domain
-data.
Reconstruct complex time-domain data from the real part of frequency-domain data.
@@ -1141,8 +1126,7 @@ All functions
- Resample a VOI to match a target image space using nearest-neighbour
-interpolation.
Resample a VOI to match a target image space using nearest-neighbour interpolation.
@@ -1158,23 +1142,19 @@ All functions
- Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water).
Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / kg of tissue water).
- Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water).
Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / kg of tissue water).
- Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / Litre of tissue).
Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / Litre of tissue).
- Convert default LCM/TARQUIN concentration scaling to molal units with partial
-volume correction.
Convert default LCM/TARQUIN concentration scaling to molal units with partial volume correction.
@@ -1222,8 +1202,7 @@ All functions
- MEGA-PRESS sequence with ideal localisation pulses and Gaussian shaped
-editing pulse.
MEGA-PRESS sequence with ideal localisation pulses and Gaussian shaped editing pulse.
@@ -1251,13 +1230,11 @@ All functions
- STEAM sequence with ideal pulses and coherence order filtering to simulate
-gradient crushers.
STEAM sequence with ideal pulses and coherence order filtering to simulate gradient crushers.
- STEAM sequence with ideal pulses using the z-rotation gradient simulation
-method described by Young et al JMR 140, 146-152 (1999).
STEAM sequence with ideal pulses using the z-rotation gradient simulation method described by Young et al JMR 140, 146-152 (1999).
@@ -1293,8 +1270,7 @@ All functions
- Set the number of time-domain data points, truncating or zero-filling as
-appropriate.
Set the number of time-domain data points, truncating or zero-filling as appropriate.
@@ -1318,18 +1294,15 @@ All functions
- Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS
-sequence. Note, ideal pulses are assumed.
Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS sequence. Note, ideal pulses are assumed.
- Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS
-sequence. Note, ideal pulses are assumed.
Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS sequence. Note, ideal pulses are assumed.
- Simulate a macromolecular and lipid basis-set suitable for 1H brain MRS
-analysis.
Simulate a macromolecular and lipid basis-set suitable for 1H brain MRS analysis.
@@ -1353,8 +1326,7 @@ All functions
- Simulate an ideal pulse excitation profile by smoothing a top-hat function
-with a Gaussian.
Simulate an ideal pulse excitation profile by smoothing a top-hat function with a Gaussian.
@@ -1374,17 +1346,19 @@ All functions
- Simulate and fit some spectra with ABfit for benchmarking purposes. Basic
-timing and performance metrics will be printed.
Simulate and fit some spectra with ABfit for benchmarking purposes. Basic timing and performance metrics will be printed.
Example MEGA-PRESS data with significant B0 drift.
+
+
+ Simulate an example fMRS dataset for a block design fMRS experiment and export a BIDS structure.
- Simulate a typical metabolite basis set for benchmarking. Timing metrics will
-be printed on completion.
Simulate a typical metabolite basis set for benchmarking. Timing metrics will be printed on completion.
@@ -1400,8 +1374,7 @@ All functions
- Convert SPM style segmentation files to a single categorical image where
-the numerical values map as: 0) Other, 1) CSF, 2) GM and 3) WM.
Convert SPM style segmentation files to a single categorical image where the numerical values map as: 0) Other, 1) CSF, 2) GM and 3) WM.
@@ -1413,8 +1386,7 @@ All functions
- Plot the fitting results of an object of class fit_result with
-individual basis set components shown.
Plot the fitting results of an object of class fit_result with individual basis set components shown.
@@ -1459,6 +1431,10 @@ All functions svs_1h_brain_batch_analysis()
Batch interface to the standard SVS 1H brain analysis pipeline.
+
+
+ Perform a t-test on spectral data points.
@@ -1518,8 +1494,7 @@ All functions
- Fade a spectrum to zero by frequency domain multiplication with a tanh
-function. Note this operation distorts data points at the end of the FID.
Fade a spectrum to zero by frequency domain multiplication with a tanh function. Note this operation distorts data points at the end of the FID.
@@ -1549,7 +1524,7 @@ All functions
diff --git a/docs/reference/int_spec.html b/docs/reference/int_spec.html
index c7060fe7..783325a8 100644
--- a/docs/reference/int_spec.html
+++ b/docs/reference/int_spec.html
@@ -1,5 +1,5 @@
-Integrate a spectral region. — int_spec • Spectroscopy Analysis Tools (spant) Integrate a spectral region. — int_spec • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -118,7 +118,7 @@ Value
diff --git a/docs/reference/interleave_dyns.html b/docs/reference/interleave_dyns.html
index effe5543..441eff27 100644
--- a/docs/reference/interleave_dyns.html
+++ b/docs/reference/interleave_dyns.html
@@ -1,5 +1,5 @@
-Interleave the first and second half of a dynamic series. — interleave_dyns • Spectroscopy Analysis Tools (spant) Interleave the first and second half of a dynamic series. — interleave_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/inv_even_dyns.html b/docs/reference/inv_even_dyns.html
index 9f9d4fff..dcb781dc 100644
--- a/docs/reference/inv_even_dyns.html
+++ b/docs/reference/inv_even_dyns.html
@@ -1,5 +1,5 @@
-Invert even numbered dynamic scans starting from 1 (2,4,6...). — inv_even_dyns • Spectroscopy Analysis Tools (spant) Invert even numbered dynamic scans starting from 1 (2,4,6...). — inv_even_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/inv_odd_dyns.html b/docs/reference/inv_odd_dyns.html
index 26212e2b..78d64660 100644
--- a/docs/reference/inv_odd_dyns.html
+++ b/docs/reference/inv_odd_dyns.html
@@ -1,5 +1,5 @@
-Invert odd numbered dynamic scans starting from 1 (1,3,5...). — inv_odd_dyns • Spectroscopy Analysis Tools (spant) Invert odd numbered dynamic scans starting from 1 (1,3,5...). — inv_odd_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/is.def.html b/docs/reference/is.def.html
index f196ffd0..a67b9eba 100644
--- a/docs/reference/is.def.html
+++ b/docs/reference/is.def.html
@@ -1,5 +1,5 @@
-Check if an object is defined, which is the same as being not NULL. — is.def • Spectroscopy Analysis Tools (spant) Check if an object is defined, which is the same as being not NULL. — is.def • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/is_fd.html b/docs/reference/is_fd.html
index 3b0ca165..18a193aa 100644
--- a/docs/reference/is_fd.html
+++ b/docs/reference/is_fd.html
@@ -1,7 +1,5 @@
-Check if the chemical shift dimension of an MRS data object is in the
-frequency domain. — is_fd • Spectroscopy Analysis Tools (spant) Check if the chemical shift dimension of an MRS data object is in the frequency domain. — is_fd • Spectroscopy Analysis Tools (spant) Transform 2D MRSI data from k-space to image space in the x-y direction. — kspace2img_xy • Spectroscopy Analysis Tools (spant) Transform 2D MRSI data from k-space to image space in the x-y direction. — kspace2img_xy • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/l2_reg.html b/docs/reference/l2_reg.html
index 3d781d80..21aa9849 100644
--- a/docs/reference/l2_reg.html
+++ b/docs/reference/l2_reg.html
@@ -1,5 +1,5 @@
-Perform l2 regularisation artefact suppression. — l2_reg • Spectroscopy Analysis Tools (spant) Perform l2 regularisation artefact suppression. — l2_reg • Spectroscopy Analysis Tools (spant) Apply line-broadening (apodisation) to MRS data or basis object. — lb • Spectroscopy Analysis Tools (spant) Apply line-broadening (apodisation) to MRS data or basis object. — lb • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -123,7 +123,7 @@ Value
diff --git a/docs/reference/lofdc.html b/docs/reference/lofdc.html
index 5419b1ec..31347a25 100644
--- a/docs/reference/lofdc.html
+++ b/docs/reference/lofdc.html
@@ -1,5 +1,5 @@
-Correct linear frequency drift. — lofdc • Spectroscopy Analysis Tools (spant) Correct linear frequency drift. — lofdc • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -138,7 +138,7 @@ Value
diff --git a/docs/reference/lw2alpha.html b/docs/reference/lw2alpha.html
index b83db682..25da229b 100644
--- a/docs/reference/lw2alpha.html
+++ b/docs/reference/lw2alpha.html
@@ -1,7 +1,5 @@
-Covert a linewidth in Hz to an equivalent alpha value in the time-domain ie:
-x * exp(-t * alpha). — lw2alpha • Spectroscopy Analysis Tools (spant) Covert a linewidth in Hz to an equivalent alpha value in the time-domain ie: x * exp(-t * alpha). — lw2alpha • Spectroscopy Analysis Tools (spant) Covert a linewidth in Hz to an equivalent beta value in the time-domain ie:
-x * exp(-t * t * beta). — lw2beta • Spectroscopy Analysis Tools (spant) Covert a linewidth in Hz to an equivalent beta value in the time-domain ie: x * exp(-t * t * beta). — lw2beta • Spectroscopy Analysis Tools (spant) Make a basis-set object from a directory containing LCModel formatted RAW
-files. — make_basis_from_raw • Spectroscopy Analysis Tools (spant) Make a basis-set object from a directory containing LCModel formatted RAW files. — make_basis_from_raw • Spectroscopy Analysis Tools (spant) Mask an MRS dataset in the dynamic dimension. — mask_dyns • Spectroscopy Analysis Tools (spant) Mask an MRS dataset in the dynamic dimension. — mask_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/mask_fit_res.html b/docs/reference/mask_fit_res.html
index 97baaa3f..ebd91a99 100644
--- a/docs/reference/mask_fit_res.html
+++ b/docs/reference/mask_fit_res.html
@@ -1,5 +1,5 @@
-Mask fit result spectra depending on a vector of bool values. — mask_fit_res • Spectroscopy Analysis Tools (spant) Mask fit result spectra depending on a vector of bool values. — mask_fit_res • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -116,7 +116,7 @@ Value
diff --git a/docs/reference/mask_xy.html b/docs/reference/mask_xy.html
index 11bb577c..b0d38619 100644
--- a/docs/reference/mask_xy.html
+++ b/docs/reference/mask_xy.html
@@ -1,5 +1,5 @@
-Mask an MRSI dataset in the x-y direction — mask_xy • Spectroscopy Analysis Tools (spant) Mask an MRSI dataset in the x-y direction — mask_xy • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/mask_xy_corners.html b/docs/reference/mask_xy_corners.html
index 09b16cd2..2d13839d 100644
--- a/docs/reference/mask_xy_corners.html
+++ b/docs/reference/mask_xy_corners.html
@@ -1,5 +1,5 @@
-Mask the four corners of an MRSI dataset in the x-y plane. — mask_xy_corners • Spectroscopy Analysis Tools (spant) Mask the four corners of an MRSI dataset in the x-y plane. — mask_xy_corners • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/mask_xy_ellipse.html b/docs/reference/mask_xy_ellipse.html
index 1d8b02e4..e2e749ef 100644
--- a/docs/reference/mask_xy_ellipse.html
+++ b/docs/reference/mask_xy_ellipse.html
@@ -1,7 +1,5 @@
-Mask the voxels outside an elliptical region spanning the MRSI dataset in the
-x-y plane. — mask_xy_ellipse • Spectroscopy Analysis Tools (spant) Mask the voxels outside an elliptical region spanning the MRSI dataset in the x-y plane. — mask_xy_ellipse • Spectroscopy Analysis Tools (spant) Mask a 2D MRSI dataset in the x-y dimension. — mask_xy_mat • Spectroscopy Analysis Tools (spant) Mask a 2D MRSI dataset in the x-y dimension. — mask_xy_mat • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Value
diff --git a/docs/reference/mat2mrs_data.html b/docs/reference/mat2mrs_data.html
index 2e2895f3..ae55665f 100644
--- a/docs/reference/mat2mrs_data.html
+++ b/docs/reference/mat2mrs_data.html
@@ -1,7 +1,5 @@
-Convert a matrix (with spectral points in the column dimension and dynamics
-in the row dimensions) into a mrs_data object. — mat2mrs_data • Spectroscopy Analysis Tools (spant) Convert a matrix (with spectral points in the column dimension and dynamics in the row dimensions) into a mrs_data object. — mat2mrs_data • Spectroscopy Analysis Tools (spant) Matrix exponential function taken from complexplus package to reduce the
-number of spant dependencies. — matexp • Spectroscopy Analysis Tools (spant) Matrix exponential function taken from complexplus package to reduce the number of spant dependencies. — matexp • Spectroscopy Analysis Tools (spant) Apply the max operator to an MRS dataset. — max_mrs • Spectroscopy Analysis Tools (spant) Apply the max operator to an MRS dataset. — max_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/max_mrs_interp.html b/docs/reference/max_mrs_interp.html
index e4474764..52e63f3e 100644
--- a/docs/reference/max_mrs_interp.html
+++ b/docs/reference/max_mrs_interp.html
@@ -1,5 +1,5 @@
-Apply the max operator to an interpolated MRS dataset. — max_mrs_interp • Spectroscopy Analysis Tools (spant) Apply the max operator to an interpolated MRS dataset. — max_mrs_interp • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/mean.list.html b/docs/reference/mean.list.html
index b8eb3463..048306fd 100644
--- a/docs/reference/mean.list.html
+++ b/docs/reference/mean.list.html
@@ -1,5 +1,5 @@
-Calculate the mean spectrum from an mrs_data object. — mean.list • Spectroscopy Analysis Tools (spant) Calculate the mean spectrum from an mrs_data object. — mean.list • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/mean.mrs_data.html b/docs/reference/mean.mrs_data.html
index 5531a28d..79515014 100644
--- a/docs/reference/mean.mrs_data.html
+++ b/docs/reference/mean.mrs_data.html
@@ -1,5 +1,5 @@
-Calculate the mean spectrum from an mrs_data object. — mean.mrs_data • Spectroscopy Analysis Tools (spant) Calculate the mean spectrum from an mrs_data object. — mean.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/mean_dyn_blocks.html b/docs/reference/mean_dyn_blocks.html
index 10467098..4c042448 100644
--- a/docs/reference/mean_dyn_blocks.html
+++ b/docs/reference/mean_dyn_blocks.html
@@ -1,5 +1,5 @@
-Calculate the mean of adjacent dynamic scans. — mean_dyn_blocks • Spectroscopy Analysis Tools (spant) Calculate the mean of adjacent dynamic scans. — mean_dyn_blocks • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/mean_dyn_pairs.html b/docs/reference/mean_dyn_pairs.html
index 63e909ea..1a241126 100644
--- a/docs/reference/mean_dyn_pairs.html
+++ b/docs/reference/mean_dyn_pairs.html
@@ -1,5 +1,5 @@
-Calculate the pairwise means across a dynamic data set. — mean_dyn_pairs • Spectroscopy Analysis Tools (spant) Calculate the pairwise means across a dynamic data set. — mean_dyn_pairs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/mean_dyns.html b/docs/reference/mean_dyns.html
index 73fdbfa7..0daa27df 100644
--- a/docs/reference/mean_dyns.html
+++ b/docs/reference/mean_dyns.html
@@ -1,5 +1,5 @@
-Calculate the mean dynamic data. — mean_dyns • Spectroscopy Analysis Tools (spant) Calculate the mean dynamic data. — mean_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/mean_mrs_list.html b/docs/reference/mean_mrs_list.html
index 808b6c50..10d842c0 100644
--- a/docs/reference/mean_mrs_list.html
+++ b/docs/reference/mean_mrs_list.html
@@ -1,5 +1,5 @@
-Return the mean of a list of mrs_data objects. — mean_mrs_list • Spectroscopy Analysis Tools (spant) Return the mean of a list of mrs_data objects. — mean_mrs_list • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/mean_vec_blocks.html b/docs/reference/mean_vec_blocks.html
index 8fc92eaa..dd78b122 100644
--- a/docs/reference/mean_vec_blocks.html
+++ b/docs/reference/mean_vec_blocks.html
@@ -1,5 +1,5 @@
-Calculate the mean of adjacent blocks in a vector. — mean_vec_blocks • Spectroscopy Analysis Tools (spant) Calculate the mean of adjacent blocks in a vector. — mean_vec_blocks • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/median_dyns.html b/docs/reference/median_dyns.html
index 1039d4b5..9a085b10 100644
--- a/docs/reference/median_dyns.html
+++ b/docs/reference/median_dyns.html
@@ -1,5 +1,5 @@
-Calculate the median dynamic data. — median_dyns • Spectroscopy Analysis Tools (spant) Calculate the median dynamic data. — median_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/mod_td.html b/docs/reference/mod_td.html
index 76ad0a40..141ef09e 100644
--- a/docs/reference/mod_td.html
+++ b/docs/reference/mod_td.html
@@ -1,5 +1,5 @@
-Apply the Modulus operator to the time-domain MRS signal. — mod_td • Spectroscopy Analysis Tools (spant) Apply the Modulus operator to the time-domain MRS signal. — mod_td • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/mrs_data2basis.html b/docs/reference/mrs_data2basis.html
index 62f7d749..11797b91 100644
--- a/docs/reference/mrs_data2basis.html
+++ b/docs/reference/mrs_data2basis.html
@@ -1,7 +1,5 @@
-Convert an mrs_data object to basis object - where basis signals are spread
-across the dynamic dimension in the MRS data. — mrs_data2basis • Spectroscopy Analysis Tools (spant) Convert an mrs_data object to basis object - where basis signals are spread across the dynamic dimension in the MRS data. — mrs_data2basis • Spectroscopy Analysis Tools (spant) Create a BIDS file structure from a vector of MRS data paths or list of mrs_data objects. — mrs_data2bids • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Create a BIDS file structure from a vector of MRS data paths or list of mrs_data objects.
+ Source: R/fmrs.R
+ mrs_data2bids.Rd
+
+
+
+ Create a BIDS file structure from a vector of MRS data paths or list of
+mrs_data objects.
+
+
+
+ mrs_data2bids(
+ mrs_data,
+ output_dir,
+ suffix = NULL,
+ sub = NULL,
+ ses = NULL,
+ task = NULL,
+ acq = NULL,
+ nuc = NULL,
+ voi = NULL,
+ rec = NULL,
+ run = NULL,
+ echo = NULL,
+ inv = NULL,
+ skip_existing = TRUE
+)
+
+
+
+ Arguments
+ - mrs_data
+vector of MRS data paths or list of mrs_data objects.
- output_dir
+the base directory to create the BIDS structure.
- suffix
+optional vector of file suffixes. Default behaviour is to
+automatically determine these from the input data, however it is recommended
+that they are specified to allow more efficient skipping of existing data.
- sub
+optional vector of subject labels. If not specified, these will be
+automatically generated as a series of increasing zero-padded integer values
+corresponding to the mrs_data input indices.
- ses
+optional vector of session labels.
- task
+optional vector of task labels.
- acq
+optional vector of acquisition labels.
- nuc
+optional vector of nucleus labels.
- voi
+optional vector of volume of interest labels.
- rec
+optional vector of reconstruction labels.
- run
+optional vector of run indices.
- echo
+optional vector of echo time indices.
- inv
+optional vector of inversion indices.
- skip_existing
+skip any data files that have already been converted.
+Defaults to TRUE, set to FALSE to force an overwrite of any existing data
+files.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/mrs_data2mat.html b/docs/reference/mrs_data2mat.html
index cf5ff28c..9e47688a 100644
--- a/docs/reference/mrs_data2mat.html
+++ b/docs/reference/mrs_data2mat.html
@@ -1,7 +1,5 @@
-Convert mrs_data object to a matrix, with spectral points in the column
-dimension and dynamics in the row dimension. — mrs_data2mat • Spectroscopy Analysis Tools (spant) Convert mrs_data object to a matrix, with spectral points in the column dimension and dynamics in the row dimension. — mrs_data2mat • Spectroscopy Analysis Tools (spant) Convert mrs_data object to a matrix, with spectral points in the column dimension and dynamics in the row dimension. — mrs_data2spec_mat • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Convert mrs_data object to a matrix, with spectral points in the column dimension and dynamics in the row dimension.
+ Source: R/mrs_data_proc.R
+ mrs_data2spec_mat.Rd
+
+
+
+ Convert mrs_data object to a matrix, with spectral points in the column
+dimension and dynamics in the row dimension.
+
+
+
+ mrs_data2spec_mat(mrs_data, collapse = TRUE)
+
+
+
+ Arguments
+ - mrs_data
+MRS data object or list of MRS data objects.
- collapse
+collapse all other dimensions along the dynamic dimension, eg
+a 16x16 MRSI grid would be first collapsed across 256 dynamic scans.
+
+ Value
+
+
+MRS data matrix.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/mrs_data2vec.html b/docs/reference/mrs_data2vec.html
index fb172d68..a1fd654d 100644
--- a/docs/reference/mrs_data2vec.html
+++ b/docs/reference/mrs_data2vec.html
@@ -1,5 +1,5 @@
-Convert mrs_data object to a vector. — mrs_data2vec • Spectroscopy Analysis Tools (spant) Convert mrs_data object to a vector. — mrs_data2vec • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -126,7 +126,7 @@ Value
diff --git a/docs/reference/mvfftshift.html b/docs/reference/mvfftshift.html
index 92b0841b..976b3410 100644
--- a/docs/reference/mvfftshift.html
+++ b/docs/reference/mvfftshift.html
@@ -1,7 +1,5 @@
-Perform a fftshift on a matrix, with each column replaced by its shifted
-result. — mvfftshift • Spectroscopy Analysis Tools (spant) Perform a fftshift on a matrix, with each column replaced by its shifted result. — mvfftshift • Spectroscopy Analysis Tools (spant) Perform an ifftshift on a matrix, with each column replaced by its shifted
-result. — mvifftshift • Spectroscopy Analysis Tools (spant) Perform an ifftshift on a matrix, with each column replaced by its shifted result. — mvifftshift • Spectroscopy Analysis Tools (spant) Print fit coordinates from a single index. — n2coord • Spectroscopy Analysis Tools (spant) Print fit coordinates from a single index. — n2coord • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/nifti_flip_lr.html b/docs/reference/nifti_flip_lr.html
index 730abe3c..19860b3c 100644
--- a/docs/reference/nifti_flip_lr.html
+++ b/docs/reference/nifti_flip_lr.html
@@ -1,9 +1,5 @@
-Flip the x data dimension order of a nifti image. This corresponds to
-flipping MRI data in the left-right direction, assuming the data in save in
-neurological format (can check with fslorient program). — nifti_flip_lr • Spectroscopy Analysis Tools (spant) Flip the x data dimension order of a nifti image. This corresponds to flipping MRI data in the left-right direction, assuming the data in save in neurological format (can check with fslorient program). — nifti_flip_lr • Spectroscopy Analysis Tools (spant) Export a one-page pdf of a single fit result — one_page_pdf • Spectroscopy Analysis Tools (spant) Export a one-page pdf of a single fit result — one_page_pdf • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -108,7 +108,7 @@ Arguments
diff --git a/docs/reference/ortho3.html b/docs/reference/ortho3.html
index 13ade97d..5d7dd2fd 100644
--- a/docs/reference/ortho3.html
+++ b/docs/reference/ortho3.html
@@ -1,5 +1,5 @@
-Display an orthographic projection plot of a nifti object. — ortho3 • Spectroscopy Analysis Tools (spant) Display an orthographic projection plot of a nifti object. — ortho3 • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -172,7 +172,7 @@ Arguments
diff --git a/docs/reference/ortho3_inter.html b/docs/reference/ortho3_inter.html
index 090cc5e5..15948899 100644
--- a/docs/reference/ortho3_inter.html
+++ b/docs/reference/ortho3_inter.html
@@ -1,5 +1,5 @@
-Display an interactive orthographic projection plot of a nifti object. — ortho3_inter • Spectroscopy Analysis Tools (spant) Display an interactive orthographic projection plot of a nifti object. — ortho3_inter • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -132,7 +132,7 @@ Arguments
diff --git a/docs/reference/peak_info.html b/docs/reference/peak_info.html
index 09058bd8..41c8ffaf 100644
--- a/docs/reference/peak_info.html
+++ b/docs/reference/peak_info.html
@@ -1,7 +1,5 @@
-Search for the highest peak in a spectral region and return the frequency,
-height and FWHM. — peak_info • Spectroscopy Analysis Tools (spant) Search for the highest peak in a spectral region and return the frequency, height and FWHM. — peak_info • Spectroscopy Analysis Tools (spant) Papoulis-Gerchberg (PG) algorithm method for k-space extrapolation. — pg_extrap_xy • Spectroscopy Analysis Tools (spant) Papoulis-Gerchberg (PG) algorithm method for k-space extrapolation. — pg_extrap_xy • Spectroscopy Analysis Tools (spant) Apply phasing parameters to MRS data. — phase • Spectroscopy Analysis Tools (spant) Apply phasing parameters to MRS data. — phase • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/phase_ref_1h_brain.html b/docs/reference/phase_ref_1h_brain.html
new file mode 100644
index 00000000..8707a74a
--- /dev/null
+++ b/docs/reference/phase_ref_1h_brain.html
@@ -0,0 +1,131 @@
+
+Corrected zero order phase and chemical shift offset in 1H MRS data from the brain. — phase_ref_1h_brain • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Corrected zero order phase and chemical shift offset in 1H MRS data from the brain.
+ Source: R/rats.R
+ phase_ref_1h_brain.Rd
+
+
+
+ Corrected zero order phase and chemical shift offset in 1H MRS data from the
+brain.
+
+
+
+ phase_ref_1h_brain(mrs_data, mean_ref = FALSE, ret_corr_only = TRUE)
+
+
+
+ Arguments
+ - mrs_data
+MRS data to be corrected.
- mean_ref
+apply the phase and offset of the mean spectrum to all
+others. Default is FALSE.
- ret_corr_only
+return the corrected data only.
+
+ Value
+
+
+corrected MRS data.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/plot.fit_result.html b/docs/reference/plot.fit_result.html
index e54d3bc1..836a53ee 100644
--- a/docs/reference/plot.fit_result.html
+++ b/docs/reference/plot.fit_result.html
@@ -1,5 +1,5 @@
-Plot the fitting results of an object of class fit_result. — plot.fit_result • Spectroscopy Analysis Tools (spant) Plot the fitting results of an object of class fit_result. — plot.fit_result • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -207,7 +207,7 @@ Arguments
diff --git a/docs/reference/plot.mrs_data.html b/docs/reference/plot.mrs_data.html
index fabcc35b..bb2ec651 100644
--- a/docs/reference/plot.mrs_data.html
+++ b/docs/reference/plot.mrs_data.html
@@ -1,5 +1,5 @@
-Plotting method for objects of class mrs_data. — plot.mrs_data • Spectroscopy Analysis Tools (spant) Plotting method for objects of class mrs_data. — plot.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -287,7 +287,7 @@ Arguments
diff --git a/docs/reference/plot_bc.html b/docs/reference/plot_bc.html
index 4f8309b4..b48142cc 100644
--- a/docs/reference/plot_bc.html
+++ b/docs/reference/plot_bc.html
@@ -1,5 +1,5 @@
-Convenience function to plot a baseline estimate with the original data. — plot_bc • Spectroscopy Analysis Tools (spant) Convenience function to plot a baseline estimate with the original data. — plot_bc • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -108,7 +108,7 @@ Arguments
diff --git a/docs/reference/plot_reg.html b/docs/reference/plot_reg.html
index ae1acbe7..2addb2f6 100644
--- a/docs/reference/plot_reg.html
+++ b/docs/reference/plot_reg.html
@@ -1,5 +1,5 @@
-Plot regressors as an image. — plot_reg • Spectroscopy Analysis Tools (spant) Plot regressors as an image. — plot_reg • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/plot_slice_fit.html b/docs/reference/plot_slice_fit.html
index fbc7b560..57f1af8a 100644
--- a/docs/reference/plot_slice_fit.html
+++ b/docs/reference/plot_slice_fit.html
@@ -1,5 +1,5 @@
-Plot a 2D slice from an MRSI fit result object. — plot_slice_fit • Spectroscopy Analysis Tools (spant) Plot a 2D slice from an MRSI fit result object. — plot_slice_fit • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -129,7 +129,7 @@ Arguments
diff --git a/docs/reference/plot_slice_fit_inter.html b/docs/reference/plot_slice_fit_inter.html
index 4eed104a..da105a7d 100644
--- a/docs/reference/plot_slice_fit_inter.html
+++ b/docs/reference/plot_slice_fit_inter.html
@@ -1,5 +1,5 @@
-Plot a 2D slice from an MRSI fit result object. — plot_slice_fit_inter • Spectroscopy Analysis Tools (spant) Plot a 2D slice from an MRSI fit result object. — plot_slice_fit_inter • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -134,7 +134,7 @@ Arguments
diff --git a/docs/reference/plot_slice_map.html b/docs/reference/plot_slice_map.html
index 553e9ac8..ffb2a134 100644
--- a/docs/reference/plot_slice_map.html
+++ b/docs/reference/plot_slice_map.html
@@ -1,5 +1,5 @@
-Plot a slice from a 7 dimensional array. — plot_slice_map • Spectroscopy Analysis Tools (spant) Plot a slice from a 7 dimensional array. — plot_slice_map • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -153,7 +153,7 @@ Arguments
diff --git a/docs/reference/plot_slice_map_inter.html b/docs/reference/plot_slice_map_inter.html
index 40d33b42..90968f66 100644
--- a/docs/reference/plot_slice_map_inter.html
+++ b/docs/reference/plot_slice_map_inter.html
@@ -1,7 +1,5 @@
-Plot an interactive slice map from a data array where voxels can be selected
-to display a corresponding spectrum. — plot_slice_map_inter • Spectroscopy Analysis Tools (spant) Plot an interactive slice map from a data array where voxels can be selected to display a corresponding spectrum. — plot_slice_map_inter • Spectroscopy Analysis Tools (spant) Plot the spectral standard deviation. — plot_spec_sd • Spectroscopy Analysis Tools (spant) Plot the spectral standard deviation. — plot_spec_sd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Arguments
diff --git a/docs/reference/plot_voi_overlay.html b/docs/reference/plot_voi_overlay.html
index 9a782e88..bbbbf35e 100644
--- a/docs/reference/plot_voi_overlay.html
+++ b/docs/reference/plot_voi_overlay.html
@@ -1,5 +1,5 @@
-Plot a volume as an image overlay. — plot_voi_overlay • Spectroscopy Analysis Tools (spant) Plot a volume as an image overlay. — plot_voi_overlay • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -116,7 +116,7 @@ Arguments
diff --git a/docs/reference/plot_voi_overlay_seg.html b/docs/reference/plot_voi_overlay_seg.html
index 3d4e74ff..0e800ff2 100644
--- a/docs/reference/plot_voi_overlay_seg.html
+++ b/docs/reference/plot_voi_overlay_seg.html
@@ -1,5 +1,5 @@
-Plot a volume as an overlay on a segmented brain volume. — plot_voi_overlay_seg • Spectroscopy Analysis Tools (spant) Plot a volume as an overlay on a segmented brain volume. — plot_voi_overlay_seg • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Arguments
diff --git a/docs/reference/ppm.html b/docs/reference/ppm.html
index c352327a..ee4696e2 100644
--- a/docs/reference/ppm.html
+++ b/docs/reference/ppm.html
@@ -1,5 +1,5 @@
-Return the ppm scale of an MRS dataset or fit result. — ppm • Spectroscopy Analysis Tools (spant) Return the ppm scale of an MRS dataset or fit result. — ppm • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -132,7 +132,7 @@ Value
diff --git a/docs/reference/precomp.html b/docs/reference/precomp.html
index 822d7336..df3d2c6c 100644
--- a/docs/reference/precomp.html
+++ b/docs/reference/precomp.html
@@ -1,7 +1,5 @@
-Save function results to file and load on subsequent calls to avoid repeat
-computation. — precomp • Spectroscopy Analysis Tools (spant) Save function results to file and load on subsequent calls to avoid repeat computation. — precomp • Spectroscopy Analysis Tools (spant) Preprocess and perform quality assessment of a single SVS data set. — preproc_svs • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Preprocess and perform quality assessment of a single SVS data set.
+ Source: R/fmrs.R
+ preproc_svs.Rd
+
+
+
+ Preprocess and perform quality assessment of a single SVS data set.
+
+
+
+ preproc_svs(path, label = NULL, output_dir = NULL, ref_inds = NULL)
+
+
+
+ Arguments
+ - path
+path to the fMRS data file or IMA directory.
- label
+a label to describe the data set.
- output_dir
+output directory.
- ref_inds
+a vector of 1-based indices for any water reference dynamic
+scans.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/preproc_svs_dataset.html b/docs/reference/preproc_svs_dataset.html
new file mode 100644
index 00000000..07c3a29b
--- /dev/null
+++ b/docs/reference/preproc_svs_dataset.html
@@ -0,0 +1,148 @@
+
+Preprocess and perform quality assessment of one or more SVS data sets. — preproc_svs_dataset • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Preprocess and perform quality assessment of one or more SVS data sets.
+ Source: R/fmrs.R
+ preproc_svs_dataset.Rd
+
+
+
+ Preprocess and perform quality assessment of one or more SVS data sets.
+
+
+
+ preproc_svs_dataset(
+ paths,
+ labels = NULL,
+ output_dir = "spant_analysis",
+ exclude_labels = NULL,
+ overwrite = FALSE,
+ ref_inds = NULL,
+ return_results = FALSE
+)
+
+
+
+ Arguments
+ - paths
+paths to the fMRS data file or IMA directory.
- labels
+labels to describe each data set.
- output_dir
+output directory.
- exclude_labels
+vector of labels of scans to exclude, eg poor quality
+data.
- overwrite
+overwrite saved results, defaults to FALSE.
- ref_inds
+a vector of 1-based indices for any water reference dynamic
+scans.
- return_results
+function will return key outputs, defaults to FALSE.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/print.fit_result.html b/docs/reference/print.fit_result.html
index 297f28dc..5f434e57 100644
--- a/docs/reference/print.fit_result.html
+++ b/docs/reference/print.fit_result.html
@@ -1,5 +1,5 @@
-Print a summary of an object of class fit_result. — print.fit_result • Spectroscopy Analysis Tools (spant) Print a summary of an object of class fit_result. — print.fit_result • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -105,7 +105,7 @@ Arguments
diff --git a/docs/reference/print.mrs_data.html b/docs/reference/print.mrs_data.html
index 51199017..e1561eb2 100644
--- a/docs/reference/print.mrs_data.html
+++ b/docs/reference/print.mrs_data.html
@@ -1,5 +1,5 @@
-Print a summary of mrs_data parameters. — print.mrs_data • Spectroscopy Analysis Tools (spant) Print a summary of mrs_data parameters. — print.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -109,7 +109,7 @@ Arguments
diff --git a/docs/reference/qn_states.html b/docs/reference/qn_states.html
index 0f42f2f9..d7aa6715 100644
--- a/docs/reference/qn_states.html
+++ b/docs/reference/qn_states.html
@@ -1,5 +1,5 @@
-Get the quantum coherence matrix for a spin system. — qn_states • Spectroscopy Analysis Tools (spant) Get the quantum coherence matrix for a spin system. — qn_states • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/rats.html b/docs/reference/rats.html
index 5a39a396..93585e08 100644
--- a/docs/reference/rats.html
+++ b/docs/reference/rats.html
@@ -1,5 +1,5 @@
-Robust Alignment to a Target Spectrum (RATS). — rats • Spectroscopy Analysis Tools (spant) Robust Alignment to a Target Spectrum (RATS). — rats • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -207,7 +207,7 @@ Value
diff --git a/docs/reference/re_weighting.html b/docs/reference/re_weighting.html
index d21caf21..8b0b070a 100644
--- a/docs/reference/re_weighting.html
+++ b/docs/reference/re_weighting.html
@@ -1,5 +1,5 @@
-Apply a weighting to the FID to enhance spectral resolution. — re_weighting • Spectroscopy Analysis Tools (spant) Apply a weighting to the FID to enhance spectral resolution. — re_weighting • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/read_basis.html b/docs/reference/read_basis.html
index da9b94af..eb6f8557 100644
--- a/docs/reference/read_basis.html
+++ b/docs/reference/read_basis.html
@@ -1,5 +1,5 @@
-Read a basis file in LCModel .basis format. — read_basis • Spectroscopy Analysis Tools (spant) Read a basis file in LCModel .basis format. — read_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/read_ima_coil_dir.html b/docs/reference/read_ima_coil_dir.html
index 28c02de0..4f073cd8 100644
--- a/docs/reference/read_ima_coil_dir.html
+++ b/docs/reference/read_ima_coil_dir.html
@@ -1,9 +1,5 @@
-Read a directory containing Siemens MRS IMA files and combine along the coil
-dimension. Note that the coil ID is inferred from the sorted file name and
-should be checked when consistency is required between two directories. — read_ima_coil_dir • Spectroscopy Analysis Tools (spant) Read a directory containing Siemens MRS IMA files and combine along the coil dimension. Note that the coil ID is inferred from the sorted file name and should be checked when consistency is required between two directories. — read_ima_coil_dir • Spectroscopy Analysis Tools (spant) Read a directory containing Siemens MRS IMA files and combine along the
-dynamic dimension. Note that the coil ID is inferred from the sorted file
-name and should be checked when consistency is required. — read_ima_dyn_dir • Spectroscopy Analysis Tools (spant) Read a directory containing Siemens MRS IMA files and combine along the dynamic dimension. Note that the coil ID is inferred from the sorted file name and should be checked when consistency is required. — read_ima_dyn_dir • Spectroscopy Analysis Tools (spant) Read an LCModel formatted coord file containing fit information. — read_lcm_coord • Spectroscopy Analysis Tools (spant) Read an LCModel formatted coord file containing fit information. — read_lcm_coord • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -107,7 +107,7 @@ Value
diff --git a/docs/reference/read_mrs.html b/docs/reference/read_mrs.html
index 3ac2a36b..2cf36b20 100644
--- a/docs/reference/read_mrs.html
+++ b/docs/reference/read_mrs.html
@@ -1,5 +1,5 @@
-Read MRS data from a file. — read_mrs • Spectroscopy Analysis Tools (spant) Read MRS data from a file. — read_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -88,7 +88,8 @@ Read MRS data from a file.
full_fid = FALSE,
omit_svs_ref_scans = TRUE,
verbose = FALSE,
- extra = NULL
+ extra = NULL,
+ fid_filt_dist = NULL
)
@@ -140,6 +141,13 @@ Arguments
an optional data frame to provide additional variables for use
in subsequent analysis steps, eg id or grouping variables.
fid_filt_dist
+indicate if the data has a distorted FID due to a
+brick-wall filter being used to downsample the data. Default is to auto
+detect this from the data, but TRUE or FALSE options can be given to override
+detection.
Value
@@ -183,7 +191,7 @@ Examples
diff --git a/docs/reference/read_mrs_tqn.html b/docs/reference/read_mrs_tqn.html
index 5766362f..84bdaf3a 100644
--- a/docs/reference/read_mrs_tqn.html
+++ b/docs/reference/read_mrs_tqn.html
@@ -1,5 +1,5 @@
-Read MRS data using the TARQUIN software package. — read_mrs_tqn • Spectroscopy Analysis Tools (spant) Read MRS data using the TARQUIN software package. — read_mrs_tqn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -131,7 +131,7 @@ Examples
diff --git a/docs/reference/read_pulse_ascii.html b/docs/reference/read_pulse_ascii.html
index c9e0d43c..ab11c9cc 100644
--- a/docs/reference/read_pulse_ascii.html
+++ b/docs/reference/read_pulse_ascii.html
@@ -1,5 +1,5 @@
-Read an ASCII formatted pulse file. — read_pulse_ascii • Spectroscopy Analysis Tools (spant) Read an ASCII formatted pulse file. — read_pulse_ascii • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/read_pulse_bruker.html b/docs/reference/read_pulse_bruker.html
index c92bf76a..dbe9073b 100644
--- a/docs/reference/read_pulse_bruker.html
+++ b/docs/reference/read_pulse_bruker.html
@@ -1,5 +1,5 @@
-Read a Bruker formatted pulse file — read_pulse_bruker • Spectroscopy Analysis Tools (spant) Read a Bruker formatted pulse file — read_pulse_bruker • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/read_pulse_pta.html b/docs/reference/read_pulse_pta.html
index 72e1b6d4..a0fac3c3 100644
--- a/docs/reference/read_pulse_pta.html
+++ b/docs/reference/read_pulse_pta.html
@@ -1,5 +1,5 @@
-Read a .pta formatted pulse file compatible with Siemens PulseTool. — read_pulse_pta • Spectroscopy Analysis Tools (spant) Read a .pta formatted pulse file compatible with Siemens PulseTool. — read_pulse_pta • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/read_siemens_txt_hdr.html b/docs/reference/read_siemens_txt_hdr.html
index 23fb8c70..3a17d87c 100644
--- a/docs/reference/read_siemens_txt_hdr.html
+++ b/docs/reference/read_siemens_txt_hdr.html
@@ -1,5 +1,5 @@
-Read the text format header found in Siemens IMA and TWIX data files. — read_siemens_txt_hdr • Spectroscopy Analysis Tools (spant) Read the text format header found in Siemens IMA and TWIX data files. — read_siemens_txt_hdr • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -78,7 +78,7 @@ Read the text format header found in Siemens IMA and TWIX data files.
- read_siemens_txt_hdr(input, version = "vd", verbose, offset = 0)
+ read_siemens_txt_hdr(input, version = "vd", verbose = FALSE, offset = 0)
@@ -118,7 +118,7 @@ Value
diff --git a/docs/reference/read_tqn_fit.html b/docs/reference/read_tqn_fit.html
index 4da6c25e..a1630420 100644
--- a/docs/reference/read_tqn_fit.html
+++ b/docs/reference/read_tqn_fit.html
@@ -1,5 +1,5 @@
-Reader for csv fit results generated by TARQUIN. — read_tqn_fit • Spectroscopy Analysis Tools (spant) Reader for csv fit results generated by TARQUIN. — read_tqn_fit • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -113,7 +113,7 @@ Examples
diff --git a/docs/reference/read_tqn_result.html b/docs/reference/read_tqn_result.html
index 36659714..68a3e98c 100644
--- a/docs/reference/read_tqn_result.html
+++ b/docs/reference/read_tqn_result.html
@@ -1,5 +1,5 @@
-Reader for csv results generated by TARQUIN. — read_tqn_result • Spectroscopy Analysis Tools (spant) Reader for csv results generated by TARQUIN. — read_tqn_result • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -117,7 +117,7 @@ Examples
diff --git a/docs/reference/recon_imag.html b/docs/reference/recon_imag.html
index d2a72225..5bc3b1eb 100644
--- a/docs/reference/recon_imag.html
+++ b/docs/reference/recon_imag.html
@@ -1,7 +1,5 @@
-Reconstruct complex time-domain data from the real part of frequency-domain
-data. — recon_imag • Spectroscopy Analysis Tools (spant) Reconstruct complex time-domain data from the real part of frequency-domain data. — recon_imag • Spectroscopy Analysis Tools (spant) Reconstruct complex time-domain data from the real part of frequency-domain
-data. — recon_imag_vec • Spectroscopy Analysis Tools (spant) Reconstruct complex time-domain data from the real part of frequency-domain data. — recon_imag_vec • Spectroscopy Analysis Tools (spant) Reconstruct 2D MRSI data from a twix file loaded with read_mrs. — recon_twix_2d_mrsi • Spectroscopy Analysis Tools (spant) Reconstruct 2D MRSI data from a twix file loaded with read_mrs. — recon_twix_2d_mrsi • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/rectangular_mask.html b/docs/reference/rectangular_mask.html
index a2117283..6e469bc9 100644
--- a/docs/reference/rectangular_mask.html
+++ b/docs/reference/rectangular_mask.html
@@ -1,5 +1,5 @@
-Create a rectangular mask stored as a matrix of logical values. — rectangular_mask • Spectroscopy Analysis Tools (spant) Create a rectangular mask stored as a matrix of logical values. — rectangular_mask • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -130,7 +130,7 @@ Value
diff --git a/docs/reference/reexports.html b/docs/reference/reexports.html
index 694a75d1..a59e8379 100644
--- a/docs/reference/reexports.html
+++ b/docs/reference/reexports.html
@@ -1,5 +1,5 @@
-Objects exported from other packages — reexports • Spectroscopy Analysis Tools (spant) Objects exported from other packages — reexports • Spectroscopy Analysis Tools (spant)
Spectroscopy Analysis Tools (spant)
- 2.21.0
+ 2.22.0
@@ -103,7 +103,7 @@ Objects exported from other packages
diff --git a/docs/reference/rep_array_dim.html b/docs/reference/rep_array_dim.html
index b9c49b4a..48c0a5ed 100644
--- a/docs/reference/rep_array_dim.html
+++ b/docs/reference/rep_array_dim.html
@@ -1,5 +1,5 @@
-Repeat an array over a given dimension. — rep_array_dim • Spectroscopy Analysis Tools (spant) Repeat an array over a given dimension. — rep_array_dim • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/rep_dyn.html b/docs/reference/rep_dyn.html
index 6bbfb0ef..89a4bb9b 100644
--- a/docs/reference/rep_dyn.html
+++ b/docs/reference/rep_dyn.html
@@ -1,5 +1,5 @@
-Replicate a scan in the dynamic dimension. — rep_dyn • Spectroscopy Analysis Tools (spant) Replicate a scan in the dynamic dimension. — rep_dyn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/rep_mrs.html b/docs/reference/rep_mrs.html
index 67730b5c..becb8f00 100644
--- a/docs/reference/rep_mrs.html
+++ b/docs/reference/rep_mrs.html
@@ -1,5 +1,5 @@
-Replicate a scan over a given dimension. — rep_mrs • Spectroscopy Analysis Tools (spant) Replicate a scan over a given dimension. — rep_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -138,7 +138,7 @@ Value
diff --git a/docs/reference/resample_basis.html b/docs/reference/resample_basis.html
index b0f2ab17..c7a6222a 100644
--- a/docs/reference/resample_basis.html
+++ b/docs/reference/resample_basis.html
@@ -1,5 +1,5 @@
-Resample a basis-set to match a mrs_data acquisition. — resample_basis • Spectroscopy Analysis Tools (spant) Resample a basis-set to match a mrs_data acquisition. — resample_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -116,7 +116,7 @@ Value
diff --git a/docs/reference/resample_img.html b/docs/reference/resample_img.html
index f1e7beaf..b0cc8f71 100644
--- a/docs/reference/resample_img.html
+++ b/docs/reference/resample_img.html
@@ -1,5 +1,5 @@
-Resample an image to match a target image space. — resample_img • Spectroscopy Analysis Tools (spant) Resample an image to match a target image space. — resample_img • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/resample_voi.html b/docs/reference/resample_voi.html
index 8fbfa836..a29ab096 100644
--- a/docs/reference/resample_voi.html
+++ b/docs/reference/resample_voi.html
@@ -1,7 +1,5 @@
-Resample a VOI to match a target image space using nearest-neighbour
-interpolation. — resample_voi • Spectroscopy Analysis Tools (spant) Resample a VOI to match a target image space using nearest-neighbour interpolation. — resample_voi • Spectroscopy Analysis Tools (spant) Reslice a nifti object to match the orientation of mrs data. — reslice_to_mrs • Spectroscopy Analysis Tools (spant) Reslice a nifti object to match the orientation of mrs data. — reslice_to_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/reson_table2mrs_data.html b/docs/reference/reson_table2mrs_data.html
index d75579ee..c5a2167a 100644
--- a/docs/reference/reson_table2mrs_data.html
+++ b/docs/reference/reson_table2mrs_data.html
@@ -1,5 +1,5 @@
-Generate mrs_data from a table of single Lorentzian resonances. — reson_table2mrs_data • Spectroscopy Analysis Tools (spant) Generate mrs_data from a table of single Lorentzian resonances. — reson_table2mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -119,7 +119,7 @@ Value
diff --git a/docs/reference/rm_dyns.html b/docs/reference/rm_dyns.html
index 5d5ef692..573e1f51 100644
--- a/docs/reference/rm_dyns.html
+++ b/docs/reference/rm_dyns.html
@@ -1,5 +1,5 @@
-Remove a subset of dynamic scans. — rm_dyns • Spectroscopy Analysis Tools (spant) Remove a subset of dynamic scans. — rm_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/scale_amp_molal.html b/docs/reference/scale_amp_molal.html
index aaeee1f2..7acb8cb0 100644
--- a/docs/reference/scale_amp_molal.html
+++ b/docs/reference/scale_amp_molal.html
@@ -1,7 +1,5 @@
-Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water). — scale_amp_molal • Spectroscopy Analysis Tools (spant) Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / kg of tissue water). — scale_amp_molal • Spectroscopy Analysis Tools (spant)
Spectroscopy Analysis Tools (spant)
- 2.21.0
+ 2.22.0
@@ -76,8 +74,7 @@
- Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water).
+ Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / kg of tissue water).
Source: R/amp_scaling.R
scale_amp_molal.Rd
@@ -163,7 +160,7 @@ Value
diff --git a/docs/reference/scale_amp_molal_pvc.html b/docs/reference/scale_amp_molal_pvc.html
index 962d6afc..4d194abd 100644
--- a/docs/reference/scale_amp_molal_pvc.html
+++ b/docs/reference/scale_amp_molal_pvc.html
@@ -1,7 +1,5 @@
-Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water). — scale_amp_molal_pvc • Spectroscopy Analysis Tools (spant)
@@ -75,8 +73,7 @@
- Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water).
+ Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / kg of tissue water).
Source: R/amp_scaling.R
scale_amp_molal_pvc.Rd
@@ -141,7 +138,7 @@ Value
diff --git a/docs/reference/scale_amp_molar.html b/docs/reference/scale_amp_molar.html
index 02358d91..dc87a338 100644
--- a/docs/reference/scale_amp_molar.html
+++ b/docs/reference/scale_amp_molar.html
@@ -1,7 +1,5 @@
-Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / Litre of tissue). — scale_amp_molar • Spectroscopy Analysis Tools (spant) Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / Litre of tissue). — scale_amp_molar • Spectroscopy Analysis Tools (spant) Convert default LCM/TARQUIN concentration scaling to molal units with partial
-volume correction. — scale_amp_molar2molal_pvc • Spectroscopy Analysis Tools (spant) Convert default LCM/TARQUIN concentration scaling to molal units with partial volume correction. — scale_amp_molar2molal_pvc • Spectroscopy Analysis Tools (spant) Scale fitted amplitudes to a ratio of signal amplitude. — scale_amp_ratio • Spectroscopy Analysis Tools (spant) Scale fitted amplitudes to a ratio of signal amplitude. — scale_amp_ratio • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -116,7 +116,7 @@ Value
diff --git a/docs/reference/scale_amp_ratio_value.html b/docs/reference/scale_amp_ratio_value.html
index 2036837a..6af8ac51 100644
--- a/docs/reference/scale_amp_ratio_value.html
+++ b/docs/reference/scale_amp_ratio_value.html
@@ -1,5 +1,5 @@
-Scale fitted amplitudes to a ratio of signal amplitude. — scale_amp_ratio_value • Spectroscopy Analysis Tools (spant) Scale fitted amplitudes to a ratio of signal amplitude. — scale_amp_ratio_value • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/scale_amp_water_ratio.html b/docs/reference/scale_amp_water_ratio.html
index 5b25e884..35a76b00 100644
--- a/docs/reference/scale_amp_water_ratio.html
+++ b/docs/reference/scale_amp_water_ratio.html
@@ -1,5 +1,5 @@
-Scale metabolite amplitudes as a ratio to the unsuppressed water amplitude. — scale_amp_water_ratio • Spectroscopy Analysis Tools (spant) Scale metabolite amplitudes as a ratio to the unsuppressed water amplitude. — scale_amp_water_ratio • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/scale_basis_amp.html b/docs/reference/scale_basis_amp.html
index 9401c3f1..5a58b5e5 100644
--- a/docs/reference/scale_basis_amp.html
+++ b/docs/reference/scale_basis_amp.html
@@ -1,5 +1,5 @@
-Scale a basis object by a scalar. — scale_basis_amp • Spectroscopy Analysis Tools (spant) Scale a basis object by a scalar. — scale_basis_amp • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/scale_basis_from_singlet.html b/docs/reference/scale_basis_from_singlet.html
index 0d542bc8..c9a19e77 100644
--- a/docs/reference/scale_basis_from_singlet.html
+++ b/docs/reference/scale_basis_from_singlet.html
@@ -1,5 +1,5 @@
-Scale a basis-set to be consistent with spant assumptions for water scaling. — scale_basis_from_singlet • Spectroscopy Analysis Tools (spant) Scale a basis-set to be consistent with spant assumptions for water scaling. — scale_basis_from_singlet • Spectroscopy Analysis Tools (spant)
Spectroscopy Analysis Tools (spant)
- 2.21.0
+ 2.22.0
@@ -127,7 +127,7 @@ Value
diff --git a/docs/reference/scale_mrs_amp.html b/docs/reference/scale_mrs_amp.html
index b5501a0d..990f058a 100644
--- a/docs/reference/scale_mrs_amp.html
+++ b/docs/reference/scale_mrs_amp.html
@@ -1,5 +1,5 @@
-Scale an mrs_data object by a scalar or vector or amplitudes. — scale_mrs_amp • Spectroscopy Analysis Tools (spant) Scale an mrs_data object by a scalar or vector or amplitudes. — scale_mrs_amp • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/scale_spec.html b/docs/reference/scale_spec.html
index 4f6ea835..6b3ddba4 100644
--- a/docs/reference/scale_spec.html
+++ b/docs/reference/scale_spec.html
@@ -1,5 +1,5 @@
-Scale mrs_data to a spectral region. — scale_spec • Spectroscopy Analysis Tools (spant) Scale mrs_data to a spectral region. — scale_spec • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -141,7 +141,7 @@ Value
diff --git a/docs/reference/sd.html b/docs/reference/sd.html
index ea1eec9f..3ae4dfd4 100644
--- a/docs/reference/sd.html
+++ b/docs/reference/sd.html
@@ -1,5 +1,5 @@
-Calculate the standard deviation spectrum from an mrs_data object. — sd • Spectroscopy Analysis Tools (spant) Calculate the standard deviation spectrum from an mrs_data object. — sd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/sd.mrs_data.html b/docs/reference/sd.mrs_data.html
index 3f92a49f..13bdda85 100644
--- a/docs/reference/sd.mrs_data.html
+++ b/docs/reference/sd.mrs_data.html
@@ -1,5 +1,5 @@
-Calculate the standard deviation spectrum from an mrs_data object. — sd.mrs_data • Spectroscopy Analysis Tools (spant) Calculate the standard deviation spectrum from an mrs_data object. — sd.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/seconds.html b/docs/reference/seconds.html
index b34d6627..467ee17f 100644
--- a/docs/reference/seconds.html
+++ b/docs/reference/seconds.html
@@ -1,5 +1,5 @@
-Return a time scale vector to match the FID of an MRS data object. — seconds • Spectroscopy Analysis Tools (spant) Return a time scale vector to match the FID of an MRS data object. — seconds • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/seq_cpmg_ideal.html b/docs/reference/seq_cpmg_ideal.html
index 547e96ab..45727c86 100644
--- a/docs/reference/seq_cpmg_ideal.html
+++ b/docs/reference/seq_cpmg_ideal.html
@@ -1,5 +1,5 @@
-CPMG style sequence with ideal pulses. — seq_cpmg_ideal • Spectroscopy Analysis Tools (spant) CPMG style sequence with ideal pulses. — seq_cpmg_ideal • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/seq_mega_press_ideal.html b/docs/reference/seq_mega_press_ideal.html
index 0769b8b4..a9cd7fa0 100644
--- a/docs/reference/seq_mega_press_ideal.html
+++ b/docs/reference/seq_mega_press_ideal.html
@@ -1,7 +1,5 @@
-MEGA-PRESS sequence with ideal localisation pulses and Gaussian shaped
-editing pulse. — seq_mega_press_ideal • Spectroscopy Analysis Tools (spant) MEGA-PRESS sequence with ideal localisation pulses and Gaussian shaped editing pulse. — seq_mega_press_ideal • Spectroscopy Analysis Tools (spant) PRESS sequence with shaped refocusing pulses. — seq_press_2d_shaped • Spectroscopy Analysis Tools (spant) PRESS sequence with shaped refocusing pulses. — seq_press_2d_shaped • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -165,7 +165,7 @@ Value
diff --git a/docs/reference/seq_press_ideal.html b/docs/reference/seq_press_ideal.html
index 8c976856..72c3af3d 100644
--- a/docs/reference/seq_press_ideal.html
+++ b/docs/reference/seq_press_ideal.html
@@ -1,5 +1,5 @@
-PRESS sequence with ideal pulses. — seq_press_ideal • Spectroscopy Analysis Tools (spant) PRESS sequence with ideal pulses. — seq_press_ideal • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/seq_pulse_acquire.html b/docs/reference/seq_pulse_acquire.html
index 4a88fc64..ad80571e 100644
--- a/docs/reference/seq_pulse_acquire.html
+++ b/docs/reference/seq_pulse_acquire.html
@@ -1,5 +1,5 @@
-Simple pulse and acquire sequence with ideal pulses. — seq_pulse_acquire • Spectroscopy Analysis Tools (spant) Simple pulse and acquire sequence with ideal pulses. — seq_pulse_acquire • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/seq_slaser_ideal.html b/docs/reference/seq_slaser_ideal.html
index 74688f4d..eb83e8e3 100644
--- a/docs/reference/seq_slaser_ideal.html
+++ b/docs/reference/seq_slaser_ideal.html
@@ -1,5 +1,5 @@
-sLASER sequence with ideal pulses. — seq_slaser_ideal • Spectroscopy Analysis Tools (spant) sLASER sequence with ideal pulses. — seq_slaser_ideal • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -126,7 +126,7 @@ Value
diff --git a/docs/reference/seq_spin_echo_ideal.html b/docs/reference/seq_spin_echo_ideal.html
index e23271de..4248716f 100644
--- a/docs/reference/seq_spin_echo_ideal.html
+++ b/docs/reference/seq_spin_echo_ideal.html
@@ -1,5 +1,5 @@
-Spin echo sequence with ideal pulses. — seq_spin_echo_ideal • Spectroscopy Analysis Tools (spant) Spin echo sequence with ideal pulses. — seq_spin_echo_ideal • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/seq_steam_ideal.html b/docs/reference/seq_steam_ideal.html
index a60685a8..1c8115d7 100644
--- a/docs/reference/seq_steam_ideal.html
+++ b/docs/reference/seq_steam_ideal.html
@@ -1,5 +1,5 @@
-STEAM sequence with ideal pulses. — seq_steam_ideal • Spectroscopy Analysis Tools (spant) STEAM sequence with ideal pulses. — seq_steam_ideal • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -128,7 +128,7 @@ Value
diff --git a/docs/reference/seq_steam_ideal_cof.html b/docs/reference/seq_steam_ideal_cof.html
index 8f225740..cba7af91 100644
--- a/docs/reference/seq_steam_ideal_cof.html
+++ b/docs/reference/seq_steam_ideal_cof.html
@@ -1,7 +1,5 @@
-STEAM sequence with ideal pulses and coherence order filtering to simulate
-gradient crushers. — seq_steam_ideal_cof • Spectroscopy Analysis Tools (spant) STEAM sequence with ideal pulses and coherence order filtering to simulate gradient crushers. — seq_steam_ideal_cof • Spectroscopy Analysis Tools (spant) STEAM sequence with ideal pulses using the z-rotation gradient simulation
-method described by Young et al JMR 140, 146-152 (1999). — seq_steam_ideal_young • Spectroscopy Analysis Tools (spant) STEAM sequence with ideal pulses using the z-rotation gradient simulation method described by Young et al JMR 140, 146-152 (1999). — seq_steam_ideal_young • Spectroscopy Analysis Tools (spant) Set the number of transients for an mrs_data object. — set_Ntrans • Spectroscopy Analysis Tools (spant) Set the number of transients for an mrs_data object. — set_Ntrans • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/set_def_acq_paras.html b/docs/reference/set_def_acq_paras.html
index 3e1b4004..cc2ada9c 100644
--- a/docs/reference/set_def_acq_paras.html
+++ b/docs/reference/set_def_acq_paras.html
@@ -1,5 +1,5 @@
-Set the default acquisition parameters. — set_def_acq_paras • Spectroscopy Analysis Tools (spant) Set the default acquisition parameters. — set_def_acq_paras • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Arguments
diff --git a/docs/reference/set_lcm_cmd.html b/docs/reference/set_lcm_cmd.html
index 2056ed01..42bb2f24 100644
--- a/docs/reference/set_lcm_cmd.html
+++ b/docs/reference/set_lcm_cmd.html
@@ -1,5 +1,5 @@
-Set the command to run the LCModel command-line program. — set_lcm_cmd • Spectroscopy Analysis Tools (spant) Set the command to run the LCModel command-line program. — set_lcm_cmd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/set_lw.html b/docs/reference/set_lw.html
index b64ec851..bb176c62 100644
--- a/docs/reference/set_lw.html
+++ b/docs/reference/set_lw.html
@@ -1,5 +1,5 @@
-Apply line-broadening to an mrs_data object to achieve a specified linewidth. — set_lw • Spectroscopy Analysis Tools (spant) Apply line-broadening to an mrs_data object to achieve a specified linewidth. — set_lw • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -123,7 +123,7 @@ Value
diff --git a/docs/reference/set_mask_xy_mat.html b/docs/reference/set_mask_xy_mat.html
index 49dc5d4e..52c4b617 100644
--- a/docs/reference/set_mask_xy_mat.html
+++ b/docs/reference/set_mask_xy_mat.html
@@ -1,5 +1,5 @@
-Set the masked voxels in a 2D MRSI dataset to given spectrum. — set_mask_xy_mat • Spectroscopy Analysis Tools (spant) Set the masked voxels in a 2D MRSI dataset to given spectrum. — set_mask_xy_mat • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Value
diff --git a/docs/reference/set_precomp_mode.html b/docs/reference/set_precomp_mode.html
index f44bd5d3..47c28e3b 100644
--- a/docs/reference/set_precomp_mode.html
+++ b/docs/reference/set_precomp_mode.html
@@ -1,5 +1,5 @@
-Set the precompute mode. — set_precomp_mode • Spectroscopy Analysis Tools (spant) Set the precompute mode. — set_precomp_mode • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/set_precomp_verbose.html b/docs/reference/set_precomp_verbose.html
index 1453a231..9c613505 100644
--- a/docs/reference/set_precomp_verbose.html
+++ b/docs/reference/set_precomp_verbose.html
@@ -1,5 +1,5 @@
-Set the verbosity of the precompute function. — set_precomp_verbose • Spectroscopy Analysis Tools (spant) Set the verbosity of the precompute function. — set_precomp_verbose • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/set_ref.html b/docs/reference/set_ref.html
index 8953fa50..5436dfa2 100644
--- a/docs/reference/set_ref.html
+++ b/docs/reference/set_ref.html
@@ -1,5 +1,5 @@
-Set the ppm reference value (eg ppm value at 0Hz). — set_ref • Spectroscopy Analysis Tools (spant) Set the ppm reference value (eg ppm value at 0Hz). — set_ref • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/set_td_pts.html b/docs/reference/set_td_pts.html
index 8a80d42a..586459ff 100644
--- a/docs/reference/set_td_pts.html
+++ b/docs/reference/set_td_pts.html
@@ -1,7 +1,5 @@
-Set the number of time-domain data points, truncating or zero-filling as
-appropriate. — set_td_pts • Spectroscopy Analysis Tools (spant) Set the number of time-domain data points, truncating or zero-filling as appropriate. — set_td_pts • Spectroscopy Analysis Tools (spant) Set the command to run the TARQUIN command-line program. — set_tqn_cmd • Spectroscopy Analysis Tools (spant) Set the command to run the TARQUIN command-line program. — set_tqn_cmd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/set_tr.html b/docs/reference/set_tr.html
index b2109ab0..65c9df5f 100644
--- a/docs/reference/set_tr.html
+++ b/docs/reference/set_tr.html
@@ -1,5 +1,5 @@
-Set the repetition time of an MRS dataset. — set_tr • Spectroscopy Analysis Tools (spant) Set the repetition time of an MRS dataset. — set_tr • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/shift.html b/docs/reference/shift.html
index ab0fe724..034591d0 100644
--- a/docs/reference/shift.html
+++ b/docs/reference/shift.html
@@ -1,5 +1,5 @@
-Apply a frequency shift to MRS data. — shift • Spectroscopy Analysis Tools (spant) Apply a frequency shift to MRS data. — shift • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/shift_basis.html b/docs/reference/shift_basis.html
index 2884be19..f55a65e0 100644
--- a/docs/reference/shift_basis.html
+++ b/docs/reference/shift_basis.html
@@ -1,5 +1,5 @@
-Apply frequency shifts to basis set signals. — shift_basis • Spectroscopy Analysis Tools (spant) Apply frequency shifts to basis set signals. — shift_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Value
diff --git a/docs/reference/sim_basis.html b/docs/reference/sim_basis.html
index c7838c46..bb5fefc6 100644
--- a/docs/reference/sim_basis.html
+++ b/docs/reference/sim_basis.html
@@ -1,5 +1,5 @@
-Simulate a basis set object. — sim_basis • Spectroscopy Analysis Tools (spant) Simulate a basis set object. — sim_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -136,7 +136,7 @@ Value
diff --git a/docs/reference/sim_basis_1h_brain.html b/docs/reference/sim_basis_1h_brain.html
index 62ed7389..f71ffa0b 100644
--- a/docs/reference/sim_basis_1h_brain.html
+++ b/docs/reference/sim_basis_1h_brain.html
@@ -1,7 +1,5 @@
-Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS
-sequence. Note, ideal pulses are assumed. — sim_basis_1h_brain • Spectroscopy Analysis Tools (spant) Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS sequence. Note, ideal pulses are assumed. — sim_basis_1h_brain • Spectroscopy Analysis Tools (spant) Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS
-sequence. Note, ideal pulses are assumed. — sim_basis_1h_brain_press • Spectroscopy Analysis Tools (spant) Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS sequence. Note, ideal pulses are assumed. — sim_basis_1h_brain_press • Spectroscopy Analysis Tools (spant) Simulate a macromolecular and lipid basis-set suitable for 1H brain MRS
-analysis. — sim_basis_mm_lip_lcm • Spectroscopy Analysis Tools (spant) Simulate a macromolecular and lipid basis-set suitable for 1H brain MRS analysis. — sim_basis_mm_lip_lcm • Spectroscopy Analysis Tools (spant) Simulate a basis file using TARQUIN. — sim_basis_tqn • Spectroscopy Analysis Tools (spant) Simulate a basis file using TARQUIN. — sim_basis_tqn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -129,7 +129,7 @@ Examples
diff --git a/docs/reference/sim_brain_1h.html b/docs/reference/sim_brain_1h.html
index 2044cf1a..717ee289 100644
--- a/docs/reference/sim_brain_1h.html
+++ b/docs/reference/sim_brain_1h.html
@@ -1,5 +1,5 @@
-Simulate MRS data with a similar appearance to normal brain (by default). — sim_brain_1h • Spectroscopy Analysis Tools (spant) Simulate MRS data with a similar appearance to normal brain (by default). — sim_brain_1h • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -159,7 +159,7 @@ Value
diff --git a/docs/reference/sim_mol.html b/docs/reference/sim_mol.html
index 23bcef50..77f76a50 100644
--- a/docs/reference/sim_mol.html
+++ b/docs/reference/sim_mol.html
@@ -1,5 +1,5 @@
-Simulate a mol_parameter object. — sim_mol • Spectroscopy Analysis Tools (spant) Simulate a mol_parameter object. — sim_mol • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -143,7 +143,7 @@ Value
diff --git a/docs/reference/sim_noise.html b/docs/reference/sim_noise.html
index 23875f79..a71477d4 100644
--- a/docs/reference/sim_noise.html
+++ b/docs/reference/sim_noise.html
@@ -1,5 +1,5 @@
-Simulate an mrs_data object containing simulated Gaussian noise. — sim_noise • Spectroscopy Analysis Tools (spant) Simulate an mrs_data object containing simulated Gaussian noise. — sim_noise • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -84,6 +84,7 @@ Simulate an mrs_data object containing simulated Gaussian noise.
ft = def_ft(),
N = def_N(),
ref = def_ref(),
+ nuc = def_nuc(),
dyns = 1,
fd = TRUE
)
@@ -111,6 +112,10 @@ Arguments
reference value for ppm scale.
nuc
+resonant nucleus.
dyns
number of dynamic scans to generate.
Value
diff --git a/docs/reference/sim_resonances.html b/docs/reference/sim_resonances.html
index 19e9a8a4..d4f8d7c0 100644
--- a/docs/reference/sim_resonances.html
+++ b/docs/reference/sim_resonances.html
@@ -1,5 +1,5 @@
-Simulate a MRS data object containing a set of simulated resonances. — sim_resonances • Spectroscopy Analysis Tools (spant) Simulate a MRS data object containing a set of simulated resonances. — sim_resonances • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -161,7 +161,7 @@ Examples
diff --git a/docs/reference/sim_th_excit_profile.html b/docs/reference/sim_th_excit_profile.html
index 5535c5ef..e781cab1 100644
--- a/docs/reference/sim_th_excit_profile.html
+++ b/docs/reference/sim_th_excit_profile.html
@@ -1,7 +1,5 @@
-Simulate an ideal pulse excitation profile by smoothing a top-hat function
-with a Gaussian. — sim_th_excit_profile • Spectroscopy Analysis Tools (spant) Simulate an ideal pulse excitation profile by smoothing a top-hat function with a Gaussian. — sim_th_excit_profile • Spectroscopy Analysis Tools (spant) Simulate an mrs_data object containing complex zero valued samples. — sim_zero • Spectroscopy Analysis Tools (spant) Simulate an mrs_data object containing complex zero valued samples. — sim_zero • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -78,7 +78,14 @@ Simulate an mrs_data object containing complex zero valued samples.
-
+
@@ -99,6 +106,10 @@ Arguments
reference value for ppm scale.
nuc
+resonant nucleus.
dyns
number of dynamic scans to generate.
Value
diff --git a/docs/reference/smooth_dyns.html b/docs/reference/smooth_dyns.html
index 4cc8da50..accf3a51 100644
--- a/docs/reference/smooth_dyns.html
+++ b/docs/reference/smooth_dyns.html
@@ -1,5 +1,5 @@
-Smooth data across the dynamic dimension with a Gaussian kernel. — smooth_dyns • Spectroscopy Analysis Tools (spant) Smooth data across the dynamic dimension with a Gaussian kernel. — smooth_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/sort_basis.html b/docs/reference/sort_basis.html
index 6a676ea2..d25cc006 100644
--- a/docs/reference/sort_basis.html
+++ b/docs/reference/sort_basis.html
@@ -1,5 +1,5 @@
-Sort the basis-set elements alphabetically. — sort_basis • Spectroscopy Analysis Tools (spant) Sort the basis-set elements alphabetically. — sort_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/spant-package.html b/docs/reference/spant-package.html
index b3dd8e21..90f19ec3 100644
--- a/docs/reference/spant-package.html
+++ b/docs/reference/spant-package.html
@@ -1,5 +1,5 @@
-spant: spectroscopy analysis tools. — spant-package • Spectroscopy Analysis Tools (spant) spant: spectroscopy analysis tools. — spant-package • Spectroscopy Analysis Tools (spant) Simulate and fit some spectra with ABfit for benchmarking purposes. Basic
-timing and performance metrics will be printed. — spant_abfit_benchmark • Spectroscopy Analysis Tools (spant) Simulate and fit some spectra with ABfit for benchmarking purposes. Basic timing and performance metrics will be printed. — spant_abfit_benchmark • Spectroscopy Analysis Tools (spant) Example MEGA-PRESS data with significant B0 drift. — spant_mpress_drift • Spectroscopy Analysis Tools (spant) Example MEGA-PRESS data with significant B0 drift. — spant_mpress_drift • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -83,7 +83,7 @@ Example MEGA-PRESS data with significant B0 drift.
Format
- An object of class mrs_data of length 13.
+ An object of class mrs_data of dimension 1 x 1 x 1 x 1 x 40 x 1 x 1024.
@@ -98,7 +98,7 @@ Format
diff --git a/docs/reference/spant_sim_fmrs_dataset.html b/docs/reference/spant_sim_fmrs_dataset.html
new file mode 100644
index 00000000..00e48b56
--- /dev/null
+++ b/docs/reference/spant_sim_fmrs_dataset.html
@@ -0,0 +1,117 @@
+
+Simulate an example fMRS dataset for a block design fMRS experiment and export a BIDS structure. — spant_sim_fmrs_dataset • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Simulate an example fMRS dataset for a block design fMRS experiment and export a BIDS structure.
+ Source: R/fmrs.R
+ spant_sim_fmrs_dataset.Rd
+
+
+
+ Simulate an example fMRS dataset for a block design fMRS experiment and
+export a BIDS structure.
+
+
+
+ spant_sim_fmrs_dataset(output_dir = NULL)
+
+
+
+ Arguments
+ - output_dir
+output directory for the BIDS data. Defaults to :
+"HOME/sim_fmrs_dataset/data".
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/spant_simulation_benchmark.html b/docs/reference/spant_simulation_benchmark.html
index 32daa8bf..d8cc6841 100644
--- a/docs/reference/spant_simulation_benchmark.html
+++ b/docs/reference/spant_simulation_benchmark.html
@@ -1,7 +1,5 @@
-Simulate a typical metabolite basis set for benchmarking. Timing metrics will
-be printed on completion. — spant_simulation_benchmark • Spectroscopy Analysis Tools (spant) Simulate a typical metabolite basis set for benchmarking. Timing metrics will be printed on completion. — spant_simulation_benchmark • Spectroscopy Analysis Tools (spant) Decompose an mrs_data object into white and gray matter spectra. — spec_decomp • Spectroscopy Analysis Tools (spant) Perform a mathematical operation on a spectral region. — spec_op • Spectroscopy Analysis Tools (spant) Perform a mathematical operation on a spectral region. — spec_op • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -98,8 +98,8 @@ Arguments
operator
-can be "sum" (default), "mean", "l2", "max", "min" or
-"max-min".
can be "sum" (default), "mean", "l2", "max", "max_cplx,
+"min" or "max-min".
freq_scale
@@ -129,7 +129,7 @@ Value
diff --git a/docs/reference/spin_sys.html b/docs/reference/spin_sys.html
index 853423a4..1eaa9e76 100644
--- a/docs/reference/spin_sys.html
+++ b/docs/reference/spin_sys.html
@@ -1,5 +1,5 @@
-Create a spin system object for pulse sequence simulation. — spin_sys • Spectroscopy Analysis Tools (spant) Create a spin system object for pulse sequence simulation. — spin_sys • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/spm_pve2categorical.html b/docs/reference/spm_pve2categorical.html
index 23a1bad9..70f10729 100644
--- a/docs/reference/spm_pve2categorical.html
+++ b/docs/reference/spm_pve2categorical.html
@@ -1,7 +1,5 @@
-Convert SPM style segmentation files to a single categorical image where
-the numerical values map as: 0) Other, 1) CSF, 2) GM and 3) WM. — spm_pve2categorical • Spectroscopy Analysis Tools (spant) Convert SPM style segmentation files to a single categorical image where the numerical values map as: 0) Other, 1) CSF, 2) GM and 3) WM. — spm_pve2categorical • Spectroscopy Analysis Tools (spant) Signal space projection method for lipid suppression. — ssp • Spectroscopy Analysis Tools (spant) Signal space projection method for lipid suppression. — ssp • Spectroscopy Analysis Tools (spant) Plot the fitting results of an object of class fit_result with
-individual basis set components shown. — stackplot.fit_result • Spectroscopy Analysis Tools (spant) Plot the fitting results of an object of class fit_result with individual basis set components shown. — stackplot.fit_result • Spectroscopy Analysis Tools (spant) Produce a plot with multiple traces. — stackplot • Spectroscopy Analysis Tools (spant) Produce a plot with multiple traces. — stackplot • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/stackplot.mrs_data.html b/docs/reference/stackplot.mrs_data.html
index 17ff5648..64eea445 100644
--- a/docs/reference/stackplot.mrs_data.html
+++ b/docs/reference/stackplot.mrs_data.html
@@ -1,5 +1,5 @@
-Stackplot plotting method for objects of class mrs_data. — stackplot.mrs_data • Spectroscopy Analysis Tools (spant) Stackplot plotting method for objects of class mrs_data. — stackplot.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -255,7 +255,7 @@ Arguments
diff --git a/docs/reference/sub_first_dyn.html b/docs/reference/sub_first_dyn.html
index dbd7f831..493b7242 100644
--- a/docs/reference/sub_first_dyn.html
+++ b/docs/reference/sub_first_dyn.html
@@ -1,5 +1,5 @@
-Subtract the first dynamic spectrum from a dynamic series. — sub_first_dyn • Spectroscopy Analysis Tools (spant) Subtract the first dynamic spectrum from a dynamic series. — sub_first_dyn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/sub_mean_dyns.html b/docs/reference/sub_mean_dyns.html
index 6e3bb2df..221bd0c1 100644
--- a/docs/reference/sub_mean_dyns.html
+++ b/docs/reference/sub_mean_dyns.html
@@ -1,5 +1,5 @@
-Subtract the mean dynamic spectrum from a dynamic series. — sub_mean_dyns • Spectroscopy Analysis Tools (spant) Subtract the mean dynamic spectrum from a dynamic series. — sub_mean_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/sub_median_dyns.html b/docs/reference/sub_median_dyns.html
index 134c495d..1e834f14 100644
--- a/docs/reference/sub_median_dyns.html
+++ b/docs/reference/sub_median_dyns.html
@@ -1,5 +1,5 @@
-Subtract the median dynamic spectrum from a dynamic series. — sub_median_dyns • Spectroscopy Analysis Tools (spant) Subtract the median dynamic spectrum from a dynamic series. — sub_median_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/sum_coils.html b/docs/reference/sum_coils.html
index 7bf559f2..e1ab3cc0 100644
--- a/docs/reference/sum_coils.html
+++ b/docs/reference/sum_coils.html
@@ -1,5 +1,5 @@
-Calculate the sum across receiver coil elements. — sum_coils • Spectroscopy Analysis Tools (spant) Calculate the sum across receiver coil elements. — sum_coils • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/sum_dyns.html b/docs/reference/sum_dyns.html
index a0be19d3..bbda2ffc 100644
--- a/docs/reference/sum_dyns.html
+++ b/docs/reference/sum_dyns.html
@@ -1,5 +1,5 @@
-Calculate the sum of data dynamics. — sum_dyns • Spectroscopy Analysis Tools (spant) Calculate the sum of data dynamics. — sum_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/sum_mrs.html b/docs/reference/sum_mrs.html
index a22f215b..3cc3ab9e 100644
--- a/docs/reference/sum_mrs.html
+++ b/docs/reference/sum_mrs.html
@@ -1,5 +1,5 @@
-Sum two mrs_data objects. — sum_mrs • Spectroscopy Analysis Tools (spant) Sum two mrs_data objects. — sum_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Value
diff --git a/docs/reference/sum_mrs_list.html b/docs/reference/sum_mrs_list.html
index f4e09aea..c3584348 100644
--- a/docs/reference/sum_mrs_list.html
+++ b/docs/reference/sum_mrs_list.html
@@ -1,5 +1,5 @@
-Return the sum of a list of mrs_data objects. — sum_mrs_list • Spectroscopy Analysis Tools (spant) Return the sum of a list of mrs_data objects. — sum_mrs_list • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/svs_1h_brain_analysis.html b/docs/reference/svs_1h_brain_analysis.html
index 8ce514db..dff0ef7d 100644
--- a/docs/reference/svs_1h_brain_analysis.html
+++ b/docs/reference/svs_1h_brain_analysis.html
@@ -1,5 +1,5 @@
-Standard SVS 1H brain analysis pipeline. — svs_1h_brain_analysis • Spectroscopy Analysis Tools (spant) Standard SVS 1H brain analysis pipeline. — svs_1h_brain_analysis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -199,7 +199,7 @@ Value
diff --git a/docs/reference/svs_1h_brain_analysis_dev.html b/docs/reference/svs_1h_brain_analysis_dev.html
index d70a14d3..d71bfea2 100644
--- a/docs/reference/svs_1h_brain_analysis_dev.html
+++ b/docs/reference/svs_1h_brain_analysis_dev.html
@@ -1,5 +1,5 @@
-Standard SVS 1H brain analysis pipeline. — svs_1h_brain_analysis_dev • Spectroscopy Analysis Tools (spant) Standard SVS 1H brain analysis pipeline. — svs_1h_brain_analysis_dev • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -193,7 +193,7 @@ Examples
diff --git a/docs/reference/svs_1h_brain_batch_analysis.html b/docs/reference/svs_1h_brain_batch_analysis.html
index 5631e8cc..15f7223e 100644
--- a/docs/reference/svs_1h_brain_batch_analysis.html
+++ b/docs/reference/svs_1h_brain_batch_analysis.html
@@ -1,5 +1,5 @@
-Batch interface to the standard SVS 1H brain analysis pipeline. — svs_1h_brain_batch_analysis • Spectroscopy Analysis Tools (spant) Batch interface to the standard SVS 1H brain analysis pipeline. — svs_1h_brain_batch_analysis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -144,7 +144,7 @@ Value
diff --git a/docs/reference/t_test_spec.html b/docs/reference/t_test_spec.html
new file mode 100644
index 00000000..56a7ea1b
--- /dev/null
+++ b/docs/reference/t_test_spec.html
@@ -0,0 +1,124 @@
+
+Perform a t-test on spectral data points. — t_test_spec • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+
+
+ Perform a t-test on spectral data points.
+
+
+
+ t_test_spec(mrs_data, group)
+
+
+
+ Arguments
+ - mrs_data
+an mrs_data object with spectra in the dynamic dimension.
- group
+vector describing the group membership of each dynamic spectrum.
+
+ Value
+
+
+a list of statistical results.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/td2fd.html b/docs/reference/td2fd.html
index 6748a6a8..f31ed524 100644
--- a/docs/reference/td2fd.html
+++ b/docs/reference/td2fd.html
@@ -1,5 +1,5 @@
-Transform time-domain data to the frequency-domain. — td2fd • Spectroscopy Analysis Tools (spant) Transform time-domain data to the frequency-domain. — td2fd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/td_conv_filt.html b/docs/reference/td_conv_filt.html
index a9f340c3..106b9b00 100644
--- a/docs/reference/td_conv_filt.html
+++ b/docs/reference/td_conv_filt.html
@@ -1,5 +1,5 @@
-Time-domain convolution based filter. — td_conv_filt • Spectroscopy Analysis Tools (spant) Time-domain convolution based filter. — td_conv_filt • Spectroscopy Analysis Tools (spant) Time-domain spectral registration. — tdsr • Spectroscopy Analysis Tools (spant) Time-domain spectral registration. — tdsr • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -121,7 +121,7 @@ Value
diff --git a/docs/reference/te.html b/docs/reference/te.html
index 010361b1..4a65711d 100644
--- a/docs/reference/te.html
+++ b/docs/reference/te.html
@@ -1,5 +1,5 @@
-Return the echo time of an MRS dataset. — te • Spectroscopy Analysis Tools (spant) Return the echo time of an MRS dataset. — te • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/tr.html b/docs/reference/tr.html
index 0c0bd63b..2e749e02 100644
--- a/docs/reference/tr.html
+++ b/docs/reference/tr.html
@@ -1,5 +1,5 @@
-Return the repetition time of an MRS dataset. — tr • Spectroscopy Analysis Tools (spant) Return the repetition time of an MRS dataset. — tr • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/varpro_3_para_opts.html b/docs/reference/varpro_3_para_opts.html
index c2270a16..52d7cd84 100644
--- a/docs/reference/varpro_3_para_opts.html
+++ b/docs/reference/varpro_3_para_opts.html
@@ -1,5 +1,5 @@
-Return a list of options for VARPRO based fitting with 3 free parameters. — varpro_3_para_opts • Spectroscopy Analysis Tools (spant) Return a list of options for VARPRO based fitting with 3 free parameters. — varpro_3_para_opts • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -141,7 +141,7 @@ Value
diff --git a/docs/reference/varpro_basic_opts.html b/docs/reference/varpro_basic_opts.html
index 32c86d22..c5104891 100644
--- a/docs/reference/varpro_basic_opts.html
+++ b/docs/reference/varpro_basic_opts.html
@@ -1,5 +1,5 @@
-Return a list of options for a basic VARPRO analysis. — varpro_basic_opts • Spectroscopy Analysis Tools (spant) Return a list of options for a basic VARPRO analysis. — varpro_basic_opts • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -118,7 +118,7 @@ Value
diff --git a/docs/reference/varpro_opts.html b/docs/reference/varpro_opts.html
index 2aabf11d..6332f730 100644
--- a/docs/reference/varpro_opts.html
+++ b/docs/reference/varpro_opts.html
@@ -1,5 +1,5 @@
-Return a list of options for VARPRO based fitting. — varpro_opts • Spectroscopy Analysis Tools (spant) Return a list of options for VARPRO based fitting. — varpro_opts • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -177,7 +177,7 @@ Examples
diff --git a/docs/reference/vec2mrs_data.html b/docs/reference/vec2mrs_data.html
index 0cccd73b..f0d58bf0 100644
--- a/docs/reference/vec2mrs_data.html
+++ b/docs/reference/vec2mrs_data.html
@@ -1,5 +1,5 @@
-Convert a vector into a mrs_data object. — vec2mrs_data • Spectroscopy Analysis Tools (spant) Convert a vector into a mrs_data object. — vec2mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -80,10 +80,11 @@ Convert a vector into a mrs_data object.
vec2mrs_data(
vec,
- fs = def_fs(),
- ft = def_ft(),
- ref = def_ref(),
- nuc = def_nuc(),
+ mrs_data = NULL,
+ fs = NULL,
+ ft = NULL,
+ ref = NULL,
+ nuc = NULL,
dyns = 1,
fd = FALSE
)
@@ -95,6 +96,10 @@ Arguments
the data vector.
mrs_data
+example data to copy acquisition parameters from.
fs
sampling frequency in Hz.
Arguments
fd
-flag to indicate if the matrix is in the frequency domain (logical).
flag to indicate if the vector is in the frequency domain (logical).
Value
diff --git a/docs/reference/write_basis.html b/docs/reference/write_basis.html
index b6e27cbd..94c5e021 100644
--- a/docs/reference/write_basis.html
+++ b/docs/reference/write_basis.html
@@ -1,5 +1,5 @@
-Write a basis object to an LCModel .basis formatted file. — write_basis • Spectroscopy Analysis Tools (spant) Write a basis object to an LCModel .basis formatted file. — write_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -108,7 +108,7 @@ Arguments
diff --git a/docs/reference/write_basis_tqn.html b/docs/reference/write_basis_tqn.html
index 6aa51c1d..116c73ec 100644
--- a/docs/reference/write_basis_tqn.html
+++ b/docs/reference/write_basis_tqn.html
@@ -1,5 +1,5 @@
-Generate a basis file using TARQUIN. — write_basis_tqn • Spectroscopy Analysis Tools (spant) Generate a basis file using TARQUIN. — write_basis_tqn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Examples
diff --git a/docs/reference/write_mrs.html b/docs/reference/write_mrs.html
index fff25f15..124b9dc4 100644
--- a/docs/reference/write_mrs.html
+++ b/docs/reference/write_mrs.html
@@ -1,5 +1,5 @@
-Write MRS data object to file. — write_mrs • Spectroscopy Analysis Tools (spant) Write MRS data object to file. — write_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Arguments
diff --git a/docs/reference/write_mrs_nifti.html b/docs/reference/write_mrs_nifti.html
index f4bf1921..bd3ed4b7 100644
--- a/docs/reference/write_mrs_nifti.html
+++ b/docs/reference/write_mrs_nifti.html
@@ -1,5 +1,5 @@
-Write MRS data object to file in NIFTI format. — write_mrs_nifti • Spectroscopy Analysis Tools (spant) Write MRS data object to file in NIFTI format. — write_mrs_nifti • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/write_pulse_ascii.html b/docs/reference/write_pulse_ascii.html
index 067ae086..221f8ebb 100644
--- a/docs/reference/write_pulse_ascii.html
+++ b/docs/reference/write_pulse_ascii.html
@@ -1,5 +1,5 @@
-Write an ASCII formatted pulse file. — write_pulse_ascii • Spectroscopy Analysis Tools (spant) Write an ASCII formatted pulse file. — write_pulse_ascii • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/zero_fade_spec.html b/docs/reference/zero_fade_spec.html
index c703745c..c8b572c3 100644
--- a/docs/reference/zero_fade_spec.html
+++ b/docs/reference/zero_fade_spec.html
@@ -1,7 +1,5 @@
-Fade a spectrum to zero by frequency domain multiplication with a tanh
-function. Note this operation distorts data points at the end of the FID. — zero_fade_spec • Spectroscopy Analysis Tools (spant) Fade a spectrum to zero by frequency domain multiplication with a tanh function. Note this operation distorts data points at the end of the FID. — zero_fade_spec • Spectroscopy Analysis Tools (spant) Zero all coherences including and above a given order. — zero_higher_orders • Spectroscopy Analysis Tools (spant) Zero all coherences including and above a given order. — zero_higher_orders • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Value
diff --git a/docs/reference/zero_td_pts_end.html b/docs/reference/zero_td_pts_end.html
index 8c1123c8..71d24ebb 100644
--- a/docs/reference/zero_td_pts_end.html
+++ b/docs/reference/zero_td_pts_end.html
@@ -1,5 +1,5 @@
-Set mrs_data object data points at the end of the FID to zero. — zero_td_pts_end • Spectroscopy Analysis Tools (spant) Set mrs_data object data points at the end of the FID to zero. — zero_td_pts_end • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/zf.html b/docs/reference/zf.html
index 85e2013c..baf50256 100644
--- a/docs/reference/zf.html
+++ b/docs/reference/zf.html
@@ -1,5 +1,5 @@
-Zero-fill MRS data in the time domain. — zf • Spectroscopy Analysis Tools (spant) Zero-fill MRS data in the time domain. — zf • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -125,7 +125,7 @@ Value
diff --git a/docs/reference/zf_xy.html b/docs/reference/zf_xy.html
index ebca3999..c4104a74 100644
--- a/docs/reference/zf_xy.html
+++ b/docs/reference/zf_xy.html
@@ -1,5 +1,5 @@
-Zero-fill MRSI data in the k-space x-y direction. — zf_xy • Spectroscopy Analysis Tools (spant) Zero-fill MRSI data in the k-space x-y direction. — zf_xy • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -113,7 +113,7 @@ Value
diff --git a/docs/sitemap.xml b/docs/sitemap.xml
index e2139f71..4c39f515 100644
--- a/docs/sitemap.xml
+++ b/docs/sitemap.xml
@@ -216,6 +216,12 @@
https://martin3141.github.io/spant/reference/comb_coils_fp_pc.html
+
+ https://martin3141.github.io/spant/reference/comb_coils_mrsi_gls.html
+
+
+ https://martin3141.github.io/spant/reference/comb_coils_svs_gls.html
+
https://martin3141.github.io/spant/reference/comb_csv_results.html
@@ -411,6 +417,9 @@
https://martin3141.github.io/spant/reference/gen_conv_reg.html
+
+ https://martin3141.github.io/spant/reference/gen_group_reg.html
+
https://martin3141.github.io/spant/reference/gen_impulse_reg.html
@@ -555,6 +564,15 @@
https://martin3141.github.io/spant/reference/glm_spec.html
+
+ https://martin3141.github.io/spant/reference/glm_spec_fmrs_fl.html
+
+
+ https://martin3141.github.io/spant/reference/glm_spec_fmrs_group.html
+
+
+ https://martin3141.github.io/spant/reference/glm_spec_group_linhyp.html
+
https://martin3141.github.io/spant/reference/grid_shift_xy.html
@@ -690,9 +708,15 @@
https://martin3141.github.io/spant/reference/mrs_data2basis.html
+
+ https://martin3141.github.io/spant/reference/mrs_data2bids.html
+
https://martin3141.github.io/spant/reference/mrs_data2mat.html
+
+ https://martin3141.github.io/spant/reference/mrs_data2spec_mat.html
+
https://martin3141.github.io/spant/reference/mrs_data2vec.html
@@ -741,6 +765,9 @@
https://martin3141.github.io/spant/reference/phase.html
+
+ https://martin3141.github.io/spant/reference/phase_ref_1h_brain.html
+
https://martin3141.github.io/spant/reference/plot.fit_result.html
@@ -780,6 +807,12 @@
https://martin3141.github.io/spant/reference/precomp.html
+
+ https://martin3141.github.io/spant/reference/preproc_svs.html
+
+
+ https://martin3141.github.io/spant/reference/preproc_svs_dataset.html
+
https://martin3141.github.io/spant/reference/print.fit_result.html
@@ -1050,6 +1083,9 @@
https://martin3141.github.io/spant/reference/spant_mpress_drift.html
+
+ https://martin3141.github.io/spant/reference/spant_sim_fmrs_dataset.html
+
https://martin3141.github.io/spant/reference/spant_simulation_benchmark.html
@@ -1107,6 +1143,9 @@
https://martin3141.github.io/spant/reference/svs_1h_brain_batch_analysis.html
+
+ https://martin3141.github.io/spant/reference/t_test_spec.html
+
https://martin3141.github.io/spant/reference/td2fd.html
Generate regressors by convolving a specified response function with a -stimulus.
Generate regressors by convolving a specified response function with a stimulus.
Expand a regressor matrix for a group analysis.
All functions
- Return a character vector of common 1H molecules found in healthy human
-brain.
Return a character vector of common 1H molecules found in healthy human brain.
- Return a list of mol_parameter objects suitable for 1H brain MRS
-analyses.
Return a list of mol_parameter objects suitable for 1H brain MRS analyses.
- Return a list of mol_parameter objects suitable for 1H brain MRS
-analyses.
Return a list of mol_parameter objects suitable for 1H brain MRS analyses.
- Return a list of mol_parameter objects suitable for 1H brain MRS
-analyses.
Return a list of mol_parameter objects suitable for 1H brain MRS analyses.
- Return a list of mol_parameter objects suitable for 1H brain MRS
-analyses.
Return a list of mol_parameter objects suitable for 1H brain MRS analyses.
@@ -582,8 +566,7 @@ All functions
- Return a character vector of molecules included in the Gold Star Phantoms
-SPECTRE phantom.
Return a character vector of molecules included in the Gold Star Phantoms SPECTRE phantom.
@@ -635,8 +618,7 @@ All functions
- Return a character array of names that may be used with the
-get_mol_paras function.
Return a character array of names that may be used with the get_mol_paras function.
@@ -700,8 +682,7 @@ All functions
- Return an array of amplitudes derived from fitting the initial points in the
-time domain and extrapolating back to t=0.
Return an array of amplitudes derived from fitting the initial points in the time domain and extrapolating back to t=0.
@@ -709,8 +690,7 @@ All functions
- Generate a mol_parameters object for a simple spin system with one
-resonance.
Generate a mol_parameters object for a simple spin system with one resonance.
@@ -731,6 +711,18 @@ All functions glm_spec()
Perform a GLM analysis of dynamic MRS data in the spectral domain.
+
+
+ Perform first-level spectral GLM analysis of an fMRS dataset.
+
+
+ Perform group-level spectral GLM analysis of an fMRS dataset.
+
+
+ Test a group-level spectral GLM linear hypothesis.
@@ -766,8 +758,7 @@ All functions
- Perform an ifft and ifftshift on a matrix with each column replaced by its
-shifted ifft.
Perform an ifft and ifftshift on a matrix with each column replaced by its shifted ifft.
@@ -799,8 +790,7 @@ All functions
- Check if the chemical shift dimension of an MRS data object is in the
-frequency domain.
Check if the chemical shift dimension of an MRS data object is in the frequency domain.
@@ -820,18 +810,15 @@ All functions
- Covert a linewidth in Hz to an equivalent alpha value in the time-domain ie:
-x * exp(-t * alpha).
Covert a linewidth in Hz to an equivalent alpha value in the time-domain ie: x * exp(-t * alpha).
- Covert a linewidth in Hz to an equivalent beta value in the time-domain ie:
-x * exp(-t * t * beta).
Covert a linewidth in Hz to an equivalent beta value in the time-domain ie: x * exp(-t * t * beta).
- Make a basis-set object from a directory containing LCModel formatted RAW
-files.
Make a basis-set object from a directory containing LCModel formatted RAW files.
@@ -851,8 +838,7 @@ All functions
- Mask the voxels outside an elliptical region spanning the MRSI dataset in the
-x-y plane.
Mask the voxels outside an elliptical region spanning the MRSI dataset in the x-y plane.
@@ -860,13 +846,11 @@ All functions
- Convert a matrix (with spectral points in the column dimension and dynamics
-in the row dimensions) into a mrs_data object.
Convert a matrix (with spectral points in the column dimension and dynamics in the row dimensions) into a mrs_data object.
- Matrix exponential function taken from complexplus package to reduce the
-number of spant dependencies.
Matrix exponential function taken from complexplus package to reduce the number of spant dependencies.
@@ -914,31 +898,31 @@ All functions
- Convert an mrs_data object to basis object - where basis signals are spread
-across the dynamic dimension in the MRS data.
Convert an mrs_data object to basis object - where basis signals are spread across the dynamic dimension in the MRS data.
+
+
+ Create a BIDS file structure from a vector of MRS data paths or list of mrs_data objects.
- Convert mrs_data object to a matrix, with spectral points in the column
-dimension and dynamics in the row dimension.
Convert mrs_data object to a matrix, with spectral points in the column dimension and dynamics in the row dimension.
-
+
- Convert mrs_data object to a vector.
Convert mrs_data object to a matrix, with spectral points in the column dimension and dynamics in the row dimension.
-
+
- Create a BIDS directory and file structure from a list of mrs_data objects.
Convert mrs_data object to a vector.
- Perform a fftshift on a matrix, with each column replaced by its shifted
-result.
Perform a fftshift on a matrix, with each column replaced by its shifted result.
- Perform an ifftshift on a matrix, with each column replaced by its shifted
-result.
Perform an ifftshift on a matrix, with each column replaced by its shifted result.
@@ -946,9 +930,7 @@ All functions
- Flip the x data dimension order of a nifti image. This corresponds to
-flipping MRI data in the left-right direction, assuming the data in save in
-neurological format (can check with fslorient program).
Flip the x data dimension order of a nifti image. This corresponds to flipping MRI data in the left-right direction, assuming the data in save in neurological format (can check with fslorient program).
@@ -964,8 +946,7 @@ All functions
- Search for the highest peak in a spectral region and return the frequency,
-height and FWHM.
Search for the highest peak in a spectral region and return the frequency, height and FWHM.
@@ -974,6 +955,10 @@ All functions phase()
Apply phasing parameters to MRS data.
+
+
+ Corrected zero order phase and chemical shift offset in 1H MRS data from the brain.
@@ -1005,8 +990,7 @@ All functions
- Plot an interactive slice map from a data array where voxels can be selected
-to display a corresponding spectrum.
Plot an interactive slice map from a data array where voxels can be selected to display a corresponding spectrum.
@@ -1026,8 +1010,15 @@ All functions
- Save function results to file and load on subsequent calls to avoid repeat
-computation.
Save function results to file and load on subsequent calls to avoid repeat computation.
+
+
+ Preprocess and perform quality assessment of a single SVS data set.
+
+
+ Preprocess and perform quality assessment of one or more SVS data sets.
@@ -1055,15 +1046,11 @@ All functions
- Read a directory containing Siemens MRS IMA files and combine along the coil
-dimension. Note that the coil ID is inferred from the sorted file name and
-should be checked when consistency is required between two directories.
Read a directory containing Siemens MRS IMA files and combine along the coil dimension. Note that the coil ID is inferred from the sorted file name and should be checked when consistency is required between two directories.
- Read a directory containing Siemens MRS IMA files and combine along the
-dynamic dimension. Note that the coil ID is inferred from the sorted file
-name and should be checked when consistency is required.
Read a directory containing Siemens MRS IMA files and combine along the dynamic dimension. Note that the coil ID is inferred from the sorted file name and should be checked when consistency is required.
@@ -1103,13 +1090,11 @@ All functions
- Reconstruct complex time-domain data from the real part of frequency-domain
-data.
Reconstruct complex time-domain data from the real part of frequency-domain data.
- Reconstruct complex time-domain data from the real part of frequency-domain
-data.
Reconstruct complex time-domain data from the real part of frequency-domain data.
@@ -1141,8 +1126,7 @@ All functions
- Resample a VOI to match a target image space using nearest-neighbour
-interpolation.
Resample a VOI to match a target image space using nearest-neighbour interpolation.
@@ -1158,23 +1142,19 @@ All functions
- Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water).
Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / kg of tissue water).
- Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water).
Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / kg of tissue water).
- Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / Litre of tissue).
Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / Litre of tissue).
- Convert default LCM/TARQUIN concentration scaling to molal units with partial
-volume correction.
Convert default LCM/TARQUIN concentration scaling to molal units with partial volume correction.
@@ -1222,8 +1202,7 @@ All functions
- MEGA-PRESS sequence with ideal localisation pulses and Gaussian shaped
-editing pulse.
MEGA-PRESS sequence with ideal localisation pulses and Gaussian shaped editing pulse.
@@ -1251,13 +1230,11 @@ All functions
- STEAM sequence with ideal pulses and coherence order filtering to simulate
-gradient crushers.
STEAM sequence with ideal pulses and coherence order filtering to simulate gradient crushers.
- STEAM sequence with ideal pulses using the z-rotation gradient simulation
-method described by Young et al JMR 140, 146-152 (1999).
STEAM sequence with ideal pulses using the z-rotation gradient simulation method described by Young et al JMR 140, 146-152 (1999).
@@ -1293,8 +1270,7 @@ All functions
- Set the number of time-domain data points, truncating or zero-filling as
-appropriate.
Set the number of time-domain data points, truncating or zero-filling as appropriate.
@@ -1318,18 +1294,15 @@ All functions
- Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS
-sequence. Note, ideal pulses are assumed.
Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS sequence. Note, ideal pulses are assumed.
- Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS
-sequence. Note, ideal pulses are assumed.
Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS sequence. Note, ideal pulses are assumed.
- Simulate a macromolecular and lipid basis-set suitable for 1H brain MRS
-analysis.
Simulate a macromolecular and lipid basis-set suitable for 1H brain MRS analysis.
@@ -1353,8 +1326,7 @@ All functions
- Simulate an ideal pulse excitation profile by smoothing a top-hat function
-with a Gaussian.
Simulate an ideal pulse excitation profile by smoothing a top-hat function with a Gaussian.
@@ -1374,17 +1346,19 @@ All functions
- Simulate and fit some spectra with ABfit for benchmarking purposes. Basic
-timing and performance metrics will be printed.
Simulate and fit some spectra with ABfit for benchmarking purposes. Basic timing and performance metrics will be printed.
Example MEGA-PRESS data with significant B0 drift.
+
+
+ Simulate an example fMRS dataset for a block design fMRS experiment and export a BIDS structure.
- Simulate a typical metabolite basis set for benchmarking. Timing metrics will
-be printed on completion.
Simulate a typical metabolite basis set for benchmarking. Timing metrics will be printed on completion.
@@ -1400,8 +1374,7 @@ All functions
- Convert SPM style segmentation files to a single categorical image where
-the numerical values map as: 0) Other, 1) CSF, 2) GM and 3) WM.
Convert SPM style segmentation files to a single categorical image where the numerical values map as: 0) Other, 1) CSF, 2) GM and 3) WM.
@@ -1413,8 +1386,7 @@ All functions
- Plot the fitting results of an object of class fit_result with
-individual basis set components shown.
Plot the fitting results of an object of class fit_result with individual basis set components shown.
@@ -1459,6 +1431,10 @@ All functions svs_1h_brain_batch_analysis()
Batch interface to the standard SVS 1H brain analysis pipeline.
+
+
+ Perform a t-test on spectral data points.
@@ -1518,8 +1494,7 @@ All functions
- Fade a spectrum to zero by frequency domain multiplication with a tanh
-function. Note this operation distorts data points at the end of the FID.
Fade a spectrum to zero by frequency domain multiplication with a tanh function. Note this operation distorts data points at the end of the FID.
@@ -1549,7 +1524,7 @@ All functions
diff --git a/docs/reference/int_spec.html b/docs/reference/int_spec.html
index c7060fe7..783325a8 100644
--- a/docs/reference/int_spec.html
+++ b/docs/reference/int_spec.html
@@ -1,5 +1,5 @@
-Integrate a spectral region. — int_spec • Spectroscopy Analysis Tools (spant) Integrate a spectral region. — int_spec • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -118,7 +118,7 @@ Value
diff --git a/docs/reference/interleave_dyns.html b/docs/reference/interleave_dyns.html
index effe5543..441eff27 100644
--- a/docs/reference/interleave_dyns.html
+++ b/docs/reference/interleave_dyns.html
@@ -1,5 +1,5 @@
-Interleave the first and second half of a dynamic series. — interleave_dyns • Spectroscopy Analysis Tools (spant) Interleave the first and second half of a dynamic series. — interleave_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/inv_even_dyns.html b/docs/reference/inv_even_dyns.html
index 9f9d4fff..dcb781dc 100644
--- a/docs/reference/inv_even_dyns.html
+++ b/docs/reference/inv_even_dyns.html
@@ -1,5 +1,5 @@
-Invert even numbered dynamic scans starting from 1 (2,4,6...). — inv_even_dyns • Spectroscopy Analysis Tools (spant) Invert even numbered dynamic scans starting from 1 (2,4,6...). — inv_even_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/inv_odd_dyns.html b/docs/reference/inv_odd_dyns.html
index 26212e2b..78d64660 100644
--- a/docs/reference/inv_odd_dyns.html
+++ b/docs/reference/inv_odd_dyns.html
@@ -1,5 +1,5 @@
-Invert odd numbered dynamic scans starting from 1 (1,3,5...). — inv_odd_dyns • Spectroscopy Analysis Tools (spant) Invert odd numbered dynamic scans starting from 1 (1,3,5...). — inv_odd_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/is.def.html b/docs/reference/is.def.html
index f196ffd0..a67b9eba 100644
--- a/docs/reference/is.def.html
+++ b/docs/reference/is.def.html
@@ -1,5 +1,5 @@
-Check if an object is defined, which is the same as being not NULL. — is.def • Spectroscopy Analysis Tools (spant) Check if an object is defined, which is the same as being not NULL. — is.def • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/is_fd.html b/docs/reference/is_fd.html
index 3b0ca165..18a193aa 100644
--- a/docs/reference/is_fd.html
+++ b/docs/reference/is_fd.html
@@ -1,7 +1,5 @@
-Check if the chemical shift dimension of an MRS data object is in the
-frequency domain. — is_fd • Spectroscopy Analysis Tools (spant) Check if the chemical shift dimension of an MRS data object is in the frequency domain. — is_fd • Spectroscopy Analysis Tools (spant) Transform 2D MRSI data from k-space to image space in the x-y direction. — kspace2img_xy • Spectroscopy Analysis Tools (spant) Transform 2D MRSI data from k-space to image space in the x-y direction. — kspace2img_xy • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/l2_reg.html b/docs/reference/l2_reg.html
index 3d781d80..21aa9849 100644
--- a/docs/reference/l2_reg.html
+++ b/docs/reference/l2_reg.html
@@ -1,5 +1,5 @@
-Perform l2 regularisation artefact suppression. — l2_reg • Spectroscopy Analysis Tools (spant) Perform l2 regularisation artefact suppression. — l2_reg • Spectroscopy Analysis Tools (spant) Apply line-broadening (apodisation) to MRS data or basis object. — lb • Spectroscopy Analysis Tools (spant) Apply line-broadening (apodisation) to MRS data or basis object. — lb • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -123,7 +123,7 @@ Value
diff --git a/docs/reference/lofdc.html b/docs/reference/lofdc.html
index 5419b1ec..31347a25 100644
--- a/docs/reference/lofdc.html
+++ b/docs/reference/lofdc.html
@@ -1,5 +1,5 @@
-Correct linear frequency drift. — lofdc • Spectroscopy Analysis Tools (spant) Correct linear frequency drift. — lofdc • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -138,7 +138,7 @@ Value
diff --git a/docs/reference/lw2alpha.html b/docs/reference/lw2alpha.html
index b83db682..25da229b 100644
--- a/docs/reference/lw2alpha.html
+++ b/docs/reference/lw2alpha.html
@@ -1,7 +1,5 @@
-Covert a linewidth in Hz to an equivalent alpha value in the time-domain ie:
-x * exp(-t * alpha). — lw2alpha • Spectroscopy Analysis Tools (spant) Covert a linewidth in Hz to an equivalent alpha value in the time-domain ie: x * exp(-t * alpha). — lw2alpha • Spectroscopy Analysis Tools (spant) Covert a linewidth in Hz to an equivalent beta value in the time-domain ie:
-x * exp(-t * t * beta). — lw2beta • Spectroscopy Analysis Tools (spant) Covert a linewidth in Hz to an equivalent beta value in the time-domain ie: x * exp(-t * t * beta). — lw2beta • Spectroscopy Analysis Tools (spant) Make a basis-set object from a directory containing LCModel formatted RAW
-files. — make_basis_from_raw • Spectroscopy Analysis Tools (spant) Make a basis-set object from a directory containing LCModel formatted RAW files. — make_basis_from_raw • Spectroscopy Analysis Tools (spant) Mask an MRS dataset in the dynamic dimension. — mask_dyns • Spectroscopy Analysis Tools (spant) Mask an MRS dataset in the dynamic dimension. — mask_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/mask_fit_res.html b/docs/reference/mask_fit_res.html
index 97baaa3f..ebd91a99 100644
--- a/docs/reference/mask_fit_res.html
+++ b/docs/reference/mask_fit_res.html
@@ -1,5 +1,5 @@
-Mask fit result spectra depending on a vector of bool values. — mask_fit_res • Spectroscopy Analysis Tools (spant) Mask fit result spectra depending on a vector of bool values. — mask_fit_res • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -116,7 +116,7 @@ Value
diff --git a/docs/reference/mask_xy.html b/docs/reference/mask_xy.html
index 11bb577c..b0d38619 100644
--- a/docs/reference/mask_xy.html
+++ b/docs/reference/mask_xy.html
@@ -1,5 +1,5 @@
-Mask an MRSI dataset in the x-y direction — mask_xy • Spectroscopy Analysis Tools (spant) Mask an MRSI dataset in the x-y direction — mask_xy • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/mask_xy_corners.html b/docs/reference/mask_xy_corners.html
index 09b16cd2..2d13839d 100644
--- a/docs/reference/mask_xy_corners.html
+++ b/docs/reference/mask_xy_corners.html
@@ -1,5 +1,5 @@
-Mask the four corners of an MRSI dataset in the x-y plane. — mask_xy_corners • Spectroscopy Analysis Tools (spant) Mask the four corners of an MRSI dataset in the x-y plane. — mask_xy_corners • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/mask_xy_ellipse.html b/docs/reference/mask_xy_ellipse.html
index 1d8b02e4..e2e749ef 100644
--- a/docs/reference/mask_xy_ellipse.html
+++ b/docs/reference/mask_xy_ellipse.html
@@ -1,7 +1,5 @@
-Mask the voxels outside an elliptical region spanning the MRSI dataset in the
-x-y plane. — mask_xy_ellipse • Spectroscopy Analysis Tools (spant) Mask the voxels outside an elliptical region spanning the MRSI dataset in the x-y plane. — mask_xy_ellipse • Spectroscopy Analysis Tools (spant) Mask a 2D MRSI dataset in the x-y dimension. — mask_xy_mat • Spectroscopy Analysis Tools (spant) Mask a 2D MRSI dataset in the x-y dimension. — mask_xy_mat • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Value
diff --git a/docs/reference/mat2mrs_data.html b/docs/reference/mat2mrs_data.html
index 2e2895f3..ae55665f 100644
--- a/docs/reference/mat2mrs_data.html
+++ b/docs/reference/mat2mrs_data.html
@@ -1,7 +1,5 @@
-Convert a matrix (with spectral points in the column dimension and dynamics
-in the row dimensions) into a mrs_data object. — mat2mrs_data • Spectroscopy Analysis Tools (spant) Convert a matrix (with spectral points in the column dimension and dynamics in the row dimensions) into a mrs_data object. — mat2mrs_data • Spectroscopy Analysis Tools (spant) Matrix exponential function taken from complexplus package to reduce the
-number of spant dependencies. — matexp • Spectroscopy Analysis Tools (spant) Matrix exponential function taken from complexplus package to reduce the number of spant dependencies. — matexp • Spectroscopy Analysis Tools (spant) Apply the max operator to an MRS dataset. — max_mrs • Spectroscopy Analysis Tools (spant) Apply the max operator to an MRS dataset. — max_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/max_mrs_interp.html b/docs/reference/max_mrs_interp.html
index e4474764..52e63f3e 100644
--- a/docs/reference/max_mrs_interp.html
+++ b/docs/reference/max_mrs_interp.html
@@ -1,5 +1,5 @@
-Apply the max operator to an interpolated MRS dataset. — max_mrs_interp • Spectroscopy Analysis Tools (spant) Apply the max operator to an interpolated MRS dataset. — max_mrs_interp • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/mean.list.html b/docs/reference/mean.list.html
index b8eb3463..048306fd 100644
--- a/docs/reference/mean.list.html
+++ b/docs/reference/mean.list.html
@@ -1,5 +1,5 @@
-Calculate the mean spectrum from an mrs_data object. — mean.list • Spectroscopy Analysis Tools (spant) Calculate the mean spectrum from an mrs_data object. — mean.list • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/mean.mrs_data.html b/docs/reference/mean.mrs_data.html
index 5531a28d..79515014 100644
--- a/docs/reference/mean.mrs_data.html
+++ b/docs/reference/mean.mrs_data.html
@@ -1,5 +1,5 @@
-Calculate the mean spectrum from an mrs_data object. — mean.mrs_data • Spectroscopy Analysis Tools (spant) Calculate the mean spectrum from an mrs_data object. — mean.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/mean_dyn_blocks.html b/docs/reference/mean_dyn_blocks.html
index 10467098..4c042448 100644
--- a/docs/reference/mean_dyn_blocks.html
+++ b/docs/reference/mean_dyn_blocks.html
@@ -1,5 +1,5 @@
-Calculate the mean of adjacent dynamic scans. — mean_dyn_blocks • Spectroscopy Analysis Tools (spant) Calculate the mean of adjacent dynamic scans. — mean_dyn_blocks • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/mean_dyn_pairs.html b/docs/reference/mean_dyn_pairs.html
index 63e909ea..1a241126 100644
--- a/docs/reference/mean_dyn_pairs.html
+++ b/docs/reference/mean_dyn_pairs.html
@@ -1,5 +1,5 @@
-Calculate the pairwise means across a dynamic data set. — mean_dyn_pairs • Spectroscopy Analysis Tools (spant) Calculate the pairwise means across a dynamic data set. — mean_dyn_pairs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/mean_dyns.html b/docs/reference/mean_dyns.html
index 73fdbfa7..0daa27df 100644
--- a/docs/reference/mean_dyns.html
+++ b/docs/reference/mean_dyns.html
@@ -1,5 +1,5 @@
-Calculate the mean dynamic data. — mean_dyns • Spectroscopy Analysis Tools (spant) Calculate the mean dynamic data. — mean_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/mean_mrs_list.html b/docs/reference/mean_mrs_list.html
index 808b6c50..10d842c0 100644
--- a/docs/reference/mean_mrs_list.html
+++ b/docs/reference/mean_mrs_list.html
@@ -1,5 +1,5 @@
-Return the mean of a list of mrs_data objects. — mean_mrs_list • Spectroscopy Analysis Tools (spant) Return the mean of a list of mrs_data objects. — mean_mrs_list • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/mean_vec_blocks.html b/docs/reference/mean_vec_blocks.html
index 8fc92eaa..dd78b122 100644
--- a/docs/reference/mean_vec_blocks.html
+++ b/docs/reference/mean_vec_blocks.html
@@ -1,5 +1,5 @@
-Calculate the mean of adjacent blocks in a vector. — mean_vec_blocks • Spectroscopy Analysis Tools (spant) Calculate the mean of adjacent blocks in a vector. — mean_vec_blocks • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/median_dyns.html b/docs/reference/median_dyns.html
index 1039d4b5..9a085b10 100644
--- a/docs/reference/median_dyns.html
+++ b/docs/reference/median_dyns.html
@@ -1,5 +1,5 @@
-Calculate the median dynamic data. — median_dyns • Spectroscopy Analysis Tools (spant) Calculate the median dynamic data. — median_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/mod_td.html b/docs/reference/mod_td.html
index 76ad0a40..141ef09e 100644
--- a/docs/reference/mod_td.html
+++ b/docs/reference/mod_td.html
@@ -1,5 +1,5 @@
-Apply the Modulus operator to the time-domain MRS signal. — mod_td • Spectroscopy Analysis Tools (spant) Apply the Modulus operator to the time-domain MRS signal. — mod_td • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/mrs_data2basis.html b/docs/reference/mrs_data2basis.html
index 62f7d749..11797b91 100644
--- a/docs/reference/mrs_data2basis.html
+++ b/docs/reference/mrs_data2basis.html
@@ -1,7 +1,5 @@
-Convert an mrs_data object to basis object - where basis signals are spread
-across the dynamic dimension in the MRS data. — mrs_data2basis • Spectroscopy Analysis Tools (spant) Convert an mrs_data object to basis object - where basis signals are spread across the dynamic dimension in the MRS data. — mrs_data2basis • Spectroscopy Analysis Tools (spant) Create a BIDS file structure from a vector of MRS data paths or list of mrs_data objects. — mrs_data2bids • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Create a BIDS file structure from a vector of MRS data paths or list of mrs_data objects.
+ Source: R/fmrs.R
+ mrs_data2bids.Rd
+
+
+
+ Create a BIDS file structure from a vector of MRS data paths or list of
+mrs_data objects.
+
+
+
+ mrs_data2bids(
+ mrs_data,
+ output_dir,
+ suffix = NULL,
+ sub = NULL,
+ ses = NULL,
+ task = NULL,
+ acq = NULL,
+ nuc = NULL,
+ voi = NULL,
+ rec = NULL,
+ run = NULL,
+ echo = NULL,
+ inv = NULL,
+ skip_existing = TRUE
+)
+
+
+
+ Arguments
+ - mrs_data
+vector of MRS data paths or list of mrs_data objects.
- output_dir
+the base directory to create the BIDS structure.
- suffix
+optional vector of file suffixes. Default behaviour is to
+automatically determine these from the input data, however it is recommended
+that they are specified to allow more efficient skipping of existing data.
- sub
+optional vector of subject labels. If not specified, these will be
+automatically generated as a series of increasing zero-padded integer values
+corresponding to the mrs_data input indices.
- ses
+optional vector of session labels.
- task
+optional vector of task labels.
- acq
+optional vector of acquisition labels.
- nuc
+optional vector of nucleus labels.
- voi
+optional vector of volume of interest labels.
- rec
+optional vector of reconstruction labels.
- run
+optional vector of run indices.
- echo
+optional vector of echo time indices.
- inv
+optional vector of inversion indices.
- skip_existing
+skip any data files that have already been converted.
+Defaults to TRUE, set to FALSE to force an overwrite of any existing data
+files.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/mrs_data2mat.html b/docs/reference/mrs_data2mat.html
index cf5ff28c..9e47688a 100644
--- a/docs/reference/mrs_data2mat.html
+++ b/docs/reference/mrs_data2mat.html
@@ -1,7 +1,5 @@
-Convert mrs_data object to a matrix, with spectral points in the column
-dimension and dynamics in the row dimension. — mrs_data2mat • Spectroscopy Analysis Tools (spant) Convert mrs_data object to a matrix, with spectral points in the column dimension and dynamics in the row dimension. — mrs_data2mat • Spectroscopy Analysis Tools (spant) Convert mrs_data object to a matrix, with spectral points in the column dimension and dynamics in the row dimension. — mrs_data2spec_mat • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Convert mrs_data object to a matrix, with spectral points in the column dimension and dynamics in the row dimension.
+ Source: R/mrs_data_proc.R
+ mrs_data2spec_mat.Rd
+
+
+
+ Convert mrs_data object to a matrix, with spectral points in the column
+dimension and dynamics in the row dimension.
+
+
+
+ mrs_data2spec_mat(mrs_data, collapse = TRUE)
+
+
+
+ Arguments
+ - mrs_data
+MRS data object or list of MRS data objects.
- collapse
+collapse all other dimensions along the dynamic dimension, eg
+a 16x16 MRSI grid would be first collapsed across 256 dynamic scans.
+
+ Value
+
+
+MRS data matrix.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/mrs_data2vec.html b/docs/reference/mrs_data2vec.html
index fb172d68..a1fd654d 100644
--- a/docs/reference/mrs_data2vec.html
+++ b/docs/reference/mrs_data2vec.html
@@ -1,5 +1,5 @@
-Convert mrs_data object to a vector. — mrs_data2vec • Spectroscopy Analysis Tools (spant) Convert mrs_data object to a vector. — mrs_data2vec • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -126,7 +126,7 @@ Value
diff --git a/docs/reference/mvfftshift.html b/docs/reference/mvfftshift.html
index 92b0841b..976b3410 100644
--- a/docs/reference/mvfftshift.html
+++ b/docs/reference/mvfftshift.html
@@ -1,7 +1,5 @@
-Perform a fftshift on a matrix, with each column replaced by its shifted
-result. — mvfftshift • Spectroscopy Analysis Tools (spant) Perform a fftshift on a matrix, with each column replaced by its shifted result. — mvfftshift • Spectroscopy Analysis Tools (spant) Perform an ifftshift on a matrix, with each column replaced by its shifted
-result. — mvifftshift • Spectroscopy Analysis Tools (spant) Perform an ifftshift on a matrix, with each column replaced by its shifted result. — mvifftshift • Spectroscopy Analysis Tools (spant) Print fit coordinates from a single index. — n2coord • Spectroscopy Analysis Tools (spant) Print fit coordinates from a single index. — n2coord • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/nifti_flip_lr.html b/docs/reference/nifti_flip_lr.html
index 730abe3c..19860b3c 100644
--- a/docs/reference/nifti_flip_lr.html
+++ b/docs/reference/nifti_flip_lr.html
@@ -1,9 +1,5 @@
-Flip the x data dimension order of a nifti image. This corresponds to
-flipping MRI data in the left-right direction, assuming the data in save in
-neurological format (can check with fslorient program). — nifti_flip_lr • Spectroscopy Analysis Tools (spant) Flip the x data dimension order of a nifti image. This corresponds to flipping MRI data in the left-right direction, assuming the data in save in neurological format (can check with fslorient program). — nifti_flip_lr • Spectroscopy Analysis Tools (spant) Export a one-page pdf of a single fit result — one_page_pdf • Spectroscopy Analysis Tools (spant) Export a one-page pdf of a single fit result — one_page_pdf • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -108,7 +108,7 @@ Arguments
diff --git a/docs/reference/ortho3.html b/docs/reference/ortho3.html
index 13ade97d..5d7dd2fd 100644
--- a/docs/reference/ortho3.html
+++ b/docs/reference/ortho3.html
@@ -1,5 +1,5 @@
-Display an orthographic projection plot of a nifti object. — ortho3 • Spectroscopy Analysis Tools (spant) Display an orthographic projection plot of a nifti object. — ortho3 • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -172,7 +172,7 @@ Arguments
diff --git a/docs/reference/ortho3_inter.html b/docs/reference/ortho3_inter.html
index 090cc5e5..15948899 100644
--- a/docs/reference/ortho3_inter.html
+++ b/docs/reference/ortho3_inter.html
@@ -1,5 +1,5 @@
-Display an interactive orthographic projection plot of a nifti object. — ortho3_inter • Spectroscopy Analysis Tools (spant) Display an interactive orthographic projection plot of a nifti object. — ortho3_inter • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -132,7 +132,7 @@ Arguments
diff --git a/docs/reference/peak_info.html b/docs/reference/peak_info.html
index 09058bd8..41c8ffaf 100644
--- a/docs/reference/peak_info.html
+++ b/docs/reference/peak_info.html
@@ -1,7 +1,5 @@
-Search for the highest peak in a spectral region and return the frequency,
-height and FWHM. — peak_info • Spectroscopy Analysis Tools (spant) Search for the highest peak in a spectral region and return the frequency, height and FWHM. — peak_info • Spectroscopy Analysis Tools (spant) Papoulis-Gerchberg (PG) algorithm method for k-space extrapolation. — pg_extrap_xy • Spectroscopy Analysis Tools (spant) Papoulis-Gerchberg (PG) algorithm method for k-space extrapolation. — pg_extrap_xy • Spectroscopy Analysis Tools (spant) Apply phasing parameters to MRS data. — phase • Spectroscopy Analysis Tools (spant) Apply phasing parameters to MRS data. — phase • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/phase_ref_1h_brain.html b/docs/reference/phase_ref_1h_brain.html
new file mode 100644
index 00000000..8707a74a
--- /dev/null
+++ b/docs/reference/phase_ref_1h_brain.html
@@ -0,0 +1,131 @@
+
+Corrected zero order phase and chemical shift offset in 1H MRS data from the brain. — phase_ref_1h_brain • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Corrected zero order phase and chemical shift offset in 1H MRS data from the brain.
+ Source: R/rats.R
+ phase_ref_1h_brain.Rd
+
+
+
+ Corrected zero order phase and chemical shift offset in 1H MRS data from the
+brain.
+
+
+
+ phase_ref_1h_brain(mrs_data, mean_ref = FALSE, ret_corr_only = TRUE)
+
+
+
+ Arguments
+ - mrs_data
+MRS data to be corrected.
- mean_ref
+apply the phase and offset of the mean spectrum to all
+others. Default is FALSE.
- ret_corr_only
+return the corrected data only.
+
+ Value
+
+
+corrected MRS data.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/plot.fit_result.html b/docs/reference/plot.fit_result.html
index e54d3bc1..836a53ee 100644
--- a/docs/reference/plot.fit_result.html
+++ b/docs/reference/plot.fit_result.html
@@ -1,5 +1,5 @@
-Plot the fitting results of an object of class fit_result. — plot.fit_result • Spectroscopy Analysis Tools (spant) Plot the fitting results of an object of class fit_result. — plot.fit_result • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -207,7 +207,7 @@ Arguments
diff --git a/docs/reference/plot.mrs_data.html b/docs/reference/plot.mrs_data.html
index fabcc35b..bb2ec651 100644
--- a/docs/reference/plot.mrs_data.html
+++ b/docs/reference/plot.mrs_data.html
@@ -1,5 +1,5 @@
-Plotting method for objects of class mrs_data. — plot.mrs_data • Spectroscopy Analysis Tools (spant) Plotting method for objects of class mrs_data. — plot.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -287,7 +287,7 @@ Arguments
diff --git a/docs/reference/plot_bc.html b/docs/reference/plot_bc.html
index 4f8309b4..b48142cc 100644
--- a/docs/reference/plot_bc.html
+++ b/docs/reference/plot_bc.html
@@ -1,5 +1,5 @@
-Convenience function to plot a baseline estimate with the original data. — plot_bc • Spectroscopy Analysis Tools (spant) Convenience function to plot a baseline estimate with the original data. — plot_bc • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -108,7 +108,7 @@ Arguments
diff --git a/docs/reference/plot_reg.html b/docs/reference/plot_reg.html
index ae1acbe7..2addb2f6 100644
--- a/docs/reference/plot_reg.html
+++ b/docs/reference/plot_reg.html
@@ -1,5 +1,5 @@
-Plot regressors as an image. — plot_reg • Spectroscopy Analysis Tools (spant) Plot regressors as an image. — plot_reg • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/plot_slice_fit.html b/docs/reference/plot_slice_fit.html
index fbc7b560..57f1af8a 100644
--- a/docs/reference/plot_slice_fit.html
+++ b/docs/reference/plot_slice_fit.html
@@ -1,5 +1,5 @@
-Plot a 2D slice from an MRSI fit result object. — plot_slice_fit • Spectroscopy Analysis Tools (spant) Plot a 2D slice from an MRSI fit result object. — plot_slice_fit • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -129,7 +129,7 @@ Arguments
diff --git a/docs/reference/plot_slice_fit_inter.html b/docs/reference/plot_slice_fit_inter.html
index 4eed104a..da105a7d 100644
--- a/docs/reference/plot_slice_fit_inter.html
+++ b/docs/reference/plot_slice_fit_inter.html
@@ -1,5 +1,5 @@
-Plot a 2D slice from an MRSI fit result object. — plot_slice_fit_inter • Spectroscopy Analysis Tools (spant) Plot a 2D slice from an MRSI fit result object. — plot_slice_fit_inter • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -134,7 +134,7 @@ Arguments
diff --git a/docs/reference/plot_slice_map.html b/docs/reference/plot_slice_map.html
index 553e9ac8..ffb2a134 100644
--- a/docs/reference/plot_slice_map.html
+++ b/docs/reference/plot_slice_map.html
@@ -1,5 +1,5 @@
-Plot a slice from a 7 dimensional array. — plot_slice_map • Spectroscopy Analysis Tools (spant) Plot a slice from a 7 dimensional array. — plot_slice_map • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -153,7 +153,7 @@ Arguments
diff --git a/docs/reference/plot_slice_map_inter.html b/docs/reference/plot_slice_map_inter.html
index 40d33b42..90968f66 100644
--- a/docs/reference/plot_slice_map_inter.html
+++ b/docs/reference/plot_slice_map_inter.html
@@ -1,7 +1,5 @@
-Plot an interactive slice map from a data array where voxels can be selected
-to display a corresponding spectrum. — plot_slice_map_inter • Spectroscopy Analysis Tools (spant) Plot an interactive slice map from a data array where voxels can be selected to display a corresponding spectrum. — plot_slice_map_inter • Spectroscopy Analysis Tools (spant) Plot the spectral standard deviation. — plot_spec_sd • Spectroscopy Analysis Tools (spant) Plot the spectral standard deviation. — plot_spec_sd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Arguments
diff --git a/docs/reference/plot_voi_overlay.html b/docs/reference/plot_voi_overlay.html
index 9a782e88..bbbbf35e 100644
--- a/docs/reference/plot_voi_overlay.html
+++ b/docs/reference/plot_voi_overlay.html
@@ -1,5 +1,5 @@
-Plot a volume as an image overlay. — plot_voi_overlay • Spectroscopy Analysis Tools (spant) Plot a volume as an image overlay. — plot_voi_overlay • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -116,7 +116,7 @@ Arguments
diff --git a/docs/reference/plot_voi_overlay_seg.html b/docs/reference/plot_voi_overlay_seg.html
index 3d4e74ff..0e800ff2 100644
--- a/docs/reference/plot_voi_overlay_seg.html
+++ b/docs/reference/plot_voi_overlay_seg.html
@@ -1,5 +1,5 @@
-Plot a volume as an overlay on a segmented brain volume. — plot_voi_overlay_seg • Spectroscopy Analysis Tools (spant) Plot a volume as an overlay on a segmented brain volume. — plot_voi_overlay_seg • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Arguments
diff --git a/docs/reference/ppm.html b/docs/reference/ppm.html
index c352327a..ee4696e2 100644
--- a/docs/reference/ppm.html
+++ b/docs/reference/ppm.html
@@ -1,5 +1,5 @@
-Return the ppm scale of an MRS dataset or fit result. — ppm • Spectroscopy Analysis Tools (spant) Return the ppm scale of an MRS dataset or fit result. — ppm • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -132,7 +132,7 @@ Value
diff --git a/docs/reference/precomp.html b/docs/reference/precomp.html
index 822d7336..df3d2c6c 100644
--- a/docs/reference/precomp.html
+++ b/docs/reference/precomp.html
@@ -1,7 +1,5 @@
-Save function results to file and load on subsequent calls to avoid repeat
-computation. — precomp • Spectroscopy Analysis Tools (spant) Save function results to file and load on subsequent calls to avoid repeat computation. — precomp • Spectroscopy Analysis Tools (spant) Preprocess and perform quality assessment of a single SVS data set. — preproc_svs • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Preprocess and perform quality assessment of a single SVS data set.
+ Source: R/fmrs.R
+ preproc_svs.Rd
+
+
+
+ Preprocess and perform quality assessment of a single SVS data set.
+
+
+
+ preproc_svs(path, label = NULL, output_dir = NULL, ref_inds = NULL)
+
+
+
+ Arguments
+ - path
+path to the fMRS data file or IMA directory.
- label
+a label to describe the data set.
- output_dir
+output directory.
- ref_inds
+a vector of 1-based indices for any water reference dynamic
+scans.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/preproc_svs_dataset.html b/docs/reference/preproc_svs_dataset.html
new file mode 100644
index 00000000..07c3a29b
--- /dev/null
+++ b/docs/reference/preproc_svs_dataset.html
@@ -0,0 +1,148 @@
+
+Preprocess and perform quality assessment of one or more SVS data sets. — preproc_svs_dataset • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Preprocess and perform quality assessment of one or more SVS data sets.
+ Source: R/fmrs.R
+ preproc_svs_dataset.Rd
+
+
+
+ Preprocess and perform quality assessment of one or more SVS data sets.
+
+
+
+ preproc_svs_dataset(
+ paths,
+ labels = NULL,
+ output_dir = "spant_analysis",
+ exclude_labels = NULL,
+ overwrite = FALSE,
+ ref_inds = NULL,
+ return_results = FALSE
+)
+
+
+
+ Arguments
+ - paths
+paths to the fMRS data file or IMA directory.
- labels
+labels to describe each data set.
- output_dir
+output directory.
- exclude_labels
+vector of labels of scans to exclude, eg poor quality
+data.
- overwrite
+overwrite saved results, defaults to FALSE.
- ref_inds
+a vector of 1-based indices for any water reference dynamic
+scans.
- return_results
+function will return key outputs, defaults to FALSE.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/print.fit_result.html b/docs/reference/print.fit_result.html
index 297f28dc..5f434e57 100644
--- a/docs/reference/print.fit_result.html
+++ b/docs/reference/print.fit_result.html
@@ -1,5 +1,5 @@
-Print a summary of an object of class fit_result. — print.fit_result • Spectroscopy Analysis Tools (spant) Print a summary of an object of class fit_result. — print.fit_result • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -105,7 +105,7 @@ Arguments
diff --git a/docs/reference/print.mrs_data.html b/docs/reference/print.mrs_data.html
index 51199017..e1561eb2 100644
--- a/docs/reference/print.mrs_data.html
+++ b/docs/reference/print.mrs_data.html
@@ -1,5 +1,5 @@
-Print a summary of mrs_data parameters. — print.mrs_data • Spectroscopy Analysis Tools (spant) Print a summary of mrs_data parameters. — print.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -109,7 +109,7 @@ Arguments
diff --git a/docs/reference/qn_states.html b/docs/reference/qn_states.html
index 0f42f2f9..d7aa6715 100644
--- a/docs/reference/qn_states.html
+++ b/docs/reference/qn_states.html
@@ -1,5 +1,5 @@
-Get the quantum coherence matrix for a spin system. — qn_states • Spectroscopy Analysis Tools (spant) Get the quantum coherence matrix for a spin system. — qn_states • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/rats.html b/docs/reference/rats.html
index 5a39a396..93585e08 100644
--- a/docs/reference/rats.html
+++ b/docs/reference/rats.html
@@ -1,5 +1,5 @@
-Robust Alignment to a Target Spectrum (RATS). — rats • Spectroscopy Analysis Tools (spant) Robust Alignment to a Target Spectrum (RATS). — rats • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -207,7 +207,7 @@ Value
diff --git a/docs/reference/re_weighting.html b/docs/reference/re_weighting.html
index d21caf21..8b0b070a 100644
--- a/docs/reference/re_weighting.html
+++ b/docs/reference/re_weighting.html
@@ -1,5 +1,5 @@
-Apply a weighting to the FID to enhance spectral resolution. — re_weighting • Spectroscopy Analysis Tools (spant) Apply a weighting to the FID to enhance spectral resolution. — re_weighting • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/read_basis.html b/docs/reference/read_basis.html
index da9b94af..eb6f8557 100644
--- a/docs/reference/read_basis.html
+++ b/docs/reference/read_basis.html
@@ -1,5 +1,5 @@
-Read a basis file in LCModel .basis format. — read_basis • Spectroscopy Analysis Tools (spant) Read a basis file in LCModel .basis format. — read_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/read_ima_coil_dir.html b/docs/reference/read_ima_coil_dir.html
index 28c02de0..4f073cd8 100644
--- a/docs/reference/read_ima_coil_dir.html
+++ b/docs/reference/read_ima_coil_dir.html
@@ -1,9 +1,5 @@
-Read a directory containing Siemens MRS IMA files and combine along the coil
-dimension. Note that the coil ID is inferred from the sorted file name and
-should be checked when consistency is required between two directories. — read_ima_coil_dir • Spectroscopy Analysis Tools (spant) Read a directory containing Siemens MRS IMA files and combine along the coil dimension. Note that the coil ID is inferred from the sorted file name and should be checked when consistency is required between two directories. — read_ima_coil_dir • Spectroscopy Analysis Tools (spant) Read a directory containing Siemens MRS IMA files and combine along the
-dynamic dimension. Note that the coil ID is inferred from the sorted file
-name and should be checked when consistency is required. — read_ima_dyn_dir • Spectroscopy Analysis Tools (spant) Read a directory containing Siemens MRS IMA files and combine along the dynamic dimension. Note that the coil ID is inferred from the sorted file name and should be checked when consistency is required. — read_ima_dyn_dir • Spectroscopy Analysis Tools (spant) Read an LCModel formatted coord file containing fit information. — read_lcm_coord • Spectroscopy Analysis Tools (spant) Read an LCModel formatted coord file containing fit information. — read_lcm_coord • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -107,7 +107,7 @@ Value
diff --git a/docs/reference/read_mrs.html b/docs/reference/read_mrs.html
index 3ac2a36b..2cf36b20 100644
--- a/docs/reference/read_mrs.html
+++ b/docs/reference/read_mrs.html
@@ -1,5 +1,5 @@
-Read MRS data from a file. — read_mrs • Spectroscopy Analysis Tools (spant) Read MRS data from a file. — read_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -88,7 +88,8 @@ Read MRS data from a file.
full_fid = FALSE,
omit_svs_ref_scans = TRUE,
verbose = FALSE,
- extra = NULL
+ extra = NULL,
+ fid_filt_dist = NULL
)
@@ -140,6 +141,13 @@ Arguments
an optional data frame to provide additional variables for use
in subsequent analysis steps, eg id or grouping variables.
fid_filt_dist
+indicate if the data has a distorted FID due to a
+brick-wall filter being used to downsample the data. Default is to auto
+detect this from the data, but TRUE or FALSE options can be given to override
+detection.
Value
@@ -183,7 +191,7 @@ Examples
diff --git a/docs/reference/read_mrs_tqn.html b/docs/reference/read_mrs_tqn.html
index 5766362f..84bdaf3a 100644
--- a/docs/reference/read_mrs_tqn.html
+++ b/docs/reference/read_mrs_tqn.html
@@ -1,5 +1,5 @@
-Read MRS data using the TARQUIN software package. — read_mrs_tqn • Spectroscopy Analysis Tools (spant) Read MRS data using the TARQUIN software package. — read_mrs_tqn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -131,7 +131,7 @@ Examples
diff --git a/docs/reference/read_pulse_ascii.html b/docs/reference/read_pulse_ascii.html
index c9e0d43c..ab11c9cc 100644
--- a/docs/reference/read_pulse_ascii.html
+++ b/docs/reference/read_pulse_ascii.html
@@ -1,5 +1,5 @@
-Read an ASCII formatted pulse file. — read_pulse_ascii • Spectroscopy Analysis Tools (spant) Read an ASCII formatted pulse file. — read_pulse_ascii • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/read_pulse_bruker.html b/docs/reference/read_pulse_bruker.html
index c92bf76a..dbe9073b 100644
--- a/docs/reference/read_pulse_bruker.html
+++ b/docs/reference/read_pulse_bruker.html
@@ -1,5 +1,5 @@
-Read a Bruker formatted pulse file — read_pulse_bruker • Spectroscopy Analysis Tools (spant) Read a Bruker formatted pulse file — read_pulse_bruker • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/read_pulse_pta.html b/docs/reference/read_pulse_pta.html
index 72e1b6d4..a0fac3c3 100644
--- a/docs/reference/read_pulse_pta.html
+++ b/docs/reference/read_pulse_pta.html
@@ -1,5 +1,5 @@
-Read a .pta formatted pulse file compatible with Siemens PulseTool. — read_pulse_pta • Spectroscopy Analysis Tools (spant) Read a .pta formatted pulse file compatible with Siemens PulseTool. — read_pulse_pta • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/read_siemens_txt_hdr.html b/docs/reference/read_siemens_txt_hdr.html
index 23fb8c70..3a17d87c 100644
--- a/docs/reference/read_siemens_txt_hdr.html
+++ b/docs/reference/read_siemens_txt_hdr.html
@@ -1,5 +1,5 @@
-Read the text format header found in Siemens IMA and TWIX data files. — read_siemens_txt_hdr • Spectroscopy Analysis Tools (spant) Read the text format header found in Siemens IMA and TWIX data files. — read_siemens_txt_hdr • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -78,7 +78,7 @@ Read the text format header found in Siemens IMA and TWIX data files.
- read_siemens_txt_hdr(input, version = "vd", verbose, offset = 0)
+ read_siemens_txt_hdr(input, version = "vd", verbose = FALSE, offset = 0)
@@ -118,7 +118,7 @@ Value
diff --git a/docs/reference/read_tqn_fit.html b/docs/reference/read_tqn_fit.html
index 4da6c25e..a1630420 100644
--- a/docs/reference/read_tqn_fit.html
+++ b/docs/reference/read_tqn_fit.html
@@ -1,5 +1,5 @@
-Reader for csv fit results generated by TARQUIN. — read_tqn_fit • Spectroscopy Analysis Tools (spant) Reader for csv fit results generated by TARQUIN. — read_tqn_fit • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -113,7 +113,7 @@ Examples
diff --git a/docs/reference/read_tqn_result.html b/docs/reference/read_tqn_result.html
index 36659714..68a3e98c 100644
--- a/docs/reference/read_tqn_result.html
+++ b/docs/reference/read_tqn_result.html
@@ -1,5 +1,5 @@
-Reader for csv results generated by TARQUIN. — read_tqn_result • Spectroscopy Analysis Tools (spant) Reader for csv results generated by TARQUIN. — read_tqn_result • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -117,7 +117,7 @@ Examples
diff --git a/docs/reference/recon_imag.html b/docs/reference/recon_imag.html
index d2a72225..5bc3b1eb 100644
--- a/docs/reference/recon_imag.html
+++ b/docs/reference/recon_imag.html
@@ -1,7 +1,5 @@
-Reconstruct complex time-domain data from the real part of frequency-domain
-data. — recon_imag • Spectroscopy Analysis Tools (spant) Reconstruct complex time-domain data from the real part of frequency-domain data. — recon_imag • Spectroscopy Analysis Tools (spant) Reconstruct complex time-domain data from the real part of frequency-domain
-data. — recon_imag_vec • Spectroscopy Analysis Tools (spant) Reconstruct complex time-domain data from the real part of frequency-domain data. — recon_imag_vec • Spectroscopy Analysis Tools (spant) Reconstruct 2D MRSI data from a twix file loaded with read_mrs. — recon_twix_2d_mrsi • Spectroscopy Analysis Tools (spant) Reconstruct 2D MRSI data from a twix file loaded with read_mrs. — recon_twix_2d_mrsi • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/rectangular_mask.html b/docs/reference/rectangular_mask.html
index a2117283..6e469bc9 100644
--- a/docs/reference/rectangular_mask.html
+++ b/docs/reference/rectangular_mask.html
@@ -1,5 +1,5 @@
-Create a rectangular mask stored as a matrix of logical values. — rectangular_mask • Spectroscopy Analysis Tools (spant) Create a rectangular mask stored as a matrix of logical values. — rectangular_mask • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -130,7 +130,7 @@ Value
diff --git a/docs/reference/reexports.html b/docs/reference/reexports.html
index 694a75d1..a59e8379 100644
--- a/docs/reference/reexports.html
+++ b/docs/reference/reexports.html
@@ -1,5 +1,5 @@
-Objects exported from other packages — reexports • Spectroscopy Analysis Tools (spant) Objects exported from other packages — reexports • Spectroscopy Analysis Tools (spant)
Spectroscopy Analysis Tools (spant)
- 2.21.0
+ 2.22.0
@@ -103,7 +103,7 @@ Objects exported from other packages
diff --git a/docs/reference/rep_array_dim.html b/docs/reference/rep_array_dim.html
index b9c49b4a..48c0a5ed 100644
--- a/docs/reference/rep_array_dim.html
+++ b/docs/reference/rep_array_dim.html
@@ -1,5 +1,5 @@
-Repeat an array over a given dimension. — rep_array_dim • Spectroscopy Analysis Tools (spant) Repeat an array over a given dimension. — rep_array_dim • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/rep_dyn.html b/docs/reference/rep_dyn.html
index 6bbfb0ef..89a4bb9b 100644
--- a/docs/reference/rep_dyn.html
+++ b/docs/reference/rep_dyn.html
@@ -1,5 +1,5 @@
-Replicate a scan in the dynamic dimension. — rep_dyn • Spectroscopy Analysis Tools (spant) Replicate a scan in the dynamic dimension. — rep_dyn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/rep_mrs.html b/docs/reference/rep_mrs.html
index 67730b5c..becb8f00 100644
--- a/docs/reference/rep_mrs.html
+++ b/docs/reference/rep_mrs.html
@@ -1,5 +1,5 @@
-Replicate a scan over a given dimension. — rep_mrs • Spectroscopy Analysis Tools (spant) Replicate a scan over a given dimension. — rep_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -138,7 +138,7 @@ Value
diff --git a/docs/reference/resample_basis.html b/docs/reference/resample_basis.html
index b0f2ab17..c7a6222a 100644
--- a/docs/reference/resample_basis.html
+++ b/docs/reference/resample_basis.html
@@ -1,5 +1,5 @@
-Resample a basis-set to match a mrs_data acquisition. — resample_basis • Spectroscopy Analysis Tools (spant) Resample a basis-set to match a mrs_data acquisition. — resample_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -116,7 +116,7 @@ Value
diff --git a/docs/reference/resample_img.html b/docs/reference/resample_img.html
index f1e7beaf..b0cc8f71 100644
--- a/docs/reference/resample_img.html
+++ b/docs/reference/resample_img.html
@@ -1,5 +1,5 @@
-Resample an image to match a target image space. — resample_img • Spectroscopy Analysis Tools (spant) Resample an image to match a target image space. — resample_img • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/resample_voi.html b/docs/reference/resample_voi.html
index 8fbfa836..a29ab096 100644
--- a/docs/reference/resample_voi.html
+++ b/docs/reference/resample_voi.html
@@ -1,7 +1,5 @@
-Resample a VOI to match a target image space using nearest-neighbour
-interpolation. — resample_voi • Spectroscopy Analysis Tools (spant) Resample a VOI to match a target image space using nearest-neighbour interpolation. — resample_voi • Spectroscopy Analysis Tools (spant) Reslice a nifti object to match the orientation of mrs data. — reslice_to_mrs • Spectroscopy Analysis Tools (spant) Reslice a nifti object to match the orientation of mrs data. — reslice_to_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/reson_table2mrs_data.html b/docs/reference/reson_table2mrs_data.html
index d75579ee..c5a2167a 100644
--- a/docs/reference/reson_table2mrs_data.html
+++ b/docs/reference/reson_table2mrs_data.html
@@ -1,5 +1,5 @@
-Generate mrs_data from a table of single Lorentzian resonances. — reson_table2mrs_data • Spectroscopy Analysis Tools (spant) Generate mrs_data from a table of single Lorentzian resonances. — reson_table2mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -119,7 +119,7 @@ Value
diff --git a/docs/reference/rm_dyns.html b/docs/reference/rm_dyns.html
index 5d5ef692..573e1f51 100644
--- a/docs/reference/rm_dyns.html
+++ b/docs/reference/rm_dyns.html
@@ -1,5 +1,5 @@
-Remove a subset of dynamic scans. — rm_dyns • Spectroscopy Analysis Tools (spant) Remove a subset of dynamic scans. — rm_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/scale_amp_molal.html b/docs/reference/scale_amp_molal.html
index aaeee1f2..7acb8cb0 100644
--- a/docs/reference/scale_amp_molal.html
+++ b/docs/reference/scale_amp_molal.html
@@ -1,7 +1,5 @@
-Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water). — scale_amp_molal • Spectroscopy Analysis Tools (spant) Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / kg of tissue water). — scale_amp_molal • Spectroscopy Analysis Tools (spant)
Spectroscopy Analysis Tools (spant)
- 2.21.0
+ 2.22.0
@@ -76,8 +74,7 @@
- Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water).
+ Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / kg of tissue water).
Source: R/amp_scaling.R
scale_amp_molal.Rd
@@ -163,7 +160,7 @@ Value
diff --git a/docs/reference/scale_amp_molal_pvc.html b/docs/reference/scale_amp_molal_pvc.html
index 962d6afc..4d194abd 100644
--- a/docs/reference/scale_amp_molal_pvc.html
+++ b/docs/reference/scale_amp_molal_pvc.html
@@ -1,7 +1,5 @@
-Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water). — scale_amp_molal_pvc • Spectroscopy Analysis Tools (spant)
@@ -75,8 +73,7 @@
- Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water).
+ Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / kg of tissue water).
Source: R/amp_scaling.R
scale_amp_molal_pvc.Rd
@@ -141,7 +138,7 @@ Value
diff --git a/docs/reference/scale_amp_molar.html b/docs/reference/scale_amp_molar.html
index 02358d91..dc87a338 100644
--- a/docs/reference/scale_amp_molar.html
+++ b/docs/reference/scale_amp_molar.html
@@ -1,7 +1,5 @@
-Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / Litre of tissue). — scale_amp_molar • Spectroscopy Analysis Tools (spant) Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / Litre of tissue). — scale_amp_molar • Spectroscopy Analysis Tools (spant) Convert default LCM/TARQUIN concentration scaling to molal units with partial
-volume correction. — scale_amp_molar2molal_pvc • Spectroscopy Analysis Tools (spant) Convert default LCM/TARQUIN concentration scaling to molal units with partial volume correction. — scale_amp_molar2molal_pvc • Spectroscopy Analysis Tools (spant) Scale fitted amplitudes to a ratio of signal amplitude. — scale_amp_ratio • Spectroscopy Analysis Tools (spant) Scale fitted amplitudes to a ratio of signal amplitude. — scale_amp_ratio • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -116,7 +116,7 @@ Value
diff --git a/docs/reference/scale_amp_ratio_value.html b/docs/reference/scale_amp_ratio_value.html
index 2036837a..6af8ac51 100644
--- a/docs/reference/scale_amp_ratio_value.html
+++ b/docs/reference/scale_amp_ratio_value.html
@@ -1,5 +1,5 @@
-Scale fitted amplitudes to a ratio of signal amplitude. — scale_amp_ratio_value • Spectroscopy Analysis Tools (spant) Scale fitted amplitudes to a ratio of signal amplitude. — scale_amp_ratio_value • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/scale_amp_water_ratio.html b/docs/reference/scale_amp_water_ratio.html
index 5b25e884..35a76b00 100644
--- a/docs/reference/scale_amp_water_ratio.html
+++ b/docs/reference/scale_amp_water_ratio.html
@@ -1,5 +1,5 @@
-Scale metabolite amplitudes as a ratio to the unsuppressed water amplitude. — scale_amp_water_ratio • Spectroscopy Analysis Tools (spant) Scale metabolite amplitudes as a ratio to the unsuppressed water amplitude. — scale_amp_water_ratio • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/scale_basis_amp.html b/docs/reference/scale_basis_amp.html
index 9401c3f1..5a58b5e5 100644
--- a/docs/reference/scale_basis_amp.html
+++ b/docs/reference/scale_basis_amp.html
@@ -1,5 +1,5 @@
-Scale a basis object by a scalar. — scale_basis_amp • Spectroscopy Analysis Tools (spant) Scale a basis object by a scalar. — scale_basis_amp • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/scale_basis_from_singlet.html b/docs/reference/scale_basis_from_singlet.html
index 0d542bc8..c9a19e77 100644
--- a/docs/reference/scale_basis_from_singlet.html
+++ b/docs/reference/scale_basis_from_singlet.html
@@ -1,5 +1,5 @@
-Scale a basis-set to be consistent with spant assumptions for water scaling. — scale_basis_from_singlet • Spectroscopy Analysis Tools (spant) Scale a basis-set to be consistent with spant assumptions for water scaling. — scale_basis_from_singlet • Spectroscopy Analysis Tools (spant)
Spectroscopy Analysis Tools (spant)
- 2.21.0
+ 2.22.0
@@ -127,7 +127,7 @@ Value
diff --git a/docs/reference/scale_mrs_amp.html b/docs/reference/scale_mrs_amp.html
index b5501a0d..990f058a 100644
--- a/docs/reference/scale_mrs_amp.html
+++ b/docs/reference/scale_mrs_amp.html
@@ -1,5 +1,5 @@
-Scale an mrs_data object by a scalar or vector or amplitudes. — scale_mrs_amp • Spectroscopy Analysis Tools (spant) Scale an mrs_data object by a scalar or vector or amplitudes. — scale_mrs_amp • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/scale_spec.html b/docs/reference/scale_spec.html
index 4f6ea835..6b3ddba4 100644
--- a/docs/reference/scale_spec.html
+++ b/docs/reference/scale_spec.html
@@ -1,5 +1,5 @@
-Scale mrs_data to a spectral region. — scale_spec • Spectroscopy Analysis Tools (spant) Scale mrs_data to a spectral region. — scale_spec • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -141,7 +141,7 @@ Value
diff --git a/docs/reference/sd.html b/docs/reference/sd.html
index ea1eec9f..3ae4dfd4 100644
--- a/docs/reference/sd.html
+++ b/docs/reference/sd.html
@@ -1,5 +1,5 @@
-Calculate the standard deviation spectrum from an mrs_data object. — sd • Spectroscopy Analysis Tools (spant) Calculate the standard deviation spectrum from an mrs_data object. — sd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/sd.mrs_data.html b/docs/reference/sd.mrs_data.html
index 3f92a49f..13bdda85 100644
--- a/docs/reference/sd.mrs_data.html
+++ b/docs/reference/sd.mrs_data.html
@@ -1,5 +1,5 @@
-Calculate the standard deviation spectrum from an mrs_data object. — sd.mrs_data • Spectroscopy Analysis Tools (spant) Calculate the standard deviation spectrum from an mrs_data object. — sd.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/seconds.html b/docs/reference/seconds.html
index b34d6627..467ee17f 100644
--- a/docs/reference/seconds.html
+++ b/docs/reference/seconds.html
@@ -1,5 +1,5 @@
-Return a time scale vector to match the FID of an MRS data object. — seconds • Spectroscopy Analysis Tools (spant) Return a time scale vector to match the FID of an MRS data object. — seconds • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/seq_cpmg_ideal.html b/docs/reference/seq_cpmg_ideal.html
index 547e96ab..45727c86 100644
--- a/docs/reference/seq_cpmg_ideal.html
+++ b/docs/reference/seq_cpmg_ideal.html
@@ -1,5 +1,5 @@
-CPMG style sequence with ideal pulses. — seq_cpmg_ideal • Spectroscopy Analysis Tools (spant) CPMG style sequence with ideal pulses. — seq_cpmg_ideal • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/seq_mega_press_ideal.html b/docs/reference/seq_mega_press_ideal.html
index 0769b8b4..a9cd7fa0 100644
--- a/docs/reference/seq_mega_press_ideal.html
+++ b/docs/reference/seq_mega_press_ideal.html
@@ -1,7 +1,5 @@
-MEGA-PRESS sequence with ideal localisation pulses and Gaussian shaped
-editing pulse. — seq_mega_press_ideal • Spectroscopy Analysis Tools (spant) MEGA-PRESS sequence with ideal localisation pulses and Gaussian shaped editing pulse. — seq_mega_press_ideal • Spectroscopy Analysis Tools (spant) PRESS sequence with shaped refocusing pulses. — seq_press_2d_shaped • Spectroscopy Analysis Tools (spant) PRESS sequence with shaped refocusing pulses. — seq_press_2d_shaped • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -165,7 +165,7 @@ Value
diff --git a/docs/reference/seq_press_ideal.html b/docs/reference/seq_press_ideal.html
index 8c976856..72c3af3d 100644
--- a/docs/reference/seq_press_ideal.html
+++ b/docs/reference/seq_press_ideal.html
@@ -1,5 +1,5 @@
-PRESS sequence with ideal pulses. — seq_press_ideal • Spectroscopy Analysis Tools (spant) PRESS sequence with ideal pulses. — seq_press_ideal • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/seq_pulse_acquire.html b/docs/reference/seq_pulse_acquire.html
index 4a88fc64..ad80571e 100644
--- a/docs/reference/seq_pulse_acquire.html
+++ b/docs/reference/seq_pulse_acquire.html
@@ -1,5 +1,5 @@
-Simple pulse and acquire sequence with ideal pulses. — seq_pulse_acquire • Spectroscopy Analysis Tools (spant) Simple pulse and acquire sequence with ideal pulses. — seq_pulse_acquire • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/seq_slaser_ideal.html b/docs/reference/seq_slaser_ideal.html
index 74688f4d..eb83e8e3 100644
--- a/docs/reference/seq_slaser_ideal.html
+++ b/docs/reference/seq_slaser_ideal.html
@@ -1,5 +1,5 @@
-sLASER sequence with ideal pulses. — seq_slaser_ideal • Spectroscopy Analysis Tools (spant) sLASER sequence with ideal pulses. — seq_slaser_ideal • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -126,7 +126,7 @@ Value
diff --git a/docs/reference/seq_spin_echo_ideal.html b/docs/reference/seq_spin_echo_ideal.html
index e23271de..4248716f 100644
--- a/docs/reference/seq_spin_echo_ideal.html
+++ b/docs/reference/seq_spin_echo_ideal.html
@@ -1,5 +1,5 @@
-Spin echo sequence with ideal pulses. — seq_spin_echo_ideal • Spectroscopy Analysis Tools (spant) Spin echo sequence with ideal pulses. — seq_spin_echo_ideal • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/seq_steam_ideal.html b/docs/reference/seq_steam_ideal.html
index a60685a8..1c8115d7 100644
--- a/docs/reference/seq_steam_ideal.html
+++ b/docs/reference/seq_steam_ideal.html
@@ -1,5 +1,5 @@
-STEAM sequence with ideal pulses. — seq_steam_ideal • Spectroscopy Analysis Tools (spant) STEAM sequence with ideal pulses. — seq_steam_ideal • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -128,7 +128,7 @@ Value
diff --git a/docs/reference/seq_steam_ideal_cof.html b/docs/reference/seq_steam_ideal_cof.html
index 8f225740..cba7af91 100644
--- a/docs/reference/seq_steam_ideal_cof.html
+++ b/docs/reference/seq_steam_ideal_cof.html
@@ -1,7 +1,5 @@
-STEAM sequence with ideal pulses and coherence order filtering to simulate
-gradient crushers. — seq_steam_ideal_cof • Spectroscopy Analysis Tools (spant) STEAM sequence with ideal pulses and coherence order filtering to simulate gradient crushers. — seq_steam_ideal_cof • Spectroscopy Analysis Tools (spant) STEAM sequence with ideal pulses using the z-rotation gradient simulation
-method described by Young et al JMR 140, 146-152 (1999). — seq_steam_ideal_young • Spectroscopy Analysis Tools (spant) STEAM sequence with ideal pulses using the z-rotation gradient simulation method described by Young et al JMR 140, 146-152 (1999). — seq_steam_ideal_young • Spectroscopy Analysis Tools (spant) Set the number of transients for an mrs_data object. — set_Ntrans • Spectroscopy Analysis Tools (spant) Set the number of transients for an mrs_data object. — set_Ntrans • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/set_def_acq_paras.html b/docs/reference/set_def_acq_paras.html
index 3e1b4004..cc2ada9c 100644
--- a/docs/reference/set_def_acq_paras.html
+++ b/docs/reference/set_def_acq_paras.html
@@ -1,5 +1,5 @@
-Set the default acquisition parameters. — set_def_acq_paras • Spectroscopy Analysis Tools (spant) Set the default acquisition parameters. — set_def_acq_paras • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Arguments
diff --git a/docs/reference/set_lcm_cmd.html b/docs/reference/set_lcm_cmd.html
index 2056ed01..42bb2f24 100644
--- a/docs/reference/set_lcm_cmd.html
+++ b/docs/reference/set_lcm_cmd.html
@@ -1,5 +1,5 @@
-Set the command to run the LCModel command-line program. — set_lcm_cmd • Spectroscopy Analysis Tools (spant) Set the command to run the LCModel command-line program. — set_lcm_cmd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/set_lw.html b/docs/reference/set_lw.html
index b64ec851..bb176c62 100644
--- a/docs/reference/set_lw.html
+++ b/docs/reference/set_lw.html
@@ -1,5 +1,5 @@
-Apply line-broadening to an mrs_data object to achieve a specified linewidth. — set_lw • Spectroscopy Analysis Tools (spant) Apply line-broadening to an mrs_data object to achieve a specified linewidth. — set_lw • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -123,7 +123,7 @@ Value
diff --git a/docs/reference/set_mask_xy_mat.html b/docs/reference/set_mask_xy_mat.html
index 49dc5d4e..52c4b617 100644
--- a/docs/reference/set_mask_xy_mat.html
+++ b/docs/reference/set_mask_xy_mat.html
@@ -1,5 +1,5 @@
-Set the masked voxels in a 2D MRSI dataset to given spectrum. — set_mask_xy_mat • Spectroscopy Analysis Tools (spant) Set the masked voxels in a 2D MRSI dataset to given spectrum. — set_mask_xy_mat • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Value
diff --git a/docs/reference/set_precomp_mode.html b/docs/reference/set_precomp_mode.html
index f44bd5d3..47c28e3b 100644
--- a/docs/reference/set_precomp_mode.html
+++ b/docs/reference/set_precomp_mode.html
@@ -1,5 +1,5 @@
-Set the precompute mode. — set_precomp_mode • Spectroscopy Analysis Tools (spant) Set the precompute mode. — set_precomp_mode • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/set_precomp_verbose.html b/docs/reference/set_precomp_verbose.html
index 1453a231..9c613505 100644
--- a/docs/reference/set_precomp_verbose.html
+++ b/docs/reference/set_precomp_verbose.html
@@ -1,5 +1,5 @@
-Set the verbosity of the precompute function. — set_precomp_verbose • Spectroscopy Analysis Tools (spant) Set the verbosity of the precompute function. — set_precomp_verbose • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/set_ref.html b/docs/reference/set_ref.html
index 8953fa50..5436dfa2 100644
--- a/docs/reference/set_ref.html
+++ b/docs/reference/set_ref.html
@@ -1,5 +1,5 @@
-Set the ppm reference value (eg ppm value at 0Hz). — set_ref • Spectroscopy Analysis Tools (spant) Set the ppm reference value (eg ppm value at 0Hz). — set_ref • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/set_td_pts.html b/docs/reference/set_td_pts.html
index 8a80d42a..586459ff 100644
--- a/docs/reference/set_td_pts.html
+++ b/docs/reference/set_td_pts.html
@@ -1,7 +1,5 @@
-Set the number of time-domain data points, truncating or zero-filling as
-appropriate. — set_td_pts • Spectroscopy Analysis Tools (spant) Set the number of time-domain data points, truncating or zero-filling as appropriate. — set_td_pts • Spectroscopy Analysis Tools (spant) Set the command to run the TARQUIN command-line program. — set_tqn_cmd • Spectroscopy Analysis Tools (spant) Set the command to run the TARQUIN command-line program. — set_tqn_cmd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/set_tr.html b/docs/reference/set_tr.html
index b2109ab0..65c9df5f 100644
--- a/docs/reference/set_tr.html
+++ b/docs/reference/set_tr.html
@@ -1,5 +1,5 @@
-Set the repetition time of an MRS dataset. — set_tr • Spectroscopy Analysis Tools (spant) Set the repetition time of an MRS dataset. — set_tr • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/shift.html b/docs/reference/shift.html
index ab0fe724..034591d0 100644
--- a/docs/reference/shift.html
+++ b/docs/reference/shift.html
@@ -1,5 +1,5 @@
-Apply a frequency shift to MRS data. — shift • Spectroscopy Analysis Tools (spant) Apply a frequency shift to MRS data. — shift • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/shift_basis.html b/docs/reference/shift_basis.html
index 2884be19..f55a65e0 100644
--- a/docs/reference/shift_basis.html
+++ b/docs/reference/shift_basis.html
@@ -1,5 +1,5 @@
-Apply frequency shifts to basis set signals. — shift_basis • Spectroscopy Analysis Tools (spant) Apply frequency shifts to basis set signals. — shift_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Value
diff --git a/docs/reference/sim_basis.html b/docs/reference/sim_basis.html
index c7838c46..bb5fefc6 100644
--- a/docs/reference/sim_basis.html
+++ b/docs/reference/sim_basis.html
@@ -1,5 +1,5 @@
-Simulate a basis set object. — sim_basis • Spectroscopy Analysis Tools (spant) Simulate a basis set object. — sim_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -136,7 +136,7 @@ Value
diff --git a/docs/reference/sim_basis_1h_brain.html b/docs/reference/sim_basis_1h_brain.html
index 62ed7389..f71ffa0b 100644
--- a/docs/reference/sim_basis_1h_brain.html
+++ b/docs/reference/sim_basis_1h_brain.html
@@ -1,7 +1,5 @@
-Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS
-sequence. Note, ideal pulses are assumed. — sim_basis_1h_brain • Spectroscopy Analysis Tools (spant) Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS sequence. Note, ideal pulses are assumed. — sim_basis_1h_brain • Spectroscopy Analysis Tools (spant) Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS
-sequence. Note, ideal pulses are assumed. — sim_basis_1h_brain_press • Spectroscopy Analysis Tools (spant) Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS sequence. Note, ideal pulses are assumed. — sim_basis_1h_brain_press • Spectroscopy Analysis Tools (spant) Simulate a macromolecular and lipid basis-set suitable for 1H brain MRS
-analysis. — sim_basis_mm_lip_lcm • Spectroscopy Analysis Tools (spant) Simulate a macromolecular and lipid basis-set suitable for 1H brain MRS analysis. — sim_basis_mm_lip_lcm • Spectroscopy Analysis Tools (spant) Simulate a basis file using TARQUIN. — sim_basis_tqn • Spectroscopy Analysis Tools (spant) Simulate a basis file using TARQUIN. — sim_basis_tqn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -129,7 +129,7 @@ Examples
diff --git a/docs/reference/sim_brain_1h.html b/docs/reference/sim_brain_1h.html
index 2044cf1a..717ee289 100644
--- a/docs/reference/sim_brain_1h.html
+++ b/docs/reference/sim_brain_1h.html
@@ -1,5 +1,5 @@
-Simulate MRS data with a similar appearance to normal brain (by default). — sim_brain_1h • Spectroscopy Analysis Tools (spant) Simulate MRS data with a similar appearance to normal brain (by default). — sim_brain_1h • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -159,7 +159,7 @@ Value
diff --git a/docs/reference/sim_mol.html b/docs/reference/sim_mol.html
index 23bcef50..77f76a50 100644
--- a/docs/reference/sim_mol.html
+++ b/docs/reference/sim_mol.html
@@ -1,5 +1,5 @@
-Simulate a mol_parameter object. — sim_mol • Spectroscopy Analysis Tools (spant) Simulate a mol_parameter object. — sim_mol • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -143,7 +143,7 @@ Value
diff --git a/docs/reference/sim_noise.html b/docs/reference/sim_noise.html
index 23875f79..a71477d4 100644
--- a/docs/reference/sim_noise.html
+++ b/docs/reference/sim_noise.html
@@ -1,5 +1,5 @@
-Simulate an mrs_data object containing simulated Gaussian noise. — sim_noise • Spectroscopy Analysis Tools (spant) Simulate an mrs_data object containing simulated Gaussian noise. — sim_noise • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -84,6 +84,7 @@ Simulate an mrs_data object containing simulated Gaussian noise.
ft = def_ft(),
N = def_N(),
ref = def_ref(),
+ nuc = def_nuc(),
dyns = 1,
fd = TRUE
)
@@ -111,6 +112,10 @@ Arguments
reference value for ppm scale.
nuc
+resonant nucleus.
dyns
number of dynamic scans to generate.
Value
diff --git a/docs/reference/sim_resonances.html b/docs/reference/sim_resonances.html
index 19e9a8a4..d4f8d7c0 100644
--- a/docs/reference/sim_resonances.html
+++ b/docs/reference/sim_resonances.html
@@ -1,5 +1,5 @@
-Simulate a MRS data object containing a set of simulated resonances. — sim_resonances • Spectroscopy Analysis Tools (spant) Simulate a MRS data object containing a set of simulated resonances. — sim_resonances • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -161,7 +161,7 @@ Examples
diff --git a/docs/reference/sim_th_excit_profile.html b/docs/reference/sim_th_excit_profile.html
index 5535c5ef..e781cab1 100644
--- a/docs/reference/sim_th_excit_profile.html
+++ b/docs/reference/sim_th_excit_profile.html
@@ -1,7 +1,5 @@
-Simulate an ideal pulse excitation profile by smoothing a top-hat function
-with a Gaussian. — sim_th_excit_profile • Spectroscopy Analysis Tools (spant) Simulate an ideal pulse excitation profile by smoothing a top-hat function with a Gaussian. — sim_th_excit_profile • Spectroscopy Analysis Tools (spant) Simulate an mrs_data object containing complex zero valued samples. — sim_zero • Spectroscopy Analysis Tools (spant) Simulate an mrs_data object containing complex zero valued samples. — sim_zero • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -78,7 +78,14 @@ Simulate an mrs_data object containing complex zero valued samples.
-
+
@@ -99,6 +106,10 @@ Arguments
reference value for ppm scale.
nuc
+resonant nucleus.
dyns
number of dynamic scans to generate.
Value
diff --git a/docs/reference/smooth_dyns.html b/docs/reference/smooth_dyns.html
index 4cc8da50..accf3a51 100644
--- a/docs/reference/smooth_dyns.html
+++ b/docs/reference/smooth_dyns.html
@@ -1,5 +1,5 @@
-Smooth data across the dynamic dimension with a Gaussian kernel. — smooth_dyns • Spectroscopy Analysis Tools (spant) Smooth data across the dynamic dimension with a Gaussian kernel. — smooth_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/sort_basis.html b/docs/reference/sort_basis.html
index 6a676ea2..d25cc006 100644
--- a/docs/reference/sort_basis.html
+++ b/docs/reference/sort_basis.html
@@ -1,5 +1,5 @@
-Sort the basis-set elements alphabetically. — sort_basis • Spectroscopy Analysis Tools (spant) Sort the basis-set elements alphabetically. — sort_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/spant-package.html b/docs/reference/spant-package.html
index b3dd8e21..90f19ec3 100644
--- a/docs/reference/spant-package.html
+++ b/docs/reference/spant-package.html
@@ -1,5 +1,5 @@
-spant: spectroscopy analysis tools. — spant-package • Spectroscopy Analysis Tools (spant) spant: spectroscopy analysis tools. — spant-package • Spectroscopy Analysis Tools (spant) Simulate and fit some spectra with ABfit for benchmarking purposes. Basic
-timing and performance metrics will be printed. — spant_abfit_benchmark • Spectroscopy Analysis Tools (spant) Simulate and fit some spectra with ABfit for benchmarking purposes. Basic timing and performance metrics will be printed. — spant_abfit_benchmark • Spectroscopy Analysis Tools (spant) Example MEGA-PRESS data with significant B0 drift. — spant_mpress_drift • Spectroscopy Analysis Tools (spant) Example MEGA-PRESS data with significant B0 drift. — spant_mpress_drift • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -83,7 +83,7 @@ Example MEGA-PRESS data with significant B0 drift.
Format
- An object of class mrs_data of length 13.
+ An object of class mrs_data of dimension 1 x 1 x 1 x 1 x 40 x 1 x 1024.
@@ -98,7 +98,7 @@ Format
diff --git a/docs/reference/spant_sim_fmrs_dataset.html b/docs/reference/spant_sim_fmrs_dataset.html
new file mode 100644
index 00000000..00e48b56
--- /dev/null
+++ b/docs/reference/spant_sim_fmrs_dataset.html
@@ -0,0 +1,117 @@
+
+Simulate an example fMRS dataset for a block design fMRS experiment and export a BIDS structure. — spant_sim_fmrs_dataset • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Simulate an example fMRS dataset for a block design fMRS experiment and export a BIDS structure.
+ Source: R/fmrs.R
+ spant_sim_fmrs_dataset.Rd
+
+
+
+ Simulate an example fMRS dataset for a block design fMRS experiment and
+export a BIDS structure.
+
+
+
+ spant_sim_fmrs_dataset(output_dir = NULL)
+
+
+
+ Arguments
+ - output_dir
+output directory for the BIDS data. Defaults to :
+"HOME/sim_fmrs_dataset/data".
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/spant_simulation_benchmark.html b/docs/reference/spant_simulation_benchmark.html
index 32daa8bf..d8cc6841 100644
--- a/docs/reference/spant_simulation_benchmark.html
+++ b/docs/reference/spant_simulation_benchmark.html
@@ -1,7 +1,5 @@
-Simulate a typical metabolite basis set for benchmarking. Timing metrics will
-be printed on completion. — spant_simulation_benchmark • Spectroscopy Analysis Tools (spant) Simulate a typical metabolite basis set for benchmarking. Timing metrics will be printed on completion. — spant_simulation_benchmark • Spectroscopy Analysis Tools (spant) Decompose an mrs_data object into white and gray matter spectra. — spec_decomp • Spectroscopy Analysis Tools (spant) Perform a mathematical operation on a spectral region. — spec_op • Spectroscopy Analysis Tools (spant) Perform a mathematical operation on a spectral region. — spec_op • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -98,8 +98,8 @@ Arguments
operator
-can be "sum" (default), "mean", "l2", "max", "min" or
-"max-min".
can be "sum" (default), "mean", "l2", "max", "max_cplx,
+"min" or "max-min".
freq_scale
@@ -129,7 +129,7 @@ Value
diff --git a/docs/reference/spin_sys.html b/docs/reference/spin_sys.html
index 853423a4..1eaa9e76 100644
--- a/docs/reference/spin_sys.html
+++ b/docs/reference/spin_sys.html
@@ -1,5 +1,5 @@
-Create a spin system object for pulse sequence simulation. — spin_sys • Spectroscopy Analysis Tools (spant) Create a spin system object for pulse sequence simulation. — spin_sys • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/spm_pve2categorical.html b/docs/reference/spm_pve2categorical.html
index 23a1bad9..70f10729 100644
--- a/docs/reference/spm_pve2categorical.html
+++ b/docs/reference/spm_pve2categorical.html
@@ -1,7 +1,5 @@
-Convert SPM style segmentation files to a single categorical image where
-the numerical values map as: 0) Other, 1) CSF, 2) GM and 3) WM. — spm_pve2categorical • Spectroscopy Analysis Tools (spant) Convert SPM style segmentation files to a single categorical image where the numerical values map as: 0) Other, 1) CSF, 2) GM and 3) WM. — spm_pve2categorical • Spectroscopy Analysis Tools (spant) Signal space projection method for lipid suppression. — ssp • Spectroscopy Analysis Tools (spant) Signal space projection method for lipid suppression. — ssp • Spectroscopy Analysis Tools (spant) Plot the fitting results of an object of class fit_result with
-individual basis set components shown. — stackplot.fit_result • Spectroscopy Analysis Tools (spant) Plot the fitting results of an object of class fit_result with individual basis set components shown. — stackplot.fit_result • Spectroscopy Analysis Tools (spant) Produce a plot with multiple traces. — stackplot • Spectroscopy Analysis Tools (spant) Produce a plot with multiple traces. — stackplot • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/stackplot.mrs_data.html b/docs/reference/stackplot.mrs_data.html
index 17ff5648..64eea445 100644
--- a/docs/reference/stackplot.mrs_data.html
+++ b/docs/reference/stackplot.mrs_data.html
@@ -1,5 +1,5 @@
-Stackplot plotting method for objects of class mrs_data. — stackplot.mrs_data • Spectroscopy Analysis Tools (spant) Stackplot plotting method for objects of class mrs_data. — stackplot.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -255,7 +255,7 @@ Arguments
diff --git a/docs/reference/sub_first_dyn.html b/docs/reference/sub_first_dyn.html
index dbd7f831..493b7242 100644
--- a/docs/reference/sub_first_dyn.html
+++ b/docs/reference/sub_first_dyn.html
@@ -1,5 +1,5 @@
-Subtract the first dynamic spectrum from a dynamic series. — sub_first_dyn • Spectroscopy Analysis Tools (spant) Subtract the first dynamic spectrum from a dynamic series. — sub_first_dyn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/sub_mean_dyns.html b/docs/reference/sub_mean_dyns.html
index 6e3bb2df..221bd0c1 100644
--- a/docs/reference/sub_mean_dyns.html
+++ b/docs/reference/sub_mean_dyns.html
@@ -1,5 +1,5 @@
-Subtract the mean dynamic spectrum from a dynamic series. — sub_mean_dyns • Spectroscopy Analysis Tools (spant) Subtract the mean dynamic spectrum from a dynamic series. — sub_mean_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/sub_median_dyns.html b/docs/reference/sub_median_dyns.html
index 134c495d..1e834f14 100644
--- a/docs/reference/sub_median_dyns.html
+++ b/docs/reference/sub_median_dyns.html
@@ -1,5 +1,5 @@
-Subtract the median dynamic spectrum from a dynamic series. — sub_median_dyns • Spectroscopy Analysis Tools (spant) Subtract the median dynamic spectrum from a dynamic series. — sub_median_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/sum_coils.html b/docs/reference/sum_coils.html
index 7bf559f2..e1ab3cc0 100644
--- a/docs/reference/sum_coils.html
+++ b/docs/reference/sum_coils.html
@@ -1,5 +1,5 @@
-Calculate the sum across receiver coil elements. — sum_coils • Spectroscopy Analysis Tools (spant) Calculate the sum across receiver coil elements. — sum_coils • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/sum_dyns.html b/docs/reference/sum_dyns.html
index a0be19d3..bbda2ffc 100644
--- a/docs/reference/sum_dyns.html
+++ b/docs/reference/sum_dyns.html
@@ -1,5 +1,5 @@
-Calculate the sum of data dynamics. — sum_dyns • Spectroscopy Analysis Tools (spant) Calculate the sum of data dynamics. — sum_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/sum_mrs.html b/docs/reference/sum_mrs.html
index a22f215b..3cc3ab9e 100644
--- a/docs/reference/sum_mrs.html
+++ b/docs/reference/sum_mrs.html
@@ -1,5 +1,5 @@
-Sum two mrs_data objects. — sum_mrs • Spectroscopy Analysis Tools (spant) Sum two mrs_data objects. — sum_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Value
diff --git a/docs/reference/sum_mrs_list.html b/docs/reference/sum_mrs_list.html
index f4e09aea..c3584348 100644
--- a/docs/reference/sum_mrs_list.html
+++ b/docs/reference/sum_mrs_list.html
@@ -1,5 +1,5 @@
-Return the sum of a list of mrs_data objects. — sum_mrs_list • Spectroscopy Analysis Tools (spant) Return the sum of a list of mrs_data objects. — sum_mrs_list • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/svs_1h_brain_analysis.html b/docs/reference/svs_1h_brain_analysis.html
index 8ce514db..dff0ef7d 100644
--- a/docs/reference/svs_1h_brain_analysis.html
+++ b/docs/reference/svs_1h_brain_analysis.html
@@ -1,5 +1,5 @@
-Standard SVS 1H brain analysis pipeline. — svs_1h_brain_analysis • Spectroscopy Analysis Tools (spant) Standard SVS 1H brain analysis pipeline. — svs_1h_brain_analysis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -199,7 +199,7 @@ Value
diff --git a/docs/reference/svs_1h_brain_analysis_dev.html b/docs/reference/svs_1h_brain_analysis_dev.html
index d70a14d3..d71bfea2 100644
--- a/docs/reference/svs_1h_brain_analysis_dev.html
+++ b/docs/reference/svs_1h_brain_analysis_dev.html
@@ -1,5 +1,5 @@
-Standard SVS 1H brain analysis pipeline. — svs_1h_brain_analysis_dev • Spectroscopy Analysis Tools (spant) Standard SVS 1H brain analysis pipeline. — svs_1h_brain_analysis_dev • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -193,7 +193,7 @@ Examples
diff --git a/docs/reference/svs_1h_brain_batch_analysis.html b/docs/reference/svs_1h_brain_batch_analysis.html
index 5631e8cc..15f7223e 100644
--- a/docs/reference/svs_1h_brain_batch_analysis.html
+++ b/docs/reference/svs_1h_brain_batch_analysis.html
@@ -1,5 +1,5 @@
-Batch interface to the standard SVS 1H brain analysis pipeline. — svs_1h_brain_batch_analysis • Spectroscopy Analysis Tools (spant) Batch interface to the standard SVS 1H brain analysis pipeline. — svs_1h_brain_batch_analysis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -144,7 +144,7 @@ Value
diff --git a/docs/reference/t_test_spec.html b/docs/reference/t_test_spec.html
new file mode 100644
index 00000000..56a7ea1b
--- /dev/null
+++ b/docs/reference/t_test_spec.html
@@ -0,0 +1,124 @@
+
+Perform a t-test on spectral data points. — t_test_spec • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+
+
+ Perform a t-test on spectral data points.
+
+
+
+ t_test_spec(mrs_data, group)
+
+
+
+ Arguments
+ - mrs_data
+an mrs_data object with spectra in the dynamic dimension.
- group
+vector describing the group membership of each dynamic spectrum.
+
+ Value
+
+
+a list of statistical results.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/td2fd.html b/docs/reference/td2fd.html
index 6748a6a8..f31ed524 100644
--- a/docs/reference/td2fd.html
+++ b/docs/reference/td2fd.html
@@ -1,5 +1,5 @@
-Transform time-domain data to the frequency-domain. — td2fd • Spectroscopy Analysis Tools (spant) Transform time-domain data to the frequency-domain. — td2fd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/td_conv_filt.html b/docs/reference/td_conv_filt.html
index a9f340c3..106b9b00 100644
--- a/docs/reference/td_conv_filt.html
+++ b/docs/reference/td_conv_filt.html
@@ -1,5 +1,5 @@
-Time-domain convolution based filter. — td_conv_filt • Spectroscopy Analysis Tools (spant) Time-domain convolution based filter. — td_conv_filt • Spectroscopy Analysis Tools (spant) Time-domain spectral registration. — tdsr • Spectroscopy Analysis Tools (spant) Time-domain spectral registration. — tdsr • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -121,7 +121,7 @@ Value
diff --git a/docs/reference/te.html b/docs/reference/te.html
index 010361b1..4a65711d 100644
--- a/docs/reference/te.html
+++ b/docs/reference/te.html
@@ -1,5 +1,5 @@
-Return the echo time of an MRS dataset. — te • Spectroscopy Analysis Tools (spant) Return the echo time of an MRS dataset. — te • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/tr.html b/docs/reference/tr.html
index 0c0bd63b..2e749e02 100644
--- a/docs/reference/tr.html
+++ b/docs/reference/tr.html
@@ -1,5 +1,5 @@
-Return the repetition time of an MRS dataset. — tr • Spectroscopy Analysis Tools (spant) Return the repetition time of an MRS dataset. — tr • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/varpro_3_para_opts.html b/docs/reference/varpro_3_para_opts.html
index c2270a16..52d7cd84 100644
--- a/docs/reference/varpro_3_para_opts.html
+++ b/docs/reference/varpro_3_para_opts.html
@@ -1,5 +1,5 @@
-Return a list of options for VARPRO based fitting with 3 free parameters. — varpro_3_para_opts • Spectroscopy Analysis Tools (spant) Return a list of options for VARPRO based fitting with 3 free parameters. — varpro_3_para_opts • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -141,7 +141,7 @@ Value
diff --git a/docs/reference/varpro_basic_opts.html b/docs/reference/varpro_basic_opts.html
index 32c86d22..c5104891 100644
--- a/docs/reference/varpro_basic_opts.html
+++ b/docs/reference/varpro_basic_opts.html
@@ -1,5 +1,5 @@
-Return a list of options for a basic VARPRO analysis. — varpro_basic_opts • Spectroscopy Analysis Tools (spant) Return a list of options for a basic VARPRO analysis. — varpro_basic_opts • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -118,7 +118,7 @@ Value
diff --git a/docs/reference/varpro_opts.html b/docs/reference/varpro_opts.html
index 2aabf11d..6332f730 100644
--- a/docs/reference/varpro_opts.html
+++ b/docs/reference/varpro_opts.html
@@ -1,5 +1,5 @@
-Return a list of options for VARPRO based fitting. — varpro_opts • Spectroscopy Analysis Tools (spant) Return a list of options for VARPRO based fitting. — varpro_opts • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -177,7 +177,7 @@ Examples
diff --git a/docs/reference/vec2mrs_data.html b/docs/reference/vec2mrs_data.html
index 0cccd73b..f0d58bf0 100644
--- a/docs/reference/vec2mrs_data.html
+++ b/docs/reference/vec2mrs_data.html
@@ -1,5 +1,5 @@
-Convert a vector into a mrs_data object. — vec2mrs_data • Spectroscopy Analysis Tools (spant) Convert a vector into a mrs_data object. — vec2mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -80,10 +80,11 @@ Convert a vector into a mrs_data object.
vec2mrs_data(
vec,
- fs = def_fs(),
- ft = def_ft(),
- ref = def_ref(),
- nuc = def_nuc(),
+ mrs_data = NULL,
+ fs = NULL,
+ ft = NULL,
+ ref = NULL,
+ nuc = NULL,
dyns = 1,
fd = FALSE
)
@@ -95,6 +96,10 @@ Arguments
the data vector.
mrs_data
+example data to copy acquisition parameters from.
fs
sampling frequency in Hz.
Arguments
fd
-flag to indicate if the matrix is in the frequency domain (logical).
flag to indicate if the vector is in the frequency domain (logical).
Value
diff --git a/docs/reference/write_basis.html b/docs/reference/write_basis.html
index b6e27cbd..94c5e021 100644
--- a/docs/reference/write_basis.html
+++ b/docs/reference/write_basis.html
@@ -1,5 +1,5 @@
-Write a basis object to an LCModel .basis formatted file. — write_basis • Spectroscopy Analysis Tools (spant) Write a basis object to an LCModel .basis formatted file. — write_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -108,7 +108,7 @@ Arguments
diff --git a/docs/reference/write_basis_tqn.html b/docs/reference/write_basis_tqn.html
index 6aa51c1d..116c73ec 100644
--- a/docs/reference/write_basis_tqn.html
+++ b/docs/reference/write_basis_tqn.html
@@ -1,5 +1,5 @@
-Generate a basis file using TARQUIN. — write_basis_tqn • Spectroscopy Analysis Tools (spant) Generate a basis file using TARQUIN. — write_basis_tqn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Examples
diff --git a/docs/reference/write_mrs.html b/docs/reference/write_mrs.html
index fff25f15..124b9dc4 100644
--- a/docs/reference/write_mrs.html
+++ b/docs/reference/write_mrs.html
@@ -1,5 +1,5 @@
-Write MRS data object to file. — write_mrs • Spectroscopy Analysis Tools (spant) Write MRS data object to file. — write_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Arguments
diff --git a/docs/reference/write_mrs_nifti.html b/docs/reference/write_mrs_nifti.html
index f4bf1921..bd3ed4b7 100644
--- a/docs/reference/write_mrs_nifti.html
+++ b/docs/reference/write_mrs_nifti.html
@@ -1,5 +1,5 @@
-Write MRS data object to file in NIFTI format. — write_mrs_nifti • Spectroscopy Analysis Tools (spant) Write MRS data object to file in NIFTI format. — write_mrs_nifti • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/write_pulse_ascii.html b/docs/reference/write_pulse_ascii.html
index 067ae086..221f8ebb 100644
--- a/docs/reference/write_pulse_ascii.html
+++ b/docs/reference/write_pulse_ascii.html
@@ -1,5 +1,5 @@
-Write an ASCII formatted pulse file. — write_pulse_ascii • Spectroscopy Analysis Tools (spant) Write an ASCII formatted pulse file. — write_pulse_ascii • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/zero_fade_spec.html b/docs/reference/zero_fade_spec.html
index c703745c..c8b572c3 100644
--- a/docs/reference/zero_fade_spec.html
+++ b/docs/reference/zero_fade_spec.html
@@ -1,7 +1,5 @@
-Fade a spectrum to zero by frequency domain multiplication with a tanh
-function. Note this operation distorts data points at the end of the FID. — zero_fade_spec • Spectroscopy Analysis Tools (spant) Fade a spectrum to zero by frequency domain multiplication with a tanh function. Note this operation distorts data points at the end of the FID. — zero_fade_spec • Spectroscopy Analysis Tools (spant) Zero all coherences including and above a given order. — zero_higher_orders • Spectroscopy Analysis Tools (spant) Zero all coherences including and above a given order. — zero_higher_orders • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Value
diff --git a/docs/reference/zero_td_pts_end.html b/docs/reference/zero_td_pts_end.html
index 8c1123c8..71d24ebb 100644
--- a/docs/reference/zero_td_pts_end.html
+++ b/docs/reference/zero_td_pts_end.html
@@ -1,5 +1,5 @@
-Set mrs_data object data points at the end of the FID to zero. — zero_td_pts_end • Spectroscopy Analysis Tools (spant) Set mrs_data object data points at the end of the FID to zero. — zero_td_pts_end • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/zf.html b/docs/reference/zf.html
index 85e2013c..baf50256 100644
--- a/docs/reference/zf.html
+++ b/docs/reference/zf.html
@@ -1,5 +1,5 @@
-Zero-fill MRS data in the time domain. — zf • Spectroscopy Analysis Tools (spant) Zero-fill MRS data in the time domain. — zf • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -125,7 +125,7 @@ Value
diff --git a/docs/reference/zf_xy.html b/docs/reference/zf_xy.html
index ebca3999..c4104a74 100644
--- a/docs/reference/zf_xy.html
+++ b/docs/reference/zf_xy.html
@@ -1,5 +1,5 @@
-Zero-fill MRSI data in the k-space x-y direction. — zf_xy • Spectroscopy Analysis Tools (spant) Zero-fill MRSI data in the k-space x-y direction. — zf_xy • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -113,7 +113,7 @@ Value
diff --git a/docs/sitemap.xml b/docs/sitemap.xml
index e2139f71..4c39f515 100644
--- a/docs/sitemap.xml
+++ b/docs/sitemap.xml
@@ -216,6 +216,12 @@
https://martin3141.github.io/spant/reference/comb_coils_fp_pc.html
+
+ https://martin3141.github.io/spant/reference/comb_coils_mrsi_gls.html
+
+
+ https://martin3141.github.io/spant/reference/comb_coils_svs_gls.html
+
https://martin3141.github.io/spant/reference/comb_csv_results.html
@@ -411,6 +417,9 @@
https://martin3141.github.io/spant/reference/gen_conv_reg.html
+
+ https://martin3141.github.io/spant/reference/gen_group_reg.html
+
https://martin3141.github.io/spant/reference/gen_impulse_reg.html
@@ -555,6 +564,15 @@
https://martin3141.github.io/spant/reference/glm_spec.html
+
+ https://martin3141.github.io/spant/reference/glm_spec_fmrs_fl.html
+
+
+ https://martin3141.github.io/spant/reference/glm_spec_fmrs_group.html
+
+
+ https://martin3141.github.io/spant/reference/glm_spec_group_linhyp.html
+
https://martin3141.github.io/spant/reference/grid_shift_xy.html
@@ -690,9 +708,15 @@
https://martin3141.github.io/spant/reference/mrs_data2basis.html
+
+ https://martin3141.github.io/spant/reference/mrs_data2bids.html
+
https://martin3141.github.io/spant/reference/mrs_data2mat.html
+
+ https://martin3141.github.io/spant/reference/mrs_data2spec_mat.html
+
https://martin3141.github.io/spant/reference/mrs_data2vec.html
@@ -741,6 +765,9 @@
https://martin3141.github.io/spant/reference/phase.html
+
+ https://martin3141.github.io/spant/reference/phase_ref_1h_brain.html
+
https://martin3141.github.io/spant/reference/plot.fit_result.html
@@ -780,6 +807,12 @@
https://martin3141.github.io/spant/reference/precomp.html
+
+ https://martin3141.github.io/spant/reference/preproc_svs.html
+
+
+ https://martin3141.github.io/spant/reference/preproc_svs_dataset.html
+
https://martin3141.github.io/spant/reference/print.fit_result.html
@@ -1050,6 +1083,9 @@
https://martin3141.github.io/spant/reference/spant_mpress_drift.html
+
+ https://martin3141.github.io/spant/reference/spant_sim_fmrs_dataset.html
+
https://martin3141.github.io/spant/reference/spant_simulation_benchmark.html
@@ -1107,6 +1143,9 @@
https://martin3141.github.io/spant/reference/svs_1h_brain_batch_analysis.html
+
+ https://martin3141.github.io/spant/reference/t_test_spec.html
+
https://martin3141.github.io/spant/reference/td2fd.html
Return a character vector of common 1H molecules found in healthy human -brain.
Return a character vector of common 1H molecules found in healthy human brain.
Return a list of mol_parameter objects suitable for 1H brain MRS
-analyses.
Return a list of mol_parameter objects suitable for 1H brain MRS analyses.
Return a list of mol_parameter objects suitable for 1H brain MRS
-analyses.
Return a list of mol_parameter objects suitable for 1H brain MRS analyses.
Return a list of mol_parameter objects suitable for 1H brain MRS
-analyses.
Return a list of mol_parameter objects suitable for 1H brain MRS analyses.
Return a list of mol_parameter objects suitable for 1H brain MRS
-analyses.
Return a list of mol_parameter objects suitable for 1H brain MRS analyses.
All functions
- Return a character vector of molecules included in the Gold Star Phantoms
-SPECTRE phantom.
Return a character vector of molecules included in the Gold Star Phantoms SPECTRE phantom.
@@ -635,8 +618,7 @@ All functions
- Return a character array of names that may be used with the
-get_mol_paras function.
Return a character array of names that may be used with the get_mol_paras function.
@@ -700,8 +682,7 @@ All functions
- Return an array of amplitudes derived from fitting the initial points in the
-time domain and extrapolating back to t=0.
Return an array of amplitudes derived from fitting the initial points in the time domain and extrapolating back to t=0.
@@ -709,8 +690,7 @@ All functions
- Generate a mol_parameters object for a simple spin system with one
-resonance.
Generate a mol_parameters object for a simple spin system with one resonance.
@@ -731,6 +711,18 @@ All functions glm_spec()
Perform a GLM analysis of dynamic MRS data in the spectral domain.
+
+
+ Perform first-level spectral GLM analysis of an fMRS dataset.
+
+
+ Perform group-level spectral GLM analysis of an fMRS dataset.
+
+
+ Test a group-level spectral GLM linear hypothesis.
@@ -766,8 +758,7 @@ All functions
- Perform an ifft and ifftshift on a matrix with each column replaced by its
-shifted ifft.
Perform an ifft and ifftshift on a matrix with each column replaced by its shifted ifft.
@@ -799,8 +790,7 @@ All functions
- Check if the chemical shift dimension of an MRS data object is in the
-frequency domain.
Check if the chemical shift dimension of an MRS data object is in the frequency domain.
@@ -820,18 +810,15 @@ All functions
- Covert a linewidth in Hz to an equivalent alpha value in the time-domain ie:
-x * exp(-t * alpha).
Covert a linewidth in Hz to an equivalent alpha value in the time-domain ie: x * exp(-t * alpha).
- Covert a linewidth in Hz to an equivalent beta value in the time-domain ie:
-x * exp(-t * t * beta).
Covert a linewidth in Hz to an equivalent beta value in the time-domain ie: x * exp(-t * t * beta).
- Make a basis-set object from a directory containing LCModel formatted RAW
-files.
Make a basis-set object from a directory containing LCModel formatted RAW files.
@@ -851,8 +838,7 @@ All functions
- Mask the voxels outside an elliptical region spanning the MRSI dataset in the
-x-y plane.
Mask the voxels outside an elliptical region spanning the MRSI dataset in the x-y plane.
@@ -860,13 +846,11 @@ All functions
- Convert a matrix (with spectral points in the column dimension and dynamics
-in the row dimensions) into a mrs_data object.
Convert a matrix (with spectral points in the column dimension and dynamics in the row dimensions) into a mrs_data object.
- Matrix exponential function taken from complexplus package to reduce the
-number of spant dependencies.
Matrix exponential function taken from complexplus package to reduce the number of spant dependencies.
@@ -914,31 +898,31 @@ All functions
- Convert an mrs_data object to basis object - where basis signals are spread
-across the dynamic dimension in the MRS data.
Convert an mrs_data object to basis object - where basis signals are spread across the dynamic dimension in the MRS data.
+
+
+ Create a BIDS file structure from a vector of MRS data paths or list of mrs_data objects.
- Convert mrs_data object to a matrix, with spectral points in the column
-dimension and dynamics in the row dimension.
Convert mrs_data object to a matrix, with spectral points in the column dimension and dynamics in the row dimension.
-
+
- Convert mrs_data object to a vector.
Convert mrs_data object to a matrix, with spectral points in the column dimension and dynamics in the row dimension.
-
+
- Create a BIDS directory and file structure from a list of mrs_data objects.
Convert mrs_data object to a vector.
- Perform a fftshift on a matrix, with each column replaced by its shifted
-result.
Perform a fftshift on a matrix, with each column replaced by its shifted result.
- Perform an ifftshift on a matrix, with each column replaced by its shifted
-result.
Perform an ifftshift on a matrix, with each column replaced by its shifted result.
@@ -946,9 +930,7 @@ All functions
- Flip the x data dimension order of a nifti image. This corresponds to
-flipping MRI data in the left-right direction, assuming the data in save in
-neurological format (can check with fslorient program).
Flip the x data dimension order of a nifti image. This corresponds to flipping MRI data in the left-right direction, assuming the data in save in neurological format (can check with fslorient program).
@@ -964,8 +946,7 @@ All functions
- Search for the highest peak in a spectral region and return the frequency,
-height and FWHM.
Search for the highest peak in a spectral region and return the frequency, height and FWHM.
@@ -974,6 +955,10 @@ All functions phase()
Apply phasing parameters to MRS data.
+
+
+ Corrected zero order phase and chemical shift offset in 1H MRS data from the brain.
@@ -1005,8 +990,7 @@ All functions
- Plot an interactive slice map from a data array where voxels can be selected
-to display a corresponding spectrum.
Plot an interactive slice map from a data array where voxels can be selected to display a corresponding spectrum.
@@ -1026,8 +1010,15 @@ All functions
- Save function results to file and load on subsequent calls to avoid repeat
-computation.
Save function results to file and load on subsequent calls to avoid repeat computation.
+
+
+ Preprocess and perform quality assessment of a single SVS data set.
+
+
+ Preprocess and perform quality assessment of one or more SVS data sets.
@@ -1055,15 +1046,11 @@ All functions
- Read a directory containing Siemens MRS IMA files and combine along the coil
-dimension. Note that the coil ID is inferred from the sorted file name and
-should be checked when consistency is required between two directories.
Read a directory containing Siemens MRS IMA files and combine along the coil dimension. Note that the coil ID is inferred from the sorted file name and should be checked when consistency is required between two directories.
- Read a directory containing Siemens MRS IMA files and combine along the
-dynamic dimension. Note that the coil ID is inferred from the sorted file
-name and should be checked when consistency is required.
Read a directory containing Siemens MRS IMA files and combine along the dynamic dimension. Note that the coil ID is inferred from the sorted file name and should be checked when consistency is required.
@@ -1103,13 +1090,11 @@ All functions
- Reconstruct complex time-domain data from the real part of frequency-domain
-data.
Reconstruct complex time-domain data from the real part of frequency-domain data.
- Reconstruct complex time-domain data from the real part of frequency-domain
-data.
Reconstruct complex time-domain data from the real part of frequency-domain data.
@@ -1141,8 +1126,7 @@ All functions
- Resample a VOI to match a target image space using nearest-neighbour
-interpolation.
Resample a VOI to match a target image space using nearest-neighbour interpolation.
@@ -1158,23 +1142,19 @@ All functions
- Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water).
Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / kg of tissue water).
- Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water).
Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / kg of tissue water).
- Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / Litre of tissue).
Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / Litre of tissue).
- Convert default LCM/TARQUIN concentration scaling to molal units with partial
-volume correction.
Convert default LCM/TARQUIN concentration scaling to molal units with partial volume correction.
@@ -1222,8 +1202,7 @@ All functions
- MEGA-PRESS sequence with ideal localisation pulses and Gaussian shaped
-editing pulse.
MEGA-PRESS sequence with ideal localisation pulses and Gaussian shaped editing pulse.
@@ -1251,13 +1230,11 @@ All functions
- STEAM sequence with ideal pulses and coherence order filtering to simulate
-gradient crushers.
STEAM sequence with ideal pulses and coherence order filtering to simulate gradient crushers.
- STEAM sequence with ideal pulses using the z-rotation gradient simulation
-method described by Young et al JMR 140, 146-152 (1999).
STEAM sequence with ideal pulses using the z-rotation gradient simulation method described by Young et al JMR 140, 146-152 (1999).
@@ -1293,8 +1270,7 @@ All functions
- Set the number of time-domain data points, truncating or zero-filling as
-appropriate.
Set the number of time-domain data points, truncating or zero-filling as appropriate.
@@ -1318,18 +1294,15 @@ All functions
- Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS
-sequence. Note, ideal pulses are assumed.
Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS sequence. Note, ideal pulses are assumed.
- Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS
-sequence. Note, ideal pulses are assumed.
Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS sequence. Note, ideal pulses are assumed.
- Simulate a macromolecular and lipid basis-set suitable for 1H brain MRS
-analysis.
Simulate a macromolecular and lipid basis-set suitable for 1H brain MRS analysis.
@@ -1353,8 +1326,7 @@ All functions
- Simulate an ideal pulse excitation profile by smoothing a top-hat function
-with a Gaussian.
Simulate an ideal pulse excitation profile by smoothing a top-hat function with a Gaussian.
@@ -1374,17 +1346,19 @@ All functions
- Simulate and fit some spectra with ABfit for benchmarking purposes. Basic
-timing and performance metrics will be printed.
Simulate and fit some spectra with ABfit for benchmarking purposes. Basic timing and performance metrics will be printed.
Example MEGA-PRESS data with significant B0 drift.
+
+
+ Simulate an example fMRS dataset for a block design fMRS experiment and export a BIDS structure.
- Simulate a typical metabolite basis set for benchmarking. Timing metrics will
-be printed on completion.
Simulate a typical metabolite basis set for benchmarking. Timing metrics will be printed on completion.
@@ -1400,8 +1374,7 @@ All functions
- Convert SPM style segmentation files to a single categorical image where
-the numerical values map as: 0) Other, 1) CSF, 2) GM and 3) WM.
Convert SPM style segmentation files to a single categorical image where the numerical values map as: 0) Other, 1) CSF, 2) GM and 3) WM.
@@ -1413,8 +1386,7 @@ All functions
- Plot the fitting results of an object of class fit_result with
-individual basis set components shown.
Plot the fitting results of an object of class fit_result with individual basis set components shown.
@@ -1459,6 +1431,10 @@ All functions svs_1h_brain_batch_analysis()
Batch interface to the standard SVS 1H brain analysis pipeline.
+
+
+ Perform a t-test on spectral data points.
@@ -1518,8 +1494,7 @@ All functions
- Fade a spectrum to zero by frequency domain multiplication with a tanh
-function. Note this operation distorts data points at the end of the FID.
Fade a spectrum to zero by frequency domain multiplication with a tanh function. Note this operation distorts data points at the end of the FID.
@@ -1549,7 +1524,7 @@ All functions
diff --git a/docs/reference/int_spec.html b/docs/reference/int_spec.html
index c7060fe7..783325a8 100644
--- a/docs/reference/int_spec.html
+++ b/docs/reference/int_spec.html
@@ -1,5 +1,5 @@
-Integrate a spectral region. — int_spec • Spectroscopy Analysis Tools (spant) Integrate a spectral region. — int_spec • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -118,7 +118,7 @@ Value
diff --git a/docs/reference/interleave_dyns.html b/docs/reference/interleave_dyns.html
index effe5543..441eff27 100644
--- a/docs/reference/interleave_dyns.html
+++ b/docs/reference/interleave_dyns.html
@@ -1,5 +1,5 @@
-Interleave the first and second half of a dynamic series. — interleave_dyns • Spectroscopy Analysis Tools (spant) Interleave the first and second half of a dynamic series. — interleave_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/inv_even_dyns.html b/docs/reference/inv_even_dyns.html
index 9f9d4fff..dcb781dc 100644
--- a/docs/reference/inv_even_dyns.html
+++ b/docs/reference/inv_even_dyns.html
@@ -1,5 +1,5 @@
-Invert even numbered dynamic scans starting from 1 (2,4,6...). — inv_even_dyns • Spectroscopy Analysis Tools (spant) Invert even numbered dynamic scans starting from 1 (2,4,6...). — inv_even_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/inv_odd_dyns.html b/docs/reference/inv_odd_dyns.html
index 26212e2b..78d64660 100644
--- a/docs/reference/inv_odd_dyns.html
+++ b/docs/reference/inv_odd_dyns.html
@@ -1,5 +1,5 @@
-Invert odd numbered dynamic scans starting from 1 (1,3,5...). — inv_odd_dyns • Spectroscopy Analysis Tools (spant) Invert odd numbered dynamic scans starting from 1 (1,3,5...). — inv_odd_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/is.def.html b/docs/reference/is.def.html
index f196ffd0..a67b9eba 100644
--- a/docs/reference/is.def.html
+++ b/docs/reference/is.def.html
@@ -1,5 +1,5 @@
-Check if an object is defined, which is the same as being not NULL. — is.def • Spectroscopy Analysis Tools (spant) Check if an object is defined, which is the same as being not NULL. — is.def • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/is_fd.html b/docs/reference/is_fd.html
index 3b0ca165..18a193aa 100644
--- a/docs/reference/is_fd.html
+++ b/docs/reference/is_fd.html
@@ -1,7 +1,5 @@
-Check if the chemical shift dimension of an MRS data object is in the
-frequency domain. — is_fd • Spectroscopy Analysis Tools (spant) Check if the chemical shift dimension of an MRS data object is in the frequency domain. — is_fd • Spectroscopy Analysis Tools (spant) Transform 2D MRSI data from k-space to image space in the x-y direction. — kspace2img_xy • Spectroscopy Analysis Tools (spant) Transform 2D MRSI data from k-space to image space in the x-y direction. — kspace2img_xy • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/l2_reg.html b/docs/reference/l2_reg.html
index 3d781d80..21aa9849 100644
--- a/docs/reference/l2_reg.html
+++ b/docs/reference/l2_reg.html
@@ -1,5 +1,5 @@
-Perform l2 regularisation artefact suppression. — l2_reg • Spectroscopy Analysis Tools (spant) Perform l2 regularisation artefact suppression. — l2_reg • Spectroscopy Analysis Tools (spant) Apply line-broadening (apodisation) to MRS data or basis object. — lb • Spectroscopy Analysis Tools (spant) Apply line-broadening (apodisation) to MRS data or basis object. — lb • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -123,7 +123,7 @@ Value
diff --git a/docs/reference/lofdc.html b/docs/reference/lofdc.html
index 5419b1ec..31347a25 100644
--- a/docs/reference/lofdc.html
+++ b/docs/reference/lofdc.html
@@ -1,5 +1,5 @@
-Correct linear frequency drift. — lofdc • Spectroscopy Analysis Tools (spant) Correct linear frequency drift. — lofdc • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -138,7 +138,7 @@ Value
diff --git a/docs/reference/lw2alpha.html b/docs/reference/lw2alpha.html
index b83db682..25da229b 100644
--- a/docs/reference/lw2alpha.html
+++ b/docs/reference/lw2alpha.html
@@ -1,7 +1,5 @@
-Covert a linewidth in Hz to an equivalent alpha value in the time-domain ie:
-x * exp(-t * alpha). — lw2alpha • Spectroscopy Analysis Tools (spant) Covert a linewidth in Hz to an equivalent alpha value in the time-domain ie: x * exp(-t * alpha). — lw2alpha • Spectroscopy Analysis Tools (spant) Covert a linewidth in Hz to an equivalent beta value in the time-domain ie:
-x * exp(-t * t * beta). — lw2beta • Spectroscopy Analysis Tools (spant) Covert a linewidth in Hz to an equivalent beta value in the time-domain ie: x * exp(-t * t * beta). — lw2beta • Spectroscopy Analysis Tools (spant) Make a basis-set object from a directory containing LCModel formatted RAW
-files. — make_basis_from_raw • Spectroscopy Analysis Tools (spant) Make a basis-set object from a directory containing LCModel formatted RAW files. — make_basis_from_raw • Spectroscopy Analysis Tools (spant) Mask an MRS dataset in the dynamic dimension. — mask_dyns • Spectroscopy Analysis Tools (spant) Mask an MRS dataset in the dynamic dimension. — mask_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/mask_fit_res.html b/docs/reference/mask_fit_res.html
index 97baaa3f..ebd91a99 100644
--- a/docs/reference/mask_fit_res.html
+++ b/docs/reference/mask_fit_res.html
@@ -1,5 +1,5 @@
-Mask fit result spectra depending on a vector of bool values. — mask_fit_res • Spectroscopy Analysis Tools (spant) Mask fit result spectra depending on a vector of bool values. — mask_fit_res • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -116,7 +116,7 @@ Value
diff --git a/docs/reference/mask_xy.html b/docs/reference/mask_xy.html
index 11bb577c..b0d38619 100644
--- a/docs/reference/mask_xy.html
+++ b/docs/reference/mask_xy.html
@@ -1,5 +1,5 @@
-Mask an MRSI dataset in the x-y direction — mask_xy • Spectroscopy Analysis Tools (spant) Mask an MRSI dataset in the x-y direction — mask_xy • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/mask_xy_corners.html b/docs/reference/mask_xy_corners.html
index 09b16cd2..2d13839d 100644
--- a/docs/reference/mask_xy_corners.html
+++ b/docs/reference/mask_xy_corners.html
@@ -1,5 +1,5 @@
-Mask the four corners of an MRSI dataset in the x-y plane. — mask_xy_corners • Spectroscopy Analysis Tools (spant) Mask the four corners of an MRSI dataset in the x-y plane. — mask_xy_corners • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/mask_xy_ellipse.html b/docs/reference/mask_xy_ellipse.html
index 1d8b02e4..e2e749ef 100644
--- a/docs/reference/mask_xy_ellipse.html
+++ b/docs/reference/mask_xy_ellipse.html
@@ -1,7 +1,5 @@
-Mask the voxels outside an elliptical region spanning the MRSI dataset in the
-x-y plane. — mask_xy_ellipse • Spectroscopy Analysis Tools (spant) Mask the voxels outside an elliptical region spanning the MRSI dataset in the x-y plane. — mask_xy_ellipse • Spectroscopy Analysis Tools (spant) Mask a 2D MRSI dataset in the x-y dimension. — mask_xy_mat • Spectroscopy Analysis Tools (spant) Mask a 2D MRSI dataset in the x-y dimension. — mask_xy_mat • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Value
diff --git a/docs/reference/mat2mrs_data.html b/docs/reference/mat2mrs_data.html
index 2e2895f3..ae55665f 100644
--- a/docs/reference/mat2mrs_data.html
+++ b/docs/reference/mat2mrs_data.html
@@ -1,7 +1,5 @@
-Convert a matrix (with spectral points in the column dimension and dynamics
-in the row dimensions) into a mrs_data object. — mat2mrs_data • Spectroscopy Analysis Tools (spant) Convert a matrix (with spectral points in the column dimension and dynamics in the row dimensions) into a mrs_data object. — mat2mrs_data • Spectroscopy Analysis Tools (spant) Matrix exponential function taken from complexplus package to reduce the
-number of spant dependencies. — matexp • Spectroscopy Analysis Tools (spant) Matrix exponential function taken from complexplus package to reduce the number of spant dependencies. — matexp • Spectroscopy Analysis Tools (spant) Apply the max operator to an MRS dataset. — max_mrs • Spectroscopy Analysis Tools (spant) Apply the max operator to an MRS dataset. — max_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/max_mrs_interp.html b/docs/reference/max_mrs_interp.html
index e4474764..52e63f3e 100644
--- a/docs/reference/max_mrs_interp.html
+++ b/docs/reference/max_mrs_interp.html
@@ -1,5 +1,5 @@
-Apply the max operator to an interpolated MRS dataset. — max_mrs_interp • Spectroscopy Analysis Tools (spant) Apply the max operator to an interpolated MRS dataset. — max_mrs_interp • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/mean.list.html b/docs/reference/mean.list.html
index b8eb3463..048306fd 100644
--- a/docs/reference/mean.list.html
+++ b/docs/reference/mean.list.html
@@ -1,5 +1,5 @@
-Calculate the mean spectrum from an mrs_data object. — mean.list • Spectroscopy Analysis Tools (spant) Calculate the mean spectrum from an mrs_data object. — mean.list • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/mean.mrs_data.html b/docs/reference/mean.mrs_data.html
index 5531a28d..79515014 100644
--- a/docs/reference/mean.mrs_data.html
+++ b/docs/reference/mean.mrs_data.html
@@ -1,5 +1,5 @@
-Calculate the mean spectrum from an mrs_data object. — mean.mrs_data • Spectroscopy Analysis Tools (spant) Calculate the mean spectrum from an mrs_data object. — mean.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/mean_dyn_blocks.html b/docs/reference/mean_dyn_blocks.html
index 10467098..4c042448 100644
--- a/docs/reference/mean_dyn_blocks.html
+++ b/docs/reference/mean_dyn_blocks.html
@@ -1,5 +1,5 @@
-Calculate the mean of adjacent dynamic scans. — mean_dyn_blocks • Spectroscopy Analysis Tools (spant) Calculate the mean of adjacent dynamic scans. — mean_dyn_blocks • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/mean_dyn_pairs.html b/docs/reference/mean_dyn_pairs.html
index 63e909ea..1a241126 100644
--- a/docs/reference/mean_dyn_pairs.html
+++ b/docs/reference/mean_dyn_pairs.html
@@ -1,5 +1,5 @@
-Calculate the pairwise means across a dynamic data set. — mean_dyn_pairs • Spectroscopy Analysis Tools (spant) Calculate the pairwise means across a dynamic data set. — mean_dyn_pairs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/mean_dyns.html b/docs/reference/mean_dyns.html
index 73fdbfa7..0daa27df 100644
--- a/docs/reference/mean_dyns.html
+++ b/docs/reference/mean_dyns.html
@@ -1,5 +1,5 @@
-Calculate the mean dynamic data. — mean_dyns • Spectroscopy Analysis Tools (spant) Calculate the mean dynamic data. — mean_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/mean_mrs_list.html b/docs/reference/mean_mrs_list.html
index 808b6c50..10d842c0 100644
--- a/docs/reference/mean_mrs_list.html
+++ b/docs/reference/mean_mrs_list.html
@@ -1,5 +1,5 @@
-Return the mean of a list of mrs_data objects. — mean_mrs_list • Spectroscopy Analysis Tools (spant) Return the mean of a list of mrs_data objects. — mean_mrs_list • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/mean_vec_blocks.html b/docs/reference/mean_vec_blocks.html
index 8fc92eaa..dd78b122 100644
--- a/docs/reference/mean_vec_blocks.html
+++ b/docs/reference/mean_vec_blocks.html
@@ -1,5 +1,5 @@
-Calculate the mean of adjacent blocks in a vector. — mean_vec_blocks • Spectroscopy Analysis Tools (spant) Calculate the mean of adjacent blocks in a vector. — mean_vec_blocks • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/median_dyns.html b/docs/reference/median_dyns.html
index 1039d4b5..9a085b10 100644
--- a/docs/reference/median_dyns.html
+++ b/docs/reference/median_dyns.html
@@ -1,5 +1,5 @@
-Calculate the median dynamic data. — median_dyns • Spectroscopy Analysis Tools (spant) Calculate the median dynamic data. — median_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/mod_td.html b/docs/reference/mod_td.html
index 76ad0a40..141ef09e 100644
--- a/docs/reference/mod_td.html
+++ b/docs/reference/mod_td.html
@@ -1,5 +1,5 @@
-Apply the Modulus operator to the time-domain MRS signal. — mod_td • Spectroscopy Analysis Tools (spant) Apply the Modulus operator to the time-domain MRS signal. — mod_td • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/mrs_data2basis.html b/docs/reference/mrs_data2basis.html
index 62f7d749..11797b91 100644
--- a/docs/reference/mrs_data2basis.html
+++ b/docs/reference/mrs_data2basis.html
@@ -1,7 +1,5 @@
-Convert an mrs_data object to basis object - where basis signals are spread
-across the dynamic dimension in the MRS data. — mrs_data2basis • Spectroscopy Analysis Tools (spant) Convert an mrs_data object to basis object - where basis signals are spread across the dynamic dimension in the MRS data. — mrs_data2basis • Spectroscopy Analysis Tools (spant) Create a BIDS file structure from a vector of MRS data paths or list of mrs_data objects. — mrs_data2bids • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Create a BIDS file structure from a vector of MRS data paths or list of mrs_data objects.
+ Source: R/fmrs.R
+ mrs_data2bids.Rd
+
+
+
+ Create a BIDS file structure from a vector of MRS data paths or list of
+mrs_data objects.
+
+
+
+ mrs_data2bids(
+ mrs_data,
+ output_dir,
+ suffix = NULL,
+ sub = NULL,
+ ses = NULL,
+ task = NULL,
+ acq = NULL,
+ nuc = NULL,
+ voi = NULL,
+ rec = NULL,
+ run = NULL,
+ echo = NULL,
+ inv = NULL,
+ skip_existing = TRUE
+)
+
+
+
+ Arguments
+ - mrs_data
+vector of MRS data paths or list of mrs_data objects.
- output_dir
+the base directory to create the BIDS structure.
- suffix
+optional vector of file suffixes. Default behaviour is to
+automatically determine these from the input data, however it is recommended
+that they are specified to allow more efficient skipping of existing data.
- sub
+optional vector of subject labels. If not specified, these will be
+automatically generated as a series of increasing zero-padded integer values
+corresponding to the mrs_data input indices.
- ses
+optional vector of session labels.
- task
+optional vector of task labels.
- acq
+optional vector of acquisition labels.
- nuc
+optional vector of nucleus labels.
- voi
+optional vector of volume of interest labels.
- rec
+optional vector of reconstruction labels.
- run
+optional vector of run indices.
- echo
+optional vector of echo time indices.
- inv
+optional vector of inversion indices.
- skip_existing
+skip any data files that have already been converted.
+Defaults to TRUE, set to FALSE to force an overwrite of any existing data
+files.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/mrs_data2mat.html b/docs/reference/mrs_data2mat.html
index cf5ff28c..9e47688a 100644
--- a/docs/reference/mrs_data2mat.html
+++ b/docs/reference/mrs_data2mat.html
@@ -1,7 +1,5 @@
-Convert mrs_data object to a matrix, with spectral points in the column
-dimension and dynamics in the row dimension. — mrs_data2mat • Spectroscopy Analysis Tools (spant) Convert mrs_data object to a matrix, with spectral points in the column dimension and dynamics in the row dimension. — mrs_data2mat • Spectroscopy Analysis Tools (spant) Convert mrs_data object to a matrix, with spectral points in the column dimension and dynamics in the row dimension. — mrs_data2spec_mat • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Convert mrs_data object to a matrix, with spectral points in the column dimension and dynamics in the row dimension.
+ Source: R/mrs_data_proc.R
+ mrs_data2spec_mat.Rd
+
+
+
+ Convert mrs_data object to a matrix, with spectral points in the column
+dimension and dynamics in the row dimension.
+
+
+
+ mrs_data2spec_mat(mrs_data, collapse = TRUE)
+
+
+
+ Arguments
+ - mrs_data
+MRS data object or list of MRS data objects.
- collapse
+collapse all other dimensions along the dynamic dimension, eg
+a 16x16 MRSI grid would be first collapsed across 256 dynamic scans.
+
+ Value
+
+
+MRS data matrix.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/mrs_data2vec.html b/docs/reference/mrs_data2vec.html
index fb172d68..a1fd654d 100644
--- a/docs/reference/mrs_data2vec.html
+++ b/docs/reference/mrs_data2vec.html
@@ -1,5 +1,5 @@
-Convert mrs_data object to a vector. — mrs_data2vec • Spectroscopy Analysis Tools (spant) Convert mrs_data object to a vector. — mrs_data2vec • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -126,7 +126,7 @@ Value
diff --git a/docs/reference/mvfftshift.html b/docs/reference/mvfftshift.html
index 92b0841b..976b3410 100644
--- a/docs/reference/mvfftshift.html
+++ b/docs/reference/mvfftshift.html
@@ -1,7 +1,5 @@
-Perform a fftshift on a matrix, with each column replaced by its shifted
-result. — mvfftshift • Spectroscopy Analysis Tools (spant) Perform a fftshift on a matrix, with each column replaced by its shifted result. — mvfftshift • Spectroscopy Analysis Tools (spant) Perform an ifftshift on a matrix, with each column replaced by its shifted
-result. — mvifftshift • Spectroscopy Analysis Tools (spant) Perform an ifftshift on a matrix, with each column replaced by its shifted result. — mvifftshift • Spectroscopy Analysis Tools (spant) Print fit coordinates from a single index. — n2coord • Spectroscopy Analysis Tools (spant) Print fit coordinates from a single index. — n2coord • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/nifti_flip_lr.html b/docs/reference/nifti_flip_lr.html
index 730abe3c..19860b3c 100644
--- a/docs/reference/nifti_flip_lr.html
+++ b/docs/reference/nifti_flip_lr.html
@@ -1,9 +1,5 @@
-Flip the x data dimension order of a nifti image. This corresponds to
-flipping MRI data in the left-right direction, assuming the data in save in
-neurological format (can check with fslorient program). — nifti_flip_lr • Spectroscopy Analysis Tools (spant) Flip the x data dimension order of a nifti image. This corresponds to flipping MRI data in the left-right direction, assuming the data in save in neurological format (can check with fslorient program). — nifti_flip_lr • Spectroscopy Analysis Tools (spant) Export a one-page pdf of a single fit result — one_page_pdf • Spectroscopy Analysis Tools (spant) Export a one-page pdf of a single fit result — one_page_pdf • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -108,7 +108,7 @@ Arguments
diff --git a/docs/reference/ortho3.html b/docs/reference/ortho3.html
index 13ade97d..5d7dd2fd 100644
--- a/docs/reference/ortho3.html
+++ b/docs/reference/ortho3.html
@@ -1,5 +1,5 @@
-Display an orthographic projection plot of a nifti object. — ortho3 • Spectroscopy Analysis Tools (spant) Display an orthographic projection plot of a nifti object. — ortho3 • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -172,7 +172,7 @@ Arguments
diff --git a/docs/reference/ortho3_inter.html b/docs/reference/ortho3_inter.html
index 090cc5e5..15948899 100644
--- a/docs/reference/ortho3_inter.html
+++ b/docs/reference/ortho3_inter.html
@@ -1,5 +1,5 @@
-Display an interactive orthographic projection plot of a nifti object. — ortho3_inter • Spectroscopy Analysis Tools (spant) Display an interactive orthographic projection plot of a nifti object. — ortho3_inter • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -132,7 +132,7 @@ Arguments
diff --git a/docs/reference/peak_info.html b/docs/reference/peak_info.html
index 09058bd8..41c8ffaf 100644
--- a/docs/reference/peak_info.html
+++ b/docs/reference/peak_info.html
@@ -1,7 +1,5 @@
-Search for the highest peak in a spectral region and return the frequency,
-height and FWHM. — peak_info • Spectroscopy Analysis Tools (spant) Search for the highest peak in a spectral region and return the frequency, height and FWHM. — peak_info • Spectroscopy Analysis Tools (spant) Papoulis-Gerchberg (PG) algorithm method for k-space extrapolation. — pg_extrap_xy • Spectroscopy Analysis Tools (spant) Papoulis-Gerchberg (PG) algorithm method for k-space extrapolation. — pg_extrap_xy • Spectroscopy Analysis Tools (spant) Apply phasing parameters to MRS data. — phase • Spectroscopy Analysis Tools (spant) Apply phasing parameters to MRS data. — phase • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/phase_ref_1h_brain.html b/docs/reference/phase_ref_1h_brain.html
new file mode 100644
index 00000000..8707a74a
--- /dev/null
+++ b/docs/reference/phase_ref_1h_brain.html
@@ -0,0 +1,131 @@
+
+Corrected zero order phase and chemical shift offset in 1H MRS data from the brain. — phase_ref_1h_brain • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Corrected zero order phase and chemical shift offset in 1H MRS data from the brain.
+ Source: R/rats.R
+ phase_ref_1h_brain.Rd
+
+
+
+ Corrected zero order phase and chemical shift offset in 1H MRS data from the
+brain.
+
+
+
+ phase_ref_1h_brain(mrs_data, mean_ref = FALSE, ret_corr_only = TRUE)
+
+
+
+ Arguments
+ - mrs_data
+MRS data to be corrected.
- mean_ref
+apply the phase and offset of the mean spectrum to all
+others. Default is FALSE.
- ret_corr_only
+return the corrected data only.
+
+ Value
+
+
+corrected MRS data.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/plot.fit_result.html b/docs/reference/plot.fit_result.html
index e54d3bc1..836a53ee 100644
--- a/docs/reference/plot.fit_result.html
+++ b/docs/reference/plot.fit_result.html
@@ -1,5 +1,5 @@
-Plot the fitting results of an object of class fit_result. — plot.fit_result • Spectroscopy Analysis Tools (spant) Plot the fitting results of an object of class fit_result. — plot.fit_result • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -207,7 +207,7 @@ Arguments
diff --git a/docs/reference/plot.mrs_data.html b/docs/reference/plot.mrs_data.html
index fabcc35b..bb2ec651 100644
--- a/docs/reference/plot.mrs_data.html
+++ b/docs/reference/plot.mrs_data.html
@@ -1,5 +1,5 @@
-Plotting method for objects of class mrs_data. — plot.mrs_data • Spectroscopy Analysis Tools (spant) Plotting method for objects of class mrs_data. — plot.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -287,7 +287,7 @@ Arguments
diff --git a/docs/reference/plot_bc.html b/docs/reference/plot_bc.html
index 4f8309b4..b48142cc 100644
--- a/docs/reference/plot_bc.html
+++ b/docs/reference/plot_bc.html
@@ -1,5 +1,5 @@
-Convenience function to plot a baseline estimate with the original data. — plot_bc • Spectroscopy Analysis Tools (spant) Convenience function to plot a baseline estimate with the original data. — plot_bc • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -108,7 +108,7 @@ Arguments
diff --git a/docs/reference/plot_reg.html b/docs/reference/plot_reg.html
index ae1acbe7..2addb2f6 100644
--- a/docs/reference/plot_reg.html
+++ b/docs/reference/plot_reg.html
@@ -1,5 +1,5 @@
-Plot regressors as an image. — plot_reg • Spectroscopy Analysis Tools (spant) Plot regressors as an image. — plot_reg • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/plot_slice_fit.html b/docs/reference/plot_slice_fit.html
index fbc7b560..57f1af8a 100644
--- a/docs/reference/plot_slice_fit.html
+++ b/docs/reference/plot_slice_fit.html
@@ -1,5 +1,5 @@
-Plot a 2D slice from an MRSI fit result object. — plot_slice_fit • Spectroscopy Analysis Tools (spant) Plot a 2D slice from an MRSI fit result object. — plot_slice_fit • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -129,7 +129,7 @@ Arguments
diff --git a/docs/reference/plot_slice_fit_inter.html b/docs/reference/plot_slice_fit_inter.html
index 4eed104a..da105a7d 100644
--- a/docs/reference/plot_slice_fit_inter.html
+++ b/docs/reference/plot_slice_fit_inter.html
@@ -1,5 +1,5 @@
-Plot a 2D slice from an MRSI fit result object. — plot_slice_fit_inter • Spectroscopy Analysis Tools (spant) Plot a 2D slice from an MRSI fit result object. — plot_slice_fit_inter • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -134,7 +134,7 @@ Arguments
diff --git a/docs/reference/plot_slice_map.html b/docs/reference/plot_slice_map.html
index 553e9ac8..ffb2a134 100644
--- a/docs/reference/plot_slice_map.html
+++ b/docs/reference/plot_slice_map.html
@@ -1,5 +1,5 @@
-Plot a slice from a 7 dimensional array. — plot_slice_map • Spectroscopy Analysis Tools (spant) Plot a slice from a 7 dimensional array. — plot_slice_map • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -153,7 +153,7 @@ Arguments
diff --git a/docs/reference/plot_slice_map_inter.html b/docs/reference/plot_slice_map_inter.html
index 40d33b42..90968f66 100644
--- a/docs/reference/plot_slice_map_inter.html
+++ b/docs/reference/plot_slice_map_inter.html
@@ -1,7 +1,5 @@
-Plot an interactive slice map from a data array where voxels can be selected
-to display a corresponding spectrum. — plot_slice_map_inter • Spectroscopy Analysis Tools (spant) Plot an interactive slice map from a data array where voxels can be selected to display a corresponding spectrum. — plot_slice_map_inter • Spectroscopy Analysis Tools (spant) Plot the spectral standard deviation. — plot_spec_sd • Spectroscopy Analysis Tools (spant) Plot the spectral standard deviation. — plot_spec_sd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Arguments
diff --git a/docs/reference/plot_voi_overlay.html b/docs/reference/plot_voi_overlay.html
index 9a782e88..bbbbf35e 100644
--- a/docs/reference/plot_voi_overlay.html
+++ b/docs/reference/plot_voi_overlay.html
@@ -1,5 +1,5 @@
-Plot a volume as an image overlay. — plot_voi_overlay • Spectroscopy Analysis Tools (spant) Plot a volume as an image overlay. — plot_voi_overlay • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -116,7 +116,7 @@ Arguments
diff --git a/docs/reference/plot_voi_overlay_seg.html b/docs/reference/plot_voi_overlay_seg.html
index 3d4e74ff..0e800ff2 100644
--- a/docs/reference/plot_voi_overlay_seg.html
+++ b/docs/reference/plot_voi_overlay_seg.html
@@ -1,5 +1,5 @@
-Plot a volume as an overlay on a segmented brain volume. — plot_voi_overlay_seg • Spectroscopy Analysis Tools (spant) Plot a volume as an overlay on a segmented brain volume. — plot_voi_overlay_seg • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Arguments
diff --git a/docs/reference/ppm.html b/docs/reference/ppm.html
index c352327a..ee4696e2 100644
--- a/docs/reference/ppm.html
+++ b/docs/reference/ppm.html
@@ -1,5 +1,5 @@
-Return the ppm scale of an MRS dataset or fit result. — ppm • Spectroscopy Analysis Tools (spant) Return the ppm scale of an MRS dataset or fit result. — ppm • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -132,7 +132,7 @@ Value
diff --git a/docs/reference/precomp.html b/docs/reference/precomp.html
index 822d7336..df3d2c6c 100644
--- a/docs/reference/precomp.html
+++ b/docs/reference/precomp.html
@@ -1,7 +1,5 @@
-Save function results to file and load on subsequent calls to avoid repeat
-computation. — precomp • Spectroscopy Analysis Tools (spant) Save function results to file and load on subsequent calls to avoid repeat computation. — precomp • Spectroscopy Analysis Tools (spant) Preprocess and perform quality assessment of a single SVS data set. — preproc_svs • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Preprocess and perform quality assessment of a single SVS data set.
+ Source: R/fmrs.R
+ preproc_svs.Rd
+
+
+
+ Preprocess and perform quality assessment of a single SVS data set.
+
+
+
+ preproc_svs(path, label = NULL, output_dir = NULL, ref_inds = NULL)
+
+
+
+ Arguments
+ - path
+path to the fMRS data file or IMA directory.
- label
+a label to describe the data set.
- output_dir
+output directory.
- ref_inds
+a vector of 1-based indices for any water reference dynamic
+scans.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/preproc_svs_dataset.html b/docs/reference/preproc_svs_dataset.html
new file mode 100644
index 00000000..07c3a29b
--- /dev/null
+++ b/docs/reference/preproc_svs_dataset.html
@@ -0,0 +1,148 @@
+
+Preprocess and perform quality assessment of one or more SVS data sets. — preproc_svs_dataset • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Preprocess and perform quality assessment of one or more SVS data sets.
+ Source: R/fmrs.R
+ preproc_svs_dataset.Rd
+
+
+
+ Preprocess and perform quality assessment of one or more SVS data sets.
+
+
+
+ preproc_svs_dataset(
+ paths,
+ labels = NULL,
+ output_dir = "spant_analysis",
+ exclude_labels = NULL,
+ overwrite = FALSE,
+ ref_inds = NULL,
+ return_results = FALSE
+)
+
+
+
+ Arguments
+ - paths
+paths to the fMRS data file or IMA directory.
- labels
+labels to describe each data set.
- output_dir
+output directory.
- exclude_labels
+vector of labels of scans to exclude, eg poor quality
+data.
- overwrite
+overwrite saved results, defaults to FALSE.
- ref_inds
+a vector of 1-based indices for any water reference dynamic
+scans.
- return_results
+function will return key outputs, defaults to FALSE.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/print.fit_result.html b/docs/reference/print.fit_result.html
index 297f28dc..5f434e57 100644
--- a/docs/reference/print.fit_result.html
+++ b/docs/reference/print.fit_result.html
@@ -1,5 +1,5 @@
-Print a summary of an object of class fit_result. — print.fit_result • Spectroscopy Analysis Tools (spant) Print a summary of an object of class fit_result. — print.fit_result • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -105,7 +105,7 @@ Arguments
diff --git a/docs/reference/print.mrs_data.html b/docs/reference/print.mrs_data.html
index 51199017..e1561eb2 100644
--- a/docs/reference/print.mrs_data.html
+++ b/docs/reference/print.mrs_data.html
@@ -1,5 +1,5 @@
-Print a summary of mrs_data parameters. — print.mrs_data • Spectroscopy Analysis Tools (spant) Print a summary of mrs_data parameters. — print.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -109,7 +109,7 @@ Arguments
diff --git a/docs/reference/qn_states.html b/docs/reference/qn_states.html
index 0f42f2f9..d7aa6715 100644
--- a/docs/reference/qn_states.html
+++ b/docs/reference/qn_states.html
@@ -1,5 +1,5 @@
-Get the quantum coherence matrix for a spin system. — qn_states • Spectroscopy Analysis Tools (spant) Get the quantum coherence matrix for a spin system. — qn_states • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/rats.html b/docs/reference/rats.html
index 5a39a396..93585e08 100644
--- a/docs/reference/rats.html
+++ b/docs/reference/rats.html
@@ -1,5 +1,5 @@
-Robust Alignment to a Target Spectrum (RATS). — rats • Spectroscopy Analysis Tools (spant) Robust Alignment to a Target Spectrum (RATS). — rats • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -207,7 +207,7 @@ Value
diff --git a/docs/reference/re_weighting.html b/docs/reference/re_weighting.html
index d21caf21..8b0b070a 100644
--- a/docs/reference/re_weighting.html
+++ b/docs/reference/re_weighting.html
@@ -1,5 +1,5 @@
-Apply a weighting to the FID to enhance spectral resolution. — re_weighting • Spectroscopy Analysis Tools (spant) Apply a weighting to the FID to enhance spectral resolution. — re_weighting • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/read_basis.html b/docs/reference/read_basis.html
index da9b94af..eb6f8557 100644
--- a/docs/reference/read_basis.html
+++ b/docs/reference/read_basis.html
@@ -1,5 +1,5 @@
-Read a basis file in LCModel .basis format. — read_basis • Spectroscopy Analysis Tools (spant) Read a basis file in LCModel .basis format. — read_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/read_ima_coil_dir.html b/docs/reference/read_ima_coil_dir.html
index 28c02de0..4f073cd8 100644
--- a/docs/reference/read_ima_coil_dir.html
+++ b/docs/reference/read_ima_coil_dir.html
@@ -1,9 +1,5 @@
-Read a directory containing Siemens MRS IMA files and combine along the coil
-dimension. Note that the coil ID is inferred from the sorted file name and
-should be checked when consistency is required between two directories. — read_ima_coil_dir • Spectroscopy Analysis Tools (spant) Read a directory containing Siemens MRS IMA files and combine along the coil dimension. Note that the coil ID is inferred from the sorted file name and should be checked when consistency is required between two directories. — read_ima_coil_dir • Spectroscopy Analysis Tools (spant) Read a directory containing Siemens MRS IMA files and combine along the
-dynamic dimension. Note that the coil ID is inferred from the sorted file
-name and should be checked when consistency is required. — read_ima_dyn_dir • Spectroscopy Analysis Tools (spant) Read a directory containing Siemens MRS IMA files and combine along the dynamic dimension. Note that the coil ID is inferred from the sorted file name and should be checked when consistency is required. — read_ima_dyn_dir • Spectroscopy Analysis Tools (spant) Read an LCModel formatted coord file containing fit information. — read_lcm_coord • Spectroscopy Analysis Tools (spant) Read an LCModel formatted coord file containing fit information. — read_lcm_coord • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -107,7 +107,7 @@ Value
diff --git a/docs/reference/read_mrs.html b/docs/reference/read_mrs.html
index 3ac2a36b..2cf36b20 100644
--- a/docs/reference/read_mrs.html
+++ b/docs/reference/read_mrs.html
@@ -1,5 +1,5 @@
-Read MRS data from a file. — read_mrs • Spectroscopy Analysis Tools (spant) Read MRS data from a file. — read_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -88,7 +88,8 @@ Read MRS data from a file.
full_fid = FALSE,
omit_svs_ref_scans = TRUE,
verbose = FALSE,
- extra = NULL
+ extra = NULL,
+ fid_filt_dist = NULL
)
@@ -140,6 +141,13 @@ Arguments
an optional data frame to provide additional variables for use
in subsequent analysis steps, eg id or grouping variables.
fid_filt_dist
+indicate if the data has a distorted FID due to a
+brick-wall filter being used to downsample the data. Default is to auto
+detect this from the data, but TRUE or FALSE options can be given to override
+detection.
Value
@@ -183,7 +191,7 @@ Examples
diff --git a/docs/reference/read_mrs_tqn.html b/docs/reference/read_mrs_tqn.html
index 5766362f..84bdaf3a 100644
--- a/docs/reference/read_mrs_tqn.html
+++ b/docs/reference/read_mrs_tqn.html
@@ -1,5 +1,5 @@
-Read MRS data using the TARQUIN software package. — read_mrs_tqn • Spectroscopy Analysis Tools (spant) Read MRS data using the TARQUIN software package. — read_mrs_tqn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -131,7 +131,7 @@ Examples
diff --git a/docs/reference/read_pulse_ascii.html b/docs/reference/read_pulse_ascii.html
index c9e0d43c..ab11c9cc 100644
--- a/docs/reference/read_pulse_ascii.html
+++ b/docs/reference/read_pulse_ascii.html
@@ -1,5 +1,5 @@
-Read an ASCII formatted pulse file. — read_pulse_ascii • Spectroscopy Analysis Tools (spant) Read an ASCII formatted pulse file. — read_pulse_ascii • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/read_pulse_bruker.html b/docs/reference/read_pulse_bruker.html
index c92bf76a..dbe9073b 100644
--- a/docs/reference/read_pulse_bruker.html
+++ b/docs/reference/read_pulse_bruker.html
@@ -1,5 +1,5 @@
-Read a Bruker formatted pulse file — read_pulse_bruker • Spectroscopy Analysis Tools (spant) Read a Bruker formatted pulse file — read_pulse_bruker • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/read_pulse_pta.html b/docs/reference/read_pulse_pta.html
index 72e1b6d4..a0fac3c3 100644
--- a/docs/reference/read_pulse_pta.html
+++ b/docs/reference/read_pulse_pta.html
@@ -1,5 +1,5 @@
-Read a .pta formatted pulse file compatible with Siemens PulseTool. — read_pulse_pta • Spectroscopy Analysis Tools (spant) Read a .pta formatted pulse file compatible with Siemens PulseTool. — read_pulse_pta • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/read_siemens_txt_hdr.html b/docs/reference/read_siemens_txt_hdr.html
index 23fb8c70..3a17d87c 100644
--- a/docs/reference/read_siemens_txt_hdr.html
+++ b/docs/reference/read_siemens_txt_hdr.html
@@ -1,5 +1,5 @@
-Read the text format header found in Siemens IMA and TWIX data files. — read_siemens_txt_hdr • Spectroscopy Analysis Tools (spant) Read the text format header found in Siemens IMA and TWIX data files. — read_siemens_txt_hdr • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -78,7 +78,7 @@ Read the text format header found in Siemens IMA and TWIX data files.
- read_siemens_txt_hdr(input, version = "vd", verbose, offset = 0)
+ read_siemens_txt_hdr(input, version = "vd", verbose = FALSE, offset = 0)
@@ -118,7 +118,7 @@ Value
diff --git a/docs/reference/read_tqn_fit.html b/docs/reference/read_tqn_fit.html
index 4da6c25e..a1630420 100644
--- a/docs/reference/read_tqn_fit.html
+++ b/docs/reference/read_tqn_fit.html
@@ -1,5 +1,5 @@
-Reader for csv fit results generated by TARQUIN. — read_tqn_fit • Spectroscopy Analysis Tools (spant) Reader for csv fit results generated by TARQUIN. — read_tqn_fit • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -113,7 +113,7 @@ Examples
diff --git a/docs/reference/read_tqn_result.html b/docs/reference/read_tqn_result.html
index 36659714..68a3e98c 100644
--- a/docs/reference/read_tqn_result.html
+++ b/docs/reference/read_tqn_result.html
@@ -1,5 +1,5 @@
-Reader for csv results generated by TARQUIN. — read_tqn_result • Spectroscopy Analysis Tools (spant) Reader for csv results generated by TARQUIN. — read_tqn_result • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -117,7 +117,7 @@ Examples
diff --git a/docs/reference/recon_imag.html b/docs/reference/recon_imag.html
index d2a72225..5bc3b1eb 100644
--- a/docs/reference/recon_imag.html
+++ b/docs/reference/recon_imag.html
@@ -1,7 +1,5 @@
-Reconstruct complex time-domain data from the real part of frequency-domain
-data. — recon_imag • Spectroscopy Analysis Tools (spant) Reconstruct complex time-domain data from the real part of frequency-domain data. — recon_imag • Spectroscopy Analysis Tools (spant) Reconstruct complex time-domain data from the real part of frequency-domain
-data. — recon_imag_vec • Spectroscopy Analysis Tools (spant) Reconstruct complex time-domain data from the real part of frequency-domain data. — recon_imag_vec • Spectroscopy Analysis Tools (spant) Reconstruct 2D MRSI data from a twix file loaded with read_mrs. — recon_twix_2d_mrsi • Spectroscopy Analysis Tools (spant) Reconstruct 2D MRSI data from a twix file loaded with read_mrs. — recon_twix_2d_mrsi • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/rectangular_mask.html b/docs/reference/rectangular_mask.html
index a2117283..6e469bc9 100644
--- a/docs/reference/rectangular_mask.html
+++ b/docs/reference/rectangular_mask.html
@@ -1,5 +1,5 @@
-Create a rectangular mask stored as a matrix of logical values. — rectangular_mask • Spectroscopy Analysis Tools (spant) Create a rectangular mask stored as a matrix of logical values. — rectangular_mask • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -130,7 +130,7 @@ Value
diff --git a/docs/reference/reexports.html b/docs/reference/reexports.html
index 694a75d1..a59e8379 100644
--- a/docs/reference/reexports.html
+++ b/docs/reference/reexports.html
@@ -1,5 +1,5 @@
-Objects exported from other packages — reexports • Spectroscopy Analysis Tools (spant) Objects exported from other packages — reexports • Spectroscopy Analysis Tools (spant)
Spectroscopy Analysis Tools (spant)
- 2.21.0
+ 2.22.0
@@ -103,7 +103,7 @@ Objects exported from other packages
diff --git a/docs/reference/rep_array_dim.html b/docs/reference/rep_array_dim.html
index b9c49b4a..48c0a5ed 100644
--- a/docs/reference/rep_array_dim.html
+++ b/docs/reference/rep_array_dim.html
@@ -1,5 +1,5 @@
-Repeat an array over a given dimension. — rep_array_dim • Spectroscopy Analysis Tools (spant) Repeat an array over a given dimension. — rep_array_dim • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/rep_dyn.html b/docs/reference/rep_dyn.html
index 6bbfb0ef..89a4bb9b 100644
--- a/docs/reference/rep_dyn.html
+++ b/docs/reference/rep_dyn.html
@@ -1,5 +1,5 @@
-Replicate a scan in the dynamic dimension. — rep_dyn • Spectroscopy Analysis Tools (spant) Replicate a scan in the dynamic dimension. — rep_dyn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/rep_mrs.html b/docs/reference/rep_mrs.html
index 67730b5c..becb8f00 100644
--- a/docs/reference/rep_mrs.html
+++ b/docs/reference/rep_mrs.html
@@ -1,5 +1,5 @@
-Replicate a scan over a given dimension. — rep_mrs • Spectroscopy Analysis Tools (spant) Replicate a scan over a given dimension. — rep_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -138,7 +138,7 @@ Value
diff --git a/docs/reference/resample_basis.html b/docs/reference/resample_basis.html
index b0f2ab17..c7a6222a 100644
--- a/docs/reference/resample_basis.html
+++ b/docs/reference/resample_basis.html
@@ -1,5 +1,5 @@
-Resample a basis-set to match a mrs_data acquisition. — resample_basis • Spectroscopy Analysis Tools (spant) Resample a basis-set to match a mrs_data acquisition. — resample_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -116,7 +116,7 @@ Value
diff --git a/docs/reference/resample_img.html b/docs/reference/resample_img.html
index f1e7beaf..b0cc8f71 100644
--- a/docs/reference/resample_img.html
+++ b/docs/reference/resample_img.html
@@ -1,5 +1,5 @@
-Resample an image to match a target image space. — resample_img • Spectroscopy Analysis Tools (spant) Resample an image to match a target image space. — resample_img • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/resample_voi.html b/docs/reference/resample_voi.html
index 8fbfa836..a29ab096 100644
--- a/docs/reference/resample_voi.html
+++ b/docs/reference/resample_voi.html
@@ -1,7 +1,5 @@
-Resample a VOI to match a target image space using nearest-neighbour
-interpolation. — resample_voi • Spectroscopy Analysis Tools (spant) Resample a VOI to match a target image space using nearest-neighbour interpolation. — resample_voi • Spectroscopy Analysis Tools (spant) Reslice a nifti object to match the orientation of mrs data. — reslice_to_mrs • Spectroscopy Analysis Tools (spant) Reslice a nifti object to match the orientation of mrs data. — reslice_to_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/reson_table2mrs_data.html b/docs/reference/reson_table2mrs_data.html
index d75579ee..c5a2167a 100644
--- a/docs/reference/reson_table2mrs_data.html
+++ b/docs/reference/reson_table2mrs_data.html
@@ -1,5 +1,5 @@
-Generate mrs_data from a table of single Lorentzian resonances. — reson_table2mrs_data • Spectroscopy Analysis Tools (spant) Generate mrs_data from a table of single Lorentzian resonances. — reson_table2mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -119,7 +119,7 @@ Value
diff --git a/docs/reference/rm_dyns.html b/docs/reference/rm_dyns.html
index 5d5ef692..573e1f51 100644
--- a/docs/reference/rm_dyns.html
+++ b/docs/reference/rm_dyns.html
@@ -1,5 +1,5 @@
-Remove a subset of dynamic scans. — rm_dyns • Spectroscopy Analysis Tools (spant) Remove a subset of dynamic scans. — rm_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/scale_amp_molal.html b/docs/reference/scale_amp_molal.html
index aaeee1f2..7acb8cb0 100644
--- a/docs/reference/scale_amp_molal.html
+++ b/docs/reference/scale_amp_molal.html
@@ -1,7 +1,5 @@
-Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water). — scale_amp_molal • Spectroscopy Analysis Tools (spant) Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / kg of tissue water). — scale_amp_molal • Spectroscopy Analysis Tools (spant)
Spectroscopy Analysis Tools (spant)
- 2.21.0
+ 2.22.0
@@ -76,8 +74,7 @@
- Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water).
+ Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / kg of tissue water).
Source: R/amp_scaling.R
scale_amp_molal.Rd
@@ -163,7 +160,7 @@ Value
diff --git a/docs/reference/scale_amp_molal_pvc.html b/docs/reference/scale_amp_molal_pvc.html
index 962d6afc..4d194abd 100644
--- a/docs/reference/scale_amp_molal_pvc.html
+++ b/docs/reference/scale_amp_molal_pvc.html
@@ -1,7 +1,5 @@
-Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water). — scale_amp_molal_pvc • Spectroscopy Analysis Tools (spant)
@@ -75,8 +73,7 @@
- Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water).
+ Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / kg of tissue water).
Source: R/amp_scaling.R
scale_amp_molal_pvc.Rd
@@ -141,7 +138,7 @@ Value
diff --git a/docs/reference/scale_amp_molar.html b/docs/reference/scale_amp_molar.html
index 02358d91..dc87a338 100644
--- a/docs/reference/scale_amp_molar.html
+++ b/docs/reference/scale_amp_molar.html
@@ -1,7 +1,5 @@
-Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / Litre of tissue). — scale_amp_molar • Spectroscopy Analysis Tools (spant) Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / Litre of tissue). — scale_amp_molar • Spectroscopy Analysis Tools (spant) Convert default LCM/TARQUIN concentration scaling to molal units with partial
-volume correction. — scale_amp_molar2molal_pvc • Spectroscopy Analysis Tools (spant) Convert default LCM/TARQUIN concentration scaling to molal units with partial volume correction. — scale_amp_molar2molal_pvc • Spectroscopy Analysis Tools (spant) Scale fitted amplitudes to a ratio of signal amplitude. — scale_amp_ratio • Spectroscopy Analysis Tools (spant) Scale fitted amplitudes to a ratio of signal amplitude. — scale_amp_ratio • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -116,7 +116,7 @@ Value
diff --git a/docs/reference/scale_amp_ratio_value.html b/docs/reference/scale_amp_ratio_value.html
index 2036837a..6af8ac51 100644
--- a/docs/reference/scale_amp_ratio_value.html
+++ b/docs/reference/scale_amp_ratio_value.html
@@ -1,5 +1,5 @@
-Scale fitted amplitudes to a ratio of signal amplitude. — scale_amp_ratio_value • Spectroscopy Analysis Tools (spant) Scale fitted amplitudes to a ratio of signal amplitude. — scale_amp_ratio_value • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/scale_amp_water_ratio.html b/docs/reference/scale_amp_water_ratio.html
index 5b25e884..35a76b00 100644
--- a/docs/reference/scale_amp_water_ratio.html
+++ b/docs/reference/scale_amp_water_ratio.html
@@ -1,5 +1,5 @@
-Scale metabolite amplitudes as a ratio to the unsuppressed water amplitude. — scale_amp_water_ratio • Spectroscopy Analysis Tools (spant) Scale metabolite amplitudes as a ratio to the unsuppressed water amplitude. — scale_amp_water_ratio • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/scale_basis_amp.html b/docs/reference/scale_basis_amp.html
index 9401c3f1..5a58b5e5 100644
--- a/docs/reference/scale_basis_amp.html
+++ b/docs/reference/scale_basis_amp.html
@@ -1,5 +1,5 @@
-Scale a basis object by a scalar. — scale_basis_amp • Spectroscopy Analysis Tools (spant) Scale a basis object by a scalar. — scale_basis_amp • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/scale_basis_from_singlet.html b/docs/reference/scale_basis_from_singlet.html
index 0d542bc8..c9a19e77 100644
--- a/docs/reference/scale_basis_from_singlet.html
+++ b/docs/reference/scale_basis_from_singlet.html
@@ -1,5 +1,5 @@
-Scale a basis-set to be consistent with spant assumptions for water scaling. — scale_basis_from_singlet • Spectroscopy Analysis Tools (spant) Scale a basis-set to be consistent with spant assumptions for water scaling. — scale_basis_from_singlet • Spectroscopy Analysis Tools (spant)
Spectroscopy Analysis Tools (spant)
- 2.21.0
+ 2.22.0
@@ -127,7 +127,7 @@ Value
diff --git a/docs/reference/scale_mrs_amp.html b/docs/reference/scale_mrs_amp.html
index b5501a0d..990f058a 100644
--- a/docs/reference/scale_mrs_amp.html
+++ b/docs/reference/scale_mrs_amp.html
@@ -1,5 +1,5 @@
-Scale an mrs_data object by a scalar or vector or amplitudes. — scale_mrs_amp • Spectroscopy Analysis Tools (spant) Scale an mrs_data object by a scalar or vector or amplitudes. — scale_mrs_amp • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/scale_spec.html b/docs/reference/scale_spec.html
index 4f6ea835..6b3ddba4 100644
--- a/docs/reference/scale_spec.html
+++ b/docs/reference/scale_spec.html
@@ -1,5 +1,5 @@
-Scale mrs_data to a spectral region. — scale_spec • Spectroscopy Analysis Tools (spant) Scale mrs_data to a spectral region. — scale_spec • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -141,7 +141,7 @@ Value
diff --git a/docs/reference/sd.html b/docs/reference/sd.html
index ea1eec9f..3ae4dfd4 100644
--- a/docs/reference/sd.html
+++ b/docs/reference/sd.html
@@ -1,5 +1,5 @@
-Calculate the standard deviation spectrum from an mrs_data object. — sd • Spectroscopy Analysis Tools (spant) Calculate the standard deviation spectrum from an mrs_data object. — sd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/sd.mrs_data.html b/docs/reference/sd.mrs_data.html
index 3f92a49f..13bdda85 100644
--- a/docs/reference/sd.mrs_data.html
+++ b/docs/reference/sd.mrs_data.html
@@ -1,5 +1,5 @@
-Calculate the standard deviation spectrum from an mrs_data object. — sd.mrs_data • Spectroscopy Analysis Tools (spant) Calculate the standard deviation spectrum from an mrs_data object. — sd.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/seconds.html b/docs/reference/seconds.html
index b34d6627..467ee17f 100644
--- a/docs/reference/seconds.html
+++ b/docs/reference/seconds.html
@@ -1,5 +1,5 @@
-Return a time scale vector to match the FID of an MRS data object. — seconds • Spectroscopy Analysis Tools (spant) Return a time scale vector to match the FID of an MRS data object. — seconds • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/seq_cpmg_ideal.html b/docs/reference/seq_cpmg_ideal.html
index 547e96ab..45727c86 100644
--- a/docs/reference/seq_cpmg_ideal.html
+++ b/docs/reference/seq_cpmg_ideal.html
@@ -1,5 +1,5 @@
-CPMG style sequence with ideal pulses. — seq_cpmg_ideal • Spectroscopy Analysis Tools (spant) CPMG style sequence with ideal pulses. — seq_cpmg_ideal • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/seq_mega_press_ideal.html b/docs/reference/seq_mega_press_ideal.html
index 0769b8b4..a9cd7fa0 100644
--- a/docs/reference/seq_mega_press_ideal.html
+++ b/docs/reference/seq_mega_press_ideal.html
@@ -1,7 +1,5 @@
-MEGA-PRESS sequence with ideal localisation pulses and Gaussian shaped
-editing pulse. — seq_mega_press_ideal • Spectroscopy Analysis Tools (spant) MEGA-PRESS sequence with ideal localisation pulses and Gaussian shaped editing pulse. — seq_mega_press_ideal • Spectroscopy Analysis Tools (spant) PRESS sequence with shaped refocusing pulses. — seq_press_2d_shaped • Spectroscopy Analysis Tools (spant) PRESS sequence with shaped refocusing pulses. — seq_press_2d_shaped • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -165,7 +165,7 @@ Value
diff --git a/docs/reference/seq_press_ideal.html b/docs/reference/seq_press_ideal.html
index 8c976856..72c3af3d 100644
--- a/docs/reference/seq_press_ideal.html
+++ b/docs/reference/seq_press_ideal.html
@@ -1,5 +1,5 @@
-PRESS sequence with ideal pulses. — seq_press_ideal • Spectroscopy Analysis Tools (spant) PRESS sequence with ideal pulses. — seq_press_ideal • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/seq_pulse_acquire.html b/docs/reference/seq_pulse_acquire.html
index 4a88fc64..ad80571e 100644
--- a/docs/reference/seq_pulse_acquire.html
+++ b/docs/reference/seq_pulse_acquire.html
@@ -1,5 +1,5 @@
-Simple pulse and acquire sequence with ideal pulses. — seq_pulse_acquire • Spectroscopy Analysis Tools (spant) Simple pulse and acquire sequence with ideal pulses. — seq_pulse_acquire • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/seq_slaser_ideal.html b/docs/reference/seq_slaser_ideal.html
index 74688f4d..eb83e8e3 100644
--- a/docs/reference/seq_slaser_ideal.html
+++ b/docs/reference/seq_slaser_ideal.html
@@ -1,5 +1,5 @@
-sLASER sequence with ideal pulses. — seq_slaser_ideal • Spectroscopy Analysis Tools (spant) sLASER sequence with ideal pulses. — seq_slaser_ideal • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -126,7 +126,7 @@ Value
diff --git a/docs/reference/seq_spin_echo_ideal.html b/docs/reference/seq_spin_echo_ideal.html
index e23271de..4248716f 100644
--- a/docs/reference/seq_spin_echo_ideal.html
+++ b/docs/reference/seq_spin_echo_ideal.html
@@ -1,5 +1,5 @@
-Spin echo sequence with ideal pulses. — seq_spin_echo_ideal • Spectroscopy Analysis Tools (spant) Spin echo sequence with ideal pulses. — seq_spin_echo_ideal • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/seq_steam_ideal.html b/docs/reference/seq_steam_ideal.html
index a60685a8..1c8115d7 100644
--- a/docs/reference/seq_steam_ideal.html
+++ b/docs/reference/seq_steam_ideal.html
@@ -1,5 +1,5 @@
-STEAM sequence with ideal pulses. — seq_steam_ideal • Spectroscopy Analysis Tools (spant) STEAM sequence with ideal pulses. — seq_steam_ideal • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -128,7 +128,7 @@ Value
diff --git a/docs/reference/seq_steam_ideal_cof.html b/docs/reference/seq_steam_ideal_cof.html
index 8f225740..cba7af91 100644
--- a/docs/reference/seq_steam_ideal_cof.html
+++ b/docs/reference/seq_steam_ideal_cof.html
@@ -1,7 +1,5 @@
-STEAM sequence with ideal pulses and coherence order filtering to simulate
-gradient crushers. — seq_steam_ideal_cof • Spectroscopy Analysis Tools (spant) STEAM sequence with ideal pulses and coherence order filtering to simulate gradient crushers. — seq_steam_ideal_cof • Spectroscopy Analysis Tools (spant) STEAM sequence with ideal pulses using the z-rotation gradient simulation
-method described by Young et al JMR 140, 146-152 (1999). — seq_steam_ideal_young • Spectroscopy Analysis Tools (spant) STEAM sequence with ideal pulses using the z-rotation gradient simulation method described by Young et al JMR 140, 146-152 (1999). — seq_steam_ideal_young • Spectroscopy Analysis Tools (spant) Set the number of transients for an mrs_data object. — set_Ntrans • Spectroscopy Analysis Tools (spant) Set the number of transients for an mrs_data object. — set_Ntrans • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/set_def_acq_paras.html b/docs/reference/set_def_acq_paras.html
index 3e1b4004..cc2ada9c 100644
--- a/docs/reference/set_def_acq_paras.html
+++ b/docs/reference/set_def_acq_paras.html
@@ -1,5 +1,5 @@
-Set the default acquisition parameters. — set_def_acq_paras • Spectroscopy Analysis Tools (spant) Set the default acquisition parameters. — set_def_acq_paras • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Arguments
diff --git a/docs/reference/set_lcm_cmd.html b/docs/reference/set_lcm_cmd.html
index 2056ed01..42bb2f24 100644
--- a/docs/reference/set_lcm_cmd.html
+++ b/docs/reference/set_lcm_cmd.html
@@ -1,5 +1,5 @@
-Set the command to run the LCModel command-line program. — set_lcm_cmd • Spectroscopy Analysis Tools (spant) Set the command to run the LCModel command-line program. — set_lcm_cmd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/set_lw.html b/docs/reference/set_lw.html
index b64ec851..bb176c62 100644
--- a/docs/reference/set_lw.html
+++ b/docs/reference/set_lw.html
@@ -1,5 +1,5 @@
-Apply line-broadening to an mrs_data object to achieve a specified linewidth. — set_lw • Spectroscopy Analysis Tools (spant) Apply line-broadening to an mrs_data object to achieve a specified linewidth. — set_lw • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -123,7 +123,7 @@ Value
diff --git a/docs/reference/set_mask_xy_mat.html b/docs/reference/set_mask_xy_mat.html
index 49dc5d4e..52c4b617 100644
--- a/docs/reference/set_mask_xy_mat.html
+++ b/docs/reference/set_mask_xy_mat.html
@@ -1,5 +1,5 @@
-Set the masked voxels in a 2D MRSI dataset to given spectrum. — set_mask_xy_mat • Spectroscopy Analysis Tools (spant) Set the masked voxels in a 2D MRSI dataset to given spectrum. — set_mask_xy_mat • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Value
diff --git a/docs/reference/set_precomp_mode.html b/docs/reference/set_precomp_mode.html
index f44bd5d3..47c28e3b 100644
--- a/docs/reference/set_precomp_mode.html
+++ b/docs/reference/set_precomp_mode.html
@@ -1,5 +1,5 @@
-Set the precompute mode. — set_precomp_mode • Spectroscopy Analysis Tools (spant) Set the precompute mode. — set_precomp_mode • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/set_precomp_verbose.html b/docs/reference/set_precomp_verbose.html
index 1453a231..9c613505 100644
--- a/docs/reference/set_precomp_verbose.html
+++ b/docs/reference/set_precomp_verbose.html
@@ -1,5 +1,5 @@
-Set the verbosity of the precompute function. — set_precomp_verbose • Spectroscopy Analysis Tools (spant) Set the verbosity of the precompute function. — set_precomp_verbose • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/set_ref.html b/docs/reference/set_ref.html
index 8953fa50..5436dfa2 100644
--- a/docs/reference/set_ref.html
+++ b/docs/reference/set_ref.html
@@ -1,5 +1,5 @@
-Set the ppm reference value (eg ppm value at 0Hz). — set_ref • Spectroscopy Analysis Tools (spant) Set the ppm reference value (eg ppm value at 0Hz). — set_ref • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/set_td_pts.html b/docs/reference/set_td_pts.html
index 8a80d42a..586459ff 100644
--- a/docs/reference/set_td_pts.html
+++ b/docs/reference/set_td_pts.html
@@ -1,7 +1,5 @@
-Set the number of time-domain data points, truncating or zero-filling as
-appropriate. — set_td_pts • Spectroscopy Analysis Tools (spant) Set the number of time-domain data points, truncating or zero-filling as appropriate. — set_td_pts • Spectroscopy Analysis Tools (spant) Set the command to run the TARQUIN command-line program. — set_tqn_cmd • Spectroscopy Analysis Tools (spant) Set the command to run the TARQUIN command-line program. — set_tqn_cmd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/set_tr.html b/docs/reference/set_tr.html
index b2109ab0..65c9df5f 100644
--- a/docs/reference/set_tr.html
+++ b/docs/reference/set_tr.html
@@ -1,5 +1,5 @@
-Set the repetition time of an MRS dataset. — set_tr • Spectroscopy Analysis Tools (spant) Set the repetition time of an MRS dataset. — set_tr • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/shift.html b/docs/reference/shift.html
index ab0fe724..034591d0 100644
--- a/docs/reference/shift.html
+++ b/docs/reference/shift.html
@@ -1,5 +1,5 @@
-Apply a frequency shift to MRS data. — shift • Spectroscopy Analysis Tools (spant) Apply a frequency shift to MRS data. — shift • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/shift_basis.html b/docs/reference/shift_basis.html
index 2884be19..f55a65e0 100644
--- a/docs/reference/shift_basis.html
+++ b/docs/reference/shift_basis.html
@@ -1,5 +1,5 @@
-Apply frequency shifts to basis set signals. — shift_basis • Spectroscopy Analysis Tools (spant) Apply frequency shifts to basis set signals. — shift_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Value
diff --git a/docs/reference/sim_basis.html b/docs/reference/sim_basis.html
index c7838c46..bb5fefc6 100644
--- a/docs/reference/sim_basis.html
+++ b/docs/reference/sim_basis.html
@@ -1,5 +1,5 @@
-Simulate a basis set object. — sim_basis • Spectroscopy Analysis Tools (spant) Simulate a basis set object. — sim_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -136,7 +136,7 @@ Value
diff --git a/docs/reference/sim_basis_1h_brain.html b/docs/reference/sim_basis_1h_brain.html
index 62ed7389..f71ffa0b 100644
--- a/docs/reference/sim_basis_1h_brain.html
+++ b/docs/reference/sim_basis_1h_brain.html
@@ -1,7 +1,5 @@
-Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS
-sequence. Note, ideal pulses are assumed. — sim_basis_1h_brain • Spectroscopy Analysis Tools (spant) Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS sequence. Note, ideal pulses are assumed. — sim_basis_1h_brain • Spectroscopy Analysis Tools (spant) Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS
-sequence. Note, ideal pulses are assumed. — sim_basis_1h_brain_press • Spectroscopy Analysis Tools (spant) Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS sequence. Note, ideal pulses are assumed. — sim_basis_1h_brain_press • Spectroscopy Analysis Tools (spant) Simulate a macromolecular and lipid basis-set suitable for 1H brain MRS
-analysis. — sim_basis_mm_lip_lcm • Spectroscopy Analysis Tools (spant) Simulate a macromolecular and lipid basis-set suitable for 1H brain MRS analysis. — sim_basis_mm_lip_lcm • Spectroscopy Analysis Tools (spant) Simulate a basis file using TARQUIN. — sim_basis_tqn • Spectroscopy Analysis Tools (spant) Simulate a basis file using TARQUIN. — sim_basis_tqn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -129,7 +129,7 @@ Examples
diff --git a/docs/reference/sim_brain_1h.html b/docs/reference/sim_brain_1h.html
index 2044cf1a..717ee289 100644
--- a/docs/reference/sim_brain_1h.html
+++ b/docs/reference/sim_brain_1h.html
@@ -1,5 +1,5 @@
-Simulate MRS data with a similar appearance to normal brain (by default). — sim_brain_1h • Spectroscopy Analysis Tools (spant) Simulate MRS data with a similar appearance to normal brain (by default). — sim_brain_1h • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -159,7 +159,7 @@ Value
diff --git a/docs/reference/sim_mol.html b/docs/reference/sim_mol.html
index 23bcef50..77f76a50 100644
--- a/docs/reference/sim_mol.html
+++ b/docs/reference/sim_mol.html
@@ -1,5 +1,5 @@
-Simulate a mol_parameter object. — sim_mol • Spectroscopy Analysis Tools (spant) Simulate a mol_parameter object. — sim_mol • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -143,7 +143,7 @@ Value
diff --git a/docs/reference/sim_noise.html b/docs/reference/sim_noise.html
index 23875f79..a71477d4 100644
--- a/docs/reference/sim_noise.html
+++ b/docs/reference/sim_noise.html
@@ -1,5 +1,5 @@
-Simulate an mrs_data object containing simulated Gaussian noise. — sim_noise • Spectroscopy Analysis Tools (spant) Simulate an mrs_data object containing simulated Gaussian noise. — sim_noise • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -84,6 +84,7 @@ Simulate an mrs_data object containing simulated Gaussian noise.
ft = def_ft(),
N = def_N(),
ref = def_ref(),
+ nuc = def_nuc(),
dyns = 1,
fd = TRUE
)
@@ -111,6 +112,10 @@ Arguments
reference value for ppm scale.
nuc
+resonant nucleus.
dyns
number of dynamic scans to generate.
Value
diff --git a/docs/reference/sim_resonances.html b/docs/reference/sim_resonances.html
index 19e9a8a4..d4f8d7c0 100644
--- a/docs/reference/sim_resonances.html
+++ b/docs/reference/sim_resonances.html
@@ -1,5 +1,5 @@
-Simulate a MRS data object containing a set of simulated resonances. — sim_resonances • Spectroscopy Analysis Tools (spant) Simulate a MRS data object containing a set of simulated resonances. — sim_resonances • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -161,7 +161,7 @@ Examples
diff --git a/docs/reference/sim_th_excit_profile.html b/docs/reference/sim_th_excit_profile.html
index 5535c5ef..e781cab1 100644
--- a/docs/reference/sim_th_excit_profile.html
+++ b/docs/reference/sim_th_excit_profile.html
@@ -1,7 +1,5 @@
-Simulate an ideal pulse excitation profile by smoothing a top-hat function
-with a Gaussian. — sim_th_excit_profile • Spectroscopy Analysis Tools (spant) Simulate an ideal pulse excitation profile by smoothing a top-hat function with a Gaussian. — sim_th_excit_profile • Spectroscopy Analysis Tools (spant) Simulate an mrs_data object containing complex zero valued samples. — sim_zero • Spectroscopy Analysis Tools (spant) Simulate an mrs_data object containing complex zero valued samples. — sim_zero • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -78,7 +78,14 @@ Simulate an mrs_data object containing complex zero valued samples.
-
+
@@ -99,6 +106,10 @@ Arguments
reference value for ppm scale.
nuc
+resonant nucleus.
dyns
number of dynamic scans to generate.
Value
diff --git a/docs/reference/smooth_dyns.html b/docs/reference/smooth_dyns.html
index 4cc8da50..accf3a51 100644
--- a/docs/reference/smooth_dyns.html
+++ b/docs/reference/smooth_dyns.html
@@ -1,5 +1,5 @@
-Smooth data across the dynamic dimension with a Gaussian kernel. — smooth_dyns • Spectroscopy Analysis Tools (spant) Smooth data across the dynamic dimension with a Gaussian kernel. — smooth_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/sort_basis.html b/docs/reference/sort_basis.html
index 6a676ea2..d25cc006 100644
--- a/docs/reference/sort_basis.html
+++ b/docs/reference/sort_basis.html
@@ -1,5 +1,5 @@
-Sort the basis-set elements alphabetically. — sort_basis • Spectroscopy Analysis Tools (spant) Sort the basis-set elements alphabetically. — sort_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/spant-package.html b/docs/reference/spant-package.html
index b3dd8e21..90f19ec3 100644
--- a/docs/reference/spant-package.html
+++ b/docs/reference/spant-package.html
@@ -1,5 +1,5 @@
-spant: spectroscopy analysis tools. — spant-package • Spectroscopy Analysis Tools (spant) spant: spectroscopy analysis tools. — spant-package • Spectroscopy Analysis Tools (spant) Simulate and fit some spectra with ABfit for benchmarking purposes. Basic
-timing and performance metrics will be printed. — spant_abfit_benchmark • Spectroscopy Analysis Tools (spant) Simulate and fit some spectra with ABfit for benchmarking purposes. Basic timing and performance metrics will be printed. — spant_abfit_benchmark • Spectroscopy Analysis Tools (spant) Example MEGA-PRESS data with significant B0 drift. — spant_mpress_drift • Spectroscopy Analysis Tools (spant) Example MEGA-PRESS data with significant B0 drift. — spant_mpress_drift • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -83,7 +83,7 @@ Example MEGA-PRESS data with significant B0 drift.
Format
- An object of class mrs_data of length 13.
+ An object of class mrs_data of dimension 1 x 1 x 1 x 1 x 40 x 1 x 1024.
@@ -98,7 +98,7 @@ Format
diff --git a/docs/reference/spant_sim_fmrs_dataset.html b/docs/reference/spant_sim_fmrs_dataset.html
new file mode 100644
index 00000000..00e48b56
--- /dev/null
+++ b/docs/reference/spant_sim_fmrs_dataset.html
@@ -0,0 +1,117 @@
+
+Simulate an example fMRS dataset for a block design fMRS experiment and export a BIDS structure. — spant_sim_fmrs_dataset • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Simulate an example fMRS dataset for a block design fMRS experiment and export a BIDS structure.
+ Source: R/fmrs.R
+ spant_sim_fmrs_dataset.Rd
+
+
+
+ Simulate an example fMRS dataset for a block design fMRS experiment and
+export a BIDS structure.
+
+
+
+ spant_sim_fmrs_dataset(output_dir = NULL)
+
+
+
+ Arguments
+ - output_dir
+output directory for the BIDS data. Defaults to :
+"HOME/sim_fmrs_dataset/data".
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/spant_simulation_benchmark.html b/docs/reference/spant_simulation_benchmark.html
index 32daa8bf..d8cc6841 100644
--- a/docs/reference/spant_simulation_benchmark.html
+++ b/docs/reference/spant_simulation_benchmark.html
@@ -1,7 +1,5 @@
-Simulate a typical metabolite basis set for benchmarking. Timing metrics will
-be printed on completion. — spant_simulation_benchmark • Spectroscopy Analysis Tools (spant) Simulate a typical metabolite basis set for benchmarking. Timing metrics will be printed on completion. — spant_simulation_benchmark • Spectroscopy Analysis Tools (spant) Decompose an mrs_data object into white and gray matter spectra. — spec_decomp • Spectroscopy Analysis Tools (spant) Perform a mathematical operation on a spectral region. — spec_op • Spectroscopy Analysis Tools (spant) Perform a mathematical operation on a spectral region. — spec_op • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -98,8 +98,8 @@ Arguments
operator
-can be "sum" (default), "mean", "l2", "max", "min" or
-"max-min".
can be "sum" (default), "mean", "l2", "max", "max_cplx,
+"min" or "max-min".
freq_scale
@@ -129,7 +129,7 @@ Value
diff --git a/docs/reference/spin_sys.html b/docs/reference/spin_sys.html
index 853423a4..1eaa9e76 100644
--- a/docs/reference/spin_sys.html
+++ b/docs/reference/spin_sys.html
@@ -1,5 +1,5 @@
-Create a spin system object for pulse sequence simulation. — spin_sys • Spectroscopy Analysis Tools (spant) Create a spin system object for pulse sequence simulation. — spin_sys • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/spm_pve2categorical.html b/docs/reference/spm_pve2categorical.html
index 23a1bad9..70f10729 100644
--- a/docs/reference/spm_pve2categorical.html
+++ b/docs/reference/spm_pve2categorical.html
@@ -1,7 +1,5 @@
-Convert SPM style segmentation files to a single categorical image where
-the numerical values map as: 0) Other, 1) CSF, 2) GM and 3) WM. — spm_pve2categorical • Spectroscopy Analysis Tools (spant) Convert SPM style segmentation files to a single categorical image where the numerical values map as: 0) Other, 1) CSF, 2) GM and 3) WM. — spm_pve2categorical • Spectroscopy Analysis Tools (spant) Signal space projection method for lipid suppression. — ssp • Spectroscopy Analysis Tools (spant) Signal space projection method for lipid suppression. — ssp • Spectroscopy Analysis Tools (spant) Plot the fitting results of an object of class fit_result with
-individual basis set components shown. — stackplot.fit_result • Spectroscopy Analysis Tools (spant) Plot the fitting results of an object of class fit_result with individual basis set components shown. — stackplot.fit_result • Spectroscopy Analysis Tools (spant) Produce a plot with multiple traces. — stackplot • Spectroscopy Analysis Tools (spant) Produce a plot with multiple traces. — stackplot • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/stackplot.mrs_data.html b/docs/reference/stackplot.mrs_data.html
index 17ff5648..64eea445 100644
--- a/docs/reference/stackplot.mrs_data.html
+++ b/docs/reference/stackplot.mrs_data.html
@@ -1,5 +1,5 @@
-Stackplot plotting method for objects of class mrs_data. — stackplot.mrs_data • Spectroscopy Analysis Tools (spant) Stackplot plotting method for objects of class mrs_data. — stackplot.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -255,7 +255,7 @@ Arguments
diff --git a/docs/reference/sub_first_dyn.html b/docs/reference/sub_first_dyn.html
index dbd7f831..493b7242 100644
--- a/docs/reference/sub_first_dyn.html
+++ b/docs/reference/sub_first_dyn.html
@@ -1,5 +1,5 @@
-Subtract the first dynamic spectrum from a dynamic series. — sub_first_dyn • Spectroscopy Analysis Tools (spant) Subtract the first dynamic spectrum from a dynamic series. — sub_first_dyn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/sub_mean_dyns.html b/docs/reference/sub_mean_dyns.html
index 6e3bb2df..221bd0c1 100644
--- a/docs/reference/sub_mean_dyns.html
+++ b/docs/reference/sub_mean_dyns.html
@@ -1,5 +1,5 @@
-Subtract the mean dynamic spectrum from a dynamic series. — sub_mean_dyns • Spectroscopy Analysis Tools (spant) Subtract the mean dynamic spectrum from a dynamic series. — sub_mean_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/sub_median_dyns.html b/docs/reference/sub_median_dyns.html
index 134c495d..1e834f14 100644
--- a/docs/reference/sub_median_dyns.html
+++ b/docs/reference/sub_median_dyns.html
@@ -1,5 +1,5 @@
-Subtract the median dynamic spectrum from a dynamic series. — sub_median_dyns • Spectroscopy Analysis Tools (spant) Subtract the median dynamic spectrum from a dynamic series. — sub_median_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/sum_coils.html b/docs/reference/sum_coils.html
index 7bf559f2..e1ab3cc0 100644
--- a/docs/reference/sum_coils.html
+++ b/docs/reference/sum_coils.html
@@ -1,5 +1,5 @@
-Calculate the sum across receiver coil elements. — sum_coils • Spectroscopy Analysis Tools (spant) Calculate the sum across receiver coil elements. — sum_coils • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/sum_dyns.html b/docs/reference/sum_dyns.html
index a0be19d3..bbda2ffc 100644
--- a/docs/reference/sum_dyns.html
+++ b/docs/reference/sum_dyns.html
@@ -1,5 +1,5 @@
-Calculate the sum of data dynamics. — sum_dyns • Spectroscopy Analysis Tools (spant) Calculate the sum of data dynamics. — sum_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/sum_mrs.html b/docs/reference/sum_mrs.html
index a22f215b..3cc3ab9e 100644
--- a/docs/reference/sum_mrs.html
+++ b/docs/reference/sum_mrs.html
@@ -1,5 +1,5 @@
-Sum two mrs_data objects. — sum_mrs • Spectroscopy Analysis Tools (spant) Sum two mrs_data objects. — sum_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Value
diff --git a/docs/reference/sum_mrs_list.html b/docs/reference/sum_mrs_list.html
index f4e09aea..c3584348 100644
--- a/docs/reference/sum_mrs_list.html
+++ b/docs/reference/sum_mrs_list.html
@@ -1,5 +1,5 @@
-Return the sum of a list of mrs_data objects. — sum_mrs_list • Spectroscopy Analysis Tools (spant) Return the sum of a list of mrs_data objects. — sum_mrs_list • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/svs_1h_brain_analysis.html b/docs/reference/svs_1h_brain_analysis.html
index 8ce514db..dff0ef7d 100644
--- a/docs/reference/svs_1h_brain_analysis.html
+++ b/docs/reference/svs_1h_brain_analysis.html
@@ -1,5 +1,5 @@
-Standard SVS 1H brain analysis pipeline. — svs_1h_brain_analysis • Spectroscopy Analysis Tools (spant) Standard SVS 1H brain analysis pipeline. — svs_1h_brain_analysis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -199,7 +199,7 @@ Value
diff --git a/docs/reference/svs_1h_brain_analysis_dev.html b/docs/reference/svs_1h_brain_analysis_dev.html
index d70a14d3..d71bfea2 100644
--- a/docs/reference/svs_1h_brain_analysis_dev.html
+++ b/docs/reference/svs_1h_brain_analysis_dev.html
@@ -1,5 +1,5 @@
-Standard SVS 1H brain analysis pipeline. — svs_1h_brain_analysis_dev • Spectroscopy Analysis Tools (spant) Standard SVS 1H brain analysis pipeline. — svs_1h_brain_analysis_dev • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -193,7 +193,7 @@ Examples
diff --git a/docs/reference/svs_1h_brain_batch_analysis.html b/docs/reference/svs_1h_brain_batch_analysis.html
index 5631e8cc..15f7223e 100644
--- a/docs/reference/svs_1h_brain_batch_analysis.html
+++ b/docs/reference/svs_1h_brain_batch_analysis.html
@@ -1,5 +1,5 @@
-Batch interface to the standard SVS 1H brain analysis pipeline. — svs_1h_brain_batch_analysis • Spectroscopy Analysis Tools (spant) Batch interface to the standard SVS 1H brain analysis pipeline. — svs_1h_brain_batch_analysis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -144,7 +144,7 @@ Value
diff --git a/docs/reference/t_test_spec.html b/docs/reference/t_test_spec.html
new file mode 100644
index 00000000..56a7ea1b
--- /dev/null
+++ b/docs/reference/t_test_spec.html
@@ -0,0 +1,124 @@
+
+Perform a t-test on spectral data points. — t_test_spec • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+
+
+ Perform a t-test on spectral data points.
+
+
+
+ t_test_spec(mrs_data, group)
+
+
+
+ Arguments
+ - mrs_data
+an mrs_data object with spectra in the dynamic dimension.
- group
+vector describing the group membership of each dynamic spectrum.
+
+ Value
+
+
+a list of statistical results.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/td2fd.html b/docs/reference/td2fd.html
index 6748a6a8..f31ed524 100644
--- a/docs/reference/td2fd.html
+++ b/docs/reference/td2fd.html
@@ -1,5 +1,5 @@
-Transform time-domain data to the frequency-domain. — td2fd • Spectroscopy Analysis Tools (spant) Transform time-domain data to the frequency-domain. — td2fd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/td_conv_filt.html b/docs/reference/td_conv_filt.html
index a9f340c3..106b9b00 100644
--- a/docs/reference/td_conv_filt.html
+++ b/docs/reference/td_conv_filt.html
@@ -1,5 +1,5 @@
-Time-domain convolution based filter. — td_conv_filt • Spectroscopy Analysis Tools (spant) Time-domain convolution based filter. — td_conv_filt • Spectroscopy Analysis Tools (spant) Time-domain spectral registration. — tdsr • Spectroscopy Analysis Tools (spant) Time-domain spectral registration. — tdsr • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -121,7 +121,7 @@ Value
diff --git a/docs/reference/te.html b/docs/reference/te.html
index 010361b1..4a65711d 100644
--- a/docs/reference/te.html
+++ b/docs/reference/te.html
@@ -1,5 +1,5 @@
-Return the echo time of an MRS dataset. — te • Spectroscopy Analysis Tools (spant) Return the echo time of an MRS dataset. — te • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/tr.html b/docs/reference/tr.html
index 0c0bd63b..2e749e02 100644
--- a/docs/reference/tr.html
+++ b/docs/reference/tr.html
@@ -1,5 +1,5 @@
-Return the repetition time of an MRS dataset. — tr • Spectroscopy Analysis Tools (spant) Return the repetition time of an MRS dataset. — tr • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/varpro_3_para_opts.html b/docs/reference/varpro_3_para_opts.html
index c2270a16..52d7cd84 100644
--- a/docs/reference/varpro_3_para_opts.html
+++ b/docs/reference/varpro_3_para_opts.html
@@ -1,5 +1,5 @@
-Return a list of options for VARPRO based fitting with 3 free parameters. — varpro_3_para_opts • Spectroscopy Analysis Tools (spant) Return a list of options for VARPRO based fitting with 3 free parameters. — varpro_3_para_opts • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -141,7 +141,7 @@ Value
diff --git a/docs/reference/varpro_basic_opts.html b/docs/reference/varpro_basic_opts.html
index 32c86d22..c5104891 100644
--- a/docs/reference/varpro_basic_opts.html
+++ b/docs/reference/varpro_basic_opts.html
@@ -1,5 +1,5 @@
-Return a list of options for a basic VARPRO analysis. — varpro_basic_opts • Spectroscopy Analysis Tools (spant) Return a list of options for a basic VARPRO analysis. — varpro_basic_opts • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -118,7 +118,7 @@ Value
diff --git a/docs/reference/varpro_opts.html b/docs/reference/varpro_opts.html
index 2aabf11d..6332f730 100644
--- a/docs/reference/varpro_opts.html
+++ b/docs/reference/varpro_opts.html
@@ -1,5 +1,5 @@
-Return a list of options for VARPRO based fitting. — varpro_opts • Spectroscopy Analysis Tools (spant) Return a list of options for VARPRO based fitting. — varpro_opts • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -177,7 +177,7 @@ Examples
diff --git a/docs/reference/vec2mrs_data.html b/docs/reference/vec2mrs_data.html
index 0cccd73b..f0d58bf0 100644
--- a/docs/reference/vec2mrs_data.html
+++ b/docs/reference/vec2mrs_data.html
@@ -1,5 +1,5 @@
-Convert a vector into a mrs_data object. — vec2mrs_data • Spectroscopy Analysis Tools (spant) Convert a vector into a mrs_data object. — vec2mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -80,10 +80,11 @@ Convert a vector into a mrs_data object.
vec2mrs_data(
vec,
- fs = def_fs(),
- ft = def_ft(),
- ref = def_ref(),
- nuc = def_nuc(),
+ mrs_data = NULL,
+ fs = NULL,
+ ft = NULL,
+ ref = NULL,
+ nuc = NULL,
dyns = 1,
fd = FALSE
)
@@ -95,6 +96,10 @@ Arguments
the data vector.
mrs_data
+example data to copy acquisition parameters from.
fs
sampling frequency in Hz.
Arguments
fd
-flag to indicate if the matrix is in the frequency domain (logical).
flag to indicate if the vector is in the frequency domain (logical).
Value
diff --git a/docs/reference/write_basis.html b/docs/reference/write_basis.html
index b6e27cbd..94c5e021 100644
--- a/docs/reference/write_basis.html
+++ b/docs/reference/write_basis.html
@@ -1,5 +1,5 @@
-Write a basis object to an LCModel .basis formatted file. — write_basis • Spectroscopy Analysis Tools (spant) Write a basis object to an LCModel .basis formatted file. — write_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -108,7 +108,7 @@ Arguments
diff --git a/docs/reference/write_basis_tqn.html b/docs/reference/write_basis_tqn.html
index 6aa51c1d..116c73ec 100644
--- a/docs/reference/write_basis_tqn.html
+++ b/docs/reference/write_basis_tqn.html
@@ -1,5 +1,5 @@
-Generate a basis file using TARQUIN. — write_basis_tqn • Spectroscopy Analysis Tools (spant) Generate a basis file using TARQUIN. — write_basis_tqn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Examples
diff --git a/docs/reference/write_mrs.html b/docs/reference/write_mrs.html
index fff25f15..124b9dc4 100644
--- a/docs/reference/write_mrs.html
+++ b/docs/reference/write_mrs.html
@@ -1,5 +1,5 @@
-Write MRS data object to file. — write_mrs • Spectroscopy Analysis Tools (spant) Write MRS data object to file. — write_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Arguments
diff --git a/docs/reference/write_mrs_nifti.html b/docs/reference/write_mrs_nifti.html
index f4bf1921..bd3ed4b7 100644
--- a/docs/reference/write_mrs_nifti.html
+++ b/docs/reference/write_mrs_nifti.html
@@ -1,5 +1,5 @@
-Write MRS data object to file in NIFTI format. — write_mrs_nifti • Spectroscopy Analysis Tools (spant) Write MRS data object to file in NIFTI format. — write_mrs_nifti • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/write_pulse_ascii.html b/docs/reference/write_pulse_ascii.html
index 067ae086..221f8ebb 100644
--- a/docs/reference/write_pulse_ascii.html
+++ b/docs/reference/write_pulse_ascii.html
@@ -1,5 +1,5 @@
-Write an ASCII formatted pulse file. — write_pulse_ascii • Spectroscopy Analysis Tools (spant) Write an ASCII formatted pulse file. — write_pulse_ascii • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/zero_fade_spec.html b/docs/reference/zero_fade_spec.html
index c703745c..c8b572c3 100644
--- a/docs/reference/zero_fade_spec.html
+++ b/docs/reference/zero_fade_spec.html
@@ -1,7 +1,5 @@
-Fade a spectrum to zero by frequency domain multiplication with a tanh
-function. Note this operation distorts data points at the end of the FID. — zero_fade_spec • Spectroscopy Analysis Tools (spant) Fade a spectrum to zero by frequency domain multiplication with a tanh function. Note this operation distorts data points at the end of the FID. — zero_fade_spec • Spectroscopy Analysis Tools (spant) Zero all coherences including and above a given order. — zero_higher_orders • Spectroscopy Analysis Tools (spant) Zero all coherences including and above a given order. — zero_higher_orders • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Value
diff --git a/docs/reference/zero_td_pts_end.html b/docs/reference/zero_td_pts_end.html
index 8c1123c8..71d24ebb 100644
--- a/docs/reference/zero_td_pts_end.html
+++ b/docs/reference/zero_td_pts_end.html
@@ -1,5 +1,5 @@
-Set mrs_data object data points at the end of the FID to zero. — zero_td_pts_end • Spectroscopy Analysis Tools (spant) Set mrs_data object data points at the end of the FID to zero. — zero_td_pts_end • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/zf.html b/docs/reference/zf.html
index 85e2013c..baf50256 100644
--- a/docs/reference/zf.html
+++ b/docs/reference/zf.html
@@ -1,5 +1,5 @@
-Zero-fill MRS data in the time domain. — zf • Spectroscopy Analysis Tools (spant) Zero-fill MRS data in the time domain. — zf • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -125,7 +125,7 @@ Value
diff --git a/docs/reference/zf_xy.html b/docs/reference/zf_xy.html
index ebca3999..c4104a74 100644
--- a/docs/reference/zf_xy.html
+++ b/docs/reference/zf_xy.html
@@ -1,5 +1,5 @@
-Zero-fill MRSI data in the k-space x-y direction. — zf_xy • Spectroscopy Analysis Tools (spant) Zero-fill MRSI data in the k-space x-y direction. — zf_xy • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -113,7 +113,7 @@ Value
diff --git a/docs/sitemap.xml b/docs/sitemap.xml
index e2139f71..4c39f515 100644
--- a/docs/sitemap.xml
+++ b/docs/sitemap.xml
@@ -216,6 +216,12 @@
https://martin3141.github.io/spant/reference/comb_coils_fp_pc.html
+
+ https://martin3141.github.io/spant/reference/comb_coils_mrsi_gls.html
+
+
+ https://martin3141.github.io/spant/reference/comb_coils_svs_gls.html
+
https://martin3141.github.io/spant/reference/comb_csv_results.html
@@ -411,6 +417,9 @@
https://martin3141.github.io/spant/reference/gen_conv_reg.html
+
+ https://martin3141.github.io/spant/reference/gen_group_reg.html
+
https://martin3141.github.io/spant/reference/gen_impulse_reg.html
@@ -555,6 +564,15 @@
https://martin3141.github.io/spant/reference/glm_spec.html
+
+ https://martin3141.github.io/spant/reference/glm_spec_fmrs_fl.html
+
+
+ https://martin3141.github.io/spant/reference/glm_spec_fmrs_group.html
+
+
+ https://martin3141.github.io/spant/reference/glm_spec_group_linhyp.html
+
https://martin3141.github.io/spant/reference/grid_shift_xy.html
@@ -690,9 +708,15 @@
https://martin3141.github.io/spant/reference/mrs_data2basis.html
+
+ https://martin3141.github.io/spant/reference/mrs_data2bids.html
+
https://martin3141.github.io/spant/reference/mrs_data2mat.html
+
+ https://martin3141.github.io/spant/reference/mrs_data2spec_mat.html
+
https://martin3141.github.io/spant/reference/mrs_data2vec.html
@@ -741,6 +765,9 @@
https://martin3141.github.io/spant/reference/phase.html
+
+ https://martin3141.github.io/spant/reference/phase_ref_1h_brain.html
+
https://martin3141.github.io/spant/reference/plot.fit_result.html
@@ -780,6 +807,12 @@
https://martin3141.github.io/spant/reference/precomp.html
+
+ https://martin3141.github.io/spant/reference/preproc_svs.html
+
+
+ https://martin3141.github.io/spant/reference/preproc_svs_dataset.html
+
https://martin3141.github.io/spant/reference/print.fit_result.html
@@ -1050,6 +1083,9 @@
https://martin3141.github.io/spant/reference/spant_mpress_drift.html
+
+ https://martin3141.github.io/spant/reference/spant_sim_fmrs_dataset.html
+
https://martin3141.github.io/spant/reference/spant_simulation_benchmark.html
@@ -1107,6 +1143,9 @@
https://martin3141.github.io/spant/reference/svs_1h_brain_batch_analysis.html
+
+ https://martin3141.github.io/spant/reference/t_test_spec.html
+
https://martin3141.github.io/spant/reference/td2fd.html
Return a character vector of molecules included in the Gold Star Phantoms -SPECTRE phantom.
Return a character vector of molecules included in the Gold Star Phantoms SPECTRE phantom.
All functions
- Return a character array of names that may be used with the
-get_mol_paras function.
Return a character array of names that may be used with the get_mol_paras function.
@@ -700,8 +682,7 @@ All functions
- Return an array of amplitudes derived from fitting the initial points in the
-time domain and extrapolating back to t=0.
Return an array of amplitudes derived from fitting the initial points in the time domain and extrapolating back to t=0.
@@ -709,8 +690,7 @@ All functions
- Generate a mol_parameters object for a simple spin system with one
-resonance.
Generate a mol_parameters object for a simple spin system with one resonance.
@@ -731,6 +711,18 @@ All functions glm_spec()
Perform a GLM analysis of dynamic MRS data in the spectral domain.
+
+
+ Perform first-level spectral GLM analysis of an fMRS dataset.
+
+
+ Perform group-level spectral GLM analysis of an fMRS dataset.
+
+
+ Test a group-level spectral GLM linear hypothesis.
@@ -766,8 +758,7 @@ All functions
- Perform an ifft and ifftshift on a matrix with each column replaced by its
-shifted ifft.
Perform an ifft and ifftshift on a matrix with each column replaced by its shifted ifft.
@@ -799,8 +790,7 @@ All functions
- Check if the chemical shift dimension of an MRS data object is in the
-frequency domain.
Check if the chemical shift dimension of an MRS data object is in the frequency domain.
@@ -820,18 +810,15 @@ All functions
- Covert a linewidth in Hz to an equivalent alpha value in the time-domain ie:
-x * exp(-t * alpha).
Covert a linewidth in Hz to an equivalent alpha value in the time-domain ie: x * exp(-t * alpha).
- Covert a linewidth in Hz to an equivalent beta value in the time-domain ie:
-x * exp(-t * t * beta).
Covert a linewidth in Hz to an equivalent beta value in the time-domain ie: x * exp(-t * t * beta).
- Make a basis-set object from a directory containing LCModel formatted RAW
-files.
Make a basis-set object from a directory containing LCModel formatted RAW files.
@@ -851,8 +838,7 @@ All functions
- Mask the voxels outside an elliptical region spanning the MRSI dataset in the
-x-y plane.
Mask the voxels outside an elliptical region spanning the MRSI dataset in the x-y plane.
@@ -860,13 +846,11 @@ All functions
- Convert a matrix (with spectral points in the column dimension and dynamics
-in the row dimensions) into a mrs_data object.
Convert a matrix (with spectral points in the column dimension and dynamics in the row dimensions) into a mrs_data object.
- Matrix exponential function taken from complexplus package to reduce the
-number of spant dependencies.
Matrix exponential function taken from complexplus package to reduce the number of spant dependencies.
@@ -914,31 +898,31 @@ All functions
- Convert an mrs_data object to basis object - where basis signals are spread
-across the dynamic dimension in the MRS data.
Convert an mrs_data object to basis object - where basis signals are spread across the dynamic dimension in the MRS data.
+
+
+ Create a BIDS file structure from a vector of MRS data paths or list of mrs_data objects.
- Convert mrs_data object to a matrix, with spectral points in the column
-dimension and dynamics in the row dimension.
Convert mrs_data object to a matrix, with spectral points in the column dimension and dynamics in the row dimension.
-
+
- Convert mrs_data object to a vector.
Convert mrs_data object to a matrix, with spectral points in the column dimension and dynamics in the row dimension.
-
+
- Create a BIDS directory and file structure from a list of mrs_data objects.
Convert mrs_data object to a vector.
- Perform a fftshift on a matrix, with each column replaced by its shifted
-result.
Perform a fftshift on a matrix, with each column replaced by its shifted result.
- Perform an ifftshift on a matrix, with each column replaced by its shifted
-result.
Perform an ifftshift on a matrix, with each column replaced by its shifted result.
@@ -946,9 +930,7 @@ All functions
- Flip the x data dimension order of a nifti image. This corresponds to
-flipping MRI data in the left-right direction, assuming the data in save in
-neurological format (can check with fslorient program).
Flip the x data dimension order of a nifti image. This corresponds to flipping MRI data in the left-right direction, assuming the data in save in neurological format (can check with fslorient program).
@@ -964,8 +946,7 @@ All functions
- Search for the highest peak in a spectral region and return the frequency,
-height and FWHM.
Search for the highest peak in a spectral region and return the frequency, height and FWHM.
@@ -974,6 +955,10 @@ All functions phase()
Apply phasing parameters to MRS data.
+
+
+ Corrected zero order phase and chemical shift offset in 1H MRS data from the brain.
@@ -1005,8 +990,7 @@ All functions
- Plot an interactive slice map from a data array where voxels can be selected
-to display a corresponding spectrum.
Plot an interactive slice map from a data array where voxels can be selected to display a corresponding spectrum.
@@ -1026,8 +1010,15 @@ All functions
- Save function results to file and load on subsequent calls to avoid repeat
-computation.
Save function results to file and load on subsequent calls to avoid repeat computation.
+
+
+ Preprocess and perform quality assessment of a single SVS data set.
+
+
+ Preprocess and perform quality assessment of one or more SVS data sets.
@@ -1055,15 +1046,11 @@ All functions
- Read a directory containing Siemens MRS IMA files and combine along the coil
-dimension. Note that the coil ID is inferred from the sorted file name and
-should be checked when consistency is required between two directories.
Read a directory containing Siemens MRS IMA files and combine along the coil dimension. Note that the coil ID is inferred from the sorted file name and should be checked when consistency is required between two directories.
- Read a directory containing Siemens MRS IMA files and combine along the
-dynamic dimension. Note that the coil ID is inferred from the sorted file
-name and should be checked when consistency is required.
Read a directory containing Siemens MRS IMA files and combine along the dynamic dimension. Note that the coil ID is inferred from the sorted file name and should be checked when consistency is required.
@@ -1103,13 +1090,11 @@ All functions
- Reconstruct complex time-domain data from the real part of frequency-domain
-data.
Reconstruct complex time-domain data from the real part of frequency-domain data.
- Reconstruct complex time-domain data from the real part of frequency-domain
-data.
Reconstruct complex time-domain data from the real part of frequency-domain data.
@@ -1141,8 +1126,7 @@ All functions
- Resample a VOI to match a target image space using nearest-neighbour
-interpolation.
Resample a VOI to match a target image space using nearest-neighbour interpolation.
@@ -1158,23 +1142,19 @@ All functions
- Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water).
Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / kg of tissue water).
- Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water).
Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / kg of tissue water).
- Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / Litre of tissue).
Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / Litre of tissue).
- Convert default LCM/TARQUIN concentration scaling to molal units with partial
-volume correction.
Convert default LCM/TARQUIN concentration scaling to molal units with partial volume correction.
@@ -1222,8 +1202,7 @@ All functions
- MEGA-PRESS sequence with ideal localisation pulses and Gaussian shaped
-editing pulse.
MEGA-PRESS sequence with ideal localisation pulses and Gaussian shaped editing pulse.
@@ -1251,13 +1230,11 @@ All functions
- STEAM sequence with ideal pulses and coherence order filtering to simulate
-gradient crushers.
STEAM sequence with ideal pulses and coherence order filtering to simulate gradient crushers.
- STEAM sequence with ideal pulses using the z-rotation gradient simulation
-method described by Young et al JMR 140, 146-152 (1999).
STEAM sequence with ideal pulses using the z-rotation gradient simulation method described by Young et al JMR 140, 146-152 (1999).
@@ -1293,8 +1270,7 @@ All functions
- Set the number of time-domain data points, truncating or zero-filling as
-appropriate.
Set the number of time-domain data points, truncating or zero-filling as appropriate.
@@ -1318,18 +1294,15 @@ All functions
- Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS
-sequence. Note, ideal pulses are assumed.
Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS sequence. Note, ideal pulses are assumed.
- Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS
-sequence. Note, ideal pulses are assumed.
Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS sequence. Note, ideal pulses are assumed.
- Simulate a macromolecular and lipid basis-set suitable for 1H brain MRS
-analysis.
Simulate a macromolecular and lipid basis-set suitable for 1H brain MRS analysis.
@@ -1353,8 +1326,7 @@ All functions
- Simulate an ideal pulse excitation profile by smoothing a top-hat function
-with a Gaussian.
Simulate an ideal pulse excitation profile by smoothing a top-hat function with a Gaussian.
@@ -1374,17 +1346,19 @@ All functions
- Simulate and fit some spectra with ABfit for benchmarking purposes. Basic
-timing and performance metrics will be printed.
Simulate and fit some spectra with ABfit for benchmarking purposes. Basic timing and performance metrics will be printed.
Example MEGA-PRESS data with significant B0 drift.
+
+
+ Simulate an example fMRS dataset for a block design fMRS experiment and export a BIDS structure.
- Simulate a typical metabolite basis set for benchmarking. Timing metrics will
-be printed on completion.
Simulate a typical metabolite basis set for benchmarking. Timing metrics will be printed on completion.
@@ -1400,8 +1374,7 @@ All functions
- Convert SPM style segmentation files to a single categorical image where
-the numerical values map as: 0) Other, 1) CSF, 2) GM and 3) WM.
Convert SPM style segmentation files to a single categorical image where the numerical values map as: 0) Other, 1) CSF, 2) GM and 3) WM.
@@ -1413,8 +1386,7 @@ All functions
- Plot the fitting results of an object of class fit_result with
-individual basis set components shown.
Plot the fitting results of an object of class fit_result with individual basis set components shown.
@@ -1459,6 +1431,10 @@ All functions svs_1h_brain_batch_analysis()
Batch interface to the standard SVS 1H brain analysis pipeline.
+
+
+ Perform a t-test on spectral data points.
@@ -1518,8 +1494,7 @@ All functions
- Fade a spectrum to zero by frequency domain multiplication with a tanh
-function. Note this operation distorts data points at the end of the FID.
Fade a spectrum to zero by frequency domain multiplication with a tanh function. Note this operation distorts data points at the end of the FID.
@@ -1549,7 +1524,7 @@ All functions
diff --git a/docs/reference/int_spec.html b/docs/reference/int_spec.html
index c7060fe7..783325a8 100644
--- a/docs/reference/int_spec.html
+++ b/docs/reference/int_spec.html
@@ -1,5 +1,5 @@
-Integrate a spectral region. — int_spec • Spectroscopy Analysis Tools (spant) Integrate a spectral region. — int_spec • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -118,7 +118,7 @@ Value
diff --git a/docs/reference/interleave_dyns.html b/docs/reference/interleave_dyns.html
index effe5543..441eff27 100644
--- a/docs/reference/interleave_dyns.html
+++ b/docs/reference/interleave_dyns.html
@@ -1,5 +1,5 @@
-Interleave the first and second half of a dynamic series. — interleave_dyns • Spectroscopy Analysis Tools (spant) Interleave the first and second half of a dynamic series. — interleave_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/inv_even_dyns.html b/docs/reference/inv_even_dyns.html
index 9f9d4fff..dcb781dc 100644
--- a/docs/reference/inv_even_dyns.html
+++ b/docs/reference/inv_even_dyns.html
@@ -1,5 +1,5 @@
-Invert even numbered dynamic scans starting from 1 (2,4,6...). — inv_even_dyns • Spectroscopy Analysis Tools (spant) Invert even numbered dynamic scans starting from 1 (2,4,6...). — inv_even_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/inv_odd_dyns.html b/docs/reference/inv_odd_dyns.html
index 26212e2b..78d64660 100644
--- a/docs/reference/inv_odd_dyns.html
+++ b/docs/reference/inv_odd_dyns.html
@@ -1,5 +1,5 @@
-Invert odd numbered dynamic scans starting from 1 (1,3,5...). — inv_odd_dyns • Spectroscopy Analysis Tools (spant) Invert odd numbered dynamic scans starting from 1 (1,3,5...). — inv_odd_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/is.def.html b/docs/reference/is.def.html
index f196ffd0..a67b9eba 100644
--- a/docs/reference/is.def.html
+++ b/docs/reference/is.def.html
@@ -1,5 +1,5 @@
-Check if an object is defined, which is the same as being not NULL. — is.def • Spectroscopy Analysis Tools (spant) Check if an object is defined, which is the same as being not NULL. — is.def • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/is_fd.html b/docs/reference/is_fd.html
index 3b0ca165..18a193aa 100644
--- a/docs/reference/is_fd.html
+++ b/docs/reference/is_fd.html
@@ -1,7 +1,5 @@
-Check if the chemical shift dimension of an MRS data object is in the
-frequency domain. — is_fd • Spectroscopy Analysis Tools (spant) Check if the chemical shift dimension of an MRS data object is in the frequency domain. — is_fd • Spectroscopy Analysis Tools (spant) Transform 2D MRSI data from k-space to image space in the x-y direction. — kspace2img_xy • Spectroscopy Analysis Tools (spant) Transform 2D MRSI data from k-space to image space in the x-y direction. — kspace2img_xy • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/l2_reg.html b/docs/reference/l2_reg.html
index 3d781d80..21aa9849 100644
--- a/docs/reference/l2_reg.html
+++ b/docs/reference/l2_reg.html
@@ -1,5 +1,5 @@
-Perform l2 regularisation artefact suppression. — l2_reg • Spectroscopy Analysis Tools (spant) Perform l2 regularisation artefact suppression. — l2_reg • Spectroscopy Analysis Tools (spant) Apply line-broadening (apodisation) to MRS data or basis object. — lb • Spectroscopy Analysis Tools (spant) Apply line-broadening (apodisation) to MRS data or basis object. — lb • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -123,7 +123,7 @@ Value
diff --git a/docs/reference/lofdc.html b/docs/reference/lofdc.html
index 5419b1ec..31347a25 100644
--- a/docs/reference/lofdc.html
+++ b/docs/reference/lofdc.html
@@ -1,5 +1,5 @@
-Correct linear frequency drift. — lofdc • Spectroscopy Analysis Tools (spant) Correct linear frequency drift. — lofdc • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -138,7 +138,7 @@ Value
diff --git a/docs/reference/lw2alpha.html b/docs/reference/lw2alpha.html
index b83db682..25da229b 100644
--- a/docs/reference/lw2alpha.html
+++ b/docs/reference/lw2alpha.html
@@ -1,7 +1,5 @@
-Covert a linewidth in Hz to an equivalent alpha value in the time-domain ie:
-x * exp(-t * alpha). — lw2alpha • Spectroscopy Analysis Tools (spant) Covert a linewidth in Hz to an equivalent alpha value in the time-domain ie: x * exp(-t * alpha). — lw2alpha • Spectroscopy Analysis Tools (spant) Covert a linewidth in Hz to an equivalent beta value in the time-domain ie:
-x * exp(-t * t * beta). — lw2beta • Spectroscopy Analysis Tools (spant) Covert a linewidth in Hz to an equivalent beta value in the time-domain ie: x * exp(-t * t * beta). — lw2beta • Spectroscopy Analysis Tools (spant) Make a basis-set object from a directory containing LCModel formatted RAW
-files. — make_basis_from_raw • Spectroscopy Analysis Tools (spant) Make a basis-set object from a directory containing LCModel formatted RAW files. — make_basis_from_raw • Spectroscopy Analysis Tools (spant) Mask an MRS dataset in the dynamic dimension. — mask_dyns • Spectroscopy Analysis Tools (spant) Mask an MRS dataset in the dynamic dimension. — mask_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/mask_fit_res.html b/docs/reference/mask_fit_res.html
index 97baaa3f..ebd91a99 100644
--- a/docs/reference/mask_fit_res.html
+++ b/docs/reference/mask_fit_res.html
@@ -1,5 +1,5 @@
-Mask fit result spectra depending on a vector of bool values. — mask_fit_res • Spectroscopy Analysis Tools (spant) Mask fit result spectra depending on a vector of bool values. — mask_fit_res • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -116,7 +116,7 @@ Value
diff --git a/docs/reference/mask_xy.html b/docs/reference/mask_xy.html
index 11bb577c..b0d38619 100644
--- a/docs/reference/mask_xy.html
+++ b/docs/reference/mask_xy.html
@@ -1,5 +1,5 @@
-Mask an MRSI dataset in the x-y direction — mask_xy • Spectroscopy Analysis Tools (spant) Mask an MRSI dataset in the x-y direction — mask_xy • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/mask_xy_corners.html b/docs/reference/mask_xy_corners.html
index 09b16cd2..2d13839d 100644
--- a/docs/reference/mask_xy_corners.html
+++ b/docs/reference/mask_xy_corners.html
@@ -1,5 +1,5 @@
-Mask the four corners of an MRSI dataset in the x-y plane. — mask_xy_corners • Spectroscopy Analysis Tools (spant) Mask the four corners of an MRSI dataset in the x-y plane. — mask_xy_corners • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/mask_xy_ellipse.html b/docs/reference/mask_xy_ellipse.html
index 1d8b02e4..e2e749ef 100644
--- a/docs/reference/mask_xy_ellipse.html
+++ b/docs/reference/mask_xy_ellipse.html
@@ -1,7 +1,5 @@
-Mask the voxels outside an elliptical region spanning the MRSI dataset in the
-x-y plane. — mask_xy_ellipse • Spectroscopy Analysis Tools (spant) Mask the voxels outside an elliptical region spanning the MRSI dataset in the x-y plane. — mask_xy_ellipse • Spectroscopy Analysis Tools (spant) Mask a 2D MRSI dataset in the x-y dimension. — mask_xy_mat • Spectroscopy Analysis Tools (spant) Mask a 2D MRSI dataset in the x-y dimension. — mask_xy_mat • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Value
diff --git a/docs/reference/mat2mrs_data.html b/docs/reference/mat2mrs_data.html
index 2e2895f3..ae55665f 100644
--- a/docs/reference/mat2mrs_data.html
+++ b/docs/reference/mat2mrs_data.html
@@ -1,7 +1,5 @@
-Convert a matrix (with spectral points in the column dimension and dynamics
-in the row dimensions) into a mrs_data object. — mat2mrs_data • Spectroscopy Analysis Tools (spant) Convert a matrix (with spectral points in the column dimension and dynamics in the row dimensions) into a mrs_data object. — mat2mrs_data • Spectroscopy Analysis Tools (spant) Matrix exponential function taken from complexplus package to reduce the
-number of spant dependencies. — matexp • Spectroscopy Analysis Tools (spant) Matrix exponential function taken from complexplus package to reduce the number of spant dependencies. — matexp • Spectroscopy Analysis Tools (spant) Apply the max operator to an MRS dataset. — max_mrs • Spectroscopy Analysis Tools (spant) Apply the max operator to an MRS dataset. — max_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/max_mrs_interp.html b/docs/reference/max_mrs_interp.html
index e4474764..52e63f3e 100644
--- a/docs/reference/max_mrs_interp.html
+++ b/docs/reference/max_mrs_interp.html
@@ -1,5 +1,5 @@
-Apply the max operator to an interpolated MRS dataset. — max_mrs_interp • Spectroscopy Analysis Tools (spant) Apply the max operator to an interpolated MRS dataset. — max_mrs_interp • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/mean.list.html b/docs/reference/mean.list.html
index b8eb3463..048306fd 100644
--- a/docs/reference/mean.list.html
+++ b/docs/reference/mean.list.html
@@ -1,5 +1,5 @@
-Calculate the mean spectrum from an mrs_data object. — mean.list • Spectroscopy Analysis Tools (spant) Calculate the mean spectrum from an mrs_data object. — mean.list • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/mean.mrs_data.html b/docs/reference/mean.mrs_data.html
index 5531a28d..79515014 100644
--- a/docs/reference/mean.mrs_data.html
+++ b/docs/reference/mean.mrs_data.html
@@ -1,5 +1,5 @@
-Calculate the mean spectrum from an mrs_data object. — mean.mrs_data • Spectroscopy Analysis Tools (spant) Calculate the mean spectrum from an mrs_data object. — mean.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/mean_dyn_blocks.html b/docs/reference/mean_dyn_blocks.html
index 10467098..4c042448 100644
--- a/docs/reference/mean_dyn_blocks.html
+++ b/docs/reference/mean_dyn_blocks.html
@@ -1,5 +1,5 @@
-Calculate the mean of adjacent dynamic scans. — mean_dyn_blocks • Spectroscopy Analysis Tools (spant) Calculate the mean of adjacent dynamic scans. — mean_dyn_blocks • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/mean_dyn_pairs.html b/docs/reference/mean_dyn_pairs.html
index 63e909ea..1a241126 100644
--- a/docs/reference/mean_dyn_pairs.html
+++ b/docs/reference/mean_dyn_pairs.html
@@ -1,5 +1,5 @@
-Calculate the pairwise means across a dynamic data set. — mean_dyn_pairs • Spectroscopy Analysis Tools (spant) Calculate the pairwise means across a dynamic data set. — mean_dyn_pairs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/mean_dyns.html b/docs/reference/mean_dyns.html
index 73fdbfa7..0daa27df 100644
--- a/docs/reference/mean_dyns.html
+++ b/docs/reference/mean_dyns.html
@@ -1,5 +1,5 @@
-Calculate the mean dynamic data. — mean_dyns • Spectroscopy Analysis Tools (spant) Calculate the mean dynamic data. — mean_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/mean_mrs_list.html b/docs/reference/mean_mrs_list.html
index 808b6c50..10d842c0 100644
--- a/docs/reference/mean_mrs_list.html
+++ b/docs/reference/mean_mrs_list.html
@@ -1,5 +1,5 @@
-Return the mean of a list of mrs_data objects. — mean_mrs_list • Spectroscopy Analysis Tools (spant) Return the mean of a list of mrs_data objects. — mean_mrs_list • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/mean_vec_blocks.html b/docs/reference/mean_vec_blocks.html
index 8fc92eaa..dd78b122 100644
--- a/docs/reference/mean_vec_blocks.html
+++ b/docs/reference/mean_vec_blocks.html
@@ -1,5 +1,5 @@
-Calculate the mean of adjacent blocks in a vector. — mean_vec_blocks • Spectroscopy Analysis Tools (spant) Calculate the mean of adjacent blocks in a vector. — mean_vec_blocks • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/median_dyns.html b/docs/reference/median_dyns.html
index 1039d4b5..9a085b10 100644
--- a/docs/reference/median_dyns.html
+++ b/docs/reference/median_dyns.html
@@ -1,5 +1,5 @@
-Calculate the median dynamic data. — median_dyns • Spectroscopy Analysis Tools (spant) Calculate the median dynamic data. — median_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/mod_td.html b/docs/reference/mod_td.html
index 76ad0a40..141ef09e 100644
--- a/docs/reference/mod_td.html
+++ b/docs/reference/mod_td.html
@@ -1,5 +1,5 @@
-Apply the Modulus operator to the time-domain MRS signal. — mod_td • Spectroscopy Analysis Tools (spant) Apply the Modulus operator to the time-domain MRS signal. — mod_td • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/mrs_data2basis.html b/docs/reference/mrs_data2basis.html
index 62f7d749..11797b91 100644
--- a/docs/reference/mrs_data2basis.html
+++ b/docs/reference/mrs_data2basis.html
@@ -1,7 +1,5 @@
-Convert an mrs_data object to basis object - where basis signals are spread
-across the dynamic dimension in the MRS data. — mrs_data2basis • Spectroscopy Analysis Tools (spant) Convert an mrs_data object to basis object - where basis signals are spread across the dynamic dimension in the MRS data. — mrs_data2basis • Spectroscopy Analysis Tools (spant) Create a BIDS file structure from a vector of MRS data paths or list of mrs_data objects. — mrs_data2bids • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Create a BIDS file structure from a vector of MRS data paths or list of mrs_data objects.
+ Source: R/fmrs.R
+ mrs_data2bids.Rd
+
+
+
+ Create a BIDS file structure from a vector of MRS data paths or list of
+mrs_data objects.
+
+
+
+ mrs_data2bids(
+ mrs_data,
+ output_dir,
+ suffix = NULL,
+ sub = NULL,
+ ses = NULL,
+ task = NULL,
+ acq = NULL,
+ nuc = NULL,
+ voi = NULL,
+ rec = NULL,
+ run = NULL,
+ echo = NULL,
+ inv = NULL,
+ skip_existing = TRUE
+)
+
+
+
+ Arguments
+ - mrs_data
+vector of MRS data paths or list of mrs_data objects.
- output_dir
+the base directory to create the BIDS structure.
- suffix
+optional vector of file suffixes. Default behaviour is to
+automatically determine these from the input data, however it is recommended
+that they are specified to allow more efficient skipping of existing data.
- sub
+optional vector of subject labels. If not specified, these will be
+automatically generated as a series of increasing zero-padded integer values
+corresponding to the mrs_data input indices.
- ses
+optional vector of session labels.
- task
+optional vector of task labels.
- acq
+optional vector of acquisition labels.
- nuc
+optional vector of nucleus labels.
- voi
+optional vector of volume of interest labels.
- rec
+optional vector of reconstruction labels.
- run
+optional vector of run indices.
- echo
+optional vector of echo time indices.
- inv
+optional vector of inversion indices.
- skip_existing
+skip any data files that have already been converted.
+Defaults to TRUE, set to FALSE to force an overwrite of any existing data
+files.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/mrs_data2mat.html b/docs/reference/mrs_data2mat.html
index cf5ff28c..9e47688a 100644
--- a/docs/reference/mrs_data2mat.html
+++ b/docs/reference/mrs_data2mat.html
@@ -1,7 +1,5 @@
-Convert mrs_data object to a matrix, with spectral points in the column
-dimension and dynamics in the row dimension. — mrs_data2mat • Spectroscopy Analysis Tools (spant) Convert mrs_data object to a matrix, with spectral points in the column dimension and dynamics in the row dimension. — mrs_data2mat • Spectroscopy Analysis Tools (spant) Convert mrs_data object to a matrix, with spectral points in the column dimension and dynamics in the row dimension. — mrs_data2spec_mat • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Convert mrs_data object to a matrix, with spectral points in the column dimension and dynamics in the row dimension.
+ Source: R/mrs_data_proc.R
+ mrs_data2spec_mat.Rd
+
+
+
+ Convert mrs_data object to a matrix, with spectral points in the column
+dimension and dynamics in the row dimension.
+
+
+
+ mrs_data2spec_mat(mrs_data, collapse = TRUE)
+
+
+
+ Arguments
+ - mrs_data
+MRS data object or list of MRS data objects.
- collapse
+collapse all other dimensions along the dynamic dimension, eg
+a 16x16 MRSI grid would be first collapsed across 256 dynamic scans.
+
+ Value
+
+
+MRS data matrix.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/mrs_data2vec.html b/docs/reference/mrs_data2vec.html
index fb172d68..a1fd654d 100644
--- a/docs/reference/mrs_data2vec.html
+++ b/docs/reference/mrs_data2vec.html
@@ -1,5 +1,5 @@
-Convert mrs_data object to a vector. — mrs_data2vec • Spectroscopy Analysis Tools (spant) Convert mrs_data object to a vector. — mrs_data2vec • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -126,7 +126,7 @@ Value
diff --git a/docs/reference/mvfftshift.html b/docs/reference/mvfftshift.html
index 92b0841b..976b3410 100644
--- a/docs/reference/mvfftshift.html
+++ b/docs/reference/mvfftshift.html
@@ -1,7 +1,5 @@
-Perform a fftshift on a matrix, with each column replaced by its shifted
-result. — mvfftshift • Spectroscopy Analysis Tools (spant) Perform a fftshift on a matrix, with each column replaced by its shifted result. — mvfftshift • Spectroscopy Analysis Tools (spant) Perform an ifftshift on a matrix, with each column replaced by its shifted
-result. — mvifftshift • Spectroscopy Analysis Tools (spant) Perform an ifftshift on a matrix, with each column replaced by its shifted result. — mvifftshift • Spectroscopy Analysis Tools (spant) Print fit coordinates from a single index. — n2coord • Spectroscopy Analysis Tools (spant) Print fit coordinates from a single index. — n2coord • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/nifti_flip_lr.html b/docs/reference/nifti_flip_lr.html
index 730abe3c..19860b3c 100644
--- a/docs/reference/nifti_flip_lr.html
+++ b/docs/reference/nifti_flip_lr.html
@@ -1,9 +1,5 @@
-Flip the x data dimension order of a nifti image. This corresponds to
-flipping MRI data in the left-right direction, assuming the data in save in
-neurological format (can check with fslorient program). — nifti_flip_lr • Spectroscopy Analysis Tools (spant) Flip the x data dimension order of a nifti image. This corresponds to flipping MRI data in the left-right direction, assuming the data in save in neurological format (can check with fslorient program). — nifti_flip_lr • Spectroscopy Analysis Tools (spant) Export a one-page pdf of a single fit result — one_page_pdf • Spectroscopy Analysis Tools (spant) Export a one-page pdf of a single fit result — one_page_pdf • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -108,7 +108,7 @@ Arguments
diff --git a/docs/reference/ortho3.html b/docs/reference/ortho3.html
index 13ade97d..5d7dd2fd 100644
--- a/docs/reference/ortho3.html
+++ b/docs/reference/ortho3.html
@@ -1,5 +1,5 @@
-Display an orthographic projection plot of a nifti object. — ortho3 • Spectroscopy Analysis Tools (spant) Display an orthographic projection plot of a nifti object. — ortho3 • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -172,7 +172,7 @@ Arguments
diff --git a/docs/reference/ortho3_inter.html b/docs/reference/ortho3_inter.html
index 090cc5e5..15948899 100644
--- a/docs/reference/ortho3_inter.html
+++ b/docs/reference/ortho3_inter.html
@@ -1,5 +1,5 @@
-Display an interactive orthographic projection plot of a nifti object. — ortho3_inter • Spectroscopy Analysis Tools (spant) Display an interactive orthographic projection plot of a nifti object. — ortho3_inter • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -132,7 +132,7 @@ Arguments
diff --git a/docs/reference/peak_info.html b/docs/reference/peak_info.html
index 09058bd8..41c8ffaf 100644
--- a/docs/reference/peak_info.html
+++ b/docs/reference/peak_info.html
@@ -1,7 +1,5 @@
-Search for the highest peak in a spectral region and return the frequency,
-height and FWHM. — peak_info • Spectroscopy Analysis Tools (spant) Search for the highest peak in a spectral region and return the frequency, height and FWHM. — peak_info • Spectroscopy Analysis Tools (spant) Papoulis-Gerchberg (PG) algorithm method for k-space extrapolation. — pg_extrap_xy • Spectroscopy Analysis Tools (spant) Papoulis-Gerchberg (PG) algorithm method for k-space extrapolation. — pg_extrap_xy • Spectroscopy Analysis Tools (spant) Apply phasing parameters to MRS data. — phase • Spectroscopy Analysis Tools (spant) Apply phasing parameters to MRS data. — phase • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/phase_ref_1h_brain.html b/docs/reference/phase_ref_1h_brain.html
new file mode 100644
index 00000000..8707a74a
--- /dev/null
+++ b/docs/reference/phase_ref_1h_brain.html
@@ -0,0 +1,131 @@
+
+Corrected zero order phase and chemical shift offset in 1H MRS data from the brain. — phase_ref_1h_brain • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Corrected zero order phase and chemical shift offset in 1H MRS data from the brain.
+ Source: R/rats.R
+ phase_ref_1h_brain.Rd
+
+
+
+ Corrected zero order phase and chemical shift offset in 1H MRS data from the
+brain.
+
+
+
+ phase_ref_1h_brain(mrs_data, mean_ref = FALSE, ret_corr_only = TRUE)
+
+
+
+ Arguments
+ - mrs_data
+MRS data to be corrected.
- mean_ref
+apply the phase and offset of the mean spectrum to all
+others. Default is FALSE.
- ret_corr_only
+return the corrected data only.
+
+ Value
+
+
+corrected MRS data.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/plot.fit_result.html b/docs/reference/plot.fit_result.html
index e54d3bc1..836a53ee 100644
--- a/docs/reference/plot.fit_result.html
+++ b/docs/reference/plot.fit_result.html
@@ -1,5 +1,5 @@
-Plot the fitting results of an object of class fit_result. — plot.fit_result • Spectroscopy Analysis Tools (spant) Plot the fitting results of an object of class fit_result. — plot.fit_result • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -207,7 +207,7 @@ Arguments
diff --git a/docs/reference/plot.mrs_data.html b/docs/reference/plot.mrs_data.html
index fabcc35b..bb2ec651 100644
--- a/docs/reference/plot.mrs_data.html
+++ b/docs/reference/plot.mrs_data.html
@@ -1,5 +1,5 @@
-Plotting method for objects of class mrs_data. — plot.mrs_data • Spectroscopy Analysis Tools (spant) Plotting method for objects of class mrs_data. — plot.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -287,7 +287,7 @@ Arguments
diff --git a/docs/reference/plot_bc.html b/docs/reference/plot_bc.html
index 4f8309b4..b48142cc 100644
--- a/docs/reference/plot_bc.html
+++ b/docs/reference/plot_bc.html
@@ -1,5 +1,5 @@
-Convenience function to plot a baseline estimate with the original data. — plot_bc • Spectroscopy Analysis Tools (spant) Convenience function to plot a baseline estimate with the original data. — plot_bc • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -108,7 +108,7 @@ Arguments
diff --git a/docs/reference/plot_reg.html b/docs/reference/plot_reg.html
index ae1acbe7..2addb2f6 100644
--- a/docs/reference/plot_reg.html
+++ b/docs/reference/plot_reg.html
@@ -1,5 +1,5 @@
-Plot regressors as an image. — plot_reg • Spectroscopy Analysis Tools (spant) Plot regressors as an image. — plot_reg • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/plot_slice_fit.html b/docs/reference/plot_slice_fit.html
index fbc7b560..57f1af8a 100644
--- a/docs/reference/plot_slice_fit.html
+++ b/docs/reference/plot_slice_fit.html
@@ -1,5 +1,5 @@
-Plot a 2D slice from an MRSI fit result object. — plot_slice_fit • Spectroscopy Analysis Tools (spant) Plot a 2D slice from an MRSI fit result object. — plot_slice_fit • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -129,7 +129,7 @@ Arguments
diff --git a/docs/reference/plot_slice_fit_inter.html b/docs/reference/plot_slice_fit_inter.html
index 4eed104a..da105a7d 100644
--- a/docs/reference/plot_slice_fit_inter.html
+++ b/docs/reference/plot_slice_fit_inter.html
@@ -1,5 +1,5 @@
-Plot a 2D slice from an MRSI fit result object. — plot_slice_fit_inter • Spectroscopy Analysis Tools (spant) Plot a 2D slice from an MRSI fit result object. — plot_slice_fit_inter • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -134,7 +134,7 @@ Arguments
diff --git a/docs/reference/plot_slice_map.html b/docs/reference/plot_slice_map.html
index 553e9ac8..ffb2a134 100644
--- a/docs/reference/plot_slice_map.html
+++ b/docs/reference/plot_slice_map.html
@@ -1,5 +1,5 @@
-Plot a slice from a 7 dimensional array. — plot_slice_map • Spectroscopy Analysis Tools (spant) Plot a slice from a 7 dimensional array. — plot_slice_map • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -153,7 +153,7 @@ Arguments
diff --git a/docs/reference/plot_slice_map_inter.html b/docs/reference/plot_slice_map_inter.html
index 40d33b42..90968f66 100644
--- a/docs/reference/plot_slice_map_inter.html
+++ b/docs/reference/plot_slice_map_inter.html
@@ -1,7 +1,5 @@
-Plot an interactive slice map from a data array where voxels can be selected
-to display a corresponding spectrum. — plot_slice_map_inter • Spectroscopy Analysis Tools (spant) Plot an interactive slice map from a data array where voxels can be selected to display a corresponding spectrum. — plot_slice_map_inter • Spectroscopy Analysis Tools (spant) Plot the spectral standard deviation. — plot_spec_sd • Spectroscopy Analysis Tools (spant) Plot the spectral standard deviation. — plot_spec_sd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Arguments
diff --git a/docs/reference/plot_voi_overlay.html b/docs/reference/plot_voi_overlay.html
index 9a782e88..bbbbf35e 100644
--- a/docs/reference/plot_voi_overlay.html
+++ b/docs/reference/plot_voi_overlay.html
@@ -1,5 +1,5 @@
-Plot a volume as an image overlay. — plot_voi_overlay • Spectroscopy Analysis Tools (spant) Plot a volume as an image overlay. — plot_voi_overlay • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -116,7 +116,7 @@ Arguments
diff --git a/docs/reference/plot_voi_overlay_seg.html b/docs/reference/plot_voi_overlay_seg.html
index 3d4e74ff..0e800ff2 100644
--- a/docs/reference/plot_voi_overlay_seg.html
+++ b/docs/reference/plot_voi_overlay_seg.html
@@ -1,5 +1,5 @@
-Plot a volume as an overlay on a segmented brain volume. — plot_voi_overlay_seg • Spectroscopy Analysis Tools (spant) Plot a volume as an overlay on a segmented brain volume. — plot_voi_overlay_seg • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Arguments
diff --git a/docs/reference/ppm.html b/docs/reference/ppm.html
index c352327a..ee4696e2 100644
--- a/docs/reference/ppm.html
+++ b/docs/reference/ppm.html
@@ -1,5 +1,5 @@
-Return the ppm scale of an MRS dataset or fit result. — ppm • Spectroscopy Analysis Tools (spant) Return the ppm scale of an MRS dataset or fit result. — ppm • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -132,7 +132,7 @@ Value
diff --git a/docs/reference/precomp.html b/docs/reference/precomp.html
index 822d7336..df3d2c6c 100644
--- a/docs/reference/precomp.html
+++ b/docs/reference/precomp.html
@@ -1,7 +1,5 @@
-Save function results to file and load on subsequent calls to avoid repeat
-computation. — precomp • Spectroscopy Analysis Tools (spant) Save function results to file and load on subsequent calls to avoid repeat computation. — precomp • Spectroscopy Analysis Tools (spant) Preprocess and perform quality assessment of a single SVS data set. — preproc_svs • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Preprocess and perform quality assessment of a single SVS data set.
+ Source: R/fmrs.R
+ preproc_svs.Rd
+
+
+
+ Preprocess and perform quality assessment of a single SVS data set.
+
+
+
+ preproc_svs(path, label = NULL, output_dir = NULL, ref_inds = NULL)
+
+
+
+ Arguments
+ - path
+path to the fMRS data file or IMA directory.
- label
+a label to describe the data set.
- output_dir
+output directory.
- ref_inds
+a vector of 1-based indices for any water reference dynamic
+scans.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/preproc_svs_dataset.html b/docs/reference/preproc_svs_dataset.html
new file mode 100644
index 00000000..07c3a29b
--- /dev/null
+++ b/docs/reference/preproc_svs_dataset.html
@@ -0,0 +1,148 @@
+
+Preprocess and perform quality assessment of one or more SVS data sets. — preproc_svs_dataset • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Preprocess and perform quality assessment of one or more SVS data sets.
+ Source: R/fmrs.R
+ preproc_svs_dataset.Rd
+
+
+
+ Preprocess and perform quality assessment of one or more SVS data sets.
+
+
+
+ preproc_svs_dataset(
+ paths,
+ labels = NULL,
+ output_dir = "spant_analysis",
+ exclude_labels = NULL,
+ overwrite = FALSE,
+ ref_inds = NULL,
+ return_results = FALSE
+)
+
+
+
+ Arguments
+ - paths
+paths to the fMRS data file or IMA directory.
- labels
+labels to describe each data set.
- output_dir
+output directory.
- exclude_labels
+vector of labels of scans to exclude, eg poor quality
+data.
- overwrite
+overwrite saved results, defaults to FALSE.
- ref_inds
+a vector of 1-based indices for any water reference dynamic
+scans.
- return_results
+function will return key outputs, defaults to FALSE.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/print.fit_result.html b/docs/reference/print.fit_result.html
index 297f28dc..5f434e57 100644
--- a/docs/reference/print.fit_result.html
+++ b/docs/reference/print.fit_result.html
@@ -1,5 +1,5 @@
-Print a summary of an object of class fit_result. — print.fit_result • Spectroscopy Analysis Tools (spant) Print a summary of an object of class fit_result. — print.fit_result • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -105,7 +105,7 @@ Arguments
diff --git a/docs/reference/print.mrs_data.html b/docs/reference/print.mrs_data.html
index 51199017..e1561eb2 100644
--- a/docs/reference/print.mrs_data.html
+++ b/docs/reference/print.mrs_data.html
@@ -1,5 +1,5 @@
-Print a summary of mrs_data parameters. — print.mrs_data • Spectroscopy Analysis Tools (spant) Print a summary of mrs_data parameters. — print.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -109,7 +109,7 @@ Arguments
diff --git a/docs/reference/qn_states.html b/docs/reference/qn_states.html
index 0f42f2f9..d7aa6715 100644
--- a/docs/reference/qn_states.html
+++ b/docs/reference/qn_states.html
@@ -1,5 +1,5 @@
-Get the quantum coherence matrix for a spin system. — qn_states • Spectroscopy Analysis Tools (spant) Get the quantum coherence matrix for a spin system. — qn_states • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/rats.html b/docs/reference/rats.html
index 5a39a396..93585e08 100644
--- a/docs/reference/rats.html
+++ b/docs/reference/rats.html
@@ -1,5 +1,5 @@
-Robust Alignment to a Target Spectrum (RATS). — rats • Spectroscopy Analysis Tools (spant) Robust Alignment to a Target Spectrum (RATS). — rats • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -207,7 +207,7 @@ Value
diff --git a/docs/reference/re_weighting.html b/docs/reference/re_weighting.html
index d21caf21..8b0b070a 100644
--- a/docs/reference/re_weighting.html
+++ b/docs/reference/re_weighting.html
@@ -1,5 +1,5 @@
-Apply a weighting to the FID to enhance spectral resolution. — re_weighting • Spectroscopy Analysis Tools (spant) Apply a weighting to the FID to enhance spectral resolution. — re_weighting • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/read_basis.html b/docs/reference/read_basis.html
index da9b94af..eb6f8557 100644
--- a/docs/reference/read_basis.html
+++ b/docs/reference/read_basis.html
@@ -1,5 +1,5 @@
-Read a basis file in LCModel .basis format. — read_basis • Spectroscopy Analysis Tools (spant) Read a basis file in LCModel .basis format. — read_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/read_ima_coil_dir.html b/docs/reference/read_ima_coil_dir.html
index 28c02de0..4f073cd8 100644
--- a/docs/reference/read_ima_coil_dir.html
+++ b/docs/reference/read_ima_coil_dir.html
@@ -1,9 +1,5 @@
-Read a directory containing Siemens MRS IMA files and combine along the coil
-dimension. Note that the coil ID is inferred from the sorted file name and
-should be checked when consistency is required between two directories. — read_ima_coil_dir • Spectroscopy Analysis Tools (spant) Read a directory containing Siemens MRS IMA files and combine along the coil dimension. Note that the coil ID is inferred from the sorted file name and should be checked when consistency is required between two directories. — read_ima_coil_dir • Spectroscopy Analysis Tools (spant) Read a directory containing Siemens MRS IMA files and combine along the
-dynamic dimension. Note that the coil ID is inferred from the sorted file
-name and should be checked when consistency is required. — read_ima_dyn_dir • Spectroscopy Analysis Tools (spant) Read a directory containing Siemens MRS IMA files and combine along the dynamic dimension. Note that the coil ID is inferred from the sorted file name and should be checked when consistency is required. — read_ima_dyn_dir • Spectroscopy Analysis Tools (spant) Read an LCModel formatted coord file containing fit information. — read_lcm_coord • Spectroscopy Analysis Tools (spant) Read an LCModel formatted coord file containing fit information. — read_lcm_coord • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -107,7 +107,7 @@ Value
diff --git a/docs/reference/read_mrs.html b/docs/reference/read_mrs.html
index 3ac2a36b..2cf36b20 100644
--- a/docs/reference/read_mrs.html
+++ b/docs/reference/read_mrs.html
@@ -1,5 +1,5 @@
-Read MRS data from a file. — read_mrs • Spectroscopy Analysis Tools (spant) Read MRS data from a file. — read_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -88,7 +88,8 @@ Read MRS data from a file.
full_fid = FALSE,
omit_svs_ref_scans = TRUE,
verbose = FALSE,
- extra = NULL
+ extra = NULL,
+ fid_filt_dist = NULL
)
@@ -140,6 +141,13 @@ Arguments
an optional data frame to provide additional variables for use
in subsequent analysis steps, eg id or grouping variables.
fid_filt_dist
+indicate if the data has a distorted FID due to a
+brick-wall filter being used to downsample the data. Default is to auto
+detect this from the data, but TRUE or FALSE options can be given to override
+detection.
Value
@@ -183,7 +191,7 @@ Examples
diff --git a/docs/reference/read_mrs_tqn.html b/docs/reference/read_mrs_tqn.html
index 5766362f..84bdaf3a 100644
--- a/docs/reference/read_mrs_tqn.html
+++ b/docs/reference/read_mrs_tqn.html
@@ -1,5 +1,5 @@
-Read MRS data using the TARQUIN software package. — read_mrs_tqn • Spectroscopy Analysis Tools (spant) Read MRS data using the TARQUIN software package. — read_mrs_tqn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -131,7 +131,7 @@ Examples
diff --git a/docs/reference/read_pulse_ascii.html b/docs/reference/read_pulse_ascii.html
index c9e0d43c..ab11c9cc 100644
--- a/docs/reference/read_pulse_ascii.html
+++ b/docs/reference/read_pulse_ascii.html
@@ -1,5 +1,5 @@
-Read an ASCII formatted pulse file. — read_pulse_ascii • Spectroscopy Analysis Tools (spant) Read an ASCII formatted pulse file. — read_pulse_ascii • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/read_pulse_bruker.html b/docs/reference/read_pulse_bruker.html
index c92bf76a..dbe9073b 100644
--- a/docs/reference/read_pulse_bruker.html
+++ b/docs/reference/read_pulse_bruker.html
@@ -1,5 +1,5 @@
-Read a Bruker formatted pulse file — read_pulse_bruker • Spectroscopy Analysis Tools (spant) Read a Bruker formatted pulse file — read_pulse_bruker • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/read_pulse_pta.html b/docs/reference/read_pulse_pta.html
index 72e1b6d4..a0fac3c3 100644
--- a/docs/reference/read_pulse_pta.html
+++ b/docs/reference/read_pulse_pta.html
@@ -1,5 +1,5 @@
-Read a .pta formatted pulse file compatible with Siemens PulseTool. — read_pulse_pta • Spectroscopy Analysis Tools (spant) Read a .pta formatted pulse file compatible with Siemens PulseTool. — read_pulse_pta • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/read_siemens_txt_hdr.html b/docs/reference/read_siemens_txt_hdr.html
index 23fb8c70..3a17d87c 100644
--- a/docs/reference/read_siemens_txt_hdr.html
+++ b/docs/reference/read_siemens_txt_hdr.html
@@ -1,5 +1,5 @@
-Read the text format header found in Siemens IMA and TWIX data files. — read_siemens_txt_hdr • Spectroscopy Analysis Tools (spant) Read the text format header found in Siemens IMA and TWIX data files. — read_siemens_txt_hdr • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -78,7 +78,7 @@ Read the text format header found in Siemens IMA and TWIX data files.
- read_siemens_txt_hdr(input, version = "vd", verbose, offset = 0)
+ read_siemens_txt_hdr(input, version = "vd", verbose = FALSE, offset = 0)
@@ -118,7 +118,7 @@ Value
diff --git a/docs/reference/read_tqn_fit.html b/docs/reference/read_tqn_fit.html
index 4da6c25e..a1630420 100644
--- a/docs/reference/read_tqn_fit.html
+++ b/docs/reference/read_tqn_fit.html
@@ -1,5 +1,5 @@
-Reader for csv fit results generated by TARQUIN. — read_tqn_fit • Spectroscopy Analysis Tools (spant) Reader for csv fit results generated by TARQUIN. — read_tqn_fit • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -113,7 +113,7 @@ Examples
diff --git a/docs/reference/read_tqn_result.html b/docs/reference/read_tqn_result.html
index 36659714..68a3e98c 100644
--- a/docs/reference/read_tqn_result.html
+++ b/docs/reference/read_tqn_result.html
@@ -1,5 +1,5 @@
-Reader for csv results generated by TARQUIN. — read_tqn_result • Spectroscopy Analysis Tools (spant) Reader for csv results generated by TARQUIN. — read_tqn_result • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -117,7 +117,7 @@ Examples
diff --git a/docs/reference/recon_imag.html b/docs/reference/recon_imag.html
index d2a72225..5bc3b1eb 100644
--- a/docs/reference/recon_imag.html
+++ b/docs/reference/recon_imag.html
@@ -1,7 +1,5 @@
-Reconstruct complex time-domain data from the real part of frequency-domain
-data. — recon_imag • Spectroscopy Analysis Tools (spant) Reconstruct complex time-domain data from the real part of frequency-domain data. — recon_imag • Spectroscopy Analysis Tools (spant) Reconstruct complex time-domain data from the real part of frequency-domain
-data. — recon_imag_vec • Spectroscopy Analysis Tools (spant) Reconstruct complex time-domain data from the real part of frequency-domain data. — recon_imag_vec • Spectroscopy Analysis Tools (spant) Reconstruct 2D MRSI data from a twix file loaded with read_mrs. — recon_twix_2d_mrsi • Spectroscopy Analysis Tools (spant) Reconstruct 2D MRSI data from a twix file loaded with read_mrs. — recon_twix_2d_mrsi • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/rectangular_mask.html b/docs/reference/rectangular_mask.html
index a2117283..6e469bc9 100644
--- a/docs/reference/rectangular_mask.html
+++ b/docs/reference/rectangular_mask.html
@@ -1,5 +1,5 @@
-Create a rectangular mask stored as a matrix of logical values. — rectangular_mask • Spectroscopy Analysis Tools (spant) Create a rectangular mask stored as a matrix of logical values. — rectangular_mask • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -130,7 +130,7 @@ Value
diff --git a/docs/reference/reexports.html b/docs/reference/reexports.html
index 694a75d1..a59e8379 100644
--- a/docs/reference/reexports.html
+++ b/docs/reference/reexports.html
@@ -1,5 +1,5 @@
-Objects exported from other packages — reexports • Spectroscopy Analysis Tools (spant) Objects exported from other packages — reexports • Spectroscopy Analysis Tools (spant)
Spectroscopy Analysis Tools (spant)
- 2.21.0
+ 2.22.0
@@ -103,7 +103,7 @@ Objects exported from other packages
diff --git a/docs/reference/rep_array_dim.html b/docs/reference/rep_array_dim.html
index b9c49b4a..48c0a5ed 100644
--- a/docs/reference/rep_array_dim.html
+++ b/docs/reference/rep_array_dim.html
@@ -1,5 +1,5 @@
-Repeat an array over a given dimension. — rep_array_dim • Spectroscopy Analysis Tools (spant) Repeat an array over a given dimension. — rep_array_dim • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/rep_dyn.html b/docs/reference/rep_dyn.html
index 6bbfb0ef..89a4bb9b 100644
--- a/docs/reference/rep_dyn.html
+++ b/docs/reference/rep_dyn.html
@@ -1,5 +1,5 @@
-Replicate a scan in the dynamic dimension. — rep_dyn • Spectroscopy Analysis Tools (spant) Replicate a scan in the dynamic dimension. — rep_dyn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/rep_mrs.html b/docs/reference/rep_mrs.html
index 67730b5c..becb8f00 100644
--- a/docs/reference/rep_mrs.html
+++ b/docs/reference/rep_mrs.html
@@ -1,5 +1,5 @@
-Replicate a scan over a given dimension. — rep_mrs • Spectroscopy Analysis Tools (spant) Replicate a scan over a given dimension. — rep_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -138,7 +138,7 @@ Value
diff --git a/docs/reference/resample_basis.html b/docs/reference/resample_basis.html
index b0f2ab17..c7a6222a 100644
--- a/docs/reference/resample_basis.html
+++ b/docs/reference/resample_basis.html
@@ -1,5 +1,5 @@
-Resample a basis-set to match a mrs_data acquisition. — resample_basis • Spectroscopy Analysis Tools (spant) Resample a basis-set to match a mrs_data acquisition. — resample_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -116,7 +116,7 @@ Value
diff --git a/docs/reference/resample_img.html b/docs/reference/resample_img.html
index f1e7beaf..b0cc8f71 100644
--- a/docs/reference/resample_img.html
+++ b/docs/reference/resample_img.html
@@ -1,5 +1,5 @@
-Resample an image to match a target image space. — resample_img • Spectroscopy Analysis Tools (spant) Resample an image to match a target image space. — resample_img • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/resample_voi.html b/docs/reference/resample_voi.html
index 8fbfa836..a29ab096 100644
--- a/docs/reference/resample_voi.html
+++ b/docs/reference/resample_voi.html
@@ -1,7 +1,5 @@
-Resample a VOI to match a target image space using nearest-neighbour
-interpolation. — resample_voi • Spectroscopy Analysis Tools (spant) Resample a VOI to match a target image space using nearest-neighbour interpolation. — resample_voi • Spectroscopy Analysis Tools (spant) Reslice a nifti object to match the orientation of mrs data. — reslice_to_mrs • Spectroscopy Analysis Tools (spant) Reslice a nifti object to match the orientation of mrs data. — reslice_to_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/reson_table2mrs_data.html b/docs/reference/reson_table2mrs_data.html
index d75579ee..c5a2167a 100644
--- a/docs/reference/reson_table2mrs_data.html
+++ b/docs/reference/reson_table2mrs_data.html
@@ -1,5 +1,5 @@
-Generate mrs_data from a table of single Lorentzian resonances. — reson_table2mrs_data • Spectroscopy Analysis Tools (spant) Generate mrs_data from a table of single Lorentzian resonances. — reson_table2mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -119,7 +119,7 @@ Value
diff --git a/docs/reference/rm_dyns.html b/docs/reference/rm_dyns.html
index 5d5ef692..573e1f51 100644
--- a/docs/reference/rm_dyns.html
+++ b/docs/reference/rm_dyns.html
@@ -1,5 +1,5 @@
-Remove a subset of dynamic scans. — rm_dyns • Spectroscopy Analysis Tools (spant) Remove a subset of dynamic scans. — rm_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/scale_amp_molal.html b/docs/reference/scale_amp_molal.html
index aaeee1f2..7acb8cb0 100644
--- a/docs/reference/scale_amp_molal.html
+++ b/docs/reference/scale_amp_molal.html
@@ -1,7 +1,5 @@
-Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water). — scale_amp_molal • Spectroscopy Analysis Tools (spant) Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / kg of tissue water). — scale_amp_molal • Spectroscopy Analysis Tools (spant)
Spectroscopy Analysis Tools (spant)
- 2.21.0
+ 2.22.0
@@ -76,8 +74,7 @@
- Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water).
+ Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / kg of tissue water).
Source: R/amp_scaling.R
scale_amp_molal.Rd
@@ -163,7 +160,7 @@ Value
diff --git a/docs/reference/scale_amp_molal_pvc.html b/docs/reference/scale_amp_molal_pvc.html
index 962d6afc..4d194abd 100644
--- a/docs/reference/scale_amp_molal_pvc.html
+++ b/docs/reference/scale_amp_molal_pvc.html
@@ -1,7 +1,5 @@
-Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water). — scale_amp_molal_pvc • Spectroscopy Analysis Tools (spant)
@@ -75,8 +73,7 @@
- Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water).
+ Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / kg of tissue water).
Source: R/amp_scaling.R
scale_amp_molal_pvc.Rd
@@ -141,7 +138,7 @@ Value
diff --git a/docs/reference/scale_amp_molar.html b/docs/reference/scale_amp_molar.html
index 02358d91..dc87a338 100644
--- a/docs/reference/scale_amp_molar.html
+++ b/docs/reference/scale_amp_molar.html
@@ -1,7 +1,5 @@
-Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / Litre of tissue). — scale_amp_molar • Spectroscopy Analysis Tools (spant) Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / Litre of tissue). — scale_amp_molar • Spectroscopy Analysis Tools (spant) Convert default LCM/TARQUIN concentration scaling to molal units with partial
-volume correction. — scale_amp_molar2molal_pvc • Spectroscopy Analysis Tools (spant) Convert default LCM/TARQUIN concentration scaling to molal units with partial volume correction. — scale_amp_molar2molal_pvc • Spectroscopy Analysis Tools (spant) Scale fitted amplitudes to a ratio of signal amplitude. — scale_amp_ratio • Spectroscopy Analysis Tools (spant) Scale fitted amplitudes to a ratio of signal amplitude. — scale_amp_ratio • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -116,7 +116,7 @@ Value
diff --git a/docs/reference/scale_amp_ratio_value.html b/docs/reference/scale_amp_ratio_value.html
index 2036837a..6af8ac51 100644
--- a/docs/reference/scale_amp_ratio_value.html
+++ b/docs/reference/scale_amp_ratio_value.html
@@ -1,5 +1,5 @@
-Scale fitted amplitudes to a ratio of signal amplitude. — scale_amp_ratio_value • Spectroscopy Analysis Tools (spant) Scale fitted amplitudes to a ratio of signal amplitude. — scale_amp_ratio_value • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/scale_amp_water_ratio.html b/docs/reference/scale_amp_water_ratio.html
index 5b25e884..35a76b00 100644
--- a/docs/reference/scale_amp_water_ratio.html
+++ b/docs/reference/scale_amp_water_ratio.html
@@ -1,5 +1,5 @@
-Scale metabolite amplitudes as a ratio to the unsuppressed water amplitude. — scale_amp_water_ratio • Spectroscopy Analysis Tools (spant) Scale metabolite amplitudes as a ratio to the unsuppressed water amplitude. — scale_amp_water_ratio • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/scale_basis_amp.html b/docs/reference/scale_basis_amp.html
index 9401c3f1..5a58b5e5 100644
--- a/docs/reference/scale_basis_amp.html
+++ b/docs/reference/scale_basis_amp.html
@@ -1,5 +1,5 @@
-Scale a basis object by a scalar. — scale_basis_amp • Spectroscopy Analysis Tools (spant) Scale a basis object by a scalar. — scale_basis_amp • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/scale_basis_from_singlet.html b/docs/reference/scale_basis_from_singlet.html
index 0d542bc8..c9a19e77 100644
--- a/docs/reference/scale_basis_from_singlet.html
+++ b/docs/reference/scale_basis_from_singlet.html
@@ -1,5 +1,5 @@
-Scale a basis-set to be consistent with spant assumptions for water scaling. — scale_basis_from_singlet • Spectroscopy Analysis Tools (spant) Scale a basis-set to be consistent with spant assumptions for water scaling. — scale_basis_from_singlet • Spectroscopy Analysis Tools (spant)
Spectroscopy Analysis Tools (spant)
- 2.21.0
+ 2.22.0
@@ -127,7 +127,7 @@ Value
diff --git a/docs/reference/scale_mrs_amp.html b/docs/reference/scale_mrs_amp.html
index b5501a0d..990f058a 100644
--- a/docs/reference/scale_mrs_amp.html
+++ b/docs/reference/scale_mrs_amp.html
@@ -1,5 +1,5 @@
-Scale an mrs_data object by a scalar or vector or amplitudes. — scale_mrs_amp • Spectroscopy Analysis Tools (spant) Scale an mrs_data object by a scalar or vector or amplitudes. — scale_mrs_amp • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/scale_spec.html b/docs/reference/scale_spec.html
index 4f6ea835..6b3ddba4 100644
--- a/docs/reference/scale_spec.html
+++ b/docs/reference/scale_spec.html
@@ -1,5 +1,5 @@
-Scale mrs_data to a spectral region. — scale_spec • Spectroscopy Analysis Tools (spant) Scale mrs_data to a spectral region. — scale_spec • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -141,7 +141,7 @@ Value
diff --git a/docs/reference/sd.html b/docs/reference/sd.html
index ea1eec9f..3ae4dfd4 100644
--- a/docs/reference/sd.html
+++ b/docs/reference/sd.html
@@ -1,5 +1,5 @@
-Calculate the standard deviation spectrum from an mrs_data object. — sd • Spectroscopy Analysis Tools (spant) Calculate the standard deviation spectrum from an mrs_data object. — sd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/sd.mrs_data.html b/docs/reference/sd.mrs_data.html
index 3f92a49f..13bdda85 100644
--- a/docs/reference/sd.mrs_data.html
+++ b/docs/reference/sd.mrs_data.html
@@ -1,5 +1,5 @@
-Calculate the standard deviation spectrum from an mrs_data object. — sd.mrs_data • Spectroscopy Analysis Tools (spant) Calculate the standard deviation spectrum from an mrs_data object. — sd.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/seconds.html b/docs/reference/seconds.html
index b34d6627..467ee17f 100644
--- a/docs/reference/seconds.html
+++ b/docs/reference/seconds.html
@@ -1,5 +1,5 @@
-Return a time scale vector to match the FID of an MRS data object. — seconds • Spectroscopy Analysis Tools (spant) Return a time scale vector to match the FID of an MRS data object. — seconds • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/seq_cpmg_ideal.html b/docs/reference/seq_cpmg_ideal.html
index 547e96ab..45727c86 100644
--- a/docs/reference/seq_cpmg_ideal.html
+++ b/docs/reference/seq_cpmg_ideal.html
@@ -1,5 +1,5 @@
-CPMG style sequence with ideal pulses. — seq_cpmg_ideal • Spectroscopy Analysis Tools (spant) CPMG style sequence with ideal pulses. — seq_cpmg_ideal • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/seq_mega_press_ideal.html b/docs/reference/seq_mega_press_ideal.html
index 0769b8b4..a9cd7fa0 100644
--- a/docs/reference/seq_mega_press_ideal.html
+++ b/docs/reference/seq_mega_press_ideal.html
@@ -1,7 +1,5 @@
-MEGA-PRESS sequence with ideal localisation pulses and Gaussian shaped
-editing pulse. — seq_mega_press_ideal • Spectroscopy Analysis Tools (spant) MEGA-PRESS sequence with ideal localisation pulses and Gaussian shaped editing pulse. — seq_mega_press_ideal • Spectroscopy Analysis Tools (spant) PRESS sequence with shaped refocusing pulses. — seq_press_2d_shaped • Spectroscopy Analysis Tools (spant) PRESS sequence with shaped refocusing pulses. — seq_press_2d_shaped • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -165,7 +165,7 @@ Value
diff --git a/docs/reference/seq_press_ideal.html b/docs/reference/seq_press_ideal.html
index 8c976856..72c3af3d 100644
--- a/docs/reference/seq_press_ideal.html
+++ b/docs/reference/seq_press_ideal.html
@@ -1,5 +1,5 @@
-PRESS sequence with ideal pulses. — seq_press_ideal • Spectroscopy Analysis Tools (spant) PRESS sequence with ideal pulses. — seq_press_ideal • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/seq_pulse_acquire.html b/docs/reference/seq_pulse_acquire.html
index 4a88fc64..ad80571e 100644
--- a/docs/reference/seq_pulse_acquire.html
+++ b/docs/reference/seq_pulse_acquire.html
@@ -1,5 +1,5 @@
-Simple pulse and acquire sequence with ideal pulses. — seq_pulse_acquire • Spectroscopy Analysis Tools (spant) Simple pulse and acquire sequence with ideal pulses. — seq_pulse_acquire • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/seq_slaser_ideal.html b/docs/reference/seq_slaser_ideal.html
index 74688f4d..eb83e8e3 100644
--- a/docs/reference/seq_slaser_ideal.html
+++ b/docs/reference/seq_slaser_ideal.html
@@ -1,5 +1,5 @@
-sLASER sequence with ideal pulses. — seq_slaser_ideal • Spectroscopy Analysis Tools (spant) sLASER sequence with ideal pulses. — seq_slaser_ideal • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -126,7 +126,7 @@ Value
diff --git a/docs/reference/seq_spin_echo_ideal.html b/docs/reference/seq_spin_echo_ideal.html
index e23271de..4248716f 100644
--- a/docs/reference/seq_spin_echo_ideal.html
+++ b/docs/reference/seq_spin_echo_ideal.html
@@ -1,5 +1,5 @@
-Spin echo sequence with ideal pulses. — seq_spin_echo_ideal • Spectroscopy Analysis Tools (spant) Spin echo sequence with ideal pulses. — seq_spin_echo_ideal • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/seq_steam_ideal.html b/docs/reference/seq_steam_ideal.html
index a60685a8..1c8115d7 100644
--- a/docs/reference/seq_steam_ideal.html
+++ b/docs/reference/seq_steam_ideal.html
@@ -1,5 +1,5 @@
-STEAM sequence with ideal pulses. — seq_steam_ideal • Spectroscopy Analysis Tools (spant) STEAM sequence with ideal pulses. — seq_steam_ideal • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -128,7 +128,7 @@ Value
diff --git a/docs/reference/seq_steam_ideal_cof.html b/docs/reference/seq_steam_ideal_cof.html
index 8f225740..cba7af91 100644
--- a/docs/reference/seq_steam_ideal_cof.html
+++ b/docs/reference/seq_steam_ideal_cof.html
@@ -1,7 +1,5 @@
-STEAM sequence with ideal pulses and coherence order filtering to simulate
-gradient crushers. — seq_steam_ideal_cof • Spectroscopy Analysis Tools (spant) STEAM sequence with ideal pulses and coherence order filtering to simulate gradient crushers. — seq_steam_ideal_cof • Spectroscopy Analysis Tools (spant) STEAM sequence with ideal pulses using the z-rotation gradient simulation
-method described by Young et al JMR 140, 146-152 (1999). — seq_steam_ideal_young • Spectroscopy Analysis Tools (spant) STEAM sequence with ideal pulses using the z-rotation gradient simulation method described by Young et al JMR 140, 146-152 (1999). — seq_steam_ideal_young • Spectroscopy Analysis Tools (spant) Set the number of transients for an mrs_data object. — set_Ntrans • Spectroscopy Analysis Tools (spant) Set the number of transients for an mrs_data object. — set_Ntrans • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/set_def_acq_paras.html b/docs/reference/set_def_acq_paras.html
index 3e1b4004..cc2ada9c 100644
--- a/docs/reference/set_def_acq_paras.html
+++ b/docs/reference/set_def_acq_paras.html
@@ -1,5 +1,5 @@
-Set the default acquisition parameters. — set_def_acq_paras • Spectroscopy Analysis Tools (spant) Set the default acquisition parameters. — set_def_acq_paras • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Arguments
diff --git a/docs/reference/set_lcm_cmd.html b/docs/reference/set_lcm_cmd.html
index 2056ed01..42bb2f24 100644
--- a/docs/reference/set_lcm_cmd.html
+++ b/docs/reference/set_lcm_cmd.html
@@ -1,5 +1,5 @@
-Set the command to run the LCModel command-line program. — set_lcm_cmd • Spectroscopy Analysis Tools (spant) Set the command to run the LCModel command-line program. — set_lcm_cmd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/set_lw.html b/docs/reference/set_lw.html
index b64ec851..bb176c62 100644
--- a/docs/reference/set_lw.html
+++ b/docs/reference/set_lw.html
@@ -1,5 +1,5 @@
-Apply line-broadening to an mrs_data object to achieve a specified linewidth. — set_lw • Spectroscopy Analysis Tools (spant) Apply line-broadening to an mrs_data object to achieve a specified linewidth. — set_lw • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -123,7 +123,7 @@ Value
diff --git a/docs/reference/set_mask_xy_mat.html b/docs/reference/set_mask_xy_mat.html
index 49dc5d4e..52c4b617 100644
--- a/docs/reference/set_mask_xy_mat.html
+++ b/docs/reference/set_mask_xy_mat.html
@@ -1,5 +1,5 @@
-Set the masked voxels in a 2D MRSI dataset to given spectrum. — set_mask_xy_mat • Spectroscopy Analysis Tools (spant) Set the masked voxels in a 2D MRSI dataset to given spectrum. — set_mask_xy_mat • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Value
diff --git a/docs/reference/set_precomp_mode.html b/docs/reference/set_precomp_mode.html
index f44bd5d3..47c28e3b 100644
--- a/docs/reference/set_precomp_mode.html
+++ b/docs/reference/set_precomp_mode.html
@@ -1,5 +1,5 @@
-Set the precompute mode. — set_precomp_mode • Spectroscopy Analysis Tools (spant) Set the precompute mode. — set_precomp_mode • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/set_precomp_verbose.html b/docs/reference/set_precomp_verbose.html
index 1453a231..9c613505 100644
--- a/docs/reference/set_precomp_verbose.html
+++ b/docs/reference/set_precomp_verbose.html
@@ -1,5 +1,5 @@
-Set the verbosity of the precompute function. — set_precomp_verbose • Spectroscopy Analysis Tools (spant) Set the verbosity of the precompute function. — set_precomp_verbose • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/set_ref.html b/docs/reference/set_ref.html
index 8953fa50..5436dfa2 100644
--- a/docs/reference/set_ref.html
+++ b/docs/reference/set_ref.html
@@ -1,5 +1,5 @@
-Set the ppm reference value (eg ppm value at 0Hz). — set_ref • Spectroscopy Analysis Tools (spant) Set the ppm reference value (eg ppm value at 0Hz). — set_ref • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/set_td_pts.html b/docs/reference/set_td_pts.html
index 8a80d42a..586459ff 100644
--- a/docs/reference/set_td_pts.html
+++ b/docs/reference/set_td_pts.html
@@ -1,7 +1,5 @@
-Set the number of time-domain data points, truncating or zero-filling as
-appropriate. — set_td_pts • Spectroscopy Analysis Tools (spant) Set the number of time-domain data points, truncating or zero-filling as appropriate. — set_td_pts • Spectroscopy Analysis Tools (spant) Set the command to run the TARQUIN command-line program. — set_tqn_cmd • Spectroscopy Analysis Tools (spant) Set the command to run the TARQUIN command-line program. — set_tqn_cmd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/set_tr.html b/docs/reference/set_tr.html
index b2109ab0..65c9df5f 100644
--- a/docs/reference/set_tr.html
+++ b/docs/reference/set_tr.html
@@ -1,5 +1,5 @@
-Set the repetition time of an MRS dataset. — set_tr • Spectroscopy Analysis Tools (spant) Set the repetition time of an MRS dataset. — set_tr • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/shift.html b/docs/reference/shift.html
index ab0fe724..034591d0 100644
--- a/docs/reference/shift.html
+++ b/docs/reference/shift.html
@@ -1,5 +1,5 @@
-Apply a frequency shift to MRS data. — shift • Spectroscopy Analysis Tools (spant) Apply a frequency shift to MRS data. — shift • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/shift_basis.html b/docs/reference/shift_basis.html
index 2884be19..f55a65e0 100644
--- a/docs/reference/shift_basis.html
+++ b/docs/reference/shift_basis.html
@@ -1,5 +1,5 @@
-Apply frequency shifts to basis set signals. — shift_basis • Spectroscopy Analysis Tools (spant) Apply frequency shifts to basis set signals. — shift_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Value
diff --git a/docs/reference/sim_basis.html b/docs/reference/sim_basis.html
index c7838c46..bb5fefc6 100644
--- a/docs/reference/sim_basis.html
+++ b/docs/reference/sim_basis.html
@@ -1,5 +1,5 @@
-Simulate a basis set object. — sim_basis • Spectroscopy Analysis Tools (spant) Simulate a basis set object. — sim_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -136,7 +136,7 @@ Value
diff --git a/docs/reference/sim_basis_1h_brain.html b/docs/reference/sim_basis_1h_brain.html
index 62ed7389..f71ffa0b 100644
--- a/docs/reference/sim_basis_1h_brain.html
+++ b/docs/reference/sim_basis_1h_brain.html
@@ -1,7 +1,5 @@
-Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS
-sequence. Note, ideal pulses are assumed. — sim_basis_1h_brain • Spectroscopy Analysis Tools (spant) Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS sequence. Note, ideal pulses are assumed. — sim_basis_1h_brain • Spectroscopy Analysis Tools (spant) Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS
-sequence. Note, ideal pulses are assumed. — sim_basis_1h_brain_press • Spectroscopy Analysis Tools (spant) Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS sequence. Note, ideal pulses are assumed. — sim_basis_1h_brain_press • Spectroscopy Analysis Tools (spant) Simulate a macromolecular and lipid basis-set suitable for 1H brain MRS
-analysis. — sim_basis_mm_lip_lcm • Spectroscopy Analysis Tools (spant) Simulate a macromolecular and lipid basis-set suitable for 1H brain MRS analysis. — sim_basis_mm_lip_lcm • Spectroscopy Analysis Tools (spant) Simulate a basis file using TARQUIN. — sim_basis_tqn • Spectroscopy Analysis Tools (spant) Simulate a basis file using TARQUIN. — sim_basis_tqn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -129,7 +129,7 @@ Examples
diff --git a/docs/reference/sim_brain_1h.html b/docs/reference/sim_brain_1h.html
index 2044cf1a..717ee289 100644
--- a/docs/reference/sim_brain_1h.html
+++ b/docs/reference/sim_brain_1h.html
@@ -1,5 +1,5 @@
-Simulate MRS data with a similar appearance to normal brain (by default). — sim_brain_1h • Spectroscopy Analysis Tools (spant) Simulate MRS data with a similar appearance to normal brain (by default). — sim_brain_1h • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -159,7 +159,7 @@ Value
diff --git a/docs/reference/sim_mol.html b/docs/reference/sim_mol.html
index 23bcef50..77f76a50 100644
--- a/docs/reference/sim_mol.html
+++ b/docs/reference/sim_mol.html
@@ -1,5 +1,5 @@
-Simulate a mol_parameter object. — sim_mol • Spectroscopy Analysis Tools (spant) Simulate a mol_parameter object. — sim_mol • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -143,7 +143,7 @@ Value
diff --git a/docs/reference/sim_noise.html b/docs/reference/sim_noise.html
index 23875f79..a71477d4 100644
--- a/docs/reference/sim_noise.html
+++ b/docs/reference/sim_noise.html
@@ -1,5 +1,5 @@
-Simulate an mrs_data object containing simulated Gaussian noise. — sim_noise • Spectroscopy Analysis Tools (spant) Simulate an mrs_data object containing simulated Gaussian noise. — sim_noise • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -84,6 +84,7 @@ Simulate an mrs_data object containing simulated Gaussian noise.
ft = def_ft(),
N = def_N(),
ref = def_ref(),
+ nuc = def_nuc(),
dyns = 1,
fd = TRUE
)
@@ -111,6 +112,10 @@ Arguments
reference value for ppm scale.
nuc
+resonant nucleus.
dyns
number of dynamic scans to generate.
Value
diff --git a/docs/reference/sim_resonances.html b/docs/reference/sim_resonances.html
index 19e9a8a4..d4f8d7c0 100644
--- a/docs/reference/sim_resonances.html
+++ b/docs/reference/sim_resonances.html
@@ -1,5 +1,5 @@
-Simulate a MRS data object containing a set of simulated resonances. — sim_resonances • Spectroscopy Analysis Tools (spant) Simulate a MRS data object containing a set of simulated resonances. — sim_resonances • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -161,7 +161,7 @@ Examples
diff --git a/docs/reference/sim_th_excit_profile.html b/docs/reference/sim_th_excit_profile.html
index 5535c5ef..e781cab1 100644
--- a/docs/reference/sim_th_excit_profile.html
+++ b/docs/reference/sim_th_excit_profile.html
@@ -1,7 +1,5 @@
-Simulate an ideal pulse excitation profile by smoothing a top-hat function
-with a Gaussian. — sim_th_excit_profile • Spectroscopy Analysis Tools (spant) Simulate an ideal pulse excitation profile by smoothing a top-hat function with a Gaussian. — sim_th_excit_profile • Spectroscopy Analysis Tools (spant) Simulate an mrs_data object containing complex zero valued samples. — sim_zero • Spectroscopy Analysis Tools (spant) Simulate an mrs_data object containing complex zero valued samples. — sim_zero • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -78,7 +78,14 @@ Simulate an mrs_data object containing complex zero valued samples.
-
+
@@ -99,6 +106,10 @@ Arguments
reference value for ppm scale.
nuc
+resonant nucleus.
dyns
number of dynamic scans to generate.
Value
diff --git a/docs/reference/smooth_dyns.html b/docs/reference/smooth_dyns.html
index 4cc8da50..accf3a51 100644
--- a/docs/reference/smooth_dyns.html
+++ b/docs/reference/smooth_dyns.html
@@ -1,5 +1,5 @@
-Smooth data across the dynamic dimension with a Gaussian kernel. — smooth_dyns • Spectroscopy Analysis Tools (spant) Smooth data across the dynamic dimension with a Gaussian kernel. — smooth_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/sort_basis.html b/docs/reference/sort_basis.html
index 6a676ea2..d25cc006 100644
--- a/docs/reference/sort_basis.html
+++ b/docs/reference/sort_basis.html
@@ -1,5 +1,5 @@
-Sort the basis-set elements alphabetically. — sort_basis • Spectroscopy Analysis Tools (spant) Sort the basis-set elements alphabetically. — sort_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/spant-package.html b/docs/reference/spant-package.html
index b3dd8e21..90f19ec3 100644
--- a/docs/reference/spant-package.html
+++ b/docs/reference/spant-package.html
@@ -1,5 +1,5 @@
-spant: spectroscopy analysis tools. — spant-package • Spectroscopy Analysis Tools (spant) spant: spectroscopy analysis tools. — spant-package • Spectroscopy Analysis Tools (spant) Simulate and fit some spectra with ABfit for benchmarking purposes. Basic
-timing and performance metrics will be printed. — spant_abfit_benchmark • Spectroscopy Analysis Tools (spant) Simulate and fit some spectra with ABfit for benchmarking purposes. Basic timing and performance metrics will be printed. — spant_abfit_benchmark • Spectroscopy Analysis Tools (spant) Example MEGA-PRESS data with significant B0 drift. — spant_mpress_drift • Spectroscopy Analysis Tools (spant) Example MEGA-PRESS data with significant B0 drift. — spant_mpress_drift • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -83,7 +83,7 @@ Example MEGA-PRESS data with significant B0 drift.
Format
- An object of class mrs_data of length 13.
+ An object of class mrs_data of dimension 1 x 1 x 1 x 1 x 40 x 1 x 1024.
@@ -98,7 +98,7 @@ Format
diff --git a/docs/reference/spant_sim_fmrs_dataset.html b/docs/reference/spant_sim_fmrs_dataset.html
new file mode 100644
index 00000000..00e48b56
--- /dev/null
+++ b/docs/reference/spant_sim_fmrs_dataset.html
@@ -0,0 +1,117 @@
+
+Simulate an example fMRS dataset for a block design fMRS experiment and export a BIDS structure. — spant_sim_fmrs_dataset • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Simulate an example fMRS dataset for a block design fMRS experiment and export a BIDS structure.
+ Source: R/fmrs.R
+ spant_sim_fmrs_dataset.Rd
+
+
+
+ Simulate an example fMRS dataset for a block design fMRS experiment and
+export a BIDS structure.
+
+
+
+ spant_sim_fmrs_dataset(output_dir = NULL)
+
+
+
+ Arguments
+ - output_dir
+output directory for the BIDS data. Defaults to :
+"HOME/sim_fmrs_dataset/data".
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/spant_simulation_benchmark.html b/docs/reference/spant_simulation_benchmark.html
index 32daa8bf..d8cc6841 100644
--- a/docs/reference/spant_simulation_benchmark.html
+++ b/docs/reference/spant_simulation_benchmark.html
@@ -1,7 +1,5 @@
-Simulate a typical metabolite basis set for benchmarking. Timing metrics will
-be printed on completion. — spant_simulation_benchmark • Spectroscopy Analysis Tools (spant) Simulate a typical metabolite basis set for benchmarking. Timing metrics will be printed on completion. — spant_simulation_benchmark • Spectroscopy Analysis Tools (spant) Decompose an mrs_data object into white and gray matter spectra. — spec_decomp • Spectroscopy Analysis Tools (spant) Perform a mathematical operation on a spectral region. — spec_op • Spectroscopy Analysis Tools (spant) Perform a mathematical operation on a spectral region. — spec_op • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -98,8 +98,8 @@ Arguments
operator
-can be "sum" (default), "mean", "l2", "max", "min" or
-"max-min".
can be "sum" (default), "mean", "l2", "max", "max_cplx,
+"min" or "max-min".
freq_scale
@@ -129,7 +129,7 @@ Value
diff --git a/docs/reference/spin_sys.html b/docs/reference/spin_sys.html
index 853423a4..1eaa9e76 100644
--- a/docs/reference/spin_sys.html
+++ b/docs/reference/spin_sys.html
@@ -1,5 +1,5 @@
-Create a spin system object for pulse sequence simulation. — spin_sys • Spectroscopy Analysis Tools (spant) Create a spin system object for pulse sequence simulation. — spin_sys • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/spm_pve2categorical.html b/docs/reference/spm_pve2categorical.html
index 23a1bad9..70f10729 100644
--- a/docs/reference/spm_pve2categorical.html
+++ b/docs/reference/spm_pve2categorical.html
@@ -1,7 +1,5 @@
-Convert SPM style segmentation files to a single categorical image where
-the numerical values map as: 0) Other, 1) CSF, 2) GM and 3) WM. — spm_pve2categorical • Spectroscopy Analysis Tools (spant) Convert SPM style segmentation files to a single categorical image where the numerical values map as: 0) Other, 1) CSF, 2) GM and 3) WM. — spm_pve2categorical • Spectroscopy Analysis Tools (spant) Signal space projection method for lipid suppression. — ssp • Spectroscopy Analysis Tools (spant) Signal space projection method for lipid suppression. — ssp • Spectroscopy Analysis Tools (spant) Plot the fitting results of an object of class fit_result with
-individual basis set components shown. — stackplot.fit_result • Spectroscopy Analysis Tools (spant) Plot the fitting results of an object of class fit_result with individual basis set components shown. — stackplot.fit_result • Spectroscopy Analysis Tools (spant) Produce a plot with multiple traces. — stackplot • Spectroscopy Analysis Tools (spant) Produce a plot with multiple traces. — stackplot • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/stackplot.mrs_data.html b/docs/reference/stackplot.mrs_data.html
index 17ff5648..64eea445 100644
--- a/docs/reference/stackplot.mrs_data.html
+++ b/docs/reference/stackplot.mrs_data.html
@@ -1,5 +1,5 @@
-Stackplot plotting method for objects of class mrs_data. — stackplot.mrs_data • Spectroscopy Analysis Tools (spant) Stackplot plotting method for objects of class mrs_data. — stackplot.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -255,7 +255,7 @@ Arguments
diff --git a/docs/reference/sub_first_dyn.html b/docs/reference/sub_first_dyn.html
index dbd7f831..493b7242 100644
--- a/docs/reference/sub_first_dyn.html
+++ b/docs/reference/sub_first_dyn.html
@@ -1,5 +1,5 @@
-Subtract the first dynamic spectrum from a dynamic series. — sub_first_dyn • Spectroscopy Analysis Tools (spant) Subtract the first dynamic spectrum from a dynamic series. — sub_first_dyn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/sub_mean_dyns.html b/docs/reference/sub_mean_dyns.html
index 6e3bb2df..221bd0c1 100644
--- a/docs/reference/sub_mean_dyns.html
+++ b/docs/reference/sub_mean_dyns.html
@@ -1,5 +1,5 @@
-Subtract the mean dynamic spectrum from a dynamic series. — sub_mean_dyns • Spectroscopy Analysis Tools (spant) Subtract the mean dynamic spectrum from a dynamic series. — sub_mean_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/sub_median_dyns.html b/docs/reference/sub_median_dyns.html
index 134c495d..1e834f14 100644
--- a/docs/reference/sub_median_dyns.html
+++ b/docs/reference/sub_median_dyns.html
@@ -1,5 +1,5 @@
-Subtract the median dynamic spectrum from a dynamic series. — sub_median_dyns • Spectroscopy Analysis Tools (spant) Subtract the median dynamic spectrum from a dynamic series. — sub_median_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/sum_coils.html b/docs/reference/sum_coils.html
index 7bf559f2..e1ab3cc0 100644
--- a/docs/reference/sum_coils.html
+++ b/docs/reference/sum_coils.html
@@ -1,5 +1,5 @@
-Calculate the sum across receiver coil elements. — sum_coils • Spectroscopy Analysis Tools (spant) Calculate the sum across receiver coil elements. — sum_coils • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/sum_dyns.html b/docs/reference/sum_dyns.html
index a0be19d3..bbda2ffc 100644
--- a/docs/reference/sum_dyns.html
+++ b/docs/reference/sum_dyns.html
@@ -1,5 +1,5 @@
-Calculate the sum of data dynamics. — sum_dyns • Spectroscopy Analysis Tools (spant) Calculate the sum of data dynamics. — sum_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/sum_mrs.html b/docs/reference/sum_mrs.html
index a22f215b..3cc3ab9e 100644
--- a/docs/reference/sum_mrs.html
+++ b/docs/reference/sum_mrs.html
@@ -1,5 +1,5 @@
-Sum two mrs_data objects. — sum_mrs • Spectroscopy Analysis Tools (spant) Sum two mrs_data objects. — sum_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Value
diff --git a/docs/reference/sum_mrs_list.html b/docs/reference/sum_mrs_list.html
index f4e09aea..c3584348 100644
--- a/docs/reference/sum_mrs_list.html
+++ b/docs/reference/sum_mrs_list.html
@@ -1,5 +1,5 @@
-Return the sum of a list of mrs_data objects. — sum_mrs_list • Spectroscopy Analysis Tools (spant) Return the sum of a list of mrs_data objects. — sum_mrs_list • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/svs_1h_brain_analysis.html b/docs/reference/svs_1h_brain_analysis.html
index 8ce514db..dff0ef7d 100644
--- a/docs/reference/svs_1h_brain_analysis.html
+++ b/docs/reference/svs_1h_brain_analysis.html
@@ -1,5 +1,5 @@
-Standard SVS 1H brain analysis pipeline. — svs_1h_brain_analysis • Spectroscopy Analysis Tools (spant) Standard SVS 1H brain analysis pipeline. — svs_1h_brain_analysis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -199,7 +199,7 @@ Value
diff --git a/docs/reference/svs_1h_brain_analysis_dev.html b/docs/reference/svs_1h_brain_analysis_dev.html
index d70a14d3..d71bfea2 100644
--- a/docs/reference/svs_1h_brain_analysis_dev.html
+++ b/docs/reference/svs_1h_brain_analysis_dev.html
@@ -1,5 +1,5 @@
-Standard SVS 1H brain analysis pipeline. — svs_1h_brain_analysis_dev • Spectroscopy Analysis Tools (spant) Standard SVS 1H brain analysis pipeline. — svs_1h_brain_analysis_dev • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -193,7 +193,7 @@ Examples
diff --git a/docs/reference/svs_1h_brain_batch_analysis.html b/docs/reference/svs_1h_brain_batch_analysis.html
index 5631e8cc..15f7223e 100644
--- a/docs/reference/svs_1h_brain_batch_analysis.html
+++ b/docs/reference/svs_1h_brain_batch_analysis.html
@@ -1,5 +1,5 @@
-Batch interface to the standard SVS 1H brain analysis pipeline. — svs_1h_brain_batch_analysis • Spectroscopy Analysis Tools (spant) Batch interface to the standard SVS 1H brain analysis pipeline. — svs_1h_brain_batch_analysis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -144,7 +144,7 @@ Value
diff --git a/docs/reference/t_test_spec.html b/docs/reference/t_test_spec.html
new file mode 100644
index 00000000..56a7ea1b
--- /dev/null
+++ b/docs/reference/t_test_spec.html
@@ -0,0 +1,124 @@
+
+Perform a t-test on spectral data points. — t_test_spec • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+
+
+ Perform a t-test on spectral data points.
+
+
+
+ t_test_spec(mrs_data, group)
+
+
+
+ Arguments
+ - mrs_data
+an mrs_data object with spectra in the dynamic dimension.
- group
+vector describing the group membership of each dynamic spectrum.
+
+ Value
+
+
+a list of statistical results.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/td2fd.html b/docs/reference/td2fd.html
index 6748a6a8..f31ed524 100644
--- a/docs/reference/td2fd.html
+++ b/docs/reference/td2fd.html
@@ -1,5 +1,5 @@
-Transform time-domain data to the frequency-domain. — td2fd • Spectroscopy Analysis Tools (spant) Transform time-domain data to the frequency-domain. — td2fd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/td_conv_filt.html b/docs/reference/td_conv_filt.html
index a9f340c3..106b9b00 100644
--- a/docs/reference/td_conv_filt.html
+++ b/docs/reference/td_conv_filt.html
@@ -1,5 +1,5 @@
-Time-domain convolution based filter. — td_conv_filt • Spectroscopy Analysis Tools (spant) Time-domain convolution based filter. — td_conv_filt • Spectroscopy Analysis Tools (spant) Time-domain spectral registration. — tdsr • Spectroscopy Analysis Tools (spant) Time-domain spectral registration. — tdsr • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -121,7 +121,7 @@ Value
diff --git a/docs/reference/te.html b/docs/reference/te.html
index 010361b1..4a65711d 100644
--- a/docs/reference/te.html
+++ b/docs/reference/te.html
@@ -1,5 +1,5 @@
-Return the echo time of an MRS dataset. — te • Spectroscopy Analysis Tools (spant) Return the echo time of an MRS dataset. — te • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/tr.html b/docs/reference/tr.html
index 0c0bd63b..2e749e02 100644
--- a/docs/reference/tr.html
+++ b/docs/reference/tr.html
@@ -1,5 +1,5 @@
-Return the repetition time of an MRS dataset. — tr • Spectroscopy Analysis Tools (spant) Return the repetition time of an MRS dataset. — tr • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/varpro_3_para_opts.html b/docs/reference/varpro_3_para_opts.html
index c2270a16..52d7cd84 100644
--- a/docs/reference/varpro_3_para_opts.html
+++ b/docs/reference/varpro_3_para_opts.html
@@ -1,5 +1,5 @@
-Return a list of options for VARPRO based fitting with 3 free parameters. — varpro_3_para_opts • Spectroscopy Analysis Tools (spant) Return a list of options for VARPRO based fitting with 3 free parameters. — varpro_3_para_opts • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -141,7 +141,7 @@ Value
diff --git a/docs/reference/varpro_basic_opts.html b/docs/reference/varpro_basic_opts.html
index 32c86d22..c5104891 100644
--- a/docs/reference/varpro_basic_opts.html
+++ b/docs/reference/varpro_basic_opts.html
@@ -1,5 +1,5 @@
-Return a list of options for a basic VARPRO analysis. — varpro_basic_opts • Spectroscopy Analysis Tools (spant) Return a list of options for a basic VARPRO analysis. — varpro_basic_opts • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -118,7 +118,7 @@ Value
diff --git a/docs/reference/varpro_opts.html b/docs/reference/varpro_opts.html
index 2aabf11d..6332f730 100644
--- a/docs/reference/varpro_opts.html
+++ b/docs/reference/varpro_opts.html
@@ -1,5 +1,5 @@
-Return a list of options for VARPRO based fitting. — varpro_opts • Spectroscopy Analysis Tools (spant) Return a list of options for VARPRO based fitting. — varpro_opts • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -177,7 +177,7 @@ Examples
diff --git a/docs/reference/vec2mrs_data.html b/docs/reference/vec2mrs_data.html
index 0cccd73b..f0d58bf0 100644
--- a/docs/reference/vec2mrs_data.html
+++ b/docs/reference/vec2mrs_data.html
@@ -1,5 +1,5 @@
-Convert a vector into a mrs_data object. — vec2mrs_data • Spectroscopy Analysis Tools (spant) Convert a vector into a mrs_data object. — vec2mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -80,10 +80,11 @@ Convert a vector into a mrs_data object.
vec2mrs_data(
vec,
- fs = def_fs(),
- ft = def_ft(),
- ref = def_ref(),
- nuc = def_nuc(),
+ mrs_data = NULL,
+ fs = NULL,
+ ft = NULL,
+ ref = NULL,
+ nuc = NULL,
dyns = 1,
fd = FALSE
)
@@ -95,6 +96,10 @@ Arguments
the data vector.
mrs_data
+example data to copy acquisition parameters from.
fs
sampling frequency in Hz.
Arguments
fd
-flag to indicate if the matrix is in the frequency domain (logical).
flag to indicate if the vector is in the frequency domain (logical).
Value
diff --git a/docs/reference/write_basis.html b/docs/reference/write_basis.html
index b6e27cbd..94c5e021 100644
--- a/docs/reference/write_basis.html
+++ b/docs/reference/write_basis.html
@@ -1,5 +1,5 @@
-Write a basis object to an LCModel .basis formatted file. — write_basis • Spectroscopy Analysis Tools (spant) Write a basis object to an LCModel .basis formatted file. — write_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -108,7 +108,7 @@ Arguments
diff --git a/docs/reference/write_basis_tqn.html b/docs/reference/write_basis_tqn.html
index 6aa51c1d..116c73ec 100644
--- a/docs/reference/write_basis_tqn.html
+++ b/docs/reference/write_basis_tqn.html
@@ -1,5 +1,5 @@
-Generate a basis file using TARQUIN. — write_basis_tqn • Spectroscopy Analysis Tools (spant) Generate a basis file using TARQUIN. — write_basis_tqn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Examples
diff --git a/docs/reference/write_mrs.html b/docs/reference/write_mrs.html
index fff25f15..124b9dc4 100644
--- a/docs/reference/write_mrs.html
+++ b/docs/reference/write_mrs.html
@@ -1,5 +1,5 @@
-Write MRS data object to file. — write_mrs • Spectroscopy Analysis Tools (spant) Write MRS data object to file. — write_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Arguments
diff --git a/docs/reference/write_mrs_nifti.html b/docs/reference/write_mrs_nifti.html
index f4bf1921..bd3ed4b7 100644
--- a/docs/reference/write_mrs_nifti.html
+++ b/docs/reference/write_mrs_nifti.html
@@ -1,5 +1,5 @@
-Write MRS data object to file in NIFTI format. — write_mrs_nifti • Spectroscopy Analysis Tools (spant) Write MRS data object to file in NIFTI format. — write_mrs_nifti • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/write_pulse_ascii.html b/docs/reference/write_pulse_ascii.html
index 067ae086..221f8ebb 100644
--- a/docs/reference/write_pulse_ascii.html
+++ b/docs/reference/write_pulse_ascii.html
@@ -1,5 +1,5 @@
-Write an ASCII formatted pulse file. — write_pulse_ascii • Spectroscopy Analysis Tools (spant) Write an ASCII formatted pulse file. — write_pulse_ascii • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/zero_fade_spec.html b/docs/reference/zero_fade_spec.html
index c703745c..c8b572c3 100644
--- a/docs/reference/zero_fade_spec.html
+++ b/docs/reference/zero_fade_spec.html
@@ -1,7 +1,5 @@
-Fade a spectrum to zero by frequency domain multiplication with a tanh
-function. Note this operation distorts data points at the end of the FID. — zero_fade_spec • Spectroscopy Analysis Tools (spant) Fade a spectrum to zero by frequency domain multiplication with a tanh function. Note this operation distorts data points at the end of the FID. — zero_fade_spec • Spectroscopy Analysis Tools (spant) Zero all coherences including and above a given order. — zero_higher_orders • Spectroscopy Analysis Tools (spant) Zero all coherences including and above a given order. — zero_higher_orders • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Value
diff --git a/docs/reference/zero_td_pts_end.html b/docs/reference/zero_td_pts_end.html
index 8c1123c8..71d24ebb 100644
--- a/docs/reference/zero_td_pts_end.html
+++ b/docs/reference/zero_td_pts_end.html
@@ -1,5 +1,5 @@
-Set mrs_data object data points at the end of the FID to zero. — zero_td_pts_end • Spectroscopy Analysis Tools (spant) Set mrs_data object data points at the end of the FID to zero. — zero_td_pts_end • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/zf.html b/docs/reference/zf.html
index 85e2013c..baf50256 100644
--- a/docs/reference/zf.html
+++ b/docs/reference/zf.html
@@ -1,5 +1,5 @@
-Zero-fill MRS data in the time domain. — zf • Spectroscopy Analysis Tools (spant) Zero-fill MRS data in the time domain. — zf • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -125,7 +125,7 @@ Value
diff --git a/docs/reference/zf_xy.html b/docs/reference/zf_xy.html
index ebca3999..c4104a74 100644
--- a/docs/reference/zf_xy.html
+++ b/docs/reference/zf_xy.html
@@ -1,5 +1,5 @@
-Zero-fill MRSI data in the k-space x-y direction. — zf_xy • Spectroscopy Analysis Tools (spant) Zero-fill MRSI data in the k-space x-y direction. — zf_xy • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -113,7 +113,7 @@ Value
diff --git a/docs/sitemap.xml b/docs/sitemap.xml
index e2139f71..4c39f515 100644
--- a/docs/sitemap.xml
+++ b/docs/sitemap.xml
@@ -216,6 +216,12 @@
https://martin3141.github.io/spant/reference/comb_coils_fp_pc.html
+
+ https://martin3141.github.io/spant/reference/comb_coils_mrsi_gls.html
+
+
+ https://martin3141.github.io/spant/reference/comb_coils_svs_gls.html
+
https://martin3141.github.io/spant/reference/comb_csv_results.html
@@ -411,6 +417,9 @@
https://martin3141.github.io/spant/reference/gen_conv_reg.html
+
+ https://martin3141.github.io/spant/reference/gen_group_reg.html
+
https://martin3141.github.io/spant/reference/gen_impulse_reg.html
@@ -555,6 +564,15 @@
https://martin3141.github.io/spant/reference/glm_spec.html
+
+ https://martin3141.github.io/spant/reference/glm_spec_fmrs_fl.html
+
+
+ https://martin3141.github.io/spant/reference/glm_spec_fmrs_group.html
+
+
+ https://martin3141.github.io/spant/reference/glm_spec_group_linhyp.html
+
https://martin3141.github.io/spant/reference/grid_shift_xy.html
@@ -690,9 +708,15 @@
https://martin3141.github.io/spant/reference/mrs_data2basis.html
+
+ https://martin3141.github.io/spant/reference/mrs_data2bids.html
+
https://martin3141.github.io/spant/reference/mrs_data2mat.html
+
+ https://martin3141.github.io/spant/reference/mrs_data2spec_mat.html
+
https://martin3141.github.io/spant/reference/mrs_data2vec.html
@@ -741,6 +765,9 @@
https://martin3141.github.io/spant/reference/phase.html
+
+ https://martin3141.github.io/spant/reference/phase_ref_1h_brain.html
+
https://martin3141.github.io/spant/reference/plot.fit_result.html
@@ -780,6 +807,12 @@
https://martin3141.github.io/spant/reference/precomp.html
+
+ https://martin3141.github.io/spant/reference/preproc_svs.html
+
+
+ https://martin3141.github.io/spant/reference/preproc_svs_dataset.html
+
https://martin3141.github.io/spant/reference/print.fit_result.html
@@ -1050,6 +1083,9 @@
https://martin3141.github.io/spant/reference/spant_mpress_drift.html
+
+ https://martin3141.github.io/spant/reference/spant_sim_fmrs_dataset.html
+
https://martin3141.github.io/spant/reference/spant_simulation_benchmark.html
@@ -1107,6 +1143,9 @@
https://martin3141.github.io/spant/reference/svs_1h_brain_batch_analysis.html
+
+ https://martin3141.github.io/spant/reference/t_test_spec.html
+
https://martin3141.github.io/spant/reference/td2fd.html
Return a character array of names that may be used with the
-get_mol_paras function.
Return a character array of names that may be used with the get_mol_paras function.
All functions
- Return an array of amplitudes derived from fitting the initial points in the
-time domain and extrapolating back to t=0.
Return an array of amplitudes derived from fitting the initial points in the time domain and extrapolating back to t=0.
@@ -709,8 +690,7 @@ All functions
- Generate a mol_parameters object for a simple spin system with one
-resonance.
Generate a mol_parameters object for a simple spin system with one resonance.
@@ -731,6 +711,18 @@ All functions glm_spec()
Perform a GLM analysis of dynamic MRS data in the spectral domain.
+
+
+ Perform first-level spectral GLM analysis of an fMRS dataset.
+
+
+ Perform group-level spectral GLM analysis of an fMRS dataset.
+
+
+ Test a group-level spectral GLM linear hypothesis.
@@ -766,8 +758,7 @@ All functions
- Perform an ifft and ifftshift on a matrix with each column replaced by its
-shifted ifft.
Perform an ifft and ifftshift on a matrix with each column replaced by its shifted ifft.
@@ -799,8 +790,7 @@ All functions
- Check if the chemical shift dimension of an MRS data object is in the
-frequency domain.
Check if the chemical shift dimension of an MRS data object is in the frequency domain.
@@ -820,18 +810,15 @@ All functions
- Covert a linewidth in Hz to an equivalent alpha value in the time-domain ie:
-x * exp(-t * alpha).
Covert a linewidth in Hz to an equivalent alpha value in the time-domain ie: x * exp(-t * alpha).
- Covert a linewidth in Hz to an equivalent beta value in the time-domain ie:
-x * exp(-t * t * beta).
Covert a linewidth in Hz to an equivalent beta value in the time-domain ie: x * exp(-t * t * beta).
- Make a basis-set object from a directory containing LCModel formatted RAW
-files.
Make a basis-set object from a directory containing LCModel formatted RAW files.
@@ -851,8 +838,7 @@ All functions
- Mask the voxels outside an elliptical region spanning the MRSI dataset in the
-x-y plane.
Mask the voxels outside an elliptical region spanning the MRSI dataset in the x-y plane.
@@ -860,13 +846,11 @@ All functions
- Convert a matrix (with spectral points in the column dimension and dynamics
-in the row dimensions) into a mrs_data object.
Convert a matrix (with spectral points in the column dimension and dynamics in the row dimensions) into a mrs_data object.
- Matrix exponential function taken from complexplus package to reduce the
-number of spant dependencies.
Matrix exponential function taken from complexplus package to reduce the number of spant dependencies.
@@ -914,31 +898,31 @@ All functions
- Convert an mrs_data object to basis object - where basis signals are spread
-across the dynamic dimension in the MRS data.
Convert an mrs_data object to basis object - where basis signals are spread across the dynamic dimension in the MRS data.
+
+
+ Create a BIDS file structure from a vector of MRS data paths or list of mrs_data objects.
- Convert mrs_data object to a matrix, with spectral points in the column
-dimension and dynamics in the row dimension.
Convert mrs_data object to a matrix, with spectral points in the column dimension and dynamics in the row dimension.
-
+
- Convert mrs_data object to a vector.
Convert mrs_data object to a matrix, with spectral points in the column dimension and dynamics in the row dimension.
-
+
- Create a BIDS directory and file structure from a list of mrs_data objects.
Convert mrs_data object to a vector.
- Perform a fftshift on a matrix, with each column replaced by its shifted
-result.
Perform a fftshift on a matrix, with each column replaced by its shifted result.
- Perform an ifftshift on a matrix, with each column replaced by its shifted
-result.
Perform an ifftshift on a matrix, with each column replaced by its shifted result.
@@ -946,9 +930,7 @@ All functions
- Flip the x data dimension order of a nifti image. This corresponds to
-flipping MRI data in the left-right direction, assuming the data in save in
-neurological format (can check with fslorient program).
Flip the x data dimension order of a nifti image. This corresponds to flipping MRI data in the left-right direction, assuming the data in save in neurological format (can check with fslorient program).
@@ -964,8 +946,7 @@ All functions
- Search for the highest peak in a spectral region and return the frequency,
-height and FWHM.
Search for the highest peak in a spectral region and return the frequency, height and FWHM.
@@ -974,6 +955,10 @@ All functions phase()
Apply phasing parameters to MRS data.
+
+
+ Corrected zero order phase and chemical shift offset in 1H MRS data from the brain.
@@ -1005,8 +990,7 @@ All functions
- Plot an interactive slice map from a data array where voxels can be selected
-to display a corresponding spectrum.
Plot an interactive slice map from a data array where voxels can be selected to display a corresponding spectrum.
@@ -1026,8 +1010,15 @@ All functions
- Save function results to file and load on subsequent calls to avoid repeat
-computation.
Save function results to file and load on subsequent calls to avoid repeat computation.
+
+
+ Preprocess and perform quality assessment of a single SVS data set.
+
+
+ Preprocess and perform quality assessment of one or more SVS data sets.
@@ -1055,15 +1046,11 @@ All functions
- Read a directory containing Siemens MRS IMA files and combine along the coil
-dimension. Note that the coil ID is inferred from the sorted file name and
-should be checked when consistency is required between two directories.
Read a directory containing Siemens MRS IMA files and combine along the coil dimension. Note that the coil ID is inferred from the sorted file name and should be checked when consistency is required between two directories.
- Read a directory containing Siemens MRS IMA files and combine along the
-dynamic dimension. Note that the coil ID is inferred from the sorted file
-name and should be checked when consistency is required.
Read a directory containing Siemens MRS IMA files and combine along the dynamic dimension. Note that the coil ID is inferred from the sorted file name and should be checked when consistency is required.
@@ -1103,13 +1090,11 @@ All functions
- Reconstruct complex time-domain data from the real part of frequency-domain
-data.
Reconstruct complex time-domain data from the real part of frequency-domain data.
- Reconstruct complex time-domain data from the real part of frequency-domain
-data.
Reconstruct complex time-domain data from the real part of frequency-domain data.
@@ -1141,8 +1126,7 @@ All functions
- Resample a VOI to match a target image space using nearest-neighbour
-interpolation.
Resample a VOI to match a target image space using nearest-neighbour interpolation.
@@ -1158,23 +1142,19 @@ All functions
- Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water).
Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / kg of tissue water).
- Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water).
Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / kg of tissue water).
- Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / Litre of tissue).
Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / Litre of tissue).
- Convert default LCM/TARQUIN concentration scaling to molal units with partial
-volume correction.
Convert default LCM/TARQUIN concentration scaling to molal units with partial volume correction.
@@ -1222,8 +1202,7 @@ All functions
- MEGA-PRESS sequence with ideal localisation pulses and Gaussian shaped
-editing pulse.
MEGA-PRESS sequence with ideal localisation pulses and Gaussian shaped editing pulse.
@@ -1251,13 +1230,11 @@ All functions
- STEAM sequence with ideal pulses and coherence order filtering to simulate
-gradient crushers.
STEAM sequence with ideal pulses and coherence order filtering to simulate gradient crushers.
- STEAM sequence with ideal pulses using the z-rotation gradient simulation
-method described by Young et al JMR 140, 146-152 (1999).
STEAM sequence with ideal pulses using the z-rotation gradient simulation method described by Young et al JMR 140, 146-152 (1999).
@@ -1293,8 +1270,7 @@ All functions
- Set the number of time-domain data points, truncating or zero-filling as
-appropriate.
Set the number of time-domain data points, truncating or zero-filling as appropriate.
@@ -1318,18 +1294,15 @@ All functions
- Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS
-sequence. Note, ideal pulses are assumed.
Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS sequence. Note, ideal pulses are assumed.
- Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS
-sequence. Note, ideal pulses are assumed.
Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS sequence. Note, ideal pulses are assumed.
- Simulate a macromolecular and lipid basis-set suitable for 1H brain MRS
-analysis.
Simulate a macromolecular and lipid basis-set suitable for 1H brain MRS analysis.
@@ -1353,8 +1326,7 @@ All functions
- Simulate an ideal pulse excitation profile by smoothing a top-hat function
-with a Gaussian.
Simulate an ideal pulse excitation profile by smoothing a top-hat function with a Gaussian.
@@ -1374,17 +1346,19 @@ All functions
- Simulate and fit some spectra with ABfit for benchmarking purposes. Basic
-timing and performance metrics will be printed.
Simulate and fit some spectra with ABfit for benchmarking purposes. Basic timing and performance metrics will be printed.
Example MEGA-PRESS data with significant B0 drift.
+
+
+ Simulate an example fMRS dataset for a block design fMRS experiment and export a BIDS structure.
- Simulate a typical metabolite basis set for benchmarking. Timing metrics will
-be printed on completion.
Simulate a typical metabolite basis set for benchmarking. Timing metrics will be printed on completion.
@@ -1400,8 +1374,7 @@ All functions
- Convert SPM style segmentation files to a single categorical image where
-the numerical values map as: 0) Other, 1) CSF, 2) GM and 3) WM.
Convert SPM style segmentation files to a single categorical image where the numerical values map as: 0) Other, 1) CSF, 2) GM and 3) WM.
@@ -1413,8 +1386,7 @@ All functions
- Plot the fitting results of an object of class fit_result with
-individual basis set components shown.
Plot the fitting results of an object of class fit_result with individual basis set components shown.
@@ -1459,6 +1431,10 @@ All functions svs_1h_brain_batch_analysis()
Batch interface to the standard SVS 1H brain analysis pipeline.
+
+
+ Perform a t-test on spectral data points.
@@ -1518,8 +1494,7 @@ All functions
- Fade a spectrum to zero by frequency domain multiplication with a tanh
-function. Note this operation distorts data points at the end of the FID.
Fade a spectrum to zero by frequency domain multiplication with a tanh function. Note this operation distorts data points at the end of the FID.
@@ -1549,7 +1524,7 @@ All functions
diff --git a/docs/reference/int_spec.html b/docs/reference/int_spec.html
index c7060fe7..783325a8 100644
--- a/docs/reference/int_spec.html
+++ b/docs/reference/int_spec.html
@@ -1,5 +1,5 @@
-Integrate a spectral region. — int_spec • Spectroscopy Analysis Tools (spant) Integrate a spectral region. — int_spec • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -118,7 +118,7 @@ Value
diff --git a/docs/reference/interleave_dyns.html b/docs/reference/interleave_dyns.html
index effe5543..441eff27 100644
--- a/docs/reference/interleave_dyns.html
+++ b/docs/reference/interleave_dyns.html
@@ -1,5 +1,5 @@
-Interleave the first and second half of a dynamic series. — interleave_dyns • Spectroscopy Analysis Tools (spant) Interleave the first and second half of a dynamic series. — interleave_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/inv_even_dyns.html b/docs/reference/inv_even_dyns.html
index 9f9d4fff..dcb781dc 100644
--- a/docs/reference/inv_even_dyns.html
+++ b/docs/reference/inv_even_dyns.html
@@ -1,5 +1,5 @@
-Invert even numbered dynamic scans starting from 1 (2,4,6...). — inv_even_dyns • Spectroscopy Analysis Tools (spant) Invert even numbered dynamic scans starting from 1 (2,4,6...). — inv_even_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/inv_odd_dyns.html b/docs/reference/inv_odd_dyns.html
index 26212e2b..78d64660 100644
--- a/docs/reference/inv_odd_dyns.html
+++ b/docs/reference/inv_odd_dyns.html
@@ -1,5 +1,5 @@
-Invert odd numbered dynamic scans starting from 1 (1,3,5...). — inv_odd_dyns • Spectroscopy Analysis Tools (spant) Invert odd numbered dynamic scans starting from 1 (1,3,5...). — inv_odd_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/is.def.html b/docs/reference/is.def.html
index f196ffd0..a67b9eba 100644
--- a/docs/reference/is.def.html
+++ b/docs/reference/is.def.html
@@ -1,5 +1,5 @@
-Check if an object is defined, which is the same as being not NULL. — is.def • Spectroscopy Analysis Tools (spant) Check if an object is defined, which is the same as being not NULL. — is.def • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/is_fd.html b/docs/reference/is_fd.html
index 3b0ca165..18a193aa 100644
--- a/docs/reference/is_fd.html
+++ b/docs/reference/is_fd.html
@@ -1,7 +1,5 @@
-Check if the chemical shift dimension of an MRS data object is in the
-frequency domain. — is_fd • Spectroscopy Analysis Tools (spant) Check if the chemical shift dimension of an MRS data object is in the frequency domain. — is_fd • Spectroscopy Analysis Tools (spant) Transform 2D MRSI data from k-space to image space in the x-y direction. — kspace2img_xy • Spectroscopy Analysis Tools (spant) Transform 2D MRSI data from k-space to image space in the x-y direction. — kspace2img_xy • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/l2_reg.html b/docs/reference/l2_reg.html
index 3d781d80..21aa9849 100644
--- a/docs/reference/l2_reg.html
+++ b/docs/reference/l2_reg.html
@@ -1,5 +1,5 @@
-Perform l2 regularisation artefact suppression. — l2_reg • Spectroscopy Analysis Tools (spant) Perform l2 regularisation artefact suppression. — l2_reg • Spectroscopy Analysis Tools (spant) Apply line-broadening (apodisation) to MRS data or basis object. — lb • Spectroscopy Analysis Tools (spant) Apply line-broadening (apodisation) to MRS data or basis object. — lb • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -123,7 +123,7 @@ Value
diff --git a/docs/reference/lofdc.html b/docs/reference/lofdc.html
index 5419b1ec..31347a25 100644
--- a/docs/reference/lofdc.html
+++ b/docs/reference/lofdc.html
@@ -1,5 +1,5 @@
-Correct linear frequency drift. — lofdc • Spectroscopy Analysis Tools (spant) Correct linear frequency drift. — lofdc • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -138,7 +138,7 @@ Value
diff --git a/docs/reference/lw2alpha.html b/docs/reference/lw2alpha.html
index b83db682..25da229b 100644
--- a/docs/reference/lw2alpha.html
+++ b/docs/reference/lw2alpha.html
@@ -1,7 +1,5 @@
-Covert a linewidth in Hz to an equivalent alpha value in the time-domain ie:
-x * exp(-t * alpha). — lw2alpha • Spectroscopy Analysis Tools (spant) Covert a linewidth in Hz to an equivalent alpha value in the time-domain ie: x * exp(-t * alpha). — lw2alpha • Spectroscopy Analysis Tools (spant) Covert a linewidth in Hz to an equivalent beta value in the time-domain ie:
-x * exp(-t * t * beta). — lw2beta • Spectroscopy Analysis Tools (spant) Covert a linewidth in Hz to an equivalent beta value in the time-domain ie: x * exp(-t * t * beta). — lw2beta • Spectroscopy Analysis Tools (spant) Make a basis-set object from a directory containing LCModel formatted RAW
-files. — make_basis_from_raw • Spectroscopy Analysis Tools (spant) Make a basis-set object from a directory containing LCModel formatted RAW files. — make_basis_from_raw • Spectroscopy Analysis Tools (spant) Mask an MRS dataset in the dynamic dimension. — mask_dyns • Spectroscopy Analysis Tools (spant) Mask an MRS dataset in the dynamic dimension. — mask_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/mask_fit_res.html b/docs/reference/mask_fit_res.html
index 97baaa3f..ebd91a99 100644
--- a/docs/reference/mask_fit_res.html
+++ b/docs/reference/mask_fit_res.html
@@ -1,5 +1,5 @@
-Mask fit result spectra depending on a vector of bool values. — mask_fit_res • Spectroscopy Analysis Tools (spant) Mask fit result spectra depending on a vector of bool values. — mask_fit_res • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -116,7 +116,7 @@ Value
diff --git a/docs/reference/mask_xy.html b/docs/reference/mask_xy.html
index 11bb577c..b0d38619 100644
--- a/docs/reference/mask_xy.html
+++ b/docs/reference/mask_xy.html
@@ -1,5 +1,5 @@
-Mask an MRSI dataset in the x-y direction — mask_xy • Spectroscopy Analysis Tools (spant) Mask an MRSI dataset in the x-y direction — mask_xy • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/mask_xy_corners.html b/docs/reference/mask_xy_corners.html
index 09b16cd2..2d13839d 100644
--- a/docs/reference/mask_xy_corners.html
+++ b/docs/reference/mask_xy_corners.html
@@ -1,5 +1,5 @@
-Mask the four corners of an MRSI dataset in the x-y plane. — mask_xy_corners • Spectroscopy Analysis Tools (spant) Mask the four corners of an MRSI dataset in the x-y plane. — mask_xy_corners • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/mask_xy_ellipse.html b/docs/reference/mask_xy_ellipse.html
index 1d8b02e4..e2e749ef 100644
--- a/docs/reference/mask_xy_ellipse.html
+++ b/docs/reference/mask_xy_ellipse.html
@@ -1,7 +1,5 @@
-Mask the voxels outside an elliptical region spanning the MRSI dataset in the
-x-y plane. — mask_xy_ellipse • Spectroscopy Analysis Tools (spant) Mask the voxels outside an elliptical region spanning the MRSI dataset in the x-y plane. — mask_xy_ellipse • Spectroscopy Analysis Tools (spant) Mask a 2D MRSI dataset in the x-y dimension. — mask_xy_mat • Spectroscopy Analysis Tools (spant) Mask a 2D MRSI dataset in the x-y dimension. — mask_xy_mat • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Value
diff --git a/docs/reference/mat2mrs_data.html b/docs/reference/mat2mrs_data.html
index 2e2895f3..ae55665f 100644
--- a/docs/reference/mat2mrs_data.html
+++ b/docs/reference/mat2mrs_data.html
@@ -1,7 +1,5 @@
-Convert a matrix (with spectral points in the column dimension and dynamics
-in the row dimensions) into a mrs_data object. — mat2mrs_data • Spectroscopy Analysis Tools (spant) Convert a matrix (with spectral points in the column dimension and dynamics in the row dimensions) into a mrs_data object. — mat2mrs_data • Spectroscopy Analysis Tools (spant) Matrix exponential function taken from complexplus package to reduce the
-number of spant dependencies. — matexp • Spectroscopy Analysis Tools (spant) Matrix exponential function taken from complexplus package to reduce the number of spant dependencies. — matexp • Spectroscopy Analysis Tools (spant) Apply the max operator to an MRS dataset. — max_mrs • Spectroscopy Analysis Tools (spant) Apply the max operator to an MRS dataset. — max_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/max_mrs_interp.html b/docs/reference/max_mrs_interp.html
index e4474764..52e63f3e 100644
--- a/docs/reference/max_mrs_interp.html
+++ b/docs/reference/max_mrs_interp.html
@@ -1,5 +1,5 @@
-Apply the max operator to an interpolated MRS dataset. — max_mrs_interp • Spectroscopy Analysis Tools (spant) Apply the max operator to an interpolated MRS dataset. — max_mrs_interp • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/mean.list.html b/docs/reference/mean.list.html
index b8eb3463..048306fd 100644
--- a/docs/reference/mean.list.html
+++ b/docs/reference/mean.list.html
@@ -1,5 +1,5 @@
-Calculate the mean spectrum from an mrs_data object. — mean.list • Spectroscopy Analysis Tools (spant) Calculate the mean spectrum from an mrs_data object. — mean.list • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/mean.mrs_data.html b/docs/reference/mean.mrs_data.html
index 5531a28d..79515014 100644
--- a/docs/reference/mean.mrs_data.html
+++ b/docs/reference/mean.mrs_data.html
@@ -1,5 +1,5 @@
-Calculate the mean spectrum from an mrs_data object. — mean.mrs_data • Spectroscopy Analysis Tools (spant) Calculate the mean spectrum from an mrs_data object. — mean.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/mean_dyn_blocks.html b/docs/reference/mean_dyn_blocks.html
index 10467098..4c042448 100644
--- a/docs/reference/mean_dyn_blocks.html
+++ b/docs/reference/mean_dyn_blocks.html
@@ -1,5 +1,5 @@
-Calculate the mean of adjacent dynamic scans. — mean_dyn_blocks • Spectroscopy Analysis Tools (spant) Calculate the mean of adjacent dynamic scans. — mean_dyn_blocks • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/mean_dyn_pairs.html b/docs/reference/mean_dyn_pairs.html
index 63e909ea..1a241126 100644
--- a/docs/reference/mean_dyn_pairs.html
+++ b/docs/reference/mean_dyn_pairs.html
@@ -1,5 +1,5 @@
-Calculate the pairwise means across a dynamic data set. — mean_dyn_pairs • Spectroscopy Analysis Tools (spant) Calculate the pairwise means across a dynamic data set. — mean_dyn_pairs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/mean_dyns.html b/docs/reference/mean_dyns.html
index 73fdbfa7..0daa27df 100644
--- a/docs/reference/mean_dyns.html
+++ b/docs/reference/mean_dyns.html
@@ -1,5 +1,5 @@
-Calculate the mean dynamic data. — mean_dyns • Spectroscopy Analysis Tools (spant) Calculate the mean dynamic data. — mean_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/mean_mrs_list.html b/docs/reference/mean_mrs_list.html
index 808b6c50..10d842c0 100644
--- a/docs/reference/mean_mrs_list.html
+++ b/docs/reference/mean_mrs_list.html
@@ -1,5 +1,5 @@
-Return the mean of a list of mrs_data objects. — mean_mrs_list • Spectroscopy Analysis Tools (spant) Return the mean of a list of mrs_data objects. — mean_mrs_list • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/mean_vec_blocks.html b/docs/reference/mean_vec_blocks.html
index 8fc92eaa..dd78b122 100644
--- a/docs/reference/mean_vec_blocks.html
+++ b/docs/reference/mean_vec_blocks.html
@@ -1,5 +1,5 @@
-Calculate the mean of adjacent blocks in a vector. — mean_vec_blocks • Spectroscopy Analysis Tools (spant) Calculate the mean of adjacent blocks in a vector. — mean_vec_blocks • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/median_dyns.html b/docs/reference/median_dyns.html
index 1039d4b5..9a085b10 100644
--- a/docs/reference/median_dyns.html
+++ b/docs/reference/median_dyns.html
@@ -1,5 +1,5 @@
-Calculate the median dynamic data. — median_dyns • Spectroscopy Analysis Tools (spant) Calculate the median dynamic data. — median_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/mod_td.html b/docs/reference/mod_td.html
index 76ad0a40..141ef09e 100644
--- a/docs/reference/mod_td.html
+++ b/docs/reference/mod_td.html
@@ -1,5 +1,5 @@
-Apply the Modulus operator to the time-domain MRS signal. — mod_td • Spectroscopy Analysis Tools (spant) Apply the Modulus operator to the time-domain MRS signal. — mod_td • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/mrs_data2basis.html b/docs/reference/mrs_data2basis.html
index 62f7d749..11797b91 100644
--- a/docs/reference/mrs_data2basis.html
+++ b/docs/reference/mrs_data2basis.html
@@ -1,7 +1,5 @@
-Convert an mrs_data object to basis object - where basis signals are spread
-across the dynamic dimension in the MRS data. — mrs_data2basis • Spectroscopy Analysis Tools (spant) Convert an mrs_data object to basis object - where basis signals are spread across the dynamic dimension in the MRS data. — mrs_data2basis • Spectroscopy Analysis Tools (spant) Create a BIDS file structure from a vector of MRS data paths or list of mrs_data objects. — mrs_data2bids • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Create a BIDS file structure from a vector of MRS data paths or list of mrs_data objects.
+ Source: R/fmrs.R
+ mrs_data2bids.Rd
+
+
+
+ Create a BIDS file structure from a vector of MRS data paths or list of
+mrs_data objects.
+
+
+
+ mrs_data2bids(
+ mrs_data,
+ output_dir,
+ suffix = NULL,
+ sub = NULL,
+ ses = NULL,
+ task = NULL,
+ acq = NULL,
+ nuc = NULL,
+ voi = NULL,
+ rec = NULL,
+ run = NULL,
+ echo = NULL,
+ inv = NULL,
+ skip_existing = TRUE
+)
+
+
+
+ Arguments
+ - mrs_data
+vector of MRS data paths or list of mrs_data objects.
- output_dir
+the base directory to create the BIDS structure.
- suffix
+optional vector of file suffixes. Default behaviour is to
+automatically determine these from the input data, however it is recommended
+that they are specified to allow more efficient skipping of existing data.
- sub
+optional vector of subject labels. If not specified, these will be
+automatically generated as a series of increasing zero-padded integer values
+corresponding to the mrs_data input indices.
- ses
+optional vector of session labels.
- task
+optional vector of task labels.
- acq
+optional vector of acquisition labels.
- nuc
+optional vector of nucleus labels.
- voi
+optional vector of volume of interest labels.
- rec
+optional vector of reconstruction labels.
- run
+optional vector of run indices.
- echo
+optional vector of echo time indices.
- inv
+optional vector of inversion indices.
- skip_existing
+skip any data files that have already been converted.
+Defaults to TRUE, set to FALSE to force an overwrite of any existing data
+files.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/mrs_data2mat.html b/docs/reference/mrs_data2mat.html
index cf5ff28c..9e47688a 100644
--- a/docs/reference/mrs_data2mat.html
+++ b/docs/reference/mrs_data2mat.html
@@ -1,7 +1,5 @@
-Convert mrs_data object to a matrix, with spectral points in the column
-dimension and dynamics in the row dimension. — mrs_data2mat • Spectroscopy Analysis Tools (spant) Convert mrs_data object to a matrix, with spectral points in the column dimension and dynamics in the row dimension. — mrs_data2mat • Spectroscopy Analysis Tools (spant) Convert mrs_data object to a matrix, with spectral points in the column dimension and dynamics in the row dimension. — mrs_data2spec_mat • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Convert mrs_data object to a matrix, with spectral points in the column dimension and dynamics in the row dimension.
+ Source: R/mrs_data_proc.R
+ mrs_data2spec_mat.Rd
+
+
+
+ Convert mrs_data object to a matrix, with spectral points in the column
+dimension and dynamics in the row dimension.
+
+
+
+ mrs_data2spec_mat(mrs_data, collapse = TRUE)
+
+
+
+ Arguments
+ - mrs_data
+MRS data object or list of MRS data objects.
- collapse
+collapse all other dimensions along the dynamic dimension, eg
+a 16x16 MRSI grid would be first collapsed across 256 dynamic scans.
+
+ Value
+
+
+MRS data matrix.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/mrs_data2vec.html b/docs/reference/mrs_data2vec.html
index fb172d68..a1fd654d 100644
--- a/docs/reference/mrs_data2vec.html
+++ b/docs/reference/mrs_data2vec.html
@@ -1,5 +1,5 @@
-Convert mrs_data object to a vector. — mrs_data2vec • Spectroscopy Analysis Tools (spant) Convert mrs_data object to a vector. — mrs_data2vec • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -126,7 +126,7 @@ Value
diff --git a/docs/reference/mvfftshift.html b/docs/reference/mvfftshift.html
index 92b0841b..976b3410 100644
--- a/docs/reference/mvfftshift.html
+++ b/docs/reference/mvfftshift.html
@@ -1,7 +1,5 @@
-Perform a fftshift on a matrix, with each column replaced by its shifted
-result. — mvfftshift • Spectroscopy Analysis Tools (spant) Perform a fftshift on a matrix, with each column replaced by its shifted result. — mvfftshift • Spectroscopy Analysis Tools (spant) Perform an ifftshift on a matrix, with each column replaced by its shifted
-result. — mvifftshift • Spectroscopy Analysis Tools (spant) Perform an ifftshift on a matrix, with each column replaced by its shifted result. — mvifftshift • Spectroscopy Analysis Tools (spant) Print fit coordinates from a single index. — n2coord • Spectroscopy Analysis Tools (spant) Print fit coordinates from a single index. — n2coord • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/nifti_flip_lr.html b/docs/reference/nifti_flip_lr.html
index 730abe3c..19860b3c 100644
--- a/docs/reference/nifti_flip_lr.html
+++ b/docs/reference/nifti_flip_lr.html
@@ -1,9 +1,5 @@
-Flip the x data dimension order of a nifti image. This corresponds to
-flipping MRI data in the left-right direction, assuming the data in save in
-neurological format (can check with fslorient program). — nifti_flip_lr • Spectroscopy Analysis Tools (spant) Flip the x data dimension order of a nifti image. This corresponds to flipping MRI data in the left-right direction, assuming the data in save in neurological format (can check with fslorient program). — nifti_flip_lr • Spectroscopy Analysis Tools (spant) Export a one-page pdf of a single fit result — one_page_pdf • Spectroscopy Analysis Tools (spant) Export a one-page pdf of a single fit result — one_page_pdf • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -108,7 +108,7 @@ Arguments
diff --git a/docs/reference/ortho3.html b/docs/reference/ortho3.html
index 13ade97d..5d7dd2fd 100644
--- a/docs/reference/ortho3.html
+++ b/docs/reference/ortho3.html
@@ -1,5 +1,5 @@
-Display an orthographic projection plot of a nifti object. — ortho3 • Spectroscopy Analysis Tools (spant) Display an orthographic projection plot of a nifti object. — ortho3 • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -172,7 +172,7 @@ Arguments
diff --git a/docs/reference/ortho3_inter.html b/docs/reference/ortho3_inter.html
index 090cc5e5..15948899 100644
--- a/docs/reference/ortho3_inter.html
+++ b/docs/reference/ortho3_inter.html
@@ -1,5 +1,5 @@
-Display an interactive orthographic projection plot of a nifti object. — ortho3_inter • Spectroscopy Analysis Tools (spant) Display an interactive orthographic projection plot of a nifti object. — ortho3_inter • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -132,7 +132,7 @@ Arguments
diff --git a/docs/reference/peak_info.html b/docs/reference/peak_info.html
index 09058bd8..41c8ffaf 100644
--- a/docs/reference/peak_info.html
+++ b/docs/reference/peak_info.html
@@ -1,7 +1,5 @@
-Search for the highest peak in a spectral region and return the frequency,
-height and FWHM. — peak_info • Spectroscopy Analysis Tools (spant) Search for the highest peak in a spectral region and return the frequency, height and FWHM. — peak_info • Spectroscopy Analysis Tools (spant) Papoulis-Gerchberg (PG) algorithm method for k-space extrapolation. — pg_extrap_xy • Spectroscopy Analysis Tools (spant) Papoulis-Gerchberg (PG) algorithm method for k-space extrapolation. — pg_extrap_xy • Spectroscopy Analysis Tools (spant) Apply phasing parameters to MRS data. — phase • Spectroscopy Analysis Tools (spant) Apply phasing parameters to MRS data. — phase • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/phase_ref_1h_brain.html b/docs/reference/phase_ref_1h_brain.html
new file mode 100644
index 00000000..8707a74a
--- /dev/null
+++ b/docs/reference/phase_ref_1h_brain.html
@@ -0,0 +1,131 @@
+
+Corrected zero order phase and chemical shift offset in 1H MRS data from the brain. — phase_ref_1h_brain • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Corrected zero order phase and chemical shift offset in 1H MRS data from the brain.
+ Source: R/rats.R
+ phase_ref_1h_brain.Rd
+
+
+
+ Corrected zero order phase and chemical shift offset in 1H MRS data from the
+brain.
+
+
+
+ phase_ref_1h_brain(mrs_data, mean_ref = FALSE, ret_corr_only = TRUE)
+
+
+
+ Arguments
+ - mrs_data
+MRS data to be corrected.
- mean_ref
+apply the phase and offset of the mean spectrum to all
+others. Default is FALSE.
- ret_corr_only
+return the corrected data only.
+
+ Value
+
+
+corrected MRS data.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/plot.fit_result.html b/docs/reference/plot.fit_result.html
index e54d3bc1..836a53ee 100644
--- a/docs/reference/plot.fit_result.html
+++ b/docs/reference/plot.fit_result.html
@@ -1,5 +1,5 @@
-Plot the fitting results of an object of class fit_result. — plot.fit_result • Spectroscopy Analysis Tools (spant) Plot the fitting results of an object of class fit_result. — plot.fit_result • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -207,7 +207,7 @@ Arguments
diff --git a/docs/reference/plot.mrs_data.html b/docs/reference/plot.mrs_data.html
index fabcc35b..bb2ec651 100644
--- a/docs/reference/plot.mrs_data.html
+++ b/docs/reference/plot.mrs_data.html
@@ -1,5 +1,5 @@
-Plotting method for objects of class mrs_data. — plot.mrs_data • Spectroscopy Analysis Tools (spant) Plotting method for objects of class mrs_data. — plot.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -287,7 +287,7 @@ Arguments
diff --git a/docs/reference/plot_bc.html b/docs/reference/plot_bc.html
index 4f8309b4..b48142cc 100644
--- a/docs/reference/plot_bc.html
+++ b/docs/reference/plot_bc.html
@@ -1,5 +1,5 @@
-Convenience function to plot a baseline estimate with the original data. — plot_bc • Spectroscopy Analysis Tools (spant) Convenience function to plot a baseline estimate with the original data. — plot_bc • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -108,7 +108,7 @@ Arguments
diff --git a/docs/reference/plot_reg.html b/docs/reference/plot_reg.html
index ae1acbe7..2addb2f6 100644
--- a/docs/reference/plot_reg.html
+++ b/docs/reference/plot_reg.html
@@ -1,5 +1,5 @@
-Plot regressors as an image. — plot_reg • Spectroscopy Analysis Tools (spant) Plot regressors as an image. — plot_reg • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/plot_slice_fit.html b/docs/reference/plot_slice_fit.html
index fbc7b560..57f1af8a 100644
--- a/docs/reference/plot_slice_fit.html
+++ b/docs/reference/plot_slice_fit.html
@@ -1,5 +1,5 @@
-Plot a 2D slice from an MRSI fit result object. — plot_slice_fit • Spectroscopy Analysis Tools (spant) Plot a 2D slice from an MRSI fit result object. — plot_slice_fit • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -129,7 +129,7 @@ Arguments
diff --git a/docs/reference/plot_slice_fit_inter.html b/docs/reference/plot_slice_fit_inter.html
index 4eed104a..da105a7d 100644
--- a/docs/reference/plot_slice_fit_inter.html
+++ b/docs/reference/plot_slice_fit_inter.html
@@ -1,5 +1,5 @@
-Plot a 2D slice from an MRSI fit result object. — plot_slice_fit_inter • Spectroscopy Analysis Tools (spant) Plot a 2D slice from an MRSI fit result object. — plot_slice_fit_inter • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -134,7 +134,7 @@ Arguments
diff --git a/docs/reference/plot_slice_map.html b/docs/reference/plot_slice_map.html
index 553e9ac8..ffb2a134 100644
--- a/docs/reference/plot_slice_map.html
+++ b/docs/reference/plot_slice_map.html
@@ -1,5 +1,5 @@
-Plot a slice from a 7 dimensional array. — plot_slice_map • Spectroscopy Analysis Tools (spant) Plot a slice from a 7 dimensional array. — plot_slice_map • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -153,7 +153,7 @@ Arguments
diff --git a/docs/reference/plot_slice_map_inter.html b/docs/reference/plot_slice_map_inter.html
index 40d33b42..90968f66 100644
--- a/docs/reference/plot_slice_map_inter.html
+++ b/docs/reference/plot_slice_map_inter.html
@@ -1,7 +1,5 @@
-Plot an interactive slice map from a data array where voxels can be selected
-to display a corresponding spectrum. — plot_slice_map_inter • Spectroscopy Analysis Tools (spant) Plot an interactive slice map from a data array where voxels can be selected to display a corresponding spectrum. — plot_slice_map_inter • Spectroscopy Analysis Tools (spant) Plot the spectral standard deviation. — plot_spec_sd • Spectroscopy Analysis Tools (spant) Plot the spectral standard deviation. — plot_spec_sd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Arguments
diff --git a/docs/reference/plot_voi_overlay.html b/docs/reference/plot_voi_overlay.html
index 9a782e88..bbbbf35e 100644
--- a/docs/reference/plot_voi_overlay.html
+++ b/docs/reference/plot_voi_overlay.html
@@ -1,5 +1,5 @@
-Plot a volume as an image overlay. — plot_voi_overlay • Spectroscopy Analysis Tools (spant) Plot a volume as an image overlay. — plot_voi_overlay • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -116,7 +116,7 @@ Arguments
diff --git a/docs/reference/plot_voi_overlay_seg.html b/docs/reference/plot_voi_overlay_seg.html
index 3d4e74ff..0e800ff2 100644
--- a/docs/reference/plot_voi_overlay_seg.html
+++ b/docs/reference/plot_voi_overlay_seg.html
@@ -1,5 +1,5 @@
-Plot a volume as an overlay on a segmented brain volume. — plot_voi_overlay_seg • Spectroscopy Analysis Tools (spant) Plot a volume as an overlay on a segmented brain volume. — plot_voi_overlay_seg • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Arguments
diff --git a/docs/reference/ppm.html b/docs/reference/ppm.html
index c352327a..ee4696e2 100644
--- a/docs/reference/ppm.html
+++ b/docs/reference/ppm.html
@@ -1,5 +1,5 @@
-Return the ppm scale of an MRS dataset or fit result. — ppm • Spectroscopy Analysis Tools (spant) Return the ppm scale of an MRS dataset or fit result. — ppm • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -132,7 +132,7 @@ Value
diff --git a/docs/reference/precomp.html b/docs/reference/precomp.html
index 822d7336..df3d2c6c 100644
--- a/docs/reference/precomp.html
+++ b/docs/reference/precomp.html
@@ -1,7 +1,5 @@
-Save function results to file and load on subsequent calls to avoid repeat
-computation. — precomp • Spectroscopy Analysis Tools (spant) Save function results to file and load on subsequent calls to avoid repeat computation. — precomp • Spectroscopy Analysis Tools (spant) Preprocess and perform quality assessment of a single SVS data set. — preproc_svs • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Preprocess and perform quality assessment of a single SVS data set.
+ Source: R/fmrs.R
+ preproc_svs.Rd
+
+
+
+ Preprocess and perform quality assessment of a single SVS data set.
+
+
+
+ preproc_svs(path, label = NULL, output_dir = NULL, ref_inds = NULL)
+
+
+
+ Arguments
+ - path
+path to the fMRS data file or IMA directory.
- label
+a label to describe the data set.
- output_dir
+output directory.
- ref_inds
+a vector of 1-based indices for any water reference dynamic
+scans.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/preproc_svs_dataset.html b/docs/reference/preproc_svs_dataset.html
new file mode 100644
index 00000000..07c3a29b
--- /dev/null
+++ b/docs/reference/preproc_svs_dataset.html
@@ -0,0 +1,148 @@
+
+Preprocess and perform quality assessment of one or more SVS data sets. — preproc_svs_dataset • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Preprocess and perform quality assessment of one or more SVS data sets.
+ Source: R/fmrs.R
+ preproc_svs_dataset.Rd
+
+
+
+ Preprocess and perform quality assessment of one or more SVS data sets.
+
+
+
+ preproc_svs_dataset(
+ paths,
+ labels = NULL,
+ output_dir = "spant_analysis",
+ exclude_labels = NULL,
+ overwrite = FALSE,
+ ref_inds = NULL,
+ return_results = FALSE
+)
+
+
+
+ Arguments
+ - paths
+paths to the fMRS data file or IMA directory.
- labels
+labels to describe each data set.
- output_dir
+output directory.
- exclude_labels
+vector of labels of scans to exclude, eg poor quality
+data.
- overwrite
+overwrite saved results, defaults to FALSE.
- ref_inds
+a vector of 1-based indices for any water reference dynamic
+scans.
- return_results
+function will return key outputs, defaults to FALSE.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/print.fit_result.html b/docs/reference/print.fit_result.html
index 297f28dc..5f434e57 100644
--- a/docs/reference/print.fit_result.html
+++ b/docs/reference/print.fit_result.html
@@ -1,5 +1,5 @@
-Print a summary of an object of class fit_result. — print.fit_result • Spectroscopy Analysis Tools (spant) Print a summary of an object of class fit_result. — print.fit_result • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -105,7 +105,7 @@ Arguments
diff --git a/docs/reference/print.mrs_data.html b/docs/reference/print.mrs_data.html
index 51199017..e1561eb2 100644
--- a/docs/reference/print.mrs_data.html
+++ b/docs/reference/print.mrs_data.html
@@ -1,5 +1,5 @@
-Print a summary of mrs_data parameters. — print.mrs_data • Spectroscopy Analysis Tools (spant) Print a summary of mrs_data parameters. — print.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -109,7 +109,7 @@ Arguments
diff --git a/docs/reference/qn_states.html b/docs/reference/qn_states.html
index 0f42f2f9..d7aa6715 100644
--- a/docs/reference/qn_states.html
+++ b/docs/reference/qn_states.html
@@ -1,5 +1,5 @@
-Get the quantum coherence matrix for a spin system. — qn_states • Spectroscopy Analysis Tools (spant) Get the quantum coherence matrix for a spin system. — qn_states • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/rats.html b/docs/reference/rats.html
index 5a39a396..93585e08 100644
--- a/docs/reference/rats.html
+++ b/docs/reference/rats.html
@@ -1,5 +1,5 @@
-Robust Alignment to a Target Spectrum (RATS). — rats • Spectroscopy Analysis Tools (spant) Robust Alignment to a Target Spectrum (RATS). — rats • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -207,7 +207,7 @@ Value
diff --git a/docs/reference/re_weighting.html b/docs/reference/re_weighting.html
index d21caf21..8b0b070a 100644
--- a/docs/reference/re_weighting.html
+++ b/docs/reference/re_weighting.html
@@ -1,5 +1,5 @@
-Apply a weighting to the FID to enhance spectral resolution. — re_weighting • Spectroscopy Analysis Tools (spant) Apply a weighting to the FID to enhance spectral resolution. — re_weighting • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/read_basis.html b/docs/reference/read_basis.html
index da9b94af..eb6f8557 100644
--- a/docs/reference/read_basis.html
+++ b/docs/reference/read_basis.html
@@ -1,5 +1,5 @@
-Read a basis file in LCModel .basis format. — read_basis • Spectroscopy Analysis Tools (spant) Read a basis file in LCModel .basis format. — read_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/read_ima_coil_dir.html b/docs/reference/read_ima_coil_dir.html
index 28c02de0..4f073cd8 100644
--- a/docs/reference/read_ima_coil_dir.html
+++ b/docs/reference/read_ima_coil_dir.html
@@ -1,9 +1,5 @@
-Read a directory containing Siemens MRS IMA files and combine along the coil
-dimension. Note that the coil ID is inferred from the sorted file name and
-should be checked when consistency is required between two directories. — read_ima_coil_dir • Spectroscopy Analysis Tools (spant) Read a directory containing Siemens MRS IMA files and combine along the coil dimension. Note that the coil ID is inferred from the sorted file name and should be checked when consistency is required between two directories. — read_ima_coil_dir • Spectroscopy Analysis Tools (spant) Read a directory containing Siemens MRS IMA files and combine along the
-dynamic dimension. Note that the coil ID is inferred from the sorted file
-name and should be checked when consistency is required. — read_ima_dyn_dir • Spectroscopy Analysis Tools (spant) Read a directory containing Siemens MRS IMA files and combine along the dynamic dimension. Note that the coil ID is inferred from the sorted file name and should be checked when consistency is required. — read_ima_dyn_dir • Spectroscopy Analysis Tools (spant) Read an LCModel formatted coord file containing fit information. — read_lcm_coord • Spectroscopy Analysis Tools (spant) Read an LCModel formatted coord file containing fit information. — read_lcm_coord • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -107,7 +107,7 @@ Value
diff --git a/docs/reference/read_mrs.html b/docs/reference/read_mrs.html
index 3ac2a36b..2cf36b20 100644
--- a/docs/reference/read_mrs.html
+++ b/docs/reference/read_mrs.html
@@ -1,5 +1,5 @@
-Read MRS data from a file. — read_mrs • Spectroscopy Analysis Tools (spant) Read MRS data from a file. — read_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -88,7 +88,8 @@ Read MRS data from a file.
full_fid = FALSE,
omit_svs_ref_scans = TRUE,
verbose = FALSE,
- extra = NULL
+ extra = NULL,
+ fid_filt_dist = NULL
)
@@ -140,6 +141,13 @@ Arguments
an optional data frame to provide additional variables for use
in subsequent analysis steps, eg id or grouping variables.
fid_filt_dist
+indicate if the data has a distorted FID due to a
+brick-wall filter being used to downsample the data. Default is to auto
+detect this from the data, but TRUE or FALSE options can be given to override
+detection.
Value
@@ -183,7 +191,7 @@ Examples
diff --git a/docs/reference/read_mrs_tqn.html b/docs/reference/read_mrs_tqn.html
index 5766362f..84bdaf3a 100644
--- a/docs/reference/read_mrs_tqn.html
+++ b/docs/reference/read_mrs_tqn.html
@@ -1,5 +1,5 @@
-Read MRS data using the TARQUIN software package. — read_mrs_tqn • Spectroscopy Analysis Tools (spant) Read MRS data using the TARQUIN software package. — read_mrs_tqn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -131,7 +131,7 @@ Examples
diff --git a/docs/reference/read_pulse_ascii.html b/docs/reference/read_pulse_ascii.html
index c9e0d43c..ab11c9cc 100644
--- a/docs/reference/read_pulse_ascii.html
+++ b/docs/reference/read_pulse_ascii.html
@@ -1,5 +1,5 @@
-Read an ASCII formatted pulse file. — read_pulse_ascii • Spectroscopy Analysis Tools (spant) Read an ASCII formatted pulse file. — read_pulse_ascii • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/read_pulse_bruker.html b/docs/reference/read_pulse_bruker.html
index c92bf76a..dbe9073b 100644
--- a/docs/reference/read_pulse_bruker.html
+++ b/docs/reference/read_pulse_bruker.html
@@ -1,5 +1,5 @@
-Read a Bruker formatted pulse file — read_pulse_bruker • Spectroscopy Analysis Tools (spant) Read a Bruker formatted pulse file — read_pulse_bruker • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/read_pulse_pta.html b/docs/reference/read_pulse_pta.html
index 72e1b6d4..a0fac3c3 100644
--- a/docs/reference/read_pulse_pta.html
+++ b/docs/reference/read_pulse_pta.html
@@ -1,5 +1,5 @@
-Read a .pta formatted pulse file compatible with Siemens PulseTool. — read_pulse_pta • Spectroscopy Analysis Tools (spant) Read a .pta formatted pulse file compatible with Siemens PulseTool. — read_pulse_pta • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/read_siemens_txt_hdr.html b/docs/reference/read_siemens_txt_hdr.html
index 23fb8c70..3a17d87c 100644
--- a/docs/reference/read_siemens_txt_hdr.html
+++ b/docs/reference/read_siemens_txt_hdr.html
@@ -1,5 +1,5 @@
-Read the text format header found in Siemens IMA and TWIX data files. — read_siemens_txt_hdr • Spectroscopy Analysis Tools (spant) Read the text format header found in Siemens IMA and TWIX data files. — read_siemens_txt_hdr • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -78,7 +78,7 @@ Read the text format header found in Siemens IMA and TWIX data files.
- read_siemens_txt_hdr(input, version = "vd", verbose, offset = 0)
+ read_siemens_txt_hdr(input, version = "vd", verbose = FALSE, offset = 0)
@@ -118,7 +118,7 @@ Value
diff --git a/docs/reference/read_tqn_fit.html b/docs/reference/read_tqn_fit.html
index 4da6c25e..a1630420 100644
--- a/docs/reference/read_tqn_fit.html
+++ b/docs/reference/read_tqn_fit.html
@@ -1,5 +1,5 @@
-Reader for csv fit results generated by TARQUIN. — read_tqn_fit • Spectroscopy Analysis Tools (spant) Reader for csv fit results generated by TARQUIN. — read_tqn_fit • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -113,7 +113,7 @@ Examples
diff --git a/docs/reference/read_tqn_result.html b/docs/reference/read_tqn_result.html
index 36659714..68a3e98c 100644
--- a/docs/reference/read_tqn_result.html
+++ b/docs/reference/read_tqn_result.html
@@ -1,5 +1,5 @@
-Reader for csv results generated by TARQUIN. — read_tqn_result • Spectroscopy Analysis Tools (spant) Reader for csv results generated by TARQUIN. — read_tqn_result • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -117,7 +117,7 @@ Examples
diff --git a/docs/reference/recon_imag.html b/docs/reference/recon_imag.html
index d2a72225..5bc3b1eb 100644
--- a/docs/reference/recon_imag.html
+++ b/docs/reference/recon_imag.html
@@ -1,7 +1,5 @@
-Reconstruct complex time-domain data from the real part of frequency-domain
-data. — recon_imag • Spectroscopy Analysis Tools (spant) Reconstruct complex time-domain data from the real part of frequency-domain data. — recon_imag • Spectroscopy Analysis Tools (spant) Reconstruct complex time-domain data from the real part of frequency-domain
-data. — recon_imag_vec • Spectroscopy Analysis Tools (spant) Reconstruct complex time-domain data from the real part of frequency-domain data. — recon_imag_vec • Spectroscopy Analysis Tools (spant) Reconstruct 2D MRSI data from a twix file loaded with read_mrs. — recon_twix_2d_mrsi • Spectroscopy Analysis Tools (spant) Reconstruct 2D MRSI data from a twix file loaded with read_mrs. — recon_twix_2d_mrsi • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/rectangular_mask.html b/docs/reference/rectangular_mask.html
index a2117283..6e469bc9 100644
--- a/docs/reference/rectangular_mask.html
+++ b/docs/reference/rectangular_mask.html
@@ -1,5 +1,5 @@
-Create a rectangular mask stored as a matrix of logical values. — rectangular_mask • Spectroscopy Analysis Tools (spant) Create a rectangular mask stored as a matrix of logical values. — rectangular_mask • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -130,7 +130,7 @@ Value
diff --git a/docs/reference/reexports.html b/docs/reference/reexports.html
index 694a75d1..a59e8379 100644
--- a/docs/reference/reexports.html
+++ b/docs/reference/reexports.html
@@ -1,5 +1,5 @@
-Objects exported from other packages — reexports • Spectroscopy Analysis Tools (spant) Objects exported from other packages — reexports • Spectroscopy Analysis Tools (spant)
Spectroscopy Analysis Tools (spant)
- 2.21.0
+ 2.22.0
@@ -103,7 +103,7 @@ Objects exported from other packages
diff --git a/docs/reference/rep_array_dim.html b/docs/reference/rep_array_dim.html
index b9c49b4a..48c0a5ed 100644
--- a/docs/reference/rep_array_dim.html
+++ b/docs/reference/rep_array_dim.html
@@ -1,5 +1,5 @@
-Repeat an array over a given dimension. — rep_array_dim • Spectroscopy Analysis Tools (spant) Repeat an array over a given dimension. — rep_array_dim • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/rep_dyn.html b/docs/reference/rep_dyn.html
index 6bbfb0ef..89a4bb9b 100644
--- a/docs/reference/rep_dyn.html
+++ b/docs/reference/rep_dyn.html
@@ -1,5 +1,5 @@
-Replicate a scan in the dynamic dimension. — rep_dyn • Spectroscopy Analysis Tools (spant) Replicate a scan in the dynamic dimension. — rep_dyn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/rep_mrs.html b/docs/reference/rep_mrs.html
index 67730b5c..becb8f00 100644
--- a/docs/reference/rep_mrs.html
+++ b/docs/reference/rep_mrs.html
@@ -1,5 +1,5 @@
-Replicate a scan over a given dimension. — rep_mrs • Spectroscopy Analysis Tools (spant) Replicate a scan over a given dimension. — rep_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -138,7 +138,7 @@ Value
diff --git a/docs/reference/resample_basis.html b/docs/reference/resample_basis.html
index b0f2ab17..c7a6222a 100644
--- a/docs/reference/resample_basis.html
+++ b/docs/reference/resample_basis.html
@@ -1,5 +1,5 @@
-Resample a basis-set to match a mrs_data acquisition. — resample_basis • Spectroscopy Analysis Tools (spant) Resample a basis-set to match a mrs_data acquisition. — resample_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -116,7 +116,7 @@ Value
diff --git a/docs/reference/resample_img.html b/docs/reference/resample_img.html
index f1e7beaf..b0cc8f71 100644
--- a/docs/reference/resample_img.html
+++ b/docs/reference/resample_img.html
@@ -1,5 +1,5 @@
-Resample an image to match a target image space. — resample_img • Spectroscopy Analysis Tools (spant) Resample an image to match a target image space. — resample_img • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/resample_voi.html b/docs/reference/resample_voi.html
index 8fbfa836..a29ab096 100644
--- a/docs/reference/resample_voi.html
+++ b/docs/reference/resample_voi.html
@@ -1,7 +1,5 @@
-Resample a VOI to match a target image space using nearest-neighbour
-interpolation. — resample_voi • Spectroscopy Analysis Tools (spant) Resample a VOI to match a target image space using nearest-neighbour interpolation. — resample_voi • Spectroscopy Analysis Tools (spant) Reslice a nifti object to match the orientation of mrs data. — reslice_to_mrs • Spectroscopy Analysis Tools (spant) Reslice a nifti object to match the orientation of mrs data. — reslice_to_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/reson_table2mrs_data.html b/docs/reference/reson_table2mrs_data.html
index d75579ee..c5a2167a 100644
--- a/docs/reference/reson_table2mrs_data.html
+++ b/docs/reference/reson_table2mrs_data.html
@@ -1,5 +1,5 @@
-Generate mrs_data from a table of single Lorentzian resonances. — reson_table2mrs_data • Spectroscopy Analysis Tools (spant) Generate mrs_data from a table of single Lorentzian resonances. — reson_table2mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -119,7 +119,7 @@ Value
diff --git a/docs/reference/rm_dyns.html b/docs/reference/rm_dyns.html
index 5d5ef692..573e1f51 100644
--- a/docs/reference/rm_dyns.html
+++ b/docs/reference/rm_dyns.html
@@ -1,5 +1,5 @@
-Remove a subset of dynamic scans. — rm_dyns • Spectroscopy Analysis Tools (spant) Remove a subset of dynamic scans. — rm_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/scale_amp_molal.html b/docs/reference/scale_amp_molal.html
index aaeee1f2..7acb8cb0 100644
--- a/docs/reference/scale_amp_molal.html
+++ b/docs/reference/scale_amp_molal.html
@@ -1,7 +1,5 @@
-Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water). — scale_amp_molal • Spectroscopy Analysis Tools (spant) Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / kg of tissue water). — scale_amp_molal • Spectroscopy Analysis Tools (spant)
Spectroscopy Analysis Tools (spant)
- 2.21.0
+ 2.22.0
@@ -76,8 +74,7 @@
- Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water).
+ Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / kg of tissue water).
Source: R/amp_scaling.R
scale_amp_molal.Rd
@@ -163,7 +160,7 @@ Value
diff --git a/docs/reference/scale_amp_molal_pvc.html b/docs/reference/scale_amp_molal_pvc.html
index 962d6afc..4d194abd 100644
--- a/docs/reference/scale_amp_molal_pvc.html
+++ b/docs/reference/scale_amp_molal_pvc.html
@@ -1,7 +1,5 @@
-Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water). — scale_amp_molal_pvc • Spectroscopy Analysis Tools (spant)
@@ -75,8 +73,7 @@
- Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water).
+ Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / kg of tissue water).
Source: R/amp_scaling.R
scale_amp_molal_pvc.Rd
@@ -141,7 +138,7 @@ Value
diff --git a/docs/reference/scale_amp_molar.html b/docs/reference/scale_amp_molar.html
index 02358d91..dc87a338 100644
--- a/docs/reference/scale_amp_molar.html
+++ b/docs/reference/scale_amp_molar.html
@@ -1,7 +1,5 @@
-Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / Litre of tissue). — scale_amp_molar • Spectroscopy Analysis Tools (spant) Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / Litre of tissue). — scale_amp_molar • Spectroscopy Analysis Tools (spant) Convert default LCM/TARQUIN concentration scaling to molal units with partial
-volume correction. — scale_amp_molar2molal_pvc • Spectroscopy Analysis Tools (spant) Convert default LCM/TARQUIN concentration scaling to molal units with partial volume correction. — scale_amp_molar2molal_pvc • Spectroscopy Analysis Tools (spant) Scale fitted amplitudes to a ratio of signal amplitude. — scale_amp_ratio • Spectroscopy Analysis Tools (spant) Scale fitted amplitudes to a ratio of signal amplitude. — scale_amp_ratio • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -116,7 +116,7 @@ Value
diff --git a/docs/reference/scale_amp_ratio_value.html b/docs/reference/scale_amp_ratio_value.html
index 2036837a..6af8ac51 100644
--- a/docs/reference/scale_amp_ratio_value.html
+++ b/docs/reference/scale_amp_ratio_value.html
@@ -1,5 +1,5 @@
-Scale fitted amplitudes to a ratio of signal amplitude. — scale_amp_ratio_value • Spectroscopy Analysis Tools (spant) Scale fitted amplitudes to a ratio of signal amplitude. — scale_amp_ratio_value • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/scale_amp_water_ratio.html b/docs/reference/scale_amp_water_ratio.html
index 5b25e884..35a76b00 100644
--- a/docs/reference/scale_amp_water_ratio.html
+++ b/docs/reference/scale_amp_water_ratio.html
@@ -1,5 +1,5 @@
-Scale metabolite amplitudes as a ratio to the unsuppressed water amplitude. — scale_amp_water_ratio • Spectroscopy Analysis Tools (spant) Scale metabolite amplitudes as a ratio to the unsuppressed water amplitude. — scale_amp_water_ratio • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/scale_basis_amp.html b/docs/reference/scale_basis_amp.html
index 9401c3f1..5a58b5e5 100644
--- a/docs/reference/scale_basis_amp.html
+++ b/docs/reference/scale_basis_amp.html
@@ -1,5 +1,5 @@
-Scale a basis object by a scalar. — scale_basis_amp • Spectroscopy Analysis Tools (spant) Scale a basis object by a scalar. — scale_basis_amp • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/scale_basis_from_singlet.html b/docs/reference/scale_basis_from_singlet.html
index 0d542bc8..c9a19e77 100644
--- a/docs/reference/scale_basis_from_singlet.html
+++ b/docs/reference/scale_basis_from_singlet.html
@@ -1,5 +1,5 @@
-Scale a basis-set to be consistent with spant assumptions for water scaling. — scale_basis_from_singlet • Spectroscopy Analysis Tools (spant) Scale a basis-set to be consistent with spant assumptions for water scaling. — scale_basis_from_singlet • Spectroscopy Analysis Tools (spant)
Spectroscopy Analysis Tools (spant)
- 2.21.0
+ 2.22.0
@@ -127,7 +127,7 @@ Value
diff --git a/docs/reference/scale_mrs_amp.html b/docs/reference/scale_mrs_amp.html
index b5501a0d..990f058a 100644
--- a/docs/reference/scale_mrs_amp.html
+++ b/docs/reference/scale_mrs_amp.html
@@ -1,5 +1,5 @@
-Scale an mrs_data object by a scalar or vector or amplitudes. — scale_mrs_amp • Spectroscopy Analysis Tools (spant) Scale an mrs_data object by a scalar or vector or amplitudes. — scale_mrs_amp • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/scale_spec.html b/docs/reference/scale_spec.html
index 4f6ea835..6b3ddba4 100644
--- a/docs/reference/scale_spec.html
+++ b/docs/reference/scale_spec.html
@@ -1,5 +1,5 @@
-Scale mrs_data to a spectral region. — scale_spec • Spectroscopy Analysis Tools (spant) Scale mrs_data to a spectral region. — scale_spec • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -141,7 +141,7 @@ Value
diff --git a/docs/reference/sd.html b/docs/reference/sd.html
index ea1eec9f..3ae4dfd4 100644
--- a/docs/reference/sd.html
+++ b/docs/reference/sd.html
@@ -1,5 +1,5 @@
-Calculate the standard deviation spectrum from an mrs_data object. — sd • Spectroscopy Analysis Tools (spant) Calculate the standard deviation spectrum from an mrs_data object. — sd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/sd.mrs_data.html b/docs/reference/sd.mrs_data.html
index 3f92a49f..13bdda85 100644
--- a/docs/reference/sd.mrs_data.html
+++ b/docs/reference/sd.mrs_data.html
@@ -1,5 +1,5 @@
-Calculate the standard deviation spectrum from an mrs_data object. — sd.mrs_data • Spectroscopy Analysis Tools (spant) Calculate the standard deviation spectrum from an mrs_data object. — sd.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/seconds.html b/docs/reference/seconds.html
index b34d6627..467ee17f 100644
--- a/docs/reference/seconds.html
+++ b/docs/reference/seconds.html
@@ -1,5 +1,5 @@
-Return a time scale vector to match the FID of an MRS data object. — seconds • Spectroscopy Analysis Tools (spant) Return a time scale vector to match the FID of an MRS data object. — seconds • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/seq_cpmg_ideal.html b/docs/reference/seq_cpmg_ideal.html
index 547e96ab..45727c86 100644
--- a/docs/reference/seq_cpmg_ideal.html
+++ b/docs/reference/seq_cpmg_ideal.html
@@ -1,5 +1,5 @@
-CPMG style sequence with ideal pulses. — seq_cpmg_ideal • Spectroscopy Analysis Tools (spant) CPMG style sequence with ideal pulses. — seq_cpmg_ideal • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/seq_mega_press_ideal.html b/docs/reference/seq_mega_press_ideal.html
index 0769b8b4..a9cd7fa0 100644
--- a/docs/reference/seq_mega_press_ideal.html
+++ b/docs/reference/seq_mega_press_ideal.html
@@ -1,7 +1,5 @@
-MEGA-PRESS sequence with ideal localisation pulses and Gaussian shaped
-editing pulse. — seq_mega_press_ideal • Spectroscopy Analysis Tools (spant) MEGA-PRESS sequence with ideal localisation pulses and Gaussian shaped editing pulse. — seq_mega_press_ideal • Spectroscopy Analysis Tools (spant) PRESS sequence with shaped refocusing pulses. — seq_press_2d_shaped • Spectroscopy Analysis Tools (spant) PRESS sequence with shaped refocusing pulses. — seq_press_2d_shaped • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -165,7 +165,7 @@ Value
diff --git a/docs/reference/seq_press_ideal.html b/docs/reference/seq_press_ideal.html
index 8c976856..72c3af3d 100644
--- a/docs/reference/seq_press_ideal.html
+++ b/docs/reference/seq_press_ideal.html
@@ -1,5 +1,5 @@
-PRESS sequence with ideal pulses. — seq_press_ideal • Spectroscopy Analysis Tools (spant) PRESS sequence with ideal pulses. — seq_press_ideal • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/seq_pulse_acquire.html b/docs/reference/seq_pulse_acquire.html
index 4a88fc64..ad80571e 100644
--- a/docs/reference/seq_pulse_acquire.html
+++ b/docs/reference/seq_pulse_acquire.html
@@ -1,5 +1,5 @@
-Simple pulse and acquire sequence with ideal pulses. — seq_pulse_acquire • Spectroscopy Analysis Tools (spant) Simple pulse and acquire sequence with ideal pulses. — seq_pulse_acquire • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/seq_slaser_ideal.html b/docs/reference/seq_slaser_ideal.html
index 74688f4d..eb83e8e3 100644
--- a/docs/reference/seq_slaser_ideal.html
+++ b/docs/reference/seq_slaser_ideal.html
@@ -1,5 +1,5 @@
-sLASER sequence with ideal pulses. — seq_slaser_ideal • Spectroscopy Analysis Tools (spant) sLASER sequence with ideal pulses. — seq_slaser_ideal • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -126,7 +126,7 @@ Value
diff --git a/docs/reference/seq_spin_echo_ideal.html b/docs/reference/seq_spin_echo_ideal.html
index e23271de..4248716f 100644
--- a/docs/reference/seq_spin_echo_ideal.html
+++ b/docs/reference/seq_spin_echo_ideal.html
@@ -1,5 +1,5 @@
-Spin echo sequence with ideal pulses. — seq_spin_echo_ideal • Spectroscopy Analysis Tools (spant) Spin echo sequence with ideal pulses. — seq_spin_echo_ideal • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/seq_steam_ideal.html b/docs/reference/seq_steam_ideal.html
index a60685a8..1c8115d7 100644
--- a/docs/reference/seq_steam_ideal.html
+++ b/docs/reference/seq_steam_ideal.html
@@ -1,5 +1,5 @@
-STEAM sequence with ideal pulses. — seq_steam_ideal • Spectroscopy Analysis Tools (spant) STEAM sequence with ideal pulses. — seq_steam_ideal • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -128,7 +128,7 @@ Value
diff --git a/docs/reference/seq_steam_ideal_cof.html b/docs/reference/seq_steam_ideal_cof.html
index 8f225740..cba7af91 100644
--- a/docs/reference/seq_steam_ideal_cof.html
+++ b/docs/reference/seq_steam_ideal_cof.html
@@ -1,7 +1,5 @@
-STEAM sequence with ideal pulses and coherence order filtering to simulate
-gradient crushers. — seq_steam_ideal_cof • Spectroscopy Analysis Tools (spant) STEAM sequence with ideal pulses and coherence order filtering to simulate gradient crushers. — seq_steam_ideal_cof • Spectroscopy Analysis Tools (spant) STEAM sequence with ideal pulses using the z-rotation gradient simulation
-method described by Young et al JMR 140, 146-152 (1999). — seq_steam_ideal_young • Spectroscopy Analysis Tools (spant) STEAM sequence with ideal pulses using the z-rotation gradient simulation method described by Young et al JMR 140, 146-152 (1999). — seq_steam_ideal_young • Spectroscopy Analysis Tools (spant) Set the number of transients for an mrs_data object. — set_Ntrans • Spectroscopy Analysis Tools (spant) Set the number of transients for an mrs_data object. — set_Ntrans • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/set_def_acq_paras.html b/docs/reference/set_def_acq_paras.html
index 3e1b4004..cc2ada9c 100644
--- a/docs/reference/set_def_acq_paras.html
+++ b/docs/reference/set_def_acq_paras.html
@@ -1,5 +1,5 @@
-Set the default acquisition parameters. — set_def_acq_paras • Spectroscopy Analysis Tools (spant) Set the default acquisition parameters. — set_def_acq_paras • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Arguments
diff --git a/docs/reference/set_lcm_cmd.html b/docs/reference/set_lcm_cmd.html
index 2056ed01..42bb2f24 100644
--- a/docs/reference/set_lcm_cmd.html
+++ b/docs/reference/set_lcm_cmd.html
@@ -1,5 +1,5 @@
-Set the command to run the LCModel command-line program. — set_lcm_cmd • Spectroscopy Analysis Tools (spant) Set the command to run the LCModel command-line program. — set_lcm_cmd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/set_lw.html b/docs/reference/set_lw.html
index b64ec851..bb176c62 100644
--- a/docs/reference/set_lw.html
+++ b/docs/reference/set_lw.html
@@ -1,5 +1,5 @@
-Apply line-broadening to an mrs_data object to achieve a specified linewidth. — set_lw • Spectroscopy Analysis Tools (spant) Apply line-broadening to an mrs_data object to achieve a specified linewidth. — set_lw • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -123,7 +123,7 @@ Value
diff --git a/docs/reference/set_mask_xy_mat.html b/docs/reference/set_mask_xy_mat.html
index 49dc5d4e..52c4b617 100644
--- a/docs/reference/set_mask_xy_mat.html
+++ b/docs/reference/set_mask_xy_mat.html
@@ -1,5 +1,5 @@
-Set the masked voxels in a 2D MRSI dataset to given spectrum. — set_mask_xy_mat • Spectroscopy Analysis Tools (spant) Set the masked voxels in a 2D MRSI dataset to given spectrum. — set_mask_xy_mat • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Value
diff --git a/docs/reference/set_precomp_mode.html b/docs/reference/set_precomp_mode.html
index f44bd5d3..47c28e3b 100644
--- a/docs/reference/set_precomp_mode.html
+++ b/docs/reference/set_precomp_mode.html
@@ -1,5 +1,5 @@
-Set the precompute mode. — set_precomp_mode • Spectroscopy Analysis Tools (spant) Set the precompute mode. — set_precomp_mode • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/set_precomp_verbose.html b/docs/reference/set_precomp_verbose.html
index 1453a231..9c613505 100644
--- a/docs/reference/set_precomp_verbose.html
+++ b/docs/reference/set_precomp_verbose.html
@@ -1,5 +1,5 @@
-Set the verbosity of the precompute function. — set_precomp_verbose • Spectroscopy Analysis Tools (spant) Set the verbosity of the precompute function. — set_precomp_verbose • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/set_ref.html b/docs/reference/set_ref.html
index 8953fa50..5436dfa2 100644
--- a/docs/reference/set_ref.html
+++ b/docs/reference/set_ref.html
@@ -1,5 +1,5 @@
-Set the ppm reference value (eg ppm value at 0Hz). — set_ref • Spectroscopy Analysis Tools (spant) Set the ppm reference value (eg ppm value at 0Hz). — set_ref • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/set_td_pts.html b/docs/reference/set_td_pts.html
index 8a80d42a..586459ff 100644
--- a/docs/reference/set_td_pts.html
+++ b/docs/reference/set_td_pts.html
@@ -1,7 +1,5 @@
-Set the number of time-domain data points, truncating or zero-filling as
-appropriate. — set_td_pts • Spectroscopy Analysis Tools (spant) Set the number of time-domain data points, truncating or zero-filling as appropriate. — set_td_pts • Spectroscopy Analysis Tools (spant) Set the command to run the TARQUIN command-line program. — set_tqn_cmd • Spectroscopy Analysis Tools (spant) Set the command to run the TARQUIN command-line program. — set_tqn_cmd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/set_tr.html b/docs/reference/set_tr.html
index b2109ab0..65c9df5f 100644
--- a/docs/reference/set_tr.html
+++ b/docs/reference/set_tr.html
@@ -1,5 +1,5 @@
-Set the repetition time of an MRS dataset. — set_tr • Spectroscopy Analysis Tools (spant) Set the repetition time of an MRS dataset. — set_tr • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/shift.html b/docs/reference/shift.html
index ab0fe724..034591d0 100644
--- a/docs/reference/shift.html
+++ b/docs/reference/shift.html
@@ -1,5 +1,5 @@
-Apply a frequency shift to MRS data. — shift • Spectroscopy Analysis Tools (spant) Apply a frequency shift to MRS data. — shift • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/shift_basis.html b/docs/reference/shift_basis.html
index 2884be19..f55a65e0 100644
--- a/docs/reference/shift_basis.html
+++ b/docs/reference/shift_basis.html
@@ -1,5 +1,5 @@
-Apply frequency shifts to basis set signals. — shift_basis • Spectroscopy Analysis Tools (spant) Apply frequency shifts to basis set signals. — shift_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Value
diff --git a/docs/reference/sim_basis.html b/docs/reference/sim_basis.html
index c7838c46..bb5fefc6 100644
--- a/docs/reference/sim_basis.html
+++ b/docs/reference/sim_basis.html
@@ -1,5 +1,5 @@
-Simulate a basis set object. — sim_basis • Spectroscopy Analysis Tools (spant) Simulate a basis set object. — sim_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -136,7 +136,7 @@ Value
diff --git a/docs/reference/sim_basis_1h_brain.html b/docs/reference/sim_basis_1h_brain.html
index 62ed7389..f71ffa0b 100644
--- a/docs/reference/sim_basis_1h_brain.html
+++ b/docs/reference/sim_basis_1h_brain.html
@@ -1,7 +1,5 @@
-Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS
-sequence. Note, ideal pulses are assumed. — sim_basis_1h_brain • Spectroscopy Analysis Tools (spant) Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS sequence. Note, ideal pulses are assumed. — sim_basis_1h_brain • Spectroscopy Analysis Tools (spant) Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS
-sequence. Note, ideal pulses are assumed. — sim_basis_1h_brain_press • Spectroscopy Analysis Tools (spant) Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS sequence. Note, ideal pulses are assumed. — sim_basis_1h_brain_press • Spectroscopy Analysis Tools (spant) Simulate a macromolecular and lipid basis-set suitable for 1H brain MRS
-analysis. — sim_basis_mm_lip_lcm • Spectroscopy Analysis Tools (spant) Simulate a macromolecular and lipid basis-set suitable for 1H brain MRS analysis. — sim_basis_mm_lip_lcm • Spectroscopy Analysis Tools (spant) Simulate a basis file using TARQUIN. — sim_basis_tqn • Spectroscopy Analysis Tools (spant) Simulate a basis file using TARQUIN. — sim_basis_tqn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -129,7 +129,7 @@ Examples
diff --git a/docs/reference/sim_brain_1h.html b/docs/reference/sim_brain_1h.html
index 2044cf1a..717ee289 100644
--- a/docs/reference/sim_brain_1h.html
+++ b/docs/reference/sim_brain_1h.html
@@ -1,5 +1,5 @@
-Simulate MRS data with a similar appearance to normal brain (by default). — sim_brain_1h • Spectroscopy Analysis Tools (spant) Simulate MRS data with a similar appearance to normal brain (by default). — sim_brain_1h • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -159,7 +159,7 @@ Value
diff --git a/docs/reference/sim_mol.html b/docs/reference/sim_mol.html
index 23bcef50..77f76a50 100644
--- a/docs/reference/sim_mol.html
+++ b/docs/reference/sim_mol.html
@@ -1,5 +1,5 @@
-Simulate a mol_parameter object. — sim_mol • Spectroscopy Analysis Tools (spant) Simulate a mol_parameter object. — sim_mol • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -143,7 +143,7 @@ Value
diff --git a/docs/reference/sim_noise.html b/docs/reference/sim_noise.html
index 23875f79..a71477d4 100644
--- a/docs/reference/sim_noise.html
+++ b/docs/reference/sim_noise.html
@@ -1,5 +1,5 @@
-Simulate an mrs_data object containing simulated Gaussian noise. — sim_noise • Spectroscopy Analysis Tools (spant) Simulate an mrs_data object containing simulated Gaussian noise. — sim_noise • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -84,6 +84,7 @@ Simulate an mrs_data object containing simulated Gaussian noise.
ft = def_ft(),
N = def_N(),
ref = def_ref(),
+ nuc = def_nuc(),
dyns = 1,
fd = TRUE
)
@@ -111,6 +112,10 @@ Arguments
reference value for ppm scale.
nuc
+resonant nucleus.
dyns
number of dynamic scans to generate.
Value
diff --git a/docs/reference/sim_resonances.html b/docs/reference/sim_resonances.html
index 19e9a8a4..d4f8d7c0 100644
--- a/docs/reference/sim_resonances.html
+++ b/docs/reference/sim_resonances.html
@@ -1,5 +1,5 @@
-Simulate a MRS data object containing a set of simulated resonances. — sim_resonances • Spectroscopy Analysis Tools (spant) Simulate a MRS data object containing a set of simulated resonances. — sim_resonances • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -161,7 +161,7 @@ Examples
diff --git a/docs/reference/sim_th_excit_profile.html b/docs/reference/sim_th_excit_profile.html
index 5535c5ef..e781cab1 100644
--- a/docs/reference/sim_th_excit_profile.html
+++ b/docs/reference/sim_th_excit_profile.html
@@ -1,7 +1,5 @@
-Simulate an ideal pulse excitation profile by smoothing a top-hat function
-with a Gaussian. — sim_th_excit_profile • Spectroscopy Analysis Tools (spant) Simulate an ideal pulse excitation profile by smoothing a top-hat function with a Gaussian. — sim_th_excit_profile • Spectroscopy Analysis Tools (spant) Simulate an mrs_data object containing complex zero valued samples. — sim_zero • Spectroscopy Analysis Tools (spant) Simulate an mrs_data object containing complex zero valued samples. — sim_zero • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -78,7 +78,14 @@ Simulate an mrs_data object containing complex zero valued samples.
-
+
@@ -99,6 +106,10 @@ Arguments
reference value for ppm scale.
nuc
+resonant nucleus.
dyns
number of dynamic scans to generate.
Value
diff --git a/docs/reference/smooth_dyns.html b/docs/reference/smooth_dyns.html
index 4cc8da50..accf3a51 100644
--- a/docs/reference/smooth_dyns.html
+++ b/docs/reference/smooth_dyns.html
@@ -1,5 +1,5 @@
-Smooth data across the dynamic dimension with a Gaussian kernel. — smooth_dyns • Spectroscopy Analysis Tools (spant) Smooth data across the dynamic dimension with a Gaussian kernel. — smooth_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/sort_basis.html b/docs/reference/sort_basis.html
index 6a676ea2..d25cc006 100644
--- a/docs/reference/sort_basis.html
+++ b/docs/reference/sort_basis.html
@@ -1,5 +1,5 @@
-Sort the basis-set elements alphabetically. — sort_basis • Spectroscopy Analysis Tools (spant) Sort the basis-set elements alphabetically. — sort_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/spant-package.html b/docs/reference/spant-package.html
index b3dd8e21..90f19ec3 100644
--- a/docs/reference/spant-package.html
+++ b/docs/reference/spant-package.html
@@ -1,5 +1,5 @@
-spant: spectroscopy analysis tools. — spant-package • Spectroscopy Analysis Tools (spant) spant: spectroscopy analysis tools. — spant-package • Spectroscopy Analysis Tools (spant) Simulate and fit some spectra with ABfit for benchmarking purposes. Basic
-timing and performance metrics will be printed. — spant_abfit_benchmark • Spectroscopy Analysis Tools (spant) Simulate and fit some spectra with ABfit for benchmarking purposes. Basic timing and performance metrics will be printed. — spant_abfit_benchmark • Spectroscopy Analysis Tools (spant) Example MEGA-PRESS data with significant B0 drift. — spant_mpress_drift • Spectroscopy Analysis Tools (spant) Example MEGA-PRESS data with significant B0 drift. — spant_mpress_drift • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -83,7 +83,7 @@ Example MEGA-PRESS data with significant B0 drift.
Format
- An object of class mrs_data of length 13.
+ An object of class mrs_data of dimension 1 x 1 x 1 x 1 x 40 x 1 x 1024.
@@ -98,7 +98,7 @@ Format
diff --git a/docs/reference/spant_sim_fmrs_dataset.html b/docs/reference/spant_sim_fmrs_dataset.html
new file mode 100644
index 00000000..00e48b56
--- /dev/null
+++ b/docs/reference/spant_sim_fmrs_dataset.html
@@ -0,0 +1,117 @@
+
+Simulate an example fMRS dataset for a block design fMRS experiment and export a BIDS structure. — spant_sim_fmrs_dataset • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Simulate an example fMRS dataset for a block design fMRS experiment and export a BIDS structure.
+ Source: R/fmrs.R
+ spant_sim_fmrs_dataset.Rd
+
+
+
+ Simulate an example fMRS dataset for a block design fMRS experiment and
+export a BIDS structure.
+
+
+
+ spant_sim_fmrs_dataset(output_dir = NULL)
+
+
+
+ Arguments
+ - output_dir
+output directory for the BIDS data. Defaults to :
+"HOME/sim_fmrs_dataset/data".
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/spant_simulation_benchmark.html b/docs/reference/spant_simulation_benchmark.html
index 32daa8bf..d8cc6841 100644
--- a/docs/reference/spant_simulation_benchmark.html
+++ b/docs/reference/spant_simulation_benchmark.html
@@ -1,7 +1,5 @@
-Simulate a typical metabolite basis set for benchmarking. Timing metrics will
-be printed on completion. — spant_simulation_benchmark • Spectroscopy Analysis Tools (spant) Simulate a typical metabolite basis set for benchmarking. Timing metrics will be printed on completion. — spant_simulation_benchmark • Spectroscopy Analysis Tools (spant) Decompose an mrs_data object into white and gray matter spectra. — spec_decomp • Spectroscopy Analysis Tools (spant) Perform a mathematical operation on a spectral region. — spec_op • Spectroscopy Analysis Tools (spant) Perform a mathematical operation on a spectral region. — spec_op • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -98,8 +98,8 @@ Arguments
operator
-can be "sum" (default), "mean", "l2", "max", "min" or
-"max-min".
can be "sum" (default), "mean", "l2", "max", "max_cplx,
+"min" or "max-min".
freq_scale
@@ -129,7 +129,7 @@ Value
diff --git a/docs/reference/spin_sys.html b/docs/reference/spin_sys.html
index 853423a4..1eaa9e76 100644
--- a/docs/reference/spin_sys.html
+++ b/docs/reference/spin_sys.html
@@ -1,5 +1,5 @@
-Create a spin system object for pulse sequence simulation. — spin_sys • Spectroscopy Analysis Tools (spant) Create a spin system object for pulse sequence simulation. — spin_sys • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/spm_pve2categorical.html b/docs/reference/spm_pve2categorical.html
index 23a1bad9..70f10729 100644
--- a/docs/reference/spm_pve2categorical.html
+++ b/docs/reference/spm_pve2categorical.html
@@ -1,7 +1,5 @@
-Convert SPM style segmentation files to a single categorical image where
-the numerical values map as: 0) Other, 1) CSF, 2) GM and 3) WM. — spm_pve2categorical • Spectroscopy Analysis Tools (spant) Convert SPM style segmentation files to a single categorical image where the numerical values map as: 0) Other, 1) CSF, 2) GM and 3) WM. — spm_pve2categorical • Spectroscopy Analysis Tools (spant) Signal space projection method for lipid suppression. — ssp • Spectroscopy Analysis Tools (spant) Signal space projection method for lipid suppression. — ssp • Spectroscopy Analysis Tools (spant) Plot the fitting results of an object of class fit_result with
-individual basis set components shown. — stackplot.fit_result • Spectroscopy Analysis Tools (spant) Plot the fitting results of an object of class fit_result with individual basis set components shown. — stackplot.fit_result • Spectroscopy Analysis Tools (spant) Produce a plot with multiple traces. — stackplot • Spectroscopy Analysis Tools (spant) Produce a plot with multiple traces. — stackplot • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/stackplot.mrs_data.html b/docs/reference/stackplot.mrs_data.html
index 17ff5648..64eea445 100644
--- a/docs/reference/stackplot.mrs_data.html
+++ b/docs/reference/stackplot.mrs_data.html
@@ -1,5 +1,5 @@
-Stackplot plotting method for objects of class mrs_data. — stackplot.mrs_data • Spectroscopy Analysis Tools (spant) Stackplot plotting method for objects of class mrs_data. — stackplot.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -255,7 +255,7 @@ Arguments
diff --git a/docs/reference/sub_first_dyn.html b/docs/reference/sub_first_dyn.html
index dbd7f831..493b7242 100644
--- a/docs/reference/sub_first_dyn.html
+++ b/docs/reference/sub_first_dyn.html
@@ -1,5 +1,5 @@
-Subtract the first dynamic spectrum from a dynamic series. — sub_first_dyn • Spectroscopy Analysis Tools (spant) Subtract the first dynamic spectrum from a dynamic series. — sub_first_dyn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/sub_mean_dyns.html b/docs/reference/sub_mean_dyns.html
index 6e3bb2df..221bd0c1 100644
--- a/docs/reference/sub_mean_dyns.html
+++ b/docs/reference/sub_mean_dyns.html
@@ -1,5 +1,5 @@
-Subtract the mean dynamic spectrum from a dynamic series. — sub_mean_dyns • Spectroscopy Analysis Tools (spant) Subtract the mean dynamic spectrum from a dynamic series. — sub_mean_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/sub_median_dyns.html b/docs/reference/sub_median_dyns.html
index 134c495d..1e834f14 100644
--- a/docs/reference/sub_median_dyns.html
+++ b/docs/reference/sub_median_dyns.html
@@ -1,5 +1,5 @@
-Subtract the median dynamic spectrum from a dynamic series. — sub_median_dyns • Spectroscopy Analysis Tools (spant) Subtract the median dynamic spectrum from a dynamic series. — sub_median_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/sum_coils.html b/docs/reference/sum_coils.html
index 7bf559f2..e1ab3cc0 100644
--- a/docs/reference/sum_coils.html
+++ b/docs/reference/sum_coils.html
@@ -1,5 +1,5 @@
-Calculate the sum across receiver coil elements. — sum_coils • Spectroscopy Analysis Tools (spant) Calculate the sum across receiver coil elements. — sum_coils • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/sum_dyns.html b/docs/reference/sum_dyns.html
index a0be19d3..bbda2ffc 100644
--- a/docs/reference/sum_dyns.html
+++ b/docs/reference/sum_dyns.html
@@ -1,5 +1,5 @@
-Calculate the sum of data dynamics. — sum_dyns • Spectroscopy Analysis Tools (spant) Calculate the sum of data dynamics. — sum_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/sum_mrs.html b/docs/reference/sum_mrs.html
index a22f215b..3cc3ab9e 100644
--- a/docs/reference/sum_mrs.html
+++ b/docs/reference/sum_mrs.html
@@ -1,5 +1,5 @@
-Sum two mrs_data objects. — sum_mrs • Spectroscopy Analysis Tools (spant) Sum two mrs_data objects. — sum_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Value
diff --git a/docs/reference/sum_mrs_list.html b/docs/reference/sum_mrs_list.html
index f4e09aea..c3584348 100644
--- a/docs/reference/sum_mrs_list.html
+++ b/docs/reference/sum_mrs_list.html
@@ -1,5 +1,5 @@
-Return the sum of a list of mrs_data objects. — sum_mrs_list • Spectroscopy Analysis Tools (spant) Return the sum of a list of mrs_data objects. — sum_mrs_list • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/svs_1h_brain_analysis.html b/docs/reference/svs_1h_brain_analysis.html
index 8ce514db..dff0ef7d 100644
--- a/docs/reference/svs_1h_brain_analysis.html
+++ b/docs/reference/svs_1h_brain_analysis.html
@@ -1,5 +1,5 @@
-Standard SVS 1H brain analysis pipeline. — svs_1h_brain_analysis • Spectroscopy Analysis Tools (spant) Standard SVS 1H brain analysis pipeline. — svs_1h_brain_analysis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -199,7 +199,7 @@ Value
diff --git a/docs/reference/svs_1h_brain_analysis_dev.html b/docs/reference/svs_1h_brain_analysis_dev.html
index d70a14d3..d71bfea2 100644
--- a/docs/reference/svs_1h_brain_analysis_dev.html
+++ b/docs/reference/svs_1h_brain_analysis_dev.html
@@ -1,5 +1,5 @@
-Standard SVS 1H brain analysis pipeline. — svs_1h_brain_analysis_dev • Spectroscopy Analysis Tools (spant) Standard SVS 1H brain analysis pipeline. — svs_1h_brain_analysis_dev • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -193,7 +193,7 @@ Examples
diff --git a/docs/reference/svs_1h_brain_batch_analysis.html b/docs/reference/svs_1h_brain_batch_analysis.html
index 5631e8cc..15f7223e 100644
--- a/docs/reference/svs_1h_brain_batch_analysis.html
+++ b/docs/reference/svs_1h_brain_batch_analysis.html
@@ -1,5 +1,5 @@
-Batch interface to the standard SVS 1H brain analysis pipeline. — svs_1h_brain_batch_analysis • Spectroscopy Analysis Tools (spant) Batch interface to the standard SVS 1H brain analysis pipeline. — svs_1h_brain_batch_analysis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -144,7 +144,7 @@ Value
diff --git a/docs/reference/t_test_spec.html b/docs/reference/t_test_spec.html
new file mode 100644
index 00000000..56a7ea1b
--- /dev/null
+++ b/docs/reference/t_test_spec.html
@@ -0,0 +1,124 @@
+
+Perform a t-test on spectral data points. — t_test_spec • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+
+
+ Perform a t-test on spectral data points.
+
+
+
+ t_test_spec(mrs_data, group)
+
+
+
+ Arguments
+ - mrs_data
+an mrs_data object with spectra in the dynamic dimension.
- group
+vector describing the group membership of each dynamic spectrum.
+
+ Value
+
+
+a list of statistical results.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/td2fd.html b/docs/reference/td2fd.html
index 6748a6a8..f31ed524 100644
--- a/docs/reference/td2fd.html
+++ b/docs/reference/td2fd.html
@@ -1,5 +1,5 @@
-Transform time-domain data to the frequency-domain. — td2fd • Spectroscopy Analysis Tools (spant) Transform time-domain data to the frequency-domain. — td2fd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/td_conv_filt.html b/docs/reference/td_conv_filt.html
index a9f340c3..106b9b00 100644
--- a/docs/reference/td_conv_filt.html
+++ b/docs/reference/td_conv_filt.html
@@ -1,5 +1,5 @@
-Time-domain convolution based filter. — td_conv_filt • Spectroscopy Analysis Tools (spant) Time-domain convolution based filter. — td_conv_filt • Spectroscopy Analysis Tools (spant) Time-domain spectral registration. — tdsr • Spectroscopy Analysis Tools (spant) Time-domain spectral registration. — tdsr • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -121,7 +121,7 @@ Value
diff --git a/docs/reference/te.html b/docs/reference/te.html
index 010361b1..4a65711d 100644
--- a/docs/reference/te.html
+++ b/docs/reference/te.html
@@ -1,5 +1,5 @@
-Return the echo time of an MRS dataset. — te • Spectroscopy Analysis Tools (spant) Return the echo time of an MRS dataset. — te • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/tr.html b/docs/reference/tr.html
index 0c0bd63b..2e749e02 100644
--- a/docs/reference/tr.html
+++ b/docs/reference/tr.html
@@ -1,5 +1,5 @@
-Return the repetition time of an MRS dataset. — tr • Spectroscopy Analysis Tools (spant) Return the repetition time of an MRS dataset. — tr • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/varpro_3_para_opts.html b/docs/reference/varpro_3_para_opts.html
index c2270a16..52d7cd84 100644
--- a/docs/reference/varpro_3_para_opts.html
+++ b/docs/reference/varpro_3_para_opts.html
@@ -1,5 +1,5 @@
-Return a list of options for VARPRO based fitting with 3 free parameters. — varpro_3_para_opts • Spectroscopy Analysis Tools (spant) Return a list of options for VARPRO based fitting with 3 free parameters. — varpro_3_para_opts • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -141,7 +141,7 @@ Value
diff --git a/docs/reference/varpro_basic_opts.html b/docs/reference/varpro_basic_opts.html
index 32c86d22..c5104891 100644
--- a/docs/reference/varpro_basic_opts.html
+++ b/docs/reference/varpro_basic_opts.html
@@ -1,5 +1,5 @@
-Return a list of options for a basic VARPRO analysis. — varpro_basic_opts • Spectroscopy Analysis Tools (spant) Return a list of options for a basic VARPRO analysis. — varpro_basic_opts • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -118,7 +118,7 @@ Value
diff --git a/docs/reference/varpro_opts.html b/docs/reference/varpro_opts.html
index 2aabf11d..6332f730 100644
--- a/docs/reference/varpro_opts.html
+++ b/docs/reference/varpro_opts.html
@@ -1,5 +1,5 @@
-Return a list of options for VARPRO based fitting. — varpro_opts • Spectroscopy Analysis Tools (spant) Return a list of options for VARPRO based fitting. — varpro_opts • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -177,7 +177,7 @@ Examples
diff --git a/docs/reference/vec2mrs_data.html b/docs/reference/vec2mrs_data.html
index 0cccd73b..f0d58bf0 100644
--- a/docs/reference/vec2mrs_data.html
+++ b/docs/reference/vec2mrs_data.html
@@ -1,5 +1,5 @@
-Convert a vector into a mrs_data object. — vec2mrs_data • Spectroscopy Analysis Tools (spant) Convert a vector into a mrs_data object. — vec2mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -80,10 +80,11 @@ Convert a vector into a mrs_data object.
vec2mrs_data(
vec,
- fs = def_fs(),
- ft = def_ft(),
- ref = def_ref(),
- nuc = def_nuc(),
+ mrs_data = NULL,
+ fs = NULL,
+ ft = NULL,
+ ref = NULL,
+ nuc = NULL,
dyns = 1,
fd = FALSE
)
@@ -95,6 +96,10 @@ Arguments
the data vector.
mrs_data
+example data to copy acquisition parameters from.
fs
sampling frequency in Hz.
Arguments
fd
-flag to indicate if the matrix is in the frequency domain (logical).
flag to indicate if the vector is in the frequency domain (logical).
Value
diff --git a/docs/reference/write_basis.html b/docs/reference/write_basis.html
index b6e27cbd..94c5e021 100644
--- a/docs/reference/write_basis.html
+++ b/docs/reference/write_basis.html
@@ -1,5 +1,5 @@
-Write a basis object to an LCModel .basis formatted file. — write_basis • Spectroscopy Analysis Tools (spant) Write a basis object to an LCModel .basis formatted file. — write_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -108,7 +108,7 @@ Arguments
diff --git a/docs/reference/write_basis_tqn.html b/docs/reference/write_basis_tqn.html
index 6aa51c1d..116c73ec 100644
--- a/docs/reference/write_basis_tqn.html
+++ b/docs/reference/write_basis_tqn.html
@@ -1,5 +1,5 @@
-Generate a basis file using TARQUIN. — write_basis_tqn • Spectroscopy Analysis Tools (spant) Generate a basis file using TARQUIN. — write_basis_tqn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Examples
diff --git a/docs/reference/write_mrs.html b/docs/reference/write_mrs.html
index fff25f15..124b9dc4 100644
--- a/docs/reference/write_mrs.html
+++ b/docs/reference/write_mrs.html
@@ -1,5 +1,5 @@
-Write MRS data object to file. — write_mrs • Spectroscopy Analysis Tools (spant) Write MRS data object to file. — write_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Arguments
diff --git a/docs/reference/write_mrs_nifti.html b/docs/reference/write_mrs_nifti.html
index f4bf1921..bd3ed4b7 100644
--- a/docs/reference/write_mrs_nifti.html
+++ b/docs/reference/write_mrs_nifti.html
@@ -1,5 +1,5 @@
-Write MRS data object to file in NIFTI format. — write_mrs_nifti • Spectroscopy Analysis Tools (spant) Write MRS data object to file in NIFTI format. — write_mrs_nifti • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/write_pulse_ascii.html b/docs/reference/write_pulse_ascii.html
index 067ae086..221f8ebb 100644
--- a/docs/reference/write_pulse_ascii.html
+++ b/docs/reference/write_pulse_ascii.html
@@ -1,5 +1,5 @@
-Write an ASCII formatted pulse file. — write_pulse_ascii • Spectroscopy Analysis Tools (spant) Write an ASCII formatted pulse file. — write_pulse_ascii • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/zero_fade_spec.html b/docs/reference/zero_fade_spec.html
index c703745c..c8b572c3 100644
--- a/docs/reference/zero_fade_spec.html
+++ b/docs/reference/zero_fade_spec.html
@@ -1,7 +1,5 @@
-Fade a spectrum to zero by frequency domain multiplication with a tanh
-function. Note this operation distorts data points at the end of the FID. — zero_fade_spec • Spectroscopy Analysis Tools (spant) Fade a spectrum to zero by frequency domain multiplication with a tanh function. Note this operation distorts data points at the end of the FID. — zero_fade_spec • Spectroscopy Analysis Tools (spant) Zero all coherences including and above a given order. — zero_higher_orders • Spectroscopy Analysis Tools (spant) Zero all coherences including and above a given order. — zero_higher_orders • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Value
diff --git a/docs/reference/zero_td_pts_end.html b/docs/reference/zero_td_pts_end.html
index 8c1123c8..71d24ebb 100644
--- a/docs/reference/zero_td_pts_end.html
+++ b/docs/reference/zero_td_pts_end.html
@@ -1,5 +1,5 @@
-Set mrs_data object data points at the end of the FID to zero. — zero_td_pts_end • Spectroscopy Analysis Tools (spant) Set mrs_data object data points at the end of the FID to zero. — zero_td_pts_end • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/zf.html b/docs/reference/zf.html
index 85e2013c..baf50256 100644
--- a/docs/reference/zf.html
+++ b/docs/reference/zf.html
@@ -1,5 +1,5 @@
-Zero-fill MRS data in the time domain. — zf • Spectroscopy Analysis Tools (spant) Zero-fill MRS data in the time domain. — zf • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -125,7 +125,7 @@ Value
diff --git a/docs/reference/zf_xy.html b/docs/reference/zf_xy.html
index ebca3999..c4104a74 100644
--- a/docs/reference/zf_xy.html
+++ b/docs/reference/zf_xy.html
@@ -1,5 +1,5 @@
-Zero-fill MRSI data in the k-space x-y direction. — zf_xy • Spectroscopy Analysis Tools (spant) Zero-fill MRSI data in the k-space x-y direction. — zf_xy • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -113,7 +113,7 @@ Value
diff --git a/docs/sitemap.xml b/docs/sitemap.xml
index e2139f71..4c39f515 100644
--- a/docs/sitemap.xml
+++ b/docs/sitemap.xml
@@ -216,6 +216,12 @@
https://martin3141.github.io/spant/reference/comb_coils_fp_pc.html
+
+ https://martin3141.github.io/spant/reference/comb_coils_mrsi_gls.html
+
+
+ https://martin3141.github.io/spant/reference/comb_coils_svs_gls.html
+
https://martin3141.github.io/spant/reference/comb_csv_results.html
@@ -411,6 +417,9 @@
https://martin3141.github.io/spant/reference/gen_conv_reg.html
+
+ https://martin3141.github.io/spant/reference/gen_group_reg.html
+
https://martin3141.github.io/spant/reference/gen_impulse_reg.html
@@ -555,6 +564,15 @@
https://martin3141.github.io/spant/reference/glm_spec.html
+
+ https://martin3141.github.io/spant/reference/glm_spec_fmrs_fl.html
+
+
+ https://martin3141.github.io/spant/reference/glm_spec_fmrs_group.html
+
+
+ https://martin3141.github.io/spant/reference/glm_spec_group_linhyp.html
+
https://martin3141.github.io/spant/reference/grid_shift_xy.html
@@ -690,9 +708,15 @@
https://martin3141.github.io/spant/reference/mrs_data2basis.html
+
+ https://martin3141.github.io/spant/reference/mrs_data2bids.html
+
https://martin3141.github.io/spant/reference/mrs_data2mat.html
+
+ https://martin3141.github.io/spant/reference/mrs_data2spec_mat.html
+
https://martin3141.github.io/spant/reference/mrs_data2vec.html
@@ -741,6 +765,9 @@
https://martin3141.github.io/spant/reference/phase.html
+
+ https://martin3141.github.io/spant/reference/phase_ref_1h_brain.html
+
https://martin3141.github.io/spant/reference/plot.fit_result.html
@@ -780,6 +807,12 @@
https://martin3141.github.io/spant/reference/precomp.html
+
+ https://martin3141.github.io/spant/reference/preproc_svs.html
+
+
+ https://martin3141.github.io/spant/reference/preproc_svs_dataset.html
+
https://martin3141.github.io/spant/reference/print.fit_result.html
@@ -1050,6 +1083,9 @@
https://martin3141.github.io/spant/reference/spant_mpress_drift.html
+
+ https://martin3141.github.io/spant/reference/spant_sim_fmrs_dataset.html
+
https://martin3141.github.io/spant/reference/spant_simulation_benchmark.html
@@ -1107,6 +1143,9 @@
https://martin3141.github.io/spant/reference/svs_1h_brain_batch_analysis.html
+
+ https://martin3141.github.io/spant/reference/t_test_spec.html
+
https://martin3141.github.io/spant/reference/td2fd.html
Return an array of amplitudes derived from fitting the initial points in the -time domain and extrapolating back to t=0.
Return an array of amplitudes derived from fitting the initial points in the time domain and extrapolating back to t=0.
All functions
- Generate a mol_parameters object for a simple spin system with one
-resonance.
Generate a mol_parameters object for a simple spin system with one resonance.
@@ -731,6 +711,18 @@ All functions glm_spec()
Perform a GLM analysis of dynamic MRS data in the spectral domain.
+
+
+ Perform first-level spectral GLM analysis of an fMRS dataset.
+
+
+ Perform group-level spectral GLM analysis of an fMRS dataset.
+
+
+ Test a group-level spectral GLM linear hypothesis.
@@ -766,8 +758,7 @@ All functions
- Perform an ifft and ifftshift on a matrix with each column replaced by its
-shifted ifft.
Perform an ifft and ifftshift on a matrix with each column replaced by its shifted ifft.
@@ -799,8 +790,7 @@ All functions
- Check if the chemical shift dimension of an MRS data object is in the
-frequency domain.
Check if the chemical shift dimension of an MRS data object is in the frequency domain.
@@ -820,18 +810,15 @@ All functions
- Covert a linewidth in Hz to an equivalent alpha value in the time-domain ie:
-x * exp(-t * alpha).
Covert a linewidth in Hz to an equivalent alpha value in the time-domain ie: x * exp(-t * alpha).
- Covert a linewidth in Hz to an equivalent beta value in the time-domain ie:
-x * exp(-t * t * beta).
Covert a linewidth in Hz to an equivalent beta value in the time-domain ie: x * exp(-t * t * beta).
- Make a basis-set object from a directory containing LCModel formatted RAW
-files.
Make a basis-set object from a directory containing LCModel formatted RAW files.
@@ -851,8 +838,7 @@ All functions
- Mask the voxels outside an elliptical region spanning the MRSI dataset in the
-x-y plane.
Mask the voxels outside an elliptical region spanning the MRSI dataset in the x-y plane.
@@ -860,13 +846,11 @@ All functions
- Convert a matrix (with spectral points in the column dimension and dynamics
-in the row dimensions) into a mrs_data object.
Convert a matrix (with spectral points in the column dimension and dynamics in the row dimensions) into a mrs_data object.
- Matrix exponential function taken from complexplus package to reduce the
-number of spant dependencies.
Matrix exponential function taken from complexplus package to reduce the number of spant dependencies.
@@ -914,31 +898,31 @@ All functions
- Convert an mrs_data object to basis object - where basis signals are spread
-across the dynamic dimension in the MRS data.
Convert an mrs_data object to basis object - where basis signals are spread across the dynamic dimension in the MRS data.
+
+
+ Create a BIDS file structure from a vector of MRS data paths or list of mrs_data objects.
- Convert mrs_data object to a matrix, with spectral points in the column
-dimension and dynamics in the row dimension.
Convert mrs_data object to a matrix, with spectral points in the column dimension and dynamics in the row dimension.
-
+
- Convert mrs_data object to a vector.
Convert mrs_data object to a matrix, with spectral points in the column dimension and dynamics in the row dimension.
-
+
- Create a BIDS directory and file structure from a list of mrs_data objects.
Convert mrs_data object to a vector.
- Perform a fftshift on a matrix, with each column replaced by its shifted
-result.
Perform a fftshift on a matrix, with each column replaced by its shifted result.
- Perform an ifftshift on a matrix, with each column replaced by its shifted
-result.
Perform an ifftshift on a matrix, with each column replaced by its shifted result.
@@ -946,9 +930,7 @@ All functions
- Flip the x data dimension order of a nifti image. This corresponds to
-flipping MRI data in the left-right direction, assuming the data in save in
-neurological format (can check with fslorient program).
Flip the x data dimension order of a nifti image. This corresponds to flipping MRI data in the left-right direction, assuming the data in save in neurological format (can check with fslorient program).
@@ -964,8 +946,7 @@ All functions
- Search for the highest peak in a spectral region and return the frequency,
-height and FWHM.
Search for the highest peak in a spectral region and return the frequency, height and FWHM.
@@ -974,6 +955,10 @@ All functions phase()
Apply phasing parameters to MRS data.
+
+
+ Corrected zero order phase and chemical shift offset in 1H MRS data from the brain.
@@ -1005,8 +990,7 @@ All functions
- Plot an interactive slice map from a data array where voxels can be selected
-to display a corresponding spectrum.
Plot an interactive slice map from a data array where voxels can be selected to display a corresponding spectrum.
@@ -1026,8 +1010,15 @@ All functions
- Save function results to file and load on subsequent calls to avoid repeat
-computation.
Save function results to file and load on subsequent calls to avoid repeat computation.
+
+
+ Preprocess and perform quality assessment of a single SVS data set.
+
+
+ Preprocess and perform quality assessment of one or more SVS data sets.
@@ -1055,15 +1046,11 @@ All functions
- Read a directory containing Siemens MRS IMA files and combine along the coil
-dimension. Note that the coil ID is inferred from the sorted file name and
-should be checked when consistency is required between two directories.
Read a directory containing Siemens MRS IMA files and combine along the coil dimension. Note that the coil ID is inferred from the sorted file name and should be checked when consistency is required between two directories.
- Read a directory containing Siemens MRS IMA files and combine along the
-dynamic dimension. Note that the coil ID is inferred from the sorted file
-name and should be checked when consistency is required.
Read a directory containing Siemens MRS IMA files and combine along the dynamic dimension. Note that the coil ID is inferred from the sorted file name and should be checked when consistency is required.
@@ -1103,13 +1090,11 @@ All functions
- Reconstruct complex time-domain data from the real part of frequency-domain
-data.
Reconstruct complex time-domain data from the real part of frequency-domain data.
- Reconstruct complex time-domain data from the real part of frequency-domain
-data.
Reconstruct complex time-domain data from the real part of frequency-domain data.
@@ -1141,8 +1126,7 @@ All functions
- Resample a VOI to match a target image space using nearest-neighbour
-interpolation.
Resample a VOI to match a target image space using nearest-neighbour interpolation.
@@ -1158,23 +1142,19 @@ All functions
- Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water).
Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / kg of tissue water).
- Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water).
Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / kg of tissue water).
- Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / Litre of tissue).
Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / Litre of tissue).
- Convert default LCM/TARQUIN concentration scaling to molal units with partial
-volume correction.
Convert default LCM/TARQUIN concentration scaling to molal units with partial volume correction.
@@ -1222,8 +1202,7 @@ All functions
- MEGA-PRESS sequence with ideal localisation pulses and Gaussian shaped
-editing pulse.
MEGA-PRESS sequence with ideal localisation pulses and Gaussian shaped editing pulse.
@@ -1251,13 +1230,11 @@ All functions
- STEAM sequence with ideal pulses and coherence order filtering to simulate
-gradient crushers.
STEAM sequence with ideal pulses and coherence order filtering to simulate gradient crushers.
- STEAM sequence with ideal pulses using the z-rotation gradient simulation
-method described by Young et al JMR 140, 146-152 (1999).
STEAM sequence with ideal pulses using the z-rotation gradient simulation method described by Young et al JMR 140, 146-152 (1999).
@@ -1293,8 +1270,7 @@ All functions
- Set the number of time-domain data points, truncating or zero-filling as
-appropriate.
Set the number of time-domain data points, truncating or zero-filling as appropriate.
@@ -1318,18 +1294,15 @@ All functions
- Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS
-sequence. Note, ideal pulses are assumed.
Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS sequence. Note, ideal pulses are assumed.
- Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS
-sequence. Note, ideal pulses are assumed.
Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS sequence. Note, ideal pulses are assumed.
- Simulate a macromolecular and lipid basis-set suitable for 1H brain MRS
-analysis.
Simulate a macromolecular and lipid basis-set suitable for 1H brain MRS analysis.
@@ -1353,8 +1326,7 @@ All functions
- Simulate an ideal pulse excitation profile by smoothing a top-hat function
-with a Gaussian.
Simulate an ideal pulse excitation profile by smoothing a top-hat function with a Gaussian.
@@ -1374,17 +1346,19 @@ All functions
- Simulate and fit some spectra with ABfit for benchmarking purposes. Basic
-timing and performance metrics will be printed.
Simulate and fit some spectra with ABfit for benchmarking purposes. Basic timing and performance metrics will be printed.
Example MEGA-PRESS data with significant B0 drift.
+
+
+ Simulate an example fMRS dataset for a block design fMRS experiment and export a BIDS structure.
- Simulate a typical metabolite basis set for benchmarking. Timing metrics will
-be printed on completion.
Simulate a typical metabolite basis set for benchmarking. Timing metrics will be printed on completion.
@@ -1400,8 +1374,7 @@ All functions
- Convert SPM style segmentation files to a single categorical image where
-the numerical values map as: 0) Other, 1) CSF, 2) GM and 3) WM.
Convert SPM style segmentation files to a single categorical image where the numerical values map as: 0) Other, 1) CSF, 2) GM and 3) WM.
@@ -1413,8 +1386,7 @@ All functions
- Plot the fitting results of an object of class fit_result with
-individual basis set components shown.
Plot the fitting results of an object of class fit_result with individual basis set components shown.
@@ -1459,6 +1431,10 @@ All functions svs_1h_brain_batch_analysis()
Batch interface to the standard SVS 1H brain analysis pipeline.
+
+
+ Perform a t-test on spectral data points.
@@ -1518,8 +1494,7 @@ All functions
- Fade a spectrum to zero by frequency domain multiplication with a tanh
-function. Note this operation distorts data points at the end of the FID.
Fade a spectrum to zero by frequency domain multiplication with a tanh function. Note this operation distorts data points at the end of the FID.
@@ -1549,7 +1524,7 @@ All functions
diff --git a/docs/reference/int_spec.html b/docs/reference/int_spec.html
index c7060fe7..783325a8 100644
--- a/docs/reference/int_spec.html
+++ b/docs/reference/int_spec.html
@@ -1,5 +1,5 @@
-Integrate a spectral region. — int_spec • Spectroscopy Analysis Tools (spant) Integrate a spectral region. — int_spec • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -118,7 +118,7 @@ Value
diff --git a/docs/reference/interleave_dyns.html b/docs/reference/interleave_dyns.html
index effe5543..441eff27 100644
--- a/docs/reference/interleave_dyns.html
+++ b/docs/reference/interleave_dyns.html
@@ -1,5 +1,5 @@
-Interleave the first and second half of a dynamic series. — interleave_dyns • Spectroscopy Analysis Tools (spant) Interleave the first and second half of a dynamic series. — interleave_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/inv_even_dyns.html b/docs/reference/inv_even_dyns.html
index 9f9d4fff..dcb781dc 100644
--- a/docs/reference/inv_even_dyns.html
+++ b/docs/reference/inv_even_dyns.html
@@ -1,5 +1,5 @@
-Invert even numbered dynamic scans starting from 1 (2,4,6...). — inv_even_dyns • Spectroscopy Analysis Tools (spant) Invert even numbered dynamic scans starting from 1 (2,4,6...). — inv_even_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/inv_odd_dyns.html b/docs/reference/inv_odd_dyns.html
index 26212e2b..78d64660 100644
--- a/docs/reference/inv_odd_dyns.html
+++ b/docs/reference/inv_odd_dyns.html
@@ -1,5 +1,5 @@
-Invert odd numbered dynamic scans starting from 1 (1,3,5...). — inv_odd_dyns • Spectroscopy Analysis Tools (spant) Invert odd numbered dynamic scans starting from 1 (1,3,5...). — inv_odd_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/is.def.html b/docs/reference/is.def.html
index f196ffd0..a67b9eba 100644
--- a/docs/reference/is.def.html
+++ b/docs/reference/is.def.html
@@ -1,5 +1,5 @@
-Check if an object is defined, which is the same as being not NULL. — is.def • Spectroscopy Analysis Tools (spant) Check if an object is defined, which is the same as being not NULL. — is.def • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/is_fd.html b/docs/reference/is_fd.html
index 3b0ca165..18a193aa 100644
--- a/docs/reference/is_fd.html
+++ b/docs/reference/is_fd.html
@@ -1,7 +1,5 @@
-Check if the chemical shift dimension of an MRS data object is in the
-frequency domain. — is_fd • Spectroscopy Analysis Tools (spant) Check if the chemical shift dimension of an MRS data object is in the frequency domain. — is_fd • Spectroscopy Analysis Tools (spant) Transform 2D MRSI data from k-space to image space in the x-y direction. — kspace2img_xy • Spectroscopy Analysis Tools (spant) Transform 2D MRSI data from k-space to image space in the x-y direction. — kspace2img_xy • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/l2_reg.html b/docs/reference/l2_reg.html
index 3d781d80..21aa9849 100644
--- a/docs/reference/l2_reg.html
+++ b/docs/reference/l2_reg.html
@@ -1,5 +1,5 @@
-Perform l2 regularisation artefact suppression. — l2_reg • Spectroscopy Analysis Tools (spant) Perform l2 regularisation artefact suppression. — l2_reg • Spectroscopy Analysis Tools (spant) Apply line-broadening (apodisation) to MRS data or basis object. — lb • Spectroscopy Analysis Tools (spant) Apply line-broadening (apodisation) to MRS data or basis object. — lb • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -123,7 +123,7 @@ Value
diff --git a/docs/reference/lofdc.html b/docs/reference/lofdc.html
index 5419b1ec..31347a25 100644
--- a/docs/reference/lofdc.html
+++ b/docs/reference/lofdc.html
@@ -1,5 +1,5 @@
-Correct linear frequency drift. — lofdc • Spectroscopy Analysis Tools (spant) Correct linear frequency drift. — lofdc • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -138,7 +138,7 @@ Value
diff --git a/docs/reference/lw2alpha.html b/docs/reference/lw2alpha.html
index b83db682..25da229b 100644
--- a/docs/reference/lw2alpha.html
+++ b/docs/reference/lw2alpha.html
@@ -1,7 +1,5 @@
-Covert a linewidth in Hz to an equivalent alpha value in the time-domain ie:
-x * exp(-t * alpha). — lw2alpha • Spectroscopy Analysis Tools (spant) Covert a linewidth in Hz to an equivalent alpha value in the time-domain ie: x * exp(-t * alpha). — lw2alpha • Spectroscopy Analysis Tools (spant) Covert a linewidth in Hz to an equivalent beta value in the time-domain ie:
-x * exp(-t * t * beta). — lw2beta • Spectroscopy Analysis Tools (spant) Covert a linewidth in Hz to an equivalent beta value in the time-domain ie: x * exp(-t * t * beta). — lw2beta • Spectroscopy Analysis Tools (spant) Make a basis-set object from a directory containing LCModel formatted RAW
-files. — make_basis_from_raw • Spectroscopy Analysis Tools (spant) Make a basis-set object from a directory containing LCModel formatted RAW files. — make_basis_from_raw • Spectroscopy Analysis Tools (spant) Mask an MRS dataset in the dynamic dimension. — mask_dyns • Spectroscopy Analysis Tools (spant) Mask an MRS dataset in the dynamic dimension. — mask_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/mask_fit_res.html b/docs/reference/mask_fit_res.html
index 97baaa3f..ebd91a99 100644
--- a/docs/reference/mask_fit_res.html
+++ b/docs/reference/mask_fit_res.html
@@ -1,5 +1,5 @@
-Mask fit result spectra depending on a vector of bool values. — mask_fit_res • Spectroscopy Analysis Tools (spant) Mask fit result spectra depending on a vector of bool values. — mask_fit_res • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -116,7 +116,7 @@ Value
diff --git a/docs/reference/mask_xy.html b/docs/reference/mask_xy.html
index 11bb577c..b0d38619 100644
--- a/docs/reference/mask_xy.html
+++ b/docs/reference/mask_xy.html
@@ -1,5 +1,5 @@
-Mask an MRSI dataset in the x-y direction — mask_xy • Spectroscopy Analysis Tools (spant) Mask an MRSI dataset in the x-y direction — mask_xy • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/mask_xy_corners.html b/docs/reference/mask_xy_corners.html
index 09b16cd2..2d13839d 100644
--- a/docs/reference/mask_xy_corners.html
+++ b/docs/reference/mask_xy_corners.html
@@ -1,5 +1,5 @@
-Mask the four corners of an MRSI dataset in the x-y plane. — mask_xy_corners • Spectroscopy Analysis Tools (spant) Mask the four corners of an MRSI dataset in the x-y plane. — mask_xy_corners • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/mask_xy_ellipse.html b/docs/reference/mask_xy_ellipse.html
index 1d8b02e4..e2e749ef 100644
--- a/docs/reference/mask_xy_ellipse.html
+++ b/docs/reference/mask_xy_ellipse.html
@@ -1,7 +1,5 @@
-Mask the voxels outside an elliptical region spanning the MRSI dataset in the
-x-y plane. — mask_xy_ellipse • Spectroscopy Analysis Tools (spant) Mask the voxels outside an elliptical region spanning the MRSI dataset in the x-y plane. — mask_xy_ellipse • Spectroscopy Analysis Tools (spant) Mask a 2D MRSI dataset in the x-y dimension. — mask_xy_mat • Spectroscopy Analysis Tools (spant) Mask a 2D MRSI dataset in the x-y dimension. — mask_xy_mat • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Value
diff --git a/docs/reference/mat2mrs_data.html b/docs/reference/mat2mrs_data.html
index 2e2895f3..ae55665f 100644
--- a/docs/reference/mat2mrs_data.html
+++ b/docs/reference/mat2mrs_data.html
@@ -1,7 +1,5 @@
-Convert a matrix (with spectral points in the column dimension and dynamics
-in the row dimensions) into a mrs_data object. — mat2mrs_data • Spectroscopy Analysis Tools (spant) Convert a matrix (with spectral points in the column dimension and dynamics in the row dimensions) into a mrs_data object. — mat2mrs_data • Spectroscopy Analysis Tools (spant) Matrix exponential function taken from complexplus package to reduce the
-number of spant dependencies. — matexp • Spectroscopy Analysis Tools (spant) Matrix exponential function taken from complexplus package to reduce the number of spant dependencies. — matexp • Spectroscopy Analysis Tools (spant) Apply the max operator to an MRS dataset. — max_mrs • Spectroscopy Analysis Tools (spant) Apply the max operator to an MRS dataset. — max_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/max_mrs_interp.html b/docs/reference/max_mrs_interp.html
index e4474764..52e63f3e 100644
--- a/docs/reference/max_mrs_interp.html
+++ b/docs/reference/max_mrs_interp.html
@@ -1,5 +1,5 @@
-Apply the max operator to an interpolated MRS dataset. — max_mrs_interp • Spectroscopy Analysis Tools (spant) Apply the max operator to an interpolated MRS dataset. — max_mrs_interp • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/mean.list.html b/docs/reference/mean.list.html
index b8eb3463..048306fd 100644
--- a/docs/reference/mean.list.html
+++ b/docs/reference/mean.list.html
@@ -1,5 +1,5 @@
-Calculate the mean spectrum from an mrs_data object. — mean.list • Spectroscopy Analysis Tools (spant) Calculate the mean spectrum from an mrs_data object. — mean.list • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/mean.mrs_data.html b/docs/reference/mean.mrs_data.html
index 5531a28d..79515014 100644
--- a/docs/reference/mean.mrs_data.html
+++ b/docs/reference/mean.mrs_data.html
@@ -1,5 +1,5 @@
-Calculate the mean spectrum from an mrs_data object. — mean.mrs_data • Spectroscopy Analysis Tools (spant) Calculate the mean spectrum from an mrs_data object. — mean.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/mean_dyn_blocks.html b/docs/reference/mean_dyn_blocks.html
index 10467098..4c042448 100644
--- a/docs/reference/mean_dyn_blocks.html
+++ b/docs/reference/mean_dyn_blocks.html
@@ -1,5 +1,5 @@
-Calculate the mean of adjacent dynamic scans. — mean_dyn_blocks • Spectroscopy Analysis Tools (spant) Calculate the mean of adjacent dynamic scans. — mean_dyn_blocks • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/mean_dyn_pairs.html b/docs/reference/mean_dyn_pairs.html
index 63e909ea..1a241126 100644
--- a/docs/reference/mean_dyn_pairs.html
+++ b/docs/reference/mean_dyn_pairs.html
@@ -1,5 +1,5 @@
-Calculate the pairwise means across a dynamic data set. — mean_dyn_pairs • Spectroscopy Analysis Tools (spant) Calculate the pairwise means across a dynamic data set. — mean_dyn_pairs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/mean_dyns.html b/docs/reference/mean_dyns.html
index 73fdbfa7..0daa27df 100644
--- a/docs/reference/mean_dyns.html
+++ b/docs/reference/mean_dyns.html
@@ -1,5 +1,5 @@
-Calculate the mean dynamic data. — mean_dyns • Spectroscopy Analysis Tools (spant) Calculate the mean dynamic data. — mean_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/mean_mrs_list.html b/docs/reference/mean_mrs_list.html
index 808b6c50..10d842c0 100644
--- a/docs/reference/mean_mrs_list.html
+++ b/docs/reference/mean_mrs_list.html
@@ -1,5 +1,5 @@
-Return the mean of a list of mrs_data objects. — mean_mrs_list • Spectroscopy Analysis Tools (spant) Return the mean of a list of mrs_data objects. — mean_mrs_list • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/mean_vec_blocks.html b/docs/reference/mean_vec_blocks.html
index 8fc92eaa..dd78b122 100644
--- a/docs/reference/mean_vec_blocks.html
+++ b/docs/reference/mean_vec_blocks.html
@@ -1,5 +1,5 @@
-Calculate the mean of adjacent blocks in a vector. — mean_vec_blocks • Spectroscopy Analysis Tools (spant) Calculate the mean of adjacent blocks in a vector. — mean_vec_blocks • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/median_dyns.html b/docs/reference/median_dyns.html
index 1039d4b5..9a085b10 100644
--- a/docs/reference/median_dyns.html
+++ b/docs/reference/median_dyns.html
@@ -1,5 +1,5 @@
-Calculate the median dynamic data. — median_dyns • Spectroscopy Analysis Tools (spant) Calculate the median dynamic data. — median_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/mod_td.html b/docs/reference/mod_td.html
index 76ad0a40..141ef09e 100644
--- a/docs/reference/mod_td.html
+++ b/docs/reference/mod_td.html
@@ -1,5 +1,5 @@
-Apply the Modulus operator to the time-domain MRS signal. — mod_td • Spectroscopy Analysis Tools (spant) Apply the Modulus operator to the time-domain MRS signal. — mod_td • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/mrs_data2basis.html b/docs/reference/mrs_data2basis.html
index 62f7d749..11797b91 100644
--- a/docs/reference/mrs_data2basis.html
+++ b/docs/reference/mrs_data2basis.html
@@ -1,7 +1,5 @@
-Convert an mrs_data object to basis object - where basis signals are spread
-across the dynamic dimension in the MRS data. — mrs_data2basis • Spectroscopy Analysis Tools (spant) Convert an mrs_data object to basis object - where basis signals are spread across the dynamic dimension in the MRS data. — mrs_data2basis • Spectroscopy Analysis Tools (spant) Create a BIDS file structure from a vector of MRS data paths or list of mrs_data objects. — mrs_data2bids • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Create a BIDS file structure from a vector of MRS data paths or list of mrs_data objects.
+ Source: R/fmrs.R
+ mrs_data2bids.Rd
+
+
+
+ Create a BIDS file structure from a vector of MRS data paths or list of
+mrs_data objects.
+
+
+
+ mrs_data2bids(
+ mrs_data,
+ output_dir,
+ suffix = NULL,
+ sub = NULL,
+ ses = NULL,
+ task = NULL,
+ acq = NULL,
+ nuc = NULL,
+ voi = NULL,
+ rec = NULL,
+ run = NULL,
+ echo = NULL,
+ inv = NULL,
+ skip_existing = TRUE
+)
+
+
+
+ Arguments
+ - mrs_data
+vector of MRS data paths or list of mrs_data objects.
- output_dir
+the base directory to create the BIDS structure.
- suffix
+optional vector of file suffixes. Default behaviour is to
+automatically determine these from the input data, however it is recommended
+that they are specified to allow more efficient skipping of existing data.
- sub
+optional vector of subject labels. If not specified, these will be
+automatically generated as a series of increasing zero-padded integer values
+corresponding to the mrs_data input indices.
- ses
+optional vector of session labels.
- task
+optional vector of task labels.
- acq
+optional vector of acquisition labels.
- nuc
+optional vector of nucleus labels.
- voi
+optional vector of volume of interest labels.
- rec
+optional vector of reconstruction labels.
- run
+optional vector of run indices.
- echo
+optional vector of echo time indices.
- inv
+optional vector of inversion indices.
- skip_existing
+skip any data files that have already been converted.
+Defaults to TRUE, set to FALSE to force an overwrite of any existing data
+files.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/mrs_data2mat.html b/docs/reference/mrs_data2mat.html
index cf5ff28c..9e47688a 100644
--- a/docs/reference/mrs_data2mat.html
+++ b/docs/reference/mrs_data2mat.html
@@ -1,7 +1,5 @@
-Convert mrs_data object to a matrix, with spectral points in the column
-dimension and dynamics in the row dimension. — mrs_data2mat • Spectroscopy Analysis Tools (spant) Convert mrs_data object to a matrix, with spectral points in the column dimension and dynamics in the row dimension. — mrs_data2mat • Spectroscopy Analysis Tools (spant) Convert mrs_data object to a matrix, with spectral points in the column dimension and dynamics in the row dimension. — mrs_data2spec_mat • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Convert mrs_data object to a matrix, with spectral points in the column dimension and dynamics in the row dimension.
+ Source: R/mrs_data_proc.R
+ mrs_data2spec_mat.Rd
+
+
+
+ Convert mrs_data object to a matrix, with spectral points in the column
+dimension and dynamics in the row dimension.
+
+
+
+ mrs_data2spec_mat(mrs_data, collapse = TRUE)
+
+
+
+ Arguments
+ - mrs_data
+MRS data object or list of MRS data objects.
- collapse
+collapse all other dimensions along the dynamic dimension, eg
+a 16x16 MRSI grid would be first collapsed across 256 dynamic scans.
+
+ Value
+
+
+MRS data matrix.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/mrs_data2vec.html b/docs/reference/mrs_data2vec.html
index fb172d68..a1fd654d 100644
--- a/docs/reference/mrs_data2vec.html
+++ b/docs/reference/mrs_data2vec.html
@@ -1,5 +1,5 @@
-Convert mrs_data object to a vector. — mrs_data2vec • Spectroscopy Analysis Tools (spant) Convert mrs_data object to a vector. — mrs_data2vec • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -126,7 +126,7 @@ Value
diff --git a/docs/reference/mvfftshift.html b/docs/reference/mvfftshift.html
index 92b0841b..976b3410 100644
--- a/docs/reference/mvfftshift.html
+++ b/docs/reference/mvfftshift.html
@@ -1,7 +1,5 @@
-Perform a fftshift on a matrix, with each column replaced by its shifted
-result. — mvfftshift • Spectroscopy Analysis Tools (spant) Perform a fftshift on a matrix, with each column replaced by its shifted result. — mvfftshift • Spectroscopy Analysis Tools (spant) Perform an ifftshift on a matrix, with each column replaced by its shifted
-result. — mvifftshift • Spectroscopy Analysis Tools (spant) Perform an ifftshift on a matrix, with each column replaced by its shifted result. — mvifftshift • Spectroscopy Analysis Tools (spant) Print fit coordinates from a single index. — n2coord • Spectroscopy Analysis Tools (spant) Print fit coordinates from a single index. — n2coord • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/nifti_flip_lr.html b/docs/reference/nifti_flip_lr.html
index 730abe3c..19860b3c 100644
--- a/docs/reference/nifti_flip_lr.html
+++ b/docs/reference/nifti_flip_lr.html
@@ -1,9 +1,5 @@
-Flip the x data dimension order of a nifti image. This corresponds to
-flipping MRI data in the left-right direction, assuming the data in save in
-neurological format (can check with fslorient program). — nifti_flip_lr • Spectroscopy Analysis Tools (spant) Flip the x data dimension order of a nifti image. This corresponds to flipping MRI data in the left-right direction, assuming the data in save in neurological format (can check with fslorient program). — nifti_flip_lr • Spectroscopy Analysis Tools (spant) Export a one-page pdf of a single fit result — one_page_pdf • Spectroscopy Analysis Tools (spant) Export a one-page pdf of a single fit result — one_page_pdf • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -108,7 +108,7 @@ Arguments
diff --git a/docs/reference/ortho3.html b/docs/reference/ortho3.html
index 13ade97d..5d7dd2fd 100644
--- a/docs/reference/ortho3.html
+++ b/docs/reference/ortho3.html
@@ -1,5 +1,5 @@
-Display an orthographic projection plot of a nifti object. — ortho3 • Spectroscopy Analysis Tools (spant) Display an orthographic projection plot of a nifti object. — ortho3 • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -172,7 +172,7 @@ Arguments
diff --git a/docs/reference/ortho3_inter.html b/docs/reference/ortho3_inter.html
index 090cc5e5..15948899 100644
--- a/docs/reference/ortho3_inter.html
+++ b/docs/reference/ortho3_inter.html
@@ -1,5 +1,5 @@
-Display an interactive orthographic projection plot of a nifti object. — ortho3_inter • Spectroscopy Analysis Tools (spant) Display an interactive orthographic projection plot of a nifti object. — ortho3_inter • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -132,7 +132,7 @@ Arguments
diff --git a/docs/reference/peak_info.html b/docs/reference/peak_info.html
index 09058bd8..41c8ffaf 100644
--- a/docs/reference/peak_info.html
+++ b/docs/reference/peak_info.html
@@ -1,7 +1,5 @@
-Search for the highest peak in a spectral region and return the frequency,
-height and FWHM. — peak_info • Spectroscopy Analysis Tools (spant) Search for the highest peak in a spectral region and return the frequency, height and FWHM. — peak_info • Spectroscopy Analysis Tools (spant) Papoulis-Gerchberg (PG) algorithm method for k-space extrapolation. — pg_extrap_xy • Spectroscopy Analysis Tools (spant) Papoulis-Gerchberg (PG) algorithm method for k-space extrapolation. — pg_extrap_xy • Spectroscopy Analysis Tools (spant) Apply phasing parameters to MRS data. — phase • Spectroscopy Analysis Tools (spant) Apply phasing parameters to MRS data. — phase • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/phase_ref_1h_brain.html b/docs/reference/phase_ref_1h_brain.html
new file mode 100644
index 00000000..8707a74a
--- /dev/null
+++ b/docs/reference/phase_ref_1h_brain.html
@@ -0,0 +1,131 @@
+
+Corrected zero order phase and chemical shift offset in 1H MRS data from the brain. — phase_ref_1h_brain • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Corrected zero order phase and chemical shift offset in 1H MRS data from the brain.
+ Source: R/rats.R
+ phase_ref_1h_brain.Rd
+
+
+
+ Corrected zero order phase and chemical shift offset in 1H MRS data from the
+brain.
+
+
+
+ phase_ref_1h_brain(mrs_data, mean_ref = FALSE, ret_corr_only = TRUE)
+
+
+
+ Arguments
+ - mrs_data
+MRS data to be corrected.
- mean_ref
+apply the phase and offset of the mean spectrum to all
+others. Default is FALSE.
- ret_corr_only
+return the corrected data only.
+
+ Value
+
+
+corrected MRS data.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/plot.fit_result.html b/docs/reference/plot.fit_result.html
index e54d3bc1..836a53ee 100644
--- a/docs/reference/plot.fit_result.html
+++ b/docs/reference/plot.fit_result.html
@@ -1,5 +1,5 @@
-Plot the fitting results of an object of class fit_result. — plot.fit_result • Spectroscopy Analysis Tools (spant) Plot the fitting results of an object of class fit_result. — plot.fit_result • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -207,7 +207,7 @@ Arguments
diff --git a/docs/reference/plot.mrs_data.html b/docs/reference/plot.mrs_data.html
index fabcc35b..bb2ec651 100644
--- a/docs/reference/plot.mrs_data.html
+++ b/docs/reference/plot.mrs_data.html
@@ -1,5 +1,5 @@
-Plotting method for objects of class mrs_data. — plot.mrs_data • Spectroscopy Analysis Tools (spant) Plotting method for objects of class mrs_data. — plot.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -287,7 +287,7 @@ Arguments
diff --git a/docs/reference/plot_bc.html b/docs/reference/plot_bc.html
index 4f8309b4..b48142cc 100644
--- a/docs/reference/plot_bc.html
+++ b/docs/reference/plot_bc.html
@@ -1,5 +1,5 @@
-Convenience function to plot a baseline estimate with the original data. — plot_bc • Spectroscopy Analysis Tools (spant) Convenience function to plot a baseline estimate with the original data. — plot_bc • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -108,7 +108,7 @@ Arguments
diff --git a/docs/reference/plot_reg.html b/docs/reference/plot_reg.html
index ae1acbe7..2addb2f6 100644
--- a/docs/reference/plot_reg.html
+++ b/docs/reference/plot_reg.html
@@ -1,5 +1,5 @@
-Plot regressors as an image. — plot_reg • Spectroscopy Analysis Tools (spant) Plot regressors as an image. — plot_reg • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/plot_slice_fit.html b/docs/reference/plot_slice_fit.html
index fbc7b560..57f1af8a 100644
--- a/docs/reference/plot_slice_fit.html
+++ b/docs/reference/plot_slice_fit.html
@@ -1,5 +1,5 @@
-Plot a 2D slice from an MRSI fit result object. — plot_slice_fit • Spectroscopy Analysis Tools (spant) Plot a 2D slice from an MRSI fit result object. — plot_slice_fit • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -129,7 +129,7 @@ Arguments
diff --git a/docs/reference/plot_slice_fit_inter.html b/docs/reference/plot_slice_fit_inter.html
index 4eed104a..da105a7d 100644
--- a/docs/reference/plot_slice_fit_inter.html
+++ b/docs/reference/plot_slice_fit_inter.html
@@ -1,5 +1,5 @@
-Plot a 2D slice from an MRSI fit result object. — plot_slice_fit_inter • Spectroscopy Analysis Tools (spant) Plot a 2D slice from an MRSI fit result object. — plot_slice_fit_inter • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -134,7 +134,7 @@ Arguments
diff --git a/docs/reference/plot_slice_map.html b/docs/reference/plot_slice_map.html
index 553e9ac8..ffb2a134 100644
--- a/docs/reference/plot_slice_map.html
+++ b/docs/reference/plot_slice_map.html
@@ -1,5 +1,5 @@
-Plot a slice from a 7 dimensional array. — plot_slice_map • Spectroscopy Analysis Tools (spant) Plot a slice from a 7 dimensional array. — plot_slice_map • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -153,7 +153,7 @@ Arguments
diff --git a/docs/reference/plot_slice_map_inter.html b/docs/reference/plot_slice_map_inter.html
index 40d33b42..90968f66 100644
--- a/docs/reference/plot_slice_map_inter.html
+++ b/docs/reference/plot_slice_map_inter.html
@@ -1,7 +1,5 @@
-Plot an interactive slice map from a data array where voxels can be selected
-to display a corresponding spectrum. — plot_slice_map_inter • Spectroscopy Analysis Tools (spant) Plot an interactive slice map from a data array where voxels can be selected to display a corresponding spectrum. — plot_slice_map_inter • Spectroscopy Analysis Tools (spant) Plot the spectral standard deviation. — plot_spec_sd • Spectroscopy Analysis Tools (spant) Plot the spectral standard deviation. — plot_spec_sd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Arguments
diff --git a/docs/reference/plot_voi_overlay.html b/docs/reference/plot_voi_overlay.html
index 9a782e88..bbbbf35e 100644
--- a/docs/reference/plot_voi_overlay.html
+++ b/docs/reference/plot_voi_overlay.html
@@ -1,5 +1,5 @@
-Plot a volume as an image overlay. — plot_voi_overlay • Spectroscopy Analysis Tools (spant) Plot a volume as an image overlay. — plot_voi_overlay • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -116,7 +116,7 @@ Arguments
diff --git a/docs/reference/plot_voi_overlay_seg.html b/docs/reference/plot_voi_overlay_seg.html
index 3d4e74ff..0e800ff2 100644
--- a/docs/reference/plot_voi_overlay_seg.html
+++ b/docs/reference/plot_voi_overlay_seg.html
@@ -1,5 +1,5 @@
-Plot a volume as an overlay on a segmented brain volume. — plot_voi_overlay_seg • Spectroscopy Analysis Tools (spant) Plot a volume as an overlay on a segmented brain volume. — plot_voi_overlay_seg • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Arguments
diff --git a/docs/reference/ppm.html b/docs/reference/ppm.html
index c352327a..ee4696e2 100644
--- a/docs/reference/ppm.html
+++ b/docs/reference/ppm.html
@@ -1,5 +1,5 @@
-Return the ppm scale of an MRS dataset or fit result. — ppm • Spectroscopy Analysis Tools (spant) Return the ppm scale of an MRS dataset or fit result. — ppm • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -132,7 +132,7 @@ Value
diff --git a/docs/reference/precomp.html b/docs/reference/precomp.html
index 822d7336..df3d2c6c 100644
--- a/docs/reference/precomp.html
+++ b/docs/reference/precomp.html
@@ -1,7 +1,5 @@
-Save function results to file and load on subsequent calls to avoid repeat
-computation. — precomp • Spectroscopy Analysis Tools (spant) Save function results to file and load on subsequent calls to avoid repeat computation. — precomp • Spectroscopy Analysis Tools (spant) Preprocess and perform quality assessment of a single SVS data set. — preproc_svs • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Preprocess and perform quality assessment of a single SVS data set.
+ Source: R/fmrs.R
+ preproc_svs.Rd
+
+
+
+ Preprocess and perform quality assessment of a single SVS data set.
+
+
+
+ preproc_svs(path, label = NULL, output_dir = NULL, ref_inds = NULL)
+
+
+
+ Arguments
+ - path
+path to the fMRS data file or IMA directory.
- label
+a label to describe the data set.
- output_dir
+output directory.
- ref_inds
+a vector of 1-based indices for any water reference dynamic
+scans.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/preproc_svs_dataset.html b/docs/reference/preproc_svs_dataset.html
new file mode 100644
index 00000000..07c3a29b
--- /dev/null
+++ b/docs/reference/preproc_svs_dataset.html
@@ -0,0 +1,148 @@
+
+Preprocess and perform quality assessment of one or more SVS data sets. — preproc_svs_dataset • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Preprocess and perform quality assessment of one or more SVS data sets.
+ Source: R/fmrs.R
+ preproc_svs_dataset.Rd
+
+
+
+ Preprocess and perform quality assessment of one or more SVS data sets.
+
+
+
+ preproc_svs_dataset(
+ paths,
+ labels = NULL,
+ output_dir = "spant_analysis",
+ exclude_labels = NULL,
+ overwrite = FALSE,
+ ref_inds = NULL,
+ return_results = FALSE
+)
+
+
+
+ Arguments
+ - paths
+paths to the fMRS data file or IMA directory.
- labels
+labels to describe each data set.
- output_dir
+output directory.
- exclude_labels
+vector of labels of scans to exclude, eg poor quality
+data.
- overwrite
+overwrite saved results, defaults to FALSE.
- ref_inds
+a vector of 1-based indices for any water reference dynamic
+scans.
- return_results
+function will return key outputs, defaults to FALSE.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/print.fit_result.html b/docs/reference/print.fit_result.html
index 297f28dc..5f434e57 100644
--- a/docs/reference/print.fit_result.html
+++ b/docs/reference/print.fit_result.html
@@ -1,5 +1,5 @@
-Print a summary of an object of class fit_result. — print.fit_result • Spectroscopy Analysis Tools (spant) Print a summary of an object of class fit_result. — print.fit_result • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -105,7 +105,7 @@ Arguments
diff --git a/docs/reference/print.mrs_data.html b/docs/reference/print.mrs_data.html
index 51199017..e1561eb2 100644
--- a/docs/reference/print.mrs_data.html
+++ b/docs/reference/print.mrs_data.html
@@ -1,5 +1,5 @@
-Print a summary of mrs_data parameters. — print.mrs_data • Spectroscopy Analysis Tools (spant) Print a summary of mrs_data parameters. — print.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -109,7 +109,7 @@ Arguments
diff --git a/docs/reference/qn_states.html b/docs/reference/qn_states.html
index 0f42f2f9..d7aa6715 100644
--- a/docs/reference/qn_states.html
+++ b/docs/reference/qn_states.html
@@ -1,5 +1,5 @@
-Get the quantum coherence matrix for a spin system. — qn_states • Spectroscopy Analysis Tools (spant) Get the quantum coherence matrix for a spin system. — qn_states • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/rats.html b/docs/reference/rats.html
index 5a39a396..93585e08 100644
--- a/docs/reference/rats.html
+++ b/docs/reference/rats.html
@@ -1,5 +1,5 @@
-Robust Alignment to a Target Spectrum (RATS). — rats • Spectroscopy Analysis Tools (spant) Robust Alignment to a Target Spectrum (RATS). — rats • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -207,7 +207,7 @@ Value
diff --git a/docs/reference/re_weighting.html b/docs/reference/re_weighting.html
index d21caf21..8b0b070a 100644
--- a/docs/reference/re_weighting.html
+++ b/docs/reference/re_weighting.html
@@ -1,5 +1,5 @@
-Apply a weighting to the FID to enhance spectral resolution. — re_weighting • Spectroscopy Analysis Tools (spant) Apply a weighting to the FID to enhance spectral resolution. — re_weighting • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/read_basis.html b/docs/reference/read_basis.html
index da9b94af..eb6f8557 100644
--- a/docs/reference/read_basis.html
+++ b/docs/reference/read_basis.html
@@ -1,5 +1,5 @@
-Read a basis file in LCModel .basis format. — read_basis • Spectroscopy Analysis Tools (spant) Read a basis file in LCModel .basis format. — read_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/read_ima_coil_dir.html b/docs/reference/read_ima_coil_dir.html
index 28c02de0..4f073cd8 100644
--- a/docs/reference/read_ima_coil_dir.html
+++ b/docs/reference/read_ima_coil_dir.html
@@ -1,9 +1,5 @@
-Read a directory containing Siemens MRS IMA files and combine along the coil
-dimension. Note that the coil ID is inferred from the sorted file name and
-should be checked when consistency is required between two directories. — read_ima_coil_dir • Spectroscopy Analysis Tools (spant) Read a directory containing Siemens MRS IMA files and combine along the coil dimension. Note that the coil ID is inferred from the sorted file name and should be checked when consistency is required between two directories. — read_ima_coil_dir • Spectroscopy Analysis Tools (spant) Read a directory containing Siemens MRS IMA files and combine along the
-dynamic dimension. Note that the coil ID is inferred from the sorted file
-name and should be checked when consistency is required. — read_ima_dyn_dir • Spectroscopy Analysis Tools (spant) Read a directory containing Siemens MRS IMA files and combine along the dynamic dimension. Note that the coil ID is inferred from the sorted file name and should be checked when consistency is required. — read_ima_dyn_dir • Spectroscopy Analysis Tools (spant) Read an LCModel formatted coord file containing fit information. — read_lcm_coord • Spectroscopy Analysis Tools (spant) Read an LCModel formatted coord file containing fit information. — read_lcm_coord • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -107,7 +107,7 @@ Value
diff --git a/docs/reference/read_mrs.html b/docs/reference/read_mrs.html
index 3ac2a36b..2cf36b20 100644
--- a/docs/reference/read_mrs.html
+++ b/docs/reference/read_mrs.html
@@ -1,5 +1,5 @@
-Read MRS data from a file. — read_mrs • Spectroscopy Analysis Tools (spant) Read MRS data from a file. — read_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -88,7 +88,8 @@ Read MRS data from a file.
full_fid = FALSE,
omit_svs_ref_scans = TRUE,
verbose = FALSE,
- extra = NULL
+ extra = NULL,
+ fid_filt_dist = NULL
)
@@ -140,6 +141,13 @@ Arguments
an optional data frame to provide additional variables for use
in subsequent analysis steps, eg id or grouping variables.
fid_filt_dist
+indicate if the data has a distorted FID due to a
+brick-wall filter being used to downsample the data. Default is to auto
+detect this from the data, but TRUE or FALSE options can be given to override
+detection.
Value
@@ -183,7 +191,7 @@ Examples
diff --git a/docs/reference/read_mrs_tqn.html b/docs/reference/read_mrs_tqn.html
index 5766362f..84bdaf3a 100644
--- a/docs/reference/read_mrs_tqn.html
+++ b/docs/reference/read_mrs_tqn.html
@@ -1,5 +1,5 @@
-Read MRS data using the TARQUIN software package. — read_mrs_tqn • Spectroscopy Analysis Tools (spant) Read MRS data using the TARQUIN software package. — read_mrs_tqn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -131,7 +131,7 @@ Examples
diff --git a/docs/reference/read_pulse_ascii.html b/docs/reference/read_pulse_ascii.html
index c9e0d43c..ab11c9cc 100644
--- a/docs/reference/read_pulse_ascii.html
+++ b/docs/reference/read_pulse_ascii.html
@@ -1,5 +1,5 @@
-Read an ASCII formatted pulse file. — read_pulse_ascii • Spectroscopy Analysis Tools (spant) Read an ASCII formatted pulse file. — read_pulse_ascii • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/read_pulse_bruker.html b/docs/reference/read_pulse_bruker.html
index c92bf76a..dbe9073b 100644
--- a/docs/reference/read_pulse_bruker.html
+++ b/docs/reference/read_pulse_bruker.html
@@ -1,5 +1,5 @@
-Read a Bruker formatted pulse file — read_pulse_bruker • Spectroscopy Analysis Tools (spant) Read a Bruker formatted pulse file — read_pulse_bruker • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/read_pulse_pta.html b/docs/reference/read_pulse_pta.html
index 72e1b6d4..a0fac3c3 100644
--- a/docs/reference/read_pulse_pta.html
+++ b/docs/reference/read_pulse_pta.html
@@ -1,5 +1,5 @@
-Read a .pta formatted pulse file compatible with Siemens PulseTool. — read_pulse_pta • Spectroscopy Analysis Tools (spant) Read a .pta formatted pulse file compatible with Siemens PulseTool. — read_pulse_pta • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/read_siemens_txt_hdr.html b/docs/reference/read_siemens_txt_hdr.html
index 23fb8c70..3a17d87c 100644
--- a/docs/reference/read_siemens_txt_hdr.html
+++ b/docs/reference/read_siemens_txt_hdr.html
@@ -1,5 +1,5 @@
-Read the text format header found in Siemens IMA and TWIX data files. — read_siemens_txt_hdr • Spectroscopy Analysis Tools (spant) Read the text format header found in Siemens IMA and TWIX data files. — read_siemens_txt_hdr • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -78,7 +78,7 @@ Read the text format header found in Siemens IMA and TWIX data files.
- read_siemens_txt_hdr(input, version = "vd", verbose, offset = 0)
+ read_siemens_txt_hdr(input, version = "vd", verbose = FALSE, offset = 0)
@@ -118,7 +118,7 @@ Value
diff --git a/docs/reference/read_tqn_fit.html b/docs/reference/read_tqn_fit.html
index 4da6c25e..a1630420 100644
--- a/docs/reference/read_tqn_fit.html
+++ b/docs/reference/read_tqn_fit.html
@@ -1,5 +1,5 @@
-Reader for csv fit results generated by TARQUIN. — read_tqn_fit • Spectroscopy Analysis Tools (spant) Reader for csv fit results generated by TARQUIN. — read_tqn_fit • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -113,7 +113,7 @@ Examples
diff --git a/docs/reference/read_tqn_result.html b/docs/reference/read_tqn_result.html
index 36659714..68a3e98c 100644
--- a/docs/reference/read_tqn_result.html
+++ b/docs/reference/read_tqn_result.html
@@ -1,5 +1,5 @@
-Reader for csv results generated by TARQUIN. — read_tqn_result • Spectroscopy Analysis Tools (spant) Reader for csv results generated by TARQUIN. — read_tqn_result • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -117,7 +117,7 @@ Examples
diff --git a/docs/reference/recon_imag.html b/docs/reference/recon_imag.html
index d2a72225..5bc3b1eb 100644
--- a/docs/reference/recon_imag.html
+++ b/docs/reference/recon_imag.html
@@ -1,7 +1,5 @@
-Reconstruct complex time-domain data from the real part of frequency-domain
-data. — recon_imag • Spectroscopy Analysis Tools (spant) Reconstruct complex time-domain data from the real part of frequency-domain data. — recon_imag • Spectroscopy Analysis Tools (spant) Reconstruct complex time-domain data from the real part of frequency-domain
-data. — recon_imag_vec • Spectroscopy Analysis Tools (spant) Reconstruct complex time-domain data from the real part of frequency-domain data. — recon_imag_vec • Spectroscopy Analysis Tools (spant) Reconstruct 2D MRSI data from a twix file loaded with read_mrs. — recon_twix_2d_mrsi • Spectroscopy Analysis Tools (spant) Reconstruct 2D MRSI data from a twix file loaded with read_mrs. — recon_twix_2d_mrsi • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/rectangular_mask.html b/docs/reference/rectangular_mask.html
index a2117283..6e469bc9 100644
--- a/docs/reference/rectangular_mask.html
+++ b/docs/reference/rectangular_mask.html
@@ -1,5 +1,5 @@
-Create a rectangular mask stored as a matrix of logical values. — rectangular_mask • Spectroscopy Analysis Tools (spant) Create a rectangular mask stored as a matrix of logical values. — rectangular_mask • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -130,7 +130,7 @@ Value
diff --git a/docs/reference/reexports.html b/docs/reference/reexports.html
index 694a75d1..a59e8379 100644
--- a/docs/reference/reexports.html
+++ b/docs/reference/reexports.html
@@ -1,5 +1,5 @@
-Objects exported from other packages — reexports • Spectroscopy Analysis Tools (spant) Objects exported from other packages — reexports • Spectroscopy Analysis Tools (spant)
Spectroscopy Analysis Tools (spant)
- 2.21.0
+ 2.22.0
@@ -103,7 +103,7 @@ Objects exported from other packages
diff --git a/docs/reference/rep_array_dim.html b/docs/reference/rep_array_dim.html
index b9c49b4a..48c0a5ed 100644
--- a/docs/reference/rep_array_dim.html
+++ b/docs/reference/rep_array_dim.html
@@ -1,5 +1,5 @@
-Repeat an array over a given dimension. — rep_array_dim • Spectroscopy Analysis Tools (spant) Repeat an array over a given dimension. — rep_array_dim • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/rep_dyn.html b/docs/reference/rep_dyn.html
index 6bbfb0ef..89a4bb9b 100644
--- a/docs/reference/rep_dyn.html
+++ b/docs/reference/rep_dyn.html
@@ -1,5 +1,5 @@
-Replicate a scan in the dynamic dimension. — rep_dyn • Spectroscopy Analysis Tools (spant) Replicate a scan in the dynamic dimension. — rep_dyn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/rep_mrs.html b/docs/reference/rep_mrs.html
index 67730b5c..becb8f00 100644
--- a/docs/reference/rep_mrs.html
+++ b/docs/reference/rep_mrs.html
@@ -1,5 +1,5 @@
-Replicate a scan over a given dimension. — rep_mrs • Spectroscopy Analysis Tools (spant) Replicate a scan over a given dimension. — rep_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -138,7 +138,7 @@ Value
diff --git a/docs/reference/resample_basis.html b/docs/reference/resample_basis.html
index b0f2ab17..c7a6222a 100644
--- a/docs/reference/resample_basis.html
+++ b/docs/reference/resample_basis.html
@@ -1,5 +1,5 @@
-Resample a basis-set to match a mrs_data acquisition. — resample_basis • Spectroscopy Analysis Tools (spant) Resample a basis-set to match a mrs_data acquisition. — resample_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -116,7 +116,7 @@ Value
diff --git a/docs/reference/resample_img.html b/docs/reference/resample_img.html
index f1e7beaf..b0cc8f71 100644
--- a/docs/reference/resample_img.html
+++ b/docs/reference/resample_img.html
@@ -1,5 +1,5 @@
-Resample an image to match a target image space. — resample_img • Spectroscopy Analysis Tools (spant) Resample an image to match a target image space. — resample_img • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/resample_voi.html b/docs/reference/resample_voi.html
index 8fbfa836..a29ab096 100644
--- a/docs/reference/resample_voi.html
+++ b/docs/reference/resample_voi.html
@@ -1,7 +1,5 @@
-Resample a VOI to match a target image space using nearest-neighbour
-interpolation. — resample_voi • Spectroscopy Analysis Tools (spant) Resample a VOI to match a target image space using nearest-neighbour interpolation. — resample_voi • Spectroscopy Analysis Tools (spant) Reslice a nifti object to match the orientation of mrs data. — reslice_to_mrs • Spectroscopy Analysis Tools (spant) Reslice a nifti object to match the orientation of mrs data. — reslice_to_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/reson_table2mrs_data.html b/docs/reference/reson_table2mrs_data.html
index d75579ee..c5a2167a 100644
--- a/docs/reference/reson_table2mrs_data.html
+++ b/docs/reference/reson_table2mrs_data.html
@@ -1,5 +1,5 @@
-Generate mrs_data from a table of single Lorentzian resonances. — reson_table2mrs_data • Spectroscopy Analysis Tools (spant) Generate mrs_data from a table of single Lorentzian resonances. — reson_table2mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -119,7 +119,7 @@ Value
diff --git a/docs/reference/rm_dyns.html b/docs/reference/rm_dyns.html
index 5d5ef692..573e1f51 100644
--- a/docs/reference/rm_dyns.html
+++ b/docs/reference/rm_dyns.html
@@ -1,5 +1,5 @@
-Remove a subset of dynamic scans. — rm_dyns • Spectroscopy Analysis Tools (spant) Remove a subset of dynamic scans. — rm_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/scale_amp_molal.html b/docs/reference/scale_amp_molal.html
index aaeee1f2..7acb8cb0 100644
--- a/docs/reference/scale_amp_molal.html
+++ b/docs/reference/scale_amp_molal.html
@@ -1,7 +1,5 @@
-Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water). — scale_amp_molal • Spectroscopy Analysis Tools (spant) Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / kg of tissue water). — scale_amp_molal • Spectroscopy Analysis Tools (spant)
Spectroscopy Analysis Tools (spant)
- 2.21.0
+ 2.22.0
@@ -76,8 +74,7 @@
- Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water).
+ Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / kg of tissue water).
Source: R/amp_scaling.R
scale_amp_molal.Rd
@@ -163,7 +160,7 @@ Value
diff --git a/docs/reference/scale_amp_molal_pvc.html b/docs/reference/scale_amp_molal_pvc.html
index 962d6afc..4d194abd 100644
--- a/docs/reference/scale_amp_molal_pvc.html
+++ b/docs/reference/scale_amp_molal_pvc.html
@@ -1,7 +1,5 @@
-Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water). — scale_amp_molal_pvc • Spectroscopy Analysis Tools (spant)
@@ -75,8 +73,7 @@
- Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water).
+ Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / kg of tissue water).
Source: R/amp_scaling.R
scale_amp_molal_pvc.Rd
@@ -141,7 +138,7 @@ Value
diff --git a/docs/reference/scale_amp_molar.html b/docs/reference/scale_amp_molar.html
index 02358d91..dc87a338 100644
--- a/docs/reference/scale_amp_molar.html
+++ b/docs/reference/scale_amp_molar.html
@@ -1,7 +1,5 @@
-Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / Litre of tissue). — scale_amp_molar • Spectroscopy Analysis Tools (spant) Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / Litre of tissue). — scale_amp_molar • Spectroscopy Analysis Tools (spant) Convert default LCM/TARQUIN concentration scaling to molal units with partial
-volume correction. — scale_amp_molar2molal_pvc • Spectroscopy Analysis Tools (spant) Convert default LCM/TARQUIN concentration scaling to molal units with partial volume correction. — scale_amp_molar2molal_pvc • Spectroscopy Analysis Tools (spant) Scale fitted amplitudes to a ratio of signal amplitude. — scale_amp_ratio • Spectroscopy Analysis Tools (spant) Scale fitted amplitudes to a ratio of signal amplitude. — scale_amp_ratio • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -116,7 +116,7 @@ Value
diff --git a/docs/reference/scale_amp_ratio_value.html b/docs/reference/scale_amp_ratio_value.html
index 2036837a..6af8ac51 100644
--- a/docs/reference/scale_amp_ratio_value.html
+++ b/docs/reference/scale_amp_ratio_value.html
@@ -1,5 +1,5 @@
-Scale fitted amplitudes to a ratio of signal amplitude. — scale_amp_ratio_value • Spectroscopy Analysis Tools (spant) Scale fitted amplitudes to a ratio of signal amplitude. — scale_amp_ratio_value • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/scale_amp_water_ratio.html b/docs/reference/scale_amp_water_ratio.html
index 5b25e884..35a76b00 100644
--- a/docs/reference/scale_amp_water_ratio.html
+++ b/docs/reference/scale_amp_water_ratio.html
@@ -1,5 +1,5 @@
-Scale metabolite amplitudes as a ratio to the unsuppressed water amplitude. — scale_amp_water_ratio • Spectroscopy Analysis Tools (spant) Scale metabolite amplitudes as a ratio to the unsuppressed water amplitude. — scale_amp_water_ratio • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/scale_basis_amp.html b/docs/reference/scale_basis_amp.html
index 9401c3f1..5a58b5e5 100644
--- a/docs/reference/scale_basis_amp.html
+++ b/docs/reference/scale_basis_amp.html
@@ -1,5 +1,5 @@
-Scale a basis object by a scalar. — scale_basis_amp • Spectroscopy Analysis Tools (spant) Scale a basis object by a scalar. — scale_basis_amp • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/scale_basis_from_singlet.html b/docs/reference/scale_basis_from_singlet.html
index 0d542bc8..c9a19e77 100644
--- a/docs/reference/scale_basis_from_singlet.html
+++ b/docs/reference/scale_basis_from_singlet.html
@@ -1,5 +1,5 @@
-Scale a basis-set to be consistent with spant assumptions for water scaling. — scale_basis_from_singlet • Spectroscopy Analysis Tools (spant) Scale a basis-set to be consistent with spant assumptions for water scaling. — scale_basis_from_singlet • Spectroscopy Analysis Tools (spant)
Spectroscopy Analysis Tools (spant)
- 2.21.0
+ 2.22.0
@@ -127,7 +127,7 @@ Value
diff --git a/docs/reference/scale_mrs_amp.html b/docs/reference/scale_mrs_amp.html
index b5501a0d..990f058a 100644
--- a/docs/reference/scale_mrs_amp.html
+++ b/docs/reference/scale_mrs_amp.html
@@ -1,5 +1,5 @@
-Scale an mrs_data object by a scalar or vector or amplitudes. — scale_mrs_amp • Spectroscopy Analysis Tools (spant) Scale an mrs_data object by a scalar or vector or amplitudes. — scale_mrs_amp • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/scale_spec.html b/docs/reference/scale_spec.html
index 4f6ea835..6b3ddba4 100644
--- a/docs/reference/scale_spec.html
+++ b/docs/reference/scale_spec.html
@@ -1,5 +1,5 @@
-Scale mrs_data to a spectral region. — scale_spec • Spectroscopy Analysis Tools (spant) Scale mrs_data to a spectral region. — scale_spec • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -141,7 +141,7 @@ Value
diff --git a/docs/reference/sd.html b/docs/reference/sd.html
index ea1eec9f..3ae4dfd4 100644
--- a/docs/reference/sd.html
+++ b/docs/reference/sd.html
@@ -1,5 +1,5 @@
-Calculate the standard deviation spectrum from an mrs_data object. — sd • Spectroscopy Analysis Tools (spant) Calculate the standard deviation spectrum from an mrs_data object. — sd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/sd.mrs_data.html b/docs/reference/sd.mrs_data.html
index 3f92a49f..13bdda85 100644
--- a/docs/reference/sd.mrs_data.html
+++ b/docs/reference/sd.mrs_data.html
@@ -1,5 +1,5 @@
-Calculate the standard deviation spectrum from an mrs_data object. — sd.mrs_data • Spectroscopy Analysis Tools (spant) Calculate the standard deviation spectrum from an mrs_data object. — sd.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/seconds.html b/docs/reference/seconds.html
index b34d6627..467ee17f 100644
--- a/docs/reference/seconds.html
+++ b/docs/reference/seconds.html
@@ -1,5 +1,5 @@
-Return a time scale vector to match the FID of an MRS data object. — seconds • Spectroscopy Analysis Tools (spant) Return a time scale vector to match the FID of an MRS data object. — seconds • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/seq_cpmg_ideal.html b/docs/reference/seq_cpmg_ideal.html
index 547e96ab..45727c86 100644
--- a/docs/reference/seq_cpmg_ideal.html
+++ b/docs/reference/seq_cpmg_ideal.html
@@ -1,5 +1,5 @@
-CPMG style sequence with ideal pulses. — seq_cpmg_ideal • Spectroscopy Analysis Tools (spant) CPMG style sequence with ideal pulses. — seq_cpmg_ideal • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/seq_mega_press_ideal.html b/docs/reference/seq_mega_press_ideal.html
index 0769b8b4..a9cd7fa0 100644
--- a/docs/reference/seq_mega_press_ideal.html
+++ b/docs/reference/seq_mega_press_ideal.html
@@ -1,7 +1,5 @@
-MEGA-PRESS sequence with ideal localisation pulses and Gaussian shaped
-editing pulse. — seq_mega_press_ideal • Spectroscopy Analysis Tools (spant) MEGA-PRESS sequence with ideal localisation pulses and Gaussian shaped editing pulse. — seq_mega_press_ideal • Spectroscopy Analysis Tools (spant) PRESS sequence with shaped refocusing pulses. — seq_press_2d_shaped • Spectroscopy Analysis Tools (spant) PRESS sequence with shaped refocusing pulses. — seq_press_2d_shaped • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -165,7 +165,7 @@ Value
diff --git a/docs/reference/seq_press_ideal.html b/docs/reference/seq_press_ideal.html
index 8c976856..72c3af3d 100644
--- a/docs/reference/seq_press_ideal.html
+++ b/docs/reference/seq_press_ideal.html
@@ -1,5 +1,5 @@
-PRESS sequence with ideal pulses. — seq_press_ideal • Spectroscopy Analysis Tools (spant) PRESS sequence with ideal pulses. — seq_press_ideal • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/seq_pulse_acquire.html b/docs/reference/seq_pulse_acquire.html
index 4a88fc64..ad80571e 100644
--- a/docs/reference/seq_pulse_acquire.html
+++ b/docs/reference/seq_pulse_acquire.html
@@ -1,5 +1,5 @@
-Simple pulse and acquire sequence with ideal pulses. — seq_pulse_acquire • Spectroscopy Analysis Tools (spant) Simple pulse and acquire sequence with ideal pulses. — seq_pulse_acquire • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/seq_slaser_ideal.html b/docs/reference/seq_slaser_ideal.html
index 74688f4d..eb83e8e3 100644
--- a/docs/reference/seq_slaser_ideal.html
+++ b/docs/reference/seq_slaser_ideal.html
@@ -1,5 +1,5 @@
-sLASER sequence with ideal pulses. — seq_slaser_ideal • Spectroscopy Analysis Tools (spant) sLASER sequence with ideal pulses. — seq_slaser_ideal • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -126,7 +126,7 @@ Value
diff --git a/docs/reference/seq_spin_echo_ideal.html b/docs/reference/seq_spin_echo_ideal.html
index e23271de..4248716f 100644
--- a/docs/reference/seq_spin_echo_ideal.html
+++ b/docs/reference/seq_spin_echo_ideal.html
@@ -1,5 +1,5 @@
-Spin echo sequence with ideal pulses. — seq_spin_echo_ideal • Spectroscopy Analysis Tools (spant) Spin echo sequence with ideal pulses. — seq_spin_echo_ideal • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/seq_steam_ideal.html b/docs/reference/seq_steam_ideal.html
index a60685a8..1c8115d7 100644
--- a/docs/reference/seq_steam_ideal.html
+++ b/docs/reference/seq_steam_ideal.html
@@ -1,5 +1,5 @@
-STEAM sequence with ideal pulses. — seq_steam_ideal • Spectroscopy Analysis Tools (spant) STEAM sequence with ideal pulses. — seq_steam_ideal • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -128,7 +128,7 @@ Value
diff --git a/docs/reference/seq_steam_ideal_cof.html b/docs/reference/seq_steam_ideal_cof.html
index 8f225740..cba7af91 100644
--- a/docs/reference/seq_steam_ideal_cof.html
+++ b/docs/reference/seq_steam_ideal_cof.html
@@ -1,7 +1,5 @@
-STEAM sequence with ideal pulses and coherence order filtering to simulate
-gradient crushers. — seq_steam_ideal_cof • Spectroscopy Analysis Tools (spant) STEAM sequence with ideal pulses and coherence order filtering to simulate gradient crushers. — seq_steam_ideal_cof • Spectroscopy Analysis Tools (spant) STEAM sequence with ideal pulses using the z-rotation gradient simulation
-method described by Young et al JMR 140, 146-152 (1999). — seq_steam_ideal_young • Spectroscopy Analysis Tools (spant) STEAM sequence with ideal pulses using the z-rotation gradient simulation method described by Young et al JMR 140, 146-152 (1999). — seq_steam_ideal_young • Spectroscopy Analysis Tools (spant) Set the number of transients for an mrs_data object. — set_Ntrans • Spectroscopy Analysis Tools (spant) Set the number of transients for an mrs_data object. — set_Ntrans • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/set_def_acq_paras.html b/docs/reference/set_def_acq_paras.html
index 3e1b4004..cc2ada9c 100644
--- a/docs/reference/set_def_acq_paras.html
+++ b/docs/reference/set_def_acq_paras.html
@@ -1,5 +1,5 @@
-Set the default acquisition parameters. — set_def_acq_paras • Spectroscopy Analysis Tools (spant) Set the default acquisition parameters. — set_def_acq_paras • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Arguments
diff --git a/docs/reference/set_lcm_cmd.html b/docs/reference/set_lcm_cmd.html
index 2056ed01..42bb2f24 100644
--- a/docs/reference/set_lcm_cmd.html
+++ b/docs/reference/set_lcm_cmd.html
@@ -1,5 +1,5 @@
-Set the command to run the LCModel command-line program. — set_lcm_cmd • Spectroscopy Analysis Tools (spant) Set the command to run the LCModel command-line program. — set_lcm_cmd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/set_lw.html b/docs/reference/set_lw.html
index b64ec851..bb176c62 100644
--- a/docs/reference/set_lw.html
+++ b/docs/reference/set_lw.html
@@ -1,5 +1,5 @@
-Apply line-broadening to an mrs_data object to achieve a specified linewidth. — set_lw • Spectroscopy Analysis Tools (spant) Apply line-broadening to an mrs_data object to achieve a specified linewidth. — set_lw • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -123,7 +123,7 @@ Value
diff --git a/docs/reference/set_mask_xy_mat.html b/docs/reference/set_mask_xy_mat.html
index 49dc5d4e..52c4b617 100644
--- a/docs/reference/set_mask_xy_mat.html
+++ b/docs/reference/set_mask_xy_mat.html
@@ -1,5 +1,5 @@
-Set the masked voxels in a 2D MRSI dataset to given spectrum. — set_mask_xy_mat • Spectroscopy Analysis Tools (spant) Set the masked voxels in a 2D MRSI dataset to given spectrum. — set_mask_xy_mat • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Value
diff --git a/docs/reference/set_precomp_mode.html b/docs/reference/set_precomp_mode.html
index f44bd5d3..47c28e3b 100644
--- a/docs/reference/set_precomp_mode.html
+++ b/docs/reference/set_precomp_mode.html
@@ -1,5 +1,5 @@
-Set the precompute mode. — set_precomp_mode • Spectroscopy Analysis Tools (spant) Set the precompute mode. — set_precomp_mode • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/set_precomp_verbose.html b/docs/reference/set_precomp_verbose.html
index 1453a231..9c613505 100644
--- a/docs/reference/set_precomp_verbose.html
+++ b/docs/reference/set_precomp_verbose.html
@@ -1,5 +1,5 @@
-Set the verbosity of the precompute function. — set_precomp_verbose • Spectroscopy Analysis Tools (spant) Set the verbosity of the precompute function. — set_precomp_verbose • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/set_ref.html b/docs/reference/set_ref.html
index 8953fa50..5436dfa2 100644
--- a/docs/reference/set_ref.html
+++ b/docs/reference/set_ref.html
@@ -1,5 +1,5 @@
-Set the ppm reference value (eg ppm value at 0Hz). — set_ref • Spectroscopy Analysis Tools (spant) Set the ppm reference value (eg ppm value at 0Hz). — set_ref • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/set_td_pts.html b/docs/reference/set_td_pts.html
index 8a80d42a..586459ff 100644
--- a/docs/reference/set_td_pts.html
+++ b/docs/reference/set_td_pts.html
@@ -1,7 +1,5 @@
-Set the number of time-domain data points, truncating or zero-filling as
-appropriate. — set_td_pts • Spectroscopy Analysis Tools (spant) Set the number of time-domain data points, truncating or zero-filling as appropriate. — set_td_pts • Spectroscopy Analysis Tools (spant) Set the command to run the TARQUIN command-line program. — set_tqn_cmd • Spectroscopy Analysis Tools (spant) Set the command to run the TARQUIN command-line program. — set_tqn_cmd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/set_tr.html b/docs/reference/set_tr.html
index b2109ab0..65c9df5f 100644
--- a/docs/reference/set_tr.html
+++ b/docs/reference/set_tr.html
@@ -1,5 +1,5 @@
-Set the repetition time of an MRS dataset. — set_tr • Spectroscopy Analysis Tools (spant) Set the repetition time of an MRS dataset. — set_tr • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/shift.html b/docs/reference/shift.html
index ab0fe724..034591d0 100644
--- a/docs/reference/shift.html
+++ b/docs/reference/shift.html
@@ -1,5 +1,5 @@
-Apply a frequency shift to MRS data. — shift • Spectroscopy Analysis Tools (spant) Apply a frequency shift to MRS data. — shift • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/shift_basis.html b/docs/reference/shift_basis.html
index 2884be19..f55a65e0 100644
--- a/docs/reference/shift_basis.html
+++ b/docs/reference/shift_basis.html
@@ -1,5 +1,5 @@
-Apply frequency shifts to basis set signals. — shift_basis • Spectroscopy Analysis Tools (spant) Apply frequency shifts to basis set signals. — shift_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Value
diff --git a/docs/reference/sim_basis.html b/docs/reference/sim_basis.html
index c7838c46..bb5fefc6 100644
--- a/docs/reference/sim_basis.html
+++ b/docs/reference/sim_basis.html
@@ -1,5 +1,5 @@
-Simulate a basis set object. — sim_basis • Spectroscopy Analysis Tools (spant) Simulate a basis set object. — sim_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -136,7 +136,7 @@ Value
diff --git a/docs/reference/sim_basis_1h_brain.html b/docs/reference/sim_basis_1h_brain.html
index 62ed7389..f71ffa0b 100644
--- a/docs/reference/sim_basis_1h_brain.html
+++ b/docs/reference/sim_basis_1h_brain.html
@@ -1,7 +1,5 @@
-Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS
-sequence. Note, ideal pulses are assumed. — sim_basis_1h_brain • Spectroscopy Analysis Tools (spant) Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS sequence. Note, ideal pulses are assumed. — sim_basis_1h_brain • Spectroscopy Analysis Tools (spant) Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS
-sequence. Note, ideal pulses are assumed. — sim_basis_1h_brain_press • Spectroscopy Analysis Tools (spant) Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS sequence. Note, ideal pulses are assumed. — sim_basis_1h_brain_press • Spectroscopy Analysis Tools (spant) Simulate a macromolecular and lipid basis-set suitable for 1H brain MRS
-analysis. — sim_basis_mm_lip_lcm • Spectroscopy Analysis Tools (spant) Simulate a macromolecular and lipid basis-set suitable for 1H brain MRS analysis. — sim_basis_mm_lip_lcm • Spectroscopy Analysis Tools (spant) Simulate a basis file using TARQUIN. — sim_basis_tqn • Spectroscopy Analysis Tools (spant) Simulate a basis file using TARQUIN. — sim_basis_tqn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -129,7 +129,7 @@ Examples
diff --git a/docs/reference/sim_brain_1h.html b/docs/reference/sim_brain_1h.html
index 2044cf1a..717ee289 100644
--- a/docs/reference/sim_brain_1h.html
+++ b/docs/reference/sim_brain_1h.html
@@ -1,5 +1,5 @@
-Simulate MRS data with a similar appearance to normal brain (by default). — sim_brain_1h • Spectroscopy Analysis Tools (spant) Simulate MRS data with a similar appearance to normal brain (by default). — sim_brain_1h • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -159,7 +159,7 @@ Value
diff --git a/docs/reference/sim_mol.html b/docs/reference/sim_mol.html
index 23bcef50..77f76a50 100644
--- a/docs/reference/sim_mol.html
+++ b/docs/reference/sim_mol.html
@@ -1,5 +1,5 @@
-Simulate a mol_parameter object. — sim_mol • Spectroscopy Analysis Tools (spant) Simulate a mol_parameter object. — sim_mol • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -143,7 +143,7 @@ Value
diff --git a/docs/reference/sim_noise.html b/docs/reference/sim_noise.html
index 23875f79..a71477d4 100644
--- a/docs/reference/sim_noise.html
+++ b/docs/reference/sim_noise.html
@@ -1,5 +1,5 @@
-Simulate an mrs_data object containing simulated Gaussian noise. — sim_noise • Spectroscopy Analysis Tools (spant) Simulate an mrs_data object containing simulated Gaussian noise. — sim_noise • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -84,6 +84,7 @@ Simulate an mrs_data object containing simulated Gaussian noise.
ft = def_ft(),
N = def_N(),
ref = def_ref(),
+ nuc = def_nuc(),
dyns = 1,
fd = TRUE
)
@@ -111,6 +112,10 @@ Arguments
reference value for ppm scale.
nuc
+resonant nucleus.
dyns
number of dynamic scans to generate.
Value
diff --git a/docs/reference/sim_resonances.html b/docs/reference/sim_resonances.html
index 19e9a8a4..d4f8d7c0 100644
--- a/docs/reference/sim_resonances.html
+++ b/docs/reference/sim_resonances.html
@@ -1,5 +1,5 @@
-Simulate a MRS data object containing a set of simulated resonances. — sim_resonances • Spectroscopy Analysis Tools (spant) Simulate a MRS data object containing a set of simulated resonances. — sim_resonances • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -161,7 +161,7 @@ Examples
diff --git a/docs/reference/sim_th_excit_profile.html b/docs/reference/sim_th_excit_profile.html
index 5535c5ef..e781cab1 100644
--- a/docs/reference/sim_th_excit_profile.html
+++ b/docs/reference/sim_th_excit_profile.html
@@ -1,7 +1,5 @@
-Simulate an ideal pulse excitation profile by smoothing a top-hat function
-with a Gaussian. — sim_th_excit_profile • Spectroscopy Analysis Tools (spant) Simulate an ideal pulse excitation profile by smoothing a top-hat function with a Gaussian. — sim_th_excit_profile • Spectroscopy Analysis Tools (spant) Simulate an mrs_data object containing complex zero valued samples. — sim_zero • Spectroscopy Analysis Tools (spant) Simulate an mrs_data object containing complex zero valued samples. — sim_zero • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -78,7 +78,14 @@ Simulate an mrs_data object containing complex zero valued samples.
-
+
@@ -99,6 +106,10 @@ Arguments
reference value for ppm scale.
nuc
+resonant nucleus.
dyns
number of dynamic scans to generate.
Value
diff --git a/docs/reference/smooth_dyns.html b/docs/reference/smooth_dyns.html
index 4cc8da50..accf3a51 100644
--- a/docs/reference/smooth_dyns.html
+++ b/docs/reference/smooth_dyns.html
@@ -1,5 +1,5 @@
-Smooth data across the dynamic dimension with a Gaussian kernel. — smooth_dyns • Spectroscopy Analysis Tools (spant) Smooth data across the dynamic dimension with a Gaussian kernel. — smooth_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/sort_basis.html b/docs/reference/sort_basis.html
index 6a676ea2..d25cc006 100644
--- a/docs/reference/sort_basis.html
+++ b/docs/reference/sort_basis.html
@@ -1,5 +1,5 @@
-Sort the basis-set elements alphabetically. — sort_basis • Spectroscopy Analysis Tools (spant) Sort the basis-set elements alphabetically. — sort_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/spant-package.html b/docs/reference/spant-package.html
index b3dd8e21..90f19ec3 100644
--- a/docs/reference/spant-package.html
+++ b/docs/reference/spant-package.html
@@ -1,5 +1,5 @@
-spant: spectroscopy analysis tools. — spant-package • Spectroscopy Analysis Tools (spant) spant: spectroscopy analysis tools. — spant-package • Spectroscopy Analysis Tools (spant) Simulate and fit some spectra with ABfit for benchmarking purposes. Basic
-timing and performance metrics will be printed. — spant_abfit_benchmark • Spectroscopy Analysis Tools (spant) Simulate and fit some spectra with ABfit for benchmarking purposes. Basic timing and performance metrics will be printed. — spant_abfit_benchmark • Spectroscopy Analysis Tools (spant) Example MEGA-PRESS data with significant B0 drift. — spant_mpress_drift • Spectroscopy Analysis Tools (spant) Example MEGA-PRESS data with significant B0 drift. — spant_mpress_drift • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -83,7 +83,7 @@ Example MEGA-PRESS data with significant B0 drift.
Format
- An object of class mrs_data of length 13.
+ An object of class mrs_data of dimension 1 x 1 x 1 x 1 x 40 x 1 x 1024.
@@ -98,7 +98,7 @@ Format
diff --git a/docs/reference/spant_sim_fmrs_dataset.html b/docs/reference/spant_sim_fmrs_dataset.html
new file mode 100644
index 00000000..00e48b56
--- /dev/null
+++ b/docs/reference/spant_sim_fmrs_dataset.html
@@ -0,0 +1,117 @@
+
+Simulate an example fMRS dataset for a block design fMRS experiment and export a BIDS structure. — spant_sim_fmrs_dataset • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Simulate an example fMRS dataset for a block design fMRS experiment and export a BIDS structure.
+ Source: R/fmrs.R
+ spant_sim_fmrs_dataset.Rd
+
+
+
+ Simulate an example fMRS dataset for a block design fMRS experiment and
+export a BIDS structure.
+
+
+
+ spant_sim_fmrs_dataset(output_dir = NULL)
+
+
+
+ Arguments
+ - output_dir
+output directory for the BIDS data. Defaults to :
+"HOME/sim_fmrs_dataset/data".
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/spant_simulation_benchmark.html b/docs/reference/spant_simulation_benchmark.html
index 32daa8bf..d8cc6841 100644
--- a/docs/reference/spant_simulation_benchmark.html
+++ b/docs/reference/spant_simulation_benchmark.html
@@ -1,7 +1,5 @@
-Simulate a typical metabolite basis set for benchmarking. Timing metrics will
-be printed on completion. — spant_simulation_benchmark • Spectroscopy Analysis Tools (spant) Simulate a typical metabolite basis set for benchmarking. Timing metrics will be printed on completion. — spant_simulation_benchmark • Spectroscopy Analysis Tools (spant) Decompose an mrs_data object into white and gray matter spectra. — spec_decomp • Spectroscopy Analysis Tools (spant) Perform a mathematical operation on a spectral region. — spec_op • Spectroscopy Analysis Tools (spant) Perform a mathematical operation on a spectral region. — spec_op • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -98,8 +98,8 @@ Arguments
operator
-can be "sum" (default), "mean", "l2", "max", "min" or
-"max-min".
can be "sum" (default), "mean", "l2", "max", "max_cplx,
+"min" or "max-min".
freq_scale
@@ -129,7 +129,7 @@ Value
diff --git a/docs/reference/spin_sys.html b/docs/reference/spin_sys.html
index 853423a4..1eaa9e76 100644
--- a/docs/reference/spin_sys.html
+++ b/docs/reference/spin_sys.html
@@ -1,5 +1,5 @@
-Create a spin system object for pulse sequence simulation. — spin_sys • Spectroscopy Analysis Tools (spant) Create a spin system object for pulse sequence simulation. — spin_sys • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/spm_pve2categorical.html b/docs/reference/spm_pve2categorical.html
index 23a1bad9..70f10729 100644
--- a/docs/reference/spm_pve2categorical.html
+++ b/docs/reference/spm_pve2categorical.html
@@ -1,7 +1,5 @@
-Convert SPM style segmentation files to a single categorical image where
-the numerical values map as: 0) Other, 1) CSF, 2) GM and 3) WM. — spm_pve2categorical • Spectroscopy Analysis Tools (spant) Convert SPM style segmentation files to a single categorical image where the numerical values map as: 0) Other, 1) CSF, 2) GM and 3) WM. — spm_pve2categorical • Spectroscopy Analysis Tools (spant) Signal space projection method for lipid suppression. — ssp • Spectroscopy Analysis Tools (spant) Signal space projection method for lipid suppression. — ssp • Spectroscopy Analysis Tools (spant) Plot the fitting results of an object of class fit_result with
-individual basis set components shown. — stackplot.fit_result • Spectroscopy Analysis Tools (spant) Plot the fitting results of an object of class fit_result with individual basis set components shown. — stackplot.fit_result • Spectroscopy Analysis Tools (spant) Produce a plot with multiple traces. — stackplot • Spectroscopy Analysis Tools (spant) Produce a plot with multiple traces. — stackplot • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/stackplot.mrs_data.html b/docs/reference/stackplot.mrs_data.html
index 17ff5648..64eea445 100644
--- a/docs/reference/stackplot.mrs_data.html
+++ b/docs/reference/stackplot.mrs_data.html
@@ -1,5 +1,5 @@
-Stackplot plotting method for objects of class mrs_data. — stackplot.mrs_data • Spectroscopy Analysis Tools (spant) Stackplot plotting method for objects of class mrs_data. — stackplot.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -255,7 +255,7 @@ Arguments
diff --git a/docs/reference/sub_first_dyn.html b/docs/reference/sub_first_dyn.html
index dbd7f831..493b7242 100644
--- a/docs/reference/sub_first_dyn.html
+++ b/docs/reference/sub_first_dyn.html
@@ -1,5 +1,5 @@
-Subtract the first dynamic spectrum from a dynamic series. — sub_first_dyn • Spectroscopy Analysis Tools (spant) Subtract the first dynamic spectrum from a dynamic series. — sub_first_dyn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/sub_mean_dyns.html b/docs/reference/sub_mean_dyns.html
index 6e3bb2df..221bd0c1 100644
--- a/docs/reference/sub_mean_dyns.html
+++ b/docs/reference/sub_mean_dyns.html
@@ -1,5 +1,5 @@
-Subtract the mean dynamic spectrum from a dynamic series. — sub_mean_dyns • Spectroscopy Analysis Tools (spant) Subtract the mean dynamic spectrum from a dynamic series. — sub_mean_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/sub_median_dyns.html b/docs/reference/sub_median_dyns.html
index 134c495d..1e834f14 100644
--- a/docs/reference/sub_median_dyns.html
+++ b/docs/reference/sub_median_dyns.html
@@ -1,5 +1,5 @@
-Subtract the median dynamic spectrum from a dynamic series. — sub_median_dyns • Spectroscopy Analysis Tools (spant) Subtract the median dynamic spectrum from a dynamic series. — sub_median_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/sum_coils.html b/docs/reference/sum_coils.html
index 7bf559f2..e1ab3cc0 100644
--- a/docs/reference/sum_coils.html
+++ b/docs/reference/sum_coils.html
@@ -1,5 +1,5 @@
-Calculate the sum across receiver coil elements. — sum_coils • Spectroscopy Analysis Tools (spant) Calculate the sum across receiver coil elements. — sum_coils • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/sum_dyns.html b/docs/reference/sum_dyns.html
index a0be19d3..bbda2ffc 100644
--- a/docs/reference/sum_dyns.html
+++ b/docs/reference/sum_dyns.html
@@ -1,5 +1,5 @@
-Calculate the sum of data dynamics. — sum_dyns • Spectroscopy Analysis Tools (spant) Calculate the sum of data dynamics. — sum_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/sum_mrs.html b/docs/reference/sum_mrs.html
index a22f215b..3cc3ab9e 100644
--- a/docs/reference/sum_mrs.html
+++ b/docs/reference/sum_mrs.html
@@ -1,5 +1,5 @@
-Sum two mrs_data objects. — sum_mrs • Spectroscopy Analysis Tools (spant) Sum two mrs_data objects. — sum_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Value
diff --git a/docs/reference/sum_mrs_list.html b/docs/reference/sum_mrs_list.html
index f4e09aea..c3584348 100644
--- a/docs/reference/sum_mrs_list.html
+++ b/docs/reference/sum_mrs_list.html
@@ -1,5 +1,5 @@
-Return the sum of a list of mrs_data objects. — sum_mrs_list • Spectroscopy Analysis Tools (spant) Return the sum of a list of mrs_data objects. — sum_mrs_list • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/svs_1h_brain_analysis.html b/docs/reference/svs_1h_brain_analysis.html
index 8ce514db..dff0ef7d 100644
--- a/docs/reference/svs_1h_brain_analysis.html
+++ b/docs/reference/svs_1h_brain_analysis.html
@@ -1,5 +1,5 @@
-Standard SVS 1H brain analysis pipeline. — svs_1h_brain_analysis • Spectroscopy Analysis Tools (spant) Standard SVS 1H brain analysis pipeline. — svs_1h_brain_analysis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -199,7 +199,7 @@ Value
diff --git a/docs/reference/svs_1h_brain_analysis_dev.html b/docs/reference/svs_1h_brain_analysis_dev.html
index d70a14d3..d71bfea2 100644
--- a/docs/reference/svs_1h_brain_analysis_dev.html
+++ b/docs/reference/svs_1h_brain_analysis_dev.html
@@ -1,5 +1,5 @@
-Standard SVS 1H brain analysis pipeline. — svs_1h_brain_analysis_dev • Spectroscopy Analysis Tools (spant) Standard SVS 1H brain analysis pipeline. — svs_1h_brain_analysis_dev • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -193,7 +193,7 @@ Examples
diff --git a/docs/reference/svs_1h_brain_batch_analysis.html b/docs/reference/svs_1h_brain_batch_analysis.html
index 5631e8cc..15f7223e 100644
--- a/docs/reference/svs_1h_brain_batch_analysis.html
+++ b/docs/reference/svs_1h_brain_batch_analysis.html
@@ -1,5 +1,5 @@
-Batch interface to the standard SVS 1H brain analysis pipeline. — svs_1h_brain_batch_analysis • Spectroscopy Analysis Tools (spant) Batch interface to the standard SVS 1H brain analysis pipeline. — svs_1h_brain_batch_analysis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -144,7 +144,7 @@ Value
diff --git a/docs/reference/t_test_spec.html b/docs/reference/t_test_spec.html
new file mode 100644
index 00000000..56a7ea1b
--- /dev/null
+++ b/docs/reference/t_test_spec.html
@@ -0,0 +1,124 @@
+
+Perform a t-test on spectral data points. — t_test_spec • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+
+
+ Perform a t-test on spectral data points.
+
+
+
+ t_test_spec(mrs_data, group)
+
+
+
+ Arguments
+ - mrs_data
+an mrs_data object with spectra in the dynamic dimension.
- group
+vector describing the group membership of each dynamic spectrum.
+
+ Value
+
+
+a list of statistical results.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/td2fd.html b/docs/reference/td2fd.html
index 6748a6a8..f31ed524 100644
--- a/docs/reference/td2fd.html
+++ b/docs/reference/td2fd.html
@@ -1,5 +1,5 @@
-Transform time-domain data to the frequency-domain. — td2fd • Spectroscopy Analysis Tools (spant) Transform time-domain data to the frequency-domain. — td2fd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/td_conv_filt.html b/docs/reference/td_conv_filt.html
index a9f340c3..106b9b00 100644
--- a/docs/reference/td_conv_filt.html
+++ b/docs/reference/td_conv_filt.html
@@ -1,5 +1,5 @@
-Time-domain convolution based filter. — td_conv_filt • Spectroscopy Analysis Tools (spant) Time-domain convolution based filter. — td_conv_filt • Spectroscopy Analysis Tools (spant) Time-domain spectral registration. — tdsr • Spectroscopy Analysis Tools (spant) Time-domain spectral registration. — tdsr • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -121,7 +121,7 @@ Value
diff --git a/docs/reference/te.html b/docs/reference/te.html
index 010361b1..4a65711d 100644
--- a/docs/reference/te.html
+++ b/docs/reference/te.html
@@ -1,5 +1,5 @@
-Return the echo time of an MRS dataset. — te • Spectroscopy Analysis Tools (spant) Return the echo time of an MRS dataset. — te • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/tr.html b/docs/reference/tr.html
index 0c0bd63b..2e749e02 100644
--- a/docs/reference/tr.html
+++ b/docs/reference/tr.html
@@ -1,5 +1,5 @@
-Return the repetition time of an MRS dataset. — tr • Spectroscopy Analysis Tools (spant) Return the repetition time of an MRS dataset. — tr • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/varpro_3_para_opts.html b/docs/reference/varpro_3_para_opts.html
index c2270a16..52d7cd84 100644
--- a/docs/reference/varpro_3_para_opts.html
+++ b/docs/reference/varpro_3_para_opts.html
@@ -1,5 +1,5 @@
-Return a list of options for VARPRO based fitting with 3 free parameters. — varpro_3_para_opts • Spectroscopy Analysis Tools (spant) Return a list of options for VARPRO based fitting with 3 free parameters. — varpro_3_para_opts • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -141,7 +141,7 @@ Value
diff --git a/docs/reference/varpro_basic_opts.html b/docs/reference/varpro_basic_opts.html
index 32c86d22..c5104891 100644
--- a/docs/reference/varpro_basic_opts.html
+++ b/docs/reference/varpro_basic_opts.html
@@ -1,5 +1,5 @@
-Return a list of options for a basic VARPRO analysis. — varpro_basic_opts • Spectroscopy Analysis Tools (spant) Return a list of options for a basic VARPRO analysis. — varpro_basic_opts • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -118,7 +118,7 @@ Value
diff --git a/docs/reference/varpro_opts.html b/docs/reference/varpro_opts.html
index 2aabf11d..6332f730 100644
--- a/docs/reference/varpro_opts.html
+++ b/docs/reference/varpro_opts.html
@@ -1,5 +1,5 @@
-Return a list of options for VARPRO based fitting. — varpro_opts • Spectroscopy Analysis Tools (spant) Return a list of options for VARPRO based fitting. — varpro_opts • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -177,7 +177,7 @@ Examples
diff --git a/docs/reference/vec2mrs_data.html b/docs/reference/vec2mrs_data.html
index 0cccd73b..f0d58bf0 100644
--- a/docs/reference/vec2mrs_data.html
+++ b/docs/reference/vec2mrs_data.html
@@ -1,5 +1,5 @@
-Convert a vector into a mrs_data object. — vec2mrs_data • Spectroscopy Analysis Tools (spant) Convert a vector into a mrs_data object. — vec2mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -80,10 +80,11 @@ Convert a vector into a mrs_data object.
vec2mrs_data(
vec,
- fs = def_fs(),
- ft = def_ft(),
- ref = def_ref(),
- nuc = def_nuc(),
+ mrs_data = NULL,
+ fs = NULL,
+ ft = NULL,
+ ref = NULL,
+ nuc = NULL,
dyns = 1,
fd = FALSE
)
@@ -95,6 +96,10 @@ Arguments
the data vector.
mrs_data
+example data to copy acquisition parameters from.
fs
sampling frequency in Hz.
Arguments
fd
-flag to indicate if the matrix is in the frequency domain (logical).
flag to indicate if the vector is in the frequency domain (logical).
Value
diff --git a/docs/reference/write_basis.html b/docs/reference/write_basis.html
index b6e27cbd..94c5e021 100644
--- a/docs/reference/write_basis.html
+++ b/docs/reference/write_basis.html
@@ -1,5 +1,5 @@
-Write a basis object to an LCModel .basis formatted file. — write_basis • Spectroscopy Analysis Tools (spant) Write a basis object to an LCModel .basis formatted file. — write_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -108,7 +108,7 @@ Arguments
diff --git a/docs/reference/write_basis_tqn.html b/docs/reference/write_basis_tqn.html
index 6aa51c1d..116c73ec 100644
--- a/docs/reference/write_basis_tqn.html
+++ b/docs/reference/write_basis_tqn.html
@@ -1,5 +1,5 @@
-Generate a basis file using TARQUIN. — write_basis_tqn • Spectroscopy Analysis Tools (spant) Generate a basis file using TARQUIN. — write_basis_tqn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Examples
diff --git a/docs/reference/write_mrs.html b/docs/reference/write_mrs.html
index fff25f15..124b9dc4 100644
--- a/docs/reference/write_mrs.html
+++ b/docs/reference/write_mrs.html
@@ -1,5 +1,5 @@
-Write MRS data object to file. — write_mrs • Spectroscopy Analysis Tools (spant) Write MRS data object to file. — write_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Arguments
diff --git a/docs/reference/write_mrs_nifti.html b/docs/reference/write_mrs_nifti.html
index f4bf1921..bd3ed4b7 100644
--- a/docs/reference/write_mrs_nifti.html
+++ b/docs/reference/write_mrs_nifti.html
@@ -1,5 +1,5 @@
-Write MRS data object to file in NIFTI format. — write_mrs_nifti • Spectroscopy Analysis Tools (spant) Write MRS data object to file in NIFTI format. — write_mrs_nifti • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/write_pulse_ascii.html b/docs/reference/write_pulse_ascii.html
index 067ae086..221f8ebb 100644
--- a/docs/reference/write_pulse_ascii.html
+++ b/docs/reference/write_pulse_ascii.html
@@ -1,5 +1,5 @@
-Write an ASCII formatted pulse file. — write_pulse_ascii • Spectroscopy Analysis Tools (spant) Write an ASCII formatted pulse file. — write_pulse_ascii • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/zero_fade_spec.html b/docs/reference/zero_fade_spec.html
index c703745c..c8b572c3 100644
--- a/docs/reference/zero_fade_spec.html
+++ b/docs/reference/zero_fade_spec.html
@@ -1,7 +1,5 @@
-Fade a spectrum to zero by frequency domain multiplication with a tanh
-function. Note this operation distorts data points at the end of the FID. — zero_fade_spec • Spectroscopy Analysis Tools (spant) Fade a spectrum to zero by frequency domain multiplication with a tanh function. Note this operation distorts data points at the end of the FID. — zero_fade_spec • Spectroscopy Analysis Tools (spant) Zero all coherences including and above a given order. — zero_higher_orders • Spectroscopy Analysis Tools (spant) Zero all coherences including and above a given order. — zero_higher_orders • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Value
diff --git a/docs/reference/zero_td_pts_end.html b/docs/reference/zero_td_pts_end.html
index 8c1123c8..71d24ebb 100644
--- a/docs/reference/zero_td_pts_end.html
+++ b/docs/reference/zero_td_pts_end.html
@@ -1,5 +1,5 @@
-Set mrs_data object data points at the end of the FID to zero. — zero_td_pts_end • Spectroscopy Analysis Tools (spant) Set mrs_data object data points at the end of the FID to zero. — zero_td_pts_end • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/zf.html b/docs/reference/zf.html
index 85e2013c..baf50256 100644
--- a/docs/reference/zf.html
+++ b/docs/reference/zf.html
@@ -1,5 +1,5 @@
-Zero-fill MRS data in the time domain. — zf • Spectroscopy Analysis Tools (spant) Zero-fill MRS data in the time domain. — zf • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -125,7 +125,7 @@ Value
diff --git a/docs/reference/zf_xy.html b/docs/reference/zf_xy.html
index ebca3999..c4104a74 100644
--- a/docs/reference/zf_xy.html
+++ b/docs/reference/zf_xy.html
@@ -1,5 +1,5 @@
-Zero-fill MRSI data in the k-space x-y direction. — zf_xy • Spectroscopy Analysis Tools (spant) Zero-fill MRSI data in the k-space x-y direction. — zf_xy • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -113,7 +113,7 @@ Value
diff --git a/docs/sitemap.xml b/docs/sitemap.xml
index e2139f71..4c39f515 100644
--- a/docs/sitemap.xml
+++ b/docs/sitemap.xml
@@ -216,6 +216,12 @@
https://martin3141.github.io/spant/reference/comb_coils_fp_pc.html
+
+ https://martin3141.github.io/spant/reference/comb_coils_mrsi_gls.html
+
+
+ https://martin3141.github.io/spant/reference/comb_coils_svs_gls.html
+
https://martin3141.github.io/spant/reference/comb_csv_results.html
@@ -411,6 +417,9 @@
https://martin3141.github.io/spant/reference/gen_conv_reg.html
+
+ https://martin3141.github.io/spant/reference/gen_group_reg.html
+
https://martin3141.github.io/spant/reference/gen_impulse_reg.html
@@ -555,6 +564,15 @@
https://martin3141.github.io/spant/reference/glm_spec.html
+
+ https://martin3141.github.io/spant/reference/glm_spec_fmrs_fl.html
+
+
+ https://martin3141.github.io/spant/reference/glm_spec_fmrs_group.html
+
+
+ https://martin3141.github.io/spant/reference/glm_spec_group_linhyp.html
+
https://martin3141.github.io/spant/reference/grid_shift_xy.html
@@ -690,9 +708,15 @@
https://martin3141.github.io/spant/reference/mrs_data2basis.html
+
+ https://martin3141.github.io/spant/reference/mrs_data2bids.html
+
https://martin3141.github.io/spant/reference/mrs_data2mat.html
+
+ https://martin3141.github.io/spant/reference/mrs_data2spec_mat.html
+
https://martin3141.github.io/spant/reference/mrs_data2vec.html
@@ -741,6 +765,9 @@
https://martin3141.github.io/spant/reference/phase.html
+
+ https://martin3141.github.io/spant/reference/phase_ref_1h_brain.html
+
https://martin3141.github.io/spant/reference/plot.fit_result.html
@@ -780,6 +807,12 @@
https://martin3141.github.io/spant/reference/precomp.html
+
+ https://martin3141.github.io/spant/reference/preproc_svs.html
+
+
+ https://martin3141.github.io/spant/reference/preproc_svs_dataset.html
+
https://martin3141.github.io/spant/reference/print.fit_result.html
@@ -1050,6 +1083,9 @@
https://martin3141.github.io/spant/reference/spant_mpress_drift.html
+
+ https://martin3141.github.io/spant/reference/spant_sim_fmrs_dataset.html
+
https://martin3141.github.io/spant/reference/spant_simulation_benchmark.html
@@ -1107,6 +1143,9 @@
https://martin3141.github.io/spant/reference/svs_1h_brain_batch_analysis.html
+
+ https://martin3141.github.io/spant/reference/t_test_spec.html
+
https://martin3141.github.io/spant/reference/td2fd.html
Generate a mol_parameters object for a simple spin system with one
-resonance.
Generate a mol_parameters object for a simple spin system with one resonance.
All functions glm_spec()
Perform a GLM analysis of dynamic MRS data in the spectral domain.
Perform a GLM analysis of dynamic MRS data in the spectral domain.
Perform first-level spectral GLM analysis of an fMRS dataset.
Perform group-level spectral GLM analysis of an fMRS dataset.
Test a group-level spectral GLM linear hypothesis.
All functions
- Perform an ifft and ifftshift on a matrix with each column replaced by its
-shifted ifft.
Perform an ifft and ifftshift on a matrix with each column replaced by its shifted ifft.
@@ -799,8 +790,7 @@ All functions
- Check if the chemical shift dimension of an MRS data object is in the
-frequency domain.
Check if the chemical shift dimension of an MRS data object is in the frequency domain.
@@ -820,18 +810,15 @@ All functions
- Covert a linewidth in Hz to an equivalent alpha value in the time-domain ie:
-x * exp(-t * alpha).
Covert a linewidth in Hz to an equivalent alpha value in the time-domain ie: x * exp(-t * alpha).
- Covert a linewidth in Hz to an equivalent beta value in the time-domain ie:
-x * exp(-t * t * beta).
Covert a linewidth in Hz to an equivalent beta value in the time-domain ie: x * exp(-t * t * beta).
- Make a basis-set object from a directory containing LCModel formatted RAW
-files.
Make a basis-set object from a directory containing LCModel formatted RAW files.
@@ -851,8 +838,7 @@ All functions
- Mask the voxels outside an elliptical region spanning the MRSI dataset in the
-x-y plane.
Mask the voxels outside an elliptical region spanning the MRSI dataset in the x-y plane.
@@ -860,13 +846,11 @@ All functions
- Convert a matrix (with spectral points in the column dimension and dynamics
-in the row dimensions) into a mrs_data object.
Convert a matrix (with spectral points in the column dimension and dynamics in the row dimensions) into a mrs_data object.
- Matrix exponential function taken from complexplus package to reduce the
-number of spant dependencies.
Matrix exponential function taken from complexplus package to reduce the number of spant dependencies.
@@ -914,31 +898,31 @@ All functions
- Convert an mrs_data object to basis object - where basis signals are spread
-across the dynamic dimension in the MRS data.
Convert an mrs_data object to basis object - where basis signals are spread across the dynamic dimension in the MRS data.
+
+
+ Create a BIDS file structure from a vector of MRS data paths or list of mrs_data objects.
- Convert mrs_data object to a matrix, with spectral points in the column
-dimension and dynamics in the row dimension.
Convert mrs_data object to a matrix, with spectral points in the column dimension and dynamics in the row dimension.
-
+
- Convert mrs_data object to a vector.
Convert mrs_data object to a matrix, with spectral points in the column dimension and dynamics in the row dimension.
-
+
- Create a BIDS directory and file structure from a list of mrs_data objects.
Convert mrs_data object to a vector.
- Perform a fftshift on a matrix, with each column replaced by its shifted
-result.
Perform a fftshift on a matrix, with each column replaced by its shifted result.
- Perform an ifftshift on a matrix, with each column replaced by its shifted
-result.
Perform an ifftshift on a matrix, with each column replaced by its shifted result.
@@ -946,9 +930,7 @@ All functions
- Flip the x data dimension order of a nifti image. This corresponds to
-flipping MRI data in the left-right direction, assuming the data in save in
-neurological format (can check with fslorient program).
Flip the x data dimension order of a nifti image. This corresponds to flipping MRI data in the left-right direction, assuming the data in save in neurological format (can check with fslorient program).
@@ -964,8 +946,7 @@ All functions
- Search for the highest peak in a spectral region and return the frequency,
-height and FWHM.
Search for the highest peak in a spectral region and return the frequency, height and FWHM.
@@ -974,6 +955,10 @@ All functions phase()
Apply phasing parameters to MRS data.
+
+
+ Corrected zero order phase and chemical shift offset in 1H MRS data from the brain.
@@ -1005,8 +990,7 @@ All functions
- Plot an interactive slice map from a data array where voxels can be selected
-to display a corresponding spectrum.
Plot an interactive slice map from a data array where voxels can be selected to display a corresponding spectrum.
@@ -1026,8 +1010,15 @@ All functions
- Save function results to file and load on subsequent calls to avoid repeat
-computation.
Save function results to file and load on subsequent calls to avoid repeat computation.
+
+
+ Preprocess and perform quality assessment of a single SVS data set.
+
+
+ Preprocess and perform quality assessment of one or more SVS data sets.
@@ -1055,15 +1046,11 @@ All functions
- Read a directory containing Siemens MRS IMA files and combine along the coil
-dimension. Note that the coil ID is inferred from the sorted file name and
-should be checked when consistency is required between two directories.
Read a directory containing Siemens MRS IMA files and combine along the coil dimension. Note that the coil ID is inferred from the sorted file name and should be checked when consistency is required between two directories.
- Read a directory containing Siemens MRS IMA files and combine along the
-dynamic dimension. Note that the coil ID is inferred from the sorted file
-name and should be checked when consistency is required.
Read a directory containing Siemens MRS IMA files and combine along the dynamic dimension. Note that the coil ID is inferred from the sorted file name and should be checked when consistency is required.
@@ -1103,13 +1090,11 @@ All functions
- Reconstruct complex time-domain data from the real part of frequency-domain
-data.
Reconstruct complex time-domain data from the real part of frequency-domain data.
- Reconstruct complex time-domain data from the real part of frequency-domain
-data.
Reconstruct complex time-domain data from the real part of frequency-domain data.
@@ -1141,8 +1126,7 @@ All functions
- Resample a VOI to match a target image space using nearest-neighbour
-interpolation.
Resample a VOI to match a target image space using nearest-neighbour interpolation.
@@ -1158,23 +1142,19 @@ All functions
- Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water).
Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / kg of tissue water).
- Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water).
Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / kg of tissue water).
- Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / Litre of tissue).
Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / Litre of tissue).
- Convert default LCM/TARQUIN concentration scaling to molal units with partial
-volume correction.
Convert default LCM/TARQUIN concentration scaling to molal units with partial volume correction.
@@ -1222,8 +1202,7 @@ All functions
- MEGA-PRESS sequence with ideal localisation pulses and Gaussian shaped
-editing pulse.
MEGA-PRESS sequence with ideal localisation pulses and Gaussian shaped editing pulse.
@@ -1251,13 +1230,11 @@ All functions
- STEAM sequence with ideal pulses and coherence order filtering to simulate
-gradient crushers.
STEAM sequence with ideal pulses and coherence order filtering to simulate gradient crushers.
- STEAM sequence with ideal pulses using the z-rotation gradient simulation
-method described by Young et al JMR 140, 146-152 (1999).
STEAM sequence with ideal pulses using the z-rotation gradient simulation method described by Young et al JMR 140, 146-152 (1999).
@@ -1293,8 +1270,7 @@ All functions
- Set the number of time-domain data points, truncating or zero-filling as
-appropriate.
Set the number of time-domain data points, truncating or zero-filling as appropriate.
@@ -1318,18 +1294,15 @@ All functions
- Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS
-sequence. Note, ideal pulses are assumed.
Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS sequence. Note, ideal pulses are assumed.
- Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS
-sequence. Note, ideal pulses are assumed.
Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS sequence. Note, ideal pulses are assumed.
- Simulate a macromolecular and lipid basis-set suitable for 1H brain MRS
-analysis.
Simulate a macromolecular and lipid basis-set suitable for 1H brain MRS analysis.
@@ -1353,8 +1326,7 @@ All functions
- Simulate an ideal pulse excitation profile by smoothing a top-hat function
-with a Gaussian.
Simulate an ideal pulse excitation profile by smoothing a top-hat function with a Gaussian.
@@ -1374,17 +1346,19 @@ All functions
- Simulate and fit some spectra with ABfit for benchmarking purposes. Basic
-timing and performance metrics will be printed.
Simulate and fit some spectra with ABfit for benchmarking purposes. Basic timing and performance metrics will be printed.
Example MEGA-PRESS data with significant B0 drift.
+
+
+ Simulate an example fMRS dataset for a block design fMRS experiment and export a BIDS structure.
- Simulate a typical metabolite basis set for benchmarking. Timing metrics will
-be printed on completion.
Simulate a typical metabolite basis set for benchmarking. Timing metrics will be printed on completion.
@@ -1400,8 +1374,7 @@ All functions
- Convert SPM style segmentation files to a single categorical image where
-the numerical values map as: 0) Other, 1) CSF, 2) GM and 3) WM.
Convert SPM style segmentation files to a single categorical image where the numerical values map as: 0) Other, 1) CSF, 2) GM and 3) WM.
@@ -1413,8 +1386,7 @@ All functions
- Plot the fitting results of an object of class fit_result with
-individual basis set components shown.
Plot the fitting results of an object of class fit_result with individual basis set components shown.
@@ -1459,6 +1431,10 @@ All functions svs_1h_brain_batch_analysis()
Batch interface to the standard SVS 1H brain analysis pipeline.
+
+
+ Perform a t-test on spectral data points.
@@ -1518,8 +1494,7 @@ All functions
- Fade a spectrum to zero by frequency domain multiplication with a tanh
-function. Note this operation distorts data points at the end of the FID.
Fade a spectrum to zero by frequency domain multiplication with a tanh function. Note this operation distorts data points at the end of the FID.
@@ -1549,7 +1524,7 @@ All functions
diff --git a/docs/reference/int_spec.html b/docs/reference/int_spec.html
index c7060fe7..783325a8 100644
--- a/docs/reference/int_spec.html
+++ b/docs/reference/int_spec.html
@@ -1,5 +1,5 @@
-Integrate a spectral region. — int_spec • Spectroscopy Analysis Tools (spant) Integrate a spectral region. — int_spec • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -118,7 +118,7 @@ Value
diff --git a/docs/reference/interleave_dyns.html b/docs/reference/interleave_dyns.html
index effe5543..441eff27 100644
--- a/docs/reference/interleave_dyns.html
+++ b/docs/reference/interleave_dyns.html
@@ -1,5 +1,5 @@
-Interleave the first and second half of a dynamic series. — interleave_dyns • Spectroscopy Analysis Tools (spant) Interleave the first and second half of a dynamic series. — interleave_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/inv_even_dyns.html b/docs/reference/inv_even_dyns.html
index 9f9d4fff..dcb781dc 100644
--- a/docs/reference/inv_even_dyns.html
+++ b/docs/reference/inv_even_dyns.html
@@ -1,5 +1,5 @@
-Invert even numbered dynamic scans starting from 1 (2,4,6...). — inv_even_dyns • Spectroscopy Analysis Tools (spant) Invert even numbered dynamic scans starting from 1 (2,4,6...). — inv_even_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/inv_odd_dyns.html b/docs/reference/inv_odd_dyns.html
index 26212e2b..78d64660 100644
--- a/docs/reference/inv_odd_dyns.html
+++ b/docs/reference/inv_odd_dyns.html
@@ -1,5 +1,5 @@
-Invert odd numbered dynamic scans starting from 1 (1,3,5...). — inv_odd_dyns • Spectroscopy Analysis Tools (spant) Invert odd numbered dynamic scans starting from 1 (1,3,5...). — inv_odd_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/is.def.html b/docs/reference/is.def.html
index f196ffd0..a67b9eba 100644
--- a/docs/reference/is.def.html
+++ b/docs/reference/is.def.html
@@ -1,5 +1,5 @@
-Check if an object is defined, which is the same as being not NULL. — is.def • Spectroscopy Analysis Tools (spant) Check if an object is defined, which is the same as being not NULL. — is.def • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/is_fd.html b/docs/reference/is_fd.html
index 3b0ca165..18a193aa 100644
--- a/docs/reference/is_fd.html
+++ b/docs/reference/is_fd.html
@@ -1,7 +1,5 @@
-Check if the chemical shift dimension of an MRS data object is in the
-frequency domain. — is_fd • Spectroscopy Analysis Tools (spant) Check if the chemical shift dimension of an MRS data object is in the frequency domain. — is_fd • Spectroscopy Analysis Tools (spant) Transform 2D MRSI data from k-space to image space in the x-y direction. — kspace2img_xy • Spectroscopy Analysis Tools (spant) Transform 2D MRSI data from k-space to image space in the x-y direction. — kspace2img_xy • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/l2_reg.html b/docs/reference/l2_reg.html
index 3d781d80..21aa9849 100644
--- a/docs/reference/l2_reg.html
+++ b/docs/reference/l2_reg.html
@@ -1,5 +1,5 @@
-Perform l2 regularisation artefact suppression. — l2_reg • Spectroscopy Analysis Tools (spant) Perform l2 regularisation artefact suppression. — l2_reg • Spectroscopy Analysis Tools (spant) Apply line-broadening (apodisation) to MRS data or basis object. — lb • Spectroscopy Analysis Tools (spant) Apply line-broadening (apodisation) to MRS data or basis object. — lb • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -123,7 +123,7 @@ Value
diff --git a/docs/reference/lofdc.html b/docs/reference/lofdc.html
index 5419b1ec..31347a25 100644
--- a/docs/reference/lofdc.html
+++ b/docs/reference/lofdc.html
@@ -1,5 +1,5 @@
-Correct linear frequency drift. — lofdc • Spectroscopy Analysis Tools (spant) Correct linear frequency drift. — lofdc • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -138,7 +138,7 @@ Value
diff --git a/docs/reference/lw2alpha.html b/docs/reference/lw2alpha.html
index b83db682..25da229b 100644
--- a/docs/reference/lw2alpha.html
+++ b/docs/reference/lw2alpha.html
@@ -1,7 +1,5 @@
-Covert a linewidth in Hz to an equivalent alpha value in the time-domain ie:
-x * exp(-t * alpha). — lw2alpha • Spectroscopy Analysis Tools (spant) Covert a linewidth in Hz to an equivalent alpha value in the time-domain ie: x * exp(-t * alpha). — lw2alpha • Spectroscopy Analysis Tools (spant) Covert a linewidth in Hz to an equivalent beta value in the time-domain ie:
-x * exp(-t * t * beta). — lw2beta • Spectroscopy Analysis Tools (spant) Covert a linewidth in Hz to an equivalent beta value in the time-domain ie: x * exp(-t * t * beta). — lw2beta • Spectroscopy Analysis Tools (spant) Make a basis-set object from a directory containing LCModel formatted RAW
-files. — make_basis_from_raw • Spectroscopy Analysis Tools (spant) Make a basis-set object from a directory containing LCModel formatted RAW files. — make_basis_from_raw • Spectroscopy Analysis Tools (spant) Mask an MRS dataset in the dynamic dimension. — mask_dyns • Spectroscopy Analysis Tools (spant) Mask an MRS dataset in the dynamic dimension. — mask_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/mask_fit_res.html b/docs/reference/mask_fit_res.html
index 97baaa3f..ebd91a99 100644
--- a/docs/reference/mask_fit_res.html
+++ b/docs/reference/mask_fit_res.html
@@ -1,5 +1,5 @@
-Mask fit result spectra depending on a vector of bool values. — mask_fit_res • Spectroscopy Analysis Tools (spant) Mask fit result spectra depending on a vector of bool values. — mask_fit_res • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -116,7 +116,7 @@ Value
diff --git a/docs/reference/mask_xy.html b/docs/reference/mask_xy.html
index 11bb577c..b0d38619 100644
--- a/docs/reference/mask_xy.html
+++ b/docs/reference/mask_xy.html
@@ -1,5 +1,5 @@
-Mask an MRSI dataset in the x-y direction — mask_xy • Spectroscopy Analysis Tools (spant) Mask an MRSI dataset in the x-y direction — mask_xy • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/mask_xy_corners.html b/docs/reference/mask_xy_corners.html
index 09b16cd2..2d13839d 100644
--- a/docs/reference/mask_xy_corners.html
+++ b/docs/reference/mask_xy_corners.html
@@ -1,5 +1,5 @@
-Mask the four corners of an MRSI dataset in the x-y plane. — mask_xy_corners • Spectroscopy Analysis Tools (spant) Mask the four corners of an MRSI dataset in the x-y plane. — mask_xy_corners • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/mask_xy_ellipse.html b/docs/reference/mask_xy_ellipse.html
index 1d8b02e4..e2e749ef 100644
--- a/docs/reference/mask_xy_ellipse.html
+++ b/docs/reference/mask_xy_ellipse.html
@@ -1,7 +1,5 @@
-Mask the voxels outside an elliptical region spanning the MRSI dataset in the
-x-y plane. — mask_xy_ellipse • Spectroscopy Analysis Tools (spant) Mask the voxels outside an elliptical region spanning the MRSI dataset in the x-y plane. — mask_xy_ellipse • Spectroscopy Analysis Tools (spant) Mask a 2D MRSI dataset in the x-y dimension. — mask_xy_mat • Spectroscopy Analysis Tools (spant) Mask a 2D MRSI dataset in the x-y dimension. — mask_xy_mat • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Value
diff --git a/docs/reference/mat2mrs_data.html b/docs/reference/mat2mrs_data.html
index 2e2895f3..ae55665f 100644
--- a/docs/reference/mat2mrs_data.html
+++ b/docs/reference/mat2mrs_data.html
@@ -1,7 +1,5 @@
-Convert a matrix (with spectral points in the column dimension and dynamics
-in the row dimensions) into a mrs_data object. — mat2mrs_data • Spectroscopy Analysis Tools (spant) Convert a matrix (with spectral points in the column dimension and dynamics in the row dimensions) into a mrs_data object. — mat2mrs_data • Spectroscopy Analysis Tools (spant) Matrix exponential function taken from complexplus package to reduce the
-number of spant dependencies. — matexp • Spectroscopy Analysis Tools (spant) Matrix exponential function taken from complexplus package to reduce the number of spant dependencies. — matexp • Spectroscopy Analysis Tools (spant) Apply the max operator to an MRS dataset. — max_mrs • Spectroscopy Analysis Tools (spant) Apply the max operator to an MRS dataset. — max_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/max_mrs_interp.html b/docs/reference/max_mrs_interp.html
index e4474764..52e63f3e 100644
--- a/docs/reference/max_mrs_interp.html
+++ b/docs/reference/max_mrs_interp.html
@@ -1,5 +1,5 @@
-Apply the max operator to an interpolated MRS dataset. — max_mrs_interp • Spectroscopy Analysis Tools (spant) Apply the max operator to an interpolated MRS dataset. — max_mrs_interp • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/mean.list.html b/docs/reference/mean.list.html
index b8eb3463..048306fd 100644
--- a/docs/reference/mean.list.html
+++ b/docs/reference/mean.list.html
@@ -1,5 +1,5 @@
-Calculate the mean spectrum from an mrs_data object. — mean.list • Spectroscopy Analysis Tools (spant) Calculate the mean spectrum from an mrs_data object. — mean.list • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/mean.mrs_data.html b/docs/reference/mean.mrs_data.html
index 5531a28d..79515014 100644
--- a/docs/reference/mean.mrs_data.html
+++ b/docs/reference/mean.mrs_data.html
@@ -1,5 +1,5 @@
-Calculate the mean spectrum from an mrs_data object. — mean.mrs_data • Spectroscopy Analysis Tools (spant) Calculate the mean spectrum from an mrs_data object. — mean.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/mean_dyn_blocks.html b/docs/reference/mean_dyn_blocks.html
index 10467098..4c042448 100644
--- a/docs/reference/mean_dyn_blocks.html
+++ b/docs/reference/mean_dyn_blocks.html
@@ -1,5 +1,5 @@
-Calculate the mean of adjacent dynamic scans. — mean_dyn_blocks • Spectroscopy Analysis Tools (spant) Calculate the mean of adjacent dynamic scans. — mean_dyn_blocks • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/mean_dyn_pairs.html b/docs/reference/mean_dyn_pairs.html
index 63e909ea..1a241126 100644
--- a/docs/reference/mean_dyn_pairs.html
+++ b/docs/reference/mean_dyn_pairs.html
@@ -1,5 +1,5 @@
-Calculate the pairwise means across a dynamic data set. — mean_dyn_pairs • Spectroscopy Analysis Tools (spant) Calculate the pairwise means across a dynamic data set. — mean_dyn_pairs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/mean_dyns.html b/docs/reference/mean_dyns.html
index 73fdbfa7..0daa27df 100644
--- a/docs/reference/mean_dyns.html
+++ b/docs/reference/mean_dyns.html
@@ -1,5 +1,5 @@
-Calculate the mean dynamic data. — mean_dyns • Spectroscopy Analysis Tools (spant) Calculate the mean dynamic data. — mean_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/mean_mrs_list.html b/docs/reference/mean_mrs_list.html
index 808b6c50..10d842c0 100644
--- a/docs/reference/mean_mrs_list.html
+++ b/docs/reference/mean_mrs_list.html
@@ -1,5 +1,5 @@
-Return the mean of a list of mrs_data objects. — mean_mrs_list • Spectroscopy Analysis Tools (spant) Return the mean of a list of mrs_data objects. — mean_mrs_list • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/mean_vec_blocks.html b/docs/reference/mean_vec_blocks.html
index 8fc92eaa..dd78b122 100644
--- a/docs/reference/mean_vec_blocks.html
+++ b/docs/reference/mean_vec_blocks.html
@@ -1,5 +1,5 @@
-Calculate the mean of adjacent blocks in a vector. — mean_vec_blocks • Spectroscopy Analysis Tools (spant) Calculate the mean of adjacent blocks in a vector. — mean_vec_blocks • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/median_dyns.html b/docs/reference/median_dyns.html
index 1039d4b5..9a085b10 100644
--- a/docs/reference/median_dyns.html
+++ b/docs/reference/median_dyns.html
@@ -1,5 +1,5 @@
-Calculate the median dynamic data. — median_dyns • Spectroscopy Analysis Tools (spant) Calculate the median dynamic data. — median_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/mod_td.html b/docs/reference/mod_td.html
index 76ad0a40..141ef09e 100644
--- a/docs/reference/mod_td.html
+++ b/docs/reference/mod_td.html
@@ -1,5 +1,5 @@
-Apply the Modulus operator to the time-domain MRS signal. — mod_td • Spectroscopy Analysis Tools (spant) Apply the Modulus operator to the time-domain MRS signal. — mod_td • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/mrs_data2basis.html b/docs/reference/mrs_data2basis.html
index 62f7d749..11797b91 100644
--- a/docs/reference/mrs_data2basis.html
+++ b/docs/reference/mrs_data2basis.html
@@ -1,7 +1,5 @@
-Convert an mrs_data object to basis object - where basis signals are spread
-across the dynamic dimension in the MRS data. — mrs_data2basis • Spectroscopy Analysis Tools (spant) Convert an mrs_data object to basis object - where basis signals are spread across the dynamic dimension in the MRS data. — mrs_data2basis • Spectroscopy Analysis Tools (spant) Create a BIDS file structure from a vector of MRS data paths or list of mrs_data objects. — mrs_data2bids • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Create a BIDS file structure from a vector of MRS data paths or list of mrs_data objects.
+ Source: R/fmrs.R
+ mrs_data2bids.Rd
+
+
+
+ Create a BIDS file structure from a vector of MRS data paths or list of
+mrs_data objects.
+
+
+
+ mrs_data2bids(
+ mrs_data,
+ output_dir,
+ suffix = NULL,
+ sub = NULL,
+ ses = NULL,
+ task = NULL,
+ acq = NULL,
+ nuc = NULL,
+ voi = NULL,
+ rec = NULL,
+ run = NULL,
+ echo = NULL,
+ inv = NULL,
+ skip_existing = TRUE
+)
+
+
+
+ Arguments
+ - mrs_data
+vector of MRS data paths or list of mrs_data objects.
- output_dir
+the base directory to create the BIDS structure.
- suffix
+optional vector of file suffixes. Default behaviour is to
+automatically determine these from the input data, however it is recommended
+that they are specified to allow more efficient skipping of existing data.
- sub
+optional vector of subject labels. If not specified, these will be
+automatically generated as a series of increasing zero-padded integer values
+corresponding to the mrs_data input indices.
- ses
+optional vector of session labels.
- task
+optional vector of task labels.
- acq
+optional vector of acquisition labels.
- nuc
+optional vector of nucleus labels.
- voi
+optional vector of volume of interest labels.
- rec
+optional vector of reconstruction labels.
- run
+optional vector of run indices.
- echo
+optional vector of echo time indices.
- inv
+optional vector of inversion indices.
- skip_existing
+skip any data files that have already been converted.
+Defaults to TRUE, set to FALSE to force an overwrite of any existing data
+files.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/mrs_data2mat.html b/docs/reference/mrs_data2mat.html
index cf5ff28c..9e47688a 100644
--- a/docs/reference/mrs_data2mat.html
+++ b/docs/reference/mrs_data2mat.html
@@ -1,7 +1,5 @@
-Convert mrs_data object to a matrix, with spectral points in the column
-dimension and dynamics in the row dimension. — mrs_data2mat • Spectroscopy Analysis Tools (spant) Convert mrs_data object to a matrix, with spectral points in the column dimension and dynamics in the row dimension. — mrs_data2mat • Spectroscopy Analysis Tools (spant) Convert mrs_data object to a matrix, with spectral points in the column dimension and dynamics in the row dimension. — mrs_data2spec_mat • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Convert mrs_data object to a matrix, with spectral points in the column dimension and dynamics in the row dimension.
+ Source: R/mrs_data_proc.R
+ mrs_data2spec_mat.Rd
+
+
+
+ Convert mrs_data object to a matrix, with spectral points in the column
+dimension and dynamics in the row dimension.
+
+
+
+ mrs_data2spec_mat(mrs_data, collapse = TRUE)
+
+
+
+ Arguments
+ - mrs_data
+MRS data object or list of MRS data objects.
- collapse
+collapse all other dimensions along the dynamic dimension, eg
+a 16x16 MRSI grid would be first collapsed across 256 dynamic scans.
+
+ Value
+
+
+MRS data matrix.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/mrs_data2vec.html b/docs/reference/mrs_data2vec.html
index fb172d68..a1fd654d 100644
--- a/docs/reference/mrs_data2vec.html
+++ b/docs/reference/mrs_data2vec.html
@@ -1,5 +1,5 @@
-Convert mrs_data object to a vector. — mrs_data2vec • Spectroscopy Analysis Tools (spant) Convert mrs_data object to a vector. — mrs_data2vec • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -126,7 +126,7 @@ Value
diff --git a/docs/reference/mvfftshift.html b/docs/reference/mvfftshift.html
index 92b0841b..976b3410 100644
--- a/docs/reference/mvfftshift.html
+++ b/docs/reference/mvfftshift.html
@@ -1,7 +1,5 @@
-Perform a fftshift on a matrix, with each column replaced by its shifted
-result. — mvfftshift • Spectroscopy Analysis Tools (spant) Perform a fftshift on a matrix, with each column replaced by its shifted result. — mvfftshift • Spectroscopy Analysis Tools (spant) Perform an ifftshift on a matrix, with each column replaced by its shifted
-result. — mvifftshift • Spectroscopy Analysis Tools (spant) Perform an ifftshift on a matrix, with each column replaced by its shifted result. — mvifftshift • Spectroscopy Analysis Tools (spant) Print fit coordinates from a single index. — n2coord • Spectroscopy Analysis Tools (spant) Print fit coordinates from a single index. — n2coord • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/nifti_flip_lr.html b/docs/reference/nifti_flip_lr.html
index 730abe3c..19860b3c 100644
--- a/docs/reference/nifti_flip_lr.html
+++ b/docs/reference/nifti_flip_lr.html
@@ -1,9 +1,5 @@
-Flip the x data dimension order of a nifti image. This corresponds to
-flipping MRI data in the left-right direction, assuming the data in save in
-neurological format (can check with fslorient program). — nifti_flip_lr • Spectroscopy Analysis Tools (spant) Flip the x data dimension order of a nifti image. This corresponds to flipping MRI data in the left-right direction, assuming the data in save in neurological format (can check with fslorient program). — nifti_flip_lr • Spectroscopy Analysis Tools (spant) Export a one-page pdf of a single fit result — one_page_pdf • Spectroscopy Analysis Tools (spant) Export a one-page pdf of a single fit result — one_page_pdf • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -108,7 +108,7 @@ Arguments
diff --git a/docs/reference/ortho3.html b/docs/reference/ortho3.html
index 13ade97d..5d7dd2fd 100644
--- a/docs/reference/ortho3.html
+++ b/docs/reference/ortho3.html
@@ -1,5 +1,5 @@
-Display an orthographic projection plot of a nifti object. — ortho3 • Spectroscopy Analysis Tools (spant) Display an orthographic projection plot of a nifti object. — ortho3 • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -172,7 +172,7 @@ Arguments
diff --git a/docs/reference/ortho3_inter.html b/docs/reference/ortho3_inter.html
index 090cc5e5..15948899 100644
--- a/docs/reference/ortho3_inter.html
+++ b/docs/reference/ortho3_inter.html
@@ -1,5 +1,5 @@
-Display an interactive orthographic projection plot of a nifti object. — ortho3_inter • Spectroscopy Analysis Tools (spant) Display an interactive orthographic projection plot of a nifti object. — ortho3_inter • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -132,7 +132,7 @@ Arguments
diff --git a/docs/reference/peak_info.html b/docs/reference/peak_info.html
index 09058bd8..41c8ffaf 100644
--- a/docs/reference/peak_info.html
+++ b/docs/reference/peak_info.html
@@ -1,7 +1,5 @@
-Search for the highest peak in a spectral region and return the frequency,
-height and FWHM. — peak_info • Spectroscopy Analysis Tools (spant) Search for the highest peak in a spectral region and return the frequency, height and FWHM. — peak_info • Spectroscopy Analysis Tools (spant) Papoulis-Gerchberg (PG) algorithm method for k-space extrapolation. — pg_extrap_xy • Spectroscopy Analysis Tools (spant) Papoulis-Gerchberg (PG) algorithm method for k-space extrapolation. — pg_extrap_xy • Spectroscopy Analysis Tools (spant) Apply phasing parameters to MRS data. — phase • Spectroscopy Analysis Tools (spant) Apply phasing parameters to MRS data. — phase • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/phase_ref_1h_brain.html b/docs/reference/phase_ref_1h_brain.html
new file mode 100644
index 00000000..8707a74a
--- /dev/null
+++ b/docs/reference/phase_ref_1h_brain.html
@@ -0,0 +1,131 @@
+
+Corrected zero order phase and chemical shift offset in 1H MRS data from the brain. — phase_ref_1h_brain • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Corrected zero order phase and chemical shift offset in 1H MRS data from the brain.
+ Source: R/rats.R
+ phase_ref_1h_brain.Rd
+
+
+
+ Corrected zero order phase and chemical shift offset in 1H MRS data from the
+brain.
+
+
+
+ phase_ref_1h_brain(mrs_data, mean_ref = FALSE, ret_corr_only = TRUE)
+
+
+
+ Arguments
+ - mrs_data
+MRS data to be corrected.
- mean_ref
+apply the phase and offset of the mean spectrum to all
+others. Default is FALSE.
- ret_corr_only
+return the corrected data only.
+
+ Value
+
+
+corrected MRS data.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/plot.fit_result.html b/docs/reference/plot.fit_result.html
index e54d3bc1..836a53ee 100644
--- a/docs/reference/plot.fit_result.html
+++ b/docs/reference/plot.fit_result.html
@@ -1,5 +1,5 @@
-Plot the fitting results of an object of class fit_result. — plot.fit_result • Spectroscopy Analysis Tools (spant) Plot the fitting results of an object of class fit_result. — plot.fit_result • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -207,7 +207,7 @@ Arguments
diff --git a/docs/reference/plot.mrs_data.html b/docs/reference/plot.mrs_data.html
index fabcc35b..bb2ec651 100644
--- a/docs/reference/plot.mrs_data.html
+++ b/docs/reference/plot.mrs_data.html
@@ -1,5 +1,5 @@
-Plotting method for objects of class mrs_data. — plot.mrs_data • Spectroscopy Analysis Tools (spant) Plotting method for objects of class mrs_data. — plot.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -287,7 +287,7 @@ Arguments
diff --git a/docs/reference/plot_bc.html b/docs/reference/plot_bc.html
index 4f8309b4..b48142cc 100644
--- a/docs/reference/plot_bc.html
+++ b/docs/reference/plot_bc.html
@@ -1,5 +1,5 @@
-Convenience function to plot a baseline estimate with the original data. — plot_bc • Spectroscopy Analysis Tools (spant) Convenience function to plot a baseline estimate with the original data. — plot_bc • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -108,7 +108,7 @@ Arguments
diff --git a/docs/reference/plot_reg.html b/docs/reference/plot_reg.html
index ae1acbe7..2addb2f6 100644
--- a/docs/reference/plot_reg.html
+++ b/docs/reference/plot_reg.html
@@ -1,5 +1,5 @@
-Plot regressors as an image. — plot_reg • Spectroscopy Analysis Tools (spant) Plot regressors as an image. — plot_reg • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/plot_slice_fit.html b/docs/reference/plot_slice_fit.html
index fbc7b560..57f1af8a 100644
--- a/docs/reference/plot_slice_fit.html
+++ b/docs/reference/plot_slice_fit.html
@@ -1,5 +1,5 @@
-Plot a 2D slice from an MRSI fit result object. — plot_slice_fit • Spectroscopy Analysis Tools (spant) Plot a 2D slice from an MRSI fit result object. — plot_slice_fit • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -129,7 +129,7 @@ Arguments
diff --git a/docs/reference/plot_slice_fit_inter.html b/docs/reference/plot_slice_fit_inter.html
index 4eed104a..da105a7d 100644
--- a/docs/reference/plot_slice_fit_inter.html
+++ b/docs/reference/plot_slice_fit_inter.html
@@ -1,5 +1,5 @@
-Plot a 2D slice from an MRSI fit result object. — plot_slice_fit_inter • Spectroscopy Analysis Tools (spant) Plot a 2D slice from an MRSI fit result object. — plot_slice_fit_inter • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -134,7 +134,7 @@ Arguments
diff --git a/docs/reference/plot_slice_map.html b/docs/reference/plot_slice_map.html
index 553e9ac8..ffb2a134 100644
--- a/docs/reference/plot_slice_map.html
+++ b/docs/reference/plot_slice_map.html
@@ -1,5 +1,5 @@
-Plot a slice from a 7 dimensional array. — plot_slice_map • Spectroscopy Analysis Tools (spant) Plot a slice from a 7 dimensional array. — plot_slice_map • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -153,7 +153,7 @@ Arguments
diff --git a/docs/reference/plot_slice_map_inter.html b/docs/reference/plot_slice_map_inter.html
index 40d33b42..90968f66 100644
--- a/docs/reference/plot_slice_map_inter.html
+++ b/docs/reference/plot_slice_map_inter.html
@@ -1,7 +1,5 @@
-Plot an interactive slice map from a data array where voxels can be selected
-to display a corresponding spectrum. — plot_slice_map_inter • Spectroscopy Analysis Tools (spant) Plot an interactive slice map from a data array where voxels can be selected to display a corresponding spectrum. — plot_slice_map_inter • Spectroscopy Analysis Tools (spant) Plot the spectral standard deviation. — plot_spec_sd • Spectroscopy Analysis Tools (spant) Plot the spectral standard deviation. — plot_spec_sd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Arguments
diff --git a/docs/reference/plot_voi_overlay.html b/docs/reference/plot_voi_overlay.html
index 9a782e88..bbbbf35e 100644
--- a/docs/reference/plot_voi_overlay.html
+++ b/docs/reference/plot_voi_overlay.html
@@ -1,5 +1,5 @@
-Plot a volume as an image overlay. — plot_voi_overlay • Spectroscopy Analysis Tools (spant) Plot a volume as an image overlay. — plot_voi_overlay • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -116,7 +116,7 @@ Arguments
diff --git a/docs/reference/plot_voi_overlay_seg.html b/docs/reference/plot_voi_overlay_seg.html
index 3d4e74ff..0e800ff2 100644
--- a/docs/reference/plot_voi_overlay_seg.html
+++ b/docs/reference/plot_voi_overlay_seg.html
@@ -1,5 +1,5 @@
-Plot a volume as an overlay on a segmented brain volume. — plot_voi_overlay_seg • Spectroscopy Analysis Tools (spant) Plot a volume as an overlay on a segmented brain volume. — plot_voi_overlay_seg • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Arguments
diff --git a/docs/reference/ppm.html b/docs/reference/ppm.html
index c352327a..ee4696e2 100644
--- a/docs/reference/ppm.html
+++ b/docs/reference/ppm.html
@@ -1,5 +1,5 @@
-Return the ppm scale of an MRS dataset or fit result. — ppm • Spectroscopy Analysis Tools (spant) Return the ppm scale of an MRS dataset or fit result. — ppm • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -132,7 +132,7 @@ Value
diff --git a/docs/reference/precomp.html b/docs/reference/precomp.html
index 822d7336..df3d2c6c 100644
--- a/docs/reference/precomp.html
+++ b/docs/reference/precomp.html
@@ -1,7 +1,5 @@
-Save function results to file and load on subsequent calls to avoid repeat
-computation. — precomp • Spectroscopy Analysis Tools (spant) Save function results to file and load on subsequent calls to avoid repeat computation. — precomp • Spectroscopy Analysis Tools (spant) Preprocess and perform quality assessment of a single SVS data set. — preproc_svs • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Preprocess and perform quality assessment of a single SVS data set.
+ Source: R/fmrs.R
+ preproc_svs.Rd
+
+
+
+ Preprocess and perform quality assessment of a single SVS data set.
+
+
+
+ preproc_svs(path, label = NULL, output_dir = NULL, ref_inds = NULL)
+
+
+
+ Arguments
+ - path
+path to the fMRS data file or IMA directory.
- label
+a label to describe the data set.
- output_dir
+output directory.
- ref_inds
+a vector of 1-based indices for any water reference dynamic
+scans.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/preproc_svs_dataset.html b/docs/reference/preproc_svs_dataset.html
new file mode 100644
index 00000000..07c3a29b
--- /dev/null
+++ b/docs/reference/preproc_svs_dataset.html
@@ -0,0 +1,148 @@
+
+Preprocess and perform quality assessment of one or more SVS data sets. — preproc_svs_dataset • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Preprocess and perform quality assessment of one or more SVS data sets.
+ Source: R/fmrs.R
+ preproc_svs_dataset.Rd
+
+
+
+ Preprocess and perform quality assessment of one or more SVS data sets.
+
+
+
+ preproc_svs_dataset(
+ paths,
+ labels = NULL,
+ output_dir = "spant_analysis",
+ exclude_labels = NULL,
+ overwrite = FALSE,
+ ref_inds = NULL,
+ return_results = FALSE
+)
+
+
+
+ Arguments
+ - paths
+paths to the fMRS data file or IMA directory.
- labels
+labels to describe each data set.
- output_dir
+output directory.
- exclude_labels
+vector of labels of scans to exclude, eg poor quality
+data.
- overwrite
+overwrite saved results, defaults to FALSE.
- ref_inds
+a vector of 1-based indices for any water reference dynamic
+scans.
- return_results
+function will return key outputs, defaults to FALSE.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/print.fit_result.html b/docs/reference/print.fit_result.html
index 297f28dc..5f434e57 100644
--- a/docs/reference/print.fit_result.html
+++ b/docs/reference/print.fit_result.html
@@ -1,5 +1,5 @@
-Print a summary of an object of class fit_result. — print.fit_result • Spectroscopy Analysis Tools (spant) Print a summary of an object of class fit_result. — print.fit_result • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -105,7 +105,7 @@ Arguments
diff --git a/docs/reference/print.mrs_data.html b/docs/reference/print.mrs_data.html
index 51199017..e1561eb2 100644
--- a/docs/reference/print.mrs_data.html
+++ b/docs/reference/print.mrs_data.html
@@ -1,5 +1,5 @@
-Print a summary of mrs_data parameters. — print.mrs_data • Spectroscopy Analysis Tools (spant) Print a summary of mrs_data parameters. — print.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -109,7 +109,7 @@ Arguments
diff --git a/docs/reference/qn_states.html b/docs/reference/qn_states.html
index 0f42f2f9..d7aa6715 100644
--- a/docs/reference/qn_states.html
+++ b/docs/reference/qn_states.html
@@ -1,5 +1,5 @@
-Get the quantum coherence matrix for a spin system. — qn_states • Spectroscopy Analysis Tools (spant) Get the quantum coherence matrix for a spin system. — qn_states • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/rats.html b/docs/reference/rats.html
index 5a39a396..93585e08 100644
--- a/docs/reference/rats.html
+++ b/docs/reference/rats.html
@@ -1,5 +1,5 @@
-Robust Alignment to a Target Spectrum (RATS). — rats • Spectroscopy Analysis Tools (spant) Robust Alignment to a Target Spectrum (RATS). — rats • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -207,7 +207,7 @@ Value
diff --git a/docs/reference/re_weighting.html b/docs/reference/re_weighting.html
index d21caf21..8b0b070a 100644
--- a/docs/reference/re_weighting.html
+++ b/docs/reference/re_weighting.html
@@ -1,5 +1,5 @@
-Apply a weighting to the FID to enhance spectral resolution. — re_weighting • Spectroscopy Analysis Tools (spant) Apply a weighting to the FID to enhance spectral resolution. — re_weighting • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/read_basis.html b/docs/reference/read_basis.html
index da9b94af..eb6f8557 100644
--- a/docs/reference/read_basis.html
+++ b/docs/reference/read_basis.html
@@ -1,5 +1,5 @@
-Read a basis file in LCModel .basis format. — read_basis • Spectroscopy Analysis Tools (spant) Read a basis file in LCModel .basis format. — read_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/read_ima_coil_dir.html b/docs/reference/read_ima_coil_dir.html
index 28c02de0..4f073cd8 100644
--- a/docs/reference/read_ima_coil_dir.html
+++ b/docs/reference/read_ima_coil_dir.html
@@ -1,9 +1,5 @@
-Read a directory containing Siemens MRS IMA files and combine along the coil
-dimension. Note that the coil ID is inferred from the sorted file name and
-should be checked when consistency is required between two directories. — read_ima_coil_dir • Spectroscopy Analysis Tools (spant) Read a directory containing Siemens MRS IMA files and combine along the coil dimension. Note that the coil ID is inferred from the sorted file name and should be checked when consistency is required between two directories. — read_ima_coil_dir • Spectroscopy Analysis Tools (spant) Read a directory containing Siemens MRS IMA files and combine along the
-dynamic dimension. Note that the coil ID is inferred from the sorted file
-name and should be checked when consistency is required. — read_ima_dyn_dir • Spectroscopy Analysis Tools (spant) Read a directory containing Siemens MRS IMA files and combine along the dynamic dimension. Note that the coil ID is inferred from the sorted file name and should be checked when consistency is required. — read_ima_dyn_dir • Spectroscopy Analysis Tools (spant) Read an LCModel formatted coord file containing fit information. — read_lcm_coord • Spectroscopy Analysis Tools (spant) Read an LCModel formatted coord file containing fit information. — read_lcm_coord • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -107,7 +107,7 @@ Value
diff --git a/docs/reference/read_mrs.html b/docs/reference/read_mrs.html
index 3ac2a36b..2cf36b20 100644
--- a/docs/reference/read_mrs.html
+++ b/docs/reference/read_mrs.html
@@ -1,5 +1,5 @@
-Read MRS data from a file. — read_mrs • Spectroscopy Analysis Tools (spant) Read MRS data from a file. — read_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -88,7 +88,8 @@ Read MRS data from a file.
full_fid = FALSE,
omit_svs_ref_scans = TRUE,
verbose = FALSE,
- extra = NULL
+ extra = NULL,
+ fid_filt_dist = NULL
)
@@ -140,6 +141,13 @@ Arguments
an optional data frame to provide additional variables for use
in subsequent analysis steps, eg id or grouping variables.
fid_filt_dist
+indicate if the data has a distorted FID due to a
+brick-wall filter being used to downsample the data. Default is to auto
+detect this from the data, but TRUE or FALSE options can be given to override
+detection.
Value
@@ -183,7 +191,7 @@ Examples
diff --git a/docs/reference/read_mrs_tqn.html b/docs/reference/read_mrs_tqn.html
index 5766362f..84bdaf3a 100644
--- a/docs/reference/read_mrs_tqn.html
+++ b/docs/reference/read_mrs_tqn.html
@@ -1,5 +1,5 @@
-Read MRS data using the TARQUIN software package. — read_mrs_tqn • Spectroscopy Analysis Tools (spant) Read MRS data using the TARQUIN software package. — read_mrs_tqn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -131,7 +131,7 @@ Examples
diff --git a/docs/reference/read_pulse_ascii.html b/docs/reference/read_pulse_ascii.html
index c9e0d43c..ab11c9cc 100644
--- a/docs/reference/read_pulse_ascii.html
+++ b/docs/reference/read_pulse_ascii.html
@@ -1,5 +1,5 @@
-Read an ASCII formatted pulse file. — read_pulse_ascii • Spectroscopy Analysis Tools (spant) Read an ASCII formatted pulse file. — read_pulse_ascii • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/read_pulse_bruker.html b/docs/reference/read_pulse_bruker.html
index c92bf76a..dbe9073b 100644
--- a/docs/reference/read_pulse_bruker.html
+++ b/docs/reference/read_pulse_bruker.html
@@ -1,5 +1,5 @@
-Read a Bruker formatted pulse file — read_pulse_bruker • Spectroscopy Analysis Tools (spant) Read a Bruker formatted pulse file — read_pulse_bruker • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/read_pulse_pta.html b/docs/reference/read_pulse_pta.html
index 72e1b6d4..a0fac3c3 100644
--- a/docs/reference/read_pulse_pta.html
+++ b/docs/reference/read_pulse_pta.html
@@ -1,5 +1,5 @@
-Read a .pta formatted pulse file compatible with Siemens PulseTool. — read_pulse_pta • Spectroscopy Analysis Tools (spant) Read a .pta formatted pulse file compatible with Siemens PulseTool. — read_pulse_pta • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/read_siemens_txt_hdr.html b/docs/reference/read_siemens_txt_hdr.html
index 23fb8c70..3a17d87c 100644
--- a/docs/reference/read_siemens_txt_hdr.html
+++ b/docs/reference/read_siemens_txt_hdr.html
@@ -1,5 +1,5 @@
-Read the text format header found in Siemens IMA and TWIX data files. — read_siemens_txt_hdr • Spectroscopy Analysis Tools (spant) Read the text format header found in Siemens IMA and TWIX data files. — read_siemens_txt_hdr • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -78,7 +78,7 @@ Read the text format header found in Siemens IMA and TWIX data files.
- read_siemens_txt_hdr(input, version = "vd", verbose, offset = 0)
+ read_siemens_txt_hdr(input, version = "vd", verbose = FALSE, offset = 0)
@@ -118,7 +118,7 @@ Value
diff --git a/docs/reference/read_tqn_fit.html b/docs/reference/read_tqn_fit.html
index 4da6c25e..a1630420 100644
--- a/docs/reference/read_tqn_fit.html
+++ b/docs/reference/read_tqn_fit.html
@@ -1,5 +1,5 @@
-Reader for csv fit results generated by TARQUIN. — read_tqn_fit • Spectroscopy Analysis Tools (spant) Reader for csv fit results generated by TARQUIN. — read_tqn_fit • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -113,7 +113,7 @@ Examples
diff --git a/docs/reference/read_tqn_result.html b/docs/reference/read_tqn_result.html
index 36659714..68a3e98c 100644
--- a/docs/reference/read_tqn_result.html
+++ b/docs/reference/read_tqn_result.html
@@ -1,5 +1,5 @@
-Reader for csv results generated by TARQUIN. — read_tqn_result • Spectroscopy Analysis Tools (spant) Reader for csv results generated by TARQUIN. — read_tqn_result • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -117,7 +117,7 @@ Examples
diff --git a/docs/reference/recon_imag.html b/docs/reference/recon_imag.html
index d2a72225..5bc3b1eb 100644
--- a/docs/reference/recon_imag.html
+++ b/docs/reference/recon_imag.html
@@ -1,7 +1,5 @@
-Reconstruct complex time-domain data from the real part of frequency-domain
-data. — recon_imag • Spectroscopy Analysis Tools (spant) Reconstruct complex time-domain data from the real part of frequency-domain data. — recon_imag • Spectroscopy Analysis Tools (spant) Reconstruct complex time-domain data from the real part of frequency-domain
-data. — recon_imag_vec • Spectroscopy Analysis Tools (spant) Reconstruct complex time-domain data from the real part of frequency-domain data. — recon_imag_vec • Spectroscopy Analysis Tools (spant) Reconstruct 2D MRSI data from a twix file loaded with read_mrs. — recon_twix_2d_mrsi • Spectroscopy Analysis Tools (spant) Reconstruct 2D MRSI data from a twix file loaded with read_mrs. — recon_twix_2d_mrsi • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/rectangular_mask.html b/docs/reference/rectangular_mask.html
index a2117283..6e469bc9 100644
--- a/docs/reference/rectangular_mask.html
+++ b/docs/reference/rectangular_mask.html
@@ -1,5 +1,5 @@
-Create a rectangular mask stored as a matrix of logical values. — rectangular_mask • Spectroscopy Analysis Tools (spant) Create a rectangular mask stored as a matrix of logical values. — rectangular_mask • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -130,7 +130,7 @@ Value
diff --git a/docs/reference/reexports.html b/docs/reference/reexports.html
index 694a75d1..a59e8379 100644
--- a/docs/reference/reexports.html
+++ b/docs/reference/reexports.html
@@ -1,5 +1,5 @@
-Objects exported from other packages — reexports • Spectroscopy Analysis Tools (spant) Objects exported from other packages — reexports • Spectroscopy Analysis Tools (spant)
Spectroscopy Analysis Tools (spant)
- 2.21.0
+ 2.22.0
@@ -103,7 +103,7 @@ Objects exported from other packages
diff --git a/docs/reference/rep_array_dim.html b/docs/reference/rep_array_dim.html
index b9c49b4a..48c0a5ed 100644
--- a/docs/reference/rep_array_dim.html
+++ b/docs/reference/rep_array_dim.html
@@ -1,5 +1,5 @@
-Repeat an array over a given dimension. — rep_array_dim • Spectroscopy Analysis Tools (spant) Repeat an array over a given dimension. — rep_array_dim • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/rep_dyn.html b/docs/reference/rep_dyn.html
index 6bbfb0ef..89a4bb9b 100644
--- a/docs/reference/rep_dyn.html
+++ b/docs/reference/rep_dyn.html
@@ -1,5 +1,5 @@
-Replicate a scan in the dynamic dimension. — rep_dyn • Spectroscopy Analysis Tools (spant) Replicate a scan in the dynamic dimension. — rep_dyn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/rep_mrs.html b/docs/reference/rep_mrs.html
index 67730b5c..becb8f00 100644
--- a/docs/reference/rep_mrs.html
+++ b/docs/reference/rep_mrs.html
@@ -1,5 +1,5 @@
-Replicate a scan over a given dimension. — rep_mrs • Spectroscopy Analysis Tools (spant) Replicate a scan over a given dimension. — rep_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -138,7 +138,7 @@ Value
diff --git a/docs/reference/resample_basis.html b/docs/reference/resample_basis.html
index b0f2ab17..c7a6222a 100644
--- a/docs/reference/resample_basis.html
+++ b/docs/reference/resample_basis.html
@@ -1,5 +1,5 @@
-Resample a basis-set to match a mrs_data acquisition. — resample_basis • Spectroscopy Analysis Tools (spant) Resample a basis-set to match a mrs_data acquisition. — resample_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -116,7 +116,7 @@ Value
diff --git a/docs/reference/resample_img.html b/docs/reference/resample_img.html
index f1e7beaf..b0cc8f71 100644
--- a/docs/reference/resample_img.html
+++ b/docs/reference/resample_img.html
@@ -1,5 +1,5 @@
-Resample an image to match a target image space. — resample_img • Spectroscopy Analysis Tools (spant) Resample an image to match a target image space. — resample_img • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/resample_voi.html b/docs/reference/resample_voi.html
index 8fbfa836..a29ab096 100644
--- a/docs/reference/resample_voi.html
+++ b/docs/reference/resample_voi.html
@@ -1,7 +1,5 @@
-Resample a VOI to match a target image space using nearest-neighbour
-interpolation. — resample_voi • Spectroscopy Analysis Tools (spant) Resample a VOI to match a target image space using nearest-neighbour interpolation. — resample_voi • Spectroscopy Analysis Tools (spant) Reslice a nifti object to match the orientation of mrs data. — reslice_to_mrs • Spectroscopy Analysis Tools (spant) Reslice a nifti object to match the orientation of mrs data. — reslice_to_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/reson_table2mrs_data.html b/docs/reference/reson_table2mrs_data.html
index d75579ee..c5a2167a 100644
--- a/docs/reference/reson_table2mrs_data.html
+++ b/docs/reference/reson_table2mrs_data.html
@@ -1,5 +1,5 @@
-Generate mrs_data from a table of single Lorentzian resonances. — reson_table2mrs_data • Spectroscopy Analysis Tools (spant) Generate mrs_data from a table of single Lorentzian resonances. — reson_table2mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -119,7 +119,7 @@ Value
diff --git a/docs/reference/rm_dyns.html b/docs/reference/rm_dyns.html
index 5d5ef692..573e1f51 100644
--- a/docs/reference/rm_dyns.html
+++ b/docs/reference/rm_dyns.html
@@ -1,5 +1,5 @@
-Remove a subset of dynamic scans. — rm_dyns • Spectroscopy Analysis Tools (spant) Remove a subset of dynamic scans. — rm_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/scale_amp_molal.html b/docs/reference/scale_amp_molal.html
index aaeee1f2..7acb8cb0 100644
--- a/docs/reference/scale_amp_molal.html
+++ b/docs/reference/scale_amp_molal.html
@@ -1,7 +1,5 @@
-Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water). — scale_amp_molal • Spectroscopy Analysis Tools (spant) Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / kg of tissue water). — scale_amp_molal • Spectroscopy Analysis Tools (spant)
Spectroscopy Analysis Tools (spant)
- 2.21.0
+ 2.22.0
@@ -76,8 +74,7 @@
- Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water).
+ Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / kg of tissue water).
Source: R/amp_scaling.R
scale_amp_molal.Rd
@@ -163,7 +160,7 @@ Value
diff --git a/docs/reference/scale_amp_molal_pvc.html b/docs/reference/scale_amp_molal_pvc.html
index 962d6afc..4d194abd 100644
--- a/docs/reference/scale_amp_molal_pvc.html
+++ b/docs/reference/scale_amp_molal_pvc.html
@@ -1,7 +1,5 @@
-Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water). — scale_amp_molal_pvc • Spectroscopy Analysis Tools (spant)
@@ -75,8 +73,7 @@
- Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water).
+ Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / kg of tissue water).
Source: R/amp_scaling.R
scale_amp_molal_pvc.Rd
@@ -141,7 +138,7 @@ Value
diff --git a/docs/reference/scale_amp_molar.html b/docs/reference/scale_amp_molar.html
index 02358d91..dc87a338 100644
--- a/docs/reference/scale_amp_molar.html
+++ b/docs/reference/scale_amp_molar.html
@@ -1,7 +1,5 @@
-Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / Litre of tissue). — scale_amp_molar • Spectroscopy Analysis Tools (spant) Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / Litre of tissue). — scale_amp_molar • Spectroscopy Analysis Tools (spant) Convert default LCM/TARQUIN concentration scaling to molal units with partial
-volume correction. — scale_amp_molar2molal_pvc • Spectroscopy Analysis Tools (spant) Convert default LCM/TARQUIN concentration scaling to molal units with partial volume correction. — scale_amp_molar2molal_pvc • Spectroscopy Analysis Tools (spant) Scale fitted amplitudes to a ratio of signal amplitude. — scale_amp_ratio • Spectroscopy Analysis Tools (spant) Scale fitted amplitudes to a ratio of signal amplitude. — scale_amp_ratio • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -116,7 +116,7 @@ Value
diff --git a/docs/reference/scale_amp_ratio_value.html b/docs/reference/scale_amp_ratio_value.html
index 2036837a..6af8ac51 100644
--- a/docs/reference/scale_amp_ratio_value.html
+++ b/docs/reference/scale_amp_ratio_value.html
@@ -1,5 +1,5 @@
-Scale fitted amplitudes to a ratio of signal amplitude. — scale_amp_ratio_value • Spectroscopy Analysis Tools (spant) Scale fitted amplitudes to a ratio of signal amplitude. — scale_amp_ratio_value • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/scale_amp_water_ratio.html b/docs/reference/scale_amp_water_ratio.html
index 5b25e884..35a76b00 100644
--- a/docs/reference/scale_amp_water_ratio.html
+++ b/docs/reference/scale_amp_water_ratio.html
@@ -1,5 +1,5 @@
-Scale metabolite amplitudes as a ratio to the unsuppressed water amplitude. — scale_amp_water_ratio • Spectroscopy Analysis Tools (spant) Scale metabolite amplitudes as a ratio to the unsuppressed water amplitude. — scale_amp_water_ratio • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/scale_basis_amp.html b/docs/reference/scale_basis_amp.html
index 9401c3f1..5a58b5e5 100644
--- a/docs/reference/scale_basis_amp.html
+++ b/docs/reference/scale_basis_amp.html
@@ -1,5 +1,5 @@
-Scale a basis object by a scalar. — scale_basis_amp • Spectroscopy Analysis Tools (spant) Scale a basis object by a scalar. — scale_basis_amp • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/scale_basis_from_singlet.html b/docs/reference/scale_basis_from_singlet.html
index 0d542bc8..c9a19e77 100644
--- a/docs/reference/scale_basis_from_singlet.html
+++ b/docs/reference/scale_basis_from_singlet.html
@@ -1,5 +1,5 @@
-Scale a basis-set to be consistent with spant assumptions for water scaling. — scale_basis_from_singlet • Spectroscopy Analysis Tools (spant) Scale a basis-set to be consistent with spant assumptions for water scaling. — scale_basis_from_singlet • Spectroscopy Analysis Tools (spant)
Spectroscopy Analysis Tools (spant)
- 2.21.0
+ 2.22.0
@@ -127,7 +127,7 @@ Value
diff --git a/docs/reference/scale_mrs_amp.html b/docs/reference/scale_mrs_amp.html
index b5501a0d..990f058a 100644
--- a/docs/reference/scale_mrs_amp.html
+++ b/docs/reference/scale_mrs_amp.html
@@ -1,5 +1,5 @@
-Scale an mrs_data object by a scalar or vector or amplitudes. — scale_mrs_amp • Spectroscopy Analysis Tools (spant) Scale an mrs_data object by a scalar or vector or amplitudes. — scale_mrs_amp • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/scale_spec.html b/docs/reference/scale_spec.html
index 4f6ea835..6b3ddba4 100644
--- a/docs/reference/scale_spec.html
+++ b/docs/reference/scale_spec.html
@@ -1,5 +1,5 @@
-Scale mrs_data to a spectral region. — scale_spec • Spectroscopy Analysis Tools (spant) Scale mrs_data to a spectral region. — scale_spec • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -141,7 +141,7 @@ Value
diff --git a/docs/reference/sd.html b/docs/reference/sd.html
index ea1eec9f..3ae4dfd4 100644
--- a/docs/reference/sd.html
+++ b/docs/reference/sd.html
@@ -1,5 +1,5 @@
-Calculate the standard deviation spectrum from an mrs_data object. — sd • Spectroscopy Analysis Tools (spant) Calculate the standard deviation spectrum from an mrs_data object. — sd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/sd.mrs_data.html b/docs/reference/sd.mrs_data.html
index 3f92a49f..13bdda85 100644
--- a/docs/reference/sd.mrs_data.html
+++ b/docs/reference/sd.mrs_data.html
@@ -1,5 +1,5 @@
-Calculate the standard deviation spectrum from an mrs_data object. — sd.mrs_data • Spectroscopy Analysis Tools (spant) Calculate the standard deviation spectrum from an mrs_data object. — sd.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/seconds.html b/docs/reference/seconds.html
index b34d6627..467ee17f 100644
--- a/docs/reference/seconds.html
+++ b/docs/reference/seconds.html
@@ -1,5 +1,5 @@
-Return a time scale vector to match the FID of an MRS data object. — seconds • Spectroscopy Analysis Tools (spant) Return a time scale vector to match the FID of an MRS data object. — seconds • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/seq_cpmg_ideal.html b/docs/reference/seq_cpmg_ideal.html
index 547e96ab..45727c86 100644
--- a/docs/reference/seq_cpmg_ideal.html
+++ b/docs/reference/seq_cpmg_ideal.html
@@ -1,5 +1,5 @@
-CPMG style sequence with ideal pulses. — seq_cpmg_ideal • Spectroscopy Analysis Tools (spant) CPMG style sequence with ideal pulses. — seq_cpmg_ideal • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/seq_mega_press_ideal.html b/docs/reference/seq_mega_press_ideal.html
index 0769b8b4..a9cd7fa0 100644
--- a/docs/reference/seq_mega_press_ideal.html
+++ b/docs/reference/seq_mega_press_ideal.html
@@ -1,7 +1,5 @@
-MEGA-PRESS sequence with ideal localisation pulses and Gaussian shaped
-editing pulse. — seq_mega_press_ideal • Spectroscopy Analysis Tools (spant) MEGA-PRESS sequence with ideal localisation pulses and Gaussian shaped editing pulse. — seq_mega_press_ideal • Spectroscopy Analysis Tools (spant) PRESS sequence with shaped refocusing pulses. — seq_press_2d_shaped • Spectroscopy Analysis Tools (spant) PRESS sequence with shaped refocusing pulses. — seq_press_2d_shaped • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -165,7 +165,7 @@ Value
diff --git a/docs/reference/seq_press_ideal.html b/docs/reference/seq_press_ideal.html
index 8c976856..72c3af3d 100644
--- a/docs/reference/seq_press_ideal.html
+++ b/docs/reference/seq_press_ideal.html
@@ -1,5 +1,5 @@
-PRESS sequence with ideal pulses. — seq_press_ideal • Spectroscopy Analysis Tools (spant) PRESS sequence with ideal pulses. — seq_press_ideal • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/seq_pulse_acquire.html b/docs/reference/seq_pulse_acquire.html
index 4a88fc64..ad80571e 100644
--- a/docs/reference/seq_pulse_acquire.html
+++ b/docs/reference/seq_pulse_acquire.html
@@ -1,5 +1,5 @@
-Simple pulse and acquire sequence with ideal pulses. — seq_pulse_acquire • Spectroscopy Analysis Tools (spant) Simple pulse and acquire sequence with ideal pulses. — seq_pulse_acquire • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/seq_slaser_ideal.html b/docs/reference/seq_slaser_ideal.html
index 74688f4d..eb83e8e3 100644
--- a/docs/reference/seq_slaser_ideal.html
+++ b/docs/reference/seq_slaser_ideal.html
@@ -1,5 +1,5 @@
-sLASER sequence with ideal pulses. — seq_slaser_ideal • Spectroscopy Analysis Tools (spant) sLASER sequence with ideal pulses. — seq_slaser_ideal • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -126,7 +126,7 @@ Value
diff --git a/docs/reference/seq_spin_echo_ideal.html b/docs/reference/seq_spin_echo_ideal.html
index e23271de..4248716f 100644
--- a/docs/reference/seq_spin_echo_ideal.html
+++ b/docs/reference/seq_spin_echo_ideal.html
@@ -1,5 +1,5 @@
-Spin echo sequence with ideal pulses. — seq_spin_echo_ideal • Spectroscopy Analysis Tools (spant) Spin echo sequence with ideal pulses. — seq_spin_echo_ideal • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/seq_steam_ideal.html b/docs/reference/seq_steam_ideal.html
index a60685a8..1c8115d7 100644
--- a/docs/reference/seq_steam_ideal.html
+++ b/docs/reference/seq_steam_ideal.html
@@ -1,5 +1,5 @@
-STEAM sequence with ideal pulses. — seq_steam_ideal • Spectroscopy Analysis Tools (spant) STEAM sequence with ideal pulses. — seq_steam_ideal • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -128,7 +128,7 @@ Value
diff --git a/docs/reference/seq_steam_ideal_cof.html b/docs/reference/seq_steam_ideal_cof.html
index 8f225740..cba7af91 100644
--- a/docs/reference/seq_steam_ideal_cof.html
+++ b/docs/reference/seq_steam_ideal_cof.html
@@ -1,7 +1,5 @@
-STEAM sequence with ideal pulses and coherence order filtering to simulate
-gradient crushers. — seq_steam_ideal_cof • Spectroscopy Analysis Tools (spant) STEAM sequence with ideal pulses and coherence order filtering to simulate gradient crushers. — seq_steam_ideal_cof • Spectroscopy Analysis Tools (spant) STEAM sequence with ideal pulses using the z-rotation gradient simulation
-method described by Young et al JMR 140, 146-152 (1999). — seq_steam_ideal_young • Spectroscopy Analysis Tools (spant) STEAM sequence with ideal pulses using the z-rotation gradient simulation method described by Young et al JMR 140, 146-152 (1999). — seq_steam_ideal_young • Spectroscopy Analysis Tools (spant) Set the number of transients for an mrs_data object. — set_Ntrans • Spectroscopy Analysis Tools (spant) Set the number of transients for an mrs_data object. — set_Ntrans • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/set_def_acq_paras.html b/docs/reference/set_def_acq_paras.html
index 3e1b4004..cc2ada9c 100644
--- a/docs/reference/set_def_acq_paras.html
+++ b/docs/reference/set_def_acq_paras.html
@@ -1,5 +1,5 @@
-Set the default acquisition parameters. — set_def_acq_paras • Spectroscopy Analysis Tools (spant) Set the default acquisition parameters. — set_def_acq_paras • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Arguments
diff --git a/docs/reference/set_lcm_cmd.html b/docs/reference/set_lcm_cmd.html
index 2056ed01..42bb2f24 100644
--- a/docs/reference/set_lcm_cmd.html
+++ b/docs/reference/set_lcm_cmd.html
@@ -1,5 +1,5 @@
-Set the command to run the LCModel command-line program. — set_lcm_cmd • Spectroscopy Analysis Tools (spant) Set the command to run the LCModel command-line program. — set_lcm_cmd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/set_lw.html b/docs/reference/set_lw.html
index b64ec851..bb176c62 100644
--- a/docs/reference/set_lw.html
+++ b/docs/reference/set_lw.html
@@ -1,5 +1,5 @@
-Apply line-broadening to an mrs_data object to achieve a specified linewidth. — set_lw • Spectroscopy Analysis Tools (spant) Apply line-broadening to an mrs_data object to achieve a specified linewidth. — set_lw • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -123,7 +123,7 @@ Value
diff --git a/docs/reference/set_mask_xy_mat.html b/docs/reference/set_mask_xy_mat.html
index 49dc5d4e..52c4b617 100644
--- a/docs/reference/set_mask_xy_mat.html
+++ b/docs/reference/set_mask_xy_mat.html
@@ -1,5 +1,5 @@
-Set the masked voxels in a 2D MRSI dataset to given spectrum. — set_mask_xy_mat • Spectroscopy Analysis Tools (spant) Set the masked voxels in a 2D MRSI dataset to given spectrum. — set_mask_xy_mat • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Value
diff --git a/docs/reference/set_precomp_mode.html b/docs/reference/set_precomp_mode.html
index f44bd5d3..47c28e3b 100644
--- a/docs/reference/set_precomp_mode.html
+++ b/docs/reference/set_precomp_mode.html
@@ -1,5 +1,5 @@
-Set the precompute mode. — set_precomp_mode • Spectroscopy Analysis Tools (spant) Set the precompute mode. — set_precomp_mode • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/set_precomp_verbose.html b/docs/reference/set_precomp_verbose.html
index 1453a231..9c613505 100644
--- a/docs/reference/set_precomp_verbose.html
+++ b/docs/reference/set_precomp_verbose.html
@@ -1,5 +1,5 @@
-Set the verbosity of the precompute function. — set_precomp_verbose • Spectroscopy Analysis Tools (spant) Set the verbosity of the precompute function. — set_precomp_verbose • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/set_ref.html b/docs/reference/set_ref.html
index 8953fa50..5436dfa2 100644
--- a/docs/reference/set_ref.html
+++ b/docs/reference/set_ref.html
@@ -1,5 +1,5 @@
-Set the ppm reference value (eg ppm value at 0Hz). — set_ref • Spectroscopy Analysis Tools (spant) Set the ppm reference value (eg ppm value at 0Hz). — set_ref • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/set_td_pts.html b/docs/reference/set_td_pts.html
index 8a80d42a..586459ff 100644
--- a/docs/reference/set_td_pts.html
+++ b/docs/reference/set_td_pts.html
@@ -1,7 +1,5 @@
-Set the number of time-domain data points, truncating or zero-filling as
-appropriate. — set_td_pts • Spectroscopy Analysis Tools (spant) Set the number of time-domain data points, truncating or zero-filling as appropriate. — set_td_pts • Spectroscopy Analysis Tools (spant) Set the command to run the TARQUIN command-line program. — set_tqn_cmd • Spectroscopy Analysis Tools (spant) Set the command to run the TARQUIN command-line program. — set_tqn_cmd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/set_tr.html b/docs/reference/set_tr.html
index b2109ab0..65c9df5f 100644
--- a/docs/reference/set_tr.html
+++ b/docs/reference/set_tr.html
@@ -1,5 +1,5 @@
-Set the repetition time of an MRS dataset. — set_tr • Spectroscopy Analysis Tools (spant) Set the repetition time of an MRS dataset. — set_tr • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/shift.html b/docs/reference/shift.html
index ab0fe724..034591d0 100644
--- a/docs/reference/shift.html
+++ b/docs/reference/shift.html
@@ -1,5 +1,5 @@
-Apply a frequency shift to MRS data. — shift • Spectroscopy Analysis Tools (spant) Apply a frequency shift to MRS data. — shift • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/shift_basis.html b/docs/reference/shift_basis.html
index 2884be19..f55a65e0 100644
--- a/docs/reference/shift_basis.html
+++ b/docs/reference/shift_basis.html
@@ -1,5 +1,5 @@
-Apply frequency shifts to basis set signals. — shift_basis • Spectroscopy Analysis Tools (spant) Apply frequency shifts to basis set signals. — shift_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Value
diff --git a/docs/reference/sim_basis.html b/docs/reference/sim_basis.html
index c7838c46..bb5fefc6 100644
--- a/docs/reference/sim_basis.html
+++ b/docs/reference/sim_basis.html
@@ -1,5 +1,5 @@
-Simulate a basis set object. — sim_basis • Spectroscopy Analysis Tools (spant) Simulate a basis set object. — sim_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -136,7 +136,7 @@ Value
diff --git a/docs/reference/sim_basis_1h_brain.html b/docs/reference/sim_basis_1h_brain.html
index 62ed7389..f71ffa0b 100644
--- a/docs/reference/sim_basis_1h_brain.html
+++ b/docs/reference/sim_basis_1h_brain.html
@@ -1,7 +1,5 @@
-Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS
-sequence. Note, ideal pulses are assumed. — sim_basis_1h_brain • Spectroscopy Analysis Tools (spant) Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS sequence. Note, ideal pulses are assumed. — sim_basis_1h_brain • Spectroscopy Analysis Tools (spant) Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS
-sequence. Note, ideal pulses are assumed. — sim_basis_1h_brain_press • Spectroscopy Analysis Tools (spant) Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS sequence. Note, ideal pulses are assumed. — sim_basis_1h_brain_press • Spectroscopy Analysis Tools (spant) Simulate a macromolecular and lipid basis-set suitable for 1H brain MRS
-analysis. — sim_basis_mm_lip_lcm • Spectroscopy Analysis Tools (spant) Simulate a macromolecular and lipid basis-set suitable for 1H brain MRS analysis. — sim_basis_mm_lip_lcm • Spectroscopy Analysis Tools (spant) Simulate a basis file using TARQUIN. — sim_basis_tqn • Spectroscopy Analysis Tools (spant) Simulate a basis file using TARQUIN. — sim_basis_tqn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -129,7 +129,7 @@ Examples
diff --git a/docs/reference/sim_brain_1h.html b/docs/reference/sim_brain_1h.html
index 2044cf1a..717ee289 100644
--- a/docs/reference/sim_brain_1h.html
+++ b/docs/reference/sim_brain_1h.html
@@ -1,5 +1,5 @@
-Simulate MRS data with a similar appearance to normal brain (by default). — sim_brain_1h • Spectroscopy Analysis Tools (spant) Simulate MRS data with a similar appearance to normal brain (by default). — sim_brain_1h • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -159,7 +159,7 @@ Value
diff --git a/docs/reference/sim_mol.html b/docs/reference/sim_mol.html
index 23bcef50..77f76a50 100644
--- a/docs/reference/sim_mol.html
+++ b/docs/reference/sim_mol.html
@@ -1,5 +1,5 @@
-Simulate a mol_parameter object. — sim_mol • Spectroscopy Analysis Tools (spant) Simulate a mol_parameter object. — sim_mol • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -143,7 +143,7 @@ Value
diff --git a/docs/reference/sim_noise.html b/docs/reference/sim_noise.html
index 23875f79..a71477d4 100644
--- a/docs/reference/sim_noise.html
+++ b/docs/reference/sim_noise.html
@@ -1,5 +1,5 @@
-Simulate an mrs_data object containing simulated Gaussian noise. — sim_noise • Spectroscopy Analysis Tools (spant) Simulate an mrs_data object containing simulated Gaussian noise. — sim_noise • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -84,6 +84,7 @@ Simulate an mrs_data object containing simulated Gaussian noise.
ft = def_ft(),
N = def_N(),
ref = def_ref(),
+ nuc = def_nuc(),
dyns = 1,
fd = TRUE
)
@@ -111,6 +112,10 @@ Arguments
reference value for ppm scale.
nuc
+resonant nucleus.
dyns
number of dynamic scans to generate.
Value
diff --git a/docs/reference/sim_resonances.html b/docs/reference/sim_resonances.html
index 19e9a8a4..d4f8d7c0 100644
--- a/docs/reference/sim_resonances.html
+++ b/docs/reference/sim_resonances.html
@@ -1,5 +1,5 @@
-Simulate a MRS data object containing a set of simulated resonances. — sim_resonances • Spectroscopy Analysis Tools (spant) Simulate a MRS data object containing a set of simulated resonances. — sim_resonances • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -161,7 +161,7 @@ Examples
diff --git a/docs/reference/sim_th_excit_profile.html b/docs/reference/sim_th_excit_profile.html
index 5535c5ef..e781cab1 100644
--- a/docs/reference/sim_th_excit_profile.html
+++ b/docs/reference/sim_th_excit_profile.html
@@ -1,7 +1,5 @@
-Simulate an ideal pulse excitation profile by smoothing a top-hat function
-with a Gaussian. — sim_th_excit_profile • Spectroscopy Analysis Tools (spant) Simulate an ideal pulse excitation profile by smoothing a top-hat function with a Gaussian. — sim_th_excit_profile • Spectroscopy Analysis Tools (spant) Simulate an mrs_data object containing complex zero valued samples. — sim_zero • Spectroscopy Analysis Tools (spant) Simulate an mrs_data object containing complex zero valued samples. — sim_zero • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -78,7 +78,14 @@ Simulate an mrs_data object containing complex zero valued samples.
-
+
@@ -99,6 +106,10 @@ Arguments
reference value for ppm scale.
nuc
+resonant nucleus.
dyns
number of dynamic scans to generate.
Value
diff --git a/docs/reference/smooth_dyns.html b/docs/reference/smooth_dyns.html
index 4cc8da50..accf3a51 100644
--- a/docs/reference/smooth_dyns.html
+++ b/docs/reference/smooth_dyns.html
@@ -1,5 +1,5 @@
-Smooth data across the dynamic dimension with a Gaussian kernel. — smooth_dyns • Spectroscopy Analysis Tools (spant) Smooth data across the dynamic dimension with a Gaussian kernel. — smooth_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/sort_basis.html b/docs/reference/sort_basis.html
index 6a676ea2..d25cc006 100644
--- a/docs/reference/sort_basis.html
+++ b/docs/reference/sort_basis.html
@@ -1,5 +1,5 @@
-Sort the basis-set elements alphabetically. — sort_basis • Spectroscopy Analysis Tools (spant) Sort the basis-set elements alphabetically. — sort_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/spant-package.html b/docs/reference/spant-package.html
index b3dd8e21..90f19ec3 100644
--- a/docs/reference/spant-package.html
+++ b/docs/reference/spant-package.html
@@ -1,5 +1,5 @@
-spant: spectroscopy analysis tools. — spant-package • Spectroscopy Analysis Tools (spant) spant: spectroscopy analysis tools. — spant-package • Spectroscopy Analysis Tools (spant) Simulate and fit some spectra with ABfit for benchmarking purposes. Basic
-timing and performance metrics will be printed. — spant_abfit_benchmark • Spectroscopy Analysis Tools (spant) Simulate and fit some spectra with ABfit for benchmarking purposes. Basic timing and performance metrics will be printed. — spant_abfit_benchmark • Spectroscopy Analysis Tools (spant) Example MEGA-PRESS data with significant B0 drift. — spant_mpress_drift • Spectroscopy Analysis Tools (spant) Example MEGA-PRESS data with significant B0 drift. — spant_mpress_drift • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -83,7 +83,7 @@ Example MEGA-PRESS data with significant B0 drift.
Format
- An object of class mrs_data of length 13.
+ An object of class mrs_data of dimension 1 x 1 x 1 x 1 x 40 x 1 x 1024.
@@ -98,7 +98,7 @@ Format
diff --git a/docs/reference/spant_sim_fmrs_dataset.html b/docs/reference/spant_sim_fmrs_dataset.html
new file mode 100644
index 00000000..00e48b56
--- /dev/null
+++ b/docs/reference/spant_sim_fmrs_dataset.html
@@ -0,0 +1,117 @@
+
+Simulate an example fMRS dataset for a block design fMRS experiment and export a BIDS structure. — spant_sim_fmrs_dataset • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Simulate an example fMRS dataset for a block design fMRS experiment and export a BIDS structure.
+ Source: R/fmrs.R
+ spant_sim_fmrs_dataset.Rd
+
+
+
+ Simulate an example fMRS dataset for a block design fMRS experiment and
+export a BIDS structure.
+
+
+
+ spant_sim_fmrs_dataset(output_dir = NULL)
+
+
+
+ Arguments
+ - output_dir
+output directory for the BIDS data. Defaults to :
+"HOME/sim_fmrs_dataset/data".
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/spant_simulation_benchmark.html b/docs/reference/spant_simulation_benchmark.html
index 32daa8bf..d8cc6841 100644
--- a/docs/reference/spant_simulation_benchmark.html
+++ b/docs/reference/spant_simulation_benchmark.html
@@ -1,7 +1,5 @@
-Simulate a typical metabolite basis set for benchmarking. Timing metrics will
-be printed on completion. — spant_simulation_benchmark • Spectroscopy Analysis Tools (spant) Simulate a typical metabolite basis set for benchmarking. Timing metrics will be printed on completion. — spant_simulation_benchmark • Spectroscopy Analysis Tools (spant) Decompose an mrs_data object into white and gray matter spectra. — spec_decomp • Spectroscopy Analysis Tools (spant) Perform a mathematical operation on a spectral region. — spec_op • Spectroscopy Analysis Tools (spant) Perform a mathematical operation on a spectral region. — spec_op • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -98,8 +98,8 @@ Arguments
operator
-can be "sum" (default), "mean", "l2", "max", "min" or
-"max-min".
can be "sum" (default), "mean", "l2", "max", "max_cplx,
+"min" or "max-min".
freq_scale
@@ -129,7 +129,7 @@ Value
diff --git a/docs/reference/spin_sys.html b/docs/reference/spin_sys.html
index 853423a4..1eaa9e76 100644
--- a/docs/reference/spin_sys.html
+++ b/docs/reference/spin_sys.html
@@ -1,5 +1,5 @@
-Create a spin system object for pulse sequence simulation. — spin_sys • Spectroscopy Analysis Tools (spant) Create a spin system object for pulse sequence simulation. — spin_sys • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/spm_pve2categorical.html b/docs/reference/spm_pve2categorical.html
index 23a1bad9..70f10729 100644
--- a/docs/reference/spm_pve2categorical.html
+++ b/docs/reference/spm_pve2categorical.html
@@ -1,7 +1,5 @@
-Convert SPM style segmentation files to a single categorical image where
-the numerical values map as: 0) Other, 1) CSF, 2) GM and 3) WM. — spm_pve2categorical • Spectroscopy Analysis Tools (spant) Convert SPM style segmentation files to a single categorical image where the numerical values map as: 0) Other, 1) CSF, 2) GM and 3) WM. — spm_pve2categorical • Spectroscopy Analysis Tools (spant) Signal space projection method for lipid suppression. — ssp • Spectroscopy Analysis Tools (spant) Signal space projection method for lipid suppression. — ssp • Spectroscopy Analysis Tools (spant) Plot the fitting results of an object of class fit_result with
-individual basis set components shown. — stackplot.fit_result • Spectroscopy Analysis Tools (spant) Plot the fitting results of an object of class fit_result with individual basis set components shown. — stackplot.fit_result • Spectroscopy Analysis Tools (spant) Produce a plot with multiple traces. — stackplot • Spectroscopy Analysis Tools (spant) Produce a plot with multiple traces. — stackplot • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/stackplot.mrs_data.html b/docs/reference/stackplot.mrs_data.html
index 17ff5648..64eea445 100644
--- a/docs/reference/stackplot.mrs_data.html
+++ b/docs/reference/stackplot.mrs_data.html
@@ -1,5 +1,5 @@
-Stackplot plotting method for objects of class mrs_data. — stackplot.mrs_data • Spectroscopy Analysis Tools (spant) Stackplot plotting method for objects of class mrs_data. — stackplot.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -255,7 +255,7 @@ Arguments
diff --git a/docs/reference/sub_first_dyn.html b/docs/reference/sub_first_dyn.html
index dbd7f831..493b7242 100644
--- a/docs/reference/sub_first_dyn.html
+++ b/docs/reference/sub_first_dyn.html
@@ -1,5 +1,5 @@
-Subtract the first dynamic spectrum from a dynamic series. — sub_first_dyn • Spectroscopy Analysis Tools (spant) Subtract the first dynamic spectrum from a dynamic series. — sub_first_dyn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/sub_mean_dyns.html b/docs/reference/sub_mean_dyns.html
index 6e3bb2df..221bd0c1 100644
--- a/docs/reference/sub_mean_dyns.html
+++ b/docs/reference/sub_mean_dyns.html
@@ -1,5 +1,5 @@
-Subtract the mean dynamic spectrum from a dynamic series. — sub_mean_dyns • Spectroscopy Analysis Tools (spant) Subtract the mean dynamic spectrum from a dynamic series. — sub_mean_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/sub_median_dyns.html b/docs/reference/sub_median_dyns.html
index 134c495d..1e834f14 100644
--- a/docs/reference/sub_median_dyns.html
+++ b/docs/reference/sub_median_dyns.html
@@ -1,5 +1,5 @@
-Subtract the median dynamic spectrum from a dynamic series. — sub_median_dyns • Spectroscopy Analysis Tools (spant) Subtract the median dynamic spectrum from a dynamic series. — sub_median_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/sum_coils.html b/docs/reference/sum_coils.html
index 7bf559f2..e1ab3cc0 100644
--- a/docs/reference/sum_coils.html
+++ b/docs/reference/sum_coils.html
@@ -1,5 +1,5 @@
-Calculate the sum across receiver coil elements. — sum_coils • Spectroscopy Analysis Tools (spant) Calculate the sum across receiver coil elements. — sum_coils • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/sum_dyns.html b/docs/reference/sum_dyns.html
index a0be19d3..bbda2ffc 100644
--- a/docs/reference/sum_dyns.html
+++ b/docs/reference/sum_dyns.html
@@ -1,5 +1,5 @@
-Calculate the sum of data dynamics. — sum_dyns • Spectroscopy Analysis Tools (spant) Calculate the sum of data dynamics. — sum_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/sum_mrs.html b/docs/reference/sum_mrs.html
index a22f215b..3cc3ab9e 100644
--- a/docs/reference/sum_mrs.html
+++ b/docs/reference/sum_mrs.html
@@ -1,5 +1,5 @@
-Sum two mrs_data objects. — sum_mrs • Spectroscopy Analysis Tools (spant) Sum two mrs_data objects. — sum_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Value
diff --git a/docs/reference/sum_mrs_list.html b/docs/reference/sum_mrs_list.html
index f4e09aea..c3584348 100644
--- a/docs/reference/sum_mrs_list.html
+++ b/docs/reference/sum_mrs_list.html
@@ -1,5 +1,5 @@
-Return the sum of a list of mrs_data objects. — sum_mrs_list • Spectroscopy Analysis Tools (spant) Return the sum of a list of mrs_data objects. — sum_mrs_list • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/svs_1h_brain_analysis.html b/docs/reference/svs_1h_brain_analysis.html
index 8ce514db..dff0ef7d 100644
--- a/docs/reference/svs_1h_brain_analysis.html
+++ b/docs/reference/svs_1h_brain_analysis.html
@@ -1,5 +1,5 @@
-Standard SVS 1H brain analysis pipeline. — svs_1h_brain_analysis • Spectroscopy Analysis Tools (spant) Standard SVS 1H brain analysis pipeline. — svs_1h_brain_analysis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -199,7 +199,7 @@ Value
diff --git a/docs/reference/svs_1h_brain_analysis_dev.html b/docs/reference/svs_1h_brain_analysis_dev.html
index d70a14d3..d71bfea2 100644
--- a/docs/reference/svs_1h_brain_analysis_dev.html
+++ b/docs/reference/svs_1h_brain_analysis_dev.html
@@ -1,5 +1,5 @@
-Standard SVS 1H brain analysis pipeline. — svs_1h_brain_analysis_dev • Spectroscopy Analysis Tools (spant) Standard SVS 1H brain analysis pipeline. — svs_1h_brain_analysis_dev • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -193,7 +193,7 @@ Examples
diff --git a/docs/reference/svs_1h_brain_batch_analysis.html b/docs/reference/svs_1h_brain_batch_analysis.html
index 5631e8cc..15f7223e 100644
--- a/docs/reference/svs_1h_brain_batch_analysis.html
+++ b/docs/reference/svs_1h_brain_batch_analysis.html
@@ -1,5 +1,5 @@
-Batch interface to the standard SVS 1H brain analysis pipeline. — svs_1h_brain_batch_analysis • Spectroscopy Analysis Tools (spant) Batch interface to the standard SVS 1H brain analysis pipeline. — svs_1h_brain_batch_analysis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -144,7 +144,7 @@ Value
diff --git a/docs/reference/t_test_spec.html b/docs/reference/t_test_spec.html
new file mode 100644
index 00000000..56a7ea1b
--- /dev/null
+++ b/docs/reference/t_test_spec.html
@@ -0,0 +1,124 @@
+
+Perform a t-test on spectral data points. — t_test_spec • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+
+
+ Perform a t-test on spectral data points.
+
+
+
+ t_test_spec(mrs_data, group)
+
+
+
+ Arguments
+ - mrs_data
+an mrs_data object with spectra in the dynamic dimension.
- group
+vector describing the group membership of each dynamic spectrum.
+
+ Value
+
+
+a list of statistical results.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/td2fd.html b/docs/reference/td2fd.html
index 6748a6a8..f31ed524 100644
--- a/docs/reference/td2fd.html
+++ b/docs/reference/td2fd.html
@@ -1,5 +1,5 @@
-Transform time-domain data to the frequency-domain. — td2fd • Spectroscopy Analysis Tools (spant) Transform time-domain data to the frequency-domain. — td2fd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/td_conv_filt.html b/docs/reference/td_conv_filt.html
index a9f340c3..106b9b00 100644
--- a/docs/reference/td_conv_filt.html
+++ b/docs/reference/td_conv_filt.html
@@ -1,5 +1,5 @@
-Time-domain convolution based filter. — td_conv_filt • Spectroscopy Analysis Tools (spant) Time-domain convolution based filter. — td_conv_filt • Spectroscopy Analysis Tools (spant) Time-domain spectral registration. — tdsr • Spectroscopy Analysis Tools (spant) Time-domain spectral registration. — tdsr • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -121,7 +121,7 @@ Value
diff --git a/docs/reference/te.html b/docs/reference/te.html
index 010361b1..4a65711d 100644
--- a/docs/reference/te.html
+++ b/docs/reference/te.html
@@ -1,5 +1,5 @@
-Return the echo time of an MRS dataset. — te • Spectroscopy Analysis Tools (spant) Return the echo time of an MRS dataset. — te • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/tr.html b/docs/reference/tr.html
index 0c0bd63b..2e749e02 100644
--- a/docs/reference/tr.html
+++ b/docs/reference/tr.html
@@ -1,5 +1,5 @@
-Return the repetition time of an MRS dataset. — tr • Spectroscopy Analysis Tools (spant) Return the repetition time of an MRS dataset. — tr • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/varpro_3_para_opts.html b/docs/reference/varpro_3_para_opts.html
index c2270a16..52d7cd84 100644
--- a/docs/reference/varpro_3_para_opts.html
+++ b/docs/reference/varpro_3_para_opts.html
@@ -1,5 +1,5 @@
-Return a list of options for VARPRO based fitting with 3 free parameters. — varpro_3_para_opts • Spectroscopy Analysis Tools (spant) Return a list of options for VARPRO based fitting with 3 free parameters. — varpro_3_para_opts • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -141,7 +141,7 @@ Value
diff --git a/docs/reference/varpro_basic_opts.html b/docs/reference/varpro_basic_opts.html
index 32c86d22..c5104891 100644
--- a/docs/reference/varpro_basic_opts.html
+++ b/docs/reference/varpro_basic_opts.html
@@ -1,5 +1,5 @@
-Return a list of options for a basic VARPRO analysis. — varpro_basic_opts • Spectroscopy Analysis Tools (spant) Return a list of options for a basic VARPRO analysis. — varpro_basic_opts • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -118,7 +118,7 @@ Value
diff --git a/docs/reference/varpro_opts.html b/docs/reference/varpro_opts.html
index 2aabf11d..6332f730 100644
--- a/docs/reference/varpro_opts.html
+++ b/docs/reference/varpro_opts.html
@@ -1,5 +1,5 @@
-Return a list of options for VARPRO based fitting. — varpro_opts • Spectroscopy Analysis Tools (spant) Return a list of options for VARPRO based fitting. — varpro_opts • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -177,7 +177,7 @@ Examples
diff --git a/docs/reference/vec2mrs_data.html b/docs/reference/vec2mrs_data.html
index 0cccd73b..f0d58bf0 100644
--- a/docs/reference/vec2mrs_data.html
+++ b/docs/reference/vec2mrs_data.html
@@ -1,5 +1,5 @@
-Convert a vector into a mrs_data object. — vec2mrs_data • Spectroscopy Analysis Tools (spant) Convert a vector into a mrs_data object. — vec2mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -80,10 +80,11 @@ Convert a vector into a mrs_data object.
vec2mrs_data(
vec,
- fs = def_fs(),
- ft = def_ft(),
- ref = def_ref(),
- nuc = def_nuc(),
+ mrs_data = NULL,
+ fs = NULL,
+ ft = NULL,
+ ref = NULL,
+ nuc = NULL,
dyns = 1,
fd = FALSE
)
@@ -95,6 +96,10 @@ Arguments
the data vector.
mrs_data
+example data to copy acquisition parameters from.
fs
sampling frequency in Hz.
Arguments
fd
-flag to indicate if the matrix is in the frequency domain (logical).
flag to indicate if the vector is in the frequency domain (logical).
Value
diff --git a/docs/reference/write_basis.html b/docs/reference/write_basis.html
index b6e27cbd..94c5e021 100644
--- a/docs/reference/write_basis.html
+++ b/docs/reference/write_basis.html
@@ -1,5 +1,5 @@
-Write a basis object to an LCModel .basis formatted file. — write_basis • Spectroscopy Analysis Tools (spant) Write a basis object to an LCModel .basis formatted file. — write_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -108,7 +108,7 @@ Arguments
diff --git a/docs/reference/write_basis_tqn.html b/docs/reference/write_basis_tqn.html
index 6aa51c1d..116c73ec 100644
--- a/docs/reference/write_basis_tqn.html
+++ b/docs/reference/write_basis_tqn.html
@@ -1,5 +1,5 @@
-Generate a basis file using TARQUIN. — write_basis_tqn • Spectroscopy Analysis Tools (spant) Generate a basis file using TARQUIN. — write_basis_tqn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Examples
diff --git a/docs/reference/write_mrs.html b/docs/reference/write_mrs.html
index fff25f15..124b9dc4 100644
--- a/docs/reference/write_mrs.html
+++ b/docs/reference/write_mrs.html
@@ -1,5 +1,5 @@
-Write MRS data object to file. — write_mrs • Spectroscopy Analysis Tools (spant) Write MRS data object to file. — write_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Arguments
diff --git a/docs/reference/write_mrs_nifti.html b/docs/reference/write_mrs_nifti.html
index f4bf1921..bd3ed4b7 100644
--- a/docs/reference/write_mrs_nifti.html
+++ b/docs/reference/write_mrs_nifti.html
@@ -1,5 +1,5 @@
-Write MRS data object to file in NIFTI format. — write_mrs_nifti • Spectroscopy Analysis Tools (spant) Write MRS data object to file in NIFTI format. — write_mrs_nifti • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/write_pulse_ascii.html b/docs/reference/write_pulse_ascii.html
index 067ae086..221f8ebb 100644
--- a/docs/reference/write_pulse_ascii.html
+++ b/docs/reference/write_pulse_ascii.html
@@ -1,5 +1,5 @@
-Write an ASCII formatted pulse file. — write_pulse_ascii • Spectroscopy Analysis Tools (spant) Write an ASCII formatted pulse file. — write_pulse_ascii • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/zero_fade_spec.html b/docs/reference/zero_fade_spec.html
index c703745c..c8b572c3 100644
--- a/docs/reference/zero_fade_spec.html
+++ b/docs/reference/zero_fade_spec.html
@@ -1,7 +1,5 @@
-Fade a spectrum to zero by frequency domain multiplication with a tanh
-function. Note this operation distorts data points at the end of the FID. — zero_fade_spec • Spectroscopy Analysis Tools (spant) Fade a spectrum to zero by frequency domain multiplication with a tanh function. Note this operation distorts data points at the end of the FID. — zero_fade_spec • Spectroscopy Analysis Tools (spant) Zero all coherences including and above a given order. — zero_higher_orders • Spectroscopy Analysis Tools (spant) Zero all coherences including and above a given order. — zero_higher_orders • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Value
diff --git a/docs/reference/zero_td_pts_end.html b/docs/reference/zero_td_pts_end.html
index 8c1123c8..71d24ebb 100644
--- a/docs/reference/zero_td_pts_end.html
+++ b/docs/reference/zero_td_pts_end.html
@@ -1,5 +1,5 @@
-Set mrs_data object data points at the end of the FID to zero. — zero_td_pts_end • Spectroscopy Analysis Tools (spant) Set mrs_data object data points at the end of the FID to zero. — zero_td_pts_end • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/zf.html b/docs/reference/zf.html
index 85e2013c..baf50256 100644
--- a/docs/reference/zf.html
+++ b/docs/reference/zf.html
@@ -1,5 +1,5 @@
-Zero-fill MRS data in the time domain. — zf • Spectroscopy Analysis Tools (spant) Zero-fill MRS data in the time domain. — zf • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -125,7 +125,7 @@ Value
diff --git a/docs/reference/zf_xy.html b/docs/reference/zf_xy.html
index ebca3999..c4104a74 100644
--- a/docs/reference/zf_xy.html
+++ b/docs/reference/zf_xy.html
@@ -1,5 +1,5 @@
-Zero-fill MRSI data in the k-space x-y direction. — zf_xy • Spectroscopy Analysis Tools (spant) Zero-fill MRSI data in the k-space x-y direction. — zf_xy • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -113,7 +113,7 @@ Value
diff --git a/docs/sitemap.xml b/docs/sitemap.xml
index e2139f71..4c39f515 100644
--- a/docs/sitemap.xml
+++ b/docs/sitemap.xml
@@ -216,6 +216,12 @@
https://martin3141.github.io/spant/reference/comb_coils_fp_pc.html
+
+ https://martin3141.github.io/spant/reference/comb_coils_mrsi_gls.html
+
+
+ https://martin3141.github.io/spant/reference/comb_coils_svs_gls.html
+
https://martin3141.github.io/spant/reference/comb_csv_results.html
@@ -411,6 +417,9 @@
https://martin3141.github.io/spant/reference/gen_conv_reg.html
+
+ https://martin3141.github.io/spant/reference/gen_group_reg.html
+
https://martin3141.github.io/spant/reference/gen_impulse_reg.html
@@ -555,6 +564,15 @@
https://martin3141.github.io/spant/reference/glm_spec.html
+
+ https://martin3141.github.io/spant/reference/glm_spec_fmrs_fl.html
+
+
+ https://martin3141.github.io/spant/reference/glm_spec_fmrs_group.html
+
+
+ https://martin3141.github.io/spant/reference/glm_spec_group_linhyp.html
+
https://martin3141.github.io/spant/reference/grid_shift_xy.html
@@ -690,9 +708,15 @@
https://martin3141.github.io/spant/reference/mrs_data2basis.html
+
+ https://martin3141.github.io/spant/reference/mrs_data2bids.html
+
https://martin3141.github.io/spant/reference/mrs_data2mat.html
+
+ https://martin3141.github.io/spant/reference/mrs_data2spec_mat.html
+
https://martin3141.github.io/spant/reference/mrs_data2vec.html
@@ -741,6 +765,9 @@
https://martin3141.github.io/spant/reference/phase.html
+
+ https://martin3141.github.io/spant/reference/phase_ref_1h_brain.html
+
https://martin3141.github.io/spant/reference/plot.fit_result.html
@@ -780,6 +807,12 @@
https://martin3141.github.io/spant/reference/precomp.html
+
+ https://martin3141.github.io/spant/reference/preproc_svs.html
+
+
+ https://martin3141.github.io/spant/reference/preproc_svs_dataset.html
+
https://martin3141.github.io/spant/reference/print.fit_result.html
@@ -1050,6 +1083,9 @@
https://martin3141.github.io/spant/reference/spant_mpress_drift.html
+
+ https://martin3141.github.io/spant/reference/spant_sim_fmrs_dataset.html
+
https://martin3141.github.io/spant/reference/spant_simulation_benchmark.html
@@ -1107,6 +1143,9 @@
https://martin3141.github.io/spant/reference/svs_1h_brain_batch_analysis.html
+
+ https://martin3141.github.io/spant/reference/t_test_spec.html
+
https://martin3141.github.io/spant/reference/td2fd.html
Perform an ifft and ifftshift on a matrix with each column replaced by its -shifted ifft.
Perform an ifft and ifftshift on a matrix with each column replaced by its shifted ifft.
All functions
- Check if the chemical shift dimension of an MRS data object is in the
-frequency domain.
Check if the chemical shift dimension of an MRS data object is in the frequency domain.
@@ -820,18 +810,15 @@ All functions
- Covert a linewidth in Hz to an equivalent alpha value in the time-domain ie:
-x * exp(-t * alpha).
Covert a linewidth in Hz to an equivalent alpha value in the time-domain ie: x * exp(-t * alpha).
- Covert a linewidth in Hz to an equivalent beta value in the time-domain ie:
-x * exp(-t * t * beta).
Covert a linewidth in Hz to an equivalent beta value in the time-domain ie: x * exp(-t * t * beta).
- Make a basis-set object from a directory containing LCModel formatted RAW
-files.
Make a basis-set object from a directory containing LCModel formatted RAW files.
@@ -851,8 +838,7 @@ All functions
- Mask the voxels outside an elliptical region spanning the MRSI dataset in the
-x-y plane.
Mask the voxels outside an elliptical region spanning the MRSI dataset in the x-y plane.
@@ -860,13 +846,11 @@ All functions
- Convert a matrix (with spectral points in the column dimension and dynamics
-in the row dimensions) into a mrs_data object.
Convert a matrix (with spectral points in the column dimension and dynamics in the row dimensions) into a mrs_data object.
- Matrix exponential function taken from complexplus package to reduce the
-number of spant dependencies.
Matrix exponential function taken from complexplus package to reduce the number of spant dependencies.
@@ -914,31 +898,31 @@ All functions
- Convert an mrs_data object to basis object - where basis signals are spread
-across the dynamic dimension in the MRS data.
Convert an mrs_data object to basis object - where basis signals are spread across the dynamic dimension in the MRS data.
+
+
+ Create a BIDS file structure from a vector of MRS data paths or list of mrs_data objects.
- Convert mrs_data object to a matrix, with spectral points in the column
-dimension and dynamics in the row dimension.
Convert mrs_data object to a matrix, with spectral points in the column dimension and dynamics in the row dimension.
-
+
- Convert mrs_data object to a vector.
Convert mrs_data object to a matrix, with spectral points in the column dimension and dynamics in the row dimension.
-
+
- Create a BIDS directory and file structure from a list of mrs_data objects.
Convert mrs_data object to a vector.
- Perform a fftshift on a matrix, with each column replaced by its shifted
-result.
Perform a fftshift on a matrix, with each column replaced by its shifted result.
- Perform an ifftshift on a matrix, with each column replaced by its shifted
-result.
Perform an ifftshift on a matrix, with each column replaced by its shifted result.
@@ -946,9 +930,7 @@ All functions
- Flip the x data dimension order of a nifti image. This corresponds to
-flipping MRI data in the left-right direction, assuming the data in save in
-neurological format (can check with fslorient program).
Flip the x data dimension order of a nifti image. This corresponds to flipping MRI data in the left-right direction, assuming the data in save in neurological format (can check with fslorient program).
@@ -964,8 +946,7 @@ All functions
- Search for the highest peak in a spectral region and return the frequency,
-height and FWHM.
Search for the highest peak in a spectral region and return the frequency, height and FWHM.
@@ -974,6 +955,10 @@ All functions phase()
Apply phasing parameters to MRS data.
+
+
+ Corrected zero order phase and chemical shift offset in 1H MRS data from the brain.
@@ -1005,8 +990,7 @@ All functions
- Plot an interactive slice map from a data array where voxels can be selected
-to display a corresponding spectrum.
Plot an interactive slice map from a data array where voxels can be selected to display a corresponding spectrum.
@@ -1026,8 +1010,15 @@ All functions
- Save function results to file and load on subsequent calls to avoid repeat
-computation.
Save function results to file and load on subsequent calls to avoid repeat computation.
+
+
+ Preprocess and perform quality assessment of a single SVS data set.
+
+
+ Preprocess and perform quality assessment of one or more SVS data sets.
@@ -1055,15 +1046,11 @@ All functions
- Read a directory containing Siemens MRS IMA files and combine along the coil
-dimension. Note that the coil ID is inferred from the sorted file name and
-should be checked when consistency is required between two directories.
Read a directory containing Siemens MRS IMA files and combine along the coil dimension. Note that the coil ID is inferred from the sorted file name and should be checked when consistency is required between two directories.
- Read a directory containing Siemens MRS IMA files and combine along the
-dynamic dimension. Note that the coil ID is inferred from the sorted file
-name and should be checked when consistency is required.
Read a directory containing Siemens MRS IMA files and combine along the dynamic dimension. Note that the coil ID is inferred from the sorted file name and should be checked when consistency is required.
@@ -1103,13 +1090,11 @@ All functions
- Reconstruct complex time-domain data from the real part of frequency-domain
-data.
Reconstruct complex time-domain data from the real part of frequency-domain data.
- Reconstruct complex time-domain data from the real part of frequency-domain
-data.
Reconstruct complex time-domain data from the real part of frequency-domain data.
@@ -1141,8 +1126,7 @@ All functions
- Resample a VOI to match a target image space using nearest-neighbour
-interpolation.
Resample a VOI to match a target image space using nearest-neighbour interpolation.
@@ -1158,23 +1142,19 @@ All functions
- Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water).
Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / kg of tissue water).
- Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water).
Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / kg of tissue water).
- Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / Litre of tissue).
Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / Litre of tissue).
- Convert default LCM/TARQUIN concentration scaling to molal units with partial
-volume correction.
Convert default LCM/TARQUIN concentration scaling to molal units with partial volume correction.
@@ -1222,8 +1202,7 @@ All functions
- MEGA-PRESS sequence with ideal localisation pulses and Gaussian shaped
-editing pulse.
MEGA-PRESS sequence with ideal localisation pulses and Gaussian shaped editing pulse.
@@ -1251,13 +1230,11 @@ All functions
- STEAM sequence with ideal pulses and coherence order filtering to simulate
-gradient crushers.
STEAM sequence with ideal pulses and coherence order filtering to simulate gradient crushers.
- STEAM sequence with ideal pulses using the z-rotation gradient simulation
-method described by Young et al JMR 140, 146-152 (1999).
STEAM sequence with ideal pulses using the z-rotation gradient simulation method described by Young et al JMR 140, 146-152 (1999).
@@ -1293,8 +1270,7 @@ All functions
- Set the number of time-domain data points, truncating or zero-filling as
-appropriate.
Set the number of time-domain data points, truncating or zero-filling as appropriate.
@@ -1318,18 +1294,15 @@ All functions
- Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS
-sequence. Note, ideal pulses are assumed.
Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS sequence. Note, ideal pulses are assumed.
- Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS
-sequence. Note, ideal pulses are assumed.
Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS sequence. Note, ideal pulses are assumed.
- Simulate a macromolecular and lipid basis-set suitable for 1H brain MRS
-analysis.
Simulate a macromolecular and lipid basis-set suitable for 1H brain MRS analysis.
@@ -1353,8 +1326,7 @@ All functions
- Simulate an ideal pulse excitation profile by smoothing a top-hat function
-with a Gaussian.
Simulate an ideal pulse excitation profile by smoothing a top-hat function with a Gaussian.
@@ -1374,17 +1346,19 @@ All functions
- Simulate and fit some spectra with ABfit for benchmarking purposes. Basic
-timing and performance metrics will be printed.
Simulate and fit some spectra with ABfit for benchmarking purposes. Basic timing and performance metrics will be printed.
Example MEGA-PRESS data with significant B0 drift.
+
+
+ Simulate an example fMRS dataset for a block design fMRS experiment and export a BIDS structure.
- Simulate a typical metabolite basis set for benchmarking. Timing metrics will
-be printed on completion.
Simulate a typical metabolite basis set for benchmarking. Timing metrics will be printed on completion.
@@ -1400,8 +1374,7 @@ All functions
- Convert SPM style segmentation files to a single categorical image where
-the numerical values map as: 0) Other, 1) CSF, 2) GM and 3) WM.
Convert SPM style segmentation files to a single categorical image where the numerical values map as: 0) Other, 1) CSF, 2) GM and 3) WM.
@@ -1413,8 +1386,7 @@ All functions
- Plot the fitting results of an object of class fit_result with
-individual basis set components shown.
Plot the fitting results of an object of class fit_result with individual basis set components shown.
@@ -1459,6 +1431,10 @@ All functions svs_1h_brain_batch_analysis()
Batch interface to the standard SVS 1H brain analysis pipeline.
+
+
+ Perform a t-test on spectral data points.
@@ -1518,8 +1494,7 @@ All functions
- Fade a spectrum to zero by frequency domain multiplication with a tanh
-function. Note this operation distorts data points at the end of the FID.
Fade a spectrum to zero by frequency domain multiplication with a tanh function. Note this operation distorts data points at the end of the FID.
@@ -1549,7 +1524,7 @@ All functions
diff --git a/docs/reference/int_spec.html b/docs/reference/int_spec.html
index c7060fe7..783325a8 100644
--- a/docs/reference/int_spec.html
+++ b/docs/reference/int_spec.html
@@ -1,5 +1,5 @@
-Integrate a spectral region. — int_spec • Spectroscopy Analysis Tools (spant) Integrate a spectral region. — int_spec • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -118,7 +118,7 @@ Value
diff --git a/docs/reference/interleave_dyns.html b/docs/reference/interleave_dyns.html
index effe5543..441eff27 100644
--- a/docs/reference/interleave_dyns.html
+++ b/docs/reference/interleave_dyns.html
@@ -1,5 +1,5 @@
-Interleave the first and second half of a dynamic series. — interleave_dyns • Spectroscopy Analysis Tools (spant) Interleave the first and second half of a dynamic series. — interleave_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/inv_even_dyns.html b/docs/reference/inv_even_dyns.html
index 9f9d4fff..dcb781dc 100644
--- a/docs/reference/inv_even_dyns.html
+++ b/docs/reference/inv_even_dyns.html
@@ -1,5 +1,5 @@
-Invert even numbered dynamic scans starting from 1 (2,4,6...). — inv_even_dyns • Spectroscopy Analysis Tools (spant) Invert even numbered dynamic scans starting from 1 (2,4,6...). — inv_even_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/inv_odd_dyns.html b/docs/reference/inv_odd_dyns.html
index 26212e2b..78d64660 100644
--- a/docs/reference/inv_odd_dyns.html
+++ b/docs/reference/inv_odd_dyns.html
@@ -1,5 +1,5 @@
-Invert odd numbered dynamic scans starting from 1 (1,3,5...). — inv_odd_dyns • Spectroscopy Analysis Tools (spant) Invert odd numbered dynamic scans starting from 1 (1,3,5...). — inv_odd_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/is.def.html b/docs/reference/is.def.html
index f196ffd0..a67b9eba 100644
--- a/docs/reference/is.def.html
+++ b/docs/reference/is.def.html
@@ -1,5 +1,5 @@
-Check if an object is defined, which is the same as being not NULL. — is.def • Spectroscopy Analysis Tools (spant) Check if an object is defined, which is the same as being not NULL. — is.def • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/is_fd.html b/docs/reference/is_fd.html
index 3b0ca165..18a193aa 100644
--- a/docs/reference/is_fd.html
+++ b/docs/reference/is_fd.html
@@ -1,7 +1,5 @@
-Check if the chemical shift dimension of an MRS data object is in the
-frequency domain. — is_fd • Spectroscopy Analysis Tools (spant) Check if the chemical shift dimension of an MRS data object is in the frequency domain. — is_fd • Spectroscopy Analysis Tools (spant) Transform 2D MRSI data from k-space to image space in the x-y direction. — kspace2img_xy • Spectroscopy Analysis Tools (spant) Transform 2D MRSI data from k-space to image space in the x-y direction. — kspace2img_xy • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/l2_reg.html b/docs/reference/l2_reg.html
index 3d781d80..21aa9849 100644
--- a/docs/reference/l2_reg.html
+++ b/docs/reference/l2_reg.html
@@ -1,5 +1,5 @@
-Perform l2 regularisation artefact suppression. — l2_reg • Spectroscopy Analysis Tools (spant) Perform l2 regularisation artefact suppression. — l2_reg • Spectroscopy Analysis Tools (spant) Apply line-broadening (apodisation) to MRS data or basis object. — lb • Spectroscopy Analysis Tools (spant) Apply line-broadening (apodisation) to MRS data or basis object. — lb • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -123,7 +123,7 @@ Value
diff --git a/docs/reference/lofdc.html b/docs/reference/lofdc.html
index 5419b1ec..31347a25 100644
--- a/docs/reference/lofdc.html
+++ b/docs/reference/lofdc.html
@@ -1,5 +1,5 @@
-Correct linear frequency drift. — lofdc • Spectroscopy Analysis Tools (spant) Correct linear frequency drift. — lofdc • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -138,7 +138,7 @@ Value
diff --git a/docs/reference/lw2alpha.html b/docs/reference/lw2alpha.html
index b83db682..25da229b 100644
--- a/docs/reference/lw2alpha.html
+++ b/docs/reference/lw2alpha.html
@@ -1,7 +1,5 @@
-Covert a linewidth in Hz to an equivalent alpha value in the time-domain ie:
-x * exp(-t * alpha). — lw2alpha • Spectroscopy Analysis Tools (spant) Covert a linewidth in Hz to an equivalent alpha value in the time-domain ie: x * exp(-t * alpha). — lw2alpha • Spectroscopy Analysis Tools (spant) Covert a linewidth in Hz to an equivalent beta value in the time-domain ie:
-x * exp(-t * t * beta). — lw2beta • Spectroscopy Analysis Tools (spant) Covert a linewidth in Hz to an equivalent beta value in the time-domain ie: x * exp(-t * t * beta). — lw2beta • Spectroscopy Analysis Tools (spant) Make a basis-set object from a directory containing LCModel formatted RAW
-files. — make_basis_from_raw • Spectroscopy Analysis Tools (spant) Make a basis-set object from a directory containing LCModel formatted RAW files. — make_basis_from_raw • Spectroscopy Analysis Tools (spant) Mask an MRS dataset in the dynamic dimension. — mask_dyns • Spectroscopy Analysis Tools (spant) Mask an MRS dataset in the dynamic dimension. — mask_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/mask_fit_res.html b/docs/reference/mask_fit_res.html
index 97baaa3f..ebd91a99 100644
--- a/docs/reference/mask_fit_res.html
+++ b/docs/reference/mask_fit_res.html
@@ -1,5 +1,5 @@
-Mask fit result spectra depending on a vector of bool values. — mask_fit_res • Spectroscopy Analysis Tools (spant) Mask fit result spectra depending on a vector of bool values. — mask_fit_res • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -116,7 +116,7 @@ Value
diff --git a/docs/reference/mask_xy.html b/docs/reference/mask_xy.html
index 11bb577c..b0d38619 100644
--- a/docs/reference/mask_xy.html
+++ b/docs/reference/mask_xy.html
@@ -1,5 +1,5 @@
-Mask an MRSI dataset in the x-y direction — mask_xy • Spectroscopy Analysis Tools (spant) Mask an MRSI dataset in the x-y direction — mask_xy • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/mask_xy_corners.html b/docs/reference/mask_xy_corners.html
index 09b16cd2..2d13839d 100644
--- a/docs/reference/mask_xy_corners.html
+++ b/docs/reference/mask_xy_corners.html
@@ -1,5 +1,5 @@
-Mask the four corners of an MRSI dataset in the x-y plane. — mask_xy_corners • Spectroscopy Analysis Tools (spant) Mask the four corners of an MRSI dataset in the x-y plane. — mask_xy_corners • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/mask_xy_ellipse.html b/docs/reference/mask_xy_ellipse.html
index 1d8b02e4..e2e749ef 100644
--- a/docs/reference/mask_xy_ellipse.html
+++ b/docs/reference/mask_xy_ellipse.html
@@ -1,7 +1,5 @@
-Mask the voxels outside an elliptical region spanning the MRSI dataset in the
-x-y plane. — mask_xy_ellipse • Spectroscopy Analysis Tools (spant) Mask the voxels outside an elliptical region spanning the MRSI dataset in the x-y plane. — mask_xy_ellipse • Spectroscopy Analysis Tools (spant) Mask a 2D MRSI dataset in the x-y dimension. — mask_xy_mat • Spectroscopy Analysis Tools (spant) Mask a 2D MRSI dataset in the x-y dimension. — mask_xy_mat • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Value
diff --git a/docs/reference/mat2mrs_data.html b/docs/reference/mat2mrs_data.html
index 2e2895f3..ae55665f 100644
--- a/docs/reference/mat2mrs_data.html
+++ b/docs/reference/mat2mrs_data.html
@@ -1,7 +1,5 @@
-Convert a matrix (with spectral points in the column dimension and dynamics
-in the row dimensions) into a mrs_data object. — mat2mrs_data • Spectroscopy Analysis Tools (spant) Convert a matrix (with spectral points in the column dimension and dynamics in the row dimensions) into a mrs_data object. — mat2mrs_data • Spectroscopy Analysis Tools (spant) Matrix exponential function taken from complexplus package to reduce the
-number of spant dependencies. — matexp • Spectroscopy Analysis Tools (spant) Matrix exponential function taken from complexplus package to reduce the number of spant dependencies. — matexp • Spectroscopy Analysis Tools (spant) Apply the max operator to an MRS dataset. — max_mrs • Spectroscopy Analysis Tools (spant) Apply the max operator to an MRS dataset. — max_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/max_mrs_interp.html b/docs/reference/max_mrs_interp.html
index e4474764..52e63f3e 100644
--- a/docs/reference/max_mrs_interp.html
+++ b/docs/reference/max_mrs_interp.html
@@ -1,5 +1,5 @@
-Apply the max operator to an interpolated MRS dataset. — max_mrs_interp • Spectroscopy Analysis Tools (spant) Apply the max operator to an interpolated MRS dataset. — max_mrs_interp • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/mean.list.html b/docs/reference/mean.list.html
index b8eb3463..048306fd 100644
--- a/docs/reference/mean.list.html
+++ b/docs/reference/mean.list.html
@@ -1,5 +1,5 @@
-Calculate the mean spectrum from an mrs_data object. — mean.list • Spectroscopy Analysis Tools (spant) Calculate the mean spectrum from an mrs_data object. — mean.list • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/mean.mrs_data.html b/docs/reference/mean.mrs_data.html
index 5531a28d..79515014 100644
--- a/docs/reference/mean.mrs_data.html
+++ b/docs/reference/mean.mrs_data.html
@@ -1,5 +1,5 @@
-Calculate the mean spectrum from an mrs_data object. — mean.mrs_data • Spectroscopy Analysis Tools (spant) Calculate the mean spectrum from an mrs_data object. — mean.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/mean_dyn_blocks.html b/docs/reference/mean_dyn_blocks.html
index 10467098..4c042448 100644
--- a/docs/reference/mean_dyn_blocks.html
+++ b/docs/reference/mean_dyn_blocks.html
@@ -1,5 +1,5 @@
-Calculate the mean of adjacent dynamic scans. — mean_dyn_blocks • Spectroscopy Analysis Tools (spant) Calculate the mean of adjacent dynamic scans. — mean_dyn_blocks • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/mean_dyn_pairs.html b/docs/reference/mean_dyn_pairs.html
index 63e909ea..1a241126 100644
--- a/docs/reference/mean_dyn_pairs.html
+++ b/docs/reference/mean_dyn_pairs.html
@@ -1,5 +1,5 @@
-Calculate the pairwise means across a dynamic data set. — mean_dyn_pairs • Spectroscopy Analysis Tools (spant) Calculate the pairwise means across a dynamic data set. — mean_dyn_pairs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/mean_dyns.html b/docs/reference/mean_dyns.html
index 73fdbfa7..0daa27df 100644
--- a/docs/reference/mean_dyns.html
+++ b/docs/reference/mean_dyns.html
@@ -1,5 +1,5 @@
-Calculate the mean dynamic data. — mean_dyns • Spectroscopy Analysis Tools (spant) Calculate the mean dynamic data. — mean_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/mean_mrs_list.html b/docs/reference/mean_mrs_list.html
index 808b6c50..10d842c0 100644
--- a/docs/reference/mean_mrs_list.html
+++ b/docs/reference/mean_mrs_list.html
@@ -1,5 +1,5 @@
-Return the mean of a list of mrs_data objects. — mean_mrs_list • Spectroscopy Analysis Tools (spant) Return the mean of a list of mrs_data objects. — mean_mrs_list • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/mean_vec_blocks.html b/docs/reference/mean_vec_blocks.html
index 8fc92eaa..dd78b122 100644
--- a/docs/reference/mean_vec_blocks.html
+++ b/docs/reference/mean_vec_blocks.html
@@ -1,5 +1,5 @@
-Calculate the mean of adjacent blocks in a vector. — mean_vec_blocks • Spectroscopy Analysis Tools (spant) Calculate the mean of adjacent blocks in a vector. — mean_vec_blocks • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/median_dyns.html b/docs/reference/median_dyns.html
index 1039d4b5..9a085b10 100644
--- a/docs/reference/median_dyns.html
+++ b/docs/reference/median_dyns.html
@@ -1,5 +1,5 @@
-Calculate the median dynamic data. — median_dyns • Spectroscopy Analysis Tools (spant) Calculate the median dynamic data. — median_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/mod_td.html b/docs/reference/mod_td.html
index 76ad0a40..141ef09e 100644
--- a/docs/reference/mod_td.html
+++ b/docs/reference/mod_td.html
@@ -1,5 +1,5 @@
-Apply the Modulus operator to the time-domain MRS signal. — mod_td • Spectroscopy Analysis Tools (spant) Apply the Modulus operator to the time-domain MRS signal. — mod_td • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/mrs_data2basis.html b/docs/reference/mrs_data2basis.html
index 62f7d749..11797b91 100644
--- a/docs/reference/mrs_data2basis.html
+++ b/docs/reference/mrs_data2basis.html
@@ -1,7 +1,5 @@
-Convert an mrs_data object to basis object - where basis signals are spread
-across the dynamic dimension in the MRS data. — mrs_data2basis • Spectroscopy Analysis Tools (spant) Convert an mrs_data object to basis object - where basis signals are spread across the dynamic dimension in the MRS data. — mrs_data2basis • Spectroscopy Analysis Tools (spant) Create a BIDS file structure from a vector of MRS data paths or list of mrs_data objects. — mrs_data2bids • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Create a BIDS file structure from a vector of MRS data paths or list of mrs_data objects.
+ Source: R/fmrs.R
+ mrs_data2bids.Rd
+
+
+
+ Create a BIDS file structure from a vector of MRS data paths or list of
+mrs_data objects.
+
+
+
+ mrs_data2bids(
+ mrs_data,
+ output_dir,
+ suffix = NULL,
+ sub = NULL,
+ ses = NULL,
+ task = NULL,
+ acq = NULL,
+ nuc = NULL,
+ voi = NULL,
+ rec = NULL,
+ run = NULL,
+ echo = NULL,
+ inv = NULL,
+ skip_existing = TRUE
+)
+
+
+
+ Arguments
+ - mrs_data
+vector of MRS data paths or list of mrs_data objects.
- output_dir
+the base directory to create the BIDS structure.
- suffix
+optional vector of file suffixes. Default behaviour is to
+automatically determine these from the input data, however it is recommended
+that they are specified to allow more efficient skipping of existing data.
- sub
+optional vector of subject labels. If not specified, these will be
+automatically generated as a series of increasing zero-padded integer values
+corresponding to the mrs_data input indices.
- ses
+optional vector of session labels.
- task
+optional vector of task labels.
- acq
+optional vector of acquisition labels.
- nuc
+optional vector of nucleus labels.
- voi
+optional vector of volume of interest labels.
- rec
+optional vector of reconstruction labels.
- run
+optional vector of run indices.
- echo
+optional vector of echo time indices.
- inv
+optional vector of inversion indices.
- skip_existing
+skip any data files that have already been converted.
+Defaults to TRUE, set to FALSE to force an overwrite of any existing data
+files.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/mrs_data2mat.html b/docs/reference/mrs_data2mat.html
index cf5ff28c..9e47688a 100644
--- a/docs/reference/mrs_data2mat.html
+++ b/docs/reference/mrs_data2mat.html
@@ -1,7 +1,5 @@
-Convert mrs_data object to a matrix, with spectral points in the column
-dimension and dynamics in the row dimension. — mrs_data2mat • Spectroscopy Analysis Tools (spant) Convert mrs_data object to a matrix, with spectral points in the column dimension and dynamics in the row dimension. — mrs_data2mat • Spectroscopy Analysis Tools (spant) Convert mrs_data object to a matrix, with spectral points in the column dimension and dynamics in the row dimension. — mrs_data2spec_mat • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Convert mrs_data object to a matrix, with spectral points in the column dimension and dynamics in the row dimension.
+ Source: R/mrs_data_proc.R
+ mrs_data2spec_mat.Rd
+
+
+
+ Convert mrs_data object to a matrix, with spectral points in the column
+dimension and dynamics in the row dimension.
+
+
+
+ mrs_data2spec_mat(mrs_data, collapse = TRUE)
+
+
+
+ Arguments
+ - mrs_data
+MRS data object or list of MRS data objects.
- collapse
+collapse all other dimensions along the dynamic dimension, eg
+a 16x16 MRSI grid would be first collapsed across 256 dynamic scans.
+
+ Value
+
+
+MRS data matrix.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/mrs_data2vec.html b/docs/reference/mrs_data2vec.html
index fb172d68..a1fd654d 100644
--- a/docs/reference/mrs_data2vec.html
+++ b/docs/reference/mrs_data2vec.html
@@ -1,5 +1,5 @@
-Convert mrs_data object to a vector. — mrs_data2vec • Spectroscopy Analysis Tools (spant) Convert mrs_data object to a vector. — mrs_data2vec • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -126,7 +126,7 @@ Value
diff --git a/docs/reference/mvfftshift.html b/docs/reference/mvfftshift.html
index 92b0841b..976b3410 100644
--- a/docs/reference/mvfftshift.html
+++ b/docs/reference/mvfftshift.html
@@ -1,7 +1,5 @@
-Perform a fftshift on a matrix, with each column replaced by its shifted
-result. — mvfftshift • Spectroscopy Analysis Tools (spant) Perform a fftshift on a matrix, with each column replaced by its shifted result. — mvfftshift • Spectroscopy Analysis Tools (spant) Perform an ifftshift on a matrix, with each column replaced by its shifted
-result. — mvifftshift • Spectroscopy Analysis Tools (spant) Perform an ifftshift on a matrix, with each column replaced by its shifted result. — mvifftshift • Spectroscopy Analysis Tools (spant) Print fit coordinates from a single index. — n2coord • Spectroscopy Analysis Tools (spant) Print fit coordinates from a single index. — n2coord • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/nifti_flip_lr.html b/docs/reference/nifti_flip_lr.html
index 730abe3c..19860b3c 100644
--- a/docs/reference/nifti_flip_lr.html
+++ b/docs/reference/nifti_flip_lr.html
@@ -1,9 +1,5 @@
-Flip the x data dimension order of a nifti image. This corresponds to
-flipping MRI data in the left-right direction, assuming the data in save in
-neurological format (can check with fslorient program). — nifti_flip_lr • Spectroscopy Analysis Tools (spant) Flip the x data dimension order of a nifti image. This corresponds to flipping MRI data in the left-right direction, assuming the data in save in neurological format (can check with fslorient program). — nifti_flip_lr • Spectroscopy Analysis Tools (spant) Export a one-page pdf of a single fit result — one_page_pdf • Spectroscopy Analysis Tools (spant) Export a one-page pdf of a single fit result — one_page_pdf • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -108,7 +108,7 @@ Arguments
diff --git a/docs/reference/ortho3.html b/docs/reference/ortho3.html
index 13ade97d..5d7dd2fd 100644
--- a/docs/reference/ortho3.html
+++ b/docs/reference/ortho3.html
@@ -1,5 +1,5 @@
-Display an orthographic projection plot of a nifti object. — ortho3 • Spectroscopy Analysis Tools (spant) Display an orthographic projection plot of a nifti object. — ortho3 • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -172,7 +172,7 @@ Arguments
diff --git a/docs/reference/ortho3_inter.html b/docs/reference/ortho3_inter.html
index 090cc5e5..15948899 100644
--- a/docs/reference/ortho3_inter.html
+++ b/docs/reference/ortho3_inter.html
@@ -1,5 +1,5 @@
-Display an interactive orthographic projection plot of a nifti object. — ortho3_inter • Spectroscopy Analysis Tools (spant) Display an interactive orthographic projection plot of a nifti object. — ortho3_inter • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -132,7 +132,7 @@ Arguments
diff --git a/docs/reference/peak_info.html b/docs/reference/peak_info.html
index 09058bd8..41c8ffaf 100644
--- a/docs/reference/peak_info.html
+++ b/docs/reference/peak_info.html
@@ -1,7 +1,5 @@
-Search for the highest peak in a spectral region and return the frequency,
-height and FWHM. — peak_info • Spectroscopy Analysis Tools (spant) Search for the highest peak in a spectral region and return the frequency, height and FWHM. — peak_info • Spectroscopy Analysis Tools (spant) Papoulis-Gerchberg (PG) algorithm method for k-space extrapolation. — pg_extrap_xy • Spectroscopy Analysis Tools (spant) Papoulis-Gerchberg (PG) algorithm method for k-space extrapolation. — pg_extrap_xy • Spectroscopy Analysis Tools (spant) Apply phasing parameters to MRS data. — phase • Spectroscopy Analysis Tools (spant) Apply phasing parameters to MRS data. — phase • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/phase_ref_1h_brain.html b/docs/reference/phase_ref_1h_brain.html
new file mode 100644
index 00000000..8707a74a
--- /dev/null
+++ b/docs/reference/phase_ref_1h_brain.html
@@ -0,0 +1,131 @@
+
+Corrected zero order phase and chemical shift offset in 1H MRS data from the brain. — phase_ref_1h_brain • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Corrected zero order phase and chemical shift offset in 1H MRS data from the brain.
+ Source: R/rats.R
+ phase_ref_1h_brain.Rd
+
+
+
+ Corrected zero order phase and chemical shift offset in 1H MRS data from the
+brain.
+
+
+
+ phase_ref_1h_brain(mrs_data, mean_ref = FALSE, ret_corr_only = TRUE)
+
+
+
+ Arguments
+ - mrs_data
+MRS data to be corrected.
- mean_ref
+apply the phase and offset of the mean spectrum to all
+others. Default is FALSE.
- ret_corr_only
+return the corrected data only.
+
+ Value
+
+
+corrected MRS data.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/plot.fit_result.html b/docs/reference/plot.fit_result.html
index e54d3bc1..836a53ee 100644
--- a/docs/reference/plot.fit_result.html
+++ b/docs/reference/plot.fit_result.html
@@ -1,5 +1,5 @@
-Plot the fitting results of an object of class fit_result. — plot.fit_result • Spectroscopy Analysis Tools (spant) Plot the fitting results of an object of class fit_result. — plot.fit_result • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -207,7 +207,7 @@ Arguments
diff --git a/docs/reference/plot.mrs_data.html b/docs/reference/plot.mrs_data.html
index fabcc35b..bb2ec651 100644
--- a/docs/reference/plot.mrs_data.html
+++ b/docs/reference/plot.mrs_data.html
@@ -1,5 +1,5 @@
-Plotting method for objects of class mrs_data. — plot.mrs_data • Spectroscopy Analysis Tools (spant) Plotting method for objects of class mrs_data. — plot.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -287,7 +287,7 @@ Arguments
diff --git a/docs/reference/plot_bc.html b/docs/reference/plot_bc.html
index 4f8309b4..b48142cc 100644
--- a/docs/reference/plot_bc.html
+++ b/docs/reference/plot_bc.html
@@ -1,5 +1,5 @@
-Convenience function to plot a baseline estimate with the original data. — plot_bc • Spectroscopy Analysis Tools (spant) Convenience function to plot a baseline estimate with the original data. — plot_bc • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -108,7 +108,7 @@ Arguments
diff --git a/docs/reference/plot_reg.html b/docs/reference/plot_reg.html
index ae1acbe7..2addb2f6 100644
--- a/docs/reference/plot_reg.html
+++ b/docs/reference/plot_reg.html
@@ -1,5 +1,5 @@
-Plot regressors as an image. — plot_reg • Spectroscopy Analysis Tools (spant) Plot regressors as an image. — plot_reg • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/plot_slice_fit.html b/docs/reference/plot_slice_fit.html
index fbc7b560..57f1af8a 100644
--- a/docs/reference/plot_slice_fit.html
+++ b/docs/reference/plot_slice_fit.html
@@ -1,5 +1,5 @@
-Plot a 2D slice from an MRSI fit result object. — plot_slice_fit • Spectroscopy Analysis Tools (spant) Plot a 2D slice from an MRSI fit result object. — plot_slice_fit • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -129,7 +129,7 @@ Arguments
diff --git a/docs/reference/plot_slice_fit_inter.html b/docs/reference/plot_slice_fit_inter.html
index 4eed104a..da105a7d 100644
--- a/docs/reference/plot_slice_fit_inter.html
+++ b/docs/reference/plot_slice_fit_inter.html
@@ -1,5 +1,5 @@
-Plot a 2D slice from an MRSI fit result object. — plot_slice_fit_inter • Spectroscopy Analysis Tools (spant) Plot a 2D slice from an MRSI fit result object. — plot_slice_fit_inter • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -134,7 +134,7 @@ Arguments
diff --git a/docs/reference/plot_slice_map.html b/docs/reference/plot_slice_map.html
index 553e9ac8..ffb2a134 100644
--- a/docs/reference/plot_slice_map.html
+++ b/docs/reference/plot_slice_map.html
@@ -1,5 +1,5 @@
-Plot a slice from a 7 dimensional array. — plot_slice_map • Spectroscopy Analysis Tools (spant) Plot a slice from a 7 dimensional array. — plot_slice_map • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -153,7 +153,7 @@ Arguments
diff --git a/docs/reference/plot_slice_map_inter.html b/docs/reference/plot_slice_map_inter.html
index 40d33b42..90968f66 100644
--- a/docs/reference/plot_slice_map_inter.html
+++ b/docs/reference/plot_slice_map_inter.html
@@ -1,7 +1,5 @@
-Plot an interactive slice map from a data array where voxels can be selected
-to display a corresponding spectrum. — plot_slice_map_inter • Spectroscopy Analysis Tools (spant) Plot an interactive slice map from a data array where voxels can be selected to display a corresponding spectrum. — plot_slice_map_inter • Spectroscopy Analysis Tools (spant) Plot the spectral standard deviation. — plot_spec_sd • Spectroscopy Analysis Tools (spant) Plot the spectral standard deviation. — plot_spec_sd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Arguments
diff --git a/docs/reference/plot_voi_overlay.html b/docs/reference/plot_voi_overlay.html
index 9a782e88..bbbbf35e 100644
--- a/docs/reference/plot_voi_overlay.html
+++ b/docs/reference/plot_voi_overlay.html
@@ -1,5 +1,5 @@
-Plot a volume as an image overlay. — plot_voi_overlay • Spectroscopy Analysis Tools (spant) Plot a volume as an image overlay. — plot_voi_overlay • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -116,7 +116,7 @@ Arguments
diff --git a/docs/reference/plot_voi_overlay_seg.html b/docs/reference/plot_voi_overlay_seg.html
index 3d4e74ff..0e800ff2 100644
--- a/docs/reference/plot_voi_overlay_seg.html
+++ b/docs/reference/plot_voi_overlay_seg.html
@@ -1,5 +1,5 @@
-Plot a volume as an overlay on a segmented brain volume. — plot_voi_overlay_seg • Spectroscopy Analysis Tools (spant) Plot a volume as an overlay on a segmented brain volume. — plot_voi_overlay_seg • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Arguments
diff --git a/docs/reference/ppm.html b/docs/reference/ppm.html
index c352327a..ee4696e2 100644
--- a/docs/reference/ppm.html
+++ b/docs/reference/ppm.html
@@ -1,5 +1,5 @@
-Return the ppm scale of an MRS dataset or fit result. — ppm • Spectroscopy Analysis Tools (spant) Return the ppm scale of an MRS dataset or fit result. — ppm • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -132,7 +132,7 @@ Value
diff --git a/docs/reference/precomp.html b/docs/reference/precomp.html
index 822d7336..df3d2c6c 100644
--- a/docs/reference/precomp.html
+++ b/docs/reference/precomp.html
@@ -1,7 +1,5 @@
-Save function results to file and load on subsequent calls to avoid repeat
-computation. — precomp • Spectroscopy Analysis Tools (spant) Save function results to file and load on subsequent calls to avoid repeat computation. — precomp • Spectroscopy Analysis Tools (spant) Preprocess and perform quality assessment of a single SVS data set. — preproc_svs • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Preprocess and perform quality assessment of a single SVS data set.
+ Source: R/fmrs.R
+ preproc_svs.Rd
+
+
+
+ Preprocess and perform quality assessment of a single SVS data set.
+
+
+
+ preproc_svs(path, label = NULL, output_dir = NULL, ref_inds = NULL)
+
+
+
+ Arguments
+ - path
+path to the fMRS data file or IMA directory.
- label
+a label to describe the data set.
- output_dir
+output directory.
- ref_inds
+a vector of 1-based indices for any water reference dynamic
+scans.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/preproc_svs_dataset.html b/docs/reference/preproc_svs_dataset.html
new file mode 100644
index 00000000..07c3a29b
--- /dev/null
+++ b/docs/reference/preproc_svs_dataset.html
@@ -0,0 +1,148 @@
+
+Preprocess and perform quality assessment of one or more SVS data sets. — preproc_svs_dataset • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Preprocess and perform quality assessment of one or more SVS data sets.
+ Source: R/fmrs.R
+ preproc_svs_dataset.Rd
+
+
+
+ Preprocess and perform quality assessment of one or more SVS data sets.
+
+
+
+ preproc_svs_dataset(
+ paths,
+ labels = NULL,
+ output_dir = "spant_analysis",
+ exclude_labels = NULL,
+ overwrite = FALSE,
+ ref_inds = NULL,
+ return_results = FALSE
+)
+
+
+
+ Arguments
+ - paths
+paths to the fMRS data file or IMA directory.
- labels
+labels to describe each data set.
- output_dir
+output directory.
- exclude_labels
+vector of labels of scans to exclude, eg poor quality
+data.
- overwrite
+overwrite saved results, defaults to FALSE.
- ref_inds
+a vector of 1-based indices for any water reference dynamic
+scans.
- return_results
+function will return key outputs, defaults to FALSE.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/print.fit_result.html b/docs/reference/print.fit_result.html
index 297f28dc..5f434e57 100644
--- a/docs/reference/print.fit_result.html
+++ b/docs/reference/print.fit_result.html
@@ -1,5 +1,5 @@
-Print a summary of an object of class fit_result. — print.fit_result • Spectroscopy Analysis Tools (spant) Print a summary of an object of class fit_result. — print.fit_result • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -105,7 +105,7 @@ Arguments
diff --git a/docs/reference/print.mrs_data.html b/docs/reference/print.mrs_data.html
index 51199017..e1561eb2 100644
--- a/docs/reference/print.mrs_data.html
+++ b/docs/reference/print.mrs_data.html
@@ -1,5 +1,5 @@
-Print a summary of mrs_data parameters. — print.mrs_data • Spectroscopy Analysis Tools (spant) Print a summary of mrs_data parameters. — print.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -109,7 +109,7 @@ Arguments
diff --git a/docs/reference/qn_states.html b/docs/reference/qn_states.html
index 0f42f2f9..d7aa6715 100644
--- a/docs/reference/qn_states.html
+++ b/docs/reference/qn_states.html
@@ -1,5 +1,5 @@
-Get the quantum coherence matrix for a spin system. — qn_states • Spectroscopy Analysis Tools (spant) Get the quantum coherence matrix for a spin system. — qn_states • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/rats.html b/docs/reference/rats.html
index 5a39a396..93585e08 100644
--- a/docs/reference/rats.html
+++ b/docs/reference/rats.html
@@ -1,5 +1,5 @@
-Robust Alignment to a Target Spectrum (RATS). — rats • Spectroscopy Analysis Tools (spant) Robust Alignment to a Target Spectrum (RATS). — rats • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -207,7 +207,7 @@ Value
diff --git a/docs/reference/re_weighting.html b/docs/reference/re_weighting.html
index d21caf21..8b0b070a 100644
--- a/docs/reference/re_weighting.html
+++ b/docs/reference/re_weighting.html
@@ -1,5 +1,5 @@
-Apply a weighting to the FID to enhance spectral resolution. — re_weighting • Spectroscopy Analysis Tools (spant) Apply a weighting to the FID to enhance spectral resolution. — re_weighting • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/read_basis.html b/docs/reference/read_basis.html
index da9b94af..eb6f8557 100644
--- a/docs/reference/read_basis.html
+++ b/docs/reference/read_basis.html
@@ -1,5 +1,5 @@
-Read a basis file in LCModel .basis format. — read_basis • Spectroscopy Analysis Tools (spant) Read a basis file in LCModel .basis format. — read_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/read_ima_coil_dir.html b/docs/reference/read_ima_coil_dir.html
index 28c02de0..4f073cd8 100644
--- a/docs/reference/read_ima_coil_dir.html
+++ b/docs/reference/read_ima_coil_dir.html
@@ -1,9 +1,5 @@
-Read a directory containing Siemens MRS IMA files and combine along the coil
-dimension. Note that the coil ID is inferred from the sorted file name and
-should be checked when consistency is required between two directories. — read_ima_coil_dir • Spectroscopy Analysis Tools (spant) Read a directory containing Siemens MRS IMA files and combine along the coil dimension. Note that the coil ID is inferred from the sorted file name and should be checked when consistency is required between two directories. — read_ima_coil_dir • Spectroscopy Analysis Tools (spant) Read a directory containing Siemens MRS IMA files and combine along the
-dynamic dimension. Note that the coil ID is inferred from the sorted file
-name and should be checked when consistency is required. — read_ima_dyn_dir • Spectroscopy Analysis Tools (spant) Read a directory containing Siemens MRS IMA files and combine along the dynamic dimension. Note that the coil ID is inferred from the sorted file name and should be checked when consistency is required. — read_ima_dyn_dir • Spectroscopy Analysis Tools (spant) Read an LCModel formatted coord file containing fit information. — read_lcm_coord • Spectroscopy Analysis Tools (spant) Read an LCModel formatted coord file containing fit information. — read_lcm_coord • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -107,7 +107,7 @@ Value
diff --git a/docs/reference/read_mrs.html b/docs/reference/read_mrs.html
index 3ac2a36b..2cf36b20 100644
--- a/docs/reference/read_mrs.html
+++ b/docs/reference/read_mrs.html
@@ -1,5 +1,5 @@
-Read MRS data from a file. — read_mrs • Spectroscopy Analysis Tools (spant) Read MRS data from a file. — read_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -88,7 +88,8 @@ Read MRS data from a file.
full_fid = FALSE,
omit_svs_ref_scans = TRUE,
verbose = FALSE,
- extra = NULL
+ extra = NULL,
+ fid_filt_dist = NULL
)
@@ -140,6 +141,13 @@ Arguments
an optional data frame to provide additional variables for use
in subsequent analysis steps, eg id or grouping variables.
fid_filt_dist
+indicate if the data has a distorted FID due to a
+brick-wall filter being used to downsample the data. Default is to auto
+detect this from the data, but TRUE or FALSE options can be given to override
+detection.
Value
@@ -183,7 +191,7 @@ Examples
diff --git a/docs/reference/read_mrs_tqn.html b/docs/reference/read_mrs_tqn.html
index 5766362f..84bdaf3a 100644
--- a/docs/reference/read_mrs_tqn.html
+++ b/docs/reference/read_mrs_tqn.html
@@ -1,5 +1,5 @@
-Read MRS data using the TARQUIN software package. — read_mrs_tqn • Spectroscopy Analysis Tools (spant) Read MRS data using the TARQUIN software package. — read_mrs_tqn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -131,7 +131,7 @@ Examples
diff --git a/docs/reference/read_pulse_ascii.html b/docs/reference/read_pulse_ascii.html
index c9e0d43c..ab11c9cc 100644
--- a/docs/reference/read_pulse_ascii.html
+++ b/docs/reference/read_pulse_ascii.html
@@ -1,5 +1,5 @@
-Read an ASCII formatted pulse file. — read_pulse_ascii • Spectroscopy Analysis Tools (spant) Read an ASCII formatted pulse file. — read_pulse_ascii • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/read_pulse_bruker.html b/docs/reference/read_pulse_bruker.html
index c92bf76a..dbe9073b 100644
--- a/docs/reference/read_pulse_bruker.html
+++ b/docs/reference/read_pulse_bruker.html
@@ -1,5 +1,5 @@
-Read a Bruker formatted pulse file — read_pulse_bruker • Spectroscopy Analysis Tools (spant) Read a Bruker formatted pulse file — read_pulse_bruker • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/read_pulse_pta.html b/docs/reference/read_pulse_pta.html
index 72e1b6d4..a0fac3c3 100644
--- a/docs/reference/read_pulse_pta.html
+++ b/docs/reference/read_pulse_pta.html
@@ -1,5 +1,5 @@
-Read a .pta formatted pulse file compatible with Siemens PulseTool. — read_pulse_pta • Spectroscopy Analysis Tools (spant) Read a .pta formatted pulse file compatible with Siemens PulseTool. — read_pulse_pta • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/read_siemens_txt_hdr.html b/docs/reference/read_siemens_txt_hdr.html
index 23fb8c70..3a17d87c 100644
--- a/docs/reference/read_siemens_txt_hdr.html
+++ b/docs/reference/read_siemens_txt_hdr.html
@@ -1,5 +1,5 @@
-Read the text format header found in Siemens IMA and TWIX data files. — read_siemens_txt_hdr • Spectroscopy Analysis Tools (spant) Read the text format header found in Siemens IMA and TWIX data files. — read_siemens_txt_hdr • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -78,7 +78,7 @@ Read the text format header found in Siemens IMA and TWIX data files.
- read_siemens_txt_hdr(input, version = "vd", verbose, offset = 0)
+ read_siemens_txt_hdr(input, version = "vd", verbose = FALSE, offset = 0)
@@ -118,7 +118,7 @@ Value
diff --git a/docs/reference/read_tqn_fit.html b/docs/reference/read_tqn_fit.html
index 4da6c25e..a1630420 100644
--- a/docs/reference/read_tqn_fit.html
+++ b/docs/reference/read_tqn_fit.html
@@ -1,5 +1,5 @@
-Reader for csv fit results generated by TARQUIN. — read_tqn_fit • Spectroscopy Analysis Tools (spant) Reader for csv fit results generated by TARQUIN. — read_tqn_fit • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -113,7 +113,7 @@ Examples
diff --git a/docs/reference/read_tqn_result.html b/docs/reference/read_tqn_result.html
index 36659714..68a3e98c 100644
--- a/docs/reference/read_tqn_result.html
+++ b/docs/reference/read_tqn_result.html
@@ -1,5 +1,5 @@
-Reader for csv results generated by TARQUIN. — read_tqn_result • Spectroscopy Analysis Tools (spant) Reader for csv results generated by TARQUIN. — read_tqn_result • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -117,7 +117,7 @@ Examples
diff --git a/docs/reference/recon_imag.html b/docs/reference/recon_imag.html
index d2a72225..5bc3b1eb 100644
--- a/docs/reference/recon_imag.html
+++ b/docs/reference/recon_imag.html
@@ -1,7 +1,5 @@
-Reconstruct complex time-domain data from the real part of frequency-domain
-data. — recon_imag • Spectroscopy Analysis Tools (spant) Reconstruct complex time-domain data from the real part of frequency-domain data. — recon_imag • Spectroscopy Analysis Tools (spant) Reconstruct complex time-domain data from the real part of frequency-domain
-data. — recon_imag_vec • Spectroscopy Analysis Tools (spant) Reconstruct complex time-domain data from the real part of frequency-domain data. — recon_imag_vec • Spectroscopy Analysis Tools (spant) Reconstruct 2D MRSI data from a twix file loaded with read_mrs. — recon_twix_2d_mrsi • Spectroscopy Analysis Tools (spant) Reconstruct 2D MRSI data from a twix file loaded with read_mrs. — recon_twix_2d_mrsi • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/rectangular_mask.html b/docs/reference/rectangular_mask.html
index a2117283..6e469bc9 100644
--- a/docs/reference/rectangular_mask.html
+++ b/docs/reference/rectangular_mask.html
@@ -1,5 +1,5 @@
-Create a rectangular mask stored as a matrix of logical values. — rectangular_mask • Spectroscopy Analysis Tools (spant) Create a rectangular mask stored as a matrix of logical values. — rectangular_mask • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -130,7 +130,7 @@ Value
diff --git a/docs/reference/reexports.html b/docs/reference/reexports.html
index 694a75d1..a59e8379 100644
--- a/docs/reference/reexports.html
+++ b/docs/reference/reexports.html
@@ -1,5 +1,5 @@
-Objects exported from other packages — reexports • Spectroscopy Analysis Tools (spant) Objects exported from other packages — reexports • Spectroscopy Analysis Tools (spant)
Spectroscopy Analysis Tools (spant)
- 2.21.0
+ 2.22.0
@@ -103,7 +103,7 @@ Objects exported from other packages
diff --git a/docs/reference/rep_array_dim.html b/docs/reference/rep_array_dim.html
index b9c49b4a..48c0a5ed 100644
--- a/docs/reference/rep_array_dim.html
+++ b/docs/reference/rep_array_dim.html
@@ -1,5 +1,5 @@
-Repeat an array over a given dimension. — rep_array_dim • Spectroscopy Analysis Tools (spant) Repeat an array over a given dimension. — rep_array_dim • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/rep_dyn.html b/docs/reference/rep_dyn.html
index 6bbfb0ef..89a4bb9b 100644
--- a/docs/reference/rep_dyn.html
+++ b/docs/reference/rep_dyn.html
@@ -1,5 +1,5 @@
-Replicate a scan in the dynamic dimension. — rep_dyn • Spectroscopy Analysis Tools (spant) Replicate a scan in the dynamic dimension. — rep_dyn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/rep_mrs.html b/docs/reference/rep_mrs.html
index 67730b5c..becb8f00 100644
--- a/docs/reference/rep_mrs.html
+++ b/docs/reference/rep_mrs.html
@@ -1,5 +1,5 @@
-Replicate a scan over a given dimension. — rep_mrs • Spectroscopy Analysis Tools (spant) Replicate a scan over a given dimension. — rep_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -138,7 +138,7 @@ Value
diff --git a/docs/reference/resample_basis.html b/docs/reference/resample_basis.html
index b0f2ab17..c7a6222a 100644
--- a/docs/reference/resample_basis.html
+++ b/docs/reference/resample_basis.html
@@ -1,5 +1,5 @@
-Resample a basis-set to match a mrs_data acquisition. — resample_basis • Spectroscopy Analysis Tools (spant) Resample a basis-set to match a mrs_data acquisition. — resample_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -116,7 +116,7 @@ Value
diff --git a/docs/reference/resample_img.html b/docs/reference/resample_img.html
index f1e7beaf..b0cc8f71 100644
--- a/docs/reference/resample_img.html
+++ b/docs/reference/resample_img.html
@@ -1,5 +1,5 @@
-Resample an image to match a target image space. — resample_img • Spectroscopy Analysis Tools (spant) Resample an image to match a target image space. — resample_img • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/resample_voi.html b/docs/reference/resample_voi.html
index 8fbfa836..a29ab096 100644
--- a/docs/reference/resample_voi.html
+++ b/docs/reference/resample_voi.html
@@ -1,7 +1,5 @@
-Resample a VOI to match a target image space using nearest-neighbour
-interpolation. — resample_voi • Spectroscopy Analysis Tools (spant) Resample a VOI to match a target image space using nearest-neighbour interpolation. — resample_voi • Spectroscopy Analysis Tools (spant) Reslice a nifti object to match the orientation of mrs data. — reslice_to_mrs • Spectroscopy Analysis Tools (spant) Reslice a nifti object to match the orientation of mrs data. — reslice_to_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/reson_table2mrs_data.html b/docs/reference/reson_table2mrs_data.html
index d75579ee..c5a2167a 100644
--- a/docs/reference/reson_table2mrs_data.html
+++ b/docs/reference/reson_table2mrs_data.html
@@ -1,5 +1,5 @@
-Generate mrs_data from a table of single Lorentzian resonances. — reson_table2mrs_data • Spectroscopy Analysis Tools (spant) Generate mrs_data from a table of single Lorentzian resonances. — reson_table2mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -119,7 +119,7 @@ Value
diff --git a/docs/reference/rm_dyns.html b/docs/reference/rm_dyns.html
index 5d5ef692..573e1f51 100644
--- a/docs/reference/rm_dyns.html
+++ b/docs/reference/rm_dyns.html
@@ -1,5 +1,5 @@
-Remove a subset of dynamic scans. — rm_dyns • Spectroscopy Analysis Tools (spant) Remove a subset of dynamic scans. — rm_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/scale_amp_molal.html b/docs/reference/scale_amp_molal.html
index aaeee1f2..7acb8cb0 100644
--- a/docs/reference/scale_amp_molal.html
+++ b/docs/reference/scale_amp_molal.html
@@ -1,7 +1,5 @@
-Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water). — scale_amp_molal • Spectroscopy Analysis Tools (spant) Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / kg of tissue water). — scale_amp_molal • Spectroscopy Analysis Tools (spant)
Spectroscopy Analysis Tools (spant)
- 2.21.0
+ 2.22.0
@@ -76,8 +74,7 @@
- Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water).
+ Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / kg of tissue water).
Source: R/amp_scaling.R
scale_amp_molal.Rd
@@ -163,7 +160,7 @@ Value
diff --git a/docs/reference/scale_amp_molal_pvc.html b/docs/reference/scale_amp_molal_pvc.html
index 962d6afc..4d194abd 100644
--- a/docs/reference/scale_amp_molal_pvc.html
+++ b/docs/reference/scale_amp_molal_pvc.html
@@ -1,7 +1,5 @@
-Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water). — scale_amp_molal_pvc • Spectroscopy Analysis Tools (spant)
@@ -75,8 +73,7 @@
- Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water).
+ Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / kg of tissue water).
Source: R/amp_scaling.R
scale_amp_molal_pvc.Rd
@@ -141,7 +138,7 @@ Value
diff --git a/docs/reference/scale_amp_molar.html b/docs/reference/scale_amp_molar.html
index 02358d91..dc87a338 100644
--- a/docs/reference/scale_amp_molar.html
+++ b/docs/reference/scale_amp_molar.html
@@ -1,7 +1,5 @@
-Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / Litre of tissue). — scale_amp_molar • Spectroscopy Analysis Tools (spant) Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / Litre of tissue). — scale_amp_molar • Spectroscopy Analysis Tools (spant) Convert default LCM/TARQUIN concentration scaling to molal units with partial
-volume correction. — scale_amp_molar2molal_pvc • Spectroscopy Analysis Tools (spant) Convert default LCM/TARQUIN concentration scaling to molal units with partial volume correction. — scale_amp_molar2molal_pvc • Spectroscopy Analysis Tools (spant) Scale fitted amplitudes to a ratio of signal amplitude. — scale_amp_ratio • Spectroscopy Analysis Tools (spant) Scale fitted amplitudes to a ratio of signal amplitude. — scale_amp_ratio • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -116,7 +116,7 @@ Value
diff --git a/docs/reference/scale_amp_ratio_value.html b/docs/reference/scale_amp_ratio_value.html
index 2036837a..6af8ac51 100644
--- a/docs/reference/scale_amp_ratio_value.html
+++ b/docs/reference/scale_amp_ratio_value.html
@@ -1,5 +1,5 @@
-Scale fitted amplitudes to a ratio of signal amplitude. — scale_amp_ratio_value • Spectroscopy Analysis Tools (spant) Scale fitted amplitudes to a ratio of signal amplitude. — scale_amp_ratio_value • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/scale_amp_water_ratio.html b/docs/reference/scale_amp_water_ratio.html
index 5b25e884..35a76b00 100644
--- a/docs/reference/scale_amp_water_ratio.html
+++ b/docs/reference/scale_amp_water_ratio.html
@@ -1,5 +1,5 @@
-Scale metabolite amplitudes as a ratio to the unsuppressed water amplitude. — scale_amp_water_ratio • Spectroscopy Analysis Tools (spant) Scale metabolite amplitudes as a ratio to the unsuppressed water amplitude. — scale_amp_water_ratio • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/scale_basis_amp.html b/docs/reference/scale_basis_amp.html
index 9401c3f1..5a58b5e5 100644
--- a/docs/reference/scale_basis_amp.html
+++ b/docs/reference/scale_basis_amp.html
@@ -1,5 +1,5 @@
-Scale a basis object by a scalar. — scale_basis_amp • Spectroscopy Analysis Tools (spant) Scale a basis object by a scalar. — scale_basis_amp • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/scale_basis_from_singlet.html b/docs/reference/scale_basis_from_singlet.html
index 0d542bc8..c9a19e77 100644
--- a/docs/reference/scale_basis_from_singlet.html
+++ b/docs/reference/scale_basis_from_singlet.html
@@ -1,5 +1,5 @@
-Scale a basis-set to be consistent with spant assumptions for water scaling. — scale_basis_from_singlet • Spectroscopy Analysis Tools (spant) Scale a basis-set to be consistent with spant assumptions for water scaling. — scale_basis_from_singlet • Spectroscopy Analysis Tools (spant)
Spectroscopy Analysis Tools (spant)
- 2.21.0
+ 2.22.0
@@ -127,7 +127,7 @@ Value
diff --git a/docs/reference/scale_mrs_amp.html b/docs/reference/scale_mrs_amp.html
index b5501a0d..990f058a 100644
--- a/docs/reference/scale_mrs_amp.html
+++ b/docs/reference/scale_mrs_amp.html
@@ -1,5 +1,5 @@
-Scale an mrs_data object by a scalar or vector or amplitudes. — scale_mrs_amp • Spectroscopy Analysis Tools (spant) Scale an mrs_data object by a scalar or vector or amplitudes. — scale_mrs_amp • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/scale_spec.html b/docs/reference/scale_spec.html
index 4f6ea835..6b3ddba4 100644
--- a/docs/reference/scale_spec.html
+++ b/docs/reference/scale_spec.html
@@ -1,5 +1,5 @@
-Scale mrs_data to a spectral region. — scale_spec • Spectroscopy Analysis Tools (spant) Scale mrs_data to a spectral region. — scale_spec • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -141,7 +141,7 @@ Value
diff --git a/docs/reference/sd.html b/docs/reference/sd.html
index ea1eec9f..3ae4dfd4 100644
--- a/docs/reference/sd.html
+++ b/docs/reference/sd.html
@@ -1,5 +1,5 @@
-Calculate the standard deviation spectrum from an mrs_data object. — sd • Spectroscopy Analysis Tools (spant) Calculate the standard deviation spectrum from an mrs_data object. — sd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/sd.mrs_data.html b/docs/reference/sd.mrs_data.html
index 3f92a49f..13bdda85 100644
--- a/docs/reference/sd.mrs_data.html
+++ b/docs/reference/sd.mrs_data.html
@@ -1,5 +1,5 @@
-Calculate the standard deviation spectrum from an mrs_data object. — sd.mrs_data • Spectroscopy Analysis Tools (spant) Calculate the standard deviation spectrum from an mrs_data object. — sd.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/seconds.html b/docs/reference/seconds.html
index b34d6627..467ee17f 100644
--- a/docs/reference/seconds.html
+++ b/docs/reference/seconds.html
@@ -1,5 +1,5 @@
-Return a time scale vector to match the FID of an MRS data object. — seconds • Spectroscopy Analysis Tools (spant) Return a time scale vector to match the FID of an MRS data object. — seconds • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/seq_cpmg_ideal.html b/docs/reference/seq_cpmg_ideal.html
index 547e96ab..45727c86 100644
--- a/docs/reference/seq_cpmg_ideal.html
+++ b/docs/reference/seq_cpmg_ideal.html
@@ -1,5 +1,5 @@
-CPMG style sequence with ideal pulses. — seq_cpmg_ideal • Spectroscopy Analysis Tools (spant) CPMG style sequence with ideal pulses. — seq_cpmg_ideal • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/seq_mega_press_ideal.html b/docs/reference/seq_mega_press_ideal.html
index 0769b8b4..a9cd7fa0 100644
--- a/docs/reference/seq_mega_press_ideal.html
+++ b/docs/reference/seq_mega_press_ideal.html
@@ -1,7 +1,5 @@
-MEGA-PRESS sequence with ideal localisation pulses and Gaussian shaped
-editing pulse. — seq_mega_press_ideal • Spectroscopy Analysis Tools (spant) MEGA-PRESS sequence with ideal localisation pulses and Gaussian shaped editing pulse. — seq_mega_press_ideal • Spectroscopy Analysis Tools (spant) PRESS sequence with shaped refocusing pulses. — seq_press_2d_shaped • Spectroscopy Analysis Tools (spant) PRESS sequence with shaped refocusing pulses. — seq_press_2d_shaped • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -165,7 +165,7 @@ Value
diff --git a/docs/reference/seq_press_ideal.html b/docs/reference/seq_press_ideal.html
index 8c976856..72c3af3d 100644
--- a/docs/reference/seq_press_ideal.html
+++ b/docs/reference/seq_press_ideal.html
@@ -1,5 +1,5 @@
-PRESS sequence with ideal pulses. — seq_press_ideal • Spectroscopy Analysis Tools (spant) PRESS sequence with ideal pulses. — seq_press_ideal • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/seq_pulse_acquire.html b/docs/reference/seq_pulse_acquire.html
index 4a88fc64..ad80571e 100644
--- a/docs/reference/seq_pulse_acquire.html
+++ b/docs/reference/seq_pulse_acquire.html
@@ -1,5 +1,5 @@
-Simple pulse and acquire sequence with ideal pulses. — seq_pulse_acquire • Spectroscopy Analysis Tools (spant) Simple pulse and acquire sequence with ideal pulses. — seq_pulse_acquire • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/seq_slaser_ideal.html b/docs/reference/seq_slaser_ideal.html
index 74688f4d..eb83e8e3 100644
--- a/docs/reference/seq_slaser_ideal.html
+++ b/docs/reference/seq_slaser_ideal.html
@@ -1,5 +1,5 @@
-sLASER sequence with ideal pulses. — seq_slaser_ideal • Spectroscopy Analysis Tools (spant) sLASER sequence with ideal pulses. — seq_slaser_ideal • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -126,7 +126,7 @@ Value
diff --git a/docs/reference/seq_spin_echo_ideal.html b/docs/reference/seq_spin_echo_ideal.html
index e23271de..4248716f 100644
--- a/docs/reference/seq_spin_echo_ideal.html
+++ b/docs/reference/seq_spin_echo_ideal.html
@@ -1,5 +1,5 @@
-Spin echo sequence with ideal pulses. — seq_spin_echo_ideal • Spectroscopy Analysis Tools (spant) Spin echo sequence with ideal pulses. — seq_spin_echo_ideal • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/seq_steam_ideal.html b/docs/reference/seq_steam_ideal.html
index a60685a8..1c8115d7 100644
--- a/docs/reference/seq_steam_ideal.html
+++ b/docs/reference/seq_steam_ideal.html
@@ -1,5 +1,5 @@
-STEAM sequence with ideal pulses. — seq_steam_ideal • Spectroscopy Analysis Tools (spant) STEAM sequence with ideal pulses. — seq_steam_ideal • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -128,7 +128,7 @@ Value
diff --git a/docs/reference/seq_steam_ideal_cof.html b/docs/reference/seq_steam_ideal_cof.html
index 8f225740..cba7af91 100644
--- a/docs/reference/seq_steam_ideal_cof.html
+++ b/docs/reference/seq_steam_ideal_cof.html
@@ -1,7 +1,5 @@
-STEAM sequence with ideal pulses and coherence order filtering to simulate
-gradient crushers. — seq_steam_ideal_cof • Spectroscopy Analysis Tools (spant) STEAM sequence with ideal pulses and coherence order filtering to simulate gradient crushers. — seq_steam_ideal_cof • Spectroscopy Analysis Tools (spant) STEAM sequence with ideal pulses using the z-rotation gradient simulation
-method described by Young et al JMR 140, 146-152 (1999). — seq_steam_ideal_young • Spectroscopy Analysis Tools (spant) STEAM sequence with ideal pulses using the z-rotation gradient simulation method described by Young et al JMR 140, 146-152 (1999). — seq_steam_ideal_young • Spectroscopy Analysis Tools (spant) Set the number of transients for an mrs_data object. — set_Ntrans • Spectroscopy Analysis Tools (spant) Set the number of transients for an mrs_data object. — set_Ntrans • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/set_def_acq_paras.html b/docs/reference/set_def_acq_paras.html
index 3e1b4004..cc2ada9c 100644
--- a/docs/reference/set_def_acq_paras.html
+++ b/docs/reference/set_def_acq_paras.html
@@ -1,5 +1,5 @@
-Set the default acquisition parameters. — set_def_acq_paras • Spectroscopy Analysis Tools (spant) Set the default acquisition parameters. — set_def_acq_paras • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Arguments
diff --git a/docs/reference/set_lcm_cmd.html b/docs/reference/set_lcm_cmd.html
index 2056ed01..42bb2f24 100644
--- a/docs/reference/set_lcm_cmd.html
+++ b/docs/reference/set_lcm_cmd.html
@@ -1,5 +1,5 @@
-Set the command to run the LCModel command-line program. — set_lcm_cmd • Spectroscopy Analysis Tools (spant) Set the command to run the LCModel command-line program. — set_lcm_cmd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/set_lw.html b/docs/reference/set_lw.html
index b64ec851..bb176c62 100644
--- a/docs/reference/set_lw.html
+++ b/docs/reference/set_lw.html
@@ -1,5 +1,5 @@
-Apply line-broadening to an mrs_data object to achieve a specified linewidth. — set_lw • Spectroscopy Analysis Tools (spant) Apply line-broadening to an mrs_data object to achieve a specified linewidth. — set_lw • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -123,7 +123,7 @@ Value
diff --git a/docs/reference/set_mask_xy_mat.html b/docs/reference/set_mask_xy_mat.html
index 49dc5d4e..52c4b617 100644
--- a/docs/reference/set_mask_xy_mat.html
+++ b/docs/reference/set_mask_xy_mat.html
@@ -1,5 +1,5 @@
-Set the masked voxels in a 2D MRSI dataset to given spectrum. — set_mask_xy_mat • Spectroscopy Analysis Tools (spant) Set the masked voxels in a 2D MRSI dataset to given spectrum. — set_mask_xy_mat • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Value
diff --git a/docs/reference/set_precomp_mode.html b/docs/reference/set_precomp_mode.html
index f44bd5d3..47c28e3b 100644
--- a/docs/reference/set_precomp_mode.html
+++ b/docs/reference/set_precomp_mode.html
@@ -1,5 +1,5 @@
-Set the precompute mode. — set_precomp_mode • Spectroscopy Analysis Tools (spant) Set the precompute mode. — set_precomp_mode • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/set_precomp_verbose.html b/docs/reference/set_precomp_verbose.html
index 1453a231..9c613505 100644
--- a/docs/reference/set_precomp_verbose.html
+++ b/docs/reference/set_precomp_verbose.html
@@ -1,5 +1,5 @@
-Set the verbosity of the precompute function. — set_precomp_verbose • Spectroscopy Analysis Tools (spant) Set the verbosity of the precompute function. — set_precomp_verbose • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/set_ref.html b/docs/reference/set_ref.html
index 8953fa50..5436dfa2 100644
--- a/docs/reference/set_ref.html
+++ b/docs/reference/set_ref.html
@@ -1,5 +1,5 @@
-Set the ppm reference value (eg ppm value at 0Hz). — set_ref • Spectroscopy Analysis Tools (spant) Set the ppm reference value (eg ppm value at 0Hz). — set_ref • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/set_td_pts.html b/docs/reference/set_td_pts.html
index 8a80d42a..586459ff 100644
--- a/docs/reference/set_td_pts.html
+++ b/docs/reference/set_td_pts.html
@@ -1,7 +1,5 @@
-Set the number of time-domain data points, truncating or zero-filling as
-appropriate. — set_td_pts • Spectroscopy Analysis Tools (spant) Set the number of time-domain data points, truncating or zero-filling as appropriate. — set_td_pts • Spectroscopy Analysis Tools (spant) Set the command to run the TARQUIN command-line program. — set_tqn_cmd • Spectroscopy Analysis Tools (spant) Set the command to run the TARQUIN command-line program. — set_tqn_cmd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/set_tr.html b/docs/reference/set_tr.html
index b2109ab0..65c9df5f 100644
--- a/docs/reference/set_tr.html
+++ b/docs/reference/set_tr.html
@@ -1,5 +1,5 @@
-Set the repetition time of an MRS dataset. — set_tr • Spectroscopy Analysis Tools (spant) Set the repetition time of an MRS dataset. — set_tr • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/shift.html b/docs/reference/shift.html
index ab0fe724..034591d0 100644
--- a/docs/reference/shift.html
+++ b/docs/reference/shift.html
@@ -1,5 +1,5 @@
-Apply a frequency shift to MRS data. — shift • Spectroscopy Analysis Tools (spant) Apply a frequency shift to MRS data. — shift • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/shift_basis.html b/docs/reference/shift_basis.html
index 2884be19..f55a65e0 100644
--- a/docs/reference/shift_basis.html
+++ b/docs/reference/shift_basis.html
@@ -1,5 +1,5 @@
-Apply frequency shifts to basis set signals. — shift_basis • Spectroscopy Analysis Tools (spant) Apply frequency shifts to basis set signals. — shift_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Value
diff --git a/docs/reference/sim_basis.html b/docs/reference/sim_basis.html
index c7838c46..bb5fefc6 100644
--- a/docs/reference/sim_basis.html
+++ b/docs/reference/sim_basis.html
@@ -1,5 +1,5 @@
-Simulate a basis set object. — sim_basis • Spectroscopy Analysis Tools (spant) Simulate a basis set object. — sim_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -136,7 +136,7 @@ Value
diff --git a/docs/reference/sim_basis_1h_brain.html b/docs/reference/sim_basis_1h_brain.html
index 62ed7389..f71ffa0b 100644
--- a/docs/reference/sim_basis_1h_brain.html
+++ b/docs/reference/sim_basis_1h_brain.html
@@ -1,7 +1,5 @@
-Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS
-sequence. Note, ideal pulses are assumed. — sim_basis_1h_brain • Spectroscopy Analysis Tools (spant) Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS sequence. Note, ideal pulses are assumed. — sim_basis_1h_brain • Spectroscopy Analysis Tools (spant) Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS
-sequence. Note, ideal pulses are assumed. — sim_basis_1h_brain_press • Spectroscopy Analysis Tools (spant) Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS sequence. Note, ideal pulses are assumed. — sim_basis_1h_brain_press • Spectroscopy Analysis Tools (spant) Simulate a macromolecular and lipid basis-set suitable for 1H brain MRS
-analysis. — sim_basis_mm_lip_lcm • Spectroscopy Analysis Tools (spant) Simulate a macromolecular and lipid basis-set suitable for 1H brain MRS analysis. — sim_basis_mm_lip_lcm • Spectroscopy Analysis Tools (spant) Simulate a basis file using TARQUIN. — sim_basis_tqn • Spectroscopy Analysis Tools (spant) Simulate a basis file using TARQUIN. — sim_basis_tqn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -129,7 +129,7 @@ Examples
diff --git a/docs/reference/sim_brain_1h.html b/docs/reference/sim_brain_1h.html
index 2044cf1a..717ee289 100644
--- a/docs/reference/sim_brain_1h.html
+++ b/docs/reference/sim_brain_1h.html
@@ -1,5 +1,5 @@
-Simulate MRS data with a similar appearance to normal brain (by default). — sim_brain_1h • Spectroscopy Analysis Tools (spant) Simulate MRS data with a similar appearance to normal brain (by default). — sim_brain_1h • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -159,7 +159,7 @@ Value
diff --git a/docs/reference/sim_mol.html b/docs/reference/sim_mol.html
index 23bcef50..77f76a50 100644
--- a/docs/reference/sim_mol.html
+++ b/docs/reference/sim_mol.html
@@ -1,5 +1,5 @@
-Simulate a mol_parameter object. — sim_mol • Spectroscopy Analysis Tools (spant) Simulate a mol_parameter object. — sim_mol • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -143,7 +143,7 @@ Value
diff --git a/docs/reference/sim_noise.html b/docs/reference/sim_noise.html
index 23875f79..a71477d4 100644
--- a/docs/reference/sim_noise.html
+++ b/docs/reference/sim_noise.html
@@ -1,5 +1,5 @@
-Simulate an mrs_data object containing simulated Gaussian noise. — sim_noise • Spectroscopy Analysis Tools (spant) Simulate an mrs_data object containing simulated Gaussian noise. — sim_noise • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -84,6 +84,7 @@ Simulate an mrs_data object containing simulated Gaussian noise.
ft = def_ft(),
N = def_N(),
ref = def_ref(),
+ nuc = def_nuc(),
dyns = 1,
fd = TRUE
)
@@ -111,6 +112,10 @@ Arguments
reference value for ppm scale.
nuc
+resonant nucleus.
dyns
number of dynamic scans to generate.
Value
diff --git a/docs/reference/sim_resonances.html b/docs/reference/sim_resonances.html
index 19e9a8a4..d4f8d7c0 100644
--- a/docs/reference/sim_resonances.html
+++ b/docs/reference/sim_resonances.html
@@ -1,5 +1,5 @@
-Simulate a MRS data object containing a set of simulated resonances. — sim_resonances • Spectroscopy Analysis Tools (spant) Simulate a MRS data object containing a set of simulated resonances. — sim_resonances • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -161,7 +161,7 @@ Examples
diff --git a/docs/reference/sim_th_excit_profile.html b/docs/reference/sim_th_excit_profile.html
index 5535c5ef..e781cab1 100644
--- a/docs/reference/sim_th_excit_profile.html
+++ b/docs/reference/sim_th_excit_profile.html
@@ -1,7 +1,5 @@
-Simulate an ideal pulse excitation profile by smoothing a top-hat function
-with a Gaussian. — sim_th_excit_profile • Spectroscopy Analysis Tools (spant) Simulate an ideal pulse excitation profile by smoothing a top-hat function with a Gaussian. — sim_th_excit_profile • Spectroscopy Analysis Tools (spant) Simulate an mrs_data object containing complex zero valued samples. — sim_zero • Spectroscopy Analysis Tools (spant) Simulate an mrs_data object containing complex zero valued samples. — sim_zero • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -78,7 +78,14 @@ Simulate an mrs_data object containing complex zero valued samples.
-
+
@@ -99,6 +106,10 @@ Arguments
reference value for ppm scale.
nuc
+resonant nucleus.
dyns
number of dynamic scans to generate.
Value
diff --git a/docs/reference/smooth_dyns.html b/docs/reference/smooth_dyns.html
index 4cc8da50..accf3a51 100644
--- a/docs/reference/smooth_dyns.html
+++ b/docs/reference/smooth_dyns.html
@@ -1,5 +1,5 @@
-Smooth data across the dynamic dimension with a Gaussian kernel. — smooth_dyns • Spectroscopy Analysis Tools (spant) Smooth data across the dynamic dimension with a Gaussian kernel. — smooth_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/sort_basis.html b/docs/reference/sort_basis.html
index 6a676ea2..d25cc006 100644
--- a/docs/reference/sort_basis.html
+++ b/docs/reference/sort_basis.html
@@ -1,5 +1,5 @@
-Sort the basis-set elements alphabetically. — sort_basis • Spectroscopy Analysis Tools (spant) Sort the basis-set elements alphabetically. — sort_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/spant-package.html b/docs/reference/spant-package.html
index b3dd8e21..90f19ec3 100644
--- a/docs/reference/spant-package.html
+++ b/docs/reference/spant-package.html
@@ -1,5 +1,5 @@
-spant: spectroscopy analysis tools. — spant-package • Spectroscopy Analysis Tools (spant) spant: spectroscopy analysis tools. — spant-package • Spectroscopy Analysis Tools (spant) Simulate and fit some spectra with ABfit for benchmarking purposes. Basic
-timing and performance metrics will be printed. — spant_abfit_benchmark • Spectroscopy Analysis Tools (spant) Simulate and fit some spectra with ABfit for benchmarking purposes. Basic timing and performance metrics will be printed. — spant_abfit_benchmark • Spectroscopy Analysis Tools (spant) Example MEGA-PRESS data with significant B0 drift. — spant_mpress_drift • Spectroscopy Analysis Tools (spant) Example MEGA-PRESS data with significant B0 drift. — spant_mpress_drift • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -83,7 +83,7 @@ Example MEGA-PRESS data with significant B0 drift.
Format
- An object of class mrs_data of length 13.
+ An object of class mrs_data of dimension 1 x 1 x 1 x 1 x 40 x 1 x 1024.
@@ -98,7 +98,7 @@ Format
diff --git a/docs/reference/spant_sim_fmrs_dataset.html b/docs/reference/spant_sim_fmrs_dataset.html
new file mode 100644
index 00000000..00e48b56
--- /dev/null
+++ b/docs/reference/spant_sim_fmrs_dataset.html
@@ -0,0 +1,117 @@
+
+Simulate an example fMRS dataset for a block design fMRS experiment and export a BIDS structure. — spant_sim_fmrs_dataset • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Simulate an example fMRS dataset for a block design fMRS experiment and export a BIDS structure.
+ Source: R/fmrs.R
+ spant_sim_fmrs_dataset.Rd
+
+
+
+ Simulate an example fMRS dataset for a block design fMRS experiment and
+export a BIDS structure.
+
+
+
+ spant_sim_fmrs_dataset(output_dir = NULL)
+
+
+
+ Arguments
+ - output_dir
+output directory for the BIDS data. Defaults to :
+"HOME/sim_fmrs_dataset/data".
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/spant_simulation_benchmark.html b/docs/reference/spant_simulation_benchmark.html
index 32daa8bf..d8cc6841 100644
--- a/docs/reference/spant_simulation_benchmark.html
+++ b/docs/reference/spant_simulation_benchmark.html
@@ -1,7 +1,5 @@
-Simulate a typical metabolite basis set for benchmarking. Timing metrics will
-be printed on completion. — spant_simulation_benchmark • Spectroscopy Analysis Tools (spant) Simulate a typical metabolite basis set for benchmarking. Timing metrics will be printed on completion. — spant_simulation_benchmark • Spectroscopy Analysis Tools (spant) Decompose an mrs_data object into white and gray matter spectra. — spec_decomp • Spectroscopy Analysis Tools (spant) Perform a mathematical operation on a spectral region. — spec_op • Spectroscopy Analysis Tools (spant) Perform a mathematical operation on a spectral region. — spec_op • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -98,8 +98,8 @@ Arguments
operator
-can be "sum" (default), "mean", "l2", "max", "min" or
-"max-min".
can be "sum" (default), "mean", "l2", "max", "max_cplx,
+"min" or "max-min".
freq_scale
@@ -129,7 +129,7 @@ Value
diff --git a/docs/reference/spin_sys.html b/docs/reference/spin_sys.html
index 853423a4..1eaa9e76 100644
--- a/docs/reference/spin_sys.html
+++ b/docs/reference/spin_sys.html
@@ -1,5 +1,5 @@
-Create a spin system object for pulse sequence simulation. — spin_sys • Spectroscopy Analysis Tools (spant) Create a spin system object for pulse sequence simulation. — spin_sys • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/spm_pve2categorical.html b/docs/reference/spm_pve2categorical.html
index 23a1bad9..70f10729 100644
--- a/docs/reference/spm_pve2categorical.html
+++ b/docs/reference/spm_pve2categorical.html
@@ -1,7 +1,5 @@
-Convert SPM style segmentation files to a single categorical image where
-the numerical values map as: 0) Other, 1) CSF, 2) GM and 3) WM. — spm_pve2categorical • Spectroscopy Analysis Tools (spant) Convert SPM style segmentation files to a single categorical image where the numerical values map as: 0) Other, 1) CSF, 2) GM and 3) WM. — spm_pve2categorical • Spectroscopy Analysis Tools (spant) Signal space projection method for lipid suppression. — ssp • Spectroscopy Analysis Tools (spant) Signal space projection method for lipid suppression. — ssp • Spectroscopy Analysis Tools (spant) Plot the fitting results of an object of class fit_result with
-individual basis set components shown. — stackplot.fit_result • Spectroscopy Analysis Tools (spant) Plot the fitting results of an object of class fit_result with individual basis set components shown. — stackplot.fit_result • Spectroscopy Analysis Tools (spant) Produce a plot with multiple traces. — stackplot • Spectroscopy Analysis Tools (spant) Produce a plot with multiple traces. — stackplot • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/stackplot.mrs_data.html b/docs/reference/stackplot.mrs_data.html
index 17ff5648..64eea445 100644
--- a/docs/reference/stackplot.mrs_data.html
+++ b/docs/reference/stackplot.mrs_data.html
@@ -1,5 +1,5 @@
-Stackplot plotting method for objects of class mrs_data. — stackplot.mrs_data • Spectroscopy Analysis Tools (spant) Stackplot plotting method for objects of class mrs_data. — stackplot.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -255,7 +255,7 @@ Arguments
diff --git a/docs/reference/sub_first_dyn.html b/docs/reference/sub_first_dyn.html
index dbd7f831..493b7242 100644
--- a/docs/reference/sub_first_dyn.html
+++ b/docs/reference/sub_first_dyn.html
@@ -1,5 +1,5 @@
-Subtract the first dynamic spectrum from a dynamic series. — sub_first_dyn • Spectroscopy Analysis Tools (spant) Subtract the first dynamic spectrum from a dynamic series. — sub_first_dyn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/sub_mean_dyns.html b/docs/reference/sub_mean_dyns.html
index 6e3bb2df..221bd0c1 100644
--- a/docs/reference/sub_mean_dyns.html
+++ b/docs/reference/sub_mean_dyns.html
@@ -1,5 +1,5 @@
-Subtract the mean dynamic spectrum from a dynamic series. — sub_mean_dyns • Spectroscopy Analysis Tools (spant) Subtract the mean dynamic spectrum from a dynamic series. — sub_mean_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/sub_median_dyns.html b/docs/reference/sub_median_dyns.html
index 134c495d..1e834f14 100644
--- a/docs/reference/sub_median_dyns.html
+++ b/docs/reference/sub_median_dyns.html
@@ -1,5 +1,5 @@
-Subtract the median dynamic spectrum from a dynamic series. — sub_median_dyns • Spectroscopy Analysis Tools (spant) Subtract the median dynamic spectrum from a dynamic series. — sub_median_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/sum_coils.html b/docs/reference/sum_coils.html
index 7bf559f2..e1ab3cc0 100644
--- a/docs/reference/sum_coils.html
+++ b/docs/reference/sum_coils.html
@@ -1,5 +1,5 @@
-Calculate the sum across receiver coil elements. — sum_coils • Spectroscopy Analysis Tools (spant) Calculate the sum across receiver coil elements. — sum_coils • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/sum_dyns.html b/docs/reference/sum_dyns.html
index a0be19d3..bbda2ffc 100644
--- a/docs/reference/sum_dyns.html
+++ b/docs/reference/sum_dyns.html
@@ -1,5 +1,5 @@
-Calculate the sum of data dynamics. — sum_dyns • Spectroscopy Analysis Tools (spant) Calculate the sum of data dynamics. — sum_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/sum_mrs.html b/docs/reference/sum_mrs.html
index a22f215b..3cc3ab9e 100644
--- a/docs/reference/sum_mrs.html
+++ b/docs/reference/sum_mrs.html
@@ -1,5 +1,5 @@
-Sum two mrs_data objects. — sum_mrs • Spectroscopy Analysis Tools (spant) Sum two mrs_data objects. — sum_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Value
diff --git a/docs/reference/sum_mrs_list.html b/docs/reference/sum_mrs_list.html
index f4e09aea..c3584348 100644
--- a/docs/reference/sum_mrs_list.html
+++ b/docs/reference/sum_mrs_list.html
@@ -1,5 +1,5 @@
-Return the sum of a list of mrs_data objects. — sum_mrs_list • Spectroscopy Analysis Tools (spant) Return the sum of a list of mrs_data objects. — sum_mrs_list • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/svs_1h_brain_analysis.html b/docs/reference/svs_1h_brain_analysis.html
index 8ce514db..dff0ef7d 100644
--- a/docs/reference/svs_1h_brain_analysis.html
+++ b/docs/reference/svs_1h_brain_analysis.html
@@ -1,5 +1,5 @@
-Standard SVS 1H brain analysis pipeline. — svs_1h_brain_analysis • Spectroscopy Analysis Tools (spant) Standard SVS 1H brain analysis pipeline. — svs_1h_brain_analysis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -199,7 +199,7 @@ Value
diff --git a/docs/reference/svs_1h_brain_analysis_dev.html b/docs/reference/svs_1h_brain_analysis_dev.html
index d70a14d3..d71bfea2 100644
--- a/docs/reference/svs_1h_brain_analysis_dev.html
+++ b/docs/reference/svs_1h_brain_analysis_dev.html
@@ -1,5 +1,5 @@
-Standard SVS 1H brain analysis pipeline. — svs_1h_brain_analysis_dev • Spectroscopy Analysis Tools (spant) Standard SVS 1H brain analysis pipeline. — svs_1h_brain_analysis_dev • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -193,7 +193,7 @@ Examples
diff --git a/docs/reference/svs_1h_brain_batch_analysis.html b/docs/reference/svs_1h_brain_batch_analysis.html
index 5631e8cc..15f7223e 100644
--- a/docs/reference/svs_1h_brain_batch_analysis.html
+++ b/docs/reference/svs_1h_brain_batch_analysis.html
@@ -1,5 +1,5 @@
-Batch interface to the standard SVS 1H brain analysis pipeline. — svs_1h_brain_batch_analysis • Spectroscopy Analysis Tools (spant) Batch interface to the standard SVS 1H brain analysis pipeline. — svs_1h_brain_batch_analysis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -144,7 +144,7 @@ Value
diff --git a/docs/reference/t_test_spec.html b/docs/reference/t_test_spec.html
new file mode 100644
index 00000000..56a7ea1b
--- /dev/null
+++ b/docs/reference/t_test_spec.html
@@ -0,0 +1,124 @@
+
+Perform a t-test on spectral data points. — t_test_spec • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+
+
+ Perform a t-test on spectral data points.
+
+
+
+ t_test_spec(mrs_data, group)
+
+
+
+ Arguments
+ - mrs_data
+an mrs_data object with spectra in the dynamic dimension.
- group
+vector describing the group membership of each dynamic spectrum.
+
+ Value
+
+
+a list of statistical results.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/td2fd.html b/docs/reference/td2fd.html
index 6748a6a8..f31ed524 100644
--- a/docs/reference/td2fd.html
+++ b/docs/reference/td2fd.html
@@ -1,5 +1,5 @@
-Transform time-domain data to the frequency-domain. — td2fd • Spectroscopy Analysis Tools (spant) Transform time-domain data to the frequency-domain. — td2fd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/td_conv_filt.html b/docs/reference/td_conv_filt.html
index a9f340c3..106b9b00 100644
--- a/docs/reference/td_conv_filt.html
+++ b/docs/reference/td_conv_filt.html
@@ -1,5 +1,5 @@
-Time-domain convolution based filter. — td_conv_filt • Spectroscopy Analysis Tools (spant) Time-domain convolution based filter. — td_conv_filt • Spectroscopy Analysis Tools (spant) Time-domain spectral registration. — tdsr • Spectroscopy Analysis Tools (spant) Time-domain spectral registration. — tdsr • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -121,7 +121,7 @@ Value
diff --git a/docs/reference/te.html b/docs/reference/te.html
index 010361b1..4a65711d 100644
--- a/docs/reference/te.html
+++ b/docs/reference/te.html
@@ -1,5 +1,5 @@
-Return the echo time of an MRS dataset. — te • Spectroscopy Analysis Tools (spant) Return the echo time of an MRS dataset. — te • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/tr.html b/docs/reference/tr.html
index 0c0bd63b..2e749e02 100644
--- a/docs/reference/tr.html
+++ b/docs/reference/tr.html
@@ -1,5 +1,5 @@
-Return the repetition time of an MRS dataset. — tr • Spectroscopy Analysis Tools (spant) Return the repetition time of an MRS dataset. — tr • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/varpro_3_para_opts.html b/docs/reference/varpro_3_para_opts.html
index c2270a16..52d7cd84 100644
--- a/docs/reference/varpro_3_para_opts.html
+++ b/docs/reference/varpro_3_para_opts.html
@@ -1,5 +1,5 @@
-Return a list of options for VARPRO based fitting with 3 free parameters. — varpro_3_para_opts • Spectroscopy Analysis Tools (spant) Return a list of options for VARPRO based fitting with 3 free parameters. — varpro_3_para_opts • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -141,7 +141,7 @@ Value
diff --git a/docs/reference/varpro_basic_opts.html b/docs/reference/varpro_basic_opts.html
index 32c86d22..c5104891 100644
--- a/docs/reference/varpro_basic_opts.html
+++ b/docs/reference/varpro_basic_opts.html
@@ -1,5 +1,5 @@
-Return a list of options for a basic VARPRO analysis. — varpro_basic_opts • Spectroscopy Analysis Tools (spant) Return a list of options for a basic VARPRO analysis. — varpro_basic_opts • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -118,7 +118,7 @@ Value
diff --git a/docs/reference/varpro_opts.html b/docs/reference/varpro_opts.html
index 2aabf11d..6332f730 100644
--- a/docs/reference/varpro_opts.html
+++ b/docs/reference/varpro_opts.html
@@ -1,5 +1,5 @@
-Return a list of options for VARPRO based fitting. — varpro_opts • Spectroscopy Analysis Tools (spant) Return a list of options for VARPRO based fitting. — varpro_opts • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -177,7 +177,7 @@ Examples
diff --git a/docs/reference/vec2mrs_data.html b/docs/reference/vec2mrs_data.html
index 0cccd73b..f0d58bf0 100644
--- a/docs/reference/vec2mrs_data.html
+++ b/docs/reference/vec2mrs_data.html
@@ -1,5 +1,5 @@
-Convert a vector into a mrs_data object. — vec2mrs_data • Spectroscopy Analysis Tools (spant) Convert a vector into a mrs_data object. — vec2mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -80,10 +80,11 @@ Convert a vector into a mrs_data object.
vec2mrs_data(
vec,
- fs = def_fs(),
- ft = def_ft(),
- ref = def_ref(),
- nuc = def_nuc(),
+ mrs_data = NULL,
+ fs = NULL,
+ ft = NULL,
+ ref = NULL,
+ nuc = NULL,
dyns = 1,
fd = FALSE
)
@@ -95,6 +96,10 @@ Arguments
the data vector.
mrs_data
+example data to copy acquisition parameters from.
fs
sampling frequency in Hz.
Arguments
fd
-flag to indicate if the matrix is in the frequency domain (logical).
flag to indicate if the vector is in the frequency domain (logical).
Value
diff --git a/docs/reference/write_basis.html b/docs/reference/write_basis.html
index b6e27cbd..94c5e021 100644
--- a/docs/reference/write_basis.html
+++ b/docs/reference/write_basis.html
@@ -1,5 +1,5 @@
-Write a basis object to an LCModel .basis formatted file. — write_basis • Spectroscopy Analysis Tools (spant) Write a basis object to an LCModel .basis formatted file. — write_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -108,7 +108,7 @@ Arguments
diff --git a/docs/reference/write_basis_tqn.html b/docs/reference/write_basis_tqn.html
index 6aa51c1d..116c73ec 100644
--- a/docs/reference/write_basis_tqn.html
+++ b/docs/reference/write_basis_tqn.html
@@ -1,5 +1,5 @@
-Generate a basis file using TARQUIN. — write_basis_tqn • Spectroscopy Analysis Tools (spant) Generate a basis file using TARQUIN. — write_basis_tqn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Examples
diff --git a/docs/reference/write_mrs.html b/docs/reference/write_mrs.html
index fff25f15..124b9dc4 100644
--- a/docs/reference/write_mrs.html
+++ b/docs/reference/write_mrs.html
@@ -1,5 +1,5 @@
-Write MRS data object to file. — write_mrs • Spectroscopy Analysis Tools (spant) Write MRS data object to file. — write_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Arguments
diff --git a/docs/reference/write_mrs_nifti.html b/docs/reference/write_mrs_nifti.html
index f4bf1921..bd3ed4b7 100644
--- a/docs/reference/write_mrs_nifti.html
+++ b/docs/reference/write_mrs_nifti.html
@@ -1,5 +1,5 @@
-Write MRS data object to file in NIFTI format. — write_mrs_nifti • Spectroscopy Analysis Tools (spant) Write MRS data object to file in NIFTI format. — write_mrs_nifti • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/write_pulse_ascii.html b/docs/reference/write_pulse_ascii.html
index 067ae086..221f8ebb 100644
--- a/docs/reference/write_pulse_ascii.html
+++ b/docs/reference/write_pulse_ascii.html
@@ -1,5 +1,5 @@
-Write an ASCII formatted pulse file. — write_pulse_ascii • Spectroscopy Analysis Tools (spant) Write an ASCII formatted pulse file. — write_pulse_ascii • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/zero_fade_spec.html b/docs/reference/zero_fade_spec.html
index c703745c..c8b572c3 100644
--- a/docs/reference/zero_fade_spec.html
+++ b/docs/reference/zero_fade_spec.html
@@ -1,7 +1,5 @@
-Fade a spectrum to zero by frequency domain multiplication with a tanh
-function. Note this operation distorts data points at the end of the FID. — zero_fade_spec • Spectroscopy Analysis Tools (spant) Fade a spectrum to zero by frequency domain multiplication with a tanh function. Note this operation distorts data points at the end of the FID. — zero_fade_spec • Spectroscopy Analysis Tools (spant) Zero all coherences including and above a given order. — zero_higher_orders • Spectroscopy Analysis Tools (spant) Zero all coherences including and above a given order. — zero_higher_orders • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Value
diff --git a/docs/reference/zero_td_pts_end.html b/docs/reference/zero_td_pts_end.html
index 8c1123c8..71d24ebb 100644
--- a/docs/reference/zero_td_pts_end.html
+++ b/docs/reference/zero_td_pts_end.html
@@ -1,5 +1,5 @@
-Set mrs_data object data points at the end of the FID to zero. — zero_td_pts_end • Spectroscopy Analysis Tools (spant) Set mrs_data object data points at the end of the FID to zero. — zero_td_pts_end • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/zf.html b/docs/reference/zf.html
index 85e2013c..baf50256 100644
--- a/docs/reference/zf.html
+++ b/docs/reference/zf.html
@@ -1,5 +1,5 @@
-Zero-fill MRS data in the time domain. — zf • Spectroscopy Analysis Tools (spant) Zero-fill MRS data in the time domain. — zf • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -125,7 +125,7 @@ Value
diff --git a/docs/reference/zf_xy.html b/docs/reference/zf_xy.html
index ebca3999..c4104a74 100644
--- a/docs/reference/zf_xy.html
+++ b/docs/reference/zf_xy.html
@@ -1,5 +1,5 @@
-Zero-fill MRSI data in the k-space x-y direction. — zf_xy • Spectroscopy Analysis Tools (spant) Zero-fill MRSI data in the k-space x-y direction. — zf_xy • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -113,7 +113,7 @@ Value
diff --git a/docs/sitemap.xml b/docs/sitemap.xml
index e2139f71..4c39f515 100644
--- a/docs/sitemap.xml
+++ b/docs/sitemap.xml
@@ -216,6 +216,12 @@
https://martin3141.github.io/spant/reference/comb_coils_fp_pc.html
+
+ https://martin3141.github.io/spant/reference/comb_coils_mrsi_gls.html
+
+
+ https://martin3141.github.io/spant/reference/comb_coils_svs_gls.html
+
https://martin3141.github.io/spant/reference/comb_csv_results.html
@@ -411,6 +417,9 @@
https://martin3141.github.io/spant/reference/gen_conv_reg.html
+
+ https://martin3141.github.io/spant/reference/gen_group_reg.html
+
https://martin3141.github.io/spant/reference/gen_impulse_reg.html
@@ -555,6 +564,15 @@
https://martin3141.github.io/spant/reference/glm_spec.html
+
+ https://martin3141.github.io/spant/reference/glm_spec_fmrs_fl.html
+
+
+ https://martin3141.github.io/spant/reference/glm_spec_fmrs_group.html
+
+
+ https://martin3141.github.io/spant/reference/glm_spec_group_linhyp.html
+
https://martin3141.github.io/spant/reference/grid_shift_xy.html
@@ -690,9 +708,15 @@
https://martin3141.github.io/spant/reference/mrs_data2basis.html
+
+ https://martin3141.github.io/spant/reference/mrs_data2bids.html
+
https://martin3141.github.io/spant/reference/mrs_data2mat.html
+
+ https://martin3141.github.io/spant/reference/mrs_data2spec_mat.html
+
https://martin3141.github.io/spant/reference/mrs_data2vec.html
@@ -741,6 +765,9 @@
https://martin3141.github.io/spant/reference/phase.html
+
+ https://martin3141.github.io/spant/reference/phase_ref_1h_brain.html
+
https://martin3141.github.io/spant/reference/plot.fit_result.html
@@ -780,6 +807,12 @@
https://martin3141.github.io/spant/reference/precomp.html
+
+ https://martin3141.github.io/spant/reference/preproc_svs.html
+
+
+ https://martin3141.github.io/spant/reference/preproc_svs_dataset.html
+
https://martin3141.github.io/spant/reference/print.fit_result.html
@@ -1050,6 +1083,9 @@
https://martin3141.github.io/spant/reference/spant_mpress_drift.html
+
+ https://martin3141.github.io/spant/reference/spant_sim_fmrs_dataset.html
+
https://martin3141.github.io/spant/reference/spant_simulation_benchmark.html
@@ -1107,6 +1143,9 @@
https://martin3141.github.io/spant/reference/svs_1h_brain_batch_analysis.html
+
+ https://martin3141.github.io/spant/reference/t_test_spec.html
+
https://martin3141.github.io/spant/reference/td2fd.html
Check if the chemical shift dimension of an MRS data object is in the -frequency domain.
Check if the chemical shift dimension of an MRS data object is in the frequency domain.
All functions
- Covert a linewidth in Hz to an equivalent alpha value in the time-domain ie:
-x * exp(-t * alpha).
Covert a linewidth in Hz to an equivalent alpha value in the time-domain ie: x * exp(-t * alpha).
- Covert a linewidth in Hz to an equivalent beta value in the time-domain ie:
-x * exp(-t * t * beta).
Covert a linewidth in Hz to an equivalent beta value in the time-domain ie: x * exp(-t * t * beta).
- Make a basis-set object from a directory containing LCModel formatted RAW
-files.
Make a basis-set object from a directory containing LCModel formatted RAW files.
@@ -851,8 +838,7 @@ All functions
- Mask the voxels outside an elliptical region spanning the MRSI dataset in the
-x-y plane.
Mask the voxels outside an elliptical region spanning the MRSI dataset in the x-y plane.
@@ -860,13 +846,11 @@ All functions
- Convert a matrix (with spectral points in the column dimension and dynamics
-in the row dimensions) into a mrs_data object.
Convert a matrix (with spectral points in the column dimension and dynamics in the row dimensions) into a mrs_data object.
- Matrix exponential function taken from complexplus package to reduce the
-number of spant dependencies.
Matrix exponential function taken from complexplus package to reduce the number of spant dependencies.
@@ -914,31 +898,31 @@ All functions
- Convert an mrs_data object to basis object - where basis signals are spread
-across the dynamic dimension in the MRS data.
Convert an mrs_data object to basis object - where basis signals are spread across the dynamic dimension in the MRS data.
+
+
+ Create a BIDS file structure from a vector of MRS data paths or list of mrs_data objects.
- Convert mrs_data object to a matrix, with spectral points in the column
-dimension and dynamics in the row dimension.
Convert mrs_data object to a matrix, with spectral points in the column dimension and dynamics in the row dimension.
-
+
- Convert mrs_data object to a vector.
Convert mrs_data object to a matrix, with spectral points in the column dimension and dynamics in the row dimension.
-
+
- Create a BIDS directory and file structure from a list of mrs_data objects.
Convert mrs_data object to a vector.
- Perform a fftshift on a matrix, with each column replaced by its shifted
-result.
Perform a fftshift on a matrix, with each column replaced by its shifted result.
- Perform an ifftshift on a matrix, with each column replaced by its shifted
-result.
Perform an ifftshift on a matrix, with each column replaced by its shifted result.
@@ -946,9 +930,7 @@ All functions
- Flip the x data dimension order of a nifti image. This corresponds to
-flipping MRI data in the left-right direction, assuming the data in save in
-neurological format (can check with fslorient program).
Flip the x data dimension order of a nifti image. This corresponds to flipping MRI data in the left-right direction, assuming the data in save in neurological format (can check with fslorient program).
@@ -964,8 +946,7 @@ All functions
- Search for the highest peak in a spectral region and return the frequency,
-height and FWHM.
Search for the highest peak in a spectral region and return the frequency, height and FWHM.
@@ -974,6 +955,10 @@ All functions phase()
Apply phasing parameters to MRS data.
+
+
+ Corrected zero order phase and chemical shift offset in 1H MRS data from the brain.
@@ -1005,8 +990,7 @@ All functions
- Plot an interactive slice map from a data array where voxels can be selected
-to display a corresponding spectrum.
Plot an interactive slice map from a data array where voxels can be selected to display a corresponding spectrum.
@@ -1026,8 +1010,15 @@ All functions
- Save function results to file and load on subsequent calls to avoid repeat
-computation.
Save function results to file and load on subsequent calls to avoid repeat computation.
+
+
+ Preprocess and perform quality assessment of a single SVS data set.
+
+
+ Preprocess and perform quality assessment of one or more SVS data sets.
@@ -1055,15 +1046,11 @@ All functions
- Read a directory containing Siemens MRS IMA files and combine along the coil
-dimension. Note that the coil ID is inferred from the sorted file name and
-should be checked when consistency is required between two directories.
Read a directory containing Siemens MRS IMA files and combine along the coil dimension. Note that the coil ID is inferred from the sorted file name and should be checked when consistency is required between two directories.
- Read a directory containing Siemens MRS IMA files and combine along the
-dynamic dimension. Note that the coil ID is inferred from the sorted file
-name and should be checked when consistency is required.
Read a directory containing Siemens MRS IMA files and combine along the dynamic dimension. Note that the coil ID is inferred from the sorted file name and should be checked when consistency is required.
@@ -1103,13 +1090,11 @@ All functions
- Reconstruct complex time-domain data from the real part of frequency-domain
-data.
Reconstruct complex time-domain data from the real part of frequency-domain data.
- Reconstruct complex time-domain data from the real part of frequency-domain
-data.
Reconstruct complex time-domain data from the real part of frequency-domain data.
@@ -1141,8 +1126,7 @@ All functions
- Resample a VOI to match a target image space using nearest-neighbour
-interpolation.
Resample a VOI to match a target image space using nearest-neighbour interpolation.
@@ -1158,23 +1142,19 @@ All functions
- Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water).
Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / kg of tissue water).
- Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water).
Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / kg of tissue water).
- Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / Litre of tissue).
Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / Litre of tissue).
- Convert default LCM/TARQUIN concentration scaling to molal units with partial
-volume correction.
Convert default LCM/TARQUIN concentration scaling to molal units with partial volume correction.
@@ -1222,8 +1202,7 @@ All functions
- MEGA-PRESS sequence with ideal localisation pulses and Gaussian shaped
-editing pulse.
MEGA-PRESS sequence with ideal localisation pulses and Gaussian shaped editing pulse.
@@ -1251,13 +1230,11 @@ All functions
- STEAM sequence with ideal pulses and coherence order filtering to simulate
-gradient crushers.
STEAM sequence with ideal pulses and coherence order filtering to simulate gradient crushers.
- STEAM sequence with ideal pulses using the z-rotation gradient simulation
-method described by Young et al JMR 140, 146-152 (1999).
STEAM sequence with ideal pulses using the z-rotation gradient simulation method described by Young et al JMR 140, 146-152 (1999).
@@ -1293,8 +1270,7 @@ All functions
- Set the number of time-domain data points, truncating or zero-filling as
-appropriate.
Set the number of time-domain data points, truncating or zero-filling as appropriate.
@@ -1318,18 +1294,15 @@ All functions
- Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS
-sequence. Note, ideal pulses are assumed.
Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS sequence. Note, ideal pulses are assumed.
- Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS
-sequence. Note, ideal pulses are assumed.
Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS sequence. Note, ideal pulses are assumed.
- Simulate a macromolecular and lipid basis-set suitable for 1H brain MRS
-analysis.
Simulate a macromolecular and lipid basis-set suitable for 1H brain MRS analysis.
@@ -1353,8 +1326,7 @@ All functions
- Simulate an ideal pulse excitation profile by smoothing a top-hat function
-with a Gaussian.
Simulate an ideal pulse excitation profile by smoothing a top-hat function with a Gaussian.
@@ -1374,17 +1346,19 @@ All functions
- Simulate and fit some spectra with ABfit for benchmarking purposes. Basic
-timing and performance metrics will be printed.
Simulate and fit some spectra with ABfit for benchmarking purposes. Basic timing and performance metrics will be printed.
Example MEGA-PRESS data with significant B0 drift.
+
+
+ Simulate an example fMRS dataset for a block design fMRS experiment and export a BIDS structure.
- Simulate a typical metabolite basis set for benchmarking. Timing metrics will
-be printed on completion.
Simulate a typical metabolite basis set for benchmarking. Timing metrics will be printed on completion.
@@ -1400,8 +1374,7 @@ All functions
- Convert SPM style segmentation files to a single categorical image where
-the numerical values map as: 0) Other, 1) CSF, 2) GM and 3) WM.
Convert SPM style segmentation files to a single categorical image where the numerical values map as: 0) Other, 1) CSF, 2) GM and 3) WM.
@@ -1413,8 +1386,7 @@ All functions
- Plot the fitting results of an object of class fit_result with
-individual basis set components shown.
Plot the fitting results of an object of class fit_result with individual basis set components shown.
@@ -1459,6 +1431,10 @@ All functions svs_1h_brain_batch_analysis()
Batch interface to the standard SVS 1H brain analysis pipeline.
+
+
+ Perform a t-test on spectral data points.
@@ -1518,8 +1494,7 @@ All functions
- Fade a spectrum to zero by frequency domain multiplication with a tanh
-function. Note this operation distorts data points at the end of the FID.
Fade a spectrum to zero by frequency domain multiplication with a tanh function. Note this operation distorts data points at the end of the FID.
@@ -1549,7 +1524,7 @@ All functions
diff --git a/docs/reference/int_spec.html b/docs/reference/int_spec.html
index c7060fe7..783325a8 100644
--- a/docs/reference/int_spec.html
+++ b/docs/reference/int_spec.html
@@ -1,5 +1,5 @@
-Integrate a spectral region. — int_spec • Spectroscopy Analysis Tools (spant) Integrate a spectral region. — int_spec • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -118,7 +118,7 @@ Value
diff --git a/docs/reference/interleave_dyns.html b/docs/reference/interleave_dyns.html
index effe5543..441eff27 100644
--- a/docs/reference/interleave_dyns.html
+++ b/docs/reference/interleave_dyns.html
@@ -1,5 +1,5 @@
-Interleave the first and second half of a dynamic series. — interleave_dyns • Spectroscopy Analysis Tools (spant) Interleave the first and second half of a dynamic series. — interleave_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/inv_even_dyns.html b/docs/reference/inv_even_dyns.html
index 9f9d4fff..dcb781dc 100644
--- a/docs/reference/inv_even_dyns.html
+++ b/docs/reference/inv_even_dyns.html
@@ -1,5 +1,5 @@
-Invert even numbered dynamic scans starting from 1 (2,4,6...). — inv_even_dyns • Spectroscopy Analysis Tools (spant) Invert even numbered dynamic scans starting from 1 (2,4,6...). — inv_even_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/inv_odd_dyns.html b/docs/reference/inv_odd_dyns.html
index 26212e2b..78d64660 100644
--- a/docs/reference/inv_odd_dyns.html
+++ b/docs/reference/inv_odd_dyns.html
@@ -1,5 +1,5 @@
-Invert odd numbered dynamic scans starting from 1 (1,3,5...). — inv_odd_dyns • Spectroscopy Analysis Tools (spant) Invert odd numbered dynamic scans starting from 1 (1,3,5...). — inv_odd_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/is.def.html b/docs/reference/is.def.html
index f196ffd0..a67b9eba 100644
--- a/docs/reference/is.def.html
+++ b/docs/reference/is.def.html
@@ -1,5 +1,5 @@
-Check if an object is defined, which is the same as being not NULL. — is.def • Spectroscopy Analysis Tools (spant) Check if an object is defined, which is the same as being not NULL. — is.def • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/is_fd.html b/docs/reference/is_fd.html
index 3b0ca165..18a193aa 100644
--- a/docs/reference/is_fd.html
+++ b/docs/reference/is_fd.html
@@ -1,7 +1,5 @@
-Check if the chemical shift dimension of an MRS data object is in the
-frequency domain. — is_fd • Spectroscopy Analysis Tools (spant) Check if the chemical shift dimension of an MRS data object is in the frequency domain. — is_fd • Spectroscopy Analysis Tools (spant) Transform 2D MRSI data from k-space to image space in the x-y direction. — kspace2img_xy • Spectroscopy Analysis Tools (spant) Transform 2D MRSI data from k-space to image space in the x-y direction. — kspace2img_xy • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/l2_reg.html b/docs/reference/l2_reg.html
index 3d781d80..21aa9849 100644
--- a/docs/reference/l2_reg.html
+++ b/docs/reference/l2_reg.html
@@ -1,5 +1,5 @@
-Perform l2 regularisation artefact suppression. — l2_reg • Spectroscopy Analysis Tools (spant) Perform l2 regularisation artefact suppression. — l2_reg • Spectroscopy Analysis Tools (spant) Apply line-broadening (apodisation) to MRS data or basis object. — lb • Spectroscopy Analysis Tools (spant) Apply line-broadening (apodisation) to MRS data or basis object. — lb • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -123,7 +123,7 @@ Value
diff --git a/docs/reference/lofdc.html b/docs/reference/lofdc.html
index 5419b1ec..31347a25 100644
--- a/docs/reference/lofdc.html
+++ b/docs/reference/lofdc.html
@@ -1,5 +1,5 @@
-Correct linear frequency drift. — lofdc • Spectroscopy Analysis Tools (spant) Correct linear frequency drift. — lofdc • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -138,7 +138,7 @@ Value
diff --git a/docs/reference/lw2alpha.html b/docs/reference/lw2alpha.html
index b83db682..25da229b 100644
--- a/docs/reference/lw2alpha.html
+++ b/docs/reference/lw2alpha.html
@@ -1,7 +1,5 @@
-Covert a linewidth in Hz to an equivalent alpha value in the time-domain ie:
-x * exp(-t * alpha). — lw2alpha • Spectroscopy Analysis Tools (spant) Covert a linewidth in Hz to an equivalent alpha value in the time-domain ie: x * exp(-t * alpha). — lw2alpha • Spectroscopy Analysis Tools (spant) Covert a linewidth in Hz to an equivalent beta value in the time-domain ie:
-x * exp(-t * t * beta). — lw2beta • Spectroscopy Analysis Tools (spant) Covert a linewidth in Hz to an equivalent beta value in the time-domain ie: x * exp(-t * t * beta). — lw2beta • Spectroscopy Analysis Tools (spant) Make a basis-set object from a directory containing LCModel formatted RAW
-files. — make_basis_from_raw • Spectroscopy Analysis Tools (spant) Make a basis-set object from a directory containing LCModel formatted RAW files. — make_basis_from_raw • Spectroscopy Analysis Tools (spant) Mask an MRS dataset in the dynamic dimension. — mask_dyns • Spectroscopy Analysis Tools (spant) Mask an MRS dataset in the dynamic dimension. — mask_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/mask_fit_res.html b/docs/reference/mask_fit_res.html
index 97baaa3f..ebd91a99 100644
--- a/docs/reference/mask_fit_res.html
+++ b/docs/reference/mask_fit_res.html
@@ -1,5 +1,5 @@
-Mask fit result spectra depending on a vector of bool values. — mask_fit_res • Spectroscopy Analysis Tools (spant) Mask fit result spectra depending on a vector of bool values. — mask_fit_res • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -116,7 +116,7 @@ Value
diff --git a/docs/reference/mask_xy.html b/docs/reference/mask_xy.html
index 11bb577c..b0d38619 100644
--- a/docs/reference/mask_xy.html
+++ b/docs/reference/mask_xy.html
@@ -1,5 +1,5 @@
-Mask an MRSI dataset in the x-y direction — mask_xy • Spectroscopy Analysis Tools (spant) Mask an MRSI dataset in the x-y direction — mask_xy • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/mask_xy_corners.html b/docs/reference/mask_xy_corners.html
index 09b16cd2..2d13839d 100644
--- a/docs/reference/mask_xy_corners.html
+++ b/docs/reference/mask_xy_corners.html
@@ -1,5 +1,5 @@
-Mask the four corners of an MRSI dataset in the x-y plane. — mask_xy_corners • Spectroscopy Analysis Tools (spant) Mask the four corners of an MRSI dataset in the x-y plane. — mask_xy_corners • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/mask_xy_ellipse.html b/docs/reference/mask_xy_ellipse.html
index 1d8b02e4..e2e749ef 100644
--- a/docs/reference/mask_xy_ellipse.html
+++ b/docs/reference/mask_xy_ellipse.html
@@ -1,7 +1,5 @@
-Mask the voxels outside an elliptical region spanning the MRSI dataset in the
-x-y plane. — mask_xy_ellipse • Spectroscopy Analysis Tools (spant) Mask the voxels outside an elliptical region spanning the MRSI dataset in the x-y plane. — mask_xy_ellipse • Spectroscopy Analysis Tools (spant) Mask a 2D MRSI dataset in the x-y dimension. — mask_xy_mat • Spectroscopy Analysis Tools (spant) Mask a 2D MRSI dataset in the x-y dimension. — mask_xy_mat • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Value
diff --git a/docs/reference/mat2mrs_data.html b/docs/reference/mat2mrs_data.html
index 2e2895f3..ae55665f 100644
--- a/docs/reference/mat2mrs_data.html
+++ b/docs/reference/mat2mrs_data.html
@@ -1,7 +1,5 @@
-Convert a matrix (with spectral points in the column dimension and dynamics
-in the row dimensions) into a mrs_data object. — mat2mrs_data • Spectroscopy Analysis Tools (spant) Convert a matrix (with spectral points in the column dimension and dynamics in the row dimensions) into a mrs_data object. — mat2mrs_data • Spectroscopy Analysis Tools (spant) Matrix exponential function taken from complexplus package to reduce the
-number of spant dependencies. — matexp • Spectroscopy Analysis Tools (spant) Matrix exponential function taken from complexplus package to reduce the number of spant dependencies. — matexp • Spectroscopy Analysis Tools (spant) Apply the max operator to an MRS dataset. — max_mrs • Spectroscopy Analysis Tools (spant) Apply the max operator to an MRS dataset. — max_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/max_mrs_interp.html b/docs/reference/max_mrs_interp.html
index e4474764..52e63f3e 100644
--- a/docs/reference/max_mrs_interp.html
+++ b/docs/reference/max_mrs_interp.html
@@ -1,5 +1,5 @@
-Apply the max operator to an interpolated MRS dataset. — max_mrs_interp • Spectroscopy Analysis Tools (spant) Apply the max operator to an interpolated MRS dataset. — max_mrs_interp • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/mean.list.html b/docs/reference/mean.list.html
index b8eb3463..048306fd 100644
--- a/docs/reference/mean.list.html
+++ b/docs/reference/mean.list.html
@@ -1,5 +1,5 @@
-Calculate the mean spectrum from an mrs_data object. — mean.list • Spectroscopy Analysis Tools (spant) Calculate the mean spectrum from an mrs_data object. — mean.list • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/mean.mrs_data.html b/docs/reference/mean.mrs_data.html
index 5531a28d..79515014 100644
--- a/docs/reference/mean.mrs_data.html
+++ b/docs/reference/mean.mrs_data.html
@@ -1,5 +1,5 @@
-Calculate the mean spectrum from an mrs_data object. — mean.mrs_data • Spectroscopy Analysis Tools (spant) Calculate the mean spectrum from an mrs_data object. — mean.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/mean_dyn_blocks.html b/docs/reference/mean_dyn_blocks.html
index 10467098..4c042448 100644
--- a/docs/reference/mean_dyn_blocks.html
+++ b/docs/reference/mean_dyn_blocks.html
@@ -1,5 +1,5 @@
-Calculate the mean of adjacent dynamic scans. — mean_dyn_blocks • Spectroscopy Analysis Tools (spant) Calculate the mean of adjacent dynamic scans. — mean_dyn_blocks • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/mean_dyn_pairs.html b/docs/reference/mean_dyn_pairs.html
index 63e909ea..1a241126 100644
--- a/docs/reference/mean_dyn_pairs.html
+++ b/docs/reference/mean_dyn_pairs.html
@@ -1,5 +1,5 @@
-Calculate the pairwise means across a dynamic data set. — mean_dyn_pairs • Spectroscopy Analysis Tools (spant) Calculate the pairwise means across a dynamic data set. — mean_dyn_pairs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/mean_dyns.html b/docs/reference/mean_dyns.html
index 73fdbfa7..0daa27df 100644
--- a/docs/reference/mean_dyns.html
+++ b/docs/reference/mean_dyns.html
@@ -1,5 +1,5 @@
-Calculate the mean dynamic data. — mean_dyns • Spectroscopy Analysis Tools (spant) Calculate the mean dynamic data. — mean_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/mean_mrs_list.html b/docs/reference/mean_mrs_list.html
index 808b6c50..10d842c0 100644
--- a/docs/reference/mean_mrs_list.html
+++ b/docs/reference/mean_mrs_list.html
@@ -1,5 +1,5 @@
-Return the mean of a list of mrs_data objects. — mean_mrs_list • Spectroscopy Analysis Tools (spant) Return the mean of a list of mrs_data objects. — mean_mrs_list • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/mean_vec_blocks.html b/docs/reference/mean_vec_blocks.html
index 8fc92eaa..dd78b122 100644
--- a/docs/reference/mean_vec_blocks.html
+++ b/docs/reference/mean_vec_blocks.html
@@ -1,5 +1,5 @@
-Calculate the mean of adjacent blocks in a vector. — mean_vec_blocks • Spectroscopy Analysis Tools (spant) Calculate the mean of adjacent blocks in a vector. — mean_vec_blocks • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/median_dyns.html b/docs/reference/median_dyns.html
index 1039d4b5..9a085b10 100644
--- a/docs/reference/median_dyns.html
+++ b/docs/reference/median_dyns.html
@@ -1,5 +1,5 @@
-Calculate the median dynamic data. — median_dyns • Spectroscopy Analysis Tools (spant) Calculate the median dynamic data. — median_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/mod_td.html b/docs/reference/mod_td.html
index 76ad0a40..141ef09e 100644
--- a/docs/reference/mod_td.html
+++ b/docs/reference/mod_td.html
@@ -1,5 +1,5 @@
-Apply the Modulus operator to the time-domain MRS signal. — mod_td • Spectroscopy Analysis Tools (spant) Apply the Modulus operator to the time-domain MRS signal. — mod_td • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/mrs_data2basis.html b/docs/reference/mrs_data2basis.html
index 62f7d749..11797b91 100644
--- a/docs/reference/mrs_data2basis.html
+++ b/docs/reference/mrs_data2basis.html
@@ -1,7 +1,5 @@
-Convert an mrs_data object to basis object - where basis signals are spread
-across the dynamic dimension in the MRS data. — mrs_data2basis • Spectroscopy Analysis Tools (spant) Convert an mrs_data object to basis object - where basis signals are spread across the dynamic dimension in the MRS data. — mrs_data2basis • Spectroscopy Analysis Tools (spant) Create a BIDS file structure from a vector of MRS data paths or list of mrs_data objects. — mrs_data2bids • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Create a BIDS file structure from a vector of MRS data paths or list of mrs_data objects.
+ Source: R/fmrs.R
+ mrs_data2bids.Rd
+
+
+
+ Create a BIDS file structure from a vector of MRS data paths or list of
+mrs_data objects.
+
+
+
+ mrs_data2bids(
+ mrs_data,
+ output_dir,
+ suffix = NULL,
+ sub = NULL,
+ ses = NULL,
+ task = NULL,
+ acq = NULL,
+ nuc = NULL,
+ voi = NULL,
+ rec = NULL,
+ run = NULL,
+ echo = NULL,
+ inv = NULL,
+ skip_existing = TRUE
+)
+
+
+
+ Arguments
+ - mrs_data
+vector of MRS data paths or list of mrs_data objects.
- output_dir
+the base directory to create the BIDS structure.
- suffix
+optional vector of file suffixes. Default behaviour is to
+automatically determine these from the input data, however it is recommended
+that they are specified to allow more efficient skipping of existing data.
- sub
+optional vector of subject labels. If not specified, these will be
+automatically generated as a series of increasing zero-padded integer values
+corresponding to the mrs_data input indices.
- ses
+optional vector of session labels.
- task
+optional vector of task labels.
- acq
+optional vector of acquisition labels.
- nuc
+optional vector of nucleus labels.
- voi
+optional vector of volume of interest labels.
- rec
+optional vector of reconstruction labels.
- run
+optional vector of run indices.
- echo
+optional vector of echo time indices.
- inv
+optional vector of inversion indices.
- skip_existing
+skip any data files that have already been converted.
+Defaults to TRUE, set to FALSE to force an overwrite of any existing data
+files.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/mrs_data2mat.html b/docs/reference/mrs_data2mat.html
index cf5ff28c..9e47688a 100644
--- a/docs/reference/mrs_data2mat.html
+++ b/docs/reference/mrs_data2mat.html
@@ -1,7 +1,5 @@
-Convert mrs_data object to a matrix, with spectral points in the column
-dimension and dynamics in the row dimension. — mrs_data2mat • Spectroscopy Analysis Tools (spant) Convert mrs_data object to a matrix, with spectral points in the column dimension and dynamics in the row dimension. — mrs_data2mat • Spectroscopy Analysis Tools (spant) Convert mrs_data object to a matrix, with spectral points in the column dimension and dynamics in the row dimension. — mrs_data2spec_mat • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Convert mrs_data object to a matrix, with spectral points in the column dimension and dynamics in the row dimension.
+ Source: R/mrs_data_proc.R
+ mrs_data2spec_mat.Rd
+
+
+
+ Convert mrs_data object to a matrix, with spectral points in the column
+dimension and dynamics in the row dimension.
+
+
+
+ mrs_data2spec_mat(mrs_data, collapse = TRUE)
+
+
+
+ Arguments
+ - mrs_data
+MRS data object or list of MRS data objects.
- collapse
+collapse all other dimensions along the dynamic dimension, eg
+a 16x16 MRSI grid would be first collapsed across 256 dynamic scans.
+
+ Value
+
+
+MRS data matrix.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/mrs_data2vec.html b/docs/reference/mrs_data2vec.html
index fb172d68..a1fd654d 100644
--- a/docs/reference/mrs_data2vec.html
+++ b/docs/reference/mrs_data2vec.html
@@ -1,5 +1,5 @@
-Convert mrs_data object to a vector. — mrs_data2vec • Spectroscopy Analysis Tools (spant) Convert mrs_data object to a vector. — mrs_data2vec • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -126,7 +126,7 @@ Value
diff --git a/docs/reference/mvfftshift.html b/docs/reference/mvfftshift.html
index 92b0841b..976b3410 100644
--- a/docs/reference/mvfftshift.html
+++ b/docs/reference/mvfftshift.html
@@ -1,7 +1,5 @@
-Perform a fftshift on a matrix, with each column replaced by its shifted
-result. — mvfftshift • Spectroscopy Analysis Tools (spant) Perform a fftshift on a matrix, with each column replaced by its shifted result. — mvfftshift • Spectroscopy Analysis Tools (spant) Perform an ifftshift on a matrix, with each column replaced by its shifted
-result. — mvifftshift • Spectroscopy Analysis Tools (spant) Perform an ifftshift on a matrix, with each column replaced by its shifted result. — mvifftshift • Spectroscopy Analysis Tools (spant) Print fit coordinates from a single index. — n2coord • Spectroscopy Analysis Tools (spant) Print fit coordinates from a single index. — n2coord • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/nifti_flip_lr.html b/docs/reference/nifti_flip_lr.html
index 730abe3c..19860b3c 100644
--- a/docs/reference/nifti_flip_lr.html
+++ b/docs/reference/nifti_flip_lr.html
@@ -1,9 +1,5 @@
-Flip the x data dimension order of a nifti image. This corresponds to
-flipping MRI data in the left-right direction, assuming the data in save in
-neurological format (can check with fslorient program). — nifti_flip_lr • Spectroscopy Analysis Tools (spant) Flip the x data dimension order of a nifti image. This corresponds to flipping MRI data in the left-right direction, assuming the data in save in neurological format (can check with fslorient program). — nifti_flip_lr • Spectroscopy Analysis Tools (spant) Export a one-page pdf of a single fit result — one_page_pdf • Spectroscopy Analysis Tools (spant) Export a one-page pdf of a single fit result — one_page_pdf • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -108,7 +108,7 @@ Arguments
diff --git a/docs/reference/ortho3.html b/docs/reference/ortho3.html
index 13ade97d..5d7dd2fd 100644
--- a/docs/reference/ortho3.html
+++ b/docs/reference/ortho3.html
@@ -1,5 +1,5 @@
-Display an orthographic projection plot of a nifti object. — ortho3 • Spectroscopy Analysis Tools (spant) Display an orthographic projection plot of a nifti object. — ortho3 • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -172,7 +172,7 @@ Arguments
diff --git a/docs/reference/ortho3_inter.html b/docs/reference/ortho3_inter.html
index 090cc5e5..15948899 100644
--- a/docs/reference/ortho3_inter.html
+++ b/docs/reference/ortho3_inter.html
@@ -1,5 +1,5 @@
-Display an interactive orthographic projection plot of a nifti object. — ortho3_inter • Spectroscopy Analysis Tools (spant) Display an interactive orthographic projection plot of a nifti object. — ortho3_inter • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -132,7 +132,7 @@ Arguments
diff --git a/docs/reference/peak_info.html b/docs/reference/peak_info.html
index 09058bd8..41c8ffaf 100644
--- a/docs/reference/peak_info.html
+++ b/docs/reference/peak_info.html
@@ -1,7 +1,5 @@
-Search for the highest peak in a spectral region and return the frequency,
-height and FWHM. — peak_info • Spectroscopy Analysis Tools (spant) Search for the highest peak in a spectral region and return the frequency, height and FWHM. — peak_info • Spectroscopy Analysis Tools (spant) Papoulis-Gerchberg (PG) algorithm method for k-space extrapolation. — pg_extrap_xy • Spectroscopy Analysis Tools (spant) Papoulis-Gerchberg (PG) algorithm method for k-space extrapolation. — pg_extrap_xy • Spectroscopy Analysis Tools (spant) Apply phasing parameters to MRS data. — phase • Spectroscopy Analysis Tools (spant) Apply phasing parameters to MRS data. — phase • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/phase_ref_1h_brain.html b/docs/reference/phase_ref_1h_brain.html
new file mode 100644
index 00000000..8707a74a
--- /dev/null
+++ b/docs/reference/phase_ref_1h_brain.html
@@ -0,0 +1,131 @@
+
+Corrected zero order phase and chemical shift offset in 1H MRS data from the brain. — phase_ref_1h_brain • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Corrected zero order phase and chemical shift offset in 1H MRS data from the brain.
+ Source: R/rats.R
+ phase_ref_1h_brain.Rd
+
+
+
+ Corrected zero order phase and chemical shift offset in 1H MRS data from the
+brain.
+
+
+
+ phase_ref_1h_brain(mrs_data, mean_ref = FALSE, ret_corr_only = TRUE)
+
+
+
+ Arguments
+ - mrs_data
+MRS data to be corrected.
- mean_ref
+apply the phase and offset of the mean spectrum to all
+others. Default is FALSE.
- ret_corr_only
+return the corrected data only.
+
+ Value
+
+
+corrected MRS data.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/plot.fit_result.html b/docs/reference/plot.fit_result.html
index e54d3bc1..836a53ee 100644
--- a/docs/reference/plot.fit_result.html
+++ b/docs/reference/plot.fit_result.html
@@ -1,5 +1,5 @@
-Plot the fitting results of an object of class fit_result. — plot.fit_result • Spectroscopy Analysis Tools (spant) Plot the fitting results of an object of class fit_result. — plot.fit_result • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -207,7 +207,7 @@ Arguments
diff --git a/docs/reference/plot.mrs_data.html b/docs/reference/plot.mrs_data.html
index fabcc35b..bb2ec651 100644
--- a/docs/reference/plot.mrs_data.html
+++ b/docs/reference/plot.mrs_data.html
@@ -1,5 +1,5 @@
-Plotting method for objects of class mrs_data. — plot.mrs_data • Spectroscopy Analysis Tools (spant) Plotting method for objects of class mrs_data. — plot.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -287,7 +287,7 @@ Arguments
diff --git a/docs/reference/plot_bc.html b/docs/reference/plot_bc.html
index 4f8309b4..b48142cc 100644
--- a/docs/reference/plot_bc.html
+++ b/docs/reference/plot_bc.html
@@ -1,5 +1,5 @@
-Convenience function to plot a baseline estimate with the original data. — plot_bc • Spectroscopy Analysis Tools (spant) Convenience function to plot a baseline estimate with the original data. — plot_bc • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -108,7 +108,7 @@ Arguments
diff --git a/docs/reference/plot_reg.html b/docs/reference/plot_reg.html
index ae1acbe7..2addb2f6 100644
--- a/docs/reference/plot_reg.html
+++ b/docs/reference/plot_reg.html
@@ -1,5 +1,5 @@
-Plot regressors as an image. — plot_reg • Spectroscopy Analysis Tools (spant) Plot regressors as an image. — plot_reg • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/plot_slice_fit.html b/docs/reference/plot_slice_fit.html
index fbc7b560..57f1af8a 100644
--- a/docs/reference/plot_slice_fit.html
+++ b/docs/reference/plot_slice_fit.html
@@ -1,5 +1,5 @@
-Plot a 2D slice from an MRSI fit result object. — plot_slice_fit • Spectroscopy Analysis Tools (spant) Plot a 2D slice from an MRSI fit result object. — plot_slice_fit • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -129,7 +129,7 @@ Arguments
diff --git a/docs/reference/plot_slice_fit_inter.html b/docs/reference/plot_slice_fit_inter.html
index 4eed104a..da105a7d 100644
--- a/docs/reference/plot_slice_fit_inter.html
+++ b/docs/reference/plot_slice_fit_inter.html
@@ -1,5 +1,5 @@
-Plot a 2D slice from an MRSI fit result object. — plot_slice_fit_inter • Spectroscopy Analysis Tools (spant) Plot a 2D slice from an MRSI fit result object. — plot_slice_fit_inter • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -134,7 +134,7 @@ Arguments
diff --git a/docs/reference/plot_slice_map.html b/docs/reference/plot_slice_map.html
index 553e9ac8..ffb2a134 100644
--- a/docs/reference/plot_slice_map.html
+++ b/docs/reference/plot_slice_map.html
@@ -1,5 +1,5 @@
-Plot a slice from a 7 dimensional array. — plot_slice_map • Spectroscopy Analysis Tools (spant) Plot a slice from a 7 dimensional array. — plot_slice_map • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -153,7 +153,7 @@ Arguments
diff --git a/docs/reference/plot_slice_map_inter.html b/docs/reference/plot_slice_map_inter.html
index 40d33b42..90968f66 100644
--- a/docs/reference/plot_slice_map_inter.html
+++ b/docs/reference/plot_slice_map_inter.html
@@ -1,7 +1,5 @@
-Plot an interactive slice map from a data array where voxels can be selected
-to display a corresponding spectrum. — plot_slice_map_inter • Spectroscopy Analysis Tools (spant) Plot an interactive slice map from a data array where voxels can be selected to display a corresponding spectrum. — plot_slice_map_inter • Spectroscopy Analysis Tools (spant) Plot the spectral standard deviation. — plot_spec_sd • Spectroscopy Analysis Tools (spant) Plot the spectral standard deviation. — plot_spec_sd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Arguments
diff --git a/docs/reference/plot_voi_overlay.html b/docs/reference/plot_voi_overlay.html
index 9a782e88..bbbbf35e 100644
--- a/docs/reference/plot_voi_overlay.html
+++ b/docs/reference/plot_voi_overlay.html
@@ -1,5 +1,5 @@
-Plot a volume as an image overlay. — plot_voi_overlay • Spectroscopy Analysis Tools (spant) Plot a volume as an image overlay. — plot_voi_overlay • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -116,7 +116,7 @@ Arguments
diff --git a/docs/reference/plot_voi_overlay_seg.html b/docs/reference/plot_voi_overlay_seg.html
index 3d4e74ff..0e800ff2 100644
--- a/docs/reference/plot_voi_overlay_seg.html
+++ b/docs/reference/plot_voi_overlay_seg.html
@@ -1,5 +1,5 @@
-Plot a volume as an overlay on a segmented brain volume. — plot_voi_overlay_seg • Spectroscopy Analysis Tools (spant) Plot a volume as an overlay on a segmented brain volume. — plot_voi_overlay_seg • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Arguments
diff --git a/docs/reference/ppm.html b/docs/reference/ppm.html
index c352327a..ee4696e2 100644
--- a/docs/reference/ppm.html
+++ b/docs/reference/ppm.html
@@ -1,5 +1,5 @@
-Return the ppm scale of an MRS dataset or fit result. — ppm • Spectroscopy Analysis Tools (spant) Return the ppm scale of an MRS dataset or fit result. — ppm • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -132,7 +132,7 @@ Value
diff --git a/docs/reference/precomp.html b/docs/reference/precomp.html
index 822d7336..df3d2c6c 100644
--- a/docs/reference/precomp.html
+++ b/docs/reference/precomp.html
@@ -1,7 +1,5 @@
-Save function results to file and load on subsequent calls to avoid repeat
-computation. — precomp • Spectroscopy Analysis Tools (spant) Save function results to file and load on subsequent calls to avoid repeat computation. — precomp • Spectroscopy Analysis Tools (spant) Preprocess and perform quality assessment of a single SVS data set. — preproc_svs • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Preprocess and perform quality assessment of a single SVS data set.
+ Source: R/fmrs.R
+ preproc_svs.Rd
+
+
+
+ Preprocess and perform quality assessment of a single SVS data set.
+
+
+
+ preproc_svs(path, label = NULL, output_dir = NULL, ref_inds = NULL)
+
+
+
+ Arguments
+ - path
+path to the fMRS data file or IMA directory.
- label
+a label to describe the data set.
- output_dir
+output directory.
- ref_inds
+a vector of 1-based indices for any water reference dynamic
+scans.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/preproc_svs_dataset.html b/docs/reference/preproc_svs_dataset.html
new file mode 100644
index 00000000..07c3a29b
--- /dev/null
+++ b/docs/reference/preproc_svs_dataset.html
@@ -0,0 +1,148 @@
+
+Preprocess and perform quality assessment of one or more SVS data sets. — preproc_svs_dataset • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Preprocess and perform quality assessment of one or more SVS data sets.
+ Source: R/fmrs.R
+ preproc_svs_dataset.Rd
+
+
+
+ Preprocess and perform quality assessment of one or more SVS data sets.
+
+
+
+ preproc_svs_dataset(
+ paths,
+ labels = NULL,
+ output_dir = "spant_analysis",
+ exclude_labels = NULL,
+ overwrite = FALSE,
+ ref_inds = NULL,
+ return_results = FALSE
+)
+
+
+
+ Arguments
+ - paths
+paths to the fMRS data file or IMA directory.
- labels
+labels to describe each data set.
- output_dir
+output directory.
- exclude_labels
+vector of labels of scans to exclude, eg poor quality
+data.
- overwrite
+overwrite saved results, defaults to FALSE.
- ref_inds
+a vector of 1-based indices for any water reference dynamic
+scans.
- return_results
+function will return key outputs, defaults to FALSE.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/print.fit_result.html b/docs/reference/print.fit_result.html
index 297f28dc..5f434e57 100644
--- a/docs/reference/print.fit_result.html
+++ b/docs/reference/print.fit_result.html
@@ -1,5 +1,5 @@
-Print a summary of an object of class fit_result. — print.fit_result • Spectroscopy Analysis Tools (spant) Print a summary of an object of class fit_result. — print.fit_result • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -105,7 +105,7 @@ Arguments
diff --git a/docs/reference/print.mrs_data.html b/docs/reference/print.mrs_data.html
index 51199017..e1561eb2 100644
--- a/docs/reference/print.mrs_data.html
+++ b/docs/reference/print.mrs_data.html
@@ -1,5 +1,5 @@
-Print a summary of mrs_data parameters. — print.mrs_data • Spectroscopy Analysis Tools (spant) Print a summary of mrs_data parameters. — print.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -109,7 +109,7 @@ Arguments
diff --git a/docs/reference/qn_states.html b/docs/reference/qn_states.html
index 0f42f2f9..d7aa6715 100644
--- a/docs/reference/qn_states.html
+++ b/docs/reference/qn_states.html
@@ -1,5 +1,5 @@
-Get the quantum coherence matrix for a spin system. — qn_states • Spectroscopy Analysis Tools (spant) Get the quantum coherence matrix for a spin system. — qn_states • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/rats.html b/docs/reference/rats.html
index 5a39a396..93585e08 100644
--- a/docs/reference/rats.html
+++ b/docs/reference/rats.html
@@ -1,5 +1,5 @@
-Robust Alignment to a Target Spectrum (RATS). — rats • Spectroscopy Analysis Tools (spant) Robust Alignment to a Target Spectrum (RATS). — rats • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -207,7 +207,7 @@ Value
diff --git a/docs/reference/re_weighting.html b/docs/reference/re_weighting.html
index d21caf21..8b0b070a 100644
--- a/docs/reference/re_weighting.html
+++ b/docs/reference/re_weighting.html
@@ -1,5 +1,5 @@
-Apply a weighting to the FID to enhance spectral resolution. — re_weighting • Spectroscopy Analysis Tools (spant) Apply a weighting to the FID to enhance spectral resolution. — re_weighting • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/read_basis.html b/docs/reference/read_basis.html
index da9b94af..eb6f8557 100644
--- a/docs/reference/read_basis.html
+++ b/docs/reference/read_basis.html
@@ -1,5 +1,5 @@
-Read a basis file in LCModel .basis format. — read_basis • Spectroscopy Analysis Tools (spant) Read a basis file in LCModel .basis format. — read_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/read_ima_coil_dir.html b/docs/reference/read_ima_coil_dir.html
index 28c02de0..4f073cd8 100644
--- a/docs/reference/read_ima_coil_dir.html
+++ b/docs/reference/read_ima_coil_dir.html
@@ -1,9 +1,5 @@
-Read a directory containing Siemens MRS IMA files and combine along the coil
-dimension. Note that the coil ID is inferred from the sorted file name and
-should be checked when consistency is required between two directories. — read_ima_coil_dir • Spectroscopy Analysis Tools (spant) Read a directory containing Siemens MRS IMA files and combine along the coil dimension. Note that the coil ID is inferred from the sorted file name and should be checked when consistency is required between two directories. — read_ima_coil_dir • Spectroscopy Analysis Tools (spant) Read a directory containing Siemens MRS IMA files and combine along the
-dynamic dimension. Note that the coil ID is inferred from the sorted file
-name and should be checked when consistency is required. — read_ima_dyn_dir • Spectroscopy Analysis Tools (spant) Read a directory containing Siemens MRS IMA files and combine along the dynamic dimension. Note that the coil ID is inferred from the sorted file name and should be checked when consistency is required. — read_ima_dyn_dir • Spectroscopy Analysis Tools (spant) Read an LCModel formatted coord file containing fit information. — read_lcm_coord • Spectroscopy Analysis Tools (spant) Read an LCModel formatted coord file containing fit information. — read_lcm_coord • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -107,7 +107,7 @@ Value
diff --git a/docs/reference/read_mrs.html b/docs/reference/read_mrs.html
index 3ac2a36b..2cf36b20 100644
--- a/docs/reference/read_mrs.html
+++ b/docs/reference/read_mrs.html
@@ -1,5 +1,5 @@
-Read MRS data from a file. — read_mrs • Spectroscopy Analysis Tools (spant) Read MRS data from a file. — read_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -88,7 +88,8 @@ Read MRS data from a file.
full_fid = FALSE,
omit_svs_ref_scans = TRUE,
verbose = FALSE,
- extra = NULL
+ extra = NULL,
+ fid_filt_dist = NULL
)
@@ -140,6 +141,13 @@ Arguments
an optional data frame to provide additional variables for use
in subsequent analysis steps, eg id or grouping variables.
fid_filt_dist
+indicate if the data has a distorted FID due to a
+brick-wall filter being used to downsample the data. Default is to auto
+detect this from the data, but TRUE or FALSE options can be given to override
+detection.
Value
@@ -183,7 +191,7 @@ Examples
diff --git a/docs/reference/read_mrs_tqn.html b/docs/reference/read_mrs_tqn.html
index 5766362f..84bdaf3a 100644
--- a/docs/reference/read_mrs_tqn.html
+++ b/docs/reference/read_mrs_tqn.html
@@ -1,5 +1,5 @@
-Read MRS data using the TARQUIN software package. — read_mrs_tqn • Spectroscopy Analysis Tools (spant) Read MRS data using the TARQUIN software package. — read_mrs_tqn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -131,7 +131,7 @@ Examples
diff --git a/docs/reference/read_pulse_ascii.html b/docs/reference/read_pulse_ascii.html
index c9e0d43c..ab11c9cc 100644
--- a/docs/reference/read_pulse_ascii.html
+++ b/docs/reference/read_pulse_ascii.html
@@ -1,5 +1,5 @@
-Read an ASCII formatted pulse file. — read_pulse_ascii • Spectroscopy Analysis Tools (spant) Read an ASCII formatted pulse file. — read_pulse_ascii • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/read_pulse_bruker.html b/docs/reference/read_pulse_bruker.html
index c92bf76a..dbe9073b 100644
--- a/docs/reference/read_pulse_bruker.html
+++ b/docs/reference/read_pulse_bruker.html
@@ -1,5 +1,5 @@
-Read a Bruker formatted pulse file — read_pulse_bruker • Spectroscopy Analysis Tools (spant) Read a Bruker formatted pulse file — read_pulse_bruker • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/read_pulse_pta.html b/docs/reference/read_pulse_pta.html
index 72e1b6d4..a0fac3c3 100644
--- a/docs/reference/read_pulse_pta.html
+++ b/docs/reference/read_pulse_pta.html
@@ -1,5 +1,5 @@
-Read a .pta formatted pulse file compatible with Siemens PulseTool. — read_pulse_pta • Spectroscopy Analysis Tools (spant) Read a .pta formatted pulse file compatible with Siemens PulseTool. — read_pulse_pta • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/read_siemens_txt_hdr.html b/docs/reference/read_siemens_txt_hdr.html
index 23fb8c70..3a17d87c 100644
--- a/docs/reference/read_siemens_txt_hdr.html
+++ b/docs/reference/read_siemens_txt_hdr.html
@@ -1,5 +1,5 @@
-Read the text format header found in Siemens IMA and TWIX data files. — read_siemens_txt_hdr • Spectroscopy Analysis Tools (spant) Read the text format header found in Siemens IMA and TWIX data files. — read_siemens_txt_hdr • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -78,7 +78,7 @@ Read the text format header found in Siemens IMA and TWIX data files.
- read_siemens_txt_hdr(input, version = "vd", verbose, offset = 0)
+ read_siemens_txt_hdr(input, version = "vd", verbose = FALSE, offset = 0)
@@ -118,7 +118,7 @@ Value
diff --git a/docs/reference/read_tqn_fit.html b/docs/reference/read_tqn_fit.html
index 4da6c25e..a1630420 100644
--- a/docs/reference/read_tqn_fit.html
+++ b/docs/reference/read_tqn_fit.html
@@ -1,5 +1,5 @@
-Reader for csv fit results generated by TARQUIN. — read_tqn_fit • Spectroscopy Analysis Tools (spant) Reader for csv fit results generated by TARQUIN. — read_tqn_fit • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -113,7 +113,7 @@ Examples
diff --git a/docs/reference/read_tqn_result.html b/docs/reference/read_tqn_result.html
index 36659714..68a3e98c 100644
--- a/docs/reference/read_tqn_result.html
+++ b/docs/reference/read_tqn_result.html
@@ -1,5 +1,5 @@
-Reader for csv results generated by TARQUIN. — read_tqn_result • Spectroscopy Analysis Tools (spant) Reader for csv results generated by TARQUIN. — read_tqn_result • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -117,7 +117,7 @@ Examples
diff --git a/docs/reference/recon_imag.html b/docs/reference/recon_imag.html
index d2a72225..5bc3b1eb 100644
--- a/docs/reference/recon_imag.html
+++ b/docs/reference/recon_imag.html
@@ -1,7 +1,5 @@
-Reconstruct complex time-domain data from the real part of frequency-domain
-data. — recon_imag • Spectroscopy Analysis Tools (spant) Reconstruct complex time-domain data from the real part of frequency-domain data. — recon_imag • Spectroscopy Analysis Tools (spant) Reconstruct complex time-domain data from the real part of frequency-domain
-data. — recon_imag_vec • Spectroscopy Analysis Tools (spant) Reconstruct complex time-domain data from the real part of frequency-domain data. — recon_imag_vec • Spectroscopy Analysis Tools (spant) Reconstruct 2D MRSI data from a twix file loaded with read_mrs. — recon_twix_2d_mrsi • Spectroscopy Analysis Tools (spant) Reconstruct 2D MRSI data from a twix file loaded with read_mrs. — recon_twix_2d_mrsi • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/rectangular_mask.html b/docs/reference/rectangular_mask.html
index a2117283..6e469bc9 100644
--- a/docs/reference/rectangular_mask.html
+++ b/docs/reference/rectangular_mask.html
@@ -1,5 +1,5 @@
-Create a rectangular mask stored as a matrix of logical values. — rectangular_mask • Spectroscopy Analysis Tools (spant) Create a rectangular mask stored as a matrix of logical values. — rectangular_mask • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -130,7 +130,7 @@ Value
diff --git a/docs/reference/reexports.html b/docs/reference/reexports.html
index 694a75d1..a59e8379 100644
--- a/docs/reference/reexports.html
+++ b/docs/reference/reexports.html
@@ -1,5 +1,5 @@
-Objects exported from other packages — reexports • Spectroscopy Analysis Tools (spant) Objects exported from other packages — reexports • Spectroscopy Analysis Tools (spant)
Spectroscopy Analysis Tools (spant)
- 2.21.0
+ 2.22.0
@@ -103,7 +103,7 @@ Objects exported from other packages
diff --git a/docs/reference/rep_array_dim.html b/docs/reference/rep_array_dim.html
index b9c49b4a..48c0a5ed 100644
--- a/docs/reference/rep_array_dim.html
+++ b/docs/reference/rep_array_dim.html
@@ -1,5 +1,5 @@
-Repeat an array over a given dimension. — rep_array_dim • Spectroscopy Analysis Tools (spant) Repeat an array over a given dimension. — rep_array_dim • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/rep_dyn.html b/docs/reference/rep_dyn.html
index 6bbfb0ef..89a4bb9b 100644
--- a/docs/reference/rep_dyn.html
+++ b/docs/reference/rep_dyn.html
@@ -1,5 +1,5 @@
-Replicate a scan in the dynamic dimension. — rep_dyn • Spectroscopy Analysis Tools (spant) Replicate a scan in the dynamic dimension. — rep_dyn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/rep_mrs.html b/docs/reference/rep_mrs.html
index 67730b5c..becb8f00 100644
--- a/docs/reference/rep_mrs.html
+++ b/docs/reference/rep_mrs.html
@@ -1,5 +1,5 @@
-Replicate a scan over a given dimension. — rep_mrs • Spectroscopy Analysis Tools (spant) Replicate a scan over a given dimension. — rep_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -138,7 +138,7 @@ Value
diff --git a/docs/reference/resample_basis.html b/docs/reference/resample_basis.html
index b0f2ab17..c7a6222a 100644
--- a/docs/reference/resample_basis.html
+++ b/docs/reference/resample_basis.html
@@ -1,5 +1,5 @@
-Resample a basis-set to match a mrs_data acquisition. — resample_basis • Spectroscopy Analysis Tools (spant) Resample a basis-set to match a mrs_data acquisition. — resample_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -116,7 +116,7 @@ Value
diff --git a/docs/reference/resample_img.html b/docs/reference/resample_img.html
index f1e7beaf..b0cc8f71 100644
--- a/docs/reference/resample_img.html
+++ b/docs/reference/resample_img.html
@@ -1,5 +1,5 @@
-Resample an image to match a target image space. — resample_img • Spectroscopy Analysis Tools (spant) Resample an image to match a target image space. — resample_img • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/resample_voi.html b/docs/reference/resample_voi.html
index 8fbfa836..a29ab096 100644
--- a/docs/reference/resample_voi.html
+++ b/docs/reference/resample_voi.html
@@ -1,7 +1,5 @@
-Resample a VOI to match a target image space using nearest-neighbour
-interpolation. — resample_voi • Spectroscopy Analysis Tools (spant) Resample a VOI to match a target image space using nearest-neighbour interpolation. — resample_voi • Spectroscopy Analysis Tools (spant) Reslice a nifti object to match the orientation of mrs data. — reslice_to_mrs • Spectroscopy Analysis Tools (spant) Reslice a nifti object to match the orientation of mrs data. — reslice_to_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/reson_table2mrs_data.html b/docs/reference/reson_table2mrs_data.html
index d75579ee..c5a2167a 100644
--- a/docs/reference/reson_table2mrs_data.html
+++ b/docs/reference/reson_table2mrs_data.html
@@ -1,5 +1,5 @@
-Generate mrs_data from a table of single Lorentzian resonances. — reson_table2mrs_data • Spectroscopy Analysis Tools (spant) Generate mrs_data from a table of single Lorentzian resonances. — reson_table2mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -119,7 +119,7 @@ Value
diff --git a/docs/reference/rm_dyns.html b/docs/reference/rm_dyns.html
index 5d5ef692..573e1f51 100644
--- a/docs/reference/rm_dyns.html
+++ b/docs/reference/rm_dyns.html
@@ -1,5 +1,5 @@
-Remove a subset of dynamic scans. — rm_dyns • Spectroscopy Analysis Tools (spant) Remove a subset of dynamic scans. — rm_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/scale_amp_molal.html b/docs/reference/scale_amp_molal.html
index aaeee1f2..7acb8cb0 100644
--- a/docs/reference/scale_amp_molal.html
+++ b/docs/reference/scale_amp_molal.html
@@ -1,7 +1,5 @@
-Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water). — scale_amp_molal • Spectroscopy Analysis Tools (spant) Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / kg of tissue water). — scale_amp_molal • Spectroscopy Analysis Tools (spant)
Spectroscopy Analysis Tools (spant)
- 2.21.0
+ 2.22.0
@@ -76,8 +74,7 @@
- Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water).
+ Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / kg of tissue water).
Source: R/amp_scaling.R
scale_amp_molal.Rd
@@ -163,7 +160,7 @@ Value
diff --git a/docs/reference/scale_amp_molal_pvc.html b/docs/reference/scale_amp_molal_pvc.html
index 962d6afc..4d194abd 100644
--- a/docs/reference/scale_amp_molal_pvc.html
+++ b/docs/reference/scale_amp_molal_pvc.html
@@ -1,7 +1,5 @@
-Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water). — scale_amp_molal_pvc • Spectroscopy Analysis Tools (spant)
@@ -75,8 +73,7 @@
- Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water).
+ Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / kg of tissue water).
Source: R/amp_scaling.R
scale_amp_molal_pvc.Rd
@@ -141,7 +138,7 @@ Value
diff --git a/docs/reference/scale_amp_molar.html b/docs/reference/scale_amp_molar.html
index 02358d91..dc87a338 100644
--- a/docs/reference/scale_amp_molar.html
+++ b/docs/reference/scale_amp_molar.html
@@ -1,7 +1,5 @@
-Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / Litre of tissue). — scale_amp_molar • Spectroscopy Analysis Tools (spant) Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / Litre of tissue). — scale_amp_molar • Spectroscopy Analysis Tools (spant) Convert default LCM/TARQUIN concentration scaling to molal units with partial
-volume correction. — scale_amp_molar2molal_pvc • Spectroscopy Analysis Tools (spant) Convert default LCM/TARQUIN concentration scaling to molal units with partial volume correction. — scale_amp_molar2molal_pvc • Spectroscopy Analysis Tools (spant) Scale fitted amplitudes to a ratio of signal amplitude. — scale_amp_ratio • Spectroscopy Analysis Tools (spant) Scale fitted amplitudes to a ratio of signal amplitude. — scale_amp_ratio • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -116,7 +116,7 @@ Value
diff --git a/docs/reference/scale_amp_ratio_value.html b/docs/reference/scale_amp_ratio_value.html
index 2036837a..6af8ac51 100644
--- a/docs/reference/scale_amp_ratio_value.html
+++ b/docs/reference/scale_amp_ratio_value.html
@@ -1,5 +1,5 @@
-Scale fitted amplitudes to a ratio of signal amplitude. — scale_amp_ratio_value • Spectroscopy Analysis Tools (spant) Scale fitted amplitudes to a ratio of signal amplitude. — scale_amp_ratio_value • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/scale_amp_water_ratio.html b/docs/reference/scale_amp_water_ratio.html
index 5b25e884..35a76b00 100644
--- a/docs/reference/scale_amp_water_ratio.html
+++ b/docs/reference/scale_amp_water_ratio.html
@@ -1,5 +1,5 @@
-Scale metabolite amplitudes as a ratio to the unsuppressed water amplitude. — scale_amp_water_ratio • Spectroscopy Analysis Tools (spant) Scale metabolite amplitudes as a ratio to the unsuppressed water amplitude. — scale_amp_water_ratio • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/scale_basis_amp.html b/docs/reference/scale_basis_amp.html
index 9401c3f1..5a58b5e5 100644
--- a/docs/reference/scale_basis_amp.html
+++ b/docs/reference/scale_basis_amp.html
@@ -1,5 +1,5 @@
-Scale a basis object by a scalar. — scale_basis_amp • Spectroscopy Analysis Tools (spant) Scale a basis object by a scalar. — scale_basis_amp • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/scale_basis_from_singlet.html b/docs/reference/scale_basis_from_singlet.html
index 0d542bc8..c9a19e77 100644
--- a/docs/reference/scale_basis_from_singlet.html
+++ b/docs/reference/scale_basis_from_singlet.html
@@ -1,5 +1,5 @@
-Scale a basis-set to be consistent with spant assumptions for water scaling. — scale_basis_from_singlet • Spectroscopy Analysis Tools (spant) Scale a basis-set to be consistent with spant assumptions for water scaling. — scale_basis_from_singlet • Spectroscopy Analysis Tools (spant)
Spectroscopy Analysis Tools (spant)
- 2.21.0
+ 2.22.0
@@ -127,7 +127,7 @@ Value
diff --git a/docs/reference/scale_mrs_amp.html b/docs/reference/scale_mrs_amp.html
index b5501a0d..990f058a 100644
--- a/docs/reference/scale_mrs_amp.html
+++ b/docs/reference/scale_mrs_amp.html
@@ -1,5 +1,5 @@
-Scale an mrs_data object by a scalar or vector or amplitudes. — scale_mrs_amp • Spectroscopy Analysis Tools (spant) Scale an mrs_data object by a scalar or vector or amplitudes. — scale_mrs_amp • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/scale_spec.html b/docs/reference/scale_spec.html
index 4f6ea835..6b3ddba4 100644
--- a/docs/reference/scale_spec.html
+++ b/docs/reference/scale_spec.html
@@ -1,5 +1,5 @@
-Scale mrs_data to a spectral region. — scale_spec • Spectroscopy Analysis Tools (spant) Scale mrs_data to a spectral region. — scale_spec • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -141,7 +141,7 @@ Value
diff --git a/docs/reference/sd.html b/docs/reference/sd.html
index ea1eec9f..3ae4dfd4 100644
--- a/docs/reference/sd.html
+++ b/docs/reference/sd.html
@@ -1,5 +1,5 @@
-Calculate the standard deviation spectrum from an mrs_data object. — sd • Spectroscopy Analysis Tools (spant) Calculate the standard deviation spectrum from an mrs_data object. — sd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/sd.mrs_data.html b/docs/reference/sd.mrs_data.html
index 3f92a49f..13bdda85 100644
--- a/docs/reference/sd.mrs_data.html
+++ b/docs/reference/sd.mrs_data.html
@@ -1,5 +1,5 @@
-Calculate the standard deviation spectrum from an mrs_data object. — sd.mrs_data • Spectroscopy Analysis Tools (spant) Calculate the standard deviation spectrum from an mrs_data object. — sd.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/seconds.html b/docs/reference/seconds.html
index b34d6627..467ee17f 100644
--- a/docs/reference/seconds.html
+++ b/docs/reference/seconds.html
@@ -1,5 +1,5 @@
-Return a time scale vector to match the FID of an MRS data object. — seconds • Spectroscopy Analysis Tools (spant) Return a time scale vector to match the FID of an MRS data object. — seconds • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/seq_cpmg_ideal.html b/docs/reference/seq_cpmg_ideal.html
index 547e96ab..45727c86 100644
--- a/docs/reference/seq_cpmg_ideal.html
+++ b/docs/reference/seq_cpmg_ideal.html
@@ -1,5 +1,5 @@
-CPMG style sequence with ideal pulses. — seq_cpmg_ideal • Spectroscopy Analysis Tools (spant) CPMG style sequence with ideal pulses. — seq_cpmg_ideal • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/seq_mega_press_ideal.html b/docs/reference/seq_mega_press_ideal.html
index 0769b8b4..a9cd7fa0 100644
--- a/docs/reference/seq_mega_press_ideal.html
+++ b/docs/reference/seq_mega_press_ideal.html
@@ -1,7 +1,5 @@
-MEGA-PRESS sequence with ideal localisation pulses and Gaussian shaped
-editing pulse. — seq_mega_press_ideal • Spectroscopy Analysis Tools (spant) MEGA-PRESS sequence with ideal localisation pulses and Gaussian shaped editing pulse. — seq_mega_press_ideal • Spectroscopy Analysis Tools (spant) PRESS sequence with shaped refocusing pulses. — seq_press_2d_shaped • Spectroscopy Analysis Tools (spant) PRESS sequence with shaped refocusing pulses. — seq_press_2d_shaped • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -165,7 +165,7 @@ Value
diff --git a/docs/reference/seq_press_ideal.html b/docs/reference/seq_press_ideal.html
index 8c976856..72c3af3d 100644
--- a/docs/reference/seq_press_ideal.html
+++ b/docs/reference/seq_press_ideal.html
@@ -1,5 +1,5 @@
-PRESS sequence with ideal pulses. — seq_press_ideal • Spectroscopy Analysis Tools (spant) PRESS sequence with ideal pulses. — seq_press_ideal • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/seq_pulse_acquire.html b/docs/reference/seq_pulse_acquire.html
index 4a88fc64..ad80571e 100644
--- a/docs/reference/seq_pulse_acquire.html
+++ b/docs/reference/seq_pulse_acquire.html
@@ -1,5 +1,5 @@
-Simple pulse and acquire sequence with ideal pulses. — seq_pulse_acquire • Spectroscopy Analysis Tools (spant) Simple pulse and acquire sequence with ideal pulses. — seq_pulse_acquire • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/seq_slaser_ideal.html b/docs/reference/seq_slaser_ideal.html
index 74688f4d..eb83e8e3 100644
--- a/docs/reference/seq_slaser_ideal.html
+++ b/docs/reference/seq_slaser_ideal.html
@@ -1,5 +1,5 @@
-sLASER sequence with ideal pulses. — seq_slaser_ideal • Spectroscopy Analysis Tools (spant) sLASER sequence with ideal pulses. — seq_slaser_ideal • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -126,7 +126,7 @@ Value
diff --git a/docs/reference/seq_spin_echo_ideal.html b/docs/reference/seq_spin_echo_ideal.html
index e23271de..4248716f 100644
--- a/docs/reference/seq_spin_echo_ideal.html
+++ b/docs/reference/seq_spin_echo_ideal.html
@@ -1,5 +1,5 @@
-Spin echo sequence with ideal pulses. — seq_spin_echo_ideal • Spectroscopy Analysis Tools (spant) Spin echo sequence with ideal pulses. — seq_spin_echo_ideal • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/seq_steam_ideal.html b/docs/reference/seq_steam_ideal.html
index a60685a8..1c8115d7 100644
--- a/docs/reference/seq_steam_ideal.html
+++ b/docs/reference/seq_steam_ideal.html
@@ -1,5 +1,5 @@
-STEAM sequence with ideal pulses. — seq_steam_ideal • Spectroscopy Analysis Tools (spant) STEAM sequence with ideal pulses. — seq_steam_ideal • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -128,7 +128,7 @@ Value
diff --git a/docs/reference/seq_steam_ideal_cof.html b/docs/reference/seq_steam_ideal_cof.html
index 8f225740..cba7af91 100644
--- a/docs/reference/seq_steam_ideal_cof.html
+++ b/docs/reference/seq_steam_ideal_cof.html
@@ -1,7 +1,5 @@
-STEAM sequence with ideal pulses and coherence order filtering to simulate
-gradient crushers. — seq_steam_ideal_cof • Spectroscopy Analysis Tools (spant) STEAM sequence with ideal pulses and coherence order filtering to simulate gradient crushers. — seq_steam_ideal_cof • Spectroscopy Analysis Tools (spant) STEAM sequence with ideal pulses using the z-rotation gradient simulation
-method described by Young et al JMR 140, 146-152 (1999). — seq_steam_ideal_young • Spectroscopy Analysis Tools (spant) STEAM sequence with ideal pulses using the z-rotation gradient simulation method described by Young et al JMR 140, 146-152 (1999). — seq_steam_ideal_young • Spectroscopy Analysis Tools (spant) Set the number of transients for an mrs_data object. — set_Ntrans • Spectroscopy Analysis Tools (spant) Set the number of transients for an mrs_data object. — set_Ntrans • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/set_def_acq_paras.html b/docs/reference/set_def_acq_paras.html
index 3e1b4004..cc2ada9c 100644
--- a/docs/reference/set_def_acq_paras.html
+++ b/docs/reference/set_def_acq_paras.html
@@ -1,5 +1,5 @@
-Set the default acquisition parameters. — set_def_acq_paras • Spectroscopy Analysis Tools (spant) Set the default acquisition parameters. — set_def_acq_paras • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Arguments
diff --git a/docs/reference/set_lcm_cmd.html b/docs/reference/set_lcm_cmd.html
index 2056ed01..42bb2f24 100644
--- a/docs/reference/set_lcm_cmd.html
+++ b/docs/reference/set_lcm_cmd.html
@@ -1,5 +1,5 @@
-Set the command to run the LCModel command-line program. — set_lcm_cmd • Spectroscopy Analysis Tools (spant) Set the command to run the LCModel command-line program. — set_lcm_cmd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/set_lw.html b/docs/reference/set_lw.html
index b64ec851..bb176c62 100644
--- a/docs/reference/set_lw.html
+++ b/docs/reference/set_lw.html
@@ -1,5 +1,5 @@
-Apply line-broadening to an mrs_data object to achieve a specified linewidth. — set_lw • Spectroscopy Analysis Tools (spant) Apply line-broadening to an mrs_data object to achieve a specified linewidth. — set_lw • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -123,7 +123,7 @@ Value
diff --git a/docs/reference/set_mask_xy_mat.html b/docs/reference/set_mask_xy_mat.html
index 49dc5d4e..52c4b617 100644
--- a/docs/reference/set_mask_xy_mat.html
+++ b/docs/reference/set_mask_xy_mat.html
@@ -1,5 +1,5 @@
-Set the masked voxels in a 2D MRSI dataset to given spectrum. — set_mask_xy_mat • Spectroscopy Analysis Tools (spant) Set the masked voxels in a 2D MRSI dataset to given spectrum. — set_mask_xy_mat • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Value
diff --git a/docs/reference/set_precomp_mode.html b/docs/reference/set_precomp_mode.html
index f44bd5d3..47c28e3b 100644
--- a/docs/reference/set_precomp_mode.html
+++ b/docs/reference/set_precomp_mode.html
@@ -1,5 +1,5 @@
-Set the precompute mode. — set_precomp_mode • Spectroscopy Analysis Tools (spant) Set the precompute mode. — set_precomp_mode • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/set_precomp_verbose.html b/docs/reference/set_precomp_verbose.html
index 1453a231..9c613505 100644
--- a/docs/reference/set_precomp_verbose.html
+++ b/docs/reference/set_precomp_verbose.html
@@ -1,5 +1,5 @@
-Set the verbosity of the precompute function. — set_precomp_verbose • Spectroscopy Analysis Tools (spant) Set the verbosity of the precompute function. — set_precomp_verbose • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/set_ref.html b/docs/reference/set_ref.html
index 8953fa50..5436dfa2 100644
--- a/docs/reference/set_ref.html
+++ b/docs/reference/set_ref.html
@@ -1,5 +1,5 @@
-Set the ppm reference value (eg ppm value at 0Hz). — set_ref • Spectroscopy Analysis Tools (spant) Set the ppm reference value (eg ppm value at 0Hz). — set_ref • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/set_td_pts.html b/docs/reference/set_td_pts.html
index 8a80d42a..586459ff 100644
--- a/docs/reference/set_td_pts.html
+++ b/docs/reference/set_td_pts.html
@@ -1,7 +1,5 @@
-Set the number of time-domain data points, truncating or zero-filling as
-appropriate. — set_td_pts • Spectroscopy Analysis Tools (spant) Set the number of time-domain data points, truncating or zero-filling as appropriate. — set_td_pts • Spectroscopy Analysis Tools (spant) Set the command to run the TARQUIN command-line program. — set_tqn_cmd • Spectroscopy Analysis Tools (spant) Set the command to run the TARQUIN command-line program. — set_tqn_cmd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/set_tr.html b/docs/reference/set_tr.html
index b2109ab0..65c9df5f 100644
--- a/docs/reference/set_tr.html
+++ b/docs/reference/set_tr.html
@@ -1,5 +1,5 @@
-Set the repetition time of an MRS dataset. — set_tr • Spectroscopy Analysis Tools (spant) Set the repetition time of an MRS dataset. — set_tr • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/shift.html b/docs/reference/shift.html
index ab0fe724..034591d0 100644
--- a/docs/reference/shift.html
+++ b/docs/reference/shift.html
@@ -1,5 +1,5 @@
-Apply a frequency shift to MRS data. — shift • Spectroscopy Analysis Tools (spant) Apply a frequency shift to MRS data. — shift • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/shift_basis.html b/docs/reference/shift_basis.html
index 2884be19..f55a65e0 100644
--- a/docs/reference/shift_basis.html
+++ b/docs/reference/shift_basis.html
@@ -1,5 +1,5 @@
-Apply frequency shifts to basis set signals. — shift_basis • Spectroscopy Analysis Tools (spant) Apply frequency shifts to basis set signals. — shift_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Value
diff --git a/docs/reference/sim_basis.html b/docs/reference/sim_basis.html
index c7838c46..bb5fefc6 100644
--- a/docs/reference/sim_basis.html
+++ b/docs/reference/sim_basis.html
@@ -1,5 +1,5 @@
-Simulate a basis set object. — sim_basis • Spectroscopy Analysis Tools (spant) Simulate a basis set object. — sim_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -136,7 +136,7 @@ Value
diff --git a/docs/reference/sim_basis_1h_brain.html b/docs/reference/sim_basis_1h_brain.html
index 62ed7389..f71ffa0b 100644
--- a/docs/reference/sim_basis_1h_brain.html
+++ b/docs/reference/sim_basis_1h_brain.html
@@ -1,7 +1,5 @@
-Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS
-sequence. Note, ideal pulses are assumed. — sim_basis_1h_brain • Spectroscopy Analysis Tools (spant) Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS sequence. Note, ideal pulses are assumed. — sim_basis_1h_brain • Spectroscopy Analysis Tools (spant) Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS
-sequence. Note, ideal pulses are assumed. — sim_basis_1h_brain_press • Spectroscopy Analysis Tools (spant) Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS sequence. Note, ideal pulses are assumed. — sim_basis_1h_brain_press • Spectroscopy Analysis Tools (spant) Simulate a macromolecular and lipid basis-set suitable for 1H brain MRS
-analysis. — sim_basis_mm_lip_lcm • Spectroscopy Analysis Tools (spant) Simulate a macromolecular and lipid basis-set suitable for 1H brain MRS analysis. — sim_basis_mm_lip_lcm • Spectroscopy Analysis Tools (spant) Simulate a basis file using TARQUIN. — sim_basis_tqn • Spectroscopy Analysis Tools (spant) Simulate a basis file using TARQUIN. — sim_basis_tqn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -129,7 +129,7 @@ Examples
diff --git a/docs/reference/sim_brain_1h.html b/docs/reference/sim_brain_1h.html
index 2044cf1a..717ee289 100644
--- a/docs/reference/sim_brain_1h.html
+++ b/docs/reference/sim_brain_1h.html
@@ -1,5 +1,5 @@
-Simulate MRS data with a similar appearance to normal brain (by default). — sim_brain_1h • Spectroscopy Analysis Tools (spant) Simulate MRS data with a similar appearance to normal brain (by default). — sim_brain_1h • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -159,7 +159,7 @@ Value
diff --git a/docs/reference/sim_mol.html b/docs/reference/sim_mol.html
index 23bcef50..77f76a50 100644
--- a/docs/reference/sim_mol.html
+++ b/docs/reference/sim_mol.html
@@ -1,5 +1,5 @@
-Simulate a mol_parameter object. — sim_mol • Spectroscopy Analysis Tools (spant) Simulate a mol_parameter object. — sim_mol • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -143,7 +143,7 @@ Value
diff --git a/docs/reference/sim_noise.html b/docs/reference/sim_noise.html
index 23875f79..a71477d4 100644
--- a/docs/reference/sim_noise.html
+++ b/docs/reference/sim_noise.html
@@ -1,5 +1,5 @@
-Simulate an mrs_data object containing simulated Gaussian noise. — sim_noise • Spectroscopy Analysis Tools (spant) Simulate an mrs_data object containing simulated Gaussian noise. — sim_noise • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -84,6 +84,7 @@ Simulate an mrs_data object containing simulated Gaussian noise.
ft = def_ft(),
N = def_N(),
ref = def_ref(),
+ nuc = def_nuc(),
dyns = 1,
fd = TRUE
)
@@ -111,6 +112,10 @@ Arguments
reference value for ppm scale.
nuc
+resonant nucleus.
dyns
number of dynamic scans to generate.
Value
diff --git a/docs/reference/sim_resonances.html b/docs/reference/sim_resonances.html
index 19e9a8a4..d4f8d7c0 100644
--- a/docs/reference/sim_resonances.html
+++ b/docs/reference/sim_resonances.html
@@ -1,5 +1,5 @@
-Simulate a MRS data object containing a set of simulated resonances. — sim_resonances • Spectroscopy Analysis Tools (spant) Simulate a MRS data object containing a set of simulated resonances. — sim_resonances • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -161,7 +161,7 @@ Examples
diff --git a/docs/reference/sim_th_excit_profile.html b/docs/reference/sim_th_excit_profile.html
index 5535c5ef..e781cab1 100644
--- a/docs/reference/sim_th_excit_profile.html
+++ b/docs/reference/sim_th_excit_profile.html
@@ -1,7 +1,5 @@
-Simulate an ideal pulse excitation profile by smoothing a top-hat function
-with a Gaussian. — sim_th_excit_profile • Spectroscopy Analysis Tools (spant) Simulate an ideal pulse excitation profile by smoothing a top-hat function with a Gaussian. — sim_th_excit_profile • Spectroscopy Analysis Tools (spant) Simulate an mrs_data object containing complex zero valued samples. — sim_zero • Spectroscopy Analysis Tools (spant) Simulate an mrs_data object containing complex zero valued samples. — sim_zero • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -78,7 +78,14 @@ Simulate an mrs_data object containing complex zero valued samples.
-
+
@@ -99,6 +106,10 @@ Arguments
reference value for ppm scale.
nuc
+resonant nucleus.
dyns
number of dynamic scans to generate.
Value
diff --git a/docs/reference/smooth_dyns.html b/docs/reference/smooth_dyns.html
index 4cc8da50..accf3a51 100644
--- a/docs/reference/smooth_dyns.html
+++ b/docs/reference/smooth_dyns.html
@@ -1,5 +1,5 @@
-Smooth data across the dynamic dimension with a Gaussian kernel. — smooth_dyns • Spectroscopy Analysis Tools (spant) Smooth data across the dynamic dimension with a Gaussian kernel. — smooth_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/sort_basis.html b/docs/reference/sort_basis.html
index 6a676ea2..d25cc006 100644
--- a/docs/reference/sort_basis.html
+++ b/docs/reference/sort_basis.html
@@ -1,5 +1,5 @@
-Sort the basis-set elements alphabetically. — sort_basis • Spectroscopy Analysis Tools (spant) Sort the basis-set elements alphabetically. — sort_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/spant-package.html b/docs/reference/spant-package.html
index b3dd8e21..90f19ec3 100644
--- a/docs/reference/spant-package.html
+++ b/docs/reference/spant-package.html
@@ -1,5 +1,5 @@
-spant: spectroscopy analysis tools. — spant-package • Spectroscopy Analysis Tools (spant) spant: spectroscopy analysis tools. — spant-package • Spectroscopy Analysis Tools (spant) Simulate and fit some spectra with ABfit for benchmarking purposes. Basic
-timing and performance metrics will be printed. — spant_abfit_benchmark • Spectroscopy Analysis Tools (spant) Simulate and fit some spectra with ABfit for benchmarking purposes. Basic timing and performance metrics will be printed. — spant_abfit_benchmark • Spectroscopy Analysis Tools (spant) Example MEGA-PRESS data with significant B0 drift. — spant_mpress_drift • Spectroscopy Analysis Tools (spant) Example MEGA-PRESS data with significant B0 drift. — spant_mpress_drift • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -83,7 +83,7 @@ Example MEGA-PRESS data with significant B0 drift.
Format
- An object of class mrs_data of length 13.
+ An object of class mrs_data of dimension 1 x 1 x 1 x 1 x 40 x 1 x 1024.
@@ -98,7 +98,7 @@ Format
diff --git a/docs/reference/spant_sim_fmrs_dataset.html b/docs/reference/spant_sim_fmrs_dataset.html
new file mode 100644
index 00000000..00e48b56
--- /dev/null
+++ b/docs/reference/spant_sim_fmrs_dataset.html
@@ -0,0 +1,117 @@
+
+Simulate an example fMRS dataset for a block design fMRS experiment and export a BIDS structure. — spant_sim_fmrs_dataset • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Simulate an example fMRS dataset for a block design fMRS experiment and export a BIDS structure.
+ Source: R/fmrs.R
+ spant_sim_fmrs_dataset.Rd
+
+
+
+ Simulate an example fMRS dataset for a block design fMRS experiment and
+export a BIDS structure.
+
+
+
+ spant_sim_fmrs_dataset(output_dir = NULL)
+
+
+
+ Arguments
+ - output_dir
+output directory for the BIDS data. Defaults to :
+"HOME/sim_fmrs_dataset/data".
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/spant_simulation_benchmark.html b/docs/reference/spant_simulation_benchmark.html
index 32daa8bf..d8cc6841 100644
--- a/docs/reference/spant_simulation_benchmark.html
+++ b/docs/reference/spant_simulation_benchmark.html
@@ -1,7 +1,5 @@
-Simulate a typical metabolite basis set for benchmarking. Timing metrics will
-be printed on completion. — spant_simulation_benchmark • Spectroscopy Analysis Tools (spant) Simulate a typical metabolite basis set for benchmarking. Timing metrics will be printed on completion. — spant_simulation_benchmark • Spectroscopy Analysis Tools (spant) Decompose an mrs_data object into white and gray matter spectra. — spec_decomp • Spectroscopy Analysis Tools (spant) Perform a mathematical operation on a spectral region. — spec_op • Spectroscopy Analysis Tools (spant) Perform a mathematical operation on a spectral region. — spec_op • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -98,8 +98,8 @@ Arguments
operator
-can be "sum" (default), "mean", "l2", "max", "min" or
-"max-min".
can be "sum" (default), "mean", "l2", "max", "max_cplx,
+"min" or "max-min".
freq_scale
@@ -129,7 +129,7 @@ Value
diff --git a/docs/reference/spin_sys.html b/docs/reference/spin_sys.html
index 853423a4..1eaa9e76 100644
--- a/docs/reference/spin_sys.html
+++ b/docs/reference/spin_sys.html
@@ -1,5 +1,5 @@
-Create a spin system object for pulse sequence simulation. — spin_sys • Spectroscopy Analysis Tools (spant) Create a spin system object for pulse sequence simulation. — spin_sys • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/spm_pve2categorical.html b/docs/reference/spm_pve2categorical.html
index 23a1bad9..70f10729 100644
--- a/docs/reference/spm_pve2categorical.html
+++ b/docs/reference/spm_pve2categorical.html
@@ -1,7 +1,5 @@
-Convert SPM style segmentation files to a single categorical image where
-the numerical values map as: 0) Other, 1) CSF, 2) GM and 3) WM. — spm_pve2categorical • Spectroscopy Analysis Tools (spant) Convert SPM style segmentation files to a single categorical image where the numerical values map as: 0) Other, 1) CSF, 2) GM and 3) WM. — spm_pve2categorical • Spectroscopy Analysis Tools (spant) Signal space projection method for lipid suppression. — ssp • Spectroscopy Analysis Tools (spant) Signal space projection method for lipid suppression. — ssp • Spectroscopy Analysis Tools (spant) Plot the fitting results of an object of class fit_result with
-individual basis set components shown. — stackplot.fit_result • Spectroscopy Analysis Tools (spant) Plot the fitting results of an object of class fit_result with individual basis set components shown. — stackplot.fit_result • Spectroscopy Analysis Tools (spant) Produce a plot with multiple traces. — stackplot • Spectroscopy Analysis Tools (spant) Produce a plot with multiple traces. — stackplot • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/stackplot.mrs_data.html b/docs/reference/stackplot.mrs_data.html
index 17ff5648..64eea445 100644
--- a/docs/reference/stackplot.mrs_data.html
+++ b/docs/reference/stackplot.mrs_data.html
@@ -1,5 +1,5 @@
-Stackplot plotting method for objects of class mrs_data. — stackplot.mrs_data • Spectroscopy Analysis Tools (spant) Stackplot plotting method for objects of class mrs_data. — stackplot.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -255,7 +255,7 @@ Arguments
diff --git a/docs/reference/sub_first_dyn.html b/docs/reference/sub_first_dyn.html
index dbd7f831..493b7242 100644
--- a/docs/reference/sub_first_dyn.html
+++ b/docs/reference/sub_first_dyn.html
@@ -1,5 +1,5 @@
-Subtract the first dynamic spectrum from a dynamic series. — sub_first_dyn • Spectroscopy Analysis Tools (spant) Subtract the first dynamic spectrum from a dynamic series. — sub_first_dyn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/sub_mean_dyns.html b/docs/reference/sub_mean_dyns.html
index 6e3bb2df..221bd0c1 100644
--- a/docs/reference/sub_mean_dyns.html
+++ b/docs/reference/sub_mean_dyns.html
@@ -1,5 +1,5 @@
-Subtract the mean dynamic spectrum from a dynamic series. — sub_mean_dyns • Spectroscopy Analysis Tools (spant) Subtract the mean dynamic spectrum from a dynamic series. — sub_mean_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/sub_median_dyns.html b/docs/reference/sub_median_dyns.html
index 134c495d..1e834f14 100644
--- a/docs/reference/sub_median_dyns.html
+++ b/docs/reference/sub_median_dyns.html
@@ -1,5 +1,5 @@
-Subtract the median dynamic spectrum from a dynamic series. — sub_median_dyns • Spectroscopy Analysis Tools (spant) Subtract the median dynamic spectrum from a dynamic series. — sub_median_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/sum_coils.html b/docs/reference/sum_coils.html
index 7bf559f2..e1ab3cc0 100644
--- a/docs/reference/sum_coils.html
+++ b/docs/reference/sum_coils.html
@@ -1,5 +1,5 @@
-Calculate the sum across receiver coil elements. — sum_coils • Spectroscopy Analysis Tools (spant) Calculate the sum across receiver coil elements. — sum_coils • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/sum_dyns.html b/docs/reference/sum_dyns.html
index a0be19d3..bbda2ffc 100644
--- a/docs/reference/sum_dyns.html
+++ b/docs/reference/sum_dyns.html
@@ -1,5 +1,5 @@
-Calculate the sum of data dynamics. — sum_dyns • Spectroscopy Analysis Tools (spant) Calculate the sum of data dynamics. — sum_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/sum_mrs.html b/docs/reference/sum_mrs.html
index a22f215b..3cc3ab9e 100644
--- a/docs/reference/sum_mrs.html
+++ b/docs/reference/sum_mrs.html
@@ -1,5 +1,5 @@
-Sum two mrs_data objects. — sum_mrs • Spectroscopy Analysis Tools (spant) Sum two mrs_data objects. — sum_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Value
diff --git a/docs/reference/sum_mrs_list.html b/docs/reference/sum_mrs_list.html
index f4e09aea..c3584348 100644
--- a/docs/reference/sum_mrs_list.html
+++ b/docs/reference/sum_mrs_list.html
@@ -1,5 +1,5 @@
-Return the sum of a list of mrs_data objects. — sum_mrs_list • Spectroscopy Analysis Tools (spant) Return the sum of a list of mrs_data objects. — sum_mrs_list • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/svs_1h_brain_analysis.html b/docs/reference/svs_1h_brain_analysis.html
index 8ce514db..dff0ef7d 100644
--- a/docs/reference/svs_1h_brain_analysis.html
+++ b/docs/reference/svs_1h_brain_analysis.html
@@ -1,5 +1,5 @@
-Standard SVS 1H brain analysis pipeline. — svs_1h_brain_analysis • Spectroscopy Analysis Tools (spant) Standard SVS 1H brain analysis pipeline. — svs_1h_brain_analysis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -199,7 +199,7 @@ Value
diff --git a/docs/reference/svs_1h_brain_analysis_dev.html b/docs/reference/svs_1h_brain_analysis_dev.html
index d70a14d3..d71bfea2 100644
--- a/docs/reference/svs_1h_brain_analysis_dev.html
+++ b/docs/reference/svs_1h_brain_analysis_dev.html
@@ -1,5 +1,5 @@
-Standard SVS 1H brain analysis pipeline. — svs_1h_brain_analysis_dev • Spectroscopy Analysis Tools (spant) Standard SVS 1H brain analysis pipeline. — svs_1h_brain_analysis_dev • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -193,7 +193,7 @@ Examples
diff --git a/docs/reference/svs_1h_brain_batch_analysis.html b/docs/reference/svs_1h_brain_batch_analysis.html
index 5631e8cc..15f7223e 100644
--- a/docs/reference/svs_1h_brain_batch_analysis.html
+++ b/docs/reference/svs_1h_brain_batch_analysis.html
@@ -1,5 +1,5 @@
-Batch interface to the standard SVS 1H brain analysis pipeline. — svs_1h_brain_batch_analysis • Spectroscopy Analysis Tools (spant) Batch interface to the standard SVS 1H brain analysis pipeline. — svs_1h_brain_batch_analysis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -144,7 +144,7 @@ Value
diff --git a/docs/reference/t_test_spec.html b/docs/reference/t_test_spec.html
new file mode 100644
index 00000000..56a7ea1b
--- /dev/null
+++ b/docs/reference/t_test_spec.html
@@ -0,0 +1,124 @@
+
+Perform a t-test on spectral data points. — t_test_spec • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+
+
+ Perform a t-test on spectral data points.
+
+
+
+ t_test_spec(mrs_data, group)
+
+
+
+ Arguments
+ - mrs_data
+an mrs_data object with spectra in the dynamic dimension.
- group
+vector describing the group membership of each dynamic spectrum.
+
+ Value
+
+
+a list of statistical results.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/td2fd.html b/docs/reference/td2fd.html
index 6748a6a8..f31ed524 100644
--- a/docs/reference/td2fd.html
+++ b/docs/reference/td2fd.html
@@ -1,5 +1,5 @@
-Transform time-domain data to the frequency-domain. — td2fd • Spectroscopy Analysis Tools (spant) Transform time-domain data to the frequency-domain. — td2fd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/td_conv_filt.html b/docs/reference/td_conv_filt.html
index a9f340c3..106b9b00 100644
--- a/docs/reference/td_conv_filt.html
+++ b/docs/reference/td_conv_filt.html
@@ -1,5 +1,5 @@
-Time-domain convolution based filter. — td_conv_filt • Spectroscopy Analysis Tools (spant) Time-domain convolution based filter. — td_conv_filt • Spectroscopy Analysis Tools (spant) Time-domain spectral registration. — tdsr • Spectroscopy Analysis Tools (spant) Time-domain spectral registration. — tdsr • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -121,7 +121,7 @@ Value
diff --git a/docs/reference/te.html b/docs/reference/te.html
index 010361b1..4a65711d 100644
--- a/docs/reference/te.html
+++ b/docs/reference/te.html
@@ -1,5 +1,5 @@
-Return the echo time of an MRS dataset. — te • Spectroscopy Analysis Tools (spant) Return the echo time of an MRS dataset. — te • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/tr.html b/docs/reference/tr.html
index 0c0bd63b..2e749e02 100644
--- a/docs/reference/tr.html
+++ b/docs/reference/tr.html
@@ -1,5 +1,5 @@
-Return the repetition time of an MRS dataset. — tr • Spectroscopy Analysis Tools (spant) Return the repetition time of an MRS dataset. — tr • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/varpro_3_para_opts.html b/docs/reference/varpro_3_para_opts.html
index c2270a16..52d7cd84 100644
--- a/docs/reference/varpro_3_para_opts.html
+++ b/docs/reference/varpro_3_para_opts.html
@@ -1,5 +1,5 @@
-Return a list of options for VARPRO based fitting with 3 free parameters. — varpro_3_para_opts • Spectroscopy Analysis Tools (spant) Return a list of options for VARPRO based fitting with 3 free parameters. — varpro_3_para_opts • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -141,7 +141,7 @@ Value
diff --git a/docs/reference/varpro_basic_opts.html b/docs/reference/varpro_basic_opts.html
index 32c86d22..c5104891 100644
--- a/docs/reference/varpro_basic_opts.html
+++ b/docs/reference/varpro_basic_opts.html
@@ -1,5 +1,5 @@
-Return a list of options for a basic VARPRO analysis. — varpro_basic_opts • Spectroscopy Analysis Tools (spant) Return a list of options for a basic VARPRO analysis. — varpro_basic_opts • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -118,7 +118,7 @@ Value
diff --git a/docs/reference/varpro_opts.html b/docs/reference/varpro_opts.html
index 2aabf11d..6332f730 100644
--- a/docs/reference/varpro_opts.html
+++ b/docs/reference/varpro_opts.html
@@ -1,5 +1,5 @@
-Return a list of options for VARPRO based fitting. — varpro_opts • Spectroscopy Analysis Tools (spant) Return a list of options for VARPRO based fitting. — varpro_opts • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -177,7 +177,7 @@ Examples
diff --git a/docs/reference/vec2mrs_data.html b/docs/reference/vec2mrs_data.html
index 0cccd73b..f0d58bf0 100644
--- a/docs/reference/vec2mrs_data.html
+++ b/docs/reference/vec2mrs_data.html
@@ -1,5 +1,5 @@
-Convert a vector into a mrs_data object. — vec2mrs_data • Spectroscopy Analysis Tools (spant) Convert a vector into a mrs_data object. — vec2mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -80,10 +80,11 @@ Convert a vector into a mrs_data object.
vec2mrs_data(
vec,
- fs = def_fs(),
- ft = def_ft(),
- ref = def_ref(),
- nuc = def_nuc(),
+ mrs_data = NULL,
+ fs = NULL,
+ ft = NULL,
+ ref = NULL,
+ nuc = NULL,
dyns = 1,
fd = FALSE
)
@@ -95,6 +96,10 @@ Arguments
the data vector.
mrs_data
+example data to copy acquisition parameters from.
fs
sampling frequency in Hz.
Arguments
fd
-flag to indicate if the matrix is in the frequency domain (logical).
flag to indicate if the vector is in the frequency domain (logical).
Value
diff --git a/docs/reference/write_basis.html b/docs/reference/write_basis.html
index b6e27cbd..94c5e021 100644
--- a/docs/reference/write_basis.html
+++ b/docs/reference/write_basis.html
@@ -1,5 +1,5 @@
-Write a basis object to an LCModel .basis formatted file. — write_basis • Spectroscopy Analysis Tools (spant) Write a basis object to an LCModel .basis formatted file. — write_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -108,7 +108,7 @@ Arguments
diff --git a/docs/reference/write_basis_tqn.html b/docs/reference/write_basis_tqn.html
index 6aa51c1d..116c73ec 100644
--- a/docs/reference/write_basis_tqn.html
+++ b/docs/reference/write_basis_tqn.html
@@ -1,5 +1,5 @@
-Generate a basis file using TARQUIN. — write_basis_tqn • Spectroscopy Analysis Tools (spant) Generate a basis file using TARQUIN. — write_basis_tqn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Examples
diff --git a/docs/reference/write_mrs.html b/docs/reference/write_mrs.html
index fff25f15..124b9dc4 100644
--- a/docs/reference/write_mrs.html
+++ b/docs/reference/write_mrs.html
@@ -1,5 +1,5 @@
-Write MRS data object to file. — write_mrs • Spectroscopy Analysis Tools (spant) Write MRS data object to file. — write_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Arguments
diff --git a/docs/reference/write_mrs_nifti.html b/docs/reference/write_mrs_nifti.html
index f4bf1921..bd3ed4b7 100644
--- a/docs/reference/write_mrs_nifti.html
+++ b/docs/reference/write_mrs_nifti.html
@@ -1,5 +1,5 @@
-Write MRS data object to file in NIFTI format. — write_mrs_nifti • Spectroscopy Analysis Tools (spant) Write MRS data object to file in NIFTI format. — write_mrs_nifti • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/write_pulse_ascii.html b/docs/reference/write_pulse_ascii.html
index 067ae086..221f8ebb 100644
--- a/docs/reference/write_pulse_ascii.html
+++ b/docs/reference/write_pulse_ascii.html
@@ -1,5 +1,5 @@
-Write an ASCII formatted pulse file. — write_pulse_ascii • Spectroscopy Analysis Tools (spant) Write an ASCII formatted pulse file. — write_pulse_ascii • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/zero_fade_spec.html b/docs/reference/zero_fade_spec.html
index c703745c..c8b572c3 100644
--- a/docs/reference/zero_fade_spec.html
+++ b/docs/reference/zero_fade_spec.html
@@ -1,7 +1,5 @@
-Fade a spectrum to zero by frequency domain multiplication with a tanh
-function. Note this operation distorts data points at the end of the FID. — zero_fade_spec • Spectroscopy Analysis Tools (spant) Fade a spectrum to zero by frequency domain multiplication with a tanh function. Note this operation distorts data points at the end of the FID. — zero_fade_spec • Spectroscopy Analysis Tools (spant) Zero all coherences including and above a given order. — zero_higher_orders • Spectroscopy Analysis Tools (spant) Zero all coherences including and above a given order. — zero_higher_orders • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Value
diff --git a/docs/reference/zero_td_pts_end.html b/docs/reference/zero_td_pts_end.html
index 8c1123c8..71d24ebb 100644
--- a/docs/reference/zero_td_pts_end.html
+++ b/docs/reference/zero_td_pts_end.html
@@ -1,5 +1,5 @@
-Set mrs_data object data points at the end of the FID to zero. — zero_td_pts_end • Spectroscopy Analysis Tools (spant) Set mrs_data object data points at the end of the FID to zero. — zero_td_pts_end • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/zf.html b/docs/reference/zf.html
index 85e2013c..baf50256 100644
--- a/docs/reference/zf.html
+++ b/docs/reference/zf.html
@@ -1,5 +1,5 @@
-Zero-fill MRS data in the time domain. — zf • Spectroscopy Analysis Tools (spant) Zero-fill MRS data in the time domain. — zf • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -125,7 +125,7 @@ Value
diff --git a/docs/reference/zf_xy.html b/docs/reference/zf_xy.html
index ebca3999..c4104a74 100644
--- a/docs/reference/zf_xy.html
+++ b/docs/reference/zf_xy.html
@@ -1,5 +1,5 @@
-Zero-fill MRSI data in the k-space x-y direction. — zf_xy • Spectroscopy Analysis Tools (spant) Zero-fill MRSI data in the k-space x-y direction. — zf_xy • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -113,7 +113,7 @@ Value
diff --git a/docs/sitemap.xml b/docs/sitemap.xml
index e2139f71..4c39f515 100644
--- a/docs/sitemap.xml
+++ b/docs/sitemap.xml
@@ -216,6 +216,12 @@
https://martin3141.github.io/spant/reference/comb_coils_fp_pc.html
+
+ https://martin3141.github.io/spant/reference/comb_coils_mrsi_gls.html
+
+
+ https://martin3141.github.io/spant/reference/comb_coils_svs_gls.html
+
https://martin3141.github.io/spant/reference/comb_csv_results.html
@@ -411,6 +417,9 @@
https://martin3141.github.io/spant/reference/gen_conv_reg.html
+
+ https://martin3141.github.io/spant/reference/gen_group_reg.html
+
https://martin3141.github.io/spant/reference/gen_impulse_reg.html
@@ -555,6 +564,15 @@
https://martin3141.github.io/spant/reference/glm_spec.html
+
+ https://martin3141.github.io/spant/reference/glm_spec_fmrs_fl.html
+
+
+ https://martin3141.github.io/spant/reference/glm_spec_fmrs_group.html
+
+
+ https://martin3141.github.io/spant/reference/glm_spec_group_linhyp.html
+
https://martin3141.github.io/spant/reference/grid_shift_xy.html
@@ -690,9 +708,15 @@
https://martin3141.github.io/spant/reference/mrs_data2basis.html
+
+ https://martin3141.github.io/spant/reference/mrs_data2bids.html
+
https://martin3141.github.io/spant/reference/mrs_data2mat.html
+
+ https://martin3141.github.io/spant/reference/mrs_data2spec_mat.html
+
https://martin3141.github.io/spant/reference/mrs_data2vec.html
@@ -741,6 +765,9 @@
https://martin3141.github.io/spant/reference/phase.html
+
+ https://martin3141.github.io/spant/reference/phase_ref_1h_brain.html
+
https://martin3141.github.io/spant/reference/plot.fit_result.html
@@ -780,6 +807,12 @@
https://martin3141.github.io/spant/reference/precomp.html
+
+ https://martin3141.github.io/spant/reference/preproc_svs.html
+
+
+ https://martin3141.github.io/spant/reference/preproc_svs_dataset.html
+
https://martin3141.github.io/spant/reference/print.fit_result.html
@@ -1050,6 +1083,9 @@
https://martin3141.github.io/spant/reference/spant_mpress_drift.html
+
+ https://martin3141.github.io/spant/reference/spant_sim_fmrs_dataset.html
+
https://martin3141.github.io/spant/reference/spant_simulation_benchmark.html
@@ -1107,6 +1143,9 @@
https://martin3141.github.io/spant/reference/svs_1h_brain_batch_analysis.html
+
+ https://martin3141.github.io/spant/reference/t_test_spec.html
+
https://martin3141.github.io/spant/reference/td2fd.html
Covert a linewidth in Hz to an equivalent alpha value in the time-domain ie: -x * exp(-t * alpha).
Covert a linewidth in Hz to an equivalent alpha value in the time-domain ie: x * exp(-t * alpha).
Covert a linewidth in Hz to an equivalent beta value in the time-domain ie: -x * exp(-t * t * beta).
Covert a linewidth in Hz to an equivalent beta value in the time-domain ie: x * exp(-t * t * beta).
Make a basis-set object from a directory containing LCModel formatted RAW -files.
Make a basis-set object from a directory containing LCModel formatted RAW files.
All functions
- Mask the voxels outside an elliptical region spanning the MRSI dataset in the
-x-y plane.
Mask the voxels outside an elliptical region spanning the MRSI dataset in the x-y plane.
@@ -860,13 +846,11 @@ All functions
- Convert a matrix (with spectral points in the column dimension and dynamics
-in the row dimensions) into a mrs_data object.
Convert a matrix (with spectral points in the column dimension and dynamics in the row dimensions) into a mrs_data object.
- Matrix exponential function taken from complexplus package to reduce the
-number of spant dependencies.
Matrix exponential function taken from complexplus package to reduce the number of spant dependencies.
@@ -914,31 +898,31 @@ All functions
- Convert an mrs_data object to basis object - where basis signals are spread
-across the dynamic dimension in the MRS data.
Convert an mrs_data object to basis object - where basis signals are spread across the dynamic dimension in the MRS data.
+
+
+ Create a BIDS file structure from a vector of MRS data paths or list of mrs_data objects.
- Convert mrs_data object to a matrix, with spectral points in the column
-dimension and dynamics in the row dimension.
Convert mrs_data object to a matrix, with spectral points in the column dimension and dynamics in the row dimension.
-
+
- Convert mrs_data object to a vector.
Convert mrs_data object to a matrix, with spectral points in the column dimension and dynamics in the row dimension.
-
+
- Create a BIDS directory and file structure from a list of mrs_data objects.
Convert mrs_data object to a vector.
- Perform a fftshift on a matrix, with each column replaced by its shifted
-result.
Perform a fftshift on a matrix, with each column replaced by its shifted result.
- Perform an ifftshift on a matrix, with each column replaced by its shifted
-result.
Perform an ifftshift on a matrix, with each column replaced by its shifted result.
@@ -946,9 +930,7 @@ All functions
- Flip the x data dimension order of a nifti image. This corresponds to
-flipping MRI data in the left-right direction, assuming the data in save in
-neurological format (can check with fslorient program).
Flip the x data dimension order of a nifti image. This corresponds to flipping MRI data in the left-right direction, assuming the data in save in neurological format (can check with fslorient program).
@@ -964,8 +946,7 @@ All functions
- Search for the highest peak in a spectral region and return the frequency,
-height and FWHM.
Search for the highest peak in a spectral region and return the frequency, height and FWHM.
@@ -974,6 +955,10 @@ All functions phase()
Apply phasing parameters to MRS data.
+
+
+ Corrected zero order phase and chemical shift offset in 1H MRS data from the brain.
@@ -1005,8 +990,7 @@ All functions
- Plot an interactive slice map from a data array where voxels can be selected
-to display a corresponding spectrum.
Plot an interactive slice map from a data array where voxels can be selected to display a corresponding spectrum.
@@ -1026,8 +1010,15 @@ All functions
- Save function results to file and load on subsequent calls to avoid repeat
-computation.
Save function results to file and load on subsequent calls to avoid repeat computation.
+
+
+ Preprocess and perform quality assessment of a single SVS data set.
+
+
+ Preprocess and perform quality assessment of one or more SVS data sets.
@@ -1055,15 +1046,11 @@ All functions
- Read a directory containing Siemens MRS IMA files and combine along the coil
-dimension. Note that the coil ID is inferred from the sorted file name and
-should be checked when consistency is required between two directories.
Read a directory containing Siemens MRS IMA files and combine along the coil dimension. Note that the coil ID is inferred from the sorted file name and should be checked when consistency is required between two directories.
- Read a directory containing Siemens MRS IMA files and combine along the
-dynamic dimension. Note that the coil ID is inferred from the sorted file
-name and should be checked when consistency is required.
Read a directory containing Siemens MRS IMA files and combine along the dynamic dimension. Note that the coil ID is inferred from the sorted file name and should be checked when consistency is required.
@@ -1103,13 +1090,11 @@ All functions
- Reconstruct complex time-domain data from the real part of frequency-domain
-data.
Reconstruct complex time-domain data from the real part of frequency-domain data.
- Reconstruct complex time-domain data from the real part of frequency-domain
-data.
Reconstruct complex time-domain data from the real part of frequency-domain data.
@@ -1141,8 +1126,7 @@ All functions
- Resample a VOI to match a target image space using nearest-neighbour
-interpolation.
Resample a VOI to match a target image space using nearest-neighbour interpolation.
@@ -1158,23 +1142,19 @@ All functions
- Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water).
Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / kg of tissue water).
- Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water).
Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / kg of tissue water).
- Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / Litre of tissue).
Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / Litre of tissue).
- Convert default LCM/TARQUIN concentration scaling to molal units with partial
-volume correction.
Convert default LCM/TARQUIN concentration scaling to molal units with partial volume correction.
@@ -1222,8 +1202,7 @@ All functions
- MEGA-PRESS sequence with ideal localisation pulses and Gaussian shaped
-editing pulse.
MEGA-PRESS sequence with ideal localisation pulses and Gaussian shaped editing pulse.
@@ -1251,13 +1230,11 @@ All functions
- STEAM sequence with ideal pulses and coherence order filtering to simulate
-gradient crushers.
STEAM sequence with ideal pulses and coherence order filtering to simulate gradient crushers.
- STEAM sequence with ideal pulses using the z-rotation gradient simulation
-method described by Young et al JMR 140, 146-152 (1999).
STEAM sequence with ideal pulses using the z-rotation gradient simulation method described by Young et al JMR 140, 146-152 (1999).
@@ -1293,8 +1270,7 @@ All functions
- Set the number of time-domain data points, truncating or zero-filling as
-appropriate.
Set the number of time-domain data points, truncating or zero-filling as appropriate.
@@ -1318,18 +1294,15 @@ All functions
- Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS
-sequence. Note, ideal pulses are assumed.
Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS sequence. Note, ideal pulses are assumed.
- Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS
-sequence. Note, ideal pulses are assumed.
Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS sequence. Note, ideal pulses are assumed.
- Simulate a macromolecular and lipid basis-set suitable for 1H brain MRS
-analysis.
Simulate a macromolecular and lipid basis-set suitable for 1H brain MRS analysis.
@@ -1353,8 +1326,7 @@ All functions
- Simulate an ideal pulse excitation profile by smoothing a top-hat function
-with a Gaussian.
Simulate an ideal pulse excitation profile by smoothing a top-hat function with a Gaussian.
@@ -1374,17 +1346,19 @@ All functions
- Simulate and fit some spectra with ABfit for benchmarking purposes. Basic
-timing and performance metrics will be printed.
Simulate and fit some spectra with ABfit for benchmarking purposes. Basic timing and performance metrics will be printed.
Example MEGA-PRESS data with significant B0 drift.
+
+
+ Simulate an example fMRS dataset for a block design fMRS experiment and export a BIDS structure.
- Simulate a typical metabolite basis set for benchmarking. Timing metrics will
-be printed on completion.
Simulate a typical metabolite basis set for benchmarking. Timing metrics will be printed on completion.
@@ -1400,8 +1374,7 @@ All functions
- Convert SPM style segmentation files to a single categorical image where
-the numerical values map as: 0) Other, 1) CSF, 2) GM and 3) WM.
Convert SPM style segmentation files to a single categorical image where the numerical values map as: 0) Other, 1) CSF, 2) GM and 3) WM.
@@ -1413,8 +1386,7 @@ All functions
- Plot the fitting results of an object of class fit_result with
-individual basis set components shown.
Plot the fitting results of an object of class fit_result with individual basis set components shown.
@@ -1459,6 +1431,10 @@ All functions svs_1h_brain_batch_analysis()
Batch interface to the standard SVS 1H brain analysis pipeline.
+
+
+ Perform a t-test on spectral data points.
@@ -1518,8 +1494,7 @@ All functions
- Fade a spectrum to zero by frequency domain multiplication with a tanh
-function. Note this operation distorts data points at the end of the FID.
Fade a spectrum to zero by frequency domain multiplication with a tanh function. Note this operation distorts data points at the end of the FID.
@@ -1549,7 +1524,7 @@ All functions
diff --git a/docs/reference/int_spec.html b/docs/reference/int_spec.html
index c7060fe7..783325a8 100644
--- a/docs/reference/int_spec.html
+++ b/docs/reference/int_spec.html
@@ -1,5 +1,5 @@
-Integrate a spectral region. — int_spec • Spectroscopy Analysis Tools (spant) Integrate a spectral region. — int_spec • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -118,7 +118,7 @@ Value
diff --git a/docs/reference/interleave_dyns.html b/docs/reference/interleave_dyns.html
index effe5543..441eff27 100644
--- a/docs/reference/interleave_dyns.html
+++ b/docs/reference/interleave_dyns.html
@@ -1,5 +1,5 @@
-Interleave the first and second half of a dynamic series. — interleave_dyns • Spectroscopy Analysis Tools (spant) Interleave the first and second half of a dynamic series. — interleave_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/inv_even_dyns.html b/docs/reference/inv_even_dyns.html
index 9f9d4fff..dcb781dc 100644
--- a/docs/reference/inv_even_dyns.html
+++ b/docs/reference/inv_even_dyns.html
@@ -1,5 +1,5 @@
-Invert even numbered dynamic scans starting from 1 (2,4,6...). — inv_even_dyns • Spectroscopy Analysis Tools (spant) Invert even numbered dynamic scans starting from 1 (2,4,6...). — inv_even_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/inv_odd_dyns.html b/docs/reference/inv_odd_dyns.html
index 26212e2b..78d64660 100644
--- a/docs/reference/inv_odd_dyns.html
+++ b/docs/reference/inv_odd_dyns.html
@@ -1,5 +1,5 @@
-Invert odd numbered dynamic scans starting from 1 (1,3,5...). — inv_odd_dyns • Spectroscopy Analysis Tools (spant) Invert odd numbered dynamic scans starting from 1 (1,3,5...). — inv_odd_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/is.def.html b/docs/reference/is.def.html
index f196ffd0..a67b9eba 100644
--- a/docs/reference/is.def.html
+++ b/docs/reference/is.def.html
@@ -1,5 +1,5 @@
-Check if an object is defined, which is the same as being not NULL. — is.def • Spectroscopy Analysis Tools (spant) Check if an object is defined, which is the same as being not NULL. — is.def • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/is_fd.html b/docs/reference/is_fd.html
index 3b0ca165..18a193aa 100644
--- a/docs/reference/is_fd.html
+++ b/docs/reference/is_fd.html
@@ -1,7 +1,5 @@
-Check if the chemical shift dimension of an MRS data object is in the
-frequency domain. — is_fd • Spectroscopy Analysis Tools (spant) Check if the chemical shift dimension of an MRS data object is in the frequency domain. — is_fd • Spectroscopy Analysis Tools (spant) Transform 2D MRSI data from k-space to image space in the x-y direction. — kspace2img_xy • Spectroscopy Analysis Tools (spant) Transform 2D MRSI data from k-space to image space in the x-y direction. — kspace2img_xy • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/l2_reg.html b/docs/reference/l2_reg.html
index 3d781d80..21aa9849 100644
--- a/docs/reference/l2_reg.html
+++ b/docs/reference/l2_reg.html
@@ -1,5 +1,5 @@
-Perform l2 regularisation artefact suppression. — l2_reg • Spectroscopy Analysis Tools (spant) Perform l2 regularisation artefact suppression. — l2_reg • Spectroscopy Analysis Tools (spant) Apply line-broadening (apodisation) to MRS data or basis object. — lb • Spectroscopy Analysis Tools (spant) Apply line-broadening (apodisation) to MRS data or basis object. — lb • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -123,7 +123,7 @@ Value
diff --git a/docs/reference/lofdc.html b/docs/reference/lofdc.html
index 5419b1ec..31347a25 100644
--- a/docs/reference/lofdc.html
+++ b/docs/reference/lofdc.html
@@ -1,5 +1,5 @@
-Correct linear frequency drift. — lofdc • Spectroscopy Analysis Tools (spant) Correct linear frequency drift. — lofdc • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -138,7 +138,7 @@ Value
diff --git a/docs/reference/lw2alpha.html b/docs/reference/lw2alpha.html
index b83db682..25da229b 100644
--- a/docs/reference/lw2alpha.html
+++ b/docs/reference/lw2alpha.html
@@ -1,7 +1,5 @@
-Covert a linewidth in Hz to an equivalent alpha value in the time-domain ie:
-x * exp(-t * alpha). — lw2alpha • Spectroscopy Analysis Tools (spant) Covert a linewidth in Hz to an equivalent alpha value in the time-domain ie: x * exp(-t * alpha). — lw2alpha • Spectroscopy Analysis Tools (spant) Covert a linewidth in Hz to an equivalent beta value in the time-domain ie:
-x * exp(-t * t * beta). — lw2beta • Spectroscopy Analysis Tools (spant) Covert a linewidth in Hz to an equivalent beta value in the time-domain ie: x * exp(-t * t * beta). — lw2beta • Spectroscopy Analysis Tools (spant) Make a basis-set object from a directory containing LCModel formatted RAW
-files. — make_basis_from_raw • Spectroscopy Analysis Tools (spant) Make a basis-set object from a directory containing LCModel formatted RAW files. — make_basis_from_raw • Spectroscopy Analysis Tools (spant) Mask an MRS dataset in the dynamic dimension. — mask_dyns • Spectroscopy Analysis Tools (spant) Mask an MRS dataset in the dynamic dimension. — mask_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/mask_fit_res.html b/docs/reference/mask_fit_res.html
index 97baaa3f..ebd91a99 100644
--- a/docs/reference/mask_fit_res.html
+++ b/docs/reference/mask_fit_res.html
@@ -1,5 +1,5 @@
-Mask fit result spectra depending on a vector of bool values. — mask_fit_res • Spectroscopy Analysis Tools (spant) Mask fit result spectra depending on a vector of bool values. — mask_fit_res • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -116,7 +116,7 @@ Value
diff --git a/docs/reference/mask_xy.html b/docs/reference/mask_xy.html
index 11bb577c..b0d38619 100644
--- a/docs/reference/mask_xy.html
+++ b/docs/reference/mask_xy.html
@@ -1,5 +1,5 @@
-Mask an MRSI dataset in the x-y direction — mask_xy • Spectroscopy Analysis Tools (spant) Mask an MRSI dataset in the x-y direction — mask_xy • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/mask_xy_corners.html b/docs/reference/mask_xy_corners.html
index 09b16cd2..2d13839d 100644
--- a/docs/reference/mask_xy_corners.html
+++ b/docs/reference/mask_xy_corners.html
@@ -1,5 +1,5 @@
-Mask the four corners of an MRSI dataset in the x-y plane. — mask_xy_corners • Spectroscopy Analysis Tools (spant) Mask the four corners of an MRSI dataset in the x-y plane. — mask_xy_corners • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/mask_xy_ellipse.html b/docs/reference/mask_xy_ellipse.html
index 1d8b02e4..e2e749ef 100644
--- a/docs/reference/mask_xy_ellipse.html
+++ b/docs/reference/mask_xy_ellipse.html
@@ -1,7 +1,5 @@
-Mask the voxels outside an elliptical region spanning the MRSI dataset in the
-x-y plane. — mask_xy_ellipse • Spectroscopy Analysis Tools (spant) Mask the voxels outside an elliptical region spanning the MRSI dataset in the x-y plane. — mask_xy_ellipse • Spectroscopy Analysis Tools (spant) Mask a 2D MRSI dataset in the x-y dimension. — mask_xy_mat • Spectroscopy Analysis Tools (spant) Mask a 2D MRSI dataset in the x-y dimension. — mask_xy_mat • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Value
diff --git a/docs/reference/mat2mrs_data.html b/docs/reference/mat2mrs_data.html
index 2e2895f3..ae55665f 100644
--- a/docs/reference/mat2mrs_data.html
+++ b/docs/reference/mat2mrs_data.html
@@ -1,7 +1,5 @@
-Convert a matrix (with spectral points in the column dimension and dynamics
-in the row dimensions) into a mrs_data object. — mat2mrs_data • Spectroscopy Analysis Tools (spant) Convert a matrix (with spectral points in the column dimension and dynamics in the row dimensions) into a mrs_data object. — mat2mrs_data • Spectroscopy Analysis Tools (spant) Matrix exponential function taken from complexplus package to reduce the
-number of spant dependencies. — matexp • Spectroscopy Analysis Tools (spant) Matrix exponential function taken from complexplus package to reduce the number of spant dependencies. — matexp • Spectroscopy Analysis Tools (spant) Apply the max operator to an MRS dataset. — max_mrs • Spectroscopy Analysis Tools (spant) Apply the max operator to an MRS dataset. — max_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/max_mrs_interp.html b/docs/reference/max_mrs_interp.html
index e4474764..52e63f3e 100644
--- a/docs/reference/max_mrs_interp.html
+++ b/docs/reference/max_mrs_interp.html
@@ -1,5 +1,5 @@
-Apply the max operator to an interpolated MRS dataset. — max_mrs_interp • Spectroscopy Analysis Tools (spant) Apply the max operator to an interpolated MRS dataset. — max_mrs_interp • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/mean.list.html b/docs/reference/mean.list.html
index b8eb3463..048306fd 100644
--- a/docs/reference/mean.list.html
+++ b/docs/reference/mean.list.html
@@ -1,5 +1,5 @@
-Calculate the mean spectrum from an mrs_data object. — mean.list • Spectroscopy Analysis Tools (spant) Calculate the mean spectrum from an mrs_data object. — mean.list • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/mean.mrs_data.html b/docs/reference/mean.mrs_data.html
index 5531a28d..79515014 100644
--- a/docs/reference/mean.mrs_data.html
+++ b/docs/reference/mean.mrs_data.html
@@ -1,5 +1,5 @@
-Calculate the mean spectrum from an mrs_data object. — mean.mrs_data • Spectroscopy Analysis Tools (spant) Calculate the mean spectrum from an mrs_data object. — mean.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/mean_dyn_blocks.html b/docs/reference/mean_dyn_blocks.html
index 10467098..4c042448 100644
--- a/docs/reference/mean_dyn_blocks.html
+++ b/docs/reference/mean_dyn_blocks.html
@@ -1,5 +1,5 @@
-Calculate the mean of adjacent dynamic scans. — mean_dyn_blocks • Spectroscopy Analysis Tools (spant) Calculate the mean of adjacent dynamic scans. — mean_dyn_blocks • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/mean_dyn_pairs.html b/docs/reference/mean_dyn_pairs.html
index 63e909ea..1a241126 100644
--- a/docs/reference/mean_dyn_pairs.html
+++ b/docs/reference/mean_dyn_pairs.html
@@ -1,5 +1,5 @@
-Calculate the pairwise means across a dynamic data set. — mean_dyn_pairs • Spectroscopy Analysis Tools (spant) Calculate the pairwise means across a dynamic data set. — mean_dyn_pairs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/mean_dyns.html b/docs/reference/mean_dyns.html
index 73fdbfa7..0daa27df 100644
--- a/docs/reference/mean_dyns.html
+++ b/docs/reference/mean_dyns.html
@@ -1,5 +1,5 @@
-Calculate the mean dynamic data. — mean_dyns • Spectroscopy Analysis Tools (spant) Calculate the mean dynamic data. — mean_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/mean_mrs_list.html b/docs/reference/mean_mrs_list.html
index 808b6c50..10d842c0 100644
--- a/docs/reference/mean_mrs_list.html
+++ b/docs/reference/mean_mrs_list.html
@@ -1,5 +1,5 @@
-Return the mean of a list of mrs_data objects. — mean_mrs_list • Spectroscopy Analysis Tools (spant) Return the mean of a list of mrs_data objects. — mean_mrs_list • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/mean_vec_blocks.html b/docs/reference/mean_vec_blocks.html
index 8fc92eaa..dd78b122 100644
--- a/docs/reference/mean_vec_blocks.html
+++ b/docs/reference/mean_vec_blocks.html
@@ -1,5 +1,5 @@
-Calculate the mean of adjacent blocks in a vector. — mean_vec_blocks • Spectroscopy Analysis Tools (spant) Calculate the mean of adjacent blocks in a vector. — mean_vec_blocks • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/median_dyns.html b/docs/reference/median_dyns.html
index 1039d4b5..9a085b10 100644
--- a/docs/reference/median_dyns.html
+++ b/docs/reference/median_dyns.html
@@ -1,5 +1,5 @@
-Calculate the median dynamic data. — median_dyns • Spectroscopy Analysis Tools (spant) Calculate the median dynamic data. — median_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/mod_td.html b/docs/reference/mod_td.html
index 76ad0a40..141ef09e 100644
--- a/docs/reference/mod_td.html
+++ b/docs/reference/mod_td.html
@@ -1,5 +1,5 @@
-Apply the Modulus operator to the time-domain MRS signal. — mod_td • Spectroscopy Analysis Tools (spant) Apply the Modulus operator to the time-domain MRS signal. — mod_td • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/mrs_data2basis.html b/docs/reference/mrs_data2basis.html
index 62f7d749..11797b91 100644
--- a/docs/reference/mrs_data2basis.html
+++ b/docs/reference/mrs_data2basis.html
@@ -1,7 +1,5 @@
-Convert an mrs_data object to basis object - where basis signals are spread
-across the dynamic dimension in the MRS data. — mrs_data2basis • Spectroscopy Analysis Tools (spant) Convert an mrs_data object to basis object - where basis signals are spread across the dynamic dimension in the MRS data. — mrs_data2basis • Spectroscopy Analysis Tools (spant) Create a BIDS file structure from a vector of MRS data paths or list of mrs_data objects. — mrs_data2bids • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Create a BIDS file structure from a vector of MRS data paths or list of mrs_data objects.
+ Source: R/fmrs.R
+ mrs_data2bids.Rd
+
+
+
+ Create a BIDS file structure from a vector of MRS data paths or list of
+mrs_data objects.
+
+
+
+ mrs_data2bids(
+ mrs_data,
+ output_dir,
+ suffix = NULL,
+ sub = NULL,
+ ses = NULL,
+ task = NULL,
+ acq = NULL,
+ nuc = NULL,
+ voi = NULL,
+ rec = NULL,
+ run = NULL,
+ echo = NULL,
+ inv = NULL,
+ skip_existing = TRUE
+)
+
+
+
+ Arguments
+ - mrs_data
+vector of MRS data paths or list of mrs_data objects.
- output_dir
+the base directory to create the BIDS structure.
- suffix
+optional vector of file suffixes. Default behaviour is to
+automatically determine these from the input data, however it is recommended
+that they are specified to allow more efficient skipping of existing data.
- sub
+optional vector of subject labels. If not specified, these will be
+automatically generated as a series of increasing zero-padded integer values
+corresponding to the mrs_data input indices.
- ses
+optional vector of session labels.
- task
+optional vector of task labels.
- acq
+optional vector of acquisition labels.
- nuc
+optional vector of nucleus labels.
- voi
+optional vector of volume of interest labels.
- rec
+optional vector of reconstruction labels.
- run
+optional vector of run indices.
- echo
+optional vector of echo time indices.
- inv
+optional vector of inversion indices.
- skip_existing
+skip any data files that have already been converted.
+Defaults to TRUE, set to FALSE to force an overwrite of any existing data
+files.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/mrs_data2mat.html b/docs/reference/mrs_data2mat.html
index cf5ff28c..9e47688a 100644
--- a/docs/reference/mrs_data2mat.html
+++ b/docs/reference/mrs_data2mat.html
@@ -1,7 +1,5 @@
-Convert mrs_data object to a matrix, with spectral points in the column
-dimension and dynamics in the row dimension. — mrs_data2mat • Spectroscopy Analysis Tools (spant) Convert mrs_data object to a matrix, with spectral points in the column dimension and dynamics in the row dimension. — mrs_data2mat • Spectroscopy Analysis Tools (spant) Convert mrs_data object to a matrix, with spectral points in the column dimension and dynamics in the row dimension. — mrs_data2spec_mat • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Convert mrs_data object to a matrix, with spectral points in the column dimension and dynamics in the row dimension.
+ Source: R/mrs_data_proc.R
+ mrs_data2spec_mat.Rd
+
+
+
+ Convert mrs_data object to a matrix, with spectral points in the column
+dimension and dynamics in the row dimension.
+
+
+
+ mrs_data2spec_mat(mrs_data, collapse = TRUE)
+
+
+
+ Arguments
+ - mrs_data
+MRS data object or list of MRS data objects.
- collapse
+collapse all other dimensions along the dynamic dimension, eg
+a 16x16 MRSI grid would be first collapsed across 256 dynamic scans.
+
+ Value
+
+
+MRS data matrix.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/mrs_data2vec.html b/docs/reference/mrs_data2vec.html
index fb172d68..a1fd654d 100644
--- a/docs/reference/mrs_data2vec.html
+++ b/docs/reference/mrs_data2vec.html
@@ -1,5 +1,5 @@
-Convert mrs_data object to a vector. — mrs_data2vec • Spectroscopy Analysis Tools (spant) Convert mrs_data object to a vector. — mrs_data2vec • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -126,7 +126,7 @@ Value
diff --git a/docs/reference/mvfftshift.html b/docs/reference/mvfftshift.html
index 92b0841b..976b3410 100644
--- a/docs/reference/mvfftshift.html
+++ b/docs/reference/mvfftshift.html
@@ -1,7 +1,5 @@
-Perform a fftshift on a matrix, with each column replaced by its shifted
-result. — mvfftshift • Spectroscopy Analysis Tools (spant) Perform a fftshift on a matrix, with each column replaced by its shifted result. — mvfftshift • Spectroscopy Analysis Tools (spant) Perform an ifftshift on a matrix, with each column replaced by its shifted
-result. — mvifftshift • Spectroscopy Analysis Tools (spant) Perform an ifftshift on a matrix, with each column replaced by its shifted result. — mvifftshift • Spectroscopy Analysis Tools (spant) Print fit coordinates from a single index. — n2coord • Spectroscopy Analysis Tools (spant) Print fit coordinates from a single index. — n2coord • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/nifti_flip_lr.html b/docs/reference/nifti_flip_lr.html
index 730abe3c..19860b3c 100644
--- a/docs/reference/nifti_flip_lr.html
+++ b/docs/reference/nifti_flip_lr.html
@@ -1,9 +1,5 @@
-Flip the x data dimension order of a nifti image. This corresponds to
-flipping MRI data in the left-right direction, assuming the data in save in
-neurological format (can check with fslorient program). — nifti_flip_lr • Spectroscopy Analysis Tools (spant) Flip the x data dimension order of a nifti image. This corresponds to flipping MRI data in the left-right direction, assuming the data in save in neurological format (can check with fslorient program). — nifti_flip_lr • Spectroscopy Analysis Tools (spant) Export a one-page pdf of a single fit result — one_page_pdf • Spectroscopy Analysis Tools (spant) Export a one-page pdf of a single fit result — one_page_pdf • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -108,7 +108,7 @@ Arguments
diff --git a/docs/reference/ortho3.html b/docs/reference/ortho3.html
index 13ade97d..5d7dd2fd 100644
--- a/docs/reference/ortho3.html
+++ b/docs/reference/ortho3.html
@@ -1,5 +1,5 @@
-Display an orthographic projection plot of a nifti object. — ortho3 • Spectroscopy Analysis Tools (spant) Display an orthographic projection plot of a nifti object. — ortho3 • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -172,7 +172,7 @@ Arguments
diff --git a/docs/reference/ortho3_inter.html b/docs/reference/ortho3_inter.html
index 090cc5e5..15948899 100644
--- a/docs/reference/ortho3_inter.html
+++ b/docs/reference/ortho3_inter.html
@@ -1,5 +1,5 @@
-Display an interactive orthographic projection plot of a nifti object. — ortho3_inter • Spectroscopy Analysis Tools (spant) Display an interactive orthographic projection plot of a nifti object. — ortho3_inter • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -132,7 +132,7 @@ Arguments
diff --git a/docs/reference/peak_info.html b/docs/reference/peak_info.html
index 09058bd8..41c8ffaf 100644
--- a/docs/reference/peak_info.html
+++ b/docs/reference/peak_info.html
@@ -1,7 +1,5 @@
-Search for the highest peak in a spectral region and return the frequency,
-height and FWHM. — peak_info • Spectroscopy Analysis Tools (spant) Search for the highest peak in a spectral region and return the frequency, height and FWHM. — peak_info • Spectroscopy Analysis Tools (spant) Papoulis-Gerchberg (PG) algorithm method for k-space extrapolation. — pg_extrap_xy • Spectroscopy Analysis Tools (spant) Papoulis-Gerchberg (PG) algorithm method for k-space extrapolation. — pg_extrap_xy • Spectroscopy Analysis Tools (spant) Apply phasing parameters to MRS data. — phase • Spectroscopy Analysis Tools (spant) Apply phasing parameters to MRS data. — phase • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/phase_ref_1h_brain.html b/docs/reference/phase_ref_1h_brain.html
new file mode 100644
index 00000000..8707a74a
--- /dev/null
+++ b/docs/reference/phase_ref_1h_brain.html
@@ -0,0 +1,131 @@
+
+Corrected zero order phase and chemical shift offset in 1H MRS data from the brain. — phase_ref_1h_brain • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Corrected zero order phase and chemical shift offset in 1H MRS data from the brain.
+ Source: R/rats.R
+ phase_ref_1h_brain.Rd
+
+
+
+ Corrected zero order phase and chemical shift offset in 1H MRS data from the
+brain.
+
+
+
+ phase_ref_1h_brain(mrs_data, mean_ref = FALSE, ret_corr_only = TRUE)
+
+
+
+ Arguments
+ - mrs_data
+MRS data to be corrected.
- mean_ref
+apply the phase and offset of the mean spectrum to all
+others. Default is FALSE.
- ret_corr_only
+return the corrected data only.
+
+ Value
+
+
+corrected MRS data.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/plot.fit_result.html b/docs/reference/plot.fit_result.html
index e54d3bc1..836a53ee 100644
--- a/docs/reference/plot.fit_result.html
+++ b/docs/reference/plot.fit_result.html
@@ -1,5 +1,5 @@
-Plot the fitting results of an object of class fit_result. — plot.fit_result • Spectroscopy Analysis Tools (spant) Plot the fitting results of an object of class fit_result. — plot.fit_result • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -207,7 +207,7 @@ Arguments
diff --git a/docs/reference/plot.mrs_data.html b/docs/reference/plot.mrs_data.html
index fabcc35b..bb2ec651 100644
--- a/docs/reference/plot.mrs_data.html
+++ b/docs/reference/plot.mrs_data.html
@@ -1,5 +1,5 @@
-Plotting method for objects of class mrs_data. — plot.mrs_data • Spectroscopy Analysis Tools (spant) Plotting method for objects of class mrs_data. — plot.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -287,7 +287,7 @@ Arguments
diff --git a/docs/reference/plot_bc.html b/docs/reference/plot_bc.html
index 4f8309b4..b48142cc 100644
--- a/docs/reference/plot_bc.html
+++ b/docs/reference/plot_bc.html
@@ -1,5 +1,5 @@
-Convenience function to plot a baseline estimate with the original data. — plot_bc • Spectroscopy Analysis Tools (spant) Convenience function to plot a baseline estimate with the original data. — plot_bc • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -108,7 +108,7 @@ Arguments
diff --git a/docs/reference/plot_reg.html b/docs/reference/plot_reg.html
index ae1acbe7..2addb2f6 100644
--- a/docs/reference/plot_reg.html
+++ b/docs/reference/plot_reg.html
@@ -1,5 +1,5 @@
-Plot regressors as an image. — plot_reg • Spectroscopy Analysis Tools (spant) Plot regressors as an image. — plot_reg • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/plot_slice_fit.html b/docs/reference/plot_slice_fit.html
index fbc7b560..57f1af8a 100644
--- a/docs/reference/plot_slice_fit.html
+++ b/docs/reference/plot_slice_fit.html
@@ -1,5 +1,5 @@
-Plot a 2D slice from an MRSI fit result object. — plot_slice_fit • Spectroscopy Analysis Tools (spant) Plot a 2D slice from an MRSI fit result object. — plot_slice_fit • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -129,7 +129,7 @@ Arguments
diff --git a/docs/reference/plot_slice_fit_inter.html b/docs/reference/plot_slice_fit_inter.html
index 4eed104a..da105a7d 100644
--- a/docs/reference/plot_slice_fit_inter.html
+++ b/docs/reference/plot_slice_fit_inter.html
@@ -1,5 +1,5 @@
-Plot a 2D slice from an MRSI fit result object. — plot_slice_fit_inter • Spectroscopy Analysis Tools (spant) Plot a 2D slice from an MRSI fit result object. — plot_slice_fit_inter • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -134,7 +134,7 @@ Arguments
diff --git a/docs/reference/plot_slice_map.html b/docs/reference/plot_slice_map.html
index 553e9ac8..ffb2a134 100644
--- a/docs/reference/plot_slice_map.html
+++ b/docs/reference/plot_slice_map.html
@@ -1,5 +1,5 @@
-Plot a slice from a 7 dimensional array. — plot_slice_map • Spectroscopy Analysis Tools (spant) Plot a slice from a 7 dimensional array. — plot_slice_map • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -153,7 +153,7 @@ Arguments
diff --git a/docs/reference/plot_slice_map_inter.html b/docs/reference/plot_slice_map_inter.html
index 40d33b42..90968f66 100644
--- a/docs/reference/plot_slice_map_inter.html
+++ b/docs/reference/plot_slice_map_inter.html
@@ -1,7 +1,5 @@
-Plot an interactive slice map from a data array where voxels can be selected
-to display a corresponding spectrum. — plot_slice_map_inter • Spectroscopy Analysis Tools (spant) Plot an interactive slice map from a data array where voxels can be selected to display a corresponding spectrum. — plot_slice_map_inter • Spectroscopy Analysis Tools (spant) Plot the spectral standard deviation. — plot_spec_sd • Spectroscopy Analysis Tools (spant) Plot the spectral standard deviation. — plot_spec_sd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Arguments
diff --git a/docs/reference/plot_voi_overlay.html b/docs/reference/plot_voi_overlay.html
index 9a782e88..bbbbf35e 100644
--- a/docs/reference/plot_voi_overlay.html
+++ b/docs/reference/plot_voi_overlay.html
@@ -1,5 +1,5 @@
-Plot a volume as an image overlay. — plot_voi_overlay • Spectroscopy Analysis Tools (spant) Plot a volume as an image overlay. — plot_voi_overlay • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -116,7 +116,7 @@ Arguments
diff --git a/docs/reference/plot_voi_overlay_seg.html b/docs/reference/plot_voi_overlay_seg.html
index 3d4e74ff..0e800ff2 100644
--- a/docs/reference/plot_voi_overlay_seg.html
+++ b/docs/reference/plot_voi_overlay_seg.html
@@ -1,5 +1,5 @@
-Plot a volume as an overlay on a segmented brain volume. — plot_voi_overlay_seg • Spectroscopy Analysis Tools (spant) Plot a volume as an overlay on a segmented brain volume. — plot_voi_overlay_seg • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Arguments
diff --git a/docs/reference/ppm.html b/docs/reference/ppm.html
index c352327a..ee4696e2 100644
--- a/docs/reference/ppm.html
+++ b/docs/reference/ppm.html
@@ -1,5 +1,5 @@
-Return the ppm scale of an MRS dataset or fit result. — ppm • Spectroscopy Analysis Tools (spant) Return the ppm scale of an MRS dataset or fit result. — ppm • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -132,7 +132,7 @@ Value
diff --git a/docs/reference/precomp.html b/docs/reference/precomp.html
index 822d7336..df3d2c6c 100644
--- a/docs/reference/precomp.html
+++ b/docs/reference/precomp.html
@@ -1,7 +1,5 @@
-Save function results to file and load on subsequent calls to avoid repeat
-computation. — precomp • Spectroscopy Analysis Tools (spant) Save function results to file and load on subsequent calls to avoid repeat computation. — precomp • Spectroscopy Analysis Tools (spant) Preprocess and perform quality assessment of a single SVS data set. — preproc_svs • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Preprocess and perform quality assessment of a single SVS data set.
+ Source: R/fmrs.R
+ preproc_svs.Rd
+
+
+
+ Preprocess and perform quality assessment of a single SVS data set.
+
+
+
+ preproc_svs(path, label = NULL, output_dir = NULL, ref_inds = NULL)
+
+
+
+ Arguments
+ - path
+path to the fMRS data file or IMA directory.
- label
+a label to describe the data set.
- output_dir
+output directory.
- ref_inds
+a vector of 1-based indices for any water reference dynamic
+scans.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/preproc_svs_dataset.html b/docs/reference/preproc_svs_dataset.html
new file mode 100644
index 00000000..07c3a29b
--- /dev/null
+++ b/docs/reference/preproc_svs_dataset.html
@@ -0,0 +1,148 @@
+
+Preprocess and perform quality assessment of one or more SVS data sets. — preproc_svs_dataset • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Preprocess and perform quality assessment of one or more SVS data sets.
+ Source: R/fmrs.R
+ preproc_svs_dataset.Rd
+
+
+
+ Preprocess and perform quality assessment of one or more SVS data sets.
+
+
+
+ preproc_svs_dataset(
+ paths,
+ labels = NULL,
+ output_dir = "spant_analysis",
+ exclude_labels = NULL,
+ overwrite = FALSE,
+ ref_inds = NULL,
+ return_results = FALSE
+)
+
+
+
+ Arguments
+ - paths
+paths to the fMRS data file or IMA directory.
- labels
+labels to describe each data set.
- output_dir
+output directory.
- exclude_labels
+vector of labels of scans to exclude, eg poor quality
+data.
- overwrite
+overwrite saved results, defaults to FALSE.
- ref_inds
+a vector of 1-based indices for any water reference dynamic
+scans.
- return_results
+function will return key outputs, defaults to FALSE.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/print.fit_result.html b/docs/reference/print.fit_result.html
index 297f28dc..5f434e57 100644
--- a/docs/reference/print.fit_result.html
+++ b/docs/reference/print.fit_result.html
@@ -1,5 +1,5 @@
-Print a summary of an object of class fit_result. — print.fit_result • Spectroscopy Analysis Tools (spant) Print a summary of an object of class fit_result. — print.fit_result • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -105,7 +105,7 @@ Arguments
diff --git a/docs/reference/print.mrs_data.html b/docs/reference/print.mrs_data.html
index 51199017..e1561eb2 100644
--- a/docs/reference/print.mrs_data.html
+++ b/docs/reference/print.mrs_data.html
@@ -1,5 +1,5 @@
-Print a summary of mrs_data parameters. — print.mrs_data • Spectroscopy Analysis Tools (spant) Print a summary of mrs_data parameters. — print.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -109,7 +109,7 @@ Arguments
diff --git a/docs/reference/qn_states.html b/docs/reference/qn_states.html
index 0f42f2f9..d7aa6715 100644
--- a/docs/reference/qn_states.html
+++ b/docs/reference/qn_states.html
@@ -1,5 +1,5 @@
-Get the quantum coherence matrix for a spin system. — qn_states • Spectroscopy Analysis Tools (spant) Get the quantum coherence matrix for a spin system. — qn_states • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/rats.html b/docs/reference/rats.html
index 5a39a396..93585e08 100644
--- a/docs/reference/rats.html
+++ b/docs/reference/rats.html
@@ -1,5 +1,5 @@
-Robust Alignment to a Target Spectrum (RATS). — rats • Spectroscopy Analysis Tools (spant) Robust Alignment to a Target Spectrum (RATS). — rats • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -207,7 +207,7 @@ Value
diff --git a/docs/reference/re_weighting.html b/docs/reference/re_weighting.html
index d21caf21..8b0b070a 100644
--- a/docs/reference/re_weighting.html
+++ b/docs/reference/re_weighting.html
@@ -1,5 +1,5 @@
-Apply a weighting to the FID to enhance spectral resolution. — re_weighting • Spectroscopy Analysis Tools (spant) Apply a weighting to the FID to enhance spectral resolution. — re_weighting • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/read_basis.html b/docs/reference/read_basis.html
index da9b94af..eb6f8557 100644
--- a/docs/reference/read_basis.html
+++ b/docs/reference/read_basis.html
@@ -1,5 +1,5 @@
-Read a basis file in LCModel .basis format. — read_basis • Spectroscopy Analysis Tools (spant) Read a basis file in LCModel .basis format. — read_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/read_ima_coil_dir.html b/docs/reference/read_ima_coil_dir.html
index 28c02de0..4f073cd8 100644
--- a/docs/reference/read_ima_coil_dir.html
+++ b/docs/reference/read_ima_coil_dir.html
@@ -1,9 +1,5 @@
-Read a directory containing Siemens MRS IMA files and combine along the coil
-dimension. Note that the coil ID is inferred from the sorted file name and
-should be checked when consistency is required between two directories. — read_ima_coil_dir • Spectroscopy Analysis Tools (spant) Read a directory containing Siemens MRS IMA files and combine along the coil dimension. Note that the coil ID is inferred from the sorted file name and should be checked when consistency is required between two directories. — read_ima_coil_dir • Spectroscopy Analysis Tools (spant) Read a directory containing Siemens MRS IMA files and combine along the
-dynamic dimension. Note that the coil ID is inferred from the sorted file
-name and should be checked when consistency is required. — read_ima_dyn_dir • Spectroscopy Analysis Tools (spant) Read a directory containing Siemens MRS IMA files and combine along the dynamic dimension. Note that the coil ID is inferred from the sorted file name and should be checked when consistency is required. — read_ima_dyn_dir • Spectroscopy Analysis Tools (spant) Read an LCModel formatted coord file containing fit information. — read_lcm_coord • Spectroscopy Analysis Tools (spant) Read an LCModel formatted coord file containing fit information. — read_lcm_coord • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -107,7 +107,7 @@ Value
diff --git a/docs/reference/read_mrs.html b/docs/reference/read_mrs.html
index 3ac2a36b..2cf36b20 100644
--- a/docs/reference/read_mrs.html
+++ b/docs/reference/read_mrs.html
@@ -1,5 +1,5 @@
-Read MRS data from a file. — read_mrs • Spectroscopy Analysis Tools (spant) Read MRS data from a file. — read_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -88,7 +88,8 @@ Read MRS data from a file.
full_fid = FALSE,
omit_svs_ref_scans = TRUE,
verbose = FALSE,
- extra = NULL
+ extra = NULL,
+ fid_filt_dist = NULL
)
@@ -140,6 +141,13 @@ Arguments
an optional data frame to provide additional variables for use
in subsequent analysis steps, eg id or grouping variables.
fid_filt_dist
+indicate if the data has a distorted FID due to a
+brick-wall filter being used to downsample the data. Default is to auto
+detect this from the data, but TRUE or FALSE options can be given to override
+detection.
Value
@@ -183,7 +191,7 @@ Examples
diff --git a/docs/reference/read_mrs_tqn.html b/docs/reference/read_mrs_tqn.html
index 5766362f..84bdaf3a 100644
--- a/docs/reference/read_mrs_tqn.html
+++ b/docs/reference/read_mrs_tqn.html
@@ -1,5 +1,5 @@
-Read MRS data using the TARQUIN software package. — read_mrs_tqn • Spectroscopy Analysis Tools (spant) Read MRS data using the TARQUIN software package. — read_mrs_tqn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -131,7 +131,7 @@ Examples
diff --git a/docs/reference/read_pulse_ascii.html b/docs/reference/read_pulse_ascii.html
index c9e0d43c..ab11c9cc 100644
--- a/docs/reference/read_pulse_ascii.html
+++ b/docs/reference/read_pulse_ascii.html
@@ -1,5 +1,5 @@
-Read an ASCII formatted pulse file. — read_pulse_ascii • Spectroscopy Analysis Tools (spant) Read an ASCII formatted pulse file. — read_pulse_ascii • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/read_pulse_bruker.html b/docs/reference/read_pulse_bruker.html
index c92bf76a..dbe9073b 100644
--- a/docs/reference/read_pulse_bruker.html
+++ b/docs/reference/read_pulse_bruker.html
@@ -1,5 +1,5 @@
-Read a Bruker formatted pulse file — read_pulse_bruker • Spectroscopy Analysis Tools (spant) Read a Bruker formatted pulse file — read_pulse_bruker • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/read_pulse_pta.html b/docs/reference/read_pulse_pta.html
index 72e1b6d4..a0fac3c3 100644
--- a/docs/reference/read_pulse_pta.html
+++ b/docs/reference/read_pulse_pta.html
@@ -1,5 +1,5 @@
-Read a .pta formatted pulse file compatible with Siemens PulseTool. — read_pulse_pta • Spectroscopy Analysis Tools (spant) Read a .pta formatted pulse file compatible with Siemens PulseTool. — read_pulse_pta • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/read_siemens_txt_hdr.html b/docs/reference/read_siemens_txt_hdr.html
index 23fb8c70..3a17d87c 100644
--- a/docs/reference/read_siemens_txt_hdr.html
+++ b/docs/reference/read_siemens_txt_hdr.html
@@ -1,5 +1,5 @@
-Read the text format header found in Siemens IMA and TWIX data files. — read_siemens_txt_hdr • Spectroscopy Analysis Tools (spant) Read the text format header found in Siemens IMA and TWIX data files. — read_siemens_txt_hdr • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -78,7 +78,7 @@ Read the text format header found in Siemens IMA and TWIX data files.
- read_siemens_txt_hdr(input, version = "vd", verbose, offset = 0)
+ read_siemens_txt_hdr(input, version = "vd", verbose = FALSE, offset = 0)
@@ -118,7 +118,7 @@ Value
diff --git a/docs/reference/read_tqn_fit.html b/docs/reference/read_tqn_fit.html
index 4da6c25e..a1630420 100644
--- a/docs/reference/read_tqn_fit.html
+++ b/docs/reference/read_tqn_fit.html
@@ -1,5 +1,5 @@
-Reader for csv fit results generated by TARQUIN. — read_tqn_fit • Spectroscopy Analysis Tools (spant) Reader for csv fit results generated by TARQUIN. — read_tqn_fit • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -113,7 +113,7 @@ Examples
diff --git a/docs/reference/read_tqn_result.html b/docs/reference/read_tqn_result.html
index 36659714..68a3e98c 100644
--- a/docs/reference/read_tqn_result.html
+++ b/docs/reference/read_tqn_result.html
@@ -1,5 +1,5 @@
-Reader for csv results generated by TARQUIN. — read_tqn_result • Spectroscopy Analysis Tools (spant) Reader for csv results generated by TARQUIN. — read_tqn_result • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -117,7 +117,7 @@ Examples
diff --git a/docs/reference/recon_imag.html b/docs/reference/recon_imag.html
index d2a72225..5bc3b1eb 100644
--- a/docs/reference/recon_imag.html
+++ b/docs/reference/recon_imag.html
@@ -1,7 +1,5 @@
-Reconstruct complex time-domain data from the real part of frequency-domain
-data. — recon_imag • Spectroscopy Analysis Tools (spant) Reconstruct complex time-domain data from the real part of frequency-domain data. — recon_imag • Spectroscopy Analysis Tools (spant) Reconstruct complex time-domain data from the real part of frequency-domain
-data. — recon_imag_vec • Spectroscopy Analysis Tools (spant) Reconstruct complex time-domain data from the real part of frequency-domain data. — recon_imag_vec • Spectroscopy Analysis Tools (spant) Reconstruct 2D MRSI data from a twix file loaded with read_mrs. — recon_twix_2d_mrsi • Spectroscopy Analysis Tools (spant) Reconstruct 2D MRSI data from a twix file loaded with read_mrs. — recon_twix_2d_mrsi • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/rectangular_mask.html b/docs/reference/rectangular_mask.html
index a2117283..6e469bc9 100644
--- a/docs/reference/rectangular_mask.html
+++ b/docs/reference/rectangular_mask.html
@@ -1,5 +1,5 @@
-Create a rectangular mask stored as a matrix of logical values. — rectangular_mask • Spectroscopy Analysis Tools (spant) Create a rectangular mask stored as a matrix of logical values. — rectangular_mask • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -130,7 +130,7 @@ Value
diff --git a/docs/reference/reexports.html b/docs/reference/reexports.html
index 694a75d1..a59e8379 100644
--- a/docs/reference/reexports.html
+++ b/docs/reference/reexports.html
@@ -1,5 +1,5 @@
-Objects exported from other packages — reexports • Spectroscopy Analysis Tools (spant) Objects exported from other packages — reexports • Spectroscopy Analysis Tools (spant)
Spectroscopy Analysis Tools (spant)
- 2.21.0
+ 2.22.0
@@ -103,7 +103,7 @@ Objects exported from other packages
diff --git a/docs/reference/rep_array_dim.html b/docs/reference/rep_array_dim.html
index b9c49b4a..48c0a5ed 100644
--- a/docs/reference/rep_array_dim.html
+++ b/docs/reference/rep_array_dim.html
@@ -1,5 +1,5 @@
-Repeat an array over a given dimension. — rep_array_dim • Spectroscopy Analysis Tools (spant) Repeat an array over a given dimension. — rep_array_dim • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/rep_dyn.html b/docs/reference/rep_dyn.html
index 6bbfb0ef..89a4bb9b 100644
--- a/docs/reference/rep_dyn.html
+++ b/docs/reference/rep_dyn.html
@@ -1,5 +1,5 @@
-Replicate a scan in the dynamic dimension. — rep_dyn • Spectroscopy Analysis Tools (spant) Replicate a scan in the dynamic dimension. — rep_dyn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/rep_mrs.html b/docs/reference/rep_mrs.html
index 67730b5c..becb8f00 100644
--- a/docs/reference/rep_mrs.html
+++ b/docs/reference/rep_mrs.html
@@ -1,5 +1,5 @@
-Replicate a scan over a given dimension. — rep_mrs • Spectroscopy Analysis Tools (spant) Replicate a scan over a given dimension. — rep_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -138,7 +138,7 @@ Value
diff --git a/docs/reference/resample_basis.html b/docs/reference/resample_basis.html
index b0f2ab17..c7a6222a 100644
--- a/docs/reference/resample_basis.html
+++ b/docs/reference/resample_basis.html
@@ -1,5 +1,5 @@
-Resample a basis-set to match a mrs_data acquisition. — resample_basis • Spectroscopy Analysis Tools (spant) Resample a basis-set to match a mrs_data acquisition. — resample_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -116,7 +116,7 @@ Value
diff --git a/docs/reference/resample_img.html b/docs/reference/resample_img.html
index f1e7beaf..b0cc8f71 100644
--- a/docs/reference/resample_img.html
+++ b/docs/reference/resample_img.html
@@ -1,5 +1,5 @@
-Resample an image to match a target image space. — resample_img • Spectroscopy Analysis Tools (spant) Resample an image to match a target image space. — resample_img • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/resample_voi.html b/docs/reference/resample_voi.html
index 8fbfa836..a29ab096 100644
--- a/docs/reference/resample_voi.html
+++ b/docs/reference/resample_voi.html
@@ -1,7 +1,5 @@
-Resample a VOI to match a target image space using nearest-neighbour
-interpolation. — resample_voi • Spectroscopy Analysis Tools (spant) Resample a VOI to match a target image space using nearest-neighbour interpolation. — resample_voi • Spectroscopy Analysis Tools (spant) Reslice a nifti object to match the orientation of mrs data. — reslice_to_mrs • Spectroscopy Analysis Tools (spant) Reslice a nifti object to match the orientation of mrs data. — reslice_to_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/reson_table2mrs_data.html b/docs/reference/reson_table2mrs_data.html
index d75579ee..c5a2167a 100644
--- a/docs/reference/reson_table2mrs_data.html
+++ b/docs/reference/reson_table2mrs_data.html
@@ -1,5 +1,5 @@
-Generate mrs_data from a table of single Lorentzian resonances. — reson_table2mrs_data • Spectroscopy Analysis Tools (spant) Generate mrs_data from a table of single Lorentzian resonances. — reson_table2mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -119,7 +119,7 @@ Value
diff --git a/docs/reference/rm_dyns.html b/docs/reference/rm_dyns.html
index 5d5ef692..573e1f51 100644
--- a/docs/reference/rm_dyns.html
+++ b/docs/reference/rm_dyns.html
@@ -1,5 +1,5 @@
-Remove a subset of dynamic scans. — rm_dyns • Spectroscopy Analysis Tools (spant) Remove a subset of dynamic scans. — rm_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/scale_amp_molal.html b/docs/reference/scale_amp_molal.html
index aaeee1f2..7acb8cb0 100644
--- a/docs/reference/scale_amp_molal.html
+++ b/docs/reference/scale_amp_molal.html
@@ -1,7 +1,5 @@
-Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water). — scale_amp_molal • Spectroscopy Analysis Tools (spant) Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / kg of tissue water). — scale_amp_molal • Spectroscopy Analysis Tools (spant)
Spectroscopy Analysis Tools (spant)
- 2.21.0
+ 2.22.0
@@ -76,8 +74,7 @@
- Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water).
+ Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / kg of tissue water).
Source: R/amp_scaling.R
scale_amp_molal.Rd
@@ -163,7 +160,7 @@ Value
diff --git a/docs/reference/scale_amp_molal_pvc.html b/docs/reference/scale_amp_molal_pvc.html
index 962d6afc..4d194abd 100644
--- a/docs/reference/scale_amp_molal_pvc.html
+++ b/docs/reference/scale_amp_molal_pvc.html
@@ -1,7 +1,5 @@
-Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water). — scale_amp_molal_pvc • Spectroscopy Analysis Tools (spant)
@@ -75,8 +73,7 @@
- Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water).
+ Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / kg of tissue water).
Source: R/amp_scaling.R
scale_amp_molal_pvc.Rd
@@ -141,7 +138,7 @@ Value
diff --git a/docs/reference/scale_amp_molar.html b/docs/reference/scale_amp_molar.html
index 02358d91..dc87a338 100644
--- a/docs/reference/scale_amp_molar.html
+++ b/docs/reference/scale_amp_molar.html
@@ -1,7 +1,5 @@
-Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / Litre of tissue). — scale_amp_molar • Spectroscopy Analysis Tools (spant) Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / Litre of tissue). — scale_amp_molar • Spectroscopy Analysis Tools (spant) Convert default LCM/TARQUIN concentration scaling to molal units with partial
-volume correction. — scale_amp_molar2molal_pvc • Spectroscopy Analysis Tools (spant) Convert default LCM/TARQUIN concentration scaling to molal units with partial volume correction. — scale_amp_molar2molal_pvc • Spectroscopy Analysis Tools (spant) Scale fitted amplitudes to a ratio of signal amplitude. — scale_amp_ratio • Spectroscopy Analysis Tools (spant) Scale fitted amplitudes to a ratio of signal amplitude. — scale_amp_ratio • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -116,7 +116,7 @@ Value
diff --git a/docs/reference/scale_amp_ratio_value.html b/docs/reference/scale_amp_ratio_value.html
index 2036837a..6af8ac51 100644
--- a/docs/reference/scale_amp_ratio_value.html
+++ b/docs/reference/scale_amp_ratio_value.html
@@ -1,5 +1,5 @@
-Scale fitted amplitudes to a ratio of signal amplitude. — scale_amp_ratio_value • Spectroscopy Analysis Tools (spant) Scale fitted amplitudes to a ratio of signal amplitude. — scale_amp_ratio_value • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/scale_amp_water_ratio.html b/docs/reference/scale_amp_water_ratio.html
index 5b25e884..35a76b00 100644
--- a/docs/reference/scale_amp_water_ratio.html
+++ b/docs/reference/scale_amp_water_ratio.html
@@ -1,5 +1,5 @@
-Scale metabolite amplitudes as a ratio to the unsuppressed water amplitude. — scale_amp_water_ratio • Spectroscopy Analysis Tools (spant) Scale metabolite amplitudes as a ratio to the unsuppressed water amplitude. — scale_amp_water_ratio • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/scale_basis_amp.html b/docs/reference/scale_basis_amp.html
index 9401c3f1..5a58b5e5 100644
--- a/docs/reference/scale_basis_amp.html
+++ b/docs/reference/scale_basis_amp.html
@@ -1,5 +1,5 @@
-Scale a basis object by a scalar. — scale_basis_amp • Spectroscopy Analysis Tools (spant) Scale a basis object by a scalar. — scale_basis_amp • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/scale_basis_from_singlet.html b/docs/reference/scale_basis_from_singlet.html
index 0d542bc8..c9a19e77 100644
--- a/docs/reference/scale_basis_from_singlet.html
+++ b/docs/reference/scale_basis_from_singlet.html
@@ -1,5 +1,5 @@
-Scale a basis-set to be consistent with spant assumptions for water scaling. — scale_basis_from_singlet • Spectroscopy Analysis Tools (spant) Scale a basis-set to be consistent with spant assumptions for water scaling. — scale_basis_from_singlet • Spectroscopy Analysis Tools (spant)
Spectroscopy Analysis Tools (spant)
- 2.21.0
+ 2.22.0
@@ -127,7 +127,7 @@ Value
diff --git a/docs/reference/scale_mrs_amp.html b/docs/reference/scale_mrs_amp.html
index b5501a0d..990f058a 100644
--- a/docs/reference/scale_mrs_amp.html
+++ b/docs/reference/scale_mrs_amp.html
@@ -1,5 +1,5 @@
-Scale an mrs_data object by a scalar or vector or amplitudes. — scale_mrs_amp • Spectroscopy Analysis Tools (spant) Scale an mrs_data object by a scalar or vector or amplitudes. — scale_mrs_amp • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/scale_spec.html b/docs/reference/scale_spec.html
index 4f6ea835..6b3ddba4 100644
--- a/docs/reference/scale_spec.html
+++ b/docs/reference/scale_spec.html
@@ -1,5 +1,5 @@
-Scale mrs_data to a spectral region. — scale_spec • Spectroscopy Analysis Tools (spant) Scale mrs_data to a spectral region. — scale_spec • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -141,7 +141,7 @@ Value
diff --git a/docs/reference/sd.html b/docs/reference/sd.html
index ea1eec9f..3ae4dfd4 100644
--- a/docs/reference/sd.html
+++ b/docs/reference/sd.html
@@ -1,5 +1,5 @@
-Calculate the standard deviation spectrum from an mrs_data object. — sd • Spectroscopy Analysis Tools (spant) Calculate the standard deviation spectrum from an mrs_data object. — sd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/sd.mrs_data.html b/docs/reference/sd.mrs_data.html
index 3f92a49f..13bdda85 100644
--- a/docs/reference/sd.mrs_data.html
+++ b/docs/reference/sd.mrs_data.html
@@ -1,5 +1,5 @@
-Calculate the standard deviation spectrum from an mrs_data object. — sd.mrs_data • Spectroscopy Analysis Tools (spant) Calculate the standard deviation spectrum from an mrs_data object. — sd.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/seconds.html b/docs/reference/seconds.html
index b34d6627..467ee17f 100644
--- a/docs/reference/seconds.html
+++ b/docs/reference/seconds.html
@@ -1,5 +1,5 @@
-Return a time scale vector to match the FID of an MRS data object. — seconds • Spectroscopy Analysis Tools (spant) Return a time scale vector to match the FID of an MRS data object. — seconds • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/seq_cpmg_ideal.html b/docs/reference/seq_cpmg_ideal.html
index 547e96ab..45727c86 100644
--- a/docs/reference/seq_cpmg_ideal.html
+++ b/docs/reference/seq_cpmg_ideal.html
@@ -1,5 +1,5 @@
-CPMG style sequence with ideal pulses. — seq_cpmg_ideal • Spectroscopy Analysis Tools (spant) CPMG style sequence with ideal pulses. — seq_cpmg_ideal • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/seq_mega_press_ideal.html b/docs/reference/seq_mega_press_ideal.html
index 0769b8b4..a9cd7fa0 100644
--- a/docs/reference/seq_mega_press_ideal.html
+++ b/docs/reference/seq_mega_press_ideal.html
@@ -1,7 +1,5 @@
-MEGA-PRESS sequence with ideal localisation pulses and Gaussian shaped
-editing pulse. — seq_mega_press_ideal • Spectroscopy Analysis Tools (spant) MEGA-PRESS sequence with ideal localisation pulses and Gaussian shaped editing pulse. — seq_mega_press_ideal • Spectroscopy Analysis Tools (spant) PRESS sequence with shaped refocusing pulses. — seq_press_2d_shaped • Spectroscopy Analysis Tools (spant) PRESS sequence with shaped refocusing pulses. — seq_press_2d_shaped • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -165,7 +165,7 @@ Value
diff --git a/docs/reference/seq_press_ideal.html b/docs/reference/seq_press_ideal.html
index 8c976856..72c3af3d 100644
--- a/docs/reference/seq_press_ideal.html
+++ b/docs/reference/seq_press_ideal.html
@@ -1,5 +1,5 @@
-PRESS sequence with ideal pulses. — seq_press_ideal • Spectroscopy Analysis Tools (spant) PRESS sequence with ideal pulses. — seq_press_ideal • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/seq_pulse_acquire.html b/docs/reference/seq_pulse_acquire.html
index 4a88fc64..ad80571e 100644
--- a/docs/reference/seq_pulse_acquire.html
+++ b/docs/reference/seq_pulse_acquire.html
@@ -1,5 +1,5 @@
-Simple pulse and acquire sequence with ideal pulses. — seq_pulse_acquire • Spectroscopy Analysis Tools (spant) Simple pulse and acquire sequence with ideal pulses. — seq_pulse_acquire • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/seq_slaser_ideal.html b/docs/reference/seq_slaser_ideal.html
index 74688f4d..eb83e8e3 100644
--- a/docs/reference/seq_slaser_ideal.html
+++ b/docs/reference/seq_slaser_ideal.html
@@ -1,5 +1,5 @@
-sLASER sequence with ideal pulses. — seq_slaser_ideal • Spectroscopy Analysis Tools (spant) sLASER sequence with ideal pulses. — seq_slaser_ideal • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -126,7 +126,7 @@ Value
diff --git a/docs/reference/seq_spin_echo_ideal.html b/docs/reference/seq_spin_echo_ideal.html
index e23271de..4248716f 100644
--- a/docs/reference/seq_spin_echo_ideal.html
+++ b/docs/reference/seq_spin_echo_ideal.html
@@ -1,5 +1,5 @@
-Spin echo sequence with ideal pulses. — seq_spin_echo_ideal • Spectroscopy Analysis Tools (spant) Spin echo sequence with ideal pulses. — seq_spin_echo_ideal • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/seq_steam_ideal.html b/docs/reference/seq_steam_ideal.html
index a60685a8..1c8115d7 100644
--- a/docs/reference/seq_steam_ideal.html
+++ b/docs/reference/seq_steam_ideal.html
@@ -1,5 +1,5 @@
-STEAM sequence with ideal pulses. — seq_steam_ideal • Spectroscopy Analysis Tools (spant) STEAM sequence with ideal pulses. — seq_steam_ideal • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -128,7 +128,7 @@ Value
diff --git a/docs/reference/seq_steam_ideal_cof.html b/docs/reference/seq_steam_ideal_cof.html
index 8f225740..cba7af91 100644
--- a/docs/reference/seq_steam_ideal_cof.html
+++ b/docs/reference/seq_steam_ideal_cof.html
@@ -1,7 +1,5 @@
-STEAM sequence with ideal pulses and coherence order filtering to simulate
-gradient crushers. — seq_steam_ideal_cof • Spectroscopy Analysis Tools (spant) STEAM sequence with ideal pulses and coherence order filtering to simulate gradient crushers. — seq_steam_ideal_cof • Spectroscopy Analysis Tools (spant) STEAM sequence with ideal pulses using the z-rotation gradient simulation
-method described by Young et al JMR 140, 146-152 (1999). — seq_steam_ideal_young • Spectroscopy Analysis Tools (spant) STEAM sequence with ideal pulses using the z-rotation gradient simulation method described by Young et al JMR 140, 146-152 (1999). — seq_steam_ideal_young • Spectroscopy Analysis Tools (spant) Set the number of transients for an mrs_data object. — set_Ntrans • Spectroscopy Analysis Tools (spant) Set the number of transients for an mrs_data object. — set_Ntrans • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/set_def_acq_paras.html b/docs/reference/set_def_acq_paras.html
index 3e1b4004..cc2ada9c 100644
--- a/docs/reference/set_def_acq_paras.html
+++ b/docs/reference/set_def_acq_paras.html
@@ -1,5 +1,5 @@
-Set the default acquisition parameters. — set_def_acq_paras • Spectroscopy Analysis Tools (spant) Set the default acquisition parameters. — set_def_acq_paras • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Arguments
diff --git a/docs/reference/set_lcm_cmd.html b/docs/reference/set_lcm_cmd.html
index 2056ed01..42bb2f24 100644
--- a/docs/reference/set_lcm_cmd.html
+++ b/docs/reference/set_lcm_cmd.html
@@ -1,5 +1,5 @@
-Set the command to run the LCModel command-line program. — set_lcm_cmd • Spectroscopy Analysis Tools (spant) Set the command to run the LCModel command-line program. — set_lcm_cmd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/set_lw.html b/docs/reference/set_lw.html
index b64ec851..bb176c62 100644
--- a/docs/reference/set_lw.html
+++ b/docs/reference/set_lw.html
@@ -1,5 +1,5 @@
-Apply line-broadening to an mrs_data object to achieve a specified linewidth. — set_lw • Spectroscopy Analysis Tools (spant) Apply line-broadening to an mrs_data object to achieve a specified linewidth. — set_lw • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -123,7 +123,7 @@ Value
diff --git a/docs/reference/set_mask_xy_mat.html b/docs/reference/set_mask_xy_mat.html
index 49dc5d4e..52c4b617 100644
--- a/docs/reference/set_mask_xy_mat.html
+++ b/docs/reference/set_mask_xy_mat.html
@@ -1,5 +1,5 @@
-Set the masked voxels in a 2D MRSI dataset to given spectrum. — set_mask_xy_mat • Spectroscopy Analysis Tools (spant) Set the masked voxels in a 2D MRSI dataset to given spectrum. — set_mask_xy_mat • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Value
diff --git a/docs/reference/set_precomp_mode.html b/docs/reference/set_precomp_mode.html
index f44bd5d3..47c28e3b 100644
--- a/docs/reference/set_precomp_mode.html
+++ b/docs/reference/set_precomp_mode.html
@@ -1,5 +1,5 @@
-Set the precompute mode. — set_precomp_mode • Spectroscopy Analysis Tools (spant) Set the precompute mode. — set_precomp_mode • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/set_precomp_verbose.html b/docs/reference/set_precomp_verbose.html
index 1453a231..9c613505 100644
--- a/docs/reference/set_precomp_verbose.html
+++ b/docs/reference/set_precomp_verbose.html
@@ -1,5 +1,5 @@
-Set the verbosity of the precompute function. — set_precomp_verbose • Spectroscopy Analysis Tools (spant) Set the verbosity of the precompute function. — set_precomp_verbose • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/set_ref.html b/docs/reference/set_ref.html
index 8953fa50..5436dfa2 100644
--- a/docs/reference/set_ref.html
+++ b/docs/reference/set_ref.html
@@ -1,5 +1,5 @@
-Set the ppm reference value (eg ppm value at 0Hz). — set_ref • Spectroscopy Analysis Tools (spant) Set the ppm reference value (eg ppm value at 0Hz). — set_ref • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/set_td_pts.html b/docs/reference/set_td_pts.html
index 8a80d42a..586459ff 100644
--- a/docs/reference/set_td_pts.html
+++ b/docs/reference/set_td_pts.html
@@ -1,7 +1,5 @@
-Set the number of time-domain data points, truncating or zero-filling as
-appropriate. — set_td_pts • Spectroscopy Analysis Tools (spant) Set the number of time-domain data points, truncating or zero-filling as appropriate. — set_td_pts • Spectroscopy Analysis Tools (spant) Set the command to run the TARQUIN command-line program. — set_tqn_cmd • Spectroscopy Analysis Tools (spant) Set the command to run the TARQUIN command-line program. — set_tqn_cmd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/set_tr.html b/docs/reference/set_tr.html
index b2109ab0..65c9df5f 100644
--- a/docs/reference/set_tr.html
+++ b/docs/reference/set_tr.html
@@ -1,5 +1,5 @@
-Set the repetition time of an MRS dataset. — set_tr • Spectroscopy Analysis Tools (spant) Set the repetition time of an MRS dataset. — set_tr • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/shift.html b/docs/reference/shift.html
index ab0fe724..034591d0 100644
--- a/docs/reference/shift.html
+++ b/docs/reference/shift.html
@@ -1,5 +1,5 @@
-Apply a frequency shift to MRS data. — shift • Spectroscopy Analysis Tools (spant) Apply a frequency shift to MRS data. — shift • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/shift_basis.html b/docs/reference/shift_basis.html
index 2884be19..f55a65e0 100644
--- a/docs/reference/shift_basis.html
+++ b/docs/reference/shift_basis.html
@@ -1,5 +1,5 @@
-Apply frequency shifts to basis set signals. — shift_basis • Spectroscopy Analysis Tools (spant) Apply frequency shifts to basis set signals. — shift_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Value
diff --git a/docs/reference/sim_basis.html b/docs/reference/sim_basis.html
index c7838c46..bb5fefc6 100644
--- a/docs/reference/sim_basis.html
+++ b/docs/reference/sim_basis.html
@@ -1,5 +1,5 @@
-Simulate a basis set object. — sim_basis • Spectroscopy Analysis Tools (spant) Simulate a basis set object. — sim_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -136,7 +136,7 @@ Value
diff --git a/docs/reference/sim_basis_1h_brain.html b/docs/reference/sim_basis_1h_brain.html
index 62ed7389..f71ffa0b 100644
--- a/docs/reference/sim_basis_1h_brain.html
+++ b/docs/reference/sim_basis_1h_brain.html
@@ -1,7 +1,5 @@
-Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS
-sequence. Note, ideal pulses are assumed. — sim_basis_1h_brain • Spectroscopy Analysis Tools (spant) Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS sequence. Note, ideal pulses are assumed. — sim_basis_1h_brain • Spectroscopy Analysis Tools (spant) Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS
-sequence. Note, ideal pulses are assumed. — sim_basis_1h_brain_press • Spectroscopy Analysis Tools (spant) Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS sequence. Note, ideal pulses are assumed. — sim_basis_1h_brain_press • Spectroscopy Analysis Tools (spant) Simulate a macromolecular and lipid basis-set suitable for 1H brain MRS
-analysis. — sim_basis_mm_lip_lcm • Spectroscopy Analysis Tools (spant) Simulate a macromolecular and lipid basis-set suitable for 1H brain MRS analysis. — sim_basis_mm_lip_lcm • Spectroscopy Analysis Tools (spant) Simulate a basis file using TARQUIN. — sim_basis_tqn • Spectroscopy Analysis Tools (spant) Simulate a basis file using TARQUIN. — sim_basis_tqn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -129,7 +129,7 @@ Examples
diff --git a/docs/reference/sim_brain_1h.html b/docs/reference/sim_brain_1h.html
index 2044cf1a..717ee289 100644
--- a/docs/reference/sim_brain_1h.html
+++ b/docs/reference/sim_brain_1h.html
@@ -1,5 +1,5 @@
-Simulate MRS data with a similar appearance to normal brain (by default). — sim_brain_1h • Spectroscopy Analysis Tools (spant) Simulate MRS data with a similar appearance to normal brain (by default). — sim_brain_1h • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -159,7 +159,7 @@ Value
diff --git a/docs/reference/sim_mol.html b/docs/reference/sim_mol.html
index 23bcef50..77f76a50 100644
--- a/docs/reference/sim_mol.html
+++ b/docs/reference/sim_mol.html
@@ -1,5 +1,5 @@
-Simulate a mol_parameter object. — sim_mol • Spectroscopy Analysis Tools (spant) Simulate a mol_parameter object. — sim_mol • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -143,7 +143,7 @@ Value
diff --git a/docs/reference/sim_noise.html b/docs/reference/sim_noise.html
index 23875f79..a71477d4 100644
--- a/docs/reference/sim_noise.html
+++ b/docs/reference/sim_noise.html
@@ -1,5 +1,5 @@
-Simulate an mrs_data object containing simulated Gaussian noise. — sim_noise • Spectroscopy Analysis Tools (spant) Simulate an mrs_data object containing simulated Gaussian noise. — sim_noise • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -84,6 +84,7 @@ Simulate an mrs_data object containing simulated Gaussian noise.
ft = def_ft(),
N = def_N(),
ref = def_ref(),
+ nuc = def_nuc(),
dyns = 1,
fd = TRUE
)
@@ -111,6 +112,10 @@ Arguments
reference value for ppm scale.
nuc
+resonant nucleus.
dyns
number of dynamic scans to generate.
Value
diff --git a/docs/reference/sim_resonances.html b/docs/reference/sim_resonances.html
index 19e9a8a4..d4f8d7c0 100644
--- a/docs/reference/sim_resonances.html
+++ b/docs/reference/sim_resonances.html
@@ -1,5 +1,5 @@
-Simulate a MRS data object containing a set of simulated resonances. — sim_resonances • Spectroscopy Analysis Tools (spant) Simulate a MRS data object containing a set of simulated resonances. — sim_resonances • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -161,7 +161,7 @@ Examples
diff --git a/docs/reference/sim_th_excit_profile.html b/docs/reference/sim_th_excit_profile.html
index 5535c5ef..e781cab1 100644
--- a/docs/reference/sim_th_excit_profile.html
+++ b/docs/reference/sim_th_excit_profile.html
@@ -1,7 +1,5 @@
-Simulate an ideal pulse excitation profile by smoothing a top-hat function
-with a Gaussian. — sim_th_excit_profile • Spectroscopy Analysis Tools (spant) Simulate an ideal pulse excitation profile by smoothing a top-hat function with a Gaussian. — sim_th_excit_profile • Spectroscopy Analysis Tools (spant) Simulate an mrs_data object containing complex zero valued samples. — sim_zero • Spectroscopy Analysis Tools (spant) Simulate an mrs_data object containing complex zero valued samples. — sim_zero • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -78,7 +78,14 @@ Simulate an mrs_data object containing complex zero valued samples.
-
+
@@ -99,6 +106,10 @@ Arguments
reference value for ppm scale.
nuc
+resonant nucleus.
dyns
number of dynamic scans to generate.
Value
diff --git a/docs/reference/smooth_dyns.html b/docs/reference/smooth_dyns.html
index 4cc8da50..accf3a51 100644
--- a/docs/reference/smooth_dyns.html
+++ b/docs/reference/smooth_dyns.html
@@ -1,5 +1,5 @@
-Smooth data across the dynamic dimension with a Gaussian kernel. — smooth_dyns • Spectroscopy Analysis Tools (spant) Smooth data across the dynamic dimension with a Gaussian kernel. — smooth_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/sort_basis.html b/docs/reference/sort_basis.html
index 6a676ea2..d25cc006 100644
--- a/docs/reference/sort_basis.html
+++ b/docs/reference/sort_basis.html
@@ -1,5 +1,5 @@
-Sort the basis-set elements alphabetically. — sort_basis • Spectroscopy Analysis Tools (spant) Sort the basis-set elements alphabetically. — sort_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/spant-package.html b/docs/reference/spant-package.html
index b3dd8e21..90f19ec3 100644
--- a/docs/reference/spant-package.html
+++ b/docs/reference/spant-package.html
@@ -1,5 +1,5 @@
-spant: spectroscopy analysis tools. — spant-package • Spectroscopy Analysis Tools (spant) spant: spectroscopy analysis tools. — spant-package • Spectroscopy Analysis Tools (spant) Simulate and fit some spectra with ABfit for benchmarking purposes. Basic
-timing and performance metrics will be printed. — spant_abfit_benchmark • Spectroscopy Analysis Tools (spant) Simulate and fit some spectra with ABfit for benchmarking purposes. Basic timing and performance metrics will be printed. — spant_abfit_benchmark • Spectroscopy Analysis Tools (spant) Example MEGA-PRESS data with significant B0 drift. — spant_mpress_drift • Spectroscopy Analysis Tools (spant) Example MEGA-PRESS data with significant B0 drift. — spant_mpress_drift • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -83,7 +83,7 @@ Example MEGA-PRESS data with significant B0 drift.
Format
- An object of class mrs_data of length 13.
+ An object of class mrs_data of dimension 1 x 1 x 1 x 1 x 40 x 1 x 1024.
@@ -98,7 +98,7 @@ Format
diff --git a/docs/reference/spant_sim_fmrs_dataset.html b/docs/reference/spant_sim_fmrs_dataset.html
new file mode 100644
index 00000000..00e48b56
--- /dev/null
+++ b/docs/reference/spant_sim_fmrs_dataset.html
@@ -0,0 +1,117 @@
+
+Simulate an example fMRS dataset for a block design fMRS experiment and export a BIDS structure. — spant_sim_fmrs_dataset • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Simulate an example fMRS dataset for a block design fMRS experiment and export a BIDS structure.
+ Source: R/fmrs.R
+ spant_sim_fmrs_dataset.Rd
+
+
+
+ Simulate an example fMRS dataset for a block design fMRS experiment and
+export a BIDS structure.
+
+
+
+ spant_sim_fmrs_dataset(output_dir = NULL)
+
+
+
+ Arguments
+ - output_dir
+output directory for the BIDS data. Defaults to :
+"HOME/sim_fmrs_dataset/data".
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/spant_simulation_benchmark.html b/docs/reference/spant_simulation_benchmark.html
index 32daa8bf..d8cc6841 100644
--- a/docs/reference/spant_simulation_benchmark.html
+++ b/docs/reference/spant_simulation_benchmark.html
@@ -1,7 +1,5 @@
-Simulate a typical metabolite basis set for benchmarking. Timing metrics will
-be printed on completion. — spant_simulation_benchmark • Spectroscopy Analysis Tools (spant) Simulate a typical metabolite basis set for benchmarking. Timing metrics will be printed on completion. — spant_simulation_benchmark • Spectroscopy Analysis Tools (spant) Decompose an mrs_data object into white and gray matter spectra. — spec_decomp • Spectroscopy Analysis Tools (spant) Perform a mathematical operation on a spectral region. — spec_op • Spectroscopy Analysis Tools (spant) Perform a mathematical operation on a spectral region. — spec_op • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -98,8 +98,8 @@ Arguments
operator
-can be "sum" (default), "mean", "l2", "max", "min" or
-"max-min".
can be "sum" (default), "mean", "l2", "max", "max_cplx,
+"min" or "max-min".
freq_scale
@@ -129,7 +129,7 @@ Value
diff --git a/docs/reference/spin_sys.html b/docs/reference/spin_sys.html
index 853423a4..1eaa9e76 100644
--- a/docs/reference/spin_sys.html
+++ b/docs/reference/spin_sys.html
@@ -1,5 +1,5 @@
-Create a spin system object for pulse sequence simulation. — spin_sys • Spectroscopy Analysis Tools (spant) Create a spin system object for pulse sequence simulation. — spin_sys • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/spm_pve2categorical.html b/docs/reference/spm_pve2categorical.html
index 23a1bad9..70f10729 100644
--- a/docs/reference/spm_pve2categorical.html
+++ b/docs/reference/spm_pve2categorical.html
@@ -1,7 +1,5 @@
-Convert SPM style segmentation files to a single categorical image where
-the numerical values map as: 0) Other, 1) CSF, 2) GM and 3) WM. — spm_pve2categorical • Spectroscopy Analysis Tools (spant) Convert SPM style segmentation files to a single categorical image where the numerical values map as: 0) Other, 1) CSF, 2) GM and 3) WM. — spm_pve2categorical • Spectroscopy Analysis Tools (spant) Signal space projection method for lipid suppression. — ssp • Spectroscopy Analysis Tools (spant) Signal space projection method for lipid suppression. — ssp • Spectroscopy Analysis Tools (spant) Plot the fitting results of an object of class fit_result with
-individual basis set components shown. — stackplot.fit_result • Spectroscopy Analysis Tools (spant) Plot the fitting results of an object of class fit_result with individual basis set components shown. — stackplot.fit_result • Spectroscopy Analysis Tools (spant) Produce a plot with multiple traces. — stackplot • Spectroscopy Analysis Tools (spant) Produce a plot with multiple traces. — stackplot • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/stackplot.mrs_data.html b/docs/reference/stackplot.mrs_data.html
index 17ff5648..64eea445 100644
--- a/docs/reference/stackplot.mrs_data.html
+++ b/docs/reference/stackplot.mrs_data.html
@@ -1,5 +1,5 @@
-Stackplot plotting method for objects of class mrs_data. — stackplot.mrs_data • Spectroscopy Analysis Tools (spant) Stackplot plotting method for objects of class mrs_data. — stackplot.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -255,7 +255,7 @@ Arguments
diff --git a/docs/reference/sub_first_dyn.html b/docs/reference/sub_first_dyn.html
index dbd7f831..493b7242 100644
--- a/docs/reference/sub_first_dyn.html
+++ b/docs/reference/sub_first_dyn.html
@@ -1,5 +1,5 @@
-Subtract the first dynamic spectrum from a dynamic series. — sub_first_dyn • Spectroscopy Analysis Tools (spant) Subtract the first dynamic spectrum from a dynamic series. — sub_first_dyn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/sub_mean_dyns.html b/docs/reference/sub_mean_dyns.html
index 6e3bb2df..221bd0c1 100644
--- a/docs/reference/sub_mean_dyns.html
+++ b/docs/reference/sub_mean_dyns.html
@@ -1,5 +1,5 @@
-Subtract the mean dynamic spectrum from a dynamic series. — sub_mean_dyns • Spectroscopy Analysis Tools (spant) Subtract the mean dynamic spectrum from a dynamic series. — sub_mean_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/sub_median_dyns.html b/docs/reference/sub_median_dyns.html
index 134c495d..1e834f14 100644
--- a/docs/reference/sub_median_dyns.html
+++ b/docs/reference/sub_median_dyns.html
@@ -1,5 +1,5 @@
-Subtract the median dynamic spectrum from a dynamic series. — sub_median_dyns • Spectroscopy Analysis Tools (spant) Subtract the median dynamic spectrum from a dynamic series. — sub_median_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/sum_coils.html b/docs/reference/sum_coils.html
index 7bf559f2..e1ab3cc0 100644
--- a/docs/reference/sum_coils.html
+++ b/docs/reference/sum_coils.html
@@ -1,5 +1,5 @@
-Calculate the sum across receiver coil elements. — sum_coils • Spectroscopy Analysis Tools (spant) Calculate the sum across receiver coil elements. — sum_coils • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/sum_dyns.html b/docs/reference/sum_dyns.html
index a0be19d3..bbda2ffc 100644
--- a/docs/reference/sum_dyns.html
+++ b/docs/reference/sum_dyns.html
@@ -1,5 +1,5 @@
-Calculate the sum of data dynamics. — sum_dyns • Spectroscopy Analysis Tools (spant) Calculate the sum of data dynamics. — sum_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/sum_mrs.html b/docs/reference/sum_mrs.html
index a22f215b..3cc3ab9e 100644
--- a/docs/reference/sum_mrs.html
+++ b/docs/reference/sum_mrs.html
@@ -1,5 +1,5 @@
-Sum two mrs_data objects. — sum_mrs • Spectroscopy Analysis Tools (spant) Sum two mrs_data objects. — sum_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Value
diff --git a/docs/reference/sum_mrs_list.html b/docs/reference/sum_mrs_list.html
index f4e09aea..c3584348 100644
--- a/docs/reference/sum_mrs_list.html
+++ b/docs/reference/sum_mrs_list.html
@@ -1,5 +1,5 @@
-Return the sum of a list of mrs_data objects. — sum_mrs_list • Spectroscopy Analysis Tools (spant) Return the sum of a list of mrs_data objects. — sum_mrs_list • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/svs_1h_brain_analysis.html b/docs/reference/svs_1h_brain_analysis.html
index 8ce514db..dff0ef7d 100644
--- a/docs/reference/svs_1h_brain_analysis.html
+++ b/docs/reference/svs_1h_brain_analysis.html
@@ -1,5 +1,5 @@
-Standard SVS 1H brain analysis pipeline. — svs_1h_brain_analysis • Spectroscopy Analysis Tools (spant) Standard SVS 1H brain analysis pipeline. — svs_1h_brain_analysis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -199,7 +199,7 @@ Value
diff --git a/docs/reference/svs_1h_brain_analysis_dev.html b/docs/reference/svs_1h_brain_analysis_dev.html
index d70a14d3..d71bfea2 100644
--- a/docs/reference/svs_1h_brain_analysis_dev.html
+++ b/docs/reference/svs_1h_brain_analysis_dev.html
@@ -1,5 +1,5 @@
-Standard SVS 1H brain analysis pipeline. — svs_1h_brain_analysis_dev • Spectroscopy Analysis Tools (spant) Standard SVS 1H brain analysis pipeline. — svs_1h_brain_analysis_dev • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -193,7 +193,7 @@ Examples
diff --git a/docs/reference/svs_1h_brain_batch_analysis.html b/docs/reference/svs_1h_brain_batch_analysis.html
index 5631e8cc..15f7223e 100644
--- a/docs/reference/svs_1h_brain_batch_analysis.html
+++ b/docs/reference/svs_1h_brain_batch_analysis.html
@@ -1,5 +1,5 @@
-Batch interface to the standard SVS 1H brain analysis pipeline. — svs_1h_brain_batch_analysis • Spectroscopy Analysis Tools (spant) Batch interface to the standard SVS 1H brain analysis pipeline. — svs_1h_brain_batch_analysis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -144,7 +144,7 @@ Value
diff --git a/docs/reference/t_test_spec.html b/docs/reference/t_test_spec.html
new file mode 100644
index 00000000..56a7ea1b
--- /dev/null
+++ b/docs/reference/t_test_spec.html
@@ -0,0 +1,124 @@
+
+Perform a t-test on spectral data points. — t_test_spec • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+
+
+ Perform a t-test on spectral data points.
+
+
+
+ t_test_spec(mrs_data, group)
+
+
+
+ Arguments
+ - mrs_data
+an mrs_data object with spectra in the dynamic dimension.
- group
+vector describing the group membership of each dynamic spectrum.
+
+ Value
+
+
+a list of statistical results.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/td2fd.html b/docs/reference/td2fd.html
index 6748a6a8..f31ed524 100644
--- a/docs/reference/td2fd.html
+++ b/docs/reference/td2fd.html
@@ -1,5 +1,5 @@
-Transform time-domain data to the frequency-domain. — td2fd • Spectroscopy Analysis Tools (spant) Transform time-domain data to the frequency-domain. — td2fd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/td_conv_filt.html b/docs/reference/td_conv_filt.html
index a9f340c3..106b9b00 100644
--- a/docs/reference/td_conv_filt.html
+++ b/docs/reference/td_conv_filt.html
@@ -1,5 +1,5 @@
-Time-domain convolution based filter. — td_conv_filt • Spectroscopy Analysis Tools (spant) Time-domain convolution based filter. — td_conv_filt • Spectroscopy Analysis Tools (spant) Time-domain spectral registration. — tdsr • Spectroscopy Analysis Tools (spant) Time-domain spectral registration. — tdsr • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -121,7 +121,7 @@ Value
diff --git a/docs/reference/te.html b/docs/reference/te.html
index 010361b1..4a65711d 100644
--- a/docs/reference/te.html
+++ b/docs/reference/te.html
@@ -1,5 +1,5 @@
-Return the echo time of an MRS dataset. — te • Spectroscopy Analysis Tools (spant) Return the echo time of an MRS dataset. — te • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/tr.html b/docs/reference/tr.html
index 0c0bd63b..2e749e02 100644
--- a/docs/reference/tr.html
+++ b/docs/reference/tr.html
@@ -1,5 +1,5 @@
-Return the repetition time of an MRS dataset. — tr • Spectroscopy Analysis Tools (spant) Return the repetition time of an MRS dataset. — tr • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/varpro_3_para_opts.html b/docs/reference/varpro_3_para_opts.html
index c2270a16..52d7cd84 100644
--- a/docs/reference/varpro_3_para_opts.html
+++ b/docs/reference/varpro_3_para_opts.html
@@ -1,5 +1,5 @@
-Return a list of options for VARPRO based fitting with 3 free parameters. — varpro_3_para_opts • Spectroscopy Analysis Tools (spant) Return a list of options for VARPRO based fitting with 3 free parameters. — varpro_3_para_opts • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -141,7 +141,7 @@ Value
diff --git a/docs/reference/varpro_basic_opts.html b/docs/reference/varpro_basic_opts.html
index 32c86d22..c5104891 100644
--- a/docs/reference/varpro_basic_opts.html
+++ b/docs/reference/varpro_basic_opts.html
@@ -1,5 +1,5 @@
-Return a list of options for a basic VARPRO analysis. — varpro_basic_opts • Spectroscopy Analysis Tools (spant) Return a list of options for a basic VARPRO analysis. — varpro_basic_opts • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -118,7 +118,7 @@ Value
diff --git a/docs/reference/varpro_opts.html b/docs/reference/varpro_opts.html
index 2aabf11d..6332f730 100644
--- a/docs/reference/varpro_opts.html
+++ b/docs/reference/varpro_opts.html
@@ -1,5 +1,5 @@
-Return a list of options for VARPRO based fitting. — varpro_opts • Spectroscopy Analysis Tools (spant) Return a list of options for VARPRO based fitting. — varpro_opts • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -177,7 +177,7 @@ Examples
diff --git a/docs/reference/vec2mrs_data.html b/docs/reference/vec2mrs_data.html
index 0cccd73b..f0d58bf0 100644
--- a/docs/reference/vec2mrs_data.html
+++ b/docs/reference/vec2mrs_data.html
@@ -1,5 +1,5 @@
-Convert a vector into a mrs_data object. — vec2mrs_data • Spectroscopy Analysis Tools (spant) Convert a vector into a mrs_data object. — vec2mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -80,10 +80,11 @@ Convert a vector into a mrs_data object.
vec2mrs_data(
vec,
- fs = def_fs(),
- ft = def_ft(),
- ref = def_ref(),
- nuc = def_nuc(),
+ mrs_data = NULL,
+ fs = NULL,
+ ft = NULL,
+ ref = NULL,
+ nuc = NULL,
dyns = 1,
fd = FALSE
)
@@ -95,6 +96,10 @@ Arguments
the data vector.
mrs_data
+example data to copy acquisition parameters from.
fs
sampling frequency in Hz.
Arguments
fd
-flag to indicate if the matrix is in the frequency domain (logical).
flag to indicate if the vector is in the frequency domain (logical).
Value
diff --git a/docs/reference/write_basis.html b/docs/reference/write_basis.html
index b6e27cbd..94c5e021 100644
--- a/docs/reference/write_basis.html
+++ b/docs/reference/write_basis.html
@@ -1,5 +1,5 @@
-Write a basis object to an LCModel .basis formatted file. — write_basis • Spectroscopy Analysis Tools (spant) Write a basis object to an LCModel .basis formatted file. — write_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -108,7 +108,7 @@ Arguments
diff --git a/docs/reference/write_basis_tqn.html b/docs/reference/write_basis_tqn.html
index 6aa51c1d..116c73ec 100644
--- a/docs/reference/write_basis_tqn.html
+++ b/docs/reference/write_basis_tqn.html
@@ -1,5 +1,5 @@
-Generate a basis file using TARQUIN. — write_basis_tqn • Spectroscopy Analysis Tools (spant) Generate a basis file using TARQUIN. — write_basis_tqn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Examples
diff --git a/docs/reference/write_mrs.html b/docs/reference/write_mrs.html
index fff25f15..124b9dc4 100644
--- a/docs/reference/write_mrs.html
+++ b/docs/reference/write_mrs.html
@@ -1,5 +1,5 @@
-Write MRS data object to file. — write_mrs • Spectroscopy Analysis Tools (spant) Write MRS data object to file. — write_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Arguments
diff --git a/docs/reference/write_mrs_nifti.html b/docs/reference/write_mrs_nifti.html
index f4bf1921..bd3ed4b7 100644
--- a/docs/reference/write_mrs_nifti.html
+++ b/docs/reference/write_mrs_nifti.html
@@ -1,5 +1,5 @@
-Write MRS data object to file in NIFTI format. — write_mrs_nifti • Spectroscopy Analysis Tools (spant) Write MRS data object to file in NIFTI format. — write_mrs_nifti • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/write_pulse_ascii.html b/docs/reference/write_pulse_ascii.html
index 067ae086..221f8ebb 100644
--- a/docs/reference/write_pulse_ascii.html
+++ b/docs/reference/write_pulse_ascii.html
@@ -1,5 +1,5 @@
-Write an ASCII formatted pulse file. — write_pulse_ascii • Spectroscopy Analysis Tools (spant) Write an ASCII formatted pulse file. — write_pulse_ascii • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/zero_fade_spec.html b/docs/reference/zero_fade_spec.html
index c703745c..c8b572c3 100644
--- a/docs/reference/zero_fade_spec.html
+++ b/docs/reference/zero_fade_spec.html
@@ -1,7 +1,5 @@
-Fade a spectrum to zero by frequency domain multiplication with a tanh
-function. Note this operation distorts data points at the end of the FID. — zero_fade_spec • Spectroscopy Analysis Tools (spant) Fade a spectrum to zero by frequency domain multiplication with a tanh function. Note this operation distorts data points at the end of the FID. — zero_fade_spec • Spectroscopy Analysis Tools (spant) Zero all coherences including and above a given order. — zero_higher_orders • Spectroscopy Analysis Tools (spant) Zero all coherences including and above a given order. — zero_higher_orders • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Value
diff --git a/docs/reference/zero_td_pts_end.html b/docs/reference/zero_td_pts_end.html
index 8c1123c8..71d24ebb 100644
--- a/docs/reference/zero_td_pts_end.html
+++ b/docs/reference/zero_td_pts_end.html
@@ -1,5 +1,5 @@
-Set mrs_data object data points at the end of the FID to zero. — zero_td_pts_end • Spectroscopy Analysis Tools (spant) Set mrs_data object data points at the end of the FID to zero. — zero_td_pts_end • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/zf.html b/docs/reference/zf.html
index 85e2013c..baf50256 100644
--- a/docs/reference/zf.html
+++ b/docs/reference/zf.html
@@ -1,5 +1,5 @@
-Zero-fill MRS data in the time domain. — zf • Spectroscopy Analysis Tools (spant) Zero-fill MRS data in the time domain. — zf • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -125,7 +125,7 @@ Value
diff --git a/docs/reference/zf_xy.html b/docs/reference/zf_xy.html
index ebca3999..c4104a74 100644
--- a/docs/reference/zf_xy.html
+++ b/docs/reference/zf_xy.html
@@ -1,5 +1,5 @@
-Zero-fill MRSI data in the k-space x-y direction. — zf_xy • Spectroscopy Analysis Tools (spant) Zero-fill MRSI data in the k-space x-y direction. — zf_xy • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -113,7 +113,7 @@ Value
diff --git a/docs/sitemap.xml b/docs/sitemap.xml
index e2139f71..4c39f515 100644
--- a/docs/sitemap.xml
+++ b/docs/sitemap.xml
@@ -216,6 +216,12 @@
https://martin3141.github.io/spant/reference/comb_coils_fp_pc.html
+
+ https://martin3141.github.io/spant/reference/comb_coils_mrsi_gls.html
+
+
+ https://martin3141.github.io/spant/reference/comb_coils_svs_gls.html
+
https://martin3141.github.io/spant/reference/comb_csv_results.html
@@ -411,6 +417,9 @@
https://martin3141.github.io/spant/reference/gen_conv_reg.html
+
+ https://martin3141.github.io/spant/reference/gen_group_reg.html
+
https://martin3141.github.io/spant/reference/gen_impulse_reg.html
@@ -555,6 +564,15 @@
https://martin3141.github.io/spant/reference/glm_spec.html
+
+ https://martin3141.github.io/spant/reference/glm_spec_fmrs_fl.html
+
+
+ https://martin3141.github.io/spant/reference/glm_spec_fmrs_group.html
+
+
+ https://martin3141.github.io/spant/reference/glm_spec_group_linhyp.html
+
https://martin3141.github.io/spant/reference/grid_shift_xy.html
@@ -690,9 +708,15 @@
https://martin3141.github.io/spant/reference/mrs_data2basis.html
+
+ https://martin3141.github.io/spant/reference/mrs_data2bids.html
+
https://martin3141.github.io/spant/reference/mrs_data2mat.html
+
+ https://martin3141.github.io/spant/reference/mrs_data2spec_mat.html
+
https://martin3141.github.io/spant/reference/mrs_data2vec.html
@@ -741,6 +765,9 @@
https://martin3141.github.io/spant/reference/phase.html
+
+ https://martin3141.github.io/spant/reference/phase_ref_1h_brain.html
+
https://martin3141.github.io/spant/reference/plot.fit_result.html
@@ -780,6 +807,12 @@
https://martin3141.github.io/spant/reference/precomp.html
+
+ https://martin3141.github.io/spant/reference/preproc_svs.html
+
+
+ https://martin3141.github.io/spant/reference/preproc_svs_dataset.html
+
https://martin3141.github.io/spant/reference/print.fit_result.html
@@ -1050,6 +1083,9 @@
https://martin3141.github.io/spant/reference/spant_mpress_drift.html
+
+ https://martin3141.github.io/spant/reference/spant_sim_fmrs_dataset.html
+
https://martin3141.github.io/spant/reference/spant_simulation_benchmark.html
@@ -1107,6 +1143,9 @@
https://martin3141.github.io/spant/reference/svs_1h_brain_batch_analysis.html
+
+ https://martin3141.github.io/spant/reference/t_test_spec.html
+
https://martin3141.github.io/spant/reference/td2fd.html
Mask the voxels outside an elliptical region spanning the MRSI dataset in the -x-y plane.
Mask the voxels outside an elliptical region spanning the MRSI dataset in the x-y plane.
All functions
- Convert a matrix (with spectral points in the column dimension and dynamics
-in the row dimensions) into a mrs_data object.
Convert a matrix (with spectral points in the column dimension and dynamics in the row dimensions) into a mrs_data object.
- Matrix exponential function taken from complexplus package to reduce the
-number of spant dependencies.
Matrix exponential function taken from complexplus package to reduce the number of spant dependencies.
@@ -914,31 +898,31 @@ All functions
- Convert an mrs_data object to basis object - where basis signals are spread
-across the dynamic dimension in the MRS data.
Convert an mrs_data object to basis object - where basis signals are spread across the dynamic dimension in the MRS data.
+
+
+ Create a BIDS file structure from a vector of MRS data paths or list of mrs_data objects.
- Convert mrs_data object to a matrix, with spectral points in the column
-dimension and dynamics in the row dimension.
Convert mrs_data object to a matrix, with spectral points in the column dimension and dynamics in the row dimension.
-
+
- Convert mrs_data object to a vector.
Convert mrs_data object to a matrix, with spectral points in the column dimension and dynamics in the row dimension.
-
+
- Create a BIDS directory and file structure from a list of mrs_data objects.
Convert mrs_data object to a vector.
- Perform a fftshift on a matrix, with each column replaced by its shifted
-result.
Perform a fftshift on a matrix, with each column replaced by its shifted result.
- Perform an ifftshift on a matrix, with each column replaced by its shifted
-result.
Perform an ifftshift on a matrix, with each column replaced by its shifted result.
@@ -946,9 +930,7 @@ All functions
- Flip the x data dimension order of a nifti image. This corresponds to
-flipping MRI data in the left-right direction, assuming the data in save in
-neurological format (can check with fslorient program).
Flip the x data dimension order of a nifti image. This corresponds to flipping MRI data in the left-right direction, assuming the data in save in neurological format (can check with fslorient program).
@@ -964,8 +946,7 @@ All functions
- Search for the highest peak in a spectral region and return the frequency,
-height and FWHM.
Search for the highest peak in a spectral region and return the frequency, height and FWHM.
@@ -974,6 +955,10 @@ All functions phase()
Apply phasing parameters to MRS data.
+
+
+ Corrected zero order phase and chemical shift offset in 1H MRS data from the brain.
@@ -1005,8 +990,7 @@ All functions
- Plot an interactive slice map from a data array where voxels can be selected
-to display a corresponding spectrum.
Plot an interactive slice map from a data array where voxels can be selected to display a corresponding spectrum.
@@ -1026,8 +1010,15 @@ All functions
- Save function results to file and load on subsequent calls to avoid repeat
-computation.
Save function results to file and load on subsequent calls to avoid repeat computation.
+
+
+ Preprocess and perform quality assessment of a single SVS data set.
+
+
+ Preprocess and perform quality assessment of one or more SVS data sets.
@@ -1055,15 +1046,11 @@ All functions
- Read a directory containing Siemens MRS IMA files and combine along the coil
-dimension. Note that the coil ID is inferred from the sorted file name and
-should be checked when consistency is required between two directories.
Read a directory containing Siemens MRS IMA files and combine along the coil dimension. Note that the coil ID is inferred from the sorted file name and should be checked when consistency is required between two directories.
- Read a directory containing Siemens MRS IMA files and combine along the
-dynamic dimension. Note that the coil ID is inferred from the sorted file
-name and should be checked when consistency is required.
Read a directory containing Siemens MRS IMA files and combine along the dynamic dimension. Note that the coil ID is inferred from the sorted file name and should be checked when consistency is required.
@@ -1103,13 +1090,11 @@ All functions
- Reconstruct complex time-domain data from the real part of frequency-domain
-data.
Reconstruct complex time-domain data from the real part of frequency-domain data.
- Reconstruct complex time-domain data from the real part of frequency-domain
-data.
Reconstruct complex time-domain data from the real part of frequency-domain data.
@@ -1141,8 +1126,7 @@ All functions
- Resample a VOI to match a target image space using nearest-neighbour
-interpolation.
Resample a VOI to match a target image space using nearest-neighbour interpolation.
@@ -1158,23 +1142,19 @@ All functions
- Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water).
Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / kg of tissue water).
- Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water).
Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / kg of tissue water).
- Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / Litre of tissue).
Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / Litre of tissue).
- Convert default LCM/TARQUIN concentration scaling to molal units with partial
-volume correction.
Convert default LCM/TARQUIN concentration scaling to molal units with partial volume correction.
@@ -1222,8 +1202,7 @@ All functions
- MEGA-PRESS sequence with ideal localisation pulses and Gaussian shaped
-editing pulse.
MEGA-PRESS sequence with ideal localisation pulses and Gaussian shaped editing pulse.
@@ -1251,13 +1230,11 @@ All functions
- STEAM sequence with ideal pulses and coherence order filtering to simulate
-gradient crushers.
STEAM sequence with ideal pulses and coherence order filtering to simulate gradient crushers.
- STEAM sequence with ideal pulses using the z-rotation gradient simulation
-method described by Young et al JMR 140, 146-152 (1999).
STEAM sequence with ideal pulses using the z-rotation gradient simulation method described by Young et al JMR 140, 146-152 (1999).
@@ -1293,8 +1270,7 @@ All functions
- Set the number of time-domain data points, truncating or zero-filling as
-appropriate.
Set the number of time-domain data points, truncating or zero-filling as appropriate.
@@ -1318,18 +1294,15 @@ All functions
- Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS
-sequence. Note, ideal pulses are assumed.
Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS sequence. Note, ideal pulses are assumed.
- Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS
-sequence. Note, ideal pulses are assumed.
Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS sequence. Note, ideal pulses are assumed.
- Simulate a macromolecular and lipid basis-set suitable for 1H brain MRS
-analysis.
Simulate a macromolecular and lipid basis-set suitable for 1H brain MRS analysis.
@@ -1353,8 +1326,7 @@ All functions
- Simulate an ideal pulse excitation profile by smoothing a top-hat function
-with a Gaussian.
Simulate an ideal pulse excitation profile by smoothing a top-hat function with a Gaussian.
@@ -1374,17 +1346,19 @@ All functions
- Simulate and fit some spectra with ABfit for benchmarking purposes. Basic
-timing and performance metrics will be printed.
Simulate and fit some spectra with ABfit for benchmarking purposes. Basic timing and performance metrics will be printed.
Example MEGA-PRESS data with significant B0 drift.
+
+
+ Simulate an example fMRS dataset for a block design fMRS experiment and export a BIDS structure.
- Simulate a typical metabolite basis set for benchmarking. Timing metrics will
-be printed on completion.
Simulate a typical metabolite basis set for benchmarking. Timing metrics will be printed on completion.
@@ -1400,8 +1374,7 @@ All functions
- Convert SPM style segmentation files to a single categorical image where
-the numerical values map as: 0) Other, 1) CSF, 2) GM and 3) WM.
Convert SPM style segmentation files to a single categorical image where the numerical values map as: 0) Other, 1) CSF, 2) GM and 3) WM.
@@ -1413,8 +1386,7 @@ All functions
- Plot the fitting results of an object of class fit_result with
-individual basis set components shown.
Plot the fitting results of an object of class fit_result with individual basis set components shown.
@@ -1459,6 +1431,10 @@ All functions svs_1h_brain_batch_analysis()
Batch interface to the standard SVS 1H brain analysis pipeline.
+
+
+ Perform a t-test on spectral data points.
@@ -1518,8 +1494,7 @@ All functions
- Fade a spectrum to zero by frequency domain multiplication with a tanh
-function. Note this operation distorts data points at the end of the FID.
Fade a spectrum to zero by frequency domain multiplication with a tanh function. Note this operation distorts data points at the end of the FID.
@@ -1549,7 +1524,7 @@ All functions
diff --git a/docs/reference/int_spec.html b/docs/reference/int_spec.html
index c7060fe7..783325a8 100644
--- a/docs/reference/int_spec.html
+++ b/docs/reference/int_spec.html
@@ -1,5 +1,5 @@
-Integrate a spectral region. — int_spec • Spectroscopy Analysis Tools (spant) Integrate a spectral region. — int_spec • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -118,7 +118,7 @@ Value
diff --git a/docs/reference/interleave_dyns.html b/docs/reference/interleave_dyns.html
index effe5543..441eff27 100644
--- a/docs/reference/interleave_dyns.html
+++ b/docs/reference/interleave_dyns.html
@@ -1,5 +1,5 @@
-Interleave the first and second half of a dynamic series. — interleave_dyns • Spectroscopy Analysis Tools (spant) Interleave the first and second half of a dynamic series. — interleave_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/inv_even_dyns.html b/docs/reference/inv_even_dyns.html
index 9f9d4fff..dcb781dc 100644
--- a/docs/reference/inv_even_dyns.html
+++ b/docs/reference/inv_even_dyns.html
@@ -1,5 +1,5 @@
-Invert even numbered dynamic scans starting from 1 (2,4,6...). — inv_even_dyns • Spectroscopy Analysis Tools (spant) Invert even numbered dynamic scans starting from 1 (2,4,6...). — inv_even_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/inv_odd_dyns.html b/docs/reference/inv_odd_dyns.html
index 26212e2b..78d64660 100644
--- a/docs/reference/inv_odd_dyns.html
+++ b/docs/reference/inv_odd_dyns.html
@@ -1,5 +1,5 @@
-Invert odd numbered dynamic scans starting from 1 (1,3,5...). — inv_odd_dyns • Spectroscopy Analysis Tools (spant) Invert odd numbered dynamic scans starting from 1 (1,3,5...). — inv_odd_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/is.def.html b/docs/reference/is.def.html
index f196ffd0..a67b9eba 100644
--- a/docs/reference/is.def.html
+++ b/docs/reference/is.def.html
@@ -1,5 +1,5 @@
-Check if an object is defined, which is the same as being not NULL. — is.def • Spectroscopy Analysis Tools (spant) Check if an object is defined, which is the same as being not NULL. — is.def • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/is_fd.html b/docs/reference/is_fd.html
index 3b0ca165..18a193aa 100644
--- a/docs/reference/is_fd.html
+++ b/docs/reference/is_fd.html
@@ -1,7 +1,5 @@
-Check if the chemical shift dimension of an MRS data object is in the
-frequency domain. — is_fd • Spectroscopy Analysis Tools (spant) Check if the chemical shift dimension of an MRS data object is in the frequency domain. — is_fd • Spectroscopy Analysis Tools (spant) Transform 2D MRSI data from k-space to image space in the x-y direction. — kspace2img_xy • Spectroscopy Analysis Tools (spant) Transform 2D MRSI data from k-space to image space in the x-y direction. — kspace2img_xy • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/l2_reg.html b/docs/reference/l2_reg.html
index 3d781d80..21aa9849 100644
--- a/docs/reference/l2_reg.html
+++ b/docs/reference/l2_reg.html
@@ -1,5 +1,5 @@
-Perform l2 regularisation artefact suppression. — l2_reg • Spectroscopy Analysis Tools (spant) Perform l2 regularisation artefact suppression. — l2_reg • Spectroscopy Analysis Tools (spant) Apply line-broadening (apodisation) to MRS data or basis object. — lb • Spectroscopy Analysis Tools (spant) Apply line-broadening (apodisation) to MRS data or basis object. — lb • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -123,7 +123,7 @@ Value
diff --git a/docs/reference/lofdc.html b/docs/reference/lofdc.html
index 5419b1ec..31347a25 100644
--- a/docs/reference/lofdc.html
+++ b/docs/reference/lofdc.html
@@ -1,5 +1,5 @@
-Correct linear frequency drift. — lofdc • Spectroscopy Analysis Tools (spant) Correct linear frequency drift. — lofdc • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -138,7 +138,7 @@ Value
diff --git a/docs/reference/lw2alpha.html b/docs/reference/lw2alpha.html
index b83db682..25da229b 100644
--- a/docs/reference/lw2alpha.html
+++ b/docs/reference/lw2alpha.html
@@ -1,7 +1,5 @@
-Covert a linewidth in Hz to an equivalent alpha value in the time-domain ie:
-x * exp(-t * alpha). — lw2alpha • Spectroscopy Analysis Tools (spant) Covert a linewidth in Hz to an equivalent alpha value in the time-domain ie: x * exp(-t * alpha). — lw2alpha • Spectroscopy Analysis Tools (spant) Covert a linewidth in Hz to an equivalent beta value in the time-domain ie:
-x * exp(-t * t * beta). — lw2beta • Spectroscopy Analysis Tools (spant) Covert a linewidth in Hz to an equivalent beta value in the time-domain ie: x * exp(-t * t * beta). — lw2beta • Spectroscopy Analysis Tools (spant) Make a basis-set object from a directory containing LCModel formatted RAW
-files. — make_basis_from_raw • Spectroscopy Analysis Tools (spant) Make a basis-set object from a directory containing LCModel formatted RAW files. — make_basis_from_raw • Spectroscopy Analysis Tools (spant) Mask an MRS dataset in the dynamic dimension. — mask_dyns • Spectroscopy Analysis Tools (spant) Mask an MRS dataset in the dynamic dimension. — mask_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/mask_fit_res.html b/docs/reference/mask_fit_res.html
index 97baaa3f..ebd91a99 100644
--- a/docs/reference/mask_fit_res.html
+++ b/docs/reference/mask_fit_res.html
@@ -1,5 +1,5 @@
-Mask fit result spectra depending on a vector of bool values. — mask_fit_res • Spectroscopy Analysis Tools (spant) Mask fit result spectra depending on a vector of bool values. — mask_fit_res • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -116,7 +116,7 @@ Value
diff --git a/docs/reference/mask_xy.html b/docs/reference/mask_xy.html
index 11bb577c..b0d38619 100644
--- a/docs/reference/mask_xy.html
+++ b/docs/reference/mask_xy.html
@@ -1,5 +1,5 @@
-Mask an MRSI dataset in the x-y direction — mask_xy • Spectroscopy Analysis Tools (spant) Mask an MRSI dataset in the x-y direction — mask_xy • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/mask_xy_corners.html b/docs/reference/mask_xy_corners.html
index 09b16cd2..2d13839d 100644
--- a/docs/reference/mask_xy_corners.html
+++ b/docs/reference/mask_xy_corners.html
@@ -1,5 +1,5 @@
-Mask the four corners of an MRSI dataset in the x-y plane. — mask_xy_corners • Spectroscopy Analysis Tools (spant) Mask the four corners of an MRSI dataset in the x-y plane. — mask_xy_corners • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/mask_xy_ellipse.html b/docs/reference/mask_xy_ellipse.html
index 1d8b02e4..e2e749ef 100644
--- a/docs/reference/mask_xy_ellipse.html
+++ b/docs/reference/mask_xy_ellipse.html
@@ -1,7 +1,5 @@
-Mask the voxels outside an elliptical region spanning the MRSI dataset in the
-x-y plane. — mask_xy_ellipse • Spectroscopy Analysis Tools (spant) Mask the voxels outside an elliptical region spanning the MRSI dataset in the x-y plane. — mask_xy_ellipse • Spectroscopy Analysis Tools (spant) Mask a 2D MRSI dataset in the x-y dimension. — mask_xy_mat • Spectroscopy Analysis Tools (spant) Mask a 2D MRSI dataset in the x-y dimension. — mask_xy_mat • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Value
diff --git a/docs/reference/mat2mrs_data.html b/docs/reference/mat2mrs_data.html
index 2e2895f3..ae55665f 100644
--- a/docs/reference/mat2mrs_data.html
+++ b/docs/reference/mat2mrs_data.html
@@ -1,7 +1,5 @@
-Convert a matrix (with spectral points in the column dimension and dynamics
-in the row dimensions) into a mrs_data object. — mat2mrs_data • Spectroscopy Analysis Tools (spant) Convert a matrix (with spectral points in the column dimension and dynamics in the row dimensions) into a mrs_data object. — mat2mrs_data • Spectroscopy Analysis Tools (spant) Matrix exponential function taken from complexplus package to reduce the
-number of spant dependencies. — matexp • Spectroscopy Analysis Tools (spant) Matrix exponential function taken from complexplus package to reduce the number of spant dependencies. — matexp • Spectroscopy Analysis Tools (spant) Apply the max operator to an MRS dataset. — max_mrs • Spectroscopy Analysis Tools (spant) Apply the max operator to an MRS dataset. — max_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/max_mrs_interp.html b/docs/reference/max_mrs_interp.html
index e4474764..52e63f3e 100644
--- a/docs/reference/max_mrs_interp.html
+++ b/docs/reference/max_mrs_interp.html
@@ -1,5 +1,5 @@
-Apply the max operator to an interpolated MRS dataset. — max_mrs_interp • Spectroscopy Analysis Tools (spant) Apply the max operator to an interpolated MRS dataset. — max_mrs_interp • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/mean.list.html b/docs/reference/mean.list.html
index b8eb3463..048306fd 100644
--- a/docs/reference/mean.list.html
+++ b/docs/reference/mean.list.html
@@ -1,5 +1,5 @@
-Calculate the mean spectrum from an mrs_data object. — mean.list • Spectroscopy Analysis Tools (spant) Calculate the mean spectrum from an mrs_data object. — mean.list • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/mean.mrs_data.html b/docs/reference/mean.mrs_data.html
index 5531a28d..79515014 100644
--- a/docs/reference/mean.mrs_data.html
+++ b/docs/reference/mean.mrs_data.html
@@ -1,5 +1,5 @@
-Calculate the mean spectrum from an mrs_data object. — mean.mrs_data • Spectroscopy Analysis Tools (spant) Calculate the mean spectrum from an mrs_data object. — mean.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/mean_dyn_blocks.html b/docs/reference/mean_dyn_blocks.html
index 10467098..4c042448 100644
--- a/docs/reference/mean_dyn_blocks.html
+++ b/docs/reference/mean_dyn_blocks.html
@@ -1,5 +1,5 @@
-Calculate the mean of adjacent dynamic scans. — mean_dyn_blocks • Spectroscopy Analysis Tools (spant) Calculate the mean of adjacent dynamic scans. — mean_dyn_blocks • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/mean_dyn_pairs.html b/docs/reference/mean_dyn_pairs.html
index 63e909ea..1a241126 100644
--- a/docs/reference/mean_dyn_pairs.html
+++ b/docs/reference/mean_dyn_pairs.html
@@ -1,5 +1,5 @@
-Calculate the pairwise means across a dynamic data set. — mean_dyn_pairs • Spectroscopy Analysis Tools (spant) Calculate the pairwise means across a dynamic data set. — mean_dyn_pairs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/mean_dyns.html b/docs/reference/mean_dyns.html
index 73fdbfa7..0daa27df 100644
--- a/docs/reference/mean_dyns.html
+++ b/docs/reference/mean_dyns.html
@@ -1,5 +1,5 @@
-Calculate the mean dynamic data. — mean_dyns • Spectroscopy Analysis Tools (spant) Calculate the mean dynamic data. — mean_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/mean_mrs_list.html b/docs/reference/mean_mrs_list.html
index 808b6c50..10d842c0 100644
--- a/docs/reference/mean_mrs_list.html
+++ b/docs/reference/mean_mrs_list.html
@@ -1,5 +1,5 @@
-Return the mean of a list of mrs_data objects. — mean_mrs_list • Spectroscopy Analysis Tools (spant) Return the mean of a list of mrs_data objects. — mean_mrs_list • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/mean_vec_blocks.html b/docs/reference/mean_vec_blocks.html
index 8fc92eaa..dd78b122 100644
--- a/docs/reference/mean_vec_blocks.html
+++ b/docs/reference/mean_vec_blocks.html
@@ -1,5 +1,5 @@
-Calculate the mean of adjacent blocks in a vector. — mean_vec_blocks • Spectroscopy Analysis Tools (spant) Calculate the mean of adjacent blocks in a vector. — mean_vec_blocks • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/median_dyns.html b/docs/reference/median_dyns.html
index 1039d4b5..9a085b10 100644
--- a/docs/reference/median_dyns.html
+++ b/docs/reference/median_dyns.html
@@ -1,5 +1,5 @@
-Calculate the median dynamic data. — median_dyns • Spectroscopy Analysis Tools (spant) Calculate the median dynamic data. — median_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/mod_td.html b/docs/reference/mod_td.html
index 76ad0a40..141ef09e 100644
--- a/docs/reference/mod_td.html
+++ b/docs/reference/mod_td.html
@@ -1,5 +1,5 @@
-Apply the Modulus operator to the time-domain MRS signal. — mod_td • Spectroscopy Analysis Tools (spant) Apply the Modulus operator to the time-domain MRS signal. — mod_td • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/mrs_data2basis.html b/docs/reference/mrs_data2basis.html
index 62f7d749..11797b91 100644
--- a/docs/reference/mrs_data2basis.html
+++ b/docs/reference/mrs_data2basis.html
@@ -1,7 +1,5 @@
-Convert an mrs_data object to basis object - where basis signals are spread
-across the dynamic dimension in the MRS data. — mrs_data2basis • Spectroscopy Analysis Tools (spant) Convert an mrs_data object to basis object - where basis signals are spread across the dynamic dimension in the MRS data. — mrs_data2basis • Spectroscopy Analysis Tools (spant) Create a BIDS file structure from a vector of MRS data paths or list of mrs_data objects. — mrs_data2bids • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Create a BIDS file structure from a vector of MRS data paths or list of mrs_data objects.
+ Source: R/fmrs.R
+ mrs_data2bids.Rd
+
+
+
+ Create a BIDS file structure from a vector of MRS data paths or list of
+mrs_data objects.
+
+
+
+ mrs_data2bids(
+ mrs_data,
+ output_dir,
+ suffix = NULL,
+ sub = NULL,
+ ses = NULL,
+ task = NULL,
+ acq = NULL,
+ nuc = NULL,
+ voi = NULL,
+ rec = NULL,
+ run = NULL,
+ echo = NULL,
+ inv = NULL,
+ skip_existing = TRUE
+)
+
+
+
+ Arguments
+ - mrs_data
+vector of MRS data paths or list of mrs_data objects.
- output_dir
+the base directory to create the BIDS structure.
- suffix
+optional vector of file suffixes. Default behaviour is to
+automatically determine these from the input data, however it is recommended
+that they are specified to allow more efficient skipping of existing data.
- sub
+optional vector of subject labels. If not specified, these will be
+automatically generated as a series of increasing zero-padded integer values
+corresponding to the mrs_data input indices.
- ses
+optional vector of session labels.
- task
+optional vector of task labels.
- acq
+optional vector of acquisition labels.
- nuc
+optional vector of nucleus labels.
- voi
+optional vector of volume of interest labels.
- rec
+optional vector of reconstruction labels.
- run
+optional vector of run indices.
- echo
+optional vector of echo time indices.
- inv
+optional vector of inversion indices.
- skip_existing
+skip any data files that have already been converted.
+Defaults to TRUE, set to FALSE to force an overwrite of any existing data
+files.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/mrs_data2mat.html b/docs/reference/mrs_data2mat.html
index cf5ff28c..9e47688a 100644
--- a/docs/reference/mrs_data2mat.html
+++ b/docs/reference/mrs_data2mat.html
@@ -1,7 +1,5 @@
-Convert mrs_data object to a matrix, with spectral points in the column
-dimension and dynamics in the row dimension. — mrs_data2mat • Spectroscopy Analysis Tools (spant) Convert mrs_data object to a matrix, with spectral points in the column dimension and dynamics in the row dimension. — mrs_data2mat • Spectroscopy Analysis Tools (spant) Convert mrs_data object to a matrix, with spectral points in the column dimension and dynamics in the row dimension. — mrs_data2spec_mat • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Convert mrs_data object to a matrix, with spectral points in the column dimension and dynamics in the row dimension.
+ Source: R/mrs_data_proc.R
+ mrs_data2spec_mat.Rd
+
+
+
+ Convert mrs_data object to a matrix, with spectral points in the column
+dimension and dynamics in the row dimension.
+
+
+
+ mrs_data2spec_mat(mrs_data, collapse = TRUE)
+
+
+
+ Arguments
+ - mrs_data
+MRS data object or list of MRS data objects.
- collapse
+collapse all other dimensions along the dynamic dimension, eg
+a 16x16 MRSI grid would be first collapsed across 256 dynamic scans.
+
+ Value
+
+
+MRS data matrix.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/mrs_data2vec.html b/docs/reference/mrs_data2vec.html
index fb172d68..a1fd654d 100644
--- a/docs/reference/mrs_data2vec.html
+++ b/docs/reference/mrs_data2vec.html
@@ -1,5 +1,5 @@
-Convert mrs_data object to a vector. — mrs_data2vec • Spectroscopy Analysis Tools (spant) Convert mrs_data object to a vector. — mrs_data2vec • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -126,7 +126,7 @@ Value
diff --git a/docs/reference/mvfftshift.html b/docs/reference/mvfftshift.html
index 92b0841b..976b3410 100644
--- a/docs/reference/mvfftshift.html
+++ b/docs/reference/mvfftshift.html
@@ -1,7 +1,5 @@
-Perform a fftshift on a matrix, with each column replaced by its shifted
-result. — mvfftshift • Spectroscopy Analysis Tools (spant) Perform a fftshift on a matrix, with each column replaced by its shifted result. — mvfftshift • Spectroscopy Analysis Tools (spant) Perform an ifftshift on a matrix, with each column replaced by its shifted
-result. — mvifftshift • Spectroscopy Analysis Tools (spant) Perform an ifftshift on a matrix, with each column replaced by its shifted result. — mvifftshift • Spectroscopy Analysis Tools (spant) Print fit coordinates from a single index. — n2coord • Spectroscopy Analysis Tools (spant) Print fit coordinates from a single index. — n2coord • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/nifti_flip_lr.html b/docs/reference/nifti_flip_lr.html
index 730abe3c..19860b3c 100644
--- a/docs/reference/nifti_flip_lr.html
+++ b/docs/reference/nifti_flip_lr.html
@@ -1,9 +1,5 @@
-Flip the x data dimension order of a nifti image. This corresponds to
-flipping MRI data in the left-right direction, assuming the data in save in
-neurological format (can check with fslorient program). — nifti_flip_lr • Spectroscopy Analysis Tools (spant) Flip the x data dimension order of a nifti image. This corresponds to flipping MRI data in the left-right direction, assuming the data in save in neurological format (can check with fslorient program). — nifti_flip_lr • Spectroscopy Analysis Tools (spant) Export a one-page pdf of a single fit result — one_page_pdf • Spectroscopy Analysis Tools (spant) Export a one-page pdf of a single fit result — one_page_pdf • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -108,7 +108,7 @@ Arguments
diff --git a/docs/reference/ortho3.html b/docs/reference/ortho3.html
index 13ade97d..5d7dd2fd 100644
--- a/docs/reference/ortho3.html
+++ b/docs/reference/ortho3.html
@@ -1,5 +1,5 @@
-Display an orthographic projection plot of a nifti object. — ortho3 • Spectroscopy Analysis Tools (spant) Display an orthographic projection plot of a nifti object. — ortho3 • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -172,7 +172,7 @@ Arguments
diff --git a/docs/reference/ortho3_inter.html b/docs/reference/ortho3_inter.html
index 090cc5e5..15948899 100644
--- a/docs/reference/ortho3_inter.html
+++ b/docs/reference/ortho3_inter.html
@@ -1,5 +1,5 @@
-Display an interactive orthographic projection plot of a nifti object. — ortho3_inter • Spectroscopy Analysis Tools (spant) Display an interactive orthographic projection plot of a nifti object. — ortho3_inter • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -132,7 +132,7 @@ Arguments
diff --git a/docs/reference/peak_info.html b/docs/reference/peak_info.html
index 09058bd8..41c8ffaf 100644
--- a/docs/reference/peak_info.html
+++ b/docs/reference/peak_info.html
@@ -1,7 +1,5 @@
-Search for the highest peak in a spectral region and return the frequency,
-height and FWHM. — peak_info • Spectroscopy Analysis Tools (spant) Search for the highest peak in a spectral region and return the frequency, height and FWHM. — peak_info • Spectroscopy Analysis Tools (spant) Papoulis-Gerchberg (PG) algorithm method for k-space extrapolation. — pg_extrap_xy • Spectroscopy Analysis Tools (spant) Papoulis-Gerchberg (PG) algorithm method for k-space extrapolation. — pg_extrap_xy • Spectroscopy Analysis Tools (spant) Apply phasing parameters to MRS data. — phase • Spectroscopy Analysis Tools (spant) Apply phasing parameters to MRS data. — phase • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/phase_ref_1h_brain.html b/docs/reference/phase_ref_1h_brain.html
new file mode 100644
index 00000000..8707a74a
--- /dev/null
+++ b/docs/reference/phase_ref_1h_brain.html
@@ -0,0 +1,131 @@
+
+Corrected zero order phase and chemical shift offset in 1H MRS data from the brain. — phase_ref_1h_brain • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Corrected zero order phase and chemical shift offset in 1H MRS data from the brain.
+ Source: R/rats.R
+ phase_ref_1h_brain.Rd
+
+
+
+ Corrected zero order phase and chemical shift offset in 1H MRS data from the
+brain.
+
+
+
+ phase_ref_1h_brain(mrs_data, mean_ref = FALSE, ret_corr_only = TRUE)
+
+
+
+ Arguments
+ - mrs_data
+MRS data to be corrected.
- mean_ref
+apply the phase and offset of the mean spectrum to all
+others. Default is FALSE.
- ret_corr_only
+return the corrected data only.
+
+ Value
+
+
+corrected MRS data.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/plot.fit_result.html b/docs/reference/plot.fit_result.html
index e54d3bc1..836a53ee 100644
--- a/docs/reference/plot.fit_result.html
+++ b/docs/reference/plot.fit_result.html
@@ -1,5 +1,5 @@
-Plot the fitting results of an object of class fit_result. — plot.fit_result • Spectroscopy Analysis Tools (spant) Plot the fitting results of an object of class fit_result. — plot.fit_result • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -207,7 +207,7 @@ Arguments
diff --git a/docs/reference/plot.mrs_data.html b/docs/reference/plot.mrs_data.html
index fabcc35b..bb2ec651 100644
--- a/docs/reference/plot.mrs_data.html
+++ b/docs/reference/plot.mrs_data.html
@@ -1,5 +1,5 @@
-Plotting method for objects of class mrs_data. — plot.mrs_data • Spectroscopy Analysis Tools (spant) Plotting method for objects of class mrs_data. — plot.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -287,7 +287,7 @@ Arguments
diff --git a/docs/reference/plot_bc.html b/docs/reference/plot_bc.html
index 4f8309b4..b48142cc 100644
--- a/docs/reference/plot_bc.html
+++ b/docs/reference/plot_bc.html
@@ -1,5 +1,5 @@
-Convenience function to plot a baseline estimate with the original data. — plot_bc • Spectroscopy Analysis Tools (spant) Convenience function to plot a baseline estimate with the original data. — plot_bc • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -108,7 +108,7 @@ Arguments
diff --git a/docs/reference/plot_reg.html b/docs/reference/plot_reg.html
index ae1acbe7..2addb2f6 100644
--- a/docs/reference/plot_reg.html
+++ b/docs/reference/plot_reg.html
@@ -1,5 +1,5 @@
-Plot regressors as an image. — plot_reg • Spectroscopy Analysis Tools (spant) Plot regressors as an image. — plot_reg • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/plot_slice_fit.html b/docs/reference/plot_slice_fit.html
index fbc7b560..57f1af8a 100644
--- a/docs/reference/plot_slice_fit.html
+++ b/docs/reference/plot_slice_fit.html
@@ -1,5 +1,5 @@
-Plot a 2D slice from an MRSI fit result object. — plot_slice_fit • Spectroscopy Analysis Tools (spant) Plot a 2D slice from an MRSI fit result object. — plot_slice_fit • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -129,7 +129,7 @@ Arguments
diff --git a/docs/reference/plot_slice_fit_inter.html b/docs/reference/plot_slice_fit_inter.html
index 4eed104a..da105a7d 100644
--- a/docs/reference/plot_slice_fit_inter.html
+++ b/docs/reference/plot_slice_fit_inter.html
@@ -1,5 +1,5 @@
-Plot a 2D slice from an MRSI fit result object. — plot_slice_fit_inter • Spectroscopy Analysis Tools (spant) Plot a 2D slice from an MRSI fit result object. — plot_slice_fit_inter • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -134,7 +134,7 @@ Arguments
diff --git a/docs/reference/plot_slice_map.html b/docs/reference/plot_slice_map.html
index 553e9ac8..ffb2a134 100644
--- a/docs/reference/plot_slice_map.html
+++ b/docs/reference/plot_slice_map.html
@@ -1,5 +1,5 @@
-Plot a slice from a 7 dimensional array. — plot_slice_map • Spectroscopy Analysis Tools (spant) Plot a slice from a 7 dimensional array. — plot_slice_map • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -153,7 +153,7 @@ Arguments
diff --git a/docs/reference/plot_slice_map_inter.html b/docs/reference/plot_slice_map_inter.html
index 40d33b42..90968f66 100644
--- a/docs/reference/plot_slice_map_inter.html
+++ b/docs/reference/plot_slice_map_inter.html
@@ -1,7 +1,5 @@
-Plot an interactive slice map from a data array where voxels can be selected
-to display a corresponding spectrum. — plot_slice_map_inter • Spectroscopy Analysis Tools (spant) Plot an interactive slice map from a data array where voxels can be selected to display a corresponding spectrum. — plot_slice_map_inter • Spectroscopy Analysis Tools (spant) Plot the spectral standard deviation. — plot_spec_sd • Spectroscopy Analysis Tools (spant) Plot the spectral standard deviation. — plot_spec_sd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Arguments
diff --git a/docs/reference/plot_voi_overlay.html b/docs/reference/plot_voi_overlay.html
index 9a782e88..bbbbf35e 100644
--- a/docs/reference/plot_voi_overlay.html
+++ b/docs/reference/plot_voi_overlay.html
@@ -1,5 +1,5 @@
-Plot a volume as an image overlay. — plot_voi_overlay • Spectroscopy Analysis Tools (spant) Plot a volume as an image overlay. — plot_voi_overlay • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -116,7 +116,7 @@ Arguments
diff --git a/docs/reference/plot_voi_overlay_seg.html b/docs/reference/plot_voi_overlay_seg.html
index 3d4e74ff..0e800ff2 100644
--- a/docs/reference/plot_voi_overlay_seg.html
+++ b/docs/reference/plot_voi_overlay_seg.html
@@ -1,5 +1,5 @@
-Plot a volume as an overlay on a segmented brain volume. — plot_voi_overlay_seg • Spectroscopy Analysis Tools (spant) Plot a volume as an overlay on a segmented brain volume. — plot_voi_overlay_seg • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Arguments
diff --git a/docs/reference/ppm.html b/docs/reference/ppm.html
index c352327a..ee4696e2 100644
--- a/docs/reference/ppm.html
+++ b/docs/reference/ppm.html
@@ -1,5 +1,5 @@
-Return the ppm scale of an MRS dataset or fit result. — ppm • Spectroscopy Analysis Tools (spant) Return the ppm scale of an MRS dataset or fit result. — ppm • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -132,7 +132,7 @@ Value
diff --git a/docs/reference/precomp.html b/docs/reference/precomp.html
index 822d7336..df3d2c6c 100644
--- a/docs/reference/precomp.html
+++ b/docs/reference/precomp.html
@@ -1,7 +1,5 @@
-Save function results to file and load on subsequent calls to avoid repeat
-computation. — precomp • Spectroscopy Analysis Tools (spant) Save function results to file and load on subsequent calls to avoid repeat computation. — precomp • Spectroscopy Analysis Tools (spant) Preprocess and perform quality assessment of a single SVS data set. — preproc_svs • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Preprocess and perform quality assessment of a single SVS data set.
+ Source: R/fmrs.R
+ preproc_svs.Rd
+
+
+
+ Preprocess and perform quality assessment of a single SVS data set.
+
+
+
+ preproc_svs(path, label = NULL, output_dir = NULL, ref_inds = NULL)
+
+
+
+ Arguments
+ - path
+path to the fMRS data file or IMA directory.
- label
+a label to describe the data set.
- output_dir
+output directory.
- ref_inds
+a vector of 1-based indices for any water reference dynamic
+scans.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/preproc_svs_dataset.html b/docs/reference/preproc_svs_dataset.html
new file mode 100644
index 00000000..07c3a29b
--- /dev/null
+++ b/docs/reference/preproc_svs_dataset.html
@@ -0,0 +1,148 @@
+
+Preprocess and perform quality assessment of one or more SVS data sets. — preproc_svs_dataset • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Preprocess and perform quality assessment of one or more SVS data sets.
+ Source: R/fmrs.R
+ preproc_svs_dataset.Rd
+
+
+
+ Preprocess and perform quality assessment of one or more SVS data sets.
+
+
+
+ preproc_svs_dataset(
+ paths,
+ labels = NULL,
+ output_dir = "spant_analysis",
+ exclude_labels = NULL,
+ overwrite = FALSE,
+ ref_inds = NULL,
+ return_results = FALSE
+)
+
+
+
+ Arguments
+ - paths
+paths to the fMRS data file or IMA directory.
- labels
+labels to describe each data set.
- output_dir
+output directory.
- exclude_labels
+vector of labels of scans to exclude, eg poor quality
+data.
- overwrite
+overwrite saved results, defaults to FALSE.
- ref_inds
+a vector of 1-based indices for any water reference dynamic
+scans.
- return_results
+function will return key outputs, defaults to FALSE.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/print.fit_result.html b/docs/reference/print.fit_result.html
index 297f28dc..5f434e57 100644
--- a/docs/reference/print.fit_result.html
+++ b/docs/reference/print.fit_result.html
@@ -1,5 +1,5 @@
-Print a summary of an object of class fit_result. — print.fit_result • Spectroscopy Analysis Tools (spant) Print a summary of an object of class fit_result. — print.fit_result • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -105,7 +105,7 @@ Arguments
diff --git a/docs/reference/print.mrs_data.html b/docs/reference/print.mrs_data.html
index 51199017..e1561eb2 100644
--- a/docs/reference/print.mrs_data.html
+++ b/docs/reference/print.mrs_data.html
@@ -1,5 +1,5 @@
-Print a summary of mrs_data parameters. — print.mrs_data • Spectroscopy Analysis Tools (spant) Print a summary of mrs_data parameters. — print.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -109,7 +109,7 @@ Arguments
diff --git a/docs/reference/qn_states.html b/docs/reference/qn_states.html
index 0f42f2f9..d7aa6715 100644
--- a/docs/reference/qn_states.html
+++ b/docs/reference/qn_states.html
@@ -1,5 +1,5 @@
-Get the quantum coherence matrix for a spin system. — qn_states • Spectroscopy Analysis Tools (spant) Get the quantum coherence matrix for a spin system. — qn_states • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/rats.html b/docs/reference/rats.html
index 5a39a396..93585e08 100644
--- a/docs/reference/rats.html
+++ b/docs/reference/rats.html
@@ -1,5 +1,5 @@
-Robust Alignment to a Target Spectrum (RATS). — rats • Spectroscopy Analysis Tools (spant) Robust Alignment to a Target Spectrum (RATS). — rats • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -207,7 +207,7 @@ Value
diff --git a/docs/reference/re_weighting.html b/docs/reference/re_weighting.html
index d21caf21..8b0b070a 100644
--- a/docs/reference/re_weighting.html
+++ b/docs/reference/re_weighting.html
@@ -1,5 +1,5 @@
-Apply a weighting to the FID to enhance spectral resolution. — re_weighting • Spectroscopy Analysis Tools (spant) Apply a weighting to the FID to enhance spectral resolution. — re_weighting • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/read_basis.html b/docs/reference/read_basis.html
index da9b94af..eb6f8557 100644
--- a/docs/reference/read_basis.html
+++ b/docs/reference/read_basis.html
@@ -1,5 +1,5 @@
-Read a basis file in LCModel .basis format. — read_basis • Spectroscopy Analysis Tools (spant) Read a basis file in LCModel .basis format. — read_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/read_ima_coil_dir.html b/docs/reference/read_ima_coil_dir.html
index 28c02de0..4f073cd8 100644
--- a/docs/reference/read_ima_coil_dir.html
+++ b/docs/reference/read_ima_coil_dir.html
@@ -1,9 +1,5 @@
-Read a directory containing Siemens MRS IMA files and combine along the coil
-dimension. Note that the coil ID is inferred from the sorted file name and
-should be checked when consistency is required between two directories. — read_ima_coil_dir • Spectroscopy Analysis Tools (spant) Read a directory containing Siemens MRS IMA files and combine along the coil dimension. Note that the coil ID is inferred from the sorted file name and should be checked when consistency is required between two directories. — read_ima_coil_dir • Spectroscopy Analysis Tools (spant) Read a directory containing Siemens MRS IMA files and combine along the
-dynamic dimension. Note that the coil ID is inferred from the sorted file
-name and should be checked when consistency is required. — read_ima_dyn_dir • Spectroscopy Analysis Tools (spant) Read a directory containing Siemens MRS IMA files and combine along the dynamic dimension. Note that the coil ID is inferred from the sorted file name and should be checked when consistency is required. — read_ima_dyn_dir • Spectroscopy Analysis Tools (spant) Read an LCModel formatted coord file containing fit information. — read_lcm_coord • Spectroscopy Analysis Tools (spant) Read an LCModel formatted coord file containing fit information. — read_lcm_coord • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -107,7 +107,7 @@ Value
diff --git a/docs/reference/read_mrs.html b/docs/reference/read_mrs.html
index 3ac2a36b..2cf36b20 100644
--- a/docs/reference/read_mrs.html
+++ b/docs/reference/read_mrs.html
@@ -1,5 +1,5 @@
-Read MRS data from a file. — read_mrs • Spectroscopy Analysis Tools (spant) Read MRS data from a file. — read_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -88,7 +88,8 @@ Read MRS data from a file.
full_fid = FALSE,
omit_svs_ref_scans = TRUE,
verbose = FALSE,
- extra = NULL
+ extra = NULL,
+ fid_filt_dist = NULL
)
@@ -140,6 +141,13 @@ Arguments
an optional data frame to provide additional variables for use
in subsequent analysis steps, eg id or grouping variables.
fid_filt_dist
+indicate if the data has a distorted FID due to a
+brick-wall filter being used to downsample the data. Default is to auto
+detect this from the data, but TRUE or FALSE options can be given to override
+detection.
Value
@@ -183,7 +191,7 @@ Examples
diff --git a/docs/reference/read_mrs_tqn.html b/docs/reference/read_mrs_tqn.html
index 5766362f..84bdaf3a 100644
--- a/docs/reference/read_mrs_tqn.html
+++ b/docs/reference/read_mrs_tqn.html
@@ -1,5 +1,5 @@
-Read MRS data using the TARQUIN software package. — read_mrs_tqn • Spectroscopy Analysis Tools (spant) Read MRS data using the TARQUIN software package. — read_mrs_tqn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -131,7 +131,7 @@ Examples
diff --git a/docs/reference/read_pulse_ascii.html b/docs/reference/read_pulse_ascii.html
index c9e0d43c..ab11c9cc 100644
--- a/docs/reference/read_pulse_ascii.html
+++ b/docs/reference/read_pulse_ascii.html
@@ -1,5 +1,5 @@
-Read an ASCII formatted pulse file. — read_pulse_ascii • Spectroscopy Analysis Tools (spant) Read an ASCII formatted pulse file. — read_pulse_ascii • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/read_pulse_bruker.html b/docs/reference/read_pulse_bruker.html
index c92bf76a..dbe9073b 100644
--- a/docs/reference/read_pulse_bruker.html
+++ b/docs/reference/read_pulse_bruker.html
@@ -1,5 +1,5 @@
-Read a Bruker formatted pulse file — read_pulse_bruker • Spectroscopy Analysis Tools (spant) Read a Bruker formatted pulse file — read_pulse_bruker • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/read_pulse_pta.html b/docs/reference/read_pulse_pta.html
index 72e1b6d4..a0fac3c3 100644
--- a/docs/reference/read_pulse_pta.html
+++ b/docs/reference/read_pulse_pta.html
@@ -1,5 +1,5 @@
-Read a .pta formatted pulse file compatible with Siemens PulseTool. — read_pulse_pta • Spectroscopy Analysis Tools (spant) Read a .pta formatted pulse file compatible with Siemens PulseTool. — read_pulse_pta • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/read_siemens_txt_hdr.html b/docs/reference/read_siemens_txt_hdr.html
index 23fb8c70..3a17d87c 100644
--- a/docs/reference/read_siemens_txt_hdr.html
+++ b/docs/reference/read_siemens_txt_hdr.html
@@ -1,5 +1,5 @@
-Read the text format header found in Siemens IMA and TWIX data files. — read_siemens_txt_hdr • Spectroscopy Analysis Tools (spant) Read the text format header found in Siemens IMA and TWIX data files. — read_siemens_txt_hdr • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -78,7 +78,7 @@ Read the text format header found in Siemens IMA and TWIX data files.
- read_siemens_txt_hdr(input, version = "vd", verbose, offset = 0)
+ read_siemens_txt_hdr(input, version = "vd", verbose = FALSE, offset = 0)
@@ -118,7 +118,7 @@ Value
diff --git a/docs/reference/read_tqn_fit.html b/docs/reference/read_tqn_fit.html
index 4da6c25e..a1630420 100644
--- a/docs/reference/read_tqn_fit.html
+++ b/docs/reference/read_tqn_fit.html
@@ -1,5 +1,5 @@
-Reader for csv fit results generated by TARQUIN. — read_tqn_fit • Spectroscopy Analysis Tools (spant) Reader for csv fit results generated by TARQUIN. — read_tqn_fit • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -113,7 +113,7 @@ Examples
diff --git a/docs/reference/read_tqn_result.html b/docs/reference/read_tqn_result.html
index 36659714..68a3e98c 100644
--- a/docs/reference/read_tqn_result.html
+++ b/docs/reference/read_tqn_result.html
@@ -1,5 +1,5 @@
-Reader for csv results generated by TARQUIN. — read_tqn_result • Spectroscopy Analysis Tools (spant) Reader for csv results generated by TARQUIN. — read_tqn_result • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -117,7 +117,7 @@ Examples
diff --git a/docs/reference/recon_imag.html b/docs/reference/recon_imag.html
index d2a72225..5bc3b1eb 100644
--- a/docs/reference/recon_imag.html
+++ b/docs/reference/recon_imag.html
@@ -1,7 +1,5 @@
-Reconstruct complex time-domain data from the real part of frequency-domain
-data. — recon_imag • Spectroscopy Analysis Tools (spant) Reconstruct complex time-domain data from the real part of frequency-domain data. — recon_imag • Spectroscopy Analysis Tools (spant) Reconstruct complex time-domain data from the real part of frequency-domain
-data. — recon_imag_vec • Spectroscopy Analysis Tools (spant) Reconstruct complex time-domain data from the real part of frequency-domain data. — recon_imag_vec • Spectroscopy Analysis Tools (spant) Reconstruct 2D MRSI data from a twix file loaded with read_mrs. — recon_twix_2d_mrsi • Spectroscopy Analysis Tools (spant) Reconstruct 2D MRSI data from a twix file loaded with read_mrs. — recon_twix_2d_mrsi • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/rectangular_mask.html b/docs/reference/rectangular_mask.html
index a2117283..6e469bc9 100644
--- a/docs/reference/rectangular_mask.html
+++ b/docs/reference/rectangular_mask.html
@@ -1,5 +1,5 @@
-Create a rectangular mask stored as a matrix of logical values. — rectangular_mask • Spectroscopy Analysis Tools (spant) Create a rectangular mask stored as a matrix of logical values. — rectangular_mask • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -130,7 +130,7 @@ Value
diff --git a/docs/reference/reexports.html b/docs/reference/reexports.html
index 694a75d1..a59e8379 100644
--- a/docs/reference/reexports.html
+++ b/docs/reference/reexports.html
@@ -1,5 +1,5 @@
-Objects exported from other packages — reexports • Spectroscopy Analysis Tools (spant) Objects exported from other packages — reexports • Spectroscopy Analysis Tools (spant)
Spectroscopy Analysis Tools (spant)
- 2.21.0
+ 2.22.0
@@ -103,7 +103,7 @@ Objects exported from other packages
diff --git a/docs/reference/rep_array_dim.html b/docs/reference/rep_array_dim.html
index b9c49b4a..48c0a5ed 100644
--- a/docs/reference/rep_array_dim.html
+++ b/docs/reference/rep_array_dim.html
@@ -1,5 +1,5 @@
-Repeat an array over a given dimension. — rep_array_dim • Spectroscopy Analysis Tools (spant) Repeat an array over a given dimension. — rep_array_dim • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/rep_dyn.html b/docs/reference/rep_dyn.html
index 6bbfb0ef..89a4bb9b 100644
--- a/docs/reference/rep_dyn.html
+++ b/docs/reference/rep_dyn.html
@@ -1,5 +1,5 @@
-Replicate a scan in the dynamic dimension. — rep_dyn • Spectroscopy Analysis Tools (spant) Replicate a scan in the dynamic dimension. — rep_dyn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/rep_mrs.html b/docs/reference/rep_mrs.html
index 67730b5c..becb8f00 100644
--- a/docs/reference/rep_mrs.html
+++ b/docs/reference/rep_mrs.html
@@ -1,5 +1,5 @@
-Replicate a scan over a given dimension. — rep_mrs • Spectroscopy Analysis Tools (spant) Replicate a scan over a given dimension. — rep_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -138,7 +138,7 @@ Value
diff --git a/docs/reference/resample_basis.html b/docs/reference/resample_basis.html
index b0f2ab17..c7a6222a 100644
--- a/docs/reference/resample_basis.html
+++ b/docs/reference/resample_basis.html
@@ -1,5 +1,5 @@
-Resample a basis-set to match a mrs_data acquisition. — resample_basis • Spectroscopy Analysis Tools (spant) Resample a basis-set to match a mrs_data acquisition. — resample_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -116,7 +116,7 @@ Value
diff --git a/docs/reference/resample_img.html b/docs/reference/resample_img.html
index f1e7beaf..b0cc8f71 100644
--- a/docs/reference/resample_img.html
+++ b/docs/reference/resample_img.html
@@ -1,5 +1,5 @@
-Resample an image to match a target image space. — resample_img • Spectroscopy Analysis Tools (spant) Resample an image to match a target image space. — resample_img • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/resample_voi.html b/docs/reference/resample_voi.html
index 8fbfa836..a29ab096 100644
--- a/docs/reference/resample_voi.html
+++ b/docs/reference/resample_voi.html
@@ -1,7 +1,5 @@
-Resample a VOI to match a target image space using nearest-neighbour
-interpolation. — resample_voi • Spectroscopy Analysis Tools (spant) Resample a VOI to match a target image space using nearest-neighbour interpolation. — resample_voi • Spectroscopy Analysis Tools (spant) Reslice a nifti object to match the orientation of mrs data. — reslice_to_mrs • Spectroscopy Analysis Tools (spant) Reslice a nifti object to match the orientation of mrs data. — reslice_to_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/reson_table2mrs_data.html b/docs/reference/reson_table2mrs_data.html
index d75579ee..c5a2167a 100644
--- a/docs/reference/reson_table2mrs_data.html
+++ b/docs/reference/reson_table2mrs_data.html
@@ -1,5 +1,5 @@
-Generate mrs_data from a table of single Lorentzian resonances. — reson_table2mrs_data • Spectroscopy Analysis Tools (spant) Generate mrs_data from a table of single Lorentzian resonances. — reson_table2mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -119,7 +119,7 @@ Value
diff --git a/docs/reference/rm_dyns.html b/docs/reference/rm_dyns.html
index 5d5ef692..573e1f51 100644
--- a/docs/reference/rm_dyns.html
+++ b/docs/reference/rm_dyns.html
@@ -1,5 +1,5 @@
-Remove a subset of dynamic scans. — rm_dyns • Spectroscopy Analysis Tools (spant) Remove a subset of dynamic scans. — rm_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/scale_amp_molal.html b/docs/reference/scale_amp_molal.html
index aaeee1f2..7acb8cb0 100644
--- a/docs/reference/scale_amp_molal.html
+++ b/docs/reference/scale_amp_molal.html
@@ -1,7 +1,5 @@
-Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water). — scale_amp_molal • Spectroscopy Analysis Tools (spant) Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / kg of tissue water). — scale_amp_molal • Spectroscopy Analysis Tools (spant)
Spectroscopy Analysis Tools (spant)
- 2.21.0
+ 2.22.0
@@ -76,8 +74,7 @@
- Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water).
+ Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / kg of tissue water).
Source: R/amp_scaling.R
scale_amp_molal.Rd
@@ -163,7 +160,7 @@ Value
diff --git a/docs/reference/scale_amp_molal_pvc.html b/docs/reference/scale_amp_molal_pvc.html
index 962d6afc..4d194abd 100644
--- a/docs/reference/scale_amp_molal_pvc.html
+++ b/docs/reference/scale_amp_molal_pvc.html
@@ -1,7 +1,5 @@
-Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water). — scale_amp_molal_pvc • Spectroscopy Analysis Tools (spant)
@@ -75,8 +73,7 @@
- Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water).
+ Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / kg of tissue water).
Source: R/amp_scaling.R
scale_amp_molal_pvc.Rd
@@ -141,7 +138,7 @@ Value
diff --git a/docs/reference/scale_amp_molar.html b/docs/reference/scale_amp_molar.html
index 02358d91..dc87a338 100644
--- a/docs/reference/scale_amp_molar.html
+++ b/docs/reference/scale_amp_molar.html
@@ -1,7 +1,5 @@
-Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / Litre of tissue). — scale_amp_molar • Spectroscopy Analysis Tools (spant) Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / Litre of tissue). — scale_amp_molar • Spectroscopy Analysis Tools (spant) Convert default LCM/TARQUIN concentration scaling to molal units with partial
-volume correction. — scale_amp_molar2molal_pvc • Spectroscopy Analysis Tools (spant) Convert default LCM/TARQUIN concentration scaling to molal units with partial volume correction. — scale_amp_molar2molal_pvc • Spectroscopy Analysis Tools (spant) Scale fitted amplitudes to a ratio of signal amplitude. — scale_amp_ratio • Spectroscopy Analysis Tools (spant) Scale fitted amplitudes to a ratio of signal amplitude. — scale_amp_ratio • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -116,7 +116,7 @@ Value
diff --git a/docs/reference/scale_amp_ratio_value.html b/docs/reference/scale_amp_ratio_value.html
index 2036837a..6af8ac51 100644
--- a/docs/reference/scale_amp_ratio_value.html
+++ b/docs/reference/scale_amp_ratio_value.html
@@ -1,5 +1,5 @@
-Scale fitted amplitudes to a ratio of signal amplitude. — scale_amp_ratio_value • Spectroscopy Analysis Tools (spant) Scale fitted amplitudes to a ratio of signal amplitude. — scale_amp_ratio_value • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/scale_amp_water_ratio.html b/docs/reference/scale_amp_water_ratio.html
index 5b25e884..35a76b00 100644
--- a/docs/reference/scale_amp_water_ratio.html
+++ b/docs/reference/scale_amp_water_ratio.html
@@ -1,5 +1,5 @@
-Scale metabolite amplitudes as a ratio to the unsuppressed water amplitude. — scale_amp_water_ratio • Spectroscopy Analysis Tools (spant) Scale metabolite amplitudes as a ratio to the unsuppressed water amplitude. — scale_amp_water_ratio • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/scale_basis_amp.html b/docs/reference/scale_basis_amp.html
index 9401c3f1..5a58b5e5 100644
--- a/docs/reference/scale_basis_amp.html
+++ b/docs/reference/scale_basis_amp.html
@@ -1,5 +1,5 @@
-Scale a basis object by a scalar. — scale_basis_amp • Spectroscopy Analysis Tools (spant) Scale a basis object by a scalar. — scale_basis_amp • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/scale_basis_from_singlet.html b/docs/reference/scale_basis_from_singlet.html
index 0d542bc8..c9a19e77 100644
--- a/docs/reference/scale_basis_from_singlet.html
+++ b/docs/reference/scale_basis_from_singlet.html
@@ -1,5 +1,5 @@
-Scale a basis-set to be consistent with spant assumptions for water scaling. — scale_basis_from_singlet • Spectroscopy Analysis Tools (spant) Scale a basis-set to be consistent with spant assumptions for water scaling. — scale_basis_from_singlet • Spectroscopy Analysis Tools (spant)
Spectroscopy Analysis Tools (spant)
- 2.21.0
+ 2.22.0
@@ -127,7 +127,7 @@ Value
diff --git a/docs/reference/scale_mrs_amp.html b/docs/reference/scale_mrs_amp.html
index b5501a0d..990f058a 100644
--- a/docs/reference/scale_mrs_amp.html
+++ b/docs/reference/scale_mrs_amp.html
@@ -1,5 +1,5 @@
-Scale an mrs_data object by a scalar or vector or amplitudes. — scale_mrs_amp • Spectroscopy Analysis Tools (spant) Scale an mrs_data object by a scalar or vector or amplitudes. — scale_mrs_amp • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/scale_spec.html b/docs/reference/scale_spec.html
index 4f6ea835..6b3ddba4 100644
--- a/docs/reference/scale_spec.html
+++ b/docs/reference/scale_spec.html
@@ -1,5 +1,5 @@
-Scale mrs_data to a spectral region. — scale_spec • Spectroscopy Analysis Tools (spant) Scale mrs_data to a spectral region. — scale_spec • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -141,7 +141,7 @@ Value
diff --git a/docs/reference/sd.html b/docs/reference/sd.html
index ea1eec9f..3ae4dfd4 100644
--- a/docs/reference/sd.html
+++ b/docs/reference/sd.html
@@ -1,5 +1,5 @@
-Calculate the standard deviation spectrum from an mrs_data object. — sd • Spectroscopy Analysis Tools (spant) Calculate the standard deviation spectrum from an mrs_data object. — sd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/sd.mrs_data.html b/docs/reference/sd.mrs_data.html
index 3f92a49f..13bdda85 100644
--- a/docs/reference/sd.mrs_data.html
+++ b/docs/reference/sd.mrs_data.html
@@ -1,5 +1,5 @@
-Calculate the standard deviation spectrum from an mrs_data object. — sd.mrs_data • Spectroscopy Analysis Tools (spant) Calculate the standard deviation spectrum from an mrs_data object. — sd.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/seconds.html b/docs/reference/seconds.html
index b34d6627..467ee17f 100644
--- a/docs/reference/seconds.html
+++ b/docs/reference/seconds.html
@@ -1,5 +1,5 @@
-Return a time scale vector to match the FID of an MRS data object. — seconds • Spectroscopy Analysis Tools (spant) Return a time scale vector to match the FID of an MRS data object. — seconds • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/seq_cpmg_ideal.html b/docs/reference/seq_cpmg_ideal.html
index 547e96ab..45727c86 100644
--- a/docs/reference/seq_cpmg_ideal.html
+++ b/docs/reference/seq_cpmg_ideal.html
@@ -1,5 +1,5 @@
-CPMG style sequence with ideal pulses. — seq_cpmg_ideal • Spectroscopy Analysis Tools (spant) CPMG style sequence with ideal pulses. — seq_cpmg_ideal • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/seq_mega_press_ideal.html b/docs/reference/seq_mega_press_ideal.html
index 0769b8b4..a9cd7fa0 100644
--- a/docs/reference/seq_mega_press_ideal.html
+++ b/docs/reference/seq_mega_press_ideal.html
@@ -1,7 +1,5 @@
-MEGA-PRESS sequence with ideal localisation pulses and Gaussian shaped
-editing pulse. — seq_mega_press_ideal • Spectroscopy Analysis Tools (spant) MEGA-PRESS sequence with ideal localisation pulses and Gaussian shaped editing pulse. — seq_mega_press_ideal • Spectroscopy Analysis Tools (spant) PRESS sequence with shaped refocusing pulses. — seq_press_2d_shaped • Spectroscopy Analysis Tools (spant) PRESS sequence with shaped refocusing pulses. — seq_press_2d_shaped • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -165,7 +165,7 @@ Value
diff --git a/docs/reference/seq_press_ideal.html b/docs/reference/seq_press_ideal.html
index 8c976856..72c3af3d 100644
--- a/docs/reference/seq_press_ideal.html
+++ b/docs/reference/seq_press_ideal.html
@@ -1,5 +1,5 @@
-PRESS sequence with ideal pulses. — seq_press_ideal • Spectroscopy Analysis Tools (spant) PRESS sequence with ideal pulses. — seq_press_ideal • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/seq_pulse_acquire.html b/docs/reference/seq_pulse_acquire.html
index 4a88fc64..ad80571e 100644
--- a/docs/reference/seq_pulse_acquire.html
+++ b/docs/reference/seq_pulse_acquire.html
@@ -1,5 +1,5 @@
-Simple pulse and acquire sequence with ideal pulses. — seq_pulse_acquire • Spectroscopy Analysis Tools (spant) Simple pulse and acquire sequence with ideal pulses. — seq_pulse_acquire • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/seq_slaser_ideal.html b/docs/reference/seq_slaser_ideal.html
index 74688f4d..eb83e8e3 100644
--- a/docs/reference/seq_slaser_ideal.html
+++ b/docs/reference/seq_slaser_ideal.html
@@ -1,5 +1,5 @@
-sLASER sequence with ideal pulses. — seq_slaser_ideal • Spectroscopy Analysis Tools (spant) sLASER sequence with ideal pulses. — seq_slaser_ideal • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -126,7 +126,7 @@ Value
diff --git a/docs/reference/seq_spin_echo_ideal.html b/docs/reference/seq_spin_echo_ideal.html
index e23271de..4248716f 100644
--- a/docs/reference/seq_spin_echo_ideal.html
+++ b/docs/reference/seq_spin_echo_ideal.html
@@ -1,5 +1,5 @@
-Spin echo sequence with ideal pulses. — seq_spin_echo_ideal • Spectroscopy Analysis Tools (spant) Spin echo sequence with ideal pulses. — seq_spin_echo_ideal • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/seq_steam_ideal.html b/docs/reference/seq_steam_ideal.html
index a60685a8..1c8115d7 100644
--- a/docs/reference/seq_steam_ideal.html
+++ b/docs/reference/seq_steam_ideal.html
@@ -1,5 +1,5 @@
-STEAM sequence with ideal pulses. — seq_steam_ideal • Spectroscopy Analysis Tools (spant) STEAM sequence with ideal pulses. — seq_steam_ideal • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -128,7 +128,7 @@ Value
diff --git a/docs/reference/seq_steam_ideal_cof.html b/docs/reference/seq_steam_ideal_cof.html
index 8f225740..cba7af91 100644
--- a/docs/reference/seq_steam_ideal_cof.html
+++ b/docs/reference/seq_steam_ideal_cof.html
@@ -1,7 +1,5 @@
-STEAM sequence with ideal pulses and coherence order filtering to simulate
-gradient crushers. — seq_steam_ideal_cof • Spectroscopy Analysis Tools (spant) STEAM sequence with ideal pulses and coherence order filtering to simulate gradient crushers. — seq_steam_ideal_cof • Spectroscopy Analysis Tools (spant) STEAM sequence with ideal pulses using the z-rotation gradient simulation
-method described by Young et al JMR 140, 146-152 (1999). — seq_steam_ideal_young • Spectroscopy Analysis Tools (spant) STEAM sequence with ideal pulses using the z-rotation gradient simulation method described by Young et al JMR 140, 146-152 (1999). — seq_steam_ideal_young • Spectroscopy Analysis Tools (spant) Set the number of transients for an mrs_data object. — set_Ntrans • Spectroscopy Analysis Tools (spant) Set the number of transients for an mrs_data object. — set_Ntrans • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/set_def_acq_paras.html b/docs/reference/set_def_acq_paras.html
index 3e1b4004..cc2ada9c 100644
--- a/docs/reference/set_def_acq_paras.html
+++ b/docs/reference/set_def_acq_paras.html
@@ -1,5 +1,5 @@
-Set the default acquisition parameters. — set_def_acq_paras • Spectroscopy Analysis Tools (spant) Set the default acquisition parameters. — set_def_acq_paras • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Arguments
diff --git a/docs/reference/set_lcm_cmd.html b/docs/reference/set_lcm_cmd.html
index 2056ed01..42bb2f24 100644
--- a/docs/reference/set_lcm_cmd.html
+++ b/docs/reference/set_lcm_cmd.html
@@ -1,5 +1,5 @@
-Set the command to run the LCModel command-line program. — set_lcm_cmd • Spectroscopy Analysis Tools (spant) Set the command to run the LCModel command-line program. — set_lcm_cmd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/set_lw.html b/docs/reference/set_lw.html
index b64ec851..bb176c62 100644
--- a/docs/reference/set_lw.html
+++ b/docs/reference/set_lw.html
@@ -1,5 +1,5 @@
-Apply line-broadening to an mrs_data object to achieve a specified linewidth. — set_lw • Spectroscopy Analysis Tools (spant) Apply line-broadening to an mrs_data object to achieve a specified linewidth. — set_lw • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -123,7 +123,7 @@ Value
diff --git a/docs/reference/set_mask_xy_mat.html b/docs/reference/set_mask_xy_mat.html
index 49dc5d4e..52c4b617 100644
--- a/docs/reference/set_mask_xy_mat.html
+++ b/docs/reference/set_mask_xy_mat.html
@@ -1,5 +1,5 @@
-Set the masked voxels in a 2D MRSI dataset to given spectrum. — set_mask_xy_mat • Spectroscopy Analysis Tools (spant) Set the masked voxels in a 2D MRSI dataset to given spectrum. — set_mask_xy_mat • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Value
diff --git a/docs/reference/set_precomp_mode.html b/docs/reference/set_precomp_mode.html
index f44bd5d3..47c28e3b 100644
--- a/docs/reference/set_precomp_mode.html
+++ b/docs/reference/set_precomp_mode.html
@@ -1,5 +1,5 @@
-Set the precompute mode. — set_precomp_mode • Spectroscopy Analysis Tools (spant) Set the precompute mode. — set_precomp_mode • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/set_precomp_verbose.html b/docs/reference/set_precomp_verbose.html
index 1453a231..9c613505 100644
--- a/docs/reference/set_precomp_verbose.html
+++ b/docs/reference/set_precomp_verbose.html
@@ -1,5 +1,5 @@
-Set the verbosity of the precompute function. — set_precomp_verbose • Spectroscopy Analysis Tools (spant) Set the verbosity of the precompute function. — set_precomp_verbose • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/set_ref.html b/docs/reference/set_ref.html
index 8953fa50..5436dfa2 100644
--- a/docs/reference/set_ref.html
+++ b/docs/reference/set_ref.html
@@ -1,5 +1,5 @@
-Set the ppm reference value (eg ppm value at 0Hz). — set_ref • Spectroscopy Analysis Tools (spant) Set the ppm reference value (eg ppm value at 0Hz). — set_ref • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/set_td_pts.html b/docs/reference/set_td_pts.html
index 8a80d42a..586459ff 100644
--- a/docs/reference/set_td_pts.html
+++ b/docs/reference/set_td_pts.html
@@ -1,7 +1,5 @@
-Set the number of time-domain data points, truncating or zero-filling as
-appropriate. — set_td_pts • Spectroscopy Analysis Tools (spant) Set the number of time-domain data points, truncating or zero-filling as appropriate. — set_td_pts • Spectroscopy Analysis Tools (spant) Set the command to run the TARQUIN command-line program. — set_tqn_cmd • Spectroscopy Analysis Tools (spant) Set the command to run the TARQUIN command-line program. — set_tqn_cmd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/set_tr.html b/docs/reference/set_tr.html
index b2109ab0..65c9df5f 100644
--- a/docs/reference/set_tr.html
+++ b/docs/reference/set_tr.html
@@ -1,5 +1,5 @@
-Set the repetition time of an MRS dataset. — set_tr • Spectroscopy Analysis Tools (spant) Set the repetition time of an MRS dataset. — set_tr • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/shift.html b/docs/reference/shift.html
index ab0fe724..034591d0 100644
--- a/docs/reference/shift.html
+++ b/docs/reference/shift.html
@@ -1,5 +1,5 @@
-Apply a frequency shift to MRS data. — shift • Spectroscopy Analysis Tools (spant) Apply a frequency shift to MRS data. — shift • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/shift_basis.html b/docs/reference/shift_basis.html
index 2884be19..f55a65e0 100644
--- a/docs/reference/shift_basis.html
+++ b/docs/reference/shift_basis.html
@@ -1,5 +1,5 @@
-Apply frequency shifts to basis set signals. — shift_basis • Spectroscopy Analysis Tools (spant) Apply frequency shifts to basis set signals. — shift_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Value
diff --git a/docs/reference/sim_basis.html b/docs/reference/sim_basis.html
index c7838c46..bb5fefc6 100644
--- a/docs/reference/sim_basis.html
+++ b/docs/reference/sim_basis.html
@@ -1,5 +1,5 @@
-Simulate a basis set object. — sim_basis • Spectroscopy Analysis Tools (spant) Simulate a basis set object. — sim_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -136,7 +136,7 @@ Value
diff --git a/docs/reference/sim_basis_1h_brain.html b/docs/reference/sim_basis_1h_brain.html
index 62ed7389..f71ffa0b 100644
--- a/docs/reference/sim_basis_1h_brain.html
+++ b/docs/reference/sim_basis_1h_brain.html
@@ -1,7 +1,5 @@
-Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS
-sequence. Note, ideal pulses are assumed. — sim_basis_1h_brain • Spectroscopy Analysis Tools (spant) Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS sequence. Note, ideal pulses are assumed. — sim_basis_1h_brain • Spectroscopy Analysis Tools (spant) Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS
-sequence. Note, ideal pulses are assumed. — sim_basis_1h_brain_press • Spectroscopy Analysis Tools (spant) Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS sequence. Note, ideal pulses are assumed. — sim_basis_1h_brain_press • Spectroscopy Analysis Tools (spant) Simulate a macromolecular and lipid basis-set suitable for 1H brain MRS
-analysis. — sim_basis_mm_lip_lcm • Spectroscopy Analysis Tools (spant) Simulate a macromolecular and lipid basis-set suitable for 1H brain MRS analysis. — sim_basis_mm_lip_lcm • Spectroscopy Analysis Tools (spant) Simulate a basis file using TARQUIN. — sim_basis_tqn • Spectroscopy Analysis Tools (spant) Simulate a basis file using TARQUIN. — sim_basis_tqn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -129,7 +129,7 @@ Examples
diff --git a/docs/reference/sim_brain_1h.html b/docs/reference/sim_brain_1h.html
index 2044cf1a..717ee289 100644
--- a/docs/reference/sim_brain_1h.html
+++ b/docs/reference/sim_brain_1h.html
@@ -1,5 +1,5 @@
-Simulate MRS data with a similar appearance to normal brain (by default). — sim_brain_1h • Spectroscopy Analysis Tools (spant) Simulate MRS data with a similar appearance to normal brain (by default). — sim_brain_1h • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -159,7 +159,7 @@ Value
diff --git a/docs/reference/sim_mol.html b/docs/reference/sim_mol.html
index 23bcef50..77f76a50 100644
--- a/docs/reference/sim_mol.html
+++ b/docs/reference/sim_mol.html
@@ -1,5 +1,5 @@
-Simulate a mol_parameter object. — sim_mol • Spectroscopy Analysis Tools (spant) Simulate a mol_parameter object. — sim_mol • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -143,7 +143,7 @@ Value
diff --git a/docs/reference/sim_noise.html b/docs/reference/sim_noise.html
index 23875f79..a71477d4 100644
--- a/docs/reference/sim_noise.html
+++ b/docs/reference/sim_noise.html
@@ -1,5 +1,5 @@
-Simulate an mrs_data object containing simulated Gaussian noise. — sim_noise • Spectroscopy Analysis Tools (spant) Simulate an mrs_data object containing simulated Gaussian noise. — sim_noise • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -84,6 +84,7 @@ Simulate an mrs_data object containing simulated Gaussian noise.
ft = def_ft(),
N = def_N(),
ref = def_ref(),
+ nuc = def_nuc(),
dyns = 1,
fd = TRUE
)
@@ -111,6 +112,10 @@ Arguments
reference value for ppm scale.
nuc
+resonant nucleus.
dyns
number of dynamic scans to generate.
Value
diff --git a/docs/reference/sim_resonances.html b/docs/reference/sim_resonances.html
index 19e9a8a4..d4f8d7c0 100644
--- a/docs/reference/sim_resonances.html
+++ b/docs/reference/sim_resonances.html
@@ -1,5 +1,5 @@
-Simulate a MRS data object containing a set of simulated resonances. — sim_resonances • Spectroscopy Analysis Tools (spant) Simulate a MRS data object containing a set of simulated resonances. — sim_resonances • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -161,7 +161,7 @@ Examples
diff --git a/docs/reference/sim_th_excit_profile.html b/docs/reference/sim_th_excit_profile.html
index 5535c5ef..e781cab1 100644
--- a/docs/reference/sim_th_excit_profile.html
+++ b/docs/reference/sim_th_excit_profile.html
@@ -1,7 +1,5 @@
-Simulate an ideal pulse excitation profile by smoothing a top-hat function
-with a Gaussian. — sim_th_excit_profile • Spectroscopy Analysis Tools (spant) Simulate an ideal pulse excitation profile by smoothing a top-hat function with a Gaussian. — sim_th_excit_profile • Spectroscopy Analysis Tools (spant) Simulate an mrs_data object containing complex zero valued samples. — sim_zero • Spectroscopy Analysis Tools (spant) Simulate an mrs_data object containing complex zero valued samples. — sim_zero • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -78,7 +78,14 @@ Simulate an mrs_data object containing complex zero valued samples.
-
+
@@ -99,6 +106,10 @@ Arguments
reference value for ppm scale.
nuc
+resonant nucleus.
dyns
number of dynamic scans to generate.
Value
diff --git a/docs/reference/smooth_dyns.html b/docs/reference/smooth_dyns.html
index 4cc8da50..accf3a51 100644
--- a/docs/reference/smooth_dyns.html
+++ b/docs/reference/smooth_dyns.html
@@ -1,5 +1,5 @@
-Smooth data across the dynamic dimension with a Gaussian kernel. — smooth_dyns • Spectroscopy Analysis Tools (spant) Smooth data across the dynamic dimension with a Gaussian kernel. — smooth_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/sort_basis.html b/docs/reference/sort_basis.html
index 6a676ea2..d25cc006 100644
--- a/docs/reference/sort_basis.html
+++ b/docs/reference/sort_basis.html
@@ -1,5 +1,5 @@
-Sort the basis-set elements alphabetically. — sort_basis • Spectroscopy Analysis Tools (spant) Sort the basis-set elements alphabetically. — sort_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/spant-package.html b/docs/reference/spant-package.html
index b3dd8e21..90f19ec3 100644
--- a/docs/reference/spant-package.html
+++ b/docs/reference/spant-package.html
@@ -1,5 +1,5 @@
-spant: spectroscopy analysis tools. — spant-package • Spectroscopy Analysis Tools (spant) spant: spectroscopy analysis tools. — spant-package • Spectroscopy Analysis Tools (spant) Simulate and fit some spectra with ABfit for benchmarking purposes. Basic
-timing and performance metrics will be printed. — spant_abfit_benchmark • Spectroscopy Analysis Tools (spant) Simulate and fit some spectra with ABfit for benchmarking purposes. Basic timing and performance metrics will be printed. — spant_abfit_benchmark • Spectroscopy Analysis Tools (spant) Example MEGA-PRESS data with significant B0 drift. — spant_mpress_drift • Spectroscopy Analysis Tools (spant) Example MEGA-PRESS data with significant B0 drift. — spant_mpress_drift • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -83,7 +83,7 @@ Example MEGA-PRESS data with significant B0 drift.
Format
- An object of class mrs_data of length 13.
+ An object of class mrs_data of dimension 1 x 1 x 1 x 1 x 40 x 1 x 1024.
@@ -98,7 +98,7 @@ Format
diff --git a/docs/reference/spant_sim_fmrs_dataset.html b/docs/reference/spant_sim_fmrs_dataset.html
new file mode 100644
index 00000000..00e48b56
--- /dev/null
+++ b/docs/reference/spant_sim_fmrs_dataset.html
@@ -0,0 +1,117 @@
+
+Simulate an example fMRS dataset for a block design fMRS experiment and export a BIDS structure. — spant_sim_fmrs_dataset • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Simulate an example fMRS dataset for a block design fMRS experiment and export a BIDS structure.
+ Source: R/fmrs.R
+ spant_sim_fmrs_dataset.Rd
+
+
+
+ Simulate an example fMRS dataset for a block design fMRS experiment and
+export a BIDS structure.
+
+
+
+ spant_sim_fmrs_dataset(output_dir = NULL)
+
+
+
+ Arguments
+ - output_dir
+output directory for the BIDS data. Defaults to :
+"HOME/sim_fmrs_dataset/data".
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/spant_simulation_benchmark.html b/docs/reference/spant_simulation_benchmark.html
index 32daa8bf..d8cc6841 100644
--- a/docs/reference/spant_simulation_benchmark.html
+++ b/docs/reference/spant_simulation_benchmark.html
@@ -1,7 +1,5 @@
-Simulate a typical metabolite basis set for benchmarking. Timing metrics will
-be printed on completion. — spant_simulation_benchmark • Spectroscopy Analysis Tools (spant) Simulate a typical metabolite basis set for benchmarking. Timing metrics will be printed on completion. — spant_simulation_benchmark • Spectroscopy Analysis Tools (spant) Decompose an mrs_data object into white and gray matter spectra. — spec_decomp • Spectroscopy Analysis Tools (spant) Perform a mathematical operation on a spectral region. — spec_op • Spectroscopy Analysis Tools (spant) Perform a mathematical operation on a spectral region. — spec_op • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -98,8 +98,8 @@ Arguments
operator
-can be "sum" (default), "mean", "l2", "max", "min" or
-"max-min".
can be "sum" (default), "mean", "l2", "max", "max_cplx,
+"min" or "max-min".
freq_scale
@@ -129,7 +129,7 @@ Value
diff --git a/docs/reference/spin_sys.html b/docs/reference/spin_sys.html
index 853423a4..1eaa9e76 100644
--- a/docs/reference/spin_sys.html
+++ b/docs/reference/spin_sys.html
@@ -1,5 +1,5 @@
-Create a spin system object for pulse sequence simulation. — spin_sys • Spectroscopy Analysis Tools (spant) Create a spin system object for pulse sequence simulation. — spin_sys • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/spm_pve2categorical.html b/docs/reference/spm_pve2categorical.html
index 23a1bad9..70f10729 100644
--- a/docs/reference/spm_pve2categorical.html
+++ b/docs/reference/spm_pve2categorical.html
@@ -1,7 +1,5 @@
-Convert SPM style segmentation files to a single categorical image where
-the numerical values map as: 0) Other, 1) CSF, 2) GM and 3) WM. — spm_pve2categorical • Spectroscopy Analysis Tools (spant) Convert SPM style segmentation files to a single categorical image where the numerical values map as: 0) Other, 1) CSF, 2) GM and 3) WM. — spm_pve2categorical • Spectroscopy Analysis Tools (spant) Signal space projection method for lipid suppression. — ssp • Spectroscopy Analysis Tools (spant) Signal space projection method for lipid suppression. — ssp • Spectroscopy Analysis Tools (spant) Plot the fitting results of an object of class fit_result with
-individual basis set components shown. — stackplot.fit_result • Spectroscopy Analysis Tools (spant) Plot the fitting results of an object of class fit_result with individual basis set components shown. — stackplot.fit_result • Spectroscopy Analysis Tools (spant) Produce a plot with multiple traces. — stackplot • Spectroscopy Analysis Tools (spant) Produce a plot with multiple traces. — stackplot • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/stackplot.mrs_data.html b/docs/reference/stackplot.mrs_data.html
index 17ff5648..64eea445 100644
--- a/docs/reference/stackplot.mrs_data.html
+++ b/docs/reference/stackplot.mrs_data.html
@@ -1,5 +1,5 @@
-Stackplot plotting method for objects of class mrs_data. — stackplot.mrs_data • Spectroscopy Analysis Tools (spant) Stackplot plotting method for objects of class mrs_data. — stackplot.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -255,7 +255,7 @@ Arguments
diff --git a/docs/reference/sub_first_dyn.html b/docs/reference/sub_first_dyn.html
index dbd7f831..493b7242 100644
--- a/docs/reference/sub_first_dyn.html
+++ b/docs/reference/sub_first_dyn.html
@@ -1,5 +1,5 @@
-Subtract the first dynamic spectrum from a dynamic series. — sub_first_dyn • Spectroscopy Analysis Tools (spant) Subtract the first dynamic spectrum from a dynamic series. — sub_first_dyn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/sub_mean_dyns.html b/docs/reference/sub_mean_dyns.html
index 6e3bb2df..221bd0c1 100644
--- a/docs/reference/sub_mean_dyns.html
+++ b/docs/reference/sub_mean_dyns.html
@@ -1,5 +1,5 @@
-Subtract the mean dynamic spectrum from a dynamic series. — sub_mean_dyns • Spectroscopy Analysis Tools (spant) Subtract the mean dynamic spectrum from a dynamic series. — sub_mean_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/sub_median_dyns.html b/docs/reference/sub_median_dyns.html
index 134c495d..1e834f14 100644
--- a/docs/reference/sub_median_dyns.html
+++ b/docs/reference/sub_median_dyns.html
@@ -1,5 +1,5 @@
-Subtract the median dynamic spectrum from a dynamic series. — sub_median_dyns • Spectroscopy Analysis Tools (spant) Subtract the median dynamic spectrum from a dynamic series. — sub_median_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/sum_coils.html b/docs/reference/sum_coils.html
index 7bf559f2..e1ab3cc0 100644
--- a/docs/reference/sum_coils.html
+++ b/docs/reference/sum_coils.html
@@ -1,5 +1,5 @@
-Calculate the sum across receiver coil elements. — sum_coils • Spectroscopy Analysis Tools (spant) Calculate the sum across receiver coil elements. — sum_coils • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/sum_dyns.html b/docs/reference/sum_dyns.html
index a0be19d3..bbda2ffc 100644
--- a/docs/reference/sum_dyns.html
+++ b/docs/reference/sum_dyns.html
@@ -1,5 +1,5 @@
-Calculate the sum of data dynamics. — sum_dyns • Spectroscopy Analysis Tools (spant) Calculate the sum of data dynamics. — sum_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/sum_mrs.html b/docs/reference/sum_mrs.html
index a22f215b..3cc3ab9e 100644
--- a/docs/reference/sum_mrs.html
+++ b/docs/reference/sum_mrs.html
@@ -1,5 +1,5 @@
-Sum two mrs_data objects. — sum_mrs • Spectroscopy Analysis Tools (spant) Sum two mrs_data objects. — sum_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Value
diff --git a/docs/reference/sum_mrs_list.html b/docs/reference/sum_mrs_list.html
index f4e09aea..c3584348 100644
--- a/docs/reference/sum_mrs_list.html
+++ b/docs/reference/sum_mrs_list.html
@@ -1,5 +1,5 @@
-Return the sum of a list of mrs_data objects. — sum_mrs_list • Spectroscopy Analysis Tools (spant) Return the sum of a list of mrs_data objects. — sum_mrs_list • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/svs_1h_brain_analysis.html b/docs/reference/svs_1h_brain_analysis.html
index 8ce514db..dff0ef7d 100644
--- a/docs/reference/svs_1h_brain_analysis.html
+++ b/docs/reference/svs_1h_brain_analysis.html
@@ -1,5 +1,5 @@
-Standard SVS 1H brain analysis pipeline. — svs_1h_brain_analysis • Spectroscopy Analysis Tools (spant) Standard SVS 1H brain analysis pipeline. — svs_1h_brain_analysis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -199,7 +199,7 @@ Value
diff --git a/docs/reference/svs_1h_brain_analysis_dev.html b/docs/reference/svs_1h_brain_analysis_dev.html
index d70a14d3..d71bfea2 100644
--- a/docs/reference/svs_1h_brain_analysis_dev.html
+++ b/docs/reference/svs_1h_brain_analysis_dev.html
@@ -1,5 +1,5 @@
-Standard SVS 1H brain analysis pipeline. — svs_1h_brain_analysis_dev • Spectroscopy Analysis Tools (spant) Standard SVS 1H brain analysis pipeline. — svs_1h_brain_analysis_dev • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -193,7 +193,7 @@ Examples
diff --git a/docs/reference/svs_1h_brain_batch_analysis.html b/docs/reference/svs_1h_brain_batch_analysis.html
index 5631e8cc..15f7223e 100644
--- a/docs/reference/svs_1h_brain_batch_analysis.html
+++ b/docs/reference/svs_1h_brain_batch_analysis.html
@@ -1,5 +1,5 @@
-Batch interface to the standard SVS 1H brain analysis pipeline. — svs_1h_brain_batch_analysis • Spectroscopy Analysis Tools (spant) Batch interface to the standard SVS 1H brain analysis pipeline. — svs_1h_brain_batch_analysis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -144,7 +144,7 @@ Value
diff --git a/docs/reference/t_test_spec.html b/docs/reference/t_test_spec.html
new file mode 100644
index 00000000..56a7ea1b
--- /dev/null
+++ b/docs/reference/t_test_spec.html
@@ -0,0 +1,124 @@
+
+Perform a t-test on spectral data points. — t_test_spec • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+
+
+ Perform a t-test on spectral data points.
+
+
+
+ t_test_spec(mrs_data, group)
+
+
+
+ Arguments
+ - mrs_data
+an mrs_data object with spectra in the dynamic dimension.
- group
+vector describing the group membership of each dynamic spectrum.
+
+ Value
+
+
+a list of statistical results.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/td2fd.html b/docs/reference/td2fd.html
index 6748a6a8..f31ed524 100644
--- a/docs/reference/td2fd.html
+++ b/docs/reference/td2fd.html
@@ -1,5 +1,5 @@
-Transform time-domain data to the frequency-domain. — td2fd • Spectroscopy Analysis Tools (spant) Transform time-domain data to the frequency-domain. — td2fd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/td_conv_filt.html b/docs/reference/td_conv_filt.html
index a9f340c3..106b9b00 100644
--- a/docs/reference/td_conv_filt.html
+++ b/docs/reference/td_conv_filt.html
@@ -1,5 +1,5 @@
-Time-domain convolution based filter. — td_conv_filt • Spectroscopy Analysis Tools (spant) Time-domain convolution based filter. — td_conv_filt • Spectroscopy Analysis Tools (spant) Time-domain spectral registration. — tdsr • Spectroscopy Analysis Tools (spant) Time-domain spectral registration. — tdsr • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -121,7 +121,7 @@ Value
diff --git a/docs/reference/te.html b/docs/reference/te.html
index 010361b1..4a65711d 100644
--- a/docs/reference/te.html
+++ b/docs/reference/te.html
@@ -1,5 +1,5 @@
-Return the echo time of an MRS dataset. — te • Spectroscopy Analysis Tools (spant) Return the echo time of an MRS dataset. — te • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/tr.html b/docs/reference/tr.html
index 0c0bd63b..2e749e02 100644
--- a/docs/reference/tr.html
+++ b/docs/reference/tr.html
@@ -1,5 +1,5 @@
-Return the repetition time of an MRS dataset. — tr • Spectroscopy Analysis Tools (spant) Return the repetition time of an MRS dataset. — tr • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/varpro_3_para_opts.html b/docs/reference/varpro_3_para_opts.html
index c2270a16..52d7cd84 100644
--- a/docs/reference/varpro_3_para_opts.html
+++ b/docs/reference/varpro_3_para_opts.html
@@ -1,5 +1,5 @@
-Return a list of options for VARPRO based fitting with 3 free parameters. — varpro_3_para_opts • Spectroscopy Analysis Tools (spant) Return a list of options for VARPRO based fitting with 3 free parameters. — varpro_3_para_opts • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -141,7 +141,7 @@ Value
diff --git a/docs/reference/varpro_basic_opts.html b/docs/reference/varpro_basic_opts.html
index 32c86d22..c5104891 100644
--- a/docs/reference/varpro_basic_opts.html
+++ b/docs/reference/varpro_basic_opts.html
@@ -1,5 +1,5 @@
-Return a list of options for a basic VARPRO analysis. — varpro_basic_opts • Spectroscopy Analysis Tools (spant) Return a list of options for a basic VARPRO analysis. — varpro_basic_opts • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -118,7 +118,7 @@ Value
diff --git a/docs/reference/varpro_opts.html b/docs/reference/varpro_opts.html
index 2aabf11d..6332f730 100644
--- a/docs/reference/varpro_opts.html
+++ b/docs/reference/varpro_opts.html
@@ -1,5 +1,5 @@
-Return a list of options for VARPRO based fitting. — varpro_opts • Spectroscopy Analysis Tools (spant) Return a list of options for VARPRO based fitting. — varpro_opts • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -177,7 +177,7 @@ Examples
diff --git a/docs/reference/vec2mrs_data.html b/docs/reference/vec2mrs_data.html
index 0cccd73b..f0d58bf0 100644
--- a/docs/reference/vec2mrs_data.html
+++ b/docs/reference/vec2mrs_data.html
@@ -1,5 +1,5 @@
-Convert a vector into a mrs_data object. — vec2mrs_data • Spectroscopy Analysis Tools (spant) Convert a vector into a mrs_data object. — vec2mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -80,10 +80,11 @@ Convert a vector into a mrs_data object.
vec2mrs_data(
vec,
- fs = def_fs(),
- ft = def_ft(),
- ref = def_ref(),
- nuc = def_nuc(),
+ mrs_data = NULL,
+ fs = NULL,
+ ft = NULL,
+ ref = NULL,
+ nuc = NULL,
dyns = 1,
fd = FALSE
)
@@ -95,6 +96,10 @@ Arguments
the data vector.
mrs_data
+example data to copy acquisition parameters from.
fs
sampling frequency in Hz.
Arguments
fd
-flag to indicate if the matrix is in the frequency domain (logical).
flag to indicate if the vector is in the frequency domain (logical).
Value
diff --git a/docs/reference/write_basis.html b/docs/reference/write_basis.html
index b6e27cbd..94c5e021 100644
--- a/docs/reference/write_basis.html
+++ b/docs/reference/write_basis.html
@@ -1,5 +1,5 @@
-Write a basis object to an LCModel .basis formatted file. — write_basis • Spectroscopy Analysis Tools (spant) Write a basis object to an LCModel .basis formatted file. — write_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -108,7 +108,7 @@ Arguments
diff --git a/docs/reference/write_basis_tqn.html b/docs/reference/write_basis_tqn.html
index 6aa51c1d..116c73ec 100644
--- a/docs/reference/write_basis_tqn.html
+++ b/docs/reference/write_basis_tqn.html
@@ -1,5 +1,5 @@
-Generate a basis file using TARQUIN. — write_basis_tqn • Spectroscopy Analysis Tools (spant) Generate a basis file using TARQUIN. — write_basis_tqn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Examples
diff --git a/docs/reference/write_mrs.html b/docs/reference/write_mrs.html
index fff25f15..124b9dc4 100644
--- a/docs/reference/write_mrs.html
+++ b/docs/reference/write_mrs.html
@@ -1,5 +1,5 @@
-Write MRS data object to file. — write_mrs • Spectroscopy Analysis Tools (spant) Write MRS data object to file. — write_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Arguments
diff --git a/docs/reference/write_mrs_nifti.html b/docs/reference/write_mrs_nifti.html
index f4bf1921..bd3ed4b7 100644
--- a/docs/reference/write_mrs_nifti.html
+++ b/docs/reference/write_mrs_nifti.html
@@ -1,5 +1,5 @@
-Write MRS data object to file in NIFTI format. — write_mrs_nifti • Spectroscopy Analysis Tools (spant) Write MRS data object to file in NIFTI format. — write_mrs_nifti • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/write_pulse_ascii.html b/docs/reference/write_pulse_ascii.html
index 067ae086..221f8ebb 100644
--- a/docs/reference/write_pulse_ascii.html
+++ b/docs/reference/write_pulse_ascii.html
@@ -1,5 +1,5 @@
-Write an ASCII formatted pulse file. — write_pulse_ascii • Spectroscopy Analysis Tools (spant) Write an ASCII formatted pulse file. — write_pulse_ascii • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/zero_fade_spec.html b/docs/reference/zero_fade_spec.html
index c703745c..c8b572c3 100644
--- a/docs/reference/zero_fade_spec.html
+++ b/docs/reference/zero_fade_spec.html
@@ -1,7 +1,5 @@
-Fade a spectrum to zero by frequency domain multiplication with a tanh
-function. Note this operation distorts data points at the end of the FID. — zero_fade_spec • Spectroscopy Analysis Tools (spant) Fade a spectrum to zero by frequency domain multiplication with a tanh function. Note this operation distorts data points at the end of the FID. — zero_fade_spec • Spectroscopy Analysis Tools (spant) Zero all coherences including and above a given order. — zero_higher_orders • Spectroscopy Analysis Tools (spant) Zero all coherences including and above a given order. — zero_higher_orders • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Value
diff --git a/docs/reference/zero_td_pts_end.html b/docs/reference/zero_td_pts_end.html
index 8c1123c8..71d24ebb 100644
--- a/docs/reference/zero_td_pts_end.html
+++ b/docs/reference/zero_td_pts_end.html
@@ -1,5 +1,5 @@
-Set mrs_data object data points at the end of the FID to zero. — zero_td_pts_end • Spectroscopy Analysis Tools (spant) Set mrs_data object data points at the end of the FID to zero. — zero_td_pts_end • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/zf.html b/docs/reference/zf.html
index 85e2013c..baf50256 100644
--- a/docs/reference/zf.html
+++ b/docs/reference/zf.html
@@ -1,5 +1,5 @@
-Zero-fill MRS data in the time domain. — zf • Spectroscopy Analysis Tools (spant) Zero-fill MRS data in the time domain. — zf • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -125,7 +125,7 @@ Value
diff --git a/docs/reference/zf_xy.html b/docs/reference/zf_xy.html
index ebca3999..c4104a74 100644
--- a/docs/reference/zf_xy.html
+++ b/docs/reference/zf_xy.html
@@ -1,5 +1,5 @@
-Zero-fill MRSI data in the k-space x-y direction. — zf_xy • Spectroscopy Analysis Tools (spant) Zero-fill MRSI data in the k-space x-y direction. — zf_xy • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -113,7 +113,7 @@ Value
diff --git a/docs/sitemap.xml b/docs/sitemap.xml
index e2139f71..4c39f515 100644
--- a/docs/sitemap.xml
+++ b/docs/sitemap.xml
@@ -216,6 +216,12 @@
https://martin3141.github.io/spant/reference/comb_coils_fp_pc.html
+
+ https://martin3141.github.io/spant/reference/comb_coils_mrsi_gls.html
+
+
+ https://martin3141.github.io/spant/reference/comb_coils_svs_gls.html
+
https://martin3141.github.io/spant/reference/comb_csv_results.html
@@ -411,6 +417,9 @@
https://martin3141.github.io/spant/reference/gen_conv_reg.html
+
+ https://martin3141.github.io/spant/reference/gen_group_reg.html
+
https://martin3141.github.io/spant/reference/gen_impulse_reg.html
@@ -555,6 +564,15 @@
https://martin3141.github.io/spant/reference/glm_spec.html
+
+ https://martin3141.github.io/spant/reference/glm_spec_fmrs_fl.html
+
+
+ https://martin3141.github.io/spant/reference/glm_spec_fmrs_group.html
+
+
+ https://martin3141.github.io/spant/reference/glm_spec_group_linhyp.html
+
https://martin3141.github.io/spant/reference/grid_shift_xy.html
@@ -690,9 +708,15 @@
https://martin3141.github.io/spant/reference/mrs_data2basis.html
+
+ https://martin3141.github.io/spant/reference/mrs_data2bids.html
+
https://martin3141.github.io/spant/reference/mrs_data2mat.html
+
+ https://martin3141.github.io/spant/reference/mrs_data2spec_mat.html
+
https://martin3141.github.io/spant/reference/mrs_data2vec.html
@@ -741,6 +765,9 @@
https://martin3141.github.io/spant/reference/phase.html
+
+ https://martin3141.github.io/spant/reference/phase_ref_1h_brain.html
+
https://martin3141.github.io/spant/reference/plot.fit_result.html
@@ -780,6 +807,12 @@
https://martin3141.github.io/spant/reference/precomp.html
+
+ https://martin3141.github.io/spant/reference/preproc_svs.html
+
+
+ https://martin3141.github.io/spant/reference/preproc_svs_dataset.html
+
https://martin3141.github.io/spant/reference/print.fit_result.html
@@ -1050,6 +1083,9 @@
https://martin3141.github.io/spant/reference/spant_mpress_drift.html
+
+ https://martin3141.github.io/spant/reference/spant_sim_fmrs_dataset.html
+
https://martin3141.github.io/spant/reference/spant_simulation_benchmark.html
@@ -1107,6 +1143,9 @@
https://martin3141.github.io/spant/reference/svs_1h_brain_batch_analysis.html
+
+ https://martin3141.github.io/spant/reference/t_test_spec.html
+
https://martin3141.github.io/spant/reference/td2fd.html
Convert a matrix (with spectral points in the column dimension and dynamics -in the row dimensions) into a mrs_data object.
Convert a matrix (with spectral points in the column dimension and dynamics in the row dimensions) into a mrs_data object.
Matrix exponential function taken from complexplus package to reduce the -number of spant dependencies.
Matrix exponential function taken from complexplus package to reduce the number of spant dependencies.
All functions
- Convert an mrs_data object to basis object - where basis signals are spread
-across the dynamic dimension in the MRS data.
Convert an mrs_data object to basis object - where basis signals are spread across the dynamic dimension in the MRS data.
+
+
+ Create a BIDS file structure from a vector of MRS data paths or list of mrs_data objects.
- Convert mrs_data object to a matrix, with spectral points in the column
-dimension and dynamics in the row dimension.
Convert mrs_data object to a matrix, with spectral points in the column dimension and dynamics in the row dimension.
-
+
- Convert mrs_data object to a vector.
Convert mrs_data object to a matrix, with spectral points in the column dimension and dynamics in the row dimension.
-
+
- Create a BIDS directory and file structure from a list of mrs_data objects.
Convert mrs_data object to a vector.
- Perform a fftshift on a matrix, with each column replaced by its shifted
-result.
Perform a fftshift on a matrix, with each column replaced by its shifted result.
- Perform an ifftshift on a matrix, with each column replaced by its shifted
-result.
Perform an ifftshift on a matrix, with each column replaced by its shifted result.
@@ -946,9 +930,7 @@ All functions
- Flip the x data dimension order of a nifti image. This corresponds to
-flipping MRI data in the left-right direction, assuming the data in save in
-neurological format (can check with fslorient program).
Flip the x data dimension order of a nifti image. This corresponds to flipping MRI data in the left-right direction, assuming the data in save in neurological format (can check with fslorient program).
@@ -964,8 +946,7 @@ All functions
- Search for the highest peak in a spectral region and return the frequency,
-height and FWHM.
Search for the highest peak in a spectral region and return the frequency, height and FWHM.
@@ -974,6 +955,10 @@ All functions phase()
Apply phasing parameters to MRS data.
+
+
+ Corrected zero order phase and chemical shift offset in 1H MRS data from the brain.
@@ -1005,8 +990,7 @@ All functions
- Plot an interactive slice map from a data array where voxels can be selected
-to display a corresponding spectrum.
Plot an interactive slice map from a data array where voxels can be selected to display a corresponding spectrum.
@@ -1026,8 +1010,15 @@ All functions
- Save function results to file and load on subsequent calls to avoid repeat
-computation.
Save function results to file and load on subsequent calls to avoid repeat computation.
+
+
+ Preprocess and perform quality assessment of a single SVS data set.
+
+
+ Preprocess and perform quality assessment of one or more SVS data sets.
@@ -1055,15 +1046,11 @@ All functions
- Read a directory containing Siemens MRS IMA files and combine along the coil
-dimension. Note that the coil ID is inferred from the sorted file name and
-should be checked when consistency is required between two directories.
Read a directory containing Siemens MRS IMA files and combine along the coil dimension. Note that the coil ID is inferred from the sorted file name and should be checked when consistency is required between two directories.
- Read a directory containing Siemens MRS IMA files and combine along the
-dynamic dimension. Note that the coil ID is inferred from the sorted file
-name and should be checked when consistency is required.
Read a directory containing Siemens MRS IMA files and combine along the dynamic dimension. Note that the coil ID is inferred from the sorted file name and should be checked when consistency is required.
@@ -1103,13 +1090,11 @@ All functions
- Reconstruct complex time-domain data from the real part of frequency-domain
-data.
Reconstruct complex time-domain data from the real part of frequency-domain data.
- Reconstruct complex time-domain data from the real part of frequency-domain
-data.
Reconstruct complex time-domain data from the real part of frequency-domain data.
@@ -1141,8 +1126,7 @@ All functions
- Resample a VOI to match a target image space using nearest-neighbour
-interpolation.
Resample a VOI to match a target image space using nearest-neighbour interpolation.
@@ -1158,23 +1142,19 @@ All functions
- Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water).
Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / kg of tissue water).
- Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water).
Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / kg of tissue water).
- Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / Litre of tissue).
Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / Litre of tissue).
- Convert default LCM/TARQUIN concentration scaling to molal units with partial
-volume correction.
Convert default LCM/TARQUIN concentration scaling to molal units with partial volume correction.
@@ -1222,8 +1202,7 @@ All functions
- MEGA-PRESS sequence with ideal localisation pulses and Gaussian shaped
-editing pulse.
MEGA-PRESS sequence with ideal localisation pulses and Gaussian shaped editing pulse.
@@ -1251,13 +1230,11 @@ All functions
- STEAM sequence with ideal pulses and coherence order filtering to simulate
-gradient crushers.
STEAM sequence with ideal pulses and coherence order filtering to simulate gradient crushers.
- STEAM sequence with ideal pulses using the z-rotation gradient simulation
-method described by Young et al JMR 140, 146-152 (1999).
STEAM sequence with ideal pulses using the z-rotation gradient simulation method described by Young et al JMR 140, 146-152 (1999).
@@ -1293,8 +1270,7 @@ All functions
- Set the number of time-domain data points, truncating or zero-filling as
-appropriate.
Set the number of time-domain data points, truncating or zero-filling as appropriate.
@@ -1318,18 +1294,15 @@ All functions
- Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS
-sequence. Note, ideal pulses are assumed.
Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS sequence. Note, ideal pulses are assumed.
- Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS
-sequence. Note, ideal pulses are assumed.
Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS sequence. Note, ideal pulses are assumed.
- Simulate a macromolecular and lipid basis-set suitable for 1H brain MRS
-analysis.
Simulate a macromolecular and lipid basis-set suitable for 1H brain MRS analysis.
@@ -1353,8 +1326,7 @@ All functions
- Simulate an ideal pulse excitation profile by smoothing a top-hat function
-with a Gaussian.
Simulate an ideal pulse excitation profile by smoothing a top-hat function with a Gaussian.
@@ -1374,17 +1346,19 @@ All functions
- Simulate and fit some spectra with ABfit for benchmarking purposes. Basic
-timing and performance metrics will be printed.
Simulate and fit some spectra with ABfit for benchmarking purposes. Basic timing and performance metrics will be printed.
Example MEGA-PRESS data with significant B0 drift.
+
+
+ Simulate an example fMRS dataset for a block design fMRS experiment and export a BIDS structure.
- Simulate a typical metabolite basis set for benchmarking. Timing metrics will
-be printed on completion.
Simulate a typical metabolite basis set for benchmarking. Timing metrics will be printed on completion.
@@ -1400,8 +1374,7 @@ All functions
- Convert SPM style segmentation files to a single categorical image where
-the numerical values map as: 0) Other, 1) CSF, 2) GM and 3) WM.
Convert SPM style segmentation files to a single categorical image where the numerical values map as: 0) Other, 1) CSF, 2) GM and 3) WM.
@@ -1413,8 +1386,7 @@ All functions
- Plot the fitting results of an object of class fit_result with
-individual basis set components shown.
Plot the fitting results of an object of class fit_result with individual basis set components shown.
@@ -1459,6 +1431,10 @@ All functions svs_1h_brain_batch_analysis()
Batch interface to the standard SVS 1H brain analysis pipeline.
+
+
+ Perform a t-test on spectral data points.
@@ -1518,8 +1494,7 @@ All functions
- Fade a spectrum to zero by frequency domain multiplication with a tanh
-function. Note this operation distorts data points at the end of the FID.
Fade a spectrum to zero by frequency domain multiplication with a tanh function. Note this operation distorts data points at the end of the FID.
@@ -1549,7 +1524,7 @@ All functions
diff --git a/docs/reference/int_spec.html b/docs/reference/int_spec.html
index c7060fe7..783325a8 100644
--- a/docs/reference/int_spec.html
+++ b/docs/reference/int_spec.html
@@ -1,5 +1,5 @@
-Integrate a spectral region. — int_spec • Spectroscopy Analysis Tools (spant) Integrate a spectral region. — int_spec • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -118,7 +118,7 @@ Value
diff --git a/docs/reference/interleave_dyns.html b/docs/reference/interleave_dyns.html
index effe5543..441eff27 100644
--- a/docs/reference/interleave_dyns.html
+++ b/docs/reference/interleave_dyns.html
@@ -1,5 +1,5 @@
-Interleave the first and second half of a dynamic series. — interleave_dyns • Spectroscopy Analysis Tools (spant) Interleave the first and second half of a dynamic series. — interleave_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/inv_even_dyns.html b/docs/reference/inv_even_dyns.html
index 9f9d4fff..dcb781dc 100644
--- a/docs/reference/inv_even_dyns.html
+++ b/docs/reference/inv_even_dyns.html
@@ -1,5 +1,5 @@
-Invert even numbered dynamic scans starting from 1 (2,4,6...). — inv_even_dyns • Spectroscopy Analysis Tools (spant) Invert even numbered dynamic scans starting from 1 (2,4,6...). — inv_even_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/inv_odd_dyns.html b/docs/reference/inv_odd_dyns.html
index 26212e2b..78d64660 100644
--- a/docs/reference/inv_odd_dyns.html
+++ b/docs/reference/inv_odd_dyns.html
@@ -1,5 +1,5 @@
-Invert odd numbered dynamic scans starting from 1 (1,3,5...). — inv_odd_dyns • Spectroscopy Analysis Tools (spant) Invert odd numbered dynamic scans starting from 1 (1,3,5...). — inv_odd_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/is.def.html b/docs/reference/is.def.html
index f196ffd0..a67b9eba 100644
--- a/docs/reference/is.def.html
+++ b/docs/reference/is.def.html
@@ -1,5 +1,5 @@
-Check if an object is defined, which is the same as being not NULL. — is.def • Spectroscopy Analysis Tools (spant) Check if an object is defined, which is the same as being not NULL. — is.def • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/is_fd.html b/docs/reference/is_fd.html
index 3b0ca165..18a193aa 100644
--- a/docs/reference/is_fd.html
+++ b/docs/reference/is_fd.html
@@ -1,7 +1,5 @@
-Check if the chemical shift dimension of an MRS data object is in the
-frequency domain. — is_fd • Spectroscopy Analysis Tools (spant) Check if the chemical shift dimension of an MRS data object is in the frequency domain. — is_fd • Spectroscopy Analysis Tools (spant) Transform 2D MRSI data from k-space to image space in the x-y direction. — kspace2img_xy • Spectroscopy Analysis Tools (spant) Transform 2D MRSI data from k-space to image space in the x-y direction. — kspace2img_xy • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/l2_reg.html b/docs/reference/l2_reg.html
index 3d781d80..21aa9849 100644
--- a/docs/reference/l2_reg.html
+++ b/docs/reference/l2_reg.html
@@ -1,5 +1,5 @@
-Perform l2 regularisation artefact suppression. — l2_reg • Spectroscopy Analysis Tools (spant) Perform l2 regularisation artefact suppression. — l2_reg • Spectroscopy Analysis Tools (spant) Apply line-broadening (apodisation) to MRS data or basis object. — lb • Spectroscopy Analysis Tools (spant) Apply line-broadening (apodisation) to MRS data or basis object. — lb • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -123,7 +123,7 @@ Value
diff --git a/docs/reference/lofdc.html b/docs/reference/lofdc.html
index 5419b1ec..31347a25 100644
--- a/docs/reference/lofdc.html
+++ b/docs/reference/lofdc.html
@@ -1,5 +1,5 @@
-Correct linear frequency drift. — lofdc • Spectroscopy Analysis Tools (spant) Correct linear frequency drift. — lofdc • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -138,7 +138,7 @@ Value
diff --git a/docs/reference/lw2alpha.html b/docs/reference/lw2alpha.html
index b83db682..25da229b 100644
--- a/docs/reference/lw2alpha.html
+++ b/docs/reference/lw2alpha.html
@@ -1,7 +1,5 @@
-Covert a linewidth in Hz to an equivalent alpha value in the time-domain ie:
-x * exp(-t * alpha). — lw2alpha • Spectroscopy Analysis Tools (spant) Covert a linewidth in Hz to an equivalent alpha value in the time-domain ie: x * exp(-t * alpha). — lw2alpha • Spectroscopy Analysis Tools (spant) Covert a linewidth in Hz to an equivalent beta value in the time-domain ie:
-x * exp(-t * t * beta). — lw2beta • Spectroscopy Analysis Tools (spant) Covert a linewidth in Hz to an equivalent beta value in the time-domain ie: x * exp(-t * t * beta). — lw2beta • Spectroscopy Analysis Tools (spant) Make a basis-set object from a directory containing LCModel formatted RAW
-files. — make_basis_from_raw • Spectroscopy Analysis Tools (spant) Make a basis-set object from a directory containing LCModel formatted RAW files. — make_basis_from_raw • Spectroscopy Analysis Tools (spant) Mask an MRS dataset in the dynamic dimension. — mask_dyns • Spectroscopy Analysis Tools (spant) Mask an MRS dataset in the dynamic dimension. — mask_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/mask_fit_res.html b/docs/reference/mask_fit_res.html
index 97baaa3f..ebd91a99 100644
--- a/docs/reference/mask_fit_res.html
+++ b/docs/reference/mask_fit_res.html
@@ -1,5 +1,5 @@
-Mask fit result spectra depending on a vector of bool values. — mask_fit_res • Spectroscopy Analysis Tools (spant) Mask fit result spectra depending on a vector of bool values. — mask_fit_res • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -116,7 +116,7 @@ Value
diff --git a/docs/reference/mask_xy.html b/docs/reference/mask_xy.html
index 11bb577c..b0d38619 100644
--- a/docs/reference/mask_xy.html
+++ b/docs/reference/mask_xy.html
@@ -1,5 +1,5 @@
-Mask an MRSI dataset in the x-y direction — mask_xy • Spectroscopy Analysis Tools (spant) Mask an MRSI dataset in the x-y direction — mask_xy • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/mask_xy_corners.html b/docs/reference/mask_xy_corners.html
index 09b16cd2..2d13839d 100644
--- a/docs/reference/mask_xy_corners.html
+++ b/docs/reference/mask_xy_corners.html
@@ -1,5 +1,5 @@
-Mask the four corners of an MRSI dataset in the x-y plane. — mask_xy_corners • Spectroscopy Analysis Tools (spant) Mask the four corners of an MRSI dataset in the x-y plane. — mask_xy_corners • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/mask_xy_ellipse.html b/docs/reference/mask_xy_ellipse.html
index 1d8b02e4..e2e749ef 100644
--- a/docs/reference/mask_xy_ellipse.html
+++ b/docs/reference/mask_xy_ellipse.html
@@ -1,7 +1,5 @@
-Mask the voxels outside an elliptical region spanning the MRSI dataset in the
-x-y plane. — mask_xy_ellipse • Spectroscopy Analysis Tools (spant) Mask the voxels outside an elliptical region spanning the MRSI dataset in the x-y plane. — mask_xy_ellipse • Spectroscopy Analysis Tools (spant) Mask a 2D MRSI dataset in the x-y dimension. — mask_xy_mat • Spectroscopy Analysis Tools (spant) Mask a 2D MRSI dataset in the x-y dimension. — mask_xy_mat • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Value
diff --git a/docs/reference/mat2mrs_data.html b/docs/reference/mat2mrs_data.html
index 2e2895f3..ae55665f 100644
--- a/docs/reference/mat2mrs_data.html
+++ b/docs/reference/mat2mrs_data.html
@@ -1,7 +1,5 @@
-Convert a matrix (with spectral points in the column dimension and dynamics
-in the row dimensions) into a mrs_data object. — mat2mrs_data • Spectroscopy Analysis Tools (spant) Convert a matrix (with spectral points in the column dimension and dynamics in the row dimensions) into a mrs_data object. — mat2mrs_data • Spectroscopy Analysis Tools (spant) Matrix exponential function taken from complexplus package to reduce the
-number of spant dependencies. — matexp • Spectroscopy Analysis Tools (spant) Matrix exponential function taken from complexplus package to reduce the number of spant dependencies. — matexp • Spectroscopy Analysis Tools (spant) Apply the max operator to an MRS dataset. — max_mrs • Spectroscopy Analysis Tools (spant) Apply the max operator to an MRS dataset. — max_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/max_mrs_interp.html b/docs/reference/max_mrs_interp.html
index e4474764..52e63f3e 100644
--- a/docs/reference/max_mrs_interp.html
+++ b/docs/reference/max_mrs_interp.html
@@ -1,5 +1,5 @@
-Apply the max operator to an interpolated MRS dataset. — max_mrs_interp • Spectroscopy Analysis Tools (spant) Apply the max operator to an interpolated MRS dataset. — max_mrs_interp • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/mean.list.html b/docs/reference/mean.list.html
index b8eb3463..048306fd 100644
--- a/docs/reference/mean.list.html
+++ b/docs/reference/mean.list.html
@@ -1,5 +1,5 @@
-Calculate the mean spectrum from an mrs_data object. — mean.list • Spectroscopy Analysis Tools (spant) Calculate the mean spectrum from an mrs_data object. — mean.list • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/mean.mrs_data.html b/docs/reference/mean.mrs_data.html
index 5531a28d..79515014 100644
--- a/docs/reference/mean.mrs_data.html
+++ b/docs/reference/mean.mrs_data.html
@@ -1,5 +1,5 @@
-Calculate the mean spectrum from an mrs_data object. — mean.mrs_data • Spectroscopy Analysis Tools (spant) Calculate the mean spectrum from an mrs_data object. — mean.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/mean_dyn_blocks.html b/docs/reference/mean_dyn_blocks.html
index 10467098..4c042448 100644
--- a/docs/reference/mean_dyn_blocks.html
+++ b/docs/reference/mean_dyn_blocks.html
@@ -1,5 +1,5 @@
-Calculate the mean of adjacent dynamic scans. — mean_dyn_blocks • Spectroscopy Analysis Tools (spant) Calculate the mean of adjacent dynamic scans. — mean_dyn_blocks • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/mean_dyn_pairs.html b/docs/reference/mean_dyn_pairs.html
index 63e909ea..1a241126 100644
--- a/docs/reference/mean_dyn_pairs.html
+++ b/docs/reference/mean_dyn_pairs.html
@@ -1,5 +1,5 @@
-Calculate the pairwise means across a dynamic data set. — mean_dyn_pairs • Spectroscopy Analysis Tools (spant) Calculate the pairwise means across a dynamic data set. — mean_dyn_pairs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/mean_dyns.html b/docs/reference/mean_dyns.html
index 73fdbfa7..0daa27df 100644
--- a/docs/reference/mean_dyns.html
+++ b/docs/reference/mean_dyns.html
@@ -1,5 +1,5 @@
-Calculate the mean dynamic data. — mean_dyns • Spectroscopy Analysis Tools (spant) Calculate the mean dynamic data. — mean_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/mean_mrs_list.html b/docs/reference/mean_mrs_list.html
index 808b6c50..10d842c0 100644
--- a/docs/reference/mean_mrs_list.html
+++ b/docs/reference/mean_mrs_list.html
@@ -1,5 +1,5 @@
-Return the mean of a list of mrs_data objects. — mean_mrs_list • Spectroscopy Analysis Tools (spant) Return the mean of a list of mrs_data objects. — mean_mrs_list • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/mean_vec_blocks.html b/docs/reference/mean_vec_blocks.html
index 8fc92eaa..dd78b122 100644
--- a/docs/reference/mean_vec_blocks.html
+++ b/docs/reference/mean_vec_blocks.html
@@ -1,5 +1,5 @@
-Calculate the mean of adjacent blocks in a vector. — mean_vec_blocks • Spectroscopy Analysis Tools (spant) Calculate the mean of adjacent blocks in a vector. — mean_vec_blocks • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/median_dyns.html b/docs/reference/median_dyns.html
index 1039d4b5..9a085b10 100644
--- a/docs/reference/median_dyns.html
+++ b/docs/reference/median_dyns.html
@@ -1,5 +1,5 @@
-Calculate the median dynamic data. — median_dyns • Spectroscopy Analysis Tools (spant) Calculate the median dynamic data. — median_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/mod_td.html b/docs/reference/mod_td.html
index 76ad0a40..141ef09e 100644
--- a/docs/reference/mod_td.html
+++ b/docs/reference/mod_td.html
@@ -1,5 +1,5 @@
-Apply the Modulus operator to the time-domain MRS signal. — mod_td • Spectroscopy Analysis Tools (spant) Apply the Modulus operator to the time-domain MRS signal. — mod_td • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/mrs_data2basis.html b/docs/reference/mrs_data2basis.html
index 62f7d749..11797b91 100644
--- a/docs/reference/mrs_data2basis.html
+++ b/docs/reference/mrs_data2basis.html
@@ -1,7 +1,5 @@
-Convert an mrs_data object to basis object - where basis signals are spread
-across the dynamic dimension in the MRS data. — mrs_data2basis • Spectroscopy Analysis Tools (spant) Convert an mrs_data object to basis object - where basis signals are spread across the dynamic dimension in the MRS data. — mrs_data2basis • Spectroscopy Analysis Tools (spant) Create a BIDS file structure from a vector of MRS data paths or list of mrs_data objects. — mrs_data2bids • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Create a BIDS file structure from a vector of MRS data paths or list of mrs_data objects.
+ Source: R/fmrs.R
+ mrs_data2bids.Rd
+
+
+
+ Create a BIDS file structure from a vector of MRS data paths or list of
+mrs_data objects.
+
+
+
+ mrs_data2bids(
+ mrs_data,
+ output_dir,
+ suffix = NULL,
+ sub = NULL,
+ ses = NULL,
+ task = NULL,
+ acq = NULL,
+ nuc = NULL,
+ voi = NULL,
+ rec = NULL,
+ run = NULL,
+ echo = NULL,
+ inv = NULL,
+ skip_existing = TRUE
+)
+
+
+
+ Arguments
+ - mrs_data
+vector of MRS data paths or list of mrs_data objects.
- output_dir
+the base directory to create the BIDS structure.
- suffix
+optional vector of file suffixes. Default behaviour is to
+automatically determine these from the input data, however it is recommended
+that they are specified to allow more efficient skipping of existing data.
- sub
+optional vector of subject labels. If not specified, these will be
+automatically generated as a series of increasing zero-padded integer values
+corresponding to the mrs_data input indices.
- ses
+optional vector of session labels.
- task
+optional vector of task labels.
- acq
+optional vector of acquisition labels.
- nuc
+optional vector of nucleus labels.
- voi
+optional vector of volume of interest labels.
- rec
+optional vector of reconstruction labels.
- run
+optional vector of run indices.
- echo
+optional vector of echo time indices.
- inv
+optional vector of inversion indices.
- skip_existing
+skip any data files that have already been converted.
+Defaults to TRUE, set to FALSE to force an overwrite of any existing data
+files.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/mrs_data2mat.html b/docs/reference/mrs_data2mat.html
index cf5ff28c..9e47688a 100644
--- a/docs/reference/mrs_data2mat.html
+++ b/docs/reference/mrs_data2mat.html
@@ -1,7 +1,5 @@
-Convert mrs_data object to a matrix, with spectral points in the column
-dimension and dynamics in the row dimension. — mrs_data2mat • Spectroscopy Analysis Tools (spant) Convert mrs_data object to a matrix, with spectral points in the column dimension and dynamics in the row dimension. — mrs_data2mat • Spectroscopy Analysis Tools (spant) Convert mrs_data object to a matrix, with spectral points in the column dimension and dynamics in the row dimension. — mrs_data2spec_mat • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Convert mrs_data object to a matrix, with spectral points in the column dimension and dynamics in the row dimension.
+ Source: R/mrs_data_proc.R
+ mrs_data2spec_mat.Rd
+
+
+
+ Convert mrs_data object to a matrix, with spectral points in the column
+dimension and dynamics in the row dimension.
+
+
+
+ mrs_data2spec_mat(mrs_data, collapse = TRUE)
+
+
+
+ Arguments
+ - mrs_data
+MRS data object or list of MRS data objects.
- collapse
+collapse all other dimensions along the dynamic dimension, eg
+a 16x16 MRSI grid would be first collapsed across 256 dynamic scans.
+
+ Value
+
+
+MRS data matrix.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/mrs_data2vec.html b/docs/reference/mrs_data2vec.html
index fb172d68..a1fd654d 100644
--- a/docs/reference/mrs_data2vec.html
+++ b/docs/reference/mrs_data2vec.html
@@ -1,5 +1,5 @@
-Convert mrs_data object to a vector. — mrs_data2vec • Spectroscopy Analysis Tools (spant) Convert mrs_data object to a vector. — mrs_data2vec • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -126,7 +126,7 @@ Value
diff --git a/docs/reference/mvfftshift.html b/docs/reference/mvfftshift.html
index 92b0841b..976b3410 100644
--- a/docs/reference/mvfftshift.html
+++ b/docs/reference/mvfftshift.html
@@ -1,7 +1,5 @@
-Perform a fftshift on a matrix, with each column replaced by its shifted
-result. — mvfftshift • Spectroscopy Analysis Tools (spant) Perform a fftshift on a matrix, with each column replaced by its shifted result. — mvfftshift • Spectroscopy Analysis Tools (spant) Perform an ifftshift on a matrix, with each column replaced by its shifted
-result. — mvifftshift • Spectroscopy Analysis Tools (spant) Perform an ifftshift on a matrix, with each column replaced by its shifted result. — mvifftshift • Spectroscopy Analysis Tools (spant) Print fit coordinates from a single index. — n2coord • Spectroscopy Analysis Tools (spant) Print fit coordinates from a single index. — n2coord • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/nifti_flip_lr.html b/docs/reference/nifti_flip_lr.html
index 730abe3c..19860b3c 100644
--- a/docs/reference/nifti_flip_lr.html
+++ b/docs/reference/nifti_flip_lr.html
@@ -1,9 +1,5 @@
-Flip the x data dimension order of a nifti image. This corresponds to
-flipping MRI data in the left-right direction, assuming the data in save in
-neurological format (can check with fslorient program). — nifti_flip_lr • Spectroscopy Analysis Tools (spant) Flip the x data dimension order of a nifti image. This corresponds to flipping MRI data in the left-right direction, assuming the data in save in neurological format (can check with fslorient program). — nifti_flip_lr • Spectroscopy Analysis Tools (spant) Export a one-page pdf of a single fit result — one_page_pdf • Spectroscopy Analysis Tools (spant) Export a one-page pdf of a single fit result — one_page_pdf • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -108,7 +108,7 @@ Arguments
diff --git a/docs/reference/ortho3.html b/docs/reference/ortho3.html
index 13ade97d..5d7dd2fd 100644
--- a/docs/reference/ortho3.html
+++ b/docs/reference/ortho3.html
@@ -1,5 +1,5 @@
-Display an orthographic projection plot of a nifti object. — ortho3 • Spectroscopy Analysis Tools (spant) Display an orthographic projection plot of a nifti object. — ortho3 • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -172,7 +172,7 @@ Arguments
diff --git a/docs/reference/ortho3_inter.html b/docs/reference/ortho3_inter.html
index 090cc5e5..15948899 100644
--- a/docs/reference/ortho3_inter.html
+++ b/docs/reference/ortho3_inter.html
@@ -1,5 +1,5 @@
-Display an interactive orthographic projection plot of a nifti object. — ortho3_inter • Spectroscopy Analysis Tools (spant) Display an interactive orthographic projection plot of a nifti object. — ortho3_inter • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -132,7 +132,7 @@ Arguments
diff --git a/docs/reference/peak_info.html b/docs/reference/peak_info.html
index 09058bd8..41c8ffaf 100644
--- a/docs/reference/peak_info.html
+++ b/docs/reference/peak_info.html
@@ -1,7 +1,5 @@
-Search for the highest peak in a spectral region and return the frequency,
-height and FWHM. — peak_info • Spectroscopy Analysis Tools (spant) Search for the highest peak in a spectral region and return the frequency, height and FWHM. — peak_info • Spectroscopy Analysis Tools (spant) Papoulis-Gerchberg (PG) algorithm method for k-space extrapolation. — pg_extrap_xy • Spectroscopy Analysis Tools (spant) Papoulis-Gerchberg (PG) algorithm method for k-space extrapolation. — pg_extrap_xy • Spectroscopy Analysis Tools (spant) Apply phasing parameters to MRS data. — phase • Spectroscopy Analysis Tools (spant) Apply phasing parameters to MRS data. — phase • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/phase_ref_1h_brain.html b/docs/reference/phase_ref_1h_brain.html
new file mode 100644
index 00000000..8707a74a
--- /dev/null
+++ b/docs/reference/phase_ref_1h_brain.html
@@ -0,0 +1,131 @@
+
+Corrected zero order phase and chemical shift offset in 1H MRS data from the brain. — phase_ref_1h_brain • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Corrected zero order phase and chemical shift offset in 1H MRS data from the brain.
+ Source: R/rats.R
+ phase_ref_1h_brain.Rd
+
+
+
+ Corrected zero order phase and chemical shift offset in 1H MRS data from the
+brain.
+
+
+
+ phase_ref_1h_brain(mrs_data, mean_ref = FALSE, ret_corr_only = TRUE)
+
+
+
+ Arguments
+ - mrs_data
+MRS data to be corrected.
- mean_ref
+apply the phase and offset of the mean spectrum to all
+others. Default is FALSE.
- ret_corr_only
+return the corrected data only.
+
+ Value
+
+
+corrected MRS data.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/plot.fit_result.html b/docs/reference/plot.fit_result.html
index e54d3bc1..836a53ee 100644
--- a/docs/reference/plot.fit_result.html
+++ b/docs/reference/plot.fit_result.html
@@ -1,5 +1,5 @@
-Plot the fitting results of an object of class fit_result. — plot.fit_result • Spectroscopy Analysis Tools (spant) Plot the fitting results of an object of class fit_result. — plot.fit_result • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -207,7 +207,7 @@ Arguments
diff --git a/docs/reference/plot.mrs_data.html b/docs/reference/plot.mrs_data.html
index fabcc35b..bb2ec651 100644
--- a/docs/reference/plot.mrs_data.html
+++ b/docs/reference/plot.mrs_data.html
@@ -1,5 +1,5 @@
-Plotting method for objects of class mrs_data. — plot.mrs_data • Spectroscopy Analysis Tools (spant) Plotting method for objects of class mrs_data. — plot.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -287,7 +287,7 @@ Arguments
diff --git a/docs/reference/plot_bc.html b/docs/reference/plot_bc.html
index 4f8309b4..b48142cc 100644
--- a/docs/reference/plot_bc.html
+++ b/docs/reference/plot_bc.html
@@ -1,5 +1,5 @@
-Convenience function to plot a baseline estimate with the original data. — plot_bc • Spectroscopy Analysis Tools (spant) Convenience function to plot a baseline estimate with the original data. — plot_bc • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -108,7 +108,7 @@ Arguments
diff --git a/docs/reference/plot_reg.html b/docs/reference/plot_reg.html
index ae1acbe7..2addb2f6 100644
--- a/docs/reference/plot_reg.html
+++ b/docs/reference/plot_reg.html
@@ -1,5 +1,5 @@
-Plot regressors as an image. — plot_reg • Spectroscopy Analysis Tools (spant) Plot regressors as an image. — plot_reg • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/plot_slice_fit.html b/docs/reference/plot_slice_fit.html
index fbc7b560..57f1af8a 100644
--- a/docs/reference/plot_slice_fit.html
+++ b/docs/reference/plot_slice_fit.html
@@ -1,5 +1,5 @@
-Plot a 2D slice from an MRSI fit result object. — plot_slice_fit • Spectroscopy Analysis Tools (spant) Plot a 2D slice from an MRSI fit result object. — plot_slice_fit • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -129,7 +129,7 @@ Arguments
diff --git a/docs/reference/plot_slice_fit_inter.html b/docs/reference/plot_slice_fit_inter.html
index 4eed104a..da105a7d 100644
--- a/docs/reference/plot_slice_fit_inter.html
+++ b/docs/reference/plot_slice_fit_inter.html
@@ -1,5 +1,5 @@
-Plot a 2D slice from an MRSI fit result object. — plot_slice_fit_inter • Spectroscopy Analysis Tools (spant) Plot a 2D slice from an MRSI fit result object. — plot_slice_fit_inter • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -134,7 +134,7 @@ Arguments
diff --git a/docs/reference/plot_slice_map.html b/docs/reference/plot_slice_map.html
index 553e9ac8..ffb2a134 100644
--- a/docs/reference/plot_slice_map.html
+++ b/docs/reference/plot_slice_map.html
@@ -1,5 +1,5 @@
-Plot a slice from a 7 dimensional array. — plot_slice_map • Spectroscopy Analysis Tools (spant) Plot a slice from a 7 dimensional array. — plot_slice_map • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -153,7 +153,7 @@ Arguments
diff --git a/docs/reference/plot_slice_map_inter.html b/docs/reference/plot_slice_map_inter.html
index 40d33b42..90968f66 100644
--- a/docs/reference/plot_slice_map_inter.html
+++ b/docs/reference/plot_slice_map_inter.html
@@ -1,7 +1,5 @@
-Plot an interactive slice map from a data array where voxels can be selected
-to display a corresponding spectrum. — plot_slice_map_inter • Spectroscopy Analysis Tools (spant) Plot an interactive slice map from a data array where voxels can be selected to display a corresponding spectrum. — plot_slice_map_inter • Spectroscopy Analysis Tools (spant) Plot the spectral standard deviation. — plot_spec_sd • Spectroscopy Analysis Tools (spant) Plot the spectral standard deviation. — plot_spec_sd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Arguments
diff --git a/docs/reference/plot_voi_overlay.html b/docs/reference/plot_voi_overlay.html
index 9a782e88..bbbbf35e 100644
--- a/docs/reference/plot_voi_overlay.html
+++ b/docs/reference/plot_voi_overlay.html
@@ -1,5 +1,5 @@
-Plot a volume as an image overlay. — plot_voi_overlay • Spectroscopy Analysis Tools (spant) Plot a volume as an image overlay. — plot_voi_overlay • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -116,7 +116,7 @@ Arguments
diff --git a/docs/reference/plot_voi_overlay_seg.html b/docs/reference/plot_voi_overlay_seg.html
index 3d4e74ff..0e800ff2 100644
--- a/docs/reference/plot_voi_overlay_seg.html
+++ b/docs/reference/plot_voi_overlay_seg.html
@@ -1,5 +1,5 @@
-Plot a volume as an overlay on a segmented brain volume. — plot_voi_overlay_seg • Spectroscopy Analysis Tools (spant) Plot a volume as an overlay on a segmented brain volume. — plot_voi_overlay_seg • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Arguments
diff --git a/docs/reference/ppm.html b/docs/reference/ppm.html
index c352327a..ee4696e2 100644
--- a/docs/reference/ppm.html
+++ b/docs/reference/ppm.html
@@ -1,5 +1,5 @@
-Return the ppm scale of an MRS dataset or fit result. — ppm • Spectroscopy Analysis Tools (spant) Return the ppm scale of an MRS dataset or fit result. — ppm • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -132,7 +132,7 @@ Value
diff --git a/docs/reference/precomp.html b/docs/reference/precomp.html
index 822d7336..df3d2c6c 100644
--- a/docs/reference/precomp.html
+++ b/docs/reference/precomp.html
@@ -1,7 +1,5 @@
-Save function results to file and load on subsequent calls to avoid repeat
-computation. — precomp • Spectroscopy Analysis Tools (spant) Save function results to file and load on subsequent calls to avoid repeat computation. — precomp • Spectroscopy Analysis Tools (spant) Preprocess and perform quality assessment of a single SVS data set. — preproc_svs • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Preprocess and perform quality assessment of a single SVS data set.
+ Source: R/fmrs.R
+ preproc_svs.Rd
+
+
+
+ Preprocess and perform quality assessment of a single SVS data set.
+
+
+
+ preproc_svs(path, label = NULL, output_dir = NULL, ref_inds = NULL)
+
+
+
+ Arguments
+ - path
+path to the fMRS data file or IMA directory.
- label
+a label to describe the data set.
- output_dir
+output directory.
- ref_inds
+a vector of 1-based indices for any water reference dynamic
+scans.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/preproc_svs_dataset.html b/docs/reference/preproc_svs_dataset.html
new file mode 100644
index 00000000..07c3a29b
--- /dev/null
+++ b/docs/reference/preproc_svs_dataset.html
@@ -0,0 +1,148 @@
+
+Preprocess and perform quality assessment of one or more SVS data sets. — preproc_svs_dataset • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Preprocess and perform quality assessment of one or more SVS data sets.
+ Source: R/fmrs.R
+ preproc_svs_dataset.Rd
+
+
+
+ Preprocess and perform quality assessment of one or more SVS data sets.
+
+
+
+ preproc_svs_dataset(
+ paths,
+ labels = NULL,
+ output_dir = "spant_analysis",
+ exclude_labels = NULL,
+ overwrite = FALSE,
+ ref_inds = NULL,
+ return_results = FALSE
+)
+
+
+
+ Arguments
+ - paths
+paths to the fMRS data file or IMA directory.
- labels
+labels to describe each data set.
- output_dir
+output directory.
- exclude_labels
+vector of labels of scans to exclude, eg poor quality
+data.
- overwrite
+overwrite saved results, defaults to FALSE.
- ref_inds
+a vector of 1-based indices for any water reference dynamic
+scans.
- return_results
+function will return key outputs, defaults to FALSE.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/print.fit_result.html b/docs/reference/print.fit_result.html
index 297f28dc..5f434e57 100644
--- a/docs/reference/print.fit_result.html
+++ b/docs/reference/print.fit_result.html
@@ -1,5 +1,5 @@
-Print a summary of an object of class fit_result. — print.fit_result • Spectroscopy Analysis Tools (spant) Print a summary of an object of class fit_result. — print.fit_result • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -105,7 +105,7 @@ Arguments
diff --git a/docs/reference/print.mrs_data.html b/docs/reference/print.mrs_data.html
index 51199017..e1561eb2 100644
--- a/docs/reference/print.mrs_data.html
+++ b/docs/reference/print.mrs_data.html
@@ -1,5 +1,5 @@
-Print a summary of mrs_data parameters. — print.mrs_data • Spectroscopy Analysis Tools (spant) Print a summary of mrs_data parameters. — print.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -109,7 +109,7 @@ Arguments
diff --git a/docs/reference/qn_states.html b/docs/reference/qn_states.html
index 0f42f2f9..d7aa6715 100644
--- a/docs/reference/qn_states.html
+++ b/docs/reference/qn_states.html
@@ -1,5 +1,5 @@
-Get the quantum coherence matrix for a spin system. — qn_states • Spectroscopy Analysis Tools (spant) Get the quantum coherence matrix for a spin system. — qn_states • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/rats.html b/docs/reference/rats.html
index 5a39a396..93585e08 100644
--- a/docs/reference/rats.html
+++ b/docs/reference/rats.html
@@ -1,5 +1,5 @@
-Robust Alignment to a Target Spectrum (RATS). — rats • Spectroscopy Analysis Tools (spant) Robust Alignment to a Target Spectrum (RATS). — rats • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -207,7 +207,7 @@ Value
diff --git a/docs/reference/re_weighting.html b/docs/reference/re_weighting.html
index d21caf21..8b0b070a 100644
--- a/docs/reference/re_weighting.html
+++ b/docs/reference/re_weighting.html
@@ -1,5 +1,5 @@
-Apply a weighting to the FID to enhance spectral resolution. — re_weighting • Spectroscopy Analysis Tools (spant) Apply a weighting to the FID to enhance spectral resolution. — re_weighting • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/read_basis.html b/docs/reference/read_basis.html
index da9b94af..eb6f8557 100644
--- a/docs/reference/read_basis.html
+++ b/docs/reference/read_basis.html
@@ -1,5 +1,5 @@
-Read a basis file in LCModel .basis format. — read_basis • Spectroscopy Analysis Tools (spant) Read a basis file in LCModel .basis format. — read_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/read_ima_coil_dir.html b/docs/reference/read_ima_coil_dir.html
index 28c02de0..4f073cd8 100644
--- a/docs/reference/read_ima_coil_dir.html
+++ b/docs/reference/read_ima_coil_dir.html
@@ -1,9 +1,5 @@
-Read a directory containing Siemens MRS IMA files and combine along the coil
-dimension. Note that the coil ID is inferred from the sorted file name and
-should be checked when consistency is required between two directories. — read_ima_coil_dir • Spectroscopy Analysis Tools (spant) Read a directory containing Siemens MRS IMA files and combine along the coil dimension. Note that the coil ID is inferred from the sorted file name and should be checked when consistency is required between two directories. — read_ima_coil_dir • Spectroscopy Analysis Tools (spant) Read a directory containing Siemens MRS IMA files and combine along the
-dynamic dimension. Note that the coil ID is inferred from the sorted file
-name and should be checked when consistency is required. — read_ima_dyn_dir • Spectroscopy Analysis Tools (spant) Read a directory containing Siemens MRS IMA files and combine along the dynamic dimension. Note that the coil ID is inferred from the sorted file name and should be checked when consistency is required. — read_ima_dyn_dir • Spectroscopy Analysis Tools (spant) Read an LCModel formatted coord file containing fit information. — read_lcm_coord • Spectroscopy Analysis Tools (spant) Read an LCModel formatted coord file containing fit information. — read_lcm_coord • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -107,7 +107,7 @@ Value
diff --git a/docs/reference/read_mrs.html b/docs/reference/read_mrs.html
index 3ac2a36b..2cf36b20 100644
--- a/docs/reference/read_mrs.html
+++ b/docs/reference/read_mrs.html
@@ -1,5 +1,5 @@
-Read MRS data from a file. — read_mrs • Spectroscopy Analysis Tools (spant) Read MRS data from a file. — read_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -88,7 +88,8 @@ Read MRS data from a file.
full_fid = FALSE,
omit_svs_ref_scans = TRUE,
verbose = FALSE,
- extra = NULL
+ extra = NULL,
+ fid_filt_dist = NULL
)
@@ -140,6 +141,13 @@ Arguments
an optional data frame to provide additional variables for use
in subsequent analysis steps, eg id or grouping variables.
fid_filt_dist
+indicate if the data has a distorted FID due to a
+brick-wall filter being used to downsample the data. Default is to auto
+detect this from the data, but TRUE or FALSE options can be given to override
+detection.
Value
@@ -183,7 +191,7 @@ Examples
diff --git a/docs/reference/read_mrs_tqn.html b/docs/reference/read_mrs_tqn.html
index 5766362f..84bdaf3a 100644
--- a/docs/reference/read_mrs_tqn.html
+++ b/docs/reference/read_mrs_tqn.html
@@ -1,5 +1,5 @@
-Read MRS data using the TARQUIN software package. — read_mrs_tqn • Spectroscopy Analysis Tools (spant) Read MRS data using the TARQUIN software package. — read_mrs_tqn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -131,7 +131,7 @@ Examples
diff --git a/docs/reference/read_pulse_ascii.html b/docs/reference/read_pulse_ascii.html
index c9e0d43c..ab11c9cc 100644
--- a/docs/reference/read_pulse_ascii.html
+++ b/docs/reference/read_pulse_ascii.html
@@ -1,5 +1,5 @@
-Read an ASCII formatted pulse file. — read_pulse_ascii • Spectroscopy Analysis Tools (spant) Read an ASCII formatted pulse file. — read_pulse_ascii • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/read_pulse_bruker.html b/docs/reference/read_pulse_bruker.html
index c92bf76a..dbe9073b 100644
--- a/docs/reference/read_pulse_bruker.html
+++ b/docs/reference/read_pulse_bruker.html
@@ -1,5 +1,5 @@
-Read a Bruker formatted pulse file — read_pulse_bruker • Spectroscopy Analysis Tools (spant) Read a Bruker formatted pulse file — read_pulse_bruker • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/read_pulse_pta.html b/docs/reference/read_pulse_pta.html
index 72e1b6d4..a0fac3c3 100644
--- a/docs/reference/read_pulse_pta.html
+++ b/docs/reference/read_pulse_pta.html
@@ -1,5 +1,5 @@
-Read a .pta formatted pulse file compatible with Siemens PulseTool. — read_pulse_pta • Spectroscopy Analysis Tools (spant) Read a .pta formatted pulse file compatible with Siemens PulseTool. — read_pulse_pta • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/read_siemens_txt_hdr.html b/docs/reference/read_siemens_txt_hdr.html
index 23fb8c70..3a17d87c 100644
--- a/docs/reference/read_siemens_txt_hdr.html
+++ b/docs/reference/read_siemens_txt_hdr.html
@@ -1,5 +1,5 @@
-Read the text format header found in Siemens IMA and TWIX data files. — read_siemens_txt_hdr • Spectroscopy Analysis Tools (spant) Read the text format header found in Siemens IMA and TWIX data files. — read_siemens_txt_hdr • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -78,7 +78,7 @@ Read the text format header found in Siemens IMA and TWIX data files.
- read_siemens_txt_hdr(input, version = "vd", verbose, offset = 0)
+ read_siemens_txt_hdr(input, version = "vd", verbose = FALSE, offset = 0)
@@ -118,7 +118,7 @@ Value
diff --git a/docs/reference/read_tqn_fit.html b/docs/reference/read_tqn_fit.html
index 4da6c25e..a1630420 100644
--- a/docs/reference/read_tqn_fit.html
+++ b/docs/reference/read_tqn_fit.html
@@ -1,5 +1,5 @@
-Reader for csv fit results generated by TARQUIN. — read_tqn_fit • Spectroscopy Analysis Tools (spant) Reader for csv fit results generated by TARQUIN. — read_tqn_fit • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -113,7 +113,7 @@ Examples
diff --git a/docs/reference/read_tqn_result.html b/docs/reference/read_tqn_result.html
index 36659714..68a3e98c 100644
--- a/docs/reference/read_tqn_result.html
+++ b/docs/reference/read_tqn_result.html
@@ -1,5 +1,5 @@
-Reader for csv results generated by TARQUIN. — read_tqn_result • Spectroscopy Analysis Tools (spant) Reader for csv results generated by TARQUIN. — read_tqn_result • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -117,7 +117,7 @@ Examples
diff --git a/docs/reference/recon_imag.html b/docs/reference/recon_imag.html
index d2a72225..5bc3b1eb 100644
--- a/docs/reference/recon_imag.html
+++ b/docs/reference/recon_imag.html
@@ -1,7 +1,5 @@
-Reconstruct complex time-domain data from the real part of frequency-domain
-data. — recon_imag • Spectroscopy Analysis Tools (spant) Reconstruct complex time-domain data from the real part of frequency-domain data. — recon_imag • Spectroscopy Analysis Tools (spant) Reconstruct complex time-domain data from the real part of frequency-domain
-data. — recon_imag_vec • Spectroscopy Analysis Tools (spant) Reconstruct complex time-domain data from the real part of frequency-domain data. — recon_imag_vec • Spectroscopy Analysis Tools (spant) Reconstruct 2D MRSI data from a twix file loaded with read_mrs. — recon_twix_2d_mrsi • Spectroscopy Analysis Tools (spant) Reconstruct 2D MRSI data from a twix file loaded with read_mrs. — recon_twix_2d_mrsi • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/rectangular_mask.html b/docs/reference/rectangular_mask.html
index a2117283..6e469bc9 100644
--- a/docs/reference/rectangular_mask.html
+++ b/docs/reference/rectangular_mask.html
@@ -1,5 +1,5 @@
-Create a rectangular mask stored as a matrix of logical values. — rectangular_mask • Spectroscopy Analysis Tools (spant) Create a rectangular mask stored as a matrix of logical values. — rectangular_mask • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -130,7 +130,7 @@ Value
diff --git a/docs/reference/reexports.html b/docs/reference/reexports.html
index 694a75d1..a59e8379 100644
--- a/docs/reference/reexports.html
+++ b/docs/reference/reexports.html
@@ -1,5 +1,5 @@
-Objects exported from other packages — reexports • Spectroscopy Analysis Tools (spant) Objects exported from other packages — reexports • Spectroscopy Analysis Tools (spant)
Spectroscopy Analysis Tools (spant)
- 2.21.0
+ 2.22.0
@@ -103,7 +103,7 @@ Objects exported from other packages
diff --git a/docs/reference/rep_array_dim.html b/docs/reference/rep_array_dim.html
index b9c49b4a..48c0a5ed 100644
--- a/docs/reference/rep_array_dim.html
+++ b/docs/reference/rep_array_dim.html
@@ -1,5 +1,5 @@
-Repeat an array over a given dimension. — rep_array_dim • Spectroscopy Analysis Tools (spant) Repeat an array over a given dimension. — rep_array_dim • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/rep_dyn.html b/docs/reference/rep_dyn.html
index 6bbfb0ef..89a4bb9b 100644
--- a/docs/reference/rep_dyn.html
+++ b/docs/reference/rep_dyn.html
@@ -1,5 +1,5 @@
-Replicate a scan in the dynamic dimension. — rep_dyn • Spectroscopy Analysis Tools (spant) Replicate a scan in the dynamic dimension. — rep_dyn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/rep_mrs.html b/docs/reference/rep_mrs.html
index 67730b5c..becb8f00 100644
--- a/docs/reference/rep_mrs.html
+++ b/docs/reference/rep_mrs.html
@@ -1,5 +1,5 @@
-Replicate a scan over a given dimension. — rep_mrs • Spectroscopy Analysis Tools (spant) Replicate a scan over a given dimension. — rep_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -138,7 +138,7 @@ Value
diff --git a/docs/reference/resample_basis.html b/docs/reference/resample_basis.html
index b0f2ab17..c7a6222a 100644
--- a/docs/reference/resample_basis.html
+++ b/docs/reference/resample_basis.html
@@ -1,5 +1,5 @@
-Resample a basis-set to match a mrs_data acquisition. — resample_basis • Spectroscopy Analysis Tools (spant) Resample a basis-set to match a mrs_data acquisition. — resample_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -116,7 +116,7 @@ Value
diff --git a/docs/reference/resample_img.html b/docs/reference/resample_img.html
index f1e7beaf..b0cc8f71 100644
--- a/docs/reference/resample_img.html
+++ b/docs/reference/resample_img.html
@@ -1,5 +1,5 @@
-Resample an image to match a target image space. — resample_img • Spectroscopy Analysis Tools (spant) Resample an image to match a target image space. — resample_img • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/resample_voi.html b/docs/reference/resample_voi.html
index 8fbfa836..a29ab096 100644
--- a/docs/reference/resample_voi.html
+++ b/docs/reference/resample_voi.html
@@ -1,7 +1,5 @@
-Resample a VOI to match a target image space using nearest-neighbour
-interpolation. — resample_voi • Spectroscopy Analysis Tools (spant) Resample a VOI to match a target image space using nearest-neighbour interpolation. — resample_voi • Spectroscopy Analysis Tools (spant) Reslice a nifti object to match the orientation of mrs data. — reslice_to_mrs • Spectroscopy Analysis Tools (spant) Reslice a nifti object to match the orientation of mrs data. — reslice_to_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/reson_table2mrs_data.html b/docs/reference/reson_table2mrs_data.html
index d75579ee..c5a2167a 100644
--- a/docs/reference/reson_table2mrs_data.html
+++ b/docs/reference/reson_table2mrs_data.html
@@ -1,5 +1,5 @@
-Generate mrs_data from a table of single Lorentzian resonances. — reson_table2mrs_data • Spectroscopy Analysis Tools (spant) Generate mrs_data from a table of single Lorentzian resonances. — reson_table2mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -119,7 +119,7 @@ Value
diff --git a/docs/reference/rm_dyns.html b/docs/reference/rm_dyns.html
index 5d5ef692..573e1f51 100644
--- a/docs/reference/rm_dyns.html
+++ b/docs/reference/rm_dyns.html
@@ -1,5 +1,5 @@
-Remove a subset of dynamic scans. — rm_dyns • Spectroscopy Analysis Tools (spant) Remove a subset of dynamic scans. — rm_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/scale_amp_molal.html b/docs/reference/scale_amp_molal.html
index aaeee1f2..7acb8cb0 100644
--- a/docs/reference/scale_amp_molal.html
+++ b/docs/reference/scale_amp_molal.html
@@ -1,7 +1,5 @@
-Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water). — scale_amp_molal • Spectroscopy Analysis Tools (spant) Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / kg of tissue water). — scale_amp_molal • Spectroscopy Analysis Tools (spant)
Spectroscopy Analysis Tools (spant)
- 2.21.0
+ 2.22.0
@@ -76,8 +74,7 @@
- Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water).
+ Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / kg of tissue water).
Source: R/amp_scaling.R
scale_amp_molal.Rd
@@ -163,7 +160,7 @@ Value
diff --git a/docs/reference/scale_amp_molal_pvc.html b/docs/reference/scale_amp_molal_pvc.html
index 962d6afc..4d194abd 100644
--- a/docs/reference/scale_amp_molal_pvc.html
+++ b/docs/reference/scale_amp_molal_pvc.html
@@ -1,7 +1,5 @@
-Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water). — scale_amp_molal_pvc • Spectroscopy Analysis Tools (spant)
@@ -75,8 +73,7 @@
- Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water).
+ Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / kg of tissue water).
Source: R/amp_scaling.R
scale_amp_molal_pvc.Rd
@@ -141,7 +138,7 @@ Value
diff --git a/docs/reference/scale_amp_molar.html b/docs/reference/scale_amp_molar.html
index 02358d91..dc87a338 100644
--- a/docs/reference/scale_amp_molar.html
+++ b/docs/reference/scale_amp_molar.html
@@ -1,7 +1,5 @@
-Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / Litre of tissue). — scale_amp_molar • Spectroscopy Analysis Tools (spant) Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / Litre of tissue). — scale_amp_molar • Spectroscopy Analysis Tools (spant) Convert default LCM/TARQUIN concentration scaling to molal units with partial
-volume correction. — scale_amp_molar2molal_pvc • Spectroscopy Analysis Tools (spant) Convert default LCM/TARQUIN concentration scaling to molal units with partial volume correction. — scale_amp_molar2molal_pvc • Spectroscopy Analysis Tools (spant) Scale fitted amplitudes to a ratio of signal amplitude. — scale_amp_ratio • Spectroscopy Analysis Tools (spant) Scale fitted amplitudes to a ratio of signal amplitude. — scale_amp_ratio • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -116,7 +116,7 @@ Value
diff --git a/docs/reference/scale_amp_ratio_value.html b/docs/reference/scale_amp_ratio_value.html
index 2036837a..6af8ac51 100644
--- a/docs/reference/scale_amp_ratio_value.html
+++ b/docs/reference/scale_amp_ratio_value.html
@@ -1,5 +1,5 @@
-Scale fitted amplitudes to a ratio of signal amplitude. — scale_amp_ratio_value • Spectroscopy Analysis Tools (spant) Scale fitted amplitudes to a ratio of signal amplitude. — scale_amp_ratio_value • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/scale_amp_water_ratio.html b/docs/reference/scale_amp_water_ratio.html
index 5b25e884..35a76b00 100644
--- a/docs/reference/scale_amp_water_ratio.html
+++ b/docs/reference/scale_amp_water_ratio.html
@@ -1,5 +1,5 @@
-Scale metabolite amplitudes as a ratio to the unsuppressed water amplitude. — scale_amp_water_ratio • Spectroscopy Analysis Tools (spant) Scale metabolite amplitudes as a ratio to the unsuppressed water amplitude. — scale_amp_water_ratio • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/scale_basis_amp.html b/docs/reference/scale_basis_amp.html
index 9401c3f1..5a58b5e5 100644
--- a/docs/reference/scale_basis_amp.html
+++ b/docs/reference/scale_basis_amp.html
@@ -1,5 +1,5 @@
-Scale a basis object by a scalar. — scale_basis_amp • Spectroscopy Analysis Tools (spant) Scale a basis object by a scalar. — scale_basis_amp • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/scale_basis_from_singlet.html b/docs/reference/scale_basis_from_singlet.html
index 0d542bc8..c9a19e77 100644
--- a/docs/reference/scale_basis_from_singlet.html
+++ b/docs/reference/scale_basis_from_singlet.html
@@ -1,5 +1,5 @@
-Scale a basis-set to be consistent with spant assumptions for water scaling. — scale_basis_from_singlet • Spectroscopy Analysis Tools (spant) Scale a basis-set to be consistent with spant assumptions for water scaling. — scale_basis_from_singlet • Spectroscopy Analysis Tools (spant)
Spectroscopy Analysis Tools (spant)
- 2.21.0
+ 2.22.0
@@ -127,7 +127,7 @@ Value
diff --git a/docs/reference/scale_mrs_amp.html b/docs/reference/scale_mrs_amp.html
index b5501a0d..990f058a 100644
--- a/docs/reference/scale_mrs_amp.html
+++ b/docs/reference/scale_mrs_amp.html
@@ -1,5 +1,5 @@
-Scale an mrs_data object by a scalar or vector or amplitudes. — scale_mrs_amp • Spectroscopy Analysis Tools (spant) Scale an mrs_data object by a scalar or vector or amplitudes. — scale_mrs_amp • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/scale_spec.html b/docs/reference/scale_spec.html
index 4f6ea835..6b3ddba4 100644
--- a/docs/reference/scale_spec.html
+++ b/docs/reference/scale_spec.html
@@ -1,5 +1,5 @@
-Scale mrs_data to a spectral region. — scale_spec • Spectroscopy Analysis Tools (spant) Scale mrs_data to a spectral region. — scale_spec • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -141,7 +141,7 @@ Value
diff --git a/docs/reference/sd.html b/docs/reference/sd.html
index ea1eec9f..3ae4dfd4 100644
--- a/docs/reference/sd.html
+++ b/docs/reference/sd.html
@@ -1,5 +1,5 @@
-Calculate the standard deviation spectrum from an mrs_data object. — sd • Spectroscopy Analysis Tools (spant) Calculate the standard deviation spectrum from an mrs_data object. — sd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/sd.mrs_data.html b/docs/reference/sd.mrs_data.html
index 3f92a49f..13bdda85 100644
--- a/docs/reference/sd.mrs_data.html
+++ b/docs/reference/sd.mrs_data.html
@@ -1,5 +1,5 @@
-Calculate the standard deviation spectrum from an mrs_data object. — sd.mrs_data • Spectroscopy Analysis Tools (spant) Calculate the standard deviation spectrum from an mrs_data object. — sd.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/seconds.html b/docs/reference/seconds.html
index b34d6627..467ee17f 100644
--- a/docs/reference/seconds.html
+++ b/docs/reference/seconds.html
@@ -1,5 +1,5 @@
-Return a time scale vector to match the FID of an MRS data object. — seconds • Spectroscopy Analysis Tools (spant) Return a time scale vector to match the FID of an MRS data object. — seconds • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/seq_cpmg_ideal.html b/docs/reference/seq_cpmg_ideal.html
index 547e96ab..45727c86 100644
--- a/docs/reference/seq_cpmg_ideal.html
+++ b/docs/reference/seq_cpmg_ideal.html
@@ -1,5 +1,5 @@
-CPMG style sequence with ideal pulses. — seq_cpmg_ideal • Spectroscopy Analysis Tools (spant) CPMG style sequence with ideal pulses. — seq_cpmg_ideal • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/seq_mega_press_ideal.html b/docs/reference/seq_mega_press_ideal.html
index 0769b8b4..a9cd7fa0 100644
--- a/docs/reference/seq_mega_press_ideal.html
+++ b/docs/reference/seq_mega_press_ideal.html
@@ -1,7 +1,5 @@
-MEGA-PRESS sequence with ideal localisation pulses and Gaussian shaped
-editing pulse. — seq_mega_press_ideal • Spectroscopy Analysis Tools (spant) MEGA-PRESS sequence with ideal localisation pulses and Gaussian shaped editing pulse. — seq_mega_press_ideal • Spectroscopy Analysis Tools (spant) PRESS sequence with shaped refocusing pulses. — seq_press_2d_shaped • Spectroscopy Analysis Tools (spant) PRESS sequence with shaped refocusing pulses. — seq_press_2d_shaped • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -165,7 +165,7 @@ Value
diff --git a/docs/reference/seq_press_ideal.html b/docs/reference/seq_press_ideal.html
index 8c976856..72c3af3d 100644
--- a/docs/reference/seq_press_ideal.html
+++ b/docs/reference/seq_press_ideal.html
@@ -1,5 +1,5 @@
-PRESS sequence with ideal pulses. — seq_press_ideal • Spectroscopy Analysis Tools (spant) PRESS sequence with ideal pulses. — seq_press_ideal • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/seq_pulse_acquire.html b/docs/reference/seq_pulse_acquire.html
index 4a88fc64..ad80571e 100644
--- a/docs/reference/seq_pulse_acquire.html
+++ b/docs/reference/seq_pulse_acquire.html
@@ -1,5 +1,5 @@
-Simple pulse and acquire sequence with ideal pulses. — seq_pulse_acquire • Spectroscopy Analysis Tools (spant) Simple pulse and acquire sequence with ideal pulses. — seq_pulse_acquire • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/seq_slaser_ideal.html b/docs/reference/seq_slaser_ideal.html
index 74688f4d..eb83e8e3 100644
--- a/docs/reference/seq_slaser_ideal.html
+++ b/docs/reference/seq_slaser_ideal.html
@@ -1,5 +1,5 @@
-sLASER sequence with ideal pulses. — seq_slaser_ideal • Spectroscopy Analysis Tools (spant) sLASER sequence with ideal pulses. — seq_slaser_ideal • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -126,7 +126,7 @@ Value
diff --git a/docs/reference/seq_spin_echo_ideal.html b/docs/reference/seq_spin_echo_ideal.html
index e23271de..4248716f 100644
--- a/docs/reference/seq_spin_echo_ideal.html
+++ b/docs/reference/seq_spin_echo_ideal.html
@@ -1,5 +1,5 @@
-Spin echo sequence with ideal pulses. — seq_spin_echo_ideal • Spectroscopy Analysis Tools (spant) Spin echo sequence with ideal pulses. — seq_spin_echo_ideal • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/seq_steam_ideal.html b/docs/reference/seq_steam_ideal.html
index a60685a8..1c8115d7 100644
--- a/docs/reference/seq_steam_ideal.html
+++ b/docs/reference/seq_steam_ideal.html
@@ -1,5 +1,5 @@
-STEAM sequence with ideal pulses. — seq_steam_ideal • Spectroscopy Analysis Tools (spant) STEAM sequence with ideal pulses. — seq_steam_ideal • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -128,7 +128,7 @@ Value
diff --git a/docs/reference/seq_steam_ideal_cof.html b/docs/reference/seq_steam_ideal_cof.html
index 8f225740..cba7af91 100644
--- a/docs/reference/seq_steam_ideal_cof.html
+++ b/docs/reference/seq_steam_ideal_cof.html
@@ -1,7 +1,5 @@
-STEAM sequence with ideal pulses and coherence order filtering to simulate
-gradient crushers. — seq_steam_ideal_cof • Spectroscopy Analysis Tools (spant) STEAM sequence with ideal pulses and coherence order filtering to simulate gradient crushers. — seq_steam_ideal_cof • Spectroscopy Analysis Tools (spant) STEAM sequence with ideal pulses using the z-rotation gradient simulation
-method described by Young et al JMR 140, 146-152 (1999). — seq_steam_ideal_young • Spectroscopy Analysis Tools (spant) STEAM sequence with ideal pulses using the z-rotation gradient simulation method described by Young et al JMR 140, 146-152 (1999). — seq_steam_ideal_young • Spectroscopy Analysis Tools (spant) Set the number of transients for an mrs_data object. — set_Ntrans • Spectroscopy Analysis Tools (spant) Set the number of transients for an mrs_data object. — set_Ntrans • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/set_def_acq_paras.html b/docs/reference/set_def_acq_paras.html
index 3e1b4004..cc2ada9c 100644
--- a/docs/reference/set_def_acq_paras.html
+++ b/docs/reference/set_def_acq_paras.html
@@ -1,5 +1,5 @@
-Set the default acquisition parameters. — set_def_acq_paras • Spectroscopy Analysis Tools (spant) Set the default acquisition parameters. — set_def_acq_paras • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Arguments
diff --git a/docs/reference/set_lcm_cmd.html b/docs/reference/set_lcm_cmd.html
index 2056ed01..42bb2f24 100644
--- a/docs/reference/set_lcm_cmd.html
+++ b/docs/reference/set_lcm_cmd.html
@@ -1,5 +1,5 @@
-Set the command to run the LCModel command-line program. — set_lcm_cmd • Spectroscopy Analysis Tools (spant) Set the command to run the LCModel command-line program. — set_lcm_cmd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/set_lw.html b/docs/reference/set_lw.html
index b64ec851..bb176c62 100644
--- a/docs/reference/set_lw.html
+++ b/docs/reference/set_lw.html
@@ -1,5 +1,5 @@
-Apply line-broadening to an mrs_data object to achieve a specified linewidth. — set_lw • Spectroscopy Analysis Tools (spant) Apply line-broadening to an mrs_data object to achieve a specified linewidth. — set_lw • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -123,7 +123,7 @@ Value
diff --git a/docs/reference/set_mask_xy_mat.html b/docs/reference/set_mask_xy_mat.html
index 49dc5d4e..52c4b617 100644
--- a/docs/reference/set_mask_xy_mat.html
+++ b/docs/reference/set_mask_xy_mat.html
@@ -1,5 +1,5 @@
-Set the masked voxels in a 2D MRSI dataset to given spectrum. — set_mask_xy_mat • Spectroscopy Analysis Tools (spant) Set the masked voxels in a 2D MRSI dataset to given spectrum. — set_mask_xy_mat • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Value
diff --git a/docs/reference/set_precomp_mode.html b/docs/reference/set_precomp_mode.html
index f44bd5d3..47c28e3b 100644
--- a/docs/reference/set_precomp_mode.html
+++ b/docs/reference/set_precomp_mode.html
@@ -1,5 +1,5 @@
-Set the precompute mode. — set_precomp_mode • Spectroscopy Analysis Tools (spant) Set the precompute mode. — set_precomp_mode • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/set_precomp_verbose.html b/docs/reference/set_precomp_verbose.html
index 1453a231..9c613505 100644
--- a/docs/reference/set_precomp_verbose.html
+++ b/docs/reference/set_precomp_verbose.html
@@ -1,5 +1,5 @@
-Set the verbosity of the precompute function. — set_precomp_verbose • Spectroscopy Analysis Tools (spant) Set the verbosity of the precompute function. — set_precomp_verbose • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/set_ref.html b/docs/reference/set_ref.html
index 8953fa50..5436dfa2 100644
--- a/docs/reference/set_ref.html
+++ b/docs/reference/set_ref.html
@@ -1,5 +1,5 @@
-Set the ppm reference value (eg ppm value at 0Hz). — set_ref • Spectroscopy Analysis Tools (spant) Set the ppm reference value (eg ppm value at 0Hz). — set_ref • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/set_td_pts.html b/docs/reference/set_td_pts.html
index 8a80d42a..586459ff 100644
--- a/docs/reference/set_td_pts.html
+++ b/docs/reference/set_td_pts.html
@@ -1,7 +1,5 @@
-Set the number of time-domain data points, truncating or zero-filling as
-appropriate. — set_td_pts • Spectroscopy Analysis Tools (spant) Set the number of time-domain data points, truncating or zero-filling as appropriate. — set_td_pts • Spectroscopy Analysis Tools (spant) Set the command to run the TARQUIN command-line program. — set_tqn_cmd • Spectroscopy Analysis Tools (spant) Set the command to run the TARQUIN command-line program. — set_tqn_cmd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/set_tr.html b/docs/reference/set_tr.html
index b2109ab0..65c9df5f 100644
--- a/docs/reference/set_tr.html
+++ b/docs/reference/set_tr.html
@@ -1,5 +1,5 @@
-Set the repetition time of an MRS dataset. — set_tr • Spectroscopy Analysis Tools (spant) Set the repetition time of an MRS dataset. — set_tr • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/shift.html b/docs/reference/shift.html
index ab0fe724..034591d0 100644
--- a/docs/reference/shift.html
+++ b/docs/reference/shift.html
@@ -1,5 +1,5 @@
-Apply a frequency shift to MRS data. — shift • Spectroscopy Analysis Tools (spant) Apply a frequency shift to MRS data. — shift • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/shift_basis.html b/docs/reference/shift_basis.html
index 2884be19..f55a65e0 100644
--- a/docs/reference/shift_basis.html
+++ b/docs/reference/shift_basis.html
@@ -1,5 +1,5 @@
-Apply frequency shifts to basis set signals. — shift_basis • Spectroscopy Analysis Tools (spant) Apply frequency shifts to basis set signals. — shift_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Value
diff --git a/docs/reference/sim_basis.html b/docs/reference/sim_basis.html
index c7838c46..bb5fefc6 100644
--- a/docs/reference/sim_basis.html
+++ b/docs/reference/sim_basis.html
@@ -1,5 +1,5 @@
-Simulate a basis set object. — sim_basis • Spectroscopy Analysis Tools (spant) Simulate a basis set object. — sim_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -136,7 +136,7 @@ Value
diff --git a/docs/reference/sim_basis_1h_brain.html b/docs/reference/sim_basis_1h_brain.html
index 62ed7389..f71ffa0b 100644
--- a/docs/reference/sim_basis_1h_brain.html
+++ b/docs/reference/sim_basis_1h_brain.html
@@ -1,7 +1,5 @@
-Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS
-sequence. Note, ideal pulses are assumed. — sim_basis_1h_brain • Spectroscopy Analysis Tools (spant) Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS sequence. Note, ideal pulses are assumed. — sim_basis_1h_brain • Spectroscopy Analysis Tools (spant) Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS
-sequence. Note, ideal pulses are assumed. — sim_basis_1h_brain_press • Spectroscopy Analysis Tools (spant) Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS sequence. Note, ideal pulses are assumed. — sim_basis_1h_brain_press • Spectroscopy Analysis Tools (spant) Simulate a macromolecular and lipid basis-set suitable for 1H brain MRS
-analysis. — sim_basis_mm_lip_lcm • Spectroscopy Analysis Tools (spant) Simulate a macromolecular and lipid basis-set suitable for 1H brain MRS analysis. — sim_basis_mm_lip_lcm • Spectroscopy Analysis Tools (spant) Simulate a basis file using TARQUIN. — sim_basis_tqn • Spectroscopy Analysis Tools (spant) Simulate a basis file using TARQUIN. — sim_basis_tqn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -129,7 +129,7 @@ Examples
diff --git a/docs/reference/sim_brain_1h.html b/docs/reference/sim_brain_1h.html
index 2044cf1a..717ee289 100644
--- a/docs/reference/sim_brain_1h.html
+++ b/docs/reference/sim_brain_1h.html
@@ -1,5 +1,5 @@
-Simulate MRS data with a similar appearance to normal brain (by default). — sim_brain_1h • Spectroscopy Analysis Tools (spant) Simulate MRS data with a similar appearance to normal brain (by default). — sim_brain_1h • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -159,7 +159,7 @@ Value
diff --git a/docs/reference/sim_mol.html b/docs/reference/sim_mol.html
index 23bcef50..77f76a50 100644
--- a/docs/reference/sim_mol.html
+++ b/docs/reference/sim_mol.html
@@ -1,5 +1,5 @@
-Simulate a mol_parameter object. — sim_mol • Spectroscopy Analysis Tools (spant) Simulate a mol_parameter object. — sim_mol • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -143,7 +143,7 @@ Value
diff --git a/docs/reference/sim_noise.html b/docs/reference/sim_noise.html
index 23875f79..a71477d4 100644
--- a/docs/reference/sim_noise.html
+++ b/docs/reference/sim_noise.html
@@ -1,5 +1,5 @@
-Simulate an mrs_data object containing simulated Gaussian noise. — sim_noise • Spectroscopy Analysis Tools (spant) Simulate an mrs_data object containing simulated Gaussian noise. — sim_noise • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -84,6 +84,7 @@ Simulate an mrs_data object containing simulated Gaussian noise.
ft = def_ft(),
N = def_N(),
ref = def_ref(),
+ nuc = def_nuc(),
dyns = 1,
fd = TRUE
)
@@ -111,6 +112,10 @@ Arguments
reference value for ppm scale.
nuc
+resonant nucleus.
dyns
number of dynamic scans to generate.
Value
diff --git a/docs/reference/sim_resonances.html b/docs/reference/sim_resonances.html
index 19e9a8a4..d4f8d7c0 100644
--- a/docs/reference/sim_resonances.html
+++ b/docs/reference/sim_resonances.html
@@ -1,5 +1,5 @@
-Simulate a MRS data object containing a set of simulated resonances. — sim_resonances • Spectroscopy Analysis Tools (spant) Simulate a MRS data object containing a set of simulated resonances. — sim_resonances • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -161,7 +161,7 @@ Examples
diff --git a/docs/reference/sim_th_excit_profile.html b/docs/reference/sim_th_excit_profile.html
index 5535c5ef..e781cab1 100644
--- a/docs/reference/sim_th_excit_profile.html
+++ b/docs/reference/sim_th_excit_profile.html
@@ -1,7 +1,5 @@
-Simulate an ideal pulse excitation profile by smoothing a top-hat function
-with a Gaussian. — sim_th_excit_profile • Spectroscopy Analysis Tools (spant) Simulate an ideal pulse excitation profile by smoothing a top-hat function with a Gaussian. — sim_th_excit_profile • Spectroscopy Analysis Tools (spant) Simulate an mrs_data object containing complex zero valued samples. — sim_zero • Spectroscopy Analysis Tools (spant) Simulate an mrs_data object containing complex zero valued samples. — sim_zero • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -78,7 +78,14 @@ Simulate an mrs_data object containing complex zero valued samples.
-
+
@@ -99,6 +106,10 @@ Arguments
reference value for ppm scale.
nuc
+resonant nucleus.
dyns
number of dynamic scans to generate.
Value
diff --git a/docs/reference/smooth_dyns.html b/docs/reference/smooth_dyns.html
index 4cc8da50..accf3a51 100644
--- a/docs/reference/smooth_dyns.html
+++ b/docs/reference/smooth_dyns.html
@@ -1,5 +1,5 @@
-Smooth data across the dynamic dimension with a Gaussian kernel. — smooth_dyns • Spectroscopy Analysis Tools (spant) Smooth data across the dynamic dimension with a Gaussian kernel. — smooth_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/sort_basis.html b/docs/reference/sort_basis.html
index 6a676ea2..d25cc006 100644
--- a/docs/reference/sort_basis.html
+++ b/docs/reference/sort_basis.html
@@ -1,5 +1,5 @@
-Sort the basis-set elements alphabetically. — sort_basis • Spectroscopy Analysis Tools (spant) Sort the basis-set elements alphabetically. — sort_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/spant-package.html b/docs/reference/spant-package.html
index b3dd8e21..90f19ec3 100644
--- a/docs/reference/spant-package.html
+++ b/docs/reference/spant-package.html
@@ -1,5 +1,5 @@
-spant: spectroscopy analysis tools. — spant-package • Spectroscopy Analysis Tools (spant) spant: spectroscopy analysis tools. — spant-package • Spectroscopy Analysis Tools (spant) Simulate and fit some spectra with ABfit for benchmarking purposes. Basic
-timing and performance metrics will be printed. — spant_abfit_benchmark • Spectroscopy Analysis Tools (spant) Simulate and fit some spectra with ABfit for benchmarking purposes. Basic timing and performance metrics will be printed. — spant_abfit_benchmark • Spectroscopy Analysis Tools (spant) Example MEGA-PRESS data with significant B0 drift. — spant_mpress_drift • Spectroscopy Analysis Tools (spant) Example MEGA-PRESS data with significant B0 drift. — spant_mpress_drift • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -83,7 +83,7 @@ Example MEGA-PRESS data with significant B0 drift.
Format
- An object of class mrs_data of length 13.
+ An object of class mrs_data of dimension 1 x 1 x 1 x 1 x 40 x 1 x 1024.
@@ -98,7 +98,7 @@ Format
diff --git a/docs/reference/spant_sim_fmrs_dataset.html b/docs/reference/spant_sim_fmrs_dataset.html
new file mode 100644
index 00000000..00e48b56
--- /dev/null
+++ b/docs/reference/spant_sim_fmrs_dataset.html
@@ -0,0 +1,117 @@
+
+Simulate an example fMRS dataset for a block design fMRS experiment and export a BIDS structure. — spant_sim_fmrs_dataset • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Simulate an example fMRS dataset for a block design fMRS experiment and export a BIDS structure.
+ Source: R/fmrs.R
+ spant_sim_fmrs_dataset.Rd
+
+
+
+ Simulate an example fMRS dataset for a block design fMRS experiment and
+export a BIDS structure.
+
+
+
+ spant_sim_fmrs_dataset(output_dir = NULL)
+
+
+
+ Arguments
+ - output_dir
+output directory for the BIDS data. Defaults to :
+"HOME/sim_fmrs_dataset/data".
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/spant_simulation_benchmark.html b/docs/reference/spant_simulation_benchmark.html
index 32daa8bf..d8cc6841 100644
--- a/docs/reference/spant_simulation_benchmark.html
+++ b/docs/reference/spant_simulation_benchmark.html
@@ -1,7 +1,5 @@
-Simulate a typical metabolite basis set for benchmarking. Timing metrics will
-be printed on completion. — spant_simulation_benchmark • Spectroscopy Analysis Tools (spant) Simulate a typical metabolite basis set for benchmarking. Timing metrics will be printed on completion. — spant_simulation_benchmark • Spectroscopy Analysis Tools (spant) Decompose an mrs_data object into white and gray matter spectra. — spec_decomp • Spectroscopy Analysis Tools (spant) Perform a mathematical operation on a spectral region. — spec_op • Spectroscopy Analysis Tools (spant) Perform a mathematical operation on a spectral region. — spec_op • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -98,8 +98,8 @@ Arguments
operator
-can be "sum" (default), "mean", "l2", "max", "min" or
-"max-min".
can be "sum" (default), "mean", "l2", "max", "max_cplx,
+"min" or "max-min".
freq_scale
@@ -129,7 +129,7 @@ Value
diff --git a/docs/reference/spin_sys.html b/docs/reference/spin_sys.html
index 853423a4..1eaa9e76 100644
--- a/docs/reference/spin_sys.html
+++ b/docs/reference/spin_sys.html
@@ -1,5 +1,5 @@
-Create a spin system object for pulse sequence simulation. — spin_sys • Spectroscopy Analysis Tools (spant) Create a spin system object for pulse sequence simulation. — spin_sys • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/spm_pve2categorical.html b/docs/reference/spm_pve2categorical.html
index 23a1bad9..70f10729 100644
--- a/docs/reference/spm_pve2categorical.html
+++ b/docs/reference/spm_pve2categorical.html
@@ -1,7 +1,5 @@
-Convert SPM style segmentation files to a single categorical image where
-the numerical values map as: 0) Other, 1) CSF, 2) GM and 3) WM. — spm_pve2categorical • Spectroscopy Analysis Tools (spant) Convert SPM style segmentation files to a single categorical image where the numerical values map as: 0) Other, 1) CSF, 2) GM and 3) WM. — spm_pve2categorical • Spectroscopy Analysis Tools (spant) Signal space projection method for lipid suppression. — ssp • Spectroscopy Analysis Tools (spant) Signal space projection method for lipid suppression. — ssp • Spectroscopy Analysis Tools (spant) Plot the fitting results of an object of class fit_result with
-individual basis set components shown. — stackplot.fit_result • Spectroscopy Analysis Tools (spant) Plot the fitting results of an object of class fit_result with individual basis set components shown. — stackplot.fit_result • Spectroscopy Analysis Tools (spant) Produce a plot with multiple traces. — stackplot • Spectroscopy Analysis Tools (spant) Produce a plot with multiple traces. — stackplot • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/stackplot.mrs_data.html b/docs/reference/stackplot.mrs_data.html
index 17ff5648..64eea445 100644
--- a/docs/reference/stackplot.mrs_data.html
+++ b/docs/reference/stackplot.mrs_data.html
@@ -1,5 +1,5 @@
-Stackplot plotting method for objects of class mrs_data. — stackplot.mrs_data • Spectroscopy Analysis Tools (spant) Stackplot plotting method for objects of class mrs_data. — stackplot.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -255,7 +255,7 @@ Arguments
diff --git a/docs/reference/sub_first_dyn.html b/docs/reference/sub_first_dyn.html
index dbd7f831..493b7242 100644
--- a/docs/reference/sub_first_dyn.html
+++ b/docs/reference/sub_first_dyn.html
@@ -1,5 +1,5 @@
-Subtract the first dynamic spectrum from a dynamic series. — sub_first_dyn • Spectroscopy Analysis Tools (spant) Subtract the first dynamic spectrum from a dynamic series. — sub_first_dyn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/sub_mean_dyns.html b/docs/reference/sub_mean_dyns.html
index 6e3bb2df..221bd0c1 100644
--- a/docs/reference/sub_mean_dyns.html
+++ b/docs/reference/sub_mean_dyns.html
@@ -1,5 +1,5 @@
-Subtract the mean dynamic spectrum from a dynamic series. — sub_mean_dyns • Spectroscopy Analysis Tools (spant) Subtract the mean dynamic spectrum from a dynamic series. — sub_mean_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/sub_median_dyns.html b/docs/reference/sub_median_dyns.html
index 134c495d..1e834f14 100644
--- a/docs/reference/sub_median_dyns.html
+++ b/docs/reference/sub_median_dyns.html
@@ -1,5 +1,5 @@
-Subtract the median dynamic spectrum from a dynamic series. — sub_median_dyns • Spectroscopy Analysis Tools (spant) Subtract the median dynamic spectrum from a dynamic series. — sub_median_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/sum_coils.html b/docs/reference/sum_coils.html
index 7bf559f2..e1ab3cc0 100644
--- a/docs/reference/sum_coils.html
+++ b/docs/reference/sum_coils.html
@@ -1,5 +1,5 @@
-Calculate the sum across receiver coil elements. — sum_coils • Spectroscopy Analysis Tools (spant) Calculate the sum across receiver coil elements. — sum_coils • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/sum_dyns.html b/docs/reference/sum_dyns.html
index a0be19d3..bbda2ffc 100644
--- a/docs/reference/sum_dyns.html
+++ b/docs/reference/sum_dyns.html
@@ -1,5 +1,5 @@
-Calculate the sum of data dynamics. — sum_dyns • Spectroscopy Analysis Tools (spant) Calculate the sum of data dynamics. — sum_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/sum_mrs.html b/docs/reference/sum_mrs.html
index a22f215b..3cc3ab9e 100644
--- a/docs/reference/sum_mrs.html
+++ b/docs/reference/sum_mrs.html
@@ -1,5 +1,5 @@
-Sum two mrs_data objects. — sum_mrs • Spectroscopy Analysis Tools (spant) Sum two mrs_data objects. — sum_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Value
diff --git a/docs/reference/sum_mrs_list.html b/docs/reference/sum_mrs_list.html
index f4e09aea..c3584348 100644
--- a/docs/reference/sum_mrs_list.html
+++ b/docs/reference/sum_mrs_list.html
@@ -1,5 +1,5 @@
-Return the sum of a list of mrs_data objects. — sum_mrs_list • Spectroscopy Analysis Tools (spant) Return the sum of a list of mrs_data objects. — sum_mrs_list • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/svs_1h_brain_analysis.html b/docs/reference/svs_1h_brain_analysis.html
index 8ce514db..dff0ef7d 100644
--- a/docs/reference/svs_1h_brain_analysis.html
+++ b/docs/reference/svs_1h_brain_analysis.html
@@ -1,5 +1,5 @@
-Standard SVS 1H brain analysis pipeline. — svs_1h_brain_analysis • Spectroscopy Analysis Tools (spant) Standard SVS 1H brain analysis pipeline. — svs_1h_brain_analysis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -199,7 +199,7 @@ Value
diff --git a/docs/reference/svs_1h_brain_analysis_dev.html b/docs/reference/svs_1h_brain_analysis_dev.html
index d70a14d3..d71bfea2 100644
--- a/docs/reference/svs_1h_brain_analysis_dev.html
+++ b/docs/reference/svs_1h_brain_analysis_dev.html
@@ -1,5 +1,5 @@
-Standard SVS 1H brain analysis pipeline. — svs_1h_brain_analysis_dev • Spectroscopy Analysis Tools (spant) Standard SVS 1H brain analysis pipeline. — svs_1h_brain_analysis_dev • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -193,7 +193,7 @@ Examples
diff --git a/docs/reference/svs_1h_brain_batch_analysis.html b/docs/reference/svs_1h_brain_batch_analysis.html
index 5631e8cc..15f7223e 100644
--- a/docs/reference/svs_1h_brain_batch_analysis.html
+++ b/docs/reference/svs_1h_brain_batch_analysis.html
@@ -1,5 +1,5 @@
-Batch interface to the standard SVS 1H brain analysis pipeline. — svs_1h_brain_batch_analysis • Spectroscopy Analysis Tools (spant) Batch interface to the standard SVS 1H brain analysis pipeline. — svs_1h_brain_batch_analysis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -144,7 +144,7 @@ Value
diff --git a/docs/reference/t_test_spec.html b/docs/reference/t_test_spec.html
new file mode 100644
index 00000000..56a7ea1b
--- /dev/null
+++ b/docs/reference/t_test_spec.html
@@ -0,0 +1,124 @@
+
+Perform a t-test on spectral data points. — t_test_spec • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+
+
+ Perform a t-test on spectral data points.
+
+
+
+ t_test_spec(mrs_data, group)
+
+
+
+ Arguments
+ - mrs_data
+an mrs_data object with spectra in the dynamic dimension.
- group
+vector describing the group membership of each dynamic spectrum.
+
+ Value
+
+
+a list of statistical results.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/td2fd.html b/docs/reference/td2fd.html
index 6748a6a8..f31ed524 100644
--- a/docs/reference/td2fd.html
+++ b/docs/reference/td2fd.html
@@ -1,5 +1,5 @@
-Transform time-domain data to the frequency-domain. — td2fd • Spectroscopy Analysis Tools (spant) Transform time-domain data to the frequency-domain. — td2fd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/td_conv_filt.html b/docs/reference/td_conv_filt.html
index a9f340c3..106b9b00 100644
--- a/docs/reference/td_conv_filt.html
+++ b/docs/reference/td_conv_filt.html
@@ -1,5 +1,5 @@
-Time-domain convolution based filter. — td_conv_filt • Spectroscopy Analysis Tools (spant) Time-domain convolution based filter. — td_conv_filt • Spectroscopy Analysis Tools (spant) Time-domain spectral registration. — tdsr • Spectroscopy Analysis Tools (spant) Time-domain spectral registration. — tdsr • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -121,7 +121,7 @@ Value
diff --git a/docs/reference/te.html b/docs/reference/te.html
index 010361b1..4a65711d 100644
--- a/docs/reference/te.html
+++ b/docs/reference/te.html
@@ -1,5 +1,5 @@
-Return the echo time of an MRS dataset. — te • Spectroscopy Analysis Tools (spant) Return the echo time of an MRS dataset. — te • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/tr.html b/docs/reference/tr.html
index 0c0bd63b..2e749e02 100644
--- a/docs/reference/tr.html
+++ b/docs/reference/tr.html
@@ -1,5 +1,5 @@
-Return the repetition time of an MRS dataset. — tr • Spectroscopy Analysis Tools (spant) Return the repetition time of an MRS dataset. — tr • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/varpro_3_para_opts.html b/docs/reference/varpro_3_para_opts.html
index c2270a16..52d7cd84 100644
--- a/docs/reference/varpro_3_para_opts.html
+++ b/docs/reference/varpro_3_para_opts.html
@@ -1,5 +1,5 @@
-Return a list of options for VARPRO based fitting with 3 free parameters. — varpro_3_para_opts • Spectroscopy Analysis Tools (spant) Return a list of options for VARPRO based fitting with 3 free parameters. — varpro_3_para_opts • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -141,7 +141,7 @@ Value
diff --git a/docs/reference/varpro_basic_opts.html b/docs/reference/varpro_basic_opts.html
index 32c86d22..c5104891 100644
--- a/docs/reference/varpro_basic_opts.html
+++ b/docs/reference/varpro_basic_opts.html
@@ -1,5 +1,5 @@
-Return a list of options for a basic VARPRO analysis. — varpro_basic_opts • Spectroscopy Analysis Tools (spant) Return a list of options for a basic VARPRO analysis. — varpro_basic_opts • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -118,7 +118,7 @@ Value
diff --git a/docs/reference/varpro_opts.html b/docs/reference/varpro_opts.html
index 2aabf11d..6332f730 100644
--- a/docs/reference/varpro_opts.html
+++ b/docs/reference/varpro_opts.html
@@ -1,5 +1,5 @@
-Return a list of options for VARPRO based fitting. — varpro_opts • Spectroscopy Analysis Tools (spant) Return a list of options for VARPRO based fitting. — varpro_opts • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -177,7 +177,7 @@ Examples
diff --git a/docs/reference/vec2mrs_data.html b/docs/reference/vec2mrs_data.html
index 0cccd73b..f0d58bf0 100644
--- a/docs/reference/vec2mrs_data.html
+++ b/docs/reference/vec2mrs_data.html
@@ -1,5 +1,5 @@
-Convert a vector into a mrs_data object. — vec2mrs_data • Spectroscopy Analysis Tools (spant) Convert a vector into a mrs_data object. — vec2mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -80,10 +80,11 @@ Convert a vector into a mrs_data object.
vec2mrs_data(
vec,
- fs = def_fs(),
- ft = def_ft(),
- ref = def_ref(),
- nuc = def_nuc(),
+ mrs_data = NULL,
+ fs = NULL,
+ ft = NULL,
+ ref = NULL,
+ nuc = NULL,
dyns = 1,
fd = FALSE
)
@@ -95,6 +96,10 @@ Arguments
the data vector.
mrs_data
+example data to copy acquisition parameters from.
fs
sampling frequency in Hz.
Arguments
fd
-flag to indicate if the matrix is in the frequency domain (logical).
flag to indicate if the vector is in the frequency domain (logical).
Value
diff --git a/docs/reference/write_basis.html b/docs/reference/write_basis.html
index b6e27cbd..94c5e021 100644
--- a/docs/reference/write_basis.html
+++ b/docs/reference/write_basis.html
@@ -1,5 +1,5 @@
-Write a basis object to an LCModel .basis formatted file. — write_basis • Spectroscopy Analysis Tools (spant) Write a basis object to an LCModel .basis formatted file. — write_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -108,7 +108,7 @@ Arguments
diff --git a/docs/reference/write_basis_tqn.html b/docs/reference/write_basis_tqn.html
index 6aa51c1d..116c73ec 100644
--- a/docs/reference/write_basis_tqn.html
+++ b/docs/reference/write_basis_tqn.html
@@ -1,5 +1,5 @@
-Generate a basis file using TARQUIN. — write_basis_tqn • Spectroscopy Analysis Tools (spant) Generate a basis file using TARQUIN. — write_basis_tqn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Examples
diff --git a/docs/reference/write_mrs.html b/docs/reference/write_mrs.html
index fff25f15..124b9dc4 100644
--- a/docs/reference/write_mrs.html
+++ b/docs/reference/write_mrs.html
@@ -1,5 +1,5 @@
-Write MRS data object to file. — write_mrs • Spectroscopy Analysis Tools (spant) Write MRS data object to file. — write_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Arguments
diff --git a/docs/reference/write_mrs_nifti.html b/docs/reference/write_mrs_nifti.html
index f4bf1921..bd3ed4b7 100644
--- a/docs/reference/write_mrs_nifti.html
+++ b/docs/reference/write_mrs_nifti.html
@@ -1,5 +1,5 @@
-Write MRS data object to file in NIFTI format. — write_mrs_nifti • Spectroscopy Analysis Tools (spant) Write MRS data object to file in NIFTI format. — write_mrs_nifti • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/write_pulse_ascii.html b/docs/reference/write_pulse_ascii.html
index 067ae086..221f8ebb 100644
--- a/docs/reference/write_pulse_ascii.html
+++ b/docs/reference/write_pulse_ascii.html
@@ -1,5 +1,5 @@
-Write an ASCII formatted pulse file. — write_pulse_ascii • Spectroscopy Analysis Tools (spant) Write an ASCII formatted pulse file. — write_pulse_ascii • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/zero_fade_spec.html b/docs/reference/zero_fade_spec.html
index c703745c..c8b572c3 100644
--- a/docs/reference/zero_fade_spec.html
+++ b/docs/reference/zero_fade_spec.html
@@ -1,7 +1,5 @@
-Fade a spectrum to zero by frequency domain multiplication with a tanh
-function. Note this operation distorts data points at the end of the FID. — zero_fade_spec • Spectroscopy Analysis Tools (spant) Fade a spectrum to zero by frequency domain multiplication with a tanh function. Note this operation distorts data points at the end of the FID. — zero_fade_spec • Spectroscopy Analysis Tools (spant) Zero all coherences including and above a given order. — zero_higher_orders • Spectroscopy Analysis Tools (spant) Zero all coherences including and above a given order. — zero_higher_orders • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Value
diff --git a/docs/reference/zero_td_pts_end.html b/docs/reference/zero_td_pts_end.html
index 8c1123c8..71d24ebb 100644
--- a/docs/reference/zero_td_pts_end.html
+++ b/docs/reference/zero_td_pts_end.html
@@ -1,5 +1,5 @@
-Set mrs_data object data points at the end of the FID to zero. — zero_td_pts_end • Spectroscopy Analysis Tools (spant) Set mrs_data object data points at the end of the FID to zero. — zero_td_pts_end • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/zf.html b/docs/reference/zf.html
index 85e2013c..baf50256 100644
--- a/docs/reference/zf.html
+++ b/docs/reference/zf.html
@@ -1,5 +1,5 @@
-Zero-fill MRS data in the time domain. — zf • Spectroscopy Analysis Tools (spant) Zero-fill MRS data in the time domain. — zf • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -125,7 +125,7 @@ Value
diff --git a/docs/reference/zf_xy.html b/docs/reference/zf_xy.html
index ebca3999..c4104a74 100644
--- a/docs/reference/zf_xy.html
+++ b/docs/reference/zf_xy.html
@@ -1,5 +1,5 @@
-Zero-fill MRSI data in the k-space x-y direction. — zf_xy • Spectroscopy Analysis Tools (spant) Zero-fill MRSI data in the k-space x-y direction. — zf_xy • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -113,7 +113,7 @@ Value
diff --git a/docs/sitemap.xml b/docs/sitemap.xml
index e2139f71..4c39f515 100644
--- a/docs/sitemap.xml
+++ b/docs/sitemap.xml
@@ -216,6 +216,12 @@
https://martin3141.github.io/spant/reference/comb_coils_fp_pc.html
+
+ https://martin3141.github.io/spant/reference/comb_coils_mrsi_gls.html
+
+
+ https://martin3141.github.io/spant/reference/comb_coils_svs_gls.html
+
https://martin3141.github.io/spant/reference/comb_csv_results.html
@@ -411,6 +417,9 @@
https://martin3141.github.io/spant/reference/gen_conv_reg.html
+
+ https://martin3141.github.io/spant/reference/gen_group_reg.html
+
https://martin3141.github.io/spant/reference/gen_impulse_reg.html
@@ -555,6 +564,15 @@
https://martin3141.github.io/spant/reference/glm_spec.html
+
+ https://martin3141.github.io/spant/reference/glm_spec_fmrs_fl.html
+
+
+ https://martin3141.github.io/spant/reference/glm_spec_fmrs_group.html
+
+
+ https://martin3141.github.io/spant/reference/glm_spec_group_linhyp.html
+
https://martin3141.github.io/spant/reference/grid_shift_xy.html
@@ -690,9 +708,15 @@
https://martin3141.github.io/spant/reference/mrs_data2basis.html
+
+ https://martin3141.github.io/spant/reference/mrs_data2bids.html
+
https://martin3141.github.io/spant/reference/mrs_data2mat.html
+
+ https://martin3141.github.io/spant/reference/mrs_data2spec_mat.html
+
https://martin3141.github.io/spant/reference/mrs_data2vec.html
@@ -741,6 +765,9 @@
https://martin3141.github.io/spant/reference/phase.html
+
+ https://martin3141.github.io/spant/reference/phase_ref_1h_brain.html
+
https://martin3141.github.io/spant/reference/plot.fit_result.html
@@ -780,6 +807,12 @@
https://martin3141.github.io/spant/reference/precomp.html
+
+ https://martin3141.github.io/spant/reference/preproc_svs.html
+
+
+ https://martin3141.github.io/spant/reference/preproc_svs_dataset.html
+
https://martin3141.github.io/spant/reference/print.fit_result.html
@@ -1050,6 +1083,9 @@
https://martin3141.github.io/spant/reference/spant_mpress_drift.html
+
+ https://martin3141.github.io/spant/reference/spant_sim_fmrs_dataset.html
+
https://martin3141.github.io/spant/reference/spant_simulation_benchmark.html
@@ -1107,6 +1143,9 @@
https://martin3141.github.io/spant/reference/svs_1h_brain_batch_analysis.html
+
+ https://martin3141.github.io/spant/reference/t_test_spec.html
+
https://martin3141.github.io/spant/reference/td2fd.html
Convert an mrs_data object to basis object - where basis signals are spread -across the dynamic dimension in the MRS data.
Convert an mrs_data object to basis object - where basis signals are spread across the dynamic dimension in the MRS data.
Create a BIDS file structure from a vector of MRS data paths or list of mrs_data objects.
Convert mrs_data object to a matrix, with spectral points in the column -dimension and dynamics in the row dimension.
Convert mrs_data object to a matrix, with spectral points in the column dimension and dynamics in the row dimension.
Convert mrs_data object to a vector.
Convert mrs_data object to a matrix, with spectral points in the column dimension and dynamics in the row dimension.
Create a BIDS directory and file structure from a list of mrs_data objects.
Convert mrs_data object to a vector.
Perform a fftshift on a matrix, with each column replaced by its shifted -result.
Perform a fftshift on a matrix, with each column replaced by its shifted result.
Perform an ifftshift on a matrix, with each column replaced by its shifted -result.
Perform an ifftshift on a matrix, with each column replaced by its shifted result.
All functions
- Flip the x data dimension order of a nifti image. This corresponds to
-flipping MRI data in the left-right direction, assuming the data in save in
-neurological format (can check with fslorient program).
Flip the x data dimension order of a nifti image. This corresponds to flipping MRI data in the left-right direction, assuming the data in save in neurological format (can check with fslorient program).
@@ -964,8 +946,7 @@ All functions
- Search for the highest peak in a spectral region and return the frequency,
-height and FWHM.
Search for the highest peak in a spectral region and return the frequency, height and FWHM.
@@ -974,6 +955,10 @@ All functions phase()
Apply phasing parameters to MRS data.
+
+
+ Corrected zero order phase and chemical shift offset in 1H MRS data from the brain.
@@ -1005,8 +990,7 @@ All functions
- Plot an interactive slice map from a data array where voxels can be selected
-to display a corresponding spectrum.
Plot an interactive slice map from a data array where voxels can be selected to display a corresponding spectrum.
@@ -1026,8 +1010,15 @@ All functions
- Save function results to file and load on subsequent calls to avoid repeat
-computation.
Save function results to file and load on subsequent calls to avoid repeat computation.
+
+
+ Preprocess and perform quality assessment of a single SVS data set.
+
+
+ Preprocess and perform quality assessment of one or more SVS data sets.
@@ -1055,15 +1046,11 @@ All functions
- Read a directory containing Siemens MRS IMA files and combine along the coil
-dimension. Note that the coil ID is inferred from the sorted file name and
-should be checked when consistency is required between two directories.
Read a directory containing Siemens MRS IMA files and combine along the coil dimension. Note that the coil ID is inferred from the sorted file name and should be checked when consistency is required between two directories.
- Read a directory containing Siemens MRS IMA files and combine along the
-dynamic dimension. Note that the coil ID is inferred from the sorted file
-name and should be checked when consistency is required.
Read a directory containing Siemens MRS IMA files and combine along the dynamic dimension. Note that the coil ID is inferred from the sorted file name and should be checked when consistency is required.
@@ -1103,13 +1090,11 @@ All functions
- Reconstruct complex time-domain data from the real part of frequency-domain
-data.
Reconstruct complex time-domain data from the real part of frequency-domain data.
- Reconstruct complex time-domain data from the real part of frequency-domain
-data.
Reconstruct complex time-domain data from the real part of frequency-domain data.
@@ -1141,8 +1126,7 @@ All functions
- Resample a VOI to match a target image space using nearest-neighbour
-interpolation.
Resample a VOI to match a target image space using nearest-neighbour interpolation.
@@ -1158,23 +1142,19 @@ All functions
- Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water).
Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / kg of tissue water).
- Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water).
Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / kg of tissue water).
- Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / Litre of tissue).
Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / Litre of tissue).
- Convert default LCM/TARQUIN concentration scaling to molal units with partial
-volume correction.
Convert default LCM/TARQUIN concentration scaling to molal units with partial volume correction.
@@ -1222,8 +1202,7 @@ All functions
- MEGA-PRESS sequence with ideal localisation pulses and Gaussian shaped
-editing pulse.
MEGA-PRESS sequence with ideal localisation pulses and Gaussian shaped editing pulse.
@@ -1251,13 +1230,11 @@ All functions
- STEAM sequence with ideal pulses and coherence order filtering to simulate
-gradient crushers.
STEAM sequence with ideal pulses and coherence order filtering to simulate gradient crushers.
- STEAM sequence with ideal pulses using the z-rotation gradient simulation
-method described by Young et al JMR 140, 146-152 (1999).
STEAM sequence with ideal pulses using the z-rotation gradient simulation method described by Young et al JMR 140, 146-152 (1999).
@@ -1293,8 +1270,7 @@ All functions
- Set the number of time-domain data points, truncating or zero-filling as
-appropriate.
Set the number of time-domain data points, truncating or zero-filling as appropriate.
@@ -1318,18 +1294,15 @@ All functions
- Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS
-sequence. Note, ideal pulses are assumed.
Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS sequence. Note, ideal pulses are assumed.
- Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS
-sequence. Note, ideal pulses are assumed.
Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS sequence. Note, ideal pulses are assumed.
- Simulate a macromolecular and lipid basis-set suitable for 1H brain MRS
-analysis.
Simulate a macromolecular and lipid basis-set suitable for 1H brain MRS analysis.
@@ -1353,8 +1326,7 @@ All functions
- Simulate an ideal pulse excitation profile by smoothing a top-hat function
-with a Gaussian.
Simulate an ideal pulse excitation profile by smoothing a top-hat function with a Gaussian.
@@ -1374,17 +1346,19 @@ All functions
- Simulate and fit some spectra with ABfit for benchmarking purposes. Basic
-timing and performance metrics will be printed.
Simulate and fit some spectra with ABfit for benchmarking purposes. Basic timing and performance metrics will be printed.
Example MEGA-PRESS data with significant B0 drift.
+
+
+ Simulate an example fMRS dataset for a block design fMRS experiment and export a BIDS structure.
- Simulate a typical metabolite basis set for benchmarking. Timing metrics will
-be printed on completion.
Simulate a typical metabolite basis set for benchmarking. Timing metrics will be printed on completion.
@@ -1400,8 +1374,7 @@ All functions
- Convert SPM style segmentation files to a single categorical image where
-the numerical values map as: 0) Other, 1) CSF, 2) GM and 3) WM.
Convert SPM style segmentation files to a single categorical image where the numerical values map as: 0) Other, 1) CSF, 2) GM and 3) WM.
@@ -1413,8 +1386,7 @@ All functions
- Plot the fitting results of an object of class fit_result with
-individual basis set components shown.
Plot the fitting results of an object of class fit_result with individual basis set components shown.
@@ -1459,6 +1431,10 @@ All functions svs_1h_brain_batch_analysis()
Batch interface to the standard SVS 1H brain analysis pipeline.
+
+
+ Perform a t-test on spectral data points.
@@ -1518,8 +1494,7 @@ All functions
- Fade a spectrum to zero by frequency domain multiplication with a tanh
-function. Note this operation distorts data points at the end of the FID.
Fade a spectrum to zero by frequency domain multiplication with a tanh function. Note this operation distorts data points at the end of the FID.
@@ -1549,7 +1524,7 @@ All functions
diff --git a/docs/reference/int_spec.html b/docs/reference/int_spec.html
index c7060fe7..783325a8 100644
--- a/docs/reference/int_spec.html
+++ b/docs/reference/int_spec.html
@@ -1,5 +1,5 @@
-Integrate a spectral region. — int_spec • Spectroscopy Analysis Tools (spant) Integrate a spectral region. — int_spec • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -118,7 +118,7 @@ Value
diff --git a/docs/reference/interleave_dyns.html b/docs/reference/interleave_dyns.html
index effe5543..441eff27 100644
--- a/docs/reference/interleave_dyns.html
+++ b/docs/reference/interleave_dyns.html
@@ -1,5 +1,5 @@
-Interleave the first and second half of a dynamic series. — interleave_dyns • Spectroscopy Analysis Tools (spant) Interleave the first and second half of a dynamic series. — interleave_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/inv_even_dyns.html b/docs/reference/inv_even_dyns.html
index 9f9d4fff..dcb781dc 100644
--- a/docs/reference/inv_even_dyns.html
+++ b/docs/reference/inv_even_dyns.html
@@ -1,5 +1,5 @@
-Invert even numbered dynamic scans starting from 1 (2,4,6...). — inv_even_dyns • Spectroscopy Analysis Tools (spant) Invert even numbered dynamic scans starting from 1 (2,4,6...). — inv_even_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/inv_odd_dyns.html b/docs/reference/inv_odd_dyns.html
index 26212e2b..78d64660 100644
--- a/docs/reference/inv_odd_dyns.html
+++ b/docs/reference/inv_odd_dyns.html
@@ -1,5 +1,5 @@
-Invert odd numbered dynamic scans starting from 1 (1,3,5...). — inv_odd_dyns • Spectroscopy Analysis Tools (spant) Invert odd numbered dynamic scans starting from 1 (1,3,5...). — inv_odd_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/is.def.html b/docs/reference/is.def.html
index f196ffd0..a67b9eba 100644
--- a/docs/reference/is.def.html
+++ b/docs/reference/is.def.html
@@ -1,5 +1,5 @@
-Check if an object is defined, which is the same as being not NULL. — is.def • Spectroscopy Analysis Tools (spant) Check if an object is defined, which is the same as being not NULL. — is.def • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/is_fd.html b/docs/reference/is_fd.html
index 3b0ca165..18a193aa 100644
--- a/docs/reference/is_fd.html
+++ b/docs/reference/is_fd.html
@@ -1,7 +1,5 @@
-Check if the chemical shift dimension of an MRS data object is in the
-frequency domain. — is_fd • Spectroscopy Analysis Tools (spant) Check if the chemical shift dimension of an MRS data object is in the frequency domain. — is_fd • Spectroscopy Analysis Tools (spant) Transform 2D MRSI data from k-space to image space in the x-y direction. — kspace2img_xy • Spectroscopy Analysis Tools (spant) Transform 2D MRSI data from k-space to image space in the x-y direction. — kspace2img_xy • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/l2_reg.html b/docs/reference/l2_reg.html
index 3d781d80..21aa9849 100644
--- a/docs/reference/l2_reg.html
+++ b/docs/reference/l2_reg.html
@@ -1,5 +1,5 @@
-Perform l2 regularisation artefact suppression. — l2_reg • Spectroscopy Analysis Tools (spant) Perform l2 regularisation artefact suppression. — l2_reg • Spectroscopy Analysis Tools (spant) Apply line-broadening (apodisation) to MRS data or basis object. — lb • Spectroscopy Analysis Tools (spant) Apply line-broadening (apodisation) to MRS data or basis object. — lb • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -123,7 +123,7 @@ Value
diff --git a/docs/reference/lofdc.html b/docs/reference/lofdc.html
index 5419b1ec..31347a25 100644
--- a/docs/reference/lofdc.html
+++ b/docs/reference/lofdc.html
@@ -1,5 +1,5 @@
-Correct linear frequency drift. — lofdc • Spectroscopy Analysis Tools (spant) Correct linear frequency drift. — lofdc • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -138,7 +138,7 @@ Value
diff --git a/docs/reference/lw2alpha.html b/docs/reference/lw2alpha.html
index b83db682..25da229b 100644
--- a/docs/reference/lw2alpha.html
+++ b/docs/reference/lw2alpha.html
@@ -1,7 +1,5 @@
-Covert a linewidth in Hz to an equivalent alpha value in the time-domain ie:
-x * exp(-t * alpha). — lw2alpha • Spectroscopy Analysis Tools (spant) Covert a linewidth in Hz to an equivalent alpha value in the time-domain ie: x * exp(-t * alpha). — lw2alpha • Spectroscopy Analysis Tools (spant) Covert a linewidth in Hz to an equivalent beta value in the time-domain ie:
-x * exp(-t * t * beta). — lw2beta • Spectroscopy Analysis Tools (spant) Covert a linewidth in Hz to an equivalent beta value in the time-domain ie: x * exp(-t * t * beta). — lw2beta • Spectroscopy Analysis Tools (spant) Make a basis-set object from a directory containing LCModel formatted RAW
-files. — make_basis_from_raw • Spectroscopy Analysis Tools (spant) Make a basis-set object from a directory containing LCModel formatted RAW files. — make_basis_from_raw • Spectroscopy Analysis Tools (spant) Mask an MRS dataset in the dynamic dimension. — mask_dyns • Spectroscopy Analysis Tools (spant) Mask an MRS dataset in the dynamic dimension. — mask_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/mask_fit_res.html b/docs/reference/mask_fit_res.html
index 97baaa3f..ebd91a99 100644
--- a/docs/reference/mask_fit_res.html
+++ b/docs/reference/mask_fit_res.html
@@ -1,5 +1,5 @@
-Mask fit result spectra depending on a vector of bool values. — mask_fit_res • Spectroscopy Analysis Tools (spant) Mask fit result spectra depending on a vector of bool values. — mask_fit_res • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -116,7 +116,7 @@ Value
diff --git a/docs/reference/mask_xy.html b/docs/reference/mask_xy.html
index 11bb577c..b0d38619 100644
--- a/docs/reference/mask_xy.html
+++ b/docs/reference/mask_xy.html
@@ -1,5 +1,5 @@
-Mask an MRSI dataset in the x-y direction — mask_xy • Spectroscopy Analysis Tools (spant) Mask an MRSI dataset in the x-y direction — mask_xy • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/mask_xy_corners.html b/docs/reference/mask_xy_corners.html
index 09b16cd2..2d13839d 100644
--- a/docs/reference/mask_xy_corners.html
+++ b/docs/reference/mask_xy_corners.html
@@ -1,5 +1,5 @@
-Mask the four corners of an MRSI dataset in the x-y plane. — mask_xy_corners • Spectroscopy Analysis Tools (spant) Mask the four corners of an MRSI dataset in the x-y plane. — mask_xy_corners • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/mask_xy_ellipse.html b/docs/reference/mask_xy_ellipse.html
index 1d8b02e4..e2e749ef 100644
--- a/docs/reference/mask_xy_ellipse.html
+++ b/docs/reference/mask_xy_ellipse.html
@@ -1,7 +1,5 @@
-Mask the voxels outside an elliptical region spanning the MRSI dataset in the
-x-y plane. — mask_xy_ellipse • Spectroscopy Analysis Tools (spant) Mask the voxels outside an elliptical region spanning the MRSI dataset in the x-y plane. — mask_xy_ellipse • Spectroscopy Analysis Tools (spant) Mask a 2D MRSI dataset in the x-y dimension. — mask_xy_mat • Spectroscopy Analysis Tools (spant) Mask a 2D MRSI dataset in the x-y dimension. — mask_xy_mat • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Value
diff --git a/docs/reference/mat2mrs_data.html b/docs/reference/mat2mrs_data.html
index 2e2895f3..ae55665f 100644
--- a/docs/reference/mat2mrs_data.html
+++ b/docs/reference/mat2mrs_data.html
@@ -1,7 +1,5 @@
-Convert a matrix (with spectral points in the column dimension and dynamics
-in the row dimensions) into a mrs_data object. — mat2mrs_data • Spectroscopy Analysis Tools (spant) Convert a matrix (with spectral points in the column dimension and dynamics in the row dimensions) into a mrs_data object. — mat2mrs_data • Spectroscopy Analysis Tools (spant) Matrix exponential function taken from complexplus package to reduce the
-number of spant dependencies. — matexp • Spectroscopy Analysis Tools (spant) Matrix exponential function taken from complexplus package to reduce the number of spant dependencies. — matexp • Spectroscopy Analysis Tools (spant) Apply the max operator to an MRS dataset. — max_mrs • Spectroscopy Analysis Tools (spant) Apply the max operator to an MRS dataset. — max_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/max_mrs_interp.html b/docs/reference/max_mrs_interp.html
index e4474764..52e63f3e 100644
--- a/docs/reference/max_mrs_interp.html
+++ b/docs/reference/max_mrs_interp.html
@@ -1,5 +1,5 @@
-Apply the max operator to an interpolated MRS dataset. — max_mrs_interp • Spectroscopy Analysis Tools (spant) Apply the max operator to an interpolated MRS dataset. — max_mrs_interp • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/mean.list.html b/docs/reference/mean.list.html
index b8eb3463..048306fd 100644
--- a/docs/reference/mean.list.html
+++ b/docs/reference/mean.list.html
@@ -1,5 +1,5 @@
-Calculate the mean spectrum from an mrs_data object. — mean.list • Spectroscopy Analysis Tools (spant) Calculate the mean spectrum from an mrs_data object. — mean.list • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/mean.mrs_data.html b/docs/reference/mean.mrs_data.html
index 5531a28d..79515014 100644
--- a/docs/reference/mean.mrs_data.html
+++ b/docs/reference/mean.mrs_data.html
@@ -1,5 +1,5 @@
-Calculate the mean spectrum from an mrs_data object. — mean.mrs_data • Spectroscopy Analysis Tools (spant) Calculate the mean spectrum from an mrs_data object. — mean.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/mean_dyn_blocks.html b/docs/reference/mean_dyn_blocks.html
index 10467098..4c042448 100644
--- a/docs/reference/mean_dyn_blocks.html
+++ b/docs/reference/mean_dyn_blocks.html
@@ -1,5 +1,5 @@
-Calculate the mean of adjacent dynamic scans. — mean_dyn_blocks • Spectroscopy Analysis Tools (spant) Calculate the mean of adjacent dynamic scans. — mean_dyn_blocks • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/mean_dyn_pairs.html b/docs/reference/mean_dyn_pairs.html
index 63e909ea..1a241126 100644
--- a/docs/reference/mean_dyn_pairs.html
+++ b/docs/reference/mean_dyn_pairs.html
@@ -1,5 +1,5 @@
-Calculate the pairwise means across a dynamic data set. — mean_dyn_pairs • Spectroscopy Analysis Tools (spant) Calculate the pairwise means across a dynamic data set. — mean_dyn_pairs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/mean_dyns.html b/docs/reference/mean_dyns.html
index 73fdbfa7..0daa27df 100644
--- a/docs/reference/mean_dyns.html
+++ b/docs/reference/mean_dyns.html
@@ -1,5 +1,5 @@
-Calculate the mean dynamic data. — mean_dyns • Spectroscopy Analysis Tools (spant) Calculate the mean dynamic data. — mean_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/mean_mrs_list.html b/docs/reference/mean_mrs_list.html
index 808b6c50..10d842c0 100644
--- a/docs/reference/mean_mrs_list.html
+++ b/docs/reference/mean_mrs_list.html
@@ -1,5 +1,5 @@
-Return the mean of a list of mrs_data objects. — mean_mrs_list • Spectroscopy Analysis Tools (spant) Return the mean of a list of mrs_data objects. — mean_mrs_list • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/mean_vec_blocks.html b/docs/reference/mean_vec_blocks.html
index 8fc92eaa..dd78b122 100644
--- a/docs/reference/mean_vec_blocks.html
+++ b/docs/reference/mean_vec_blocks.html
@@ -1,5 +1,5 @@
-Calculate the mean of adjacent blocks in a vector. — mean_vec_blocks • Spectroscopy Analysis Tools (spant) Calculate the mean of adjacent blocks in a vector. — mean_vec_blocks • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/median_dyns.html b/docs/reference/median_dyns.html
index 1039d4b5..9a085b10 100644
--- a/docs/reference/median_dyns.html
+++ b/docs/reference/median_dyns.html
@@ -1,5 +1,5 @@
-Calculate the median dynamic data. — median_dyns • Spectroscopy Analysis Tools (spant) Calculate the median dynamic data. — median_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/mod_td.html b/docs/reference/mod_td.html
index 76ad0a40..141ef09e 100644
--- a/docs/reference/mod_td.html
+++ b/docs/reference/mod_td.html
@@ -1,5 +1,5 @@
-Apply the Modulus operator to the time-domain MRS signal. — mod_td • Spectroscopy Analysis Tools (spant) Apply the Modulus operator to the time-domain MRS signal. — mod_td • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/mrs_data2basis.html b/docs/reference/mrs_data2basis.html
index 62f7d749..11797b91 100644
--- a/docs/reference/mrs_data2basis.html
+++ b/docs/reference/mrs_data2basis.html
@@ -1,7 +1,5 @@
-Convert an mrs_data object to basis object - where basis signals are spread
-across the dynamic dimension in the MRS data. — mrs_data2basis • Spectroscopy Analysis Tools (spant) Convert an mrs_data object to basis object - where basis signals are spread across the dynamic dimension in the MRS data. — mrs_data2basis • Spectroscopy Analysis Tools (spant) Create a BIDS file structure from a vector of MRS data paths or list of mrs_data objects. — mrs_data2bids • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Create a BIDS file structure from a vector of MRS data paths or list of mrs_data objects.
+ Source: R/fmrs.R
+ mrs_data2bids.Rd
+
+
+
+ Create a BIDS file structure from a vector of MRS data paths or list of
+mrs_data objects.
+
+
+
+ mrs_data2bids(
+ mrs_data,
+ output_dir,
+ suffix = NULL,
+ sub = NULL,
+ ses = NULL,
+ task = NULL,
+ acq = NULL,
+ nuc = NULL,
+ voi = NULL,
+ rec = NULL,
+ run = NULL,
+ echo = NULL,
+ inv = NULL,
+ skip_existing = TRUE
+)
+
+
+
+ Arguments
+ - mrs_data
+vector of MRS data paths or list of mrs_data objects.
- output_dir
+the base directory to create the BIDS structure.
- suffix
+optional vector of file suffixes. Default behaviour is to
+automatically determine these from the input data, however it is recommended
+that they are specified to allow more efficient skipping of existing data.
- sub
+optional vector of subject labels. If not specified, these will be
+automatically generated as a series of increasing zero-padded integer values
+corresponding to the mrs_data input indices.
- ses
+optional vector of session labels.
- task
+optional vector of task labels.
- acq
+optional vector of acquisition labels.
- nuc
+optional vector of nucleus labels.
- voi
+optional vector of volume of interest labels.
- rec
+optional vector of reconstruction labels.
- run
+optional vector of run indices.
- echo
+optional vector of echo time indices.
- inv
+optional vector of inversion indices.
- skip_existing
+skip any data files that have already been converted.
+Defaults to TRUE, set to FALSE to force an overwrite of any existing data
+files.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/mrs_data2mat.html b/docs/reference/mrs_data2mat.html
index cf5ff28c..9e47688a 100644
--- a/docs/reference/mrs_data2mat.html
+++ b/docs/reference/mrs_data2mat.html
@@ -1,7 +1,5 @@
-Convert mrs_data object to a matrix, with spectral points in the column
-dimension and dynamics in the row dimension. — mrs_data2mat • Spectroscopy Analysis Tools (spant) Convert mrs_data object to a matrix, with spectral points in the column dimension and dynamics in the row dimension. — mrs_data2mat • Spectroscopy Analysis Tools (spant) Convert mrs_data object to a matrix, with spectral points in the column dimension and dynamics in the row dimension. — mrs_data2spec_mat • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Convert mrs_data object to a matrix, with spectral points in the column dimension and dynamics in the row dimension.
+ Source: R/mrs_data_proc.R
+ mrs_data2spec_mat.Rd
+
+
+
+ Convert mrs_data object to a matrix, with spectral points in the column
+dimension and dynamics in the row dimension.
+
+
+
+ mrs_data2spec_mat(mrs_data, collapse = TRUE)
+
+
+
+ Arguments
+ - mrs_data
+MRS data object or list of MRS data objects.
- collapse
+collapse all other dimensions along the dynamic dimension, eg
+a 16x16 MRSI grid would be first collapsed across 256 dynamic scans.
+
+ Value
+
+
+MRS data matrix.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/mrs_data2vec.html b/docs/reference/mrs_data2vec.html
index fb172d68..a1fd654d 100644
--- a/docs/reference/mrs_data2vec.html
+++ b/docs/reference/mrs_data2vec.html
@@ -1,5 +1,5 @@
-Convert mrs_data object to a vector. — mrs_data2vec • Spectroscopy Analysis Tools (spant) Convert mrs_data object to a vector. — mrs_data2vec • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -126,7 +126,7 @@ Value
diff --git a/docs/reference/mvfftshift.html b/docs/reference/mvfftshift.html
index 92b0841b..976b3410 100644
--- a/docs/reference/mvfftshift.html
+++ b/docs/reference/mvfftshift.html
@@ -1,7 +1,5 @@
-Perform a fftshift on a matrix, with each column replaced by its shifted
-result. — mvfftshift • Spectroscopy Analysis Tools (spant) Perform a fftshift on a matrix, with each column replaced by its shifted result. — mvfftshift • Spectroscopy Analysis Tools (spant) Perform an ifftshift on a matrix, with each column replaced by its shifted
-result. — mvifftshift • Spectroscopy Analysis Tools (spant) Perform an ifftshift on a matrix, with each column replaced by its shifted result. — mvifftshift • Spectroscopy Analysis Tools (spant) Print fit coordinates from a single index. — n2coord • Spectroscopy Analysis Tools (spant) Print fit coordinates from a single index. — n2coord • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/nifti_flip_lr.html b/docs/reference/nifti_flip_lr.html
index 730abe3c..19860b3c 100644
--- a/docs/reference/nifti_flip_lr.html
+++ b/docs/reference/nifti_flip_lr.html
@@ -1,9 +1,5 @@
-Flip the x data dimension order of a nifti image. This corresponds to
-flipping MRI data in the left-right direction, assuming the data in save in
-neurological format (can check with fslorient program). — nifti_flip_lr • Spectroscopy Analysis Tools (spant) Flip the x data dimension order of a nifti image. This corresponds to flipping MRI data in the left-right direction, assuming the data in save in neurological format (can check with fslorient program). — nifti_flip_lr • Spectroscopy Analysis Tools (spant) Export a one-page pdf of a single fit result — one_page_pdf • Spectroscopy Analysis Tools (spant) Export a one-page pdf of a single fit result — one_page_pdf • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -108,7 +108,7 @@ Arguments
diff --git a/docs/reference/ortho3.html b/docs/reference/ortho3.html
index 13ade97d..5d7dd2fd 100644
--- a/docs/reference/ortho3.html
+++ b/docs/reference/ortho3.html
@@ -1,5 +1,5 @@
-Display an orthographic projection plot of a nifti object. — ortho3 • Spectroscopy Analysis Tools (spant) Display an orthographic projection plot of a nifti object. — ortho3 • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -172,7 +172,7 @@ Arguments
diff --git a/docs/reference/ortho3_inter.html b/docs/reference/ortho3_inter.html
index 090cc5e5..15948899 100644
--- a/docs/reference/ortho3_inter.html
+++ b/docs/reference/ortho3_inter.html
@@ -1,5 +1,5 @@
-Display an interactive orthographic projection plot of a nifti object. — ortho3_inter • Spectroscopy Analysis Tools (spant) Display an interactive orthographic projection plot of a nifti object. — ortho3_inter • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -132,7 +132,7 @@ Arguments
diff --git a/docs/reference/peak_info.html b/docs/reference/peak_info.html
index 09058bd8..41c8ffaf 100644
--- a/docs/reference/peak_info.html
+++ b/docs/reference/peak_info.html
@@ -1,7 +1,5 @@
-Search for the highest peak in a spectral region and return the frequency,
-height and FWHM. — peak_info • Spectroscopy Analysis Tools (spant) Search for the highest peak in a spectral region and return the frequency, height and FWHM. — peak_info • Spectroscopy Analysis Tools (spant) Papoulis-Gerchberg (PG) algorithm method for k-space extrapolation. — pg_extrap_xy • Spectroscopy Analysis Tools (spant) Papoulis-Gerchberg (PG) algorithm method for k-space extrapolation. — pg_extrap_xy • Spectroscopy Analysis Tools (spant) Apply phasing parameters to MRS data. — phase • Spectroscopy Analysis Tools (spant) Apply phasing parameters to MRS data. — phase • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/phase_ref_1h_brain.html b/docs/reference/phase_ref_1h_brain.html
new file mode 100644
index 00000000..8707a74a
--- /dev/null
+++ b/docs/reference/phase_ref_1h_brain.html
@@ -0,0 +1,131 @@
+
+Corrected zero order phase and chemical shift offset in 1H MRS data from the brain. — phase_ref_1h_brain • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Corrected zero order phase and chemical shift offset in 1H MRS data from the brain.
+ Source: R/rats.R
+ phase_ref_1h_brain.Rd
+
+
+
+ Corrected zero order phase and chemical shift offset in 1H MRS data from the
+brain.
+
+
+
+ phase_ref_1h_brain(mrs_data, mean_ref = FALSE, ret_corr_only = TRUE)
+
+
+
+ Arguments
+ - mrs_data
+MRS data to be corrected.
- mean_ref
+apply the phase and offset of the mean spectrum to all
+others. Default is FALSE.
- ret_corr_only
+return the corrected data only.
+
+ Value
+
+
+corrected MRS data.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/plot.fit_result.html b/docs/reference/plot.fit_result.html
index e54d3bc1..836a53ee 100644
--- a/docs/reference/plot.fit_result.html
+++ b/docs/reference/plot.fit_result.html
@@ -1,5 +1,5 @@
-Plot the fitting results of an object of class fit_result. — plot.fit_result • Spectroscopy Analysis Tools (spant) Plot the fitting results of an object of class fit_result. — plot.fit_result • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -207,7 +207,7 @@ Arguments
diff --git a/docs/reference/plot.mrs_data.html b/docs/reference/plot.mrs_data.html
index fabcc35b..bb2ec651 100644
--- a/docs/reference/plot.mrs_data.html
+++ b/docs/reference/plot.mrs_data.html
@@ -1,5 +1,5 @@
-Plotting method for objects of class mrs_data. — plot.mrs_data • Spectroscopy Analysis Tools (spant) Plotting method for objects of class mrs_data. — plot.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -287,7 +287,7 @@ Arguments
diff --git a/docs/reference/plot_bc.html b/docs/reference/plot_bc.html
index 4f8309b4..b48142cc 100644
--- a/docs/reference/plot_bc.html
+++ b/docs/reference/plot_bc.html
@@ -1,5 +1,5 @@
-Convenience function to plot a baseline estimate with the original data. — plot_bc • Spectroscopy Analysis Tools (spant) Convenience function to plot a baseline estimate with the original data. — plot_bc • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -108,7 +108,7 @@ Arguments
diff --git a/docs/reference/plot_reg.html b/docs/reference/plot_reg.html
index ae1acbe7..2addb2f6 100644
--- a/docs/reference/plot_reg.html
+++ b/docs/reference/plot_reg.html
@@ -1,5 +1,5 @@
-Plot regressors as an image. — plot_reg • Spectroscopy Analysis Tools (spant) Plot regressors as an image. — plot_reg • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/plot_slice_fit.html b/docs/reference/plot_slice_fit.html
index fbc7b560..57f1af8a 100644
--- a/docs/reference/plot_slice_fit.html
+++ b/docs/reference/plot_slice_fit.html
@@ -1,5 +1,5 @@
-Plot a 2D slice from an MRSI fit result object. — plot_slice_fit • Spectroscopy Analysis Tools (spant) Plot a 2D slice from an MRSI fit result object. — plot_slice_fit • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -129,7 +129,7 @@ Arguments
diff --git a/docs/reference/plot_slice_fit_inter.html b/docs/reference/plot_slice_fit_inter.html
index 4eed104a..da105a7d 100644
--- a/docs/reference/plot_slice_fit_inter.html
+++ b/docs/reference/plot_slice_fit_inter.html
@@ -1,5 +1,5 @@
-Plot a 2D slice from an MRSI fit result object. — plot_slice_fit_inter • Spectroscopy Analysis Tools (spant) Plot a 2D slice from an MRSI fit result object. — plot_slice_fit_inter • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -134,7 +134,7 @@ Arguments
diff --git a/docs/reference/plot_slice_map.html b/docs/reference/plot_slice_map.html
index 553e9ac8..ffb2a134 100644
--- a/docs/reference/plot_slice_map.html
+++ b/docs/reference/plot_slice_map.html
@@ -1,5 +1,5 @@
-Plot a slice from a 7 dimensional array. — plot_slice_map • Spectroscopy Analysis Tools (spant) Plot a slice from a 7 dimensional array. — plot_slice_map • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -153,7 +153,7 @@ Arguments
diff --git a/docs/reference/plot_slice_map_inter.html b/docs/reference/plot_slice_map_inter.html
index 40d33b42..90968f66 100644
--- a/docs/reference/plot_slice_map_inter.html
+++ b/docs/reference/plot_slice_map_inter.html
@@ -1,7 +1,5 @@
-Plot an interactive slice map from a data array where voxels can be selected
-to display a corresponding spectrum. — plot_slice_map_inter • Spectroscopy Analysis Tools (spant) Plot an interactive slice map from a data array where voxels can be selected to display a corresponding spectrum. — plot_slice_map_inter • Spectroscopy Analysis Tools (spant) Plot the spectral standard deviation. — plot_spec_sd • Spectroscopy Analysis Tools (spant) Plot the spectral standard deviation. — plot_spec_sd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Arguments
diff --git a/docs/reference/plot_voi_overlay.html b/docs/reference/plot_voi_overlay.html
index 9a782e88..bbbbf35e 100644
--- a/docs/reference/plot_voi_overlay.html
+++ b/docs/reference/plot_voi_overlay.html
@@ -1,5 +1,5 @@
-Plot a volume as an image overlay. — plot_voi_overlay • Spectroscopy Analysis Tools (spant) Plot a volume as an image overlay. — plot_voi_overlay • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -116,7 +116,7 @@ Arguments
diff --git a/docs/reference/plot_voi_overlay_seg.html b/docs/reference/plot_voi_overlay_seg.html
index 3d4e74ff..0e800ff2 100644
--- a/docs/reference/plot_voi_overlay_seg.html
+++ b/docs/reference/plot_voi_overlay_seg.html
@@ -1,5 +1,5 @@
-Plot a volume as an overlay on a segmented brain volume. — plot_voi_overlay_seg • Spectroscopy Analysis Tools (spant) Plot a volume as an overlay on a segmented brain volume. — plot_voi_overlay_seg • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Arguments
diff --git a/docs/reference/ppm.html b/docs/reference/ppm.html
index c352327a..ee4696e2 100644
--- a/docs/reference/ppm.html
+++ b/docs/reference/ppm.html
@@ -1,5 +1,5 @@
-Return the ppm scale of an MRS dataset or fit result. — ppm • Spectroscopy Analysis Tools (spant) Return the ppm scale of an MRS dataset or fit result. — ppm • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -132,7 +132,7 @@ Value
diff --git a/docs/reference/precomp.html b/docs/reference/precomp.html
index 822d7336..df3d2c6c 100644
--- a/docs/reference/precomp.html
+++ b/docs/reference/precomp.html
@@ -1,7 +1,5 @@
-Save function results to file and load on subsequent calls to avoid repeat
-computation. — precomp • Spectroscopy Analysis Tools (spant) Save function results to file and load on subsequent calls to avoid repeat computation. — precomp • Spectroscopy Analysis Tools (spant) Preprocess and perform quality assessment of a single SVS data set. — preproc_svs • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Preprocess and perform quality assessment of a single SVS data set.
+ Source: R/fmrs.R
+ preproc_svs.Rd
+
+
+
+ Preprocess and perform quality assessment of a single SVS data set.
+
+
+
+ preproc_svs(path, label = NULL, output_dir = NULL, ref_inds = NULL)
+
+
+
+ Arguments
+ - path
+path to the fMRS data file or IMA directory.
- label
+a label to describe the data set.
- output_dir
+output directory.
- ref_inds
+a vector of 1-based indices for any water reference dynamic
+scans.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/preproc_svs_dataset.html b/docs/reference/preproc_svs_dataset.html
new file mode 100644
index 00000000..07c3a29b
--- /dev/null
+++ b/docs/reference/preproc_svs_dataset.html
@@ -0,0 +1,148 @@
+
+Preprocess and perform quality assessment of one or more SVS data sets. — preproc_svs_dataset • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Preprocess and perform quality assessment of one or more SVS data sets.
+ Source: R/fmrs.R
+ preproc_svs_dataset.Rd
+
+
+
+ Preprocess and perform quality assessment of one or more SVS data sets.
+
+
+
+ preproc_svs_dataset(
+ paths,
+ labels = NULL,
+ output_dir = "spant_analysis",
+ exclude_labels = NULL,
+ overwrite = FALSE,
+ ref_inds = NULL,
+ return_results = FALSE
+)
+
+
+
+ Arguments
+ - paths
+paths to the fMRS data file or IMA directory.
- labels
+labels to describe each data set.
- output_dir
+output directory.
- exclude_labels
+vector of labels of scans to exclude, eg poor quality
+data.
- overwrite
+overwrite saved results, defaults to FALSE.
- ref_inds
+a vector of 1-based indices for any water reference dynamic
+scans.
- return_results
+function will return key outputs, defaults to FALSE.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/print.fit_result.html b/docs/reference/print.fit_result.html
index 297f28dc..5f434e57 100644
--- a/docs/reference/print.fit_result.html
+++ b/docs/reference/print.fit_result.html
@@ -1,5 +1,5 @@
-Print a summary of an object of class fit_result. — print.fit_result • Spectroscopy Analysis Tools (spant) Print a summary of an object of class fit_result. — print.fit_result • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -105,7 +105,7 @@ Arguments
diff --git a/docs/reference/print.mrs_data.html b/docs/reference/print.mrs_data.html
index 51199017..e1561eb2 100644
--- a/docs/reference/print.mrs_data.html
+++ b/docs/reference/print.mrs_data.html
@@ -1,5 +1,5 @@
-Print a summary of mrs_data parameters. — print.mrs_data • Spectroscopy Analysis Tools (spant) Print a summary of mrs_data parameters. — print.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -109,7 +109,7 @@ Arguments
diff --git a/docs/reference/qn_states.html b/docs/reference/qn_states.html
index 0f42f2f9..d7aa6715 100644
--- a/docs/reference/qn_states.html
+++ b/docs/reference/qn_states.html
@@ -1,5 +1,5 @@
-Get the quantum coherence matrix for a spin system. — qn_states • Spectroscopy Analysis Tools (spant) Get the quantum coherence matrix for a spin system. — qn_states • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/rats.html b/docs/reference/rats.html
index 5a39a396..93585e08 100644
--- a/docs/reference/rats.html
+++ b/docs/reference/rats.html
@@ -1,5 +1,5 @@
-Robust Alignment to a Target Spectrum (RATS). — rats • Spectroscopy Analysis Tools (spant) Robust Alignment to a Target Spectrum (RATS). — rats • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -207,7 +207,7 @@ Value
diff --git a/docs/reference/re_weighting.html b/docs/reference/re_weighting.html
index d21caf21..8b0b070a 100644
--- a/docs/reference/re_weighting.html
+++ b/docs/reference/re_weighting.html
@@ -1,5 +1,5 @@
-Apply a weighting to the FID to enhance spectral resolution. — re_weighting • Spectroscopy Analysis Tools (spant) Apply a weighting to the FID to enhance spectral resolution. — re_weighting • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/read_basis.html b/docs/reference/read_basis.html
index da9b94af..eb6f8557 100644
--- a/docs/reference/read_basis.html
+++ b/docs/reference/read_basis.html
@@ -1,5 +1,5 @@
-Read a basis file in LCModel .basis format. — read_basis • Spectroscopy Analysis Tools (spant) Read a basis file in LCModel .basis format. — read_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/read_ima_coil_dir.html b/docs/reference/read_ima_coil_dir.html
index 28c02de0..4f073cd8 100644
--- a/docs/reference/read_ima_coil_dir.html
+++ b/docs/reference/read_ima_coil_dir.html
@@ -1,9 +1,5 @@
-Read a directory containing Siemens MRS IMA files and combine along the coil
-dimension. Note that the coil ID is inferred from the sorted file name and
-should be checked when consistency is required between two directories. — read_ima_coil_dir • Spectroscopy Analysis Tools (spant) Read a directory containing Siemens MRS IMA files and combine along the coil dimension. Note that the coil ID is inferred from the sorted file name and should be checked when consistency is required between two directories. — read_ima_coil_dir • Spectroscopy Analysis Tools (spant) Read a directory containing Siemens MRS IMA files and combine along the
-dynamic dimension. Note that the coil ID is inferred from the sorted file
-name and should be checked when consistency is required. — read_ima_dyn_dir • Spectroscopy Analysis Tools (spant) Read a directory containing Siemens MRS IMA files and combine along the dynamic dimension. Note that the coil ID is inferred from the sorted file name and should be checked when consistency is required. — read_ima_dyn_dir • Spectroscopy Analysis Tools (spant) Read an LCModel formatted coord file containing fit information. — read_lcm_coord • Spectroscopy Analysis Tools (spant) Read an LCModel formatted coord file containing fit information. — read_lcm_coord • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -107,7 +107,7 @@ Value
diff --git a/docs/reference/read_mrs.html b/docs/reference/read_mrs.html
index 3ac2a36b..2cf36b20 100644
--- a/docs/reference/read_mrs.html
+++ b/docs/reference/read_mrs.html
@@ -1,5 +1,5 @@
-Read MRS data from a file. — read_mrs • Spectroscopy Analysis Tools (spant) Read MRS data from a file. — read_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -88,7 +88,8 @@ Read MRS data from a file.
full_fid = FALSE,
omit_svs_ref_scans = TRUE,
verbose = FALSE,
- extra = NULL
+ extra = NULL,
+ fid_filt_dist = NULL
)
@@ -140,6 +141,13 @@ Arguments
an optional data frame to provide additional variables for use
in subsequent analysis steps, eg id or grouping variables.
fid_filt_dist
+indicate if the data has a distorted FID due to a
+brick-wall filter being used to downsample the data. Default is to auto
+detect this from the data, but TRUE or FALSE options can be given to override
+detection.
Value
@@ -183,7 +191,7 @@ Examples
diff --git a/docs/reference/read_mrs_tqn.html b/docs/reference/read_mrs_tqn.html
index 5766362f..84bdaf3a 100644
--- a/docs/reference/read_mrs_tqn.html
+++ b/docs/reference/read_mrs_tqn.html
@@ -1,5 +1,5 @@
-Read MRS data using the TARQUIN software package. — read_mrs_tqn • Spectroscopy Analysis Tools (spant) Read MRS data using the TARQUIN software package. — read_mrs_tqn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -131,7 +131,7 @@ Examples
diff --git a/docs/reference/read_pulse_ascii.html b/docs/reference/read_pulse_ascii.html
index c9e0d43c..ab11c9cc 100644
--- a/docs/reference/read_pulse_ascii.html
+++ b/docs/reference/read_pulse_ascii.html
@@ -1,5 +1,5 @@
-Read an ASCII formatted pulse file. — read_pulse_ascii • Spectroscopy Analysis Tools (spant) Read an ASCII formatted pulse file. — read_pulse_ascii • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/read_pulse_bruker.html b/docs/reference/read_pulse_bruker.html
index c92bf76a..dbe9073b 100644
--- a/docs/reference/read_pulse_bruker.html
+++ b/docs/reference/read_pulse_bruker.html
@@ -1,5 +1,5 @@
-Read a Bruker formatted pulse file — read_pulse_bruker • Spectroscopy Analysis Tools (spant) Read a Bruker formatted pulse file — read_pulse_bruker • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/read_pulse_pta.html b/docs/reference/read_pulse_pta.html
index 72e1b6d4..a0fac3c3 100644
--- a/docs/reference/read_pulse_pta.html
+++ b/docs/reference/read_pulse_pta.html
@@ -1,5 +1,5 @@
-Read a .pta formatted pulse file compatible with Siemens PulseTool. — read_pulse_pta • Spectroscopy Analysis Tools (spant) Read a .pta formatted pulse file compatible with Siemens PulseTool. — read_pulse_pta • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/read_siemens_txt_hdr.html b/docs/reference/read_siemens_txt_hdr.html
index 23fb8c70..3a17d87c 100644
--- a/docs/reference/read_siemens_txt_hdr.html
+++ b/docs/reference/read_siemens_txt_hdr.html
@@ -1,5 +1,5 @@
-Read the text format header found in Siemens IMA and TWIX data files. — read_siemens_txt_hdr • Spectroscopy Analysis Tools (spant) Read the text format header found in Siemens IMA and TWIX data files. — read_siemens_txt_hdr • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -78,7 +78,7 @@ Read the text format header found in Siemens IMA and TWIX data files.
- read_siemens_txt_hdr(input, version = "vd", verbose, offset = 0)
+ read_siemens_txt_hdr(input, version = "vd", verbose = FALSE, offset = 0)
@@ -118,7 +118,7 @@ Value
diff --git a/docs/reference/read_tqn_fit.html b/docs/reference/read_tqn_fit.html
index 4da6c25e..a1630420 100644
--- a/docs/reference/read_tqn_fit.html
+++ b/docs/reference/read_tqn_fit.html
@@ -1,5 +1,5 @@
-Reader for csv fit results generated by TARQUIN. — read_tqn_fit • Spectroscopy Analysis Tools (spant) Reader for csv fit results generated by TARQUIN. — read_tqn_fit • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -113,7 +113,7 @@ Examples
diff --git a/docs/reference/read_tqn_result.html b/docs/reference/read_tqn_result.html
index 36659714..68a3e98c 100644
--- a/docs/reference/read_tqn_result.html
+++ b/docs/reference/read_tqn_result.html
@@ -1,5 +1,5 @@
-Reader for csv results generated by TARQUIN. — read_tqn_result • Spectroscopy Analysis Tools (spant) Reader for csv results generated by TARQUIN. — read_tqn_result • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -117,7 +117,7 @@ Examples
diff --git a/docs/reference/recon_imag.html b/docs/reference/recon_imag.html
index d2a72225..5bc3b1eb 100644
--- a/docs/reference/recon_imag.html
+++ b/docs/reference/recon_imag.html
@@ -1,7 +1,5 @@
-Reconstruct complex time-domain data from the real part of frequency-domain
-data. — recon_imag • Spectroscopy Analysis Tools (spant) Reconstruct complex time-domain data from the real part of frequency-domain data. — recon_imag • Spectroscopy Analysis Tools (spant) Reconstruct complex time-domain data from the real part of frequency-domain
-data. — recon_imag_vec • Spectroscopy Analysis Tools (spant) Reconstruct complex time-domain data from the real part of frequency-domain data. — recon_imag_vec • Spectroscopy Analysis Tools (spant) Reconstruct 2D MRSI data from a twix file loaded with read_mrs. — recon_twix_2d_mrsi • Spectroscopy Analysis Tools (spant) Reconstruct 2D MRSI data from a twix file loaded with read_mrs. — recon_twix_2d_mrsi • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/rectangular_mask.html b/docs/reference/rectangular_mask.html
index a2117283..6e469bc9 100644
--- a/docs/reference/rectangular_mask.html
+++ b/docs/reference/rectangular_mask.html
@@ -1,5 +1,5 @@
-Create a rectangular mask stored as a matrix of logical values. — rectangular_mask • Spectroscopy Analysis Tools (spant) Create a rectangular mask stored as a matrix of logical values. — rectangular_mask • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -130,7 +130,7 @@ Value
diff --git a/docs/reference/reexports.html b/docs/reference/reexports.html
index 694a75d1..a59e8379 100644
--- a/docs/reference/reexports.html
+++ b/docs/reference/reexports.html
@@ -1,5 +1,5 @@
-Objects exported from other packages — reexports • Spectroscopy Analysis Tools (spant) Objects exported from other packages — reexports • Spectroscopy Analysis Tools (spant)
Spectroscopy Analysis Tools (spant)
- 2.21.0
+ 2.22.0
@@ -103,7 +103,7 @@ Objects exported from other packages
diff --git a/docs/reference/rep_array_dim.html b/docs/reference/rep_array_dim.html
index b9c49b4a..48c0a5ed 100644
--- a/docs/reference/rep_array_dim.html
+++ b/docs/reference/rep_array_dim.html
@@ -1,5 +1,5 @@
-Repeat an array over a given dimension. — rep_array_dim • Spectroscopy Analysis Tools (spant) Repeat an array over a given dimension. — rep_array_dim • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/rep_dyn.html b/docs/reference/rep_dyn.html
index 6bbfb0ef..89a4bb9b 100644
--- a/docs/reference/rep_dyn.html
+++ b/docs/reference/rep_dyn.html
@@ -1,5 +1,5 @@
-Replicate a scan in the dynamic dimension. — rep_dyn • Spectroscopy Analysis Tools (spant) Replicate a scan in the dynamic dimension. — rep_dyn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/rep_mrs.html b/docs/reference/rep_mrs.html
index 67730b5c..becb8f00 100644
--- a/docs/reference/rep_mrs.html
+++ b/docs/reference/rep_mrs.html
@@ -1,5 +1,5 @@
-Replicate a scan over a given dimension. — rep_mrs • Spectroscopy Analysis Tools (spant) Replicate a scan over a given dimension. — rep_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -138,7 +138,7 @@ Value
diff --git a/docs/reference/resample_basis.html b/docs/reference/resample_basis.html
index b0f2ab17..c7a6222a 100644
--- a/docs/reference/resample_basis.html
+++ b/docs/reference/resample_basis.html
@@ -1,5 +1,5 @@
-Resample a basis-set to match a mrs_data acquisition. — resample_basis • Spectroscopy Analysis Tools (spant) Resample a basis-set to match a mrs_data acquisition. — resample_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -116,7 +116,7 @@ Value
diff --git a/docs/reference/resample_img.html b/docs/reference/resample_img.html
index f1e7beaf..b0cc8f71 100644
--- a/docs/reference/resample_img.html
+++ b/docs/reference/resample_img.html
@@ -1,5 +1,5 @@
-Resample an image to match a target image space. — resample_img • Spectroscopy Analysis Tools (spant) Resample an image to match a target image space. — resample_img • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/resample_voi.html b/docs/reference/resample_voi.html
index 8fbfa836..a29ab096 100644
--- a/docs/reference/resample_voi.html
+++ b/docs/reference/resample_voi.html
@@ -1,7 +1,5 @@
-Resample a VOI to match a target image space using nearest-neighbour
-interpolation. — resample_voi • Spectroscopy Analysis Tools (spant) Resample a VOI to match a target image space using nearest-neighbour interpolation. — resample_voi • Spectroscopy Analysis Tools (spant) Reslice a nifti object to match the orientation of mrs data. — reslice_to_mrs • Spectroscopy Analysis Tools (spant) Reslice a nifti object to match the orientation of mrs data. — reslice_to_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/reson_table2mrs_data.html b/docs/reference/reson_table2mrs_data.html
index d75579ee..c5a2167a 100644
--- a/docs/reference/reson_table2mrs_data.html
+++ b/docs/reference/reson_table2mrs_data.html
@@ -1,5 +1,5 @@
-Generate mrs_data from a table of single Lorentzian resonances. — reson_table2mrs_data • Spectroscopy Analysis Tools (spant) Generate mrs_data from a table of single Lorentzian resonances. — reson_table2mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -119,7 +119,7 @@ Value
diff --git a/docs/reference/rm_dyns.html b/docs/reference/rm_dyns.html
index 5d5ef692..573e1f51 100644
--- a/docs/reference/rm_dyns.html
+++ b/docs/reference/rm_dyns.html
@@ -1,5 +1,5 @@
-Remove a subset of dynamic scans. — rm_dyns • Spectroscopy Analysis Tools (spant) Remove a subset of dynamic scans. — rm_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/scale_amp_molal.html b/docs/reference/scale_amp_molal.html
index aaeee1f2..7acb8cb0 100644
--- a/docs/reference/scale_amp_molal.html
+++ b/docs/reference/scale_amp_molal.html
@@ -1,7 +1,5 @@
-Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water). — scale_amp_molal • Spectroscopy Analysis Tools (spant) Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / kg of tissue water). — scale_amp_molal • Spectroscopy Analysis Tools (spant)
Spectroscopy Analysis Tools (spant)
- 2.21.0
+ 2.22.0
@@ -76,8 +74,7 @@
- Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water).
+ Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / kg of tissue water).
Source: R/amp_scaling.R
scale_amp_molal.Rd
@@ -163,7 +160,7 @@ Value
diff --git a/docs/reference/scale_amp_molal_pvc.html b/docs/reference/scale_amp_molal_pvc.html
index 962d6afc..4d194abd 100644
--- a/docs/reference/scale_amp_molal_pvc.html
+++ b/docs/reference/scale_amp_molal_pvc.html
@@ -1,7 +1,5 @@
-Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water). — scale_amp_molal_pvc • Spectroscopy Analysis Tools (spant)
@@ -75,8 +73,7 @@
- Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water).
+ Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / kg of tissue water).
Source: R/amp_scaling.R
scale_amp_molal_pvc.Rd
@@ -141,7 +138,7 @@ Value
diff --git a/docs/reference/scale_amp_molar.html b/docs/reference/scale_amp_molar.html
index 02358d91..dc87a338 100644
--- a/docs/reference/scale_amp_molar.html
+++ b/docs/reference/scale_amp_molar.html
@@ -1,7 +1,5 @@
-Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / Litre of tissue). — scale_amp_molar • Spectroscopy Analysis Tools (spant) Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / Litre of tissue). — scale_amp_molar • Spectroscopy Analysis Tools (spant) Convert default LCM/TARQUIN concentration scaling to molal units with partial
-volume correction. — scale_amp_molar2molal_pvc • Spectroscopy Analysis Tools (spant) Convert default LCM/TARQUIN concentration scaling to molal units with partial volume correction. — scale_amp_molar2molal_pvc • Spectroscopy Analysis Tools (spant) Scale fitted amplitudes to a ratio of signal amplitude. — scale_amp_ratio • Spectroscopy Analysis Tools (spant) Scale fitted amplitudes to a ratio of signal amplitude. — scale_amp_ratio • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -116,7 +116,7 @@ Value
diff --git a/docs/reference/scale_amp_ratio_value.html b/docs/reference/scale_amp_ratio_value.html
index 2036837a..6af8ac51 100644
--- a/docs/reference/scale_amp_ratio_value.html
+++ b/docs/reference/scale_amp_ratio_value.html
@@ -1,5 +1,5 @@
-Scale fitted amplitudes to a ratio of signal amplitude. — scale_amp_ratio_value • Spectroscopy Analysis Tools (spant) Scale fitted amplitudes to a ratio of signal amplitude. — scale_amp_ratio_value • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/scale_amp_water_ratio.html b/docs/reference/scale_amp_water_ratio.html
index 5b25e884..35a76b00 100644
--- a/docs/reference/scale_amp_water_ratio.html
+++ b/docs/reference/scale_amp_water_ratio.html
@@ -1,5 +1,5 @@
-Scale metabolite amplitudes as a ratio to the unsuppressed water amplitude. — scale_amp_water_ratio • Spectroscopy Analysis Tools (spant) Scale metabolite amplitudes as a ratio to the unsuppressed water amplitude. — scale_amp_water_ratio • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/scale_basis_amp.html b/docs/reference/scale_basis_amp.html
index 9401c3f1..5a58b5e5 100644
--- a/docs/reference/scale_basis_amp.html
+++ b/docs/reference/scale_basis_amp.html
@@ -1,5 +1,5 @@
-Scale a basis object by a scalar. — scale_basis_amp • Spectroscopy Analysis Tools (spant) Scale a basis object by a scalar. — scale_basis_amp • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/scale_basis_from_singlet.html b/docs/reference/scale_basis_from_singlet.html
index 0d542bc8..c9a19e77 100644
--- a/docs/reference/scale_basis_from_singlet.html
+++ b/docs/reference/scale_basis_from_singlet.html
@@ -1,5 +1,5 @@
-Scale a basis-set to be consistent with spant assumptions for water scaling. — scale_basis_from_singlet • Spectroscopy Analysis Tools (spant) Scale a basis-set to be consistent with spant assumptions for water scaling. — scale_basis_from_singlet • Spectroscopy Analysis Tools (spant)
Spectroscopy Analysis Tools (spant)
- 2.21.0
+ 2.22.0
@@ -127,7 +127,7 @@ Value
diff --git a/docs/reference/scale_mrs_amp.html b/docs/reference/scale_mrs_amp.html
index b5501a0d..990f058a 100644
--- a/docs/reference/scale_mrs_amp.html
+++ b/docs/reference/scale_mrs_amp.html
@@ -1,5 +1,5 @@
-Scale an mrs_data object by a scalar or vector or amplitudes. — scale_mrs_amp • Spectroscopy Analysis Tools (spant) Scale an mrs_data object by a scalar or vector or amplitudes. — scale_mrs_amp • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/scale_spec.html b/docs/reference/scale_spec.html
index 4f6ea835..6b3ddba4 100644
--- a/docs/reference/scale_spec.html
+++ b/docs/reference/scale_spec.html
@@ -1,5 +1,5 @@
-Scale mrs_data to a spectral region. — scale_spec • Spectroscopy Analysis Tools (spant) Scale mrs_data to a spectral region. — scale_spec • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -141,7 +141,7 @@ Value
diff --git a/docs/reference/sd.html b/docs/reference/sd.html
index ea1eec9f..3ae4dfd4 100644
--- a/docs/reference/sd.html
+++ b/docs/reference/sd.html
@@ -1,5 +1,5 @@
-Calculate the standard deviation spectrum from an mrs_data object. — sd • Spectroscopy Analysis Tools (spant) Calculate the standard deviation spectrum from an mrs_data object. — sd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/sd.mrs_data.html b/docs/reference/sd.mrs_data.html
index 3f92a49f..13bdda85 100644
--- a/docs/reference/sd.mrs_data.html
+++ b/docs/reference/sd.mrs_data.html
@@ -1,5 +1,5 @@
-Calculate the standard deviation spectrum from an mrs_data object. — sd.mrs_data • Spectroscopy Analysis Tools (spant) Calculate the standard deviation spectrum from an mrs_data object. — sd.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/seconds.html b/docs/reference/seconds.html
index b34d6627..467ee17f 100644
--- a/docs/reference/seconds.html
+++ b/docs/reference/seconds.html
@@ -1,5 +1,5 @@
-Return a time scale vector to match the FID of an MRS data object. — seconds • Spectroscopy Analysis Tools (spant) Return a time scale vector to match the FID of an MRS data object. — seconds • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/seq_cpmg_ideal.html b/docs/reference/seq_cpmg_ideal.html
index 547e96ab..45727c86 100644
--- a/docs/reference/seq_cpmg_ideal.html
+++ b/docs/reference/seq_cpmg_ideal.html
@@ -1,5 +1,5 @@
-CPMG style sequence with ideal pulses. — seq_cpmg_ideal • Spectroscopy Analysis Tools (spant) CPMG style sequence with ideal pulses. — seq_cpmg_ideal • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/seq_mega_press_ideal.html b/docs/reference/seq_mega_press_ideal.html
index 0769b8b4..a9cd7fa0 100644
--- a/docs/reference/seq_mega_press_ideal.html
+++ b/docs/reference/seq_mega_press_ideal.html
@@ -1,7 +1,5 @@
-MEGA-PRESS sequence with ideal localisation pulses and Gaussian shaped
-editing pulse. — seq_mega_press_ideal • Spectroscopy Analysis Tools (spant) MEGA-PRESS sequence with ideal localisation pulses and Gaussian shaped editing pulse. — seq_mega_press_ideal • Spectroscopy Analysis Tools (spant) PRESS sequence with shaped refocusing pulses. — seq_press_2d_shaped • Spectroscopy Analysis Tools (spant) PRESS sequence with shaped refocusing pulses. — seq_press_2d_shaped • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -165,7 +165,7 @@ Value
diff --git a/docs/reference/seq_press_ideal.html b/docs/reference/seq_press_ideal.html
index 8c976856..72c3af3d 100644
--- a/docs/reference/seq_press_ideal.html
+++ b/docs/reference/seq_press_ideal.html
@@ -1,5 +1,5 @@
-PRESS sequence with ideal pulses. — seq_press_ideal • Spectroscopy Analysis Tools (spant) PRESS sequence with ideal pulses. — seq_press_ideal • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/seq_pulse_acquire.html b/docs/reference/seq_pulse_acquire.html
index 4a88fc64..ad80571e 100644
--- a/docs/reference/seq_pulse_acquire.html
+++ b/docs/reference/seq_pulse_acquire.html
@@ -1,5 +1,5 @@
-Simple pulse and acquire sequence with ideal pulses. — seq_pulse_acquire • Spectroscopy Analysis Tools (spant) Simple pulse and acquire sequence with ideal pulses. — seq_pulse_acquire • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/seq_slaser_ideal.html b/docs/reference/seq_slaser_ideal.html
index 74688f4d..eb83e8e3 100644
--- a/docs/reference/seq_slaser_ideal.html
+++ b/docs/reference/seq_slaser_ideal.html
@@ -1,5 +1,5 @@
-sLASER sequence with ideal pulses. — seq_slaser_ideal • Spectroscopy Analysis Tools (spant) sLASER sequence with ideal pulses. — seq_slaser_ideal • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -126,7 +126,7 @@ Value
diff --git a/docs/reference/seq_spin_echo_ideal.html b/docs/reference/seq_spin_echo_ideal.html
index e23271de..4248716f 100644
--- a/docs/reference/seq_spin_echo_ideal.html
+++ b/docs/reference/seq_spin_echo_ideal.html
@@ -1,5 +1,5 @@
-Spin echo sequence with ideal pulses. — seq_spin_echo_ideal • Spectroscopy Analysis Tools (spant) Spin echo sequence with ideal pulses. — seq_spin_echo_ideal • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/seq_steam_ideal.html b/docs/reference/seq_steam_ideal.html
index a60685a8..1c8115d7 100644
--- a/docs/reference/seq_steam_ideal.html
+++ b/docs/reference/seq_steam_ideal.html
@@ -1,5 +1,5 @@
-STEAM sequence with ideal pulses. — seq_steam_ideal • Spectroscopy Analysis Tools (spant) STEAM sequence with ideal pulses. — seq_steam_ideal • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -128,7 +128,7 @@ Value
diff --git a/docs/reference/seq_steam_ideal_cof.html b/docs/reference/seq_steam_ideal_cof.html
index 8f225740..cba7af91 100644
--- a/docs/reference/seq_steam_ideal_cof.html
+++ b/docs/reference/seq_steam_ideal_cof.html
@@ -1,7 +1,5 @@
-STEAM sequence with ideal pulses and coherence order filtering to simulate
-gradient crushers. — seq_steam_ideal_cof • Spectroscopy Analysis Tools (spant) STEAM sequence with ideal pulses and coherence order filtering to simulate gradient crushers. — seq_steam_ideal_cof • Spectroscopy Analysis Tools (spant) STEAM sequence with ideal pulses using the z-rotation gradient simulation
-method described by Young et al JMR 140, 146-152 (1999). — seq_steam_ideal_young • Spectroscopy Analysis Tools (spant) STEAM sequence with ideal pulses using the z-rotation gradient simulation method described by Young et al JMR 140, 146-152 (1999). — seq_steam_ideal_young • Spectroscopy Analysis Tools (spant) Set the number of transients for an mrs_data object. — set_Ntrans • Spectroscopy Analysis Tools (spant) Set the number of transients for an mrs_data object. — set_Ntrans • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/set_def_acq_paras.html b/docs/reference/set_def_acq_paras.html
index 3e1b4004..cc2ada9c 100644
--- a/docs/reference/set_def_acq_paras.html
+++ b/docs/reference/set_def_acq_paras.html
@@ -1,5 +1,5 @@
-Set the default acquisition parameters. — set_def_acq_paras • Spectroscopy Analysis Tools (spant) Set the default acquisition parameters. — set_def_acq_paras • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Arguments
diff --git a/docs/reference/set_lcm_cmd.html b/docs/reference/set_lcm_cmd.html
index 2056ed01..42bb2f24 100644
--- a/docs/reference/set_lcm_cmd.html
+++ b/docs/reference/set_lcm_cmd.html
@@ -1,5 +1,5 @@
-Set the command to run the LCModel command-line program. — set_lcm_cmd • Spectroscopy Analysis Tools (spant) Set the command to run the LCModel command-line program. — set_lcm_cmd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/set_lw.html b/docs/reference/set_lw.html
index b64ec851..bb176c62 100644
--- a/docs/reference/set_lw.html
+++ b/docs/reference/set_lw.html
@@ -1,5 +1,5 @@
-Apply line-broadening to an mrs_data object to achieve a specified linewidth. — set_lw • Spectroscopy Analysis Tools (spant) Apply line-broadening to an mrs_data object to achieve a specified linewidth. — set_lw • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -123,7 +123,7 @@ Value
diff --git a/docs/reference/set_mask_xy_mat.html b/docs/reference/set_mask_xy_mat.html
index 49dc5d4e..52c4b617 100644
--- a/docs/reference/set_mask_xy_mat.html
+++ b/docs/reference/set_mask_xy_mat.html
@@ -1,5 +1,5 @@
-Set the masked voxels in a 2D MRSI dataset to given spectrum. — set_mask_xy_mat • Spectroscopy Analysis Tools (spant) Set the masked voxels in a 2D MRSI dataset to given spectrum. — set_mask_xy_mat • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Value
diff --git a/docs/reference/set_precomp_mode.html b/docs/reference/set_precomp_mode.html
index f44bd5d3..47c28e3b 100644
--- a/docs/reference/set_precomp_mode.html
+++ b/docs/reference/set_precomp_mode.html
@@ -1,5 +1,5 @@
-Set the precompute mode. — set_precomp_mode • Spectroscopy Analysis Tools (spant) Set the precompute mode. — set_precomp_mode • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/set_precomp_verbose.html b/docs/reference/set_precomp_verbose.html
index 1453a231..9c613505 100644
--- a/docs/reference/set_precomp_verbose.html
+++ b/docs/reference/set_precomp_verbose.html
@@ -1,5 +1,5 @@
-Set the verbosity of the precompute function. — set_precomp_verbose • Spectroscopy Analysis Tools (spant) Set the verbosity of the precompute function. — set_precomp_verbose • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/set_ref.html b/docs/reference/set_ref.html
index 8953fa50..5436dfa2 100644
--- a/docs/reference/set_ref.html
+++ b/docs/reference/set_ref.html
@@ -1,5 +1,5 @@
-Set the ppm reference value (eg ppm value at 0Hz). — set_ref • Spectroscopy Analysis Tools (spant) Set the ppm reference value (eg ppm value at 0Hz). — set_ref • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/set_td_pts.html b/docs/reference/set_td_pts.html
index 8a80d42a..586459ff 100644
--- a/docs/reference/set_td_pts.html
+++ b/docs/reference/set_td_pts.html
@@ -1,7 +1,5 @@
-Set the number of time-domain data points, truncating or zero-filling as
-appropriate. — set_td_pts • Spectroscopy Analysis Tools (spant) Set the number of time-domain data points, truncating or zero-filling as appropriate. — set_td_pts • Spectroscopy Analysis Tools (spant) Set the command to run the TARQUIN command-line program. — set_tqn_cmd • Spectroscopy Analysis Tools (spant) Set the command to run the TARQUIN command-line program. — set_tqn_cmd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/set_tr.html b/docs/reference/set_tr.html
index b2109ab0..65c9df5f 100644
--- a/docs/reference/set_tr.html
+++ b/docs/reference/set_tr.html
@@ -1,5 +1,5 @@
-Set the repetition time of an MRS dataset. — set_tr • Spectroscopy Analysis Tools (spant) Set the repetition time of an MRS dataset. — set_tr • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/shift.html b/docs/reference/shift.html
index ab0fe724..034591d0 100644
--- a/docs/reference/shift.html
+++ b/docs/reference/shift.html
@@ -1,5 +1,5 @@
-Apply a frequency shift to MRS data. — shift • Spectroscopy Analysis Tools (spant) Apply a frequency shift to MRS data. — shift • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/shift_basis.html b/docs/reference/shift_basis.html
index 2884be19..f55a65e0 100644
--- a/docs/reference/shift_basis.html
+++ b/docs/reference/shift_basis.html
@@ -1,5 +1,5 @@
-Apply frequency shifts to basis set signals. — shift_basis • Spectroscopy Analysis Tools (spant) Apply frequency shifts to basis set signals. — shift_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Value
diff --git a/docs/reference/sim_basis.html b/docs/reference/sim_basis.html
index c7838c46..bb5fefc6 100644
--- a/docs/reference/sim_basis.html
+++ b/docs/reference/sim_basis.html
@@ -1,5 +1,5 @@
-Simulate a basis set object. — sim_basis • Spectroscopy Analysis Tools (spant) Simulate a basis set object. — sim_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -136,7 +136,7 @@ Value
diff --git a/docs/reference/sim_basis_1h_brain.html b/docs/reference/sim_basis_1h_brain.html
index 62ed7389..f71ffa0b 100644
--- a/docs/reference/sim_basis_1h_brain.html
+++ b/docs/reference/sim_basis_1h_brain.html
@@ -1,7 +1,5 @@
-Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS
-sequence. Note, ideal pulses are assumed. — sim_basis_1h_brain • Spectroscopy Analysis Tools (spant) Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS sequence. Note, ideal pulses are assumed. — sim_basis_1h_brain • Spectroscopy Analysis Tools (spant) Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS
-sequence. Note, ideal pulses are assumed. — sim_basis_1h_brain_press • Spectroscopy Analysis Tools (spant) Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS sequence. Note, ideal pulses are assumed. — sim_basis_1h_brain_press • Spectroscopy Analysis Tools (spant) Simulate a macromolecular and lipid basis-set suitable for 1H brain MRS
-analysis. — sim_basis_mm_lip_lcm • Spectroscopy Analysis Tools (spant) Simulate a macromolecular and lipid basis-set suitable for 1H brain MRS analysis. — sim_basis_mm_lip_lcm • Spectroscopy Analysis Tools (spant) Simulate a basis file using TARQUIN. — sim_basis_tqn • Spectroscopy Analysis Tools (spant) Simulate a basis file using TARQUIN. — sim_basis_tqn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -129,7 +129,7 @@ Examples
diff --git a/docs/reference/sim_brain_1h.html b/docs/reference/sim_brain_1h.html
index 2044cf1a..717ee289 100644
--- a/docs/reference/sim_brain_1h.html
+++ b/docs/reference/sim_brain_1h.html
@@ -1,5 +1,5 @@
-Simulate MRS data with a similar appearance to normal brain (by default). — sim_brain_1h • Spectroscopy Analysis Tools (spant) Simulate MRS data with a similar appearance to normal brain (by default). — sim_brain_1h • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -159,7 +159,7 @@ Value
diff --git a/docs/reference/sim_mol.html b/docs/reference/sim_mol.html
index 23bcef50..77f76a50 100644
--- a/docs/reference/sim_mol.html
+++ b/docs/reference/sim_mol.html
@@ -1,5 +1,5 @@
-Simulate a mol_parameter object. — sim_mol • Spectroscopy Analysis Tools (spant) Simulate a mol_parameter object. — sim_mol • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -143,7 +143,7 @@ Value
diff --git a/docs/reference/sim_noise.html b/docs/reference/sim_noise.html
index 23875f79..a71477d4 100644
--- a/docs/reference/sim_noise.html
+++ b/docs/reference/sim_noise.html
@@ -1,5 +1,5 @@
-Simulate an mrs_data object containing simulated Gaussian noise. — sim_noise • Spectroscopy Analysis Tools (spant) Simulate an mrs_data object containing simulated Gaussian noise. — sim_noise • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -84,6 +84,7 @@ Simulate an mrs_data object containing simulated Gaussian noise.
ft = def_ft(),
N = def_N(),
ref = def_ref(),
+ nuc = def_nuc(),
dyns = 1,
fd = TRUE
)
@@ -111,6 +112,10 @@ Arguments
reference value for ppm scale.
nuc
+resonant nucleus.
dyns
number of dynamic scans to generate.
Value
diff --git a/docs/reference/sim_resonances.html b/docs/reference/sim_resonances.html
index 19e9a8a4..d4f8d7c0 100644
--- a/docs/reference/sim_resonances.html
+++ b/docs/reference/sim_resonances.html
@@ -1,5 +1,5 @@
-Simulate a MRS data object containing a set of simulated resonances. — sim_resonances • Spectroscopy Analysis Tools (spant) Simulate a MRS data object containing a set of simulated resonances. — sim_resonances • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -161,7 +161,7 @@ Examples
diff --git a/docs/reference/sim_th_excit_profile.html b/docs/reference/sim_th_excit_profile.html
index 5535c5ef..e781cab1 100644
--- a/docs/reference/sim_th_excit_profile.html
+++ b/docs/reference/sim_th_excit_profile.html
@@ -1,7 +1,5 @@
-Simulate an ideal pulse excitation profile by smoothing a top-hat function
-with a Gaussian. — sim_th_excit_profile • Spectroscopy Analysis Tools (spant) Simulate an ideal pulse excitation profile by smoothing a top-hat function with a Gaussian. — sim_th_excit_profile • Spectroscopy Analysis Tools (spant) Simulate an mrs_data object containing complex zero valued samples. — sim_zero • Spectroscopy Analysis Tools (spant) Simulate an mrs_data object containing complex zero valued samples. — sim_zero • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -78,7 +78,14 @@ Simulate an mrs_data object containing complex zero valued samples.
-
+
@@ -99,6 +106,10 @@ Arguments
reference value for ppm scale.
nuc
+resonant nucleus.
dyns
number of dynamic scans to generate.
Value
diff --git a/docs/reference/smooth_dyns.html b/docs/reference/smooth_dyns.html
index 4cc8da50..accf3a51 100644
--- a/docs/reference/smooth_dyns.html
+++ b/docs/reference/smooth_dyns.html
@@ -1,5 +1,5 @@
-Smooth data across the dynamic dimension with a Gaussian kernel. — smooth_dyns • Spectroscopy Analysis Tools (spant) Smooth data across the dynamic dimension with a Gaussian kernel. — smooth_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/sort_basis.html b/docs/reference/sort_basis.html
index 6a676ea2..d25cc006 100644
--- a/docs/reference/sort_basis.html
+++ b/docs/reference/sort_basis.html
@@ -1,5 +1,5 @@
-Sort the basis-set elements alphabetically. — sort_basis • Spectroscopy Analysis Tools (spant) Sort the basis-set elements alphabetically. — sort_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/spant-package.html b/docs/reference/spant-package.html
index b3dd8e21..90f19ec3 100644
--- a/docs/reference/spant-package.html
+++ b/docs/reference/spant-package.html
@@ -1,5 +1,5 @@
-spant: spectroscopy analysis tools. — spant-package • Spectroscopy Analysis Tools (spant) spant: spectroscopy analysis tools. — spant-package • Spectroscopy Analysis Tools (spant) Simulate and fit some spectra with ABfit for benchmarking purposes. Basic
-timing and performance metrics will be printed. — spant_abfit_benchmark • Spectroscopy Analysis Tools (spant) Simulate and fit some spectra with ABfit for benchmarking purposes. Basic timing and performance metrics will be printed. — spant_abfit_benchmark • Spectroscopy Analysis Tools (spant) Example MEGA-PRESS data with significant B0 drift. — spant_mpress_drift • Spectroscopy Analysis Tools (spant) Example MEGA-PRESS data with significant B0 drift. — spant_mpress_drift • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -83,7 +83,7 @@ Example MEGA-PRESS data with significant B0 drift.
Format
- An object of class mrs_data of length 13.
+ An object of class mrs_data of dimension 1 x 1 x 1 x 1 x 40 x 1 x 1024.
@@ -98,7 +98,7 @@ Format
diff --git a/docs/reference/spant_sim_fmrs_dataset.html b/docs/reference/spant_sim_fmrs_dataset.html
new file mode 100644
index 00000000..00e48b56
--- /dev/null
+++ b/docs/reference/spant_sim_fmrs_dataset.html
@@ -0,0 +1,117 @@
+
+Simulate an example fMRS dataset for a block design fMRS experiment and export a BIDS structure. — spant_sim_fmrs_dataset • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Simulate an example fMRS dataset for a block design fMRS experiment and export a BIDS structure.
+ Source: R/fmrs.R
+ spant_sim_fmrs_dataset.Rd
+
+
+
+ Simulate an example fMRS dataset for a block design fMRS experiment and
+export a BIDS structure.
+
+
+
+ spant_sim_fmrs_dataset(output_dir = NULL)
+
+
+
+ Arguments
+ - output_dir
+output directory for the BIDS data. Defaults to :
+"HOME/sim_fmrs_dataset/data".
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/spant_simulation_benchmark.html b/docs/reference/spant_simulation_benchmark.html
index 32daa8bf..d8cc6841 100644
--- a/docs/reference/spant_simulation_benchmark.html
+++ b/docs/reference/spant_simulation_benchmark.html
@@ -1,7 +1,5 @@
-Simulate a typical metabolite basis set for benchmarking. Timing metrics will
-be printed on completion. — spant_simulation_benchmark • Spectroscopy Analysis Tools (spant) Simulate a typical metabolite basis set for benchmarking. Timing metrics will be printed on completion. — spant_simulation_benchmark • Spectroscopy Analysis Tools (spant) Decompose an mrs_data object into white and gray matter spectra. — spec_decomp • Spectroscopy Analysis Tools (spant) Perform a mathematical operation on a spectral region. — spec_op • Spectroscopy Analysis Tools (spant) Perform a mathematical operation on a spectral region. — spec_op • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -98,8 +98,8 @@ Arguments
operator
-can be "sum" (default), "mean", "l2", "max", "min" or
-"max-min".
can be "sum" (default), "mean", "l2", "max", "max_cplx,
+"min" or "max-min".
freq_scale
@@ -129,7 +129,7 @@ Value
diff --git a/docs/reference/spin_sys.html b/docs/reference/spin_sys.html
index 853423a4..1eaa9e76 100644
--- a/docs/reference/spin_sys.html
+++ b/docs/reference/spin_sys.html
@@ -1,5 +1,5 @@
-Create a spin system object for pulse sequence simulation. — spin_sys • Spectroscopy Analysis Tools (spant) Create a spin system object for pulse sequence simulation. — spin_sys • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/spm_pve2categorical.html b/docs/reference/spm_pve2categorical.html
index 23a1bad9..70f10729 100644
--- a/docs/reference/spm_pve2categorical.html
+++ b/docs/reference/spm_pve2categorical.html
@@ -1,7 +1,5 @@
-Convert SPM style segmentation files to a single categorical image where
-the numerical values map as: 0) Other, 1) CSF, 2) GM and 3) WM. — spm_pve2categorical • Spectroscopy Analysis Tools (spant) Convert SPM style segmentation files to a single categorical image where the numerical values map as: 0) Other, 1) CSF, 2) GM and 3) WM. — spm_pve2categorical • Spectroscopy Analysis Tools (spant) Signal space projection method for lipid suppression. — ssp • Spectroscopy Analysis Tools (spant) Signal space projection method for lipid suppression. — ssp • Spectroscopy Analysis Tools (spant) Plot the fitting results of an object of class fit_result with
-individual basis set components shown. — stackplot.fit_result • Spectroscopy Analysis Tools (spant) Plot the fitting results of an object of class fit_result with individual basis set components shown. — stackplot.fit_result • Spectroscopy Analysis Tools (spant) Produce a plot with multiple traces. — stackplot • Spectroscopy Analysis Tools (spant) Produce a plot with multiple traces. — stackplot • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/stackplot.mrs_data.html b/docs/reference/stackplot.mrs_data.html
index 17ff5648..64eea445 100644
--- a/docs/reference/stackplot.mrs_data.html
+++ b/docs/reference/stackplot.mrs_data.html
@@ -1,5 +1,5 @@
-Stackplot plotting method for objects of class mrs_data. — stackplot.mrs_data • Spectroscopy Analysis Tools (spant) Stackplot plotting method for objects of class mrs_data. — stackplot.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -255,7 +255,7 @@ Arguments
diff --git a/docs/reference/sub_first_dyn.html b/docs/reference/sub_first_dyn.html
index dbd7f831..493b7242 100644
--- a/docs/reference/sub_first_dyn.html
+++ b/docs/reference/sub_first_dyn.html
@@ -1,5 +1,5 @@
-Subtract the first dynamic spectrum from a dynamic series. — sub_first_dyn • Spectroscopy Analysis Tools (spant) Subtract the first dynamic spectrum from a dynamic series. — sub_first_dyn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/sub_mean_dyns.html b/docs/reference/sub_mean_dyns.html
index 6e3bb2df..221bd0c1 100644
--- a/docs/reference/sub_mean_dyns.html
+++ b/docs/reference/sub_mean_dyns.html
@@ -1,5 +1,5 @@
-Subtract the mean dynamic spectrum from a dynamic series. — sub_mean_dyns • Spectroscopy Analysis Tools (spant) Subtract the mean dynamic spectrum from a dynamic series. — sub_mean_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/sub_median_dyns.html b/docs/reference/sub_median_dyns.html
index 134c495d..1e834f14 100644
--- a/docs/reference/sub_median_dyns.html
+++ b/docs/reference/sub_median_dyns.html
@@ -1,5 +1,5 @@
-Subtract the median dynamic spectrum from a dynamic series. — sub_median_dyns • Spectroscopy Analysis Tools (spant) Subtract the median dynamic spectrum from a dynamic series. — sub_median_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/sum_coils.html b/docs/reference/sum_coils.html
index 7bf559f2..e1ab3cc0 100644
--- a/docs/reference/sum_coils.html
+++ b/docs/reference/sum_coils.html
@@ -1,5 +1,5 @@
-Calculate the sum across receiver coil elements. — sum_coils • Spectroscopy Analysis Tools (spant) Calculate the sum across receiver coil elements. — sum_coils • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/sum_dyns.html b/docs/reference/sum_dyns.html
index a0be19d3..bbda2ffc 100644
--- a/docs/reference/sum_dyns.html
+++ b/docs/reference/sum_dyns.html
@@ -1,5 +1,5 @@
-Calculate the sum of data dynamics. — sum_dyns • Spectroscopy Analysis Tools (spant) Calculate the sum of data dynamics. — sum_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/sum_mrs.html b/docs/reference/sum_mrs.html
index a22f215b..3cc3ab9e 100644
--- a/docs/reference/sum_mrs.html
+++ b/docs/reference/sum_mrs.html
@@ -1,5 +1,5 @@
-Sum two mrs_data objects. — sum_mrs • Spectroscopy Analysis Tools (spant) Sum two mrs_data objects. — sum_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Value
diff --git a/docs/reference/sum_mrs_list.html b/docs/reference/sum_mrs_list.html
index f4e09aea..c3584348 100644
--- a/docs/reference/sum_mrs_list.html
+++ b/docs/reference/sum_mrs_list.html
@@ -1,5 +1,5 @@
-Return the sum of a list of mrs_data objects. — sum_mrs_list • Spectroscopy Analysis Tools (spant) Return the sum of a list of mrs_data objects. — sum_mrs_list • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/svs_1h_brain_analysis.html b/docs/reference/svs_1h_brain_analysis.html
index 8ce514db..dff0ef7d 100644
--- a/docs/reference/svs_1h_brain_analysis.html
+++ b/docs/reference/svs_1h_brain_analysis.html
@@ -1,5 +1,5 @@
-Standard SVS 1H brain analysis pipeline. — svs_1h_brain_analysis • Spectroscopy Analysis Tools (spant) Standard SVS 1H brain analysis pipeline. — svs_1h_brain_analysis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -199,7 +199,7 @@ Value
diff --git a/docs/reference/svs_1h_brain_analysis_dev.html b/docs/reference/svs_1h_brain_analysis_dev.html
index d70a14d3..d71bfea2 100644
--- a/docs/reference/svs_1h_brain_analysis_dev.html
+++ b/docs/reference/svs_1h_brain_analysis_dev.html
@@ -1,5 +1,5 @@
-Standard SVS 1H brain analysis pipeline. — svs_1h_brain_analysis_dev • Spectroscopy Analysis Tools (spant) Standard SVS 1H brain analysis pipeline. — svs_1h_brain_analysis_dev • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -193,7 +193,7 @@ Examples
diff --git a/docs/reference/svs_1h_brain_batch_analysis.html b/docs/reference/svs_1h_brain_batch_analysis.html
index 5631e8cc..15f7223e 100644
--- a/docs/reference/svs_1h_brain_batch_analysis.html
+++ b/docs/reference/svs_1h_brain_batch_analysis.html
@@ -1,5 +1,5 @@
-Batch interface to the standard SVS 1H brain analysis pipeline. — svs_1h_brain_batch_analysis • Spectroscopy Analysis Tools (spant) Batch interface to the standard SVS 1H brain analysis pipeline. — svs_1h_brain_batch_analysis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -144,7 +144,7 @@ Value
diff --git a/docs/reference/t_test_spec.html b/docs/reference/t_test_spec.html
new file mode 100644
index 00000000..56a7ea1b
--- /dev/null
+++ b/docs/reference/t_test_spec.html
@@ -0,0 +1,124 @@
+
+Perform a t-test on spectral data points. — t_test_spec • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+
+
+ Perform a t-test on spectral data points.
+
+
+
+ t_test_spec(mrs_data, group)
+
+
+
+ Arguments
+ - mrs_data
+an mrs_data object with spectra in the dynamic dimension.
- group
+vector describing the group membership of each dynamic spectrum.
+
+ Value
+
+
+a list of statistical results.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/td2fd.html b/docs/reference/td2fd.html
index 6748a6a8..f31ed524 100644
--- a/docs/reference/td2fd.html
+++ b/docs/reference/td2fd.html
@@ -1,5 +1,5 @@
-Transform time-domain data to the frequency-domain. — td2fd • Spectroscopy Analysis Tools (spant) Transform time-domain data to the frequency-domain. — td2fd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/td_conv_filt.html b/docs/reference/td_conv_filt.html
index a9f340c3..106b9b00 100644
--- a/docs/reference/td_conv_filt.html
+++ b/docs/reference/td_conv_filt.html
@@ -1,5 +1,5 @@
-Time-domain convolution based filter. — td_conv_filt • Spectroscopy Analysis Tools (spant) Time-domain convolution based filter. — td_conv_filt • Spectroscopy Analysis Tools (spant) Time-domain spectral registration. — tdsr • Spectroscopy Analysis Tools (spant) Time-domain spectral registration. — tdsr • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -121,7 +121,7 @@ Value
diff --git a/docs/reference/te.html b/docs/reference/te.html
index 010361b1..4a65711d 100644
--- a/docs/reference/te.html
+++ b/docs/reference/te.html
@@ -1,5 +1,5 @@
-Return the echo time of an MRS dataset. — te • Spectroscopy Analysis Tools (spant) Return the echo time of an MRS dataset. — te • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/tr.html b/docs/reference/tr.html
index 0c0bd63b..2e749e02 100644
--- a/docs/reference/tr.html
+++ b/docs/reference/tr.html
@@ -1,5 +1,5 @@
-Return the repetition time of an MRS dataset. — tr • Spectroscopy Analysis Tools (spant) Return the repetition time of an MRS dataset. — tr • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/varpro_3_para_opts.html b/docs/reference/varpro_3_para_opts.html
index c2270a16..52d7cd84 100644
--- a/docs/reference/varpro_3_para_opts.html
+++ b/docs/reference/varpro_3_para_opts.html
@@ -1,5 +1,5 @@
-Return a list of options for VARPRO based fitting with 3 free parameters. — varpro_3_para_opts • Spectroscopy Analysis Tools (spant) Return a list of options for VARPRO based fitting with 3 free parameters. — varpro_3_para_opts • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -141,7 +141,7 @@ Value
diff --git a/docs/reference/varpro_basic_opts.html b/docs/reference/varpro_basic_opts.html
index 32c86d22..c5104891 100644
--- a/docs/reference/varpro_basic_opts.html
+++ b/docs/reference/varpro_basic_opts.html
@@ -1,5 +1,5 @@
-Return a list of options for a basic VARPRO analysis. — varpro_basic_opts • Spectroscopy Analysis Tools (spant) Return a list of options for a basic VARPRO analysis. — varpro_basic_opts • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -118,7 +118,7 @@ Value
diff --git a/docs/reference/varpro_opts.html b/docs/reference/varpro_opts.html
index 2aabf11d..6332f730 100644
--- a/docs/reference/varpro_opts.html
+++ b/docs/reference/varpro_opts.html
@@ -1,5 +1,5 @@
-Return a list of options for VARPRO based fitting. — varpro_opts • Spectroscopy Analysis Tools (spant) Return a list of options for VARPRO based fitting. — varpro_opts • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -177,7 +177,7 @@ Examples
diff --git a/docs/reference/vec2mrs_data.html b/docs/reference/vec2mrs_data.html
index 0cccd73b..f0d58bf0 100644
--- a/docs/reference/vec2mrs_data.html
+++ b/docs/reference/vec2mrs_data.html
@@ -1,5 +1,5 @@
-Convert a vector into a mrs_data object. — vec2mrs_data • Spectroscopy Analysis Tools (spant) Convert a vector into a mrs_data object. — vec2mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -80,10 +80,11 @@ Convert a vector into a mrs_data object.
vec2mrs_data(
vec,
- fs = def_fs(),
- ft = def_ft(),
- ref = def_ref(),
- nuc = def_nuc(),
+ mrs_data = NULL,
+ fs = NULL,
+ ft = NULL,
+ ref = NULL,
+ nuc = NULL,
dyns = 1,
fd = FALSE
)
@@ -95,6 +96,10 @@ Arguments
the data vector.
mrs_data
+example data to copy acquisition parameters from.
fs
sampling frequency in Hz.
Arguments
fd
-flag to indicate if the matrix is in the frequency domain (logical).
flag to indicate if the vector is in the frequency domain (logical).
Value
diff --git a/docs/reference/write_basis.html b/docs/reference/write_basis.html
index b6e27cbd..94c5e021 100644
--- a/docs/reference/write_basis.html
+++ b/docs/reference/write_basis.html
@@ -1,5 +1,5 @@
-Write a basis object to an LCModel .basis formatted file. — write_basis • Spectroscopy Analysis Tools (spant) Write a basis object to an LCModel .basis formatted file. — write_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -108,7 +108,7 @@ Arguments
diff --git a/docs/reference/write_basis_tqn.html b/docs/reference/write_basis_tqn.html
index 6aa51c1d..116c73ec 100644
--- a/docs/reference/write_basis_tqn.html
+++ b/docs/reference/write_basis_tqn.html
@@ -1,5 +1,5 @@
-Generate a basis file using TARQUIN. — write_basis_tqn • Spectroscopy Analysis Tools (spant) Generate a basis file using TARQUIN. — write_basis_tqn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Examples
diff --git a/docs/reference/write_mrs.html b/docs/reference/write_mrs.html
index fff25f15..124b9dc4 100644
--- a/docs/reference/write_mrs.html
+++ b/docs/reference/write_mrs.html
@@ -1,5 +1,5 @@
-Write MRS data object to file. — write_mrs • Spectroscopy Analysis Tools (spant) Write MRS data object to file. — write_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Arguments
diff --git a/docs/reference/write_mrs_nifti.html b/docs/reference/write_mrs_nifti.html
index f4bf1921..bd3ed4b7 100644
--- a/docs/reference/write_mrs_nifti.html
+++ b/docs/reference/write_mrs_nifti.html
@@ -1,5 +1,5 @@
-Write MRS data object to file in NIFTI format. — write_mrs_nifti • Spectroscopy Analysis Tools (spant) Write MRS data object to file in NIFTI format. — write_mrs_nifti • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/write_pulse_ascii.html b/docs/reference/write_pulse_ascii.html
index 067ae086..221f8ebb 100644
--- a/docs/reference/write_pulse_ascii.html
+++ b/docs/reference/write_pulse_ascii.html
@@ -1,5 +1,5 @@
-Write an ASCII formatted pulse file. — write_pulse_ascii • Spectroscopy Analysis Tools (spant) Write an ASCII formatted pulse file. — write_pulse_ascii • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/zero_fade_spec.html b/docs/reference/zero_fade_spec.html
index c703745c..c8b572c3 100644
--- a/docs/reference/zero_fade_spec.html
+++ b/docs/reference/zero_fade_spec.html
@@ -1,7 +1,5 @@
-Fade a spectrum to zero by frequency domain multiplication with a tanh
-function. Note this operation distorts data points at the end of the FID. — zero_fade_spec • Spectroscopy Analysis Tools (spant) Fade a spectrum to zero by frequency domain multiplication with a tanh function. Note this operation distorts data points at the end of the FID. — zero_fade_spec • Spectroscopy Analysis Tools (spant) Zero all coherences including and above a given order. — zero_higher_orders • Spectroscopy Analysis Tools (spant) Zero all coherences including and above a given order. — zero_higher_orders • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Value
diff --git a/docs/reference/zero_td_pts_end.html b/docs/reference/zero_td_pts_end.html
index 8c1123c8..71d24ebb 100644
--- a/docs/reference/zero_td_pts_end.html
+++ b/docs/reference/zero_td_pts_end.html
@@ -1,5 +1,5 @@
-Set mrs_data object data points at the end of the FID to zero. — zero_td_pts_end • Spectroscopy Analysis Tools (spant) Set mrs_data object data points at the end of the FID to zero. — zero_td_pts_end • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/zf.html b/docs/reference/zf.html
index 85e2013c..baf50256 100644
--- a/docs/reference/zf.html
+++ b/docs/reference/zf.html
@@ -1,5 +1,5 @@
-Zero-fill MRS data in the time domain. — zf • Spectroscopy Analysis Tools (spant) Zero-fill MRS data in the time domain. — zf • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -125,7 +125,7 @@ Value
diff --git a/docs/reference/zf_xy.html b/docs/reference/zf_xy.html
index ebca3999..c4104a74 100644
--- a/docs/reference/zf_xy.html
+++ b/docs/reference/zf_xy.html
@@ -1,5 +1,5 @@
-Zero-fill MRSI data in the k-space x-y direction. — zf_xy • Spectroscopy Analysis Tools (spant) Zero-fill MRSI data in the k-space x-y direction. — zf_xy • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -113,7 +113,7 @@ Value
diff --git a/docs/sitemap.xml b/docs/sitemap.xml
index e2139f71..4c39f515 100644
--- a/docs/sitemap.xml
+++ b/docs/sitemap.xml
@@ -216,6 +216,12 @@
https://martin3141.github.io/spant/reference/comb_coils_fp_pc.html
+
+ https://martin3141.github.io/spant/reference/comb_coils_mrsi_gls.html
+
+
+ https://martin3141.github.io/spant/reference/comb_coils_svs_gls.html
+
https://martin3141.github.io/spant/reference/comb_csv_results.html
@@ -411,6 +417,9 @@
https://martin3141.github.io/spant/reference/gen_conv_reg.html
+
+ https://martin3141.github.io/spant/reference/gen_group_reg.html
+
https://martin3141.github.io/spant/reference/gen_impulse_reg.html
@@ -555,6 +564,15 @@
https://martin3141.github.io/spant/reference/glm_spec.html
+
+ https://martin3141.github.io/spant/reference/glm_spec_fmrs_fl.html
+
+
+ https://martin3141.github.io/spant/reference/glm_spec_fmrs_group.html
+
+
+ https://martin3141.github.io/spant/reference/glm_spec_group_linhyp.html
+
https://martin3141.github.io/spant/reference/grid_shift_xy.html
@@ -690,9 +708,15 @@
https://martin3141.github.io/spant/reference/mrs_data2basis.html
+
+ https://martin3141.github.io/spant/reference/mrs_data2bids.html
+
https://martin3141.github.io/spant/reference/mrs_data2mat.html
+
+ https://martin3141.github.io/spant/reference/mrs_data2spec_mat.html
+
https://martin3141.github.io/spant/reference/mrs_data2vec.html
@@ -741,6 +765,9 @@
https://martin3141.github.io/spant/reference/phase.html
+
+ https://martin3141.github.io/spant/reference/phase_ref_1h_brain.html
+
https://martin3141.github.io/spant/reference/plot.fit_result.html
@@ -780,6 +807,12 @@
https://martin3141.github.io/spant/reference/precomp.html
+
+ https://martin3141.github.io/spant/reference/preproc_svs.html
+
+
+ https://martin3141.github.io/spant/reference/preproc_svs_dataset.html
+
https://martin3141.github.io/spant/reference/print.fit_result.html
@@ -1050,6 +1083,9 @@
https://martin3141.github.io/spant/reference/spant_mpress_drift.html
+
+ https://martin3141.github.io/spant/reference/spant_sim_fmrs_dataset.html
+
https://martin3141.github.io/spant/reference/spant_simulation_benchmark.html
@@ -1107,6 +1143,9 @@
https://martin3141.github.io/spant/reference/svs_1h_brain_batch_analysis.html
+
+ https://martin3141.github.io/spant/reference/t_test_spec.html
+
https://martin3141.github.io/spant/reference/td2fd.html
Flip the x data dimension order of a nifti image. This corresponds to -flipping MRI data in the left-right direction, assuming the data in save in -neurological format (can check with fslorient program).
Flip the x data dimension order of a nifti image. This corresponds to flipping MRI data in the left-right direction, assuming the data in save in neurological format (can check with fslorient program).
All functions
- Search for the highest peak in a spectral region and return the frequency,
-height and FWHM.
Search for the highest peak in a spectral region and return the frequency, height and FWHM.
@@ -974,6 +955,10 @@ All functions phase()
Apply phasing parameters to MRS data.
+
+
+ Corrected zero order phase and chemical shift offset in 1H MRS data from the brain.
@@ -1005,8 +990,7 @@ All functions
- Plot an interactive slice map from a data array where voxels can be selected
-to display a corresponding spectrum.
Plot an interactive slice map from a data array where voxels can be selected to display a corresponding spectrum.
@@ -1026,8 +1010,15 @@ All functions
- Save function results to file and load on subsequent calls to avoid repeat
-computation.
Save function results to file and load on subsequent calls to avoid repeat computation.
+
+
+ Preprocess and perform quality assessment of a single SVS data set.
+
+
+ Preprocess and perform quality assessment of one or more SVS data sets.
@@ -1055,15 +1046,11 @@ All functions
- Read a directory containing Siemens MRS IMA files and combine along the coil
-dimension. Note that the coil ID is inferred from the sorted file name and
-should be checked when consistency is required between two directories.
Read a directory containing Siemens MRS IMA files and combine along the coil dimension. Note that the coil ID is inferred from the sorted file name and should be checked when consistency is required between two directories.
- Read a directory containing Siemens MRS IMA files and combine along the
-dynamic dimension. Note that the coil ID is inferred from the sorted file
-name and should be checked when consistency is required.
Read a directory containing Siemens MRS IMA files and combine along the dynamic dimension. Note that the coil ID is inferred from the sorted file name and should be checked when consistency is required.
@@ -1103,13 +1090,11 @@ All functions
- Reconstruct complex time-domain data from the real part of frequency-domain
-data.
Reconstruct complex time-domain data from the real part of frequency-domain data.
- Reconstruct complex time-domain data from the real part of frequency-domain
-data.
Reconstruct complex time-domain data from the real part of frequency-domain data.
@@ -1141,8 +1126,7 @@ All functions
- Resample a VOI to match a target image space using nearest-neighbour
-interpolation.
Resample a VOI to match a target image space using nearest-neighbour interpolation.
@@ -1158,23 +1142,19 @@ All functions
- Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water).
Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / kg of tissue water).
- Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water).
Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / kg of tissue water).
- Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / Litre of tissue).
Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / Litre of tissue).
- Convert default LCM/TARQUIN concentration scaling to molal units with partial
-volume correction.
Convert default LCM/TARQUIN concentration scaling to molal units with partial volume correction.
@@ -1222,8 +1202,7 @@ All functions
- MEGA-PRESS sequence with ideal localisation pulses and Gaussian shaped
-editing pulse.
MEGA-PRESS sequence with ideal localisation pulses and Gaussian shaped editing pulse.
@@ -1251,13 +1230,11 @@ All functions
- STEAM sequence with ideal pulses and coherence order filtering to simulate
-gradient crushers.
STEAM sequence with ideal pulses and coherence order filtering to simulate gradient crushers.
- STEAM sequence with ideal pulses using the z-rotation gradient simulation
-method described by Young et al JMR 140, 146-152 (1999).
STEAM sequence with ideal pulses using the z-rotation gradient simulation method described by Young et al JMR 140, 146-152 (1999).
@@ -1293,8 +1270,7 @@ All functions
- Set the number of time-domain data points, truncating or zero-filling as
-appropriate.
Set the number of time-domain data points, truncating or zero-filling as appropriate.
@@ -1318,18 +1294,15 @@ All functions
- Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS
-sequence. Note, ideal pulses are assumed.
Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS sequence. Note, ideal pulses are assumed.
- Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS
-sequence. Note, ideal pulses are assumed.
Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS sequence. Note, ideal pulses are assumed.
- Simulate a macromolecular and lipid basis-set suitable for 1H brain MRS
-analysis.
Simulate a macromolecular and lipid basis-set suitable for 1H brain MRS analysis.
@@ -1353,8 +1326,7 @@ All functions
- Simulate an ideal pulse excitation profile by smoothing a top-hat function
-with a Gaussian.
Simulate an ideal pulse excitation profile by smoothing a top-hat function with a Gaussian.
@@ -1374,17 +1346,19 @@ All functions
- Simulate and fit some spectra with ABfit for benchmarking purposes. Basic
-timing and performance metrics will be printed.
Simulate and fit some spectra with ABfit for benchmarking purposes. Basic timing and performance metrics will be printed.
Example MEGA-PRESS data with significant B0 drift.
+
+
+ Simulate an example fMRS dataset for a block design fMRS experiment and export a BIDS structure.
- Simulate a typical metabolite basis set for benchmarking. Timing metrics will
-be printed on completion.
Simulate a typical metabolite basis set for benchmarking. Timing metrics will be printed on completion.
@@ -1400,8 +1374,7 @@ All functions
- Convert SPM style segmentation files to a single categorical image where
-the numerical values map as: 0) Other, 1) CSF, 2) GM and 3) WM.
Convert SPM style segmentation files to a single categorical image where the numerical values map as: 0) Other, 1) CSF, 2) GM and 3) WM.
@@ -1413,8 +1386,7 @@ All functions
- Plot the fitting results of an object of class fit_result with
-individual basis set components shown.
Plot the fitting results of an object of class fit_result with individual basis set components shown.
@@ -1459,6 +1431,10 @@ All functions svs_1h_brain_batch_analysis()
Batch interface to the standard SVS 1H brain analysis pipeline.
+
+
+ Perform a t-test on spectral data points.
@@ -1518,8 +1494,7 @@ All functions
- Fade a spectrum to zero by frequency domain multiplication with a tanh
-function. Note this operation distorts data points at the end of the FID.
Fade a spectrum to zero by frequency domain multiplication with a tanh function. Note this operation distorts data points at the end of the FID.
@@ -1549,7 +1524,7 @@ All functions
diff --git a/docs/reference/int_spec.html b/docs/reference/int_spec.html
index c7060fe7..783325a8 100644
--- a/docs/reference/int_spec.html
+++ b/docs/reference/int_spec.html
@@ -1,5 +1,5 @@
-Integrate a spectral region. — int_spec • Spectroscopy Analysis Tools (spant) Integrate a spectral region. — int_spec • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -118,7 +118,7 @@ Value
diff --git a/docs/reference/interleave_dyns.html b/docs/reference/interleave_dyns.html
index effe5543..441eff27 100644
--- a/docs/reference/interleave_dyns.html
+++ b/docs/reference/interleave_dyns.html
@@ -1,5 +1,5 @@
-Interleave the first and second half of a dynamic series. — interleave_dyns • Spectroscopy Analysis Tools (spant) Interleave the first and second half of a dynamic series. — interleave_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/inv_even_dyns.html b/docs/reference/inv_even_dyns.html
index 9f9d4fff..dcb781dc 100644
--- a/docs/reference/inv_even_dyns.html
+++ b/docs/reference/inv_even_dyns.html
@@ -1,5 +1,5 @@
-Invert even numbered dynamic scans starting from 1 (2,4,6...). — inv_even_dyns • Spectroscopy Analysis Tools (spant) Invert even numbered dynamic scans starting from 1 (2,4,6...). — inv_even_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/inv_odd_dyns.html b/docs/reference/inv_odd_dyns.html
index 26212e2b..78d64660 100644
--- a/docs/reference/inv_odd_dyns.html
+++ b/docs/reference/inv_odd_dyns.html
@@ -1,5 +1,5 @@
-Invert odd numbered dynamic scans starting from 1 (1,3,5...). — inv_odd_dyns • Spectroscopy Analysis Tools (spant) Invert odd numbered dynamic scans starting from 1 (1,3,5...). — inv_odd_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/is.def.html b/docs/reference/is.def.html
index f196ffd0..a67b9eba 100644
--- a/docs/reference/is.def.html
+++ b/docs/reference/is.def.html
@@ -1,5 +1,5 @@
-Check if an object is defined, which is the same as being not NULL. — is.def • Spectroscopy Analysis Tools (spant) Check if an object is defined, which is the same as being not NULL. — is.def • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/is_fd.html b/docs/reference/is_fd.html
index 3b0ca165..18a193aa 100644
--- a/docs/reference/is_fd.html
+++ b/docs/reference/is_fd.html
@@ -1,7 +1,5 @@
-Check if the chemical shift dimension of an MRS data object is in the
-frequency domain. — is_fd • Spectroscopy Analysis Tools (spant) Check if the chemical shift dimension of an MRS data object is in the frequency domain. — is_fd • Spectroscopy Analysis Tools (spant) Transform 2D MRSI data from k-space to image space in the x-y direction. — kspace2img_xy • Spectroscopy Analysis Tools (spant) Transform 2D MRSI data from k-space to image space in the x-y direction. — kspace2img_xy • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/l2_reg.html b/docs/reference/l2_reg.html
index 3d781d80..21aa9849 100644
--- a/docs/reference/l2_reg.html
+++ b/docs/reference/l2_reg.html
@@ -1,5 +1,5 @@
-Perform l2 regularisation artefact suppression. — l2_reg • Spectroscopy Analysis Tools (spant) Perform l2 regularisation artefact suppression. — l2_reg • Spectroscopy Analysis Tools (spant) Apply line-broadening (apodisation) to MRS data or basis object. — lb • Spectroscopy Analysis Tools (spant) Apply line-broadening (apodisation) to MRS data or basis object. — lb • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -123,7 +123,7 @@ Value
diff --git a/docs/reference/lofdc.html b/docs/reference/lofdc.html
index 5419b1ec..31347a25 100644
--- a/docs/reference/lofdc.html
+++ b/docs/reference/lofdc.html
@@ -1,5 +1,5 @@
-Correct linear frequency drift. — lofdc • Spectroscopy Analysis Tools (spant) Correct linear frequency drift. — lofdc • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -138,7 +138,7 @@ Value
diff --git a/docs/reference/lw2alpha.html b/docs/reference/lw2alpha.html
index b83db682..25da229b 100644
--- a/docs/reference/lw2alpha.html
+++ b/docs/reference/lw2alpha.html
@@ -1,7 +1,5 @@
-Covert a linewidth in Hz to an equivalent alpha value in the time-domain ie:
-x * exp(-t * alpha). — lw2alpha • Spectroscopy Analysis Tools (spant) Covert a linewidth in Hz to an equivalent alpha value in the time-domain ie: x * exp(-t * alpha). — lw2alpha • Spectroscopy Analysis Tools (spant) Covert a linewidth in Hz to an equivalent beta value in the time-domain ie:
-x * exp(-t * t * beta). — lw2beta • Spectroscopy Analysis Tools (spant) Covert a linewidth in Hz to an equivalent beta value in the time-domain ie: x * exp(-t * t * beta). — lw2beta • Spectroscopy Analysis Tools (spant) Make a basis-set object from a directory containing LCModel formatted RAW
-files. — make_basis_from_raw • Spectroscopy Analysis Tools (spant) Make a basis-set object from a directory containing LCModel formatted RAW files. — make_basis_from_raw • Spectroscopy Analysis Tools (spant) Mask an MRS dataset in the dynamic dimension. — mask_dyns • Spectroscopy Analysis Tools (spant) Mask an MRS dataset in the dynamic dimension. — mask_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/mask_fit_res.html b/docs/reference/mask_fit_res.html
index 97baaa3f..ebd91a99 100644
--- a/docs/reference/mask_fit_res.html
+++ b/docs/reference/mask_fit_res.html
@@ -1,5 +1,5 @@
-Mask fit result spectra depending on a vector of bool values. — mask_fit_res • Spectroscopy Analysis Tools (spant) Mask fit result spectra depending on a vector of bool values. — mask_fit_res • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -116,7 +116,7 @@ Value
diff --git a/docs/reference/mask_xy.html b/docs/reference/mask_xy.html
index 11bb577c..b0d38619 100644
--- a/docs/reference/mask_xy.html
+++ b/docs/reference/mask_xy.html
@@ -1,5 +1,5 @@
-Mask an MRSI dataset in the x-y direction — mask_xy • Spectroscopy Analysis Tools (spant) Mask an MRSI dataset in the x-y direction — mask_xy • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/mask_xy_corners.html b/docs/reference/mask_xy_corners.html
index 09b16cd2..2d13839d 100644
--- a/docs/reference/mask_xy_corners.html
+++ b/docs/reference/mask_xy_corners.html
@@ -1,5 +1,5 @@
-Mask the four corners of an MRSI dataset in the x-y plane. — mask_xy_corners • Spectroscopy Analysis Tools (spant) Mask the four corners of an MRSI dataset in the x-y plane. — mask_xy_corners • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/mask_xy_ellipse.html b/docs/reference/mask_xy_ellipse.html
index 1d8b02e4..e2e749ef 100644
--- a/docs/reference/mask_xy_ellipse.html
+++ b/docs/reference/mask_xy_ellipse.html
@@ -1,7 +1,5 @@
-Mask the voxels outside an elliptical region spanning the MRSI dataset in the
-x-y plane. — mask_xy_ellipse • Spectroscopy Analysis Tools (spant) Mask the voxels outside an elliptical region spanning the MRSI dataset in the x-y plane. — mask_xy_ellipse • Spectroscopy Analysis Tools (spant) Mask a 2D MRSI dataset in the x-y dimension. — mask_xy_mat • Spectroscopy Analysis Tools (spant) Mask a 2D MRSI dataset in the x-y dimension. — mask_xy_mat • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Value
diff --git a/docs/reference/mat2mrs_data.html b/docs/reference/mat2mrs_data.html
index 2e2895f3..ae55665f 100644
--- a/docs/reference/mat2mrs_data.html
+++ b/docs/reference/mat2mrs_data.html
@@ -1,7 +1,5 @@
-Convert a matrix (with spectral points in the column dimension and dynamics
-in the row dimensions) into a mrs_data object. — mat2mrs_data • Spectroscopy Analysis Tools (spant) Convert a matrix (with spectral points in the column dimension and dynamics in the row dimensions) into a mrs_data object. — mat2mrs_data • Spectroscopy Analysis Tools (spant) Matrix exponential function taken from complexplus package to reduce the
-number of spant dependencies. — matexp • Spectroscopy Analysis Tools (spant) Matrix exponential function taken from complexplus package to reduce the number of spant dependencies. — matexp • Spectroscopy Analysis Tools (spant) Apply the max operator to an MRS dataset. — max_mrs • Spectroscopy Analysis Tools (spant) Apply the max operator to an MRS dataset. — max_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/max_mrs_interp.html b/docs/reference/max_mrs_interp.html
index e4474764..52e63f3e 100644
--- a/docs/reference/max_mrs_interp.html
+++ b/docs/reference/max_mrs_interp.html
@@ -1,5 +1,5 @@
-Apply the max operator to an interpolated MRS dataset. — max_mrs_interp • Spectroscopy Analysis Tools (spant) Apply the max operator to an interpolated MRS dataset. — max_mrs_interp • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/mean.list.html b/docs/reference/mean.list.html
index b8eb3463..048306fd 100644
--- a/docs/reference/mean.list.html
+++ b/docs/reference/mean.list.html
@@ -1,5 +1,5 @@
-Calculate the mean spectrum from an mrs_data object. — mean.list • Spectroscopy Analysis Tools (spant) Calculate the mean spectrum from an mrs_data object. — mean.list • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/mean.mrs_data.html b/docs/reference/mean.mrs_data.html
index 5531a28d..79515014 100644
--- a/docs/reference/mean.mrs_data.html
+++ b/docs/reference/mean.mrs_data.html
@@ -1,5 +1,5 @@
-Calculate the mean spectrum from an mrs_data object. — mean.mrs_data • Spectroscopy Analysis Tools (spant) Calculate the mean spectrum from an mrs_data object. — mean.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/mean_dyn_blocks.html b/docs/reference/mean_dyn_blocks.html
index 10467098..4c042448 100644
--- a/docs/reference/mean_dyn_blocks.html
+++ b/docs/reference/mean_dyn_blocks.html
@@ -1,5 +1,5 @@
-Calculate the mean of adjacent dynamic scans. — mean_dyn_blocks • Spectroscopy Analysis Tools (spant) Calculate the mean of adjacent dynamic scans. — mean_dyn_blocks • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/mean_dyn_pairs.html b/docs/reference/mean_dyn_pairs.html
index 63e909ea..1a241126 100644
--- a/docs/reference/mean_dyn_pairs.html
+++ b/docs/reference/mean_dyn_pairs.html
@@ -1,5 +1,5 @@
-Calculate the pairwise means across a dynamic data set. — mean_dyn_pairs • Spectroscopy Analysis Tools (spant) Calculate the pairwise means across a dynamic data set. — mean_dyn_pairs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/mean_dyns.html b/docs/reference/mean_dyns.html
index 73fdbfa7..0daa27df 100644
--- a/docs/reference/mean_dyns.html
+++ b/docs/reference/mean_dyns.html
@@ -1,5 +1,5 @@
-Calculate the mean dynamic data. — mean_dyns • Spectroscopy Analysis Tools (spant) Calculate the mean dynamic data. — mean_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/mean_mrs_list.html b/docs/reference/mean_mrs_list.html
index 808b6c50..10d842c0 100644
--- a/docs/reference/mean_mrs_list.html
+++ b/docs/reference/mean_mrs_list.html
@@ -1,5 +1,5 @@
-Return the mean of a list of mrs_data objects. — mean_mrs_list • Spectroscopy Analysis Tools (spant) Return the mean of a list of mrs_data objects. — mean_mrs_list • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/mean_vec_blocks.html b/docs/reference/mean_vec_blocks.html
index 8fc92eaa..dd78b122 100644
--- a/docs/reference/mean_vec_blocks.html
+++ b/docs/reference/mean_vec_blocks.html
@@ -1,5 +1,5 @@
-Calculate the mean of adjacent blocks in a vector. — mean_vec_blocks • Spectroscopy Analysis Tools (spant) Calculate the mean of adjacent blocks in a vector. — mean_vec_blocks • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/median_dyns.html b/docs/reference/median_dyns.html
index 1039d4b5..9a085b10 100644
--- a/docs/reference/median_dyns.html
+++ b/docs/reference/median_dyns.html
@@ -1,5 +1,5 @@
-Calculate the median dynamic data. — median_dyns • Spectroscopy Analysis Tools (spant) Calculate the median dynamic data. — median_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/mod_td.html b/docs/reference/mod_td.html
index 76ad0a40..141ef09e 100644
--- a/docs/reference/mod_td.html
+++ b/docs/reference/mod_td.html
@@ -1,5 +1,5 @@
-Apply the Modulus operator to the time-domain MRS signal. — mod_td • Spectroscopy Analysis Tools (spant) Apply the Modulus operator to the time-domain MRS signal. — mod_td • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/mrs_data2basis.html b/docs/reference/mrs_data2basis.html
index 62f7d749..11797b91 100644
--- a/docs/reference/mrs_data2basis.html
+++ b/docs/reference/mrs_data2basis.html
@@ -1,7 +1,5 @@
-Convert an mrs_data object to basis object - where basis signals are spread
-across the dynamic dimension in the MRS data. — mrs_data2basis • Spectroscopy Analysis Tools (spant) Convert an mrs_data object to basis object - where basis signals are spread across the dynamic dimension in the MRS data. — mrs_data2basis • Spectroscopy Analysis Tools (spant) Create a BIDS file structure from a vector of MRS data paths or list of mrs_data objects. — mrs_data2bids • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Create a BIDS file structure from a vector of MRS data paths or list of mrs_data objects.
+ Source: R/fmrs.R
+ mrs_data2bids.Rd
+
+
+
+ Create a BIDS file structure from a vector of MRS data paths or list of
+mrs_data objects.
+
+
+
+ mrs_data2bids(
+ mrs_data,
+ output_dir,
+ suffix = NULL,
+ sub = NULL,
+ ses = NULL,
+ task = NULL,
+ acq = NULL,
+ nuc = NULL,
+ voi = NULL,
+ rec = NULL,
+ run = NULL,
+ echo = NULL,
+ inv = NULL,
+ skip_existing = TRUE
+)
+
+
+
+ Arguments
+ - mrs_data
+vector of MRS data paths or list of mrs_data objects.
- output_dir
+the base directory to create the BIDS structure.
- suffix
+optional vector of file suffixes. Default behaviour is to
+automatically determine these from the input data, however it is recommended
+that they are specified to allow more efficient skipping of existing data.
- sub
+optional vector of subject labels. If not specified, these will be
+automatically generated as a series of increasing zero-padded integer values
+corresponding to the mrs_data input indices.
- ses
+optional vector of session labels.
- task
+optional vector of task labels.
- acq
+optional vector of acquisition labels.
- nuc
+optional vector of nucleus labels.
- voi
+optional vector of volume of interest labels.
- rec
+optional vector of reconstruction labels.
- run
+optional vector of run indices.
- echo
+optional vector of echo time indices.
- inv
+optional vector of inversion indices.
- skip_existing
+skip any data files that have already been converted.
+Defaults to TRUE, set to FALSE to force an overwrite of any existing data
+files.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/mrs_data2mat.html b/docs/reference/mrs_data2mat.html
index cf5ff28c..9e47688a 100644
--- a/docs/reference/mrs_data2mat.html
+++ b/docs/reference/mrs_data2mat.html
@@ -1,7 +1,5 @@
-Convert mrs_data object to a matrix, with spectral points in the column
-dimension and dynamics in the row dimension. — mrs_data2mat • Spectroscopy Analysis Tools (spant) Convert mrs_data object to a matrix, with spectral points in the column dimension and dynamics in the row dimension. — mrs_data2mat • Spectroscopy Analysis Tools (spant) Convert mrs_data object to a matrix, with spectral points in the column dimension and dynamics in the row dimension. — mrs_data2spec_mat • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Convert mrs_data object to a matrix, with spectral points in the column dimension and dynamics in the row dimension.
+ Source: R/mrs_data_proc.R
+ mrs_data2spec_mat.Rd
+
+
+
+ Convert mrs_data object to a matrix, with spectral points in the column
+dimension and dynamics in the row dimension.
+
+
+
+ mrs_data2spec_mat(mrs_data, collapse = TRUE)
+
+
+
+ Arguments
+ - mrs_data
+MRS data object or list of MRS data objects.
- collapse
+collapse all other dimensions along the dynamic dimension, eg
+a 16x16 MRSI grid would be first collapsed across 256 dynamic scans.
+
+ Value
+
+
+MRS data matrix.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/mrs_data2vec.html b/docs/reference/mrs_data2vec.html
index fb172d68..a1fd654d 100644
--- a/docs/reference/mrs_data2vec.html
+++ b/docs/reference/mrs_data2vec.html
@@ -1,5 +1,5 @@
-Convert mrs_data object to a vector. — mrs_data2vec • Spectroscopy Analysis Tools (spant) Convert mrs_data object to a vector. — mrs_data2vec • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -126,7 +126,7 @@ Value
diff --git a/docs/reference/mvfftshift.html b/docs/reference/mvfftshift.html
index 92b0841b..976b3410 100644
--- a/docs/reference/mvfftshift.html
+++ b/docs/reference/mvfftshift.html
@@ -1,7 +1,5 @@
-Perform a fftshift on a matrix, with each column replaced by its shifted
-result. — mvfftshift • Spectroscopy Analysis Tools (spant) Perform a fftshift on a matrix, with each column replaced by its shifted result. — mvfftshift • Spectroscopy Analysis Tools (spant) Perform an ifftshift on a matrix, with each column replaced by its shifted
-result. — mvifftshift • Spectroscopy Analysis Tools (spant) Perform an ifftshift on a matrix, with each column replaced by its shifted result. — mvifftshift • Spectroscopy Analysis Tools (spant) Print fit coordinates from a single index. — n2coord • Spectroscopy Analysis Tools (spant) Print fit coordinates from a single index. — n2coord • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/nifti_flip_lr.html b/docs/reference/nifti_flip_lr.html
index 730abe3c..19860b3c 100644
--- a/docs/reference/nifti_flip_lr.html
+++ b/docs/reference/nifti_flip_lr.html
@@ -1,9 +1,5 @@
-Flip the x data dimension order of a nifti image. This corresponds to
-flipping MRI data in the left-right direction, assuming the data in save in
-neurological format (can check with fslorient program). — nifti_flip_lr • Spectroscopy Analysis Tools (spant) Flip the x data dimension order of a nifti image. This corresponds to flipping MRI data in the left-right direction, assuming the data in save in neurological format (can check with fslorient program). — nifti_flip_lr • Spectroscopy Analysis Tools (spant) Export a one-page pdf of a single fit result — one_page_pdf • Spectroscopy Analysis Tools (spant) Export a one-page pdf of a single fit result — one_page_pdf • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -108,7 +108,7 @@ Arguments
diff --git a/docs/reference/ortho3.html b/docs/reference/ortho3.html
index 13ade97d..5d7dd2fd 100644
--- a/docs/reference/ortho3.html
+++ b/docs/reference/ortho3.html
@@ -1,5 +1,5 @@
-Display an orthographic projection plot of a nifti object. — ortho3 • Spectroscopy Analysis Tools (spant) Display an orthographic projection plot of a nifti object. — ortho3 • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -172,7 +172,7 @@ Arguments
diff --git a/docs/reference/ortho3_inter.html b/docs/reference/ortho3_inter.html
index 090cc5e5..15948899 100644
--- a/docs/reference/ortho3_inter.html
+++ b/docs/reference/ortho3_inter.html
@@ -1,5 +1,5 @@
-Display an interactive orthographic projection plot of a nifti object. — ortho3_inter • Spectroscopy Analysis Tools (spant) Display an interactive orthographic projection plot of a nifti object. — ortho3_inter • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -132,7 +132,7 @@ Arguments
diff --git a/docs/reference/peak_info.html b/docs/reference/peak_info.html
index 09058bd8..41c8ffaf 100644
--- a/docs/reference/peak_info.html
+++ b/docs/reference/peak_info.html
@@ -1,7 +1,5 @@
-Search for the highest peak in a spectral region and return the frequency,
-height and FWHM. — peak_info • Spectroscopy Analysis Tools (spant) Search for the highest peak in a spectral region and return the frequency, height and FWHM. — peak_info • Spectroscopy Analysis Tools (spant) Papoulis-Gerchberg (PG) algorithm method for k-space extrapolation. — pg_extrap_xy • Spectroscopy Analysis Tools (spant) Papoulis-Gerchberg (PG) algorithm method for k-space extrapolation. — pg_extrap_xy • Spectroscopy Analysis Tools (spant) Apply phasing parameters to MRS data. — phase • Spectroscopy Analysis Tools (spant) Apply phasing parameters to MRS data. — phase • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/phase_ref_1h_brain.html b/docs/reference/phase_ref_1h_brain.html
new file mode 100644
index 00000000..8707a74a
--- /dev/null
+++ b/docs/reference/phase_ref_1h_brain.html
@@ -0,0 +1,131 @@
+
+Corrected zero order phase and chemical shift offset in 1H MRS data from the brain. — phase_ref_1h_brain • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Corrected zero order phase and chemical shift offset in 1H MRS data from the brain.
+ Source: R/rats.R
+ phase_ref_1h_brain.Rd
+
+
+
+ Corrected zero order phase and chemical shift offset in 1H MRS data from the
+brain.
+
+
+
+ phase_ref_1h_brain(mrs_data, mean_ref = FALSE, ret_corr_only = TRUE)
+
+
+
+ Arguments
+ - mrs_data
+MRS data to be corrected.
- mean_ref
+apply the phase and offset of the mean spectrum to all
+others. Default is FALSE.
- ret_corr_only
+return the corrected data only.
+
+ Value
+
+
+corrected MRS data.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/plot.fit_result.html b/docs/reference/plot.fit_result.html
index e54d3bc1..836a53ee 100644
--- a/docs/reference/plot.fit_result.html
+++ b/docs/reference/plot.fit_result.html
@@ -1,5 +1,5 @@
-Plot the fitting results of an object of class fit_result. — plot.fit_result • Spectroscopy Analysis Tools (spant) Plot the fitting results of an object of class fit_result. — plot.fit_result • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -207,7 +207,7 @@ Arguments
diff --git a/docs/reference/plot.mrs_data.html b/docs/reference/plot.mrs_data.html
index fabcc35b..bb2ec651 100644
--- a/docs/reference/plot.mrs_data.html
+++ b/docs/reference/plot.mrs_data.html
@@ -1,5 +1,5 @@
-Plotting method for objects of class mrs_data. — plot.mrs_data • Spectroscopy Analysis Tools (spant) Plotting method for objects of class mrs_data. — plot.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -287,7 +287,7 @@ Arguments
diff --git a/docs/reference/plot_bc.html b/docs/reference/plot_bc.html
index 4f8309b4..b48142cc 100644
--- a/docs/reference/plot_bc.html
+++ b/docs/reference/plot_bc.html
@@ -1,5 +1,5 @@
-Convenience function to plot a baseline estimate with the original data. — plot_bc • Spectroscopy Analysis Tools (spant) Convenience function to plot a baseline estimate with the original data. — plot_bc • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -108,7 +108,7 @@ Arguments
diff --git a/docs/reference/plot_reg.html b/docs/reference/plot_reg.html
index ae1acbe7..2addb2f6 100644
--- a/docs/reference/plot_reg.html
+++ b/docs/reference/plot_reg.html
@@ -1,5 +1,5 @@
-Plot regressors as an image. — plot_reg • Spectroscopy Analysis Tools (spant) Plot regressors as an image. — plot_reg • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/plot_slice_fit.html b/docs/reference/plot_slice_fit.html
index fbc7b560..57f1af8a 100644
--- a/docs/reference/plot_slice_fit.html
+++ b/docs/reference/plot_slice_fit.html
@@ -1,5 +1,5 @@
-Plot a 2D slice from an MRSI fit result object. — plot_slice_fit • Spectroscopy Analysis Tools (spant) Plot a 2D slice from an MRSI fit result object. — plot_slice_fit • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -129,7 +129,7 @@ Arguments
diff --git a/docs/reference/plot_slice_fit_inter.html b/docs/reference/plot_slice_fit_inter.html
index 4eed104a..da105a7d 100644
--- a/docs/reference/plot_slice_fit_inter.html
+++ b/docs/reference/plot_slice_fit_inter.html
@@ -1,5 +1,5 @@
-Plot a 2D slice from an MRSI fit result object. — plot_slice_fit_inter • Spectroscopy Analysis Tools (spant) Plot a 2D slice from an MRSI fit result object. — plot_slice_fit_inter • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -134,7 +134,7 @@ Arguments
diff --git a/docs/reference/plot_slice_map.html b/docs/reference/plot_slice_map.html
index 553e9ac8..ffb2a134 100644
--- a/docs/reference/plot_slice_map.html
+++ b/docs/reference/plot_slice_map.html
@@ -1,5 +1,5 @@
-Plot a slice from a 7 dimensional array. — plot_slice_map • Spectroscopy Analysis Tools (spant) Plot a slice from a 7 dimensional array. — plot_slice_map • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -153,7 +153,7 @@ Arguments
diff --git a/docs/reference/plot_slice_map_inter.html b/docs/reference/plot_slice_map_inter.html
index 40d33b42..90968f66 100644
--- a/docs/reference/plot_slice_map_inter.html
+++ b/docs/reference/plot_slice_map_inter.html
@@ -1,7 +1,5 @@
-Plot an interactive slice map from a data array where voxels can be selected
-to display a corresponding spectrum. — plot_slice_map_inter • Spectroscopy Analysis Tools (spant) Plot an interactive slice map from a data array where voxels can be selected to display a corresponding spectrum. — plot_slice_map_inter • Spectroscopy Analysis Tools (spant) Plot the spectral standard deviation. — plot_spec_sd • Spectroscopy Analysis Tools (spant) Plot the spectral standard deviation. — plot_spec_sd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Arguments
diff --git a/docs/reference/plot_voi_overlay.html b/docs/reference/plot_voi_overlay.html
index 9a782e88..bbbbf35e 100644
--- a/docs/reference/plot_voi_overlay.html
+++ b/docs/reference/plot_voi_overlay.html
@@ -1,5 +1,5 @@
-Plot a volume as an image overlay. — plot_voi_overlay • Spectroscopy Analysis Tools (spant) Plot a volume as an image overlay. — plot_voi_overlay • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -116,7 +116,7 @@ Arguments
diff --git a/docs/reference/plot_voi_overlay_seg.html b/docs/reference/plot_voi_overlay_seg.html
index 3d4e74ff..0e800ff2 100644
--- a/docs/reference/plot_voi_overlay_seg.html
+++ b/docs/reference/plot_voi_overlay_seg.html
@@ -1,5 +1,5 @@
-Plot a volume as an overlay on a segmented brain volume. — plot_voi_overlay_seg • Spectroscopy Analysis Tools (spant) Plot a volume as an overlay on a segmented brain volume. — plot_voi_overlay_seg • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Arguments
diff --git a/docs/reference/ppm.html b/docs/reference/ppm.html
index c352327a..ee4696e2 100644
--- a/docs/reference/ppm.html
+++ b/docs/reference/ppm.html
@@ -1,5 +1,5 @@
-Return the ppm scale of an MRS dataset or fit result. — ppm • Spectroscopy Analysis Tools (spant) Return the ppm scale of an MRS dataset or fit result. — ppm • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -132,7 +132,7 @@ Value
diff --git a/docs/reference/precomp.html b/docs/reference/precomp.html
index 822d7336..df3d2c6c 100644
--- a/docs/reference/precomp.html
+++ b/docs/reference/precomp.html
@@ -1,7 +1,5 @@
-Save function results to file and load on subsequent calls to avoid repeat
-computation. — precomp • Spectroscopy Analysis Tools (spant) Save function results to file and load on subsequent calls to avoid repeat computation. — precomp • Spectroscopy Analysis Tools (spant) Preprocess and perform quality assessment of a single SVS data set. — preproc_svs • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Preprocess and perform quality assessment of a single SVS data set.
+ Source: R/fmrs.R
+ preproc_svs.Rd
+
+
+
+ Preprocess and perform quality assessment of a single SVS data set.
+
+
+
+ preproc_svs(path, label = NULL, output_dir = NULL, ref_inds = NULL)
+
+
+
+ Arguments
+ - path
+path to the fMRS data file or IMA directory.
- label
+a label to describe the data set.
- output_dir
+output directory.
- ref_inds
+a vector of 1-based indices for any water reference dynamic
+scans.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/preproc_svs_dataset.html b/docs/reference/preproc_svs_dataset.html
new file mode 100644
index 00000000..07c3a29b
--- /dev/null
+++ b/docs/reference/preproc_svs_dataset.html
@@ -0,0 +1,148 @@
+
+Preprocess and perform quality assessment of one or more SVS data sets. — preproc_svs_dataset • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Preprocess and perform quality assessment of one or more SVS data sets.
+ Source: R/fmrs.R
+ preproc_svs_dataset.Rd
+
+
+
+ Preprocess and perform quality assessment of one or more SVS data sets.
+
+
+
+ preproc_svs_dataset(
+ paths,
+ labels = NULL,
+ output_dir = "spant_analysis",
+ exclude_labels = NULL,
+ overwrite = FALSE,
+ ref_inds = NULL,
+ return_results = FALSE
+)
+
+
+
+ Arguments
+ - paths
+paths to the fMRS data file or IMA directory.
- labels
+labels to describe each data set.
- output_dir
+output directory.
- exclude_labels
+vector of labels of scans to exclude, eg poor quality
+data.
- overwrite
+overwrite saved results, defaults to FALSE.
- ref_inds
+a vector of 1-based indices for any water reference dynamic
+scans.
- return_results
+function will return key outputs, defaults to FALSE.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/print.fit_result.html b/docs/reference/print.fit_result.html
index 297f28dc..5f434e57 100644
--- a/docs/reference/print.fit_result.html
+++ b/docs/reference/print.fit_result.html
@@ -1,5 +1,5 @@
-Print a summary of an object of class fit_result. — print.fit_result • Spectroscopy Analysis Tools (spant) Print a summary of an object of class fit_result. — print.fit_result • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -105,7 +105,7 @@ Arguments
diff --git a/docs/reference/print.mrs_data.html b/docs/reference/print.mrs_data.html
index 51199017..e1561eb2 100644
--- a/docs/reference/print.mrs_data.html
+++ b/docs/reference/print.mrs_data.html
@@ -1,5 +1,5 @@
-Print a summary of mrs_data parameters. — print.mrs_data • Spectroscopy Analysis Tools (spant) Print a summary of mrs_data parameters. — print.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -109,7 +109,7 @@ Arguments
diff --git a/docs/reference/qn_states.html b/docs/reference/qn_states.html
index 0f42f2f9..d7aa6715 100644
--- a/docs/reference/qn_states.html
+++ b/docs/reference/qn_states.html
@@ -1,5 +1,5 @@
-Get the quantum coherence matrix for a spin system. — qn_states • Spectroscopy Analysis Tools (spant) Get the quantum coherence matrix for a spin system. — qn_states • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/rats.html b/docs/reference/rats.html
index 5a39a396..93585e08 100644
--- a/docs/reference/rats.html
+++ b/docs/reference/rats.html
@@ -1,5 +1,5 @@
-Robust Alignment to a Target Spectrum (RATS). — rats • Spectroscopy Analysis Tools (spant) Robust Alignment to a Target Spectrum (RATS). — rats • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -207,7 +207,7 @@ Value
diff --git a/docs/reference/re_weighting.html b/docs/reference/re_weighting.html
index d21caf21..8b0b070a 100644
--- a/docs/reference/re_weighting.html
+++ b/docs/reference/re_weighting.html
@@ -1,5 +1,5 @@
-Apply a weighting to the FID to enhance spectral resolution. — re_weighting • Spectroscopy Analysis Tools (spant) Apply a weighting to the FID to enhance spectral resolution. — re_weighting • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/read_basis.html b/docs/reference/read_basis.html
index da9b94af..eb6f8557 100644
--- a/docs/reference/read_basis.html
+++ b/docs/reference/read_basis.html
@@ -1,5 +1,5 @@
-Read a basis file in LCModel .basis format. — read_basis • Spectroscopy Analysis Tools (spant) Read a basis file in LCModel .basis format. — read_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/read_ima_coil_dir.html b/docs/reference/read_ima_coil_dir.html
index 28c02de0..4f073cd8 100644
--- a/docs/reference/read_ima_coil_dir.html
+++ b/docs/reference/read_ima_coil_dir.html
@@ -1,9 +1,5 @@
-Read a directory containing Siemens MRS IMA files and combine along the coil
-dimension. Note that the coil ID is inferred from the sorted file name and
-should be checked when consistency is required between two directories. — read_ima_coil_dir • Spectroscopy Analysis Tools (spant) Read a directory containing Siemens MRS IMA files and combine along the coil dimension. Note that the coil ID is inferred from the sorted file name and should be checked when consistency is required between two directories. — read_ima_coil_dir • Spectroscopy Analysis Tools (spant) Read a directory containing Siemens MRS IMA files and combine along the
-dynamic dimension. Note that the coil ID is inferred from the sorted file
-name and should be checked when consistency is required. — read_ima_dyn_dir • Spectroscopy Analysis Tools (spant) Read a directory containing Siemens MRS IMA files and combine along the dynamic dimension. Note that the coil ID is inferred from the sorted file name and should be checked when consistency is required. — read_ima_dyn_dir • Spectroscopy Analysis Tools (spant) Read an LCModel formatted coord file containing fit information. — read_lcm_coord • Spectroscopy Analysis Tools (spant) Read an LCModel formatted coord file containing fit information. — read_lcm_coord • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -107,7 +107,7 @@ Value
diff --git a/docs/reference/read_mrs.html b/docs/reference/read_mrs.html
index 3ac2a36b..2cf36b20 100644
--- a/docs/reference/read_mrs.html
+++ b/docs/reference/read_mrs.html
@@ -1,5 +1,5 @@
-Read MRS data from a file. — read_mrs • Spectroscopy Analysis Tools (spant) Read MRS data from a file. — read_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -88,7 +88,8 @@ Read MRS data from a file.
full_fid = FALSE,
omit_svs_ref_scans = TRUE,
verbose = FALSE,
- extra = NULL
+ extra = NULL,
+ fid_filt_dist = NULL
)
@@ -140,6 +141,13 @@ Arguments
an optional data frame to provide additional variables for use
in subsequent analysis steps, eg id or grouping variables.
fid_filt_dist
+indicate if the data has a distorted FID due to a
+brick-wall filter being used to downsample the data. Default is to auto
+detect this from the data, but TRUE or FALSE options can be given to override
+detection.
Value
@@ -183,7 +191,7 @@ Examples
diff --git a/docs/reference/read_mrs_tqn.html b/docs/reference/read_mrs_tqn.html
index 5766362f..84bdaf3a 100644
--- a/docs/reference/read_mrs_tqn.html
+++ b/docs/reference/read_mrs_tqn.html
@@ -1,5 +1,5 @@
-Read MRS data using the TARQUIN software package. — read_mrs_tqn • Spectroscopy Analysis Tools (spant) Read MRS data using the TARQUIN software package. — read_mrs_tqn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -131,7 +131,7 @@ Examples
diff --git a/docs/reference/read_pulse_ascii.html b/docs/reference/read_pulse_ascii.html
index c9e0d43c..ab11c9cc 100644
--- a/docs/reference/read_pulse_ascii.html
+++ b/docs/reference/read_pulse_ascii.html
@@ -1,5 +1,5 @@
-Read an ASCII formatted pulse file. — read_pulse_ascii • Spectroscopy Analysis Tools (spant) Read an ASCII formatted pulse file. — read_pulse_ascii • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/read_pulse_bruker.html b/docs/reference/read_pulse_bruker.html
index c92bf76a..dbe9073b 100644
--- a/docs/reference/read_pulse_bruker.html
+++ b/docs/reference/read_pulse_bruker.html
@@ -1,5 +1,5 @@
-Read a Bruker formatted pulse file — read_pulse_bruker • Spectroscopy Analysis Tools (spant) Read a Bruker formatted pulse file — read_pulse_bruker • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/read_pulse_pta.html b/docs/reference/read_pulse_pta.html
index 72e1b6d4..a0fac3c3 100644
--- a/docs/reference/read_pulse_pta.html
+++ b/docs/reference/read_pulse_pta.html
@@ -1,5 +1,5 @@
-Read a .pta formatted pulse file compatible with Siemens PulseTool. — read_pulse_pta • Spectroscopy Analysis Tools (spant) Read a .pta formatted pulse file compatible with Siemens PulseTool. — read_pulse_pta • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/read_siemens_txt_hdr.html b/docs/reference/read_siemens_txt_hdr.html
index 23fb8c70..3a17d87c 100644
--- a/docs/reference/read_siemens_txt_hdr.html
+++ b/docs/reference/read_siemens_txt_hdr.html
@@ -1,5 +1,5 @@
-Read the text format header found in Siemens IMA and TWIX data files. — read_siemens_txt_hdr • Spectroscopy Analysis Tools (spant) Read the text format header found in Siemens IMA and TWIX data files. — read_siemens_txt_hdr • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -78,7 +78,7 @@ Read the text format header found in Siemens IMA and TWIX data files.
- read_siemens_txt_hdr(input, version = "vd", verbose, offset = 0)
+ read_siemens_txt_hdr(input, version = "vd", verbose = FALSE, offset = 0)
@@ -118,7 +118,7 @@ Value
diff --git a/docs/reference/read_tqn_fit.html b/docs/reference/read_tqn_fit.html
index 4da6c25e..a1630420 100644
--- a/docs/reference/read_tqn_fit.html
+++ b/docs/reference/read_tqn_fit.html
@@ -1,5 +1,5 @@
-Reader for csv fit results generated by TARQUIN. — read_tqn_fit • Spectroscopy Analysis Tools (spant) Reader for csv fit results generated by TARQUIN. — read_tqn_fit • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -113,7 +113,7 @@ Examples
diff --git a/docs/reference/read_tqn_result.html b/docs/reference/read_tqn_result.html
index 36659714..68a3e98c 100644
--- a/docs/reference/read_tqn_result.html
+++ b/docs/reference/read_tqn_result.html
@@ -1,5 +1,5 @@
-Reader for csv results generated by TARQUIN. — read_tqn_result • Spectroscopy Analysis Tools (spant) Reader for csv results generated by TARQUIN. — read_tqn_result • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -117,7 +117,7 @@ Examples
diff --git a/docs/reference/recon_imag.html b/docs/reference/recon_imag.html
index d2a72225..5bc3b1eb 100644
--- a/docs/reference/recon_imag.html
+++ b/docs/reference/recon_imag.html
@@ -1,7 +1,5 @@
-Reconstruct complex time-domain data from the real part of frequency-domain
-data. — recon_imag • Spectroscopy Analysis Tools (spant) Reconstruct complex time-domain data from the real part of frequency-domain data. — recon_imag • Spectroscopy Analysis Tools (spant) Reconstruct complex time-domain data from the real part of frequency-domain
-data. — recon_imag_vec • Spectroscopy Analysis Tools (spant) Reconstruct complex time-domain data from the real part of frequency-domain data. — recon_imag_vec • Spectroscopy Analysis Tools (spant) Reconstruct 2D MRSI data from a twix file loaded with read_mrs. — recon_twix_2d_mrsi • Spectroscopy Analysis Tools (spant) Reconstruct 2D MRSI data from a twix file loaded with read_mrs. — recon_twix_2d_mrsi • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/rectangular_mask.html b/docs/reference/rectangular_mask.html
index a2117283..6e469bc9 100644
--- a/docs/reference/rectangular_mask.html
+++ b/docs/reference/rectangular_mask.html
@@ -1,5 +1,5 @@
-Create a rectangular mask stored as a matrix of logical values. — rectangular_mask • Spectroscopy Analysis Tools (spant) Create a rectangular mask stored as a matrix of logical values. — rectangular_mask • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -130,7 +130,7 @@ Value
diff --git a/docs/reference/reexports.html b/docs/reference/reexports.html
index 694a75d1..a59e8379 100644
--- a/docs/reference/reexports.html
+++ b/docs/reference/reexports.html
@@ -1,5 +1,5 @@
-Objects exported from other packages — reexports • Spectroscopy Analysis Tools (spant) Objects exported from other packages — reexports • Spectroscopy Analysis Tools (spant)
Spectroscopy Analysis Tools (spant)
- 2.21.0
+ 2.22.0
@@ -103,7 +103,7 @@ Objects exported from other packages
diff --git a/docs/reference/rep_array_dim.html b/docs/reference/rep_array_dim.html
index b9c49b4a..48c0a5ed 100644
--- a/docs/reference/rep_array_dim.html
+++ b/docs/reference/rep_array_dim.html
@@ -1,5 +1,5 @@
-Repeat an array over a given dimension. — rep_array_dim • Spectroscopy Analysis Tools (spant) Repeat an array over a given dimension. — rep_array_dim • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/rep_dyn.html b/docs/reference/rep_dyn.html
index 6bbfb0ef..89a4bb9b 100644
--- a/docs/reference/rep_dyn.html
+++ b/docs/reference/rep_dyn.html
@@ -1,5 +1,5 @@
-Replicate a scan in the dynamic dimension. — rep_dyn • Spectroscopy Analysis Tools (spant) Replicate a scan in the dynamic dimension. — rep_dyn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/rep_mrs.html b/docs/reference/rep_mrs.html
index 67730b5c..becb8f00 100644
--- a/docs/reference/rep_mrs.html
+++ b/docs/reference/rep_mrs.html
@@ -1,5 +1,5 @@
-Replicate a scan over a given dimension. — rep_mrs • Spectroscopy Analysis Tools (spant) Replicate a scan over a given dimension. — rep_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -138,7 +138,7 @@ Value
diff --git a/docs/reference/resample_basis.html b/docs/reference/resample_basis.html
index b0f2ab17..c7a6222a 100644
--- a/docs/reference/resample_basis.html
+++ b/docs/reference/resample_basis.html
@@ -1,5 +1,5 @@
-Resample a basis-set to match a mrs_data acquisition. — resample_basis • Spectroscopy Analysis Tools (spant) Resample a basis-set to match a mrs_data acquisition. — resample_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -116,7 +116,7 @@ Value
diff --git a/docs/reference/resample_img.html b/docs/reference/resample_img.html
index f1e7beaf..b0cc8f71 100644
--- a/docs/reference/resample_img.html
+++ b/docs/reference/resample_img.html
@@ -1,5 +1,5 @@
-Resample an image to match a target image space. — resample_img • Spectroscopy Analysis Tools (spant) Resample an image to match a target image space. — resample_img • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/resample_voi.html b/docs/reference/resample_voi.html
index 8fbfa836..a29ab096 100644
--- a/docs/reference/resample_voi.html
+++ b/docs/reference/resample_voi.html
@@ -1,7 +1,5 @@
-Resample a VOI to match a target image space using nearest-neighbour
-interpolation. — resample_voi • Spectroscopy Analysis Tools (spant) Resample a VOI to match a target image space using nearest-neighbour interpolation. — resample_voi • Spectroscopy Analysis Tools (spant) Reslice a nifti object to match the orientation of mrs data. — reslice_to_mrs • Spectroscopy Analysis Tools (spant) Reslice a nifti object to match the orientation of mrs data. — reslice_to_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/reson_table2mrs_data.html b/docs/reference/reson_table2mrs_data.html
index d75579ee..c5a2167a 100644
--- a/docs/reference/reson_table2mrs_data.html
+++ b/docs/reference/reson_table2mrs_data.html
@@ -1,5 +1,5 @@
-Generate mrs_data from a table of single Lorentzian resonances. — reson_table2mrs_data • Spectroscopy Analysis Tools (spant) Generate mrs_data from a table of single Lorentzian resonances. — reson_table2mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -119,7 +119,7 @@ Value
diff --git a/docs/reference/rm_dyns.html b/docs/reference/rm_dyns.html
index 5d5ef692..573e1f51 100644
--- a/docs/reference/rm_dyns.html
+++ b/docs/reference/rm_dyns.html
@@ -1,5 +1,5 @@
-Remove a subset of dynamic scans. — rm_dyns • Spectroscopy Analysis Tools (spant) Remove a subset of dynamic scans. — rm_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/scale_amp_molal.html b/docs/reference/scale_amp_molal.html
index aaeee1f2..7acb8cb0 100644
--- a/docs/reference/scale_amp_molal.html
+++ b/docs/reference/scale_amp_molal.html
@@ -1,7 +1,5 @@
-Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water). — scale_amp_molal • Spectroscopy Analysis Tools (spant) Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / kg of tissue water). — scale_amp_molal • Spectroscopy Analysis Tools (spant)
Spectroscopy Analysis Tools (spant)
- 2.21.0
+ 2.22.0
@@ -76,8 +74,7 @@
- Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water).
+ Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / kg of tissue water).
Source: R/amp_scaling.R
scale_amp_molal.Rd
@@ -163,7 +160,7 @@ Value
diff --git a/docs/reference/scale_amp_molal_pvc.html b/docs/reference/scale_amp_molal_pvc.html
index 962d6afc..4d194abd 100644
--- a/docs/reference/scale_amp_molal_pvc.html
+++ b/docs/reference/scale_amp_molal_pvc.html
@@ -1,7 +1,5 @@
-Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water). — scale_amp_molal_pvc • Spectroscopy Analysis Tools (spant)
@@ -75,8 +73,7 @@
- Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water).
+ Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / kg of tissue water).
Source: R/amp_scaling.R
scale_amp_molal_pvc.Rd
@@ -141,7 +138,7 @@ Value
diff --git a/docs/reference/scale_amp_molar.html b/docs/reference/scale_amp_molar.html
index 02358d91..dc87a338 100644
--- a/docs/reference/scale_amp_molar.html
+++ b/docs/reference/scale_amp_molar.html
@@ -1,7 +1,5 @@
-Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / Litre of tissue). — scale_amp_molar • Spectroscopy Analysis Tools (spant) Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / Litre of tissue). — scale_amp_molar • Spectroscopy Analysis Tools (spant) Convert default LCM/TARQUIN concentration scaling to molal units with partial
-volume correction. — scale_amp_molar2molal_pvc • Spectroscopy Analysis Tools (spant) Convert default LCM/TARQUIN concentration scaling to molal units with partial volume correction. — scale_amp_molar2molal_pvc • Spectroscopy Analysis Tools (spant) Scale fitted amplitudes to a ratio of signal amplitude. — scale_amp_ratio • Spectroscopy Analysis Tools (spant) Scale fitted amplitudes to a ratio of signal amplitude. — scale_amp_ratio • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -116,7 +116,7 @@ Value
diff --git a/docs/reference/scale_amp_ratio_value.html b/docs/reference/scale_amp_ratio_value.html
index 2036837a..6af8ac51 100644
--- a/docs/reference/scale_amp_ratio_value.html
+++ b/docs/reference/scale_amp_ratio_value.html
@@ -1,5 +1,5 @@
-Scale fitted amplitudes to a ratio of signal amplitude. — scale_amp_ratio_value • Spectroscopy Analysis Tools (spant) Scale fitted amplitudes to a ratio of signal amplitude. — scale_amp_ratio_value • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/scale_amp_water_ratio.html b/docs/reference/scale_amp_water_ratio.html
index 5b25e884..35a76b00 100644
--- a/docs/reference/scale_amp_water_ratio.html
+++ b/docs/reference/scale_amp_water_ratio.html
@@ -1,5 +1,5 @@
-Scale metabolite amplitudes as a ratio to the unsuppressed water amplitude. — scale_amp_water_ratio • Spectroscopy Analysis Tools (spant) Scale metabolite amplitudes as a ratio to the unsuppressed water amplitude. — scale_amp_water_ratio • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/scale_basis_amp.html b/docs/reference/scale_basis_amp.html
index 9401c3f1..5a58b5e5 100644
--- a/docs/reference/scale_basis_amp.html
+++ b/docs/reference/scale_basis_amp.html
@@ -1,5 +1,5 @@
-Scale a basis object by a scalar. — scale_basis_amp • Spectroscopy Analysis Tools (spant) Scale a basis object by a scalar. — scale_basis_amp • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/scale_basis_from_singlet.html b/docs/reference/scale_basis_from_singlet.html
index 0d542bc8..c9a19e77 100644
--- a/docs/reference/scale_basis_from_singlet.html
+++ b/docs/reference/scale_basis_from_singlet.html
@@ -1,5 +1,5 @@
-Scale a basis-set to be consistent with spant assumptions for water scaling. — scale_basis_from_singlet • Spectroscopy Analysis Tools (spant) Scale a basis-set to be consistent with spant assumptions for water scaling. — scale_basis_from_singlet • Spectroscopy Analysis Tools (spant)
Spectroscopy Analysis Tools (spant)
- 2.21.0
+ 2.22.0
@@ -127,7 +127,7 @@ Value
diff --git a/docs/reference/scale_mrs_amp.html b/docs/reference/scale_mrs_amp.html
index b5501a0d..990f058a 100644
--- a/docs/reference/scale_mrs_amp.html
+++ b/docs/reference/scale_mrs_amp.html
@@ -1,5 +1,5 @@
-Scale an mrs_data object by a scalar or vector or amplitudes. — scale_mrs_amp • Spectroscopy Analysis Tools (spant) Scale an mrs_data object by a scalar or vector or amplitudes. — scale_mrs_amp • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/scale_spec.html b/docs/reference/scale_spec.html
index 4f6ea835..6b3ddba4 100644
--- a/docs/reference/scale_spec.html
+++ b/docs/reference/scale_spec.html
@@ -1,5 +1,5 @@
-Scale mrs_data to a spectral region. — scale_spec • Spectroscopy Analysis Tools (spant) Scale mrs_data to a spectral region. — scale_spec • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -141,7 +141,7 @@ Value
diff --git a/docs/reference/sd.html b/docs/reference/sd.html
index ea1eec9f..3ae4dfd4 100644
--- a/docs/reference/sd.html
+++ b/docs/reference/sd.html
@@ -1,5 +1,5 @@
-Calculate the standard deviation spectrum from an mrs_data object. — sd • Spectroscopy Analysis Tools (spant) Calculate the standard deviation spectrum from an mrs_data object. — sd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/sd.mrs_data.html b/docs/reference/sd.mrs_data.html
index 3f92a49f..13bdda85 100644
--- a/docs/reference/sd.mrs_data.html
+++ b/docs/reference/sd.mrs_data.html
@@ -1,5 +1,5 @@
-Calculate the standard deviation spectrum from an mrs_data object. — sd.mrs_data • Spectroscopy Analysis Tools (spant) Calculate the standard deviation spectrum from an mrs_data object. — sd.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/seconds.html b/docs/reference/seconds.html
index b34d6627..467ee17f 100644
--- a/docs/reference/seconds.html
+++ b/docs/reference/seconds.html
@@ -1,5 +1,5 @@
-Return a time scale vector to match the FID of an MRS data object. — seconds • Spectroscopy Analysis Tools (spant) Return a time scale vector to match the FID of an MRS data object. — seconds • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/seq_cpmg_ideal.html b/docs/reference/seq_cpmg_ideal.html
index 547e96ab..45727c86 100644
--- a/docs/reference/seq_cpmg_ideal.html
+++ b/docs/reference/seq_cpmg_ideal.html
@@ -1,5 +1,5 @@
-CPMG style sequence with ideal pulses. — seq_cpmg_ideal • Spectroscopy Analysis Tools (spant) CPMG style sequence with ideal pulses. — seq_cpmg_ideal • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/seq_mega_press_ideal.html b/docs/reference/seq_mega_press_ideal.html
index 0769b8b4..a9cd7fa0 100644
--- a/docs/reference/seq_mega_press_ideal.html
+++ b/docs/reference/seq_mega_press_ideal.html
@@ -1,7 +1,5 @@
-MEGA-PRESS sequence with ideal localisation pulses and Gaussian shaped
-editing pulse. — seq_mega_press_ideal • Spectroscopy Analysis Tools (spant) MEGA-PRESS sequence with ideal localisation pulses and Gaussian shaped editing pulse. — seq_mega_press_ideal • Spectroscopy Analysis Tools (spant) PRESS sequence with shaped refocusing pulses. — seq_press_2d_shaped • Spectroscopy Analysis Tools (spant) PRESS sequence with shaped refocusing pulses. — seq_press_2d_shaped • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -165,7 +165,7 @@ Value
diff --git a/docs/reference/seq_press_ideal.html b/docs/reference/seq_press_ideal.html
index 8c976856..72c3af3d 100644
--- a/docs/reference/seq_press_ideal.html
+++ b/docs/reference/seq_press_ideal.html
@@ -1,5 +1,5 @@
-PRESS sequence with ideal pulses. — seq_press_ideal • Spectroscopy Analysis Tools (spant) PRESS sequence with ideal pulses. — seq_press_ideal • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/seq_pulse_acquire.html b/docs/reference/seq_pulse_acquire.html
index 4a88fc64..ad80571e 100644
--- a/docs/reference/seq_pulse_acquire.html
+++ b/docs/reference/seq_pulse_acquire.html
@@ -1,5 +1,5 @@
-Simple pulse and acquire sequence with ideal pulses. — seq_pulse_acquire • Spectroscopy Analysis Tools (spant) Simple pulse and acquire sequence with ideal pulses. — seq_pulse_acquire • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/seq_slaser_ideal.html b/docs/reference/seq_slaser_ideal.html
index 74688f4d..eb83e8e3 100644
--- a/docs/reference/seq_slaser_ideal.html
+++ b/docs/reference/seq_slaser_ideal.html
@@ -1,5 +1,5 @@
-sLASER sequence with ideal pulses. — seq_slaser_ideal • Spectroscopy Analysis Tools (spant) sLASER sequence with ideal pulses. — seq_slaser_ideal • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -126,7 +126,7 @@ Value
diff --git a/docs/reference/seq_spin_echo_ideal.html b/docs/reference/seq_spin_echo_ideal.html
index e23271de..4248716f 100644
--- a/docs/reference/seq_spin_echo_ideal.html
+++ b/docs/reference/seq_spin_echo_ideal.html
@@ -1,5 +1,5 @@
-Spin echo sequence with ideal pulses. — seq_spin_echo_ideal • Spectroscopy Analysis Tools (spant) Spin echo sequence with ideal pulses. — seq_spin_echo_ideal • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/seq_steam_ideal.html b/docs/reference/seq_steam_ideal.html
index a60685a8..1c8115d7 100644
--- a/docs/reference/seq_steam_ideal.html
+++ b/docs/reference/seq_steam_ideal.html
@@ -1,5 +1,5 @@
-STEAM sequence with ideal pulses. — seq_steam_ideal • Spectroscopy Analysis Tools (spant) STEAM sequence with ideal pulses. — seq_steam_ideal • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -128,7 +128,7 @@ Value
diff --git a/docs/reference/seq_steam_ideal_cof.html b/docs/reference/seq_steam_ideal_cof.html
index 8f225740..cba7af91 100644
--- a/docs/reference/seq_steam_ideal_cof.html
+++ b/docs/reference/seq_steam_ideal_cof.html
@@ -1,7 +1,5 @@
-STEAM sequence with ideal pulses and coherence order filtering to simulate
-gradient crushers. — seq_steam_ideal_cof • Spectroscopy Analysis Tools (spant) STEAM sequence with ideal pulses and coherence order filtering to simulate gradient crushers. — seq_steam_ideal_cof • Spectroscopy Analysis Tools (spant) STEAM sequence with ideal pulses using the z-rotation gradient simulation
-method described by Young et al JMR 140, 146-152 (1999). — seq_steam_ideal_young • Spectroscopy Analysis Tools (spant) STEAM sequence with ideal pulses using the z-rotation gradient simulation method described by Young et al JMR 140, 146-152 (1999). — seq_steam_ideal_young • Spectroscopy Analysis Tools (spant) Set the number of transients for an mrs_data object. — set_Ntrans • Spectroscopy Analysis Tools (spant) Set the number of transients for an mrs_data object. — set_Ntrans • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/set_def_acq_paras.html b/docs/reference/set_def_acq_paras.html
index 3e1b4004..cc2ada9c 100644
--- a/docs/reference/set_def_acq_paras.html
+++ b/docs/reference/set_def_acq_paras.html
@@ -1,5 +1,5 @@
-Set the default acquisition parameters. — set_def_acq_paras • Spectroscopy Analysis Tools (spant) Set the default acquisition parameters. — set_def_acq_paras • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Arguments
diff --git a/docs/reference/set_lcm_cmd.html b/docs/reference/set_lcm_cmd.html
index 2056ed01..42bb2f24 100644
--- a/docs/reference/set_lcm_cmd.html
+++ b/docs/reference/set_lcm_cmd.html
@@ -1,5 +1,5 @@
-Set the command to run the LCModel command-line program. — set_lcm_cmd • Spectroscopy Analysis Tools (spant) Set the command to run the LCModel command-line program. — set_lcm_cmd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/set_lw.html b/docs/reference/set_lw.html
index b64ec851..bb176c62 100644
--- a/docs/reference/set_lw.html
+++ b/docs/reference/set_lw.html
@@ -1,5 +1,5 @@
-Apply line-broadening to an mrs_data object to achieve a specified linewidth. — set_lw • Spectroscopy Analysis Tools (spant) Apply line-broadening to an mrs_data object to achieve a specified linewidth. — set_lw • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -123,7 +123,7 @@ Value
diff --git a/docs/reference/set_mask_xy_mat.html b/docs/reference/set_mask_xy_mat.html
index 49dc5d4e..52c4b617 100644
--- a/docs/reference/set_mask_xy_mat.html
+++ b/docs/reference/set_mask_xy_mat.html
@@ -1,5 +1,5 @@
-Set the masked voxels in a 2D MRSI dataset to given spectrum. — set_mask_xy_mat • Spectroscopy Analysis Tools (spant) Set the masked voxels in a 2D MRSI dataset to given spectrum. — set_mask_xy_mat • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Value
diff --git a/docs/reference/set_precomp_mode.html b/docs/reference/set_precomp_mode.html
index f44bd5d3..47c28e3b 100644
--- a/docs/reference/set_precomp_mode.html
+++ b/docs/reference/set_precomp_mode.html
@@ -1,5 +1,5 @@
-Set the precompute mode. — set_precomp_mode • Spectroscopy Analysis Tools (spant) Set the precompute mode. — set_precomp_mode • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/set_precomp_verbose.html b/docs/reference/set_precomp_verbose.html
index 1453a231..9c613505 100644
--- a/docs/reference/set_precomp_verbose.html
+++ b/docs/reference/set_precomp_verbose.html
@@ -1,5 +1,5 @@
-Set the verbosity of the precompute function. — set_precomp_verbose • Spectroscopy Analysis Tools (spant) Set the verbosity of the precompute function. — set_precomp_verbose • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/set_ref.html b/docs/reference/set_ref.html
index 8953fa50..5436dfa2 100644
--- a/docs/reference/set_ref.html
+++ b/docs/reference/set_ref.html
@@ -1,5 +1,5 @@
-Set the ppm reference value (eg ppm value at 0Hz). — set_ref • Spectroscopy Analysis Tools (spant) Set the ppm reference value (eg ppm value at 0Hz). — set_ref • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/set_td_pts.html b/docs/reference/set_td_pts.html
index 8a80d42a..586459ff 100644
--- a/docs/reference/set_td_pts.html
+++ b/docs/reference/set_td_pts.html
@@ -1,7 +1,5 @@
-Set the number of time-domain data points, truncating or zero-filling as
-appropriate. — set_td_pts • Spectroscopy Analysis Tools (spant) Set the number of time-domain data points, truncating or zero-filling as appropriate. — set_td_pts • Spectroscopy Analysis Tools (spant) Set the command to run the TARQUIN command-line program. — set_tqn_cmd • Spectroscopy Analysis Tools (spant) Set the command to run the TARQUIN command-line program. — set_tqn_cmd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/set_tr.html b/docs/reference/set_tr.html
index b2109ab0..65c9df5f 100644
--- a/docs/reference/set_tr.html
+++ b/docs/reference/set_tr.html
@@ -1,5 +1,5 @@
-Set the repetition time of an MRS dataset. — set_tr • Spectroscopy Analysis Tools (spant) Set the repetition time of an MRS dataset. — set_tr • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/shift.html b/docs/reference/shift.html
index ab0fe724..034591d0 100644
--- a/docs/reference/shift.html
+++ b/docs/reference/shift.html
@@ -1,5 +1,5 @@
-Apply a frequency shift to MRS data. — shift • Spectroscopy Analysis Tools (spant) Apply a frequency shift to MRS data. — shift • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/shift_basis.html b/docs/reference/shift_basis.html
index 2884be19..f55a65e0 100644
--- a/docs/reference/shift_basis.html
+++ b/docs/reference/shift_basis.html
@@ -1,5 +1,5 @@
-Apply frequency shifts to basis set signals. — shift_basis • Spectroscopy Analysis Tools (spant) Apply frequency shifts to basis set signals. — shift_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Value
diff --git a/docs/reference/sim_basis.html b/docs/reference/sim_basis.html
index c7838c46..bb5fefc6 100644
--- a/docs/reference/sim_basis.html
+++ b/docs/reference/sim_basis.html
@@ -1,5 +1,5 @@
-Simulate a basis set object. — sim_basis • Spectroscopy Analysis Tools (spant) Simulate a basis set object. — sim_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -136,7 +136,7 @@ Value
diff --git a/docs/reference/sim_basis_1h_brain.html b/docs/reference/sim_basis_1h_brain.html
index 62ed7389..f71ffa0b 100644
--- a/docs/reference/sim_basis_1h_brain.html
+++ b/docs/reference/sim_basis_1h_brain.html
@@ -1,7 +1,5 @@
-Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS
-sequence. Note, ideal pulses are assumed. — sim_basis_1h_brain • Spectroscopy Analysis Tools (spant) Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS sequence. Note, ideal pulses are assumed. — sim_basis_1h_brain • Spectroscopy Analysis Tools (spant) Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS
-sequence. Note, ideal pulses are assumed. — sim_basis_1h_brain_press • Spectroscopy Analysis Tools (spant) Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS sequence. Note, ideal pulses are assumed. — sim_basis_1h_brain_press • Spectroscopy Analysis Tools (spant) Simulate a macromolecular and lipid basis-set suitable for 1H brain MRS
-analysis. — sim_basis_mm_lip_lcm • Spectroscopy Analysis Tools (spant) Simulate a macromolecular and lipid basis-set suitable for 1H brain MRS analysis. — sim_basis_mm_lip_lcm • Spectroscopy Analysis Tools (spant) Simulate a basis file using TARQUIN. — sim_basis_tqn • Spectroscopy Analysis Tools (spant) Simulate a basis file using TARQUIN. — sim_basis_tqn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -129,7 +129,7 @@ Examples
diff --git a/docs/reference/sim_brain_1h.html b/docs/reference/sim_brain_1h.html
index 2044cf1a..717ee289 100644
--- a/docs/reference/sim_brain_1h.html
+++ b/docs/reference/sim_brain_1h.html
@@ -1,5 +1,5 @@
-Simulate MRS data with a similar appearance to normal brain (by default). — sim_brain_1h • Spectroscopy Analysis Tools (spant) Simulate MRS data with a similar appearance to normal brain (by default). — sim_brain_1h • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -159,7 +159,7 @@ Value
diff --git a/docs/reference/sim_mol.html b/docs/reference/sim_mol.html
index 23bcef50..77f76a50 100644
--- a/docs/reference/sim_mol.html
+++ b/docs/reference/sim_mol.html
@@ -1,5 +1,5 @@
-Simulate a mol_parameter object. — sim_mol • Spectroscopy Analysis Tools (spant) Simulate a mol_parameter object. — sim_mol • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -143,7 +143,7 @@ Value
diff --git a/docs/reference/sim_noise.html b/docs/reference/sim_noise.html
index 23875f79..a71477d4 100644
--- a/docs/reference/sim_noise.html
+++ b/docs/reference/sim_noise.html
@@ -1,5 +1,5 @@
-Simulate an mrs_data object containing simulated Gaussian noise. — sim_noise • Spectroscopy Analysis Tools (spant) Simulate an mrs_data object containing simulated Gaussian noise. — sim_noise • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -84,6 +84,7 @@ Simulate an mrs_data object containing simulated Gaussian noise.
ft = def_ft(),
N = def_N(),
ref = def_ref(),
+ nuc = def_nuc(),
dyns = 1,
fd = TRUE
)
@@ -111,6 +112,10 @@ Arguments
reference value for ppm scale.
nuc
+resonant nucleus.
dyns
number of dynamic scans to generate.
Value
diff --git a/docs/reference/sim_resonances.html b/docs/reference/sim_resonances.html
index 19e9a8a4..d4f8d7c0 100644
--- a/docs/reference/sim_resonances.html
+++ b/docs/reference/sim_resonances.html
@@ -1,5 +1,5 @@
-Simulate a MRS data object containing a set of simulated resonances. — sim_resonances • Spectroscopy Analysis Tools (spant) Simulate a MRS data object containing a set of simulated resonances. — sim_resonances • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -161,7 +161,7 @@ Examples
diff --git a/docs/reference/sim_th_excit_profile.html b/docs/reference/sim_th_excit_profile.html
index 5535c5ef..e781cab1 100644
--- a/docs/reference/sim_th_excit_profile.html
+++ b/docs/reference/sim_th_excit_profile.html
@@ -1,7 +1,5 @@
-Simulate an ideal pulse excitation profile by smoothing a top-hat function
-with a Gaussian. — sim_th_excit_profile • Spectroscopy Analysis Tools (spant) Simulate an ideal pulse excitation profile by smoothing a top-hat function with a Gaussian. — sim_th_excit_profile • Spectroscopy Analysis Tools (spant) Simulate an mrs_data object containing complex zero valued samples. — sim_zero • Spectroscopy Analysis Tools (spant) Simulate an mrs_data object containing complex zero valued samples. — sim_zero • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -78,7 +78,14 @@ Simulate an mrs_data object containing complex zero valued samples.
-
+
@@ -99,6 +106,10 @@ Arguments
reference value for ppm scale.
nuc
+resonant nucleus.
dyns
number of dynamic scans to generate.
Value
diff --git a/docs/reference/smooth_dyns.html b/docs/reference/smooth_dyns.html
index 4cc8da50..accf3a51 100644
--- a/docs/reference/smooth_dyns.html
+++ b/docs/reference/smooth_dyns.html
@@ -1,5 +1,5 @@
-Smooth data across the dynamic dimension with a Gaussian kernel. — smooth_dyns • Spectroscopy Analysis Tools (spant) Smooth data across the dynamic dimension with a Gaussian kernel. — smooth_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/sort_basis.html b/docs/reference/sort_basis.html
index 6a676ea2..d25cc006 100644
--- a/docs/reference/sort_basis.html
+++ b/docs/reference/sort_basis.html
@@ -1,5 +1,5 @@
-Sort the basis-set elements alphabetically. — sort_basis • Spectroscopy Analysis Tools (spant) Sort the basis-set elements alphabetically. — sort_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/spant-package.html b/docs/reference/spant-package.html
index b3dd8e21..90f19ec3 100644
--- a/docs/reference/spant-package.html
+++ b/docs/reference/spant-package.html
@@ -1,5 +1,5 @@
-spant: spectroscopy analysis tools. — spant-package • Spectroscopy Analysis Tools (spant) spant: spectroscopy analysis tools. — spant-package • Spectroscopy Analysis Tools (spant) Simulate and fit some spectra with ABfit for benchmarking purposes. Basic
-timing and performance metrics will be printed. — spant_abfit_benchmark • Spectroscopy Analysis Tools (spant) Simulate and fit some spectra with ABfit for benchmarking purposes. Basic timing and performance metrics will be printed. — spant_abfit_benchmark • Spectroscopy Analysis Tools (spant) Example MEGA-PRESS data with significant B0 drift. — spant_mpress_drift • Spectroscopy Analysis Tools (spant) Example MEGA-PRESS data with significant B0 drift. — spant_mpress_drift • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -83,7 +83,7 @@ Example MEGA-PRESS data with significant B0 drift.
Format
- An object of class mrs_data of length 13.
+ An object of class mrs_data of dimension 1 x 1 x 1 x 1 x 40 x 1 x 1024.
@@ -98,7 +98,7 @@ Format
diff --git a/docs/reference/spant_sim_fmrs_dataset.html b/docs/reference/spant_sim_fmrs_dataset.html
new file mode 100644
index 00000000..00e48b56
--- /dev/null
+++ b/docs/reference/spant_sim_fmrs_dataset.html
@@ -0,0 +1,117 @@
+
+Simulate an example fMRS dataset for a block design fMRS experiment and export a BIDS structure. — spant_sim_fmrs_dataset • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Simulate an example fMRS dataset for a block design fMRS experiment and export a BIDS structure.
+ Source: R/fmrs.R
+ spant_sim_fmrs_dataset.Rd
+
+
+
+ Simulate an example fMRS dataset for a block design fMRS experiment and
+export a BIDS structure.
+
+
+
+ spant_sim_fmrs_dataset(output_dir = NULL)
+
+
+
+ Arguments
+ - output_dir
+output directory for the BIDS data. Defaults to :
+"HOME/sim_fmrs_dataset/data".
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/spant_simulation_benchmark.html b/docs/reference/spant_simulation_benchmark.html
index 32daa8bf..d8cc6841 100644
--- a/docs/reference/spant_simulation_benchmark.html
+++ b/docs/reference/spant_simulation_benchmark.html
@@ -1,7 +1,5 @@
-Simulate a typical metabolite basis set for benchmarking. Timing metrics will
-be printed on completion. — spant_simulation_benchmark • Spectroscopy Analysis Tools (spant) Simulate a typical metabolite basis set for benchmarking. Timing metrics will be printed on completion. — spant_simulation_benchmark • Spectroscopy Analysis Tools (spant) Decompose an mrs_data object into white and gray matter spectra. — spec_decomp • Spectroscopy Analysis Tools (spant) Perform a mathematical operation on a spectral region. — spec_op • Spectroscopy Analysis Tools (spant) Perform a mathematical operation on a spectral region. — spec_op • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -98,8 +98,8 @@ Arguments
operator
-can be "sum" (default), "mean", "l2", "max", "min" or
-"max-min".
can be "sum" (default), "mean", "l2", "max", "max_cplx,
+"min" or "max-min".
freq_scale
@@ -129,7 +129,7 @@ Value
diff --git a/docs/reference/spin_sys.html b/docs/reference/spin_sys.html
index 853423a4..1eaa9e76 100644
--- a/docs/reference/spin_sys.html
+++ b/docs/reference/spin_sys.html
@@ -1,5 +1,5 @@
-Create a spin system object for pulse sequence simulation. — spin_sys • Spectroscopy Analysis Tools (spant) Create a spin system object for pulse sequence simulation. — spin_sys • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/spm_pve2categorical.html b/docs/reference/spm_pve2categorical.html
index 23a1bad9..70f10729 100644
--- a/docs/reference/spm_pve2categorical.html
+++ b/docs/reference/spm_pve2categorical.html
@@ -1,7 +1,5 @@
-Convert SPM style segmentation files to a single categorical image where
-the numerical values map as: 0) Other, 1) CSF, 2) GM and 3) WM. — spm_pve2categorical • Spectroscopy Analysis Tools (spant) Convert SPM style segmentation files to a single categorical image where the numerical values map as: 0) Other, 1) CSF, 2) GM and 3) WM. — spm_pve2categorical • Spectroscopy Analysis Tools (spant) Signal space projection method for lipid suppression. — ssp • Spectroscopy Analysis Tools (spant) Signal space projection method for lipid suppression. — ssp • Spectroscopy Analysis Tools (spant) Plot the fitting results of an object of class fit_result with
-individual basis set components shown. — stackplot.fit_result • Spectroscopy Analysis Tools (spant) Plot the fitting results of an object of class fit_result with individual basis set components shown. — stackplot.fit_result • Spectroscopy Analysis Tools (spant) Produce a plot with multiple traces. — stackplot • Spectroscopy Analysis Tools (spant) Produce a plot with multiple traces. — stackplot • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/stackplot.mrs_data.html b/docs/reference/stackplot.mrs_data.html
index 17ff5648..64eea445 100644
--- a/docs/reference/stackplot.mrs_data.html
+++ b/docs/reference/stackplot.mrs_data.html
@@ -1,5 +1,5 @@
-Stackplot plotting method for objects of class mrs_data. — stackplot.mrs_data • Spectroscopy Analysis Tools (spant) Stackplot plotting method for objects of class mrs_data. — stackplot.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -255,7 +255,7 @@ Arguments
diff --git a/docs/reference/sub_first_dyn.html b/docs/reference/sub_first_dyn.html
index dbd7f831..493b7242 100644
--- a/docs/reference/sub_first_dyn.html
+++ b/docs/reference/sub_first_dyn.html
@@ -1,5 +1,5 @@
-Subtract the first dynamic spectrum from a dynamic series. — sub_first_dyn • Spectroscopy Analysis Tools (spant) Subtract the first dynamic spectrum from a dynamic series. — sub_first_dyn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/sub_mean_dyns.html b/docs/reference/sub_mean_dyns.html
index 6e3bb2df..221bd0c1 100644
--- a/docs/reference/sub_mean_dyns.html
+++ b/docs/reference/sub_mean_dyns.html
@@ -1,5 +1,5 @@
-Subtract the mean dynamic spectrum from a dynamic series. — sub_mean_dyns • Spectroscopy Analysis Tools (spant) Subtract the mean dynamic spectrum from a dynamic series. — sub_mean_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/sub_median_dyns.html b/docs/reference/sub_median_dyns.html
index 134c495d..1e834f14 100644
--- a/docs/reference/sub_median_dyns.html
+++ b/docs/reference/sub_median_dyns.html
@@ -1,5 +1,5 @@
-Subtract the median dynamic spectrum from a dynamic series. — sub_median_dyns • Spectroscopy Analysis Tools (spant) Subtract the median dynamic spectrum from a dynamic series. — sub_median_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/sum_coils.html b/docs/reference/sum_coils.html
index 7bf559f2..e1ab3cc0 100644
--- a/docs/reference/sum_coils.html
+++ b/docs/reference/sum_coils.html
@@ -1,5 +1,5 @@
-Calculate the sum across receiver coil elements. — sum_coils • Spectroscopy Analysis Tools (spant) Calculate the sum across receiver coil elements. — sum_coils • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/sum_dyns.html b/docs/reference/sum_dyns.html
index a0be19d3..bbda2ffc 100644
--- a/docs/reference/sum_dyns.html
+++ b/docs/reference/sum_dyns.html
@@ -1,5 +1,5 @@
-Calculate the sum of data dynamics. — sum_dyns • Spectroscopy Analysis Tools (spant) Calculate the sum of data dynamics. — sum_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/sum_mrs.html b/docs/reference/sum_mrs.html
index a22f215b..3cc3ab9e 100644
--- a/docs/reference/sum_mrs.html
+++ b/docs/reference/sum_mrs.html
@@ -1,5 +1,5 @@
-Sum two mrs_data objects. — sum_mrs • Spectroscopy Analysis Tools (spant) Sum two mrs_data objects. — sum_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Value
diff --git a/docs/reference/sum_mrs_list.html b/docs/reference/sum_mrs_list.html
index f4e09aea..c3584348 100644
--- a/docs/reference/sum_mrs_list.html
+++ b/docs/reference/sum_mrs_list.html
@@ -1,5 +1,5 @@
-Return the sum of a list of mrs_data objects. — sum_mrs_list • Spectroscopy Analysis Tools (spant) Return the sum of a list of mrs_data objects. — sum_mrs_list • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/svs_1h_brain_analysis.html b/docs/reference/svs_1h_brain_analysis.html
index 8ce514db..dff0ef7d 100644
--- a/docs/reference/svs_1h_brain_analysis.html
+++ b/docs/reference/svs_1h_brain_analysis.html
@@ -1,5 +1,5 @@
-Standard SVS 1H brain analysis pipeline. — svs_1h_brain_analysis • Spectroscopy Analysis Tools (spant) Standard SVS 1H brain analysis pipeline. — svs_1h_brain_analysis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -199,7 +199,7 @@ Value
diff --git a/docs/reference/svs_1h_brain_analysis_dev.html b/docs/reference/svs_1h_brain_analysis_dev.html
index d70a14d3..d71bfea2 100644
--- a/docs/reference/svs_1h_brain_analysis_dev.html
+++ b/docs/reference/svs_1h_brain_analysis_dev.html
@@ -1,5 +1,5 @@
-Standard SVS 1H brain analysis pipeline. — svs_1h_brain_analysis_dev • Spectroscopy Analysis Tools (spant) Standard SVS 1H brain analysis pipeline. — svs_1h_brain_analysis_dev • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -193,7 +193,7 @@ Examples
diff --git a/docs/reference/svs_1h_brain_batch_analysis.html b/docs/reference/svs_1h_brain_batch_analysis.html
index 5631e8cc..15f7223e 100644
--- a/docs/reference/svs_1h_brain_batch_analysis.html
+++ b/docs/reference/svs_1h_brain_batch_analysis.html
@@ -1,5 +1,5 @@
-Batch interface to the standard SVS 1H brain analysis pipeline. — svs_1h_brain_batch_analysis • Spectroscopy Analysis Tools (spant) Batch interface to the standard SVS 1H brain analysis pipeline. — svs_1h_brain_batch_analysis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -144,7 +144,7 @@ Value
diff --git a/docs/reference/t_test_spec.html b/docs/reference/t_test_spec.html
new file mode 100644
index 00000000..56a7ea1b
--- /dev/null
+++ b/docs/reference/t_test_spec.html
@@ -0,0 +1,124 @@
+
+Perform a t-test on spectral data points. — t_test_spec • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+
+
+ Perform a t-test on spectral data points.
+
+
+
+ t_test_spec(mrs_data, group)
+
+
+
+ Arguments
+ - mrs_data
+an mrs_data object with spectra in the dynamic dimension.
- group
+vector describing the group membership of each dynamic spectrum.
+
+ Value
+
+
+a list of statistical results.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/td2fd.html b/docs/reference/td2fd.html
index 6748a6a8..f31ed524 100644
--- a/docs/reference/td2fd.html
+++ b/docs/reference/td2fd.html
@@ -1,5 +1,5 @@
-Transform time-domain data to the frequency-domain. — td2fd • Spectroscopy Analysis Tools (spant) Transform time-domain data to the frequency-domain. — td2fd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/td_conv_filt.html b/docs/reference/td_conv_filt.html
index a9f340c3..106b9b00 100644
--- a/docs/reference/td_conv_filt.html
+++ b/docs/reference/td_conv_filt.html
@@ -1,5 +1,5 @@
-Time-domain convolution based filter. — td_conv_filt • Spectroscopy Analysis Tools (spant) Time-domain convolution based filter. — td_conv_filt • Spectroscopy Analysis Tools (spant) Time-domain spectral registration. — tdsr • Spectroscopy Analysis Tools (spant) Time-domain spectral registration. — tdsr • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -121,7 +121,7 @@ Value
diff --git a/docs/reference/te.html b/docs/reference/te.html
index 010361b1..4a65711d 100644
--- a/docs/reference/te.html
+++ b/docs/reference/te.html
@@ -1,5 +1,5 @@
-Return the echo time of an MRS dataset. — te • Spectroscopy Analysis Tools (spant) Return the echo time of an MRS dataset. — te • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/tr.html b/docs/reference/tr.html
index 0c0bd63b..2e749e02 100644
--- a/docs/reference/tr.html
+++ b/docs/reference/tr.html
@@ -1,5 +1,5 @@
-Return the repetition time of an MRS dataset. — tr • Spectroscopy Analysis Tools (spant) Return the repetition time of an MRS dataset. — tr • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/varpro_3_para_opts.html b/docs/reference/varpro_3_para_opts.html
index c2270a16..52d7cd84 100644
--- a/docs/reference/varpro_3_para_opts.html
+++ b/docs/reference/varpro_3_para_opts.html
@@ -1,5 +1,5 @@
-Return a list of options for VARPRO based fitting with 3 free parameters. — varpro_3_para_opts • Spectroscopy Analysis Tools (spant) Return a list of options for VARPRO based fitting with 3 free parameters. — varpro_3_para_opts • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -141,7 +141,7 @@ Value
diff --git a/docs/reference/varpro_basic_opts.html b/docs/reference/varpro_basic_opts.html
index 32c86d22..c5104891 100644
--- a/docs/reference/varpro_basic_opts.html
+++ b/docs/reference/varpro_basic_opts.html
@@ -1,5 +1,5 @@
-Return a list of options for a basic VARPRO analysis. — varpro_basic_opts • Spectroscopy Analysis Tools (spant) Return a list of options for a basic VARPRO analysis. — varpro_basic_opts • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -118,7 +118,7 @@ Value
diff --git a/docs/reference/varpro_opts.html b/docs/reference/varpro_opts.html
index 2aabf11d..6332f730 100644
--- a/docs/reference/varpro_opts.html
+++ b/docs/reference/varpro_opts.html
@@ -1,5 +1,5 @@
-Return a list of options for VARPRO based fitting. — varpro_opts • Spectroscopy Analysis Tools (spant) Return a list of options for VARPRO based fitting. — varpro_opts • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -177,7 +177,7 @@ Examples
diff --git a/docs/reference/vec2mrs_data.html b/docs/reference/vec2mrs_data.html
index 0cccd73b..f0d58bf0 100644
--- a/docs/reference/vec2mrs_data.html
+++ b/docs/reference/vec2mrs_data.html
@@ -1,5 +1,5 @@
-Convert a vector into a mrs_data object. — vec2mrs_data • Spectroscopy Analysis Tools (spant) Convert a vector into a mrs_data object. — vec2mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -80,10 +80,11 @@ Convert a vector into a mrs_data object.
vec2mrs_data(
vec,
- fs = def_fs(),
- ft = def_ft(),
- ref = def_ref(),
- nuc = def_nuc(),
+ mrs_data = NULL,
+ fs = NULL,
+ ft = NULL,
+ ref = NULL,
+ nuc = NULL,
dyns = 1,
fd = FALSE
)
@@ -95,6 +96,10 @@ Arguments
the data vector.
mrs_data
+example data to copy acquisition parameters from.
fs
sampling frequency in Hz.
Arguments
fd
-flag to indicate if the matrix is in the frequency domain (logical).
flag to indicate if the vector is in the frequency domain (logical).
Value
diff --git a/docs/reference/write_basis.html b/docs/reference/write_basis.html
index b6e27cbd..94c5e021 100644
--- a/docs/reference/write_basis.html
+++ b/docs/reference/write_basis.html
@@ -1,5 +1,5 @@
-Write a basis object to an LCModel .basis formatted file. — write_basis • Spectroscopy Analysis Tools (spant) Write a basis object to an LCModel .basis formatted file. — write_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -108,7 +108,7 @@ Arguments
diff --git a/docs/reference/write_basis_tqn.html b/docs/reference/write_basis_tqn.html
index 6aa51c1d..116c73ec 100644
--- a/docs/reference/write_basis_tqn.html
+++ b/docs/reference/write_basis_tqn.html
@@ -1,5 +1,5 @@
-Generate a basis file using TARQUIN. — write_basis_tqn • Spectroscopy Analysis Tools (spant) Generate a basis file using TARQUIN. — write_basis_tqn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Examples
diff --git a/docs/reference/write_mrs.html b/docs/reference/write_mrs.html
index fff25f15..124b9dc4 100644
--- a/docs/reference/write_mrs.html
+++ b/docs/reference/write_mrs.html
@@ -1,5 +1,5 @@
-Write MRS data object to file. — write_mrs • Spectroscopy Analysis Tools (spant) Write MRS data object to file. — write_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Arguments
diff --git a/docs/reference/write_mrs_nifti.html b/docs/reference/write_mrs_nifti.html
index f4bf1921..bd3ed4b7 100644
--- a/docs/reference/write_mrs_nifti.html
+++ b/docs/reference/write_mrs_nifti.html
@@ -1,5 +1,5 @@
-Write MRS data object to file in NIFTI format. — write_mrs_nifti • Spectroscopy Analysis Tools (spant) Write MRS data object to file in NIFTI format. — write_mrs_nifti • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/write_pulse_ascii.html b/docs/reference/write_pulse_ascii.html
index 067ae086..221f8ebb 100644
--- a/docs/reference/write_pulse_ascii.html
+++ b/docs/reference/write_pulse_ascii.html
@@ -1,5 +1,5 @@
-Write an ASCII formatted pulse file. — write_pulse_ascii • Spectroscopy Analysis Tools (spant) Write an ASCII formatted pulse file. — write_pulse_ascii • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/zero_fade_spec.html b/docs/reference/zero_fade_spec.html
index c703745c..c8b572c3 100644
--- a/docs/reference/zero_fade_spec.html
+++ b/docs/reference/zero_fade_spec.html
@@ -1,7 +1,5 @@
-Fade a spectrum to zero by frequency domain multiplication with a tanh
-function. Note this operation distorts data points at the end of the FID. — zero_fade_spec • Spectroscopy Analysis Tools (spant) Fade a spectrum to zero by frequency domain multiplication with a tanh function. Note this operation distorts data points at the end of the FID. — zero_fade_spec • Spectroscopy Analysis Tools (spant) Zero all coherences including and above a given order. — zero_higher_orders • Spectroscopy Analysis Tools (spant) Zero all coherences including and above a given order. — zero_higher_orders • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Value
diff --git a/docs/reference/zero_td_pts_end.html b/docs/reference/zero_td_pts_end.html
index 8c1123c8..71d24ebb 100644
--- a/docs/reference/zero_td_pts_end.html
+++ b/docs/reference/zero_td_pts_end.html
@@ -1,5 +1,5 @@
-Set mrs_data object data points at the end of the FID to zero. — zero_td_pts_end • Spectroscopy Analysis Tools (spant) Set mrs_data object data points at the end of the FID to zero. — zero_td_pts_end • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/zf.html b/docs/reference/zf.html
index 85e2013c..baf50256 100644
--- a/docs/reference/zf.html
+++ b/docs/reference/zf.html
@@ -1,5 +1,5 @@
-Zero-fill MRS data in the time domain. — zf • Spectroscopy Analysis Tools (spant) Zero-fill MRS data in the time domain. — zf • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -125,7 +125,7 @@ Value
diff --git a/docs/reference/zf_xy.html b/docs/reference/zf_xy.html
index ebca3999..c4104a74 100644
--- a/docs/reference/zf_xy.html
+++ b/docs/reference/zf_xy.html
@@ -1,5 +1,5 @@
-Zero-fill MRSI data in the k-space x-y direction. — zf_xy • Spectroscopy Analysis Tools (spant) Zero-fill MRSI data in the k-space x-y direction. — zf_xy • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -113,7 +113,7 @@ Value
diff --git a/docs/sitemap.xml b/docs/sitemap.xml
index e2139f71..4c39f515 100644
--- a/docs/sitemap.xml
+++ b/docs/sitemap.xml
@@ -216,6 +216,12 @@
https://martin3141.github.io/spant/reference/comb_coils_fp_pc.html
+
+ https://martin3141.github.io/spant/reference/comb_coils_mrsi_gls.html
+
+
+ https://martin3141.github.io/spant/reference/comb_coils_svs_gls.html
+
https://martin3141.github.io/spant/reference/comb_csv_results.html
@@ -411,6 +417,9 @@
https://martin3141.github.io/spant/reference/gen_conv_reg.html
+
+ https://martin3141.github.io/spant/reference/gen_group_reg.html
+
https://martin3141.github.io/spant/reference/gen_impulse_reg.html
@@ -555,6 +564,15 @@
https://martin3141.github.io/spant/reference/glm_spec.html
+
+ https://martin3141.github.io/spant/reference/glm_spec_fmrs_fl.html
+
+
+ https://martin3141.github.io/spant/reference/glm_spec_fmrs_group.html
+
+
+ https://martin3141.github.io/spant/reference/glm_spec_group_linhyp.html
+
https://martin3141.github.io/spant/reference/grid_shift_xy.html
@@ -690,9 +708,15 @@
https://martin3141.github.io/spant/reference/mrs_data2basis.html
+
+ https://martin3141.github.io/spant/reference/mrs_data2bids.html
+
https://martin3141.github.io/spant/reference/mrs_data2mat.html
+
+ https://martin3141.github.io/spant/reference/mrs_data2spec_mat.html
+
https://martin3141.github.io/spant/reference/mrs_data2vec.html
@@ -741,6 +765,9 @@
https://martin3141.github.io/spant/reference/phase.html
+
+ https://martin3141.github.io/spant/reference/phase_ref_1h_brain.html
+
https://martin3141.github.io/spant/reference/plot.fit_result.html
@@ -780,6 +807,12 @@
https://martin3141.github.io/spant/reference/precomp.html
+
+ https://martin3141.github.io/spant/reference/preproc_svs.html
+
+
+ https://martin3141.github.io/spant/reference/preproc_svs_dataset.html
+
https://martin3141.github.io/spant/reference/print.fit_result.html
@@ -1050,6 +1083,9 @@
https://martin3141.github.io/spant/reference/spant_mpress_drift.html
+
+ https://martin3141.github.io/spant/reference/spant_sim_fmrs_dataset.html
+
https://martin3141.github.io/spant/reference/spant_simulation_benchmark.html
@@ -1107,6 +1143,9 @@
https://martin3141.github.io/spant/reference/svs_1h_brain_batch_analysis.html
+
+ https://martin3141.github.io/spant/reference/t_test_spec.html
+
https://martin3141.github.io/spant/reference/td2fd.html
Search for the highest peak in a spectral region and return the frequency, -height and FWHM.
Search for the highest peak in a spectral region and return the frequency, height and FWHM.
All functions phase()
Apply phasing parameters to MRS data.
Apply phasing parameters to MRS data.
Corrected zero order phase and chemical shift offset in 1H MRS data from the brain.
All functions
- Plot an interactive slice map from a data array where voxels can be selected
-to display a corresponding spectrum.
Plot an interactive slice map from a data array where voxels can be selected to display a corresponding spectrum.
@@ -1026,8 +1010,15 @@ All functions
- Save function results to file and load on subsequent calls to avoid repeat
-computation.
Save function results to file and load on subsequent calls to avoid repeat computation.
+
+
+ Preprocess and perform quality assessment of a single SVS data set.
+
+
+ Preprocess and perform quality assessment of one or more SVS data sets.
@@ -1055,15 +1046,11 @@ All functions
- Read a directory containing Siemens MRS IMA files and combine along the coil
-dimension. Note that the coil ID is inferred from the sorted file name and
-should be checked when consistency is required between two directories.
Read a directory containing Siemens MRS IMA files and combine along the coil dimension. Note that the coil ID is inferred from the sorted file name and should be checked when consistency is required between two directories.
- Read a directory containing Siemens MRS IMA files and combine along the
-dynamic dimension. Note that the coil ID is inferred from the sorted file
-name and should be checked when consistency is required.
Read a directory containing Siemens MRS IMA files and combine along the dynamic dimension. Note that the coil ID is inferred from the sorted file name and should be checked when consistency is required.
@@ -1103,13 +1090,11 @@ All functions
- Reconstruct complex time-domain data from the real part of frequency-domain
-data.
Reconstruct complex time-domain data from the real part of frequency-domain data.
- Reconstruct complex time-domain data from the real part of frequency-domain
-data.
Reconstruct complex time-domain data from the real part of frequency-domain data.
@@ -1141,8 +1126,7 @@ All functions
- Resample a VOI to match a target image space using nearest-neighbour
-interpolation.
Resample a VOI to match a target image space using nearest-neighbour interpolation.
@@ -1158,23 +1142,19 @@ All functions
- Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water).
Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / kg of tissue water).
- Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water).
Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / kg of tissue water).
- Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / Litre of tissue).
Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / Litre of tissue).
- Convert default LCM/TARQUIN concentration scaling to molal units with partial
-volume correction.
Convert default LCM/TARQUIN concentration scaling to molal units with partial volume correction.
@@ -1222,8 +1202,7 @@ All functions
- MEGA-PRESS sequence with ideal localisation pulses and Gaussian shaped
-editing pulse.
MEGA-PRESS sequence with ideal localisation pulses and Gaussian shaped editing pulse.
@@ -1251,13 +1230,11 @@ All functions
- STEAM sequence with ideal pulses and coherence order filtering to simulate
-gradient crushers.
STEAM sequence with ideal pulses and coherence order filtering to simulate gradient crushers.
- STEAM sequence with ideal pulses using the z-rotation gradient simulation
-method described by Young et al JMR 140, 146-152 (1999).
STEAM sequence with ideal pulses using the z-rotation gradient simulation method described by Young et al JMR 140, 146-152 (1999).
@@ -1293,8 +1270,7 @@ All functions
- Set the number of time-domain data points, truncating or zero-filling as
-appropriate.
Set the number of time-domain data points, truncating or zero-filling as appropriate.
@@ -1318,18 +1294,15 @@ All functions
- Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS
-sequence. Note, ideal pulses are assumed.
Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS sequence. Note, ideal pulses are assumed.
- Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS
-sequence. Note, ideal pulses are assumed.
Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS sequence. Note, ideal pulses are assumed.
- Simulate a macromolecular and lipid basis-set suitable for 1H brain MRS
-analysis.
Simulate a macromolecular and lipid basis-set suitable for 1H brain MRS analysis.
@@ -1353,8 +1326,7 @@ All functions
- Simulate an ideal pulse excitation profile by smoothing a top-hat function
-with a Gaussian.
Simulate an ideal pulse excitation profile by smoothing a top-hat function with a Gaussian.
@@ -1374,17 +1346,19 @@ All functions
- Simulate and fit some spectra with ABfit for benchmarking purposes. Basic
-timing and performance metrics will be printed.
Simulate and fit some spectra with ABfit for benchmarking purposes. Basic timing and performance metrics will be printed.
Example MEGA-PRESS data with significant B0 drift.
+
+
+ Simulate an example fMRS dataset for a block design fMRS experiment and export a BIDS structure.
- Simulate a typical metabolite basis set for benchmarking. Timing metrics will
-be printed on completion.
Simulate a typical metabolite basis set for benchmarking. Timing metrics will be printed on completion.
@@ -1400,8 +1374,7 @@ All functions
- Convert SPM style segmentation files to a single categorical image where
-the numerical values map as: 0) Other, 1) CSF, 2) GM and 3) WM.
Convert SPM style segmentation files to a single categorical image where the numerical values map as: 0) Other, 1) CSF, 2) GM and 3) WM.
@@ -1413,8 +1386,7 @@ All functions
- Plot the fitting results of an object of class fit_result with
-individual basis set components shown.
Plot the fitting results of an object of class fit_result with individual basis set components shown.
@@ -1459,6 +1431,10 @@ All functions svs_1h_brain_batch_analysis()
Batch interface to the standard SVS 1H brain analysis pipeline.
+
+
+ Perform a t-test on spectral data points.
@@ -1518,8 +1494,7 @@ All functions
- Fade a spectrum to zero by frequency domain multiplication with a tanh
-function. Note this operation distorts data points at the end of the FID.
Fade a spectrum to zero by frequency domain multiplication with a tanh function. Note this operation distorts data points at the end of the FID.
@@ -1549,7 +1524,7 @@ All functions
diff --git a/docs/reference/int_spec.html b/docs/reference/int_spec.html
index c7060fe7..783325a8 100644
--- a/docs/reference/int_spec.html
+++ b/docs/reference/int_spec.html
@@ -1,5 +1,5 @@
-Integrate a spectral region. — int_spec • Spectroscopy Analysis Tools (spant) Integrate a spectral region. — int_spec • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -118,7 +118,7 @@ Value
diff --git a/docs/reference/interleave_dyns.html b/docs/reference/interleave_dyns.html
index effe5543..441eff27 100644
--- a/docs/reference/interleave_dyns.html
+++ b/docs/reference/interleave_dyns.html
@@ -1,5 +1,5 @@
-Interleave the first and second half of a dynamic series. — interleave_dyns • Spectroscopy Analysis Tools (spant) Interleave the first and second half of a dynamic series. — interleave_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/inv_even_dyns.html b/docs/reference/inv_even_dyns.html
index 9f9d4fff..dcb781dc 100644
--- a/docs/reference/inv_even_dyns.html
+++ b/docs/reference/inv_even_dyns.html
@@ -1,5 +1,5 @@
-Invert even numbered dynamic scans starting from 1 (2,4,6...). — inv_even_dyns • Spectroscopy Analysis Tools (spant) Invert even numbered dynamic scans starting from 1 (2,4,6...). — inv_even_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/inv_odd_dyns.html b/docs/reference/inv_odd_dyns.html
index 26212e2b..78d64660 100644
--- a/docs/reference/inv_odd_dyns.html
+++ b/docs/reference/inv_odd_dyns.html
@@ -1,5 +1,5 @@
-Invert odd numbered dynamic scans starting from 1 (1,3,5...). — inv_odd_dyns • Spectroscopy Analysis Tools (spant) Invert odd numbered dynamic scans starting from 1 (1,3,5...). — inv_odd_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/is.def.html b/docs/reference/is.def.html
index f196ffd0..a67b9eba 100644
--- a/docs/reference/is.def.html
+++ b/docs/reference/is.def.html
@@ -1,5 +1,5 @@
-Check if an object is defined, which is the same as being not NULL. — is.def • Spectroscopy Analysis Tools (spant) Check if an object is defined, which is the same as being not NULL. — is.def • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/is_fd.html b/docs/reference/is_fd.html
index 3b0ca165..18a193aa 100644
--- a/docs/reference/is_fd.html
+++ b/docs/reference/is_fd.html
@@ -1,7 +1,5 @@
-Check if the chemical shift dimension of an MRS data object is in the
-frequency domain. — is_fd • Spectroscopy Analysis Tools (spant) Check if the chemical shift dimension of an MRS data object is in the frequency domain. — is_fd • Spectroscopy Analysis Tools (spant) Transform 2D MRSI data from k-space to image space in the x-y direction. — kspace2img_xy • Spectroscopy Analysis Tools (spant) Transform 2D MRSI data from k-space to image space in the x-y direction. — kspace2img_xy • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/l2_reg.html b/docs/reference/l2_reg.html
index 3d781d80..21aa9849 100644
--- a/docs/reference/l2_reg.html
+++ b/docs/reference/l2_reg.html
@@ -1,5 +1,5 @@
-Perform l2 regularisation artefact suppression. — l2_reg • Spectroscopy Analysis Tools (spant) Perform l2 regularisation artefact suppression. — l2_reg • Spectroscopy Analysis Tools (spant) Apply line-broadening (apodisation) to MRS data or basis object. — lb • Spectroscopy Analysis Tools (spant) Apply line-broadening (apodisation) to MRS data or basis object. — lb • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -123,7 +123,7 @@ Value
diff --git a/docs/reference/lofdc.html b/docs/reference/lofdc.html
index 5419b1ec..31347a25 100644
--- a/docs/reference/lofdc.html
+++ b/docs/reference/lofdc.html
@@ -1,5 +1,5 @@
-Correct linear frequency drift. — lofdc • Spectroscopy Analysis Tools (spant) Correct linear frequency drift. — lofdc • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -138,7 +138,7 @@ Value
diff --git a/docs/reference/lw2alpha.html b/docs/reference/lw2alpha.html
index b83db682..25da229b 100644
--- a/docs/reference/lw2alpha.html
+++ b/docs/reference/lw2alpha.html
@@ -1,7 +1,5 @@
-Covert a linewidth in Hz to an equivalent alpha value in the time-domain ie:
-x * exp(-t * alpha). — lw2alpha • Spectroscopy Analysis Tools (spant) Covert a linewidth in Hz to an equivalent alpha value in the time-domain ie: x * exp(-t * alpha). — lw2alpha • Spectroscopy Analysis Tools (spant) Covert a linewidth in Hz to an equivalent beta value in the time-domain ie:
-x * exp(-t * t * beta). — lw2beta • Spectroscopy Analysis Tools (spant) Covert a linewidth in Hz to an equivalent beta value in the time-domain ie: x * exp(-t * t * beta). — lw2beta • Spectroscopy Analysis Tools (spant) Make a basis-set object from a directory containing LCModel formatted RAW
-files. — make_basis_from_raw • Spectroscopy Analysis Tools (spant) Make a basis-set object from a directory containing LCModel formatted RAW files. — make_basis_from_raw • Spectroscopy Analysis Tools (spant) Mask an MRS dataset in the dynamic dimension. — mask_dyns • Spectroscopy Analysis Tools (spant) Mask an MRS dataset in the dynamic dimension. — mask_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/mask_fit_res.html b/docs/reference/mask_fit_res.html
index 97baaa3f..ebd91a99 100644
--- a/docs/reference/mask_fit_res.html
+++ b/docs/reference/mask_fit_res.html
@@ -1,5 +1,5 @@
-Mask fit result spectra depending on a vector of bool values. — mask_fit_res • Spectroscopy Analysis Tools (spant) Mask fit result spectra depending on a vector of bool values. — mask_fit_res • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -116,7 +116,7 @@ Value
diff --git a/docs/reference/mask_xy.html b/docs/reference/mask_xy.html
index 11bb577c..b0d38619 100644
--- a/docs/reference/mask_xy.html
+++ b/docs/reference/mask_xy.html
@@ -1,5 +1,5 @@
-Mask an MRSI dataset in the x-y direction — mask_xy • Spectroscopy Analysis Tools (spant) Mask an MRSI dataset in the x-y direction — mask_xy • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/mask_xy_corners.html b/docs/reference/mask_xy_corners.html
index 09b16cd2..2d13839d 100644
--- a/docs/reference/mask_xy_corners.html
+++ b/docs/reference/mask_xy_corners.html
@@ -1,5 +1,5 @@
-Mask the four corners of an MRSI dataset in the x-y plane. — mask_xy_corners • Spectroscopy Analysis Tools (spant) Mask the four corners of an MRSI dataset in the x-y plane. — mask_xy_corners • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/mask_xy_ellipse.html b/docs/reference/mask_xy_ellipse.html
index 1d8b02e4..e2e749ef 100644
--- a/docs/reference/mask_xy_ellipse.html
+++ b/docs/reference/mask_xy_ellipse.html
@@ -1,7 +1,5 @@
-Mask the voxels outside an elliptical region spanning the MRSI dataset in the
-x-y plane. — mask_xy_ellipse • Spectroscopy Analysis Tools (spant) Mask the voxels outside an elliptical region spanning the MRSI dataset in the x-y plane. — mask_xy_ellipse • Spectroscopy Analysis Tools (spant) Mask a 2D MRSI dataset in the x-y dimension. — mask_xy_mat • Spectroscopy Analysis Tools (spant) Mask a 2D MRSI dataset in the x-y dimension. — mask_xy_mat • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Value
diff --git a/docs/reference/mat2mrs_data.html b/docs/reference/mat2mrs_data.html
index 2e2895f3..ae55665f 100644
--- a/docs/reference/mat2mrs_data.html
+++ b/docs/reference/mat2mrs_data.html
@@ -1,7 +1,5 @@
-Convert a matrix (with spectral points in the column dimension and dynamics
-in the row dimensions) into a mrs_data object. — mat2mrs_data • Spectroscopy Analysis Tools (spant) Convert a matrix (with spectral points in the column dimension and dynamics in the row dimensions) into a mrs_data object. — mat2mrs_data • Spectroscopy Analysis Tools (spant) Matrix exponential function taken from complexplus package to reduce the
-number of spant dependencies. — matexp • Spectroscopy Analysis Tools (spant) Matrix exponential function taken from complexplus package to reduce the number of spant dependencies. — matexp • Spectroscopy Analysis Tools (spant) Apply the max operator to an MRS dataset. — max_mrs • Spectroscopy Analysis Tools (spant) Apply the max operator to an MRS dataset. — max_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/max_mrs_interp.html b/docs/reference/max_mrs_interp.html
index e4474764..52e63f3e 100644
--- a/docs/reference/max_mrs_interp.html
+++ b/docs/reference/max_mrs_interp.html
@@ -1,5 +1,5 @@
-Apply the max operator to an interpolated MRS dataset. — max_mrs_interp • Spectroscopy Analysis Tools (spant) Apply the max operator to an interpolated MRS dataset. — max_mrs_interp • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/mean.list.html b/docs/reference/mean.list.html
index b8eb3463..048306fd 100644
--- a/docs/reference/mean.list.html
+++ b/docs/reference/mean.list.html
@@ -1,5 +1,5 @@
-Calculate the mean spectrum from an mrs_data object. — mean.list • Spectroscopy Analysis Tools (spant) Calculate the mean spectrum from an mrs_data object. — mean.list • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/mean.mrs_data.html b/docs/reference/mean.mrs_data.html
index 5531a28d..79515014 100644
--- a/docs/reference/mean.mrs_data.html
+++ b/docs/reference/mean.mrs_data.html
@@ -1,5 +1,5 @@
-Calculate the mean spectrum from an mrs_data object. — mean.mrs_data • Spectroscopy Analysis Tools (spant) Calculate the mean spectrum from an mrs_data object. — mean.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/mean_dyn_blocks.html b/docs/reference/mean_dyn_blocks.html
index 10467098..4c042448 100644
--- a/docs/reference/mean_dyn_blocks.html
+++ b/docs/reference/mean_dyn_blocks.html
@@ -1,5 +1,5 @@
-Calculate the mean of adjacent dynamic scans. — mean_dyn_blocks • Spectroscopy Analysis Tools (spant) Calculate the mean of adjacent dynamic scans. — mean_dyn_blocks • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/mean_dyn_pairs.html b/docs/reference/mean_dyn_pairs.html
index 63e909ea..1a241126 100644
--- a/docs/reference/mean_dyn_pairs.html
+++ b/docs/reference/mean_dyn_pairs.html
@@ -1,5 +1,5 @@
-Calculate the pairwise means across a dynamic data set. — mean_dyn_pairs • Spectroscopy Analysis Tools (spant) Calculate the pairwise means across a dynamic data set. — mean_dyn_pairs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/mean_dyns.html b/docs/reference/mean_dyns.html
index 73fdbfa7..0daa27df 100644
--- a/docs/reference/mean_dyns.html
+++ b/docs/reference/mean_dyns.html
@@ -1,5 +1,5 @@
-Calculate the mean dynamic data. — mean_dyns • Spectroscopy Analysis Tools (spant) Calculate the mean dynamic data. — mean_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/mean_mrs_list.html b/docs/reference/mean_mrs_list.html
index 808b6c50..10d842c0 100644
--- a/docs/reference/mean_mrs_list.html
+++ b/docs/reference/mean_mrs_list.html
@@ -1,5 +1,5 @@
-Return the mean of a list of mrs_data objects. — mean_mrs_list • Spectroscopy Analysis Tools (spant) Return the mean of a list of mrs_data objects. — mean_mrs_list • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/mean_vec_blocks.html b/docs/reference/mean_vec_blocks.html
index 8fc92eaa..dd78b122 100644
--- a/docs/reference/mean_vec_blocks.html
+++ b/docs/reference/mean_vec_blocks.html
@@ -1,5 +1,5 @@
-Calculate the mean of adjacent blocks in a vector. — mean_vec_blocks • Spectroscopy Analysis Tools (spant) Calculate the mean of adjacent blocks in a vector. — mean_vec_blocks • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/median_dyns.html b/docs/reference/median_dyns.html
index 1039d4b5..9a085b10 100644
--- a/docs/reference/median_dyns.html
+++ b/docs/reference/median_dyns.html
@@ -1,5 +1,5 @@
-Calculate the median dynamic data. — median_dyns • Spectroscopy Analysis Tools (spant) Calculate the median dynamic data. — median_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/mod_td.html b/docs/reference/mod_td.html
index 76ad0a40..141ef09e 100644
--- a/docs/reference/mod_td.html
+++ b/docs/reference/mod_td.html
@@ -1,5 +1,5 @@
-Apply the Modulus operator to the time-domain MRS signal. — mod_td • Spectroscopy Analysis Tools (spant) Apply the Modulus operator to the time-domain MRS signal. — mod_td • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/mrs_data2basis.html b/docs/reference/mrs_data2basis.html
index 62f7d749..11797b91 100644
--- a/docs/reference/mrs_data2basis.html
+++ b/docs/reference/mrs_data2basis.html
@@ -1,7 +1,5 @@
-Convert an mrs_data object to basis object - where basis signals are spread
-across the dynamic dimension in the MRS data. — mrs_data2basis • Spectroscopy Analysis Tools (spant) Convert an mrs_data object to basis object - where basis signals are spread across the dynamic dimension in the MRS data. — mrs_data2basis • Spectroscopy Analysis Tools (spant) Create a BIDS file structure from a vector of MRS data paths or list of mrs_data objects. — mrs_data2bids • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Create a BIDS file structure from a vector of MRS data paths or list of mrs_data objects.
+ Source: R/fmrs.R
+ mrs_data2bids.Rd
+
+
+
+ Create a BIDS file structure from a vector of MRS data paths or list of
+mrs_data objects.
+
+
+
+ mrs_data2bids(
+ mrs_data,
+ output_dir,
+ suffix = NULL,
+ sub = NULL,
+ ses = NULL,
+ task = NULL,
+ acq = NULL,
+ nuc = NULL,
+ voi = NULL,
+ rec = NULL,
+ run = NULL,
+ echo = NULL,
+ inv = NULL,
+ skip_existing = TRUE
+)
+
+
+
+ Arguments
+ - mrs_data
+vector of MRS data paths or list of mrs_data objects.
- output_dir
+the base directory to create the BIDS structure.
- suffix
+optional vector of file suffixes. Default behaviour is to
+automatically determine these from the input data, however it is recommended
+that they are specified to allow more efficient skipping of existing data.
- sub
+optional vector of subject labels. If not specified, these will be
+automatically generated as a series of increasing zero-padded integer values
+corresponding to the mrs_data input indices.
- ses
+optional vector of session labels.
- task
+optional vector of task labels.
- acq
+optional vector of acquisition labels.
- nuc
+optional vector of nucleus labels.
- voi
+optional vector of volume of interest labels.
- rec
+optional vector of reconstruction labels.
- run
+optional vector of run indices.
- echo
+optional vector of echo time indices.
- inv
+optional vector of inversion indices.
- skip_existing
+skip any data files that have already been converted.
+Defaults to TRUE, set to FALSE to force an overwrite of any existing data
+files.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/mrs_data2mat.html b/docs/reference/mrs_data2mat.html
index cf5ff28c..9e47688a 100644
--- a/docs/reference/mrs_data2mat.html
+++ b/docs/reference/mrs_data2mat.html
@@ -1,7 +1,5 @@
-Convert mrs_data object to a matrix, with spectral points in the column
-dimension and dynamics in the row dimension. — mrs_data2mat • Spectroscopy Analysis Tools (spant) Convert mrs_data object to a matrix, with spectral points in the column dimension and dynamics in the row dimension. — mrs_data2mat • Spectroscopy Analysis Tools (spant) Convert mrs_data object to a matrix, with spectral points in the column dimension and dynamics in the row dimension. — mrs_data2spec_mat • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Convert mrs_data object to a matrix, with spectral points in the column dimension and dynamics in the row dimension.
+ Source: R/mrs_data_proc.R
+ mrs_data2spec_mat.Rd
+
+
+
+ Convert mrs_data object to a matrix, with spectral points in the column
+dimension and dynamics in the row dimension.
+
+
+
+ mrs_data2spec_mat(mrs_data, collapse = TRUE)
+
+
+
+ Arguments
+ - mrs_data
+MRS data object or list of MRS data objects.
- collapse
+collapse all other dimensions along the dynamic dimension, eg
+a 16x16 MRSI grid would be first collapsed across 256 dynamic scans.
+
+ Value
+
+
+MRS data matrix.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/mrs_data2vec.html b/docs/reference/mrs_data2vec.html
index fb172d68..a1fd654d 100644
--- a/docs/reference/mrs_data2vec.html
+++ b/docs/reference/mrs_data2vec.html
@@ -1,5 +1,5 @@
-Convert mrs_data object to a vector. — mrs_data2vec • Spectroscopy Analysis Tools (spant) Convert mrs_data object to a vector. — mrs_data2vec • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -126,7 +126,7 @@ Value
diff --git a/docs/reference/mvfftshift.html b/docs/reference/mvfftshift.html
index 92b0841b..976b3410 100644
--- a/docs/reference/mvfftshift.html
+++ b/docs/reference/mvfftshift.html
@@ -1,7 +1,5 @@
-Perform a fftshift on a matrix, with each column replaced by its shifted
-result. — mvfftshift • Spectroscopy Analysis Tools (spant) Perform a fftshift on a matrix, with each column replaced by its shifted result. — mvfftshift • Spectroscopy Analysis Tools (spant) Perform an ifftshift on a matrix, with each column replaced by its shifted
-result. — mvifftshift • Spectroscopy Analysis Tools (spant) Perform an ifftshift on a matrix, with each column replaced by its shifted result. — mvifftshift • Spectroscopy Analysis Tools (spant) Print fit coordinates from a single index. — n2coord • Spectroscopy Analysis Tools (spant) Print fit coordinates from a single index. — n2coord • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/nifti_flip_lr.html b/docs/reference/nifti_flip_lr.html
index 730abe3c..19860b3c 100644
--- a/docs/reference/nifti_flip_lr.html
+++ b/docs/reference/nifti_flip_lr.html
@@ -1,9 +1,5 @@
-Flip the x data dimension order of a nifti image. This corresponds to
-flipping MRI data in the left-right direction, assuming the data in save in
-neurological format (can check with fslorient program). — nifti_flip_lr • Spectroscopy Analysis Tools (spant) Flip the x data dimension order of a nifti image. This corresponds to flipping MRI data in the left-right direction, assuming the data in save in neurological format (can check with fslorient program). — nifti_flip_lr • Spectroscopy Analysis Tools (spant) Export a one-page pdf of a single fit result — one_page_pdf • Spectroscopy Analysis Tools (spant) Export a one-page pdf of a single fit result — one_page_pdf • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -108,7 +108,7 @@ Arguments
diff --git a/docs/reference/ortho3.html b/docs/reference/ortho3.html
index 13ade97d..5d7dd2fd 100644
--- a/docs/reference/ortho3.html
+++ b/docs/reference/ortho3.html
@@ -1,5 +1,5 @@
-Display an orthographic projection plot of a nifti object. — ortho3 • Spectroscopy Analysis Tools (spant) Display an orthographic projection plot of a nifti object. — ortho3 • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -172,7 +172,7 @@ Arguments
diff --git a/docs/reference/ortho3_inter.html b/docs/reference/ortho3_inter.html
index 090cc5e5..15948899 100644
--- a/docs/reference/ortho3_inter.html
+++ b/docs/reference/ortho3_inter.html
@@ -1,5 +1,5 @@
-Display an interactive orthographic projection plot of a nifti object. — ortho3_inter • Spectroscopy Analysis Tools (spant) Display an interactive orthographic projection plot of a nifti object. — ortho3_inter • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -132,7 +132,7 @@ Arguments
diff --git a/docs/reference/peak_info.html b/docs/reference/peak_info.html
index 09058bd8..41c8ffaf 100644
--- a/docs/reference/peak_info.html
+++ b/docs/reference/peak_info.html
@@ -1,7 +1,5 @@
-Search for the highest peak in a spectral region and return the frequency,
-height and FWHM. — peak_info • Spectroscopy Analysis Tools (spant) Search for the highest peak in a spectral region and return the frequency, height and FWHM. — peak_info • Spectroscopy Analysis Tools (spant) Papoulis-Gerchberg (PG) algorithm method for k-space extrapolation. — pg_extrap_xy • Spectroscopy Analysis Tools (spant) Papoulis-Gerchberg (PG) algorithm method for k-space extrapolation. — pg_extrap_xy • Spectroscopy Analysis Tools (spant) Apply phasing parameters to MRS data. — phase • Spectroscopy Analysis Tools (spant) Apply phasing parameters to MRS data. — phase • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/phase_ref_1h_brain.html b/docs/reference/phase_ref_1h_brain.html
new file mode 100644
index 00000000..8707a74a
--- /dev/null
+++ b/docs/reference/phase_ref_1h_brain.html
@@ -0,0 +1,131 @@
+
+Corrected zero order phase and chemical shift offset in 1H MRS data from the brain. — phase_ref_1h_brain • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Corrected zero order phase and chemical shift offset in 1H MRS data from the brain.
+ Source: R/rats.R
+ phase_ref_1h_brain.Rd
+
+
+
+ Corrected zero order phase and chemical shift offset in 1H MRS data from the
+brain.
+
+
+
+ phase_ref_1h_brain(mrs_data, mean_ref = FALSE, ret_corr_only = TRUE)
+
+
+
+ Arguments
+ - mrs_data
+MRS data to be corrected.
- mean_ref
+apply the phase and offset of the mean spectrum to all
+others. Default is FALSE.
- ret_corr_only
+return the corrected data only.
+
+ Value
+
+
+corrected MRS data.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/plot.fit_result.html b/docs/reference/plot.fit_result.html
index e54d3bc1..836a53ee 100644
--- a/docs/reference/plot.fit_result.html
+++ b/docs/reference/plot.fit_result.html
@@ -1,5 +1,5 @@
-Plot the fitting results of an object of class fit_result. — plot.fit_result • Spectroscopy Analysis Tools (spant) Plot the fitting results of an object of class fit_result. — plot.fit_result • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -207,7 +207,7 @@ Arguments
diff --git a/docs/reference/plot.mrs_data.html b/docs/reference/plot.mrs_data.html
index fabcc35b..bb2ec651 100644
--- a/docs/reference/plot.mrs_data.html
+++ b/docs/reference/plot.mrs_data.html
@@ -1,5 +1,5 @@
-Plotting method for objects of class mrs_data. — plot.mrs_data • Spectroscopy Analysis Tools (spant) Plotting method for objects of class mrs_data. — plot.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -287,7 +287,7 @@ Arguments
diff --git a/docs/reference/plot_bc.html b/docs/reference/plot_bc.html
index 4f8309b4..b48142cc 100644
--- a/docs/reference/plot_bc.html
+++ b/docs/reference/plot_bc.html
@@ -1,5 +1,5 @@
-Convenience function to plot a baseline estimate with the original data. — plot_bc • Spectroscopy Analysis Tools (spant) Convenience function to plot a baseline estimate with the original data. — plot_bc • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -108,7 +108,7 @@ Arguments
diff --git a/docs/reference/plot_reg.html b/docs/reference/plot_reg.html
index ae1acbe7..2addb2f6 100644
--- a/docs/reference/plot_reg.html
+++ b/docs/reference/plot_reg.html
@@ -1,5 +1,5 @@
-Plot regressors as an image. — plot_reg • Spectroscopy Analysis Tools (spant) Plot regressors as an image. — plot_reg • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/plot_slice_fit.html b/docs/reference/plot_slice_fit.html
index fbc7b560..57f1af8a 100644
--- a/docs/reference/plot_slice_fit.html
+++ b/docs/reference/plot_slice_fit.html
@@ -1,5 +1,5 @@
-Plot a 2D slice from an MRSI fit result object. — plot_slice_fit • Spectroscopy Analysis Tools (spant) Plot a 2D slice from an MRSI fit result object. — plot_slice_fit • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -129,7 +129,7 @@ Arguments
diff --git a/docs/reference/plot_slice_fit_inter.html b/docs/reference/plot_slice_fit_inter.html
index 4eed104a..da105a7d 100644
--- a/docs/reference/plot_slice_fit_inter.html
+++ b/docs/reference/plot_slice_fit_inter.html
@@ -1,5 +1,5 @@
-Plot a 2D slice from an MRSI fit result object. — plot_slice_fit_inter • Spectroscopy Analysis Tools (spant) Plot a 2D slice from an MRSI fit result object. — plot_slice_fit_inter • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -134,7 +134,7 @@ Arguments
diff --git a/docs/reference/plot_slice_map.html b/docs/reference/plot_slice_map.html
index 553e9ac8..ffb2a134 100644
--- a/docs/reference/plot_slice_map.html
+++ b/docs/reference/plot_slice_map.html
@@ -1,5 +1,5 @@
-Plot a slice from a 7 dimensional array. — plot_slice_map • Spectroscopy Analysis Tools (spant) Plot a slice from a 7 dimensional array. — plot_slice_map • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -153,7 +153,7 @@ Arguments
diff --git a/docs/reference/plot_slice_map_inter.html b/docs/reference/plot_slice_map_inter.html
index 40d33b42..90968f66 100644
--- a/docs/reference/plot_slice_map_inter.html
+++ b/docs/reference/plot_slice_map_inter.html
@@ -1,7 +1,5 @@
-Plot an interactive slice map from a data array where voxels can be selected
-to display a corresponding spectrum. — plot_slice_map_inter • Spectroscopy Analysis Tools (spant) Plot an interactive slice map from a data array where voxels can be selected to display a corresponding spectrum. — plot_slice_map_inter • Spectroscopy Analysis Tools (spant) Plot the spectral standard deviation. — plot_spec_sd • Spectroscopy Analysis Tools (spant) Plot the spectral standard deviation. — plot_spec_sd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Arguments
diff --git a/docs/reference/plot_voi_overlay.html b/docs/reference/plot_voi_overlay.html
index 9a782e88..bbbbf35e 100644
--- a/docs/reference/plot_voi_overlay.html
+++ b/docs/reference/plot_voi_overlay.html
@@ -1,5 +1,5 @@
-Plot a volume as an image overlay. — plot_voi_overlay • Spectroscopy Analysis Tools (spant) Plot a volume as an image overlay. — plot_voi_overlay • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -116,7 +116,7 @@ Arguments
diff --git a/docs/reference/plot_voi_overlay_seg.html b/docs/reference/plot_voi_overlay_seg.html
index 3d4e74ff..0e800ff2 100644
--- a/docs/reference/plot_voi_overlay_seg.html
+++ b/docs/reference/plot_voi_overlay_seg.html
@@ -1,5 +1,5 @@
-Plot a volume as an overlay on a segmented brain volume. — plot_voi_overlay_seg • Spectroscopy Analysis Tools (spant) Plot a volume as an overlay on a segmented brain volume. — plot_voi_overlay_seg • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Arguments
diff --git a/docs/reference/ppm.html b/docs/reference/ppm.html
index c352327a..ee4696e2 100644
--- a/docs/reference/ppm.html
+++ b/docs/reference/ppm.html
@@ -1,5 +1,5 @@
-Return the ppm scale of an MRS dataset or fit result. — ppm • Spectroscopy Analysis Tools (spant) Return the ppm scale of an MRS dataset or fit result. — ppm • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -132,7 +132,7 @@ Value
diff --git a/docs/reference/precomp.html b/docs/reference/precomp.html
index 822d7336..df3d2c6c 100644
--- a/docs/reference/precomp.html
+++ b/docs/reference/precomp.html
@@ -1,7 +1,5 @@
-Save function results to file and load on subsequent calls to avoid repeat
-computation. — precomp • Spectroscopy Analysis Tools (spant) Save function results to file and load on subsequent calls to avoid repeat computation. — precomp • Spectroscopy Analysis Tools (spant) Preprocess and perform quality assessment of a single SVS data set. — preproc_svs • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Preprocess and perform quality assessment of a single SVS data set.
+ Source: R/fmrs.R
+ preproc_svs.Rd
+
+
+
+ Preprocess and perform quality assessment of a single SVS data set.
+
+
+
+ preproc_svs(path, label = NULL, output_dir = NULL, ref_inds = NULL)
+
+
+
+ Arguments
+ - path
+path to the fMRS data file or IMA directory.
- label
+a label to describe the data set.
- output_dir
+output directory.
- ref_inds
+a vector of 1-based indices for any water reference dynamic
+scans.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/preproc_svs_dataset.html b/docs/reference/preproc_svs_dataset.html
new file mode 100644
index 00000000..07c3a29b
--- /dev/null
+++ b/docs/reference/preproc_svs_dataset.html
@@ -0,0 +1,148 @@
+
+Preprocess and perform quality assessment of one or more SVS data sets. — preproc_svs_dataset • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Preprocess and perform quality assessment of one or more SVS data sets.
+ Source: R/fmrs.R
+ preproc_svs_dataset.Rd
+
+
+
+ Preprocess and perform quality assessment of one or more SVS data sets.
+
+
+
+ preproc_svs_dataset(
+ paths,
+ labels = NULL,
+ output_dir = "spant_analysis",
+ exclude_labels = NULL,
+ overwrite = FALSE,
+ ref_inds = NULL,
+ return_results = FALSE
+)
+
+
+
+ Arguments
+ - paths
+paths to the fMRS data file or IMA directory.
- labels
+labels to describe each data set.
- output_dir
+output directory.
- exclude_labels
+vector of labels of scans to exclude, eg poor quality
+data.
- overwrite
+overwrite saved results, defaults to FALSE.
- ref_inds
+a vector of 1-based indices for any water reference dynamic
+scans.
- return_results
+function will return key outputs, defaults to FALSE.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/print.fit_result.html b/docs/reference/print.fit_result.html
index 297f28dc..5f434e57 100644
--- a/docs/reference/print.fit_result.html
+++ b/docs/reference/print.fit_result.html
@@ -1,5 +1,5 @@
-Print a summary of an object of class fit_result. — print.fit_result • Spectroscopy Analysis Tools (spant) Print a summary of an object of class fit_result. — print.fit_result • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -105,7 +105,7 @@ Arguments
diff --git a/docs/reference/print.mrs_data.html b/docs/reference/print.mrs_data.html
index 51199017..e1561eb2 100644
--- a/docs/reference/print.mrs_data.html
+++ b/docs/reference/print.mrs_data.html
@@ -1,5 +1,5 @@
-Print a summary of mrs_data parameters. — print.mrs_data • Spectroscopy Analysis Tools (spant) Print a summary of mrs_data parameters. — print.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -109,7 +109,7 @@ Arguments
diff --git a/docs/reference/qn_states.html b/docs/reference/qn_states.html
index 0f42f2f9..d7aa6715 100644
--- a/docs/reference/qn_states.html
+++ b/docs/reference/qn_states.html
@@ -1,5 +1,5 @@
-Get the quantum coherence matrix for a spin system. — qn_states • Spectroscopy Analysis Tools (spant) Get the quantum coherence matrix for a spin system. — qn_states • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/rats.html b/docs/reference/rats.html
index 5a39a396..93585e08 100644
--- a/docs/reference/rats.html
+++ b/docs/reference/rats.html
@@ -1,5 +1,5 @@
-Robust Alignment to a Target Spectrum (RATS). — rats • Spectroscopy Analysis Tools (spant) Robust Alignment to a Target Spectrum (RATS). — rats • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -207,7 +207,7 @@ Value
diff --git a/docs/reference/re_weighting.html b/docs/reference/re_weighting.html
index d21caf21..8b0b070a 100644
--- a/docs/reference/re_weighting.html
+++ b/docs/reference/re_weighting.html
@@ -1,5 +1,5 @@
-Apply a weighting to the FID to enhance spectral resolution. — re_weighting • Spectroscopy Analysis Tools (spant) Apply a weighting to the FID to enhance spectral resolution. — re_weighting • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/read_basis.html b/docs/reference/read_basis.html
index da9b94af..eb6f8557 100644
--- a/docs/reference/read_basis.html
+++ b/docs/reference/read_basis.html
@@ -1,5 +1,5 @@
-Read a basis file in LCModel .basis format. — read_basis • Spectroscopy Analysis Tools (spant) Read a basis file in LCModel .basis format. — read_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/read_ima_coil_dir.html b/docs/reference/read_ima_coil_dir.html
index 28c02de0..4f073cd8 100644
--- a/docs/reference/read_ima_coil_dir.html
+++ b/docs/reference/read_ima_coil_dir.html
@@ -1,9 +1,5 @@
-Read a directory containing Siemens MRS IMA files and combine along the coil
-dimension. Note that the coil ID is inferred from the sorted file name and
-should be checked when consistency is required between two directories. — read_ima_coil_dir • Spectroscopy Analysis Tools (spant) Read a directory containing Siemens MRS IMA files and combine along the coil dimension. Note that the coil ID is inferred from the sorted file name and should be checked when consistency is required between two directories. — read_ima_coil_dir • Spectroscopy Analysis Tools (spant) Read a directory containing Siemens MRS IMA files and combine along the
-dynamic dimension. Note that the coil ID is inferred from the sorted file
-name and should be checked when consistency is required. — read_ima_dyn_dir • Spectroscopy Analysis Tools (spant) Read a directory containing Siemens MRS IMA files and combine along the dynamic dimension. Note that the coil ID is inferred from the sorted file name and should be checked when consistency is required. — read_ima_dyn_dir • Spectroscopy Analysis Tools (spant) Read an LCModel formatted coord file containing fit information. — read_lcm_coord • Spectroscopy Analysis Tools (spant) Read an LCModel formatted coord file containing fit information. — read_lcm_coord • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -107,7 +107,7 @@ Value
diff --git a/docs/reference/read_mrs.html b/docs/reference/read_mrs.html
index 3ac2a36b..2cf36b20 100644
--- a/docs/reference/read_mrs.html
+++ b/docs/reference/read_mrs.html
@@ -1,5 +1,5 @@
-Read MRS data from a file. — read_mrs • Spectroscopy Analysis Tools (spant) Read MRS data from a file. — read_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -88,7 +88,8 @@ Read MRS data from a file.
full_fid = FALSE,
omit_svs_ref_scans = TRUE,
verbose = FALSE,
- extra = NULL
+ extra = NULL,
+ fid_filt_dist = NULL
)
@@ -140,6 +141,13 @@ Arguments
an optional data frame to provide additional variables for use
in subsequent analysis steps, eg id or grouping variables.
fid_filt_dist
+indicate if the data has a distorted FID due to a
+brick-wall filter being used to downsample the data. Default is to auto
+detect this from the data, but TRUE or FALSE options can be given to override
+detection.
Value
@@ -183,7 +191,7 @@ Examples
diff --git a/docs/reference/read_mrs_tqn.html b/docs/reference/read_mrs_tqn.html
index 5766362f..84bdaf3a 100644
--- a/docs/reference/read_mrs_tqn.html
+++ b/docs/reference/read_mrs_tqn.html
@@ -1,5 +1,5 @@
-Read MRS data using the TARQUIN software package. — read_mrs_tqn • Spectroscopy Analysis Tools (spant) Read MRS data using the TARQUIN software package. — read_mrs_tqn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -131,7 +131,7 @@ Examples
diff --git a/docs/reference/read_pulse_ascii.html b/docs/reference/read_pulse_ascii.html
index c9e0d43c..ab11c9cc 100644
--- a/docs/reference/read_pulse_ascii.html
+++ b/docs/reference/read_pulse_ascii.html
@@ -1,5 +1,5 @@
-Read an ASCII formatted pulse file. — read_pulse_ascii • Spectroscopy Analysis Tools (spant) Read an ASCII formatted pulse file. — read_pulse_ascii • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/read_pulse_bruker.html b/docs/reference/read_pulse_bruker.html
index c92bf76a..dbe9073b 100644
--- a/docs/reference/read_pulse_bruker.html
+++ b/docs/reference/read_pulse_bruker.html
@@ -1,5 +1,5 @@
-Read a Bruker formatted pulse file — read_pulse_bruker • Spectroscopy Analysis Tools (spant) Read a Bruker formatted pulse file — read_pulse_bruker • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/read_pulse_pta.html b/docs/reference/read_pulse_pta.html
index 72e1b6d4..a0fac3c3 100644
--- a/docs/reference/read_pulse_pta.html
+++ b/docs/reference/read_pulse_pta.html
@@ -1,5 +1,5 @@
-Read a .pta formatted pulse file compatible with Siemens PulseTool. — read_pulse_pta • Spectroscopy Analysis Tools (spant) Read a .pta formatted pulse file compatible with Siemens PulseTool. — read_pulse_pta • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/read_siemens_txt_hdr.html b/docs/reference/read_siemens_txt_hdr.html
index 23fb8c70..3a17d87c 100644
--- a/docs/reference/read_siemens_txt_hdr.html
+++ b/docs/reference/read_siemens_txt_hdr.html
@@ -1,5 +1,5 @@
-Read the text format header found in Siemens IMA and TWIX data files. — read_siemens_txt_hdr • Spectroscopy Analysis Tools (spant) Read the text format header found in Siemens IMA and TWIX data files. — read_siemens_txt_hdr • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -78,7 +78,7 @@ Read the text format header found in Siemens IMA and TWIX data files.
- read_siemens_txt_hdr(input, version = "vd", verbose, offset = 0)
+ read_siemens_txt_hdr(input, version = "vd", verbose = FALSE, offset = 0)
@@ -118,7 +118,7 @@ Value
diff --git a/docs/reference/read_tqn_fit.html b/docs/reference/read_tqn_fit.html
index 4da6c25e..a1630420 100644
--- a/docs/reference/read_tqn_fit.html
+++ b/docs/reference/read_tqn_fit.html
@@ -1,5 +1,5 @@
-Reader for csv fit results generated by TARQUIN. — read_tqn_fit • Spectroscopy Analysis Tools (spant) Reader for csv fit results generated by TARQUIN. — read_tqn_fit • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -113,7 +113,7 @@ Examples
diff --git a/docs/reference/read_tqn_result.html b/docs/reference/read_tqn_result.html
index 36659714..68a3e98c 100644
--- a/docs/reference/read_tqn_result.html
+++ b/docs/reference/read_tqn_result.html
@@ -1,5 +1,5 @@
-Reader for csv results generated by TARQUIN. — read_tqn_result • Spectroscopy Analysis Tools (spant) Reader for csv results generated by TARQUIN. — read_tqn_result • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -117,7 +117,7 @@ Examples
diff --git a/docs/reference/recon_imag.html b/docs/reference/recon_imag.html
index d2a72225..5bc3b1eb 100644
--- a/docs/reference/recon_imag.html
+++ b/docs/reference/recon_imag.html
@@ -1,7 +1,5 @@
-Reconstruct complex time-domain data from the real part of frequency-domain
-data. — recon_imag • Spectroscopy Analysis Tools (spant) Reconstruct complex time-domain data from the real part of frequency-domain data. — recon_imag • Spectroscopy Analysis Tools (spant) Reconstruct complex time-domain data from the real part of frequency-domain
-data. — recon_imag_vec • Spectroscopy Analysis Tools (spant) Reconstruct complex time-domain data from the real part of frequency-domain data. — recon_imag_vec • Spectroscopy Analysis Tools (spant) Reconstruct 2D MRSI data from a twix file loaded with read_mrs. — recon_twix_2d_mrsi • Spectroscopy Analysis Tools (spant) Reconstruct 2D MRSI data from a twix file loaded with read_mrs. — recon_twix_2d_mrsi • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/rectangular_mask.html b/docs/reference/rectangular_mask.html
index a2117283..6e469bc9 100644
--- a/docs/reference/rectangular_mask.html
+++ b/docs/reference/rectangular_mask.html
@@ -1,5 +1,5 @@
-Create a rectangular mask stored as a matrix of logical values. — rectangular_mask • Spectroscopy Analysis Tools (spant) Create a rectangular mask stored as a matrix of logical values. — rectangular_mask • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -130,7 +130,7 @@ Value
diff --git a/docs/reference/reexports.html b/docs/reference/reexports.html
index 694a75d1..a59e8379 100644
--- a/docs/reference/reexports.html
+++ b/docs/reference/reexports.html
@@ -1,5 +1,5 @@
-Objects exported from other packages — reexports • Spectroscopy Analysis Tools (spant) Objects exported from other packages — reexports • Spectroscopy Analysis Tools (spant)
Spectroscopy Analysis Tools (spant)
- 2.21.0
+ 2.22.0
@@ -103,7 +103,7 @@ Objects exported from other packages
diff --git a/docs/reference/rep_array_dim.html b/docs/reference/rep_array_dim.html
index b9c49b4a..48c0a5ed 100644
--- a/docs/reference/rep_array_dim.html
+++ b/docs/reference/rep_array_dim.html
@@ -1,5 +1,5 @@
-Repeat an array over a given dimension. — rep_array_dim • Spectroscopy Analysis Tools (spant) Repeat an array over a given dimension. — rep_array_dim • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/rep_dyn.html b/docs/reference/rep_dyn.html
index 6bbfb0ef..89a4bb9b 100644
--- a/docs/reference/rep_dyn.html
+++ b/docs/reference/rep_dyn.html
@@ -1,5 +1,5 @@
-Replicate a scan in the dynamic dimension. — rep_dyn • Spectroscopy Analysis Tools (spant) Replicate a scan in the dynamic dimension. — rep_dyn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/rep_mrs.html b/docs/reference/rep_mrs.html
index 67730b5c..becb8f00 100644
--- a/docs/reference/rep_mrs.html
+++ b/docs/reference/rep_mrs.html
@@ -1,5 +1,5 @@
-Replicate a scan over a given dimension. — rep_mrs • Spectroscopy Analysis Tools (spant) Replicate a scan over a given dimension. — rep_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -138,7 +138,7 @@ Value
diff --git a/docs/reference/resample_basis.html b/docs/reference/resample_basis.html
index b0f2ab17..c7a6222a 100644
--- a/docs/reference/resample_basis.html
+++ b/docs/reference/resample_basis.html
@@ -1,5 +1,5 @@
-Resample a basis-set to match a mrs_data acquisition. — resample_basis • Spectroscopy Analysis Tools (spant) Resample a basis-set to match a mrs_data acquisition. — resample_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -116,7 +116,7 @@ Value
diff --git a/docs/reference/resample_img.html b/docs/reference/resample_img.html
index f1e7beaf..b0cc8f71 100644
--- a/docs/reference/resample_img.html
+++ b/docs/reference/resample_img.html
@@ -1,5 +1,5 @@
-Resample an image to match a target image space. — resample_img • Spectroscopy Analysis Tools (spant) Resample an image to match a target image space. — resample_img • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/resample_voi.html b/docs/reference/resample_voi.html
index 8fbfa836..a29ab096 100644
--- a/docs/reference/resample_voi.html
+++ b/docs/reference/resample_voi.html
@@ -1,7 +1,5 @@
-Resample a VOI to match a target image space using nearest-neighbour
-interpolation. — resample_voi • Spectroscopy Analysis Tools (spant) Resample a VOI to match a target image space using nearest-neighbour interpolation. — resample_voi • Spectroscopy Analysis Tools (spant) Reslice a nifti object to match the orientation of mrs data. — reslice_to_mrs • Spectroscopy Analysis Tools (spant) Reslice a nifti object to match the orientation of mrs data. — reslice_to_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/reson_table2mrs_data.html b/docs/reference/reson_table2mrs_data.html
index d75579ee..c5a2167a 100644
--- a/docs/reference/reson_table2mrs_data.html
+++ b/docs/reference/reson_table2mrs_data.html
@@ -1,5 +1,5 @@
-Generate mrs_data from a table of single Lorentzian resonances. — reson_table2mrs_data • Spectroscopy Analysis Tools (spant) Generate mrs_data from a table of single Lorentzian resonances. — reson_table2mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -119,7 +119,7 @@ Value
diff --git a/docs/reference/rm_dyns.html b/docs/reference/rm_dyns.html
index 5d5ef692..573e1f51 100644
--- a/docs/reference/rm_dyns.html
+++ b/docs/reference/rm_dyns.html
@@ -1,5 +1,5 @@
-Remove a subset of dynamic scans. — rm_dyns • Spectroscopy Analysis Tools (spant) Remove a subset of dynamic scans. — rm_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/scale_amp_molal.html b/docs/reference/scale_amp_molal.html
index aaeee1f2..7acb8cb0 100644
--- a/docs/reference/scale_amp_molal.html
+++ b/docs/reference/scale_amp_molal.html
@@ -1,7 +1,5 @@
-Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water). — scale_amp_molal • Spectroscopy Analysis Tools (spant) Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / kg of tissue water). — scale_amp_molal • Spectroscopy Analysis Tools (spant)
Spectroscopy Analysis Tools (spant)
- 2.21.0
+ 2.22.0
@@ -76,8 +74,7 @@
- Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water).
+ Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / kg of tissue water).
Source: R/amp_scaling.R
scale_amp_molal.Rd
@@ -163,7 +160,7 @@ Value
diff --git a/docs/reference/scale_amp_molal_pvc.html b/docs/reference/scale_amp_molal_pvc.html
index 962d6afc..4d194abd 100644
--- a/docs/reference/scale_amp_molal_pvc.html
+++ b/docs/reference/scale_amp_molal_pvc.html
@@ -1,7 +1,5 @@
-Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water). — scale_amp_molal_pvc • Spectroscopy Analysis Tools (spant)
@@ -75,8 +73,7 @@
- Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water).
+ Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / kg of tissue water).
Source: R/amp_scaling.R
scale_amp_molal_pvc.Rd
@@ -141,7 +138,7 @@ Value
diff --git a/docs/reference/scale_amp_molar.html b/docs/reference/scale_amp_molar.html
index 02358d91..dc87a338 100644
--- a/docs/reference/scale_amp_molar.html
+++ b/docs/reference/scale_amp_molar.html
@@ -1,7 +1,5 @@
-Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / Litre of tissue). — scale_amp_molar • Spectroscopy Analysis Tools (spant) Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / Litre of tissue). — scale_amp_molar • Spectroscopy Analysis Tools (spant) Convert default LCM/TARQUIN concentration scaling to molal units with partial
-volume correction. — scale_amp_molar2molal_pvc • Spectroscopy Analysis Tools (spant) Convert default LCM/TARQUIN concentration scaling to molal units with partial volume correction. — scale_amp_molar2molal_pvc • Spectroscopy Analysis Tools (spant) Scale fitted amplitudes to a ratio of signal amplitude. — scale_amp_ratio • Spectroscopy Analysis Tools (spant) Scale fitted amplitudes to a ratio of signal amplitude. — scale_amp_ratio • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -116,7 +116,7 @@ Value
diff --git a/docs/reference/scale_amp_ratio_value.html b/docs/reference/scale_amp_ratio_value.html
index 2036837a..6af8ac51 100644
--- a/docs/reference/scale_amp_ratio_value.html
+++ b/docs/reference/scale_amp_ratio_value.html
@@ -1,5 +1,5 @@
-Scale fitted amplitudes to a ratio of signal amplitude. — scale_amp_ratio_value • Spectroscopy Analysis Tools (spant) Scale fitted amplitudes to a ratio of signal amplitude. — scale_amp_ratio_value • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/scale_amp_water_ratio.html b/docs/reference/scale_amp_water_ratio.html
index 5b25e884..35a76b00 100644
--- a/docs/reference/scale_amp_water_ratio.html
+++ b/docs/reference/scale_amp_water_ratio.html
@@ -1,5 +1,5 @@
-Scale metabolite amplitudes as a ratio to the unsuppressed water amplitude. — scale_amp_water_ratio • Spectroscopy Analysis Tools (spant) Scale metabolite amplitudes as a ratio to the unsuppressed water amplitude. — scale_amp_water_ratio • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/scale_basis_amp.html b/docs/reference/scale_basis_amp.html
index 9401c3f1..5a58b5e5 100644
--- a/docs/reference/scale_basis_amp.html
+++ b/docs/reference/scale_basis_amp.html
@@ -1,5 +1,5 @@
-Scale a basis object by a scalar. — scale_basis_amp • Spectroscopy Analysis Tools (spant) Scale a basis object by a scalar. — scale_basis_amp • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/scale_basis_from_singlet.html b/docs/reference/scale_basis_from_singlet.html
index 0d542bc8..c9a19e77 100644
--- a/docs/reference/scale_basis_from_singlet.html
+++ b/docs/reference/scale_basis_from_singlet.html
@@ -1,5 +1,5 @@
-Scale a basis-set to be consistent with spant assumptions for water scaling. — scale_basis_from_singlet • Spectroscopy Analysis Tools (spant) Scale a basis-set to be consistent with spant assumptions for water scaling. — scale_basis_from_singlet • Spectroscopy Analysis Tools (spant)
Spectroscopy Analysis Tools (spant)
- 2.21.0
+ 2.22.0
@@ -127,7 +127,7 @@ Value
diff --git a/docs/reference/scale_mrs_amp.html b/docs/reference/scale_mrs_amp.html
index b5501a0d..990f058a 100644
--- a/docs/reference/scale_mrs_amp.html
+++ b/docs/reference/scale_mrs_amp.html
@@ -1,5 +1,5 @@
-Scale an mrs_data object by a scalar or vector or amplitudes. — scale_mrs_amp • Spectroscopy Analysis Tools (spant) Scale an mrs_data object by a scalar or vector or amplitudes. — scale_mrs_amp • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/scale_spec.html b/docs/reference/scale_spec.html
index 4f6ea835..6b3ddba4 100644
--- a/docs/reference/scale_spec.html
+++ b/docs/reference/scale_spec.html
@@ -1,5 +1,5 @@
-Scale mrs_data to a spectral region. — scale_spec • Spectroscopy Analysis Tools (spant) Scale mrs_data to a spectral region. — scale_spec • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -141,7 +141,7 @@ Value
diff --git a/docs/reference/sd.html b/docs/reference/sd.html
index ea1eec9f..3ae4dfd4 100644
--- a/docs/reference/sd.html
+++ b/docs/reference/sd.html
@@ -1,5 +1,5 @@
-Calculate the standard deviation spectrum from an mrs_data object. — sd • Spectroscopy Analysis Tools (spant) Calculate the standard deviation spectrum from an mrs_data object. — sd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/sd.mrs_data.html b/docs/reference/sd.mrs_data.html
index 3f92a49f..13bdda85 100644
--- a/docs/reference/sd.mrs_data.html
+++ b/docs/reference/sd.mrs_data.html
@@ -1,5 +1,5 @@
-Calculate the standard deviation spectrum from an mrs_data object. — sd.mrs_data • Spectroscopy Analysis Tools (spant) Calculate the standard deviation spectrum from an mrs_data object. — sd.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/seconds.html b/docs/reference/seconds.html
index b34d6627..467ee17f 100644
--- a/docs/reference/seconds.html
+++ b/docs/reference/seconds.html
@@ -1,5 +1,5 @@
-Return a time scale vector to match the FID of an MRS data object. — seconds • Spectroscopy Analysis Tools (spant) Return a time scale vector to match the FID of an MRS data object. — seconds • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/seq_cpmg_ideal.html b/docs/reference/seq_cpmg_ideal.html
index 547e96ab..45727c86 100644
--- a/docs/reference/seq_cpmg_ideal.html
+++ b/docs/reference/seq_cpmg_ideal.html
@@ -1,5 +1,5 @@
-CPMG style sequence with ideal pulses. — seq_cpmg_ideal • Spectroscopy Analysis Tools (spant) CPMG style sequence with ideal pulses. — seq_cpmg_ideal • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/seq_mega_press_ideal.html b/docs/reference/seq_mega_press_ideal.html
index 0769b8b4..a9cd7fa0 100644
--- a/docs/reference/seq_mega_press_ideal.html
+++ b/docs/reference/seq_mega_press_ideal.html
@@ -1,7 +1,5 @@
-MEGA-PRESS sequence with ideal localisation pulses and Gaussian shaped
-editing pulse. — seq_mega_press_ideal • Spectroscopy Analysis Tools (spant) MEGA-PRESS sequence with ideal localisation pulses and Gaussian shaped editing pulse. — seq_mega_press_ideal • Spectroscopy Analysis Tools (spant) PRESS sequence with shaped refocusing pulses. — seq_press_2d_shaped • Spectroscopy Analysis Tools (spant) PRESS sequence with shaped refocusing pulses. — seq_press_2d_shaped • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -165,7 +165,7 @@ Value
diff --git a/docs/reference/seq_press_ideal.html b/docs/reference/seq_press_ideal.html
index 8c976856..72c3af3d 100644
--- a/docs/reference/seq_press_ideal.html
+++ b/docs/reference/seq_press_ideal.html
@@ -1,5 +1,5 @@
-PRESS sequence with ideal pulses. — seq_press_ideal • Spectroscopy Analysis Tools (spant) PRESS sequence with ideal pulses. — seq_press_ideal • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/seq_pulse_acquire.html b/docs/reference/seq_pulse_acquire.html
index 4a88fc64..ad80571e 100644
--- a/docs/reference/seq_pulse_acquire.html
+++ b/docs/reference/seq_pulse_acquire.html
@@ -1,5 +1,5 @@
-Simple pulse and acquire sequence with ideal pulses. — seq_pulse_acquire • Spectroscopy Analysis Tools (spant) Simple pulse and acquire sequence with ideal pulses. — seq_pulse_acquire • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/seq_slaser_ideal.html b/docs/reference/seq_slaser_ideal.html
index 74688f4d..eb83e8e3 100644
--- a/docs/reference/seq_slaser_ideal.html
+++ b/docs/reference/seq_slaser_ideal.html
@@ -1,5 +1,5 @@
-sLASER sequence with ideal pulses. — seq_slaser_ideal • Spectroscopy Analysis Tools (spant) sLASER sequence with ideal pulses. — seq_slaser_ideal • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -126,7 +126,7 @@ Value
diff --git a/docs/reference/seq_spin_echo_ideal.html b/docs/reference/seq_spin_echo_ideal.html
index e23271de..4248716f 100644
--- a/docs/reference/seq_spin_echo_ideal.html
+++ b/docs/reference/seq_spin_echo_ideal.html
@@ -1,5 +1,5 @@
-Spin echo sequence with ideal pulses. — seq_spin_echo_ideal • Spectroscopy Analysis Tools (spant) Spin echo sequence with ideal pulses. — seq_spin_echo_ideal • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/seq_steam_ideal.html b/docs/reference/seq_steam_ideal.html
index a60685a8..1c8115d7 100644
--- a/docs/reference/seq_steam_ideal.html
+++ b/docs/reference/seq_steam_ideal.html
@@ -1,5 +1,5 @@
-STEAM sequence with ideal pulses. — seq_steam_ideal • Spectroscopy Analysis Tools (spant) STEAM sequence with ideal pulses. — seq_steam_ideal • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -128,7 +128,7 @@ Value
diff --git a/docs/reference/seq_steam_ideal_cof.html b/docs/reference/seq_steam_ideal_cof.html
index 8f225740..cba7af91 100644
--- a/docs/reference/seq_steam_ideal_cof.html
+++ b/docs/reference/seq_steam_ideal_cof.html
@@ -1,7 +1,5 @@
-STEAM sequence with ideal pulses and coherence order filtering to simulate
-gradient crushers. — seq_steam_ideal_cof • Spectroscopy Analysis Tools (spant) STEAM sequence with ideal pulses and coherence order filtering to simulate gradient crushers. — seq_steam_ideal_cof • Spectroscopy Analysis Tools (spant) STEAM sequence with ideal pulses using the z-rotation gradient simulation
-method described by Young et al JMR 140, 146-152 (1999). — seq_steam_ideal_young • Spectroscopy Analysis Tools (spant) STEAM sequence with ideal pulses using the z-rotation gradient simulation method described by Young et al JMR 140, 146-152 (1999). — seq_steam_ideal_young • Spectroscopy Analysis Tools (spant) Set the number of transients for an mrs_data object. — set_Ntrans • Spectroscopy Analysis Tools (spant) Set the number of transients for an mrs_data object. — set_Ntrans • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/set_def_acq_paras.html b/docs/reference/set_def_acq_paras.html
index 3e1b4004..cc2ada9c 100644
--- a/docs/reference/set_def_acq_paras.html
+++ b/docs/reference/set_def_acq_paras.html
@@ -1,5 +1,5 @@
-Set the default acquisition parameters. — set_def_acq_paras • Spectroscopy Analysis Tools (spant) Set the default acquisition parameters. — set_def_acq_paras • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Arguments
diff --git a/docs/reference/set_lcm_cmd.html b/docs/reference/set_lcm_cmd.html
index 2056ed01..42bb2f24 100644
--- a/docs/reference/set_lcm_cmd.html
+++ b/docs/reference/set_lcm_cmd.html
@@ -1,5 +1,5 @@
-Set the command to run the LCModel command-line program. — set_lcm_cmd • Spectroscopy Analysis Tools (spant) Set the command to run the LCModel command-line program. — set_lcm_cmd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/set_lw.html b/docs/reference/set_lw.html
index b64ec851..bb176c62 100644
--- a/docs/reference/set_lw.html
+++ b/docs/reference/set_lw.html
@@ -1,5 +1,5 @@
-Apply line-broadening to an mrs_data object to achieve a specified linewidth. — set_lw • Spectroscopy Analysis Tools (spant) Apply line-broadening to an mrs_data object to achieve a specified linewidth. — set_lw • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -123,7 +123,7 @@ Value
diff --git a/docs/reference/set_mask_xy_mat.html b/docs/reference/set_mask_xy_mat.html
index 49dc5d4e..52c4b617 100644
--- a/docs/reference/set_mask_xy_mat.html
+++ b/docs/reference/set_mask_xy_mat.html
@@ -1,5 +1,5 @@
-Set the masked voxels in a 2D MRSI dataset to given spectrum. — set_mask_xy_mat • Spectroscopy Analysis Tools (spant) Set the masked voxels in a 2D MRSI dataset to given spectrum. — set_mask_xy_mat • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Value
diff --git a/docs/reference/set_precomp_mode.html b/docs/reference/set_precomp_mode.html
index f44bd5d3..47c28e3b 100644
--- a/docs/reference/set_precomp_mode.html
+++ b/docs/reference/set_precomp_mode.html
@@ -1,5 +1,5 @@
-Set the precompute mode. — set_precomp_mode • Spectroscopy Analysis Tools (spant) Set the precompute mode. — set_precomp_mode • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/set_precomp_verbose.html b/docs/reference/set_precomp_verbose.html
index 1453a231..9c613505 100644
--- a/docs/reference/set_precomp_verbose.html
+++ b/docs/reference/set_precomp_verbose.html
@@ -1,5 +1,5 @@
-Set the verbosity of the precompute function. — set_precomp_verbose • Spectroscopy Analysis Tools (spant) Set the verbosity of the precompute function. — set_precomp_verbose • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/set_ref.html b/docs/reference/set_ref.html
index 8953fa50..5436dfa2 100644
--- a/docs/reference/set_ref.html
+++ b/docs/reference/set_ref.html
@@ -1,5 +1,5 @@
-Set the ppm reference value (eg ppm value at 0Hz). — set_ref • Spectroscopy Analysis Tools (spant) Set the ppm reference value (eg ppm value at 0Hz). — set_ref • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/set_td_pts.html b/docs/reference/set_td_pts.html
index 8a80d42a..586459ff 100644
--- a/docs/reference/set_td_pts.html
+++ b/docs/reference/set_td_pts.html
@@ -1,7 +1,5 @@
-Set the number of time-domain data points, truncating or zero-filling as
-appropriate. — set_td_pts • Spectroscopy Analysis Tools (spant) Set the number of time-domain data points, truncating or zero-filling as appropriate. — set_td_pts • Spectroscopy Analysis Tools (spant) Set the command to run the TARQUIN command-line program. — set_tqn_cmd • Spectroscopy Analysis Tools (spant) Set the command to run the TARQUIN command-line program. — set_tqn_cmd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/set_tr.html b/docs/reference/set_tr.html
index b2109ab0..65c9df5f 100644
--- a/docs/reference/set_tr.html
+++ b/docs/reference/set_tr.html
@@ -1,5 +1,5 @@
-Set the repetition time of an MRS dataset. — set_tr • Spectroscopy Analysis Tools (spant) Set the repetition time of an MRS dataset. — set_tr • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/shift.html b/docs/reference/shift.html
index ab0fe724..034591d0 100644
--- a/docs/reference/shift.html
+++ b/docs/reference/shift.html
@@ -1,5 +1,5 @@
-Apply a frequency shift to MRS data. — shift • Spectroscopy Analysis Tools (spant) Apply a frequency shift to MRS data. — shift • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/shift_basis.html b/docs/reference/shift_basis.html
index 2884be19..f55a65e0 100644
--- a/docs/reference/shift_basis.html
+++ b/docs/reference/shift_basis.html
@@ -1,5 +1,5 @@
-Apply frequency shifts to basis set signals. — shift_basis • Spectroscopy Analysis Tools (spant) Apply frequency shifts to basis set signals. — shift_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Value
diff --git a/docs/reference/sim_basis.html b/docs/reference/sim_basis.html
index c7838c46..bb5fefc6 100644
--- a/docs/reference/sim_basis.html
+++ b/docs/reference/sim_basis.html
@@ -1,5 +1,5 @@
-Simulate a basis set object. — sim_basis • Spectroscopy Analysis Tools (spant) Simulate a basis set object. — sim_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -136,7 +136,7 @@ Value
diff --git a/docs/reference/sim_basis_1h_brain.html b/docs/reference/sim_basis_1h_brain.html
index 62ed7389..f71ffa0b 100644
--- a/docs/reference/sim_basis_1h_brain.html
+++ b/docs/reference/sim_basis_1h_brain.html
@@ -1,7 +1,5 @@
-Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS
-sequence. Note, ideal pulses are assumed. — sim_basis_1h_brain • Spectroscopy Analysis Tools (spant) Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS sequence. Note, ideal pulses are assumed. — sim_basis_1h_brain • Spectroscopy Analysis Tools (spant) Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS
-sequence. Note, ideal pulses are assumed. — sim_basis_1h_brain_press • Spectroscopy Analysis Tools (spant) Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS sequence. Note, ideal pulses are assumed. — sim_basis_1h_brain_press • Spectroscopy Analysis Tools (spant) Simulate a macromolecular and lipid basis-set suitable for 1H brain MRS
-analysis. — sim_basis_mm_lip_lcm • Spectroscopy Analysis Tools (spant) Simulate a macromolecular and lipid basis-set suitable for 1H brain MRS analysis. — sim_basis_mm_lip_lcm • Spectroscopy Analysis Tools (spant) Simulate a basis file using TARQUIN. — sim_basis_tqn • Spectroscopy Analysis Tools (spant) Simulate a basis file using TARQUIN. — sim_basis_tqn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -129,7 +129,7 @@ Examples
diff --git a/docs/reference/sim_brain_1h.html b/docs/reference/sim_brain_1h.html
index 2044cf1a..717ee289 100644
--- a/docs/reference/sim_brain_1h.html
+++ b/docs/reference/sim_brain_1h.html
@@ -1,5 +1,5 @@
-Simulate MRS data with a similar appearance to normal brain (by default). — sim_brain_1h • Spectroscopy Analysis Tools (spant) Simulate MRS data with a similar appearance to normal brain (by default). — sim_brain_1h • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -159,7 +159,7 @@ Value
diff --git a/docs/reference/sim_mol.html b/docs/reference/sim_mol.html
index 23bcef50..77f76a50 100644
--- a/docs/reference/sim_mol.html
+++ b/docs/reference/sim_mol.html
@@ -1,5 +1,5 @@
-Simulate a mol_parameter object. — sim_mol • Spectroscopy Analysis Tools (spant) Simulate a mol_parameter object. — sim_mol • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -143,7 +143,7 @@ Value
diff --git a/docs/reference/sim_noise.html b/docs/reference/sim_noise.html
index 23875f79..a71477d4 100644
--- a/docs/reference/sim_noise.html
+++ b/docs/reference/sim_noise.html
@@ -1,5 +1,5 @@
-Simulate an mrs_data object containing simulated Gaussian noise. — sim_noise • Spectroscopy Analysis Tools (spant) Simulate an mrs_data object containing simulated Gaussian noise. — sim_noise • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -84,6 +84,7 @@ Simulate an mrs_data object containing simulated Gaussian noise.
ft = def_ft(),
N = def_N(),
ref = def_ref(),
+ nuc = def_nuc(),
dyns = 1,
fd = TRUE
)
@@ -111,6 +112,10 @@ Arguments
reference value for ppm scale.
nuc
+resonant nucleus.
dyns
number of dynamic scans to generate.
Value
diff --git a/docs/reference/sim_resonances.html b/docs/reference/sim_resonances.html
index 19e9a8a4..d4f8d7c0 100644
--- a/docs/reference/sim_resonances.html
+++ b/docs/reference/sim_resonances.html
@@ -1,5 +1,5 @@
-Simulate a MRS data object containing a set of simulated resonances. — sim_resonances • Spectroscopy Analysis Tools (spant) Simulate a MRS data object containing a set of simulated resonances. — sim_resonances • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -161,7 +161,7 @@ Examples
diff --git a/docs/reference/sim_th_excit_profile.html b/docs/reference/sim_th_excit_profile.html
index 5535c5ef..e781cab1 100644
--- a/docs/reference/sim_th_excit_profile.html
+++ b/docs/reference/sim_th_excit_profile.html
@@ -1,7 +1,5 @@
-Simulate an ideal pulse excitation profile by smoothing a top-hat function
-with a Gaussian. — sim_th_excit_profile • Spectroscopy Analysis Tools (spant) Simulate an ideal pulse excitation profile by smoothing a top-hat function with a Gaussian. — sim_th_excit_profile • Spectroscopy Analysis Tools (spant) Simulate an mrs_data object containing complex zero valued samples. — sim_zero • Spectroscopy Analysis Tools (spant) Simulate an mrs_data object containing complex zero valued samples. — sim_zero • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -78,7 +78,14 @@ Simulate an mrs_data object containing complex zero valued samples.
-
+
@@ -99,6 +106,10 @@ Arguments
reference value for ppm scale.
nuc
+resonant nucleus.
dyns
number of dynamic scans to generate.
Value
diff --git a/docs/reference/smooth_dyns.html b/docs/reference/smooth_dyns.html
index 4cc8da50..accf3a51 100644
--- a/docs/reference/smooth_dyns.html
+++ b/docs/reference/smooth_dyns.html
@@ -1,5 +1,5 @@
-Smooth data across the dynamic dimension with a Gaussian kernel. — smooth_dyns • Spectroscopy Analysis Tools (spant) Smooth data across the dynamic dimension with a Gaussian kernel. — smooth_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/sort_basis.html b/docs/reference/sort_basis.html
index 6a676ea2..d25cc006 100644
--- a/docs/reference/sort_basis.html
+++ b/docs/reference/sort_basis.html
@@ -1,5 +1,5 @@
-Sort the basis-set elements alphabetically. — sort_basis • Spectroscopy Analysis Tools (spant) Sort the basis-set elements alphabetically. — sort_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/spant-package.html b/docs/reference/spant-package.html
index b3dd8e21..90f19ec3 100644
--- a/docs/reference/spant-package.html
+++ b/docs/reference/spant-package.html
@@ -1,5 +1,5 @@
-spant: spectroscopy analysis tools. — spant-package • Spectroscopy Analysis Tools (spant) spant: spectroscopy analysis tools. — spant-package • Spectroscopy Analysis Tools (spant) Simulate and fit some spectra with ABfit for benchmarking purposes. Basic
-timing and performance metrics will be printed. — spant_abfit_benchmark • Spectroscopy Analysis Tools (spant) Simulate and fit some spectra with ABfit for benchmarking purposes. Basic timing and performance metrics will be printed. — spant_abfit_benchmark • Spectroscopy Analysis Tools (spant) Example MEGA-PRESS data with significant B0 drift. — spant_mpress_drift • Spectroscopy Analysis Tools (spant) Example MEGA-PRESS data with significant B0 drift. — spant_mpress_drift • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -83,7 +83,7 @@ Example MEGA-PRESS data with significant B0 drift.
Format
- An object of class mrs_data of length 13.
+ An object of class mrs_data of dimension 1 x 1 x 1 x 1 x 40 x 1 x 1024.
@@ -98,7 +98,7 @@ Format
diff --git a/docs/reference/spant_sim_fmrs_dataset.html b/docs/reference/spant_sim_fmrs_dataset.html
new file mode 100644
index 00000000..00e48b56
--- /dev/null
+++ b/docs/reference/spant_sim_fmrs_dataset.html
@@ -0,0 +1,117 @@
+
+Simulate an example fMRS dataset for a block design fMRS experiment and export a BIDS structure. — spant_sim_fmrs_dataset • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Simulate an example fMRS dataset for a block design fMRS experiment and export a BIDS structure.
+ Source: R/fmrs.R
+ spant_sim_fmrs_dataset.Rd
+
+
+
+ Simulate an example fMRS dataset for a block design fMRS experiment and
+export a BIDS structure.
+
+
+
+ spant_sim_fmrs_dataset(output_dir = NULL)
+
+
+
+ Arguments
+ - output_dir
+output directory for the BIDS data. Defaults to :
+"HOME/sim_fmrs_dataset/data".
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/spant_simulation_benchmark.html b/docs/reference/spant_simulation_benchmark.html
index 32daa8bf..d8cc6841 100644
--- a/docs/reference/spant_simulation_benchmark.html
+++ b/docs/reference/spant_simulation_benchmark.html
@@ -1,7 +1,5 @@
-Simulate a typical metabolite basis set for benchmarking. Timing metrics will
-be printed on completion. — spant_simulation_benchmark • Spectroscopy Analysis Tools (spant) Simulate a typical metabolite basis set for benchmarking. Timing metrics will be printed on completion. — spant_simulation_benchmark • Spectroscopy Analysis Tools (spant) Decompose an mrs_data object into white and gray matter spectra. — spec_decomp • Spectroscopy Analysis Tools (spant) Perform a mathematical operation on a spectral region. — spec_op • Spectroscopy Analysis Tools (spant) Perform a mathematical operation on a spectral region. — spec_op • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -98,8 +98,8 @@ Arguments
operator
-can be "sum" (default), "mean", "l2", "max", "min" or
-"max-min".
can be "sum" (default), "mean", "l2", "max", "max_cplx,
+"min" or "max-min".
freq_scale
@@ -129,7 +129,7 @@ Value
diff --git a/docs/reference/spin_sys.html b/docs/reference/spin_sys.html
index 853423a4..1eaa9e76 100644
--- a/docs/reference/spin_sys.html
+++ b/docs/reference/spin_sys.html
@@ -1,5 +1,5 @@
-Create a spin system object for pulse sequence simulation. — spin_sys • Spectroscopy Analysis Tools (spant) Create a spin system object for pulse sequence simulation. — spin_sys • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/spm_pve2categorical.html b/docs/reference/spm_pve2categorical.html
index 23a1bad9..70f10729 100644
--- a/docs/reference/spm_pve2categorical.html
+++ b/docs/reference/spm_pve2categorical.html
@@ -1,7 +1,5 @@
-Convert SPM style segmentation files to a single categorical image where
-the numerical values map as: 0) Other, 1) CSF, 2) GM and 3) WM. — spm_pve2categorical • Spectroscopy Analysis Tools (spant) Convert SPM style segmentation files to a single categorical image where the numerical values map as: 0) Other, 1) CSF, 2) GM and 3) WM. — spm_pve2categorical • Spectroscopy Analysis Tools (spant) Signal space projection method for lipid suppression. — ssp • Spectroscopy Analysis Tools (spant) Signal space projection method for lipid suppression. — ssp • Spectroscopy Analysis Tools (spant) Plot the fitting results of an object of class fit_result with
-individual basis set components shown. — stackplot.fit_result • Spectroscopy Analysis Tools (spant) Plot the fitting results of an object of class fit_result with individual basis set components shown. — stackplot.fit_result • Spectroscopy Analysis Tools (spant) Produce a plot with multiple traces. — stackplot • Spectroscopy Analysis Tools (spant) Produce a plot with multiple traces. — stackplot • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/stackplot.mrs_data.html b/docs/reference/stackplot.mrs_data.html
index 17ff5648..64eea445 100644
--- a/docs/reference/stackplot.mrs_data.html
+++ b/docs/reference/stackplot.mrs_data.html
@@ -1,5 +1,5 @@
-Stackplot plotting method for objects of class mrs_data. — stackplot.mrs_data • Spectroscopy Analysis Tools (spant) Stackplot plotting method for objects of class mrs_data. — stackplot.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -255,7 +255,7 @@ Arguments
diff --git a/docs/reference/sub_first_dyn.html b/docs/reference/sub_first_dyn.html
index dbd7f831..493b7242 100644
--- a/docs/reference/sub_first_dyn.html
+++ b/docs/reference/sub_first_dyn.html
@@ -1,5 +1,5 @@
-Subtract the first dynamic spectrum from a dynamic series. — sub_first_dyn • Spectroscopy Analysis Tools (spant) Subtract the first dynamic spectrum from a dynamic series. — sub_first_dyn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/sub_mean_dyns.html b/docs/reference/sub_mean_dyns.html
index 6e3bb2df..221bd0c1 100644
--- a/docs/reference/sub_mean_dyns.html
+++ b/docs/reference/sub_mean_dyns.html
@@ -1,5 +1,5 @@
-Subtract the mean dynamic spectrum from a dynamic series. — sub_mean_dyns • Spectroscopy Analysis Tools (spant) Subtract the mean dynamic spectrum from a dynamic series. — sub_mean_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/sub_median_dyns.html b/docs/reference/sub_median_dyns.html
index 134c495d..1e834f14 100644
--- a/docs/reference/sub_median_dyns.html
+++ b/docs/reference/sub_median_dyns.html
@@ -1,5 +1,5 @@
-Subtract the median dynamic spectrum from a dynamic series. — sub_median_dyns • Spectroscopy Analysis Tools (spant) Subtract the median dynamic spectrum from a dynamic series. — sub_median_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/sum_coils.html b/docs/reference/sum_coils.html
index 7bf559f2..e1ab3cc0 100644
--- a/docs/reference/sum_coils.html
+++ b/docs/reference/sum_coils.html
@@ -1,5 +1,5 @@
-Calculate the sum across receiver coil elements. — sum_coils • Spectroscopy Analysis Tools (spant) Calculate the sum across receiver coil elements. — sum_coils • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/sum_dyns.html b/docs/reference/sum_dyns.html
index a0be19d3..bbda2ffc 100644
--- a/docs/reference/sum_dyns.html
+++ b/docs/reference/sum_dyns.html
@@ -1,5 +1,5 @@
-Calculate the sum of data dynamics. — sum_dyns • Spectroscopy Analysis Tools (spant) Calculate the sum of data dynamics. — sum_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/sum_mrs.html b/docs/reference/sum_mrs.html
index a22f215b..3cc3ab9e 100644
--- a/docs/reference/sum_mrs.html
+++ b/docs/reference/sum_mrs.html
@@ -1,5 +1,5 @@
-Sum two mrs_data objects. — sum_mrs • Spectroscopy Analysis Tools (spant) Sum two mrs_data objects. — sum_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Value
diff --git a/docs/reference/sum_mrs_list.html b/docs/reference/sum_mrs_list.html
index f4e09aea..c3584348 100644
--- a/docs/reference/sum_mrs_list.html
+++ b/docs/reference/sum_mrs_list.html
@@ -1,5 +1,5 @@
-Return the sum of a list of mrs_data objects. — sum_mrs_list • Spectroscopy Analysis Tools (spant) Return the sum of a list of mrs_data objects. — sum_mrs_list • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/svs_1h_brain_analysis.html b/docs/reference/svs_1h_brain_analysis.html
index 8ce514db..dff0ef7d 100644
--- a/docs/reference/svs_1h_brain_analysis.html
+++ b/docs/reference/svs_1h_brain_analysis.html
@@ -1,5 +1,5 @@
-Standard SVS 1H brain analysis pipeline. — svs_1h_brain_analysis • Spectroscopy Analysis Tools (spant) Standard SVS 1H brain analysis pipeline. — svs_1h_brain_analysis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -199,7 +199,7 @@ Value
diff --git a/docs/reference/svs_1h_brain_analysis_dev.html b/docs/reference/svs_1h_brain_analysis_dev.html
index d70a14d3..d71bfea2 100644
--- a/docs/reference/svs_1h_brain_analysis_dev.html
+++ b/docs/reference/svs_1h_brain_analysis_dev.html
@@ -1,5 +1,5 @@
-Standard SVS 1H brain analysis pipeline. — svs_1h_brain_analysis_dev • Spectroscopy Analysis Tools (spant) Standard SVS 1H brain analysis pipeline. — svs_1h_brain_analysis_dev • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -193,7 +193,7 @@ Examples
diff --git a/docs/reference/svs_1h_brain_batch_analysis.html b/docs/reference/svs_1h_brain_batch_analysis.html
index 5631e8cc..15f7223e 100644
--- a/docs/reference/svs_1h_brain_batch_analysis.html
+++ b/docs/reference/svs_1h_brain_batch_analysis.html
@@ -1,5 +1,5 @@
-Batch interface to the standard SVS 1H brain analysis pipeline. — svs_1h_brain_batch_analysis • Spectroscopy Analysis Tools (spant) Batch interface to the standard SVS 1H brain analysis pipeline. — svs_1h_brain_batch_analysis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -144,7 +144,7 @@ Value
diff --git a/docs/reference/t_test_spec.html b/docs/reference/t_test_spec.html
new file mode 100644
index 00000000..56a7ea1b
--- /dev/null
+++ b/docs/reference/t_test_spec.html
@@ -0,0 +1,124 @@
+
+Perform a t-test on spectral data points. — t_test_spec • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+
+
+ Perform a t-test on spectral data points.
+
+
+
+ t_test_spec(mrs_data, group)
+
+
+
+ Arguments
+ - mrs_data
+an mrs_data object with spectra in the dynamic dimension.
- group
+vector describing the group membership of each dynamic spectrum.
+
+ Value
+
+
+a list of statistical results.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/td2fd.html b/docs/reference/td2fd.html
index 6748a6a8..f31ed524 100644
--- a/docs/reference/td2fd.html
+++ b/docs/reference/td2fd.html
@@ -1,5 +1,5 @@
-Transform time-domain data to the frequency-domain. — td2fd • Spectroscopy Analysis Tools (spant) Transform time-domain data to the frequency-domain. — td2fd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/td_conv_filt.html b/docs/reference/td_conv_filt.html
index a9f340c3..106b9b00 100644
--- a/docs/reference/td_conv_filt.html
+++ b/docs/reference/td_conv_filt.html
@@ -1,5 +1,5 @@
-Time-domain convolution based filter. — td_conv_filt • Spectroscopy Analysis Tools (spant) Time-domain convolution based filter. — td_conv_filt • Spectroscopy Analysis Tools (spant) Time-domain spectral registration. — tdsr • Spectroscopy Analysis Tools (spant) Time-domain spectral registration. — tdsr • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -121,7 +121,7 @@ Value
diff --git a/docs/reference/te.html b/docs/reference/te.html
index 010361b1..4a65711d 100644
--- a/docs/reference/te.html
+++ b/docs/reference/te.html
@@ -1,5 +1,5 @@
-Return the echo time of an MRS dataset. — te • Spectroscopy Analysis Tools (spant) Return the echo time of an MRS dataset. — te • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/tr.html b/docs/reference/tr.html
index 0c0bd63b..2e749e02 100644
--- a/docs/reference/tr.html
+++ b/docs/reference/tr.html
@@ -1,5 +1,5 @@
-Return the repetition time of an MRS dataset. — tr • Spectroscopy Analysis Tools (spant) Return the repetition time of an MRS dataset. — tr • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/varpro_3_para_opts.html b/docs/reference/varpro_3_para_opts.html
index c2270a16..52d7cd84 100644
--- a/docs/reference/varpro_3_para_opts.html
+++ b/docs/reference/varpro_3_para_opts.html
@@ -1,5 +1,5 @@
-Return a list of options for VARPRO based fitting with 3 free parameters. — varpro_3_para_opts • Spectroscopy Analysis Tools (spant) Return a list of options for VARPRO based fitting with 3 free parameters. — varpro_3_para_opts • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -141,7 +141,7 @@ Value
diff --git a/docs/reference/varpro_basic_opts.html b/docs/reference/varpro_basic_opts.html
index 32c86d22..c5104891 100644
--- a/docs/reference/varpro_basic_opts.html
+++ b/docs/reference/varpro_basic_opts.html
@@ -1,5 +1,5 @@
-Return a list of options for a basic VARPRO analysis. — varpro_basic_opts • Spectroscopy Analysis Tools (spant) Return a list of options for a basic VARPRO analysis. — varpro_basic_opts • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -118,7 +118,7 @@ Value
diff --git a/docs/reference/varpro_opts.html b/docs/reference/varpro_opts.html
index 2aabf11d..6332f730 100644
--- a/docs/reference/varpro_opts.html
+++ b/docs/reference/varpro_opts.html
@@ -1,5 +1,5 @@
-Return a list of options for VARPRO based fitting. — varpro_opts • Spectroscopy Analysis Tools (spant) Return a list of options for VARPRO based fitting. — varpro_opts • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -177,7 +177,7 @@ Examples
diff --git a/docs/reference/vec2mrs_data.html b/docs/reference/vec2mrs_data.html
index 0cccd73b..f0d58bf0 100644
--- a/docs/reference/vec2mrs_data.html
+++ b/docs/reference/vec2mrs_data.html
@@ -1,5 +1,5 @@
-Convert a vector into a mrs_data object. — vec2mrs_data • Spectroscopy Analysis Tools (spant) Convert a vector into a mrs_data object. — vec2mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -80,10 +80,11 @@ Convert a vector into a mrs_data object.
vec2mrs_data(
vec,
- fs = def_fs(),
- ft = def_ft(),
- ref = def_ref(),
- nuc = def_nuc(),
+ mrs_data = NULL,
+ fs = NULL,
+ ft = NULL,
+ ref = NULL,
+ nuc = NULL,
dyns = 1,
fd = FALSE
)
@@ -95,6 +96,10 @@ Arguments
the data vector.
mrs_data
+example data to copy acquisition parameters from.
fs
sampling frequency in Hz.
Arguments
fd
-flag to indicate if the matrix is in the frequency domain (logical).
flag to indicate if the vector is in the frequency domain (logical).
Value
diff --git a/docs/reference/write_basis.html b/docs/reference/write_basis.html
index b6e27cbd..94c5e021 100644
--- a/docs/reference/write_basis.html
+++ b/docs/reference/write_basis.html
@@ -1,5 +1,5 @@
-Write a basis object to an LCModel .basis formatted file. — write_basis • Spectroscopy Analysis Tools (spant) Write a basis object to an LCModel .basis formatted file. — write_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -108,7 +108,7 @@ Arguments
diff --git a/docs/reference/write_basis_tqn.html b/docs/reference/write_basis_tqn.html
index 6aa51c1d..116c73ec 100644
--- a/docs/reference/write_basis_tqn.html
+++ b/docs/reference/write_basis_tqn.html
@@ -1,5 +1,5 @@
-Generate a basis file using TARQUIN. — write_basis_tqn • Spectroscopy Analysis Tools (spant) Generate a basis file using TARQUIN. — write_basis_tqn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Examples
diff --git a/docs/reference/write_mrs.html b/docs/reference/write_mrs.html
index fff25f15..124b9dc4 100644
--- a/docs/reference/write_mrs.html
+++ b/docs/reference/write_mrs.html
@@ -1,5 +1,5 @@
-Write MRS data object to file. — write_mrs • Spectroscopy Analysis Tools (spant) Write MRS data object to file. — write_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Arguments
diff --git a/docs/reference/write_mrs_nifti.html b/docs/reference/write_mrs_nifti.html
index f4bf1921..bd3ed4b7 100644
--- a/docs/reference/write_mrs_nifti.html
+++ b/docs/reference/write_mrs_nifti.html
@@ -1,5 +1,5 @@
-Write MRS data object to file in NIFTI format. — write_mrs_nifti • Spectroscopy Analysis Tools (spant) Write MRS data object to file in NIFTI format. — write_mrs_nifti • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/write_pulse_ascii.html b/docs/reference/write_pulse_ascii.html
index 067ae086..221f8ebb 100644
--- a/docs/reference/write_pulse_ascii.html
+++ b/docs/reference/write_pulse_ascii.html
@@ -1,5 +1,5 @@
-Write an ASCII formatted pulse file. — write_pulse_ascii • Spectroscopy Analysis Tools (spant) Write an ASCII formatted pulse file. — write_pulse_ascii • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/zero_fade_spec.html b/docs/reference/zero_fade_spec.html
index c703745c..c8b572c3 100644
--- a/docs/reference/zero_fade_spec.html
+++ b/docs/reference/zero_fade_spec.html
@@ -1,7 +1,5 @@
-Fade a spectrum to zero by frequency domain multiplication with a tanh
-function. Note this operation distorts data points at the end of the FID. — zero_fade_spec • Spectroscopy Analysis Tools (spant) Fade a spectrum to zero by frequency domain multiplication with a tanh function. Note this operation distorts data points at the end of the FID. — zero_fade_spec • Spectroscopy Analysis Tools (spant) Zero all coherences including and above a given order. — zero_higher_orders • Spectroscopy Analysis Tools (spant) Zero all coherences including and above a given order. — zero_higher_orders • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Value
diff --git a/docs/reference/zero_td_pts_end.html b/docs/reference/zero_td_pts_end.html
index 8c1123c8..71d24ebb 100644
--- a/docs/reference/zero_td_pts_end.html
+++ b/docs/reference/zero_td_pts_end.html
@@ -1,5 +1,5 @@
-Set mrs_data object data points at the end of the FID to zero. — zero_td_pts_end • Spectroscopy Analysis Tools (spant) Set mrs_data object data points at the end of the FID to zero. — zero_td_pts_end • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/zf.html b/docs/reference/zf.html
index 85e2013c..baf50256 100644
--- a/docs/reference/zf.html
+++ b/docs/reference/zf.html
@@ -1,5 +1,5 @@
-Zero-fill MRS data in the time domain. — zf • Spectroscopy Analysis Tools (spant) Zero-fill MRS data in the time domain. — zf • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -125,7 +125,7 @@ Value
diff --git a/docs/reference/zf_xy.html b/docs/reference/zf_xy.html
index ebca3999..c4104a74 100644
--- a/docs/reference/zf_xy.html
+++ b/docs/reference/zf_xy.html
@@ -1,5 +1,5 @@
-Zero-fill MRSI data in the k-space x-y direction. — zf_xy • Spectroscopy Analysis Tools (spant) Zero-fill MRSI data in the k-space x-y direction. — zf_xy • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -113,7 +113,7 @@ Value
diff --git a/docs/sitemap.xml b/docs/sitemap.xml
index e2139f71..4c39f515 100644
--- a/docs/sitemap.xml
+++ b/docs/sitemap.xml
@@ -216,6 +216,12 @@
https://martin3141.github.io/spant/reference/comb_coils_fp_pc.html
+
+ https://martin3141.github.io/spant/reference/comb_coils_mrsi_gls.html
+
+
+ https://martin3141.github.io/spant/reference/comb_coils_svs_gls.html
+
https://martin3141.github.io/spant/reference/comb_csv_results.html
@@ -411,6 +417,9 @@
https://martin3141.github.io/spant/reference/gen_conv_reg.html
+
+ https://martin3141.github.io/spant/reference/gen_group_reg.html
+
https://martin3141.github.io/spant/reference/gen_impulse_reg.html
@@ -555,6 +564,15 @@
https://martin3141.github.io/spant/reference/glm_spec.html
+
+ https://martin3141.github.io/spant/reference/glm_spec_fmrs_fl.html
+
+
+ https://martin3141.github.io/spant/reference/glm_spec_fmrs_group.html
+
+
+ https://martin3141.github.io/spant/reference/glm_spec_group_linhyp.html
+
https://martin3141.github.io/spant/reference/grid_shift_xy.html
@@ -690,9 +708,15 @@
https://martin3141.github.io/spant/reference/mrs_data2basis.html
+
+ https://martin3141.github.io/spant/reference/mrs_data2bids.html
+
https://martin3141.github.io/spant/reference/mrs_data2mat.html
+
+ https://martin3141.github.io/spant/reference/mrs_data2spec_mat.html
+
https://martin3141.github.io/spant/reference/mrs_data2vec.html
@@ -741,6 +765,9 @@
https://martin3141.github.io/spant/reference/phase.html
+
+ https://martin3141.github.io/spant/reference/phase_ref_1h_brain.html
+
https://martin3141.github.io/spant/reference/plot.fit_result.html
@@ -780,6 +807,12 @@
https://martin3141.github.io/spant/reference/precomp.html
+
+ https://martin3141.github.io/spant/reference/preproc_svs.html
+
+
+ https://martin3141.github.io/spant/reference/preproc_svs_dataset.html
+
https://martin3141.github.io/spant/reference/print.fit_result.html
@@ -1050,6 +1083,9 @@
https://martin3141.github.io/spant/reference/spant_mpress_drift.html
+
+ https://martin3141.github.io/spant/reference/spant_sim_fmrs_dataset.html
+
https://martin3141.github.io/spant/reference/spant_simulation_benchmark.html
@@ -1107,6 +1143,9 @@
https://martin3141.github.io/spant/reference/svs_1h_brain_batch_analysis.html
+
+ https://martin3141.github.io/spant/reference/t_test_spec.html
+
https://martin3141.github.io/spant/reference/td2fd.html
Plot an interactive slice map from a data array where voxels can be selected -to display a corresponding spectrum.
Plot an interactive slice map from a data array where voxels can be selected to display a corresponding spectrum.
All functions
- Save function results to file and load on subsequent calls to avoid repeat
-computation.
Save function results to file and load on subsequent calls to avoid repeat computation.
+
+
+ Preprocess and perform quality assessment of a single SVS data set.
+
+
+ Preprocess and perform quality assessment of one or more SVS data sets.
@@ -1055,15 +1046,11 @@ All functions
- Read a directory containing Siemens MRS IMA files and combine along the coil
-dimension. Note that the coil ID is inferred from the sorted file name and
-should be checked when consistency is required between two directories.
Read a directory containing Siemens MRS IMA files and combine along the coil dimension. Note that the coil ID is inferred from the sorted file name and should be checked when consistency is required between two directories.
- Read a directory containing Siemens MRS IMA files and combine along the
-dynamic dimension. Note that the coil ID is inferred from the sorted file
-name and should be checked when consistency is required.
Read a directory containing Siemens MRS IMA files and combine along the dynamic dimension. Note that the coil ID is inferred from the sorted file name and should be checked when consistency is required.
@@ -1103,13 +1090,11 @@ All functions
- Reconstruct complex time-domain data from the real part of frequency-domain
-data.
Reconstruct complex time-domain data from the real part of frequency-domain data.
- Reconstruct complex time-domain data from the real part of frequency-domain
-data.
Reconstruct complex time-domain data from the real part of frequency-domain data.
@@ -1141,8 +1126,7 @@ All functions
- Resample a VOI to match a target image space using nearest-neighbour
-interpolation.
Resample a VOI to match a target image space using nearest-neighbour interpolation.
@@ -1158,23 +1142,19 @@ All functions
- Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water).
Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / kg of tissue water).
- Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water).
Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / kg of tissue water).
- Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / Litre of tissue).
Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / Litre of tissue).
- Convert default LCM/TARQUIN concentration scaling to molal units with partial
-volume correction.
Convert default LCM/TARQUIN concentration scaling to molal units with partial volume correction.
@@ -1222,8 +1202,7 @@ All functions
- MEGA-PRESS sequence with ideal localisation pulses and Gaussian shaped
-editing pulse.
MEGA-PRESS sequence with ideal localisation pulses and Gaussian shaped editing pulse.
@@ -1251,13 +1230,11 @@ All functions
- STEAM sequence with ideal pulses and coherence order filtering to simulate
-gradient crushers.
STEAM sequence with ideal pulses and coherence order filtering to simulate gradient crushers.
- STEAM sequence with ideal pulses using the z-rotation gradient simulation
-method described by Young et al JMR 140, 146-152 (1999).
STEAM sequence with ideal pulses using the z-rotation gradient simulation method described by Young et al JMR 140, 146-152 (1999).
@@ -1293,8 +1270,7 @@ All functions
- Set the number of time-domain data points, truncating or zero-filling as
-appropriate.
Set the number of time-domain data points, truncating or zero-filling as appropriate.
@@ -1318,18 +1294,15 @@ All functions
- Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS
-sequence. Note, ideal pulses are assumed.
Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS sequence. Note, ideal pulses are assumed.
- Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS
-sequence. Note, ideal pulses are assumed.
Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS sequence. Note, ideal pulses are assumed.
- Simulate a macromolecular and lipid basis-set suitable for 1H brain MRS
-analysis.
Simulate a macromolecular and lipid basis-set suitable for 1H brain MRS analysis.
@@ -1353,8 +1326,7 @@ All functions
- Simulate an ideal pulse excitation profile by smoothing a top-hat function
-with a Gaussian.
Simulate an ideal pulse excitation profile by smoothing a top-hat function with a Gaussian.
@@ -1374,17 +1346,19 @@ All functions
- Simulate and fit some spectra with ABfit for benchmarking purposes. Basic
-timing and performance metrics will be printed.
Simulate and fit some spectra with ABfit for benchmarking purposes. Basic timing and performance metrics will be printed.
Example MEGA-PRESS data with significant B0 drift.
+
+
+ Simulate an example fMRS dataset for a block design fMRS experiment and export a BIDS structure.
- Simulate a typical metabolite basis set for benchmarking. Timing metrics will
-be printed on completion.
Simulate a typical metabolite basis set for benchmarking. Timing metrics will be printed on completion.
@@ -1400,8 +1374,7 @@ All functions
- Convert SPM style segmentation files to a single categorical image where
-the numerical values map as: 0) Other, 1) CSF, 2) GM and 3) WM.
Convert SPM style segmentation files to a single categorical image where the numerical values map as: 0) Other, 1) CSF, 2) GM and 3) WM.
@@ -1413,8 +1386,7 @@ All functions
- Plot the fitting results of an object of class fit_result with
-individual basis set components shown.
Plot the fitting results of an object of class fit_result with individual basis set components shown.
@@ -1459,6 +1431,10 @@ All functions svs_1h_brain_batch_analysis()
Batch interface to the standard SVS 1H brain analysis pipeline.
+
+
+ Perform a t-test on spectral data points.
@@ -1518,8 +1494,7 @@ All functions
- Fade a spectrum to zero by frequency domain multiplication with a tanh
-function. Note this operation distorts data points at the end of the FID.
Fade a spectrum to zero by frequency domain multiplication with a tanh function. Note this operation distorts data points at the end of the FID.
@@ -1549,7 +1524,7 @@ All functions
diff --git a/docs/reference/int_spec.html b/docs/reference/int_spec.html
index c7060fe7..783325a8 100644
--- a/docs/reference/int_spec.html
+++ b/docs/reference/int_spec.html
@@ -1,5 +1,5 @@
-Integrate a spectral region. — int_spec • Spectroscopy Analysis Tools (spant) Integrate a spectral region. — int_spec • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -118,7 +118,7 @@ Value
diff --git a/docs/reference/interleave_dyns.html b/docs/reference/interleave_dyns.html
index effe5543..441eff27 100644
--- a/docs/reference/interleave_dyns.html
+++ b/docs/reference/interleave_dyns.html
@@ -1,5 +1,5 @@
-Interleave the first and second half of a dynamic series. — interleave_dyns • Spectroscopy Analysis Tools (spant) Interleave the first and second half of a dynamic series. — interleave_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/inv_even_dyns.html b/docs/reference/inv_even_dyns.html
index 9f9d4fff..dcb781dc 100644
--- a/docs/reference/inv_even_dyns.html
+++ b/docs/reference/inv_even_dyns.html
@@ -1,5 +1,5 @@
-Invert even numbered dynamic scans starting from 1 (2,4,6...). — inv_even_dyns • Spectroscopy Analysis Tools (spant) Invert even numbered dynamic scans starting from 1 (2,4,6...). — inv_even_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/inv_odd_dyns.html b/docs/reference/inv_odd_dyns.html
index 26212e2b..78d64660 100644
--- a/docs/reference/inv_odd_dyns.html
+++ b/docs/reference/inv_odd_dyns.html
@@ -1,5 +1,5 @@
-Invert odd numbered dynamic scans starting from 1 (1,3,5...). — inv_odd_dyns • Spectroscopy Analysis Tools (spant) Invert odd numbered dynamic scans starting from 1 (1,3,5...). — inv_odd_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/is.def.html b/docs/reference/is.def.html
index f196ffd0..a67b9eba 100644
--- a/docs/reference/is.def.html
+++ b/docs/reference/is.def.html
@@ -1,5 +1,5 @@
-Check if an object is defined, which is the same as being not NULL. — is.def • Spectroscopy Analysis Tools (spant) Check if an object is defined, which is the same as being not NULL. — is.def • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/is_fd.html b/docs/reference/is_fd.html
index 3b0ca165..18a193aa 100644
--- a/docs/reference/is_fd.html
+++ b/docs/reference/is_fd.html
@@ -1,7 +1,5 @@
-Check if the chemical shift dimension of an MRS data object is in the
-frequency domain. — is_fd • Spectroscopy Analysis Tools (spant) Check if the chemical shift dimension of an MRS data object is in the frequency domain. — is_fd • Spectroscopy Analysis Tools (spant) Transform 2D MRSI data from k-space to image space in the x-y direction. — kspace2img_xy • Spectroscopy Analysis Tools (spant) Transform 2D MRSI data from k-space to image space in the x-y direction. — kspace2img_xy • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/l2_reg.html b/docs/reference/l2_reg.html
index 3d781d80..21aa9849 100644
--- a/docs/reference/l2_reg.html
+++ b/docs/reference/l2_reg.html
@@ -1,5 +1,5 @@
-Perform l2 regularisation artefact suppression. — l2_reg • Spectroscopy Analysis Tools (spant) Perform l2 regularisation artefact suppression. — l2_reg • Spectroscopy Analysis Tools (spant) Apply line-broadening (apodisation) to MRS data or basis object. — lb • Spectroscopy Analysis Tools (spant) Apply line-broadening (apodisation) to MRS data or basis object. — lb • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -123,7 +123,7 @@ Value
diff --git a/docs/reference/lofdc.html b/docs/reference/lofdc.html
index 5419b1ec..31347a25 100644
--- a/docs/reference/lofdc.html
+++ b/docs/reference/lofdc.html
@@ -1,5 +1,5 @@
-Correct linear frequency drift. — lofdc • Spectroscopy Analysis Tools (spant) Correct linear frequency drift. — lofdc • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -138,7 +138,7 @@ Value
diff --git a/docs/reference/lw2alpha.html b/docs/reference/lw2alpha.html
index b83db682..25da229b 100644
--- a/docs/reference/lw2alpha.html
+++ b/docs/reference/lw2alpha.html
@@ -1,7 +1,5 @@
-Covert a linewidth in Hz to an equivalent alpha value in the time-domain ie:
-x * exp(-t * alpha). — lw2alpha • Spectroscopy Analysis Tools (spant) Covert a linewidth in Hz to an equivalent alpha value in the time-domain ie: x * exp(-t * alpha). — lw2alpha • Spectroscopy Analysis Tools (spant) Covert a linewidth in Hz to an equivalent beta value in the time-domain ie:
-x * exp(-t * t * beta). — lw2beta • Spectroscopy Analysis Tools (spant) Covert a linewidth in Hz to an equivalent beta value in the time-domain ie: x * exp(-t * t * beta). — lw2beta • Spectroscopy Analysis Tools (spant) Make a basis-set object from a directory containing LCModel formatted RAW
-files. — make_basis_from_raw • Spectroscopy Analysis Tools (spant) Make a basis-set object from a directory containing LCModel formatted RAW files. — make_basis_from_raw • Spectroscopy Analysis Tools (spant) Mask an MRS dataset in the dynamic dimension. — mask_dyns • Spectroscopy Analysis Tools (spant) Mask an MRS dataset in the dynamic dimension. — mask_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/mask_fit_res.html b/docs/reference/mask_fit_res.html
index 97baaa3f..ebd91a99 100644
--- a/docs/reference/mask_fit_res.html
+++ b/docs/reference/mask_fit_res.html
@@ -1,5 +1,5 @@
-Mask fit result spectra depending on a vector of bool values. — mask_fit_res • Spectroscopy Analysis Tools (spant) Mask fit result spectra depending on a vector of bool values. — mask_fit_res • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -116,7 +116,7 @@ Value
diff --git a/docs/reference/mask_xy.html b/docs/reference/mask_xy.html
index 11bb577c..b0d38619 100644
--- a/docs/reference/mask_xy.html
+++ b/docs/reference/mask_xy.html
@@ -1,5 +1,5 @@
-Mask an MRSI dataset in the x-y direction — mask_xy • Spectroscopy Analysis Tools (spant) Mask an MRSI dataset in the x-y direction — mask_xy • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/mask_xy_corners.html b/docs/reference/mask_xy_corners.html
index 09b16cd2..2d13839d 100644
--- a/docs/reference/mask_xy_corners.html
+++ b/docs/reference/mask_xy_corners.html
@@ -1,5 +1,5 @@
-Mask the four corners of an MRSI dataset in the x-y plane. — mask_xy_corners • Spectroscopy Analysis Tools (spant) Mask the four corners of an MRSI dataset in the x-y plane. — mask_xy_corners • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/mask_xy_ellipse.html b/docs/reference/mask_xy_ellipse.html
index 1d8b02e4..e2e749ef 100644
--- a/docs/reference/mask_xy_ellipse.html
+++ b/docs/reference/mask_xy_ellipse.html
@@ -1,7 +1,5 @@
-Mask the voxels outside an elliptical region spanning the MRSI dataset in the
-x-y plane. — mask_xy_ellipse • Spectroscopy Analysis Tools (spant) Mask the voxels outside an elliptical region spanning the MRSI dataset in the x-y plane. — mask_xy_ellipse • Spectroscopy Analysis Tools (spant) Mask a 2D MRSI dataset in the x-y dimension. — mask_xy_mat • Spectroscopy Analysis Tools (spant) Mask a 2D MRSI dataset in the x-y dimension. — mask_xy_mat • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Value
diff --git a/docs/reference/mat2mrs_data.html b/docs/reference/mat2mrs_data.html
index 2e2895f3..ae55665f 100644
--- a/docs/reference/mat2mrs_data.html
+++ b/docs/reference/mat2mrs_data.html
@@ -1,7 +1,5 @@
-Convert a matrix (with spectral points in the column dimension and dynamics
-in the row dimensions) into a mrs_data object. — mat2mrs_data • Spectroscopy Analysis Tools (spant) Convert a matrix (with spectral points in the column dimension and dynamics in the row dimensions) into a mrs_data object. — mat2mrs_data • Spectroscopy Analysis Tools (spant) Matrix exponential function taken from complexplus package to reduce the
-number of spant dependencies. — matexp • Spectroscopy Analysis Tools (spant) Matrix exponential function taken from complexplus package to reduce the number of spant dependencies. — matexp • Spectroscopy Analysis Tools (spant) Apply the max operator to an MRS dataset. — max_mrs • Spectroscopy Analysis Tools (spant) Apply the max operator to an MRS dataset. — max_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/max_mrs_interp.html b/docs/reference/max_mrs_interp.html
index e4474764..52e63f3e 100644
--- a/docs/reference/max_mrs_interp.html
+++ b/docs/reference/max_mrs_interp.html
@@ -1,5 +1,5 @@
-Apply the max operator to an interpolated MRS dataset. — max_mrs_interp • Spectroscopy Analysis Tools (spant) Apply the max operator to an interpolated MRS dataset. — max_mrs_interp • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/mean.list.html b/docs/reference/mean.list.html
index b8eb3463..048306fd 100644
--- a/docs/reference/mean.list.html
+++ b/docs/reference/mean.list.html
@@ -1,5 +1,5 @@
-Calculate the mean spectrum from an mrs_data object. — mean.list • Spectroscopy Analysis Tools (spant) Calculate the mean spectrum from an mrs_data object. — mean.list • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/mean.mrs_data.html b/docs/reference/mean.mrs_data.html
index 5531a28d..79515014 100644
--- a/docs/reference/mean.mrs_data.html
+++ b/docs/reference/mean.mrs_data.html
@@ -1,5 +1,5 @@
-Calculate the mean spectrum from an mrs_data object. — mean.mrs_data • Spectroscopy Analysis Tools (spant) Calculate the mean spectrum from an mrs_data object. — mean.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/mean_dyn_blocks.html b/docs/reference/mean_dyn_blocks.html
index 10467098..4c042448 100644
--- a/docs/reference/mean_dyn_blocks.html
+++ b/docs/reference/mean_dyn_blocks.html
@@ -1,5 +1,5 @@
-Calculate the mean of adjacent dynamic scans. — mean_dyn_blocks • Spectroscopy Analysis Tools (spant) Calculate the mean of adjacent dynamic scans. — mean_dyn_blocks • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/mean_dyn_pairs.html b/docs/reference/mean_dyn_pairs.html
index 63e909ea..1a241126 100644
--- a/docs/reference/mean_dyn_pairs.html
+++ b/docs/reference/mean_dyn_pairs.html
@@ -1,5 +1,5 @@
-Calculate the pairwise means across a dynamic data set. — mean_dyn_pairs • Spectroscopy Analysis Tools (spant) Calculate the pairwise means across a dynamic data set. — mean_dyn_pairs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/mean_dyns.html b/docs/reference/mean_dyns.html
index 73fdbfa7..0daa27df 100644
--- a/docs/reference/mean_dyns.html
+++ b/docs/reference/mean_dyns.html
@@ -1,5 +1,5 @@
-Calculate the mean dynamic data. — mean_dyns • Spectroscopy Analysis Tools (spant) Calculate the mean dynamic data. — mean_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/mean_mrs_list.html b/docs/reference/mean_mrs_list.html
index 808b6c50..10d842c0 100644
--- a/docs/reference/mean_mrs_list.html
+++ b/docs/reference/mean_mrs_list.html
@@ -1,5 +1,5 @@
-Return the mean of a list of mrs_data objects. — mean_mrs_list • Spectroscopy Analysis Tools (spant) Return the mean of a list of mrs_data objects. — mean_mrs_list • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/mean_vec_blocks.html b/docs/reference/mean_vec_blocks.html
index 8fc92eaa..dd78b122 100644
--- a/docs/reference/mean_vec_blocks.html
+++ b/docs/reference/mean_vec_blocks.html
@@ -1,5 +1,5 @@
-Calculate the mean of adjacent blocks in a vector. — mean_vec_blocks • Spectroscopy Analysis Tools (spant) Calculate the mean of adjacent blocks in a vector. — mean_vec_blocks • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/median_dyns.html b/docs/reference/median_dyns.html
index 1039d4b5..9a085b10 100644
--- a/docs/reference/median_dyns.html
+++ b/docs/reference/median_dyns.html
@@ -1,5 +1,5 @@
-Calculate the median dynamic data. — median_dyns • Spectroscopy Analysis Tools (spant) Calculate the median dynamic data. — median_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/mod_td.html b/docs/reference/mod_td.html
index 76ad0a40..141ef09e 100644
--- a/docs/reference/mod_td.html
+++ b/docs/reference/mod_td.html
@@ -1,5 +1,5 @@
-Apply the Modulus operator to the time-domain MRS signal. — mod_td • Spectroscopy Analysis Tools (spant) Apply the Modulus operator to the time-domain MRS signal. — mod_td • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/mrs_data2basis.html b/docs/reference/mrs_data2basis.html
index 62f7d749..11797b91 100644
--- a/docs/reference/mrs_data2basis.html
+++ b/docs/reference/mrs_data2basis.html
@@ -1,7 +1,5 @@
-Convert an mrs_data object to basis object - where basis signals are spread
-across the dynamic dimension in the MRS data. — mrs_data2basis • Spectroscopy Analysis Tools (spant) Convert an mrs_data object to basis object - where basis signals are spread across the dynamic dimension in the MRS data. — mrs_data2basis • Spectroscopy Analysis Tools (spant) Create a BIDS file structure from a vector of MRS data paths or list of mrs_data objects. — mrs_data2bids • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Create a BIDS file structure from a vector of MRS data paths or list of mrs_data objects.
+ Source: R/fmrs.R
+ mrs_data2bids.Rd
+
+
+
+ Create a BIDS file structure from a vector of MRS data paths or list of
+mrs_data objects.
+
+
+
+ mrs_data2bids(
+ mrs_data,
+ output_dir,
+ suffix = NULL,
+ sub = NULL,
+ ses = NULL,
+ task = NULL,
+ acq = NULL,
+ nuc = NULL,
+ voi = NULL,
+ rec = NULL,
+ run = NULL,
+ echo = NULL,
+ inv = NULL,
+ skip_existing = TRUE
+)
+
+
+
+ Arguments
+ - mrs_data
+vector of MRS data paths or list of mrs_data objects.
- output_dir
+the base directory to create the BIDS structure.
- suffix
+optional vector of file suffixes. Default behaviour is to
+automatically determine these from the input data, however it is recommended
+that they are specified to allow more efficient skipping of existing data.
- sub
+optional vector of subject labels. If not specified, these will be
+automatically generated as a series of increasing zero-padded integer values
+corresponding to the mrs_data input indices.
- ses
+optional vector of session labels.
- task
+optional vector of task labels.
- acq
+optional vector of acquisition labels.
- nuc
+optional vector of nucleus labels.
- voi
+optional vector of volume of interest labels.
- rec
+optional vector of reconstruction labels.
- run
+optional vector of run indices.
- echo
+optional vector of echo time indices.
- inv
+optional vector of inversion indices.
- skip_existing
+skip any data files that have already been converted.
+Defaults to TRUE, set to FALSE to force an overwrite of any existing data
+files.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/mrs_data2mat.html b/docs/reference/mrs_data2mat.html
index cf5ff28c..9e47688a 100644
--- a/docs/reference/mrs_data2mat.html
+++ b/docs/reference/mrs_data2mat.html
@@ -1,7 +1,5 @@
-Convert mrs_data object to a matrix, with spectral points in the column
-dimension and dynamics in the row dimension. — mrs_data2mat • Spectroscopy Analysis Tools (spant) Convert mrs_data object to a matrix, with spectral points in the column dimension and dynamics in the row dimension. — mrs_data2mat • Spectroscopy Analysis Tools (spant) Convert mrs_data object to a matrix, with spectral points in the column dimension and dynamics in the row dimension. — mrs_data2spec_mat • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Convert mrs_data object to a matrix, with spectral points in the column dimension and dynamics in the row dimension.
+ Source: R/mrs_data_proc.R
+ mrs_data2spec_mat.Rd
+
+
+
+ Convert mrs_data object to a matrix, with spectral points in the column
+dimension and dynamics in the row dimension.
+
+
+
+ mrs_data2spec_mat(mrs_data, collapse = TRUE)
+
+
+
+ Arguments
+ - mrs_data
+MRS data object or list of MRS data objects.
- collapse
+collapse all other dimensions along the dynamic dimension, eg
+a 16x16 MRSI grid would be first collapsed across 256 dynamic scans.
+
+ Value
+
+
+MRS data matrix.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/mrs_data2vec.html b/docs/reference/mrs_data2vec.html
index fb172d68..a1fd654d 100644
--- a/docs/reference/mrs_data2vec.html
+++ b/docs/reference/mrs_data2vec.html
@@ -1,5 +1,5 @@
-Convert mrs_data object to a vector. — mrs_data2vec • Spectroscopy Analysis Tools (spant) Convert mrs_data object to a vector. — mrs_data2vec • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -126,7 +126,7 @@ Value
diff --git a/docs/reference/mvfftshift.html b/docs/reference/mvfftshift.html
index 92b0841b..976b3410 100644
--- a/docs/reference/mvfftshift.html
+++ b/docs/reference/mvfftshift.html
@@ -1,7 +1,5 @@
-Perform a fftshift on a matrix, with each column replaced by its shifted
-result. — mvfftshift • Spectroscopy Analysis Tools (spant) Perform a fftshift on a matrix, with each column replaced by its shifted result. — mvfftshift • Spectroscopy Analysis Tools (spant) Perform an ifftshift on a matrix, with each column replaced by its shifted
-result. — mvifftshift • Spectroscopy Analysis Tools (spant) Perform an ifftshift on a matrix, with each column replaced by its shifted result. — mvifftshift • Spectroscopy Analysis Tools (spant) Print fit coordinates from a single index. — n2coord • Spectroscopy Analysis Tools (spant) Print fit coordinates from a single index. — n2coord • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/nifti_flip_lr.html b/docs/reference/nifti_flip_lr.html
index 730abe3c..19860b3c 100644
--- a/docs/reference/nifti_flip_lr.html
+++ b/docs/reference/nifti_flip_lr.html
@@ -1,9 +1,5 @@
-Flip the x data dimension order of a nifti image. This corresponds to
-flipping MRI data in the left-right direction, assuming the data in save in
-neurological format (can check with fslorient program). — nifti_flip_lr • Spectroscopy Analysis Tools (spant) Flip the x data dimension order of a nifti image. This corresponds to flipping MRI data in the left-right direction, assuming the data in save in neurological format (can check with fslorient program). — nifti_flip_lr • Spectroscopy Analysis Tools (spant) Export a one-page pdf of a single fit result — one_page_pdf • Spectroscopy Analysis Tools (spant) Export a one-page pdf of a single fit result — one_page_pdf • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -108,7 +108,7 @@ Arguments
diff --git a/docs/reference/ortho3.html b/docs/reference/ortho3.html
index 13ade97d..5d7dd2fd 100644
--- a/docs/reference/ortho3.html
+++ b/docs/reference/ortho3.html
@@ -1,5 +1,5 @@
-Display an orthographic projection plot of a nifti object. — ortho3 • Spectroscopy Analysis Tools (spant) Display an orthographic projection plot of a nifti object. — ortho3 • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -172,7 +172,7 @@ Arguments
diff --git a/docs/reference/ortho3_inter.html b/docs/reference/ortho3_inter.html
index 090cc5e5..15948899 100644
--- a/docs/reference/ortho3_inter.html
+++ b/docs/reference/ortho3_inter.html
@@ -1,5 +1,5 @@
-Display an interactive orthographic projection plot of a nifti object. — ortho3_inter • Spectroscopy Analysis Tools (spant) Display an interactive orthographic projection plot of a nifti object. — ortho3_inter • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -132,7 +132,7 @@ Arguments
diff --git a/docs/reference/peak_info.html b/docs/reference/peak_info.html
index 09058bd8..41c8ffaf 100644
--- a/docs/reference/peak_info.html
+++ b/docs/reference/peak_info.html
@@ -1,7 +1,5 @@
-Search for the highest peak in a spectral region and return the frequency,
-height and FWHM. — peak_info • Spectroscopy Analysis Tools (spant) Search for the highest peak in a spectral region and return the frequency, height and FWHM. — peak_info • Spectroscopy Analysis Tools (spant) Papoulis-Gerchberg (PG) algorithm method for k-space extrapolation. — pg_extrap_xy • Spectroscopy Analysis Tools (spant) Papoulis-Gerchberg (PG) algorithm method for k-space extrapolation. — pg_extrap_xy • Spectroscopy Analysis Tools (spant) Apply phasing parameters to MRS data. — phase • Spectroscopy Analysis Tools (spant) Apply phasing parameters to MRS data. — phase • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/phase_ref_1h_brain.html b/docs/reference/phase_ref_1h_brain.html
new file mode 100644
index 00000000..8707a74a
--- /dev/null
+++ b/docs/reference/phase_ref_1h_brain.html
@@ -0,0 +1,131 @@
+
+Corrected zero order phase and chemical shift offset in 1H MRS data from the brain. — phase_ref_1h_brain • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Corrected zero order phase and chemical shift offset in 1H MRS data from the brain.
+ Source: R/rats.R
+ phase_ref_1h_brain.Rd
+
+
+
+ Corrected zero order phase and chemical shift offset in 1H MRS data from the
+brain.
+
+
+
+ phase_ref_1h_brain(mrs_data, mean_ref = FALSE, ret_corr_only = TRUE)
+
+
+
+ Arguments
+ - mrs_data
+MRS data to be corrected.
- mean_ref
+apply the phase and offset of the mean spectrum to all
+others. Default is FALSE.
- ret_corr_only
+return the corrected data only.
+
+ Value
+
+
+corrected MRS data.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/plot.fit_result.html b/docs/reference/plot.fit_result.html
index e54d3bc1..836a53ee 100644
--- a/docs/reference/plot.fit_result.html
+++ b/docs/reference/plot.fit_result.html
@@ -1,5 +1,5 @@
-Plot the fitting results of an object of class fit_result. — plot.fit_result • Spectroscopy Analysis Tools (spant) Plot the fitting results of an object of class fit_result. — plot.fit_result • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -207,7 +207,7 @@ Arguments
diff --git a/docs/reference/plot.mrs_data.html b/docs/reference/plot.mrs_data.html
index fabcc35b..bb2ec651 100644
--- a/docs/reference/plot.mrs_data.html
+++ b/docs/reference/plot.mrs_data.html
@@ -1,5 +1,5 @@
-Plotting method for objects of class mrs_data. — plot.mrs_data • Spectroscopy Analysis Tools (spant) Plotting method for objects of class mrs_data. — plot.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -287,7 +287,7 @@ Arguments
diff --git a/docs/reference/plot_bc.html b/docs/reference/plot_bc.html
index 4f8309b4..b48142cc 100644
--- a/docs/reference/plot_bc.html
+++ b/docs/reference/plot_bc.html
@@ -1,5 +1,5 @@
-Convenience function to plot a baseline estimate with the original data. — plot_bc • Spectroscopy Analysis Tools (spant) Convenience function to plot a baseline estimate with the original data. — plot_bc • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -108,7 +108,7 @@ Arguments
diff --git a/docs/reference/plot_reg.html b/docs/reference/plot_reg.html
index ae1acbe7..2addb2f6 100644
--- a/docs/reference/plot_reg.html
+++ b/docs/reference/plot_reg.html
@@ -1,5 +1,5 @@
-Plot regressors as an image. — plot_reg • Spectroscopy Analysis Tools (spant) Plot regressors as an image. — plot_reg • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/plot_slice_fit.html b/docs/reference/plot_slice_fit.html
index fbc7b560..57f1af8a 100644
--- a/docs/reference/plot_slice_fit.html
+++ b/docs/reference/plot_slice_fit.html
@@ -1,5 +1,5 @@
-Plot a 2D slice from an MRSI fit result object. — plot_slice_fit • Spectroscopy Analysis Tools (spant) Plot a 2D slice from an MRSI fit result object. — plot_slice_fit • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -129,7 +129,7 @@ Arguments
diff --git a/docs/reference/plot_slice_fit_inter.html b/docs/reference/plot_slice_fit_inter.html
index 4eed104a..da105a7d 100644
--- a/docs/reference/plot_slice_fit_inter.html
+++ b/docs/reference/plot_slice_fit_inter.html
@@ -1,5 +1,5 @@
-Plot a 2D slice from an MRSI fit result object. — plot_slice_fit_inter • Spectroscopy Analysis Tools (spant) Plot a 2D slice from an MRSI fit result object. — plot_slice_fit_inter • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -134,7 +134,7 @@ Arguments
diff --git a/docs/reference/plot_slice_map.html b/docs/reference/plot_slice_map.html
index 553e9ac8..ffb2a134 100644
--- a/docs/reference/plot_slice_map.html
+++ b/docs/reference/plot_slice_map.html
@@ -1,5 +1,5 @@
-Plot a slice from a 7 dimensional array. — plot_slice_map • Spectroscopy Analysis Tools (spant) Plot a slice from a 7 dimensional array. — plot_slice_map • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -153,7 +153,7 @@ Arguments
diff --git a/docs/reference/plot_slice_map_inter.html b/docs/reference/plot_slice_map_inter.html
index 40d33b42..90968f66 100644
--- a/docs/reference/plot_slice_map_inter.html
+++ b/docs/reference/plot_slice_map_inter.html
@@ -1,7 +1,5 @@
-Plot an interactive slice map from a data array where voxels can be selected
-to display a corresponding spectrum. — plot_slice_map_inter • Spectroscopy Analysis Tools (spant) Plot an interactive slice map from a data array where voxels can be selected to display a corresponding spectrum. — plot_slice_map_inter • Spectroscopy Analysis Tools (spant) Plot the spectral standard deviation. — plot_spec_sd • Spectroscopy Analysis Tools (spant) Plot the spectral standard deviation. — plot_spec_sd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Arguments
diff --git a/docs/reference/plot_voi_overlay.html b/docs/reference/plot_voi_overlay.html
index 9a782e88..bbbbf35e 100644
--- a/docs/reference/plot_voi_overlay.html
+++ b/docs/reference/plot_voi_overlay.html
@@ -1,5 +1,5 @@
-Plot a volume as an image overlay. — plot_voi_overlay • Spectroscopy Analysis Tools (spant) Plot a volume as an image overlay. — plot_voi_overlay • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -116,7 +116,7 @@ Arguments
diff --git a/docs/reference/plot_voi_overlay_seg.html b/docs/reference/plot_voi_overlay_seg.html
index 3d4e74ff..0e800ff2 100644
--- a/docs/reference/plot_voi_overlay_seg.html
+++ b/docs/reference/plot_voi_overlay_seg.html
@@ -1,5 +1,5 @@
-Plot a volume as an overlay on a segmented brain volume. — plot_voi_overlay_seg • Spectroscopy Analysis Tools (spant) Plot a volume as an overlay on a segmented brain volume. — plot_voi_overlay_seg • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Arguments
diff --git a/docs/reference/ppm.html b/docs/reference/ppm.html
index c352327a..ee4696e2 100644
--- a/docs/reference/ppm.html
+++ b/docs/reference/ppm.html
@@ -1,5 +1,5 @@
-Return the ppm scale of an MRS dataset or fit result. — ppm • Spectroscopy Analysis Tools (spant) Return the ppm scale of an MRS dataset or fit result. — ppm • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -132,7 +132,7 @@ Value
diff --git a/docs/reference/precomp.html b/docs/reference/precomp.html
index 822d7336..df3d2c6c 100644
--- a/docs/reference/precomp.html
+++ b/docs/reference/precomp.html
@@ -1,7 +1,5 @@
-Save function results to file and load on subsequent calls to avoid repeat
-computation. — precomp • Spectroscopy Analysis Tools (spant) Save function results to file and load on subsequent calls to avoid repeat computation. — precomp • Spectroscopy Analysis Tools (spant) Preprocess and perform quality assessment of a single SVS data set. — preproc_svs • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Preprocess and perform quality assessment of a single SVS data set.
+ Source: R/fmrs.R
+ preproc_svs.Rd
+
+
+
+ Preprocess and perform quality assessment of a single SVS data set.
+
+
+
+ preproc_svs(path, label = NULL, output_dir = NULL, ref_inds = NULL)
+
+
+
+ Arguments
+ - path
+path to the fMRS data file or IMA directory.
- label
+a label to describe the data set.
- output_dir
+output directory.
- ref_inds
+a vector of 1-based indices for any water reference dynamic
+scans.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/preproc_svs_dataset.html b/docs/reference/preproc_svs_dataset.html
new file mode 100644
index 00000000..07c3a29b
--- /dev/null
+++ b/docs/reference/preproc_svs_dataset.html
@@ -0,0 +1,148 @@
+
+Preprocess and perform quality assessment of one or more SVS data sets. — preproc_svs_dataset • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Preprocess and perform quality assessment of one or more SVS data sets.
+ Source: R/fmrs.R
+ preproc_svs_dataset.Rd
+
+
+
+ Preprocess and perform quality assessment of one or more SVS data sets.
+
+
+
+ preproc_svs_dataset(
+ paths,
+ labels = NULL,
+ output_dir = "spant_analysis",
+ exclude_labels = NULL,
+ overwrite = FALSE,
+ ref_inds = NULL,
+ return_results = FALSE
+)
+
+
+
+ Arguments
+ - paths
+paths to the fMRS data file or IMA directory.
- labels
+labels to describe each data set.
- output_dir
+output directory.
- exclude_labels
+vector of labels of scans to exclude, eg poor quality
+data.
- overwrite
+overwrite saved results, defaults to FALSE.
- ref_inds
+a vector of 1-based indices for any water reference dynamic
+scans.
- return_results
+function will return key outputs, defaults to FALSE.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/print.fit_result.html b/docs/reference/print.fit_result.html
index 297f28dc..5f434e57 100644
--- a/docs/reference/print.fit_result.html
+++ b/docs/reference/print.fit_result.html
@@ -1,5 +1,5 @@
-Print a summary of an object of class fit_result. — print.fit_result • Spectroscopy Analysis Tools (spant) Print a summary of an object of class fit_result. — print.fit_result • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -105,7 +105,7 @@ Arguments
diff --git a/docs/reference/print.mrs_data.html b/docs/reference/print.mrs_data.html
index 51199017..e1561eb2 100644
--- a/docs/reference/print.mrs_data.html
+++ b/docs/reference/print.mrs_data.html
@@ -1,5 +1,5 @@
-Print a summary of mrs_data parameters. — print.mrs_data • Spectroscopy Analysis Tools (spant) Print a summary of mrs_data parameters. — print.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -109,7 +109,7 @@ Arguments
diff --git a/docs/reference/qn_states.html b/docs/reference/qn_states.html
index 0f42f2f9..d7aa6715 100644
--- a/docs/reference/qn_states.html
+++ b/docs/reference/qn_states.html
@@ -1,5 +1,5 @@
-Get the quantum coherence matrix for a spin system. — qn_states • Spectroscopy Analysis Tools (spant) Get the quantum coherence matrix for a spin system. — qn_states • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/rats.html b/docs/reference/rats.html
index 5a39a396..93585e08 100644
--- a/docs/reference/rats.html
+++ b/docs/reference/rats.html
@@ -1,5 +1,5 @@
-Robust Alignment to a Target Spectrum (RATS). — rats • Spectroscopy Analysis Tools (spant) Robust Alignment to a Target Spectrum (RATS). — rats • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -207,7 +207,7 @@ Value
diff --git a/docs/reference/re_weighting.html b/docs/reference/re_weighting.html
index d21caf21..8b0b070a 100644
--- a/docs/reference/re_weighting.html
+++ b/docs/reference/re_weighting.html
@@ -1,5 +1,5 @@
-Apply a weighting to the FID to enhance spectral resolution. — re_weighting • Spectroscopy Analysis Tools (spant) Apply a weighting to the FID to enhance spectral resolution. — re_weighting • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/read_basis.html b/docs/reference/read_basis.html
index da9b94af..eb6f8557 100644
--- a/docs/reference/read_basis.html
+++ b/docs/reference/read_basis.html
@@ -1,5 +1,5 @@
-Read a basis file in LCModel .basis format. — read_basis • Spectroscopy Analysis Tools (spant) Read a basis file in LCModel .basis format. — read_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/read_ima_coil_dir.html b/docs/reference/read_ima_coil_dir.html
index 28c02de0..4f073cd8 100644
--- a/docs/reference/read_ima_coil_dir.html
+++ b/docs/reference/read_ima_coil_dir.html
@@ -1,9 +1,5 @@
-Read a directory containing Siemens MRS IMA files and combine along the coil
-dimension. Note that the coil ID is inferred from the sorted file name and
-should be checked when consistency is required between two directories. — read_ima_coil_dir • Spectroscopy Analysis Tools (spant) Read a directory containing Siemens MRS IMA files and combine along the coil dimension. Note that the coil ID is inferred from the sorted file name and should be checked when consistency is required between two directories. — read_ima_coil_dir • Spectroscopy Analysis Tools (spant) Read a directory containing Siemens MRS IMA files and combine along the
-dynamic dimension. Note that the coil ID is inferred from the sorted file
-name and should be checked when consistency is required. — read_ima_dyn_dir • Spectroscopy Analysis Tools (spant) Read a directory containing Siemens MRS IMA files and combine along the dynamic dimension. Note that the coil ID is inferred from the sorted file name and should be checked when consistency is required. — read_ima_dyn_dir • Spectroscopy Analysis Tools (spant) Read an LCModel formatted coord file containing fit information. — read_lcm_coord • Spectroscopy Analysis Tools (spant) Read an LCModel formatted coord file containing fit information. — read_lcm_coord • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -107,7 +107,7 @@ Value
diff --git a/docs/reference/read_mrs.html b/docs/reference/read_mrs.html
index 3ac2a36b..2cf36b20 100644
--- a/docs/reference/read_mrs.html
+++ b/docs/reference/read_mrs.html
@@ -1,5 +1,5 @@
-Read MRS data from a file. — read_mrs • Spectroscopy Analysis Tools (spant) Read MRS data from a file. — read_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -88,7 +88,8 @@ Read MRS data from a file.
full_fid = FALSE,
omit_svs_ref_scans = TRUE,
verbose = FALSE,
- extra = NULL
+ extra = NULL,
+ fid_filt_dist = NULL
)
@@ -140,6 +141,13 @@ Arguments
an optional data frame to provide additional variables for use
in subsequent analysis steps, eg id or grouping variables.
fid_filt_dist
+indicate if the data has a distorted FID due to a
+brick-wall filter being used to downsample the data. Default is to auto
+detect this from the data, but TRUE or FALSE options can be given to override
+detection.
Value
@@ -183,7 +191,7 @@ Examples
diff --git a/docs/reference/read_mrs_tqn.html b/docs/reference/read_mrs_tqn.html
index 5766362f..84bdaf3a 100644
--- a/docs/reference/read_mrs_tqn.html
+++ b/docs/reference/read_mrs_tqn.html
@@ -1,5 +1,5 @@
-Read MRS data using the TARQUIN software package. — read_mrs_tqn • Spectroscopy Analysis Tools (spant) Read MRS data using the TARQUIN software package. — read_mrs_tqn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -131,7 +131,7 @@ Examples
diff --git a/docs/reference/read_pulse_ascii.html b/docs/reference/read_pulse_ascii.html
index c9e0d43c..ab11c9cc 100644
--- a/docs/reference/read_pulse_ascii.html
+++ b/docs/reference/read_pulse_ascii.html
@@ -1,5 +1,5 @@
-Read an ASCII formatted pulse file. — read_pulse_ascii • Spectroscopy Analysis Tools (spant) Read an ASCII formatted pulse file. — read_pulse_ascii • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/read_pulse_bruker.html b/docs/reference/read_pulse_bruker.html
index c92bf76a..dbe9073b 100644
--- a/docs/reference/read_pulse_bruker.html
+++ b/docs/reference/read_pulse_bruker.html
@@ -1,5 +1,5 @@
-Read a Bruker formatted pulse file — read_pulse_bruker • Spectroscopy Analysis Tools (spant) Read a Bruker formatted pulse file — read_pulse_bruker • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/read_pulse_pta.html b/docs/reference/read_pulse_pta.html
index 72e1b6d4..a0fac3c3 100644
--- a/docs/reference/read_pulse_pta.html
+++ b/docs/reference/read_pulse_pta.html
@@ -1,5 +1,5 @@
-Read a .pta formatted pulse file compatible with Siemens PulseTool. — read_pulse_pta • Spectroscopy Analysis Tools (spant) Read a .pta formatted pulse file compatible with Siemens PulseTool. — read_pulse_pta • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/read_siemens_txt_hdr.html b/docs/reference/read_siemens_txt_hdr.html
index 23fb8c70..3a17d87c 100644
--- a/docs/reference/read_siemens_txt_hdr.html
+++ b/docs/reference/read_siemens_txt_hdr.html
@@ -1,5 +1,5 @@
-Read the text format header found in Siemens IMA and TWIX data files. — read_siemens_txt_hdr • Spectroscopy Analysis Tools (spant) Read the text format header found in Siemens IMA and TWIX data files. — read_siemens_txt_hdr • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -78,7 +78,7 @@ Read the text format header found in Siemens IMA and TWIX data files.
- read_siemens_txt_hdr(input, version = "vd", verbose, offset = 0)
+ read_siemens_txt_hdr(input, version = "vd", verbose = FALSE, offset = 0)
@@ -118,7 +118,7 @@ Value
diff --git a/docs/reference/read_tqn_fit.html b/docs/reference/read_tqn_fit.html
index 4da6c25e..a1630420 100644
--- a/docs/reference/read_tqn_fit.html
+++ b/docs/reference/read_tqn_fit.html
@@ -1,5 +1,5 @@
-Reader for csv fit results generated by TARQUIN. — read_tqn_fit • Spectroscopy Analysis Tools (spant) Reader for csv fit results generated by TARQUIN. — read_tqn_fit • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -113,7 +113,7 @@ Examples
diff --git a/docs/reference/read_tqn_result.html b/docs/reference/read_tqn_result.html
index 36659714..68a3e98c 100644
--- a/docs/reference/read_tqn_result.html
+++ b/docs/reference/read_tqn_result.html
@@ -1,5 +1,5 @@
-Reader for csv results generated by TARQUIN. — read_tqn_result • Spectroscopy Analysis Tools (spant) Reader for csv results generated by TARQUIN. — read_tqn_result • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -117,7 +117,7 @@ Examples
diff --git a/docs/reference/recon_imag.html b/docs/reference/recon_imag.html
index d2a72225..5bc3b1eb 100644
--- a/docs/reference/recon_imag.html
+++ b/docs/reference/recon_imag.html
@@ -1,7 +1,5 @@
-Reconstruct complex time-domain data from the real part of frequency-domain
-data. — recon_imag • Spectroscopy Analysis Tools (spant) Reconstruct complex time-domain data from the real part of frequency-domain data. — recon_imag • Spectroscopy Analysis Tools (spant) Reconstruct complex time-domain data from the real part of frequency-domain
-data. — recon_imag_vec • Spectroscopy Analysis Tools (spant) Reconstruct complex time-domain data from the real part of frequency-domain data. — recon_imag_vec • Spectroscopy Analysis Tools (spant) Reconstruct 2D MRSI data from a twix file loaded with read_mrs. — recon_twix_2d_mrsi • Spectroscopy Analysis Tools (spant) Reconstruct 2D MRSI data from a twix file loaded with read_mrs. — recon_twix_2d_mrsi • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/rectangular_mask.html b/docs/reference/rectangular_mask.html
index a2117283..6e469bc9 100644
--- a/docs/reference/rectangular_mask.html
+++ b/docs/reference/rectangular_mask.html
@@ -1,5 +1,5 @@
-Create a rectangular mask stored as a matrix of logical values. — rectangular_mask • Spectroscopy Analysis Tools (spant) Create a rectangular mask stored as a matrix of logical values. — rectangular_mask • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -130,7 +130,7 @@ Value
diff --git a/docs/reference/reexports.html b/docs/reference/reexports.html
index 694a75d1..a59e8379 100644
--- a/docs/reference/reexports.html
+++ b/docs/reference/reexports.html
@@ -1,5 +1,5 @@
-Objects exported from other packages — reexports • Spectroscopy Analysis Tools (spant) Objects exported from other packages — reexports • Spectroscopy Analysis Tools (spant)
Spectroscopy Analysis Tools (spant)
- 2.21.0
+ 2.22.0
@@ -103,7 +103,7 @@ Objects exported from other packages
diff --git a/docs/reference/rep_array_dim.html b/docs/reference/rep_array_dim.html
index b9c49b4a..48c0a5ed 100644
--- a/docs/reference/rep_array_dim.html
+++ b/docs/reference/rep_array_dim.html
@@ -1,5 +1,5 @@
-Repeat an array over a given dimension. — rep_array_dim • Spectroscopy Analysis Tools (spant) Repeat an array over a given dimension. — rep_array_dim • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/rep_dyn.html b/docs/reference/rep_dyn.html
index 6bbfb0ef..89a4bb9b 100644
--- a/docs/reference/rep_dyn.html
+++ b/docs/reference/rep_dyn.html
@@ -1,5 +1,5 @@
-Replicate a scan in the dynamic dimension. — rep_dyn • Spectroscopy Analysis Tools (spant) Replicate a scan in the dynamic dimension. — rep_dyn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/rep_mrs.html b/docs/reference/rep_mrs.html
index 67730b5c..becb8f00 100644
--- a/docs/reference/rep_mrs.html
+++ b/docs/reference/rep_mrs.html
@@ -1,5 +1,5 @@
-Replicate a scan over a given dimension. — rep_mrs • Spectroscopy Analysis Tools (spant) Replicate a scan over a given dimension. — rep_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -138,7 +138,7 @@ Value
diff --git a/docs/reference/resample_basis.html b/docs/reference/resample_basis.html
index b0f2ab17..c7a6222a 100644
--- a/docs/reference/resample_basis.html
+++ b/docs/reference/resample_basis.html
@@ -1,5 +1,5 @@
-Resample a basis-set to match a mrs_data acquisition. — resample_basis • Spectroscopy Analysis Tools (spant) Resample a basis-set to match a mrs_data acquisition. — resample_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -116,7 +116,7 @@ Value
diff --git a/docs/reference/resample_img.html b/docs/reference/resample_img.html
index f1e7beaf..b0cc8f71 100644
--- a/docs/reference/resample_img.html
+++ b/docs/reference/resample_img.html
@@ -1,5 +1,5 @@
-Resample an image to match a target image space. — resample_img • Spectroscopy Analysis Tools (spant) Resample an image to match a target image space. — resample_img • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/resample_voi.html b/docs/reference/resample_voi.html
index 8fbfa836..a29ab096 100644
--- a/docs/reference/resample_voi.html
+++ b/docs/reference/resample_voi.html
@@ -1,7 +1,5 @@
-Resample a VOI to match a target image space using nearest-neighbour
-interpolation. — resample_voi • Spectroscopy Analysis Tools (spant) Resample a VOI to match a target image space using nearest-neighbour interpolation. — resample_voi • Spectroscopy Analysis Tools (spant) Reslice a nifti object to match the orientation of mrs data. — reslice_to_mrs • Spectroscopy Analysis Tools (spant) Reslice a nifti object to match the orientation of mrs data. — reslice_to_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/reson_table2mrs_data.html b/docs/reference/reson_table2mrs_data.html
index d75579ee..c5a2167a 100644
--- a/docs/reference/reson_table2mrs_data.html
+++ b/docs/reference/reson_table2mrs_data.html
@@ -1,5 +1,5 @@
-Generate mrs_data from a table of single Lorentzian resonances. — reson_table2mrs_data • Spectroscopy Analysis Tools (spant) Generate mrs_data from a table of single Lorentzian resonances. — reson_table2mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -119,7 +119,7 @@ Value
diff --git a/docs/reference/rm_dyns.html b/docs/reference/rm_dyns.html
index 5d5ef692..573e1f51 100644
--- a/docs/reference/rm_dyns.html
+++ b/docs/reference/rm_dyns.html
@@ -1,5 +1,5 @@
-Remove a subset of dynamic scans. — rm_dyns • Spectroscopy Analysis Tools (spant) Remove a subset of dynamic scans. — rm_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/scale_amp_molal.html b/docs/reference/scale_amp_molal.html
index aaeee1f2..7acb8cb0 100644
--- a/docs/reference/scale_amp_molal.html
+++ b/docs/reference/scale_amp_molal.html
@@ -1,7 +1,5 @@
-Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water). — scale_amp_molal • Spectroscopy Analysis Tools (spant) Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / kg of tissue water). — scale_amp_molal • Spectroscopy Analysis Tools (spant)
Spectroscopy Analysis Tools (spant)
- 2.21.0
+ 2.22.0
@@ -76,8 +74,7 @@
- Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water).
+ Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / kg of tissue water).
Source: R/amp_scaling.R
scale_amp_molal.Rd
@@ -163,7 +160,7 @@ Value
diff --git a/docs/reference/scale_amp_molal_pvc.html b/docs/reference/scale_amp_molal_pvc.html
index 962d6afc..4d194abd 100644
--- a/docs/reference/scale_amp_molal_pvc.html
+++ b/docs/reference/scale_amp_molal_pvc.html
@@ -1,7 +1,5 @@
-Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water). — scale_amp_molal_pvc • Spectroscopy Analysis Tools (spant)
@@ -75,8 +73,7 @@
- Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water).
+ Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / kg of tissue water).
Source: R/amp_scaling.R
scale_amp_molal_pvc.Rd
@@ -141,7 +138,7 @@ Value
diff --git a/docs/reference/scale_amp_molar.html b/docs/reference/scale_amp_molar.html
index 02358d91..dc87a338 100644
--- a/docs/reference/scale_amp_molar.html
+++ b/docs/reference/scale_amp_molar.html
@@ -1,7 +1,5 @@
-Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / Litre of tissue). — scale_amp_molar • Spectroscopy Analysis Tools (spant) Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / Litre of tissue). — scale_amp_molar • Spectroscopy Analysis Tools (spant) Convert default LCM/TARQUIN concentration scaling to molal units with partial
-volume correction. — scale_amp_molar2molal_pvc • Spectroscopy Analysis Tools (spant) Convert default LCM/TARQUIN concentration scaling to molal units with partial volume correction. — scale_amp_molar2molal_pvc • Spectroscopy Analysis Tools (spant) Scale fitted amplitudes to a ratio of signal amplitude. — scale_amp_ratio • Spectroscopy Analysis Tools (spant) Scale fitted amplitudes to a ratio of signal amplitude. — scale_amp_ratio • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -116,7 +116,7 @@ Value
diff --git a/docs/reference/scale_amp_ratio_value.html b/docs/reference/scale_amp_ratio_value.html
index 2036837a..6af8ac51 100644
--- a/docs/reference/scale_amp_ratio_value.html
+++ b/docs/reference/scale_amp_ratio_value.html
@@ -1,5 +1,5 @@
-Scale fitted amplitudes to a ratio of signal amplitude. — scale_amp_ratio_value • Spectroscopy Analysis Tools (spant) Scale fitted amplitudes to a ratio of signal amplitude. — scale_amp_ratio_value • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/scale_amp_water_ratio.html b/docs/reference/scale_amp_water_ratio.html
index 5b25e884..35a76b00 100644
--- a/docs/reference/scale_amp_water_ratio.html
+++ b/docs/reference/scale_amp_water_ratio.html
@@ -1,5 +1,5 @@
-Scale metabolite amplitudes as a ratio to the unsuppressed water amplitude. — scale_amp_water_ratio • Spectroscopy Analysis Tools (spant) Scale metabolite amplitudes as a ratio to the unsuppressed water amplitude. — scale_amp_water_ratio • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/scale_basis_amp.html b/docs/reference/scale_basis_amp.html
index 9401c3f1..5a58b5e5 100644
--- a/docs/reference/scale_basis_amp.html
+++ b/docs/reference/scale_basis_amp.html
@@ -1,5 +1,5 @@
-Scale a basis object by a scalar. — scale_basis_amp • Spectroscopy Analysis Tools (spant) Scale a basis object by a scalar. — scale_basis_amp • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/scale_basis_from_singlet.html b/docs/reference/scale_basis_from_singlet.html
index 0d542bc8..c9a19e77 100644
--- a/docs/reference/scale_basis_from_singlet.html
+++ b/docs/reference/scale_basis_from_singlet.html
@@ -1,5 +1,5 @@
-Scale a basis-set to be consistent with spant assumptions for water scaling. — scale_basis_from_singlet • Spectroscopy Analysis Tools (spant) Scale a basis-set to be consistent with spant assumptions for water scaling. — scale_basis_from_singlet • Spectroscopy Analysis Tools (spant)
Spectroscopy Analysis Tools (spant)
- 2.21.0
+ 2.22.0
@@ -127,7 +127,7 @@ Value
diff --git a/docs/reference/scale_mrs_amp.html b/docs/reference/scale_mrs_amp.html
index b5501a0d..990f058a 100644
--- a/docs/reference/scale_mrs_amp.html
+++ b/docs/reference/scale_mrs_amp.html
@@ -1,5 +1,5 @@
-Scale an mrs_data object by a scalar or vector or amplitudes. — scale_mrs_amp • Spectroscopy Analysis Tools (spant) Scale an mrs_data object by a scalar or vector or amplitudes. — scale_mrs_amp • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/scale_spec.html b/docs/reference/scale_spec.html
index 4f6ea835..6b3ddba4 100644
--- a/docs/reference/scale_spec.html
+++ b/docs/reference/scale_spec.html
@@ -1,5 +1,5 @@
-Scale mrs_data to a spectral region. — scale_spec • Spectroscopy Analysis Tools (spant) Scale mrs_data to a spectral region. — scale_spec • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -141,7 +141,7 @@ Value
diff --git a/docs/reference/sd.html b/docs/reference/sd.html
index ea1eec9f..3ae4dfd4 100644
--- a/docs/reference/sd.html
+++ b/docs/reference/sd.html
@@ -1,5 +1,5 @@
-Calculate the standard deviation spectrum from an mrs_data object. — sd • Spectroscopy Analysis Tools (spant) Calculate the standard deviation spectrum from an mrs_data object. — sd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/sd.mrs_data.html b/docs/reference/sd.mrs_data.html
index 3f92a49f..13bdda85 100644
--- a/docs/reference/sd.mrs_data.html
+++ b/docs/reference/sd.mrs_data.html
@@ -1,5 +1,5 @@
-Calculate the standard deviation spectrum from an mrs_data object. — sd.mrs_data • Spectroscopy Analysis Tools (spant) Calculate the standard deviation spectrum from an mrs_data object. — sd.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/seconds.html b/docs/reference/seconds.html
index b34d6627..467ee17f 100644
--- a/docs/reference/seconds.html
+++ b/docs/reference/seconds.html
@@ -1,5 +1,5 @@
-Return a time scale vector to match the FID of an MRS data object. — seconds • Spectroscopy Analysis Tools (spant) Return a time scale vector to match the FID of an MRS data object. — seconds • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/seq_cpmg_ideal.html b/docs/reference/seq_cpmg_ideal.html
index 547e96ab..45727c86 100644
--- a/docs/reference/seq_cpmg_ideal.html
+++ b/docs/reference/seq_cpmg_ideal.html
@@ -1,5 +1,5 @@
-CPMG style sequence with ideal pulses. — seq_cpmg_ideal • Spectroscopy Analysis Tools (spant) CPMG style sequence with ideal pulses. — seq_cpmg_ideal • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/seq_mega_press_ideal.html b/docs/reference/seq_mega_press_ideal.html
index 0769b8b4..a9cd7fa0 100644
--- a/docs/reference/seq_mega_press_ideal.html
+++ b/docs/reference/seq_mega_press_ideal.html
@@ -1,7 +1,5 @@
-MEGA-PRESS sequence with ideal localisation pulses and Gaussian shaped
-editing pulse. — seq_mega_press_ideal • Spectroscopy Analysis Tools (spant) MEGA-PRESS sequence with ideal localisation pulses and Gaussian shaped editing pulse. — seq_mega_press_ideal • Spectroscopy Analysis Tools (spant) PRESS sequence with shaped refocusing pulses. — seq_press_2d_shaped • Spectroscopy Analysis Tools (spant) PRESS sequence with shaped refocusing pulses. — seq_press_2d_shaped • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -165,7 +165,7 @@ Value
diff --git a/docs/reference/seq_press_ideal.html b/docs/reference/seq_press_ideal.html
index 8c976856..72c3af3d 100644
--- a/docs/reference/seq_press_ideal.html
+++ b/docs/reference/seq_press_ideal.html
@@ -1,5 +1,5 @@
-PRESS sequence with ideal pulses. — seq_press_ideal • Spectroscopy Analysis Tools (spant) PRESS sequence with ideal pulses. — seq_press_ideal • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/seq_pulse_acquire.html b/docs/reference/seq_pulse_acquire.html
index 4a88fc64..ad80571e 100644
--- a/docs/reference/seq_pulse_acquire.html
+++ b/docs/reference/seq_pulse_acquire.html
@@ -1,5 +1,5 @@
-Simple pulse and acquire sequence with ideal pulses. — seq_pulse_acquire • Spectroscopy Analysis Tools (spant) Simple pulse and acquire sequence with ideal pulses. — seq_pulse_acquire • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/seq_slaser_ideal.html b/docs/reference/seq_slaser_ideal.html
index 74688f4d..eb83e8e3 100644
--- a/docs/reference/seq_slaser_ideal.html
+++ b/docs/reference/seq_slaser_ideal.html
@@ -1,5 +1,5 @@
-sLASER sequence with ideal pulses. — seq_slaser_ideal • Spectroscopy Analysis Tools (spant) sLASER sequence with ideal pulses. — seq_slaser_ideal • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -126,7 +126,7 @@ Value
diff --git a/docs/reference/seq_spin_echo_ideal.html b/docs/reference/seq_spin_echo_ideal.html
index e23271de..4248716f 100644
--- a/docs/reference/seq_spin_echo_ideal.html
+++ b/docs/reference/seq_spin_echo_ideal.html
@@ -1,5 +1,5 @@
-Spin echo sequence with ideal pulses. — seq_spin_echo_ideal • Spectroscopy Analysis Tools (spant) Spin echo sequence with ideal pulses. — seq_spin_echo_ideal • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/seq_steam_ideal.html b/docs/reference/seq_steam_ideal.html
index a60685a8..1c8115d7 100644
--- a/docs/reference/seq_steam_ideal.html
+++ b/docs/reference/seq_steam_ideal.html
@@ -1,5 +1,5 @@
-STEAM sequence with ideal pulses. — seq_steam_ideal • Spectroscopy Analysis Tools (spant) STEAM sequence with ideal pulses. — seq_steam_ideal • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -128,7 +128,7 @@ Value
diff --git a/docs/reference/seq_steam_ideal_cof.html b/docs/reference/seq_steam_ideal_cof.html
index 8f225740..cba7af91 100644
--- a/docs/reference/seq_steam_ideal_cof.html
+++ b/docs/reference/seq_steam_ideal_cof.html
@@ -1,7 +1,5 @@
-STEAM sequence with ideal pulses and coherence order filtering to simulate
-gradient crushers. — seq_steam_ideal_cof • Spectroscopy Analysis Tools (spant) STEAM sequence with ideal pulses and coherence order filtering to simulate gradient crushers. — seq_steam_ideal_cof • Spectroscopy Analysis Tools (spant) STEAM sequence with ideal pulses using the z-rotation gradient simulation
-method described by Young et al JMR 140, 146-152 (1999). — seq_steam_ideal_young • Spectroscopy Analysis Tools (spant) STEAM sequence with ideal pulses using the z-rotation gradient simulation method described by Young et al JMR 140, 146-152 (1999). — seq_steam_ideal_young • Spectroscopy Analysis Tools (spant) Set the number of transients for an mrs_data object. — set_Ntrans • Spectroscopy Analysis Tools (spant) Set the number of transients for an mrs_data object. — set_Ntrans • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/set_def_acq_paras.html b/docs/reference/set_def_acq_paras.html
index 3e1b4004..cc2ada9c 100644
--- a/docs/reference/set_def_acq_paras.html
+++ b/docs/reference/set_def_acq_paras.html
@@ -1,5 +1,5 @@
-Set the default acquisition parameters. — set_def_acq_paras • Spectroscopy Analysis Tools (spant) Set the default acquisition parameters. — set_def_acq_paras • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Arguments
diff --git a/docs/reference/set_lcm_cmd.html b/docs/reference/set_lcm_cmd.html
index 2056ed01..42bb2f24 100644
--- a/docs/reference/set_lcm_cmd.html
+++ b/docs/reference/set_lcm_cmd.html
@@ -1,5 +1,5 @@
-Set the command to run the LCModel command-line program. — set_lcm_cmd • Spectroscopy Analysis Tools (spant) Set the command to run the LCModel command-line program. — set_lcm_cmd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/set_lw.html b/docs/reference/set_lw.html
index b64ec851..bb176c62 100644
--- a/docs/reference/set_lw.html
+++ b/docs/reference/set_lw.html
@@ -1,5 +1,5 @@
-Apply line-broadening to an mrs_data object to achieve a specified linewidth. — set_lw • Spectroscopy Analysis Tools (spant) Apply line-broadening to an mrs_data object to achieve a specified linewidth. — set_lw • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -123,7 +123,7 @@ Value
diff --git a/docs/reference/set_mask_xy_mat.html b/docs/reference/set_mask_xy_mat.html
index 49dc5d4e..52c4b617 100644
--- a/docs/reference/set_mask_xy_mat.html
+++ b/docs/reference/set_mask_xy_mat.html
@@ -1,5 +1,5 @@
-Set the masked voxels in a 2D MRSI dataset to given spectrum. — set_mask_xy_mat • Spectroscopy Analysis Tools (spant) Set the masked voxels in a 2D MRSI dataset to given spectrum. — set_mask_xy_mat • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Value
diff --git a/docs/reference/set_precomp_mode.html b/docs/reference/set_precomp_mode.html
index f44bd5d3..47c28e3b 100644
--- a/docs/reference/set_precomp_mode.html
+++ b/docs/reference/set_precomp_mode.html
@@ -1,5 +1,5 @@
-Set the precompute mode. — set_precomp_mode • Spectroscopy Analysis Tools (spant) Set the precompute mode. — set_precomp_mode • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/set_precomp_verbose.html b/docs/reference/set_precomp_verbose.html
index 1453a231..9c613505 100644
--- a/docs/reference/set_precomp_verbose.html
+++ b/docs/reference/set_precomp_verbose.html
@@ -1,5 +1,5 @@
-Set the verbosity of the precompute function. — set_precomp_verbose • Spectroscopy Analysis Tools (spant) Set the verbosity of the precompute function. — set_precomp_verbose • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/set_ref.html b/docs/reference/set_ref.html
index 8953fa50..5436dfa2 100644
--- a/docs/reference/set_ref.html
+++ b/docs/reference/set_ref.html
@@ -1,5 +1,5 @@
-Set the ppm reference value (eg ppm value at 0Hz). — set_ref • Spectroscopy Analysis Tools (spant) Set the ppm reference value (eg ppm value at 0Hz). — set_ref • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/set_td_pts.html b/docs/reference/set_td_pts.html
index 8a80d42a..586459ff 100644
--- a/docs/reference/set_td_pts.html
+++ b/docs/reference/set_td_pts.html
@@ -1,7 +1,5 @@
-Set the number of time-domain data points, truncating or zero-filling as
-appropriate. — set_td_pts • Spectroscopy Analysis Tools (spant) Set the number of time-domain data points, truncating or zero-filling as appropriate. — set_td_pts • Spectroscopy Analysis Tools (spant) Set the command to run the TARQUIN command-line program. — set_tqn_cmd • Spectroscopy Analysis Tools (spant) Set the command to run the TARQUIN command-line program. — set_tqn_cmd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/set_tr.html b/docs/reference/set_tr.html
index b2109ab0..65c9df5f 100644
--- a/docs/reference/set_tr.html
+++ b/docs/reference/set_tr.html
@@ -1,5 +1,5 @@
-Set the repetition time of an MRS dataset. — set_tr • Spectroscopy Analysis Tools (spant) Set the repetition time of an MRS dataset. — set_tr • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/shift.html b/docs/reference/shift.html
index ab0fe724..034591d0 100644
--- a/docs/reference/shift.html
+++ b/docs/reference/shift.html
@@ -1,5 +1,5 @@
-Apply a frequency shift to MRS data. — shift • Spectroscopy Analysis Tools (spant) Apply a frequency shift to MRS data. — shift • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/shift_basis.html b/docs/reference/shift_basis.html
index 2884be19..f55a65e0 100644
--- a/docs/reference/shift_basis.html
+++ b/docs/reference/shift_basis.html
@@ -1,5 +1,5 @@
-Apply frequency shifts to basis set signals. — shift_basis • Spectroscopy Analysis Tools (spant) Apply frequency shifts to basis set signals. — shift_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Value
diff --git a/docs/reference/sim_basis.html b/docs/reference/sim_basis.html
index c7838c46..bb5fefc6 100644
--- a/docs/reference/sim_basis.html
+++ b/docs/reference/sim_basis.html
@@ -1,5 +1,5 @@
-Simulate a basis set object. — sim_basis • Spectroscopy Analysis Tools (spant) Simulate a basis set object. — sim_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -136,7 +136,7 @@ Value
diff --git a/docs/reference/sim_basis_1h_brain.html b/docs/reference/sim_basis_1h_brain.html
index 62ed7389..f71ffa0b 100644
--- a/docs/reference/sim_basis_1h_brain.html
+++ b/docs/reference/sim_basis_1h_brain.html
@@ -1,7 +1,5 @@
-Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS
-sequence. Note, ideal pulses are assumed. — sim_basis_1h_brain • Spectroscopy Analysis Tools (spant) Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS sequence. Note, ideal pulses are assumed. — sim_basis_1h_brain • Spectroscopy Analysis Tools (spant) Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS
-sequence. Note, ideal pulses are assumed. — sim_basis_1h_brain_press • Spectroscopy Analysis Tools (spant) Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS sequence. Note, ideal pulses are assumed. — sim_basis_1h_brain_press • Spectroscopy Analysis Tools (spant) Simulate a macromolecular and lipid basis-set suitable for 1H brain MRS
-analysis. — sim_basis_mm_lip_lcm • Spectroscopy Analysis Tools (spant) Simulate a macromolecular and lipid basis-set suitable for 1H brain MRS analysis. — sim_basis_mm_lip_lcm • Spectroscopy Analysis Tools (spant) Simulate a basis file using TARQUIN. — sim_basis_tqn • Spectroscopy Analysis Tools (spant) Simulate a basis file using TARQUIN. — sim_basis_tqn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -129,7 +129,7 @@ Examples
diff --git a/docs/reference/sim_brain_1h.html b/docs/reference/sim_brain_1h.html
index 2044cf1a..717ee289 100644
--- a/docs/reference/sim_brain_1h.html
+++ b/docs/reference/sim_brain_1h.html
@@ -1,5 +1,5 @@
-Simulate MRS data with a similar appearance to normal brain (by default). — sim_brain_1h • Spectroscopy Analysis Tools (spant) Simulate MRS data with a similar appearance to normal brain (by default). — sim_brain_1h • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -159,7 +159,7 @@ Value
diff --git a/docs/reference/sim_mol.html b/docs/reference/sim_mol.html
index 23bcef50..77f76a50 100644
--- a/docs/reference/sim_mol.html
+++ b/docs/reference/sim_mol.html
@@ -1,5 +1,5 @@
-Simulate a mol_parameter object. — sim_mol • Spectroscopy Analysis Tools (spant) Simulate a mol_parameter object. — sim_mol • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -143,7 +143,7 @@ Value
diff --git a/docs/reference/sim_noise.html b/docs/reference/sim_noise.html
index 23875f79..a71477d4 100644
--- a/docs/reference/sim_noise.html
+++ b/docs/reference/sim_noise.html
@@ -1,5 +1,5 @@
-Simulate an mrs_data object containing simulated Gaussian noise. — sim_noise • Spectroscopy Analysis Tools (spant) Simulate an mrs_data object containing simulated Gaussian noise. — sim_noise • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -84,6 +84,7 @@ Simulate an mrs_data object containing simulated Gaussian noise.
ft = def_ft(),
N = def_N(),
ref = def_ref(),
+ nuc = def_nuc(),
dyns = 1,
fd = TRUE
)
@@ -111,6 +112,10 @@ Arguments
reference value for ppm scale.
nuc
+resonant nucleus.
dyns
number of dynamic scans to generate.
Value
diff --git a/docs/reference/sim_resonances.html b/docs/reference/sim_resonances.html
index 19e9a8a4..d4f8d7c0 100644
--- a/docs/reference/sim_resonances.html
+++ b/docs/reference/sim_resonances.html
@@ -1,5 +1,5 @@
-Simulate a MRS data object containing a set of simulated resonances. — sim_resonances • Spectroscopy Analysis Tools (spant) Simulate a MRS data object containing a set of simulated resonances. — sim_resonances • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -161,7 +161,7 @@ Examples
diff --git a/docs/reference/sim_th_excit_profile.html b/docs/reference/sim_th_excit_profile.html
index 5535c5ef..e781cab1 100644
--- a/docs/reference/sim_th_excit_profile.html
+++ b/docs/reference/sim_th_excit_profile.html
@@ -1,7 +1,5 @@
-Simulate an ideal pulse excitation profile by smoothing a top-hat function
-with a Gaussian. — sim_th_excit_profile • Spectroscopy Analysis Tools (spant) Simulate an ideal pulse excitation profile by smoothing a top-hat function with a Gaussian. — sim_th_excit_profile • Spectroscopy Analysis Tools (spant) Simulate an mrs_data object containing complex zero valued samples. — sim_zero • Spectroscopy Analysis Tools (spant) Simulate an mrs_data object containing complex zero valued samples. — sim_zero • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -78,7 +78,14 @@ Simulate an mrs_data object containing complex zero valued samples.
-
+
@@ -99,6 +106,10 @@ Arguments
reference value for ppm scale.
nuc
+resonant nucleus.
dyns
number of dynamic scans to generate.
Value
diff --git a/docs/reference/smooth_dyns.html b/docs/reference/smooth_dyns.html
index 4cc8da50..accf3a51 100644
--- a/docs/reference/smooth_dyns.html
+++ b/docs/reference/smooth_dyns.html
@@ -1,5 +1,5 @@
-Smooth data across the dynamic dimension with a Gaussian kernel. — smooth_dyns • Spectroscopy Analysis Tools (spant) Smooth data across the dynamic dimension with a Gaussian kernel. — smooth_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/sort_basis.html b/docs/reference/sort_basis.html
index 6a676ea2..d25cc006 100644
--- a/docs/reference/sort_basis.html
+++ b/docs/reference/sort_basis.html
@@ -1,5 +1,5 @@
-Sort the basis-set elements alphabetically. — sort_basis • Spectroscopy Analysis Tools (spant) Sort the basis-set elements alphabetically. — sort_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/spant-package.html b/docs/reference/spant-package.html
index b3dd8e21..90f19ec3 100644
--- a/docs/reference/spant-package.html
+++ b/docs/reference/spant-package.html
@@ -1,5 +1,5 @@
-spant: spectroscopy analysis tools. — spant-package • Spectroscopy Analysis Tools (spant) spant: spectroscopy analysis tools. — spant-package • Spectroscopy Analysis Tools (spant) Simulate and fit some spectra with ABfit for benchmarking purposes. Basic
-timing and performance metrics will be printed. — spant_abfit_benchmark • Spectroscopy Analysis Tools (spant) Simulate and fit some spectra with ABfit for benchmarking purposes. Basic timing and performance metrics will be printed. — spant_abfit_benchmark • Spectroscopy Analysis Tools (spant) Example MEGA-PRESS data with significant B0 drift. — spant_mpress_drift • Spectroscopy Analysis Tools (spant) Example MEGA-PRESS data with significant B0 drift. — spant_mpress_drift • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -83,7 +83,7 @@ Example MEGA-PRESS data with significant B0 drift.
Format
- An object of class mrs_data of length 13.
+ An object of class mrs_data of dimension 1 x 1 x 1 x 1 x 40 x 1 x 1024.
@@ -98,7 +98,7 @@ Format
diff --git a/docs/reference/spant_sim_fmrs_dataset.html b/docs/reference/spant_sim_fmrs_dataset.html
new file mode 100644
index 00000000..00e48b56
--- /dev/null
+++ b/docs/reference/spant_sim_fmrs_dataset.html
@@ -0,0 +1,117 @@
+
+Simulate an example fMRS dataset for a block design fMRS experiment and export a BIDS structure. — spant_sim_fmrs_dataset • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Simulate an example fMRS dataset for a block design fMRS experiment and export a BIDS structure.
+ Source: R/fmrs.R
+ spant_sim_fmrs_dataset.Rd
+
+
+
+ Simulate an example fMRS dataset for a block design fMRS experiment and
+export a BIDS structure.
+
+
+
+ spant_sim_fmrs_dataset(output_dir = NULL)
+
+
+
+ Arguments
+ - output_dir
+output directory for the BIDS data. Defaults to :
+"HOME/sim_fmrs_dataset/data".
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/spant_simulation_benchmark.html b/docs/reference/spant_simulation_benchmark.html
index 32daa8bf..d8cc6841 100644
--- a/docs/reference/spant_simulation_benchmark.html
+++ b/docs/reference/spant_simulation_benchmark.html
@@ -1,7 +1,5 @@
-Simulate a typical metabolite basis set for benchmarking. Timing metrics will
-be printed on completion. — spant_simulation_benchmark • Spectroscopy Analysis Tools (spant) Simulate a typical metabolite basis set for benchmarking. Timing metrics will be printed on completion. — spant_simulation_benchmark • Spectroscopy Analysis Tools (spant) Decompose an mrs_data object into white and gray matter spectra. — spec_decomp • Spectroscopy Analysis Tools (spant) Perform a mathematical operation on a spectral region. — spec_op • Spectroscopy Analysis Tools (spant) Perform a mathematical operation on a spectral region. — spec_op • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -98,8 +98,8 @@ Arguments
operator
-can be "sum" (default), "mean", "l2", "max", "min" or
-"max-min".
can be "sum" (default), "mean", "l2", "max", "max_cplx,
+"min" or "max-min".
freq_scale
@@ -129,7 +129,7 @@ Value
diff --git a/docs/reference/spin_sys.html b/docs/reference/spin_sys.html
index 853423a4..1eaa9e76 100644
--- a/docs/reference/spin_sys.html
+++ b/docs/reference/spin_sys.html
@@ -1,5 +1,5 @@
-Create a spin system object for pulse sequence simulation. — spin_sys • Spectroscopy Analysis Tools (spant) Create a spin system object for pulse sequence simulation. — spin_sys • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/spm_pve2categorical.html b/docs/reference/spm_pve2categorical.html
index 23a1bad9..70f10729 100644
--- a/docs/reference/spm_pve2categorical.html
+++ b/docs/reference/spm_pve2categorical.html
@@ -1,7 +1,5 @@
-Convert SPM style segmentation files to a single categorical image where
-the numerical values map as: 0) Other, 1) CSF, 2) GM and 3) WM. — spm_pve2categorical • Spectroscopy Analysis Tools (spant) Convert SPM style segmentation files to a single categorical image where the numerical values map as: 0) Other, 1) CSF, 2) GM and 3) WM. — spm_pve2categorical • Spectroscopy Analysis Tools (spant) Signal space projection method for lipid suppression. — ssp • Spectroscopy Analysis Tools (spant) Signal space projection method for lipid suppression. — ssp • Spectroscopy Analysis Tools (spant) Plot the fitting results of an object of class fit_result with
-individual basis set components shown. — stackplot.fit_result • Spectroscopy Analysis Tools (spant) Plot the fitting results of an object of class fit_result with individual basis set components shown. — stackplot.fit_result • Spectroscopy Analysis Tools (spant) Produce a plot with multiple traces. — stackplot • Spectroscopy Analysis Tools (spant) Produce a plot with multiple traces. — stackplot • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/stackplot.mrs_data.html b/docs/reference/stackplot.mrs_data.html
index 17ff5648..64eea445 100644
--- a/docs/reference/stackplot.mrs_data.html
+++ b/docs/reference/stackplot.mrs_data.html
@@ -1,5 +1,5 @@
-Stackplot plotting method for objects of class mrs_data. — stackplot.mrs_data • Spectroscopy Analysis Tools (spant) Stackplot plotting method for objects of class mrs_data. — stackplot.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -255,7 +255,7 @@ Arguments
diff --git a/docs/reference/sub_first_dyn.html b/docs/reference/sub_first_dyn.html
index dbd7f831..493b7242 100644
--- a/docs/reference/sub_first_dyn.html
+++ b/docs/reference/sub_first_dyn.html
@@ -1,5 +1,5 @@
-Subtract the first dynamic spectrum from a dynamic series. — sub_first_dyn • Spectroscopy Analysis Tools (spant) Subtract the first dynamic spectrum from a dynamic series. — sub_first_dyn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/sub_mean_dyns.html b/docs/reference/sub_mean_dyns.html
index 6e3bb2df..221bd0c1 100644
--- a/docs/reference/sub_mean_dyns.html
+++ b/docs/reference/sub_mean_dyns.html
@@ -1,5 +1,5 @@
-Subtract the mean dynamic spectrum from a dynamic series. — sub_mean_dyns • Spectroscopy Analysis Tools (spant) Subtract the mean dynamic spectrum from a dynamic series. — sub_mean_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/sub_median_dyns.html b/docs/reference/sub_median_dyns.html
index 134c495d..1e834f14 100644
--- a/docs/reference/sub_median_dyns.html
+++ b/docs/reference/sub_median_dyns.html
@@ -1,5 +1,5 @@
-Subtract the median dynamic spectrum from a dynamic series. — sub_median_dyns • Spectroscopy Analysis Tools (spant) Subtract the median dynamic spectrum from a dynamic series. — sub_median_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/sum_coils.html b/docs/reference/sum_coils.html
index 7bf559f2..e1ab3cc0 100644
--- a/docs/reference/sum_coils.html
+++ b/docs/reference/sum_coils.html
@@ -1,5 +1,5 @@
-Calculate the sum across receiver coil elements. — sum_coils • Spectroscopy Analysis Tools (spant) Calculate the sum across receiver coil elements. — sum_coils • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/sum_dyns.html b/docs/reference/sum_dyns.html
index a0be19d3..bbda2ffc 100644
--- a/docs/reference/sum_dyns.html
+++ b/docs/reference/sum_dyns.html
@@ -1,5 +1,5 @@
-Calculate the sum of data dynamics. — sum_dyns • Spectroscopy Analysis Tools (spant) Calculate the sum of data dynamics. — sum_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/sum_mrs.html b/docs/reference/sum_mrs.html
index a22f215b..3cc3ab9e 100644
--- a/docs/reference/sum_mrs.html
+++ b/docs/reference/sum_mrs.html
@@ -1,5 +1,5 @@
-Sum two mrs_data objects. — sum_mrs • Spectroscopy Analysis Tools (spant) Sum two mrs_data objects. — sum_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Value
diff --git a/docs/reference/sum_mrs_list.html b/docs/reference/sum_mrs_list.html
index f4e09aea..c3584348 100644
--- a/docs/reference/sum_mrs_list.html
+++ b/docs/reference/sum_mrs_list.html
@@ -1,5 +1,5 @@
-Return the sum of a list of mrs_data objects. — sum_mrs_list • Spectroscopy Analysis Tools (spant) Return the sum of a list of mrs_data objects. — sum_mrs_list • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/svs_1h_brain_analysis.html b/docs/reference/svs_1h_brain_analysis.html
index 8ce514db..dff0ef7d 100644
--- a/docs/reference/svs_1h_brain_analysis.html
+++ b/docs/reference/svs_1h_brain_analysis.html
@@ -1,5 +1,5 @@
-Standard SVS 1H brain analysis pipeline. — svs_1h_brain_analysis • Spectroscopy Analysis Tools (spant) Standard SVS 1H brain analysis pipeline. — svs_1h_brain_analysis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -199,7 +199,7 @@ Value
diff --git a/docs/reference/svs_1h_brain_analysis_dev.html b/docs/reference/svs_1h_brain_analysis_dev.html
index d70a14d3..d71bfea2 100644
--- a/docs/reference/svs_1h_brain_analysis_dev.html
+++ b/docs/reference/svs_1h_brain_analysis_dev.html
@@ -1,5 +1,5 @@
-Standard SVS 1H brain analysis pipeline. — svs_1h_brain_analysis_dev • Spectroscopy Analysis Tools (spant) Standard SVS 1H brain analysis pipeline. — svs_1h_brain_analysis_dev • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -193,7 +193,7 @@ Examples
diff --git a/docs/reference/svs_1h_brain_batch_analysis.html b/docs/reference/svs_1h_brain_batch_analysis.html
index 5631e8cc..15f7223e 100644
--- a/docs/reference/svs_1h_brain_batch_analysis.html
+++ b/docs/reference/svs_1h_brain_batch_analysis.html
@@ -1,5 +1,5 @@
-Batch interface to the standard SVS 1H brain analysis pipeline. — svs_1h_brain_batch_analysis • Spectroscopy Analysis Tools (spant) Batch interface to the standard SVS 1H brain analysis pipeline. — svs_1h_brain_batch_analysis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -144,7 +144,7 @@ Value
diff --git a/docs/reference/t_test_spec.html b/docs/reference/t_test_spec.html
new file mode 100644
index 00000000..56a7ea1b
--- /dev/null
+++ b/docs/reference/t_test_spec.html
@@ -0,0 +1,124 @@
+
+Perform a t-test on spectral data points. — t_test_spec • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+
+
+ Perform a t-test on spectral data points.
+
+
+
+ t_test_spec(mrs_data, group)
+
+
+
+ Arguments
+ - mrs_data
+an mrs_data object with spectra in the dynamic dimension.
- group
+vector describing the group membership of each dynamic spectrum.
+
+ Value
+
+
+a list of statistical results.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/td2fd.html b/docs/reference/td2fd.html
index 6748a6a8..f31ed524 100644
--- a/docs/reference/td2fd.html
+++ b/docs/reference/td2fd.html
@@ -1,5 +1,5 @@
-Transform time-domain data to the frequency-domain. — td2fd • Spectroscopy Analysis Tools (spant) Transform time-domain data to the frequency-domain. — td2fd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/td_conv_filt.html b/docs/reference/td_conv_filt.html
index a9f340c3..106b9b00 100644
--- a/docs/reference/td_conv_filt.html
+++ b/docs/reference/td_conv_filt.html
@@ -1,5 +1,5 @@
-Time-domain convolution based filter. — td_conv_filt • Spectroscopy Analysis Tools (spant) Time-domain convolution based filter. — td_conv_filt • Spectroscopy Analysis Tools (spant) Time-domain spectral registration. — tdsr • Spectroscopy Analysis Tools (spant) Time-domain spectral registration. — tdsr • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -121,7 +121,7 @@ Value
diff --git a/docs/reference/te.html b/docs/reference/te.html
index 010361b1..4a65711d 100644
--- a/docs/reference/te.html
+++ b/docs/reference/te.html
@@ -1,5 +1,5 @@
-Return the echo time of an MRS dataset. — te • Spectroscopy Analysis Tools (spant) Return the echo time of an MRS dataset. — te • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/tr.html b/docs/reference/tr.html
index 0c0bd63b..2e749e02 100644
--- a/docs/reference/tr.html
+++ b/docs/reference/tr.html
@@ -1,5 +1,5 @@
-Return the repetition time of an MRS dataset. — tr • Spectroscopy Analysis Tools (spant) Return the repetition time of an MRS dataset. — tr • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/varpro_3_para_opts.html b/docs/reference/varpro_3_para_opts.html
index c2270a16..52d7cd84 100644
--- a/docs/reference/varpro_3_para_opts.html
+++ b/docs/reference/varpro_3_para_opts.html
@@ -1,5 +1,5 @@
-Return a list of options for VARPRO based fitting with 3 free parameters. — varpro_3_para_opts • Spectroscopy Analysis Tools (spant) Return a list of options for VARPRO based fitting with 3 free parameters. — varpro_3_para_opts • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -141,7 +141,7 @@ Value
diff --git a/docs/reference/varpro_basic_opts.html b/docs/reference/varpro_basic_opts.html
index 32c86d22..c5104891 100644
--- a/docs/reference/varpro_basic_opts.html
+++ b/docs/reference/varpro_basic_opts.html
@@ -1,5 +1,5 @@
-Return a list of options for a basic VARPRO analysis. — varpro_basic_opts • Spectroscopy Analysis Tools (spant) Return a list of options for a basic VARPRO analysis. — varpro_basic_opts • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -118,7 +118,7 @@ Value
diff --git a/docs/reference/varpro_opts.html b/docs/reference/varpro_opts.html
index 2aabf11d..6332f730 100644
--- a/docs/reference/varpro_opts.html
+++ b/docs/reference/varpro_opts.html
@@ -1,5 +1,5 @@
-Return a list of options for VARPRO based fitting. — varpro_opts • Spectroscopy Analysis Tools (spant) Return a list of options for VARPRO based fitting. — varpro_opts • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -177,7 +177,7 @@ Examples
diff --git a/docs/reference/vec2mrs_data.html b/docs/reference/vec2mrs_data.html
index 0cccd73b..f0d58bf0 100644
--- a/docs/reference/vec2mrs_data.html
+++ b/docs/reference/vec2mrs_data.html
@@ -1,5 +1,5 @@
-Convert a vector into a mrs_data object. — vec2mrs_data • Spectroscopy Analysis Tools (spant) Convert a vector into a mrs_data object. — vec2mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -80,10 +80,11 @@ Convert a vector into a mrs_data object.
vec2mrs_data(
vec,
- fs = def_fs(),
- ft = def_ft(),
- ref = def_ref(),
- nuc = def_nuc(),
+ mrs_data = NULL,
+ fs = NULL,
+ ft = NULL,
+ ref = NULL,
+ nuc = NULL,
dyns = 1,
fd = FALSE
)
@@ -95,6 +96,10 @@ Arguments
the data vector.
mrs_data
+example data to copy acquisition parameters from.
fs
sampling frequency in Hz.
Arguments
fd
-flag to indicate if the matrix is in the frequency domain (logical).
flag to indicate if the vector is in the frequency domain (logical).
Value
diff --git a/docs/reference/write_basis.html b/docs/reference/write_basis.html
index b6e27cbd..94c5e021 100644
--- a/docs/reference/write_basis.html
+++ b/docs/reference/write_basis.html
@@ -1,5 +1,5 @@
-Write a basis object to an LCModel .basis formatted file. — write_basis • Spectroscopy Analysis Tools (spant) Write a basis object to an LCModel .basis formatted file. — write_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -108,7 +108,7 @@ Arguments
diff --git a/docs/reference/write_basis_tqn.html b/docs/reference/write_basis_tqn.html
index 6aa51c1d..116c73ec 100644
--- a/docs/reference/write_basis_tqn.html
+++ b/docs/reference/write_basis_tqn.html
@@ -1,5 +1,5 @@
-Generate a basis file using TARQUIN. — write_basis_tqn • Spectroscopy Analysis Tools (spant) Generate a basis file using TARQUIN. — write_basis_tqn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Examples
diff --git a/docs/reference/write_mrs.html b/docs/reference/write_mrs.html
index fff25f15..124b9dc4 100644
--- a/docs/reference/write_mrs.html
+++ b/docs/reference/write_mrs.html
@@ -1,5 +1,5 @@
-Write MRS data object to file. — write_mrs • Spectroscopy Analysis Tools (spant) Write MRS data object to file. — write_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Arguments
diff --git a/docs/reference/write_mrs_nifti.html b/docs/reference/write_mrs_nifti.html
index f4bf1921..bd3ed4b7 100644
--- a/docs/reference/write_mrs_nifti.html
+++ b/docs/reference/write_mrs_nifti.html
@@ -1,5 +1,5 @@
-Write MRS data object to file in NIFTI format. — write_mrs_nifti • Spectroscopy Analysis Tools (spant) Write MRS data object to file in NIFTI format. — write_mrs_nifti • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/write_pulse_ascii.html b/docs/reference/write_pulse_ascii.html
index 067ae086..221f8ebb 100644
--- a/docs/reference/write_pulse_ascii.html
+++ b/docs/reference/write_pulse_ascii.html
@@ -1,5 +1,5 @@
-Write an ASCII formatted pulse file. — write_pulse_ascii • Spectroscopy Analysis Tools (spant) Write an ASCII formatted pulse file. — write_pulse_ascii • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/zero_fade_spec.html b/docs/reference/zero_fade_spec.html
index c703745c..c8b572c3 100644
--- a/docs/reference/zero_fade_spec.html
+++ b/docs/reference/zero_fade_spec.html
@@ -1,7 +1,5 @@
-Fade a spectrum to zero by frequency domain multiplication with a tanh
-function. Note this operation distorts data points at the end of the FID. — zero_fade_spec • Spectroscopy Analysis Tools (spant) Fade a spectrum to zero by frequency domain multiplication with a tanh function. Note this operation distorts data points at the end of the FID. — zero_fade_spec • Spectroscopy Analysis Tools (spant) Zero all coherences including and above a given order. — zero_higher_orders • Spectroscopy Analysis Tools (spant) Zero all coherences including and above a given order. — zero_higher_orders • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Value
diff --git a/docs/reference/zero_td_pts_end.html b/docs/reference/zero_td_pts_end.html
index 8c1123c8..71d24ebb 100644
--- a/docs/reference/zero_td_pts_end.html
+++ b/docs/reference/zero_td_pts_end.html
@@ -1,5 +1,5 @@
-Set mrs_data object data points at the end of the FID to zero. — zero_td_pts_end • Spectroscopy Analysis Tools (spant) Set mrs_data object data points at the end of the FID to zero. — zero_td_pts_end • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/zf.html b/docs/reference/zf.html
index 85e2013c..baf50256 100644
--- a/docs/reference/zf.html
+++ b/docs/reference/zf.html
@@ -1,5 +1,5 @@
-Zero-fill MRS data in the time domain. — zf • Spectroscopy Analysis Tools (spant) Zero-fill MRS data in the time domain. — zf • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -125,7 +125,7 @@ Value
diff --git a/docs/reference/zf_xy.html b/docs/reference/zf_xy.html
index ebca3999..c4104a74 100644
--- a/docs/reference/zf_xy.html
+++ b/docs/reference/zf_xy.html
@@ -1,5 +1,5 @@
-Zero-fill MRSI data in the k-space x-y direction. — zf_xy • Spectroscopy Analysis Tools (spant) Zero-fill MRSI data in the k-space x-y direction. — zf_xy • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -113,7 +113,7 @@ Value
diff --git a/docs/sitemap.xml b/docs/sitemap.xml
index e2139f71..4c39f515 100644
--- a/docs/sitemap.xml
+++ b/docs/sitemap.xml
@@ -216,6 +216,12 @@
https://martin3141.github.io/spant/reference/comb_coils_fp_pc.html
+
+ https://martin3141.github.io/spant/reference/comb_coils_mrsi_gls.html
+
+
+ https://martin3141.github.io/spant/reference/comb_coils_svs_gls.html
+
https://martin3141.github.io/spant/reference/comb_csv_results.html
@@ -411,6 +417,9 @@
https://martin3141.github.io/spant/reference/gen_conv_reg.html
+
+ https://martin3141.github.io/spant/reference/gen_group_reg.html
+
https://martin3141.github.io/spant/reference/gen_impulse_reg.html
@@ -555,6 +564,15 @@
https://martin3141.github.io/spant/reference/glm_spec.html
+
+ https://martin3141.github.io/spant/reference/glm_spec_fmrs_fl.html
+
+
+ https://martin3141.github.io/spant/reference/glm_spec_fmrs_group.html
+
+
+ https://martin3141.github.io/spant/reference/glm_spec_group_linhyp.html
+
https://martin3141.github.io/spant/reference/grid_shift_xy.html
@@ -690,9 +708,15 @@
https://martin3141.github.io/spant/reference/mrs_data2basis.html
+
+ https://martin3141.github.io/spant/reference/mrs_data2bids.html
+
https://martin3141.github.io/spant/reference/mrs_data2mat.html
+
+ https://martin3141.github.io/spant/reference/mrs_data2spec_mat.html
+
https://martin3141.github.io/spant/reference/mrs_data2vec.html
@@ -741,6 +765,9 @@
https://martin3141.github.io/spant/reference/phase.html
+
+ https://martin3141.github.io/spant/reference/phase_ref_1h_brain.html
+
https://martin3141.github.io/spant/reference/plot.fit_result.html
@@ -780,6 +807,12 @@
https://martin3141.github.io/spant/reference/precomp.html
+
+ https://martin3141.github.io/spant/reference/preproc_svs.html
+
+
+ https://martin3141.github.io/spant/reference/preproc_svs_dataset.html
+
https://martin3141.github.io/spant/reference/print.fit_result.html
@@ -1050,6 +1083,9 @@
https://martin3141.github.io/spant/reference/spant_mpress_drift.html
+
+ https://martin3141.github.io/spant/reference/spant_sim_fmrs_dataset.html
+
https://martin3141.github.io/spant/reference/spant_simulation_benchmark.html
@@ -1107,6 +1143,9 @@
https://martin3141.github.io/spant/reference/svs_1h_brain_batch_analysis.html
+
+ https://martin3141.github.io/spant/reference/t_test_spec.html
+
https://martin3141.github.io/spant/reference/td2fd.html
Save function results to file and load on subsequent calls to avoid repeat -computation.
Save function results to file and load on subsequent calls to avoid repeat computation.
Preprocess and perform quality assessment of a single SVS data set.
Preprocess and perform quality assessment of one or more SVS data sets.
All functions
- Read a directory containing Siemens MRS IMA files and combine along the coil
-dimension. Note that the coil ID is inferred from the sorted file name and
-should be checked when consistency is required between two directories.
Read a directory containing Siemens MRS IMA files and combine along the coil dimension. Note that the coil ID is inferred from the sorted file name and should be checked when consistency is required between two directories.
- Read a directory containing Siemens MRS IMA files and combine along the
-dynamic dimension. Note that the coil ID is inferred from the sorted file
-name and should be checked when consistency is required.
Read a directory containing Siemens MRS IMA files and combine along the dynamic dimension. Note that the coil ID is inferred from the sorted file name and should be checked when consistency is required.
@@ -1103,13 +1090,11 @@ All functions
- Reconstruct complex time-domain data from the real part of frequency-domain
-data.
Reconstruct complex time-domain data from the real part of frequency-domain data.
- Reconstruct complex time-domain data from the real part of frequency-domain
-data.
Reconstruct complex time-domain data from the real part of frequency-domain data.
@@ -1141,8 +1126,7 @@ All functions
- Resample a VOI to match a target image space using nearest-neighbour
-interpolation.
Resample a VOI to match a target image space using nearest-neighbour interpolation.
@@ -1158,23 +1142,19 @@ All functions
- Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water).
Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / kg of tissue water).
- Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water).
Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / kg of tissue water).
- Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / Litre of tissue).
Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / Litre of tissue).
- Convert default LCM/TARQUIN concentration scaling to molal units with partial
-volume correction.
Convert default LCM/TARQUIN concentration scaling to molal units with partial volume correction.
@@ -1222,8 +1202,7 @@ All functions
- MEGA-PRESS sequence with ideal localisation pulses and Gaussian shaped
-editing pulse.
MEGA-PRESS sequence with ideal localisation pulses and Gaussian shaped editing pulse.
@@ -1251,13 +1230,11 @@ All functions
- STEAM sequence with ideal pulses and coherence order filtering to simulate
-gradient crushers.
STEAM sequence with ideal pulses and coherence order filtering to simulate gradient crushers.
- STEAM sequence with ideal pulses using the z-rotation gradient simulation
-method described by Young et al JMR 140, 146-152 (1999).
STEAM sequence with ideal pulses using the z-rotation gradient simulation method described by Young et al JMR 140, 146-152 (1999).
@@ -1293,8 +1270,7 @@ All functions
- Set the number of time-domain data points, truncating or zero-filling as
-appropriate.
Set the number of time-domain data points, truncating or zero-filling as appropriate.
@@ -1318,18 +1294,15 @@ All functions
- Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS
-sequence. Note, ideal pulses are assumed.
Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS sequence. Note, ideal pulses are assumed.
- Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS
-sequence. Note, ideal pulses are assumed.
Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS sequence. Note, ideal pulses are assumed.
- Simulate a macromolecular and lipid basis-set suitable for 1H brain MRS
-analysis.
Simulate a macromolecular and lipid basis-set suitable for 1H brain MRS analysis.
@@ -1353,8 +1326,7 @@ All functions
- Simulate an ideal pulse excitation profile by smoothing a top-hat function
-with a Gaussian.
Simulate an ideal pulse excitation profile by smoothing a top-hat function with a Gaussian.
@@ -1374,17 +1346,19 @@ All functions
- Simulate and fit some spectra with ABfit for benchmarking purposes. Basic
-timing and performance metrics will be printed.
Simulate and fit some spectra with ABfit for benchmarking purposes. Basic timing and performance metrics will be printed.
Example MEGA-PRESS data with significant B0 drift.
+
+
+ Simulate an example fMRS dataset for a block design fMRS experiment and export a BIDS structure.
- Simulate a typical metabolite basis set for benchmarking. Timing metrics will
-be printed on completion.
Simulate a typical metabolite basis set for benchmarking. Timing metrics will be printed on completion.
@@ -1400,8 +1374,7 @@ All functions
- Convert SPM style segmentation files to a single categorical image where
-the numerical values map as: 0) Other, 1) CSF, 2) GM and 3) WM.
Convert SPM style segmentation files to a single categorical image where the numerical values map as: 0) Other, 1) CSF, 2) GM and 3) WM.
@@ -1413,8 +1386,7 @@ All functions
- Plot the fitting results of an object of class fit_result with
-individual basis set components shown.
Plot the fitting results of an object of class fit_result with individual basis set components shown.
@@ -1459,6 +1431,10 @@ All functions svs_1h_brain_batch_analysis()
Batch interface to the standard SVS 1H brain analysis pipeline.
+
+
+ Perform a t-test on spectral data points.
@@ -1518,8 +1494,7 @@ All functions
- Fade a spectrum to zero by frequency domain multiplication with a tanh
-function. Note this operation distorts data points at the end of the FID.
Fade a spectrum to zero by frequency domain multiplication with a tanh function. Note this operation distorts data points at the end of the FID.
@@ -1549,7 +1524,7 @@ All functions
diff --git a/docs/reference/int_spec.html b/docs/reference/int_spec.html
index c7060fe7..783325a8 100644
--- a/docs/reference/int_spec.html
+++ b/docs/reference/int_spec.html
@@ -1,5 +1,5 @@
-Integrate a spectral region. — int_spec • Spectroscopy Analysis Tools (spant) Integrate a spectral region. — int_spec • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -118,7 +118,7 @@ Value
diff --git a/docs/reference/interleave_dyns.html b/docs/reference/interleave_dyns.html
index effe5543..441eff27 100644
--- a/docs/reference/interleave_dyns.html
+++ b/docs/reference/interleave_dyns.html
@@ -1,5 +1,5 @@
-Interleave the first and second half of a dynamic series. — interleave_dyns • Spectroscopy Analysis Tools (spant) Interleave the first and second half of a dynamic series. — interleave_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/inv_even_dyns.html b/docs/reference/inv_even_dyns.html
index 9f9d4fff..dcb781dc 100644
--- a/docs/reference/inv_even_dyns.html
+++ b/docs/reference/inv_even_dyns.html
@@ -1,5 +1,5 @@
-Invert even numbered dynamic scans starting from 1 (2,4,6...). — inv_even_dyns • Spectroscopy Analysis Tools (spant) Invert even numbered dynamic scans starting from 1 (2,4,6...). — inv_even_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/inv_odd_dyns.html b/docs/reference/inv_odd_dyns.html
index 26212e2b..78d64660 100644
--- a/docs/reference/inv_odd_dyns.html
+++ b/docs/reference/inv_odd_dyns.html
@@ -1,5 +1,5 @@
-Invert odd numbered dynamic scans starting from 1 (1,3,5...). — inv_odd_dyns • Spectroscopy Analysis Tools (spant) Invert odd numbered dynamic scans starting from 1 (1,3,5...). — inv_odd_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/is.def.html b/docs/reference/is.def.html
index f196ffd0..a67b9eba 100644
--- a/docs/reference/is.def.html
+++ b/docs/reference/is.def.html
@@ -1,5 +1,5 @@
-Check if an object is defined, which is the same as being not NULL. — is.def • Spectroscopy Analysis Tools (spant) Check if an object is defined, which is the same as being not NULL. — is.def • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/is_fd.html b/docs/reference/is_fd.html
index 3b0ca165..18a193aa 100644
--- a/docs/reference/is_fd.html
+++ b/docs/reference/is_fd.html
@@ -1,7 +1,5 @@
-Check if the chemical shift dimension of an MRS data object is in the
-frequency domain. — is_fd • Spectroscopy Analysis Tools (spant) Check if the chemical shift dimension of an MRS data object is in the frequency domain. — is_fd • Spectroscopy Analysis Tools (spant) Transform 2D MRSI data from k-space to image space in the x-y direction. — kspace2img_xy • Spectroscopy Analysis Tools (spant) Transform 2D MRSI data from k-space to image space in the x-y direction. — kspace2img_xy • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/l2_reg.html b/docs/reference/l2_reg.html
index 3d781d80..21aa9849 100644
--- a/docs/reference/l2_reg.html
+++ b/docs/reference/l2_reg.html
@@ -1,5 +1,5 @@
-Perform l2 regularisation artefact suppression. — l2_reg • Spectroscopy Analysis Tools (spant) Perform l2 regularisation artefact suppression. — l2_reg • Spectroscopy Analysis Tools (spant) Apply line-broadening (apodisation) to MRS data or basis object. — lb • Spectroscopy Analysis Tools (spant) Apply line-broadening (apodisation) to MRS data or basis object. — lb • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -123,7 +123,7 @@ Value
diff --git a/docs/reference/lofdc.html b/docs/reference/lofdc.html
index 5419b1ec..31347a25 100644
--- a/docs/reference/lofdc.html
+++ b/docs/reference/lofdc.html
@@ -1,5 +1,5 @@
-Correct linear frequency drift. — lofdc • Spectroscopy Analysis Tools (spant) Correct linear frequency drift. — lofdc • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -138,7 +138,7 @@ Value
diff --git a/docs/reference/lw2alpha.html b/docs/reference/lw2alpha.html
index b83db682..25da229b 100644
--- a/docs/reference/lw2alpha.html
+++ b/docs/reference/lw2alpha.html
@@ -1,7 +1,5 @@
-Covert a linewidth in Hz to an equivalent alpha value in the time-domain ie:
-x * exp(-t * alpha). — lw2alpha • Spectroscopy Analysis Tools (spant) Covert a linewidth in Hz to an equivalent alpha value in the time-domain ie: x * exp(-t * alpha). — lw2alpha • Spectroscopy Analysis Tools (spant) Covert a linewidth in Hz to an equivalent beta value in the time-domain ie:
-x * exp(-t * t * beta). — lw2beta • Spectroscopy Analysis Tools (spant) Covert a linewidth in Hz to an equivalent beta value in the time-domain ie: x * exp(-t * t * beta). — lw2beta • Spectroscopy Analysis Tools (spant) Make a basis-set object from a directory containing LCModel formatted RAW
-files. — make_basis_from_raw • Spectroscopy Analysis Tools (spant) Make a basis-set object from a directory containing LCModel formatted RAW files. — make_basis_from_raw • Spectroscopy Analysis Tools (spant) Mask an MRS dataset in the dynamic dimension. — mask_dyns • Spectroscopy Analysis Tools (spant) Mask an MRS dataset in the dynamic dimension. — mask_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/mask_fit_res.html b/docs/reference/mask_fit_res.html
index 97baaa3f..ebd91a99 100644
--- a/docs/reference/mask_fit_res.html
+++ b/docs/reference/mask_fit_res.html
@@ -1,5 +1,5 @@
-Mask fit result spectra depending on a vector of bool values. — mask_fit_res • Spectroscopy Analysis Tools (spant) Mask fit result spectra depending on a vector of bool values. — mask_fit_res • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -116,7 +116,7 @@ Value
diff --git a/docs/reference/mask_xy.html b/docs/reference/mask_xy.html
index 11bb577c..b0d38619 100644
--- a/docs/reference/mask_xy.html
+++ b/docs/reference/mask_xy.html
@@ -1,5 +1,5 @@
-Mask an MRSI dataset in the x-y direction — mask_xy • Spectroscopy Analysis Tools (spant) Mask an MRSI dataset in the x-y direction — mask_xy • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/mask_xy_corners.html b/docs/reference/mask_xy_corners.html
index 09b16cd2..2d13839d 100644
--- a/docs/reference/mask_xy_corners.html
+++ b/docs/reference/mask_xy_corners.html
@@ -1,5 +1,5 @@
-Mask the four corners of an MRSI dataset in the x-y plane. — mask_xy_corners • Spectroscopy Analysis Tools (spant) Mask the four corners of an MRSI dataset in the x-y plane. — mask_xy_corners • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/mask_xy_ellipse.html b/docs/reference/mask_xy_ellipse.html
index 1d8b02e4..e2e749ef 100644
--- a/docs/reference/mask_xy_ellipse.html
+++ b/docs/reference/mask_xy_ellipse.html
@@ -1,7 +1,5 @@
-Mask the voxels outside an elliptical region spanning the MRSI dataset in the
-x-y plane. — mask_xy_ellipse • Spectroscopy Analysis Tools (spant) Mask the voxels outside an elliptical region spanning the MRSI dataset in the x-y plane. — mask_xy_ellipse • Spectroscopy Analysis Tools (spant) Mask a 2D MRSI dataset in the x-y dimension. — mask_xy_mat • Spectroscopy Analysis Tools (spant) Mask a 2D MRSI dataset in the x-y dimension. — mask_xy_mat • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Value
diff --git a/docs/reference/mat2mrs_data.html b/docs/reference/mat2mrs_data.html
index 2e2895f3..ae55665f 100644
--- a/docs/reference/mat2mrs_data.html
+++ b/docs/reference/mat2mrs_data.html
@@ -1,7 +1,5 @@
-Convert a matrix (with spectral points in the column dimension and dynamics
-in the row dimensions) into a mrs_data object. — mat2mrs_data • Spectroscopy Analysis Tools (spant) Convert a matrix (with spectral points in the column dimension and dynamics in the row dimensions) into a mrs_data object. — mat2mrs_data • Spectroscopy Analysis Tools (spant) Matrix exponential function taken from complexplus package to reduce the
-number of spant dependencies. — matexp • Spectroscopy Analysis Tools (spant) Matrix exponential function taken from complexplus package to reduce the number of spant dependencies. — matexp • Spectroscopy Analysis Tools (spant) Apply the max operator to an MRS dataset. — max_mrs • Spectroscopy Analysis Tools (spant) Apply the max operator to an MRS dataset. — max_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/max_mrs_interp.html b/docs/reference/max_mrs_interp.html
index e4474764..52e63f3e 100644
--- a/docs/reference/max_mrs_interp.html
+++ b/docs/reference/max_mrs_interp.html
@@ -1,5 +1,5 @@
-Apply the max operator to an interpolated MRS dataset. — max_mrs_interp • Spectroscopy Analysis Tools (spant) Apply the max operator to an interpolated MRS dataset. — max_mrs_interp • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/mean.list.html b/docs/reference/mean.list.html
index b8eb3463..048306fd 100644
--- a/docs/reference/mean.list.html
+++ b/docs/reference/mean.list.html
@@ -1,5 +1,5 @@
-Calculate the mean spectrum from an mrs_data object. — mean.list • Spectroscopy Analysis Tools (spant) Calculate the mean spectrum from an mrs_data object. — mean.list • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/mean.mrs_data.html b/docs/reference/mean.mrs_data.html
index 5531a28d..79515014 100644
--- a/docs/reference/mean.mrs_data.html
+++ b/docs/reference/mean.mrs_data.html
@@ -1,5 +1,5 @@
-Calculate the mean spectrum from an mrs_data object. — mean.mrs_data • Spectroscopy Analysis Tools (spant) Calculate the mean spectrum from an mrs_data object. — mean.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/mean_dyn_blocks.html b/docs/reference/mean_dyn_blocks.html
index 10467098..4c042448 100644
--- a/docs/reference/mean_dyn_blocks.html
+++ b/docs/reference/mean_dyn_blocks.html
@@ -1,5 +1,5 @@
-Calculate the mean of adjacent dynamic scans. — mean_dyn_blocks • Spectroscopy Analysis Tools (spant) Calculate the mean of adjacent dynamic scans. — mean_dyn_blocks • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/mean_dyn_pairs.html b/docs/reference/mean_dyn_pairs.html
index 63e909ea..1a241126 100644
--- a/docs/reference/mean_dyn_pairs.html
+++ b/docs/reference/mean_dyn_pairs.html
@@ -1,5 +1,5 @@
-Calculate the pairwise means across a dynamic data set. — mean_dyn_pairs • Spectroscopy Analysis Tools (spant) Calculate the pairwise means across a dynamic data set. — mean_dyn_pairs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/mean_dyns.html b/docs/reference/mean_dyns.html
index 73fdbfa7..0daa27df 100644
--- a/docs/reference/mean_dyns.html
+++ b/docs/reference/mean_dyns.html
@@ -1,5 +1,5 @@
-Calculate the mean dynamic data. — mean_dyns • Spectroscopy Analysis Tools (spant) Calculate the mean dynamic data. — mean_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/mean_mrs_list.html b/docs/reference/mean_mrs_list.html
index 808b6c50..10d842c0 100644
--- a/docs/reference/mean_mrs_list.html
+++ b/docs/reference/mean_mrs_list.html
@@ -1,5 +1,5 @@
-Return the mean of a list of mrs_data objects. — mean_mrs_list • Spectroscopy Analysis Tools (spant) Return the mean of a list of mrs_data objects. — mean_mrs_list • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/mean_vec_blocks.html b/docs/reference/mean_vec_blocks.html
index 8fc92eaa..dd78b122 100644
--- a/docs/reference/mean_vec_blocks.html
+++ b/docs/reference/mean_vec_blocks.html
@@ -1,5 +1,5 @@
-Calculate the mean of adjacent blocks in a vector. — mean_vec_blocks • Spectroscopy Analysis Tools (spant) Calculate the mean of adjacent blocks in a vector. — mean_vec_blocks • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/median_dyns.html b/docs/reference/median_dyns.html
index 1039d4b5..9a085b10 100644
--- a/docs/reference/median_dyns.html
+++ b/docs/reference/median_dyns.html
@@ -1,5 +1,5 @@
-Calculate the median dynamic data. — median_dyns • Spectroscopy Analysis Tools (spant) Calculate the median dynamic data. — median_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/mod_td.html b/docs/reference/mod_td.html
index 76ad0a40..141ef09e 100644
--- a/docs/reference/mod_td.html
+++ b/docs/reference/mod_td.html
@@ -1,5 +1,5 @@
-Apply the Modulus operator to the time-domain MRS signal. — mod_td • Spectroscopy Analysis Tools (spant) Apply the Modulus operator to the time-domain MRS signal. — mod_td • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/mrs_data2basis.html b/docs/reference/mrs_data2basis.html
index 62f7d749..11797b91 100644
--- a/docs/reference/mrs_data2basis.html
+++ b/docs/reference/mrs_data2basis.html
@@ -1,7 +1,5 @@
-Convert an mrs_data object to basis object - where basis signals are spread
-across the dynamic dimension in the MRS data. — mrs_data2basis • Spectroscopy Analysis Tools (spant) Convert an mrs_data object to basis object - where basis signals are spread across the dynamic dimension in the MRS data. — mrs_data2basis • Spectroscopy Analysis Tools (spant) Create a BIDS file structure from a vector of MRS data paths or list of mrs_data objects. — mrs_data2bids • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Create a BIDS file structure from a vector of MRS data paths or list of mrs_data objects.
+ Source: R/fmrs.R
+ mrs_data2bids.Rd
+
+
+
+ Create a BIDS file structure from a vector of MRS data paths or list of
+mrs_data objects.
+
+
+
+ mrs_data2bids(
+ mrs_data,
+ output_dir,
+ suffix = NULL,
+ sub = NULL,
+ ses = NULL,
+ task = NULL,
+ acq = NULL,
+ nuc = NULL,
+ voi = NULL,
+ rec = NULL,
+ run = NULL,
+ echo = NULL,
+ inv = NULL,
+ skip_existing = TRUE
+)
+
+
+
+ Arguments
+ - mrs_data
+vector of MRS data paths or list of mrs_data objects.
- output_dir
+the base directory to create the BIDS structure.
- suffix
+optional vector of file suffixes. Default behaviour is to
+automatically determine these from the input data, however it is recommended
+that they are specified to allow more efficient skipping of existing data.
- sub
+optional vector of subject labels. If not specified, these will be
+automatically generated as a series of increasing zero-padded integer values
+corresponding to the mrs_data input indices.
- ses
+optional vector of session labels.
- task
+optional vector of task labels.
- acq
+optional vector of acquisition labels.
- nuc
+optional vector of nucleus labels.
- voi
+optional vector of volume of interest labels.
- rec
+optional vector of reconstruction labels.
- run
+optional vector of run indices.
- echo
+optional vector of echo time indices.
- inv
+optional vector of inversion indices.
- skip_existing
+skip any data files that have already been converted.
+Defaults to TRUE, set to FALSE to force an overwrite of any existing data
+files.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/mrs_data2mat.html b/docs/reference/mrs_data2mat.html
index cf5ff28c..9e47688a 100644
--- a/docs/reference/mrs_data2mat.html
+++ b/docs/reference/mrs_data2mat.html
@@ -1,7 +1,5 @@
-Convert mrs_data object to a matrix, with spectral points in the column
-dimension and dynamics in the row dimension. — mrs_data2mat • Spectroscopy Analysis Tools (spant) Convert mrs_data object to a matrix, with spectral points in the column dimension and dynamics in the row dimension. — mrs_data2mat • Spectroscopy Analysis Tools (spant) Convert mrs_data object to a matrix, with spectral points in the column dimension and dynamics in the row dimension. — mrs_data2spec_mat • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Convert mrs_data object to a matrix, with spectral points in the column dimension and dynamics in the row dimension.
+ Source: R/mrs_data_proc.R
+ mrs_data2spec_mat.Rd
+
+
+
+ Convert mrs_data object to a matrix, with spectral points in the column
+dimension and dynamics in the row dimension.
+
+
+
+ mrs_data2spec_mat(mrs_data, collapse = TRUE)
+
+
+
+ Arguments
+ - mrs_data
+MRS data object or list of MRS data objects.
- collapse
+collapse all other dimensions along the dynamic dimension, eg
+a 16x16 MRSI grid would be first collapsed across 256 dynamic scans.
+
+ Value
+
+
+MRS data matrix.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/mrs_data2vec.html b/docs/reference/mrs_data2vec.html
index fb172d68..a1fd654d 100644
--- a/docs/reference/mrs_data2vec.html
+++ b/docs/reference/mrs_data2vec.html
@@ -1,5 +1,5 @@
-Convert mrs_data object to a vector. — mrs_data2vec • Spectroscopy Analysis Tools (spant) Convert mrs_data object to a vector. — mrs_data2vec • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -126,7 +126,7 @@ Value
diff --git a/docs/reference/mvfftshift.html b/docs/reference/mvfftshift.html
index 92b0841b..976b3410 100644
--- a/docs/reference/mvfftshift.html
+++ b/docs/reference/mvfftshift.html
@@ -1,7 +1,5 @@
-Perform a fftshift on a matrix, with each column replaced by its shifted
-result. — mvfftshift • Spectroscopy Analysis Tools (spant) Perform a fftshift on a matrix, with each column replaced by its shifted result. — mvfftshift • Spectroscopy Analysis Tools (spant) Perform an ifftshift on a matrix, with each column replaced by its shifted
-result. — mvifftshift • Spectroscopy Analysis Tools (spant) Perform an ifftshift on a matrix, with each column replaced by its shifted result. — mvifftshift • Spectroscopy Analysis Tools (spant) Print fit coordinates from a single index. — n2coord • Spectroscopy Analysis Tools (spant) Print fit coordinates from a single index. — n2coord • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/nifti_flip_lr.html b/docs/reference/nifti_flip_lr.html
index 730abe3c..19860b3c 100644
--- a/docs/reference/nifti_flip_lr.html
+++ b/docs/reference/nifti_flip_lr.html
@@ -1,9 +1,5 @@
-Flip the x data dimension order of a nifti image. This corresponds to
-flipping MRI data in the left-right direction, assuming the data in save in
-neurological format (can check with fslorient program). — nifti_flip_lr • Spectroscopy Analysis Tools (spant) Flip the x data dimension order of a nifti image. This corresponds to flipping MRI data in the left-right direction, assuming the data in save in neurological format (can check with fslorient program). — nifti_flip_lr • Spectroscopy Analysis Tools (spant) Export a one-page pdf of a single fit result — one_page_pdf • Spectroscopy Analysis Tools (spant) Export a one-page pdf of a single fit result — one_page_pdf • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -108,7 +108,7 @@ Arguments
diff --git a/docs/reference/ortho3.html b/docs/reference/ortho3.html
index 13ade97d..5d7dd2fd 100644
--- a/docs/reference/ortho3.html
+++ b/docs/reference/ortho3.html
@@ -1,5 +1,5 @@
-Display an orthographic projection plot of a nifti object. — ortho3 • Spectroscopy Analysis Tools (spant) Display an orthographic projection plot of a nifti object. — ortho3 • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -172,7 +172,7 @@ Arguments
diff --git a/docs/reference/ortho3_inter.html b/docs/reference/ortho3_inter.html
index 090cc5e5..15948899 100644
--- a/docs/reference/ortho3_inter.html
+++ b/docs/reference/ortho3_inter.html
@@ -1,5 +1,5 @@
-Display an interactive orthographic projection plot of a nifti object. — ortho3_inter • Spectroscopy Analysis Tools (spant) Display an interactive orthographic projection plot of a nifti object. — ortho3_inter • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -132,7 +132,7 @@ Arguments
diff --git a/docs/reference/peak_info.html b/docs/reference/peak_info.html
index 09058bd8..41c8ffaf 100644
--- a/docs/reference/peak_info.html
+++ b/docs/reference/peak_info.html
@@ -1,7 +1,5 @@
-Search for the highest peak in a spectral region and return the frequency,
-height and FWHM. — peak_info • Spectroscopy Analysis Tools (spant) Search for the highest peak in a spectral region and return the frequency, height and FWHM. — peak_info • Spectroscopy Analysis Tools (spant) Papoulis-Gerchberg (PG) algorithm method for k-space extrapolation. — pg_extrap_xy • Spectroscopy Analysis Tools (spant) Papoulis-Gerchberg (PG) algorithm method for k-space extrapolation. — pg_extrap_xy • Spectroscopy Analysis Tools (spant) Apply phasing parameters to MRS data. — phase • Spectroscopy Analysis Tools (spant) Apply phasing parameters to MRS data. — phase • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/phase_ref_1h_brain.html b/docs/reference/phase_ref_1h_brain.html
new file mode 100644
index 00000000..8707a74a
--- /dev/null
+++ b/docs/reference/phase_ref_1h_brain.html
@@ -0,0 +1,131 @@
+
+Corrected zero order phase and chemical shift offset in 1H MRS data from the brain. — phase_ref_1h_brain • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Corrected zero order phase and chemical shift offset in 1H MRS data from the brain.
+ Source: R/rats.R
+ phase_ref_1h_brain.Rd
+
+
+
+ Corrected zero order phase and chemical shift offset in 1H MRS data from the
+brain.
+
+
+
+ phase_ref_1h_brain(mrs_data, mean_ref = FALSE, ret_corr_only = TRUE)
+
+
+
+ Arguments
+ - mrs_data
+MRS data to be corrected.
- mean_ref
+apply the phase and offset of the mean spectrum to all
+others. Default is FALSE.
- ret_corr_only
+return the corrected data only.
+
+ Value
+
+
+corrected MRS data.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/plot.fit_result.html b/docs/reference/plot.fit_result.html
index e54d3bc1..836a53ee 100644
--- a/docs/reference/plot.fit_result.html
+++ b/docs/reference/plot.fit_result.html
@@ -1,5 +1,5 @@
-Plot the fitting results of an object of class fit_result. — plot.fit_result • Spectroscopy Analysis Tools (spant) Plot the fitting results of an object of class fit_result. — plot.fit_result • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -207,7 +207,7 @@ Arguments
diff --git a/docs/reference/plot.mrs_data.html b/docs/reference/plot.mrs_data.html
index fabcc35b..bb2ec651 100644
--- a/docs/reference/plot.mrs_data.html
+++ b/docs/reference/plot.mrs_data.html
@@ -1,5 +1,5 @@
-Plotting method for objects of class mrs_data. — plot.mrs_data • Spectroscopy Analysis Tools (spant) Plotting method for objects of class mrs_data. — plot.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -287,7 +287,7 @@ Arguments
diff --git a/docs/reference/plot_bc.html b/docs/reference/plot_bc.html
index 4f8309b4..b48142cc 100644
--- a/docs/reference/plot_bc.html
+++ b/docs/reference/plot_bc.html
@@ -1,5 +1,5 @@
-Convenience function to plot a baseline estimate with the original data. — plot_bc • Spectroscopy Analysis Tools (spant) Convenience function to plot a baseline estimate with the original data. — plot_bc • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -108,7 +108,7 @@ Arguments
diff --git a/docs/reference/plot_reg.html b/docs/reference/plot_reg.html
index ae1acbe7..2addb2f6 100644
--- a/docs/reference/plot_reg.html
+++ b/docs/reference/plot_reg.html
@@ -1,5 +1,5 @@
-Plot regressors as an image. — plot_reg • Spectroscopy Analysis Tools (spant) Plot regressors as an image. — plot_reg • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/plot_slice_fit.html b/docs/reference/plot_slice_fit.html
index fbc7b560..57f1af8a 100644
--- a/docs/reference/plot_slice_fit.html
+++ b/docs/reference/plot_slice_fit.html
@@ -1,5 +1,5 @@
-Plot a 2D slice from an MRSI fit result object. — plot_slice_fit • Spectroscopy Analysis Tools (spant) Plot a 2D slice from an MRSI fit result object. — plot_slice_fit • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -129,7 +129,7 @@ Arguments
diff --git a/docs/reference/plot_slice_fit_inter.html b/docs/reference/plot_slice_fit_inter.html
index 4eed104a..da105a7d 100644
--- a/docs/reference/plot_slice_fit_inter.html
+++ b/docs/reference/plot_slice_fit_inter.html
@@ -1,5 +1,5 @@
-Plot a 2D slice from an MRSI fit result object. — plot_slice_fit_inter • Spectroscopy Analysis Tools (spant) Plot a 2D slice from an MRSI fit result object. — plot_slice_fit_inter • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -134,7 +134,7 @@ Arguments
diff --git a/docs/reference/plot_slice_map.html b/docs/reference/plot_slice_map.html
index 553e9ac8..ffb2a134 100644
--- a/docs/reference/plot_slice_map.html
+++ b/docs/reference/plot_slice_map.html
@@ -1,5 +1,5 @@
-Plot a slice from a 7 dimensional array. — plot_slice_map • Spectroscopy Analysis Tools (spant) Plot a slice from a 7 dimensional array. — plot_slice_map • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -153,7 +153,7 @@ Arguments
diff --git a/docs/reference/plot_slice_map_inter.html b/docs/reference/plot_slice_map_inter.html
index 40d33b42..90968f66 100644
--- a/docs/reference/plot_slice_map_inter.html
+++ b/docs/reference/plot_slice_map_inter.html
@@ -1,7 +1,5 @@
-Plot an interactive slice map from a data array where voxels can be selected
-to display a corresponding spectrum. — plot_slice_map_inter • Spectroscopy Analysis Tools (spant) Plot an interactive slice map from a data array where voxels can be selected to display a corresponding spectrum. — plot_slice_map_inter • Spectroscopy Analysis Tools (spant) Plot the spectral standard deviation. — plot_spec_sd • Spectroscopy Analysis Tools (spant) Plot the spectral standard deviation. — plot_spec_sd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Arguments
diff --git a/docs/reference/plot_voi_overlay.html b/docs/reference/plot_voi_overlay.html
index 9a782e88..bbbbf35e 100644
--- a/docs/reference/plot_voi_overlay.html
+++ b/docs/reference/plot_voi_overlay.html
@@ -1,5 +1,5 @@
-Plot a volume as an image overlay. — plot_voi_overlay • Spectroscopy Analysis Tools (spant) Plot a volume as an image overlay. — plot_voi_overlay • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -116,7 +116,7 @@ Arguments
diff --git a/docs/reference/plot_voi_overlay_seg.html b/docs/reference/plot_voi_overlay_seg.html
index 3d4e74ff..0e800ff2 100644
--- a/docs/reference/plot_voi_overlay_seg.html
+++ b/docs/reference/plot_voi_overlay_seg.html
@@ -1,5 +1,5 @@
-Plot a volume as an overlay on a segmented brain volume. — plot_voi_overlay_seg • Spectroscopy Analysis Tools (spant) Plot a volume as an overlay on a segmented brain volume. — plot_voi_overlay_seg • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Arguments
diff --git a/docs/reference/ppm.html b/docs/reference/ppm.html
index c352327a..ee4696e2 100644
--- a/docs/reference/ppm.html
+++ b/docs/reference/ppm.html
@@ -1,5 +1,5 @@
-Return the ppm scale of an MRS dataset or fit result. — ppm • Spectroscopy Analysis Tools (spant) Return the ppm scale of an MRS dataset or fit result. — ppm • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -132,7 +132,7 @@ Value
diff --git a/docs/reference/precomp.html b/docs/reference/precomp.html
index 822d7336..df3d2c6c 100644
--- a/docs/reference/precomp.html
+++ b/docs/reference/precomp.html
@@ -1,7 +1,5 @@
-Save function results to file and load on subsequent calls to avoid repeat
-computation. — precomp • Spectroscopy Analysis Tools (spant) Save function results to file and load on subsequent calls to avoid repeat computation. — precomp • Spectroscopy Analysis Tools (spant) Preprocess and perform quality assessment of a single SVS data set. — preproc_svs • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Preprocess and perform quality assessment of a single SVS data set.
+ Source: R/fmrs.R
+ preproc_svs.Rd
+
+
+
+ Preprocess and perform quality assessment of a single SVS data set.
+
+
+
+ preproc_svs(path, label = NULL, output_dir = NULL, ref_inds = NULL)
+
+
+
+ Arguments
+ - path
+path to the fMRS data file or IMA directory.
- label
+a label to describe the data set.
- output_dir
+output directory.
- ref_inds
+a vector of 1-based indices for any water reference dynamic
+scans.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/preproc_svs_dataset.html b/docs/reference/preproc_svs_dataset.html
new file mode 100644
index 00000000..07c3a29b
--- /dev/null
+++ b/docs/reference/preproc_svs_dataset.html
@@ -0,0 +1,148 @@
+
+Preprocess and perform quality assessment of one or more SVS data sets. — preproc_svs_dataset • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Preprocess and perform quality assessment of one or more SVS data sets.
+ Source: R/fmrs.R
+ preproc_svs_dataset.Rd
+
+
+
+ Preprocess and perform quality assessment of one or more SVS data sets.
+
+
+
+ preproc_svs_dataset(
+ paths,
+ labels = NULL,
+ output_dir = "spant_analysis",
+ exclude_labels = NULL,
+ overwrite = FALSE,
+ ref_inds = NULL,
+ return_results = FALSE
+)
+
+
+
+ Arguments
+ - paths
+paths to the fMRS data file or IMA directory.
- labels
+labels to describe each data set.
- output_dir
+output directory.
- exclude_labels
+vector of labels of scans to exclude, eg poor quality
+data.
- overwrite
+overwrite saved results, defaults to FALSE.
- ref_inds
+a vector of 1-based indices for any water reference dynamic
+scans.
- return_results
+function will return key outputs, defaults to FALSE.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/print.fit_result.html b/docs/reference/print.fit_result.html
index 297f28dc..5f434e57 100644
--- a/docs/reference/print.fit_result.html
+++ b/docs/reference/print.fit_result.html
@@ -1,5 +1,5 @@
-Print a summary of an object of class fit_result. — print.fit_result • Spectroscopy Analysis Tools (spant) Print a summary of an object of class fit_result. — print.fit_result • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -105,7 +105,7 @@ Arguments
diff --git a/docs/reference/print.mrs_data.html b/docs/reference/print.mrs_data.html
index 51199017..e1561eb2 100644
--- a/docs/reference/print.mrs_data.html
+++ b/docs/reference/print.mrs_data.html
@@ -1,5 +1,5 @@
-Print a summary of mrs_data parameters. — print.mrs_data • Spectroscopy Analysis Tools (spant) Print a summary of mrs_data parameters. — print.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -109,7 +109,7 @@ Arguments
diff --git a/docs/reference/qn_states.html b/docs/reference/qn_states.html
index 0f42f2f9..d7aa6715 100644
--- a/docs/reference/qn_states.html
+++ b/docs/reference/qn_states.html
@@ -1,5 +1,5 @@
-Get the quantum coherence matrix for a spin system. — qn_states • Spectroscopy Analysis Tools (spant) Get the quantum coherence matrix for a spin system. — qn_states • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/rats.html b/docs/reference/rats.html
index 5a39a396..93585e08 100644
--- a/docs/reference/rats.html
+++ b/docs/reference/rats.html
@@ -1,5 +1,5 @@
-Robust Alignment to a Target Spectrum (RATS). — rats • Spectroscopy Analysis Tools (spant) Robust Alignment to a Target Spectrum (RATS). — rats • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -207,7 +207,7 @@ Value
diff --git a/docs/reference/re_weighting.html b/docs/reference/re_weighting.html
index d21caf21..8b0b070a 100644
--- a/docs/reference/re_weighting.html
+++ b/docs/reference/re_weighting.html
@@ -1,5 +1,5 @@
-Apply a weighting to the FID to enhance spectral resolution. — re_weighting • Spectroscopy Analysis Tools (spant) Apply a weighting to the FID to enhance spectral resolution. — re_weighting • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/read_basis.html b/docs/reference/read_basis.html
index da9b94af..eb6f8557 100644
--- a/docs/reference/read_basis.html
+++ b/docs/reference/read_basis.html
@@ -1,5 +1,5 @@
-Read a basis file in LCModel .basis format. — read_basis • Spectroscopy Analysis Tools (spant) Read a basis file in LCModel .basis format. — read_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/read_ima_coil_dir.html b/docs/reference/read_ima_coil_dir.html
index 28c02de0..4f073cd8 100644
--- a/docs/reference/read_ima_coil_dir.html
+++ b/docs/reference/read_ima_coil_dir.html
@@ -1,9 +1,5 @@
-Read a directory containing Siemens MRS IMA files and combine along the coil
-dimension. Note that the coil ID is inferred from the sorted file name and
-should be checked when consistency is required between two directories. — read_ima_coil_dir • Spectroscopy Analysis Tools (spant) Read a directory containing Siemens MRS IMA files and combine along the coil dimension. Note that the coil ID is inferred from the sorted file name and should be checked when consistency is required between two directories. — read_ima_coil_dir • Spectroscopy Analysis Tools (spant) Read a directory containing Siemens MRS IMA files and combine along the
-dynamic dimension. Note that the coil ID is inferred from the sorted file
-name and should be checked when consistency is required. — read_ima_dyn_dir • Spectroscopy Analysis Tools (spant) Read a directory containing Siemens MRS IMA files and combine along the dynamic dimension. Note that the coil ID is inferred from the sorted file name and should be checked when consistency is required. — read_ima_dyn_dir • Spectroscopy Analysis Tools (spant) Read an LCModel formatted coord file containing fit information. — read_lcm_coord • Spectroscopy Analysis Tools (spant) Read an LCModel formatted coord file containing fit information. — read_lcm_coord • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -107,7 +107,7 @@ Value
diff --git a/docs/reference/read_mrs.html b/docs/reference/read_mrs.html
index 3ac2a36b..2cf36b20 100644
--- a/docs/reference/read_mrs.html
+++ b/docs/reference/read_mrs.html
@@ -1,5 +1,5 @@
-Read MRS data from a file. — read_mrs • Spectroscopy Analysis Tools (spant) Read MRS data from a file. — read_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -88,7 +88,8 @@ Read MRS data from a file.
full_fid = FALSE,
omit_svs_ref_scans = TRUE,
verbose = FALSE,
- extra = NULL
+ extra = NULL,
+ fid_filt_dist = NULL
)
@@ -140,6 +141,13 @@ Arguments
an optional data frame to provide additional variables for use
in subsequent analysis steps, eg id or grouping variables.
fid_filt_dist
+indicate if the data has a distorted FID due to a
+brick-wall filter being used to downsample the data. Default is to auto
+detect this from the data, but TRUE or FALSE options can be given to override
+detection.
Value
@@ -183,7 +191,7 @@ Examples
diff --git a/docs/reference/read_mrs_tqn.html b/docs/reference/read_mrs_tqn.html
index 5766362f..84bdaf3a 100644
--- a/docs/reference/read_mrs_tqn.html
+++ b/docs/reference/read_mrs_tqn.html
@@ -1,5 +1,5 @@
-Read MRS data using the TARQUIN software package. — read_mrs_tqn • Spectroscopy Analysis Tools (spant) Read MRS data using the TARQUIN software package. — read_mrs_tqn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -131,7 +131,7 @@ Examples
diff --git a/docs/reference/read_pulse_ascii.html b/docs/reference/read_pulse_ascii.html
index c9e0d43c..ab11c9cc 100644
--- a/docs/reference/read_pulse_ascii.html
+++ b/docs/reference/read_pulse_ascii.html
@@ -1,5 +1,5 @@
-Read an ASCII formatted pulse file. — read_pulse_ascii • Spectroscopy Analysis Tools (spant) Read an ASCII formatted pulse file. — read_pulse_ascii • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/read_pulse_bruker.html b/docs/reference/read_pulse_bruker.html
index c92bf76a..dbe9073b 100644
--- a/docs/reference/read_pulse_bruker.html
+++ b/docs/reference/read_pulse_bruker.html
@@ -1,5 +1,5 @@
-Read a Bruker formatted pulse file — read_pulse_bruker • Spectroscopy Analysis Tools (spant) Read a Bruker formatted pulse file — read_pulse_bruker • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/read_pulse_pta.html b/docs/reference/read_pulse_pta.html
index 72e1b6d4..a0fac3c3 100644
--- a/docs/reference/read_pulse_pta.html
+++ b/docs/reference/read_pulse_pta.html
@@ -1,5 +1,5 @@
-Read a .pta formatted pulse file compatible with Siemens PulseTool. — read_pulse_pta • Spectroscopy Analysis Tools (spant) Read a .pta formatted pulse file compatible with Siemens PulseTool. — read_pulse_pta • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/read_siemens_txt_hdr.html b/docs/reference/read_siemens_txt_hdr.html
index 23fb8c70..3a17d87c 100644
--- a/docs/reference/read_siemens_txt_hdr.html
+++ b/docs/reference/read_siemens_txt_hdr.html
@@ -1,5 +1,5 @@
-Read the text format header found in Siemens IMA and TWIX data files. — read_siemens_txt_hdr • Spectroscopy Analysis Tools (spant) Read the text format header found in Siemens IMA and TWIX data files. — read_siemens_txt_hdr • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -78,7 +78,7 @@ Read the text format header found in Siemens IMA and TWIX data files.
- read_siemens_txt_hdr(input, version = "vd", verbose, offset = 0)
+ read_siemens_txt_hdr(input, version = "vd", verbose = FALSE, offset = 0)
@@ -118,7 +118,7 @@ Value
diff --git a/docs/reference/read_tqn_fit.html b/docs/reference/read_tqn_fit.html
index 4da6c25e..a1630420 100644
--- a/docs/reference/read_tqn_fit.html
+++ b/docs/reference/read_tqn_fit.html
@@ -1,5 +1,5 @@
-Reader for csv fit results generated by TARQUIN. — read_tqn_fit • Spectroscopy Analysis Tools (spant) Reader for csv fit results generated by TARQUIN. — read_tqn_fit • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -113,7 +113,7 @@ Examples
diff --git a/docs/reference/read_tqn_result.html b/docs/reference/read_tqn_result.html
index 36659714..68a3e98c 100644
--- a/docs/reference/read_tqn_result.html
+++ b/docs/reference/read_tqn_result.html
@@ -1,5 +1,5 @@
-Reader for csv results generated by TARQUIN. — read_tqn_result • Spectroscopy Analysis Tools (spant) Reader for csv results generated by TARQUIN. — read_tqn_result • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -117,7 +117,7 @@ Examples
diff --git a/docs/reference/recon_imag.html b/docs/reference/recon_imag.html
index d2a72225..5bc3b1eb 100644
--- a/docs/reference/recon_imag.html
+++ b/docs/reference/recon_imag.html
@@ -1,7 +1,5 @@
-Reconstruct complex time-domain data from the real part of frequency-domain
-data. — recon_imag • Spectroscopy Analysis Tools (spant) Reconstruct complex time-domain data from the real part of frequency-domain data. — recon_imag • Spectroscopy Analysis Tools (spant) Reconstruct complex time-domain data from the real part of frequency-domain
-data. — recon_imag_vec • Spectroscopy Analysis Tools (spant) Reconstruct complex time-domain data from the real part of frequency-domain data. — recon_imag_vec • Spectroscopy Analysis Tools (spant) Reconstruct 2D MRSI data from a twix file loaded with read_mrs. — recon_twix_2d_mrsi • Spectroscopy Analysis Tools (spant) Reconstruct 2D MRSI data from a twix file loaded with read_mrs. — recon_twix_2d_mrsi • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/rectangular_mask.html b/docs/reference/rectangular_mask.html
index a2117283..6e469bc9 100644
--- a/docs/reference/rectangular_mask.html
+++ b/docs/reference/rectangular_mask.html
@@ -1,5 +1,5 @@
-Create a rectangular mask stored as a matrix of logical values. — rectangular_mask • Spectroscopy Analysis Tools (spant) Create a rectangular mask stored as a matrix of logical values. — rectangular_mask • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -130,7 +130,7 @@ Value
diff --git a/docs/reference/reexports.html b/docs/reference/reexports.html
index 694a75d1..a59e8379 100644
--- a/docs/reference/reexports.html
+++ b/docs/reference/reexports.html
@@ -1,5 +1,5 @@
-Objects exported from other packages — reexports • Spectroscopy Analysis Tools (spant) Objects exported from other packages — reexports • Spectroscopy Analysis Tools (spant)
Spectroscopy Analysis Tools (spant)
- 2.21.0
+ 2.22.0
@@ -103,7 +103,7 @@ Objects exported from other packages
diff --git a/docs/reference/rep_array_dim.html b/docs/reference/rep_array_dim.html
index b9c49b4a..48c0a5ed 100644
--- a/docs/reference/rep_array_dim.html
+++ b/docs/reference/rep_array_dim.html
@@ -1,5 +1,5 @@
-Repeat an array over a given dimension. — rep_array_dim • Spectroscopy Analysis Tools (spant) Repeat an array over a given dimension. — rep_array_dim • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/rep_dyn.html b/docs/reference/rep_dyn.html
index 6bbfb0ef..89a4bb9b 100644
--- a/docs/reference/rep_dyn.html
+++ b/docs/reference/rep_dyn.html
@@ -1,5 +1,5 @@
-Replicate a scan in the dynamic dimension. — rep_dyn • Spectroscopy Analysis Tools (spant) Replicate a scan in the dynamic dimension. — rep_dyn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/rep_mrs.html b/docs/reference/rep_mrs.html
index 67730b5c..becb8f00 100644
--- a/docs/reference/rep_mrs.html
+++ b/docs/reference/rep_mrs.html
@@ -1,5 +1,5 @@
-Replicate a scan over a given dimension. — rep_mrs • Spectroscopy Analysis Tools (spant) Replicate a scan over a given dimension. — rep_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -138,7 +138,7 @@ Value
diff --git a/docs/reference/resample_basis.html b/docs/reference/resample_basis.html
index b0f2ab17..c7a6222a 100644
--- a/docs/reference/resample_basis.html
+++ b/docs/reference/resample_basis.html
@@ -1,5 +1,5 @@
-Resample a basis-set to match a mrs_data acquisition. — resample_basis • Spectroscopy Analysis Tools (spant) Resample a basis-set to match a mrs_data acquisition. — resample_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -116,7 +116,7 @@ Value
diff --git a/docs/reference/resample_img.html b/docs/reference/resample_img.html
index f1e7beaf..b0cc8f71 100644
--- a/docs/reference/resample_img.html
+++ b/docs/reference/resample_img.html
@@ -1,5 +1,5 @@
-Resample an image to match a target image space. — resample_img • Spectroscopy Analysis Tools (spant) Resample an image to match a target image space. — resample_img • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/resample_voi.html b/docs/reference/resample_voi.html
index 8fbfa836..a29ab096 100644
--- a/docs/reference/resample_voi.html
+++ b/docs/reference/resample_voi.html
@@ -1,7 +1,5 @@
-Resample a VOI to match a target image space using nearest-neighbour
-interpolation. — resample_voi • Spectroscopy Analysis Tools (spant) Resample a VOI to match a target image space using nearest-neighbour interpolation. — resample_voi • Spectroscopy Analysis Tools (spant) Reslice a nifti object to match the orientation of mrs data. — reslice_to_mrs • Spectroscopy Analysis Tools (spant) Reslice a nifti object to match the orientation of mrs data. — reslice_to_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/reson_table2mrs_data.html b/docs/reference/reson_table2mrs_data.html
index d75579ee..c5a2167a 100644
--- a/docs/reference/reson_table2mrs_data.html
+++ b/docs/reference/reson_table2mrs_data.html
@@ -1,5 +1,5 @@
-Generate mrs_data from a table of single Lorentzian resonances. — reson_table2mrs_data • Spectroscopy Analysis Tools (spant) Generate mrs_data from a table of single Lorentzian resonances. — reson_table2mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -119,7 +119,7 @@ Value
diff --git a/docs/reference/rm_dyns.html b/docs/reference/rm_dyns.html
index 5d5ef692..573e1f51 100644
--- a/docs/reference/rm_dyns.html
+++ b/docs/reference/rm_dyns.html
@@ -1,5 +1,5 @@
-Remove a subset of dynamic scans. — rm_dyns • Spectroscopy Analysis Tools (spant) Remove a subset of dynamic scans. — rm_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/scale_amp_molal.html b/docs/reference/scale_amp_molal.html
index aaeee1f2..7acb8cb0 100644
--- a/docs/reference/scale_amp_molal.html
+++ b/docs/reference/scale_amp_molal.html
@@ -1,7 +1,5 @@
-Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water). — scale_amp_molal • Spectroscopy Analysis Tools (spant) Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / kg of tissue water). — scale_amp_molal • Spectroscopy Analysis Tools (spant)
Spectroscopy Analysis Tools (spant)
- 2.21.0
+ 2.22.0
@@ -76,8 +74,7 @@
- Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water).
+ Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / kg of tissue water).
Source: R/amp_scaling.R
scale_amp_molal.Rd
@@ -163,7 +160,7 @@ Value
diff --git a/docs/reference/scale_amp_molal_pvc.html b/docs/reference/scale_amp_molal_pvc.html
index 962d6afc..4d194abd 100644
--- a/docs/reference/scale_amp_molal_pvc.html
+++ b/docs/reference/scale_amp_molal_pvc.html
@@ -1,7 +1,5 @@
-Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water). — scale_amp_molal_pvc • Spectroscopy Analysis Tools (spant)
@@ -75,8 +73,7 @@
- Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water).
+ Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / kg of tissue water).
Source: R/amp_scaling.R
scale_amp_molal_pvc.Rd
@@ -141,7 +138,7 @@ Value
diff --git a/docs/reference/scale_amp_molar.html b/docs/reference/scale_amp_molar.html
index 02358d91..dc87a338 100644
--- a/docs/reference/scale_amp_molar.html
+++ b/docs/reference/scale_amp_molar.html
@@ -1,7 +1,5 @@
-Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / Litre of tissue). — scale_amp_molar • Spectroscopy Analysis Tools (spant) Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / Litre of tissue). — scale_amp_molar • Spectroscopy Analysis Tools (spant) Convert default LCM/TARQUIN concentration scaling to molal units with partial
-volume correction. — scale_amp_molar2molal_pvc • Spectroscopy Analysis Tools (spant) Convert default LCM/TARQUIN concentration scaling to molal units with partial volume correction. — scale_amp_molar2molal_pvc • Spectroscopy Analysis Tools (spant) Scale fitted amplitudes to a ratio of signal amplitude. — scale_amp_ratio • Spectroscopy Analysis Tools (spant) Scale fitted amplitudes to a ratio of signal amplitude. — scale_amp_ratio • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -116,7 +116,7 @@ Value
diff --git a/docs/reference/scale_amp_ratio_value.html b/docs/reference/scale_amp_ratio_value.html
index 2036837a..6af8ac51 100644
--- a/docs/reference/scale_amp_ratio_value.html
+++ b/docs/reference/scale_amp_ratio_value.html
@@ -1,5 +1,5 @@
-Scale fitted amplitudes to a ratio of signal amplitude. — scale_amp_ratio_value • Spectroscopy Analysis Tools (spant) Scale fitted amplitudes to a ratio of signal amplitude. — scale_amp_ratio_value • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/scale_amp_water_ratio.html b/docs/reference/scale_amp_water_ratio.html
index 5b25e884..35a76b00 100644
--- a/docs/reference/scale_amp_water_ratio.html
+++ b/docs/reference/scale_amp_water_ratio.html
@@ -1,5 +1,5 @@
-Scale metabolite amplitudes as a ratio to the unsuppressed water amplitude. — scale_amp_water_ratio • Spectroscopy Analysis Tools (spant) Scale metabolite amplitudes as a ratio to the unsuppressed water amplitude. — scale_amp_water_ratio • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/scale_basis_amp.html b/docs/reference/scale_basis_amp.html
index 9401c3f1..5a58b5e5 100644
--- a/docs/reference/scale_basis_amp.html
+++ b/docs/reference/scale_basis_amp.html
@@ -1,5 +1,5 @@
-Scale a basis object by a scalar. — scale_basis_amp • Spectroscopy Analysis Tools (spant) Scale a basis object by a scalar. — scale_basis_amp • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/scale_basis_from_singlet.html b/docs/reference/scale_basis_from_singlet.html
index 0d542bc8..c9a19e77 100644
--- a/docs/reference/scale_basis_from_singlet.html
+++ b/docs/reference/scale_basis_from_singlet.html
@@ -1,5 +1,5 @@
-Scale a basis-set to be consistent with spant assumptions for water scaling. — scale_basis_from_singlet • Spectroscopy Analysis Tools (spant) Scale a basis-set to be consistent with spant assumptions for water scaling. — scale_basis_from_singlet • Spectroscopy Analysis Tools (spant)
Spectroscopy Analysis Tools (spant)
- 2.21.0
+ 2.22.0
@@ -127,7 +127,7 @@ Value
diff --git a/docs/reference/scale_mrs_amp.html b/docs/reference/scale_mrs_amp.html
index b5501a0d..990f058a 100644
--- a/docs/reference/scale_mrs_amp.html
+++ b/docs/reference/scale_mrs_amp.html
@@ -1,5 +1,5 @@
-Scale an mrs_data object by a scalar or vector or amplitudes. — scale_mrs_amp • Spectroscopy Analysis Tools (spant) Scale an mrs_data object by a scalar or vector or amplitudes. — scale_mrs_amp • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/scale_spec.html b/docs/reference/scale_spec.html
index 4f6ea835..6b3ddba4 100644
--- a/docs/reference/scale_spec.html
+++ b/docs/reference/scale_spec.html
@@ -1,5 +1,5 @@
-Scale mrs_data to a spectral region. — scale_spec • Spectroscopy Analysis Tools (spant) Scale mrs_data to a spectral region. — scale_spec • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -141,7 +141,7 @@ Value
diff --git a/docs/reference/sd.html b/docs/reference/sd.html
index ea1eec9f..3ae4dfd4 100644
--- a/docs/reference/sd.html
+++ b/docs/reference/sd.html
@@ -1,5 +1,5 @@
-Calculate the standard deviation spectrum from an mrs_data object. — sd • Spectroscopy Analysis Tools (spant) Calculate the standard deviation spectrum from an mrs_data object. — sd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/sd.mrs_data.html b/docs/reference/sd.mrs_data.html
index 3f92a49f..13bdda85 100644
--- a/docs/reference/sd.mrs_data.html
+++ b/docs/reference/sd.mrs_data.html
@@ -1,5 +1,5 @@
-Calculate the standard deviation spectrum from an mrs_data object. — sd.mrs_data • Spectroscopy Analysis Tools (spant) Calculate the standard deviation spectrum from an mrs_data object. — sd.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/seconds.html b/docs/reference/seconds.html
index b34d6627..467ee17f 100644
--- a/docs/reference/seconds.html
+++ b/docs/reference/seconds.html
@@ -1,5 +1,5 @@
-Return a time scale vector to match the FID of an MRS data object. — seconds • Spectroscopy Analysis Tools (spant) Return a time scale vector to match the FID of an MRS data object. — seconds • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/seq_cpmg_ideal.html b/docs/reference/seq_cpmg_ideal.html
index 547e96ab..45727c86 100644
--- a/docs/reference/seq_cpmg_ideal.html
+++ b/docs/reference/seq_cpmg_ideal.html
@@ -1,5 +1,5 @@
-CPMG style sequence with ideal pulses. — seq_cpmg_ideal • Spectroscopy Analysis Tools (spant) CPMG style sequence with ideal pulses. — seq_cpmg_ideal • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/seq_mega_press_ideal.html b/docs/reference/seq_mega_press_ideal.html
index 0769b8b4..a9cd7fa0 100644
--- a/docs/reference/seq_mega_press_ideal.html
+++ b/docs/reference/seq_mega_press_ideal.html
@@ -1,7 +1,5 @@
-MEGA-PRESS sequence with ideal localisation pulses and Gaussian shaped
-editing pulse. — seq_mega_press_ideal • Spectroscopy Analysis Tools (spant) MEGA-PRESS sequence with ideal localisation pulses and Gaussian shaped editing pulse. — seq_mega_press_ideal • Spectroscopy Analysis Tools (spant) PRESS sequence with shaped refocusing pulses. — seq_press_2d_shaped • Spectroscopy Analysis Tools (spant) PRESS sequence with shaped refocusing pulses. — seq_press_2d_shaped • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -165,7 +165,7 @@ Value
diff --git a/docs/reference/seq_press_ideal.html b/docs/reference/seq_press_ideal.html
index 8c976856..72c3af3d 100644
--- a/docs/reference/seq_press_ideal.html
+++ b/docs/reference/seq_press_ideal.html
@@ -1,5 +1,5 @@
-PRESS sequence with ideal pulses. — seq_press_ideal • Spectroscopy Analysis Tools (spant) PRESS sequence with ideal pulses. — seq_press_ideal • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/seq_pulse_acquire.html b/docs/reference/seq_pulse_acquire.html
index 4a88fc64..ad80571e 100644
--- a/docs/reference/seq_pulse_acquire.html
+++ b/docs/reference/seq_pulse_acquire.html
@@ -1,5 +1,5 @@
-Simple pulse and acquire sequence with ideal pulses. — seq_pulse_acquire • Spectroscopy Analysis Tools (spant) Simple pulse and acquire sequence with ideal pulses. — seq_pulse_acquire • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/seq_slaser_ideal.html b/docs/reference/seq_slaser_ideal.html
index 74688f4d..eb83e8e3 100644
--- a/docs/reference/seq_slaser_ideal.html
+++ b/docs/reference/seq_slaser_ideal.html
@@ -1,5 +1,5 @@
-sLASER sequence with ideal pulses. — seq_slaser_ideal • Spectroscopy Analysis Tools (spant) sLASER sequence with ideal pulses. — seq_slaser_ideal • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -126,7 +126,7 @@ Value
diff --git a/docs/reference/seq_spin_echo_ideal.html b/docs/reference/seq_spin_echo_ideal.html
index e23271de..4248716f 100644
--- a/docs/reference/seq_spin_echo_ideal.html
+++ b/docs/reference/seq_spin_echo_ideal.html
@@ -1,5 +1,5 @@
-Spin echo sequence with ideal pulses. — seq_spin_echo_ideal • Spectroscopy Analysis Tools (spant) Spin echo sequence with ideal pulses. — seq_spin_echo_ideal • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/seq_steam_ideal.html b/docs/reference/seq_steam_ideal.html
index a60685a8..1c8115d7 100644
--- a/docs/reference/seq_steam_ideal.html
+++ b/docs/reference/seq_steam_ideal.html
@@ -1,5 +1,5 @@
-STEAM sequence with ideal pulses. — seq_steam_ideal • Spectroscopy Analysis Tools (spant) STEAM sequence with ideal pulses. — seq_steam_ideal • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -128,7 +128,7 @@ Value
diff --git a/docs/reference/seq_steam_ideal_cof.html b/docs/reference/seq_steam_ideal_cof.html
index 8f225740..cba7af91 100644
--- a/docs/reference/seq_steam_ideal_cof.html
+++ b/docs/reference/seq_steam_ideal_cof.html
@@ -1,7 +1,5 @@
-STEAM sequence with ideal pulses and coherence order filtering to simulate
-gradient crushers. — seq_steam_ideal_cof • Spectroscopy Analysis Tools (spant) STEAM sequence with ideal pulses and coherence order filtering to simulate gradient crushers. — seq_steam_ideal_cof • Spectroscopy Analysis Tools (spant) STEAM sequence with ideal pulses using the z-rotation gradient simulation
-method described by Young et al JMR 140, 146-152 (1999). — seq_steam_ideal_young • Spectroscopy Analysis Tools (spant) STEAM sequence with ideal pulses using the z-rotation gradient simulation method described by Young et al JMR 140, 146-152 (1999). — seq_steam_ideal_young • Spectroscopy Analysis Tools (spant) Set the number of transients for an mrs_data object. — set_Ntrans • Spectroscopy Analysis Tools (spant) Set the number of transients for an mrs_data object. — set_Ntrans • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/set_def_acq_paras.html b/docs/reference/set_def_acq_paras.html
index 3e1b4004..cc2ada9c 100644
--- a/docs/reference/set_def_acq_paras.html
+++ b/docs/reference/set_def_acq_paras.html
@@ -1,5 +1,5 @@
-Set the default acquisition parameters. — set_def_acq_paras • Spectroscopy Analysis Tools (spant) Set the default acquisition parameters. — set_def_acq_paras • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Arguments
diff --git a/docs/reference/set_lcm_cmd.html b/docs/reference/set_lcm_cmd.html
index 2056ed01..42bb2f24 100644
--- a/docs/reference/set_lcm_cmd.html
+++ b/docs/reference/set_lcm_cmd.html
@@ -1,5 +1,5 @@
-Set the command to run the LCModel command-line program. — set_lcm_cmd • Spectroscopy Analysis Tools (spant) Set the command to run the LCModel command-line program. — set_lcm_cmd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/set_lw.html b/docs/reference/set_lw.html
index b64ec851..bb176c62 100644
--- a/docs/reference/set_lw.html
+++ b/docs/reference/set_lw.html
@@ -1,5 +1,5 @@
-Apply line-broadening to an mrs_data object to achieve a specified linewidth. — set_lw • Spectroscopy Analysis Tools (spant) Apply line-broadening to an mrs_data object to achieve a specified linewidth. — set_lw • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -123,7 +123,7 @@ Value
diff --git a/docs/reference/set_mask_xy_mat.html b/docs/reference/set_mask_xy_mat.html
index 49dc5d4e..52c4b617 100644
--- a/docs/reference/set_mask_xy_mat.html
+++ b/docs/reference/set_mask_xy_mat.html
@@ -1,5 +1,5 @@
-Set the masked voxels in a 2D MRSI dataset to given spectrum. — set_mask_xy_mat • Spectroscopy Analysis Tools (spant) Set the masked voxels in a 2D MRSI dataset to given spectrum. — set_mask_xy_mat • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Value
diff --git a/docs/reference/set_precomp_mode.html b/docs/reference/set_precomp_mode.html
index f44bd5d3..47c28e3b 100644
--- a/docs/reference/set_precomp_mode.html
+++ b/docs/reference/set_precomp_mode.html
@@ -1,5 +1,5 @@
-Set the precompute mode. — set_precomp_mode • Spectroscopy Analysis Tools (spant) Set the precompute mode. — set_precomp_mode • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/set_precomp_verbose.html b/docs/reference/set_precomp_verbose.html
index 1453a231..9c613505 100644
--- a/docs/reference/set_precomp_verbose.html
+++ b/docs/reference/set_precomp_verbose.html
@@ -1,5 +1,5 @@
-Set the verbosity of the precompute function. — set_precomp_verbose • Spectroscopy Analysis Tools (spant) Set the verbosity of the precompute function. — set_precomp_verbose • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/set_ref.html b/docs/reference/set_ref.html
index 8953fa50..5436dfa2 100644
--- a/docs/reference/set_ref.html
+++ b/docs/reference/set_ref.html
@@ -1,5 +1,5 @@
-Set the ppm reference value (eg ppm value at 0Hz). — set_ref • Spectroscopy Analysis Tools (spant) Set the ppm reference value (eg ppm value at 0Hz). — set_ref • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/set_td_pts.html b/docs/reference/set_td_pts.html
index 8a80d42a..586459ff 100644
--- a/docs/reference/set_td_pts.html
+++ b/docs/reference/set_td_pts.html
@@ -1,7 +1,5 @@
-Set the number of time-domain data points, truncating or zero-filling as
-appropriate. — set_td_pts • Spectroscopy Analysis Tools (spant) Set the number of time-domain data points, truncating or zero-filling as appropriate. — set_td_pts • Spectroscopy Analysis Tools (spant) Set the command to run the TARQUIN command-line program. — set_tqn_cmd • Spectroscopy Analysis Tools (spant) Set the command to run the TARQUIN command-line program. — set_tqn_cmd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/set_tr.html b/docs/reference/set_tr.html
index b2109ab0..65c9df5f 100644
--- a/docs/reference/set_tr.html
+++ b/docs/reference/set_tr.html
@@ -1,5 +1,5 @@
-Set the repetition time of an MRS dataset. — set_tr • Spectroscopy Analysis Tools (spant) Set the repetition time of an MRS dataset. — set_tr • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/shift.html b/docs/reference/shift.html
index ab0fe724..034591d0 100644
--- a/docs/reference/shift.html
+++ b/docs/reference/shift.html
@@ -1,5 +1,5 @@
-Apply a frequency shift to MRS data. — shift • Spectroscopy Analysis Tools (spant) Apply a frequency shift to MRS data. — shift • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/shift_basis.html b/docs/reference/shift_basis.html
index 2884be19..f55a65e0 100644
--- a/docs/reference/shift_basis.html
+++ b/docs/reference/shift_basis.html
@@ -1,5 +1,5 @@
-Apply frequency shifts to basis set signals. — shift_basis • Spectroscopy Analysis Tools (spant) Apply frequency shifts to basis set signals. — shift_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Value
diff --git a/docs/reference/sim_basis.html b/docs/reference/sim_basis.html
index c7838c46..bb5fefc6 100644
--- a/docs/reference/sim_basis.html
+++ b/docs/reference/sim_basis.html
@@ -1,5 +1,5 @@
-Simulate a basis set object. — sim_basis • Spectroscopy Analysis Tools (spant) Simulate a basis set object. — sim_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -136,7 +136,7 @@ Value
diff --git a/docs/reference/sim_basis_1h_brain.html b/docs/reference/sim_basis_1h_brain.html
index 62ed7389..f71ffa0b 100644
--- a/docs/reference/sim_basis_1h_brain.html
+++ b/docs/reference/sim_basis_1h_brain.html
@@ -1,7 +1,5 @@
-Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS
-sequence. Note, ideal pulses are assumed. — sim_basis_1h_brain • Spectroscopy Analysis Tools (spant) Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS sequence. Note, ideal pulses are assumed. — sim_basis_1h_brain • Spectroscopy Analysis Tools (spant) Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS
-sequence. Note, ideal pulses are assumed. — sim_basis_1h_brain_press • Spectroscopy Analysis Tools (spant) Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS sequence. Note, ideal pulses are assumed. — sim_basis_1h_brain_press • Spectroscopy Analysis Tools (spant) Simulate a macromolecular and lipid basis-set suitable for 1H brain MRS
-analysis. — sim_basis_mm_lip_lcm • Spectroscopy Analysis Tools (spant) Simulate a macromolecular and lipid basis-set suitable for 1H brain MRS analysis. — sim_basis_mm_lip_lcm • Spectroscopy Analysis Tools (spant) Simulate a basis file using TARQUIN. — sim_basis_tqn • Spectroscopy Analysis Tools (spant) Simulate a basis file using TARQUIN. — sim_basis_tqn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -129,7 +129,7 @@ Examples
diff --git a/docs/reference/sim_brain_1h.html b/docs/reference/sim_brain_1h.html
index 2044cf1a..717ee289 100644
--- a/docs/reference/sim_brain_1h.html
+++ b/docs/reference/sim_brain_1h.html
@@ -1,5 +1,5 @@
-Simulate MRS data with a similar appearance to normal brain (by default). — sim_brain_1h • Spectroscopy Analysis Tools (spant) Simulate MRS data with a similar appearance to normal brain (by default). — sim_brain_1h • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -159,7 +159,7 @@ Value
diff --git a/docs/reference/sim_mol.html b/docs/reference/sim_mol.html
index 23bcef50..77f76a50 100644
--- a/docs/reference/sim_mol.html
+++ b/docs/reference/sim_mol.html
@@ -1,5 +1,5 @@
-Simulate a mol_parameter object. — sim_mol • Spectroscopy Analysis Tools (spant) Simulate a mol_parameter object. — sim_mol • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -143,7 +143,7 @@ Value
diff --git a/docs/reference/sim_noise.html b/docs/reference/sim_noise.html
index 23875f79..a71477d4 100644
--- a/docs/reference/sim_noise.html
+++ b/docs/reference/sim_noise.html
@@ -1,5 +1,5 @@
-Simulate an mrs_data object containing simulated Gaussian noise. — sim_noise • Spectroscopy Analysis Tools (spant) Simulate an mrs_data object containing simulated Gaussian noise. — sim_noise • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -84,6 +84,7 @@ Simulate an mrs_data object containing simulated Gaussian noise.
ft = def_ft(),
N = def_N(),
ref = def_ref(),
+ nuc = def_nuc(),
dyns = 1,
fd = TRUE
)
@@ -111,6 +112,10 @@ Arguments
reference value for ppm scale.
nuc
+resonant nucleus.
dyns
number of dynamic scans to generate.
Value
diff --git a/docs/reference/sim_resonances.html b/docs/reference/sim_resonances.html
index 19e9a8a4..d4f8d7c0 100644
--- a/docs/reference/sim_resonances.html
+++ b/docs/reference/sim_resonances.html
@@ -1,5 +1,5 @@
-Simulate a MRS data object containing a set of simulated resonances. — sim_resonances • Spectroscopy Analysis Tools (spant) Simulate a MRS data object containing a set of simulated resonances. — sim_resonances • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -161,7 +161,7 @@ Examples
diff --git a/docs/reference/sim_th_excit_profile.html b/docs/reference/sim_th_excit_profile.html
index 5535c5ef..e781cab1 100644
--- a/docs/reference/sim_th_excit_profile.html
+++ b/docs/reference/sim_th_excit_profile.html
@@ -1,7 +1,5 @@
-Simulate an ideal pulse excitation profile by smoothing a top-hat function
-with a Gaussian. — sim_th_excit_profile • Spectroscopy Analysis Tools (spant) Simulate an ideal pulse excitation profile by smoothing a top-hat function with a Gaussian. — sim_th_excit_profile • Spectroscopy Analysis Tools (spant) Simulate an mrs_data object containing complex zero valued samples. — sim_zero • Spectroscopy Analysis Tools (spant) Simulate an mrs_data object containing complex zero valued samples. — sim_zero • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -78,7 +78,14 @@ Simulate an mrs_data object containing complex zero valued samples.
-
+
@@ -99,6 +106,10 @@ Arguments
reference value for ppm scale.
nuc
+resonant nucleus.
dyns
number of dynamic scans to generate.
Value
diff --git a/docs/reference/smooth_dyns.html b/docs/reference/smooth_dyns.html
index 4cc8da50..accf3a51 100644
--- a/docs/reference/smooth_dyns.html
+++ b/docs/reference/smooth_dyns.html
@@ -1,5 +1,5 @@
-Smooth data across the dynamic dimension with a Gaussian kernel. — smooth_dyns • Spectroscopy Analysis Tools (spant) Smooth data across the dynamic dimension with a Gaussian kernel. — smooth_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/sort_basis.html b/docs/reference/sort_basis.html
index 6a676ea2..d25cc006 100644
--- a/docs/reference/sort_basis.html
+++ b/docs/reference/sort_basis.html
@@ -1,5 +1,5 @@
-Sort the basis-set elements alphabetically. — sort_basis • Spectroscopy Analysis Tools (spant) Sort the basis-set elements alphabetically. — sort_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/spant-package.html b/docs/reference/spant-package.html
index b3dd8e21..90f19ec3 100644
--- a/docs/reference/spant-package.html
+++ b/docs/reference/spant-package.html
@@ -1,5 +1,5 @@
-spant: spectroscopy analysis tools. — spant-package • Spectroscopy Analysis Tools (spant) spant: spectroscopy analysis tools. — spant-package • Spectroscopy Analysis Tools (spant) Simulate and fit some spectra with ABfit for benchmarking purposes. Basic
-timing and performance metrics will be printed. — spant_abfit_benchmark • Spectroscopy Analysis Tools (spant) Simulate and fit some spectra with ABfit for benchmarking purposes. Basic timing and performance metrics will be printed. — spant_abfit_benchmark • Spectroscopy Analysis Tools (spant) Example MEGA-PRESS data with significant B0 drift. — spant_mpress_drift • Spectroscopy Analysis Tools (spant) Example MEGA-PRESS data with significant B0 drift. — spant_mpress_drift • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -83,7 +83,7 @@ Example MEGA-PRESS data with significant B0 drift.
Format
- An object of class mrs_data of length 13.
+ An object of class mrs_data of dimension 1 x 1 x 1 x 1 x 40 x 1 x 1024.
@@ -98,7 +98,7 @@ Format
diff --git a/docs/reference/spant_sim_fmrs_dataset.html b/docs/reference/spant_sim_fmrs_dataset.html
new file mode 100644
index 00000000..00e48b56
--- /dev/null
+++ b/docs/reference/spant_sim_fmrs_dataset.html
@@ -0,0 +1,117 @@
+
+Simulate an example fMRS dataset for a block design fMRS experiment and export a BIDS structure. — spant_sim_fmrs_dataset • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Simulate an example fMRS dataset for a block design fMRS experiment and export a BIDS structure.
+ Source: R/fmrs.R
+ spant_sim_fmrs_dataset.Rd
+
+
+
+ Simulate an example fMRS dataset for a block design fMRS experiment and
+export a BIDS structure.
+
+
+
+ spant_sim_fmrs_dataset(output_dir = NULL)
+
+
+
+ Arguments
+ - output_dir
+output directory for the BIDS data. Defaults to :
+"HOME/sim_fmrs_dataset/data".
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/spant_simulation_benchmark.html b/docs/reference/spant_simulation_benchmark.html
index 32daa8bf..d8cc6841 100644
--- a/docs/reference/spant_simulation_benchmark.html
+++ b/docs/reference/spant_simulation_benchmark.html
@@ -1,7 +1,5 @@
-Simulate a typical metabolite basis set for benchmarking. Timing metrics will
-be printed on completion. — spant_simulation_benchmark • Spectroscopy Analysis Tools (spant) Simulate a typical metabolite basis set for benchmarking. Timing metrics will be printed on completion. — spant_simulation_benchmark • Spectroscopy Analysis Tools (spant) Decompose an mrs_data object into white and gray matter spectra. — spec_decomp • Spectroscopy Analysis Tools (spant) Perform a mathematical operation on a spectral region. — spec_op • Spectroscopy Analysis Tools (spant) Perform a mathematical operation on a spectral region. — spec_op • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -98,8 +98,8 @@ Arguments
operator
-can be "sum" (default), "mean", "l2", "max", "min" or
-"max-min".
can be "sum" (default), "mean", "l2", "max", "max_cplx,
+"min" or "max-min".
freq_scale
@@ -129,7 +129,7 @@ Value
diff --git a/docs/reference/spin_sys.html b/docs/reference/spin_sys.html
index 853423a4..1eaa9e76 100644
--- a/docs/reference/spin_sys.html
+++ b/docs/reference/spin_sys.html
@@ -1,5 +1,5 @@
-Create a spin system object for pulse sequence simulation. — spin_sys • Spectroscopy Analysis Tools (spant) Create a spin system object for pulse sequence simulation. — spin_sys • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/spm_pve2categorical.html b/docs/reference/spm_pve2categorical.html
index 23a1bad9..70f10729 100644
--- a/docs/reference/spm_pve2categorical.html
+++ b/docs/reference/spm_pve2categorical.html
@@ -1,7 +1,5 @@
-Convert SPM style segmentation files to a single categorical image where
-the numerical values map as: 0) Other, 1) CSF, 2) GM and 3) WM. — spm_pve2categorical • Spectroscopy Analysis Tools (spant) Convert SPM style segmentation files to a single categorical image where the numerical values map as: 0) Other, 1) CSF, 2) GM and 3) WM. — spm_pve2categorical • Spectroscopy Analysis Tools (spant) Signal space projection method for lipid suppression. — ssp • Spectroscopy Analysis Tools (spant) Signal space projection method for lipid suppression. — ssp • Spectroscopy Analysis Tools (spant) Plot the fitting results of an object of class fit_result with
-individual basis set components shown. — stackplot.fit_result • Spectroscopy Analysis Tools (spant) Plot the fitting results of an object of class fit_result with individual basis set components shown. — stackplot.fit_result • Spectroscopy Analysis Tools (spant) Produce a plot with multiple traces. — stackplot • Spectroscopy Analysis Tools (spant) Produce a plot with multiple traces. — stackplot • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/stackplot.mrs_data.html b/docs/reference/stackplot.mrs_data.html
index 17ff5648..64eea445 100644
--- a/docs/reference/stackplot.mrs_data.html
+++ b/docs/reference/stackplot.mrs_data.html
@@ -1,5 +1,5 @@
-Stackplot plotting method for objects of class mrs_data. — stackplot.mrs_data • Spectroscopy Analysis Tools (spant) Stackplot plotting method for objects of class mrs_data. — stackplot.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -255,7 +255,7 @@ Arguments
diff --git a/docs/reference/sub_first_dyn.html b/docs/reference/sub_first_dyn.html
index dbd7f831..493b7242 100644
--- a/docs/reference/sub_first_dyn.html
+++ b/docs/reference/sub_first_dyn.html
@@ -1,5 +1,5 @@
-Subtract the first dynamic spectrum from a dynamic series. — sub_first_dyn • Spectroscopy Analysis Tools (spant) Subtract the first dynamic spectrum from a dynamic series. — sub_first_dyn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/sub_mean_dyns.html b/docs/reference/sub_mean_dyns.html
index 6e3bb2df..221bd0c1 100644
--- a/docs/reference/sub_mean_dyns.html
+++ b/docs/reference/sub_mean_dyns.html
@@ -1,5 +1,5 @@
-Subtract the mean dynamic spectrum from a dynamic series. — sub_mean_dyns • Spectroscopy Analysis Tools (spant) Subtract the mean dynamic spectrum from a dynamic series. — sub_mean_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/sub_median_dyns.html b/docs/reference/sub_median_dyns.html
index 134c495d..1e834f14 100644
--- a/docs/reference/sub_median_dyns.html
+++ b/docs/reference/sub_median_dyns.html
@@ -1,5 +1,5 @@
-Subtract the median dynamic spectrum from a dynamic series. — sub_median_dyns • Spectroscopy Analysis Tools (spant) Subtract the median dynamic spectrum from a dynamic series. — sub_median_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/sum_coils.html b/docs/reference/sum_coils.html
index 7bf559f2..e1ab3cc0 100644
--- a/docs/reference/sum_coils.html
+++ b/docs/reference/sum_coils.html
@@ -1,5 +1,5 @@
-Calculate the sum across receiver coil elements. — sum_coils • Spectroscopy Analysis Tools (spant) Calculate the sum across receiver coil elements. — sum_coils • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/sum_dyns.html b/docs/reference/sum_dyns.html
index a0be19d3..bbda2ffc 100644
--- a/docs/reference/sum_dyns.html
+++ b/docs/reference/sum_dyns.html
@@ -1,5 +1,5 @@
-Calculate the sum of data dynamics. — sum_dyns • Spectroscopy Analysis Tools (spant) Calculate the sum of data dynamics. — sum_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/sum_mrs.html b/docs/reference/sum_mrs.html
index a22f215b..3cc3ab9e 100644
--- a/docs/reference/sum_mrs.html
+++ b/docs/reference/sum_mrs.html
@@ -1,5 +1,5 @@
-Sum two mrs_data objects. — sum_mrs • Spectroscopy Analysis Tools (spant) Sum two mrs_data objects. — sum_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Value
diff --git a/docs/reference/sum_mrs_list.html b/docs/reference/sum_mrs_list.html
index f4e09aea..c3584348 100644
--- a/docs/reference/sum_mrs_list.html
+++ b/docs/reference/sum_mrs_list.html
@@ -1,5 +1,5 @@
-Return the sum of a list of mrs_data objects. — sum_mrs_list • Spectroscopy Analysis Tools (spant) Return the sum of a list of mrs_data objects. — sum_mrs_list • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/svs_1h_brain_analysis.html b/docs/reference/svs_1h_brain_analysis.html
index 8ce514db..dff0ef7d 100644
--- a/docs/reference/svs_1h_brain_analysis.html
+++ b/docs/reference/svs_1h_brain_analysis.html
@@ -1,5 +1,5 @@
-Standard SVS 1H brain analysis pipeline. — svs_1h_brain_analysis • Spectroscopy Analysis Tools (spant) Standard SVS 1H brain analysis pipeline. — svs_1h_brain_analysis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -199,7 +199,7 @@ Value
diff --git a/docs/reference/svs_1h_brain_analysis_dev.html b/docs/reference/svs_1h_brain_analysis_dev.html
index d70a14d3..d71bfea2 100644
--- a/docs/reference/svs_1h_brain_analysis_dev.html
+++ b/docs/reference/svs_1h_brain_analysis_dev.html
@@ -1,5 +1,5 @@
-Standard SVS 1H brain analysis pipeline. — svs_1h_brain_analysis_dev • Spectroscopy Analysis Tools (spant) Standard SVS 1H brain analysis pipeline. — svs_1h_brain_analysis_dev • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -193,7 +193,7 @@ Examples
diff --git a/docs/reference/svs_1h_brain_batch_analysis.html b/docs/reference/svs_1h_brain_batch_analysis.html
index 5631e8cc..15f7223e 100644
--- a/docs/reference/svs_1h_brain_batch_analysis.html
+++ b/docs/reference/svs_1h_brain_batch_analysis.html
@@ -1,5 +1,5 @@
-Batch interface to the standard SVS 1H brain analysis pipeline. — svs_1h_brain_batch_analysis • Spectroscopy Analysis Tools (spant) Batch interface to the standard SVS 1H brain analysis pipeline. — svs_1h_brain_batch_analysis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -144,7 +144,7 @@ Value
diff --git a/docs/reference/t_test_spec.html b/docs/reference/t_test_spec.html
new file mode 100644
index 00000000..56a7ea1b
--- /dev/null
+++ b/docs/reference/t_test_spec.html
@@ -0,0 +1,124 @@
+
+Perform a t-test on spectral data points. — t_test_spec • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+
+
+ Perform a t-test on spectral data points.
+
+
+
+ t_test_spec(mrs_data, group)
+
+
+
+ Arguments
+ - mrs_data
+an mrs_data object with spectra in the dynamic dimension.
- group
+vector describing the group membership of each dynamic spectrum.
+
+ Value
+
+
+a list of statistical results.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/td2fd.html b/docs/reference/td2fd.html
index 6748a6a8..f31ed524 100644
--- a/docs/reference/td2fd.html
+++ b/docs/reference/td2fd.html
@@ -1,5 +1,5 @@
-Transform time-domain data to the frequency-domain. — td2fd • Spectroscopy Analysis Tools (spant) Transform time-domain data to the frequency-domain. — td2fd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/td_conv_filt.html b/docs/reference/td_conv_filt.html
index a9f340c3..106b9b00 100644
--- a/docs/reference/td_conv_filt.html
+++ b/docs/reference/td_conv_filt.html
@@ -1,5 +1,5 @@
-Time-domain convolution based filter. — td_conv_filt • Spectroscopy Analysis Tools (spant) Time-domain convolution based filter. — td_conv_filt • Spectroscopy Analysis Tools (spant) Time-domain spectral registration. — tdsr • Spectroscopy Analysis Tools (spant) Time-domain spectral registration. — tdsr • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -121,7 +121,7 @@ Value
diff --git a/docs/reference/te.html b/docs/reference/te.html
index 010361b1..4a65711d 100644
--- a/docs/reference/te.html
+++ b/docs/reference/te.html
@@ -1,5 +1,5 @@
-Return the echo time of an MRS dataset. — te • Spectroscopy Analysis Tools (spant) Return the echo time of an MRS dataset. — te • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/tr.html b/docs/reference/tr.html
index 0c0bd63b..2e749e02 100644
--- a/docs/reference/tr.html
+++ b/docs/reference/tr.html
@@ -1,5 +1,5 @@
-Return the repetition time of an MRS dataset. — tr • Spectroscopy Analysis Tools (spant) Return the repetition time of an MRS dataset. — tr • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/varpro_3_para_opts.html b/docs/reference/varpro_3_para_opts.html
index c2270a16..52d7cd84 100644
--- a/docs/reference/varpro_3_para_opts.html
+++ b/docs/reference/varpro_3_para_opts.html
@@ -1,5 +1,5 @@
-Return a list of options for VARPRO based fitting with 3 free parameters. — varpro_3_para_opts • Spectroscopy Analysis Tools (spant) Return a list of options for VARPRO based fitting with 3 free parameters. — varpro_3_para_opts • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -141,7 +141,7 @@ Value
diff --git a/docs/reference/varpro_basic_opts.html b/docs/reference/varpro_basic_opts.html
index 32c86d22..c5104891 100644
--- a/docs/reference/varpro_basic_opts.html
+++ b/docs/reference/varpro_basic_opts.html
@@ -1,5 +1,5 @@
-Return a list of options for a basic VARPRO analysis. — varpro_basic_opts • Spectroscopy Analysis Tools (spant) Return a list of options for a basic VARPRO analysis. — varpro_basic_opts • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -118,7 +118,7 @@ Value
diff --git a/docs/reference/varpro_opts.html b/docs/reference/varpro_opts.html
index 2aabf11d..6332f730 100644
--- a/docs/reference/varpro_opts.html
+++ b/docs/reference/varpro_opts.html
@@ -1,5 +1,5 @@
-Return a list of options for VARPRO based fitting. — varpro_opts • Spectroscopy Analysis Tools (spant) Return a list of options for VARPRO based fitting. — varpro_opts • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -177,7 +177,7 @@ Examples
diff --git a/docs/reference/vec2mrs_data.html b/docs/reference/vec2mrs_data.html
index 0cccd73b..f0d58bf0 100644
--- a/docs/reference/vec2mrs_data.html
+++ b/docs/reference/vec2mrs_data.html
@@ -1,5 +1,5 @@
-Convert a vector into a mrs_data object. — vec2mrs_data • Spectroscopy Analysis Tools (spant) Convert a vector into a mrs_data object. — vec2mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -80,10 +80,11 @@ Convert a vector into a mrs_data object.
vec2mrs_data(
vec,
- fs = def_fs(),
- ft = def_ft(),
- ref = def_ref(),
- nuc = def_nuc(),
+ mrs_data = NULL,
+ fs = NULL,
+ ft = NULL,
+ ref = NULL,
+ nuc = NULL,
dyns = 1,
fd = FALSE
)
@@ -95,6 +96,10 @@ Arguments
the data vector.
mrs_data
+example data to copy acquisition parameters from.
fs
sampling frequency in Hz.
Arguments
fd
-flag to indicate if the matrix is in the frequency domain (logical).
flag to indicate if the vector is in the frequency domain (logical).
Value
diff --git a/docs/reference/write_basis.html b/docs/reference/write_basis.html
index b6e27cbd..94c5e021 100644
--- a/docs/reference/write_basis.html
+++ b/docs/reference/write_basis.html
@@ -1,5 +1,5 @@
-Write a basis object to an LCModel .basis formatted file. — write_basis • Spectroscopy Analysis Tools (spant) Write a basis object to an LCModel .basis formatted file. — write_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -108,7 +108,7 @@ Arguments
diff --git a/docs/reference/write_basis_tqn.html b/docs/reference/write_basis_tqn.html
index 6aa51c1d..116c73ec 100644
--- a/docs/reference/write_basis_tqn.html
+++ b/docs/reference/write_basis_tqn.html
@@ -1,5 +1,5 @@
-Generate a basis file using TARQUIN. — write_basis_tqn • Spectroscopy Analysis Tools (spant) Generate a basis file using TARQUIN. — write_basis_tqn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Examples
diff --git a/docs/reference/write_mrs.html b/docs/reference/write_mrs.html
index fff25f15..124b9dc4 100644
--- a/docs/reference/write_mrs.html
+++ b/docs/reference/write_mrs.html
@@ -1,5 +1,5 @@
-Write MRS data object to file. — write_mrs • Spectroscopy Analysis Tools (spant) Write MRS data object to file. — write_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Arguments
diff --git a/docs/reference/write_mrs_nifti.html b/docs/reference/write_mrs_nifti.html
index f4bf1921..bd3ed4b7 100644
--- a/docs/reference/write_mrs_nifti.html
+++ b/docs/reference/write_mrs_nifti.html
@@ -1,5 +1,5 @@
-Write MRS data object to file in NIFTI format. — write_mrs_nifti • Spectroscopy Analysis Tools (spant) Write MRS data object to file in NIFTI format. — write_mrs_nifti • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/write_pulse_ascii.html b/docs/reference/write_pulse_ascii.html
index 067ae086..221f8ebb 100644
--- a/docs/reference/write_pulse_ascii.html
+++ b/docs/reference/write_pulse_ascii.html
@@ -1,5 +1,5 @@
-Write an ASCII formatted pulse file. — write_pulse_ascii • Spectroscopy Analysis Tools (spant) Write an ASCII formatted pulse file. — write_pulse_ascii • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/zero_fade_spec.html b/docs/reference/zero_fade_spec.html
index c703745c..c8b572c3 100644
--- a/docs/reference/zero_fade_spec.html
+++ b/docs/reference/zero_fade_spec.html
@@ -1,7 +1,5 @@
-Fade a spectrum to zero by frequency domain multiplication with a tanh
-function. Note this operation distorts data points at the end of the FID. — zero_fade_spec • Spectroscopy Analysis Tools (spant) Fade a spectrum to zero by frequency domain multiplication with a tanh function. Note this operation distorts data points at the end of the FID. — zero_fade_spec • Spectroscopy Analysis Tools (spant) Zero all coherences including and above a given order. — zero_higher_orders • Spectroscopy Analysis Tools (spant) Zero all coherences including and above a given order. — zero_higher_orders • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Value
diff --git a/docs/reference/zero_td_pts_end.html b/docs/reference/zero_td_pts_end.html
index 8c1123c8..71d24ebb 100644
--- a/docs/reference/zero_td_pts_end.html
+++ b/docs/reference/zero_td_pts_end.html
@@ -1,5 +1,5 @@
-Set mrs_data object data points at the end of the FID to zero. — zero_td_pts_end • Spectroscopy Analysis Tools (spant) Set mrs_data object data points at the end of the FID to zero. — zero_td_pts_end • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/zf.html b/docs/reference/zf.html
index 85e2013c..baf50256 100644
--- a/docs/reference/zf.html
+++ b/docs/reference/zf.html
@@ -1,5 +1,5 @@
-Zero-fill MRS data in the time domain. — zf • Spectroscopy Analysis Tools (spant) Zero-fill MRS data in the time domain. — zf • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -125,7 +125,7 @@ Value
diff --git a/docs/reference/zf_xy.html b/docs/reference/zf_xy.html
index ebca3999..c4104a74 100644
--- a/docs/reference/zf_xy.html
+++ b/docs/reference/zf_xy.html
@@ -1,5 +1,5 @@
-Zero-fill MRSI data in the k-space x-y direction. — zf_xy • Spectroscopy Analysis Tools (spant) Zero-fill MRSI data in the k-space x-y direction. — zf_xy • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -113,7 +113,7 @@ Value
diff --git a/docs/sitemap.xml b/docs/sitemap.xml
index e2139f71..4c39f515 100644
--- a/docs/sitemap.xml
+++ b/docs/sitemap.xml
@@ -216,6 +216,12 @@
https://martin3141.github.io/spant/reference/comb_coils_fp_pc.html
+
+ https://martin3141.github.io/spant/reference/comb_coils_mrsi_gls.html
+
+
+ https://martin3141.github.io/spant/reference/comb_coils_svs_gls.html
+
https://martin3141.github.io/spant/reference/comb_csv_results.html
@@ -411,6 +417,9 @@
https://martin3141.github.io/spant/reference/gen_conv_reg.html
+
+ https://martin3141.github.io/spant/reference/gen_group_reg.html
+
https://martin3141.github.io/spant/reference/gen_impulse_reg.html
@@ -555,6 +564,15 @@
https://martin3141.github.io/spant/reference/glm_spec.html
+
+ https://martin3141.github.io/spant/reference/glm_spec_fmrs_fl.html
+
+
+ https://martin3141.github.io/spant/reference/glm_spec_fmrs_group.html
+
+
+ https://martin3141.github.io/spant/reference/glm_spec_group_linhyp.html
+
https://martin3141.github.io/spant/reference/grid_shift_xy.html
@@ -690,9 +708,15 @@
https://martin3141.github.io/spant/reference/mrs_data2basis.html
+
+ https://martin3141.github.io/spant/reference/mrs_data2bids.html
+
https://martin3141.github.io/spant/reference/mrs_data2mat.html
+
+ https://martin3141.github.io/spant/reference/mrs_data2spec_mat.html
+
https://martin3141.github.io/spant/reference/mrs_data2vec.html
@@ -741,6 +765,9 @@
https://martin3141.github.io/spant/reference/phase.html
+
+ https://martin3141.github.io/spant/reference/phase_ref_1h_brain.html
+
https://martin3141.github.io/spant/reference/plot.fit_result.html
@@ -780,6 +807,12 @@
https://martin3141.github.io/spant/reference/precomp.html
+
+ https://martin3141.github.io/spant/reference/preproc_svs.html
+
+
+ https://martin3141.github.io/spant/reference/preproc_svs_dataset.html
+
https://martin3141.github.io/spant/reference/print.fit_result.html
@@ -1050,6 +1083,9 @@
https://martin3141.github.io/spant/reference/spant_mpress_drift.html
+
+ https://martin3141.github.io/spant/reference/spant_sim_fmrs_dataset.html
+
https://martin3141.github.io/spant/reference/spant_simulation_benchmark.html
@@ -1107,6 +1143,9 @@
https://martin3141.github.io/spant/reference/svs_1h_brain_batch_analysis.html
+
+ https://martin3141.github.io/spant/reference/t_test_spec.html
+
https://martin3141.github.io/spant/reference/td2fd.html
Read a directory containing Siemens MRS IMA files and combine along the coil -dimension. Note that the coil ID is inferred from the sorted file name and -should be checked when consistency is required between two directories.
Read a directory containing Siemens MRS IMA files and combine along the coil dimension. Note that the coil ID is inferred from the sorted file name and should be checked when consistency is required between two directories.
Read a directory containing Siemens MRS IMA files and combine along the -dynamic dimension. Note that the coil ID is inferred from the sorted file -name and should be checked when consistency is required.
Read a directory containing Siemens MRS IMA files and combine along the dynamic dimension. Note that the coil ID is inferred from the sorted file name and should be checked when consistency is required.
All functions
- Reconstruct complex time-domain data from the real part of frequency-domain
-data.
Reconstruct complex time-domain data from the real part of frequency-domain data.
- Reconstruct complex time-domain data from the real part of frequency-domain
-data.
Reconstruct complex time-domain data from the real part of frequency-domain data.
@@ -1141,8 +1126,7 @@ All functions
- Resample a VOI to match a target image space using nearest-neighbour
-interpolation.
Resample a VOI to match a target image space using nearest-neighbour interpolation.
@@ -1158,23 +1142,19 @@ All functions
- Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water).
Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / kg of tissue water).
- Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water).
Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / kg of tissue water).
- Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / Litre of tissue).
Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / Litre of tissue).
- Convert default LCM/TARQUIN concentration scaling to molal units with partial
-volume correction.
Convert default LCM/TARQUIN concentration scaling to molal units with partial volume correction.
@@ -1222,8 +1202,7 @@ All functions
- MEGA-PRESS sequence with ideal localisation pulses and Gaussian shaped
-editing pulse.
MEGA-PRESS sequence with ideal localisation pulses and Gaussian shaped editing pulse.
@@ -1251,13 +1230,11 @@ All functions
- STEAM sequence with ideal pulses and coherence order filtering to simulate
-gradient crushers.
STEAM sequence with ideal pulses and coherence order filtering to simulate gradient crushers.
- STEAM sequence with ideal pulses using the z-rotation gradient simulation
-method described by Young et al JMR 140, 146-152 (1999).
STEAM sequence with ideal pulses using the z-rotation gradient simulation method described by Young et al JMR 140, 146-152 (1999).
@@ -1293,8 +1270,7 @@ All functions
- Set the number of time-domain data points, truncating or zero-filling as
-appropriate.
Set the number of time-domain data points, truncating or zero-filling as appropriate.
@@ -1318,18 +1294,15 @@ All functions
- Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS
-sequence. Note, ideal pulses are assumed.
Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS sequence. Note, ideal pulses are assumed.
- Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS
-sequence. Note, ideal pulses are assumed.
Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS sequence. Note, ideal pulses are assumed.
- Simulate a macromolecular and lipid basis-set suitable for 1H brain MRS
-analysis.
Simulate a macromolecular and lipid basis-set suitable for 1H brain MRS analysis.
@@ -1353,8 +1326,7 @@ All functions
- Simulate an ideal pulse excitation profile by smoothing a top-hat function
-with a Gaussian.
Simulate an ideal pulse excitation profile by smoothing a top-hat function with a Gaussian.
@@ -1374,17 +1346,19 @@ All functions
- Simulate and fit some spectra with ABfit for benchmarking purposes. Basic
-timing and performance metrics will be printed.
Simulate and fit some spectra with ABfit for benchmarking purposes. Basic timing and performance metrics will be printed.
Example MEGA-PRESS data with significant B0 drift.
+
+
+ Simulate an example fMRS dataset for a block design fMRS experiment and export a BIDS structure.
- Simulate a typical metabolite basis set for benchmarking. Timing metrics will
-be printed on completion.
Simulate a typical metabolite basis set for benchmarking. Timing metrics will be printed on completion.
@@ -1400,8 +1374,7 @@ All functions
- Convert SPM style segmentation files to a single categorical image where
-the numerical values map as: 0) Other, 1) CSF, 2) GM and 3) WM.
Convert SPM style segmentation files to a single categorical image where the numerical values map as: 0) Other, 1) CSF, 2) GM and 3) WM.
@@ -1413,8 +1386,7 @@ All functions
- Plot the fitting results of an object of class fit_result with
-individual basis set components shown.
Plot the fitting results of an object of class fit_result with individual basis set components shown.
@@ -1459,6 +1431,10 @@ All functions svs_1h_brain_batch_analysis()
Batch interface to the standard SVS 1H brain analysis pipeline.
+
+
+ Perform a t-test on spectral data points.
@@ -1518,8 +1494,7 @@ All functions
- Fade a spectrum to zero by frequency domain multiplication with a tanh
-function. Note this operation distorts data points at the end of the FID.
Fade a spectrum to zero by frequency domain multiplication with a tanh function. Note this operation distorts data points at the end of the FID.
@@ -1549,7 +1524,7 @@ All functions
diff --git a/docs/reference/int_spec.html b/docs/reference/int_spec.html
index c7060fe7..783325a8 100644
--- a/docs/reference/int_spec.html
+++ b/docs/reference/int_spec.html
@@ -1,5 +1,5 @@
-Integrate a spectral region. — int_spec • Spectroscopy Analysis Tools (spant) Integrate a spectral region. — int_spec • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -118,7 +118,7 @@ Value
diff --git a/docs/reference/interleave_dyns.html b/docs/reference/interleave_dyns.html
index effe5543..441eff27 100644
--- a/docs/reference/interleave_dyns.html
+++ b/docs/reference/interleave_dyns.html
@@ -1,5 +1,5 @@
-Interleave the first and second half of a dynamic series. — interleave_dyns • Spectroscopy Analysis Tools (spant) Interleave the first and second half of a dynamic series. — interleave_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/inv_even_dyns.html b/docs/reference/inv_even_dyns.html
index 9f9d4fff..dcb781dc 100644
--- a/docs/reference/inv_even_dyns.html
+++ b/docs/reference/inv_even_dyns.html
@@ -1,5 +1,5 @@
-Invert even numbered dynamic scans starting from 1 (2,4,6...). — inv_even_dyns • Spectroscopy Analysis Tools (spant) Invert even numbered dynamic scans starting from 1 (2,4,6...). — inv_even_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/inv_odd_dyns.html b/docs/reference/inv_odd_dyns.html
index 26212e2b..78d64660 100644
--- a/docs/reference/inv_odd_dyns.html
+++ b/docs/reference/inv_odd_dyns.html
@@ -1,5 +1,5 @@
-Invert odd numbered dynamic scans starting from 1 (1,3,5...). — inv_odd_dyns • Spectroscopy Analysis Tools (spant) Invert odd numbered dynamic scans starting from 1 (1,3,5...). — inv_odd_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/is.def.html b/docs/reference/is.def.html
index f196ffd0..a67b9eba 100644
--- a/docs/reference/is.def.html
+++ b/docs/reference/is.def.html
@@ -1,5 +1,5 @@
-Check if an object is defined, which is the same as being not NULL. — is.def • Spectroscopy Analysis Tools (spant) Check if an object is defined, which is the same as being not NULL. — is.def • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/is_fd.html b/docs/reference/is_fd.html
index 3b0ca165..18a193aa 100644
--- a/docs/reference/is_fd.html
+++ b/docs/reference/is_fd.html
@@ -1,7 +1,5 @@
-Check if the chemical shift dimension of an MRS data object is in the
-frequency domain. — is_fd • Spectroscopy Analysis Tools (spant) Check if the chemical shift dimension of an MRS data object is in the frequency domain. — is_fd • Spectroscopy Analysis Tools (spant) Transform 2D MRSI data from k-space to image space in the x-y direction. — kspace2img_xy • Spectroscopy Analysis Tools (spant) Transform 2D MRSI data from k-space to image space in the x-y direction. — kspace2img_xy • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/l2_reg.html b/docs/reference/l2_reg.html
index 3d781d80..21aa9849 100644
--- a/docs/reference/l2_reg.html
+++ b/docs/reference/l2_reg.html
@@ -1,5 +1,5 @@
-Perform l2 regularisation artefact suppression. — l2_reg • Spectroscopy Analysis Tools (spant) Perform l2 regularisation artefact suppression. — l2_reg • Spectroscopy Analysis Tools (spant) Apply line-broadening (apodisation) to MRS data or basis object. — lb • Spectroscopy Analysis Tools (spant) Apply line-broadening (apodisation) to MRS data or basis object. — lb • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -123,7 +123,7 @@ Value
diff --git a/docs/reference/lofdc.html b/docs/reference/lofdc.html
index 5419b1ec..31347a25 100644
--- a/docs/reference/lofdc.html
+++ b/docs/reference/lofdc.html
@@ -1,5 +1,5 @@
-Correct linear frequency drift. — lofdc • Spectroscopy Analysis Tools (spant) Correct linear frequency drift. — lofdc • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -138,7 +138,7 @@ Value
diff --git a/docs/reference/lw2alpha.html b/docs/reference/lw2alpha.html
index b83db682..25da229b 100644
--- a/docs/reference/lw2alpha.html
+++ b/docs/reference/lw2alpha.html
@@ -1,7 +1,5 @@
-Covert a linewidth in Hz to an equivalent alpha value in the time-domain ie:
-x * exp(-t * alpha). — lw2alpha • Spectroscopy Analysis Tools (spant) Covert a linewidth in Hz to an equivalent alpha value in the time-domain ie: x * exp(-t * alpha). — lw2alpha • Spectroscopy Analysis Tools (spant) Covert a linewidth in Hz to an equivalent beta value in the time-domain ie:
-x * exp(-t * t * beta). — lw2beta • Spectroscopy Analysis Tools (spant) Covert a linewidth in Hz to an equivalent beta value in the time-domain ie: x * exp(-t * t * beta). — lw2beta • Spectroscopy Analysis Tools (spant) Make a basis-set object from a directory containing LCModel formatted RAW
-files. — make_basis_from_raw • Spectroscopy Analysis Tools (spant) Make a basis-set object from a directory containing LCModel formatted RAW files. — make_basis_from_raw • Spectroscopy Analysis Tools (spant) Mask an MRS dataset in the dynamic dimension. — mask_dyns • Spectroscopy Analysis Tools (spant) Mask an MRS dataset in the dynamic dimension. — mask_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/mask_fit_res.html b/docs/reference/mask_fit_res.html
index 97baaa3f..ebd91a99 100644
--- a/docs/reference/mask_fit_res.html
+++ b/docs/reference/mask_fit_res.html
@@ -1,5 +1,5 @@
-Mask fit result spectra depending on a vector of bool values. — mask_fit_res • Spectroscopy Analysis Tools (spant) Mask fit result spectra depending on a vector of bool values. — mask_fit_res • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -116,7 +116,7 @@ Value
diff --git a/docs/reference/mask_xy.html b/docs/reference/mask_xy.html
index 11bb577c..b0d38619 100644
--- a/docs/reference/mask_xy.html
+++ b/docs/reference/mask_xy.html
@@ -1,5 +1,5 @@
-Mask an MRSI dataset in the x-y direction — mask_xy • Spectroscopy Analysis Tools (spant) Mask an MRSI dataset in the x-y direction — mask_xy • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/mask_xy_corners.html b/docs/reference/mask_xy_corners.html
index 09b16cd2..2d13839d 100644
--- a/docs/reference/mask_xy_corners.html
+++ b/docs/reference/mask_xy_corners.html
@@ -1,5 +1,5 @@
-Mask the four corners of an MRSI dataset in the x-y plane. — mask_xy_corners • Spectroscopy Analysis Tools (spant) Mask the four corners of an MRSI dataset in the x-y plane. — mask_xy_corners • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/mask_xy_ellipse.html b/docs/reference/mask_xy_ellipse.html
index 1d8b02e4..e2e749ef 100644
--- a/docs/reference/mask_xy_ellipse.html
+++ b/docs/reference/mask_xy_ellipse.html
@@ -1,7 +1,5 @@
-Mask the voxels outside an elliptical region spanning the MRSI dataset in the
-x-y plane. — mask_xy_ellipse • Spectroscopy Analysis Tools (spant) Mask the voxels outside an elliptical region spanning the MRSI dataset in the x-y plane. — mask_xy_ellipse • Spectroscopy Analysis Tools (spant) Mask a 2D MRSI dataset in the x-y dimension. — mask_xy_mat • Spectroscopy Analysis Tools (spant) Mask a 2D MRSI dataset in the x-y dimension. — mask_xy_mat • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Value
diff --git a/docs/reference/mat2mrs_data.html b/docs/reference/mat2mrs_data.html
index 2e2895f3..ae55665f 100644
--- a/docs/reference/mat2mrs_data.html
+++ b/docs/reference/mat2mrs_data.html
@@ -1,7 +1,5 @@
-Convert a matrix (with spectral points in the column dimension and dynamics
-in the row dimensions) into a mrs_data object. — mat2mrs_data • Spectroscopy Analysis Tools (spant) Convert a matrix (with spectral points in the column dimension and dynamics in the row dimensions) into a mrs_data object. — mat2mrs_data • Spectroscopy Analysis Tools (spant) Matrix exponential function taken from complexplus package to reduce the
-number of spant dependencies. — matexp • Spectroscopy Analysis Tools (spant) Matrix exponential function taken from complexplus package to reduce the number of spant dependencies. — matexp • Spectroscopy Analysis Tools (spant) Apply the max operator to an MRS dataset. — max_mrs • Spectroscopy Analysis Tools (spant) Apply the max operator to an MRS dataset. — max_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/max_mrs_interp.html b/docs/reference/max_mrs_interp.html
index e4474764..52e63f3e 100644
--- a/docs/reference/max_mrs_interp.html
+++ b/docs/reference/max_mrs_interp.html
@@ -1,5 +1,5 @@
-Apply the max operator to an interpolated MRS dataset. — max_mrs_interp • Spectroscopy Analysis Tools (spant) Apply the max operator to an interpolated MRS dataset. — max_mrs_interp • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/mean.list.html b/docs/reference/mean.list.html
index b8eb3463..048306fd 100644
--- a/docs/reference/mean.list.html
+++ b/docs/reference/mean.list.html
@@ -1,5 +1,5 @@
-Calculate the mean spectrum from an mrs_data object. — mean.list • Spectroscopy Analysis Tools (spant) Calculate the mean spectrum from an mrs_data object. — mean.list • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/mean.mrs_data.html b/docs/reference/mean.mrs_data.html
index 5531a28d..79515014 100644
--- a/docs/reference/mean.mrs_data.html
+++ b/docs/reference/mean.mrs_data.html
@@ -1,5 +1,5 @@
-Calculate the mean spectrum from an mrs_data object. — mean.mrs_data • Spectroscopy Analysis Tools (spant) Calculate the mean spectrum from an mrs_data object. — mean.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/mean_dyn_blocks.html b/docs/reference/mean_dyn_blocks.html
index 10467098..4c042448 100644
--- a/docs/reference/mean_dyn_blocks.html
+++ b/docs/reference/mean_dyn_blocks.html
@@ -1,5 +1,5 @@
-Calculate the mean of adjacent dynamic scans. — mean_dyn_blocks • Spectroscopy Analysis Tools (spant) Calculate the mean of adjacent dynamic scans. — mean_dyn_blocks • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/mean_dyn_pairs.html b/docs/reference/mean_dyn_pairs.html
index 63e909ea..1a241126 100644
--- a/docs/reference/mean_dyn_pairs.html
+++ b/docs/reference/mean_dyn_pairs.html
@@ -1,5 +1,5 @@
-Calculate the pairwise means across a dynamic data set. — mean_dyn_pairs • Spectroscopy Analysis Tools (spant) Calculate the pairwise means across a dynamic data set. — mean_dyn_pairs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/mean_dyns.html b/docs/reference/mean_dyns.html
index 73fdbfa7..0daa27df 100644
--- a/docs/reference/mean_dyns.html
+++ b/docs/reference/mean_dyns.html
@@ -1,5 +1,5 @@
-Calculate the mean dynamic data. — mean_dyns • Spectroscopy Analysis Tools (spant) Calculate the mean dynamic data. — mean_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/mean_mrs_list.html b/docs/reference/mean_mrs_list.html
index 808b6c50..10d842c0 100644
--- a/docs/reference/mean_mrs_list.html
+++ b/docs/reference/mean_mrs_list.html
@@ -1,5 +1,5 @@
-Return the mean of a list of mrs_data objects. — mean_mrs_list • Spectroscopy Analysis Tools (spant) Return the mean of a list of mrs_data objects. — mean_mrs_list • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/mean_vec_blocks.html b/docs/reference/mean_vec_blocks.html
index 8fc92eaa..dd78b122 100644
--- a/docs/reference/mean_vec_blocks.html
+++ b/docs/reference/mean_vec_blocks.html
@@ -1,5 +1,5 @@
-Calculate the mean of adjacent blocks in a vector. — mean_vec_blocks • Spectroscopy Analysis Tools (spant) Calculate the mean of adjacent blocks in a vector. — mean_vec_blocks • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/median_dyns.html b/docs/reference/median_dyns.html
index 1039d4b5..9a085b10 100644
--- a/docs/reference/median_dyns.html
+++ b/docs/reference/median_dyns.html
@@ -1,5 +1,5 @@
-Calculate the median dynamic data. — median_dyns • Spectroscopy Analysis Tools (spant) Calculate the median dynamic data. — median_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/mod_td.html b/docs/reference/mod_td.html
index 76ad0a40..141ef09e 100644
--- a/docs/reference/mod_td.html
+++ b/docs/reference/mod_td.html
@@ -1,5 +1,5 @@
-Apply the Modulus operator to the time-domain MRS signal. — mod_td • Spectroscopy Analysis Tools (spant) Apply the Modulus operator to the time-domain MRS signal. — mod_td • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/mrs_data2basis.html b/docs/reference/mrs_data2basis.html
index 62f7d749..11797b91 100644
--- a/docs/reference/mrs_data2basis.html
+++ b/docs/reference/mrs_data2basis.html
@@ -1,7 +1,5 @@
-Convert an mrs_data object to basis object - where basis signals are spread
-across the dynamic dimension in the MRS data. — mrs_data2basis • Spectroscopy Analysis Tools (spant) Convert an mrs_data object to basis object - where basis signals are spread across the dynamic dimension in the MRS data. — mrs_data2basis • Spectroscopy Analysis Tools (spant) Create a BIDS file structure from a vector of MRS data paths or list of mrs_data objects. — mrs_data2bids • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Create a BIDS file structure from a vector of MRS data paths or list of mrs_data objects.
+ Source: R/fmrs.R
+ mrs_data2bids.Rd
+
+
+
+ Create a BIDS file structure from a vector of MRS data paths or list of
+mrs_data objects.
+
+
+
+ mrs_data2bids(
+ mrs_data,
+ output_dir,
+ suffix = NULL,
+ sub = NULL,
+ ses = NULL,
+ task = NULL,
+ acq = NULL,
+ nuc = NULL,
+ voi = NULL,
+ rec = NULL,
+ run = NULL,
+ echo = NULL,
+ inv = NULL,
+ skip_existing = TRUE
+)
+
+
+
+ Arguments
+ - mrs_data
+vector of MRS data paths or list of mrs_data objects.
- output_dir
+the base directory to create the BIDS structure.
- suffix
+optional vector of file suffixes. Default behaviour is to
+automatically determine these from the input data, however it is recommended
+that they are specified to allow more efficient skipping of existing data.
- sub
+optional vector of subject labels. If not specified, these will be
+automatically generated as a series of increasing zero-padded integer values
+corresponding to the mrs_data input indices.
- ses
+optional vector of session labels.
- task
+optional vector of task labels.
- acq
+optional vector of acquisition labels.
- nuc
+optional vector of nucleus labels.
- voi
+optional vector of volume of interest labels.
- rec
+optional vector of reconstruction labels.
- run
+optional vector of run indices.
- echo
+optional vector of echo time indices.
- inv
+optional vector of inversion indices.
- skip_existing
+skip any data files that have already been converted.
+Defaults to TRUE, set to FALSE to force an overwrite of any existing data
+files.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/mrs_data2mat.html b/docs/reference/mrs_data2mat.html
index cf5ff28c..9e47688a 100644
--- a/docs/reference/mrs_data2mat.html
+++ b/docs/reference/mrs_data2mat.html
@@ -1,7 +1,5 @@
-Convert mrs_data object to a matrix, with spectral points in the column
-dimension and dynamics in the row dimension. — mrs_data2mat • Spectroscopy Analysis Tools (spant) Convert mrs_data object to a matrix, with spectral points in the column dimension and dynamics in the row dimension. — mrs_data2mat • Spectroscopy Analysis Tools (spant) Convert mrs_data object to a matrix, with spectral points in the column dimension and dynamics in the row dimension. — mrs_data2spec_mat • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Convert mrs_data object to a matrix, with spectral points in the column dimension and dynamics in the row dimension.
+ Source: R/mrs_data_proc.R
+ mrs_data2spec_mat.Rd
+
+
+
+ Convert mrs_data object to a matrix, with spectral points in the column
+dimension and dynamics in the row dimension.
+
+
+
+ mrs_data2spec_mat(mrs_data, collapse = TRUE)
+
+
+
+ Arguments
+ - mrs_data
+MRS data object or list of MRS data objects.
- collapse
+collapse all other dimensions along the dynamic dimension, eg
+a 16x16 MRSI grid would be first collapsed across 256 dynamic scans.
+
+ Value
+
+
+MRS data matrix.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/mrs_data2vec.html b/docs/reference/mrs_data2vec.html
index fb172d68..a1fd654d 100644
--- a/docs/reference/mrs_data2vec.html
+++ b/docs/reference/mrs_data2vec.html
@@ -1,5 +1,5 @@
-Convert mrs_data object to a vector. — mrs_data2vec • Spectroscopy Analysis Tools (spant) Convert mrs_data object to a vector. — mrs_data2vec • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -126,7 +126,7 @@ Value
diff --git a/docs/reference/mvfftshift.html b/docs/reference/mvfftshift.html
index 92b0841b..976b3410 100644
--- a/docs/reference/mvfftshift.html
+++ b/docs/reference/mvfftshift.html
@@ -1,7 +1,5 @@
-Perform a fftshift on a matrix, with each column replaced by its shifted
-result. — mvfftshift • Spectroscopy Analysis Tools (spant) Perform a fftshift on a matrix, with each column replaced by its shifted result. — mvfftshift • Spectroscopy Analysis Tools (spant) Perform an ifftshift on a matrix, with each column replaced by its shifted
-result. — mvifftshift • Spectroscopy Analysis Tools (spant) Perform an ifftshift on a matrix, with each column replaced by its shifted result. — mvifftshift • Spectroscopy Analysis Tools (spant) Print fit coordinates from a single index. — n2coord • Spectroscopy Analysis Tools (spant) Print fit coordinates from a single index. — n2coord • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/nifti_flip_lr.html b/docs/reference/nifti_flip_lr.html
index 730abe3c..19860b3c 100644
--- a/docs/reference/nifti_flip_lr.html
+++ b/docs/reference/nifti_flip_lr.html
@@ -1,9 +1,5 @@
-Flip the x data dimension order of a nifti image. This corresponds to
-flipping MRI data in the left-right direction, assuming the data in save in
-neurological format (can check with fslorient program). — nifti_flip_lr • Spectroscopy Analysis Tools (spant) Flip the x data dimension order of a nifti image. This corresponds to flipping MRI data in the left-right direction, assuming the data in save in neurological format (can check with fslorient program). — nifti_flip_lr • Spectroscopy Analysis Tools (spant) Export a one-page pdf of a single fit result — one_page_pdf • Spectroscopy Analysis Tools (spant) Export a one-page pdf of a single fit result — one_page_pdf • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -108,7 +108,7 @@ Arguments
diff --git a/docs/reference/ortho3.html b/docs/reference/ortho3.html
index 13ade97d..5d7dd2fd 100644
--- a/docs/reference/ortho3.html
+++ b/docs/reference/ortho3.html
@@ -1,5 +1,5 @@
-Display an orthographic projection plot of a nifti object. — ortho3 • Spectroscopy Analysis Tools (spant) Display an orthographic projection plot of a nifti object. — ortho3 • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -172,7 +172,7 @@ Arguments
diff --git a/docs/reference/ortho3_inter.html b/docs/reference/ortho3_inter.html
index 090cc5e5..15948899 100644
--- a/docs/reference/ortho3_inter.html
+++ b/docs/reference/ortho3_inter.html
@@ -1,5 +1,5 @@
-Display an interactive orthographic projection plot of a nifti object. — ortho3_inter • Spectroscopy Analysis Tools (spant) Display an interactive orthographic projection plot of a nifti object. — ortho3_inter • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -132,7 +132,7 @@ Arguments
diff --git a/docs/reference/peak_info.html b/docs/reference/peak_info.html
index 09058bd8..41c8ffaf 100644
--- a/docs/reference/peak_info.html
+++ b/docs/reference/peak_info.html
@@ -1,7 +1,5 @@
-Search for the highest peak in a spectral region and return the frequency,
-height and FWHM. — peak_info • Spectroscopy Analysis Tools (spant) Search for the highest peak in a spectral region and return the frequency, height and FWHM. — peak_info • Spectroscopy Analysis Tools (spant) Papoulis-Gerchberg (PG) algorithm method for k-space extrapolation. — pg_extrap_xy • Spectroscopy Analysis Tools (spant) Papoulis-Gerchberg (PG) algorithm method for k-space extrapolation. — pg_extrap_xy • Spectroscopy Analysis Tools (spant) Apply phasing parameters to MRS data. — phase • Spectroscopy Analysis Tools (spant) Apply phasing parameters to MRS data. — phase • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/phase_ref_1h_brain.html b/docs/reference/phase_ref_1h_brain.html
new file mode 100644
index 00000000..8707a74a
--- /dev/null
+++ b/docs/reference/phase_ref_1h_brain.html
@@ -0,0 +1,131 @@
+
+Corrected zero order phase and chemical shift offset in 1H MRS data from the brain. — phase_ref_1h_brain • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Corrected zero order phase and chemical shift offset in 1H MRS data from the brain.
+ Source: R/rats.R
+ phase_ref_1h_brain.Rd
+
+
+
+ Corrected zero order phase and chemical shift offset in 1H MRS data from the
+brain.
+
+
+
+ phase_ref_1h_brain(mrs_data, mean_ref = FALSE, ret_corr_only = TRUE)
+
+
+
+ Arguments
+ - mrs_data
+MRS data to be corrected.
- mean_ref
+apply the phase and offset of the mean spectrum to all
+others. Default is FALSE.
- ret_corr_only
+return the corrected data only.
+
+ Value
+
+
+corrected MRS data.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/plot.fit_result.html b/docs/reference/plot.fit_result.html
index e54d3bc1..836a53ee 100644
--- a/docs/reference/plot.fit_result.html
+++ b/docs/reference/plot.fit_result.html
@@ -1,5 +1,5 @@
-Plot the fitting results of an object of class fit_result. — plot.fit_result • Spectroscopy Analysis Tools (spant) Plot the fitting results of an object of class fit_result. — plot.fit_result • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -207,7 +207,7 @@ Arguments
diff --git a/docs/reference/plot.mrs_data.html b/docs/reference/plot.mrs_data.html
index fabcc35b..bb2ec651 100644
--- a/docs/reference/plot.mrs_data.html
+++ b/docs/reference/plot.mrs_data.html
@@ -1,5 +1,5 @@
-Plotting method for objects of class mrs_data. — plot.mrs_data • Spectroscopy Analysis Tools (spant) Plotting method for objects of class mrs_data. — plot.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -287,7 +287,7 @@ Arguments
diff --git a/docs/reference/plot_bc.html b/docs/reference/plot_bc.html
index 4f8309b4..b48142cc 100644
--- a/docs/reference/plot_bc.html
+++ b/docs/reference/plot_bc.html
@@ -1,5 +1,5 @@
-Convenience function to plot a baseline estimate with the original data. — plot_bc • Spectroscopy Analysis Tools (spant) Convenience function to plot a baseline estimate with the original data. — plot_bc • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -108,7 +108,7 @@ Arguments
diff --git a/docs/reference/plot_reg.html b/docs/reference/plot_reg.html
index ae1acbe7..2addb2f6 100644
--- a/docs/reference/plot_reg.html
+++ b/docs/reference/plot_reg.html
@@ -1,5 +1,5 @@
-Plot regressors as an image. — plot_reg • Spectroscopy Analysis Tools (spant) Plot regressors as an image. — plot_reg • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/plot_slice_fit.html b/docs/reference/plot_slice_fit.html
index fbc7b560..57f1af8a 100644
--- a/docs/reference/plot_slice_fit.html
+++ b/docs/reference/plot_slice_fit.html
@@ -1,5 +1,5 @@
-Plot a 2D slice from an MRSI fit result object. — plot_slice_fit • Spectroscopy Analysis Tools (spant) Plot a 2D slice from an MRSI fit result object. — plot_slice_fit • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -129,7 +129,7 @@ Arguments
diff --git a/docs/reference/plot_slice_fit_inter.html b/docs/reference/plot_slice_fit_inter.html
index 4eed104a..da105a7d 100644
--- a/docs/reference/plot_slice_fit_inter.html
+++ b/docs/reference/plot_slice_fit_inter.html
@@ -1,5 +1,5 @@
-Plot a 2D slice from an MRSI fit result object. — plot_slice_fit_inter • Spectroscopy Analysis Tools (spant) Plot a 2D slice from an MRSI fit result object. — plot_slice_fit_inter • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -134,7 +134,7 @@ Arguments
diff --git a/docs/reference/plot_slice_map.html b/docs/reference/plot_slice_map.html
index 553e9ac8..ffb2a134 100644
--- a/docs/reference/plot_slice_map.html
+++ b/docs/reference/plot_slice_map.html
@@ -1,5 +1,5 @@
-Plot a slice from a 7 dimensional array. — plot_slice_map • Spectroscopy Analysis Tools (spant) Plot a slice from a 7 dimensional array. — plot_slice_map • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -153,7 +153,7 @@ Arguments
diff --git a/docs/reference/plot_slice_map_inter.html b/docs/reference/plot_slice_map_inter.html
index 40d33b42..90968f66 100644
--- a/docs/reference/plot_slice_map_inter.html
+++ b/docs/reference/plot_slice_map_inter.html
@@ -1,7 +1,5 @@
-Plot an interactive slice map from a data array where voxels can be selected
-to display a corresponding spectrum. — plot_slice_map_inter • Spectroscopy Analysis Tools (spant) Plot an interactive slice map from a data array where voxels can be selected to display a corresponding spectrum. — plot_slice_map_inter • Spectroscopy Analysis Tools (spant) Plot the spectral standard deviation. — plot_spec_sd • Spectroscopy Analysis Tools (spant) Plot the spectral standard deviation. — plot_spec_sd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Arguments
diff --git a/docs/reference/plot_voi_overlay.html b/docs/reference/plot_voi_overlay.html
index 9a782e88..bbbbf35e 100644
--- a/docs/reference/plot_voi_overlay.html
+++ b/docs/reference/plot_voi_overlay.html
@@ -1,5 +1,5 @@
-Plot a volume as an image overlay. — plot_voi_overlay • Spectroscopy Analysis Tools (spant) Plot a volume as an image overlay. — plot_voi_overlay • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -116,7 +116,7 @@ Arguments
diff --git a/docs/reference/plot_voi_overlay_seg.html b/docs/reference/plot_voi_overlay_seg.html
index 3d4e74ff..0e800ff2 100644
--- a/docs/reference/plot_voi_overlay_seg.html
+++ b/docs/reference/plot_voi_overlay_seg.html
@@ -1,5 +1,5 @@
-Plot a volume as an overlay on a segmented brain volume. — plot_voi_overlay_seg • Spectroscopy Analysis Tools (spant) Plot a volume as an overlay on a segmented brain volume. — plot_voi_overlay_seg • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Arguments
diff --git a/docs/reference/ppm.html b/docs/reference/ppm.html
index c352327a..ee4696e2 100644
--- a/docs/reference/ppm.html
+++ b/docs/reference/ppm.html
@@ -1,5 +1,5 @@
-Return the ppm scale of an MRS dataset or fit result. — ppm • Spectroscopy Analysis Tools (spant) Return the ppm scale of an MRS dataset or fit result. — ppm • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -132,7 +132,7 @@ Value
diff --git a/docs/reference/precomp.html b/docs/reference/precomp.html
index 822d7336..df3d2c6c 100644
--- a/docs/reference/precomp.html
+++ b/docs/reference/precomp.html
@@ -1,7 +1,5 @@
-Save function results to file and load on subsequent calls to avoid repeat
-computation. — precomp • Spectroscopy Analysis Tools (spant) Save function results to file and load on subsequent calls to avoid repeat computation. — precomp • Spectroscopy Analysis Tools (spant) Preprocess and perform quality assessment of a single SVS data set. — preproc_svs • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Preprocess and perform quality assessment of a single SVS data set.
+ Source: R/fmrs.R
+ preproc_svs.Rd
+
+
+
+ Preprocess and perform quality assessment of a single SVS data set.
+
+
+
+ preproc_svs(path, label = NULL, output_dir = NULL, ref_inds = NULL)
+
+
+
+ Arguments
+ - path
+path to the fMRS data file or IMA directory.
- label
+a label to describe the data set.
- output_dir
+output directory.
- ref_inds
+a vector of 1-based indices for any water reference dynamic
+scans.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/preproc_svs_dataset.html b/docs/reference/preproc_svs_dataset.html
new file mode 100644
index 00000000..07c3a29b
--- /dev/null
+++ b/docs/reference/preproc_svs_dataset.html
@@ -0,0 +1,148 @@
+
+Preprocess and perform quality assessment of one or more SVS data sets. — preproc_svs_dataset • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Preprocess and perform quality assessment of one or more SVS data sets.
+ Source: R/fmrs.R
+ preproc_svs_dataset.Rd
+
+
+
+ Preprocess and perform quality assessment of one or more SVS data sets.
+
+
+
+ preproc_svs_dataset(
+ paths,
+ labels = NULL,
+ output_dir = "spant_analysis",
+ exclude_labels = NULL,
+ overwrite = FALSE,
+ ref_inds = NULL,
+ return_results = FALSE
+)
+
+
+
+ Arguments
+ - paths
+paths to the fMRS data file or IMA directory.
- labels
+labels to describe each data set.
- output_dir
+output directory.
- exclude_labels
+vector of labels of scans to exclude, eg poor quality
+data.
- overwrite
+overwrite saved results, defaults to FALSE.
- ref_inds
+a vector of 1-based indices for any water reference dynamic
+scans.
- return_results
+function will return key outputs, defaults to FALSE.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/print.fit_result.html b/docs/reference/print.fit_result.html
index 297f28dc..5f434e57 100644
--- a/docs/reference/print.fit_result.html
+++ b/docs/reference/print.fit_result.html
@@ -1,5 +1,5 @@
-Print a summary of an object of class fit_result. — print.fit_result • Spectroscopy Analysis Tools (spant) Print a summary of an object of class fit_result. — print.fit_result • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -105,7 +105,7 @@ Arguments
diff --git a/docs/reference/print.mrs_data.html b/docs/reference/print.mrs_data.html
index 51199017..e1561eb2 100644
--- a/docs/reference/print.mrs_data.html
+++ b/docs/reference/print.mrs_data.html
@@ -1,5 +1,5 @@
-Print a summary of mrs_data parameters. — print.mrs_data • Spectroscopy Analysis Tools (spant) Print a summary of mrs_data parameters. — print.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -109,7 +109,7 @@ Arguments
diff --git a/docs/reference/qn_states.html b/docs/reference/qn_states.html
index 0f42f2f9..d7aa6715 100644
--- a/docs/reference/qn_states.html
+++ b/docs/reference/qn_states.html
@@ -1,5 +1,5 @@
-Get the quantum coherence matrix for a spin system. — qn_states • Spectroscopy Analysis Tools (spant) Get the quantum coherence matrix for a spin system. — qn_states • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/rats.html b/docs/reference/rats.html
index 5a39a396..93585e08 100644
--- a/docs/reference/rats.html
+++ b/docs/reference/rats.html
@@ -1,5 +1,5 @@
-Robust Alignment to a Target Spectrum (RATS). — rats • Spectroscopy Analysis Tools (spant) Robust Alignment to a Target Spectrum (RATS). — rats • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -207,7 +207,7 @@ Value
diff --git a/docs/reference/re_weighting.html b/docs/reference/re_weighting.html
index d21caf21..8b0b070a 100644
--- a/docs/reference/re_weighting.html
+++ b/docs/reference/re_weighting.html
@@ -1,5 +1,5 @@
-Apply a weighting to the FID to enhance spectral resolution. — re_weighting • Spectroscopy Analysis Tools (spant) Apply a weighting to the FID to enhance spectral resolution. — re_weighting • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/read_basis.html b/docs/reference/read_basis.html
index da9b94af..eb6f8557 100644
--- a/docs/reference/read_basis.html
+++ b/docs/reference/read_basis.html
@@ -1,5 +1,5 @@
-Read a basis file in LCModel .basis format. — read_basis • Spectroscopy Analysis Tools (spant) Read a basis file in LCModel .basis format. — read_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/read_ima_coil_dir.html b/docs/reference/read_ima_coil_dir.html
index 28c02de0..4f073cd8 100644
--- a/docs/reference/read_ima_coil_dir.html
+++ b/docs/reference/read_ima_coil_dir.html
@@ -1,9 +1,5 @@
-Read a directory containing Siemens MRS IMA files and combine along the coil
-dimension. Note that the coil ID is inferred from the sorted file name and
-should be checked when consistency is required between two directories. — read_ima_coil_dir • Spectroscopy Analysis Tools (spant) Read a directory containing Siemens MRS IMA files and combine along the coil dimension. Note that the coil ID is inferred from the sorted file name and should be checked when consistency is required between two directories. — read_ima_coil_dir • Spectroscopy Analysis Tools (spant) Read a directory containing Siemens MRS IMA files and combine along the
-dynamic dimension. Note that the coil ID is inferred from the sorted file
-name and should be checked when consistency is required. — read_ima_dyn_dir • Spectroscopy Analysis Tools (spant) Read a directory containing Siemens MRS IMA files and combine along the dynamic dimension. Note that the coil ID is inferred from the sorted file name and should be checked when consistency is required. — read_ima_dyn_dir • Spectroscopy Analysis Tools (spant) Read an LCModel formatted coord file containing fit information. — read_lcm_coord • Spectroscopy Analysis Tools (spant) Read an LCModel formatted coord file containing fit information. — read_lcm_coord • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -107,7 +107,7 @@ Value
diff --git a/docs/reference/read_mrs.html b/docs/reference/read_mrs.html
index 3ac2a36b..2cf36b20 100644
--- a/docs/reference/read_mrs.html
+++ b/docs/reference/read_mrs.html
@@ -1,5 +1,5 @@
-Read MRS data from a file. — read_mrs • Spectroscopy Analysis Tools (spant) Read MRS data from a file. — read_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -88,7 +88,8 @@ Read MRS data from a file.
full_fid = FALSE,
omit_svs_ref_scans = TRUE,
verbose = FALSE,
- extra = NULL
+ extra = NULL,
+ fid_filt_dist = NULL
)
@@ -140,6 +141,13 @@ Arguments
an optional data frame to provide additional variables for use
in subsequent analysis steps, eg id or grouping variables.
fid_filt_dist
+indicate if the data has a distorted FID due to a
+brick-wall filter being used to downsample the data. Default is to auto
+detect this from the data, but TRUE or FALSE options can be given to override
+detection.
Value
@@ -183,7 +191,7 @@ Examples
diff --git a/docs/reference/read_mrs_tqn.html b/docs/reference/read_mrs_tqn.html
index 5766362f..84bdaf3a 100644
--- a/docs/reference/read_mrs_tqn.html
+++ b/docs/reference/read_mrs_tqn.html
@@ -1,5 +1,5 @@
-Read MRS data using the TARQUIN software package. — read_mrs_tqn • Spectroscopy Analysis Tools (spant) Read MRS data using the TARQUIN software package. — read_mrs_tqn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -131,7 +131,7 @@ Examples
diff --git a/docs/reference/read_pulse_ascii.html b/docs/reference/read_pulse_ascii.html
index c9e0d43c..ab11c9cc 100644
--- a/docs/reference/read_pulse_ascii.html
+++ b/docs/reference/read_pulse_ascii.html
@@ -1,5 +1,5 @@
-Read an ASCII formatted pulse file. — read_pulse_ascii • Spectroscopy Analysis Tools (spant) Read an ASCII formatted pulse file. — read_pulse_ascii • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/read_pulse_bruker.html b/docs/reference/read_pulse_bruker.html
index c92bf76a..dbe9073b 100644
--- a/docs/reference/read_pulse_bruker.html
+++ b/docs/reference/read_pulse_bruker.html
@@ -1,5 +1,5 @@
-Read a Bruker formatted pulse file — read_pulse_bruker • Spectroscopy Analysis Tools (spant) Read a Bruker formatted pulse file — read_pulse_bruker • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/read_pulse_pta.html b/docs/reference/read_pulse_pta.html
index 72e1b6d4..a0fac3c3 100644
--- a/docs/reference/read_pulse_pta.html
+++ b/docs/reference/read_pulse_pta.html
@@ -1,5 +1,5 @@
-Read a .pta formatted pulse file compatible with Siemens PulseTool. — read_pulse_pta • Spectroscopy Analysis Tools (spant) Read a .pta formatted pulse file compatible with Siemens PulseTool. — read_pulse_pta • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/read_siemens_txt_hdr.html b/docs/reference/read_siemens_txt_hdr.html
index 23fb8c70..3a17d87c 100644
--- a/docs/reference/read_siemens_txt_hdr.html
+++ b/docs/reference/read_siemens_txt_hdr.html
@@ -1,5 +1,5 @@
-Read the text format header found in Siemens IMA and TWIX data files. — read_siemens_txt_hdr • Spectroscopy Analysis Tools (spant) Read the text format header found in Siemens IMA and TWIX data files. — read_siemens_txt_hdr • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -78,7 +78,7 @@ Read the text format header found in Siemens IMA and TWIX data files.
- read_siemens_txt_hdr(input, version = "vd", verbose, offset = 0)
+ read_siemens_txt_hdr(input, version = "vd", verbose = FALSE, offset = 0)
@@ -118,7 +118,7 @@ Value
diff --git a/docs/reference/read_tqn_fit.html b/docs/reference/read_tqn_fit.html
index 4da6c25e..a1630420 100644
--- a/docs/reference/read_tqn_fit.html
+++ b/docs/reference/read_tqn_fit.html
@@ -1,5 +1,5 @@
-Reader for csv fit results generated by TARQUIN. — read_tqn_fit • Spectroscopy Analysis Tools (spant) Reader for csv fit results generated by TARQUIN. — read_tqn_fit • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -113,7 +113,7 @@ Examples
diff --git a/docs/reference/read_tqn_result.html b/docs/reference/read_tqn_result.html
index 36659714..68a3e98c 100644
--- a/docs/reference/read_tqn_result.html
+++ b/docs/reference/read_tqn_result.html
@@ -1,5 +1,5 @@
-Reader for csv results generated by TARQUIN. — read_tqn_result • Spectroscopy Analysis Tools (spant) Reader for csv results generated by TARQUIN. — read_tqn_result • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -117,7 +117,7 @@ Examples
diff --git a/docs/reference/recon_imag.html b/docs/reference/recon_imag.html
index d2a72225..5bc3b1eb 100644
--- a/docs/reference/recon_imag.html
+++ b/docs/reference/recon_imag.html
@@ -1,7 +1,5 @@
-Reconstruct complex time-domain data from the real part of frequency-domain
-data. — recon_imag • Spectroscopy Analysis Tools (spant) Reconstruct complex time-domain data from the real part of frequency-domain data. — recon_imag • Spectroscopy Analysis Tools (spant) Reconstruct complex time-domain data from the real part of frequency-domain
-data. — recon_imag_vec • Spectroscopy Analysis Tools (spant) Reconstruct complex time-domain data from the real part of frequency-domain data. — recon_imag_vec • Spectroscopy Analysis Tools (spant) Reconstruct 2D MRSI data from a twix file loaded with read_mrs. — recon_twix_2d_mrsi • Spectroscopy Analysis Tools (spant) Reconstruct 2D MRSI data from a twix file loaded with read_mrs. — recon_twix_2d_mrsi • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/rectangular_mask.html b/docs/reference/rectangular_mask.html
index a2117283..6e469bc9 100644
--- a/docs/reference/rectangular_mask.html
+++ b/docs/reference/rectangular_mask.html
@@ -1,5 +1,5 @@
-Create a rectangular mask stored as a matrix of logical values. — rectangular_mask • Spectroscopy Analysis Tools (spant) Create a rectangular mask stored as a matrix of logical values. — rectangular_mask • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -130,7 +130,7 @@ Value
diff --git a/docs/reference/reexports.html b/docs/reference/reexports.html
index 694a75d1..a59e8379 100644
--- a/docs/reference/reexports.html
+++ b/docs/reference/reexports.html
@@ -1,5 +1,5 @@
-Objects exported from other packages — reexports • Spectroscopy Analysis Tools (spant) Objects exported from other packages — reexports • Spectroscopy Analysis Tools (spant)
Spectroscopy Analysis Tools (spant)
- 2.21.0
+ 2.22.0
@@ -103,7 +103,7 @@ Objects exported from other packages
diff --git a/docs/reference/rep_array_dim.html b/docs/reference/rep_array_dim.html
index b9c49b4a..48c0a5ed 100644
--- a/docs/reference/rep_array_dim.html
+++ b/docs/reference/rep_array_dim.html
@@ -1,5 +1,5 @@
-Repeat an array over a given dimension. — rep_array_dim • Spectroscopy Analysis Tools (spant) Repeat an array over a given dimension. — rep_array_dim • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/rep_dyn.html b/docs/reference/rep_dyn.html
index 6bbfb0ef..89a4bb9b 100644
--- a/docs/reference/rep_dyn.html
+++ b/docs/reference/rep_dyn.html
@@ -1,5 +1,5 @@
-Replicate a scan in the dynamic dimension. — rep_dyn • Spectroscopy Analysis Tools (spant) Replicate a scan in the dynamic dimension. — rep_dyn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/rep_mrs.html b/docs/reference/rep_mrs.html
index 67730b5c..becb8f00 100644
--- a/docs/reference/rep_mrs.html
+++ b/docs/reference/rep_mrs.html
@@ -1,5 +1,5 @@
-Replicate a scan over a given dimension. — rep_mrs • Spectroscopy Analysis Tools (spant) Replicate a scan over a given dimension. — rep_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -138,7 +138,7 @@ Value
diff --git a/docs/reference/resample_basis.html b/docs/reference/resample_basis.html
index b0f2ab17..c7a6222a 100644
--- a/docs/reference/resample_basis.html
+++ b/docs/reference/resample_basis.html
@@ -1,5 +1,5 @@
-Resample a basis-set to match a mrs_data acquisition. — resample_basis • Spectroscopy Analysis Tools (spant) Resample a basis-set to match a mrs_data acquisition. — resample_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -116,7 +116,7 @@ Value
diff --git a/docs/reference/resample_img.html b/docs/reference/resample_img.html
index f1e7beaf..b0cc8f71 100644
--- a/docs/reference/resample_img.html
+++ b/docs/reference/resample_img.html
@@ -1,5 +1,5 @@
-Resample an image to match a target image space. — resample_img • Spectroscopy Analysis Tools (spant) Resample an image to match a target image space. — resample_img • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/resample_voi.html b/docs/reference/resample_voi.html
index 8fbfa836..a29ab096 100644
--- a/docs/reference/resample_voi.html
+++ b/docs/reference/resample_voi.html
@@ -1,7 +1,5 @@
-Resample a VOI to match a target image space using nearest-neighbour
-interpolation. — resample_voi • Spectroscopy Analysis Tools (spant) Resample a VOI to match a target image space using nearest-neighbour interpolation. — resample_voi • Spectroscopy Analysis Tools (spant) Reslice a nifti object to match the orientation of mrs data. — reslice_to_mrs • Spectroscopy Analysis Tools (spant) Reslice a nifti object to match the orientation of mrs data. — reslice_to_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/reson_table2mrs_data.html b/docs/reference/reson_table2mrs_data.html
index d75579ee..c5a2167a 100644
--- a/docs/reference/reson_table2mrs_data.html
+++ b/docs/reference/reson_table2mrs_data.html
@@ -1,5 +1,5 @@
-Generate mrs_data from a table of single Lorentzian resonances. — reson_table2mrs_data • Spectroscopy Analysis Tools (spant) Generate mrs_data from a table of single Lorentzian resonances. — reson_table2mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -119,7 +119,7 @@ Value
diff --git a/docs/reference/rm_dyns.html b/docs/reference/rm_dyns.html
index 5d5ef692..573e1f51 100644
--- a/docs/reference/rm_dyns.html
+++ b/docs/reference/rm_dyns.html
@@ -1,5 +1,5 @@
-Remove a subset of dynamic scans. — rm_dyns • Spectroscopy Analysis Tools (spant) Remove a subset of dynamic scans. — rm_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/scale_amp_molal.html b/docs/reference/scale_amp_molal.html
index aaeee1f2..7acb8cb0 100644
--- a/docs/reference/scale_amp_molal.html
+++ b/docs/reference/scale_amp_molal.html
@@ -1,7 +1,5 @@
-Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water). — scale_amp_molal • Spectroscopy Analysis Tools (spant) Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / kg of tissue water). — scale_amp_molal • Spectroscopy Analysis Tools (spant)
Spectroscopy Analysis Tools (spant)
- 2.21.0
+ 2.22.0
@@ -76,8 +74,7 @@
- Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water).
+ Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / kg of tissue water).
Source: R/amp_scaling.R
scale_amp_molal.Rd
@@ -163,7 +160,7 @@ Value
diff --git a/docs/reference/scale_amp_molal_pvc.html b/docs/reference/scale_amp_molal_pvc.html
index 962d6afc..4d194abd 100644
--- a/docs/reference/scale_amp_molal_pvc.html
+++ b/docs/reference/scale_amp_molal_pvc.html
@@ -1,7 +1,5 @@
-Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water). — scale_amp_molal_pvc • Spectroscopy Analysis Tools (spant)
@@ -75,8 +73,7 @@
- Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water).
+ Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / kg of tissue water).
Source: R/amp_scaling.R
scale_amp_molal_pvc.Rd
@@ -141,7 +138,7 @@ Value
diff --git a/docs/reference/scale_amp_molar.html b/docs/reference/scale_amp_molar.html
index 02358d91..dc87a338 100644
--- a/docs/reference/scale_amp_molar.html
+++ b/docs/reference/scale_amp_molar.html
@@ -1,7 +1,5 @@
-Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / Litre of tissue). — scale_amp_molar • Spectroscopy Analysis Tools (spant) Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / Litre of tissue). — scale_amp_molar • Spectroscopy Analysis Tools (spant) Convert default LCM/TARQUIN concentration scaling to molal units with partial
-volume correction. — scale_amp_molar2molal_pvc • Spectroscopy Analysis Tools (spant) Convert default LCM/TARQUIN concentration scaling to molal units with partial volume correction. — scale_amp_molar2molal_pvc • Spectroscopy Analysis Tools (spant) Scale fitted amplitudes to a ratio of signal amplitude. — scale_amp_ratio • Spectroscopy Analysis Tools (spant) Scale fitted amplitudes to a ratio of signal amplitude. — scale_amp_ratio • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -116,7 +116,7 @@ Value
diff --git a/docs/reference/scale_amp_ratio_value.html b/docs/reference/scale_amp_ratio_value.html
index 2036837a..6af8ac51 100644
--- a/docs/reference/scale_amp_ratio_value.html
+++ b/docs/reference/scale_amp_ratio_value.html
@@ -1,5 +1,5 @@
-Scale fitted amplitudes to a ratio of signal amplitude. — scale_amp_ratio_value • Spectroscopy Analysis Tools (spant) Scale fitted amplitudes to a ratio of signal amplitude. — scale_amp_ratio_value • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/scale_amp_water_ratio.html b/docs/reference/scale_amp_water_ratio.html
index 5b25e884..35a76b00 100644
--- a/docs/reference/scale_amp_water_ratio.html
+++ b/docs/reference/scale_amp_water_ratio.html
@@ -1,5 +1,5 @@
-Scale metabolite amplitudes as a ratio to the unsuppressed water amplitude. — scale_amp_water_ratio • Spectroscopy Analysis Tools (spant) Scale metabolite amplitudes as a ratio to the unsuppressed water amplitude. — scale_amp_water_ratio • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/scale_basis_amp.html b/docs/reference/scale_basis_amp.html
index 9401c3f1..5a58b5e5 100644
--- a/docs/reference/scale_basis_amp.html
+++ b/docs/reference/scale_basis_amp.html
@@ -1,5 +1,5 @@
-Scale a basis object by a scalar. — scale_basis_amp • Spectroscopy Analysis Tools (spant) Scale a basis object by a scalar. — scale_basis_amp • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/scale_basis_from_singlet.html b/docs/reference/scale_basis_from_singlet.html
index 0d542bc8..c9a19e77 100644
--- a/docs/reference/scale_basis_from_singlet.html
+++ b/docs/reference/scale_basis_from_singlet.html
@@ -1,5 +1,5 @@
-Scale a basis-set to be consistent with spant assumptions for water scaling. — scale_basis_from_singlet • Spectroscopy Analysis Tools (spant) Scale a basis-set to be consistent with spant assumptions for water scaling. — scale_basis_from_singlet • Spectroscopy Analysis Tools (spant)
Spectroscopy Analysis Tools (spant)
- 2.21.0
+ 2.22.0
@@ -127,7 +127,7 @@ Value
diff --git a/docs/reference/scale_mrs_amp.html b/docs/reference/scale_mrs_amp.html
index b5501a0d..990f058a 100644
--- a/docs/reference/scale_mrs_amp.html
+++ b/docs/reference/scale_mrs_amp.html
@@ -1,5 +1,5 @@
-Scale an mrs_data object by a scalar or vector or amplitudes. — scale_mrs_amp • Spectroscopy Analysis Tools (spant) Scale an mrs_data object by a scalar or vector or amplitudes. — scale_mrs_amp • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/scale_spec.html b/docs/reference/scale_spec.html
index 4f6ea835..6b3ddba4 100644
--- a/docs/reference/scale_spec.html
+++ b/docs/reference/scale_spec.html
@@ -1,5 +1,5 @@
-Scale mrs_data to a spectral region. — scale_spec • Spectroscopy Analysis Tools (spant) Scale mrs_data to a spectral region. — scale_spec • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -141,7 +141,7 @@ Value
diff --git a/docs/reference/sd.html b/docs/reference/sd.html
index ea1eec9f..3ae4dfd4 100644
--- a/docs/reference/sd.html
+++ b/docs/reference/sd.html
@@ -1,5 +1,5 @@
-Calculate the standard deviation spectrum from an mrs_data object. — sd • Spectroscopy Analysis Tools (spant) Calculate the standard deviation spectrum from an mrs_data object. — sd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/sd.mrs_data.html b/docs/reference/sd.mrs_data.html
index 3f92a49f..13bdda85 100644
--- a/docs/reference/sd.mrs_data.html
+++ b/docs/reference/sd.mrs_data.html
@@ -1,5 +1,5 @@
-Calculate the standard deviation spectrum from an mrs_data object. — sd.mrs_data • Spectroscopy Analysis Tools (spant) Calculate the standard deviation spectrum from an mrs_data object. — sd.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/seconds.html b/docs/reference/seconds.html
index b34d6627..467ee17f 100644
--- a/docs/reference/seconds.html
+++ b/docs/reference/seconds.html
@@ -1,5 +1,5 @@
-Return a time scale vector to match the FID of an MRS data object. — seconds • Spectroscopy Analysis Tools (spant) Return a time scale vector to match the FID of an MRS data object. — seconds • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/seq_cpmg_ideal.html b/docs/reference/seq_cpmg_ideal.html
index 547e96ab..45727c86 100644
--- a/docs/reference/seq_cpmg_ideal.html
+++ b/docs/reference/seq_cpmg_ideal.html
@@ -1,5 +1,5 @@
-CPMG style sequence with ideal pulses. — seq_cpmg_ideal • Spectroscopy Analysis Tools (spant) CPMG style sequence with ideal pulses. — seq_cpmg_ideal • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/seq_mega_press_ideal.html b/docs/reference/seq_mega_press_ideal.html
index 0769b8b4..a9cd7fa0 100644
--- a/docs/reference/seq_mega_press_ideal.html
+++ b/docs/reference/seq_mega_press_ideal.html
@@ -1,7 +1,5 @@
-MEGA-PRESS sequence with ideal localisation pulses and Gaussian shaped
-editing pulse. — seq_mega_press_ideal • Spectroscopy Analysis Tools (spant) MEGA-PRESS sequence with ideal localisation pulses and Gaussian shaped editing pulse. — seq_mega_press_ideal • Spectroscopy Analysis Tools (spant) PRESS sequence with shaped refocusing pulses. — seq_press_2d_shaped • Spectroscopy Analysis Tools (spant) PRESS sequence with shaped refocusing pulses. — seq_press_2d_shaped • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -165,7 +165,7 @@ Value
diff --git a/docs/reference/seq_press_ideal.html b/docs/reference/seq_press_ideal.html
index 8c976856..72c3af3d 100644
--- a/docs/reference/seq_press_ideal.html
+++ b/docs/reference/seq_press_ideal.html
@@ -1,5 +1,5 @@
-PRESS sequence with ideal pulses. — seq_press_ideal • Spectroscopy Analysis Tools (spant) PRESS sequence with ideal pulses. — seq_press_ideal • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/seq_pulse_acquire.html b/docs/reference/seq_pulse_acquire.html
index 4a88fc64..ad80571e 100644
--- a/docs/reference/seq_pulse_acquire.html
+++ b/docs/reference/seq_pulse_acquire.html
@@ -1,5 +1,5 @@
-Simple pulse and acquire sequence with ideal pulses. — seq_pulse_acquire • Spectroscopy Analysis Tools (spant) Simple pulse and acquire sequence with ideal pulses. — seq_pulse_acquire • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/seq_slaser_ideal.html b/docs/reference/seq_slaser_ideal.html
index 74688f4d..eb83e8e3 100644
--- a/docs/reference/seq_slaser_ideal.html
+++ b/docs/reference/seq_slaser_ideal.html
@@ -1,5 +1,5 @@
-sLASER sequence with ideal pulses. — seq_slaser_ideal • Spectroscopy Analysis Tools (spant) sLASER sequence with ideal pulses. — seq_slaser_ideal • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -126,7 +126,7 @@ Value
diff --git a/docs/reference/seq_spin_echo_ideal.html b/docs/reference/seq_spin_echo_ideal.html
index e23271de..4248716f 100644
--- a/docs/reference/seq_spin_echo_ideal.html
+++ b/docs/reference/seq_spin_echo_ideal.html
@@ -1,5 +1,5 @@
-Spin echo sequence with ideal pulses. — seq_spin_echo_ideal • Spectroscopy Analysis Tools (spant) Spin echo sequence with ideal pulses. — seq_spin_echo_ideal • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/seq_steam_ideal.html b/docs/reference/seq_steam_ideal.html
index a60685a8..1c8115d7 100644
--- a/docs/reference/seq_steam_ideal.html
+++ b/docs/reference/seq_steam_ideal.html
@@ -1,5 +1,5 @@
-STEAM sequence with ideal pulses. — seq_steam_ideal • Spectroscopy Analysis Tools (spant) STEAM sequence with ideal pulses. — seq_steam_ideal • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -128,7 +128,7 @@ Value
diff --git a/docs/reference/seq_steam_ideal_cof.html b/docs/reference/seq_steam_ideal_cof.html
index 8f225740..cba7af91 100644
--- a/docs/reference/seq_steam_ideal_cof.html
+++ b/docs/reference/seq_steam_ideal_cof.html
@@ -1,7 +1,5 @@
-STEAM sequence with ideal pulses and coherence order filtering to simulate
-gradient crushers. — seq_steam_ideal_cof • Spectroscopy Analysis Tools (spant) STEAM sequence with ideal pulses and coherence order filtering to simulate gradient crushers. — seq_steam_ideal_cof • Spectroscopy Analysis Tools (spant) STEAM sequence with ideal pulses using the z-rotation gradient simulation
-method described by Young et al JMR 140, 146-152 (1999). — seq_steam_ideal_young • Spectroscopy Analysis Tools (spant) STEAM sequence with ideal pulses using the z-rotation gradient simulation method described by Young et al JMR 140, 146-152 (1999). — seq_steam_ideal_young • Spectroscopy Analysis Tools (spant) Set the number of transients for an mrs_data object. — set_Ntrans • Spectroscopy Analysis Tools (spant) Set the number of transients for an mrs_data object. — set_Ntrans • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/set_def_acq_paras.html b/docs/reference/set_def_acq_paras.html
index 3e1b4004..cc2ada9c 100644
--- a/docs/reference/set_def_acq_paras.html
+++ b/docs/reference/set_def_acq_paras.html
@@ -1,5 +1,5 @@
-Set the default acquisition parameters. — set_def_acq_paras • Spectroscopy Analysis Tools (spant) Set the default acquisition parameters. — set_def_acq_paras • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Arguments
diff --git a/docs/reference/set_lcm_cmd.html b/docs/reference/set_lcm_cmd.html
index 2056ed01..42bb2f24 100644
--- a/docs/reference/set_lcm_cmd.html
+++ b/docs/reference/set_lcm_cmd.html
@@ -1,5 +1,5 @@
-Set the command to run the LCModel command-line program. — set_lcm_cmd • Spectroscopy Analysis Tools (spant) Set the command to run the LCModel command-line program. — set_lcm_cmd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/set_lw.html b/docs/reference/set_lw.html
index b64ec851..bb176c62 100644
--- a/docs/reference/set_lw.html
+++ b/docs/reference/set_lw.html
@@ -1,5 +1,5 @@
-Apply line-broadening to an mrs_data object to achieve a specified linewidth. — set_lw • Spectroscopy Analysis Tools (spant) Apply line-broadening to an mrs_data object to achieve a specified linewidth. — set_lw • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -123,7 +123,7 @@ Value
diff --git a/docs/reference/set_mask_xy_mat.html b/docs/reference/set_mask_xy_mat.html
index 49dc5d4e..52c4b617 100644
--- a/docs/reference/set_mask_xy_mat.html
+++ b/docs/reference/set_mask_xy_mat.html
@@ -1,5 +1,5 @@
-Set the masked voxels in a 2D MRSI dataset to given spectrum. — set_mask_xy_mat • Spectroscopy Analysis Tools (spant) Set the masked voxels in a 2D MRSI dataset to given spectrum. — set_mask_xy_mat • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Value
diff --git a/docs/reference/set_precomp_mode.html b/docs/reference/set_precomp_mode.html
index f44bd5d3..47c28e3b 100644
--- a/docs/reference/set_precomp_mode.html
+++ b/docs/reference/set_precomp_mode.html
@@ -1,5 +1,5 @@
-Set the precompute mode. — set_precomp_mode • Spectroscopy Analysis Tools (spant) Set the precompute mode. — set_precomp_mode • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/set_precomp_verbose.html b/docs/reference/set_precomp_verbose.html
index 1453a231..9c613505 100644
--- a/docs/reference/set_precomp_verbose.html
+++ b/docs/reference/set_precomp_verbose.html
@@ -1,5 +1,5 @@
-Set the verbosity of the precompute function. — set_precomp_verbose • Spectroscopy Analysis Tools (spant) Set the verbosity of the precompute function. — set_precomp_verbose • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/set_ref.html b/docs/reference/set_ref.html
index 8953fa50..5436dfa2 100644
--- a/docs/reference/set_ref.html
+++ b/docs/reference/set_ref.html
@@ -1,5 +1,5 @@
-Set the ppm reference value (eg ppm value at 0Hz). — set_ref • Spectroscopy Analysis Tools (spant) Set the ppm reference value (eg ppm value at 0Hz). — set_ref • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/set_td_pts.html b/docs/reference/set_td_pts.html
index 8a80d42a..586459ff 100644
--- a/docs/reference/set_td_pts.html
+++ b/docs/reference/set_td_pts.html
@@ -1,7 +1,5 @@
-Set the number of time-domain data points, truncating or zero-filling as
-appropriate. — set_td_pts • Spectroscopy Analysis Tools (spant) Set the number of time-domain data points, truncating or zero-filling as appropriate. — set_td_pts • Spectroscopy Analysis Tools (spant) Set the command to run the TARQUIN command-line program. — set_tqn_cmd • Spectroscopy Analysis Tools (spant) Set the command to run the TARQUIN command-line program. — set_tqn_cmd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/set_tr.html b/docs/reference/set_tr.html
index b2109ab0..65c9df5f 100644
--- a/docs/reference/set_tr.html
+++ b/docs/reference/set_tr.html
@@ -1,5 +1,5 @@
-Set the repetition time of an MRS dataset. — set_tr • Spectroscopy Analysis Tools (spant) Set the repetition time of an MRS dataset. — set_tr • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/shift.html b/docs/reference/shift.html
index ab0fe724..034591d0 100644
--- a/docs/reference/shift.html
+++ b/docs/reference/shift.html
@@ -1,5 +1,5 @@
-Apply a frequency shift to MRS data. — shift • Spectroscopy Analysis Tools (spant) Apply a frequency shift to MRS data. — shift • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/shift_basis.html b/docs/reference/shift_basis.html
index 2884be19..f55a65e0 100644
--- a/docs/reference/shift_basis.html
+++ b/docs/reference/shift_basis.html
@@ -1,5 +1,5 @@
-Apply frequency shifts to basis set signals. — shift_basis • Spectroscopy Analysis Tools (spant) Apply frequency shifts to basis set signals. — shift_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Value
diff --git a/docs/reference/sim_basis.html b/docs/reference/sim_basis.html
index c7838c46..bb5fefc6 100644
--- a/docs/reference/sim_basis.html
+++ b/docs/reference/sim_basis.html
@@ -1,5 +1,5 @@
-Simulate a basis set object. — sim_basis • Spectroscopy Analysis Tools (spant) Simulate a basis set object. — sim_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -136,7 +136,7 @@ Value
diff --git a/docs/reference/sim_basis_1h_brain.html b/docs/reference/sim_basis_1h_brain.html
index 62ed7389..f71ffa0b 100644
--- a/docs/reference/sim_basis_1h_brain.html
+++ b/docs/reference/sim_basis_1h_brain.html
@@ -1,7 +1,5 @@
-Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS
-sequence. Note, ideal pulses are assumed. — sim_basis_1h_brain • Spectroscopy Analysis Tools (spant) Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS sequence. Note, ideal pulses are assumed. — sim_basis_1h_brain • Spectroscopy Analysis Tools (spant) Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS
-sequence. Note, ideal pulses are assumed. — sim_basis_1h_brain_press • Spectroscopy Analysis Tools (spant) Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS sequence. Note, ideal pulses are assumed. — sim_basis_1h_brain_press • Spectroscopy Analysis Tools (spant) Simulate a macromolecular and lipid basis-set suitable for 1H brain MRS
-analysis. — sim_basis_mm_lip_lcm • Spectroscopy Analysis Tools (spant) Simulate a macromolecular and lipid basis-set suitable for 1H brain MRS analysis. — sim_basis_mm_lip_lcm • Spectroscopy Analysis Tools (spant) Simulate a basis file using TARQUIN. — sim_basis_tqn • Spectroscopy Analysis Tools (spant) Simulate a basis file using TARQUIN. — sim_basis_tqn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -129,7 +129,7 @@ Examples
diff --git a/docs/reference/sim_brain_1h.html b/docs/reference/sim_brain_1h.html
index 2044cf1a..717ee289 100644
--- a/docs/reference/sim_brain_1h.html
+++ b/docs/reference/sim_brain_1h.html
@@ -1,5 +1,5 @@
-Simulate MRS data with a similar appearance to normal brain (by default). — sim_brain_1h • Spectroscopy Analysis Tools (spant) Simulate MRS data with a similar appearance to normal brain (by default). — sim_brain_1h • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -159,7 +159,7 @@ Value
diff --git a/docs/reference/sim_mol.html b/docs/reference/sim_mol.html
index 23bcef50..77f76a50 100644
--- a/docs/reference/sim_mol.html
+++ b/docs/reference/sim_mol.html
@@ -1,5 +1,5 @@
-Simulate a mol_parameter object. — sim_mol • Spectroscopy Analysis Tools (spant) Simulate a mol_parameter object. — sim_mol • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -143,7 +143,7 @@ Value
diff --git a/docs/reference/sim_noise.html b/docs/reference/sim_noise.html
index 23875f79..a71477d4 100644
--- a/docs/reference/sim_noise.html
+++ b/docs/reference/sim_noise.html
@@ -1,5 +1,5 @@
-Simulate an mrs_data object containing simulated Gaussian noise. — sim_noise • Spectroscopy Analysis Tools (spant) Simulate an mrs_data object containing simulated Gaussian noise. — sim_noise • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -84,6 +84,7 @@ Simulate an mrs_data object containing simulated Gaussian noise.
ft = def_ft(),
N = def_N(),
ref = def_ref(),
+ nuc = def_nuc(),
dyns = 1,
fd = TRUE
)
@@ -111,6 +112,10 @@ Arguments
reference value for ppm scale.
nuc
+resonant nucleus.
dyns
number of dynamic scans to generate.
Value
diff --git a/docs/reference/sim_resonances.html b/docs/reference/sim_resonances.html
index 19e9a8a4..d4f8d7c0 100644
--- a/docs/reference/sim_resonances.html
+++ b/docs/reference/sim_resonances.html
@@ -1,5 +1,5 @@
-Simulate a MRS data object containing a set of simulated resonances. — sim_resonances • Spectroscopy Analysis Tools (spant) Simulate a MRS data object containing a set of simulated resonances. — sim_resonances • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -161,7 +161,7 @@ Examples
diff --git a/docs/reference/sim_th_excit_profile.html b/docs/reference/sim_th_excit_profile.html
index 5535c5ef..e781cab1 100644
--- a/docs/reference/sim_th_excit_profile.html
+++ b/docs/reference/sim_th_excit_profile.html
@@ -1,7 +1,5 @@
-Simulate an ideal pulse excitation profile by smoothing a top-hat function
-with a Gaussian. — sim_th_excit_profile • Spectroscopy Analysis Tools (spant) Simulate an ideal pulse excitation profile by smoothing a top-hat function with a Gaussian. — sim_th_excit_profile • Spectroscopy Analysis Tools (spant) Simulate an mrs_data object containing complex zero valued samples. — sim_zero • Spectroscopy Analysis Tools (spant) Simulate an mrs_data object containing complex zero valued samples. — sim_zero • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -78,7 +78,14 @@ Simulate an mrs_data object containing complex zero valued samples.
-
+
@@ -99,6 +106,10 @@ Arguments
reference value for ppm scale.
nuc
+resonant nucleus.
dyns
number of dynamic scans to generate.
Value
diff --git a/docs/reference/smooth_dyns.html b/docs/reference/smooth_dyns.html
index 4cc8da50..accf3a51 100644
--- a/docs/reference/smooth_dyns.html
+++ b/docs/reference/smooth_dyns.html
@@ -1,5 +1,5 @@
-Smooth data across the dynamic dimension with a Gaussian kernel. — smooth_dyns • Spectroscopy Analysis Tools (spant) Smooth data across the dynamic dimension with a Gaussian kernel. — smooth_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/sort_basis.html b/docs/reference/sort_basis.html
index 6a676ea2..d25cc006 100644
--- a/docs/reference/sort_basis.html
+++ b/docs/reference/sort_basis.html
@@ -1,5 +1,5 @@
-Sort the basis-set elements alphabetically. — sort_basis • Spectroscopy Analysis Tools (spant) Sort the basis-set elements alphabetically. — sort_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/spant-package.html b/docs/reference/spant-package.html
index b3dd8e21..90f19ec3 100644
--- a/docs/reference/spant-package.html
+++ b/docs/reference/spant-package.html
@@ -1,5 +1,5 @@
-spant: spectroscopy analysis tools. — spant-package • Spectroscopy Analysis Tools (spant) spant: spectroscopy analysis tools. — spant-package • Spectroscopy Analysis Tools (spant) Simulate and fit some spectra with ABfit for benchmarking purposes. Basic
-timing and performance metrics will be printed. — spant_abfit_benchmark • Spectroscopy Analysis Tools (spant) Simulate and fit some spectra with ABfit for benchmarking purposes. Basic timing and performance metrics will be printed. — spant_abfit_benchmark • Spectroscopy Analysis Tools (spant) Example MEGA-PRESS data with significant B0 drift. — spant_mpress_drift • Spectroscopy Analysis Tools (spant) Example MEGA-PRESS data with significant B0 drift. — spant_mpress_drift • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -83,7 +83,7 @@ Example MEGA-PRESS data with significant B0 drift.
Format
- An object of class mrs_data of length 13.
+ An object of class mrs_data of dimension 1 x 1 x 1 x 1 x 40 x 1 x 1024.
@@ -98,7 +98,7 @@ Format
diff --git a/docs/reference/spant_sim_fmrs_dataset.html b/docs/reference/spant_sim_fmrs_dataset.html
new file mode 100644
index 00000000..00e48b56
--- /dev/null
+++ b/docs/reference/spant_sim_fmrs_dataset.html
@@ -0,0 +1,117 @@
+
+Simulate an example fMRS dataset for a block design fMRS experiment and export a BIDS structure. — spant_sim_fmrs_dataset • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Simulate an example fMRS dataset for a block design fMRS experiment and export a BIDS structure.
+ Source: R/fmrs.R
+ spant_sim_fmrs_dataset.Rd
+
+
+
+ Simulate an example fMRS dataset for a block design fMRS experiment and
+export a BIDS structure.
+
+
+
+ spant_sim_fmrs_dataset(output_dir = NULL)
+
+
+
+ Arguments
+ - output_dir
+output directory for the BIDS data. Defaults to :
+"HOME/sim_fmrs_dataset/data".
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/spant_simulation_benchmark.html b/docs/reference/spant_simulation_benchmark.html
index 32daa8bf..d8cc6841 100644
--- a/docs/reference/spant_simulation_benchmark.html
+++ b/docs/reference/spant_simulation_benchmark.html
@@ -1,7 +1,5 @@
-Simulate a typical metabolite basis set for benchmarking. Timing metrics will
-be printed on completion. — spant_simulation_benchmark • Spectroscopy Analysis Tools (spant) Simulate a typical metabolite basis set for benchmarking. Timing metrics will be printed on completion. — spant_simulation_benchmark • Spectroscopy Analysis Tools (spant) Decompose an mrs_data object into white and gray matter spectra. — spec_decomp • Spectroscopy Analysis Tools (spant) Perform a mathematical operation on a spectral region. — spec_op • Spectroscopy Analysis Tools (spant) Perform a mathematical operation on a spectral region. — spec_op • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -98,8 +98,8 @@ Arguments
operator
-can be "sum" (default), "mean", "l2", "max", "min" or
-"max-min".
can be "sum" (default), "mean", "l2", "max", "max_cplx,
+"min" or "max-min".
freq_scale
@@ -129,7 +129,7 @@ Value
diff --git a/docs/reference/spin_sys.html b/docs/reference/spin_sys.html
index 853423a4..1eaa9e76 100644
--- a/docs/reference/spin_sys.html
+++ b/docs/reference/spin_sys.html
@@ -1,5 +1,5 @@
-Create a spin system object for pulse sequence simulation. — spin_sys • Spectroscopy Analysis Tools (spant) Create a spin system object for pulse sequence simulation. — spin_sys • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/spm_pve2categorical.html b/docs/reference/spm_pve2categorical.html
index 23a1bad9..70f10729 100644
--- a/docs/reference/spm_pve2categorical.html
+++ b/docs/reference/spm_pve2categorical.html
@@ -1,7 +1,5 @@
-Convert SPM style segmentation files to a single categorical image where
-the numerical values map as: 0) Other, 1) CSF, 2) GM and 3) WM. — spm_pve2categorical • Spectroscopy Analysis Tools (spant) Convert SPM style segmentation files to a single categorical image where the numerical values map as: 0) Other, 1) CSF, 2) GM and 3) WM. — spm_pve2categorical • Spectroscopy Analysis Tools (spant) Signal space projection method for lipid suppression. — ssp • Spectroscopy Analysis Tools (spant) Signal space projection method for lipid suppression. — ssp • Spectroscopy Analysis Tools (spant) Plot the fitting results of an object of class fit_result with
-individual basis set components shown. — stackplot.fit_result • Spectroscopy Analysis Tools (spant) Plot the fitting results of an object of class fit_result with individual basis set components shown. — stackplot.fit_result • Spectroscopy Analysis Tools (spant) Produce a plot with multiple traces. — stackplot • Spectroscopy Analysis Tools (spant) Produce a plot with multiple traces. — stackplot • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/stackplot.mrs_data.html b/docs/reference/stackplot.mrs_data.html
index 17ff5648..64eea445 100644
--- a/docs/reference/stackplot.mrs_data.html
+++ b/docs/reference/stackplot.mrs_data.html
@@ -1,5 +1,5 @@
-Stackplot plotting method for objects of class mrs_data. — stackplot.mrs_data • Spectroscopy Analysis Tools (spant) Stackplot plotting method for objects of class mrs_data. — stackplot.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -255,7 +255,7 @@ Arguments
diff --git a/docs/reference/sub_first_dyn.html b/docs/reference/sub_first_dyn.html
index dbd7f831..493b7242 100644
--- a/docs/reference/sub_first_dyn.html
+++ b/docs/reference/sub_first_dyn.html
@@ -1,5 +1,5 @@
-Subtract the first dynamic spectrum from a dynamic series. — sub_first_dyn • Spectroscopy Analysis Tools (spant) Subtract the first dynamic spectrum from a dynamic series. — sub_first_dyn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/sub_mean_dyns.html b/docs/reference/sub_mean_dyns.html
index 6e3bb2df..221bd0c1 100644
--- a/docs/reference/sub_mean_dyns.html
+++ b/docs/reference/sub_mean_dyns.html
@@ -1,5 +1,5 @@
-Subtract the mean dynamic spectrum from a dynamic series. — sub_mean_dyns • Spectroscopy Analysis Tools (spant) Subtract the mean dynamic spectrum from a dynamic series. — sub_mean_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/sub_median_dyns.html b/docs/reference/sub_median_dyns.html
index 134c495d..1e834f14 100644
--- a/docs/reference/sub_median_dyns.html
+++ b/docs/reference/sub_median_dyns.html
@@ -1,5 +1,5 @@
-Subtract the median dynamic spectrum from a dynamic series. — sub_median_dyns • Spectroscopy Analysis Tools (spant) Subtract the median dynamic spectrum from a dynamic series. — sub_median_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/sum_coils.html b/docs/reference/sum_coils.html
index 7bf559f2..e1ab3cc0 100644
--- a/docs/reference/sum_coils.html
+++ b/docs/reference/sum_coils.html
@@ -1,5 +1,5 @@
-Calculate the sum across receiver coil elements. — sum_coils • Spectroscopy Analysis Tools (spant) Calculate the sum across receiver coil elements. — sum_coils • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/sum_dyns.html b/docs/reference/sum_dyns.html
index a0be19d3..bbda2ffc 100644
--- a/docs/reference/sum_dyns.html
+++ b/docs/reference/sum_dyns.html
@@ -1,5 +1,5 @@
-Calculate the sum of data dynamics. — sum_dyns • Spectroscopy Analysis Tools (spant) Calculate the sum of data dynamics. — sum_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/sum_mrs.html b/docs/reference/sum_mrs.html
index a22f215b..3cc3ab9e 100644
--- a/docs/reference/sum_mrs.html
+++ b/docs/reference/sum_mrs.html
@@ -1,5 +1,5 @@
-Sum two mrs_data objects. — sum_mrs • Spectroscopy Analysis Tools (spant) Sum two mrs_data objects. — sum_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Value
diff --git a/docs/reference/sum_mrs_list.html b/docs/reference/sum_mrs_list.html
index f4e09aea..c3584348 100644
--- a/docs/reference/sum_mrs_list.html
+++ b/docs/reference/sum_mrs_list.html
@@ -1,5 +1,5 @@
-Return the sum of a list of mrs_data objects. — sum_mrs_list • Spectroscopy Analysis Tools (spant) Return the sum of a list of mrs_data objects. — sum_mrs_list • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/svs_1h_brain_analysis.html b/docs/reference/svs_1h_brain_analysis.html
index 8ce514db..dff0ef7d 100644
--- a/docs/reference/svs_1h_brain_analysis.html
+++ b/docs/reference/svs_1h_brain_analysis.html
@@ -1,5 +1,5 @@
-Standard SVS 1H brain analysis pipeline. — svs_1h_brain_analysis • Spectroscopy Analysis Tools (spant) Standard SVS 1H brain analysis pipeline. — svs_1h_brain_analysis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -199,7 +199,7 @@ Value
diff --git a/docs/reference/svs_1h_brain_analysis_dev.html b/docs/reference/svs_1h_brain_analysis_dev.html
index d70a14d3..d71bfea2 100644
--- a/docs/reference/svs_1h_brain_analysis_dev.html
+++ b/docs/reference/svs_1h_brain_analysis_dev.html
@@ -1,5 +1,5 @@
-Standard SVS 1H brain analysis pipeline. — svs_1h_brain_analysis_dev • Spectroscopy Analysis Tools (spant) Standard SVS 1H brain analysis pipeline. — svs_1h_brain_analysis_dev • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -193,7 +193,7 @@ Examples
diff --git a/docs/reference/svs_1h_brain_batch_analysis.html b/docs/reference/svs_1h_brain_batch_analysis.html
index 5631e8cc..15f7223e 100644
--- a/docs/reference/svs_1h_brain_batch_analysis.html
+++ b/docs/reference/svs_1h_brain_batch_analysis.html
@@ -1,5 +1,5 @@
-Batch interface to the standard SVS 1H brain analysis pipeline. — svs_1h_brain_batch_analysis • Spectroscopy Analysis Tools (spant) Batch interface to the standard SVS 1H brain analysis pipeline. — svs_1h_brain_batch_analysis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -144,7 +144,7 @@ Value
diff --git a/docs/reference/t_test_spec.html b/docs/reference/t_test_spec.html
new file mode 100644
index 00000000..56a7ea1b
--- /dev/null
+++ b/docs/reference/t_test_spec.html
@@ -0,0 +1,124 @@
+
+Perform a t-test on spectral data points. — t_test_spec • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+
+
+ Perform a t-test on spectral data points.
+
+
+
+ t_test_spec(mrs_data, group)
+
+
+
+ Arguments
+ - mrs_data
+an mrs_data object with spectra in the dynamic dimension.
- group
+vector describing the group membership of each dynamic spectrum.
+
+ Value
+
+
+a list of statistical results.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/td2fd.html b/docs/reference/td2fd.html
index 6748a6a8..f31ed524 100644
--- a/docs/reference/td2fd.html
+++ b/docs/reference/td2fd.html
@@ -1,5 +1,5 @@
-Transform time-domain data to the frequency-domain. — td2fd • Spectroscopy Analysis Tools (spant) Transform time-domain data to the frequency-domain. — td2fd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/td_conv_filt.html b/docs/reference/td_conv_filt.html
index a9f340c3..106b9b00 100644
--- a/docs/reference/td_conv_filt.html
+++ b/docs/reference/td_conv_filt.html
@@ -1,5 +1,5 @@
-Time-domain convolution based filter. — td_conv_filt • Spectroscopy Analysis Tools (spant) Time-domain convolution based filter. — td_conv_filt • Spectroscopy Analysis Tools (spant) Time-domain spectral registration. — tdsr • Spectroscopy Analysis Tools (spant) Time-domain spectral registration. — tdsr • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -121,7 +121,7 @@ Value
diff --git a/docs/reference/te.html b/docs/reference/te.html
index 010361b1..4a65711d 100644
--- a/docs/reference/te.html
+++ b/docs/reference/te.html
@@ -1,5 +1,5 @@
-Return the echo time of an MRS dataset. — te • Spectroscopy Analysis Tools (spant) Return the echo time of an MRS dataset. — te • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/tr.html b/docs/reference/tr.html
index 0c0bd63b..2e749e02 100644
--- a/docs/reference/tr.html
+++ b/docs/reference/tr.html
@@ -1,5 +1,5 @@
-Return the repetition time of an MRS dataset. — tr • Spectroscopy Analysis Tools (spant) Return the repetition time of an MRS dataset. — tr • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/varpro_3_para_opts.html b/docs/reference/varpro_3_para_opts.html
index c2270a16..52d7cd84 100644
--- a/docs/reference/varpro_3_para_opts.html
+++ b/docs/reference/varpro_3_para_opts.html
@@ -1,5 +1,5 @@
-Return a list of options for VARPRO based fitting with 3 free parameters. — varpro_3_para_opts • Spectroscopy Analysis Tools (spant) Return a list of options for VARPRO based fitting with 3 free parameters. — varpro_3_para_opts • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -141,7 +141,7 @@ Value
diff --git a/docs/reference/varpro_basic_opts.html b/docs/reference/varpro_basic_opts.html
index 32c86d22..c5104891 100644
--- a/docs/reference/varpro_basic_opts.html
+++ b/docs/reference/varpro_basic_opts.html
@@ -1,5 +1,5 @@
-Return a list of options for a basic VARPRO analysis. — varpro_basic_opts • Spectroscopy Analysis Tools (spant) Return a list of options for a basic VARPRO analysis. — varpro_basic_opts • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -118,7 +118,7 @@ Value
diff --git a/docs/reference/varpro_opts.html b/docs/reference/varpro_opts.html
index 2aabf11d..6332f730 100644
--- a/docs/reference/varpro_opts.html
+++ b/docs/reference/varpro_opts.html
@@ -1,5 +1,5 @@
-Return a list of options for VARPRO based fitting. — varpro_opts • Spectroscopy Analysis Tools (spant) Return a list of options for VARPRO based fitting. — varpro_opts • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -177,7 +177,7 @@ Examples
diff --git a/docs/reference/vec2mrs_data.html b/docs/reference/vec2mrs_data.html
index 0cccd73b..f0d58bf0 100644
--- a/docs/reference/vec2mrs_data.html
+++ b/docs/reference/vec2mrs_data.html
@@ -1,5 +1,5 @@
-Convert a vector into a mrs_data object. — vec2mrs_data • Spectroscopy Analysis Tools (spant) Convert a vector into a mrs_data object. — vec2mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -80,10 +80,11 @@ Convert a vector into a mrs_data object.
vec2mrs_data(
vec,
- fs = def_fs(),
- ft = def_ft(),
- ref = def_ref(),
- nuc = def_nuc(),
+ mrs_data = NULL,
+ fs = NULL,
+ ft = NULL,
+ ref = NULL,
+ nuc = NULL,
dyns = 1,
fd = FALSE
)
@@ -95,6 +96,10 @@ Arguments
the data vector.
mrs_data
+example data to copy acquisition parameters from.
fs
sampling frequency in Hz.
Arguments
fd
-flag to indicate if the matrix is in the frequency domain (logical).
flag to indicate if the vector is in the frequency domain (logical).
Value
diff --git a/docs/reference/write_basis.html b/docs/reference/write_basis.html
index b6e27cbd..94c5e021 100644
--- a/docs/reference/write_basis.html
+++ b/docs/reference/write_basis.html
@@ -1,5 +1,5 @@
-Write a basis object to an LCModel .basis formatted file. — write_basis • Spectroscopy Analysis Tools (spant) Write a basis object to an LCModel .basis formatted file. — write_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -108,7 +108,7 @@ Arguments
diff --git a/docs/reference/write_basis_tqn.html b/docs/reference/write_basis_tqn.html
index 6aa51c1d..116c73ec 100644
--- a/docs/reference/write_basis_tqn.html
+++ b/docs/reference/write_basis_tqn.html
@@ -1,5 +1,5 @@
-Generate a basis file using TARQUIN. — write_basis_tqn • Spectroscopy Analysis Tools (spant) Generate a basis file using TARQUIN. — write_basis_tqn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Examples
diff --git a/docs/reference/write_mrs.html b/docs/reference/write_mrs.html
index fff25f15..124b9dc4 100644
--- a/docs/reference/write_mrs.html
+++ b/docs/reference/write_mrs.html
@@ -1,5 +1,5 @@
-Write MRS data object to file. — write_mrs • Spectroscopy Analysis Tools (spant) Write MRS data object to file. — write_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Arguments
diff --git a/docs/reference/write_mrs_nifti.html b/docs/reference/write_mrs_nifti.html
index f4bf1921..bd3ed4b7 100644
--- a/docs/reference/write_mrs_nifti.html
+++ b/docs/reference/write_mrs_nifti.html
@@ -1,5 +1,5 @@
-Write MRS data object to file in NIFTI format. — write_mrs_nifti • Spectroscopy Analysis Tools (spant) Write MRS data object to file in NIFTI format. — write_mrs_nifti • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/write_pulse_ascii.html b/docs/reference/write_pulse_ascii.html
index 067ae086..221f8ebb 100644
--- a/docs/reference/write_pulse_ascii.html
+++ b/docs/reference/write_pulse_ascii.html
@@ -1,5 +1,5 @@
-Write an ASCII formatted pulse file. — write_pulse_ascii • Spectroscopy Analysis Tools (spant) Write an ASCII formatted pulse file. — write_pulse_ascii • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/zero_fade_spec.html b/docs/reference/zero_fade_spec.html
index c703745c..c8b572c3 100644
--- a/docs/reference/zero_fade_spec.html
+++ b/docs/reference/zero_fade_spec.html
@@ -1,7 +1,5 @@
-Fade a spectrum to zero by frequency domain multiplication with a tanh
-function. Note this operation distorts data points at the end of the FID. — zero_fade_spec • Spectroscopy Analysis Tools (spant) Fade a spectrum to zero by frequency domain multiplication with a tanh function. Note this operation distorts data points at the end of the FID. — zero_fade_spec • Spectroscopy Analysis Tools (spant) Zero all coherences including and above a given order. — zero_higher_orders • Spectroscopy Analysis Tools (spant) Zero all coherences including and above a given order. — zero_higher_orders • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Value
diff --git a/docs/reference/zero_td_pts_end.html b/docs/reference/zero_td_pts_end.html
index 8c1123c8..71d24ebb 100644
--- a/docs/reference/zero_td_pts_end.html
+++ b/docs/reference/zero_td_pts_end.html
@@ -1,5 +1,5 @@
-Set mrs_data object data points at the end of the FID to zero. — zero_td_pts_end • Spectroscopy Analysis Tools (spant) Set mrs_data object data points at the end of the FID to zero. — zero_td_pts_end • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/zf.html b/docs/reference/zf.html
index 85e2013c..baf50256 100644
--- a/docs/reference/zf.html
+++ b/docs/reference/zf.html
@@ -1,5 +1,5 @@
-Zero-fill MRS data in the time domain. — zf • Spectroscopy Analysis Tools (spant) Zero-fill MRS data in the time domain. — zf • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -125,7 +125,7 @@ Value
diff --git a/docs/reference/zf_xy.html b/docs/reference/zf_xy.html
index ebca3999..c4104a74 100644
--- a/docs/reference/zf_xy.html
+++ b/docs/reference/zf_xy.html
@@ -1,5 +1,5 @@
-Zero-fill MRSI data in the k-space x-y direction. — zf_xy • Spectroscopy Analysis Tools (spant) Zero-fill MRSI data in the k-space x-y direction. — zf_xy • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -113,7 +113,7 @@ Value
diff --git a/docs/sitemap.xml b/docs/sitemap.xml
index e2139f71..4c39f515 100644
--- a/docs/sitemap.xml
+++ b/docs/sitemap.xml
@@ -216,6 +216,12 @@
https://martin3141.github.io/spant/reference/comb_coils_fp_pc.html
+
+ https://martin3141.github.io/spant/reference/comb_coils_mrsi_gls.html
+
+
+ https://martin3141.github.io/spant/reference/comb_coils_svs_gls.html
+
https://martin3141.github.io/spant/reference/comb_csv_results.html
@@ -411,6 +417,9 @@
https://martin3141.github.io/spant/reference/gen_conv_reg.html
+
+ https://martin3141.github.io/spant/reference/gen_group_reg.html
+
https://martin3141.github.io/spant/reference/gen_impulse_reg.html
@@ -555,6 +564,15 @@
https://martin3141.github.io/spant/reference/glm_spec.html
+
+ https://martin3141.github.io/spant/reference/glm_spec_fmrs_fl.html
+
+
+ https://martin3141.github.io/spant/reference/glm_spec_fmrs_group.html
+
+
+ https://martin3141.github.io/spant/reference/glm_spec_group_linhyp.html
+
https://martin3141.github.io/spant/reference/grid_shift_xy.html
@@ -690,9 +708,15 @@
https://martin3141.github.io/spant/reference/mrs_data2basis.html
+
+ https://martin3141.github.io/spant/reference/mrs_data2bids.html
+
https://martin3141.github.io/spant/reference/mrs_data2mat.html
+
+ https://martin3141.github.io/spant/reference/mrs_data2spec_mat.html
+
https://martin3141.github.io/spant/reference/mrs_data2vec.html
@@ -741,6 +765,9 @@
https://martin3141.github.io/spant/reference/phase.html
+
+ https://martin3141.github.io/spant/reference/phase_ref_1h_brain.html
+
https://martin3141.github.io/spant/reference/plot.fit_result.html
@@ -780,6 +807,12 @@
https://martin3141.github.io/spant/reference/precomp.html
+
+ https://martin3141.github.io/spant/reference/preproc_svs.html
+
+
+ https://martin3141.github.io/spant/reference/preproc_svs_dataset.html
+
https://martin3141.github.io/spant/reference/print.fit_result.html
@@ -1050,6 +1083,9 @@
https://martin3141.github.io/spant/reference/spant_mpress_drift.html
+
+ https://martin3141.github.io/spant/reference/spant_sim_fmrs_dataset.html
+
https://martin3141.github.io/spant/reference/spant_simulation_benchmark.html
@@ -1107,6 +1143,9 @@
https://martin3141.github.io/spant/reference/svs_1h_brain_batch_analysis.html
+
+ https://martin3141.github.io/spant/reference/t_test_spec.html
+
https://martin3141.github.io/spant/reference/td2fd.html
Reconstruct complex time-domain data from the real part of frequency-domain -data.
Reconstruct complex time-domain data from the real part of frequency-domain data.
Reconstruct complex time-domain data from the real part of frequency-domain -data.
Reconstruct complex time-domain data from the real part of frequency-domain data.
All functions
- Resample a VOI to match a target image space using nearest-neighbour
-interpolation.
Resample a VOI to match a target image space using nearest-neighbour interpolation.
@@ -1158,23 +1142,19 @@ All functions
- Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water).
Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / kg of tissue water).
- Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water).
Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / kg of tissue water).
- Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / Litre of tissue).
Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / Litre of tissue).
- Convert default LCM/TARQUIN concentration scaling to molal units with partial
-volume correction.
Convert default LCM/TARQUIN concentration scaling to molal units with partial volume correction.
@@ -1222,8 +1202,7 @@ All functions
- MEGA-PRESS sequence with ideal localisation pulses and Gaussian shaped
-editing pulse.
MEGA-PRESS sequence with ideal localisation pulses and Gaussian shaped editing pulse.
@@ -1251,13 +1230,11 @@ All functions
- STEAM sequence with ideal pulses and coherence order filtering to simulate
-gradient crushers.
STEAM sequence with ideal pulses and coherence order filtering to simulate gradient crushers.
- STEAM sequence with ideal pulses using the z-rotation gradient simulation
-method described by Young et al JMR 140, 146-152 (1999).
STEAM sequence with ideal pulses using the z-rotation gradient simulation method described by Young et al JMR 140, 146-152 (1999).
@@ -1293,8 +1270,7 @@ All functions
- Set the number of time-domain data points, truncating or zero-filling as
-appropriate.
Set the number of time-domain data points, truncating or zero-filling as appropriate.
@@ -1318,18 +1294,15 @@ All functions
- Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS
-sequence. Note, ideal pulses are assumed.
Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS sequence. Note, ideal pulses are assumed.
- Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS
-sequence. Note, ideal pulses are assumed.
Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS sequence. Note, ideal pulses are assumed.
- Simulate a macromolecular and lipid basis-set suitable for 1H brain MRS
-analysis.
Simulate a macromolecular and lipid basis-set suitable for 1H brain MRS analysis.
@@ -1353,8 +1326,7 @@ All functions
- Simulate an ideal pulse excitation profile by smoothing a top-hat function
-with a Gaussian.
Simulate an ideal pulse excitation profile by smoothing a top-hat function with a Gaussian.
@@ -1374,17 +1346,19 @@ All functions
- Simulate and fit some spectra with ABfit for benchmarking purposes. Basic
-timing and performance metrics will be printed.
Simulate and fit some spectra with ABfit for benchmarking purposes. Basic timing and performance metrics will be printed.
Example MEGA-PRESS data with significant B0 drift.
+
+
+ Simulate an example fMRS dataset for a block design fMRS experiment and export a BIDS structure.
- Simulate a typical metabolite basis set for benchmarking. Timing metrics will
-be printed on completion.
Simulate a typical metabolite basis set for benchmarking. Timing metrics will be printed on completion.
@@ -1400,8 +1374,7 @@ All functions
- Convert SPM style segmentation files to a single categorical image where
-the numerical values map as: 0) Other, 1) CSF, 2) GM and 3) WM.
Convert SPM style segmentation files to a single categorical image where the numerical values map as: 0) Other, 1) CSF, 2) GM and 3) WM.
@@ -1413,8 +1386,7 @@ All functions
- Plot the fitting results of an object of class fit_result with
-individual basis set components shown.
Plot the fitting results of an object of class fit_result with individual basis set components shown.
@@ -1459,6 +1431,10 @@ All functions svs_1h_brain_batch_analysis()
Batch interface to the standard SVS 1H brain analysis pipeline.
+
+
+ Perform a t-test on spectral data points.
@@ -1518,8 +1494,7 @@ All functions
- Fade a spectrum to zero by frequency domain multiplication with a tanh
-function. Note this operation distorts data points at the end of the FID.
Fade a spectrum to zero by frequency domain multiplication with a tanh function. Note this operation distorts data points at the end of the FID.
@@ -1549,7 +1524,7 @@ All functions
diff --git a/docs/reference/int_spec.html b/docs/reference/int_spec.html
index c7060fe7..783325a8 100644
--- a/docs/reference/int_spec.html
+++ b/docs/reference/int_spec.html
@@ -1,5 +1,5 @@
-Integrate a spectral region. — int_spec • Spectroscopy Analysis Tools (spant) Integrate a spectral region. — int_spec • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -118,7 +118,7 @@ Value
diff --git a/docs/reference/interleave_dyns.html b/docs/reference/interleave_dyns.html
index effe5543..441eff27 100644
--- a/docs/reference/interleave_dyns.html
+++ b/docs/reference/interleave_dyns.html
@@ -1,5 +1,5 @@
-Interleave the first and second half of a dynamic series. — interleave_dyns • Spectroscopy Analysis Tools (spant) Interleave the first and second half of a dynamic series. — interleave_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/inv_even_dyns.html b/docs/reference/inv_even_dyns.html
index 9f9d4fff..dcb781dc 100644
--- a/docs/reference/inv_even_dyns.html
+++ b/docs/reference/inv_even_dyns.html
@@ -1,5 +1,5 @@
-Invert even numbered dynamic scans starting from 1 (2,4,6...). — inv_even_dyns • Spectroscopy Analysis Tools (spant) Invert even numbered dynamic scans starting from 1 (2,4,6...). — inv_even_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/inv_odd_dyns.html b/docs/reference/inv_odd_dyns.html
index 26212e2b..78d64660 100644
--- a/docs/reference/inv_odd_dyns.html
+++ b/docs/reference/inv_odd_dyns.html
@@ -1,5 +1,5 @@
-Invert odd numbered dynamic scans starting from 1 (1,3,5...). — inv_odd_dyns • Spectroscopy Analysis Tools (spant) Invert odd numbered dynamic scans starting from 1 (1,3,5...). — inv_odd_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/is.def.html b/docs/reference/is.def.html
index f196ffd0..a67b9eba 100644
--- a/docs/reference/is.def.html
+++ b/docs/reference/is.def.html
@@ -1,5 +1,5 @@
-Check if an object is defined, which is the same as being not NULL. — is.def • Spectroscopy Analysis Tools (spant) Check if an object is defined, which is the same as being not NULL. — is.def • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/is_fd.html b/docs/reference/is_fd.html
index 3b0ca165..18a193aa 100644
--- a/docs/reference/is_fd.html
+++ b/docs/reference/is_fd.html
@@ -1,7 +1,5 @@
-Check if the chemical shift dimension of an MRS data object is in the
-frequency domain. — is_fd • Spectroscopy Analysis Tools (spant) Check if the chemical shift dimension of an MRS data object is in the frequency domain. — is_fd • Spectroscopy Analysis Tools (spant) Transform 2D MRSI data from k-space to image space in the x-y direction. — kspace2img_xy • Spectroscopy Analysis Tools (spant) Transform 2D MRSI data from k-space to image space in the x-y direction. — kspace2img_xy • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/l2_reg.html b/docs/reference/l2_reg.html
index 3d781d80..21aa9849 100644
--- a/docs/reference/l2_reg.html
+++ b/docs/reference/l2_reg.html
@@ -1,5 +1,5 @@
-Perform l2 regularisation artefact suppression. — l2_reg • Spectroscopy Analysis Tools (spant) Perform l2 regularisation artefact suppression. — l2_reg • Spectroscopy Analysis Tools (spant) Apply line-broadening (apodisation) to MRS data or basis object. — lb • Spectroscopy Analysis Tools (spant) Apply line-broadening (apodisation) to MRS data or basis object. — lb • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -123,7 +123,7 @@ Value
diff --git a/docs/reference/lofdc.html b/docs/reference/lofdc.html
index 5419b1ec..31347a25 100644
--- a/docs/reference/lofdc.html
+++ b/docs/reference/lofdc.html
@@ -1,5 +1,5 @@
-Correct linear frequency drift. — lofdc • Spectroscopy Analysis Tools (spant) Correct linear frequency drift. — lofdc • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -138,7 +138,7 @@ Value
diff --git a/docs/reference/lw2alpha.html b/docs/reference/lw2alpha.html
index b83db682..25da229b 100644
--- a/docs/reference/lw2alpha.html
+++ b/docs/reference/lw2alpha.html
@@ -1,7 +1,5 @@
-Covert a linewidth in Hz to an equivalent alpha value in the time-domain ie:
-x * exp(-t * alpha). — lw2alpha • Spectroscopy Analysis Tools (spant) Covert a linewidth in Hz to an equivalent alpha value in the time-domain ie: x * exp(-t * alpha). — lw2alpha • Spectroscopy Analysis Tools (spant) Covert a linewidth in Hz to an equivalent beta value in the time-domain ie:
-x * exp(-t * t * beta). — lw2beta • Spectroscopy Analysis Tools (spant) Covert a linewidth in Hz to an equivalent beta value in the time-domain ie: x * exp(-t * t * beta). — lw2beta • Spectroscopy Analysis Tools (spant) Make a basis-set object from a directory containing LCModel formatted RAW
-files. — make_basis_from_raw • Spectroscopy Analysis Tools (spant) Make a basis-set object from a directory containing LCModel formatted RAW files. — make_basis_from_raw • Spectroscopy Analysis Tools (spant) Mask an MRS dataset in the dynamic dimension. — mask_dyns • Spectroscopy Analysis Tools (spant) Mask an MRS dataset in the dynamic dimension. — mask_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/mask_fit_res.html b/docs/reference/mask_fit_res.html
index 97baaa3f..ebd91a99 100644
--- a/docs/reference/mask_fit_res.html
+++ b/docs/reference/mask_fit_res.html
@@ -1,5 +1,5 @@
-Mask fit result spectra depending on a vector of bool values. — mask_fit_res • Spectroscopy Analysis Tools (spant) Mask fit result spectra depending on a vector of bool values. — mask_fit_res • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -116,7 +116,7 @@ Value
diff --git a/docs/reference/mask_xy.html b/docs/reference/mask_xy.html
index 11bb577c..b0d38619 100644
--- a/docs/reference/mask_xy.html
+++ b/docs/reference/mask_xy.html
@@ -1,5 +1,5 @@
-Mask an MRSI dataset in the x-y direction — mask_xy • Spectroscopy Analysis Tools (spant) Mask an MRSI dataset in the x-y direction — mask_xy • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/mask_xy_corners.html b/docs/reference/mask_xy_corners.html
index 09b16cd2..2d13839d 100644
--- a/docs/reference/mask_xy_corners.html
+++ b/docs/reference/mask_xy_corners.html
@@ -1,5 +1,5 @@
-Mask the four corners of an MRSI dataset in the x-y plane. — mask_xy_corners • Spectroscopy Analysis Tools (spant) Mask the four corners of an MRSI dataset in the x-y plane. — mask_xy_corners • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/mask_xy_ellipse.html b/docs/reference/mask_xy_ellipse.html
index 1d8b02e4..e2e749ef 100644
--- a/docs/reference/mask_xy_ellipse.html
+++ b/docs/reference/mask_xy_ellipse.html
@@ -1,7 +1,5 @@
-Mask the voxels outside an elliptical region spanning the MRSI dataset in the
-x-y plane. — mask_xy_ellipse • Spectroscopy Analysis Tools (spant) Mask the voxels outside an elliptical region spanning the MRSI dataset in the x-y plane. — mask_xy_ellipse • Spectroscopy Analysis Tools (spant) Mask a 2D MRSI dataset in the x-y dimension. — mask_xy_mat • Spectroscopy Analysis Tools (spant) Mask a 2D MRSI dataset in the x-y dimension. — mask_xy_mat • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Value
diff --git a/docs/reference/mat2mrs_data.html b/docs/reference/mat2mrs_data.html
index 2e2895f3..ae55665f 100644
--- a/docs/reference/mat2mrs_data.html
+++ b/docs/reference/mat2mrs_data.html
@@ -1,7 +1,5 @@
-Convert a matrix (with spectral points in the column dimension and dynamics
-in the row dimensions) into a mrs_data object. — mat2mrs_data • Spectroscopy Analysis Tools (spant) Convert a matrix (with spectral points in the column dimension and dynamics in the row dimensions) into a mrs_data object. — mat2mrs_data • Spectroscopy Analysis Tools (spant) Matrix exponential function taken from complexplus package to reduce the
-number of spant dependencies. — matexp • Spectroscopy Analysis Tools (spant) Matrix exponential function taken from complexplus package to reduce the number of spant dependencies. — matexp • Spectroscopy Analysis Tools (spant) Apply the max operator to an MRS dataset. — max_mrs • Spectroscopy Analysis Tools (spant) Apply the max operator to an MRS dataset. — max_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/max_mrs_interp.html b/docs/reference/max_mrs_interp.html
index e4474764..52e63f3e 100644
--- a/docs/reference/max_mrs_interp.html
+++ b/docs/reference/max_mrs_interp.html
@@ -1,5 +1,5 @@
-Apply the max operator to an interpolated MRS dataset. — max_mrs_interp • Spectroscopy Analysis Tools (spant) Apply the max operator to an interpolated MRS dataset. — max_mrs_interp • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/mean.list.html b/docs/reference/mean.list.html
index b8eb3463..048306fd 100644
--- a/docs/reference/mean.list.html
+++ b/docs/reference/mean.list.html
@@ -1,5 +1,5 @@
-Calculate the mean spectrum from an mrs_data object. — mean.list • Spectroscopy Analysis Tools (spant) Calculate the mean spectrum from an mrs_data object. — mean.list • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/mean.mrs_data.html b/docs/reference/mean.mrs_data.html
index 5531a28d..79515014 100644
--- a/docs/reference/mean.mrs_data.html
+++ b/docs/reference/mean.mrs_data.html
@@ -1,5 +1,5 @@
-Calculate the mean spectrum from an mrs_data object. — mean.mrs_data • Spectroscopy Analysis Tools (spant) Calculate the mean spectrum from an mrs_data object. — mean.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/mean_dyn_blocks.html b/docs/reference/mean_dyn_blocks.html
index 10467098..4c042448 100644
--- a/docs/reference/mean_dyn_blocks.html
+++ b/docs/reference/mean_dyn_blocks.html
@@ -1,5 +1,5 @@
-Calculate the mean of adjacent dynamic scans. — mean_dyn_blocks • Spectroscopy Analysis Tools (spant) Calculate the mean of adjacent dynamic scans. — mean_dyn_blocks • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/mean_dyn_pairs.html b/docs/reference/mean_dyn_pairs.html
index 63e909ea..1a241126 100644
--- a/docs/reference/mean_dyn_pairs.html
+++ b/docs/reference/mean_dyn_pairs.html
@@ -1,5 +1,5 @@
-Calculate the pairwise means across a dynamic data set. — mean_dyn_pairs • Spectroscopy Analysis Tools (spant) Calculate the pairwise means across a dynamic data set. — mean_dyn_pairs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/mean_dyns.html b/docs/reference/mean_dyns.html
index 73fdbfa7..0daa27df 100644
--- a/docs/reference/mean_dyns.html
+++ b/docs/reference/mean_dyns.html
@@ -1,5 +1,5 @@
-Calculate the mean dynamic data. — mean_dyns • Spectroscopy Analysis Tools (spant) Calculate the mean dynamic data. — mean_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/mean_mrs_list.html b/docs/reference/mean_mrs_list.html
index 808b6c50..10d842c0 100644
--- a/docs/reference/mean_mrs_list.html
+++ b/docs/reference/mean_mrs_list.html
@@ -1,5 +1,5 @@
-Return the mean of a list of mrs_data objects. — mean_mrs_list • Spectroscopy Analysis Tools (spant) Return the mean of a list of mrs_data objects. — mean_mrs_list • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/mean_vec_blocks.html b/docs/reference/mean_vec_blocks.html
index 8fc92eaa..dd78b122 100644
--- a/docs/reference/mean_vec_blocks.html
+++ b/docs/reference/mean_vec_blocks.html
@@ -1,5 +1,5 @@
-Calculate the mean of adjacent blocks in a vector. — mean_vec_blocks • Spectroscopy Analysis Tools (spant) Calculate the mean of adjacent blocks in a vector. — mean_vec_blocks • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/median_dyns.html b/docs/reference/median_dyns.html
index 1039d4b5..9a085b10 100644
--- a/docs/reference/median_dyns.html
+++ b/docs/reference/median_dyns.html
@@ -1,5 +1,5 @@
-Calculate the median dynamic data. — median_dyns • Spectroscopy Analysis Tools (spant) Calculate the median dynamic data. — median_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/mod_td.html b/docs/reference/mod_td.html
index 76ad0a40..141ef09e 100644
--- a/docs/reference/mod_td.html
+++ b/docs/reference/mod_td.html
@@ -1,5 +1,5 @@
-Apply the Modulus operator to the time-domain MRS signal. — mod_td • Spectroscopy Analysis Tools (spant) Apply the Modulus operator to the time-domain MRS signal. — mod_td • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/mrs_data2basis.html b/docs/reference/mrs_data2basis.html
index 62f7d749..11797b91 100644
--- a/docs/reference/mrs_data2basis.html
+++ b/docs/reference/mrs_data2basis.html
@@ -1,7 +1,5 @@
-Convert an mrs_data object to basis object - where basis signals are spread
-across the dynamic dimension in the MRS data. — mrs_data2basis • Spectroscopy Analysis Tools (spant) Convert an mrs_data object to basis object - where basis signals are spread across the dynamic dimension in the MRS data. — mrs_data2basis • Spectroscopy Analysis Tools (spant) Create a BIDS file structure from a vector of MRS data paths or list of mrs_data objects. — mrs_data2bids • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Create a BIDS file structure from a vector of MRS data paths or list of mrs_data objects.
+ Source: R/fmrs.R
+ mrs_data2bids.Rd
+
+
+
+ Create a BIDS file structure from a vector of MRS data paths or list of
+mrs_data objects.
+
+
+
+ mrs_data2bids(
+ mrs_data,
+ output_dir,
+ suffix = NULL,
+ sub = NULL,
+ ses = NULL,
+ task = NULL,
+ acq = NULL,
+ nuc = NULL,
+ voi = NULL,
+ rec = NULL,
+ run = NULL,
+ echo = NULL,
+ inv = NULL,
+ skip_existing = TRUE
+)
+
+
+
+ Arguments
+ - mrs_data
+vector of MRS data paths or list of mrs_data objects.
- output_dir
+the base directory to create the BIDS structure.
- suffix
+optional vector of file suffixes. Default behaviour is to
+automatically determine these from the input data, however it is recommended
+that they are specified to allow more efficient skipping of existing data.
- sub
+optional vector of subject labels. If not specified, these will be
+automatically generated as a series of increasing zero-padded integer values
+corresponding to the mrs_data input indices.
- ses
+optional vector of session labels.
- task
+optional vector of task labels.
- acq
+optional vector of acquisition labels.
- nuc
+optional vector of nucleus labels.
- voi
+optional vector of volume of interest labels.
- rec
+optional vector of reconstruction labels.
- run
+optional vector of run indices.
- echo
+optional vector of echo time indices.
- inv
+optional vector of inversion indices.
- skip_existing
+skip any data files that have already been converted.
+Defaults to TRUE, set to FALSE to force an overwrite of any existing data
+files.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/mrs_data2mat.html b/docs/reference/mrs_data2mat.html
index cf5ff28c..9e47688a 100644
--- a/docs/reference/mrs_data2mat.html
+++ b/docs/reference/mrs_data2mat.html
@@ -1,7 +1,5 @@
-Convert mrs_data object to a matrix, with spectral points in the column
-dimension and dynamics in the row dimension. — mrs_data2mat • Spectroscopy Analysis Tools (spant) Convert mrs_data object to a matrix, with spectral points in the column dimension and dynamics in the row dimension. — mrs_data2mat • Spectroscopy Analysis Tools (spant) Convert mrs_data object to a matrix, with spectral points in the column dimension and dynamics in the row dimension. — mrs_data2spec_mat • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Convert mrs_data object to a matrix, with spectral points in the column dimension and dynamics in the row dimension.
+ Source: R/mrs_data_proc.R
+ mrs_data2spec_mat.Rd
+
+
+
+ Convert mrs_data object to a matrix, with spectral points in the column
+dimension and dynamics in the row dimension.
+
+
+
+ mrs_data2spec_mat(mrs_data, collapse = TRUE)
+
+
+
+ Arguments
+ - mrs_data
+MRS data object or list of MRS data objects.
- collapse
+collapse all other dimensions along the dynamic dimension, eg
+a 16x16 MRSI grid would be first collapsed across 256 dynamic scans.
+
+ Value
+
+
+MRS data matrix.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/mrs_data2vec.html b/docs/reference/mrs_data2vec.html
index fb172d68..a1fd654d 100644
--- a/docs/reference/mrs_data2vec.html
+++ b/docs/reference/mrs_data2vec.html
@@ -1,5 +1,5 @@
-Convert mrs_data object to a vector. — mrs_data2vec • Spectroscopy Analysis Tools (spant) Convert mrs_data object to a vector. — mrs_data2vec • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -126,7 +126,7 @@ Value
diff --git a/docs/reference/mvfftshift.html b/docs/reference/mvfftshift.html
index 92b0841b..976b3410 100644
--- a/docs/reference/mvfftshift.html
+++ b/docs/reference/mvfftshift.html
@@ -1,7 +1,5 @@
-Perform a fftshift on a matrix, with each column replaced by its shifted
-result. — mvfftshift • Spectroscopy Analysis Tools (spant) Perform a fftshift on a matrix, with each column replaced by its shifted result. — mvfftshift • Spectroscopy Analysis Tools (spant) Perform an ifftshift on a matrix, with each column replaced by its shifted
-result. — mvifftshift • Spectroscopy Analysis Tools (spant) Perform an ifftshift on a matrix, with each column replaced by its shifted result. — mvifftshift • Spectroscopy Analysis Tools (spant) Print fit coordinates from a single index. — n2coord • Spectroscopy Analysis Tools (spant) Print fit coordinates from a single index. — n2coord • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/nifti_flip_lr.html b/docs/reference/nifti_flip_lr.html
index 730abe3c..19860b3c 100644
--- a/docs/reference/nifti_flip_lr.html
+++ b/docs/reference/nifti_flip_lr.html
@@ -1,9 +1,5 @@
-Flip the x data dimension order of a nifti image. This corresponds to
-flipping MRI data in the left-right direction, assuming the data in save in
-neurological format (can check with fslorient program). — nifti_flip_lr • Spectroscopy Analysis Tools (spant) Flip the x data dimension order of a nifti image. This corresponds to flipping MRI data in the left-right direction, assuming the data in save in neurological format (can check with fslorient program). — nifti_flip_lr • Spectroscopy Analysis Tools (spant) Export a one-page pdf of a single fit result — one_page_pdf • Spectroscopy Analysis Tools (spant) Export a one-page pdf of a single fit result — one_page_pdf • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -108,7 +108,7 @@ Arguments
diff --git a/docs/reference/ortho3.html b/docs/reference/ortho3.html
index 13ade97d..5d7dd2fd 100644
--- a/docs/reference/ortho3.html
+++ b/docs/reference/ortho3.html
@@ -1,5 +1,5 @@
-Display an orthographic projection plot of a nifti object. — ortho3 • Spectroscopy Analysis Tools (spant) Display an orthographic projection plot of a nifti object. — ortho3 • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -172,7 +172,7 @@ Arguments
diff --git a/docs/reference/ortho3_inter.html b/docs/reference/ortho3_inter.html
index 090cc5e5..15948899 100644
--- a/docs/reference/ortho3_inter.html
+++ b/docs/reference/ortho3_inter.html
@@ -1,5 +1,5 @@
-Display an interactive orthographic projection plot of a nifti object. — ortho3_inter • Spectroscopy Analysis Tools (spant) Display an interactive orthographic projection plot of a nifti object. — ortho3_inter • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -132,7 +132,7 @@ Arguments
diff --git a/docs/reference/peak_info.html b/docs/reference/peak_info.html
index 09058bd8..41c8ffaf 100644
--- a/docs/reference/peak_info.html
+++ b/docs/reference/peak_info.html
@@ -1,7 +1,5 @@
-Search for the highest peak in a spectral region and return the frequency,
-height and FWHM. — peak_info • Spectroscopy Analysis Tools (spant) Search for the highest peak in a spectral region and return the frequency, height and FWHM. — peak_info • Spectroscopy Analysis Tools (spant) Papoulis-Gerchberg (PG) algorithm method for k-space extrapolation. — pg_extrap_xy • Spectroscopy Analysis Tools (spant) Papoulis-Gerchberg (PG) algorithm method for k-space extrapolation. — pg_extrap_xy • Spectroscopy Analysis Tools (spant) Apply phasing parameters to MRS data. — phase • Spectroscopy Analysis Tools (spant) Apply phasing parameters to MRS data. — phase • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/phase_ref_1h_brain.html b/docs/reference/phase_ref_1h_brain.html
new file mode 100644
index 00000000..8707a74a
--- /dev/null
+++ b/docs/reference/phase_ref_1h_brain.html
@@ -0,0 +1,131 @@
+
+Corrected zero order phase and chemical shift offset in 1H MRS data from the brain. — phase_ref_1h_brain • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Corrected zero order phase and chemical shift offset in 1H MRS data from the brain.
+ Source: R/rats.R
+ phase_ref_1h_brain.Rd
+
+
+
+ Corrected zero order phase and chemical shift offset in 1H MRS data from the
+brain.
+
+
+
+ phase_ref_1h_brain(mrs_data, mean_ref = FALSE, ret_corr_only = TRUE)
+
+
+
+ Arguments
+ - mrs_data
+MRS data to be corrected.
- mean_ref
+apply the phase and offset of the mean spectrum to all
+others. Default is FALSE.
- ret_corr_only
+return the corrected data only.
+
+ Value
+
+
+corrected MRS data.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/plot.fit_result.html b/docs/reference/plot.fit_result.html
index e54d3bc1..836a53ee 100644
--- a/docs/reference/plot.fit_result.html
+++ b/docs/reference/plot.fit_result.html
@@ -1,5 +1,5 @@
-Plot the fitting results of an object of class fit_result. — plot.fit_result • Spectroscopy Analysis Tools (spant) Plot the fitting results of an object of class fit_result. — plot.fit_result • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -207,7 +207,7 @@ Arguments
diff --git a/docs/reference/plot.mrs_data.html b/docs/reference/plot.mrs_data.html
index fabcc35b..bb2ec651 100644
--- a/docs/reference/plot.mrs_data.html
+++ b/docs/reference/plot.mrs_data.html
@@ -1,5 +1,5 @@
-Plotting method for objects of class mrs_data. — plot.mrs_data • Spectroscopy Analysis Tools (spant) Plotting method for objects of class mrs_data. — plot.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -287,7 +287,7 @@ Arguments
diff --git a/docs/reference/plot_bc.html b/docs/reference/plot_bc.html
index 4f8309b4..b48142cc 100644
--- a/docs/reference/plot_bc.html
+++ b/docs/reference/plot_bc.html
@@ -1,5 +1,5 @@
-Convenience function to plot a baseline estimate with the original data. — plot_bc • Spectroscopy Analysis Tools (spant) Convenience function to plot a baseline estimate with the original data. — plot_bc • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -108,7 +108,7 @@ Arguments
diff --git a/docs/reference/plot_reg.html b/docs/reference/plot_reg.html
index ae1acbe7..2addb2f6 100644
--- a/docs/reference/plot_reg.html
+++ b/docs/reference/plot_reg.html
@@ -1,5 +1,5 @@
-Plot regressors as an image. — plot_reg • Spectroscopy Analysis Tools (spant) Plot regressors as an image. — plot_reg • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/plot_slice_fit.html b/docs/reference/plot_slice_fit.html
index fbc7b560..57f1af8a 100644
--- a/docs/reference/plot_slice_fit.html
+++ b/docs/reference/plot_slice_fit.html
@@ -1,5 +1,5 @@
-Plot a 2D slice from an MRSI fit result object. — plot_slice_fit • Spectroscopy Analysis Tools (spant) Plot a 2D slice from an MRSI fit result object. — plot_slice_fit • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -129,7 +129,7 @@ Arguments
diff --git a/docs/reference/plot_slice_fit_inter.html b/docs/reference/plot_slice_fit_inter.html
index 4eed104a..da105a7d 100644
--- a/docs/reference/plot_slice_fit_inter.html
+++ b/docs/reference/plot_slice_fit_inter.html
@@ -1,5 +1,5 @@
-Plot a 2D slice from an MRSI fit result object. — plot_slice_fit_inter • Spectroscopy Analysis Tools (spant) Plot a 2D slice from an MRSI fit result object. — plot_slice_fit_inter • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -134,7 +134,7 @@ Arguments
diff --git a/docs/reference/plot_slice_map.html b/docs/reference/plot_slice_map.html
index 553e9ac8..ffb2a134 100644
--- a/docs/reference/plot_slice_map.html
+++ b/docs/reference/plot_slice_map.html
@@ -1,5 +1,5 @@
-Plot a slice from a 7 dimensional array. — plot_slice_map • Spectroscopy Analysis Tools (spant) Plot a slice from a 7 dimensional array. — plot_slice_map • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -153,7 +153,7 @@ Arguments
diff --git a/docs/reference/plot_slice_map_inter.html b/docs/reference/plot_slice_map_inter.html
index 40d33b42..90968f66 100644
--- a/docs/reference/plot_slice_map_inter.html
+++ b/docs/reference/plot_slice_map_inter.html
@@ -1,7 +1,5 @@
-Plot an interactive slice map from a data array where voxels can be selected
-to display a corresponding spectrum. — plot_slice_map_inter • Spectroscopy Analysis Tools (spant) Plot an interactive slice map from a data array where voxels can be selected to display a corresponding spectrum. — plot_slice_map_inter • Spectroscopy Analysis Tools (spant) Plot the spectral standard deviation. — plot_spec_sd • Spectroscopy Analysis Tools (spant) Plot the spectral standard deviation. — plot_spec_sd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Arguments
diff --git a/docs/reference/plot_voi_overlay.html b/docs/reference/plot_voi_overlay.html
index 9a782e88..bbbbf35e 100644
--- a/docs/reference/plot_voi_overlay.html
+++ b/docs/reference/plot_voi_overlay.html
@@ -1,5 +1,5 @@
-Plot a volume as an image overlay. — plot_voi_overlay • Spectroscopy Analysis Tools (spant) Plot a volume as an image overlay. — plot_voi_overlay • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -116,7 +116,7 @@ Arguments
diff --git a/docs/reference/plot_voi_overlay_seg.html b/docs/reference/plot_voi_overlay_seg.html
index 3d4e74ff..0e800ff2 100644
--- a/docs/reference/plot_voi_overlay_seg.html
+++ b/docs/reference/plot_voi_overlay_seg.html
@@ -1,5 +1,5 @@
-Plot a volume as an overlay on a segmented brain volume. — plot_voi_overlay_seg • Spectroscopy Analysis Tools (spant) Plot a volume as an overlay on a segmented brain volume. — plot_voi_overlay_seg • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Arguments
diff --git a/docs/reference/ppm.html b/docs/reference/ppm.html
index c352327a..ee4696e2 100644
--- a/docs/reference/ppm.html
+++ b/docs/reference/ppm.html
@@ -1,5 +1,5 @@
-Return the ppm scale of an MRS dataset or fit result. — ppm • Spectroscopy Analysis Tools (spant) Return the ppm scale of an MRS dataset or fit result. — ppm • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -132,7 +132,7 @@ Value
diff --git a/docs/reference/precomp.html b/docs/reference/precomp.html
index 822d7336..df3d2c6c 100644
--- a/docs/reference/precomp.html
+++ b/docs/reference/precomp.html
@@ -1,7 +1,5 @@
-Save function results to file and load on subsequent calls to avoid repeat
-computation. — precomp • Spectroscopy Analysis Tools (spant) Save function results to file and load on subsequent calls to avoid repeat computation. — precomp • Spectroscopy Analysis Tools (spant) Preprocess and perform quality assessment of a single SVS data set. — preproc_svs • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Preprocess and perform quality assessment of a single SVS data set.
+ Source: R/fmrs.R
+ preproc_svs.Rd
+
+
+
+ Preprocess and perform quality assessment of a single SVS data set.
+
+
+
+ preproc_svs(path, label = NULL, output_dir = NULL, ref_inds = NULL)
+
+
+
+ Arguments
+ - path
+path to the fMRS data file or IMA directory.
- label
+a label to describe the data set.
- output_dir
+output directory.
- ref_inds
+a vector of 1-based indices for any water reference dynamic
+scans.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/preproc_svs_dataset.html b/docs/reference/preproc_svs_dataset.html
new file mode 100644
index 00000000..07c3a29b
--- /dev/null
+++ b/docs/reference/preproc_svs_dataset.html
@@ -0,0 +1,148 @@
+
+Preprocess and perform quality assessment of one or more SVS data sets. — preproc_svs_dataset • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Preprocess and perform quality assessment of one or more SVS data sets.
+ Source: R/fmrs.R
+ preproc_svs_dataset.Rd
+
+
+
+ Preprocess and perform quality assessment of one or more SVS data sets.
+
+
+
+ preproc_svs_dataset(
+ paths,
+ labels = NULL,
+ output_dir = "spant_analysis",
+ exclude_labels = NULL,
+ overwrite = FALSE,
+ ref_inds = NULL,
+ return_results = FALSE
+)
+
+
+
+ Arguments
+ - paths
+paths to the fMRS data file or IMA directory.
- labels
+labels to describe each data set.
- output_dir
+output directory.
- exclude_labels
+vector of labels of scans to exclude, eg poor quality
+data.
- overwrite
+overwrite saved results, defaults to FALSE.
- ref_inds
+a vector of 1-based indices for any water reference dynamic
+scans.
- return_results
+function will return key outputs, defaults to FALSE.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/print.fit_result.html b/docs/reference/print.fit_result.html
index 297f28dc..5f434e57 100644
--- a/docs/reference/print.fit_result.html
+++ b/docs/reference/print.fit_result.html
@@ -1,5 +1,5 @@
-Print a summary of an object of class fit_result. — print.fit_result • Spectroscopy Analysis Tools (spant) Print a summary of an object of class fit_result. — print.fit_result • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -105,7 +105,7 @@ Arguments
diff --git a/docs/reference/print.mrs_data.html b/docs/reference/print.mrs_data.html
index 51199017..e1561eb2 100644
--- a/docs/reference/print.mrs_data.html
+++ b/docs/reference/print.mrs_data.html
@@ -1,5 +1,5 @@
-Print a summary of mrs_data parameters. — print.mrs_data • Spectroscopy Analysis Tools (spant) Print a summary of mrs_data parameters. — print.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -109,7 +109,7 @@ Arguments
diff --git a/docs/reference/qn_states.html b/docs/reference/qn_states.html
index 0f42f2f9..d7aa6715 100644
--- a/docs/reference/qn_states.html
+++ b/docs/reference/qn_states.html
@@ -1,5 +1,5 @@
-Get the quantum coherence matrix for a spin system. — qn_states • Spectroscopy Analysis Tools (spant) Get the quantum coherence matrix for a spin system. — qn_states • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/rats.html b/docs/reference/rats.html
index 5a39a396..93585e08 100644
--- a/docs/reference/rats.html
+++ b/docs/reference/rats.html
@@ -1,5 +1,5 @@
-Robust Alignment to a Target Spectrum (RATS). — rats • Spectroscopy Analysis Tools (spant) Robust Alignment to a Target Spectrum (RATS). — rats • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -207,7 +207,7 @@ Value
diff --git a/docs/reference/re_weighting.html b/docs/reference/re_weighting.html
index d21caf21..8b0b070a 100644
--- a/docs/reference/re_weighting.html
+++ b/docs/reference/re_weighting.html
@@ -1,5 +1,5 @@
-Apply a weighting to the FID to enhance spectral resolution. — re_weighting • Spectroscopy Analysis Tools (spant) Apply a weighting to the FID to enhance spectral resolution. — re_weighting • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/read_basis.html b/docs/reference/read_basis.html
index da9b94af..eb6f8557 100644
--- a/docs/reference/read_basis.html
+++ b/docs/reference/read_basis.html
@@ -1,5 +1,5 @@
-Read a basis file in LCModel .basis format. — read_basis • Spectroscopy Analysis Tools (spant) Read a basis file in LCModel .basis format. — read_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/read_ima_coil_dir.html b/docs/reference/read_ima_coil_dir.html
index 28c02de0..4f073cd8 100644
--- a/docs/reference/read_ima_coil_dir.html
+++ b/docs/reference/read_ima_coil_dir.html
@@ -1,9 +1,5 @@
-Read a directory containing Siemens MRS IMA files and combine along the coil
-dimension. Note that the coil ID is inferred from the sorted file name and
-should be checked when consistency is required between two directories. — read_ima_coil_dir • Spectroscopy Analysis Tools (spant) Read a directory containing Siemens MRS IMA files and combine along the coil dimension. Note that the coil ID is inferred from the sorted file name and should be checked when consistency is required between two directories. — read_ima_coil_dir • Spectroscopy Analysis Tools (spant) Read a directory containing Siemens MRS IMA files and combine along the
-dynamic dimension. Note that the coil ID is inferred from the sorted file
-name and should be checked when consistency is required. — read_ima_dyn_dir • Spectroscopy Analysis Tools (spant) Read a directory containing Siemens MRS IMA files and combine along the dynamic dimension. Note that the coil ID is inferred from the sorted file name and should be checked when consistency is required. — read_ima_dyn_dir • Spectroscopy Analysis Tools (spant) Read an LCModel formatted coord file containing fit information. — read_lcm_coord • Spectroscopy Analysis Tools (spant) Read an LCModel formatted coord file containing fit information. — read_lcm_coord • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -107,7 +107,7 @@ Value
diff --git a/docs/reference/read_mrs.html b/docs/reference/read_mrs.html
index 3ac2a36b..2cf36b20 100644
--- a/docs/reference/read_mrs.html
+++ b/docs/reference/read_mrs.html
@@ -1,5 +1,5 @@
-Read MRS data from a file. — read_mrs • Spectroscopy Analysis Tools (spant) Read MRS data from a file. — read_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -88,7 +88,8 @@ Read MRS data from a file.
full_fid = FALSE,
omit_svs_ref_scans = TRUE,
verbose = FALSE,
- extra = NULL
+ extra = NULL,
+ fid_filt_dist = NULL
)
@@ -140,6 +141,13 @@ Arguments
an optional data frame to provide additional variables for use
in subsequent analysis steps, eg id or grouping variables.
fid_filt_dist
+indicate if the data has a distorted FID due to a
+brick-wall filter being used to downsample the data. Default is to auto
+detect this from the data, but TRUE or FALSE options can be given to override
+detection.
Value
@@ -183,7 +191,7 @@ Examples
diff --git a/docs/reference/read_mrs_tqn.html b/docs/reference/read_mrs_tqn.html
index 5766362f..84bdaf3a 100644
--- a/docs/reference/read_mrs_tqn.html
+++ b/docs/reference/read_mrs_tqn.html
@@ -1,5 +1,5 @@
-Read MRS data using the TARQUIN software package. — read_mrs_tqn • Spectroscopy Analysis Tools (spant) Read MRS data using the TARQUIN software package. — read_mrs_tqn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -131,7 +131,7 @@ Examples
diff --git a/docs/reference/read_pulse_ascii.html b/docs/reference/read_pulse_ascii.html
index c9e0d43c..ab11c9cc 100644
--- a/docs/reference/read_pulse_ascii.html
+++ b/docs/reference/read_pulse_ascii.html
@@ -1,5 +1,5 @@
-Read an ASCII formatted pulse file. — read_pulse_ascii • Spectroscopy Analysis Tools (spant) Read an ASCII formatted pulse file. — read_pulse_ascii • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/read_pulse_bruker.html b/docs/reference/read_pulse_bruker.html
index c92bf76a..dbe9073b 100644
--- a/docs/reference/read_pulse_bruker.html
+++ b/docs/reference/read_pulse_bruker.html
@@ -1,5 +1,5 @@
-Read a Bruker formatted pulse file — read_pulse_bruker • Spectroscopy Analysis Tools (spant) Read a Bruker formatted pulse file — read_pulse_bruker • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/read_pulse_pta.html b/docs/reference/read_pulse_pta.html
index 72e1b6d4..a0fac3c3 100644
--- a/docs/reference/read_pulse_pta.html
+++ b/docs/reference/read_pulse_pta.html
@@ -1,5 +1,5 @@
-Read a .pta formatted pulse file compatible with Siemens PulseTool. — read_pulse_pta • Spectroscopy Analysis Tools (spant) Read a .pta formatted pulse file compatible with Siemens PulseTool. — read_pulse_pta • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/read_siemens_txt_hdr.html b/docs/reference/read_siemens_txt_hdr.html
index 23fb8c70..3a17d87c 100644
--- a/docs/reference/read_siemens_txt_hdr.html
+++ b/docs/reference/read_siemens_txt_hdr.html
@@ -1,5 +1,5 @@
-Read the text format header found in Siemens IMA and TWIX data files. — read_siemens_txt_hdr • Spectroscopy Analysis Tools (spant) Read the text format header found in Siemens IMA and TWIX data files. — read_siemens_txt_hdr • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -78,7 +78,7 @@ Read the text format header found in Siemens IMA and TWIX data files.
- read_siemens_txt_hdr(input, version = "vd", verbose, offset = 0)
+ read_siemens_txt_hdr(input, version = "vd", verbose = FALSE, offset = 0)
@@ -118,7 +118,7 @@ Value
diff --git a/docs/reference/read_tqn_fit.html b/docs/reference/read_tqn_fit.html
index 4da6c25e..a1630420 100644
--- a/docs/reference/read_tqn_fit.html
+++ b/docs/reference/read_tqn_fit.html
@@ -1,5 +1,5 @@
-Reader for csv fit results generated by TARQUIN. — read_tqn_fit • Spectroscopy Analysis Tools (spant) Reader for csv fit results generated by TARQUIN. — read_tqn_fit • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -113,7 +113,7 @@ Examples
diff --git a/docs/reference/read_tqn_result.html b/docs/reference/read_tqn_result.html
index 36659714..68a3e98c 100644
--- a/docs/reference/read_tqn_result.html
+++ b/docs/reference/read_tqn_result.html
@@ -1,5 +1,5 @@
-Reader for csv results generated by TARQUIN. — read_tqn_result • Spectroscopy Analysis Tools (spant) Reader for csv results generated by TARQUIN. — read_tqn_result • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -117,7 +117,7 @@ Examples
diff --git a/docs/reference/recon_imag.html b/docs/reference/recon_imag.html
index d2a72225..5bc3b1eb 100644
--- a/docs/reference/recon_imag.html
+++ b/docs/reference/recon_imag.html
@@ -1,7 +1,5 @@
-Reconstruct complex time-domain data from the real part of frequency-domain
-data. — recon_imag • Spectroscopy Analysis Tools (spant) Reconstruct complex time-domain data from the real part of frequency-domain data. — recon_imag • Spectroscopy Analysis Tools (spant) Reconstruct complex time-domain data from the real part of frequency-domain
-data. — recon_imag_vec • Spectroscopy Analysis Tools (spant) Reconstruct complex time-domain data from the real part of frequency-domain data. — recon_imag_vec • Spectroscopy Analysis Tools (spant) Reconstruct 2D MRSI data from a twix file loaded with read_mrs. — recon_twix_2d_mrsi • Spectroscopy Analysis Tools (spant) Reconstruct 2D MRSI data from a twix file loaded with read_mrs. — recon_twix_2d_mrsi • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/rectangular_mask.html b/docs/reference/rectangular_mask.html
index a2117283..6e469bc9 100644
--- a/docs/reference/rectangular_mask.html
+++ b/docs/reference/rectangular_mask.html
@@ -1,5 +1,5 @@
-Create a rectangular mask stored as a matrix of logical values. — rectangular_mask • Spectroscopy Analysis Tools (spant) Create a rectangular mask stored as a matrix of logical values. — rectangular_mask • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -130,7 +130,7 @@ Value
diff --git a/docs/reference/reexports.html b/docs/reference/reexports.html
index 694a75d1..a59e8379 100644
--- a/docs/reference/reexports.html
+++ b/docs/reference/reexports.html
@@ -1,5 +1,5 @@
-Objects exported from other packages — reexports • Spectroscopy Analysis Tools (spant) Objects exported from other packages — reexports • Spectroscopy Analysis Tools (spant)
Spectroscopy Analysis Tools (spant)
- 2.21.0
+ 2.22.0
@@ -103,7 +103,7 @@ Objects exported from other packages
diff --git a/docs/reference/rep_array_dim.html b/docs/reference/rep_array_dim.html
index b9c49b4a..48c0a5ed 100644
--- a/docs/reference/rep_array_dim.html
+++ b/docs/reference/rep_array_dim.html
@@ -1,5 +1,5 @@
-Repeat an array over a given dimension. — rep_array_dim • Spectroscopy Analysis Tools (spant) Repeat an array over a given dimension. — rep_array_dim • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/rep_dyn.html b/docs/reference/rep_dyn.html
index 6bbfb0ef..89a4bb9b 100644
--- a/docs/reference/rep_dyn.html
+++ b/docs/reference/rep_dyn.html
@@ -1,5 +1,5 @@
-Replicate a scan in the dynamic dimension. — rep_dyn • Spectroscopy Analysis Tools (spant) Replicate a scan in the dynamic dimension. — rep_dyn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/rep_mrs.html b/docs/reference/rep_mrs.html
index 67730b5c..becb8f00 100644
--- a/docs/reference/rep_mrs.html
+++ b/docs/reference/rep_mrs.html
@@ -1,5 +1,5 @@
-Replicate a scan over a given dimension. — rep_mrs • Spectroscopy Analysis Tools (spant) Replicate a scan over a given dimension. — rep_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -138,7 +138,7 @@ Value
diff --git a/docs/reference/resample_basis.html b/docs/reference/resample_basis.html
index b0f2ab17..c7a6222a 100644
--- a/docs/reference/resample_basis.html
+++ b/docs/reference/resample_basis.html
@@ -1,5 +1,5 @@
-Resample a basis-set to match a mrs_data acquisition. — resample_basis • Spectroscopy Analysis Tools (spant) Resample a basis-set to match a mrs_data acquisition. — resample_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -116,7 +116,7 @@ Value
diff --git a/docs/reference/resample_img.html b/docs/reference/resample_img.html
index f1e7beaf..b0cc8f71 100644
--- a/docs/reference/resample_img.html
+++ b/docs/reference/resample_img.html
@@ -1,5 +1,5 @@
-Resample an image to match a target image space. — resample_img • Spectroscopy Analysis Tools (spant) Resample an image to match a target image space. — resample_img • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/resample_voi.html b/docs/reference/resample_voi.html
index 8fbfa836..a29ab096 100644
--- a/docs/reference/resample_voi.html
+++ b/docs/reference/resample_voi.html
@@ -1,7 +1,5 @@
-Resample a VOI to match a target image space using nearest-neighbour
-interpolation. — resample_voi • Spectroscopy Analysis Tools (spant) Resample a VOI to match a target image space using nearest-neighbour interpolation. — resample_voi • Spectroscopy Analysis Tools (spant) Reslice a nifti object to match the orientation of mrs data. — reslice_to_mrs • Spectroscopy Analysis Tools (spant) Reslice a nifti object to match the orientation of mrs data. — reslice_to_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/reson_table2mrs_data.html b/docs/reference/reson_table2mrs_data.html
index d75579ee..c5a2167a 100644
--- a/docs/reference/reson_table2mrs_data.html
+++ b/docs/reference/reson_table2mrs_data.html
@@ -1,5 +1,5 @@
-Generate mrs_data from a table of single Lorentzian resonances. — reson_table2mrs_data • Spectroscopy Analysis Tools (spant) Generate mrs_data from a table of single Lorentzian resonances. — reson_table2mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -119,7 +119,7 @@ Value
diff --git a/docs/reference/rm_dyns.html b/docs/reference/rm_dyns.html
index 5d5ef692..573e1f51 100644
--- a/docs/reference/rm_dyns.html
+++ b/docs/reference/rm_dyns.html
@@ -1,5 +1,5 @@
-Remove a subset of dynamic scans. — rm_dyns • Spectroscopy Analysis Tools (spant) Remove a subset of dynamic scans. — rm_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/scale_amp_molal.html b/docs/reference/scale_amp_molal.html
index aaeee1f2..7acb8cb0 100644
--- a/docs/reference/scale_amp_molal.html
+++ b/docs/reference/scale_amp_molal.html
@@ -1,7 +1,5 @@
-Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water). — scale_amp_molal • Spectroscopy Analysis Tools (spant) Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / kg of tissue water). — scale_amp_molal • Spectroscopy Analysis Tools (spant)
Spectroscopy Analysis Tools (spant)
- 2.21.0
+ 2.22.0
@@ -76,8 +74,7 @@
- Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water).
+ Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / kg of tissue water).
Source: R/amp_scaling.R
scale_amp_molal.Rd
@@ -163,7 +160,7 @@ Value
diff --git a/docs/reference/scale_amp_molal_pvc.html b/docs/reference/scale_amp_molal_pvc.html
index 962d6afc..4d194abd 100644
--- a/docs/reference/scale_amp_molal_pvc.html
+++ b/docs/reference/scale_amp_molal_pvc.html
@@ -1,7 +1,5 @@
-Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water). — scale_amp_molal_pvc • Spectroscopy Analysis Tools (spant)
@@ -75,8 +73,7 @@
- Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water).
+ Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / kg of tissue water).
Source: R/amp_scaling.R
scale_amp_molal_pvc.Rd
@@ -141,7 +138,7 @@ Value
diff --git a/docs/reference/scale_amp_molar.html b/docs/reference/scale_amp_molar.html
index 02358d91..dc87a338 100644
--- a/docs/reference/scale_amp_molar.html
+++ b/docs/reference/scale_amp_molar.html
@@ -1,7 +1,5 @@
-Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / Litre of tissue). — scale_amp_molar • Spectroscopy Analysis Tools (spant) Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / Litre of tissue). — scale_amp_molar • Spectroscopy Analysis Tools (spant) Convert default LCM/TARQUIN concentration scaling to molal units with partial
-volume correction. — scale_amp_molar2molal_pvc • Spectroscopy Analysis Tools (spant) Convert default LCM/TARQUIN concentration scaling to molal units with partial volume correction. — scale_amp_molar2molal_pvc • Spectroscopy Analysis Tools (spant) Scale fitted amplitudes to a ratio of signal amplitude. — scale_amp_ratio • Spectroscopy Analysis Tools (spant) Scale fitted amplitudes to a ratio of signal amplitude. — scale_amp_ratio • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -116,7 +116,7 @@ Value
diff --git a/docs/reference/scale_amp_ratio_value.html b/docs/reference/scale_amp_ratio_value.html
index 2036837a..6af8ac51 100644
--- a/docs/reference/scale_amp_ratio_value.html
+++ b/docs/reference/scale_amp_ratio_value.html
@@ -1,5 +1,5 @@
-Scale fitted amplitudes to a ratio of signal amplitude. — scale_amp_ratio_value • Spectroscopy Analysis Tools (spant) Scale fitted amplitudes to a ratio of signal amplitude. — scale_amp_ratio_value • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/scale_amp_water_ratio.html b/docs/reference/scale_amp_water_ratio.html
index 5b25e884..35a76b00 100644
--- a/docs/reference/scale_amp_water_ratio.html
+++ b/docs/reference/scale_amp_water_ratio.html
@@ -1,5 +1,5 @@
-Scale metabolite amplitudes as a ratio to the unsuppressed water amplitude. — scale_amp_water_ratio • Spectroscopy Analysis Tools (spant) Scale metabolite amplitudes as a ratio to the unsuppressed water amplitude. — scale_amp_water_ratio • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/scale_basis_amp.html b/docs/reference/scale_basis_amp.html
index 9401c3f1..5a58b5e5 100644
--- a/docs/reference/scale_basis_amp.html
+++ b/docs/reference/scale_basis_amp.html
@@ -1,5 +1,5 @@
-Scale a basis object by a scalar. — scale_basis_amp • Spectroscopy Analysis Tools (spant) Scale a basis object by a scalar. — scale_basis_amp • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/scale_basis_from_singlet.html b/docs/reference/scale_basis_from_singlet.html
index 0d542bc8..c9a19e77 100644
--- a/docs/reference/scale_basis_from_singlet.html
+++ b/docs/reference/scale_basis_from_singlet.html
@@ -1,5 +1,5 @@
-Scale a basis-set to be consistent with spant assumptions for water scaling. — scale_basis_from_singlet • Spectroscopy Analysis Tools (spant) Scale a basis-set to be consistent with spant assumptions for water scaling. — scale_basis_from_singlet • Spectroscopy Analysis Tools (spant)
Spectroscopy Analysis Tools (spant)
- 2.21.0
+ 2.22.0
@@ -127,7 +127,7 @@ Value
diff --git a/docs/reference/scale_mrs_amp.html b/docs/reference/scale_mrs_amp.html
index b5501a0d..990f058a 100644
--- a/docs/reference/scale_mrs_amp.html
+++ b/docs/reference/scale_mrs_amp.html
@@ -1,5 +1,5 @@
-Scale an mrs_data object by a scalar or vector or amplitudes. — scale_mrs_amp • Spectroscopy Analysis Tools (spant) Scale an mrs_data object by a scalar or vector or amplitudes. — scale_mrs_amp • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/scale_spec.html b/docs/reference/scale_spec.html
index 4f6ea835..6b3ddba4 100644
--- a/docs/reference/scale_spec.html
+++ b/docs/reference/scale_spec.html
@@ -1,5 +1,5 @@
-Scale mrs_data to a spectral region. — scale_spec • Spectroscopy Analysis Tools (spant) Scale mrs_data to a spectral region. — scale_spec • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -141,7 +141,7 @@ Value
diff --git a/docs/reference/sd.html b/docs/reference/sd.html
index ea1eec9f..3ae4dfd4 100644
--- a/docs/reference/sd.html
+++ b/docs/reference/sd.html
@@ -1,5 +1,5 @@
-Calculate the standard deviation spectrum from an mrs_data object. — sd • Spectroscopy Analysis Tools (spant) Calculate the standard deviation spectrum from an mrs_data object. — sd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/sd.mrs_data.html b/docs/reference/sd.mrs_data.html
index 3f92a49f..13bdda85 100644
--- a/docs/reference/sd.mrs_data.html
+++ b/docs/reference/sd.mrs_data.html
@@ -1,5 +1,5 @@
-Calculate the standard deviation spectrum from an mrs_data object. — sd.mrs_data • Spectroscopy Analysis Tools (spant) Calculate the standard deviation spectrum from an mrs_data object. — sd.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/seconds.html b/docs/reference/seconds.html
index b34d6627..467ee17f 100644
--- a/docs/reference/seconds.html
+++ b/docs/reference/seconds.html
@@ -1,5 +1,5 @@
-Return a time scale vector to match the FID of an MRS data object. — seconds • Spectroscopy Analysis Tools (spant) Return a time scale vector to match the FID of an MRS data object. — seconds • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/seq_cpmg_ideal.html b/docs/reference/seq_cpmg_ideal.html
index 547e96ab..45727c86 100644
--- a/docs/reference/seq_cpmg_ideal.html
+++ b/docs/reference/seq_cpmg_ideal.html
@@ -1,5 +1,5 @@
-CPMG style sequence with ideal pulses. — seq_cpmg_ideal • Spectroscopy Analysis Tools (spant) CPMG style sequence with ideal pulses. — seq_cpmg_ideal • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/seq_mega_press_ideal.html b/docs/reference/seq_mega_press_ideal.html
index 0769b8b4..a9cd7fa0 100644
--- a/docs/reference/seq_mega_press_ideal.html
+++ b/docs/reference/seq_mega_press_ideal.html
@@ -1,7 +1,5 @@
-MEGA-PRESS sequence with ideal localisation pulses and Gaussian shaped
-editing pulse. — seq_mega_press_ideal • Spectroscopy Analysis Tools (spant) MEGA-PRESS sequence with ideal localisation pulses and Gaussian shaped editing pulse. — seq_mega_press_ideal • Spectroscopy Analysis Tools (spant) PRESS sequence with shaped refocusing pulses. — seq_press_2d_shaped • Spectroscopy Analysis Tools (spant) PRESS sequence with shaped refocusing pulses. — seq_press_2d_shaped • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -165,7 +165,7 @@ Value
diff --git a/docs/reference/seq_press_ideal.html b/docs/reference/seq_press_ideal.html
index 8c976856..72c3af3d 100644
--- a/docs/reference/seq_press_ideal.html
+++ b/docs/reference/seq_press_ideal.html
@@ -1,5 +1,5 @@
-PRESS sequence with ideal pulses. — seq_press_ideal • Spectroscopy Analysis Tools (spant) PRESS sequence with ideal pulses. — seq_press_ideal • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/seq_pulse_acquire.html b/docs/reference/seq_pulse_acquire.html
index 4a88fc64..ad80571e 100644
--- a/docs/reference/seq_pulse_acquire.html
+++ b/docs/reference/seq_pulse_acquire.html
@@ -1,5 +1,5 @@
-Simple pulse and acquire sequence with ideal pulses. — seq_pulse_acquire • Spectroscopy Analysis Tools (spant) Simple pulse and acquire sequence with ideal pulses. — seq_pulse_acquire • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/seq_slaser_ideal.html b/docs/reference/seq_slaser_ideal.html
index 74688f4d..eb83e8e3 100644
--- a/docs/reference/seq_slaser_ideal.html
+++ b/docs/reference/seq_slaser_ideal.html
@@ -1,5 +1,5 @@
-sLASER sequence with ideal pulses. — seq_slaser_ideal • Spectroscopy Analysis Tools (spant) sLASER sequence with ideal pulses. — seq_slaser_ideal • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -126,7 +126,7 @@ Value
diff --git a/docs/reference/seq_spin_echo_ideal.html b/docs/reference/seq_spin_echo_ideal.html
index e23271de..4248716f 100644
--- a/docs/reference/seq_spin_echo_ideal.html
+++ b/docs/reference/seq_spin_echo_ideal.html
@@ -1,5 +1,5 @@
-Spin echo sequence with ideal pulses. — seq_spin_echo_ideal • Spectroscopy Analysis Tools (spant) Spin echo sequence with ideal pulses. — seq_spin_echo_ideal • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/seq_steam_ideal.html b/docs/reference/seq_steam_ideal.html
index a60685a8..1c8115d7 100644
--- a/docs/reference/seq_steam_ideal.html
+++ b/docs/reference/seq_steam_ideal.html
@@ -1,5 +1,5 @@
-STEAM sequence with ideal pulses. — seq_steam_ideal • Spectroscopy Analysis Tools (spant) STEAM sequence with ideal pulses. — seq_steam_ideal • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -128,7 +128,7 @@ Value
diff --git a/docs/reference/seq_steam_ideal_cof.html b/docs/reference/seq_steam_ideal_cof.html
index 8f225740..cba7af91 100644
--- a/docs/reference/seq_steam_ideal_cof.html
+++ b/docs/reference/seq_steam_ideal_cof.html
@@ -1,7 +1,5 @@
-STEAM sequence with ideal pulses and coherence order filtering to simulate
-gradient crushers. — seq_steam_ideal_cof • Spectroscopy Analysis Tools (spant) STEAM sequence with ideal pulses and coherence order filtering to simulate gradient crushers. — seq_steam_ideal_cof • Spectroscopy Analysis Tools (spant) STEAM sequence with ideal pulses using the z-rotation gradient simulation
-method described by Young et al JMR 140, 146-152 (1999). — seq_steam_ideal_young • Spectroscopy Analysis Tools (spant) STEAM sequence with ideal pulses using the z-rotation gradient simulation method described by Young et al JMR 140, 146-152 (1999). — seq_steam_ideal_young • Spectroscopy Analysis Tools (spant) Set the number of transients for an mrs_data object. — set_Ntrans • Spectroscopy Analysis Tools (spant) Set the number of transients for an mrs_data object. — set_Ntrans • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/set_def_acq_paras.html b/docs/reference/set_def_acq_paras.html
index 3e1b4004..cc2ada9c 100644
--- a/docs/reference/set_def_acq_paras.html
+++ b/docs/reference/set_def_acq_paras.html
@@ -1,5 +1,5 @@
-Set the default acquisition parameters. — set_def_acq_paras • Spectroscopy Analysis Tools (spant) Set the default acquisition parameters. — set_def_acq_paras • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Arguments
diff --git a/docs/reference/set_lcm_cmd.html b/docs/reference/set_lcm_cmd.html
index 2056ed01..42bb2f24 100644
--- a/docs/reference/set_lcm_cmd.html
+++ b/docs/reference/set_lcm_cmd.html
@@ -1,5 +1,5 @@
-Set the command to run the LCModel command-line program. — set_lcm_cmd • Spectroscopy Analysis Tools (spant) Set the command to run the LCModel command-line program. — set_lcm_cmd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/set_lw.html b/docs/reference/set_lw.html
index b64ec851..bb176c62 100644
--- a/docs/reference/set_lw.html
+++ b/docs/reference/set_lw.html
@@ -1,5 +1,5 @@
-Apply line-broadening to an mrs_data object to achieve a specified linewidth. — set_lw • Spectroscopy Analysis Tools (spant) Apply line-broadening to an mrs_data object to achieve a specified linewidth. — set_lw • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -123,7 +123,7 @@ Value
diff --git a/docs/reference/set_mask_xy_mat.html b/docs/reference/set_mask_xy_mat.html
index 49dc5d4e..52c4b617 100644
--- a/docs/reference/set_mask_xy_mat.html
+++ b/docs/reference/set_mask_xy_mat.html
@@ -1,5 +1,5 @@
-Set the masked voxels in a 2D MRSI dataset to given spectrum. — set_mask_xy_mat • Spectroscopy Analysis Tools (spant) Set the masked voxels in a 2D MRSI dataset to given spectrum. — set_mask_xy_mat • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Value
diff --git a/docs/reference/set_precomp_mode.html b/docs/reference/set_precomp_mode.html
index f44bd5d3..47c28e3b 100644
--- a/docs/reference/set_precomp_mode.html
+++ b/docs/reference/set_precomp_mode.html
@@ -1,5 +1,5 @@
-Set the precompute mode. — set_precomp_mode • Spectroscopy Analysis Tools (spant) Set the precompute mode. — set_precomp_mode • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/set_precomp_verbose.html b/docs/reference/set_precomp_verbose.html
index 1453a231..9c613505 100644
--- a/docs/reference/set_precomp_verbose.html
+++ b/docs/reference/set_precomp_verbose.html
@@ -1,5 +1,5 @@
-Set the verbosity of the precompute function. — set_precomp_verbose • Spectroscopy Analysis Tools (spant) Set the verbosity of the precompute function. — set_precomp_verbose • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/set_ref.html b/docs/reference/set_ref.html
index 8953fa50..5436dfa2 100644
--- a/docs/reference/set_ref.html
+++ b/docs/reference/set_ref.html
@@ -1,5 +1,5 @@
-Set the ppm reference value (eg ppm value at 0Hz). — set_ref • Spectroscopy Analysis Tools (spant) Set the ppm reference value (eg ppm value at 0Hz). — set_ref • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/set_td_pts.html b/docs/reference/set_td_pts.html
index 8a80d42a..586459ff 100644
--- a/docs/reference/set_td_pts.html
+++ b/docs/reference/set_td_pts.html
@@ -1,7 +1,5 @@
-Set the number of time-domain data points, truncating or zero-filling as
-appropriate. — set_td_pts • Spectroscopy Analysis Tools (spant) Set the number of time-domain data points, truncating or zero-filling as appropriate. — set_td_pts • Spectroscopy Analysis Tools (spant) Set the command to run the TARQUIN command-line program. — set_tqn_cmd • Spectroscopy Analysis Tools (spant) Set the command to run the TARQUIN command-line program. — set_tqn_cmd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/set_tr.html b/docs/reference/set_tr.html
index b2109ab0..65c9df5f 100644
--- a/docs/reference/set_tr.html
+++ b/docs/reference/set_tr.html
@@ -1,5 +1,5 @@
-Set the repetition time of an MRS dataset. — set_tr • Spectroscopy Analysis Tools (spant) Set the repetition time of an MRS dataset. — set_tr • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/shift.html b/docs/reference/shift.html
index ab0fe724..034591d0 100644
--- a/docs/reference/shift.html
+++ b/docs/reference/shift.html
@@ -1,5 +1,5 @@
-Apply a frequency shift to MRS data. — shift • Spectroscopy Analysis Tools (spant) Apply a frequency shift to MRS data. — shift • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/shift_basis.html b/docs/reference/shift_basis.html
index 2884be19..f55a65e0 100644
--- a/docs/reference/shift_basis.html
+++ b/docs/reference/shift_basis.html
@@ -1,5 +1,5 @@
-Apply frequency shifts to basis set signals. — shift_basis • Spectroscopy Analysis Tools (spant) Apply frequency shifts to basis set signals. — shift_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Value
diff --git a/docs/reference/sim_basis.html b/docs/reference/sim_basis.html
index c7838c46..bb5fefc6 100644
--- a/docs/reference/sim_basis.html
+++ b/docs/reference/sim_basis.html
@@ -1,5 +1,5 @@
-Simulate a basis set object. — sim_basis • Spectroscopy Analysis Tools (spant) Simulate a basis set object. — sim_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -136,7 +136,7 @@ Value
diff --git a/docs/reference/sim_basis_1h_brain.html b/docs/reference/sim_basis_1h_brain.html
index 62ed7389..f71ffa0b 100644
--- a/docs/reference/sim_basis_1h_brain.html
+++ b/docs/reference/sim_basis_1h_brain.html
@@ -1,7 +1,5 @@
-Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS
-sequence. Note, ideal pulses are assumed. — sim_basis_1h_brain • Spectroscopy Analysis Tools (spant) Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS sequence. Note, ideal pulses are assumed. — sim_basis_1h_brain • Spectroscopy Analysis Tools (spant) Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS
-sequence. Note, ideal pulses are assumed. — sim_basis_1h_brain_press • Spectroscopy Analysis Tools (spant) Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS sequence. Note, ideal pulses are assumed. — sim_basis_1h_brain_press • Spectroscopy Analysis Tools (spant) Simulate a macromolecular and lipid basis-set suitable for 1H brain MRS
-analysis. — sim_basis_mm_lip_lcm • Spectroscopy Analysis Tools (spant) Simulate a macromolecular and lipid basis-set suitable for 1H brain MRS analysis. — sim_basis_mm_lip_lcm • Spectroscopy Analysis Tools (spant) Simulate a basis file using TARQUIN. — sim_basis_tqn • Spectroscopy Analysis Tools (spant) Simulate a basis file using TARQUIN. — sim_basis_tqn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -129,7 +129,7 @@ Examples
diff --git a/docs/reference/sim_brain_1h.html b/docs/reference/sim_brain_1h.html
index 2044cf1a..717ee289 100644
--- a/docs/reference/sim_brain_1h.html
+++ b/docs/reference/sim_brain_1h.html
@@ -1,5 +1,5 @@
-Simulate MRS data with a similar appearance to normal brain (by default). — sim_brain_1h • Spectroscopy Analysis Tools (spant) Simulate MRS data with a similar appearance to normal brain (by default). — sim_brain_1h • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -159,7 +159,7 @@ Value
diff --git a/docs/reference/sim_mol.html b/docs/reference/sim_mol.html
index 23bcef50..77f76a50 100644
--- a/docs/reference/sim_mol.html
+++ b/docs/reference/sim_mol.html
@@ -1,5 +1,5 @@
-Simulate a mol_parameter object. — sim_mol • Spectroscopy Analysis Tools (spant) Simulate a mol_parameter object. — sim_mol • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -143,7 +143,7 @@ Value
diff --git a/docs/reference/sim_noise.html b/docs/reference/sim_noise.html
index 23875f79..a71477d4 100644
--- a/docs/reference/sim_noise.html
+++ b/docs/reference/sim_noise.html
@@ -1,5 +1,5 @@
-Simulate an mrs_data object containing simulated Gaussian noise. — sim_noise • Spectroscopy Analysis Tools (spant) Simulate an mrs_data object containing simulated Gaussian noise. — sim_noise • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -84,6 +84,7 @@ Simulate an mrs_data object containing simulated Gaussian noise.
ft = def_ft(),
N = def_N(),
ref = def_ref(),
+ nuc = def_nuc(),
dyns = 1,
fd = TRUE
)
@@ -111,6 +112,10 @@ Arguments
reference value for ppm scale.
nuc
+resonant nucleus.
dyns
number of dynamic scans to generate.
Value
diff --git a/docs/reference/sim_resonances.html b/docs/reference/sim_resonances.html
index 19e9a8a4..d4f8d7c0 100644
--- a/docs/reference/sim_resonances.html
+++ b/docs/reference/sim_resonances.html
@@ -1,5 +1,5 @@
-Simulate a MRS data object containing a set of simulated resonances. — sim_resonances • Spectroscopy Analysis Tools (spant) Simulate a MRS data object containing a set of simulated resonances. — sim_resonances • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -161,7 +161,7 @@ Examples
diff --git a/docs/reference/sim_th_excit_profile.html b/docs/reference/sim_th_excit_profile.html
index 5535c5ef..e781cab1 100644
--- a/docs/reference/sim_th_excit_profile.html
+++ b/docs/reference/sim_th_excit_profile.html
@@ -1,7 +1,5 @@
-Simulate an ideal pulse excitation profile by smoothing a top-hat function
-with a Gaussian. — sim_th_excit_profile • Spectroscopy Analysis Tools (spant) Simulate an ideal pulse excitation profile by smoothing a top-hat function with a Gaussian. — sim_th_excit_profile • Spectroscopy Analysis Tools (spant) Simulate an mrs_data object containing complex zero valued samples. — sim_zero • Spectroscopy Analysis Tools (spant) Simulate an mrs_data object containing complex zero valued samples. — sim_zero • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -78,7 +78,14 @@ Simulate an mrs_data object containing complex zero valued samples.
-
+
@@ -99,6 +106,10 @@ Arguments
reference value for ppm scale.
nuc
+resonant nucleus.
dyns
number of dynamic scans to generate.
Value
diff --git a/docs/reference/smooth_dyns.html b/docs/reference/smooth_dyns.html
index 4cc8da50..accf3a51 100644
--- a/docs/reference/smooth_dyns.html
+++ b/docs/reference/smooth_dyns.html
@@ -1,5 +1,5 @@
-Smooth data across the dynamic dimension with a Gaussian kernel. — smooth_dyns • Spectroscopy Analysis Tools (spant) Smooth data across the dynamic dimension with a Gaussian kernel. — smooth_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/sort_basis.html b/docs/reference/sort_basis.html
index 6a676ea2..d25cc006 100644
--- a/docs/reference/sort_basis.html
+++ b/docs/reference/sort_basis.html
@@ -1,5 +1,5 @@
-Sort the basis-set elements alphabetically. — sort_basis • Spectroscopy Analysis Tools (spant) Sort the basis-set elements alphabetically. — sort_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/spant-package.html b/docs/reference/spant-package.html
index b3dd8e21..90f19ec3 100644
--- a/docs/reference/spant-package.html
+++ b/docs/reference/spant-package.html
@@ -1,5 +1,5 @@
-spant: spectroscopy analysis tools. — spant-package • Spectroscopy Analysis Tools (spant) spant: spectroscopy analysis tools. — spant-package • Spectroscopy Analysis Tools (spant) Simulate and fit some spectra with ABfit for benchmarking purposes. Basic
-timing and performance metrics will be printed. — spant_abfit_benchmark • Spectroscopy Analysis Tools (spant) Simulate and fit some spectra with ABfit for benchmarking purposes. Basic timing and performance metrics will be printed. — spant_abfit_benchmark • Spectroscopy Analysis Tools (spant) Example MEGA-PRESS data with significant B0 drift. — spant_mpress_drift • Spectroscopy Analysis Tools (spant) Example MEGA-PRESS data with significant B0 drift. — spant_mpress_drift • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -83,7 +83,7 @@ Example MEGA-PRESS data with significant B0 drift.
Format
- An object of class mrs_data of length 13.
+ An object of class mrs_data of dimension 1 x 1 x 1 x 1 x 40 x 1 x 1024.
@@ -98,7 +98,7 @@ Format
diff --git a/docs/reference/spant_sim_fmrs_dataset.html b/docs/reference/spant_sim_fmrs_dataset.html
new file mode 100644
index 00000000..00e48b56
--- /dev/null
+++ b/docs/reference/spant_sim_fmrs_dataset.html
@@ -0,0 +1,117 @@
+
+Simulate an example fMRS dataset for a block design fMRS experiment and export a BIDS structure. — spant_sim_fmrs_dataset • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Simulate an example fMRS dataset for a block design fMRS experiment and export a BIDS structure.
+ Source: R/fmrs.R
+ spant_sim_fmrs_dataset.Rd
+
+
+
+ Simulate an example fMRS dataset for a block design fMRS experiment and
+export a BIDS structure.
+
+
+
+ spant_sim_fmrs_dataset(output_dir = NULL)
+
+
+
+ Arguments
+ - output_dir
+output directory for the BIDS data. Defaults to :
+"HOME/sim_fmrs_dataset/data".
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/spant_simulation_benchmark.html b/docs/reference/spant_simulation_benchmark.html
index 32daa8bf..d8cc6841 100644
--- a/docs/reference/spant_simulation_benchmark.html
+++ b/docs/reference/spant_simulation_benchmark.html
@@ -1,7 +1,5 @@
-Simulate a typical metabolite basis set for benchmarking. Timing metrics will
-be printed on completion. — spant_simulation_benchmark • Spectroscopy Analysis Tools (spant) Simulate a typical metabolite basis set for benchmarking. Timing metrics will be printed on completion. — spant_simulation_benchmark • Spectroscopy Analysis Tools (spant) Decompose an mrs_data object into white and gray matter spectra. — spec_decomp • Spectroscopy Analysis Tools (spant) Perform a mathematical operation on a spectral region. — spec_op • Spectroscopy Analysis Tools (spant) Perform a mathematical operation on a spectral region. — spec_op • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -98,8 +98,8 @@ Arguments
operator
-can be "sum" (default), "mean", "l2", "max", "min" or
-"max-min".
can be "sum" (default), "mean", "l2", "max", "max_cplx,
+"min" or "max-min".
freq_scale
@@ -129,7 +129,7 @@ Value
diff --git a/docs/reference/spin_sys.html b/docs/reference/spin_sys.html
index 853423a4..1eaa9e76 100644
--- a/docs/reference/spin_sys.html
+++ b/docs/reference/spin_sys.html
@@ -1,5 +1,5 @@
-Create a spin system object for pulse sequence simulation. — spin_sys • Spectroscopy Analysis Tools (spant) Create a spin system object for pulse sequence simulation. — spin_sys • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/spm_pve2categorical.html b/docs/reference/spm_pve2categorical.html
index 23a1bad9..70f10729 100644
--- a/docs/reference/spm_pve2categorical.html
+++ b/docs/reference/spm_pve2categorical.html
@@ -1,7 +1,5 @@
-Convert SPM style segmentation files to a single categorical image where
-the numerical values map as: 0) Other, 1) CSF, 2) GM and 3) WM. — spm_pve2categorical • Spectroscopy Analysis Tools (spant) Convert SPM style segmentation files to a single categorical image where the numerical values map as: 0) Other, 1) CSF, 2) GM and 3) WM. — spm_pve2categorical • Spectroscopy Analysis Tools (spant) Signal space projection method for lipid suppression. — ssp • Spectroscopy Analysis Tools (spant) Signal space projection method for lipid suppression. — ssp • Spectroscopy Analysis Tools (spant) Plot the fitting results of an object of class fit_result with
-individual basis set components shown. — stackplot.fit_result • Spectroscopy Analysis Tools (spant) Plot the fitting results of an object of class fit_result with individual basis set components shown. — stackplot.fit_result • Spectroscopy Analysis Tools (spant) Produce a plot with multiple traces. — stackplot • Spectroscopy Analysis Tools (spant) Produce a plot with multiple traces. — stackplot • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/stackplot.mrs_data.html b/docs/reference/stackplot.mrs_data.html
index 17ff5648..64eea445 100644
--- a/docs/reference/stackplot.mrs_data.html
+++ b/docs/reference/stackplot.mrs_data.html
@@ -1,5 +1,5 @@
-Stackplot plotting method for objects of class mrs_data. — stackplot.mrs_data • Spectroscopy Analysis Tools (spant) Stackplot plotting method for objects of class mrs_data. — stackplot.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -255,7 +255,7 @@ Arguments
diff --git a/docs/reference/sub_first_dyn.html b/docs/reference/sub_first_dyn.html
index dbd7f831..493b7242 100644
--- a/docs/reference/sub_first_dyn.html
+++ b/docs/reference/sub_first_dyn.html
@@ -1,5 +1,5 @@
-Subtract the first dynamic spectrum from a dynamic series. — sub_first_dyn • Spectroscopy Analysis Tools (spant) Subtract the first dynamic spectrum from a dynamic series. — sub_first_dyn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/sub_mean_dyns.html b/docs/reference/sub_mean_dyns.html
index 6e3bb2df..221bd0c1 100644
--- a/docs/reference/sub_mean_dyns.html
+++ b/docs/reference/sub_mean_dyns.html
@@ -1,5 +1,5 @@
-Subtract the mean dynamic spectrum from a dynamic series. — sub_mean_dyns • Spectroscopy Analysis Tools (spant) Subtract the mean dynamic spectrum from a dynamic series. — sub_mean_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/sub_median_dyns.html b/docs/reference/sub_median_dyns.html
index 134c495d..1e834f14 100644
--- a/docs/reference/sub_median_dyns.html
+++ b/docs/reference/sub_median_dyns.html
@@ -1,5 +1,5 @@
-Subtract the median dynamic spectrum from a dynamic series. — sub_median_dyns • Spectroscopy Analysis Tools (spant) Subtract the median dynamic spectrum from a dynamic series. — sub_median_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/sum_coils.html b/docs/reference/sum_coils.html
index 7bf559f2..e1ab3cc0 100644
--- a/docs/reference/sum_coils.html
+++ b/docs/reference/sum_coils.html
@@ -1,5 +1,5 @@
-Calculate the sum across receiver coil elements. — sum_coils • Spectroscopy Analysis Tools (spant) Calculate the sum across receiver coil elements. — sum_coils • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/sum_dyns.html b/docs/reference/sum_dyns.html
index a0be19d3..bbda2ffc 100644
--- a/docs/reference/sum_dyns.html
+++ b/docs/reference/sum_dyns.html
@@ -1,5 +1,5 @@
-Calculate the sum of data dynamics. — sum_dyns • Spectroscopy Analysis Tools (spant) Calculate the sum of data dynamics. — sum_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/sum_mrs.html b/docs/reference/sum_mrs.html
index a22f215b..3cc3ab9e 100644
--- a/docs/reference/sum_mrs.html
+++ b/docs/reference/sum_mrs.html
@@ -1,5 +1,5 @@
-Sum two mrs_data objects. — sum_mrs • Spectroscopy Analysis Tools (spant) Sum two mrs_data objects. — sum_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Value
diff --git a/docs/reference/sum_mrs_list.html b/docs/reference/sum_mrs_list.html
index f4e09aea..c3584348 100644
--- a/docs/reference/sum_mrs_list.html
+++ b/docs/reference/sum_mrs_list.html
@@ -1,5 +1,5 @@
-Return the sum of a list of mrs_data objects. — sum_mrs_list • Spectroscopy Analysis Tools (spant) Return the sum of a list of mrs_data objects. — sum_mrs_list • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/svs_1h_brain_analysis.html b/docs/reference/svs_1h_brain_analysis.html
index 8ce514db..dff0ef7d 100644
--- a/docs/reference/svs_1h_brain_analysis.html
+++ b/docs/reference/svs_1h_brain_analysis.html
@@ -1,5 +1,5 @@
-Standard SVS 1H brain analysis pipeline. — svs_1h_brain_analysis • Spectroscopy Analysis Tools (spant) Standard SVS 1H brain analysis pipeline. — svs_1h_brain_analysis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -199,7 +199,7 @@ Value
diff --git a/docs/reference/svs_1h_brain_analysis_dev.html b/docs/reference/svs_1h_brain_analysis_dev.html
index d70a14d3..d71bfea2 100644
--- a/docs/reference/svs_1h_brain_analysis_dev.html
+++ b/docs/reference/svs_1h_brain_analysis_dev.html
@@ -1,5 +1,5 @@
-Standard SVS 1H brain analysis pipeline. — svs_1h_brain_analysis_dev • Spectroscopy Analysis Tools (spant) Standard SVS 1H brain analysis pipeline. — svs_1h_brain_analysis_dev • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -193,7 +193,7 @@ Examples
diff --git a/docs/reference/svs_1h_brain_batch_analysis.html b/docs/reference/svs_1h_brain_batch_analysis.html
index 5631e8cc..15f7223e 100644
--- a/docs/reference/svs_1h_brain_batch_analysis.html
+++ b/docs/reference/svs_1h_brain_batch_analysis.html
@@ -1,5 +1,5 @@
-Batch interface to the standard SVS 1H brain analysis pipeline. — svs_1h_brain_batch_analysis • Spectroscopy Analysis Tools (spant) Batch interface to the standard SVS 1H brain analysis pipeline. — svs_1h_brain_batch_analysis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -144,7 +144,7 @@ Value
diff --git a/docs/reference/t_test_spec.html b/docs/reference/t_test_spec.html
new file mode 100644
index 00000000..56a7ea1b
--- /dev/null
+++ b/docs/reference/t_test_spec.html
@@ -0,0 +1,124 @@
+
+Perform a t-test on spectral data points. — t_test_spec • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+
+
+ Perform a t-test on spectral data points.
+
+
+
+ t_test_spec(mrs_data, group)
+
+
+
+ Arguments
+ - mrs_data
+an mrs_data object with spectra in the dynamic dimension.
- group
+vector describing the group membership of each dynamic spectrum.
+
+ Value
+
+
+a list of statistical results.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/td2fd.html b/docs/reference/td2fd.html
index 6748a6a8..f31ed524 100644
--- a/docs/reference/td2fd.html
+++ b/docs/reference/td2fd.html
@@ -1,5 +1,5 @@
-Transform time-domain data to the frequency-domain. — td2fd • Spectroscopy Analysis Tools (spant) Transform time-domain data to the frequency-domain. — td2fd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/td_conv_filt.html b/docs/reference/td_conv_filt.html
index a9f340c3..106b9b00 100644
--- a/docs/reference/td_conv_filt.html
+++ b/docs/reference/td_conv_filt.html
@@ -1,5 +1,5 @@
-Time-domain convolution based filter. — td_conv_filt • Spectroscopy Analysis Tools (spant) Time-domain convolution based filter. — td_conv_filt • Spectroscopy Analysis Tools (spant) Time-domain spectral registration. — tdsr • Spectroscopy Analysis Tools (spant) Time-domain spectral registration. — tdsr • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -121,7 +121,7 @@ Value
diff --git a/docs/reference/te.html b/docs/reference/te.html
index 010361b1..4a65711d 100644
--- a/docs/reference/te.html
+++ b/docs/reference/te.html
@@ -1,5 +1,5 @@
-Return the echo time of an MRS dataset. — te • Spectroscopy Analysis Tools (spant) Return the echo time of an MRS dataset. — te • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/tr.html b/docs/reference/tr.html
index 0c0bd63b..2e749e02 100644
--- a/docs/reference/tr.html
+++ b/docs/reference/tr.html
@@ -1,5 +1,5 @@
-Return the repetition time of an MRS dataset. — tr • Spectroscopy Analysis Tools (spant) Return the repetition time of an MRS dataset. — tr • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/varpro_3_para_opts.html b/docs/reference/varpro_3_para_opts.html
index c2270a16..52d7cd84 100644
--- a/docs/reference/varpro_3_para_opts.html
+++ b/docs/reference/varpro_3_para_opts.html
@@ -1,5 +1,5 @@
-Return a list of options for VARPRO based fitting with 3 free parameters. — varpro_3_para_opts • Spectroscopy Analysis Tools (spant) Return a list of options for VARPRO based fitting with 3 free parameters. — varpro_3_para_opts • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -141,7 +141,7 @@ Value
diff --git a/docs/reference/varpro_basic_opts.html b/docs/reference/varpro_basic_opts.html
index 32c86d22..c5104891 100644
--- a/docs/reference/varpro_basic_opts.html
+++ b/docs/reference/varpro_basic_opts.html
@@ -1,5 +1,5 @@
-Return a list of options for a basic VARPRO analysis. — varpro_basic_opts • Spectroscopy Analysis Tools (spant) Return a list of options for a basic VARPRO analysis. — varpro_basic_opts • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -118,7 +118,7 @@ Value
diff --git a/docs/reference/varpro_opts.html b/docs/reference/varpro_opts.html
index 2aabf11d..6332f730 100644
--- a/docs/reference/varpro_opts.html
+++ b/docs/reference/varpro_opts.html
@@ -1,5 +1,5 @@
-Return a list of options for VARPRO based fitting. — varpro_opts • Spectroscopy Analysis Tools (spant) Return a list of options for VARPRO based fitting. — varpro_opts • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -177,7 +177,7 @@ Examples
diff --git a/docs/reference/vec2mrs_data.html b/docs/reference/vec2mrs_data.html
index 0cccd73b..f0d58bf0 100644
--- a/docs/reference/vec2mrs_data.html
+++ b/docs/reference/vec2mrs_data.html
@@ -1,5 +1,5 @@
-Convert a vector into a mrs_data object. — vec2mrs_data • Spectroscopy Analysis Tools (spant) Convert a vector into a mrs_data object. — vec2mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -80,10 +80,11 @@ Convert a vector into a mrs_data object.
vec2mrs_data(
vec,
- fs = def_fs(),
- ft = def_ft(),
- ref = def_ref(),
- nuc = def_nuc(),
+ mrs_data = NULL,
+ fs = NULL,
+ ft = NULL,
+ ref = NULL,
+ nuc = NULL,
dyns = 1,
fd = FALSE
)
@@ -95,6 +96,10 @@ Arguments
the data vector.
mrs_data
+example data to copy acquisition parameters from.
fs
sampling frequency in Hz.
Arguments
fd
-flag to indicate if the matrix is in the frequency domain (logical).
flag to indicate if the vector is in the frequency domain (logical).
Value
diff --git a/docs/reference/write_basis.html b/docs/reference/write_basis.html
index b6e27cbd..94c5e021 100644
--- a/docs/reference/write_basis.html
+++ b/docs/reference/write_basis.html
@@ -1,5 +1,5 @@
-Write a basis object to an LCModel .basis formatted file. — write_basis • Spectroscopy Analysis Tools (spant) Write a basis object to an LCModel .basis formatted file. — write_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -108,7 +108,7 @@ Arguments
diff --git a/docs/reference/write_basis_tqn.html b/docs/reference/write_basis_tqn.html
index 6aa51c1d..116c73ec 100644
--- a/docs/reference/write_basis_tqn.html
+++ b/docs/reference/write_basis_tqn.html
@@ -1,5 +1,5 @@
-Generate a basis file using TARQUIN. — write_basis_tqn • Spectroscopy Analysis Tools (spant) Generate a basis file using TARQUIN. — write_basis_tqn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Examples
diff --git a/docs/reference/write_mrs.html b/docs/reference/write_mrs.html
index fff25f15..124b9dc4 100644
--- a/docs/reference/write_mrs.html
+++ b/docs/reference/write_mrs.html
@@ -1,5 +1,5 @@
-Write MRS data object to file. — write_mrs • Spectroscopy Analysis Tools (spant) Write MRS data object to file. — write_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Arguments
diff --git a/docs/reference/write_mrs_nifti.html b/docs/reference/write_mrs_nifti.html
index f4bf1921..bd3ed4b7 100644
--- a/docs/reference/write_mrs_nifti.html
+++ b/docs/reference/write_mrs_nifti.html
@@ -1,5 +1,5 @@
-Write MRS data object to file in NIFTI format. — write_mrs_nifti • Spectroscopy Analysis Tools (spant) Write MRS data object to file in NIFTI format. — write_mrs_nifti • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/write_pulse_ascii.html b/docs/reference/write_pulse_ascii.html
index 067ae086..221f8ebb 100644
--- a/docs/reference/write_pulse_ascii.html
+++ b/docs/reference/write_pulse_ascii.html
@@ -1,5 +1,5 @@
-Write an ASCII formatted pulse file. — write_pulse_ascii • Spectroscopy Analysis Tools (spant) Write an ASCII formatted pulse file. — write_pulse_ascii • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/zero_fade_spec.html b/docs/reference/zero_fade_spec.html
index c703745c..c8b572c3 100644
--- a/docs/reference/zero_fade_spec.html
+++ b/docs/reference/zero_fade_spec.html
@@ -1,7 +1,5 @@
-Fade a spectrum to zero by frequency domain multiplication with a tanh
-function. Note this operation distorts data points at the end of the FID. — zero_fade_spec • Spectroscopy Analysis Tools (spant) Fade a spectrum to zero by frequency domain multiplication with a tanh function. Note this operation distorts data points at the end of the FID. — zero_fade_spec • Spectroscopy Analysis Tools (spant) Zero all coherences including and above a given order. — zero_higher_orders • Spectroscopy Analysis Tools (spant) Zero all coherences including and above a given order. — zero_higher_orders • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Value
diff --git a/docs/reference/zero_td_pts_end.html b/docs/reference/zero_td_pts_end.html
index 8c1123c8..71d24ebb 100644
--- a/docs/reference/zero_td_pts_end.html
+++ b/docs/reference/zero_td_pts_end.html
@@ -1,5 +1,5 @@
-Set mrs_data object data points at the end of the FID to zero. — zero_td_pts_end • Spectroscopy Analysis Tools (spant) Set mrs_data object data points at the end of the FID to zero. — zero_td_pts_end • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/zf.html b/docs/reference/zf.html
index 85e2013c..baf50256 100644
--- a/docs/reference/zf.html
+++ b/docs/reference/zf.html
@@ -1,5 +1,5 @@
-Zero-fill MRS data in the time domain. — zf • Spectroscopy Analysis Tools (spant) Zero-fill MRS data in the time domain. — zf • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -125,7 +125,7 @@ Value
diff --git a/docs/reference/zf_xy.html b/docs/reference/zf_xy.html
index ebca3999..c4104a74 100644
--- a/docs/reference/zf_xy.html
+++ b/docs/reference/zf_xy.html
@@ -1,5 +1,5 @@
-Zero-fill MRSI data in the k-space x-y direction. — zf_xy • Spectroscopy Analysis Tools (spant) Zero-fill MRSI data in the k-space x-y direction. — zf_xy • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -113,7 +113,7 @@ Value
diff --git a/docs/sitemap.xml b/docs/sitemap.xml
index e2139f71..4c39f515 100644
--- a/docs/sitemap.xml
+++ b/docs/sitemap.xml
@@ -216,6 +216,12 @@
https://martin3141.github.io/spant/reference/comb_coils_fp_pc.html
+
+ https://martin3141.github.io/spant/reference/comb_coils_mrsi_gls.html
+
+
+ https://martin3141.github.io/spant/reference/comb_coils_svs_gls.html
+
https://martin3141.github.io/spant/reference/comb_csv_results.html
@@ -411,6 +417,9 @@
https://martin3141.github.io/spant/reference/gen_conv_reg.html
+
+ https://martin3141.github.io/spant/reference/gen_group_reg.html
+
https://martin3141.github.io/spant/reference/gen_impulse_reg.html
@@ -555,6 +564,15 @@
https://martin3141.github.io/spant/reference/glm_spec.html
+
+ https://martin3141.github.io/spant/reference/glm_spec_fmrs_fl.html
+
+
+ https://martin3141.github.io/spant/reference/glm_spec_fmrs_group.html
+
+
+ https://martin3141.github.io/spant/reference/glm_spec_group_linhyp.html
+
https://martin3141.github.io/spant/reference/grid_shift_xy.html
@@ -690,9 +708,15 @@
https://martin3141.github.io/spant/reference/mrs_data2basis.html
+
+ https://martin3141.github.io/spant/reference/mrs_data2bids.html
+
https://martin3141.github.io/spant/reference/mrs_data2mat.html
+
+ https://martin3141.github.io/spant/reference/mrs_data2spec_mat.html
+
https://martin3141.github.io/spant/reference/mrs_data2vec.html
@@ -741,6 +765,9 @@
https://martin3141.github.io/spant/reference/phase.html
+
+ https://martin3141.github.io/spant/reference/phase_ref_1h_brain.html
+
https://martin3141.github.io/spant/reference/plot.fit_result.html
@@ -780,6 +807,12 @@
https://martin3141.github.io/spant/reference/precomp.html
+
+ https://martin3141.github.io/spant/reference/preproc_svs.html
+
+
+ https://martin3141.github.io/spant/reference/preproc_svs_dataset.html
+
https://martin3141.github.io/spant/reference/print.fit_result.html
@@ -1050,6 +1083,9 @@
https://martin3141.github.io/spant/reference/spant_mpress_drift.html
+
+ https://martin3141.github.io/spant/reference/spant_sim_fmrs_dataset.html
+
https://martin3141.github.io/spant/reference/spant_simulation_benchmark.html
@@ -1107,6 +1143,9 @@
https://martin3141.github.io/spant/reference/svs_1h_brain_batch_analysis.html
+
+ https://martin3141.github.io/spant/reference/t_test_spec.html
+
https://martin3141.github.io/spant/reference/td2fd.html
Resample a VOI to match a target image space using nearest-neighbour -interpolation.
Resample a VOI to match a target image space using nearest-neighbour interpolation.
All functions
- Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water).
Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / kg of tissue water).
- Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water).
Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / kg of tissue water).
- Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / Litre of tissue).
Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / Litre of tissue).
- Convert default LCM/TARQUIN concentration scaling to molal units with partial
-volume correction.
Convert default LCM/TARQUIN concentration scaling to molal units with partial volume correction.
@@ -1222,8 +1202,7 @@ All functions
- MEGA-PRESS sequence with ideal localisation pulses and Gaussian shaped
-editing pulse.
MEGA-PRESS sequence with ideal localisation pulses and Gaussian shaped editing pulse.
@@ -1251,13 +1230,11 @@ All functions
- STEAM sequence with ideal pulses and coherence order filtering to simulate
-gradient crushers.
STEAM sequence with ideal pulses and coherence order filtering to simulate gradient crushers.
- STEAM sequence with ideal pulses using the z-rotation gradient simulation
-method described by Young et al JMR 140, 146-152 (1999).
STEAM sequence with ideal pulses using the z-rotation gradient simulation method described by Young et al JMR 140, 146-152 (1999).
@@ -1293,8 +1270,7 @@ All functions
- Set the number of time-domain data points, truncating or zero-filling as
-appropriate.
Set the number of time-domain data points, truncating or zero-filling as appropriate.
@@ -1318,18 +1294,15 @@ All functions
- Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS
-sequence. Note, ideal pulses are assumed.
Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS sequence. Note, ideal pulses are assumed.
- Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS
-sequence. Note, ideal pulses are assumed.
Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS sequence. Note, ideal pulses are assumed.
- Simulate a macromolecular and lipid basis-set suitable for 1H brain MRS
-analysis.
Simulate a macromolecular and lipid basis-set suitable for 1H brain MRS analysis.
@@ -1353,8 +1326,7 @@ All functions
- Simulate an ideal pulse excitation profile by smoothing a top-hat function
-with a Gaussian.
Simulate an ideal pulse excitation profile by smoothing a top-hat function with a Gaussian.
@@ -1374,17 +1346,19 @@ All functions
- Simulate and fit some spectra with ABfit for benchmarking purposes. Basic
-timing and performance metrics will be printed.
Simulate and fit some spectra with ABfit for benchmarking purposes. Basic timing and performance metrics will be printed.
Example MEGA-PRESS data with significant B0 drift.
+
+
+ Simulate an example fMRS dataset for a block design fMRS experiment and export a BIDS structure.
- Simulate a typical metabolite basis set for benchmarking. Timing metrics will
-be printed on completion.
Simulate a typical metabolite basis set for benchmarking. Timing metrics will be printed on completion.
@@ -1400,8 +1374,7 @@ All functions
- Convert SPM style segmentation files to a single categorical image where
-the numerical values map as: 0) Other, 1) CSF, 2) GM and 3) WM.
Convert SPM style segmentation files to a single categorical image where the numerical values map as: 0) Other, 1) CSF, 2) GM and 3) WM.
@@ -1413,8 +1386,7 @@ All functions
- Plot the fitting results of an object of class fit_result with
-individual basis set components shown.
Plot the fitting results of an object of class fit_result with individual basis set components shown.
@@ -1459,6 +1431,10 @@ All functions svs_1h_brain_batch_analysis()
Batch interface to the standard SVS 1H brain analysis pipeline.
+
+
+ Perform a t-test on spectral data points.
@@ -1518,8 +1494,7 @@ All functions
- Fade a spectrum to zero by frequency domain multiplication with a tanh
-function. Note this operation distorts data points at the end of the FID.
Fade a spectrum to zero by frequency domain multiplication with a tanh function. Note this operation distorts data points at the end of the FID.
@@ -1549,7 +1524,7 @@ All functions
diff --git a/docs/reference/int_spec.html b/docs/reference/int_spec.html
index c7060fe7..783325a8 100644
--- a/docs/reference/int_spec.html
+++ b/docs/reference/int_spec.html
@@ -1,5 +1,5 @@
-Integrate a spectral region. — int_spec • Spectroscopy Analysis Tools (spant) Integrate a spectral region. — int_spec • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -118,7 +118,7 @@ Value
diff --git a/docs/reference/interleave_dyns.html b/docs/reference/interleave_dyns.html
index effe5543..441eff27 100644
--- a/docs/reference/interleave_dyns.html
+++ b/docs/reference/interleave_dyns.html
@@ -1,5 +1,5 @@
-Interleave the first and second half of a dynamic series. — interleave_dyns • Spectroscopy Analysis Tools (spant) Interleave the first and second half of a dynamic series. — interleave_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/inv_even_dyns.html b/docs/reference/inv_even_dyns.html
index 9f9d4fff..dcb781dc 100644
--- a/docs/reference/inv_even_dyns.html
+++ b/docs/reference/inv_even_dyns.html
@@ -1,5 +1,5 @@
-Invert even numbered dynamic scans starting from 1 (2,4,6...). — inv_even_dyns • Spectroscopy Analysis Tools (spant) Invert even numbered dynamic scans starting from 1 (2,4,6...). — inv_even_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/inv_odd_dyns.html b/docs/reference/inv_odd_dyns.html
index 26212e2b..78d64660 100644
--- a/docs/reference/inv_odd_dyns.html
+++ b/docs/reference/inv_odd_dyns.html
@@ -1,5 +1,5 @@
-Invert odd numbered dynamic scans starting from 1 (1,3,5...). — inv_odd_dyns • Spectroscopy Analysis Tools (spant) Invert odd numbered dynamic scans starting from 1 (1,3,5...). — inv_odd_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/is.def.html b/docs/reference/is.def.html
index f196ffd0..a67b9eba 100644
--- a/docs/reference/is.def.html
+++ b/docs/reference/is.def.html
@@ -1,5 +1,5 @@
-Check if an object is defined, which is the same as being not NULL. — is.def • Spectroscopy Analysis Tools (spant) Check if an object is defined, which is the same as being not NULL. — is.def • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/is_fd.html b/docs/reference/is_fd.html
index 3b0ca165..18a193aa 100644
--- a/docs/reference/is_fd.html
+++ b/docs/reference/is_fd.html
@@ -1,7 +1,5 @@
-Check if the chemical shift dimension of an MRS data object is in the
-frequency domain. — is_fd • Spectroscopy Analysis Tools (spant) Check if the chemical shift dimension of an MRS data object is in the frequency domain. — is_fd • Spectroscopy Analysis Tools (spant) Transform 2D MRSI data from k-space to image space in the x-y direction. — kspace2img_xy • Spectroscopy Analysis Tools (spant) Transform 2D MRSI data from k-space to image space in the x-y direction. — kspace2img_xy • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/l2_reg.html b/docs/reference/l2_reg.html
index 3d781d80..21aa9849 100644
--- a/docs/reference/l2_reg.html
+++ b/docs/reference/l2_reg.html
@@ -1,5 +1,5 @@
-Perform l2 regularisation artefact suppression. — l2_reg • Spectroscopy Analysis Tools (spant) Perform l2 regularisation artefact suppression. — l2_reg • Spectroscopy Analysis Tools (spant) Apply line-broadening (apodisation) to MRS data or basis object. — lb • Spectroscopy Analysis Tools (spant) Apply line-broadening (apodisation) to MRS data or basis object. — lb • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -123,7 +123,7 @@ Value
diff --git a/docs/reference/lofdc.html b/docs/reference/lofdc.html
index 5419b1ec..31347a25 100644
--- a/docs/reference/lofdc.html
+++ b/docs/reference/lofdc.html
@@ -1,5 +1,5 @@
-Correct linear frequency drift. — lofdc • Spectroscopy Analysis Tools (spant) Correct linear frequency drift. — lofdc • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -138,7 +138,7 @@ Value
diff --git a/docs/reference/lw2alpha.html b/docs/reference/lw2alpha.html
index b83db682..25da229b 100644
--- a/docs/reference/lw2alpha.html
+++ b/docs/reference/lw2alpha.html
@@ -1,7 +1,5 @@
-Covert a linewidth in Hz to an equivalent alpha value in the time-domain ie:
-x * exp(-t * alpha). — lw2alpha • Spectroscopy Analysis Tools (spant) Covert a linewidth in Hz to an equivalent alpha value in the time-domain ie: x * exp(-t * alpha). — lw2alpha • Spectroscopy Analysis Tools (spant) Covert a linewidth in Hz to an equivalent beta value in the time-domain ie:
-x * exp(-t * t * beta). — lw2beta • Spectroscopy Analysis Tools (spant) Covert a linewidth in Hz to an equivalent beta value in the time-domain ie: x * exp(-t * t * beta). — lw2beta • Spectroscopy Analysis Tools (spant) Make a basis-set object from a directory containing LCModel formatted RAW
-files. — make_basis_from_raw • Spectroscopy Analysis Tools (spant) Make a basis-set object from a directory containing LCModel formatted RAW files. — make_basis_from_raw • Spectroscopy Analysis Tools (spant) Mask an MRS dataset in the dynamic dimension. — mask_dyns • Spectroscopy Analysis Tools (spant) Mask an MRS dataset in the dynamic dimension. — mask_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/mask_fit_res.html b/docs/reference/mask_fit_res.html
index 97baaa3f..ebd91a99 100644
--- a/docs/reference/mask_fit_res.html
+++ b/docs/reference/mask_fit_res.html
@@ -1,5 +1,5 @@
-Mask fit result spectra depending on a vector of bool values. — mask_fit_res • Spectroscopy Analysis Tools (spant) Mask fit result spectra depending on a vector of bool values. — mask_fit_res • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -116,7 +116,7 @@ Value
diff --git a/docs/reference/mask_xy.html b/docs/reference/mask_xy.html
index 11bb577c..b0d38619 100644
--- a/docs/reference/mask_xy.html
+++ b/docs/reference/mask_xy.html
@@ -1,5 +1,5 @@
-Mask an MRSI dataset in the x-y direction — mask_xy • Spectroscopy Analysis Tools (spant) Mask an MRSI dataset in the x-y direction — mask_xy • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/mask_xy_corners.html b/docs/reference/mask_xy_corners.html
index 09b16cd2..2d13839d 100644
--- a/docs/reference/mask_xy_corners.html
+++ b/docs/reference/mask_xy_corners.html
@@ -1,5 +1,5 @@
-Mask the four corners of an MRSI dataset in the x-y plane. — mask_xy_corners • Spectroscopy Analysis Tools (spant) Mask the four corners of an MRSI dataset in the x-y plane. — mask_xy_corners • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/mask_xy_ellipse.html b/docs/reference/mask_xy_ellipse.html
index 1d8b02e4..e2e749ef 100644
--- a/docs/reference/mask_xy_ellipse.html
+++ b/docs/reference/mask_xy_ellipse.html
@@ -1,7 +1,5 @@
-Mask the voxels outside an elliptical region spanning the MRSI dataset in the
-x-y plane. — mask_xy_ellipse • Spectroscopy Analysis Tools (spant) Mask the voxels outside an elliptical region spanning the MRSI dataset in the x-y plane. — mask_xy_ellipse • Spectroscopy Analysis Tools (spant) Mask a 2D MRSI dataset in the x-y dimension. — mask_xy_mat • Spectroscopy Analysis Tools (spant) Mask a 2D MRSI dataset in the x-y dimension. — mask_xy_mat • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Value
diff --git a/docs/reference/mat2mrs_data.html b/docs/reference/mat2mrs_data.html
index 2e2895f3..ae55665f 100644
--- a/docs/reference/mat2mrs_data.html
+++ b/docs/reference/mat2mrs_data.html
@@ -1,7 +1,5 @@
-Convert a matrix (with spectral points in the column dimension and dynamics
-in the row dimensions) into a mrs_data object. — mat2mrs_data • Spectroscopy Analysis Tools (spant) Convert a matrix (with spectral points in the column dimension and dynamics in the row dimensions) into a mrs_data object. — mat2mrs_data • Spectroscopy Analysis Tools (spant) Matrix exponential function taken from complexplus package to reduce the
-number of spant dependencies. — matexp • Spectroscopy Analysis Tools (spant) Matrix exponential function taken from complexplus package to reduce the number of spant dependencies. — matexp • Spectroscopy Analysis Tools (spant) Apply the max operator to an MRS dataset. — max_mrs • Spectroscopy Analysis Tools (spant) Apply the max operator to an MRS dataset. — max_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/max_mrs_interp.html b/docs/reference/max_mrs_interp.html
index e4474764..52e63f3e 100644
--- a/docs/reference/max_mrs_interp.html
+++ b/docs/reference/max_mrs_interp.html
@@ -1,5 +1,5 @@
-Apply the max operator to an interpolated MRS dataset. — max_mrs_interp • Spectroscopy Analysis Tools (spant) Apply the max operator to an interpolated MRS dataset. — max_mrs_interp • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/mean.list.html b/docs/reference/mean.list.html
index b8eb3463..048306fd 100644
--- a/docs/reference/mean.list.html
+++ b/docs/reference/mean.list.html
@@ -1,5 +1,5 @@
-Calculate the mean spectrum from an mrs_data object. — mean.list • Spectroscopy Analysis Tools (spant) Calculate the mean spectrum from an mrs_data object. — mean.list • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/mean.mrs_data.html b/docs/reference/mean.mrs_data.html
index 5531a28d..79515014 100644
--- a/docs/reference/mean.mrs_data.html
+++ b/docs/reference/mean.mrs_data.html
@@ -1,5 +1,5 @@
-Calculate the mean spectrum from an mrs_data object. — mean.mrs_data • Spectroscopy Analysis Tools (spant) Calculate the mean spectrum from an mrs_data object. — mean.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/mean_dyn_blocks.html b/docs/reference/mean_dyn_blocks.html
index 10467098..4c042448 100644
--- a/docs/reference/mean_dyn_blocks.html
+++ b/docs/reference/mean_dyn_blocks.html
@@ -1,5 +1,5 @@
-Calculate the mean of adjacent dynamic scans. — mean_dyn_blocks • Spectroscopy Analysis Tools (spant) Calculate the mean of adjacent dynamic scans. — mean_dyn_blocks • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/mean_dyn_pairs.html b/docs/reference/mean_dyn_pairs.html
index 63e909ea..1a241126 100644
--- a/docs/reference/mean_dyn_pairs.html
+++ b/docs/reference/mean_dyn_pairs.html
@@ -1,5 +1,5 @@
-Calculate the pairwise means across a dynamic data set. — mean_dyn_pairs • Spectroscopy Analysis Tools (spant) Calculate the pairwise means across a dynamic data set. — mean_dyn_pairs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/mean_dyns.html b/docs/reference/mean_dyns.html
index 73fdbfa7..0daa27df 100644
--- a/docs/reference/mean_dyns.html
+++ b/docs/reference/mean_dyns.html
@@ -1,5 +1,5 @@
-Calculate the mean dynamic data. — mean_dyns • Spectroscopy Analysis Tools (spant) Calculate the mean dynamic data. — mean_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/mean_mrs_list.html b/docs/reference/mean_mrs_list.html
index 808b6c50..10d842c0 100644
--- a/docs/reference/mean_mrs_list.html
+++ b/docs/reference/mean_mrs_list.html
@@ -1,5 +1,5 @@
-Return the mean of a list of mrs_data objects. — mean_mrs_list • Spectroscopy Analysis Tools (spant) Return the mean of a list of mrs_data objects. — mean_mrs_list • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/mean_vec_blocks.html b/docs/reference/mean_vec_blocks.html
index 8fc92eaa..dd78b122 100644
--- a/docs/reference/mean_vec_blocks.html
+++ b/docs/reference/mean_vec_blocks.html
@@ -1,5 +1,5 @@
-Calculate the mean of adjacent blocks in a vector. — mean_vec_blocks • Spectroscopy Analysis Tools (spant) Calculate the mean of adjacent blocks in a vector. — mean_vec_blocks • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/median_dyns.html b/docs/reference/median_dyns.html
index 1039d4b5..9a085b10 100644
--- a/docs/reference/median_dyns.html
+++ b/docs/reference/median_dyns.html
@@ -1,5 +1,5 @@
-Calculate the median dynamic data. — median_dyns • Spectroscopy Analysis Tools (spant) Calculate the median dynamic data. — median_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/mod_td.html b/docs/reference/mod_td.html
index 76ad0a40..141ef09e 100644
--- a/docs/reference/mod_td.html
+++ b/docs/reference/mod_td.html
@@ -1,5 +1,5 @@
-Apply the Modulus operator to the time-domain MRS signal. — mod_td • Spectroscopy Analysis Tools (spant) Apply the Modulus operator to the time-domain MRS signal. — mod_td • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/mrs_data2basis.html b/docs/reference/mrs_data2basis.html
index 62f7d749..11797b91 100644
--- a/docs/reference/mrs_data2basis.html
+++ b/docs/reference/mrs_data2basis.html
@@ -1,7 +1,5 @@
-Convert an mrs_data object to basis object - where basis signals are spread
-across the dynamic dimension in the MRS data. — mrs_data2basis • Spectroscopy Analysis Tools (spant) Convert an mrs_data object to basis object - where basis signals are spread across the dynamic dimension in the MRS data. — mrs_data2basis • Spectroscopy Analysis Tools (spant) Create a BIDS file structure from a vector of MRS data paths or list of mrs_data objects. — mrs_data2bids • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Create a BIDS file structure from a vector of MRS data paths or list of mrs_data objects.
+ Source: R/fmrs.R
+ mrs_data2bids.Rd
+
+
+
+ Create a BIDS file structure from a vector of MRS data paths or list of
+mrs_data objects.
+
+
+
+ mrs_data2bids(
+ mrs_data,
+ output_dir,
+ suffix = NULL,
+ sub = NULL,
+ ses = NULL,
+ task = NULL,
+ acq = NULL,
+ nuc = NULL,
+ voi = NULL,
+ rec = NULL,
+ run = NULL,
+ echo = NULL,
+ inv = NULL,
+ skip_existing = TRUE
+)
+
+
+
+ Arguments
+ - mrs_data
+vector of MRS data paths or list of mrs_data objects.
- output_dir
+the base directory to create the BIDS structure.
- suffix
+optional vector of file suffixes. Default behaviour is to
+automatically determine these from the input data, however it is recommended
+that they are specified to allow more efficient skipping of existing data.
- sub
+optional vector of subject labels. If not specified, these will be
+automatically generated as a series of increasing zero-padded integer values
+corresponding to the mrs_data input indices.
- ses
+optional vector of session labels.
- task
+optional vector of task labels.
- acq
+optional vector of acquisition labels.
- nuc
+optional vector of nucleus labels.
- voi
+optional vector of volume of interest labels.
- rec
+optional vector of reconstruction labels.
- run
+optional vector of run indices.
- echo
+optional vector of echo time indices.
- inv
+optional vector of inversion indices.
- skip_existing
+skip any data files that have already been converted.
+Defaults to TRUE, set to FALSE to force an overwrite of any existing data
+files.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/mrs_data2mat.html b/docs/reference/mrs_data2mat.html
index cf5ff28c..9e47688a 100644
--- a/docs/reference/mrs_data2mat.html
+++ b/docs/reference/mrs_data2mat.html
@@ -1,7 +1,5 @@
-Convert mrs_data object to a matrix, with spectral points in the column
-dimension and dynamics in the row dimension. — mrs_data2mat • Spectroscopy Analysis Tools (spant) Convert mrs_data object to a matrix, with spectral points in the column dimension and dynamics in the row dimension. — mrs_data2mat • Spectroscopy Analysis Tools (spant) Convert mrs_data object to a matrix, with spectral points in the column dimension and dynamics in the row dimension. — mrs_data2spec_mat • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Convert mrs_data object to a matrix, with spectral points in the column dimension and dynamics in the row dimension.
+ Source: R/mrs_data_proc.R
+ mrs_data2spec_mat.Rd
+
+
+
+ Convert mrs_data object to a matrix, with spectral points in the column
+dimension and dynamics in the row dimension.
+
+
+
+ mrs_data2spec_mat(mrs_data, collapse = TRUE)
+
+
+
+ Arguments
+ - mrs_data
+MRS data object or list of MRS data objects.
- collapse
+collapse all other dimensions along the dynamic dimension, eg
+a 16x16 MRSI grid would be first collapsed across 256 dynamic scans.
+
+ Value
+
+
+MRS data matrix.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/mrs_data2vec.html b/docs/reference/mrs_data2vec.html
index fb172d68..a1fd654d 100644
--- a/docs/reference/mrs_data2vec.html
+++ b/docs/reference/mrs_data2vec.html
@@ -1,5 +1,5 @@
-Convert mrs_data object to a vector. — mrs_data2vec • Spectroscopy Analysis Tools (spant) Convert mrs_data object to a vector. — mrs_data2vec • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -126,7 +126,7 @@ Value
diff --git a/docs/reference/mvfftshift.html b/docs/reference/mvfftshift.html
index 92b0841b..976b3410 100644
--- a/docs/reference/mvfftshift.html
+++ b/docs/reference/mvfftshift.html
@@ -1,7 +1,5 @@
-Perform a fftshift on a matrix, with each column replaced by its shifted
-result. — mvfftshift • Spectroscopy Analysis Tools (spant) Perform a fftshift on a matrix, with each column replaced by its shifted result. — mvfftshift • Spectroscopy Analysis Tools (spant) Perform an ifftshift on a matrix, with each column replaced by its shifted
-result. — mvifftshift • Spectroscopy Analysis Tools (spant) Perform an ifftshift on a matrix, with each column replaced by its shifted result. — mvifftshift • Spectroscopy Analysis Tools (spant) Print fit coordinates from a single index. — n2coord • Spectroscopy Analysis Tools (spant) Print fit coordinates from a single index. — n2coord • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/nifti_flip_lr.html b/docs/reference/nifti_flip_lr.html
index 730abe3c..19860b3c 100644
--- a/docs/reference/nifti_flip_lr.html
+++ b/docs/reference/nifti_flip_lr.html
@@ -1,9 +1,5 @@
-Flip the x data dimension order of a nifti image. This corresponds to
-flipping MRI data in the left-right direction, assuming the data in save in
-neurological format (can check with fslorient program). — nifti_flip_lr • Spectroscopy Analysis Tools (spant) Flip the x data dimension order of a nifti image. This corresponds to flipping MRI data in the left-right direction, assuming the data in save in neurological format (can check with fslorient program). — nifti_flip_lr • Spectroscopy Analysis Tools (spant) Export a one-page pdf of a single fit result — one_page_pdf • Spectroscopy Analysis Tools (spant) Export a one-page pdf of a single fit result — one_page_pdf • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -108,7 +108,7 @@ Arguments
diff --git a/docs/reference/ortho3.html b/docs/reference/ortho3.html
index 13ade97d..5d7dd2fd 100644
--- a/docs/reference/ortho3.html
+++ b/docs/reference/ortho3.html
@@ -1,5 +1,5 @@
-Display an orthographic projection plot of a nifti object. — ortho3 • Spectroscopy Analysis Tools (spant) Display an orthographic projection plot of a nifti object. — ortho3 • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -172,7 +172,7 @@ Arguments
diff --git a/docs/reference/ortho3_inter.html b/docs/reference/ortho3_inter.html
index 090cc5e5..15948899 100644
--- a/docs/reference/ortho3_inter.html
+++ b/docs/reference/ortho3_inter.html
@@ -1,5 +1,5 @@
-Display an interactive orthographic projection plot of a nifti object. — ortho3_inter • Spectroscopy Analysis Tools (spant) Display an interactive orthographic projection plot of a nifti object. — ortho3_inter • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -132,7 +132,7 @@ Arguments
diff --git a/docs/reference/peak_info.html b/docs/reference/peak_info.html
index 09058bd8..41c8ffaf 100644
--- a/docs/reference/peak_info.html
+++ b/docs/reference/peak_info.html
@@ -1,7 +1,5 @@
-Search for the highest peak in a spectral region and return the frequency,
-height and FWHM. — peak_info • Spectroscopy Analysis Tools (spant) Search for the highest peak in a spectral region and return the frequency, height and FWHM. — peak_info • Spectroscopy Analysis Tools (spant) Papoulis-Gerchberg (PG) algorithm method for k-space extrapolation. — pg_extrap_xy • Spectroscopy Analysis Tools (spant) Papoulis-Gerchberg (PG) algorithm method for k-space extrapolation. — pg_extrap_xy • Spectroscopy Analysis Tools (spant) Apply phasing parameters to MRS data. — phase • Spectroscopy Analysis Tools (spant) Apply phasing parameters to MRS data. — phase • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/phase_ref_1h_brain.html b/docs/reference/phase_ref_1h_brain.html
new file mode 100644
index 00000000..8707a74a
--- /dev/null
+++ b/docs/reference/phase_ref_1h_brain.html
@@ -0,0 +1,131 @@
+
+Corrected zero order phase and chemical shift offset in 1H MRS data from the brain. — phase_ref_1h_brain • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Corrected zero order phase and chemical shift offset in 1H MRS data from the brain.
+ Source: R/rats.R
+ phase_ref_1h_brain.Rd
+
+
+
+ Corrected zero order phase and chemical shift offset in 1H MRS data from the
+brain.
+
+
+
+ phase_ref_1h_brain(mrs_data, mean_ref = FALSE, ret_corr_only = TRUE)
+
+
+
+ Arguments
+ - mrs_data
+MRS data to be corrected.
- mean_ref
+apply the phase and offset of the mean spectrum to all
+others. Default is FALSE.
- ret_corr_only
+return the corrected data only.
+
+ Value
+
+
+corrected MRS data.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/plot.fit_result.html b/docs/reference/plot.fit_result.html
index e54d3bc1..836a53ee 100644
--- a/docs/reference/plot.fit_result.html
+++ b/docs/reference/plot.fit_result.html
@@ -1,5 +1,5 @@
-Plot the fitting results of an object of class fit_result. — plot.fit_result • Spectroscopy Analysis Tools (spant) Plot the fitting results of an object of class fit_result. — plot.fit_result • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -207,7 +207,7 @@ Arguments
diff --git a/docs/reference/plot.mrs_data.html b/docs/reference/plot.mrs_data.html
index fabcc35b..bb2ec651 100644
--- a/docs/reference/plot.mrs_data.html
+++ b/docs/reference/plot.mrs_data.html
@@ -1,5 +1,5 @@
-Plotting method for objects of class mrs_data. — plot.mrs_data • Spectroscopy Analysis Tools (spant) Plotting method for objects of class mrs_data. — plot.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -287,7 +287,7 @@ Arguments
diff --git a/docs/reference/plot_bc.html b/docs/reference/plot_bc.html
index 4f8309b4..b48142cc 100644
--- a/docs/reference/plot_bc.html
+++ b/docs/reference/plot_bc.html
@@ -1,5 +1,5 @@
-Convenience function to plot a baseline estimate with the original data. — plot_bc • Spectroscopy Analysis Tools (spant) Convenience function to plot a baseline estimate with the original data. — plot_bc • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -108,7 +108,7 @@ Arguments
diff --git a/docs/reference/plot_reg.html b/docs/reference/plot_reg.html
index ae1acbe7..2addb2f6 100644
--- a/docs/reference/plot_reg.html
+++ b/docs/reference/plot_reg.html
@@ -1,5 +1,5 @@
-Plot regressors as an image. — plot_reg • Spectroscopy Analysis Tools (spant) Plot regressors as an image. — plot_reg • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/plot_slice_fit.html b/docs/reference/plot_slice_fit.html
index fbc7b560..57f1af8a 100644
--- a/docs/reference/plot_slice_fit.html
+++ b/docs/reference/plot_slice_fit.html
@@ -1,5 +1,5 @@
-Plot a 2D slice from an MRSI fit result object. — plot_slice_fit • Spectroscopy Analysis Tools (spant) Plot a 2D slice from an MRSI fit result object. — plot_slice_fit • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -129,7 +129,7 @@ Arguments
diff --git a/docs/reference/plot_slice_fit_inter.html b/docs/reference/plot_slice_fit_inter.html
index 4eed104a..da105a7d 100644
--- a/docs/reference/plot_slice_fit_inter.html
+++ b/docs/reference/plot_slice_fit_inter.html
@@ -1,5 +1,5 @@
-Plot a 2D slice from an MRSI fit result object. — plot_slice_fit_inter • Spectroscopy Analysis Tools (spant) Plot a 2D slice from an MRSI fit result object. — plot_slice_fit_inter • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -134,7 +134,7 @@ Arguments
diff --git a/docs/reference/plot_slice_map.html b/docs/reference/plot_slice_map.html
index 553e9ac8..ffb2a134 100644
--- a/docs/reference/plot_slice_map.html
+++ b/docs/reference/plot_slice_map.html
@@ -1,5 +1,5 @@
-Plot a slice from a 7 dimensional array. — plot_slice_map • Spectroscopy Analysis Tools (spant) Plot a slice from a 7 dimensional array. — plot_slice_map • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -153,7 +153,7 @@ Arguments
diff --git a/docs/reference/plot_slice_map_inter.html b/docs/reference/plot_slice_map_inter.html
index 40d33b42..90968f66 100644
--- a/docs/reference/plot_slice_map_inter.html
+++ b/docs/reference/plot_slice_map_inter.html
@@ -1,7 +1,5 @@
-Plot an interactive slice map from a data array where voxels can be selected
-to display a corresponding spectrum. — plot_slice_map_inter • Spectroscopy Analysis Tools (spant) Plot an interactive slice map from a data array where voxels can be selected to display a corresponding spectrum. — plot_slice_map_inter • Spectroscopy Analysis Tools (spant) Plot the spectral standard deviation. — plot_spec_sd • Spectroscopy Analysis Tools (spant) Plot the spectral standard deviation. — plot_spec_sd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Arguments
diff --git a/docs/reference/plot_voi_overlay.html b/docs/reference/plot_voi_overlay.html
index 9a782e88..bbbbf35e 100644
--- a/docs/reference/plot_voi_overlay.html
+++ b/docs/reference/plot_voi_overlay.html
@@ -1,5 +1,5 @@
-Plot a volume as an image overlay. — plot_voi_overlay • Spectroscopy Analysis Tools (spant) Plot a volume as an image overlay. — plot_voi_overlay • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -116,7 +116,7 @@ Arguments
diff --git a/docs/reference/plot_voi_overlay_seg.html b/docs/reference/plot_voi_overlay_seg.html
index 3d4e74ff..0e800ff2 100644
--- a/docs/reference/plot_voi_overlay_seg.html
+++ b/docs/reference/plot_voi_overlay_seg.html
@@ -1,5 +1,5 @@
-Plot a volume as an overlay on a segmented brain volume. — plot_voi_overlay_seg • Spectroscopy Analysis Tools (spant) Plot a volume as an overlay on a segmented brain volume. — plot_voi_overlay_seg • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Arguments
diff --git a/docs/reference/ppm.html b/docs/reference/ppm.html
index c352327a..ee4696e2 100644
--- a/docs/reference/ppm.html
+++ b/docs/reference/ppm.html
@@ -1,5 +1,5 @@
-Return the ppm scale of an MRS dataset or fit result. — ppm • Spectroscopy Analysis Tools (spant) Return the ppm scale of an MRS dataset or fit result. — ppm • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -132,7 +132,7 @@ Value
diff --git a/docs/reference/precomp.html b/docs/reference/precomp.html
index 822d7336..df3d2c6c 100644
--- a/docs/reference/precomp.html
+++ b/docs/reference/precomp.html
@@ -1,7 +1,5 @@
-Save function results to file and load on subsequent calls to avoid repeat
-computation. — precomp • Spectroscopy Analysis Tools (spant) Save function results to file and load on subsequent calls to avoid repeat computation. — precomp • Spectroscopy Analysis Tools (spant) Preprocess and perform quality assessment of a single SVS data set. — preproc_svs • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Preprocess and perform quality assessment of a single SVS data set.
+ Source: R/fmrs.R
+ preproc_svs.Rd
+
+
+
+ Preprocess and perform quality assessment of a single SVS data set.
+
+
+
+ preproc_svs(path, label = NULL, output_dir = NULL, ref_inds = NULL)
+
+
+
+ Arguments
+ - path
+path to the fMRS data file or IMA directory.
- label
+a label to describe the data set.
- output_dir
+output directory.
- ref_inds
+a vector of 1-based indices for any water reference dynamic
+scans.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/preproc_svs_dataset.html b/docs/reference/preproc_svs_dataset.html
new file mode 100644
index 00000000..07c3a29b
--- /dev/null
+++ b/docs/reference/preproc_svs_dataset.html
@@ -0,0 +1,148 @@
+
+Preprocess and perform quality assessment of one or more SVS data sets. — preproc_svs_dataset • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Preprocess and perform quality assessment of one or more SVS data sets.
+ Source: R/fmrs.R
+ preproc_svs_dataset.Rd
+
+
+
+ Preprocess and perform quality assessment of one or more SVS data sets.
+
+
+
+ preproc_svs_dataset(
+ paths,
+ labels = NULL,
+ output_dir = "spant_analysis",
+ exclude_labels = NULL,
+ overwrite = FALSE,
+ ref_inds = NULL,
+ return_results = FALSE
+)
+
+
+
+ Arguments
+ - paths
+paths to the fMRS data file or IMA directory.
- labels
+labels to describe each data set.
- output_dir
+output directory.
- exclude_labels
+vector of labels of scans to exclude, eg poor quality
+data.
- overwrite
+overwrite saved results, defaults to FALSE.
- ref_inds
+a vector of 1-based indices for any water reference dynamic
+scans.
- return_results
+function will return key outputs, defaults to FALSE.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/print.fit_result.html b/docs/reference/print.fit_result.html
index 297f28dc..5f434e57 100644
--- a/docs/reference/print.fit_result.html
+++ b/docs/reference/print.fit_result.html
@@ -1,5 +1,5 @@
-Print a summary of an object of class fit_result. — print.fit_result • Spectroscopy Analysis Tools (spant) Print a summary of an object of class fit_result. — print.fit_result • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -105,7 +105,7 @@ Arguments
diff --git a/docs/reference/print.mrs_data.html b/docs/reference/print.mrs_data.html
index 51199017..e1561eb2 100644
--- a/docs/reference/print.mrs_data.html
+++ b/docs/reference/print.mrs_data.html
@@ -1,5 +1,5 @@
-Print a summary of mrs_data parameters. — print.mrs_data • Spectroscopy Analysis Tools (spant) Print a summary of mrs_data parameters. — print.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -109,7 +109,7 @@ Arguments
diff --git a/docs/reference/qn_states.html b/docs/reference/qn_states.html
index 0f42f2f9..d7aa6715 100644
--- a/docs/reference/qn_states.html
+++ b/docs/reference/qn_states.html
@@ -1,5 +1,5 @@
-Get the quantum coherence matrix for a spin system. — qn_states • Spectroscopy Analysis Tools (spant) Get the quantum coherence matrix for a spin system. — qn_states • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/rats.html b/docs/reference/rats.html
index 5a39a396..93585e08 100644
--- a/docs/reference/rats.html
+++ b/docs/reference/rats.html
@@ -1,5 +1,5 @@
-Robust Alignment to a Target Spectrum (RATS). — rats • Spectroscopy Analysis Tools (spant) Robust Alignment to a Target Spectrum (RATS). — rats • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -207,7 +207,7 @@ Value
diff --git a/docs/reference/re_weighting.html b/docs/reference/re_weighting.html
index d21caf21..8b0b070a 100644
--- a/docs/reference/re_weighting.html
+++ b/docs/reference/re_weighting.html
@@ -1,5 +1,5 @@
-Apply a weighting to the FID to enhance spectral resolution. — re_weighting • Spectroscopy Analysis Tools (spant) Apply a weighting to the FID to enhance spectral resolution. — re_weighting • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/read_basis.html b/docs/reference/read_basis.html
index da9b94af..eb6f8557 100644
--- a/docs/reference/read_basis.html
+++ b/docs/reference/read_basis.html
@@ -1,5 +1,5 @@
-Read a basis file in LCModel .basis format. — read_basis • Spectroscopy Analysis Tools (spant) Read a basis file in LCModel .basis format. — read_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/read_ima_coil_dir.html b/docs/reference/read_ima_coil_dir.html
index 28c02de0..4f073cd8 100644
--- a/docs/reference/read_ima_coil_dir.html
+++ b/docs/reference/read_ima_coil_dir.html
@@ -1,9 +1,5 @@
-Read a directory containing Siemens MRS IMA files and combine along the coil
-dimension. Note that the coil ID is inferred from the sorted file name and
-should be checked when consistency is required between two directories. — read_ima_coil_dir • Spectroscopy Analysis Tools (spant) Read a directory containing Siemens MRS IMA files and combine along the coil dimension. Note that the coil ID is inferred from the sorted file name and should be checked when consistency is required between two directories. — read_ima_coil_dir • Spectroscopy Analysis Tools (spant) Read a directory containing Siemens MRS IMA files and combine along the
-dynamic dimension. Note that the coil ID is inferred from the sorted file
-name and should be checked when consistency is required. — read_ima_dyn_dir • Spectroscopy Analysis Tools (spant) Read a directory containing Siemens MRS IMA files and combine along the dynamic dimension. Note that the coil ID is inferred from the sorted file name and should be checked when consistency is required. — read_ima_dyn_dir • Spectroscopy Analysis Tools (spant) Read an LCModel formatted coord file containing fit information. — read_lcm_coord • Spectroscopy Analysis Tools (spant) Read an LCModel formatted coord file containing fit information. — read_lcm_coord • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -107,7 +107,7 @@ Value
diff --git a/docs/reference/read_mrs.html b/docs/reference/read_mrs.html
index 3ac2a36b..2cf36b20 100644
--- a/docs/reference/read_mrs.html
+++ b/docs/reference/read_mrs.html
@@ -1,5 +1,5 @@
-Read MRS data from a file. — read_mrs • Spectroscopy Analysis Tools (spant) Read MRS data from a file. — read_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -88,7 +88,8 @@ Read MRS data from a file.
full_fid = FALSE,
omit_svs_ref_scans = TRUE,
verbose = FALSE,
- extra = NULL
+ extra = NULL,
+ fid_filt_dist = NULL
)
@@ -140,6 +141,13 @@ Arguments
an optional data frame to provide additional variables for use
in subsequent analysis steps, eg id or grouping variables.
fid_filt_dist
+indicate if the data has a distorted FID due to a
+brick-wall filter being used to downsample the data. Default is to auto
+detect this from the data, but TRUE or FALSE options can be given to override
+detection.
Value
@@ -183,7 +191,7 @@ Examples
diff --git a/docs/reference/read_mrs_tqn.html b/docs/reference/read_mrs_tqn.html
index 5766362f..84bdaf3a 100644
--- a/docs/reference/read_mrs_tqn.html
+++ b/docs/reference/read_mrs_tqn.html
@@ -1,5 +1,5 @@
-Read MRS data using the TARQUIN software package. — read_mrs_tqn • Spectroscopy Analysis Tools (spant) Read MRS data using the TARQUIN software package. — read_mrs_tqn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -131,7 +131,7 @@ Examples
diff --git a/docs/reference/read_pulse_ascii.html b/docs/reference/read_pulse_ascii.html
index c9e0d43c..ab11c9cc 100644
--- a/docs/reference/read_pulse_ascii.html
+++ b/docs/reference/read_pulse_ascii.html
@@ -1,5 +1,5 @@
-Read an ASCII formatted pulse file. — read_pulse_ascii • Spectroscopy Analysis Tools (spant) Read an ASCII formatted pulse file. — read_pulse_ascii • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/read_pulse_bruker.html b/docs/reference/read_pulse_bruker.html
index c92bf76a..dbe9073b 100644
--- a/docs/reference/read_pulse_bruker.html
+++ b/docs/reference/read_pulse_bruker.html
@@ -1,5 +1,5 @@
-Read a Bruker formatted pulse file — read_pulse_bruker • Spectroscopy Analysis Tools (spant) Read a Bruker formatted pulse file — read_pulse_bruker • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/read_pulse_pta.html b/docs/reference/read_pulse_pta.html
index 72e1b6d4..a0fac3c3 100644
--- a/docs/reference/read_pulse_pta.html
+++ b/docs/reference/read_pulse_pta.html
@@ -1,5 +1,5 @@
-Read a .pta formatted pulse file compatible with Siemens PulseTool. — read_pulse_pta • Spectroscopy Analysis Tools (spant) Read a .pta formatted pulse file compatible with Siemens PulseTool. — read_pulse_pta • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/read_siemens_txt_hdr.html b/docs/reference/read_siemens_txt_hdr.html
index 23fb8c70..3a17d87c 100644
--- a/docs/reference/read_siemens_txt_hdr.html
+++ b/docs/reference/read_siemens_txt_hdr.html
@@ -1,5 +1,5 @@
-Read the text format header found in Siemens IMA and TWIX data files. — read_siemens_txt_hdr • Spectroscopy Analysis Tools (spant) Read the text format header found in Siemens IMA and TWIX data files. — read_siemens_txt_hdr • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -78,7 +78,7 @@ Read the text format header found in Siemens IMA and TWIX data files.
- read_siemens_txt_hdr(input, version = "vd", verbose, offset = 0)
+ read_siemens_txt_hdr(input, version = "vd", verbose = FALSE, offset = 0)
@@ -118,7 +118,7 @@ Value
diff --git a/docs/reference/read_tqn_fit.html b/docs/reference/read_tqn_fit.html
index 4da6c25e..a1630420 100644
--- a/docs/reference/read_tqn_fit.html
+++ b/docs/reference/read_tqn_fit.html
@@ -1,5 +1,5 @@
-Reader for csv fit results generated by TARQUIN. — read_tqn_fit • Spectroscopy Analysis Tools (spant) Reader for csv fit results generated by TARQUIN. — read_tqn_fit • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -113,7 +113,7 @@ Examples
diff --git a/docs/reference/read_tqn_result.html b/docs/reference/read_tqn_result.html
index 36659714..68a3e98c 100644
--- a/docs/reference/read_tqn_result.html
+++ b/docs/reference/read_tqn_result.html
@@ -1,5 +1,5 @@
-Reader for csv results generated by TARQUIN. — read_tqn_result • Spectroscopy Analysis Tools (spant) Reader for csv results generated by TARQUIN. — read_tqn_result • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -117,7 +117,7 @@ Examples
diff --git a/docs/reference/recon_imag.html b/docs/reference/recon_imag.html
index d2a72225..5bc3b1eb 100644
--- a/docs/reference/recon_imag.html
+++ b/docs/reference/recon_imag.html
@@ -1,7 +1,5 @@
-Reconstruct complex time-domain data from the real part of frequency-domain
-data. — recon_imag • Spectroscopy Analysis Tools (spant) Reconstruct complex time-domain data from the real part of frequency-domain data. — recon_imag • Spectroscopy Analysis Tools (spant) Reconstruct complex time-domain data from the real part of frequency-domain
-data. — recon_imag_vec • Spectroscopy Analysis Tools (spant) Reconstruct complex time-domain data from the real part of frequency-domain data. — recon_imag_vec • Spectroscopy Analysis Tools (spant) Reconstruct 2D MRSI data from a twix file loaded with read_mrs. — recon_twix_2d_mrsi • Spectroscopy Analysis Tools (spant) Reconstruct 2D MRSI data from a twix file loaded with read_mrs. — recon_twix_2d_mrsi • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/rectangular_mask.html b/docs/reference/rectangular_mask.html
index a2117283..6e469bc9 100644
--- a/docs/reference/rectangular_mask.html
+++ b/docs/reference/rectangular_mask.html
@@ -1,5 +1,5 @@
-Create a rectangular mask stored as a matrix of logical values. — rectangular_mask • Spectroscopy Analysis Tools (spant) Create a rectangular mask stored as a matrix of logical values. — rectangular_mask • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -130,7 +130,7 @@ Value
diff --git a/docs/reference/reexports.html b/docs/reference/reexports.html
index 694a75d1..a59e8379 100644
--- a/docs/reference/reexports.html
+++ b/docs/reference/reexports.html
@@ -1,5 +1,5 @@
-Objects exported from other packages — reexports • Spectroscopy Analysis Tools (spant) Objects exported from other packages — reexports • Spectroscopy Analysis Tools (spant)
Spectroscopy Analysis Tools (spant)
- 2.21.0
+ 2.22.0
@@ -103,7 +103,7 @@ Objects exported from other packages
diff --git a/docs/reference/rep_array_dim.html b/docs/reference/rep_array_dim.html
index b9c49b4a..48c0a5ed 100644
--- a/docs/reference/rep_array_dim.html
+++ b/docs/reference/rep_array_dim.html
@@ -1,5 +1,5 @@
-Repeat an array over a given dimension. — rep_array_dim • Spectroscopy Analysis Tools (spant) Repeat an array over a given dimension. — rep_array_dim • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/rep_dyn.html b/docs/reference/rep_dyn.html
index 6bbfb0ef..89a4bb9b 100644
--- a/docs/reference/rep_dyn.html
+++ b/docs/reference/rep_dyn.html
@@ -1,5 +1,5 @@
-Replicate a scan in the dynamic dimension. — rep_dyn • Spectroscopy Analysis Tools (spant) Replicate a scan in the dynamic dimension. — rep_dyn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/rep_mrs.html b/docs/reference/rep_mrs.html
index 67730b5c..becb8f00 100644
--- a/docs/reference/rep_mrs.html
+++ b/docs/reference/rep_mrs.html
@@ -1,5 +1,5 @@
-Replicate a scan over a given dimension. — rep_mrs • Spectroscopy Analysis Tools (spant) Replicate a scan over a given dimension. — rep_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -138,7 +138,7 @@ Value
diff --git a/docs/reference/resample_basis.html b/docs/reference/resample_basis.html
index b0f2ab17..c7a6222a 100644
--- a/docs/reference/resample_basis.html
+++ b/docs/reference/resample_basis.html
@@ -1,5 +1,5 @@
-Resample a basis-set to match a mrs_data acquisition. — resample_basis • Spectroscopy Analysis Tools (spant) Resample a basis-set to match a mrs_data acquisition. — resample_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -116,7 +116,7 @@ Value
diff --git a/docs/reference/resample_img.html b/docs/reference/resample_img.html
index f1e7beaf..b0cc8f71 100644
--- a/docs/reference/resample_img.html
+++ b/docs/reference/resample_img.html
@@ -1,5 +1,5 @@
-Resample an image to match a target image space. — resample_img • Spectroscopy Analysis Tools (spant) Resample an image to match a target image space. — resample_img • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/resample_voi.html b/docs/reference/resample_voi.html
index 8fbfa836..a29ab096 100644
--- a/docs/reference/resample_voi.html
+++ b/docs/reference/resample_voi.html
@@ -1,7 +1,5 @@
-Resample a VOI to match a target image space using nearest-neighbour
-interpolation. — resample_voi • Spectroscopy Analysis Tools (spant) Resample a VOI to match a target image space using nearest-neighbour interpolation. — resample_voi • Spectroscopy Analysis Tools (spant) Reslice a nifti object to match the orientation of mrs data. — reslice_to_mrs • Spectroscopy Analysis Tools (spant) Reslice a nifti object to match the orientation of mrs data. — reslice_to_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/reson_table2mrs_data.html b/docs/reference/reson_table2mrs_data.html
index d75579ee..c5a2167a 100644
--- a/docs/reference/reson_table2mrs_data.html
+++ b/docs/reference/reson_table2mrs_data.html
@@ -1,5 +1,5 @@
-Generate mrs_data from a table of single Lorentzian resonances. — reson_table2mrs_data • Spectroscopy Analysis Tools (spant) Generate mrs_data from a table of single Lorentzian resonances. — reson_table2mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -119,7 +119,7 @@ Value
diff --git a/docs/reference/rm_dyns.html b/docs/reference/rm_dyns.html
index 5d5ef692..573e1f51 100644
--- a/docs/reference/rm_dyns.html
+++ b/docs/reference/rm_dyns.html
@@ -1,5 +1,5 @@
-Remove a subset of dynamic scans. — rm_dyns • Spectroscopy Analysis Tools (spant) Remove a subset of dynamic scans. — rm_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/scale_amp_molal.html b/docs/reference/scale_amp_molal.html
index aaeee1f2..7acb8cb0 100644
--- a/docs/reference/scale_amp_molal.html
+++ b/docs/reference/scale_amp_molal.html
@@ -1,7 +1,5 @@
-Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water). — scale_amp_molal • Spectroscopy Analysis Tools (spant) Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / kg of tissue water). — scale_amp_molal • Spectroscopy Analysis Tools (spant)
Spectroscopy Analysis Tools (spant)
- 2.21.0
+ 2.22.0
@@ -76,8 +74,7 @@
- Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water).
+ Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / kg of tissue water).
Source: R/amp_scaling.R
scale_amp_molal.Rd
@@ -163,7 +160,7 @@ Value
diff --git a/docs/reference/scale_amp_molal_pvc.html b/docs/reference/scale_amp_molal_pvc.html
index 962d6afc..4d194abd 100644
--- a/docs/reference/scale_amp_molal_pvc.html
+++ b/docs/reference/scale_amp_molal_pvc.html
@@ -1,7 +1,5 @@
-Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water). — scale_amp_molal_pvc • Spectroscopy Analysis Tools (spant)
@@ -75,8 +73,7 @@
- Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water).
+ Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / kg of tissue water).
Source: R/amp_scaling.R
scale_amp_molal_pvc.Rd
@@ -141,7 +138,7 @@ Value
diff --git a/docs/reference/scale_amp_molar.html b/docs/reference/scale_amp_molar.html
index 02358d91..dc87a338 100644
--- a/docs/reference/scale_amp_molar.html
+++ b/docs/reference/scale_amp_molar.html
@@ -1,7 +1,5 @@
-Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / Litre of tissue). — scale_amp_molar • Spectroscopy Analysis Tools (spant) Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / Litre of tissue). — scale_amp_molar • Spectroscopy Analysis Tools (spant) Convert default LCM/TARQUIN concentration scaling to molal units with partial
-volume correction. — scale_amp_molar2molal_pvc • Spectroscopy Analysis Tools (spant) Convert default LCM/TARQUIN concentration scaling to molal units with partial volume correction. — scale_amp_molar2molal_pvc • Spectroscopy Analysis Tools (spant) Scale fitted amplitudes to a ratio of signal amplitude. — scale_amp_ratio • Spectroscopy Analysis Tools (spant) Scale fitted amplitudes to a ratio of signal amplitude. — scale_amp_ratio • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -116,7 +116,7 @@ Value
diff --git a/docs/reference/scale_amp_ratio_value.html b/docs/reference/scale_amp_ratio_value.html
index 2036837a..6af8ac51 100644
--- a/docs/reference/scale_amp_ratio_value.html
+++ b/docs/reference/scale_amp_ratio_value.html
@@ -1,5 +1,5 @@
-Scale fitted amplitudes to a ratio of signal amplitude. — scale_amp_ratio_value • Spectroscopy Analysis Tools (spant) Scale fitted amplitudes to a ratio of signal amplitude. — scale_amp_ratio_value • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/scale_amp_water_ratio.html b/docs/reference/scale_amp_water_ratio.html
index 5b25e884..35a76b00 100644
--- a/docs/reference/scale_amp_water_ratio.html
+++ b/docs/reference/scale_amp_water_ratio.html
@@ -1,5 +1,5 @@
-Scale metabolite amplitudes as a ratio to the unsuppressed water amplitude. — scale_amp_water_ratio • Spectroscopy Analysis Tools (spant) Scale metabolite amplitudes as a ratio to the unsuppressed water amplitude. — scale_amp_water_ratio • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/scale_basis_amp.html b/docs/reference/scale_basis_amp.html
index 9401c3f1..5a58b5e5 100644
--- a/docs/reference/scale_basis_amp.html
+++ b/docs/reference/scale_basis_amp.html
@@ -1,5 +1,5 @@
-Scale a basis object by a scalar. — scale_basis_amp • Spectroscopy Analysis Tools (spant) Scale a basis object by a scalar. — scale_basis_amp • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/scale_basis_from_singlet.html b/docs/reference/scale_basis_from_singlet.html
index 0d542bc8..c9a19e77 100644
--- a/docs/reference/scale_basis_from_singlet.html
+++ b/docs/reference/scale_basis_from_singlet.html
@@ -1,5 +1,5 @@
-Scale a basis-set to be consistent with spant assumptions for water scaling. — scale_basis_from_singlet • Spectroscopy Analysis Tools (spant) Scale a basis-set to be consistent with spant assumptions for water scaling. — scale_basis_from_singlet • Spectroscopy Analysis Tools (spant)
Spectroscopy Analysis Tools (spant)
- 2.21.0
+ 2.22.0
@@ -127,7 +127,7 @@ Value
diff --git a/docs/reference/scale_mrs_amp.html b/docs/reference/scale_mrs_amp.html
index b5501a0d..990f058a 100644
--- a/docs/reference/scale_mrs_amp.html
+++ b/docs/reference/scale_mrs_amp.html
@@ -1,5 +1,5 @@
-Scale an mrs_data object by a scalar or vector or amplitudes. — scale_mrs_amp • Spectroscopy Analysis Tools (spant) Scale an mrs_data object by a scalar or vector or amplitudes. — scale_mrs_amp • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/scale_spec.html b/docs/reference/scale_spec.html
index 4f6ea835..6b3ddba4 100644
--- a/docs/reference/scale_spec.html
+++ b/docs/reference/scale_spec.html
@@ -1,5 +1,5 @@
-Scale mrs_data to a spectral region. — scale_spec • Spectroscopy Analysis Tools (spant) Scale mrs_data to a spectral region. — scale_spec • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -141,7 +141,7 @@ Value
diff --git a/docs/reference/sd.html b/docs/reference/sd.html
index ea1eec9f..3ae4dfd4 100644
--- a/docs/reference/sd.html
+++ b/docs/reference/sd.html
@@ -1,5 +1,5 @@
-Calculate the standard deviation spectrum from an mrs_data object. — sd • Spectroscopy Analysis Tools (spant) Calculate the standard deviation spectrum from an mrs_data object. — sd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/sd.mrs_data.html b/docs/reference/sd.mrs_data.html
index 3f92a49f..13bdda85 100644
--- a/docs/reference/sd.mrs_data.html
+++ b/docs/reference/sd.mrs_data.html
@@ -1,5 +1,5 @@
-Calculate the standard deviation spectrum from an mrs_data object. — sd.mrs_data • Spectroscopy Analysis Tools (spant) Calculate the standard deviation spectrum from an mrs_data object. — sd.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/seconds.html b/docs/reference/seconds.html
index b34d6627..467ee17f 100644
--- a/docs/reference/seconds.html
+++ b/docs/reference/seconds.html
@@ -1,5 +1,5 @@
-Return a time scale vector to match the FID of an MRS data object. — seconds • Spectroscopy Analysis Tools (spant) Return a time scale vector to match the FID of an MRS data object. — seconds • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/seq_cpmg_ideal.html b/docs/reference/seq_cpmg_ideal.html
index 547e96ab..45727c86 100644
--- a/docs/reference/seq_cpmg_ideal.html
+++ b/docs/reference/seq_cpmg_ideal.html
@@ -1,5 +1,5 @@
-CPMG style sequence with ideal pulses. — seq_cpmg_ideal • Spectroscopy Analysis Tools (spant) CPMG style sequence with ideal pulses. — seq_cpmg_ideal • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/seq_mega_press_ideal.html b/docs/reference/seq_mega_press_ideal.html
index 0769b8b4..a9cd7fa0 100644
--- a/docs/reference/seq_mega_press_ideal.html
+++ b/docs/reference/seq_mega_press_ideal.html
@@ -1,7 +1,5 @@
-MEGA-PRESS sequence with ideal localisation pulses and Gaussian shaped
-editing pulse. — seq_mega_press_ideal • Spectroscopy Analysis Tools (spant) MEGA-PRESS sequence with ideal localisation pulses and Gaussian shaped editing pulse. — seq_mega_press_ideal • Spectroscopy Analysis Tools (spant) PRESS sequence with shaped refocusing pulses. — seq_press_2d_shaped • Spectroscopy Analysis Tools (spant) PRESS sequence with shaped refocusing pulses. — seq_press_2d_shaped • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -165,7 +165,7 @@ Value
diff --git a/docs/reference/seq_press_ideal.html b/docs/reference/seq_press_ideal.html
index 8c976856..72c3af3d 100644
--- a/docs/reference/seq_press_ideal.html
+++ b/docs/reference/seq_press_ideal.html
@@ -1,5 +1,5 @@
-PRESS sequence with ideal pulses. — seq_press_ideal • Spectroscopy Analysis Tools (spant) PRESS sequence with ideal pulses. — seq_press_ideal • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/seq_pulse_acquire.html b/docs/reference/seq_pulse_acquire.html
index 4a88fc64..ad80571e 100644
--- a/docs/reference/seq_pulse_acquire.html
+++ b/docs/reference/seq_pulse_acquire.html
@@ -1,5 +1,5 @@
-Simple pulse and acquire sequence with ideal pulses. — seq_pulse_acquire • Spectroscopy Analysis Tools (spant) Simple pulse and acquire sequence with ideal pulses. — seq_pulse_acquire • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/seq_slaser_ideal.html b/docs/reference/seq_slaser_ideal.html
index 74688f4d..eb83e8e3 100644
--- a/docs/reference/seq_slaser_ideal.html
+++ b/docs/reference/seq_slaser_ideal.html
@@ -1,5 +1,5 @@
-sLASER sequence with ideal pulses. — seq_slaser_ideal • Spectroscopy Analysis Tools (spant) sLASER sequence with ideal pulses. — seq_slaser_ideal • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -126,7 +126,7 @@ Value
diff --git a/docs/reference/seq_spin_echo_ideal.html b/docs/reference/seq_spin_echo_ideal.html
index e23271de..4248716f 100644
--- a/docs/reference/seq_spin_echo_ideal.html
+++ b/docs/reference/seq_spin_echo_ideal.html
@@ -1,5 +1,5 @@
-Spin echo sequence with ideal pulses. — seq_spin_echo_ideal • Spectroscopy Analysis Tools (spant) Spin echo sequence with ideal pulses. — seq_spin_echo_ideal • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/seq_steam_ideal.html b/docs/reference/seq_steam_ideal.html
index a60685a8..1c8115d7 100644
--- a/docs/reference/seq_steam_ideal.html
+++ b/docs/reference/seq_steam_ideal.html
@@ -1,5 +1,5 @@
-STEAM sequence with ideal pulses. — seq_steam_ideal • Spectroscopy Analysis Tools (spant) STEAM sequence with ideal pulses. — seq_steam_ideal • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -128,7 +128,7 @@ Value
diff --git a/docs/reference/seq_steam_ideal_cof.html b/docs/reference/seq_steam_ideal_cof.html
index 8f225740..cba7af91 100644
--- a/docs/reference/seq_steam_ideal_cof.html
+++ b/docs/reference/seq_steam_ideal_cof.html
@@ -1,7 +1,5 @@
-STEAM sequence with ideal pulses and coherence order filtering to simulate
-gradient crushers. — seq_steam_ideal_cof • Spectroscopy Analysis Tools (spant) STEAM sequence with ideal pulses and coherence order filtering to simulate gradient crushers. — seq_steam_ideal_cof • Spectroscopy Analysis Tools (spant) STEAM sequence with ideal pulses using the z-rotation gradient simulation
-method described by Young et al JMR 140, 146-152 (1999). — seq_steam_ideal_young • Spectroscopy Analysis Tools (spant) STEAM sequence with ideal pulses using the z-rotation gradient simulation method described by Young et al JMR 140, 146-152 (1999). — seq_steam_ideal_young • Spectroscopy Analysis Tools (spant) Set the number of transients for an mrs_data object. — set_Ntrans • Spectroscopy Analysis Tools (spant) Set the number of transients for an mrs_data object. — set_Ntrans • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/set_def_acq_paras.html b/docs/reference/set_def_acq_paras.html
index 3e1b4004..cc2ada9c 100644
--- a/docs/reference/set_def_acq_paras.html
+++ b/docs/reference/set_def_acq_paras.html
@@ -1,5 +1,5 @@
-Set the default acquisition parameters. — set_def_acq_paras • Spectroscopy Analysis Tools (spant) Set the default acquisition parameters. — set_def_acq_paras • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Arguments
diff --git a/docs/reference/set_lcm_cmd.html b/docs/reference/set_lcm_cmd.html
index 2056ed01..42bb2f24 100644
--- a/docs/reference/set_lcm_cmd.html
+++ b/docs/reference/set_lcm_cmd.html
@@ -1,5 +1,5 @@
-Set the command to run the LCModel command-line program. — set_lcm_cmd • Spectroscopy Analysis Tools (spant) Set the command to run the LCModel command-line program. — set_lcm_cmd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/set_lw.html b/docs/reference/set_lw.html
index b64ec851..bb176c62 100644
--- a/docs/reference/set_lw.html
+++ b/docs/reference/set_lw.html
@@ -1,5 +1,5 @@
-Apply line-broadening to an mrs_data object to achieve a specified linewidth. — set_lw • Spectroscopy Analysis Tools (spant) Apply line-broadening to an mrs_data object to achieve a specified linewidth. — set_lw • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -123,7 +123,7 @@ Value
diff --git a/docs/reference/set_mask_xy_mat.html b/docs/reference/set_mask_xy_mat.html
index 49dc5d4e..52c4b617 100644
--- a/docs/reference/set_mask_xy_mat.html
+++ b/docs/reference/set_mask_xy_mat.html
@@ -1,5 +1,5 @@
-Set the masked voxels in a 2D MRSI dataset to given spectrum. — set_mask_xy_mat • Spectroscopy Analysis Tools (spant) Set the masked voxels in a 2D MRSI dataset to given spectrum. — set_mask_xy_mat • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Value
diff --git a/docs/reference/set_precomp_mode.html b/docs/reference/set_precomp_mode.html
index f44bd5d3..47c28e3b 100644
--- a/docs/reference/set_precomp_mode.html
+++ b/docs/reference/set_precomp_mode.html
@@ -1,5 +1,5 @@
-Set the precompute mode. — set_precomp_mode • Spectroscopy Analysis Tools (spant) Set the precompute mode. — set_precomp_mode • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/set_precomp_verbose.html b/docs/reference/set_precomp_verbose.html
index 1453a231..9c613505 100644
--- a/docs/reference/set_precomp_verbose.html
+++ b/docs/reference/set_precomp_verbose.html
@@ -1,5 +1,5 @@
-Set the verbosity of the precompute function. — set_precomp_verbose • Spectroscopy Analysis Tools (spant) Set the verbosity of the precompute function. — set_precomp_verbose • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/set_ref.html b/docs/reference/set_ref.html
index 8953fa50..5436dfa2 100644
--- a/docs/reference/set_ref.html
+++ b/docs/reference/set_ref.html
@@ -1,5 +1,5 @@
-Set the ppm reference value (eg ppm value at 0Hz). — set_ref • Spectroscopy Analysis Tools (spant) Set the ppm reference value (eg ppm value at 0Hz). — set_ref • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/set_td_pts.html b/docs/reference/set_td_pts.html
index 8a80d42a..586459ff 100644
--- a/docs/reference/set_td_pts.html
+++ b/docs/reference/set_td_pts.html
@@ -1,7 +1,5 @@
-Set the number of time-domain data points, truncating or zero-filling as
-appropriate. — set_td_pts • Spectroscopy Analysis Tools (spant) Set the number of time-domain data points, truncating or zero-filling as appropriate. — set_td_pts • Spectroscopy Analysis Tools (spant) Set the command to run the TARQUIN command-line program. — set_tqn_cmd • Spectroscopy Analysis Tools (spant) Set the command to run the TARQUIN command-line program. — set_tqn_cmd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/set_tr.html b/docs/reference/set_tr.html
index b2109ab0..65c9df5f 100644
--- a/docs/reference/set_tr.html
+++ b/docs/reference/set_tr.html
@@ -1,5 +1,5 @@
-Set the repetition time of an MRS dataset. — set_tr • Spectroscopy Analysis Tools (spant) Set the repetition time of an MRS dataset. — set_tr • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/shift.html b/docs/reference/shift.html
index ab0fe724..034591d0 100644
--- a/docs/reference/shift.html
+++ b/docs/reference/shift.html
@@ -1,5 +1,5 @@
-Apply a frequency shift to MRS data. — shift • Spectroscopy Analysis Tools (spant) Apply a frequency shift to MRS data. — shift • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/shift_basis.html b/docs/reference/shift_basis.html
index 2884be19..f55a65e0 100644
--- a/docs/reference/shift_basis.html
+++ b/docs/reference/shift_basis.html
@@ -1,5 +1,5 @@
-Apply frequency shifts to basis set signals. — shift_basis • Spectroscopy Analysis Tools (spant) Apply frequency shifts to basis set signals. — shift_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Value
diff --git a/docs/reference/sim_basis.html b/docs/reference/sim_basis.html
index c7838c46..bb5fefc6 100644
--- a/docs/reference/sim_basis.html
+++ b/docs/reference/sim_basis.html
@@ -1,5 +1,5 @@
-Simulate a basis set object. — sim_basis • Spectroscopy Analysis Tools (spant) Simulate a basis set object. — sim_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -136,7 +136,7 @@ Value
diff --git a/docs/reference/sim_basis_1h_brain.html b/docs/reference/sim_basis_1h_brain.html
index 62ed7389..f71ffa0b 100644
--- a/docs/reference/sim_basis_1h_brain.html
+++ b/docs/reference/sim_basis_1h_brain.html
@@ -1,7 +1,5 @@
-Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS
-sequence. Note, ideal pulses are assumed. — sim_basis_1h_brain • Spectroscopy Analysis Tools (spant) Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS sequence. Note, ideal pulses are assumed. — sim_basis_1h_brain • Spectroscopy Analysis Tools (spant) Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS
-sequence. Note, ideal pulses are assumed. — sim_basis_1h_brain_press • Spectroscopy Analysis Tools (spant) Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS sequence. Note, ideal pulses are assumed. — sim_basis_1h_brain_press • Spectroscopy Analysis Tools (spant) Simulate a macromolecular and lipid basis-set suitable for 1H brain MRS
-analysis. — sim_basis_mm_lip_lcm • Spectroscopy Analysis Tools (spant) Simulate a macromolecular and lipid basis-set suitable for 1H brain MRS analysis. — sim_basis_mm_lip_lcm • Spectroscopy Analysis Tools (spant) Simulate a basis file using TARQUIN. — sim_basis_tqn • Spectroscopy Analysis Tools (spant) Simulate a basis file using TARQUIN. — sim_basis_tqn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -129,7 +129,7 @@ Examples
diff --git a/docs/reference/sim_brain_1h.html b/docs/reference/sim_brain_1h.html
index 2044cf1a..717ee289 100644
--- a/docs/reference/sim_brain_1h.html
+++ b/docs/reference/sim_brain_1h.html
@@ -1,5 +1,5 @@
-Simulate MRS data with a similar appearance to normal brain (by default). — sim_brain_1h • Spectroscopy Analysis Tools (spant) Simulate MRS data with a similar appearance to normal brain (by default). — sim_brain_1h • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -159,7 +159,7 @@ Value
diff --git a/docs/reference/sim_mol.html b/docs/reference/sim_mol.html
index 23bcef50..77f76a50 100644
--- a/docs/reference/sim_mol.html
+++ b/docs/reference/sim_mol.html
@@ -1,5 +1,5 @@
-Simulate a mol_parameter object. — sim_mol • Spectroscopy Analysis Tools (spant) Simulate a mol_parameter object. — sim_mol • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -143,7 +143,7 @@ Value
diff --git a/docs/reference/sim_noise.html b/docs/reference/sim_noise.html
index 23875f79..a71477d4 100644
--- a/docs/reference/sim_noise.html
+++ b/docs/reference/sim_noise.html
@@ -1,5 +1,5 @@
-Simulate an mrs_data object containing simulated Gaussian noise. — sim_noise • Spectroscopy Analysis Tools (spant) Simulate an mrs_data object containing simulated Gaussian noise. — sim_noise • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -84,6 +84,7 @@ Simulate an mrs_data object containing simulated Gaussian noise.
ft = def_ft(),
N = def_N(),
ref = def_ref(),
+ nuc = def_nuc(),
dyns = 1,
fd = TRUE
)
@@ -111,6 +112,10 @@ Arguments
reference value for ppm scale.
nuc
+resonant nucleus.
dyns
number of dynamic scans to generate.
Value
diff --git a/docs/reference/sim_resonances.html b/docs/reference/sim_resonances.html
index 19e9a8a4..d4f8d7c0 100644
--- a/docs/reference/sim_resonances.html
+++ b/docs/reference/sim_resonances.html
@@ -1,5 +1,5 @@
-Simulate a MRS data object containing a set of simulated resonances. — sim_resonances • Spectroscopy Analysis Tools (spant) Simulate a MRS data object containing a set of simulated resonances. — sim_resonances • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -161,7 +161,7 @@ Examples
diff --git a/docs/reference/sim_th_excit_profile.html b/docs/reference/sim_th_excit_profile.html
index 5535c5ef..e781cab1 100644
--- a/docs/reference/sim_th_excit_profile.html
+++ b/docs/reference/sim_th_excit_profile.html
@@ -1,7 +1,5 @@
-Simulate an ideal pulse excitation profile by smoothing a top-hat function
-with a Gaussian. — sim_th_excit_profile • Spectroscopy Analysis Tools (spant) Simulate an ideal pulse excitation profile by smoothing a top-hat function with a Gaussian. — sim_th_excit_profile • Spectroscopy Analysis Tools (spant) Simulate an mrs_data object containing complex zero valued samples. — sim_zero • Spectroscopy Analysis Tools (spant) Simulate an mrs_data object containing complex zero valued samples. — sim_zero • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -78,7 +78,14 @@ Simulate an mrs_data object containing complex zero valued samples.
-
+
@@ -99,6 +106,10 @@ Arguments
reference value for ppm scale.
nuc
+resonant nucleus.
dyns
number of dynamic scans to generate.
Value
diff --git a/docs/reference/smooth_dyns.html b/docs/reference/smooth_dyns.html
index 4cc8da50..accf3a51 100644
--- a/docs/reference/smooth_dyns.html
+++ b/docs/reference/smooth_dyns.html
@@ -1,5 +1,5 @@
-Smooth data across the dynamic dimension with a Gaussian kernel. — smooth_dyns • Spectroscopy Analysis Tools (spant) Smooth data across the dynamic dimension with a Gaussian kernel. — smooth_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/sort_basis.html b/docs/reference/sort_basis.html
index 6a676ea2..d25cc006 100644
--- a/docs/reference/sort_basis.html
+++ b/docs/reference/sort_basis.html
@@ -1,5 +1,5 @@
-Sort the basis-set elements alphabetically. — sort_basis • Spectroscopy Analysis Tools (spant) Sort the basis-set elements alphabetically. — sort_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/spant-package.html b/docs/reference/spant-package.html
index b3dd8e21..90f19ec3 100644
--- a/docs/reference/spant-package.html
+++ b/docs/reference/spant-package.html
@@ -1,5 +1,5 @@
-spant: spectroscopy analysis tools. — spant-package • Spectroscopy Analysis Tools (spant) spant: spectroscopy analysis tools. — spant-package • Spectroscopy Analysis Tools (spant) Simulate and fit some spectra with ABfit for benchmarking purposes. Basic
-timing and performance metrics will be printed. — spant_abfit_benchmark • Spectroscopy Analysis Tools (spant) Simulate and fit some spectra with ABfit for benchmarking purposes. Basic timing and performance metrics will be printed. — spant_abfit_benchmark • Spectroscopy Analysis Tools (spant) Example MEGA-PRESS data with significant B0 drift. — spant_mpress_drift • Spectroscopy Analysis Tools (spant) Example MEGA-PRESS data with significant B0 drift. — spant_mpress_drift • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -83,7 +83,7 @@ Example MEGA-PRESS data with significant B0 drift.
Format
- An object of class mrs_data of length 13.
+ An object of class mrs_data of dimension 1 x 1 x 1 x 1 x 40 x 1 x 1024.
@@ -98,7 +98,7 @@ Format
diff --git a/docs/reference/spant_sim_fmrs_dataset.html b/docs/reference/spant_sim_fmrs_dataset.html
new file mode 100644
index 00000000..00e48b56
--- /dev/null
+++ b/docs/reference/spant_sim_fmrs_dataset.html
@@ -0,0 +1,117 @@
+
+Simulate an example fMRS dataset for a block design fMRS experiment and export a BIDS structure. — spant_sim_fmrs_dataset • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Simulate an example fMRS dataset for a block design fMRS experiment and export a BIDS structure.
+ Source: R/fmrs.R
+ spant_sim_fmrs_dataset.Rd
+
+
+
+ Simulate an example fMRS dataset for a block design fMRS experiment and
+export a BIDS structure.
+
+
+
+ spant_sim_fmrs_dataset(output_dir = NULL)
+
+
+
+ Arguments
+ - output_dir
+output directory for the BIDS data. Defaults to :
+"HOME/sim_fmrs_dataset/data".
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/spant_simulation_benchmark.html b/docs/reference/spant_simulation_benchmark.html
index 32daa8bf..d8cc6841 100644
--- a/docs/reference/spant_simulation_benchmark.html
+++ b/docs/reference/spant_simulation_benchmark.html
@@ -1,7 +1,5 @@
-Simulate a typical metabolite basis set for benchmarking. Timing metrics will
-be printed on completion. — spant_simulation_benchmark • Spectroscopy Analysis Tools (spant) Simulate a typical metabolite basis set for benchmarking. Timing metrics will be printed on completion. — spant_simulation_benchmark • Spectroscopy Analysis Tools (spant) Decompose an mrs_data object into white and gray matter spectra. — spec_decomp • Spectroscopy Analysis Tools (spant) Perform a mathematical operation on a spectral region. — spec_op • Spectroscopy Analysis Tools (spant) Perform a mathematical operation on a spectral region. — spec_op • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -98,8 +98,8 @@ Arguments
operator
-can be "sum" (default), "mean", "l2", "max", "min" or
-"max-min".
can be "sum" (default), "mean", "l2", "max", "max_cplx,
+"min" or "max-min".
freq_scale
@@ -129,7 +129,7 @@ Value
diff --git a/docs/reference/spin_sys.html b/docs/reference/spin_sys.html
index 853423a4..1eaa9e76 100644
--- a/docs/reference/spin_sys.html
+++ b/docs/reference/spin_sys.html
@@ -1,5 +1,5 @@
-Create a spin system object for pulse sequence simulation. — spin_sys • Spectroscopy Analysis Tools (spant) Create a spin system object for pulse sequence simulation. — spin_sys • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/spm_pve2categorical.html b/docs/reference/spm_pve2categorical.html
index 23a1bad9..70f10729 100644
--- a/docs/reference/spm_pve2categorical.html
+++ b/docs/reference/spm_pve2categorical.html
@@ -1,7 +1,5 @@
-Convert SPM style segmentation files to a single categorical image where
-the numerical values map as: 0) Other, 1) CSF, 2) GM and 3) WM. — spm_pve2categorical • Spectroscopy Analysis Tools (spant) Convert SPM style segmentation files to a single categorical image where the numerical values map as: 0) Other, 1) CSF, 2) GM and 3) WM. — spm_pve2categorical • Spectroscopy Analysis Tools (spant) Signal space projection method for lipid suppression. — ssp • Spectroscopy Analysis Tools (spant) Signal space projection method for lipid suppression. — ssp • Spectroscopy Analysis Tools (spant) Plot the fitting results of an object of class fit_result with
-individual basis set components shown. — stackplot.fit_result • Spectroscopy Analysis Tools (spant) Plot the fitting results of an object of class fit_result with individual basis set components shown. — stackplot.fit_result • Spectroscopy Analysis Tools (spant) Produce a plot with multiple traces. — stackplot • Spectroscopy Analysis Tools (spant) Produce a plot with multiple traces. — stackplot • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/stackplot.mrs_data.html b/docs/reference/stackplot.mrs_data.html
index 17ff5648..64eea445 100644
--- a/docs/reference/stackplot.mrs_data.html
+++ b/docs/reference/stackplot.mrs_data.html
@@ -1,5 +1,5 @@
-Stackplot plotting method for objects of class mrs_data. — stackplot.mrs_data • Spectroscopy Analysis Tools (spant) Stackplot plotting method for objects of class mrs_data. — stackplot.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -255,7 +255,7 @@ Arguments
diff --git a/docs/reference/sub_first_dyn.html b/docs/reference/sub_first_dyn.html
index dbd7f831..493b7242 100644
--- a/docs/reference/sub_first_dyn.html
+++ b/docs/reference/sub_first_dyn.html
@@ -1,5 +1,5 @@
-Subtract the first dynamic spectrum from a dynamic series. — sub_first_dyn • Spectroscopy Analysis Tools (spant) Subtract the first dynamic spectrum from a dynamic series. — sub_first_dyn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/sub_mean_dyns.html b/docs/reference/sub_mean_dyns.html
index 6e3bb2df..221bd0c1 100644
--- a/docs/reference/sub_mean_dyns.html
+++ b/docs/reference/sub_mean_dyns.html
@@ -1,5 +1,5 @@
-Subtract the mean dynamic spectrum from a dynamic series. — sub_mean_dyns • Spectroscopy Analysis Tools (spant) Subtract the mean dynamic spectrum from a dynamic series. — sub_mean_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/sub_median_dyns.html b/docs/reference/sub_median_dyns.html
index 134c495d..1e834f14 100644
--- a/docs/reference/sub_median_dyns.html
+++ b/docs/reference/sub_median_dyns.html
@@ -1,5 +1,5 @@
-Subtract the median dynamic spectrum from a dynamic series. — sub_median_dyns • Spectroscopy Analysis Tools (spant) Subtract the median dynamic spectrum from a dynamic series. — sub_median_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/sum_coils.html b/docs/reference/sum_coils.html
index 7bf559f2..e1ab3cc0 100644
--- a/docs/reference/sum_coils.html
+++ b/docs/reference/sum_coils.html
@@ -1,5 +1,5 @@
-Calculate the sum across receiver coil elements. — sum_coils • Spectroscopy Analysis Tools (spant) Calculate the sum across receiver coil elements. — sum_coils • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/sum_dyns.html b/docs/reference/sum_dyns.html
index a0be19d3..bbda2ffc 100644
--- a/docs/reference/sum_dyns.html
+++ b/docs/reference/sum_dyns.html
@@ -1,5 +1,5 @@
-Calculate the sum of data dynamics. — sum_dyns • Spectroscopy Analysis Tools (spant) Calculate the sum of data dynamics. — sum_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/sum_mrs.html b/docs/reference/sum_mrs.html
index a22f215b..3cc3ab9e 100644
--- a/docs/reference/sum_mrs.html
+++ b/docs/reference/sum_mrs.html
@@ -1,5 +1,5 @@
-Sum two mrs_data objects. — sum_mrs • Spectroscopy Analysis Tools (spant) Sum two mrs_data objects. — sum_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Value
diff --git a/docs/reference/sum_mrs_list.html b/docs/reference/sum_mrs_list.html
index f4e09aea..c3584348 100644
--- a/docs/reference/sum_mrs_list.html
+++ b/docs/reference/sum_mrs_list.html
@@ -1,5 +1,5 @@
-Return the sum of a list of mrs_data objects. — sum_mrs_list • Spectroscopy Analysis Tools (spant) Return the sum of a list of mrs_data objects. — sum_mrs_list • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/svs_1h_brain_analysis.html b/docs/reference/svs_1h_brain_analysis.html
index 8ce514db..dff0ef7d 100644
--- a/docs/reference/svs_1h_brain_analysis.html
+++ b/docs/reference/svs_1h_brain_analysis.html
@@ -1,5 +1,5 @@
-Standard SVS 1H brain analysis pipeline. — svs_1h_brain_analysis • Spectroscopy Analysis Tools (spant) Standard SVS 1H brain analysis pipeline. — svs_1h_brain_analysis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -199,7 +199,7 @@ Value
diff --git a/docs/reference/svs_1h_brain_analysis_dev.html b/docs/reference/svs_1h_brain_analysis_dev.html
index d70a14d3..d71bfea2 100644
--- a/docs/reference/svs_1h_brain_analysis_dev.html
+++ b/docs/reference/svs_1h_brain_analysis_dev.html
@@ -1,5 +1,5 @@
-Standard SVS 1H brain analysis pipeline. — svs_1h_brain_analysis_dev • Spectroscopy Analysis Tools (spant) Standard SVS 1H brain analysis pipeline. — svs_1h_brain_analysis_dev • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -193,7 +193,7 @@ Examples
diff --git a/docs/reference/svs_1h_brain_batch_analysis.html b/docs/reference/svs_1h_brain_batch_analysis.html
index 5631e8cc..15f7223e 100644
--- a/docs/reference/svs_1h_brain_batch_analysis.html
+++ b/docs/reference/svs_1h_brain_batch_analysis.html
@@ -1,5 +1,5 @@
-Batch interface to the standard SVS 1H brain analysis pipeline. — svs_1h_brain_batch_analysis • Spectroscopy Analysis Tools (spant) Batch interface to the standard SVS 1H brain analysis pipeline. — svs_1h_brain_batch_analysis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -144,7 +144,7 @@ Value
diff --git a/docs/reference/t_test_spec.html b/docs/reference/t_test_spec.html
new file mode 100644
index 00000000..56a7ea1b
--- /dev/null
+++ b/docs/reference/t_test_spec.html
@@ -0,0 +1,124 @@
+
+Perform a t-test on spectral data points. — t_test_spec • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+
+
+ Perform a t-test on spectral data points.
+
+
+
+ t_test_spec(mrs_data, group)
+
+
+
+ Arguments
+ - mrs_data
+an mrs_data object with spectra in the dynamic dimension.
- group
+vector describing the group membership of each dynamic spectrum.
+
+ Value
+
+
+a list of statistical results.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/td2fd.html b/docs/reference/td2fd.html
index 6748a6a8..f31ed524 100644
--- a/docs/reference/td2fd.html
+++ b/docs/reference/td2fd.html
@@ -1,5 +1,5 @@
-Transform time-domain data to the frequency-domain. — td2fd • Spectroscopy Analysis Tools (spant) Transform time-domain data to the frequency-domain. — td2fd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/td_conv_filt.html b/docs/reference/td_conv_filt.html
index a9f340c3..106b9b00 100644
--- a/docs/reference/td_conv_filt.html
+++ b/docs/reference/td_conv_filt.html
@@ -1,5 +1,5 @@
-Time-domain convolution based filter. — td_conv_filt • Spectroscopy Analysis Tools (spant) Time-domain convolution based filter. — td_conv_filt • Spectroscopy Analysis Tools (spant) Time-domain spectral registration. — tdsr • Spectroscopy Analysis Tools (spant) Time-domain spectral registration. — tdsr • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -121,7 +121,7 @@ Value
diff --git a/docs/reference/te.html b/docs/reference/te.html
index 010361b1..4a65711d 100644
--- a/docs/reference/te.html
+++ b/docs/reference/te.html
@@ -1,5 +1,5 @@
-Return the echo time of an MRS dataset. — te • Spectroscopy Analysis Tools (spant) Return the echo time of an MRS dataset. — te • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/tr.html b/docs/reference/tr.html
index 0c0bd63b..2e749e02 100644
--- a/docs/reference/tr.html
+++ b/docs/reference/tr.html
@@ -1,5 +1,5 @@
-Return the repetition time of an MRS dataset. — tr • Spectroscopy Analysis Tools (spant) Return the repetition time of an MRS dataset. — tr • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/varpro_3_para_opts.html b/docs/reference/varpro_3_para_opts.html
index c2270a16..52d7cd84 100644
--- a/docs/reference/varpro_3_para_opts.html
+++ b/docs/reference/varpro_3_para_opts.html
@@ -1,5 +1,5 @@
-Return a list of options for VARPRO based fitting with 3 free parameters. — varpro_3_para_opts • Spectroscopy Analysis Tools (spant) Return a list of options for VARPRO based fitting with 3 free parameters. — varpro_3_para_opts • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -141,7 +141,7 @@ Value
diff --git a/docs/reference/varpro_basic_opts.html b/docs/reference/varpro_basic_opts.html
index 32c86d22..c5104891 100644
--- a/docs/reference/varpro_basic_opts.html
+++ b/docs/reference/varpro_basic_opts.html
@@ -1,5 +1,5 @@
-Return a list of options for a basic VARPRO analysis. — varpro_basic_opts • Spectroscopy Analysis Tools (spant) Return a list of options for a basic VARPRO analysis. — varpro_basic_opts • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -118,7 +118,7 @@ Value
diff --git a/docs/reference/varpro_opts.html b/docs/reference/varpro_opts.html
index 2aabf11d..6332f730 100644
--- a/docs/reference/varpro_opts.html
+++ b/docs/reference/varpro_opts.html
@@ -1,5 +1,5 @@
-Return a list of options for VARPRO based fitting. — varpro_opts • Spectroscopy Analysis Tools (spant) Return a list of options for VARPRO based fitting. — varpro_opts • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -177,7 +177,7 @@ Examples
diff --git a/docs/reference/vec2mrs_data.html b/docs/reference/vec2mrs_data.html
index 0cccd73b..f0d58bf0 100644
--- a/docs/reference/vec2mrs_data.html
+++ b/docs/reference/vec2mrs_data.html
@@ -1,5 +1,5 @@
-Convert a vector into a mrs_data object. — vec2mrs_data • Spectroscopy Analysis Tools (spant) Convert a vector into a mrs_data object. — vec2mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -80,10 +80,11 @@ Convert a vector into a mrs_data object.
vec2mrs_data(
vec,
- fs = def_fs(),
- ft = def_ft(),
- ref = def_ref(),
- nuc = def_nuc(),
+ mrs_data = NULL,
+ fs = NULL,
+ ft = NULL,
+ ref = NULL,
+ nuc = NULL,
dyns = 1,
fd = FALSE
)
@@ -95,6 +96,10 @@ Arguments
the data vector.
mrs_data
+example data to copy acquisition parameters from.
fs
sampling frequency in Hz.
Arguments
fd
-flag to indicate if the matrix is in the frequency domain (logical).
flag to indicate if the vector is in the frequency domain (logical).
Value
diff --git a/docs/reference/write_basis.html b/docs/reference/write_basis.html
index b6e27cbd..94c5e021 100644
--- a/docs/reference/write_basis.html
+++ b/docs/reference/write_basis.html
@@ -1,5 +1,5 @@
-Write a basis object to an LCModel .basis formatted file. — write_basis • Spectroscopy Analysis Tools (spant) Write a basis object to an LCModel .basis formatted file. — write_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -108,7 +108,7 @@ Arguments
diff --git a/docs/reference/write_basis_tqn.html b/docs/reference/write_basis_tqn.html
index 6aa51c1d..116c73ec 100644
--- a/docs/reference/write_basis_tqn.html
+++ b/docs/reference/write_basis_tqn.html
@@ -1,5 +1,5 @@
-Generate a basis file using TARQUIN. — write_basis_tqn • Spectroscopy Analysis Tools (spant) Generate a basis file using TARQUIN. — write_basis_tqn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Examples
diff --git a/docs/reference/write_mrs.html b/docs/reference/write_mrs.html
index fff25f15..124b9dc4 100644
--- a/docs/reference/write_mrs.html
+++ b/docs/reference/write_mrs.html
@@ -1,5 +1,5 @@
-Write MRS data object to file. — write_mrs • Spectroscopy Analysis Tools (spant) Write MRS data object to file. — write_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Arguments
diff --git a/docs/reference/write_mrs_nifti.html b/docs/reference/write_mrs_nifti.html
index f4bf1921..bd3ed4b7 100644
--- a/docs/reference/write_mrs_nifti.html
+++ b/docs/reference/write_mrs_nifti.html
@@ -1,5 +1,5 @@
-Write MRS data object to file in NIFTI format. — write_mrs_nifti • Spectroscopy Analysis Tools (spant) Write MRS data object to file in NIFTI format. — write_mrs_nifti • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/write_pulse_ascii.html b/docs/reference/write_pulse_ascii.html
index 067ae086..221f8ebb 100644
--- a/docs/reference/write_pulse_ascii.html
+++ b/docs/reference/write_pulse_ascii.html
@@ -1,5 +1,5 @@
-Write an ASCII formatted pulse file. — write_pulse_ascii • Spectroscopy Analysis Tools (spant) Write an ASCII formatted pulse file. — write_pulse_ascii • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/zero_fade_spec.html b/docs/reference/zero_fade_spec.html
index c703745c..c8b572c3 100644
--- a/docs/reference/zero_fade_spec.html
+++ b/docs/reference/zero_fade_spec.html
@@ -1,7 +1,5 @@
-Fade a spectrum to zero by frequency domain multiplication with a tanh
-function. Note this operation distorts data points at the end of the FID. — zero_fade_spec • Spectroscopy Analysis Tools (spant) Fade a spectrum to zero by frequency domain multiplication with a tanh function. Note this operation distorts data points at the end of the FID. — zero_fade_spec • Spectroscopy Analysis Tools (spant) Zero all coherences including and above a given order. — zero_higher_orders • Spectroscopy Analysis Tools (spant) Zero all coherences including and above a given order. — zero_higher_orders • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Value
diff --git a/docs/reference/zero_td_pts_end.html b/docs/reference/zero_td_pts_end.html
index 8c1123c8..71d24ebb 100644
--- a/docs/reference/zero_td_pts_end.html
+++ b/docs/reference/zero_td_pts_end.html
@@ -1,5 +1,5 @@
-Set mrs_data object data points at the end of the FID to zero. — zero_td_pts_end • Spectroscopy Analysis Tools (spant) Set mrs_data object data points at the end of the FID to zero. — zero_td_pts_end • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/zf.html b/docs/reference/zf.html
index 85e2013c..baf50256 100644
--- a/docs/reference/zf.html
+++ b/docs/reference/zf.html
@@ -1,5 +1,5 @@
-Zero-fill MRS data in the time domain. — zf • Spectroscopy Analysis Tools (spant) Zero-fill MRS data in the time domain. — zf • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -125,7 +125,7 @@ Value
diff --git a/docs/reference/zf_xy.html b/docs/reference/zf_xy.html
index ebca3999..c4104a74 100644
--- a/docs/reference/zf_xy.html
+++ b/docs/reference/zf_xy.html
@@ -1,5 +1,5 @@
-Zero-fill MRSI data in the k-space x-y direction. — zf_xy • Spectroscopy Analysis Tools (spant) Zero-fill MRSI data in the k-space x-y direction. — zf_xy • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -113,7 +113,7 @@ Value
diff --git a/docs/sitemap.xml b/docs/sitemap.xml
index e2139f71..4c39f515 100644
--- a/docs/sitemap.xml
+++ b/docs/sitemap.xml
@@ -216,6 +216,12 @@
https://martin3141.github.io/spant/reference/comb_coils_fp_pc.html
+
+ https://martin3141.github.io/spant/reference/comb_coils_mrsi_gls.html
+
+
+ https://martin3141.github.io/spant/reference/comb_coils_svs_gls.html
+
https://martin3141.github.io/spant/reference/comb_csv_results.html
@@ -411,6 +417,9 @@
https://martin3141.github.io/spant/reference/gen_conv_reg.html
+
+ https://martin3141.github.io/spant/reference/gen_group_reg.html
+
https://martin3141.github.io/spant/reference/gen_impulse_reg.html
@@ -555,6 +564,15 @@
https://martin3141.github.io/spant/reference/glm_spec.html
+
+ https://martin3141.github.io/spant/reference/glm_spec_fmrs_fl.html
+
+
+ https://martin3141.github.io/spant/reference/glm_spec_fmrs_group.html
+
+
+ https://martin3141.github.io/spant/reference/glm_spec_group_linhyp.html
+
https://martin3141.github.io/spant/reference/grid_shift_xy.html
@@ -690,9 +708,15 @@
https://martin3141.github.io/spant/reference/mrs_data2basis.html
+
+ https://martin3141.github.io/spant/reference/mrs_data2bids.html
+
https://martin3141.github.io/spant/reference/mrs_data2mat.html
+
+ https://martin3141.github.io/spant/reference/mrs_data2spec_mat.html
+
https://martin3141.github.io/spant/reference/mrs_data2vec.html
@@ -741,6 +765,9 @@
https://martin3141.github.io/spant/reference/phase.html
+
+ https://martin3141.github.io/spant/reference/phase_ref_1h_brain.html
+
https://martin3141.github.io/spant/reference/plot.fit_result.html
@@ -780,6 +807,12 @@
https://martin3141.github.io/spant/reference/precomp.html
+
+ https://martin3141.github.io/spant/reference/preproc_svs.html
+
+
+ https://martin3141.github.io/spant/reference/preproc_svs_dataset.html
+
https://martin3141.github.io/spant/reference/print.fit_result.html
@@ -1050,6 +1083,9 @@
https://martin3141.github.io/spant/reference/spant_mpress_drift.html
+
+ https://martin3141.github.io/spant/reference/spant_sim_fmrs_dataset.html
+
https://martin3141.github.io/spant/reference/spant_simulation_benchmark.html
@@ -1107,6 +1143,9 @@
https://martin3141.github.io/spant/reference/svs_1h_brain_batch_analysis.html
+
+ https://martin3141.github.io/spant/reference/t_test_spec.html
+
https://martin3141.github.io/spant/reference/td2fd.html
Apply water reference scaling to a fitting results object to yield metabolite -quantities in millimolar (mM) units (mol / kg of tissue water).
Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / kg of tissue water).
Apply water reference scaling to a fitting results object to yield metabolite -quantities in millimolar (mM) units (mol / kg of tissue water).
Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / kg of tissue water).
Apply water reference scaling to a fitting results object to yield metabolite -quantities in millimolar (mM) units (mol / Litre of tissue).
Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / Litre of tissue).
Convert default LCM/TARQUIN concentration scaling to molal units with partial -volume correction.
Convert default LCM/TARQUIN concentration scaling to molal units with partial volume correction.
All functions
- MEGA-PRESS sequence with ideal localisation pulses and Gaussian shaped
-editing pulse.
MEGA-PRESS sequence with ideal localisation pulses and Gaussian shaped editing pulse.
@@ -1251,13 +1230,11 @@ All functions
- STEAM sequence with ideal pulses and coherence order filtering to simulate
-gradient crushers.
STEAM sequence with ideal pulses and coherence order filtering to simulate gradient crushers.
- STEAM sequence with ideal pulses using the z-rotation gradient simulation
-method described by Young et al JMR 140, 146-152 (1999).
STEAM sequence with ideal pulses using the z-rotation gradient simulation method described by Young et al JMR 140, 146-152 (1999).
@@ -1293,8 +1270,7 @@ All functions
- Set the number of time-domain data points, truncating or zero-filling as
-appropriate.
Set the number of time-domain data points, truncating or zero-filling as appropriate.
@@ -1318,18 +1294,15 @@ All functions
- Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS
-sequence. Note, ideal pulses are assumed.
Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS sequence. Note, ideal pulses are assumed.
- Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS
-sequence. Note, ideal pulses are assumed.
Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS sequence. Note, ideal pulses are assumed.
- Simulate a macromolecular and lipid basis-set suitable for 1H brain MRS
-analysis.
Simulate a macromolecular and lipid basis-set suitable for 1H brain MRS analysis.
@@ -1353,8 +1326,7 @@ All functions
- Simulate an ideal pulse excitation profile by smoothing a top-hat function
-with a Gaussian.
Simulate an ideal pulse excitation profile by smoothing a top-hat function with a Gaussian.
@@ -1374,17 +1346,19 @@ All functions
- Simulate and fit some spectra with ABfit for benchmarking purposes. Basic
-timing and performance metrics will be printed.
Simulate and fit some spectra with ABfit for benchmarking purposes. Basic timing and performance metrics will be printed.
Example MEGA-PRESS data with significant B0 drift.
+
+
+ Simulate an example fMRS dataset for a block design fMRS experiment and export a BIDS structure.
- Simulate a typical metabolite basis set for benchmarking. Timing metrics will
-be printed on completion.
Simulate a typical metabolite basis set for benchmarking. Timing metrics will be printed on completion.
@@ -1400,8 +1374,7 @@ All functions
- Convert SPM style segmentation files to a single categorical image where
-the numerical values map as: 0) Other, 1) CSF, 2) GM and 3) WM.
Convert SPM style segmentation files to a single categorical image where the numerical values map as: 0) Other, 1) CSF, 2) GM and 3) WM.
@@ -1413,8 +1386,7 @@ All functions
- Plot the fitting results of an object of class fit_result with
-individual basis set components shown.
Plot the fitting results of an object of class fit_result with individual basis set components shown.
@@ -1459,6 +1431,10 @@ All functions svs_1h_brain_batch_analysis()
Batch interface to the standard SVS 1H brain analysis pipeline.
+
+
+ Perform a t-test on spectral data points.
@@ -1518,8 +1494,7 @@ All functions
- Fade a spectrum to zero by frequency domain multiplication with a tanh
-function. Note this operation distorts data points at the end of the FID.
Fade a spectrum to zero by frequency domain multiplication with a tanh function. Note this operation distorts data points at the end of the FID.
@@ -1549,7 +1524,7 @@ All functions
diff --git a/docs/reference/int_spec.html b/docs/reference/int_spec.html
index c7060fe7..783325a8 100644
--- a/docs/reference/int_spec.html
+++ b/docs/reference/int_spec.html
@@ -1,5 +1,5 @@
-Integrate a spectral region. — int_spec • Spectroscopy Analysis Tools (spant) Integrate a spectral region. — int_spec • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -118,7 +118,7 @@ Value
diff --git a/docs/reference/interleave_dyns.html b/docs/reference/interleave_dyns.html
index effe5543..441eff27 100644
--- a/docs/reference/interleave_dyns.html
+++ b/docs/reference/interleave_dyns.html
@@ -1,5 +1,5 @@
-Interleave the first and second half of a dynamic series. — interleave_dyns • Spectroscopy Analysis Tools (spant) Interleave the first and second half of a dynamic series. — interleave_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/inv_even_dyns.html b/docs/reference/inv_even_dyns.html
index 9f9d4fff..dcb781dc 100644
--- a/docs/reference/inv_even_dyns.html
+++ b/docs/reference/inv_even_dyns.html
@@ -1,5 +1,5 @@
-Invert even numbered dynamic scans starting from 1 (2,4,6...). — inv_even_dyns • Spectroscopy Analysis Tools (spant) Invert even numbered dynamic scans starting from 1 (2,4,6...). — inv_even_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/inv_odd_dyns.html b/docs/reference/inv_odd_dyns.html
index 26212e2b..78d64660 100644
--- a/docs/reference/inv_odd_dyns.html
+++ b/docs/reference/inv_odd_dyns.html
@@ -1,5 +1,5 @@
-Invert odd numbered dynamic scans starting from 1 (1,3,5...). — inv_odd_dyns • Spectroscopy Analysis Tools (spant) Invert odd numbered dynamic scans starting from 1 (1,3,5...). — inv_odd_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/is.def.html b/docs/reference/is.def.html
index f196ffd0..a67b9eba 100644
--- a/docs/reference/is.def.html
+++ b/docs/reference/is.def.html
@@ -1,5 +1,5 @@
-Check if an object is defined, which is the same as being not NULL. — is.def • Spectroscopy Analysis Tools (spant) Check if an object is defined, which is the same as being not NULL. — is.def • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/is_fd.html b/docs/reference/is_fd.html
index 3b0ca165..18a193aa 100644
--- a/docs/reference/is_fd.html
+++ b/docs/reference/is_fd.html
@@ -1,7 +1,5 @@
-Check if the chemical shift dimension of an MRS data object is in the
-frequency domain. — is_fd • Spectroscopy Analysis Tools (spant) Check if the chemical shift dimension of an MRS data object is in the frequency domain. — is_fd • Spectroscopy Analysis Tools (spant) Transform 2D MRSI data from k-space to image space in the x-y direction. — kspace2img_xy • Spectroscopy Analysis Tools (spant) Transform 2D MRSI data from k-space to image space in the x-y direction. — kspace2img_xy • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/l2_reg.html b/docs/reference/l2_reg.html
index 3d781d80..21aa9849 100644
--- a/docs/reference/l2_reg.html
+++ b/docs/reference/l2_reg.html
@@ -1,5 +1,5 @@
-Perform l2 regularisation artefact suppression. — l2_reg • Spectroscopy Analysis Tools (spant) Perform l2 regularisation artefact suppression. — l2_reg • Spectroscopy Analysis Tools (spant) Apply line-broadening (apodisation) to MRS data or basis object. — lb • Spectroscopy Analysis Tools (spant) Apply line-broadening (apodisation) to MRS data or basis object. — lb • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -123,7 +123,7 @@ Value
diff --git a/docs/reference/lofdc.html b/docs/reference/lofdc.html
index 5419b1ec..31347a25 100644
--- a/docs/reference/lofdc.html
+++ b/docs/reference/lofdc.html
@@ -1,5 +1,5 @@
-Correct linear frequency drift. — lofdc • Spectroscopy Analysis Tools (spant) Correct linear frequency drift. — lofdc • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -138,7 +138,7 @@ Value
diff --git a/docs/reference/lw2alpha.html b/docs/reference/lw2alpha.html
index b83db682..25da229b 100644
--- a/docs/reference/lw2alpha.html
+++ b/docs/reference/lw2alpha.html
@@ -1,7 +1,5 @@
-Covert a linewidth in Hz to an equivalent alpha value in the time-domain ie:
-x * exp(-t * alpha). — lw2alpha • Spectroscopy Analysis Tools (spant) Covert a linewidth in Hz to an equivalent alpha value in the time-domain ie: x * exp(-t * alpha). — lw2alpha • Spectroscopy Analysis Tools (spant) Covert a linewidth in Hz to an equivalent beta value in the time-domain ie:
-x * exp(-t * t * beta). — lw2beta • Spectroscopy Analysis Tools (spant) Covert a linewidth in Hz to an equivalent beta value in the time-domain ie: x * exp(-t * t * beta). — lw2beta • Spectroscopy Analysis Tools (spant) Make a basis-set object from a directory containing LCModel formatted RAW
-files. — make_basis_from_raw • Spectroscopy Analysis Tools (spant) Make a basis-set object from a directory containing LCModel formatted RAW files. — make_basis_from_raw • Spectroscopy Analysis Tools (spant) Mask an MRS dataset in the dynamic dimension. — mask_dyns • Spectroscopy Analysis Tools (spant) Mask an MRS dataset in the dynamic dimension. — mask_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/mask_fit_res.html b/docs/reference/mask_fit_res.html
index 97baaa3f..ebd91a99 100644
--- a/docs/reference/mask_fit_res.html
+++ b/docs/reference/mask_fit_res.html
@@ -1,5 +1,5 @@
-Mask fit result spectra depending on a vector of bool values. — mask_fit_res • Spectroscopy Analysis Tools (spant) Mask fit result spectra depending on a vector of bool values. — mask_fit_res • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -116,7 +116,7 @@ Value
diff --git a/docs/reference/mask_xy.html b/docs/reference/mask_xy.html
index 11bb577c..b0d38619 100644
--- a/docs/reference/mask_xy.html
+++ b/docs/reference/mask_xy.html
@@ -1,5 +1,5 @@
-Mask an MRSI dataset in the x-y direction — mask_xy • Spectroscopy Analysis Tools (spant) Mask an MRSI dataset in the x-y direction — mask_xy • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/mask_xy_corners.html b/docs/reference/mask_xy_corners.html
index 09b16cd2..2d13839d 100644
--- a/docs/reference/mask_xy_corners.html
+++ b/docs/reference/mask_xy_corners.html
@@ -1,5 +1,5 @@
-Mask the four corners of an MRSI dataset in the x-y plane. — mask_xy_corners • Spectroscopy Analysis Tools (spant) Mask the four corners of an MRSI dataset in the x-y plane. — mask_xy_corners • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/mask_xy_ellipse.html b/docs/reference/mask_xy_ellipse.html
index 1d8b02e4..e2e749ef 100644
--- a/docs/reference/mask_xy_ellipse.html
+++ b/docs/reference/mask_xy_ellipse.html
@@ -1,7 +1,5 @@
-Mask the voxels outside an elliptical region spanning the MRSI dataset in the
-x-y plane. — mask_xy_ellipse • Spectroscopy Analysis Tools (spant) Mask the voxels outside an elliptical region spanning the MRSI dataset in the x-y plane. — mask_xy_ellipse • Spectroscopy Analysis Tools (spant) Mask a 2D MRSI dataset in the x-y dimension. — mask_xy_mat • Spectroscopy Analysis Tools (spant) Mask a 2D MRSI dataset in the x-y dimension. — mask_xy_mat • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Value
diff --git a/docs/reference/mat2mrs_data.html b/docs/reference/mat2mrs_data.html
index 2e2895f3..ae55665f 100644
--- a/docs/reference/mat2mrs_data.html
+++ b/docs/reference/mat2mrs_data.html
@@ -1,7 +1,5 @@
-Convert a matrix (with spectral points in the column dimension and dynamics
-in the row dimensions) into a mrs_data object. — mat2mrs_data • Spectroscopy Analysis Tools (spant) Convert a matrix (with spectral points in the column dimension and dynamics in the row dimensions) into a mrs_data object. — mat2mrs_data • Spectroscopy Analysis Tools (spant) Matrix exponential function taken from complexplus package to reduce the
-number of spant dependencies. — matexp • Spectroscopy Analysis Tools (spant) Matrix exponential function taken from complexplus package to reduce the number of spant dependencies. — matexp • Spectroscopy Analysis Tools (spant) Apply the max operator to an MRS dataset. — max_mrs • Spectroscopy Analysis Tools (spant) Apply the max operator to an MRS dataset. — max_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/max_mrs_interp.html b/docs/reference/max_mrs_interp.html
index e4474764..52e63f3e 100644
--- a/docs/reference/max_mrs_interp.html
+++ b/docs/reference/max_mrs_interp.html
@@ -1,5 +1,5 @@
-Apply the max operator to an interpolated MRS dataset. — max_mrs_interp • Spectroscopy Analysis Tools (spant) Apply the max operator to an interpolated MRS dataset. — max_mrs_interp • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/mean.list.html b/docs/reference/mean.list.html
index b8eb3463..048306fd 100644
--- a/docs/reference/mean.list.html
+++ b/docs/reference/mean.list.html
@@ -1,5 +1,5 @@
-Calculate the mean spectrum from an mrs_data object. — mean.list • Spectroscopy Analysis Tools (spant) Calculate the mean spectrum from an mrs_data object. — mean.list • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/mean.mrs_data.html b/docs/reference/mean.mrs_data.html
index 5531a28d..79515014 100644
--- a/docs/reference/mean.mrs_data.html
+++ b/docs/reference/mean.mrs_data.html
@@ -1,5 +1,5 @@
-Calculate the mean spectrum from an mrs_data object. — mean.mrs_data • Spectroscopy Analysis Tools (spant) Calculate the mean spectrum from an mrs_data object. — mean.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/mean_dyn_blocks.html b/docs/reference/mean_dyn_blocks.html
index 10467098..4c042448 100644
--- a/docs/reference/mean_dyn_blocks.html
+++ b/docs/reference/mean_dyn_blocks.html
@@ -1,5 +1,5 @@
-Calculate the mean of adjacent dynamic scans. — mean_dyn_blocks • Spectroscopy Analysis Tools (spant) Calculate the mean of adjacent dynamic scans. — mean_dyn_blocks • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/mean_dyn_pairs.html b/docs/reference/mean_dyn_pairs.html
index 63e909ea..1a241126 100644
--- a/docs/reference/mean_dyn_pairs.html
+++ b/docs/reference/mean_dyn_pairs.html
@@ -1,5 +1,5 @@
-Calculate the pairwise means across a dynamic data set. — mean_dyn_pairs • Spectroscopy Analysis Tools (spant) Calculate the pairwise means across a dynamic data set. — mean_dyn_pairs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/mean_dyns.html b/docs/reference/mean_dyns.html
index 73fdbfa7..0daa27df 100644
--- a/docs/reference/mean_dyns.html
+++ b/docs/reference/mean_dyns.html
@@ -1,5 +1,5 @@
-Calculate the mean dynamic data. — mean_dyns • Spectroscopy Analysis Tools (spant) Calculate the mean dynamic data. — mean_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/mean_mrs_list.html b/docs/reference/mean_mrs_list.html
index 808b6c50..10d842c0 100644
--- a/docs/reference/mean_mrs_list.html
+++ b/docs/reference/mean_mrs_list.html
@@ -1,5 +1,5 @@
-Return the mean of a list of mrs_data objects. — mean_mrs_list • Spectroscopy Analysis Tools (spant) Return the mean of a list of mrs_data objects. — mean_mrs_list • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/mean_vec_blocks.html b/docs/reference/mean_vec_blocks.html
index 8fc92eaa..dd78b122 100644
--- a/docs/reference/mean_vec_blocks.html
+++ b/docs/reference/mean_vec_blocks.html
@@ -1,5 +1,5 @@
-Calculate the mean of adjacent blocks in a vector. — mean_vec_blocks • Spectroscopy Analysis Tools (spant) Calculate the mean of adjacent blocks in a vector. — mean_vec_blocks • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/median_dyns.html b/docs/reference/median_dyns.html
index 1039d4b5..9a085b10 100644
--- a/docs/reference/median_dyns.html
+++ b/docs/reference/median_dyns.html
@@ -1,5 +1,5 @@
-Calculate the median dynamic data. — median_dyns • Spectroscopy Analysis Tools (spant) Calculate the median dynamic data. — median_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/mod_td.html b/docs/reference/mod_td.html
index 76ad0a40..141ef09e 100644
--- a/docs/reference/mod_td.html
+++ b/docs/reference/mod_td.html
@@ -1,5 +1,5 @@
-Apply the Modulus operator to the time-domain MRS signal. — mod_td • Spectroscopy Analysis Tools (spant) Apply the Modulus operator to the time-domain MRS signal. — mod_td • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/mrs_data2basis.html b/docs/reference/mrs_data2basis.html
index 62f7d749..11797b91 100644
--- a/docs/reference/mrs_data2basis.html
+++ b/docs/reference/mrs_data2basis.html
@@ -1,7 +1,5 @@
-Convert an mrs_data object to basis object - where basis signals are spread
-across the dynamic dimension in the MRS data. — mrs_data2basis • Spectroscopy Analysis Tools (spant) Convert an mrs_data object to basis object - where basis signals are spread across the dynamic dimension in the MRS data. — mrs_data2basis • Spectroscopy Analysis Tools (spant) Create a BIDS file structure from a vector of MRS data paths or list of mrs_data objects. — mrs_data2bids • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Create a BIDS file structure from a vector of MRS data paths or list of mrs_data objects.
+ Source: R/fmrs.R
+ mrs_data2bids.Rd
+
+
+
+ Create a BIDS file structure from a vector of MRS data paths or list of
+mrs_data objects.
+
+
+
+ mrs_data2bids(
+ mrs_data,
+ output_dir,
+ suffix = NULL,
+ sub = NULL,
+ ses = NULL,
+ task = NULL,
+ acq = NULL,
+ nuc = NULL,
+ voi = NULL,
+ rec = NULL,
+ run = NULL,
+ echo = NULL,
+ inv = NULL,
+ skip_existing = TRUE
+)
+
+
+
+ Arguments
+ - mrs_data
+vector of MRS data paths or list of mrs_data objects.
- output_dir
+the base directory to create the BIDS structure.
- suffix
+optional vector of file suffixes. Default behaviour is to
+automatically determine these from the input data, however it is recommended
+that they are specified to allow more efficient skipping of existing data.
- sub
+optional vector of subject labels. If not specified, these will be
+automatically generated as a series of increasing zero-padded integer values
+corresponding to the mrs_data input indices.
- ses
+optional vector of session labels.
- task
+optional vector of task labels.
- acq
+optional vector of acquisition labels.
- nuc
+optional vector of nucleus labels.
- voi
+optional vector of volume of interest labels.
- rec
+optional vector of reconstruction labels.
- run
+optional vector of run indices.
- echo
+optional vector of echo time indices.
- inv
+optional vector of inversion indices.
- skip_existing
+skip any data files that have already been converted.
+Defaults to TRUE, set to FALSE to force an overwrite of any existing data
+files.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/mrs_data2mat.html b/docs/reference/mrs_data2mat.html
index cf5ff28c..9e47688a 100644
--- a/docs/reference/mrs_data2mat.html
+++ b/docs/reference/mrs_data2mat.html
@@ -1,7 +1,5 @@
-Convert mrs_data object to a matrix, with spectral points in the column
-dimension and dynamics in the row dimension. — mrs_data2mat • Spectroscopy Analysis Tools (spant) Convert mrs_data object to a matrix, with spectral points in the column dimension and dynamics in the row dimension. — mrs_data2mat • Spectroscopy Analysis Tools (spant) Convert mrs_data object to a matrix, with spectral points in the column dimension and dynamics in the row dimension. — mrs_data2spec_mat • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Convert mrs_data object to a matrix, with spectral points in the column dimension and dynamics in the row dimension.
+ Source: R/mrs_data_proc.R
+ mrs_data2spec_mat.Rd
+
+
+
+ Convert mrs_data object to a matrix, with spectral points in the column
+dimension and dynamics in the row dimension.
+
+
+
+ mrs_data2spec_mat(mrs_data, collapse = TRUE)
+
+
+
+ Arguments
+ - mrs_data
+MRS data object or list of MRS data objects.
- collapse
+collapse all other dimensions along the dynamic dimension, eg
+a 16x16 MRSI grid would be first collapsed across 256 dynamic scans.
+
+ Value
+
+
+MRS data matrix.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/mrs_data2vec.html b/docs/reference/mrs_data2vec.html
index fb172d68..a1fd654d 100644
--- a/docs/reference/mrs_data2vec.html
+++ b/docs/reference/mrs_data2vec.html
@@ -1,5 +1,5 @@
-Convert mrs_data object to a vector. — mrs_data2vec • Spectroscopy Analysis Tools (spant) Convert mrs_data object to a vector. — mrs_data2vec • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -126,7 +126,7 @@ Value
diff --git a/docs/reference/mvfftshift.html b/docs/reference/mvfftshift.html
index 92b0841b..976b3410 100644
--- a/docs/reference/mvfftshift.html
+++ b/docs/reference/mvfftshift.html
@@ -1,7 +1,5 @@
-Perform a fftshift on a matrix, with each column replaced by its shifted
-result. — mvfftshift • Spectroscopy Analysis Tools (spant) Perform a fftshift on a matrix, with each column replaced by its shifted result. — mvfftshift • Spectroscopy Analysis Tools (spant) Perform an ifftshift on a matrix, with each column replaced by its shifted
-result. — mvifftshift • Spectroscopy Analysis Tools (spant) Perform an ifftshift on a matrix, with each column replaced by its shifted result. — mvifftshift • Spectroscopy Analysis Tools (spant) Print fit coordinates from a single index. — n2coord • Spectroscopy Analysis Tools (spant) Print fit coordinates from a single index. — n2coord • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/nifti_flip_lr.html b/docs/reference/nifti_flip_lr.html
index 730abe3c..19860b3c 100644
--- a/docs/reference/nifti_flip_lr.html
+++ b/docs/reference/nifti_flip_lr.html
@@ -1,9 +1,5 @@
-Flip the x data dimension order of a nifti image. This corresponds to
-flipping MRI data in the left-right direction, assuming the data in save in
-neurological format (can check with fslorient program). — nifti_flip_lr • Spectroscopy Analysis Tools (spant) Flip the x data dimension order of a nifti image. This corresponds to flipping MRI data in the left-right direction, assuming the data in save in neurological format (can check with fslorient program). — nifti_flip_lr • Spectroscopy Analysis Tools (spant) Export a one-page pdf of a single fit result — one_page_pdf • Spectroscopy Analysis Tools (spant) Export a one-page pdf of a single fit result — one_page_pdf • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -108,7 +108,7 @@ Arguments
diff --git a/docs/reference/ortho3.html b/docs/reference/ortho3.html
index 13ade97d..5d7dd2fd 100644
--- a/docs/reference/ortho3.html
+++ b/docs/reference/ortho3.html
@@ -1,5 +1,5 @@
-Display an orthographic projection plot of a nifti object. — ortho3 • Spectroscopy Analysis Tools (spant) Display an orthographic projection plot of a nifti object. — ortho3 • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -172,7 +172,7 @@ Arguments
diff --git a/docs/reference/ortho3_inter.html b/docs/reference/ortho3_inter.html
index 090cc5e5..15948899 100644
--- a/docs/reference/ortho3_inter.html
+++ b/docs/reference/ortho3_inter.html
@@ -1,5 +1,5 @@
-Display an interactive orthographic projection plot of a nifti object. — ortho3_inter • Spectroscopy Analysis Tools (spant) Display an interactive orthographic projection plot of a nifti object. — ortho3_inter • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -132,7 +132,7 @@ Arguments
diff --git a/docs/reference/peak_info.html b/docs/reference/peak_info.html
index 09058bd8..41c8ffaf 100644
--- a/docs/reference/peak_info.html
+++ b/docs/reference/peak_info.html
@@ -1,7 +1,5 @@
-Search for the highest peak in a spectral region and return the frequency,
-height and FWHM. — peak_info • Spectroscopy Analysis Tools (spant) Search for the highest peak in a spectral region and return the frequency, height and FWHM. — peak_info • Spectroscopy Analysis Tools (spant) Papoulis-Gerchberg (PG) algorithm method for k-space extrapolation. — pg_extrap_xy • Spectroscopy Analysis Tools (spant) Papoulis-Gerchberg (PG) algorithm method for k-space extrapolation. — pg_extrap_xy • Spectroscopy Analysis Tools (spant) Apply phasing parameters to MRS data. — phase • Spectroscopy Analysis Tools (spant) Apply phasing parameters to MRS data. — phase • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/phase_ref_1h_brain.html b/docs/reference/phase_ref_1h_brain.html
new file mode 100644
index 00000000..8707a74a
--- /dev/null
+++ b/docs/reference/phase_ref_1h_brain.html
@@ -0,0 +1,131 @@
+
+Corrected zero order phase and chemical shift offset in 1H MRS data from the brain. — phase_ref_1h_brain • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Corrected zero order phase and chemical shift offset in 1H MRS data from the brain.
+ Source: R/rats.R
+ phase_ref_1h_brain.Rd
+
+
+
+ Corrected zero order phase and chemical shift offset in 1H MRS data from the
+brain.
+
+
+
+ phase_ref_1h_brain(mrs_data, mean_ref = FALSE, ret_corr_only = TRUE)
+
+
+
+ Arguments
+ - mrs_data
+MRS data to be corrected.
- mean_ref
+apply the phase and offset of the mean spectrum to all
+others. Default is FALSE.
- ret_corr_only
+return the corrected data only.
+
+ Value
+
+
+corrected MRS data.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/plot.fit_result.html b/docs/reference/plot.fit_result.html
index e54d3bc1..836a53ee 100644
--- a/docs/reference/plot.fit_result.html
+++ b/docs/reference/plot.fit_result.html
@@ -1,5 +1,5 @@
-Plot the fitting results of an object of class fit_result. — plot.fit_result • Spectroscopy Analysis Tools (spant) Plot the fitting results of an object of class fit_result. — plot.fit_result • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -207,7 +207,7 @@ Arguments
diff --git a/docs/reference/plot.mrs_data.html b/docs/reference/plot.mrs_data.html
index fabcc35b..bb2ec651 100644
--- a/docs/reference/plot.mrs_data.html
+++ b/docs/reference/plot.mrs_data.html
@@ -1,5 +1,5 @@
-Plotting method for objects of class mrs_data. — plot.mrs_data • Spectroscopy Analysis Tools (spant) Plotting method for objects of class mrs_data. — plot.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -287,7 +287,7 @@ Arguments
diff --git a/docs/reference/plot_bc.html b/docs/reference/plot_bc.html
index 4f8309b4..b48142cc 100644
--- a/docs/reference/plot_bc.html
+++ b/docs/reference/plot_bc.html
@@ -1,5 +1,5 @@
-Convenience function to plot a baseline estimate with the original data. — plot_bc • Spectroscopy Analysis Tools (spant) Convenience function to plot a baseline estimate with the original data. — plot_bc • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -108,7 +108,7 @@ Arguments
diff --git a/docs/reference/plot_reg.html b/docs/reference/plot_reg.html
index ae1acbe7..2addb2f6 100644
--- a/docs/reference/plot_reg.html
+++ b/docs/reference/plot_reg.html
@@ -1,5 +1,5 @@
-Plot regressors as an image. — plot_reg • Spectroscopy Analysis Tools (spant) Plot regressors as an image. — plot_reg • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/plot_slice_fit.html b/docs/reference/plot_slice_fit.html
index fbc7b560..57f1af8a 100644
--- a/docs/reference/plot_slice_fit.html
+++ b/docs/reference/plot_slice_fit.html
@@ -1,5 +1,5 @@
-Plot a 2D slice from an MRSI fit result object. — plot_slice_fit • Spectroscopy Analysis Tools (spant) Plot a 2D slice from an MRSI fit result object. — plot_slice_fit • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -129,7 +129,7 @@ Arguments
diff --git a/docs/reference/plot_slice_fit_inter.html b/docs/reference/plot_slice_fit_inter.html
index 4eed104a..da105a7d 100644
--- a/docs/reference/plot_slice_fit_inter.html
+++ b/docs/reference/plot_slice_fit_inter.html
@@ -1,5 +1,5 @@
-Plot a 2D slice from an MRSI fit result object. — plot_slice_fit_inter • Spectroscopy Analysis Tools (spant) Plot a 2D slice from an MRSI fit result object. — plot_slice_fit_inter • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -134,7 +134,7 @@ Arguments
diff --git a/docs/reference/plot_slice_map.html b/docs/reference/plot_slice_map.html
index 553e9ac8..ffb2a134 100644
--- a/docs/reference/plot_slice_map.html
+++ b/docs/reference/plot_slice_map.html
@@ -1,5 +1,5 @@
-Plot a slice from a 7 dimensional array. — plot_slice_map • Spectroscopy Analysis Tools (spant) Plot a slice from a 7 dimensional array. — plot_slice_map • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -153,7 +153,7 @@ Arguments
diff --git a/docs/reference/plot_slice_map_inter.html b/docs/reference/plot_slice_map_inter.html
index 40d33b42..90968f66 100644
--- a/docs/reference/plot_slice_map_inter.html
+++ b/docs/reference/plot_slice_map_inter.html
@@ -1,7 +1,5 @@
-Plot an interactive slice map from a data array where voxels can be selected
-to display a corresponding spectrum. — plot_slice_map_inter • Spectroscopy Analysis Tools (spant) Plot an interactive slice map from a data array where voxels can be selected to display a corresponding spectrum. — plot_slice_map_inter • Spectroscopy Analysis Tools (spant) Plot the spectral standard deviation. — plot_spec_sd • Spectroscopy Analysis Tools (spant) Plot the spectral standard deviation. — plot_spec_sd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Arguments
diff --git a/docs/reference/plot_voi_overlay.html b/docs/reference/plot_voi_overlay.html
index 9a782e88..bbbbf35e 100644
--- a/docs/reference/plot_voi_overlay.html
+++ b/docs/reference/plot_voi_overlay.html
@@ -1,5 +1,5 @@
-Plot a volume as an image overlay. — plot_voi_overlay • Spectroscopy Analysis Tools (spant) Plot a volume as an image overlay. — plot_voi_overlay • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -116,7 +116,7 @@ Arguments
diff --git a/docs/reference/plot_voi_overlay_seg.html b/docs/reference/plot_voi_overlay_seg.html
index 3d4e74ff..0e800ff2 100644
--- a/docs/reference/plot_voi_overlay_seg.html
+++ b/docs/reference/plot_voi_overlay_seg.html
@@ -1,5 +1,5 @@
-Plot a volume as an overlay on a segmented brain volume. — plot_voi_overlay_seg • Spectroscopy Analysis Tools (spant) Plot a volume as an overlay on a segmented brain volume. — plot_voi_overlay_seg • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Arguments
diff --git a/docs/reference/ppm.html b/docs/reference/ppm.html
index c352327a..ee4696e2 100644
--- a/docs/reference/ppm.html
+++ b/docs/reference/ppm.html
@@ -1,5 +1,5 @@
-Return the ppm scale of an MRS dataset or fit result. — ppm • Spectroscopy Analysis Tools (spant) Return the ppm scale of an MRS dataset or fit result. — ppm • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -132,7 +132,7 @@ Value
diff --git a/docs/reference/precomp.html b/docs/reference/precomp.html
index 822d7336..df3d2c6c 100644
--- a/docs/reference/precomp.html
+++ b/docs/reference/precomp.html
@@ -1,7 +1,5 @@
-Save function results to file and load on subsequent calls to avoid repeat
-computation. — precomp • Spectroscopy Analysis Tools (spant) Save function results to file and load on subsequent calls to avoid repeat computation. — precomp • Spectroscopy Analysis Tools (spant) Preprocess and perform quality assessment of a single SVS data set. — preproc_svs • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Preprocess and perform quality assessment of a single SVS data set.
+ Source: R/fmrs.R
+ preproc_svs.Rd
+
+
+
+ Preprocess and perform quality assessment of a single SVS data set.
+
+
+
+ preproc_svs(path, label = NULL, output_dir = NULL, ref_inds = NULL)
+
+
+
+ Arguments
+ - path
+path to the fMRS data file or IMA directory.
- label
+a label to describe the data set.
- output_dir
+output directory.
- ref_inds
+a vector of 1-based indices for any water reference dynamic
+scans.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/preproc_svs_dataset.html b/docs/reference/preproc_svs_dataset.html
new file mode 100644
index 00000000..07c3a29b
--- /dev/null
+++ b/docs/reference/preproc_svs_dataset.html
@@ -0,0 +1,148 @@
+
+Preprocess and perform quality assessment of one or more SVS data sets. — preproc_svs_dataset • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Preprocess and perform quality assessment of one or more SVS data sets.
+ Source: R/fmrs.R
+ preproc_svs_dataset.Rd
+
+
+
+ Preprocess and perform quality assessment of one or more SVS data sets.
+
+
+
+ preproc_svs_dataset(
+ paths,
+ labels = NULL,
+ output_dir = "spant_analysis",
+ exclude_labels = NULL,
+ overwrite = FALSE,
+ ref_inds = NULL,
+ return_results = FALSE
+)
+
+
+
+ Arguments
+ - paths
+paths to the fMRS data file or IMA directory.
- labels
+labels to describe each data set.
- output_dir
+output directory.
- exclude_labels
+vector of labels of scans to exclude, eg poor quality
+data.
- overwrite
+overwrite saved results, defaults to FALSE.
- ref_inds
+a vector of 1-based indices for any water reference dynamic
+scans.
- return_results
+function will return key outputs, defaults to FALSE.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/print.fit_result.html b/docs/reference/print.fit_result.html
index 297f28dc..5f434e57 100644
--- a/docs/reference/print.fit_result.html
+++ b/docs/reference/print.fit_result.html
@@ -1,5 +1,5 @@
-Print a summary of an object of class fit_result. — print.fit_result • Spectroscopy Analysis Tools (spant) Print a summary of an object of class fit_result. — print.fit_result • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -105,7 +105,7 @@ Arguments
diff --git a/docs/reference/print.mrs_data.html b/docs/reference/print.mrs_data.html
index 51199017..e1561eb2 100644
--- a/docs/reference/print.mrs_data.html
+++ b/docs/reference/print.mrs_data.html
@@ -1,5 +1,5 @@
-Print a summary of mrs_data parameters. — print.mrs_data • Spectroscopy Analysis Tools (spant) Print a summary of mrs_data parameters. — print.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -109,7 +109,7 @@ Arguments
diff --git a/docs/reference/qn_states.html b/docs/reference/qn_states.html
index 0f42f2f9..d7aa6715 100644
--- a/docs/reference/qn_states.html
+++ b/docs/reference/qn_states.html
@@ -1,5 +1,5 @@
-Get the quantum coherence matrix for a spin system. — qn_states • Spectroscopy Analysis Tools (spant) Get the quantum coherence matrix for a spin system. — qn_states • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/rats.html b/docs/reference/rats.html
index 5a39a396..93585e08 100644
--- a/docs/reference/rats.html
+++ b/docs/reference/rats.html
@@ -1,5 +1,5 @@
-Robust Alignment to a Target Spectrum (RATS). — rats • Spectroscopy Analysis Tools (spant) Robust Alignment to a Target Spectrum (RATS). — rats • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -207,7 +207,7 @@ Value
diff --git a/docs/reference/re_weighting.html b/docs/reference/re_weighting.html
index d21caf21..8b0b070a 100644
--- a/docs/reference/re_weighting.html
+++ b/docs/reference/re_weighting.html
@@ -1,5 +1,5 @@
-Apply a weighting to the FID to enhance spectral resolution. — re_weighting • Spectroscopy Analysis Tools (spant) Apply a weighting to the FID to enhance spectral resolution. — re_weighting • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/read_basis.html b/docs/reference/read_basis.html
index da9b94af..eb6f8557 100644
--- a/docs/reference/read_basis.html
+++ b/docs/reference/read_basis.html
@@ -1,5 +1,5 @@
-Read a basis file in LCModel .basis format. — read_basis • Spectroscopy Analysis Tools (spant) Read a basis file in LCModel .basis format. — read_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/read_ima_coil_dir.html b/docs/reference/read_ima_coil_dir.html
index 28c02de0..4f073cd8 100644
--- a/docs/reference/read_ima_coil_dir.html
+++ b/docs/reference/read_ima_coil_dir.html
@@ -1,9 +1,5 @@
-Read a directory containing Siemens MRS IMA files and combine along the coil
-dimension. Note that the coil ID is inferred from the sorted file name and
-should be checked when consistency is required between two directories. — read_ima_coil_dir • Spectroscopy Analysis Tools (spant) Read a directory containing Siemens MRS IMA files and combine along the coil dimension. Note that the coil ID is inferred from the sorted file name and should be checked when consistency is required between two directories. — read_ima_coil_dir • Spectroscopy Analysis Tools (spant) Read a directory containing Siemens MRS IMA files and combine along the
-dynamic dimension. Note that the coil ID is inferred from the sorted file
-name and should be checked when consistency is required. — read_ima_dyn_dir • Spectroscopy Analysis Tools (spant) Read a directory containing Siemens MRS IMA files and combine along the dynamic dimension. Note that the coil ID is inferred from the sorted file name and should be checked when consistency is required. — read_ima_dyn_dir • Spectroscopy Analysis Tools (spant) Read an LCModel formatted coord file containing fit information. — read_lcm_coord • Spectroscopy Analysis Tools (spant) Read an LCModel formatted coord file containing fit information. — read_lcm_coord • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -107,7 +107,7 @@ Value
diff --git a/docs/reference/read_mrs.html b/docs/reference/read_mrs.html
index 3ac2a36b..2cf36b20 100644
--- a/docs/reference/read_mrs.html
+++ b/docs/reference/read_mrs.html
@@ -1,5 +1,5 @@
-Read MRS data from a file. — read_mrs • Spectroscopy Analysis Tools (spant) Read MRS data from a file. — read_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -88,7 +88,8 @@ Read MRS data from a file.
full_fid = FALSE,
omit_svs_ref_scans = TRUE,
verbose = FALSE,
- extra = NULL
+ extra = NULL,
+ fid_filt_dist = NULL
)
@@ -140,6 +141,13 @@ Arguments
an optional data frame to provide additional variables for use
in subsequent analysis steps, eg id or grouping variables.
fid_filt_dist
+indicate if the data has a distorted FID due to a
+brick-wall filter being used to downsample the data. Default is to auto
+detect this from the data, but TRUE or FALSE options can be given to override
+detection.
Value
@@ -183,7 +191,7 @@ Examples
diff --git a/docs/reference/read_mrs_tqn.html b/docs/reference/read_mrs_tqn.html
index 5766362f..84bdaf3a 100644
--- a/docs/reference/read_mrs_tqn.html
+++ b/docs/reference/read_mrs_tqn.html
@@ -1,5 +1,5 @@
-Read MRS data using the TARQUIN software package. — read_mrs_tqn • Spectroscopy Analysis Tools (spant) Read MRS data using the TARQUIN software package. — read_mrs_tqn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -131,7 +131,7 @@ Examples
diff --git a/docs/reference/read_pulse_ascii.html b/docs/reference/read_pulse_ascii.html
index c9e0d43c..ab11c9cc 100644
--- a/docs/reference/read_pulse_ascii.html
+++ b/docs/reference/read_pulse_ascii.html
@@ -1,5 +1,5 @@
-Read an ASCII formatted pulse file. — read_pulse_ascii • Spectroscopy Analysis Tools (spant) Read an ASCII formatted pulse file. — read_pulse_ascii • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/read_pulse_bruker.html b/docs/reference/read_pulse_bruker.html
index c92bf76a..dbe9073b 100644
--- a/docs/reference/read_pulse_bruker.html
+++ b/docs/reference/read_pulse_bruker.html
@@ -1,5 +1,5 @@
-Read a Bruker formatted pulse file — read_pulse_bruker • Spectroscopy Analysis Tools (spant) Read a Bruker formatted pulse file — read_pulse_bruker • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/read_pulse_pta.html b/docs/reference/read_pulse_pta.html
index 72e1b6d4..a0fac3c3 100644
--- a/docs/reference/read_pulse_pta.html
+++ b/docs/reference/read_pulse_pta.html
@@ -1,5 +1,5 @@
-Read a .pta formatted pulse file compatible with Siemens PulseTool. — read_pulse_pta • Spectroscopy Analysis Tools (spant) Read a .pta formatted pulse file compatible with Siemens PulseTool. — read_pulse_pta • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/read_siemens_txt_hdr.html b/docs/reference/read_siemens_txt_hdr.html
index 23fb8c70..3a17d87c 100644
--- a/docs/reference/read_siemens_txt_hdr.html
+++ b/docs/reference/read_siemens_txt_hdr.html
@@ -1,5 +1,5 @@
-Read the text format header found in Siemens IMA and TWIX data files. — read_siemens_txt_hdr • Spectroscopy Analysis Tools (spant) Read the text format header found in Siemens IMA and TWIX data files. — read_siemens_txt_hdr • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -78,7 +78,7 @@ Read the text format header found in Siemens IMA and TWIX data files.
- read_siemens_txt_hdr(input, version = "vd", verbose, offset = 0)
+ read_siemens_txt_hdr(input, version = "vd", verbose = FALSE, offset = 0)
@@ -118,7 +118,7 @@ Value
diff --git a/docs/reference/read_tqn_fit.html b/docs/reference/read_tqn_fit.html
index 4da6c25e..a1630420 100644
--- a/docs/reference/read_tqn_fit.html
+++ b/docs/reference/read_tqn_fit.html
@@ -1,5 +1,5 @@
-Reader for csv fit results generated by TARQUIN. — read_tqn_fit • Spectroscopy Analysis Tools (spant) Reader for csv fit results generated by TARQUIN. — read_tqn_fit • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -113,7 +113,7 @@ Examples
diff --git a/docs/reference/read_tqn_result.html b/docs/reference/read_tqn_result.html
index 36659714..68a3e98c 100644
--- a/docs/reference/read_tqn_result.html
+++ b/docs/reference/read_tqn_result.html
@@ -1,5 +1,5 @@
-Reader for csv results generated by TARQUIN. — read_tqn_result • Spectroscopy Analysis Tools (spant) Reader for csv results generated by TARQUIN. — read_tqn_result • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -117,7 +117,7 @@ Examples
diff --git a/docs/reference/recon_imag.html b/docs/reference/recon_imag.html
index d2a72225..5bc3b1eb 100644
--- a/docs/reference/recon_imag.html
+++ b/docs/reference/recon_imag.html
@@ -1,7 +1,5 @@
-Reconstruct complex time-domain data from the real part of frequency-domain
-data. — recon_imag • Spectroscopy Analysis Tools (spant) Reconstruct complex time-domain data from the real part of frequency-domain data. — recon_imag • Spectroscopy Analysis Tools (spant) Reconstruct complex time-domain data from the real part of frequency-domain
-data. — recon_imag_vec • Spectroscopy Analysis Tools (spant) Reconstruct complex time-domain data from the real part of frequency-domain data. — recon_imag_vec • Spectroscopy Analysis Tools (spant) Reconstruct 2D MRSI data from a twix file loaded with read_mrs. — recon_twix_2d_mrsi • Spectroscopy Analysis Tools (spant) Reconstruct 2D MRSI data from a twix file loaded with read_mrs. — recon_twix_2d_mrsi • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/rectangular_mask.html b/docs/reference/rectangular_mask.html
index a2117283..6e469bc9 100644
--- a/docs/reference/rectangular_mask.html
+++ b/docs/reference/rectangular_mask.html
@@ -1,5 +1,5 @@
-Create a rectangular mask stored as a matrix of logical values. — rectangular_mask • Spectroscopy Analysis Tools (spant) Create a rectangular mask stored as a matrix of logical values. — rectangular_mask • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -130,7 +130,7 @@ Value
diff --git a/docs/reference/reexports.html b/docs/reference/reexports.html
index 694a75d1..a59e8379 100644
--- a/docs/reference/reexports.html
+++ b/docs/reference/reexports.html
@@ -1,5 +1,5 @@
-Objects exported from other packages — reexports • Spectroscopy Analysis Tools (spant) Objects exported from other packages — reexports • Spectroscopy Analysis Tools (spant)
Spectroscopy Analysis Tools (spant)
- 2.21.0
+ 2.22.0
@@ -103,7 +103,7 @@ Objects exported from other packages
diff --git a/docs/reference/rep_array_dim.html b/docs/reference/rep_array_dim.html
index b9c49b4a..48c0a5ed 100644
--- a/docs/reference/rep_array_dim.html
+++ b/docs/reference/rep_array_dim.html
@@ -1,5 +1,5 @@
-Repeat an array over a given dimension. — rep_array_dim • Spectroscopy Analysis Tools (spant) Repeat an array over a given dimension. — rep_array_dim • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/rep_dyn.html b/docs/reference/rep_dyn.html
index 6bbfb0ef..89a4bb9b 100644
--- a/docs/reference/rep_dyn.html
+++ b/docs/reference/rep_dyn.html
@@ -1,5 +1,5 @@
-Replicate a scan in the dynamic dimension. — rep_dyn • Spectroscopy Analysis Tools (spant) Replicate a scan in the dynamic dimension. — rep_dyn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/rep_mrs.html b/docs/reference/rep_mrs.html
index 67730b5c..becb8f00 100644
--- a/docs/reference/rep_mrs.html
+++ b/docs/reference/rep_mrs.html
@@ -1,5 +1,5 @@
-Replicate a scan over a given dimension. — rep_mrs • Spectroscopy Analysis Tools (spant) Replicate a scan over a given dimension. — rep_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -138,7 +138,7 @@ Value
diff --git a/docs/reference/resample_basis.html b/docs/reference/resample_basis.html
index b0f2ab17..c7a6222a 100644
--- a/docs/reference/resample_basis.html
+++ b/docs/reference/resample_basis.html
@@ -1,5 +1,5 @@
-Resample a basis-set to match a mrs_data acquisition. — resample_basis • Spectroscopy Analysis Tools (spant) Resample a basis-set to match a mrs_data acquisition. — resample_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -116,7 +116,7 @@ Value
diff --git a/docs/reference/resample_img.html b/docs/reference/resample_img.html
index f1e7beaf..b0cc8f71 100644
--- a/docs/reference/resample_img.html
+++ b/docs/reference/resample_img.html
@@ -1,5 +1,5 @@
-Resample an image to match a target image space. — resample_img • Spectroscopy Analysis Tools (spant) Resample an image to match a target image space. — resample_img • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/resample_voi.html b/docs/reference/resample_voi.html
index 8fbfa836..a29ab096 100644
--- a/docs/reference/resample_voi.html
+++ b/docs/reference/resample_voi.html
@@ -1,7 +1,5 @@
-Resample a VOI to match a target image space using nearest-neighbour
-interpolation. — resample_voi • Spectroscopy Analysis Tools (spant) Resample a VOI to match a target image space using nearest-neighbour interpolation. — resample_voi • Spectroscopy Analysis Tools (spant) Reslice a nifti object to match the orientation of mrs data. — reslice_to_mrs • Spectroscopy Analysis Tools (spant) Reslice a nifti object to match the orientation of mrs data. — reslice_to_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/reson_table2mrs_data.html b/docs/reference/reson_table2mrs_data.html
index d75579ee..c5a2167a 100644
--- a/docs/reference/reson_table2mrs_data.html
+++ b/docs/reference/reson_table2mrs_data.html
@@ -1,5 +1,5 @@
-Generate mrs_data from a table of single Lorentzian resonances. — reson_table2mrs_data • Spectroscopy Analysis Tools (spant) Generate mrs_data from a table of single Lorentzian resonances. — reson_table2mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -119,7 +119,7 @@ Value
diff --git a/docs/reference/rm_dyns.html b/docs/reference/rm_dyns.html
index 5d5ef692..573e1f51 100644
--- a/docs/reference/rm_dyns.html
+++ b/docs/reference/rm_dyns.html
@@ -1,5 +1,5 @@
-Remove a subset of dynamic scans. — rm_dyns • Spectroscopy Analysis Tools (spant) Remove a subset of dynamic scans. — rm_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/scale_amp_molal.html b/docs/reference/scale_amp_molal.html
index aaeee1f2..7acb8cb0 100644
--- a/docs/reference/scale_amp_molal.html
+++ b/docs/reference/scale_amp_molal.html
@@ -1,7 +1,5 @@
-Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water). — scale_amp_molal • Spectroscopy Analysis Tools (spant) Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / kg of tissue water). — scale_amp_molal • Spectroscopy Analysis Tools (spant)
Spectroscopy Analysis Tools (spant)
- 2.21.0
+ 2.22.0
@@ -76,8 +74,7 @@
- Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water).
+ Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / kg of tissue water).
Source: R/amp_scaling.R
scale_amp_molal.Rd
@@ -163,7 +160,7 @@ Value
diff --git a/docs/reference/scale_amp_molal_pvc.html b/docs/reference/scale_amp_molal_pvc.html
index 962d6afc..4d194abd 100644
--- a/docs/reference/scale_amp_molal_pvc.html
+++ b/docs/reference/scale_amp_molal_pvc.html
@@ -1,7 +1,5 @@
-Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water). — scale_amp_molal_pvc • Spectroscopy Analysis Tools (spant)
@@ -75,8 +73,7 @@
- Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water).
+ Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / kg of tissue water).
Source: R/amp_scaling.R
scale_amp_molal_pvc.Rd
@@ -141,7 +138,7 @@ Value
diff --git a/docs/reference/scale_amp_molar.html b/docs/reference/scale_amp_molar.html
index 02358d91..dc87a338 100644
--- a/docs/reference/scale_amp_molar.html
+++ b/docs/reference/scale_amp_molar.html
@@ -1,7 +1,5 @@
-Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / Litre of tissue). — scale_amp_molar • Spectroscopy Analysis Tools (spant) Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / Litre of tissue). — scale_amp_molar • Spectroscopy Analysis Tools (spant) Convert default LCM/TARQUIN concentration scaling to molal units with partial
-volume correction. — scale_amp_molar2molal_pvc • Spectroscopy Analysis Tools (spant) Convert default LCM/TARQUIN concentration scaling to molal units with partial volume correction. — scale_amp_molar2molal_pvc • Spectroscopy Analysis Tools (spant) Scale fitted amplitudes to a ratio of signal amplitude. — scale_amp_ratio • Spectroscopy Analysis Tools (spant) Scale fitted amplitudes to a ratio of signal amplitude. — scale_amp_ratio • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -116,7 +116,7 @@ Value
diff --git a/docs/reference/scale_amp_ratio_value.html b/docs/reference/scale_amp_ratio_value.html
index 2036837a..6af8ac51 100644
--- a/docs/reference/scale_amp_ratio_value.html
+++ b/docs/reference/scale_amp_ratio_value.html
@@ -1,5 +1,5 @@
-Scale fitted amplitudes to a ratio of signal amplitude. — scale_amp_ratio_value • Spectroscopy Analysis Tools (spant) Scale fitted amplitudes to a ratio of signal amplitude. — scale_amp_ratio_value • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/scale_amp_water_ratio.html b/docs/reference/scale_amp_water_ratio.html
index 5b25e884..35a76b00 100644
--- a/docs/reference/scale_amp_water_ratio.html
+++ b/docs/reference/scale_amp_water_ratio.html
@@ -1,5 +1,5 @@
-Scale metabolite amplitudes as a ratio to the unsuppressed water amplitude. — scale_amp_water_ratio • Spectroscopy Analysis Tools (spant) Scale metabolite amplitudes as a ratio to the unsuppressed water amplitude. — scale_amp_water_ratio • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/scale_basis_amp.html b/docs/reference/scale_basis_amp.html
index 9401c3f1..5a58b5e5 100644
--- a/docs/reference/scale_basis_amp.html
+++ b/docs/reference/scale_basis_amp.html
@@ -1,5 +1,5 @@
-Scale a basis object by a scalar. — scale_basis_amp • Spectroscopy Analysis Tools (spant) Scale a basis object by a scalar. — scale_basis_amp • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/scale_basis_from_singlet.html b/docs/reference/scale_basis_from_singlet.html
index 0d542bc8..c9a19e77 100644
--- a/docs/reference/scale_basis_from_singlet.html
+++ b/docs/reference/scale_basis_from_singlet.html
@@ -1,5 +1,5 @@
-Scale a basis-set to be consistent with spant assumptions for water scaling. — scale_basis_from_singlet • Spectroscopy Analysis Tools (spant) Scale a basis-set to be consistent with spant assumptions for water scaling. — scale_basis_from_singlet • Spectroscopy Analysis Tools (spant)
Spectroscopy Analysis Tools (spant)
- 2.21.0
+ 2.22.0
@@ -127,7 +127,7 @@ Value
diff --git a/docs/reference/scale_mrs_amp.html b/docs/reference/scale_mrs_amp.html
index b5501a0d..990f058a 100644
--- a/docs/reference/scale_mrs_amp.html
+++ b/docs/reference/scale_mrs_amp.html
@@ -1,5 +1,5 @@
-Scale an mrs_data object by a scalar or vector or amplitudes. — scale_mrs_amp • Spectroscopy Analysis Tools (spant) Scale an mrs_data object by a scalar or vector or amplitudes. — scale_mrs_amp • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/scale_spec.html b/docs/reference/scale_spec.html
index 4f6ea835..6b3ddba4 100644
--- a/docs/reference/scale_spec.html
+++ b/docs/reference/scale_spec.html
@@ -1,5 +1,5 @@
-Scale mrs_data to a spectral region. — scale_spec • Spectroscopy Analysis Tools (spant) Scale mrs_data to a spectral region. — scale_spec • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -141,7 +141,7 @@ Value
diff --git a/docs/reference/sd.html b/docs/reference/sd.html
index ea1eec9f..3ae4dfd4 100644
--- a/docs/reference/sd.html
+++ b/docs/reference/sd.html
@@ -1,5 +1,5 @@
-Calculate the standard deviation spectrum from an mrs_data object. — sd • Spectroscopy Analysis Tools (spant) Calculate the standard deviation spectrum from an mrs_data object. — sd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/sd.mrs_data.html b/docs/reference/sd.mrs_data.html
index 3f92a49f..13bdda85 100644
--- a/docs/reference/sd.mrs_data.html
+++ b/docs/reference/sd.mrs_data.html
@@ -1,5 +1,5 @@
-Calculate the standard deviation spectrum from an mrs_data object. — sd.mrs_data • Spectroscopy Analysis Tools (spant) Calculate the standard deviation spectrum from an mrs_data object. — sd.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/seconds.html b/docs/reference/seconds.html
index b34d6627..467ee17f 100644
--- a/docs/reference/seconds.html
+++ b/docs/reference/seconds.html
@@ -1,5 +1,5 @@
-Return a time scale vector to match the FID of an MRS data object. — seconds • Spectroscopy Analysis Tools (spant) Return a time scale vector to match the FID of an MRS data object. — seconds • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/seq_cpmg_ideal.html b/docs/reference/seq_cpmg_ideal.html
index 547e96ab..45727c86 100644
--- a/docs/reference/seq_cpmg_ideal.html
+++ b/docs/reference/seq_cpmg_ideal.html
@@ -1,5 +1,5 @@
-CPMG style sequence with ideal pulses. — seq_cpmg_ideal • Spectroscopy Analysis Tools (spant) CPMG style sequence with ideal pulses. — seq_cpmg_ideal • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/seq_mega_press_ideal.html b/docs/reference/seq_mega_press_ideal.html
index 0769b8b4..a9cd7fa0 100644
--- a/docs/reference/seq_mega_press_ideal.html
+++ b/docs/reference/seq_mega_press_ideal.html
@@ -1,7 +1,5 @@
-MEGA-PRESS sequence with ideal localisation pulses and Gaussian shaped
-editing pulse. — seq_mega_press_ideal • Spectroscopy Analysis Tools (spant) MEGA-PRESS sequence with ideal localisation pulses and Gaussian shaped editing pulse. — seq_mega_press_ideal • Spectroscopy Analysis Tools (spant) PRESS sequence with shaped refocusing pulses. — seq_press_2d_shaped • Spectroscopy Analysis Tools (spant) PRESS sequence with shaped refocusing pulses. — seq_press_2d_shaped • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -165,7 +165,7 @@ Value
diff --git a/docs/reference/seq_press_ideal.html b/docs/reference/seq_press_ideal.html
index 8c976856..72c3af3d 100644
--- a/docs/reference/seq_press_ideal.html
+++ b/docs/reference/seq_press_ideal.html
@@ -1,5 +1,5 @@
-PRESS sequence with ideal pulses. — seq_press_ideal • Spectroscopy Analysis Tools (spant) PRESS sequence with ideal pulses. — seq_press_ideal • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/seq_pulse_acquire.html b/docs/reference/seq_pulse_acquire.html
index 4a88fc64..ad80571e 100644
--- a/docs/reference/seq_pulse_acquire.html
+++ b/docs/reference/seq_pulse_acquire.html
@@ -1,5 +1,5 @@
-Simple pulse and acquire sequence with ideal pulses. — seq_pulse_acquire • Spectroscopy Analysis Tools (spant) Simple pulse and acquire sequence with ideal pulses. — seq_pulse_acquire • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/seq_slaser_ideal.html b/docs/reference/seq_slaser_ideal.html
index 74688f4d..eb83e8e3 100644
--- a/docs/reference/seq_slaser_ideal.html
+++ b/docs/reference/seq_slaser_ideal.html
@@ -1,5 +1,5 @@
-sLASER sequence with ideal pulses. — seq_slaser_ideal • Spectroscopy Analysis Tools (spant) sLASER sequence with ideal pulses. — seq_slaser_ideal • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -126,7 +126,7 @@ Value
diff --git a/docs/reference/seq_spin_echo_ideal.html b/docs/reference/seq_spin_echo_ideal.html
index e23271de..4248716f 100644
--- a/docs/reference/seq_spin_echo_ideal.html
+++ b/docs/reference/seq_spin_echo_ideal.html
@@ -1,5 +1,5 @@
-Spin echo sequence with ideal pulses. — seq_spin_echo_ideal • Spectroscopy Analysis Tools (spant) Spin echo sequence with ideal pulses. — seq_spin_echo_ideal • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/seq_steam_ideal.html b/docs/reference/seq_steam_ideal.html
index a60685a8..1c8115d7 100644
--- a/docs/reference/seq_steam_ideal.html
+++ b/docs/reference/seq_steam_ideal.html
@@ -1,5 +1,5 @@
-STEAM sequence with ideal pulses. — seq_steam_ideal • Spectroscopy Analysis Tools (spant) STEAM sequence with ideal pulses. — seq_steam_ideal • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -128,7 +128,7 @@ Value
diff --git a/docs/reference/seq_steam_ideal_cof.html b/docs/reference/seq_steam_ideal_cof.html
index 8f225740..cba7af91 100644
--- a/docs/reference/seq_steam_ideal_cof.html
+++ b/docs/reference/seq_steam_ideal_cof.html
@@ -1,7 +1,5 @@
-STEAM sequence with ideal pulses and coherence order filtering to simulate
-gradient crushers. — seq_steam_ideal_cof • Spectroscopy Analysis Tools (spant) STEAM sequence with ideal pulses and coherence order filtering to simulate gradient crushers. — seq_steam_ideal_cof • Spectroscopy Analysis Tools (spant) STEAM sequence with ideal pulses using the z-rotation gradient simulation
-method described by Young et al JMR 140, 146-152 (1999). — seq_steam_ideal_young • Spectroscopy Analysis Tools (spant) STEAM sequence with ideal pulses using the z-rotation gradient simulation method described by Young et al JMR 140, 146-152 (1999). — seq_steam_ideal_young • Spectroscopy Analysis Tools (spant) Set the number of transients for an mrs_data object. — set_Ntrans • Spectroscopy Analysis Tools (spant) Set the number of transients for an mrs_data object. — set_Ntrans • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/set_def_acq_paras.html b/docs/reference/set_def_acq_paras.html
index 3e1b4004..cc2ada9c 100644
--- a/docs/reference/set_def_acq_paras.html
+++ b/docs/reference/set_def_acq_paras.html
@@ -1,5 +1,5 @@
-Set the default acquisition parameters. — set_def_acq_paras • Spectroscopy Analysis Tools (spant) Set the default acquisition parameters. — set_def_acq_paras • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Arguments
diff --git a/docs/reference/set_lcm_cmd.html b/docs/reference/set_lcm_cmd.html
index 2056ed01..42bb2f24 100644
--- a/docs/reference/set_lcm_cmd.html
+++ b/docs/reference/set_lcm_cmd.html
@@ -1,5 +1,5 @@
-Set the command to run the LCModel command-line program. — set_lcm_cmd • Spectroscopy Analysis Tools (spant) Set the command to run the LCModel command-line program. — set_lcm_cmd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/set_lw.html b/docs/reference/set_lw.html
index b64ec851..bb176c62 100644
--- a/docs/reference/set_lw.html
+++ b/docs/reference/set_lw.html
@@ -1,5 +1,5 @@
-Apply line-broadening to an mrs_data object to achieve a specified linewidth. — set_lw • Spectroscopy Analysis Tools (spant) Apply line-broadening to an mrs_data object to achieve a specified linewidth. — set_lw • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -123,7 +123,7 @@ Value
diff --git a/docs/reference/set_mask_xy_mat.html b/docs/reference/set_mask_xy_mat.html
index 49dc5d4e..52c4b617 100644
--- a/docs/reference/set_mask_xy_mat.html
+++ b/docs/reference/set_mask_xy_mat.html
@@ -1,5 +1,5 @@
-Set the masked voxels in a 2D MRSI dataset to given spectrum. — set_mask_xy_mat • Spectroscopy Analysis Tools (spant) Set the masked voxels in a 2D MRSI dataset to given spectrum. — set_mask_xy_mat • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Value
diff --git a/docs/reference/set_precomp_mode.html b/docs/reference/set_precomp_mode.html
index f44bd5d3..47c28e3b 100644
--- a/docs/reference/set_precomp_mode.html
+++ b/docs/reference/set_precomp_mode.html
@@ -1,5 +1,5 @@
-Set the precompute mode. — set_precomp_mode • Spectroscopy Analysis Tools (spant) Set the precompute mode. — set_precomp_mode • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/set_precomp_verbose.html b/docs/reference/set_precomp_verbose.html
index 1453a231..9c613505 100644
--- a/docs/reference/set_precomp_verbose.html
+++ b/docs/reference/set_precomp_verbose.html
@@ -1,5 +1,5 @@
-Set the verbosity of the precompute function. — set_precomp_verbose • Spectroscopy Analysis Tools (spant) Set the verbosity of the precompute function. — set_precomp_verbose • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/set_ref.html b/docs/reference/set_ref.html
index 8953fa50..5436dfa2 100644
--- a/docs/reference/set_ref.html
+++ b/docs/reference/set_ref.html
@@ -1,5 +1,5 @@
-Set the ppm reference value (eg ppm value at 0Hz). — set_ref • Spectroscopy Analysis Tools (spant) Set the ppm reference value (eg ppm value at 0Hz). — set_ref • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/set_td_pts.html b/docs/reference/set_td_pts.html
index 8a80d42a..586459ff 100644
--- a/docs/reference/set_td_pts.html
+++ b/docs/reference/set_td_pts.html
@@ -1,7 +1,5 @@
-Set the number of time-domain data points, truncating or zero-filling as
-appropriate. — set_td_pts • Spectroscopy Analysis Tools (spant) Set the number of time-domain data points, truncating or zero-filling as appropriate. — set_td_pts • Spectroscopy Analysis Tools (spant) Set the command to run the TARQUIN command-line program. — set_tqn_cmd • Spectroscopy Analysis Tools (spant) Set the command to run the TARQUIN command-line program. — set_tqn_cmd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/set_tr.html b/docs/reference/set_tr.html
index b2109ab0..65c9df5f 100644
--- a/docs/reference/set_tr.html
+++ b/docs/reference/set_tr.html
@@ -1,5 +1,5 @@
-Set the repetition time of an MRS dataset. — set_tr • Spectroscopy Analysis Tools (spant) Set the repetition time of an MRS dataset. — set_tr • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/shift.html b/docs/reference/shift.html
index ab0fe724..034591d0 100644
--- a/docs/reference/shift.html
+++ b/docs/reference/shift.html
@@ -1,5 +1,5 @@
-Apply a frequency shift to MRS data. — shift • Spectroscopy Analysis Tools (spant) Apply a frequency shift to MRS data. — shift • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/shift_basis.html b/docs/reference/shift_basis.html
index 2884be19..f55a65e0 100644
--- a/docs/reference/shift_basis.html
+++ b/docs/reference/shift_basis.html
@@ -1,5 +1,5 @@
-Apply frequency shifts to basis set signals. — shift_basis • Spectroscopy Analysis Tools (spant) Apply frequency shifts to basis set signals. — shift_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Value
diff --git a/docs/reference/sim_basis.html b/docs/reference/sim_basis.html
index c7838c46..bb5fefc6 100644
--- a/docs/reference/sim_basis.html
+++ b/docs/reference/sim_basis.html
@@ -1,5 +1,5 @@
-Simulate a basis set object. — sim_basis • Spectroscopy Analysis Tools (spant) Simulate a basis set object. — sim_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -136,7 +136,7 @@ Value
diff --git a/docs/reference/sim_basis_1h_brain.html b/docs/reference/sim_basis_1h_brain.html
index 62ed7389..f71ffa0b 100644
--- a/docs/reference/sim_basis_1h_brain.html
+++ b/docs/reference/sim_basis_1h_brain.html
@@ -1,7 +1,5 @@
-Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS
-sequence. Note, ideal pulses are assumed. — sim_basis_1h_brain • Spectroscopy Analysis Tools (spant) Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS sequence. Note, ideal pulses are assumed. — sim_basis_1h_brain • Spectroscopy Analysis Tools (spant) Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS
-sequence. Note, ideal pulses are assumed. — sim_basis_1h_brain_press • Spectroscopy Analysis Tools (spant) Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS sequence. Note, ideal pulses are assumed. — sim_basis_1h_brain_press • Spectroscopy Analysis Tools (spant) Simulate a macromolecular and lipid basis-set suitable for 1H brain MRS
-analysis. — sim_basis_mm_lip_lcm • Spectroscopy Analysis Tools (spant) Simulate a macromolecular and lipid basis-set suitable for 1H brain MRS analysis. — sim_basis_mm_lip_lcm • Spectroscopy Analysis Tools (spant) Simulate a basis file using TARQUIN. — sim_basis_tqn • Spectroscopy Analysis Tools (spant) Simulate a basis file using TARQUIN. — sim_basis_tqn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -129,7 +129,7 @@ Examples
diff --git a/docs/reference/sim_brain_1h.html b/docs/reference/sim_brain_1h.html
index 2044cf1a..717ee289 100644
--- a/docs/reference/sim_brain_1h.html
+++ b/docs/reference/sim_brain_1h.html
@@ -1,5 +1,5 @@
-Simulate MRS data with a similar appearance to normal brain (by default). — sim_brain_1h • Spectroscopy Analysis Tools (spant) Simulate MRS data with a similar appearance to normal brain (by default). — sim_brain_1h • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -159,7 +159,7 @@ Value
diff --git a/docs/reference/sim_mol.html b/docs/reference/sim_mol.html
index 23bcef50..77f76a50 100644
--- a/docs/reference/sim_mol.html
+++ b/docs/reference/sim_mol.html
@@ -1,5 +1,5 @@
-Simulate a mol_parameter object. — sim_mol • Spectroscopy Analysis Tools (spant) Simulate a mol_parameter object. — sim_mol • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -143,7 +143,7 @@ Value
diff --git a/docs/reference/sim_noise.html b/docs/reference/sim_noise.html
index 23875f79..a71477d4 100644
--- a/docs/reference/sim_noise.html
+++ b/docs/reference/sim_noise.html
@@ -1,5 +1,5 @@
-Simulate an mrs_data object containing simulated Gaussian noise. — sim_noise • Spectroscopy Analysis Tools (spant) Simulate an mrs_data object containing simulated Gaussian noise. — sim_noise • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -84,6 +84,7 @@ Simulate an mrs_data object containing simulated Gaussian noise.
ft = def_ft(),
N = def_N(),
ref = def_ref(),
+ nuc = def_nuc(),
dyns = 1,
fd = TRUE
)
@@ -111,6 +112,10 @@ Arguments
reference value for ppm scale.
nuc
+resonant nucleus.
dyns
number of dynamic scans to generate.
Value
diff --git a/docs/reference/sim_resonances.html b/docs/reference/sim_resonances.html
index 19e9a8a4..d4f8d7c0 100644
--- a/docs/reference/sim_resonances.html
+++ b/docs/reference/sim_resonances.html
@@ -1,5 +1,5 @@
-Simulate a MRS data object containing a set of simulated resonances. — sim_resonances • Spectroscopy Analysis Tools (spant) Simulate a MRS data object containing a set of simulated resonances. — sim_resonances • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -161,7 +161,7 @@ Examples
diff --git a/docs/reference/sim_th_excit_profile.html b/docs/reference/sim_th_excit_profile.html
index 5535c5ef..e781cab1 100644
--- a/docs/reference/sim_th_excit_profile.html
+++ b/docs/reference/sim_th_excit_profile.html
@@ -1,7 +1,5 @@
-Simulate an ideal pulse excitation profile by smoothing a top-hat function
-with a Gaussian. — sim_th_excit_profile • Spectroscopy Analysis Tools (spant) Simulate an ideal pulse excitation profile by smoothing a top-hat function with a Gaussian. — sim_th_excit_profile • Spectroscopy Analysis Tools (spant) Simulate an mrs_data object containing complex zero valued samples. — sim_zero • Spectroscopy Analysis Tools (spant) Simulate an mrs_data object containing complex zero valued samples. — sim_zero • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -78,7 +78,14 @@ Simulate an mrs_data object containing complex zero valued samples.
-
+
@@ -99,6 +106,10 @@ Arguments
reference value for ppm scale.
nuc
+resonant nucleus.
dyns
number of dynamic scans to generate.
Value
diff --git a/docs/reference/smooth_dyns.html b/docs/reference/smooth_dyns.html
index 4cc8da50..accf3a51 100644
--- a/docs/reference/smooth_dyns.html
+++ b/docs/reference/smooth_dyns.html
@@ -1,5 +1,5 @@
-Smooth data across the dynamic dimension with a Gaussian kernel. — smooth_dyns • Spectroscopy Analysis Tools (spant) Smooth data across the dynamic dimension with a Gaussian kernel. — smooth_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/sort_basis.html b/docs/reference/sort_basis.html
index 6a676ea2..d25cc006 100644
--- a/docs/reference/sort_basis.html
+++ b/docs/reference/sort_basis.html
@@ -1,5 +1,5 @@
-Sort the basis-set elements alphabetically. — sort_basis • Spectroscopy Analysis Tools (spant) Sort the basis-set elements alphabetically. — sort_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/spant-package.html b/docs/reference/spant-package.html
index b3dd8e21..90f19ec3 100644
--- a/docs/reference/spant-package.html
+++ b/docs/reference/spant-package.html
@@ -1,5 +1,5 @@
-spant: spectroscopy analysis tools. — spant-package • Spectroscopy Analysis Tools (spant) spant: spectroscopy analysis tools. — spant-package • Spectroscopy Analysis Tools (spant) Simulate and fit some spectra with ABfit for benchmarking purposes. Basic
-timing and performance metrics will be printed. — spant_abfit_benchmark • Spectroscopy Analysis Tools (spant) Simulate and fit some spectra with ABfit for benchmarking purposes. Basic timing and performance metrics will be printed. — spant_abfit_benchmark • Spectroscopy Analysis Tools (spant) Example MEGA-PRESS data with significant B0 drift. — spant_mpress_drift • Spectroscopy Analysis Tools (spant) Example MEGA-PRESS data with significant B0 drift. — spant_mpress_drift • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -83,7 +83,7 @@ Example MEGA-PRESS data with significant B0 drift.
Format
- An object of class mrs_data of length 13.
+ An object of class mrs_data of dimension 1 x 1 x 1 x 1 x 40 x 1 x 1024.
@@ -98,7 +98,7 @@ Format
diff --git a/docs/reference/spant_sim_fmrs_dataset.html b/docs/reference/spant_sim_fmrs_dataset.html
new file mode 100644
index 00000000..00e48b56
--- /dev/null
+++ b/docs/reference/spant_sim_fmrs_dataset.html
@@ -0,0 +1,117 @@
+
+Simulate an example fMRS dataset for a block design fMRS experiment and export a BIDS structure. — spant_sim_fmrs_dataset • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Simulate an example fMRS dataset for a block design fMRS experiment and export a BIDS structure.
+ Source: R/fmrs.R
+ spant_sim_fmrs_dataset.Rd
+
+
+
+ Simulate an example fMRS dataset for a block design fMRS experiment and
+export a BIDS structure.
+
+
+
+ spant_sim_fmrs_dataset(output_dir = NULL)
+
+
+
+ Arguments
+ - output_dir
+output directory for the BIDS data. Defaults to :
+"HOME/sim_fmrs_dataset/data".
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/spant_simulation_benchmark.html b/docs/reference/spant_simulation_benchmark.html
index 32daa8bf..d8cc6841 100644
--- a/docs/reference/spant_simulation_benchmark.html
+++ b/docs/reference/spant_simulation_benchmark.html
@@ -1,7 +1,5 @@
-Simulate a typical metabolite basis set for benchmarking. Timing metrics will
-be printed on completion. — spant_simulation_benchmark • Spectroscopy Analysis Tools (spant) Simulate a typical metabolite basis set for benchmarking. Timing metrics will be printed on completion. — spant_simulation_benchmark • Spectroscopy Analysis Tools (spant) Decompose an mrs_data object into white and gray matter spectra. — spec_decomp • Spectroscopy Analysis Tools (spant) Perform a mathematical operation on a spectral region. — spec_op • Spectroscopy Analysis Tools (spant) Perform a mathematical operation on a spectral region. — spec_op • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -98,8 +98,8 @@ Arguments
operator
-can be "sum" (default), "mean", "l2", "max", "min" or
-"max-min".
can be "sum" (default), "mean", "l2", "max", "max_cplx,
+"min" or "max-min".
freq_scale
@@ -129,7 +129,7 @@ Value
diff --git a/docs/reference/spin_sys.html b/docs/reference/spin_sys.html
index 853423a4..1eaa9e76 100644
--- a/docs/reference/spin_sys.html
+++ b/docs/reference/spin_sys.html
@@ -1,5 +1,5 @@
-Create a spin system object for pulse sequence simulation. — spin_sys • Spectroscopy Analysis Tools (spant) Create a spin system object for pulse sequence simulation. — spin_sys • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/spm_pve2categorical.html b/docs/reference/spm_pve2categorical.html
index 23a1bad9..70f10729 100644
--- a/docs/reference/spm_pve2categorical.html
+++ b/docs/reference/spm_pve2categorical.html
@@ -1,7 +1,5 @@
-Convert SPM style segmentation files to a single categorical image where
-the numerical values map as: 0) Other, 1) CSF, 2) GM and 3) WM. — spm_pve2categorical • Spectroscopy Analysis Tools (spant) Convert SPM style segmentation files to a single categorical image where the numerical values map as: 0) Other, 1) CSF, 2) GM and 3) WM. — spm_pve2categorical • Spectroscopy Analysis Tools (spant) Signal space projection method for lipid suppression. — ssp • Spectroscopy Analysis Tools (spant) Signal space projection method for lipid suppression. — ssp • Spectroscopy Analysis Tools (spant) Plot the fitting results of an object of class fit_result with
-individual basis set components shown. — stackplot.fit_result • Spectroscopy Analysis Tools (spant) Plot the fitting results of an object of class fit_result with individual basis set components shown. — stackplot.fit_result • Spectroscopy Analysis Tools (spant) Produce a plot with multiple traces. — stackplot • Spectroscopy Analysis Tools (spant) Produce a plot with multiple traces. — stackplot • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/stackplot.mrs_data.html b/docs/reference/stackplot.mrs_data.html
index 17ff5648..64eea445 100644
--- a/docs/reference/stackplot.mrs_data.html
+++ b/docs/reference/stackplot.mrs_data.html
@@ -1,5 +1,5 @@
-Stackplot plotting method for objects of class mrs_data. — stackplot.mrs_data • Spectroscopy Analysis Tools (spant) Stackplot plotting method for objects of class mrs_data. — stackplot.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -255,7 +255,7 @@ Arguments
diff --git a/docs/reference/sub_first_dyn.html b/docs/reference/sub_first_dyn.html
index dbd7f831..493b7242 100644
--- a/docs/reference/sub_first_dyn.html
+++ b/docs/reference/sub_first_dyn.html
@@ -1,5 +1,5 @@
-Subtract the first dynamic spectrum from a dynamic series. — sub_first_dyn • Spectroscopy Analysis Tools (spant) Subtract the first dynamic spectrum from a dynamic series. — sub_first_dyn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/sub_mean_dyns.html b/docs/reference/sub_mean_dyns.html
index 6e3bb2df..221bd0c1 100644
--- a/docs/reference/sub_mean_dyns.html
+++ b/docs/reference/sub_mean_dyns.html
@@ -1,5 +1,5 @@
-Subtract the mean dynamic spectrum from a dynamic series. — sub_mean_dyns • Spectroscopy Analysis Tools (spant) Subtract the mean dynamic spectrum from a dynamic series. — sub_mean_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/sub_median_dyns.html b/docs/reference/sub_median_dyns.html
index 134c495d..1e834f14 100644
--- a/docs/reference/sub_median_dyns.html
+++ b/docs/reference/sub_median_dyns.html
@@ -1,5 +1,5 @@
-Subtract the median dynamic spectrum from a dynamic series. — sub_median_dyns • Spectroscopy Analysis Tools (spant) Subtract the median dynamic spectrum from a dynamic series. — sub_median_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/sum_coils.html b/docs/reference/sum_coils.html
index 7bf559f2..e1ab3cc0 100644
--- a/docs/reference/sum_coils.html
+++ b/docs/reference/sum_coils.html
@@ -1,5 +1,5 @@
-Calculate the sum across receiver coil elements. — sum_coils • Spectroscopy Analysis Tools (spant) Calculate the sum across receiver coil elements. — sum_coils • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/sum_dyns.html b/docs/reference/sum_dyns.html
index a0be19d3..bbda2ffc 100644
--- a/docs/reference/sum_dyns.html
+++ b/docs/reference/sum_dyns.html
@@ -1,5 +1,5 @@
-Calculate the sum of data dynamics. — sum_dyns • Spectroscopy Analysis Tools (spant) Calculate the sum of data dynamics. — sum_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/sum_mrs.html b/docs/reference/sum_mrs.html
index a22f215b..3cc3ab9e 100644
--- a/docs/reference/sum_mrs.html
+++ b/docs/reference/sum_mrs.html
@@ -1,5 +1,5 @@
-Sum two mrs_data objects. — sum_mrs • Spectroscopy Analysis Tools (spant) Sum two mrs_data objects. — sum_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Value
diff --git a/docs/reference/sum_mrs_list.html b/docs/reference/sum_mrs_list.html
index f4e09aea..c3584348 100644
--- a/docs/reference/sum_mrs_list.html
+++ b/docs/reference/sum_mrs_list.html
@@ -1,5 +1,5 @@
-Return the sum of a list of mrs_data objects. — sum_mrs_list • Spectroscopy Analysis Tools (spant) Return the sum of a list of mrs_data objects. — sum_mrs_list • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/svs_1h_brain_analysis.html b/docs/reference/svs_1h_brain_analysis.html
index 8ce514db..dff0ef7d 100644
--- a/docs/reference/svs_1h_brain_analysis.html
+++ b/docs/reference/svs_1h_brain_analysis.html
@@ -1,5 +1,5 @@
-Standard SVS 1H brain analysis pipeline. — svs_1h_brain_analysis • Spectroscopy Analysis Tools (spant) Standard SVS 1H brain analysis pipeline. — svs_1h_brain_analysis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -199,7 +199,7 @@ Value
diff --git a/docs/reference/svs_1h_brain_analysis_dev.html b/docs/reference/svs_1h_brain_analysis_dev.html
index d70a14d3..d71bfea2 100644
--- a/docs/reference/svs_1h_brain_analysis_dev.html
+++ b/docs/reference/svs_1h_brain_analysis_dev.html
@@ -1,5 +1,5 @@
-Standard SVS 1H brain analysis pipeline. — svs_1h_brain_analysis_dev • Spectroscopy Analysis Tools (spant) Standard SVS 1H brain analysis pipeline. — svs_1h_brain_analysis_dev • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -193,7 +193,7 @@ Examples
diff --git a/docs/reference/svs_1h_brain_batch_analysis.html b/docs/reference/svs_1h_brain_batch_analysis.html
index 5631e8cc..15f7223e 100644
--- a/docs/reference/svs_1h_brain_batch_analysis.html
+++ b/docs/reference/svs_1h_brain_batch_analysis.html
@@ -1,5 +1,5 @@
-Batch interface to the standard SVS 1H brain analysis pipeline. — svs_1h_brain_batch_analysis • Spectroscopy Analysis Tools (spant) Batch interface to the standard SVS 1H brain analysis pipeline. — svs_1h_brain_batch_analysis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -144,7 +144,7 @@ Value
diff --git a/docs/reference/t_test_spec.html b/docs/reference/t_test_spec.html
new file mode 100644
index 00000000..56a7ea1b
--- /dev/null
+++ b/docs/reference/t_test_spec.html
@@ -0,0 +1,124 @@
+
+Perform a t-test on spectral data points. — t_test_spec • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+
+
+ Perform a t-test on spectral data points.
+
+
+
+ t_test_spec(mrs_data, group)
+
+
+
+ Arguments
+ - mrs_data
+an mrs_data object with spectra in the dynamic dimension.
- group
+vector describing the group membership of each dynamic spectrum.
+
+ Value
+
+
+a list of statistical results.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/td2fd.html b/docs/reference/td2fd.html
index 6748a6a8..f31ed524 100644
--- a/docs/reference/td2fd.html
+++ b/docs/reference/td2fd.html
@@ -1,5 +1,5 @@
-Transform time-domain data to the frequency-domain. — td2fd • Spectroscopy Analysis Tools (spant) Transform time-domain data to the frequency-domain. — td2fd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/td_conv_filt.html b/docs/reference/td_conv_filt.html
index a9f340c3..106b9b00 100644
--- a/docs/reference/td_conv_filt.html
+++ b/docs/reference/td_conv_filt.html
@@ -1,5 +1,5 @@
-Time-domain convolution based filter. — td_conv_filt • Spectroscopy Analysis Tools (spant) Time-domain convolution based filter. — td_conv_filt • Spectroscopy Analysis Tools (spant) Time-domain spectral registration. — tdsr • Spectroscopy Analysis Tools (spant) Time-domain spectral registration. — tdsr • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -121,7 +121,7 @@ Value
diff --git a/docs/reference/te.html b/docs/reference/te.html
index 010361b1..4a65711d 100644
--- a/docs/reference/te.html
+++ b/docs/reference/te.html
@@ -1,5 +1,5 @@
-Return the echo time of an MRS dataset. — te • Spectroscopy Analysis Tools (spant) Return the echo time of an MRS dataset. — te • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/tr.html b/docs/reference/tr.html
index 0c0bd63b..2e749e02 100644
--- a/docs/reference/tr.html
+++ b/docs/reference/tr.html
@@ -1,5 +1,5 @@
-Return the repetition time of an MRS dataset. — tr • Spectroscopy Analysis Tools (spant) Return the repetition time of an MRS dataset. — tr • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/varpro_3_para_opts.html b/docs/reference/varpro_3_para_opts.html
index c2270a16..52d7cd84 100644
--- a/docs/reference/varpro_3_para_opts.html
+++ b/docs/reference/varpro_3_para_opts.html
@@ -1,5 +1,5 @@
-Return a list of options for VARPRO based fitting with 3 free parameters. — varpro_3_para_opts • Spectroscopy Analysis Tools (spant) Return a list of options for VARPRO based fitting with 3 free parameters. — varpro_3_para_opts • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -141,7 +141,7 @@ Value
diff --git a/docs/reference/varpro_basic_opts.html b/docs/reference/varpro_basic_opts.html
index 32c86d22..c5104891 100644
--- a/docs/reference/varpro_basic_opts.html
+++ b/docs/reference/varpro_basic_opts.html
@@ -1,5 +1,5 @@
-Return a list of options for a basic VARPRO analysis. — varpro_basic_opts • Spectroscopy Analysis Tools (spant) Return a list of options for a basic VARPRO analysis. — varpro_basic_opts • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -118,7 +118,7 @@ Value
diff --git a/docs/reference/varpro_opts.html b/docs/reference/varpro_opts.html
index 2aabf11d..6332f730 100644
--- a/docs/reference/varpro_opts.html
+++ b/docs/reference/varpro_opts.html
@@ -1,5 +1,5 @@
-Return a list of options for VARPRO based fitting. — varpro_opts • Spectroscopy Analysis Tools (spant) Return a list of options for VARPRO based fitting. — varpro_opts • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -177,7 +177,7 @@ Examples
diff --git a/docs/reference/vec2mrs_data.html b/docs/reference/vec2mrs_data.html
index 0cccd73b..f0d58bf0 100644
--- a/docs/reference/vec2mrs_data.html
+++ b/docs/reference/vec2mrs_data.html
@@ -1,5 +1,5 @@
-Convert a vector into a mrs_data object. — vec2mrs_data • Spectroscopy Analysis Tools (spant) Convert a vector into a mrs_data object. — vec2mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -80,10 +80,11 @@ Convert a vector into a mrs_data object.
vec2mrs_data(
vec,
- fs = def_fs(),
- ft = def_ft(),
- ref = def_ref(),
- nuc = def_nuc(),
+ mrs_data = NULL,
+ fs = NULL,
+ ft = NULL,
+ ref = NULL,
+ nuc = NULL,
dyns = 1,
fd = FALSE
)
@@ -95,6 +96,10 @@ Arguments
the data vector.
mrs_data
+example data to copy acquisition parameters from.
fs
sampling frequency in Hz.
Arguments
fd
-flag to indicate if the matrix is in the frequency domain (logical).
flag to indicate if the vector is in the frequency domain (logical).
Value
diff --git a/docs/reference/write_basis.html b/docs/reference/write_basis.html
index b6e27cbd..94c5e021 100644
--- a/docs/reference/write_basis.html
+++ b/docs/reference/write_basis.html
@@ -1,5 +1,5 @@
-Write a basis object to an LCModel .basis formatted file. — write_basis • Spectroscopy Analysis Tools (spant) Write a basis object to an LCModel .basis formatted file. — write_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -108,7 +108,7 @@ Arguments
diff --git a/docs/reference/write_basis_tqn.html b/docs/reference/write_basis_tqn.html
index 6aa51c1d..116c73ec 100644
--- a/docs/reference/write_basis_tqn.html
+++ b/docs/reference/write_basis_tqn.html
@@ -1,5 +1,5 @@
-Generate a basis file using TARQUIN. — write_basis_tqn • Spectroscopy Analysis Tools (spant) Generate a basis file using TARQUIN. — write_basis_tqn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Examples
diff --git a/docs/reference/write_mrs.html b/docs/reference/write_mrs.html
index fff25f15..124b9dc4 100644
--- a/docs/reference/write_mrs.html
+++ b/docs/reference/write_mrs.html
@@ -1,5 +1,5 @@
-Write MRS data object to file. — write_mrs • Spectroscopy Analysis Tools (spant) Write MRS data object to file. — write_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Arguments
diff --git a/docs/reference/write_mrs_nifti.html b/docs/reference/write_mrs_nifti.html
index f4bf1921..bd3ed4b7 100644
--- a/docs/reference/write_mrs_nifti.html
+++ b/docs/reference/write_mrs_nifti.html
@@ -1,5 +1,5 @@
-Write MRS data object to file in NIFTI format. — write_mrs_nifti • Spectroscopy Analysis Tools (spant) Write MRS data object to file in NIFTI format. — write_mrs_nifti • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/write_pulse_ascii.html b/docs/reference/write_pulse_ascii.html
index 067ae086..221f8ebb 100644
--- a/docs/reference/write_pulse_ascii.html
+++ b/docs/reference/write_pulse_ascii.html
@@ -1,5 +1,5 @@
-Write an ASCII formatted pulse file. — write_pulse_ascii • Spectroscopy Analysis Tools (spant) Write an ASCII formatted pulse file. — write_pulse_ascii • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/zero_fade_spec.html b/docs/reference/zero_fade_spec.html
index c703745c..c8b572c3 100644
--- a/docs/reference/zero_fade_spec.html
+++ b/docs/reference/zero_fade_spec.html
@@ -1,7 +1,5 @@
-Fade a spectrum to zero by frequency domain multiplication with a tanh
-function. Note this operation distorts data points at the end of the FID. — zero_fade_spec • Spectroscopy Analysis Tools (spant) Fade a spectrum to zero by frequency domain multiplication with a tanh function. Note this operation distorts data points at the end of the FID. — zero_fade_spec • Spectroscopy Analysis Tools (spant) Zero all coherences including and above a given order. — zero_higher_orders • Spectroscopy Analysis Tools (spant) Zero all coherences including and above a given order. — zero_higher_orders • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Value
diff --git a/docs/reference/zero_td_pts_end.html b/docs/reference/zero_td_pts_end.html
index 8c1123c8..71d24ebb 100644
--- a/docs/reference/zero_td_pts_end.html
+++ b/docs/reference/zero_td_pts_end.html
@@ -1,5 +1,5 @@
-Set mrs_data object data points at the end of the FID to zero. — zero_td_pts_end • Spectroscopy Analysis Tools (spant) Set mrs_data object data points at the end of the FID to zero. — zero_td_pts_end • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/zf.html b/docs/reference/zf.html
index 85e2013c..baf50256 100644
--- a/docs/reference/zf.html
+++ b/docs/reference/zf.html
@@ -1,5 +1,5 @@
-Zero-fill MRS data in the time domain. — zf • Spectroscopy Analysis Tools (spant) Zero-fill MRS data in the time domain. — zf • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -125,7 +125,7 @@ Value
diff --git a/docs/reference/zf_xy.html b/docs/reference/zf_xy.html
index ebca3999..c4104a74 100644
--- a/docs/reference/zf_xy.html
+++ b/docs/reference/zf_xy.html
@@ -1,5 +1,5 @@
-Zero-fill MRSI data in the k-space x-y direction. — zf_xy • Spectroscopy Analysis Tools (spant) Zero-fill MRSI data in the k-space x-y direction. — zf_xy • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -113,7 +113,7 @@ Value
diff --git a/docs/sitemap.xml b/docs/sitemap.xml
index e2139f71..4c39f515 100644
--- a/docs/sitemap.xml
+++ b/docs/sitemap.xml
@@ -216,6 +216,12 @@
https://martin3141.github.io/spant/reference/comb_coils_fp_pc.html
+
+ https://martin3141.github.io/spant/reference/comb_coils_mrsi_gls.html
+
+
+ https://martin3141.github.io/spant/reference/comb_coils_svs_gls.html
+
https://martin3141.github.io/spant/reference/comb_csv_results.html
@@ -411,6 +417,9 @@
https://martin3141.github.io/spant/reference/gen_conv_reg.html
+
+ https://martin3141.github.io/spant/reference/gen_group_reg.html
+
https://martin3141.github.io/spant/reference/gen_impulse_reg.html
@@ -555,6 +564,15 @@
https://martin3141.github.io/spant/reference/glm_spec.html
+
+ https://martin3141.github.io/spant/reference/glm_spec_fmrs_fl.html
+
+
+ https://martin3141.github.io/spant/reference/glm_spec_fmrs_group.html
+
+
+ https://martin3141.github.io/spant/reference/glm_spec_group_linhyp.html
+
https://martin3141.github.io/spant/reference/grid_shift_xy.html
@@ -690,9 +708,15 @@
https://martin3141.github.io/spant/reference/mrs_data2basis.html
+
+ https://martin3141.github.io/spant/reference/mrs_data2bids.html
+
https://martin3141.github.io/spant/reference/mrs_data2mat.html
+
+ https://martin3141.github.io/spant/reference/mrs_data2spec_mat.html
+
https://martin3141.github.io/spant/reference/mrs_data2vec.html
@@ -741,6 +765,9 @@
https://martin3141.github.io/spant/reference/phase.html
+
+ https://martin3141.github.io/spant/reference/phase_ref_1h_brain.html
+
https://martin3141.github.io/spant/reference/plot.fit_result.html
@@ -780,6 +807,12 @@
https://martin3141.github.io/spant/reference/precomp.html
+
+ https://martin3141.github.io/spant/reference/preproc_svs.html
+
+
+ https://martin3141.github.io/spant/reference/preproc_svs_dataset.html
+
https://martin3141.github.io/spant/reference/print.fit_result.html
@@ -1050,6 +1083,9 @@
https://martin3141.github.io/spant/reference/spant_mpress_drift.html
+
+ https://martin3141.github.io/spant/reference/spant_sim_fmrs_dataset.html
+
https://martin3141.github.io/spant/reference/spant_simulation_benchmark.html
@@ -1107,6 +1143,9 @@
https://martin3141.github.io/spant/reference/svs_1h_brain_batch_analysis.html
+
+ https://martin3141.github.io/spant/reference/t_test_spec.html
+
https://martin3141.github.io/spant/reference/td2fd.html
MEGA-PRESS sequence with ideal localisation pulses and Gaussian shaped -editing pulse.
MEGA-PRESS sequence with ideal localisation pulses and Gaussian shaped editing pulse.
All functions
- STEAM sequence with ideal pulses and coherence order filtering to simulate
-gradient crushers.
STEAM sequence with ideal pulses and coherence order filtering to simulate gradient crushers.
- STEAM sequence with ideal pulses using the z-rotation gradient simulation
-method described by Young et al JMR 140, 146-152 (1999).
STEAM sequence with ideal pulses using the z-rotation gradient simulation method described by Young et al JMR 140, 146-152 (1999).
@@ -1293,8 +1270,7 @@ All functions
- Set the number of time-domain data points, truncating or zero-filling as
-appropriate.
Set the number of time-domain data points, truncating or zero-filling as appropriate.
@@ -1318,18 +1294,15 @@ All functions
- Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS
-sequence. Note, ideal pulses are assumed.
Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS sequence. Note, ideal pulses are assumed.
- Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS
-sequence. Note, ideal pulses are assumed.
Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS sequence. Note, ideal pulses are assumed.
- Simulate a macromolecular and lipid basis-set suitable for 1H brain MRS
-analysis.
Simulate a macromolecular and lipid basis-set suitable for 1H brain MRS analysis.
@@ -1353,8 +1326,7 @@ All functions
- Simulate an ideal pulse excitation profile by smoothing a top-hat function
-with a Gaussian.
Simulate an ideal pulse excitation profile by smoothing a top-hat function with a Gaussian.
@@ -1374,17 +1346,19 @@ All functions
- Simulate and fit some spectra with ABfit for benchmarking purposes. Basic
-timing and performance metrics will be printed.
Simulate and fit some spectra with ABfit for benchmarking purposes. Basic timing and performance metrics will be printed.
Example MEGA-PRESS data with significant B0 drift.
+
+
+ Simulate an example fMRS dataset for a block design fMRS experiment and export a BIDS structure.
- Simulate a typical metabolite basis set for benchmarking. Timing metrics will
-be printed on completion.
Simulate a typical metabolite basis set for benchmarking. Timing metrics will be printed on completion.
@@ -1400,8 +1374,7 @@ All functions
- Convert SPM style segmentation files to a single categorical image where
-the numerical values map as: 0) Other, 1) CSF, 2) GM and 3) WM.
Convert SPM style segmentation files to a single categorical image where the numerical values map as: 0) Other, 1) CSF, 2) GM and 3) WM.
@@ -1413,8 +1386,7 @@ All functions
- Plot the fitting results of an object of class fit_result with
-individual basis set components shown.
Plot the fitting results of an object of class fit_result with individual basis set components shown.
@@ -1459,6 +1431,10 @@ All functions svs_1h_brain_batch_analysis()
Batch interface to the standard SVS 1H brain analysis pipeline.
+
+
+ Perform a t-test on spectral data points.
@@ -1518,8 +1494,7 @@ All functions
- Fade a spectrum to zero by frequency domain multiplication with a tanh
-function. Note this operation distorts data points at the end of the FID.
Fade a spectrum to zero by frequency domain multiplication with a tanh function. Note this operation distorts data points at the end of the FID.
@@ -1549,7 +1524,7 @@ All functions
diff --git a/docs/reference/int_spec.html b/docs/reference/int_spec.html
index c7060fe7..783325a8 100644
--- a/docs/reference/int_spec.html
+++ b/docs/reference/int_spec.html
@@ -1,5 +1,5 @@
-Integrate a spectral region. — int_spec • Spectroscopy Analysis Tools (spant) Integrate a spectral region. — int_spec • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -118,7 +118,7 @@ Value
diff --git a/docs/reference/interleave_dyns.html b/docs/reference/interleave_dyns.html
index effe5543..441eff27 100644
--- a/docs/reference/interleave_dyns.html
+++ b/docs/reference/interleave_dyns.html
@@ -1,5 +1,5 @@
-Interleave the first and second half of a dynamic series. — interleave_dyns • Spectroscopy Analysis Tools (spant) Interleave the first and second half of a dynamic series. — interleave_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/inv_even_dyns.html b/docs/reference/inv_even_dyns.html
index 9f9d4fff..dcb781dc 100644
--- a/docs/reference/inv_even_dyns.html
+++ b/docs/reference/inv_even_dyns.html
@@ -1,5 +1,5 @@
-Invert even numbered dynamic scans starting from 1 (2,4,6...). — inv_even_dyns • Spectroscopy Analysis Tools (spant) Invert even numbered dynamic scans starting from 1 (2,4,6...). — inv_even_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/inv_odd_dyns.html b/docs/reference/inv_odd_dyns.html
index 26212e2b..78d64660 100644
--- a/docs/reference/inv_odd_dyns.html
+++ b/docs/reference/inv_odd_dyns.html
@@ -1,5 +1,5 @@
-Invert odd numbered dynamic scans starting from 1 (1,3,5...). — inv_odd_dyns • Spectroscopy Analysis Tools (spant) Invert odd numbered dynamic scans starting from 1 (1,3,5...). — inv_odd_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/is.def.html b/docs/reference/is.def.html
index f196ffd0..a67b9eba 100644
--- a/docs/reference/is.def.html
+++ b/docs/reference/is.def.html
@@ -1,5 +1,5 @@
-Check if an object is defined, which is the same as being not NULL. — is.def • Spectroscopy Analysis Tools (spant) Check if an object is defined, which is the same as being not NULL. — is.def • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/is_fd.html b/docs/reference/is_fd.html
index 3b0ca165..18a193aa 100644
--- a/docs/reference/is_fd.html
+++ b/docs/reference/is_fd.html
@@ -1,7 +1,5 @@
-Check if the chemical shift dimension of an MRS data object is in the
-frequency domain. — is_fd • Spectroscopy Analysis Tools (spant) Check if the chemical shift dimension of an MRS data object is in the frequency domain. — is_fd • Spectroscopy Analysis Tools (spant) Transform 2D MRSI data from k-space to image space in the x-y direction. — kspace2img_xy • Spectroscopy Analysis Tools (spant) Transform 2D MRSI data from k-space to image space in the x-y direction. — kspace2img_xy • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/l2_reg.html b/docs/reference/l2_reg.html
index 3d781d80..21aa9849 100644
--- a/docs/reference/l2_reg.html
+++ b/docs/reference/l2_reg.html
@@ -1,5 +1,5 @@
-Perform l2 regularisation artefact suppression. — l2_reg • Spectroscopy Analysis Tools (spant) Perform l2 regularisation artefact suppression. — l2_reg • Spectroscopy Analysis Tools (spant) Apply line-broadening (apodisation) to MRS data or basis object. — lb • Spectroscopy Analysis Tools (spant) Apply line-broadening (apodisation) to MRS data or basis object. — lb • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -123,7 +123,7 @@ Value
diff --git a/docs/reference/lofdc.html b/docs/reference/lofdc.html
index 5419b1ec..31347a25 100644
--- a/docs/reference/lofdc.html
+++ b/docs/reference/lofdc.html
@@ -1,5 +1,5 @@
-Correct linear frequency drift. — lofdc • Spectroscopy Analysis Tools (spant) Correct linear frequency drift. — lofdc • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -138,7 +138,7 @@ Value
diff --git a/docs/reference/lw2alpha.html b/docs/reference/lw2alpha.html
index b83db682..25da229b 100644
--- a/docs/reference/lw2alpha.html
+++ b/docs/reference/lw2alpha.html
@@ -1,7 +1,5 @@
-Covert a linewidth in Hz to an equivalent alpha value in the time-domain ie:
-x * exp(-t * alpha). — lw2alpha • Spectroscopy Analysis Tools (spant) Covert a linewidth in Hz to an equivalent alpha value in the time-domain ie: x * exp(-t * alpha). — lw2alpha • Spectroscopy Analysis Tools (spant) Covert a linewidth in Hz to an equivalent beta value in the time-domain ie:
-x * exp(-t * t * beta). — lw2beta • Spectroscopy Analysis Tools (spant) Covert a linewidth in Hz to an equivalent beta value in the time-domain ie: x * exp(-t * t * beta). — lw2beta • Spectroscopy Analysis Tools (spant) Make a basis-set object from a directory containing LCModel formatted RAW
-files. — make_basis_from_raw • Spectroscopy Analysis Tools (spant) Make a basis-set object from a directory containing LCModel formatted RAW files. — make_basis_from_raw • Spectroscopy Analysis Tools (spant) Mask an MRS dataset in the dynamic dimension. — mask_dyns • Spectroscopy Analysis Tools (spant) Mask an MRS dataset in the dynamic dimension. — mask_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/mask_fit_res.html b/docs/reference/mask_fit_res.html
index 97baaa3f..ebd91a99 100644
--- a/docs/reference/mask_fit_res.html
+++ b/docs/reference/mask_fit_res.html
@@ -1,5 +1,5 @@
-Mask fit result spectra depending on a vector of bool values. — mask_fit_res • Spectroscopy Analysis Tools (spant) Mask fit result spectra depending on a vector of bool values. — mask_fit_res • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -116,7 +116,7 @@ Value
diff --git a/docs/reference/mask_xy.html b/docs/reference/mask_xy.html
index 11bb577c..b0d38619 100644
--- a/docs/reference/mask_xy.html
+++ b/docs/reference/mask_xy.html
@@ -1,5 +1,5 @@
-Mask an MRSI dataset in the x-y direction — mask_xy • Spectroscopy Analysis Tools (spant) Mask an MRSI dataset in the x-y direction — mask_xy • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/mask_xy_corners.html b/docs/reference/mask_xy_corners.html
index 09b16cd2..2d13839d 100644
--- a/docs/reference/mask_xy_corners.html
+++ b/docs/reference/mask_xy_corners.html
@@ -1,5 +1,5 @@
-Mask the four corners of an MRSI dataset in the x-y plane. — mask_xy_corners • Spectroscopy Analysis Tools (spant) Mask the four corners of an MRSI dataset in the x-y plane. — mask_xy_corners • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/mask_xy_ellipse.html b/docs/reference/mask_xy_ellipse.html
index 1d8b02e4..e2e749ef 100644
--- a/docs/reference/mask_xy_ellipse.html
+++ b/docs/reference/mask_xy_ellipse.html
@@ -1,7 +1,5 @@
-Mask the voxels outside an elliptical region spanning the MRSI dataset in the
-x-y plane. — mask_xy_ellipse • Spectroscopy Analysis Tools (spant) Mask the voxels outside an elliptical region spanning the MRSI dataset in the x-y plane. — mask_xy_ellipse • Spectroscopy Analysis Tools (spant) Mask a 2D MRSI dataset in the x-y dimension. — mask_xy_mat • Spectroscopy Analysis Tools (spant) Mask a 2D MRSI dataset in the x-y dimension. — mask_xy_mat • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Value
diff --git a/docs/reference/mat2mrs_data.html b/docs/reference/mat2mrs_data.html
index 2e2895f3..ae55665f 100644
--- a/docs/reference/mat2mrs_data.html
+++ b/docs/reference/mat2mrs_data.html
@@ -1,7 +1,5 @@
-Convert a matrix (with spectral points in the column dimension and dynamics
-in the row dimensions) into a mrs_data object. — mat2mrs_data • Spectroscopy Analysis Tools (spant) Convert a matrix (with spectral points in the column dimension and dynamics in the row dimensions) into a mrs_data object. — mat2mrs_data • Spectroscopy Analysis Tools (spant) Matrix exponential function taken from complexplus package to reduce the
-number of spant dependencies. — matexp • Spectroscopy Analysis Tools (spant) Matrix exponential function taken from complexplus package to reduce the number of spant dependencies. — matexp • Spectroscopy Analysis Tools (spant) Apply the max operator to an MRS dataset. — max_mrs • Spectroscopy Analysis Tools (spant) Apply the max operator to an MRS dataset. — max_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/max_mrs_interp.html b/docs/reference/max_mrs_interp.html
index e4474764..52e63f3e 100644
--- a/docs/reference/max_mrs_interp.html
+++ b/docs/reference/max_mrs_interp.html
@@ -1,5 +1,5 @@
-Apply the max operator to an interpolated MRS dataset. — max_mrs_interp • Spectroscopy Analysis Tools (spant) Apply the max operator to an interpolated MRS dataset. — max_mrs_interp • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/mean.list.html b/docs/reference/mean.list.html
index b8eb3463..048306fd 100644
--- a/docs/reference/mean.list.html
+++ b/docs/reference/mean.list.html
@@ -1,5 +1,5 @@
-Calculate the mean spectrum from an mrs_data object. — mean.list • Spectroscopy Analysis Tools (spant) Calculate the mean spectrum from an mrs_data object. — mean.list • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/mean.mrs_data.html b/docs/reference/mean.mrs_data.html
index 5531a28d..79515014 100644
--- a/docs/reference/mean.mrs_data.html
+++ b/docs/reference/mean.mrs_data.html
@@ -1,5 +1,5 @@
-Calculate the mean spectrum from an mrs_data object. — mean.mrs_data • Spectroscopy Analysis Tools (spant) Calculate the mean spectrum from an mrs_data object. — mean.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/mean_dyn_blocks.html b/docs/reference/mean_dyn_blocks.html
index 10467098..4c042448 100644
--- a/docs/reference/mean_dyn_blocks.html
+++ b/docs/reference/mean_dyn_blocks.html
@@ -1,5 +1,5 @@
-Calculate the mean of adjacent dynamic scans. — mean_dyn_blocks • Spectroscopy Analysis Tools (spant) Calculate the mean of adjacent dynamic scans. — mean_dyn_blocks • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/mean_dyn_pairs.html b/docs/reference/mean_dyn_pairs.html
index 63e909ea..1a241126 100644
--- a/docs/reference/mean_dyn_pairs.html
+++ b/docs/reference/mean_dyn_pairs.html
@@ -1,5 +1,5 @@
-Calculate the pairwise means across a dynamic data set. — mean_dyn_pairs • Spectroscopy Analysis Tools (spant) Calculate the pairwise means across a dynamic data set. — mean_dyn_pairs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/mean_dyns.html b/docs/reference/mean_dyns.html
index 73fdbfa7..0daa27df 100644
--- a/docs/reference/mean_dyns.html
+++ b/docs/reference/mean_dyns.html
@@ -1,5 +1,5 @@
-Calculate the mean dynamic data. — mean_dyns • Spectroscopy Analysis Tools (spant) Calculate the mean dynamic data. — mean_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/mean_mrs_list.html b/docs/reference/mean_mrs_list.html
index 808b6c50..10d842c0 100644
--- a/docs/reference/mean_mrs_list.html
+++ b/docs/reference/mean_mrs_list.html
@@ -1,5 +1,5 @@
-Return the mean of a list of mrs_data objects. — mean_mrs_list • Spectroscopy Analysis Tools (spant) Return the mean of a list of mrs_data objects. — mean_mrs_list • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/mean_vec_blocks.html b/docs/reference/mean_vec_blocks.html
index 8fc92eaa..dd78b122 100644
--- a/docs/reference/mean_vec_blocks.html
+++ b/docs/reference/mean_vec_blocks.html
@@ -1,5 +1,5 @@
-Calculate the mean of adjacent blocks in a vector. — mean_vec_blocks • Spectroscopy Analysis Tools (spant) Calculate the mean of adjacent blocks in a vector. — mean_vec_blocks • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/median_dyns.html b/docs/reference/median_dyns.html
index 1039d4b5..9a085b10 100644
--- a/docs/reference/median_dyns.html
+++ b/docs/reference/median_dyns.html
@@ -1,5 +1,5 @@
-Calculate the median dynamic data. — median_dyns • Spectroscopy Analysis Tools (spant) Calculate the median dynamic data. — median_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/mod_td.html b/docs/reference/mod_td.html
index 76ad0a40..141ef09e 100644
--- a/docs/reference/mod_td.html
+++ b/docs/reference/mod_td.html
@@ -1,5 +1,5 @@
-Apply the Modulus operator to the time-domain MRS signal. — mod_td • Spectroscopy Analysis Tools (spant) Apply the Modulus operator to the time-domain MRS signal. — mod_td • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/mrs_data2basis.html b/docs/reference/mrs_data2basis.html
index 62f7d749..11797b91 100644
--- a/docs/reference/mrs_data2basis.html
+++ b/docs/reference/mrs_data2basis.html
@@ -1,7 +1,5 @@
-Convert an mrs_data object to basis object - where basis signals are spread
-across the dynamic dimension in the MRS data. — mrs_data2basis • Spectroscopy Analysis Tools (spant) Convert an mrs_data object to basis object - where basis signals are spread across the dynamic dimension in the MRS data. — mrs_data2basis • Spectroscopy Analysis Tools (spant) Create a BIDS file structure from a vector of MRS data paths or list of mrs_data objects. — mrs_data2bids • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Create a BIDS file structure from a vector of MRS data paths or list of mrs_data objects.
+ Source: R/fmrs.R
+ mrs_data2bids.Rd
+
+
+
+ Create a BIDS file structure from a vector of MRS data paths or list of
+mrs_data objects.
+
+
+
+ mrs_data2bids(
+ mrs_data,
+ output_dir,
+ suffix = NULL,
+ sub = NULL,
+ ses = NULL,
+ task = NULL,
+ acq = NULL,
+ nuc = NULL,
+ voi = NULL,
+ rec = NULL,
+ run = NULL,
+ echo = NULL,
+ inv = NULL,
+ skip_existing = TRUE
+)
+
+
+
+ Arguments
+ - mrs_data
+vector of MRS data paths or list of mrs_data objects.
- output_dir
+the base directory to create the BIDS structure.
- suffix
+optional vector of file suffixes. Default behaviour is to
+automatically determine these from the input data, however it is recommended
+that they are specified to allow more efficient skipping of existing data.
- sub
+optional vector of subject labels. If not specified, these will be
+automatically generated as a series of increasing zero-padded integer values
+corresponding to the mrs_data input indices.
- ses
+optional vector of session labels.
- task
+optional vector of task labels.
- acq
+optional vector of acquisition labels.
- nuc
+optional vector of nucleus labels.
- voi
+optional vector of volume of interest labels.
- rec
+optional vector of reconstruction labels.
- run
+optional vector of run indices.
- echo
+optional vector of echo time indices.
- inv
+optional vector of inversion indices.
- skip_existing
+skip any data files that have already been converted.
+Defaults to TRUE, set to FALSE to force an overwrite of any existing data
+files.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/mrs_data2mat.html b/docs/reference/mrs_data2mat.html
index cf5ff28c..9e47688a 100644
--- a/docs/reference/mrs_data2mat.html
+++ b/docs/reference/mrs_data2mat.html
@@ -1,7 +1,5 @@
-Convert mrs_data object to a matrix, with spectral points in the column
-dimension and dynamics in the row dimension. — mrs_data2mat • Spectroscopy Analysis Tools (spant) Convert mrs_data object to a matrix, with spectral points in the column dimension and dynamics in the row dimension. — mrs_data2mat • Spectroscopy Analysis Tools (spant) Convert mrs_data object to a matrix, with spectral points in the column dimension and dynamics in the row dimension. — mrs_data2spec_mat • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Convert mrs_data object to a matrix, with spectral points in the column dimension and dynamics in the row dimension.
+ Source: R/mrs_data_proc.R
+ mrs_data2spec_mat.Rd
+
+
+
+ Convert mrs_data object to a matrix, with spectral points in the column
+dimension and dynamics in the row dimension.
+
+
+
+ mrs_data2spec_mat(mrs_data, collapse = TRUE)
+
+
+
+ Arguments
+ - mrs_data
+MRS data object or list of MRS data objects.
- collapse
+collapse all other dimensions along the dynamic dimension, eg
+a 16x16 MRSI grid would be first collapsed across 256 dynamic scans.
+
+ Value
+
+
+MRS data matrix.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/mrs_data2vec.html b/docs/reference/mrs_data2vec.html
index fb172d68..a1fd654d 100644
--- a/docs/reference/mrs_data2vec.html
+++ b/docs/reference/mrs_data2vec.html
@@ -1,5 +1,5 @@
-Convert mrs_data object to a vector. — mrs_data2vec • Spectroscopy Analysis Tools (spant) Convert mrs_data object to a vector. — mrs_data2vec • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -126,7 +126,7 @@ Value
diff --git a/docs/reference/mvfftshift.html b/docs/reference/mvfftshift.html
index 92b0841b..976b3410 100644
--- a/docs/reference/mvfftshift.html
+++ b/docs/reference/mvfftshift.html
@@ -1,7 +1,5 @@
-Perform a fftshift on a matrix, with each column replaced by its shifted
-result. — mvfftshift • Spectroscopy Analysis Tools (spant) Perform a fftshift on a matrix, with each column replaced by its shifted result. — mvfftshift • Spectroscopy Analysis Tools (spant) Perform an ifftshift on a matrix, with each column replaced by its shifted
-result. — mvifftshift • Spectroscopy Analysis Tools (spant) Perform an ifftshift on a matrix, with each column replaced by its shifted result. — mvifftshift • Spectroscopy Analysis Tools (spant) Print fit coordinates from a single index. — n2coord • Spectroscopy Analysis Tools (spant) Print fit coordinates from a single index. — n2coord • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/nifti_flip_lr.html b/docs/reference/nifti_flip_lr.html
index 730abe3c..19860b3c 100644
--- a/docs/reference/nifti_flip_lr.html
+++ b/docs/reference/nifti_flip_lr.html
@@ -1,9 +1,5 @@
-Flip the x data dimension order of a nifti image. This corresponds to
-flipping MRI data in the left-right direction, assuming the data in save in
-neurological format (can check with fslorient program). — nifti_flip_lr • Spectroscopy Analysis Tools (spant) Flip the x data dimension order of a nifti image. This corresponds to flipping MRI data in the left-right direction, assuming the data in save in neurological format (can check with fslorient program). — nifti_flip_lr • Spectroscopy Analysis Tools (spant) Export a one-page pdf of a single fit result — one_page_pdf • Spectroscopy Analysis Tools (spant) Export a one-page pdf of a single fit result — one_page_pdf • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -108,7 +108,7 @@ Arguments
diff --git a/docs/reference/ortho3.html b/docs/reference/ortho3.html
index 13ade97d..5d7dd2fd 100644
--- a/docs/reference/ortho3.html
+++ b/docs/reference/ortho3.html
@@ -1,5 +1,5 @@
-Display an orthographic projection plot of a nifti object. — ortho3 • Spectroscopy Analysis Tools (spant) Display an orthographic projection plot of a nifti object. — ortho3 • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -172,7 +172,7 @@ Arguments
diff --git a/docs/reference/ortho3_inter.html b/docs/reference/ortho3_inter.html
index 090cc5e5..15948899 100644
--- a/docs/reference/ortho3_inter.html
+++ b/docs/reference/ortho3_inter.html
@@ -1,5 +1,5 @@
-Display an interactive orthographic projection plot of a nifti object. — ortho3_inter • Spectroscopy Analysis Tools (spant) Display an interactive orthographic projection plot of a nifti object. — ortho3_inter • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -132,7 +132,7 @@ Arguments
diff --git a/docs/reference/peak_info.html b/docs/reference/peak_info.html
index 09058bd8..41c8ffaf 100644
--- a/docs/reference/peak_info.html
+++ b/docs/reference/peak_info.html
@@ -1,7 +1,5 @@
-Search for the highest peak in a spectral region and return the frequency,
-height and FWHM. — peak_info • Spectroscopy Analysis Tools (spant) Search for the highest peak in a spectral region and return the frequency, height and FWHM. — peak_info • Spectroscopy Analysis Tools (spant) Papoulis-Gerchberg (PG) algorithm method for k-space extrapolation. — pg_extrap_xy • Spectroscopy Analysis Tools (spant) Papoulis-Gerchberg (PG) algorithm method for k-space extrapolation. — pg_extrap_xy • Spectroscopy Analysis Tools (spant) Apply phasing parameters to MRS data. — phase • Spectroscopy Analysis Tools (spant) Apply phasing parameters to MRS data. — phase • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/phase_ref_1h_brain.html b/docs/reference/phase_ref_1h_brain.html
new file mode 100644
index 00000000..8707a74a
--- /dev/null
+++ b/docs/reference/phase_ref_1h_brain.html
@@ -0,0 +1,131 @@
+
+Corrected zero order phase and chemical shift offset in 1H MRS data from the brain. — phase_ref_1h_brain • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Corrected zero order phase and chemical shift offset in 1H MRS data from the brain.
+ Source: R/rats.R
+ phase_ref_1h_brain.Rd
+
+
+
+ Corrected zero order phase and chemical shift offset in 1H MRS data from the
+brain.
+
+
+
+ phase_ref_1h_brain(mrs_data, mean_ref = FALSE, ret_corr_only = TRUE)
+
+
+
+ Arguments
+ - mrs_data
+MRS data to be corrected.
- mean_ref
+apply the phase and offset of the mean spectrum to all
+others. Default is FALSE.
- ret_corr_only
+return the corrected data only.
+
+ Value
+
+
+corrected MRS data.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/plot.fit_result.html b/docs/reference/plot.fit_result.html
index e54d3bc1..836a53ee 100644
--- a/docs/reference/plot.fit_result.html
+++ b/docs/reference/plot.fit_result.html
@@ -1,5 +1,5 @@
-Plot the fitting results of an object of class fit_result. — plot.fit_result • Spectroscopy Analysis Tools (spant) Plot the fitting results of an object of class fit_result. — plot.fit_result • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -207,7 +207,7 @@ Arguments
diff --git a/docs/reference/plot.mrs_data.html b/docs/reference/plot.mrs_data.html
index fabcc35b..bb2ec651 100644
--- a/docs/reference/plot.mrs_data.html
+++ b/docs/reference/plot.mrs_data.html
@@ -1,5 +1,5 @@
-Plotting method for objects of class mrs_data. — plot.mrs_data • Spectroscopy Analysis Tools (spant) Plotting method for objects of class mrs_data. — plot.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -287,7 +287,7 @@ Arguments
diff --git a/docs/reference/plot_bc.html b/docs/reference/plot_bc.html
index 4f8309b4..b48142cc 100644
--- a/docs/reference/plot_bc.html
+++ b/docs/reference/plot_bc.html
@@ -1,5 +1,5 @@
-Convenience function to plot a baseline estimate with the original data. — plot_bc • Spectroscopy Analysis Tools (spant) Convenience function to plot a baseline estimate with the original data. — plot_bc • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -108,7 +108,7 @@ Arguments
diff --git a/docs/reference/plot_reg.html b/docs/reference/plot_reg.html
index ae1acbe7..2addb2f6 100644
--- a/docs/reference/plot_reg.html
+++ b/docs/reference/plot_reg.html
@@ -1,5 +1,5 @@
-Plot regressors as an image. — plot_reg • Spectroscopy Analysis Tools (spant) Plot regressors as an image. — plot_reg • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/plot_slice_fit.html b/docs/reference/plot_slice_fit.html
index fbc7b560..57f1af8a 100644
--- a/docs/reference/plot_slice_fit.html
+++ b/docs/reference/plot_slice_fit.html
@@ -1,5 +1,5 @@
-Plot a 2D slice from an MRSI fit result object. — plot_slice_fit • Spectroscopy Analysis Tools (spant) Plot a 2D slice from an MRSI fit result object. — plot_slice_fit • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -129,7 +129,7 @@ Arguments
diff --git a/docs/reference/plot_slice_fit_inter.html b/docs/reference/plot_slice_fit_inter.html
index 4eed104a..da105a7d 100644
--- a/docs/reference/plot_slice_fit_inter.html
+++ b/docs/reference/plot_slice_fit_inter.html
@@ -1,5 +1,5 @@
-Plot a 2D slice from an MRSI fit result object. — plot_slice_fit_inter • Spectroscopy Analysis Tools (spant) Plot a 2D slice from an MRSI fit result object. — plot_slice_fit_inter • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -134,7 +134,7 @@ Arguments
diff --git a/docs/reference/plot_slice_map.html b/docs/reference/plot_slice_map.html
index 553e9ac8..ffb2a134 100644
--- a/docs/reference/plot_slice_map.html
+++ b/docs/reference/plot_slice_map.html
@@ -1,5 +1,5 @@
-Plot a slice from a 7 dimensional array. — plot_slice_map • Spectroscopy Analysis Tools (spant) Plot a slice from a 7 dimensional array. — plot_slice_map • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -153,7 +153,7 @@ Arguments
diff --git a/docs/reference/plot_slice_map_inter.html b/docs/reference/plot_slice_map_inter.html
index 40d33b42..90968f66 100644
--- a/docs/reference/plot_slice_map_inter.html
+++ b/docs/reference/plot_slice_map_inter.html
@@ -1,7 +1,5 @@
-Plot an interactive slice map from a data array where voxels can be selected
-to display a corresponding spectrum. — plot_slice_map_inter • Spectroscopy Analysis Tools (spant) Plot an interactive slice map from a data array where voxels can be selected to display a corresponding spectrum. — plot_slice_map_inter • Spectroscopy Analysis Tools (spant) Plot the spectral standard deviation. — plot_spec_sd • Spectroscopy Analysis Tools (spant) Plot the spectral standard deviation. — plot_spec_sd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Arguments
diff --git a/docs/reference/plot_voi_overlay.html b/docs/reference/plot_voi_overlay.html
index 9a782e88..bbbbf35e 100644
--- a/docs/reference/plot_voi_overlay.html
+++ b/docs/reference/plot_voi_overlay.html
@@ -1,5 +1,5 @@
-Plot a volume as an image overlay. — plot_voi_overlay • Spectroscopy Analysis Tools (spant) Plot a volume as an image overlay. — plot_voi_overlay • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -116,7 +116,7 @@ Arguments
diff --git a/docs/reference/plot_voi_overlay_seg.html b/docs/reference/plot_voi_overlay_seg.html
index 3d4e74ff..0e800ff2 100644
--- a/docs/reference/plot_voi_overlay_seg.html
+++ b/docs/reference/plot_voi_overlay_seg.html
@@ -1,5 +1,5 @@
-Plot a volume as an overlay on a segmented brain volume. — plot_voi_overlay_seg • Spectroscopy Analysis Tools (spant) Plot a volume as an overlay on a segmented brain volume. — plot_voi_overlay_seg • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Arguments
diff --git a/docs/reference/ppm.html b/docs/reference/ppm.html
index c352327a..ee4696e2 100644
--- a/docs/reference/ppm.html
+++ b/docs/reference/ppm.html
@@ -1,5 +1,5 @@
-Return the ppm scale of an MRS dataset or fit result. — ppm • Spectroscopy Analysis Tools (spant) Return the ppm scale of an MRS dataset or fit result. — ppm • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -132,7 +132,7 @@ Value
diff --git a/docs/reference/precomp.html b/docs/reference/precomp.html
index 822d7336..df3d2c6c 100644
--- a/docs/reference/precomp.html
+++ b/docs/reference/precomp.html
@@ -1,7 +1,5 @@
-Save function results to file and load on subsequent calls to avoid repeat
-computation. — precomp • Spectroscopy Analysis Tools (spant) Save function results to file and load on subsequent calls to avoid repeat computation. — precomp • Spectroscopy Analysis Tools (spant) Preprocess and perform quality assessment of a single SVS data set. — preproc_svs • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Preprocess and perform quality assessment of a single SVS data set.
+ Source: R/fmrs.R
+ preproc_svs.Rd
+
+
+
+ Preprocess and perform quality assessment of a single SVS data set.
+
+
+
+ preproc_svs(path, label = NULL, output_dir = NULL, ref_inds = NULL)
+
+
+
+ Arguments
+ - path
+path to the fMRS data file or IMA directory.
- label
+a label to describe the data set.
- output_dir
+output directory.
- ref_inds
+a vector of 1-based indices for any water reference dynamic
+scans.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/preproc_svs_dataset.html b/docs/reference/preproc_svs_dataset.html
new file mode 100644
index 00000000..07c3a29b
--- /dev/null
+++ b/docs/reference/preproc_svs_dataset.html
@@ -0,0 +1,148 @@
+
+Preprocess and perform quality assessment of one or more SVS data sets. — preproc_svs_dataset • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Preprocess and perform quality assessment of one or more SVS data sets.
+ Source: R/fmrs.R
+ preproc_svs_dataset.Rd
+
+
+
+ Preprocess and perform quality assessment of one or more SVS data sets.
+
+
+
+ preproc_svs_dataset(
+ paths,
+ labels = NULL,
+ output_dir = "spant_analysis",
+ exclude_labels = NULL,
+ overwrite = FALSE,
+ ref_inds = NULL,
+ return_results = FALSE
+)
+
+
+
+ Arguments
+ - paths
+paths to the fMRS data file or IMA directory.
- labels
+labels to describe each data set.
- output_dir
+output directory.
- exclude_labels
+vector of labels of scans to exclude, eg poor quality
+data.
- overwrite
+overwrite saved results, defaults to FALSE.
- ref_inds
+a vector of 1-based indices for any water reference dynamic
+scans.
- return_results
+function will return key outputs, defaults to FALSE.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/print.fit_result.html b/docs/reference/print.fit_result.html
index 297f28dc..5f434e57 100644
--- a/docs/reference/print.fit_result.html
+++ b/docs/reference/print.fit_result.html
@@ -1,5 +1,5 @@
-Print a summary of an object of class fit_result. — print.fit_result • Spectroscopy Analysis Tools (spant) Print a summary of an object of class fit_result. — print.fit_result • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -105,7 +105,7 @@ Arguments
diff --git a/docs/reference/print.mrs_data.html b/docs/reference/print.mrs_data.html
index 51199017..e1561eb2 100644
--- a/docs/reference/print.mrs_data.html
+++ b/docs/reference/print.mrs_data.html
@@ -1,5 +1,5 @@
-Print a summary of mrs_data parameters. — print.mrs_data • Spectroscopy Analysis Tools (spant) Print a summary of mrs_data parameters. — print.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -109,7 +109,7 @@ Arguments
diff --git a/docs/reference/qn_states.html b/docs/reference/qn_states.html
index 0f42f2f9..d7aa6715 100644
--- a/docs/reference/qn_states.html
+++ b/docs/reference/qn_states.html
@@ -1,5 +1,5 @@
-Get the quantum coherence matrix for a spin system. — qn_states • Spectroscopy Analysis Tools (spant) Get the quantum coherence matrix for a spin system. — qn_states • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/rats.html b/docs/reference/rats.html
index 5a39a396..93585e08 100644
--- a/docs/reference/rats.html
+++ b/docs/reference/rats.html
@@ -1,5 +1,5 @@
-Robust Alignment to a Target Spectrum (RATS). — rats • Spectroscopy Analysis Tools (spant) Robust Alignment to a Target Spectrum (RATS). — rats • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -207,7 +207,7 @@ Value
diff --git a/docs/reference/re_weighting.html b/docs/reference/re_weighting.html
index d21caf21..8b0b070a 100644
--- a/docs/reference/re_weighting.html
+++ b/docs/reference/re_weighting.html
@@ -1,5 +1,5 @@
-Apply a weighting to the FID to enhance spectral resolution. — re_weighting • Spectroscopy Analysis Tools (spant) Apply a weighting to the FID to enhance spectral resolution. — re_weighting • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/read_basis.html b/docs/reference/read_basis.html
index da9b94af..eb6f8557 100644
--- a/docs/reference/read_basis.html
+++ b/docs/reference/read_basis.html
@@ -1,5 +1,5 @@
-Read a basis file in LCModel .basis format. — read_basis • Spectroscopy Analysis Tools (spant) Read a basis file in LCModel .basis format. — read_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/read_ima_coil_dir.html b/docs/reference/read_ima_coil_dir.html
index 28c02de0..4f073cd8 100644
--- a/docs/reference/read_ima_coil_dir.html
+++ b/docs/reference/read_ima_coil_dir.html
@@ -1,9 +1,5 @@
-Read a directory containing Siemens MRS IMA files and combine along the coil
-dimension. Note that the coil ID is inferred from the sorted file name and
-should be checked when consistency is required between two directories. — read_ima_coil_dir • Spectroscopy Analysis Tools (spant) Read a directory containing Siemens MRS IMA files and combine along the coil dimension. Note that the coil ID is inferred from the sorted file name and should be checked when consistency is required between two directories. — read_ima_coil_dir • Spectroscopy Analysis Tools (spant) Read a directory containing Siemens MRS IMA files and combine along the
-dynamic dimension. Note that the coil ID is inferred from the sorted file
-name and should be checked when consistency is required. — read_ima_dyn_dir • Spectroscopy Analysis Tools (spant) Read a directory containing Siemens MRS IMA files and combine along the dynamic dimension. Note that the coil ID is inferred from the sorted file name and should be checked when consistency is required. — read_ima_dyn_dir • Spectroscopy Analysis Tools (spant) Read an LCModel formatted coord file containing fit information. — read_lcm_coord • Spectroscopy Analysis Tools (spant) Read an LCModel formatted coord file containing fit information. — read_lcm_coord • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -107,7 +107,7 @@ Value
diff --git a/docs/reference/read_mrs.html b/docs/reference/read_mrs.html
index 3ac2a36b..2cf36b20 100644
--- a/docs/reference/read_mrs.html
+++ b/docs/reference/read_mrs.html
@@ -1,5 +1,5 @@
-Read MRS data from a file. — read_mrs • Spectroscopy Analysis Tools (spant) Read MRS data from a file. — read_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -88,7 +88,8 @@ Read MRS data from a file.
full_fid = FALSE,
omit_svs_ref_scans = TRUE,
verbose = FALSE,
- extra = NULL
+ extra = NULL,
+ fid_filt_dist = NULL
)
@@ -140,6 +141,13 @@ Arguments
an optional data frame to provide additional variables for use
in subsequent analysis steps, eg id or grouping variables.
fid_filt_dist
+indicate if the data has a distorted FID due to a
+brick-wall filter being used to downsample the data. Default is to auto
+detect this from the data, but TRUE or FALSE options can be given to override
+detection.
Value
@@ -183,7 +191,7 @@ Examples
diff --git a/docs/reference/read_mrs_tqn.html b/docs/reference/read_mrs_tqn.html
index 5766362f..84bdaf3a 100644
--- a/docs/reference/read_mrs_tqn.html
+++ b/docs/reference/read_mrs_tqn.html
@@ -1,5 +1,5 @@
-Read MRS data using the TARQUIN software package. — read_mrs_tqn • Spectroscopy Analysis Tools (spant) Read MRS data using the TARQUIN software package. — read_mrs_tqn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -131,7 +131,7 @@ Examples
diff --git a/docs/reference/read_pulse_ascii.html b/docs/reference/read_pulse_ascii.html
index c9e0d43c..ab11c9cc 100644
--- a/docs/reference/read_pulse_ascii.html
+++ b/docs/reference/read_pulse_ascii.html
@@ -1,5 +1,5 @@
-Read an ASCII formatted pulse file. — read_pulse_ascii • Spectroscopy Analysis Tools (spant) Read an ASCII formatted pulse file. — read_pulse_ascii • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/read_pulse_bruker.html b/docs/reference/read_pulse_bruker.html
index c92bf76a..dbe9073b 100644
--- a/docs/reference/read_pulse_bruker.html
+++ b/docs/reference/read_pulse_bruker.html
@@ -1,5 +1,5 @@
-Read a Bruker formatted pulse file — read_pulse_bruker • Spectroscopy Analysis Tools (spant) Read a Bruker formatted pulse file — read_pulse_bruker • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/read_pulse_pta.html b/docs/reference/read_pulse_pta.html
index 72e1b6d4..a0fac3c3 100644
--- a/docs/reference/read_pulse_pta.html
+++ b/docs/reference/read_pulse_pta.html
@@ -1,5 +1,5 @@
-Read a .pta formatted pulse file compatible with Siemens PulseTool. — read_pulse_pta • Spectroscopy Analysis Tools (spant) Read a .pta formatted pulse file compatible with Siemens PulseTool. — read_pulse_pta • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/read_siemens_txt_hdr.html b/docs/reference/read_siemens_txt_hdr.html
index 23fb8c70..3a17d87c 100644
--- a/docs/reference/read_siemens_txt_hdr.html
+++ b/docs/reference/read_siemens_txt_hdr.html
@@ -1,5 +1,5 @@
-Read the text format header found in Siemens IMA and TWIX data files. — read_siemens_txt_hdr • Spectroscopy Analysis Tools (spant) Read the text format header found in Siemens IMA and TWIX data files. — read_siemens_txt_hdr • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -78,7 +78,7 @@ Read the text format header found in Siemens IMA and TWIX data files.
- read_siemens_txt_hdr(input, version = "vd", verbose, offset = 0)
+ read_siemens_txt_hdr(input, version = "vd", verbose = FALSE, offset = 0)
@@ -118,7 +118,7 @@ Value
diff --git a/docs/reference/read_tqn_fit.html b/docs/reference/read_tqn_fit.html
index 4da6c25e..a1630420 100644
--- a/docs/reference/read_tqn_fit.html
+++ b/docs/reference/read_tqn_fit.html
@@ -1,5 +1,5 @@
-Reader for csv fit results generated by TARQUIN. — read_tqn_fit • Spectroscopy Analysis Tools (spant) Reader for csv fit results generated by TARQUIN. — read_tqn_fit • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -113,7 +113,7 @@ Examples
diff --git a/docs/reference/read_tqn_result.html b/docs/reference/read_tqn_result.html
index 36659714..68a3e98c 100644
--- a/docs/reference/read_tqn_result.html
+++ b/docs/reference/read_tqn_result.html
@@ -1,5 +1,5 @@
-Reader for csv results generated by TARQUIN. — read_tqn_result • Spectroscopy Analysis Tools (spant) Reader for csv results generated by TARQUIN. — read_tqn_result • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -117,7 +117,7 @@ Examples
diff --git a/docs/reference/recon_imag.html b/docs/reference/recon_imag.html
index d2a72225..5bc3b1eb 100644
--- a/docs/reference/recon_imag.html
+++ b/docs/reference/recon_imag.html
@@ -1,7 +1,5 @@
-Reconstruct complex time-domain data from the real part of frequency-domain
-data. — recon_imag • Spectroscopy Analysis Tools (spant) Reconstruct complex time-domain data from the real part of frequency-domain data. — recon_imag • Spectroscopy Analysis Tools (spant) Reconstruct complex time-domain data from the real part of frequency-domain
-data. — recon_imag_vec • Spectroscopy Analysis Tools (spant) Reconstruct complex time-domain data from the real part of frequency-domain data. — recon_imag_vec • Spectroscopy Analysis Tools (spant) Reconstruct 2D MRSI data from a twix file loaded with read_mrs. — recon_twix_2d_mrsi • Spectroscopy Analysis Tools (spant) Reconstruct 2D MRSI data from a twix file loaded with read_mrs. — recon_twix_2d_mrsi • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/rectangular_mask.html b/docs/reference/rectangular_mask.html
index a2117283..6e469bc9 100644
--- a/docs/reference/rectangular_mask.html
+++ b/docs/reference/rectangular_mask.html
@@ -1,5 +1,5 @@
-Create a rectangular mask stored as a matrix of logical values. — rectangular_mask • Spectroscopy Analysis Tools (spant) Create a rectangular mask stored as a matrix of logical values. — rectangular_mask • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -130,7 +130,7 @@ Value
diff --git a/docs/reference/reexports.html b/docs/reference/reexports.html
index 694a75d1..a59e8379 100644
--- a/docs/reference/reexports.html
+++ b/docs/reference/reexports.html
@@ -1,5 +1,5 @@
-Objects exported from other packages — reexports • Spectroscopy Analysis Tools (spant) Objects exported from other packages — reexports • Spectroscopy Analysis Tools (spant)
Spectroscopy Analysis Tools (spant)
- 2.21.0
+ 2.22.0
@@ -103,7 +103,7 @@ Objects exported from other packages
diff --git a/docs/reference/rep_array_dim.html b/docs/reference/rep_array_dim.html
index b9c49b4a..48c0a5ed 100644
--- a/docs/reference/rep_array_dim.html
+++ b/docs/reference/rep_array_dim.html
@@ -1,5 +1,5 @@
-Repeat an array over a given dimension. — rep_array_dim • Spectroscopy Analysis Tools (spant) Repeat an array over a given dimension. — rep_array_dim • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/rep_dyn.html b/docs/reference/rep_dyn.html
index 6bbfb0ef..89a4bb9b 100644
--- a/docs/reference/rep_dyn.html
+++ b/docs/reference/rep_dyn.html
@@ -1,5 +1,5 @@
-Replicate a scan in the dynamic dimension. — rep_dyn • Spectroscopy Analysis Tools (spant) Replicate a scan in the dynamic dimension. — rep_dyn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/rep_mrs.html b/docs/reference/rep_mrs.html
index 67730b5c..becb8f00 100644
--- a/docs/reference/rep_mrs.html
+++ b/docs/reference/rep_mrs.html
@@ -1,5 +1,5 @@
-Replicate a scan over a given dimension. — rep_mrs • Spectroscopy Analysis Tools (spant) Replicate a scan over a given dimension. — rep_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -138,7 +138,7 @@ Value
diff --git a/docs/reference/resample_basis.html b/docs/reference/resample_basis.html
index b0f2ab17..c7a6222a 100644
--- a/docs/reference/resample_basis.html
+++ b/docs/reference/resample_basis.html
@@ -1,5 +1,5 @@
-Resample a basis-set to match a mrs_data acquisition. — resample_basis • Spectroscopy Analysis Tools (spant) Resample a basis-set to match a mrs_data acquisition. — resample_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -116,7 +116,7 @@ Value
diff --git a/docs/reference/resample_img.html b/docs/reference/resample_img.html
index f1e7beaf..b0cc8f71 100644
--- a/docs/reference/resample_img.html
+++ b/docs/reference/resample_img.html
@@ -1,5 +1,5 @@
-Resample an image to match a target image space. — resample_img • Spectroscopy Analysis Tools (spant) Resample an image to match a target image space. — resample_img • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/resample_voi.html b/docs/reference/resample_voi.html
index 8fbfa836..a29ab096 100644
--- a/docs/reference/resample_voi.html
+++ b/docs/reference/resample_voi.html
@@ -1,7 +1,5 @@
-Resample a VOI to match a target image space using nearest-neighbour
-interpolation. — resample_voi • Spectroscopy Analysis Tools (spant) Resample a VOI to match a target image space using nearest-neighbour interpolation. — resample_voi • Spectroscopy Analysis Tools (spant) Reslice a nifti object to match the orientation of mrs data. — reslice_to_mrs • Spectroscopy Analysis Tools (spant) Reslice a nifti object to match the orientation of mrs data. — reslice_to_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/reson_table2mrs_data.html b/docs/reference/reson_table2mrs_data.html
index d75579ee..c5a2167a 100644
--- a/docs/reference/reson_table2mrs_data.html
+++ b/docs/reference/reson_table2mrs_data.html
@@ -1,5 +1,5 @@
-Generate mrs_data from a table of single Lorentzian resonances. — reson_table2mrs_data • Spectroscopy Analysis Tools (spant) Generate mrs_data from a table of single Lorentzian resonances. — reson_table2mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -119,7 +119,7 @@ Value
diff --git a/docs/reference/rm_dyns.html b/docs/reference/rm_dyns.html
index 5d5ef692..573e1f51 100644
--- a/docs/reference/rm_dyns.html
+++ b/docs/reference/rm_dyns.html
@@ -1,5 +1,5 @@
-Remove a subset of dynamic scans. — rm_dyns • Spectroscopy Analysis Tools (spant) Remove a subset of dynamic scans. — rm_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/scale_amp_molal.html b/docs/reference/scale_amp_molal.html
index aaeee1f2..7acb8cb0 100644
--- a/docs/reference/scale_amp_molal.html
+++ b/docs/reference/scale_amp_molal.html
@@ -1,7 +1,5 @@
-Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water). — scale_amp_molal • Spectroscopy Analysis Tools (spant) Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / kg of tissue water). — scale_amp_molal • Spectroscopy Analysis Tools (spant)
Spectroscopy Analysis Tools (spant)
- 2.21.0
+ 2.22.0
@@ -76,8 +74,7 @@
- Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water).
+ Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / kg of tissue water).
Source: R/amp_scaling.R
scale_amp_molal.Rd
@@ -163,7 +160,7 @@ Value
diff --git a/docs/reference/scale_amp_molal_pvc.html b/docs/reference/scale_amp_molal_pvc.html
index 962d6afc..4d194abd 100644
--- a/docs/reference/scale_amp_molal_pvc.html
+++ b/docs/reference/scale_amp_molal_pvc.html
@@ -1,7 +1,5 @@
-Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water). — scale_amp_molal_pvc • Spectroscopy Analysis Tools (spant)
@@ -75,8 +73,7 @@
- Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water).
+ Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / kg of tissue water).
Source: R/amp_scaling.R
scale_amp_molal_pvc.Rd
@@ -141,7 +138,7 @@ Value
diff --git a/docs/reference/scale_amp_molar.html b/docs/reference/scale_amp_molar.html
index 02358d91..dc87a338 100644
--- a/docs/reference/scale_amp_molar.html
+++ b/docs/reference/scale_amp_molar.html
@@ -1,7 +1,5 @@
-Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / Litre of tissue). — scale_amp_molar • Spectroscopy Analysis Tools (spant) Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / Litre of tissue). — scale_amp_molar • Spectroscopy Analysis Tools (spant) Convert default LCM/TARQUIN concentration scaling to molal units with partial
-volume correction. — scale_amp_molar2molal_pvc • Spectroscopy Analysis Tools (spant) Convert default LCM/TARQUIN concentration scaling to molal units with partial volume correction. — scale_amp_molar2molal_pvc • Spectroscopy Analysis Tools (spant) Scale fitted amplitudes to a ratio of signal amplitude. — scale_amp_ratio • Spectroscopy Analysis Tools (spant) Scale fitted amplitudes to a ratio of signal amplitude. — scale_amp_ratio • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -116,7 +116,7 @@ Value
diff --git a/docs/reference/scale_amp_ratio_value.html b/docs/reference/scale_amp_ratio_value.html
index 2036837a..6af8ac51 100644
--- a/docs/reference/scale_amp_ratio_value.html
+++ b/docs/reference/scale_amp_ratio_value.html
@@ -1,5 +1,5 @@
-Scale fitted amplitudes to a ratio of signal amplitude. — scale_amp_ratio_value • Spectroscopy Analysis Tools (spant) Scale fitted amplitudes to a ratio of signal amplitude. — scale_amp_ratio_value • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/scale_amp_water_ratio.html b/docs/reference/scale_amp_water_ratio.html
index 5b25e884..35a76b00 100644
--- a/docs/reference/scale_amp_water_ratio.html
+++ b/docs/reference/scale_amp_water_ratio.html
@@ -1,5 +1,5 @@
-Scale metabolite amplitudes as a ratio to the unsuppressed water amplitude. — scale_amp_water_ratio • Spectroscopy Analysis Tools (spant) Scale metabolite amplitudes as a ratio to the unsuppressed water amplitude. — scale_amp_water_ratio • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/scale_basis_amp.html b/docs/reference/scale_basis_amp.html
index 9401c3f1..5a58b5e5 100644
--- a/docs/reference/scale_basis_amp.html
+++ b/docs/reference/scale_basis_amp.html
@@ -1,5 +1,5 @@
-Scale a basis object by a scalar. — scale_basis_amp • Spectroscopy Analysis Tools (spant) Scale a basis object by a scalar. — scale_basis_amp • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/scale_basis_from_singlet.html b/docs/reference/scale_basis_from_singlet.html
index 0d542bc8..c9a19e77 100644
--- a/docs/reference/scale_basis_from_singlet.html
+++ b/docs/reference/scale_basis_from_singlet.html
@@ -1,5 +1,5 @@
-Scale a basis-set to be consistent with spant assumptions for water scaling. — scale_basis_from_singlet • Spectroscopy Analysis Tools (spant) Scale a basis-set to be consistent with spant assumptions for water scaling. — scale_basis_from_singlet • Spectroscopy Analysis Tools (spant)
Spectroscopy Analysis Tools (spant)
- 2.21.0
+ 2.22.0
@@ -127,7 +127,7 @@ Value
diff --git a/docs/reference/scale_mrs_amp.html b/docs/reference/scale_mrs_amp.html
index b5501a0d..990f058a 100644
--- a/docs/reference/scale_mrs_amp.html
+++ b/docs/reference/scale_mrs_amp.html
@@ -1,5 +1,5 @@
-Scale an mrs_data object by a scalar or vector or amplitudes. — scale_mrs_amp • Spectroscopy Analysis Tools (spant) Scale an mrs_data object by a scalar or vector or amplitudes. — scale_mrs_amp • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/scale_spec.html b/docs/reference/scale_spec.html
index 4f6ea835..6b3ddba4 100644
--- a/docs/reference/scale_spec.html
+++ b/docs/reference/scale_spec.html
@@ -1,5 +1,5 @@
-Scale mrs_data to a spectral region. — scale_spec • Spectroscopy Analysis Tools (spant) Scale mrs_data to a spectral region. — scale_spec • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -141,7 +141,7 @@ Value
diff --git a/docs/reference/sd.html b/docs/reference/sd.html
index ea1eec9f..3ae4dfd4 100644
--- a/docs/reference/sd.html
+++ b/docs/reference/sd.html
@@ -1,5 +1,5 @@
-Calculate the standard deviation spectrum from an mrs_data object. — sd • Spectroscopy Analysis Tools (spant) Calculate the standard deviation spectrum from an mrs_data object. — sd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/sd.mrs_data.html b/docs/reference/sd.mrs_data.html
index 3f92a49f..13bdda85 100644
--- a/docs/reference/sd.mrs_data.html
+++ b/docs/reference/sd.mrs_data.html
@@ -1,5 +1,5 @@
-Calculate the standard deviation spectrum from an mrs_data object. — sd.mrs_data • Spectroscopy Analysis Tools (spant) Calculate the standard deviation spectrum from an mrs_data object. — sd.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/seconds.html b/docs/reference/seconds.html
index b34d6627..467ee17f 100644
--- a/docs/reference/seconds.html
+++ b/docs/reference/seconds.html
@@ -1,5 +1,5 @@
-Return a time scale vector to match the FID of an MRS data object. — seconds • Spectroscopy Analysis Tools (spant) Return a time scale vector to match the FID of an MRS data object. — seconds • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/seq_cpmg_ideal.html b/docs/reference/seq_cpmg_ideal.html
index 547e96ab..45727c86 100644
--- a/docs/reference/seq_cpmg_ideal.html
+++ b/docs/reference/seq_cpmg_ideal.html
@@ -1,5 +1,5 @@
-CPMG style sequence with ideal pulses. — seq_cpmg_ideal • Spectroscopy Analysis Tools (spant) CPMG style sequence with ideal pulses. — seq_cpmg_ideal • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/seq_mega_press_ideal.html b/docs/reference/seq_mega_press_ideal.html
index 0769b8b4..a9cd7fa0 100644
--- a/docs/reference/seq_mega_press_ideal.html
+++ b/docs/reference/seq_mega_press_ideal.html
@@ -1,7 +1,5 @@
-MEGA-PRESS sequence with ideal localisation pulses and Gaussian shaped
-editing pulse. — seq_mega_press_ideal • Spectroscopy Analysis Tools (spant) MEGA-PRESS sequence with ideal localisation pulses and Gaussian shaped editing pulse. — seq_mega_press_ideal • Spectroscopy Analysis Tools (spant) PRESS sequence with shaped refocusing pulses. — seq_press_2d_shaped • Spectroscopy Analysis Tools (spant) PRESS sequence with shaped refocusing pulses. — seq_press_2d_shaped • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -165,7 +165,7 @@ Value
diff --git a/docs/reference/seq_press_ideal.html b/docs/reference/seq_press_ideal.html
index 8c976856..72c3af3d 100644
--- a/docs/reference/seq_press_ideal.html
+++ b/docs/reference/seq_press_ideal.html
@@ -1,5 +1,5 @@
-PRESS sequence with ideal pulses. — seq_press_ideal • Spectroscopy Analysis Tools (spant) PRESS sequence with ideal pulses. — seq_press_ideal • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/seq_pulse_acquire.html b/docs/reference/seq_pulse_acquire.html
index 4a88fc64..ad80571e 100644
--- a/docs/reference/seq_pulse_acquire.html
+++ b/docs/reference/seq_pulse_acquire.html
@@ -1,5 +1,5 @@
-Simple pulse and acquire sequence with ideal pulses. — seq_pulse_acquire • Spectroscopy Analysis Tools (spant) Simple pulse and acquire sequence with ideal pulses. — seq_pulse_acquire • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/seq_slaser_ideal.html b/docs/reference/seq_slaser_ideal.html
index 74688f4d..eb83e8e3 100644
--- a/docs/reference/seq_slaser_ideal.html
+++ b/docs/reference/seq_slaser_ideal.html
@@ -1,5 +1,5 @@
-sLASER sequence with ideal pulses. — seq_slaser_ideal • Spectroscopy Analysis Tools (spant) sLASER sequence with ideal pulses. — seq_slaser_ideal • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -126,7 +126,7 @@ Value
diff --git a/docs/reference/seq_spin_echo_ideal.html b/docs/reference/seq_spin_echo_ideal.html
index e23271de..4248716f 100644
--- a/docs/reference/seq_spin_echo_ideal.html
+++ b/docs/reference/seq_spin_echo_ideal.html
@@ -1,5 +1,5 @@
-Spin echo sequence with ideal pulses. — seq_spin_echo_ideal • Spectroscopy Analysis Tools (spant) Spin echo sequence with ideal pulses. — seq_spin_echo_ideal • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/seq_steam_ideal.html b/docs/reference/seq_steam_ideal.html
index a60685a8..1c8115d7 100644
--- a/docs/reference/seq_steam_ideal.html
+++ b/docs/reference/seq_steam_ideal.html
@@ -1,5 +1,5 @@
-STEAM sequence with ideal pulses. — seq_steam_ideal • Spectroscopy Analysis Tools (spant) STEAM sequence with ideal pulses. — seq_steam_ideal • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -128,7 +128,7 @@ Value
diff --git a/docs/reference/seq_steam_ideal_cof.html b/docs/reference/seq_steam_ideal_cof.html
index 8f225740..cba7af91 100644
--- a/docs/reference/seq_steam_ideal_cof.html
+++ b/docs/reference/seq_steam_ideal_cof.html
@@ -1,7 +1,5 @@
-STEAM sequence with ideal pulses and coherence order filtering to simulate
-gradient crushers. — seq_steam_ideal_cof • Spectroscopy Analysis Tools (spant) STEAM sequence with ideal pulses and coherence order filtering to simulate gradient crushers. — seq_steam_ideal_cof • Spectroscopy Analysis Tools (spant) STEAM sequence with ideal pulses using the z-rotation gradient simulation
-method described by Young et al JMR 140, 146-152 (1999). — seq_steam_ideal_young • Spectroscopy Analysis Tools (spant) STEAM sequence with ideal pulses using the z-rotation gradient simulation method described by Young et al JMR 140, 146-152 (1999). — seq_steam_ideal_young • Spectroscopy Analysis Tools (spant) Set the number of transients for an mrs_data object. — set_Ntrans • Spectroscopy Analysis Tools (spant) Set the number of transients for an mrs_data object. — set_Ntrans • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/set_def_acq_paras.html b/docs/reference/set_def_acq_paras.html
index 3e1b4004..cc2ada9c 100644
--- a/docs/reference/set_def_acq_paras.html
+++ b/docs/reference/set_def_acq_paras.html
@@ -1,5 +1,5 @@
-Set the default acquisition parameters. — set_def_acq_paras • Spectroscopy Analysis Tools (spant) Set the default acquisition parameters. — set_def_acq_paras • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Arguments
diff --git a/docs/reference/set_lcm_cmd.html b/docs/reference/set_lcm_cmd.html
index 2056ed01..42bb2f24 100644
--- a/docs/reference/set_lcm_cmd.html
+++ b/docs/reference/set_lcm_cmd.html
@@ -1,5 +1,5 @@
-Set the command to run the LCModel command-line program. — set_lcm_cmd • Spectroscopy Analysis Tools (spant) Set the command to run the LCModel command-line program. — set_lcm_cmd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/set_lw.html b/docs/reference/set_lw.html
index b64ec851..bb176c62 100644
--- a/docs/reference/set_lw.html
+++ b/docs/reference/set_lw.html
@@ -1,5 +1,5 @@
-Apply line-broadening to an mrs_data object to achieve a specified linewidth. — set_lw • Spectroscopy Analysis Tools (spant) Apply line-broadening to an mrs_data object to achieve a specified linewidth. — set_lw • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -123,7 +123,7 @@ Value
diff --git a/docs/reference/set_mask_xy_mat.html b/docs/reference/set_mask_xy_mat.html
index 49dc5d4e..52c4b617 100644
--- a/docs/reference/set_mask_xy_mat.html
+++ b/docs/reference/set_mask_xy_mat.html
@@ -1,5 +1,5 @@
-Set the masked voxels in a 2D MRSI dataset to given spectrum. — set_mask_xy_mat • Spectroscopy Analysis Tools (spant) Set the masked voxels in a 2D MRSI dataset to given spectrum. — set_mask_xy_mat • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Value
diff --git a/docs/reference/set_precomp_mode.html b/docs/reference/set_precomp_mode.html
index f44bd5d3..47c28e3b 100644
--- a/docs/reference/set_precomp_mode.html
+++ b/docs/reference/set_precomp_mode.html
@@ -1,5 +1,5 @@
-Set the precompute mode. — set_precomp_mode • Spectroscopy Analysis Tools (spant) Set the precompute mode. — set_precomp_mode • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/set_precomp_verbose.html b/docs/reference/set_precomp_verbose.html
index 1453a231..9c613505 100644
--- a/docs/reference/set_precomp_verbose.html
+++ b/docs/reference/set_precomp_verbose.html
@@ -1,5 +1,5 @@
-Set the verbosity of the precompute function. — set_precomp_verbose • Spectroscopy Analysis Tools (spant) Set the verbosity of the precompute function. — set_precomp_verbose • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/set_ref.html b/docs/reference/set_ref.html
index 8953fa50..5436dfa2 100644
--- a/docs/reference/set_ref.html
+++ b/docs/reference/set_ref.html
@@ -1,5 +1,5 @@
-Set the ppm reference value (eg ppm value at 0Hz). — set_ref • Spectroscopy Analysis Tools (spant) Set the ppm reference value (eg ppm value at 0Hz). — set_ref • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/set_td_pts.html b/docs/reference/set_td_pts.html
index 8a80d42a..586459ff 100644
--- a/docs/reference/set_td_pts.html
+++ b/docs/reference/set_td_pts.html
@@ -1,7 +1,5 @@
-Set the number of time-domain data points, truncating or zero-filling as
-appropriate. — set_td_pts • Spectroscopy Analysis Tools (spant) Set the number of time-domain data points, truncating or zero-filling as appropriate. — set_td_pts • Spectroscopy Analysis Tools (spant) Set the command to run the TARQUIN command-line program. — set_tqn_cmd • Spectroscopy Analysis Tools (spant) Set the command to run the TARQUIN command-line program. — set_tqn_cmd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/set_tr.html b/docs/reference/set_tr.html
index b2109ab0..65c9df5f 100644
--- a/docs/reference/set_tr.html
+++ b/docs/reference/set_tr.html
@@ -1,5 +1,5 @@
-Set the repetition time of an MRS dataset. — set_tr • Spectroscopy Analysis Tools (spant) Set the repetition time of an MRS dataset. — set_tr • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/shift.html b/docs/reference/shift.html
index ab0fe724..034591d0 100644
--- a/docs/reference/shift.html
+++ b/docs/reference/shift.html
@@ -1,5 +1,5 @@
-Apply a frequency shift to MRS data. — shift • Spectroscopy Analysis Tools (spant) Apply a frequency shift to MRS data. — shift • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/shift_basis.html b/docs/reference/shift_basis.html
index 2884be19..f55a65e0 100644
--- a/docs/reference/shift_basis.html
+++ b/docs/reference/shift_basis.html
@@ -1,5 +1,5 @@
-Apply frequency shifts to basis set signals. — shift_basis • Spectroscopy Analysis Tools (spant) Apply frequency shifts to basis set signals. — shift_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Value
diff --git a/docs/reference/sim_basis.html b/docs/reference/sim_basis.html
index c7838c46..bb5fefc6 100644
--- a/docs/reference/sim_basis.html
+++ b/docs/reference/sim_basis.html
@@ -1,5 +1,5 @@
-Simulate a basis set object. — sim_basis • Spectroscopy Analysis Tools (spant) Simulate a basis set object. — sim_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -136,7 +136,7 @@ Value
diff --git a/docs/reference/sim_basis_1h_brain.html b/docs/reference/sim_basis_1h_brain.html
index 62ed7389..f71ffa0b 100644
--- a/docs/reference/sim_basis_1h_brain.html
+++ b/docs/reference/sim_basis_1h_brain.html
@@ -1,7 +1,5 @@
-Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS
-sequence. Note, ideal pulses are assumed. — sim_basis_1h_brain • Spectroscopy Analysis Tools (spant) Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS sequence. Note, ideal pulses are assumed. — sim_basis_1h_brain • Spectroscopy Analysis Tools (spant) Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS
-sequence. Note, ideal pulses are assumed. — sim_basis_1h_brain_press • Spectroscopy Analysis Tools (spant) Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS sequence. Note, ideal pulses are assumed. — sim_basis_1h_brain_press • Spectroscopy Analysis Tools (spant) Simulate a macromolecular and lipid basis-set suitable for 1H brain MRS
-analysis. — sim_basis_mm_lip_lcm • Spectroscopy Analysis Tools (spant) Simulate a macromolecular and lipid basis-set suitable for 1H brain MRS analysis. — sim_basis_mm_lip_lcm • Spectroscopy Analysis Tools (spant) Simulate a basis file using TARQUIN. — sim_basis_tqn • Spectroscopy Analysis Tools (spant) Simulate a basis file using TARQUIN. — sim_basis_tqn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -129,7 +129,7 @@ Examples
diff --git a/docs/reference/sim_brain_1h.html b/docs/reference/sim_brain_1h.html
index 2044cf1a..717ee289 100644
--- a/docs/reference/sim_brain_1h.html
+++ b/docs/reference/sim_brain_1h.html
@@ -1,5 +1,5 @@
-Simulate MRS data with a similar appearance to normal brain (by default). — sim_brain_1h • Spectroscopy Analysis Tools (spant) Simulate MRS data with a similar appearance to normal brain (by default). — sim_brain_1h • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -159,7 +159,7 @@ Value
diff --git a/docs/reference/sim_mol.html b/docs/reference/sim_mol.html
index 23bcef50..77f76a50 100644
--- a/docs/reference/sim_mol.html
+++ b/docs/reference/sim_mol.html
@@ -1,5 +1,5 @@
-Simulate a mol_parameter object. — sim_mol • Spectroscopy Analysis Tools (spant) Simulate a mol_parameter object. — sim_mol • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -143,7 +143,7 @@ Value
diff --git a/docs/reference/sim_noise.html b/docs/reference/sim_noise.html
index 23875f79..a71477d4 100644
--- a/docs/reference/sim_noise.html
+++ b/docs/reference/sim_noise.html
@@ -1,5 +1,5 @@
-Simulate an mrs_data object containing simulated Gaussian noise. — sim_noise • Spectroscopy Analysis Tools (spant) Simulate an mrs_data object containing simulated Gaussian noise. — sim_noise • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -84,6 +84,7 @@ Simulate an mrs_data object containing simulated Gaussian noise.
ft = def_ft(),
N = def_N(),
ref = def_ref(),
+ nuc = def_nuc(),
dyns = 1,
fd = TRUE
)
@@ -111,6 +112,10 @@ Arguments
reference value for ppm scale.
nuc
+resonant nucleus.
dyns
number of dynamic scans to generate.
Value
diff --git a/docs/reference/sim_resonances.html b/docs/reference/sim_resonances.html
index 19e9a8a4..d4f8d7c0 100644
--- a/docs/reference/sim_resonances.html
+++ b/docs/reference/sim_resonances.html
@@ -1,5 +1,5 @@
-Simulate a MRS data object containing a set of simulated resonances. — sim_resonances • Spectroscopy Analysis Tools (spant) Simulate a MRS data object containing a set of simulated resonances. — sim_resonances • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -161,7 +161,7 @@ Examples
diff --git a/docs/reference/sim_th_excit_profile.html b/docs/reference/sim_th_excit_profile.html
index 5535c5ef..e781cab1 100644
--- a/docs/reference/sim_th_excit_profile.html
+++ b/docs/reference/sim_th_excit_profile.html
@@ -1,7 +1,5 @@
-Simulate an ideal pulse excitation profile by smoothing a top-hat function
-with a Gaussian. — sim_th_excit_profile • Spectroscopy Analysis Tools (spant) Simulate an ideal pulse excitation profile by smoothing a top-hat function with a Gaussian. — sim_th_excit_profile • Spectroscopy Analysis Tools (spant) Simulate an mrs_data object containing complex zero valued samples. — sim_zero • Spectroscopy Analysis Tools (spant) Simulate an mrs_data object containing complex zero valued samples. — sim_zero • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -78,7 +78,14 @@ Simulate an mrs_data object containing complex zero valued samples.
-
+
@@ -99,6 +106,10 @@ Arguments
reference value for ppm scale.
nuc
+resonant nucleus.
dyns
number of dynamic scans to generate.
Value
diff --git a/docs/reference/smooth_dyns.html b/docs/reference/smooth_dyns.html
index 4cc8da50..accf3a51 100644
--- a/docs/reference/smooth_dyns.html
+++ b/docs/reference/smooth_dyns.html
@@ -1,5 +1,5 @@
-Smooth data across the dynamic dimension with a Gaussian kernel. — smooth_dyns • Spectroscopy Analysis Tools (spant) Smooth data across the dynamic dimension with a Gaussian kernel. — smooth_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/sort_basis.html b/docs/reference/sort_basis.html
index 6a676ea2..d25cc006 100644
--- a/docs/reference/sort_basis.html
+++ b/docs/reference/sort_basis.html
@@ -1,5 +1,5 @@
-Sort the basis-set elements alphabetically. — sort_basis • Spectroscopy Analysis Tools (spant) Sort the basis-set elements alphabetically. — sort_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/spant-package.html b/docs/reference/spant-package.html
index b3dd8e21..90f19ec3 100644
--- a/docs/reference/spant-package.html
+++ b/docs/reference/spant-package.html
@@ -1,5 +1,5 @@
-spant: spectroscopy analysis tools. — spant-package • Spectroscopy Analysis Tools (spant) spant: spectroscopy analysis tools. — spant-package • Spectroscopy Analysis Tools (spant) Simulate and fit some spectra with ABfit for benchmarking purposes. Basic
-timing and performance metrics will be printed. — spant_abfit_benchmark • Spectroscopy Analysis Tools (spant) Simulate and fit some spectra with ABfit for benchmarking purposes. Basic timing and performance metrics will be printed. — spant_abfit_benchmark • Spectroscopy Analysis Tools (spant) Example MEGA-PRESS data with significant B0 drift. — spant_mpress_drift • Spectroscopy Analysis Tools (spant) Example MEGA-PRESS data with significant B0 drift. — spant_mpress_drift • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -83,7 +83,7 @@ Example MEGA-PRESS data with significant B0 drift.
Format
- An object of class mrs_data of length 13.
+ An object of class mrs_data of dimension 1 x 1 x 1 x 1 x 40 x 1 x 1024.
@@ -98,7 +98,7 @@ Format
diff --git a/docs/reference/spant_sim_fmrs_dataset.html b/docs/reference/spant_sim_fmrs_dataset.html
new file mode 100644
index 00000000..00e48b56
--- /dev/null
+++ b/docs/reference/spant_sim_fmrs_dataset.html
@@ -0,0 +1,117 @@
+
+Simulate an example fMRS dataset for a block design fMRS experiment and export a BIDS structure. — spant_sim_fmrs_dataset • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Simulate an example fMRS dataset for a block design fMRS experiment and export a BIDS structure.
+ Source: R/fmrs.R
+ spant_sim_fmrs_dataset.Rd
+
+
+
+ Simulate an example fMRS dataset for a block design fMRS experiment and
+export a BIDS structure.
+
+
+
+ spant_sim_fmrs_dataset(output_dir = NULL)
+
+
+
+ Arguments
+ - output_dir
+output directory for the BIDS data. Defaults to :
+"HOME/sim_fmrs_dataset/data".
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/spant_simulation_benchmark.html b/docs/reference/spant_simulation_benchmark.html
index 32daa8bf..d8cc6841 100644
--- a/docs/reference/spant_simulation_benchmark.html
+++ b/docs/reference/spant_simulation_benchmark.html
@@ -1,7 +1,5 @@
-Simulate a typical metabolite basis set for benchmarking. Timing metrics will
-be printed on completion. — spant_simulation_benchmark • Spectroscopy Analysis Tools (spant) Simulate a typical metabolite basis set for benchmarking. Timing metrics will be printed on completion. — spant_simulation_benchmark • Spectroscopy Analysis Tools (spant) Decompose an mrs_data object into white and gray matter spectra. — spec_decomp • Spectroscopy Analysis Tools (spant) Perform a mathematical operation on a spectral region. — spec_op • Spectroscopy Analysis Tools (spant) Perform a mathematical operation on a spectral region. — spec_op • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -98,8 +98,8 @@ Arguments
operator
-can be "sum" (default), "mean", "l2", "max", "min" or
-"max-min".
can be "sum" (default), "mean", "l2", "max", "max_cplx,
+"min" or "max-min".
freq_scale
@@ -129,7 +129,7 @@ Value
diff --git a/docs/reference/spin_sys.html b/docs/reference/spin_sys.html
index 853423a4..1eaa9e76 100644
--- a/docs/reference/spin_sys.html
+++ b/docs/reference/spin_sys.html
@@ -1,5 +1,5 @@
-Create a spin system object for pulse sequence simulation. — spin_sys • Spectroscopy Analysis Tools (spant) Create a spin system object for pulse sequence simulation. — spin_sys • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/spm_pve2categorical.html b/docs/reference/spm_pve2categorical.html
index 23a1bad9..70f10729 100644
--- a/docs/reference/spm_pve2categorical.html
+++ b/docs/reference/spm_pve2categorical.html
@@ -1,7 +1,5 @@
-Convert SPM style segmentation files to a single categorical image where
-the numerical values map as: 0) Other, 1) CSF, 2) GM and 3) WM. — spm_pve2categorical • Spectroscopy Analysis Tools (spant) Convert SPM style segmentation files to a single categorical image where the numerical values map as: 0) Other, 1) CSF, 2) GM and 3) WM. — spm_pve2categorical • Spectroscopy Analysis Tools (spant) Signal space projection method for lipid suppression. — ssp • Spectroscopy Analysis Tools (spant) Signal space projection method for lipid suppression. — ssp • Spectroscopy Analysis Tools (spant) Plot the fitting results of an object of class fit_result with
-individual basis set components shown. — stackplot.fit_result • Spectroscopy Analysis Tools (spant) Plot the fitting results of an object of class fit_result with individual basis set components shown. — stackplot.fit_result • Spectroscopy Analysis Tools (spant) Produce a plot with multiple traces. — stackplot • Spectroscopy Analysis Tools (spant) Produce a plot with multiple traces. — stackplot • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/stackplot.mrs_data.html b/docs/reference/stackplot.mrs_data.html
index 17ff5648..64eea445 100644
--- a/docs/reference/stackplot.mrs_data.html
+++ b/docs/reference/stackplot.mrs_data.html
@@ -1,5 +1,5 @@
-Stackplot plotting method for objects of class mrs_data. — stackplot.mrs_data • Spectroscopy Analysis Tools (spant) Stackplot plotting method for objects of class mrs_data. — stackplot.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -255,7 +255,7 @@ Arguments
diff --git a/docs/reference/sub_first_dyn.html b/docs/reference/sub_first_dyn.html
index dbd7f831..493b7242 100644
--- a/docs/reference/sub_first_dyn.html
+++ b/docs/reference/sub_first_dyn.html
@@ -1,5 +1,5 @@
-Subtract the first dynamic spectrum from a dynamic series. — sub_first_dyn • Spectroscopy Analysis Tools (spant) Subtract the first dynamic spectrum from a dynamic series. — sub_first_dyn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/sub_mean_dyns.html b/docs/reference/sub_mean_dyns.html
index 6e3bb2df..221bd0c1 100644
--- a/docs/reference/sub_mean_dyns.html
+++ b/docs/reference/sub_mean_dyns.html
@@ -1,5 +1,5 @@
-Subtract the mean dynamic spectrum from a dynamic series. — sub_mean_dyns • Spectroscopy Analysis Tools (spant) Subtract the mean dynamic spectrum from a dynamic series. — sub_mean_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/sub_median_dyns.html b/docs/reference/sub_median_dyns.html
index 134c495d..1e834f14 100644
--- a/docs/reference/sub_median_dyns.html
+++ b/docs/reference/sub_median_dyns.html
@@ -1,5 +1,5 @@
-Subtract the median dynamic spectrum from a dynamic series. — sub_median_dyns • Spectroscopy Analysis Tools (spant) Subtract the median dynamic spectrum from a dynamic series. — sub_median_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/sum_coils.html b/docs/reference/sum_coils.html
index 7bf559f2..e1ab3cc0 100644
--- a/docs/reference/sum_coils.html
+++ b/docs/reference/sum_coils.html
@@ -1,5 +1,5 @@
-Calculate the sum across receiver coil elements. — sum_coils • Spectroscopy Analysis Tools (spant) Calculate the sum across receiver coil elements. — sum_coils • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/sum_dyns.html b/docs/reference/sum_dyns.html
index a0be19d3..bbda2ffc 100644
--- a/docs/reference/sum_dyns.html
+++ b/docs/reference/sum_dyns.html
@@ -1,5 +1,5 @@
-Calculate the sum of data dynamics. — sum_dyns • Spectroscopy Analysis Tools (spant) Calculate the sum of data dynamics. — sum_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/sum_mrs.html b/docs/reference/sum_mrs.html
index a22f215b..3cc3ab9e 100644
--- a/docs/reference/sum_mrs.html
+++ b/docs/reference/sum_mrs.html
@@ -1,5 +1,5 @@
-Sum two mrs_data objects. — sum_mrs • Spectroscopy Analysis Tools (spant) Sum two mrs_data objects. — sum_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Value
diff --git a/docs/reference/sum_mrs_list.html b/docs/reference/sum_mrs_list.html
index f4e09aea..c3584348 100644
--- a/docs/reference/sum_mrs_list.html
+++ b/docs/reference/sum_mrs_list.html
@@ -1,5 +1,5 @@
-Return the sum of a list of mrs_data objects. — sum_mrs_list • Spectroscopy Analysis Tools (spant) Return the sum of a list of mrs_data objects. — sum_mrs_list • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/svs_1h_brain_analysis.html b/docs/reference/svs_1h_brain_analysis.html
index 8ce514db..dff0ef7d 100644
--- a/docs/reference/svs_1h_brain_analysis.html
+++ b/docs/reference/svs_1h_brain_analysis.html
@@ -1,5 +1,5 @@
-Standard SVS 1H brain analysis pipeline. — svs_1h_brain_analysis • Spectroscopy Analysis Tools (spant) Standard SVS 1H brain analysis pipeline. — svs_1h_brain_analysis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -199,7 +199,7 @@ Value
diff --git a/docs/reference/svs_1h_brain_analysis_dev.html b/docs/reference/svs_1h_brain_analysis_dev.html
index d70a14d3..d71bfea2 100644
--- a/docs/reference/svs_1h_brain_analysis_dev.html
+++ b/docs/reference/svs_1h_brain_analysis_dev.html
@@ -1,5 +1,5 @@
-Standard SVS 1H brain analysis pipeline. — svs_1h_brain_analysis_dev • Spectroscopy Analysis Tools (spant) Standard SVS 1H brain analysis pipeline. — svs_1h_brain_analysis_dev • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -193,7 +193,7 @@ Examples
diff --git a/docs/reference/svs_1h_brain_batch_analysis.html b/docs/reference/svs_1h_brain_batch_analysis.html
index 5631e8cc..15f7223e 100644
--- a/docs/reference/svs_1h_brain_batch_analysis.html
+++ b/docs/reference/svs_1h_brain_batch_analysis.html
@@ -1,5 +1,5 @@
-Batch interface to the standard SVS 1H brain analysis pipeline. — svs_1h_brain_batch_analysis • Spectroscopy Analysis Tools (spant) Batch interface to the standard SVS 1H brain analysis pipeline. — svs_1h_brain_batch_analysis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -144,7 +144,7 @@ Value
diff --git a/docs/reference/t_test_spec.html b/docs/reference/t_test_spec.html
new file mode 100644
index 00000000..56a7ea1b
--- /dev/null
+++ b/docs/reference/t_test_spec.html
@@ -0,0 +1,124 @@
+
+Perform a t-test on spectral data points. — t_test_spec • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+
+
+ Perform a t-test on spectral data points.
+
+
+
+ t_test_spec(mrs_data, group)
+
+
+
+ Arguments
+ - mrs_data
+an mrs_data object with spectra in the dynamic dimension.
- group
+vector describing the group membership of each dynamic spectrum.
+
+ Value
+
+
+a list of statistical results.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/td2fd.html b/docs/reference/td2fd.html
index 6748a6a8..f31ed524 100644
--- a/docs/reference/td2fd.html
+++ b/docs/reference/td2fd.html
@@ -1,5 +1,5 @@
-Transform time-domain data to the frequency-domain. — td2fd • Spectroscopy Analysis Tools (spant) Transform time-domain data to the frequency-domain. — td2fd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/td_conv_filt.html b/docs/reference/td_conv_filt.html
index a9f340c3..106b9b00 100644
--- a/docs/reference/td_conv_filt.html
+++ b/docs/reference/td_conv_filt.html
@@ -1,5 +1,5 @@
-Time-domain convolution based filter. — td_conv_filt • Spectroscopy Analysis Tools (spant) Time-domain convolution based filter. — td_conv_filt • Spectroscopy Analysis Tools (spant) Time-domain spectral registration. — tdsr • Spectroscopy Analysis Tools (spant) Time-domain spectral registration. — tdsr • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -121,7 +121,7 @@ Value
diff --git a/docs/reference/te.html b/docs/reference/te.html
index 010361b1..4a65711d 100644
--- a/docs/reference/te.html
+++ b/docs/reference/te.html
@@ -1,5 +1,5 @@
-Return the echo time of an MRS dataset. — te • Spectroscopy Analysis Tools (spant) Return the echo time of an MRS dataset. — te • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/tr.html b/docs/reference/tr.html
index 0c0bd63b..2e749e02 100644
--- a/docs/reference/tr.html
+++ b/docs/reference/tr.html
@@ -1,5 +1,5 @@
-Return the repetition time of an MRS dataset. — tr • Spectroscopy Analysis Tools (spant) Return the repetition time of an MRS dataset. — tr • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/varpro_3_para_opts.html b/docs/reference/varpro_3_para_opts.html
index c2270a16..52d7cd84 100644
--- a/docs/reference/varpro_3_para_opts.html
+++ b/docs/reference/varpro_3_para_opts.html
@@ -1,5 +1,5 @@
-Return a list of options for VARPRO based fitting with 3 free parameters. — varpro_3_para_opts • Spectroscopy Analysis Tools (spant) Return a list of options for VARPRO based fitting with 3 free parameters. — varpro_3_para_opts • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -141,7 +141,7 @@ Value
diff --git a/docs/reference/varpro_basic_opts.html b/docs/reference/varpro_basic_opts.html
index 32c86d22..c5104891 100644
--- a/docs/reference/varpro_basic_opts.html
+++ b/docs/reference/varpro_basic_opts.html
@@ -1,5 +1,5 @@
-Return a list of options for a basic VARPRO analysis. — varpro_basic_opts • Spectroscopy Analysis Tools (spant) Return a list of options for a basic VARPRO analysis. — varpro_basic_opts • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -118,7 +118,7 @@ Value
diff --git a/docs/reference/varpro_opts.html b/docs/reference/varpro_opts.html
index 2aabf11d..6332f730 100644
--- a/docs/reference/varpro_opts.html
+++ b/docs/reference/varpro_opts.html
@@ -1,5 +1,5 @@
-Return a list of options for VARPRO based fitting. — varpro_opts • Spectroscopy Analysis Tools (spant) Return a list of options for VARPRO based fitting. — varpro_opts • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -177,7 +177,7 @@ Examples
diff --git a/docs/reference/vec2mrs_data.html b/docs/reference/vec2mrs_data.html
index 0cccd73b..f0d58bf0 100644
--- a/docs/reference/vec2mrs_data.html
+++ b/docs/reference/vec2mrs_data.html
@@ -1,5 +1,5 @@
-Convert a vector into a mrs_data object. — vec2mrs_data • Spectroscopy Analysis Tools (spant) Convert a vector into a mrs_data object. — vec2mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -80,10 +80,11 @@ Convert a vector into a mrs_data object.
vec2mrs_data(
vec,
- fs = def_fs(),
- ft = def_ft(),
- ref = def_ref(),
- nuc = def_nuc(),
+ mrs_data = NULL,
+ fs = NULL,
+ ft = NULL,
+ ref = NULL,
+ nuc = NULL,
dyns = 1,
fd = FALSE
)
@@ -95,6 +96,10 @@ Arguments
the data vector.
mrs_data
+example data to copy acquisition parameters from.
fs
sampling frequency in Hz.
Arguments
fd
-flag to indicate if the matrix is in the frequency domain (logical).
flag to indicate if the vector is in the frequency domain (logical).
Value
diff --git a/docs/reference/write_basis.html b/docs/reference/write_basis.html
index b6e27cbd..94c5e021 100644
--- a/docs/reference/write_basis.html
+++ b/docs/reference/write_basis.html
@@ -1,5 +1,5 @@
-Write a basis object to an LCModel .basis formatted file. — write_basis • Spectroscopy Analysis Tools (spant) Write a basis object to an LCModel .basis formatted file. — write_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -108,7 +108,7 @@ Arguments
diff --git a/docs/reference/write_basis_tqn.html b/docs/reference/write_basis_tqn.html
index 6aa51c1d..116c73ec 100644
--- a/docs/reference/write_basis_tqn.html
+++ b/docs/reference/write_basis_tqn.html
@@ -1,5 +1,5 @@
-Generate a basis file using TARQUIN. — write_basis_tqn • Spectroscopy Analysis Tools (spant) Generate a basis file using TARQUIN. — write_basis_tqn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Examples
diff --git a/docs/reference/write_mrs.html b/docs/reference/write_mrs.html
index fff25f15..124b9dc4 100644
--- a/docs/reference/write_mrs.html
+++ b/docs/reference/write_mrs.html
@@ -1,5 +1,5 @@
-Write MRS data object to file. — write_mrs • Spectroscopy Analysis Tools (spant) Write MRS data object to file. — write_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Arguments
diff --git a/docs/reference/write_mrs_nifti.html b/docs/reference/write_mrs_nifti.html
index f4bf1921..bd3ed4b7 100644
--- a/docs/reference/write_mrs_nifti.html
+++ b/docs/reference/write_mrs_nifti.html
@@ -1,5 +1,5 @@
-Write MRS data object to file in NIFTI format. — write_mrs_nifti • Spectroscopy Analysis Tools (spant) Write MRS data object to file in NIFTI format. — write_mrs_nifti • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/write_pulse_ascii.html b/docs/reference/write_pulse_ascii.html
index 067ae086..221f8ebb 100644
--- a/docs/reference/write_pulse_ascii.html
+++ b/docs/reference/write_pulse_ascii.html
@@ -1,5 +1,5 @@
-Write an ASCII formatted pulse file. — write_pulse_ascii • Spectroscopy Analysis Tools (spant) Write an ASCII formatted pulse file. — write_pulse_ascii • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/zero_fade_spec.html b/docs/reference/zero_fade_spec.html
index c703745c..c8b572c3 100644
--- a/docs/reference/zero_fade_spec.html
+++ b/docs/reference/zero_fade_spec.html
@@ -1,7 +1,5 @@
-Fade a spectrum to zero by frequency domain multiplication with a tanh
-function. Note this operation distorts data points at the end of the FID. — zero_fade_spec • Spectroscopy Analysis Tools (spant) Fade a spectrum to zero by frequency domain multiplication with a tanh function. Note this operation distorts data points at the end of the FID. — zero_fade_spec • Spectroscopy Analysis Tools (spant) Zero all coherences including and above a given order. — zero_higher_orders • Spectroscopy Analysis Tools (spant) Zero all coherences including and above a given order. — zero_higher_orders • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Value
diff --git a/docs/reference/zero_td_pts_end.html b/docs/reference/zero_td_pts_end.html
index 8c1123c8..71d24ebb 100644
--- a/docs/reference/zero_td_pts_end.html
+++ b/docs/reference/zero_td_pts_end.html
@@ -1,5 +1,5 @@
-Set mrs_data object data points at the end of the FID to zero. — zero_td_pts_end • Spectroscopy Analysis Tools (spant) Set mrs_data object data points at the end of the FID to zero. — zero_td_pts_end • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/zf.html b/docs/reference/zf.html
index 85e2013c..baf50256 100644
--- a/docs/reference/zf.html
+++ b/docs/reference/zf.html
@@ -1,5 +1,5 @@
-Zero-fill MRS data in the time domain. — zf • Spectroscopy Analysis Tools (spant) Zero-fill MRS data in the time domain. — zf • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -125,7 +125,7 @@ Value
diff --git a/docs/reference/zf_xy.html b/docs/reference/zf_xy.html
index ebca3999..c4104a74 100644
--- a/docs/reference/zf_xy.html
+++ b/docs/reference/zf_xy.html
@@ -1,5 +1,5 @@
-Zero-fill MRSI data in the k-space x-y direction. — zf_xy • Spectroscopy Analysis Tools (spant) Zero-fill MRSI data in the k-space x-y direction. — zf_xy • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -113,7 +113,7 @@ Value
diff --git a/docs/sitemap.xml b/docs/sitemap.xml
index e2139f71..4c39f515 100644
--- a/docs/sitemap.xml
+++ b/docs/sitemap.xml
@@ -216,6 +216,12 @@
https://martin3141.github.io/spant/reference/comb_coils_fp_pc.html
+
+ https://martin3141.github.io/spant/reference/comb_coils_mrsi_gls.html
+
+
+ https://martin3141.github.io/spant/reference/comb_coils_svs_gls.html
+
https://martin3141.github.io/spant/reference/comb_csv_results.html
@@ -411,6 +417,9 @@
https://martin3141.github.io/spant/reference/gen_conv_reg.html
+
+ https://martin3141.github.io/spant/reference/gen_group_reg.html
+
https://martin3141.github.io/spant/reference/gen_impulse_reg.html
@@ -555,6 +564,15 @@
https://martin3141.github.io/spant/reference/glm_spec.html
+
+ https://martin3141.github.io/spant/reference/glm_spec_fmrs_fl.html
+
+
+ https://martin3141.github.io/spant/reference/glm_spec_fmrs_group.html
+
+
+ https://martin3141.github.io/spant/reference/glm_spec_group_linhyp.html
+
https://martin3141.github.io/spant/reference/grid_shift_xy.html
@@ -690,9 +708,15 @@
https://martin3141.github.io/spant/reference/mrs_data2basis.html
+
+ https://martin3141.github.io/spant/reference/mrs_data2bids.html
+
https://martin3141.github.io/spant/reference/mrs_data2mat.html
+
+ https://martin3141.github.io/spant/reference/mrs_data2spec_mat.html
+
https://martin3141.github.io/spant/reference/mrs_data2vec.html
@@ -741,6 +765,9 @@
https://martin3141.github.io/spant/reference/phase.html
+
+ https://martin3141.github.io/spant/reference/phase_ref_1h_brain.html
+
https://martin3141.github.io/spant/reference/plot.fit_result.html
@@ -780,6 +807,12 @@
https://martin3141.github.io/spant/reference/precomp.html
+
+ https://martin3141.github.io/spant/reference/preproc_svs.html
+
+
+ https://martin3141.github.io/spant/reference/preproc_svs_dataset.html
+
https://martin3141.github.io/spant/reference/print.fit_result.html
@@ -1050,6 +1083,9 @@
https://martin3141.github.io/spant/reference/spant_mpress_drift.html
+
+ https://martin3141.github.io/spant/reference/spant_sim_fmrs_dataset.html
+
https://martin3141.github.io/spant/reference/spant_simulation_benchmark.html
@@ -1107,6 +1143,9 @@
https://martin3141.github.io/spant/reference/svs_1h_brain_batch_analysis.html
+
+ https://martin3141.github.io/spant/reference/t_test_spec.html
+
https://martin3141.github.io/spant/reference/td2fd.html
STEAM sequence with ideal pulses and coherence order filtering to simulate -gradient crushers.
STEAM sequence with ideal pulses and coherence order filtering to simulate gradient crushers.
STEAM sequence with ideal pulses using the z-rotation gradient simulation -method described by Young et al JMR 140, 146-152 (1999).
STEAM sequence with ideal pulses using the z-rotation gradient simulation method described by Young et al JMR 140, 146-152 (1999).
All functions
- Set the number of time-domain data points, truncating or zero-filling as
-appropriate.
Set the number of time-domain data points, truncating or zero-filling as appropriate.
@@ -1318,18 +1294,15 @@ All functions
- Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS
-sequence. Note, ideal pulses are assumed.
Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS sequence. Note, ideal pulses are assumed.
- Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS
-sequence. Note, ideal pulses are assumed.
Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS sequence. Note, ideal pulses are assumed.
- Simulate a macromolecular and lipid basis-set suitable for 1H brain MRS
-analysis.
Simulate a macromolecular and lipid basis-set suitable for 1H brain MRS analysis.
@@ -1353,8 +1326,7 @@ All functions
- Simulate an ideal pulse excitation profile by smoothing a top-hat function
-with a Gaussian.
Simulate an ideal pulse excitation profile by smoothing a top-hat function with a Gaussian.
@@ -1374,17 +1346,19 @@ All functions
- Simulate and fit some spectra with ABfit for benchmarking purposes. Basic
-timing and performance metrics will be printed.
Simulate and fit some spectra with ABfit for benchmarking purposes. Basic timing and performance metrics will be printed.
Example MEGA-PRESS data with significant B0 drift.
+
+
+ Simulate an example fMRS dataset for a block design fMRS experiment and export a BIDS structure.
- Simulate a typical metabolite basis set for benchmarking. Timing metrics will
-be printed on completion.
Simulate a typical metabolite basis set for benchmarking. Timing metrics will be printed on completion.
@@ -1400,8 +1374,7 @@ All functions
- Convert SPM style segmentation files to a single categorical image where
-the numerical values map as: 0) Other, 1) CSF, 2) GM and 3) WM.
Convert SPM style segmentation files to a single categorical image where the numerical values map as: 0) Other, 1) CSF, 2) GM and 3) WM.
@@ -1413,8 +1386,7 @@ All functions
- Plot the fitting results of an object of class fit_result with
-individual basis set components shown.
Plot the fitting results of an object of class fit_result with individual basis set components shown.
@@ -1459,6 +1431,10 @@ All functions svs_1h_brain_batch_analysis()
Batch interface to the standard SVS 1H brain analysis pipeline.
+
+
+ Perform a t-test on spectral data points.
@@ -1518,8 +1494,7 @@ All functions
- Fade a spectrum to zero by frequency domain multiplication with a tanh
-function. Note this operation distorts data points at the end of the FID.
Fade a spectrum to zero by frequency domain multiplication with a tanh function. Note this operation distorts data points at the end of the FID.
@@ -1549,7 +1524,7 @@ All functions
diff --git a/docs/reference/int_spec.html b/docs/reference/int_spec.html
index c7060fe7..783325a8 100644
--- a/docs/reference/int_spec.html
+++ b/docs/reference/int_spec.html
@@ -1,5 +1,5 @@
-Integrate a spectral region. — int_spec • Spectroscopy Analysis Tools (spant) Integrate a spectral region. — int_spec • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -118,7 +118,7 @@ Value
diff --git a/docs/reference/interleave_dyns.html b/docs/reference/interleave_dyns.html
index effe5543..441eff27 100644
--- a/docs/reference/interleave_dyns.html
+++ b/docs/reference/interleave_dyns.html
@@ -1,5 +1,5 @@
-Interleave the first and second half of a dynamic series. — interleave_dyns • Spectroscopy Analysis Tools (spant) Interleave the first and second half of a dynamic series. — interleave_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/inv_even_dyns.html b/docs/reference/inv_even_dyns.html
index 9f9d4fff..dcb781dc 100644
--- a/docs/reference/inv_even_dyns.html
+++ b/docs/reference/inv_even_dyns.html
@@ -1,5 +1,5 @@
-Invert even numbered dynamic scans starting from 1 (2,4,6...). — inv_even_dyns • Spectroscopy Analysis Tools (spant) Invert even numbered dynamic scans starting from 1 (2,4,6...). — inv_even_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/inv_odd_dyns.html b/docs/reference/inv_odd_dyns.html
index 26212e2b..78d64660 100644
--- a/docs/reference/inv_odd_dyns.html
+++ b/docs/reference/inv_odd_dyns.html
@@ -1,5 +1,5 @@
-Invert odd numbered dynamic scans starting from 1 (1,3,5...). — inv_odd_dyns • Spectroscopy Analysis Tools (spant) Invert odd numbered dynamic scans starting from 1 (1,3,5...). — inv_odd_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/is.def.html b/docs/reference/is.def.html
index f196ffd0..a67b9eba 100644
--- a/docs/reference/is.def.html
+++ b/docs/reference/is.def.html
@@ -1,5 +1,5 @@
-Check if an object is defined, which is the same as being not NULL. — is.def • Spectroscopy Analysis Tools (spant) Check if an object is defined, which is the same as being not NULL. — is.def • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/is_fd.html b/docs/reference/is_fd.html
index 3b0ca165..18a193aa 100644
--- a/docs/reference/is_fd.html
+++ b/docs/reference/is_fd.html
@@ -1,7 +1,5 @@
-Check if the chemical shift dimension of an MRS data object is in the
-frequency domain. — is_fd • Spectroscopy Analysis Tools (spant) Check if the chemical shift dimension of an MRS data object is in the frequency domain. — is_fd • Spectroscopy Analysis Tools (spant) Transform 2D MRSI data from k-space to image space in the x-y direction. — kspace2img_xy • Spectroscopy Analysis Tools (spant) Transform 2D MRSI data from k-space to image space in the x-y direction. — kspace2img_xy • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/l2_reg.html b/docs/reference/l2_reg.html
index 3d781d80..21aa9849 100644
--- a/docs/reference/l2_reg.html
+++ b/docs/reference/l2_reg.html
@@ -1,5 +1,5 @@
-Perform l2 regularisation artefact suppression. — l2_reg • Spectroscopy Analysis Tools (spant) Perform l2 regularisation artefact suppression. — l2_reg • Spectroscopy Analysis Tools (spant) Apply line-broadening (apodisation) to MRS data or basis object. — lb • Spectroscopy Analysis Tools (spant) Apply line-broadening (apodisation) to MRS data or basis object. — lb • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -123,7 +123,7 @@ Value
diff --git a/docs/reference/lofdc.html b/docs/reference/lofdc.html
index 5419b1ec..31347a25 100644
--- a/docs/reference/lofdc.html
+++ b/docs/reference/lofdc.html
@@ -1,5 +1,5 @@
-Correct linear frequency drift. — lofdc • Spectroscopy Analysis Tools (spant) Correct linear frequency drift. — lofdc • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -138,7 +138,7 @@ Value
diff --git a/docs/reference/lw2alpha.html b/docs/reference/lw2alpha.html
index b83db682..25da229b 100644
--- a/docs/reference/lw2alpha.html
+++ b/docs/reference/lw2alpha.html
@@ -1,7 +1,5 @@
-Covert a linewidth in Hz to an equivalent alpha value in the time-domain ie:
-x * exp(-t * alpha). — lw2alpha • Spectroscopy Analysis Tools (spant) Covert a linewidth in Hz to an equivalent alpha value in the time-domain ie: x * exp(-t * alpha). — lw2alpha • Spectroscopy Analysis Tools (spant) Covert a linewidth in Hz to an equivalent beta value in the time-domain ie:
-x * exp(-t * t * beta). — lw2beta • Spectroscopy Analysis Tools (spant) Covert a linewidth in Hz to an equivalent beta value in the time-domain ie: x * exp(-t * t * beta). — lw2beta • Spectroscopy Analysis Tools (spant) Make a basis-set object from a directory containing LCModel formatted RAW
-files. — make_basis_from_raw • Spectroscopy Analysis Tools (spant) Make a basis-set object from a directory containing LCModel formatted RAW files. — make_basis_from_raw • Spectroscopy Analysis Tools (spant) Mask an MRS dataset in the dynamic dimension. — mask_dyns • Spectroscopy Analysis Tools (spant) Mask an MRS dataset in the dynamic dimension. — mask_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/mask_fit_res.html b/docs/reference/mask_fit_res.html
index 97baaa3f..ebd91a99 100644
--- a/docs/reference/mask_fit_res.html
+++ b/docs/reference/mask_fit_res.html
@@ -1,5 +1,5 @@
-Mask fit result spectra depending on a vector of bool values. — mask_fit_res • Spectroscopy Analysis Tools (spant) Mask fit result spectra depending on a vector of bool values. — mask_fit_res • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -116,7 +116,7 @@ Value
diff --git a/docs/reference/mask_xy.html b/docs/reference/mask_xy.html
index 11bb577c..b0d38619 100644
--- a/docs/reference/mask_xy.html
+++ b/docs/reference/mask_xy.html
@@ -1,5 +1,5 @@
-Mask an MRSI dataset in the x-y direction — mask_xy • Spectroscopy Analysis Tools (spant) Mask an MRSI dataset in the x-y direction — mask_xy • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/mask_xy_corners.html b/docs/reference/mask_xy_corners.html
index 09b16cd2..2d13839d 100644
--- a/docs/reference/mask_xy_corners.html
+++ b/docs/reference/mask_xy_corners.html
@@ -1,5 +1,5 @@
-Mask the four corners of an MRSI dataset in the x-y plane. — mask_xy_corners • Spectroscopy Analysis Tools (spant) Mask the four corners of an MRSI dataset in the x-y plane. — mask_xy_corners • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/mask_xy_ellipse.html b/docs/reference/mask_xy_ellipse.html
index 1d8b02e4..e2e749ef 100644
--- a/docs/reference/mask_xy_ellipse.html
+++ b/docs/reference/mask_xy_ellipse.html
@@ -1,7 +1,5 @@
-Mask the voxels outside an elliptical region spanning the MRSI dataset in the
-x-y plane. — mask_xy_ellipse • Spectroscopy Analysis Tools (spant) Mask the voxels outside an elliptical region spanning the MRSI dataset in the x-y plane. — mask_xy_ellipse • Spectroscopy Analysis Tools (spant) Mask a 2D MRSI dataset in the x-y dimension. — mask_xy_mat • Spectroscopy Analysis Tools (spant) Mask a 2D MRSI dataset in the x-y dimension. — mask_xy_mat • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Value
diff --git a/docs/reference/mat2mrs_data.html b/docs/reference/mat2mrs_data.html
index 2e2895f3..ae55665f 100644
--- a/docs/reference/mat2mrs_data.html
+++ b/docs/reference/mat2mrs_data.html
@@ -1,7 +1,5 @@
-Convert a matrix (with spectral points in the column dimension and dynamics
-in the row dimensions) into a mrs_data object. — mat2mrs_data • Spectroscopy Analysis Tools (spant) Convert a matrix (with spectral points in the column dimension and dynamics in the row dimensions) into a mrs_data object. — mat2mrs_data • Spectroscopy Analysis Tools (spant) Matrix exponential function taken from complexplus package to reduce the
-number of spant dependencies. — matexp • Spectroscopy Analysis Tools (spant) Matrix exponential function taken from complexplus package to reduce the number of spant dependencies. — matexp • Spectroscopy Analysis Tools (spant) Apply the max operator to an MRS dataset. — max_mrs • Spectroscopy Analysis Tools (spant) Apply the max operator to an MRS dataset. — max_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/max_mrs_interp.html b/docs/reference/max_mrs_interp.html
index e4474764..52e63f3e 100644
--- a/docs/reference/max_mrs_interp.html
+++ b/docs/reference/max_mrs_interp.html
@@ -1,5 +1,5 @@
-Apply the max operator to an interpolated MRS dataset. — max_mrs_interp • Spectroscopy Analysis Tools (spant) Apply the max operator to an interpolated MRS dataset. — max_mrs_interp • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/mean.list.html b/docs/reference/mean.list.html
index b8eb3463..048306fd 100644
--- a/docs/reference/mean.list.html
+++ b/docs/reference/mean.list.html
@@ -1,5 +1,5 @@
-Calculate the mean spectrum from an mrs_data object. — mean.list • Spectroscopy Analysis Tools (spant) Calculate the mean spectrum from an mrs_data object. — mean.list • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/mean.mrs_data.html b/docs/reference/mean.mrs_data.html
index 5531a28d..79515014 100644
--- a/docs/reference/mean.mrs_data.html
+++ b/docs/reference/mean.mrs_data.html
@@ -1,5 +1,5 @@
-Calculate the mean spectrum from an mrs_data object. — mean.mrs_data • Spectroscopy Analysis Tools (spant) Calculate the mean spectrum from an mrs_data object. — mean.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/mean_dyn_blocks.html b/docs/reference/mean_dyn_blocks.html
index 10467098..4c042448 100644
--- a/docs/reference/mean_dyn_blocks.html
+++ b/docs/reference/mean_dyn_blocks.html
@@ -1,5 +1,5 @@
-Calculate the mean of adjacent dynamic scans. — mean_dyn_blocks • Spectroscopy Analysis Tools (spant) Calculate the mean of adjacent dynamic scans. — mean_dyn_blocks • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/mean_dyn_pairs.html b/docs/reference/mean_dyn_pairs.html
index 63e909ea..1a241126 100644
--- a/docs/reference/mean_dyn_pairs.html
+++ b/docs/reference/mean_dyn_pairs.html
@@ -1,5 +1,5 @@
-Calculate the pairwise means across a dynamic data set. — mean_dyn_pairs • Spectroscopy Analysis Tools (spant) Calculate the pairwise means across a dynamic data set. — mean_dyn_pairs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/mean_dyns.html b/docs/reference/mean_dyns.html
index 73fdbfa7..0daa27df 100644
--- a/docs/reference/mean_dyns.html
+++ b/docs/reference/mean_dyns.html
@@ -1,5 +1,5 @@
-Calculate the mean dynamic data. — mean_dyns • Spectroscopy Analysis Tools (spant) Calculate the mean dynamic data. — mean_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/mean_mrs_list.html b/docs/reference/mean_mrs_list.html
index 808b6c50..10d842c0 100644
--- a/docs/reference/mean_mrs_list.html
+++ b/docs/reference/mean_mrs_list.html
@@ -1,5 +1,5 @@
-Return the mean of a list of mrs_data objects. — mean_mrs_list • Spectroscopy Analysis Tools (spant) Return the mean of a list of mrs_data objects. — mean_mrs_list • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/mean_vec_blocks.html b/docs/reference/mean_vec_blocks.html
index 8fc92eaa..dd78b122 100644
--- a/docs/reference/mean_vec_blocks.html
+++ b/docs/reference/mean_vec_blocks.html
@@ -1,5 +1,5 @@
-Calculate the mean of adjacent blocks in a vector. — mean_vec_blocks • Spectroscopy Analysis Tools (spant) Calculate the mean of adjacent blocks in a vector. — mean_vec_blocks • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/median_dyns.html b/docs/reference/median_dyns.html
index 1039d4b5..9a085b10 100644
--- a/docs/reference/median_dyns.html
+++ b/docs/reference/median_dyns.html
@@ -1,5 +1,5 @@
-Calculate the median dynamic data. — median_dyns • Spectroscopy Analysis Tools (spant) Calculate the median dynamic data. — median_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/mod_td.html b/docs/reference/mod_td.html
index 76ad0a40..141ef09e 100644
--- a/docs/reference/mod_td.html
+++ b/docs/reference/mod_td.html
@@ -1,5 +1,5 @@
-Apply the Modulus operator to the time-domain MRS signal. — mod_td • Spectroscopy Analysis Tools (spant) Apply the Modulus operator to the time-domain MRS signal. — mod_td • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/mrs_data2basis.html b/docs/reference/mrs_data2basis.html
index 62f7d749..11797b91 100644
--- a/docs/reference/mrs_data2basis.html
+++ b/docs/reference/mrs_data2basis.html
@@ -1,7 +1,5 @@
-Convert an mrs_data object to basis object - where basis signals are spread
-across the dynamic dimension in the MRS data. — mrs_data2basis • Spectroscopy Analysis Tools (spant) Convert an mrs_data object to basis object - where basis signals are spread across the dynamic dimension in the MRS data. — mrs_data2basis • Spectroscopy Analysis Tools (spant) Create a BIDS file structure from a vector of MRS data paths or list of mrs_data objects. — mrs_data2bids • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Create a BIDS file structure from a vector of MRS data paths or list of mrs_data objects.
+ Source: R/fmrs.R
+ mrs_data2bids.Rd
+
+
+
+ Create a BIDS file structure from a vector of MRS data paths or list of
+mrs_data objects.
+
+
+
+ mrs_data2bids(
+ mrs_data,
+ output_dir,
+ suffix = NULL,
+ sub = NULL,
+ ses = NULL,
+ task = NULL,
+ acq = NULL,
+ nuc = NULL,
+ voi = NULL,
+ rec = NULL,
+ run = NULL,
+ echo = NULL,
+ inv = NULL,
+ skip_existing = TRUE
+)
+
+
+
+ Arguments
+ - mrs_data
+vector of MRS data paths or list of mrs_data objects.
- output_dir
+the base directory to create the BIDS structure.
- suffix
+optional vector of file suffixes. Default behaviour is to
+automatically determine these from the input data, however it is recommended
+that they are specified to allow more efficient skipping of existing data.
- sub
+optional vector of subject labels. If not specified, these will be
+automatically generated as a series of increasing zero-padded integer values
+corresponding to the mrs_data input indices.
- ses
+optional vector of session labels.
- task
+optional vector of task labels.
- acq
+optional vector of acquisition labels.
- nuc
+optional vector of nucleus labels.
- voi
+optional vector of volume of interest labels.
- rec
+optional vector of reconstruction labels.
- run
+optional vector of run indices.
- echo
+optional vector of echo time indices.
- inv
+optional vector of inversion indices.
- skip_existing
+skip any data files that have already been converted.
+Defaults to TRUE, set to FALSE to force an overwrite of any existing data
+files.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/mrs_data2mat.html b/docs/reference/mrs_data2mat.html
index cf5ff28c..9e47688a 100644
--- a/docs/reference/mrs_data2mat.html
+++ b/docs/reference/mrs_data2mat.html
@@ -1,7 +1,5 @@
-Convert mrs_data object to a matrix, with spectral points in the column
-dimension and dynamics in the row dimension. — mrs_data2mat • Spectroscopy Analysis Tools (spant) Convert mrs_data object to a matrix, with spectral points in the column dimension and dynamics in the row dimension. — mrs_data2mat • Spectroscopy Analysis Tools (spant) Convert mrs_data object to a matrix, with spectral points in the column dimension and dynamics in the row dimension. — mrs_data2spec_mat • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Convert mrs_data object to a matrix, with spectral points in the column dimension and dynamics in the row dimension.
+ Source: R/mrs_data_proc.R
+ mrs_data2spec_mat.Rd
+
+
+
+ Convert mrs_data object to a matrix, with spectral points in the column
+dimension and dynamics in the row dimension.
+
+
+
+ mrs_data2spec_mat(mrs_data, collapse = TRUE)
+
+
+
+ Arguments
+ - mrs_data
+MRS data object or list of MRS data objects.
- collapse
+collapse all other dimensions along the dynamic dimension, eg
+a 16x16 MRSI grid would be first collapsed across 256 dynamic scans.
+
+ Value
+
+
+MRS data matrix.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/mrs_data2vec.html b/docs/reference/mrs_data2vec.html
index fb172d68..a1fd654d 100644
--- a/docs/reference/mrs_data2vec.html
+++ b/docs/reference/mrs_data2vec.html
@@ -1,5 +1,5 @@
-Convert mrs_data object to a vector. — mrs_data2vec • Spectroscopy Analysis Tools (spant) Convert mrs_data object to a vector. — mrs_data2vec • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -126,7 +126,7 @@ Value
diff --git a/docs/reference/mvfftshift.html b/docs/reference/mvfftshift.html
index 92b0841b..976b3410 100644
--- a/docs/reference/mvfftshift.html
+++ b/docs/reference/mvfftshift.html
@@ -1,7 +1,5 @@
-Perform a fftshift on a matrix, with each column replaced by its shifted
-result. — mvfftshift • Spectroscopy Analysis Tools (spant) Perform a fftshift on a matrix, with each column replaced by its shifted result. — mvfftshift • Spectroscopy Analysis Tools (spant) Perform an ifftshift on a matrix, with each column replaced by its shifted
-result. — mvifftshift • Spectroscopy Analysis Tools (spant) Perform an ifftshift on a matrix, with each column replaced by its shifted result. — mvifftshift • Spectroscopy Analysis Tools (spant) Print fit coordinates from a single index. — n2coord • Spectroscopy Analysis Tools (spant) Print fit coordinates from a single index. — n2coord • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/nifti_flip_lr.html b/docs/reference/nifti_flip_lr.html
index 730abe3c..19860b3c 100644
--- a/docs/reference/nifti_flip_lr.html
+++ b/docs/reference/nifti_flip_lr.html
@@ -1,9 +1,5 @@
-Flip the x data dimension order of a nifti image. This corresponds to
-flipping MRI data in the left-right direction, assuming the data in save in
-neurological format (can check with fslorient program). — nifti_flip_lr • Spectroscopy Analysis Tools (spant) Flip the x data dimension order of a nifti image. This corresponds to flipping MRI data in the left-right direction, assuming the data in save in neurological format (can check with fslorient program). — nifti_flip_lr • Spectroscopy Analysis Tools (spant) Export a one-page pdf of a single fit result — one_page_pdf • Spectroscopy Analysis Tools (spant) Export a one-page pdf of a single fit result — one_page_pdf • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -108,7 +108,7 @@ Arguments
diff --git a/docs/reference/ortho3.html b/docs/reference/ortho3.html
index 13ade97d..5d7dd2fd 100644
--- a/docs/reference/ortho3.html
+++ b/docs/reference/ortho3.html
@@ -1,5 +1,5 @@
-Display an orthographic projection plot of a nifti object. — ortho3 • Spectroscopy Analysis Tools (spant) Display an orthographic projection plot of a nifti object. — ortho3 • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -172,7 +172,7 @@ Arguments
diff --git a/docs/reference/ortho3_inter.html b/docs/reference/ortho3_inter.html
index 090cc5e5..15948899 100644
--- a/docs/reference/ortho3_inter.html
+++ b/docs/reference/ortho3_inter.html
@@ -1,5 +1,5 @@
-Display an interactive orthographic projection plot of a nifti object. — ortho3_inter • Spectroscopy Analysis Tools (spant) Display an interactive orthographic projection plot of a nifti object. — ortho3_inter • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -132,7 +132,7 @@ Arguments
diff --git a/docs/reference/peak_info.html b/docs/reference/peak_info.html
index 09058bd8..41c8ffaf 100644
--- a/docs/reference/peak_info.html
+++ b/docs/reference/peak_info.html
@@ -1,7 +1,5 @@
-Search for the highest peak in a spectral region and return the frequency,
-height and FWHM. — peak_info • Spectroscopy Analysis Tools (spant) Search for the highest peak in a spectral region and return the frequency, height and FWHM. — peak_info • Spectroscopy Analysis Tools (spant) Papoulis-Gerchberg (PG) algorithm method for k-space extrapolation. — pg_extrap_xy • Spectroscopy Analysis Tools (spant) Papoulis-Gerchberg (PG) algorithm method for k-space extrapolation. — pg_extrap_xy • Spectroscopy Analysis Tools (spant) Apply phasing parameters to MRS data. — phase • Spectroscopy Analysis Tools (spant) Apply phasing parameters to MRS data. — phase • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/phase_ref_1h_brain.html b/docs/reference/phase_ref_1h_brain.html
new file mode 100644
index 00000000..8707a74a
--- /dev/null
+++ b/docs/reference/phase_ref_1h_brain.html
@@ -0,0 +1,131 @@
+
+Corrected zero order phase and chemical shift offset in 1H MRS data from the brain. — phase_ref_1h_brain • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Corrected zero order phase and chemical shift offset in 1H MRS data from the brain.
+ Source: R/rats.R
+ phase_ref_1h_brain.Rd
+
+
+
+ Corrected zero order phase and chemical shift offset in 1H MRS data from the
+brain.
+
+
+
+ phase_ref_1h_brain(mrs_data, mean_ref = FALSE, ret_corr_only = TRUE)
+
+
+
+ Arguments
+ - mrs_data
+MRS data to be corrected.
- mean_ref
+apply the phase and offset of the mean spectrum to all
+others. Default is FALSE.
- ret_corr_only
+return the corrected data only.
+
+ Value
+
+
+corrected MRS data.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/plot.fit_result.html b/docs/reference/plot.fit_result.html
index e54d3bc1..836a53ee 100644
--- a/docs/reference/plot.fit_result.html
+++ b/docs/reference/plot.fit_result.html
@@ -1,5 +1,5 @@
-Plot the fitting results of an object of class fit_result. — plot.fit_result • Spectroscopy Analysis Tools (spant) Plot the fitting results of an object of class fit_result. — plot.fit_result • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -207,7 +207,7 @@ Arguments
diff --git a/docs/reference/plot.mrs_data.html b/docs/reference/plot.mrs_data.html
index fabcc35b..bb2ec651 100644
--- a/docs/reference/plot.mrs_data.html
+++ b/docs/reference/plot.mrs_data.html
@@ -1,5 +1,5 @@
-Plotting method for objects of class mrs_data. — plot.mrs_data • Spectroscopy Analysis Tools (spant) Plotting method for objects of class mrs_data. — plot.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -287,7 +287,7 @@ Arguments
diff --git a/docs/reference/plot_bc.html b/docs/reference/plot_bc.html
index 4f8309b4..b48142cc 100644
--- a/docs/reference/plot_bc.html
+++ b/docs/reference/plot_bc.html
@@ -1,5 +1,5 @@
-Convenience function to plot a baseline estimate with the original data. — plot_bc • Spectroscopy Analysis Tools (spant) Convenience function to plot a baseline estimate with the original data. — plot_bc • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -108,7 +108,7 @@ Arguments
diff --git a/docs/reference/plot_reg.html b/docs/reference/plot_reg.html
index ae1acbe7..2addb2f6 100644
--- a/docs/reference/plot_reg.html
+++ b/docs/reference/plot_reg.html
@@ -1,5 +1,5 @@
-Plot regressors as an image. — plot_reg • Spectroscopy Analysis Tools (spant) Plot regressors as an image. — plot_reg • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/plot_slice_fit.html b/docs/reference/plot_slice_fit.html
index fbc7b560..57f1af8a 100644
--- a/docs/reference/plot_slice_fit.html
+++ b/docs/reference/plot_slice_fit.html
@@ -1,5 +1,5 @@
-Plot a 2D slice from an MRSI fit result object. — plot_slice_fit • Spectroscopy Analysis Tools (spant) Plot a 2D slice from an MRSI fit result object. — plot_slice_fit • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -129,7 +129,7 @@ Arguments
diff --git a/docs/reference/plot_slice_fit_inter.html b/docs/reference/plot_slice_fit_inter.html
index 4eed104a..da105a7d 100644
--- a/docs/reference/plot_slice_fit_inter.html
+++ b/docs/reference/plot_slice_fit_inter.html
@@ -1,5 +1,5 @@
-Plot a 2D slice from an MRSI fit result object. — plot_slice_fit_inter • Spectroscopy Analysis Tools (spant) Plot a 2D slice from an MRSI fit result object. — plot_slice_fit_inter • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -134,7 +134,7 @@ Arguments
diff --git a/docs/reference/plot_slice_map.html b/docs/reference/plot_slice_map.html
index 553e9ac8..ffb2a134 100644
--- a/docs/reference/plot_slice_map.html
+++ b/docs/reference/plot_slice_map.html
@@ -1,5 +1,5 @@
-Plot a slice from a 7 dimensional array. — plot_slice_map • Spectroscopy Analysis Tools (spant) Plot a slice from a 7 dimensional array. — plot_slice_map • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -153,7 +153,7 @@ Arguments
diff --git a/docs/reference/plot_slice_map_inter.html b/docs/reference/plot_slice_map_inter.html
index 40d33b42..90968f66 100644
--- a/docs/reference/plot_slice_map_inter.html
+++ b/docs/reference/plot_slice_map_inter.html
@@ -1,7 +1,5 @@
-Plot an interactive slice map from a data array where voxels can be selected
-to display a corresponding spectrum. — plot_slice_map_inter • Spectroscopy Analysis Tools (spant) Plot an interactive slice map from a data array where voxels can be selected to display a corresponding spectrum. — plot_slice_map_inter • Spectroscopy Analysis Tools (spant) Plot the spectral standard deviation. — plot_spec_sd • Spectroscopy Analysis Tools (spant) Plot the spectral standard deviation. — plot_spec_sd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Arguments
diff --git a/docs/reference/plot_voi_overlay.html b/docs/reference/plot_voi_overlay.html
index 9a782e88..bbbbf35e 100644
--- a/docs/reference/plot_voi_overlay.html
+++ b/docs/reference/plot_voi_overlay.html
@@ -1,5 +1,5 @@
-Plot a volume as an image overlay. — plot_voi_overlay • Spectroscopy Analysis Tools (spant) Plot a volume as an image overlay. — plot_voi_overlay • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -116,7 +116,7 @@ Arguments
diff --git a/docs/reference/plot_voi_overlay_seg.html b/docs/reference/plot_voi_overlay_seg.html
index 3d4e74ff..0e800ff2 100644
--- a/docs/reference/plot_voi_overlay_seg.html
+++ b/docs/reference/plot_voi_overlay_seg.html
@@ -1,5 +1,5 @@
-Plot a volume as an overlay on a segmented brain volume. — plot_voi_overlay_seg • Spectroscopy Analysis Tools (spant) Plot a volume as an overlay on a segmented brain volume. — plot_voi_overlay_seg • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Arguments
diff --git a/docs/reference/ppm.html b/docs/reference/ppm.html
index c352327a..ee4696e2 100644
--- a/docs/reference/ppm.html
+++ b/docs/reference/ppm.html
@@ -1,5 +1,5 @@
-Return the ppm scale of an MRS dataset or fit result. — ppm • Spectroscopy Analysis Tools (spant) Return the ppm scale of an MRS dataset or fit result. — ppm • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -132,7 +132,7 @@ Value
diff --git a/docs/reference/precomp.html b/docs/reference/precomp.html
index 822d7336..df3d2c6c 100644
--- a/docs/reference/precomp.html
+++ b/docs/reference/precomp.html
@@ -1,7 +1,5 @@
-Save function results to file and load on subsequent calls to avoid repeat
-computation. — precomp • Spectroscopy Analysis Tools (spant) Save function results to file and load on subsequent calls to avoid repeat computation. — precomp • Spectroscopy Analysis Tools (spant) Preprocess and perform quality assessment of a single SVS data set. — preproc_svs • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Preprocess and perform quality assessment of a single SVS data set.
+ Source: R/fmrs.R
+ preproc_svs.Rd
+
+
+
+ Preprocess and perform quality assessment of a single SVS data set.
+
+
+
+ preproc_svs(path, label = NULL, output_dir = NULL, ref_inds = NULL)
+
+
+
+ Arguments
+ - path
+path to the fMRS data file or IMA directory.
- label
+a label to describe the data set.
- output_dir
+output directory.
- ref_inds
+a vector of 1-based indices for any water reference dynamic
+scans.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/preproc_svs_dataset.html b/docs/reference/preproc_svs_dataset.html
new file mode 100644
index 00000000..07c3a29b
--- /dev/null
+++ b/docs/reference/preproc_svs_dataset.html
@@ -0,0 +1,148 @@
+
+Preprocess and perform quality assessment of one or more SVS data sets. — preproc_svs_dataset • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Preprocess and perform quality assessment of one or more SVS data sets.
+ Source: R/fmrs.R
+ preproc_svs_dataset.Rd
+
+
+
+ Preprocess and perform quality assessment of one or more SVS data sets.
+
+
+
+ preproc_svs_dataset(
+ paths,
+ labels = NULL,
+ output_dir = "spant_analysis",
+ exclude_labels = NULL,
+ overwrite = FALSE,
+ ref_inds = NULL,
+ return_results = FALSE
+)
+
+
+
+ Arguments
+ - paths
+paths to the fMRS data file or IMA directory.
- labels
+labels to describe each data set.
- output_dir
+output directory.
- exclude_labels
+vector of labels of scans to exclude, eg poor quality
+data.
- overwrite
+overwrite saved results, defaults to FALSE.
- ref_inds
+a vector of 1-based indices for any water reference dynamic
+scans.
- return_results
+function will return key outputs, defaults to FALSE.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/print.fit_result.html b/docs/reference/print.fit_result.html
index 297f28dc..5f434e57 100644
--- a/docs/reference/print.fit_result.html
+++ b/docs/reference/print.fit_result.html
@@ -1,5 +1,5 @@
-Print a summary of an object of class fit_result. — print.fit_result • Spectroscopy Analysis Tools (spant) Print a summary of an object of class fit_result. — print.fit_result • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -105,7 +105,7 @@ Arguments
diff --git a/docs/reference/print.mrs_data.html b/docs/reference/print.mrs_data.html
index 51199017..e1561eb2 100644
--- a/docs/reference/print.mrs_data.html
+++ b/docs/reference/print.mrs_data.html
@@ -1,5 +1,5 @@
-Print a summary of mrs_data parameters. — print.mrs_data • Spectroscopy Analysis Tools (spant) Print a summary of mrs_data parameters. — print.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -109,7 +109,7 @@ Arguments
diff --git a/docs/reference/qn_states.html b/docs/reference/qn_states.html
index 0f42f2f9..d7aa6715 100644
--- a/docs/reference/qn_states.html
+++ b/docs/reference/qn_states.html
@@ -1,5 +1,5 @@
-Get the quantum coherence matrix for a spin system. — qn_states • Spectroscopy Analysis Tools (spant) Get the quantum coherence matrix for a spin system. — qn_states • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/rats.html b/docs/reference/rats.html
index 5a39a396..93585e08 100644
--- a/docs/reference/rats.html
+++ b/docs/reference/rats.html
@@ -1,5 +1,5 @@
-Robust Alignment to a Target Spectrum (RATS). — rats • Spectroscopy Analysis Tools (spant) Robust Alignment to a Target Spectrum (RATS). — rats • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -207,7 +207,7 @@ Value
diff --git a/docs/reference/re_weighting.html b/docs/reference/re_weighting.html
index d21caf21..8b0b070a 100644
--- a/docs/reference/re_weighting.html
+++ b/docs/reference/re_weighting.html
@@ -1,5 +1,5 @@
-Apply a weighting to the FID to enhance spectral resolution. — re_weighting • Spectroscopy Analysis Tools (spant) Apply a weighting to the FID to enhance spectral resolution. — re_weighting • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/read_basis.html b/docs/reference/read_basis.html
index da9b94af..eb6f8557 100644
--- a/docs/reference/read_basis.html
+++ b/docs/reference/read_basis.html
@@ -1,5 +1,5 @@
-Read a basis file in LCModel .basis format. — read_basis • Spectroscopy Analysis Tools (spant) Read a basis file in LCModel .basis format. — read_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/read_ima_coil_dir.html b/docs/reference/read_ima_coil_dir.html
index 28c02de0..4f073cd8 100644
--- a/docs/reference/read_ima_coil_dir.html
+++ b/docs/reference/read_ima_coil_dir.html
@@ -1,9 +1,5 @@
-Read a directory containing Siemens MRS IMA files and combine along the coil
-dimension. Note that the coil ID is inferred from the sorted file name and
-should be checked when consistency is required between two directories. — read_ima_coil_dir • Spectroscopy Analysis Tools (spant) Read a directory containing Siemens MRS IMA files and combine along the coil dimension. Note that the coil ID is inferred from the sorted file name and should be checked when consistency is required between two directories. — read_ima_coil_dir • Spectroscopy Analysis Tools (spant) Read a directory containing Siemens MRS IMA files and combine along the
-dynamic dimension. Note that the coil ID is inferred from the sorted file
-name and should be checked when consistency is required. — read_ima_dyn_dir • Spectroscopy Analysis Tools (spant) Read a directory containing Siemens MRS IMA files and combine along the dynamic dimension. Note that the coil ID is inferred from the sorted file name and should be checked when consistency is required. — read_ima_dyn_dir • Spectroscopy Analysis Tools (spant) Read an LCModel formatted coord file containing fit information. — read_lcm_coord • Spectroscopy Analysis Tools (spant) Read an LCModel formatted coord file containing fit information. — read_lcm_coord • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -107,7 +107,7 @@ Value
diff --git a/docs/reference/read_mrs.html b/docs/reference/read_mrs.html
index 3ac2a36b..2cf36b20 100644
--- a/docs/reference/read_mrs.html
+++ b/docs/reference/read_mrs.html
@@ -1,5 +1,5 @@
-Read MRS data from a file. — read_mrs • Spectroscopy Analysis Tools (spant) Read MRS data from a file. — read_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -88,7 +88,8 @@ Read MRS data from a file.
full_fid = FALSE,
omit_svs_ref_scans = TRUE,
verbose = FALSE,
- extra = NULL
+ extra = NULL,
+ fid_filt_dist = NULL
)
@@ -140,6 +141,13 @@ Arguments
an optional data frame to provide additional variables for use
in subsequent analysis steps, eg id or grouping variables.
fid_filt_dist
+indicate if the data has a distorted FID due to a
+brick-wall filter being used to downsample the data. Default is to auto
+detect this from the data, but TRUE or FALSE options can be given to override
+detection.
Value
@@ -183,7 +191,7 @@ Examples
diff --git a/docs/reference/read_mrs_tqn.html b/docs/reference/read_mrs_tqn.html
index 5766362f..84bdaf3a 100644
--- a/docs/reference/read_mrs_tqn.html
+++ b/docs/reference/read_mrs_tqn.html
@@ -1,5 +1,5 @@
-Read MRS data using the TARQUIN software package. — read_mrs_tqn • Spectroscopy Analysis Tools (spant) Read MRS data using the TARQUIN software package. — read_mrs_tqn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -131,7 +131,7 @@ Examples
diff --git a/docs/reference/read_pulse_ascii.html b/docs/reference/read_pulse_ascii.html
index c9e0d43c..ab11c9cc 100644
--- a/docs/reference/read_pulse_ascii.html
+++ b/docs/reference/read_pulse_ascii.html
@@ -1,5 +1,5 @@
-Read an ASCII formatted pulse file. — read_pulse_ascii • Spectroscopy Analysis Tools (spant) Read an ASCII formatted pulse file. — read_pulse_ascii • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/read_pulse_bruker.html b/docs/reference/read_pulse_bruker.html
index c92bf76a..dbe9073b 100644
--- a/docs/reference/read_pulse_bruker.html
+++ b/docs/reference/read_pulse_bruker.html
@@ -1,5 +1,5 @@
-Read a Bruker formatted pulse file — read_pulse_bruker • Spectroscopy Analysis Tools (spant) Read a Bruker formatted pulse file — read_pulse_bruker • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/read_pulse_pta.html b/docs/reference/read_pulse_pta.html
index 72e1b6d4..a0fac3c3 100644
--- a/docs/reference/read_pulse_pta.html
+++ b/docs/reference/read_pulse_pta.html
@@ -1,5 +1,5 @@
-Read a .pta formatted pulse file compatible with Siemens PulseTool. — read_pulse_pta • Spectroscopy Analysis Tools (spant) Read a .pta formatted pulse file compatible with Siemens PulseTool. — read_pulse_pta • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/read_siemens_txt_hdr.html b/docs/reference/read_siemens_txt_hdr.html
index 23fb8c70..3a17d87c 100644
--- a/docs/reference/read_siemens_txt_hdr.html
+++ b/docs/reference/read_siemens_txt_hdr.html
@@ -1,5 +1,5 @@
-Read the text format header found in Siemens IMA and TWIX data files. — read_siemens_txt_hdr • Spectroscopy Analysis Tools (spant) Read the text format header found in Siemens IMA and TWIX data files. — read_siemens_txt_hdr • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -78,7 +78,7 @@ Read the text format header found in Siemens IMA and TWIX data files.
- read_siemens_txt_hdr(input, version = "vd", verbose, offset = 0)
+ read_siemens_txt_hdr(input, version = "vd", verbose = FALSE, offset = 0)
@@ -118,7 +118,7 @@ Value
diff --git a/docs/reference/read_tqn_fit.html b/docs/reference/read_tqn_fit.html
index 4da6c25e..a1630420 100644
--- a/docs/reference/read_tqn_fit.html
+++ b/docs/reference/read_tqn_fit.html
@@ -1,5 +1,5 @@
-Reader for csv fit results generated by TARQUIN. — read_tqn_fit • Spectroscopy Analysis Tools (spant) Reader for csv fit results generated by TARQUIN. — read_tqn_fit • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -113,7 +113,7 @@ Examples
diff --git a/docs/reference/read_tqn_result.html b/docs/reference/read_tqn_result.html
index 36659714..68a3e98c 100644
--- a/docs/reference/read_tqn_result.html
+++ b/docs/reference/read_tqn_result.html
@@ -1,5 +1,5 @@
-Reader for csv results generated by TARQUIN. — read_tqn_result • Spectroscopy Analysis Tools (spant) Reader for csv results generated by TARQUIN. — read_tqn_result • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -117,7 +117,7 @@ Examples
diff --git a/docs/reference/recon_imag.html b/docs/reference/recon_imag.html
index d2a72225..5bc3b1eb 100644
--- a/docs/reference/recon_imag.html
+++ b/docs/reference/recon_imag.html
@@ -1,7 +1,5 @@
-Reconstruct complex time-domain data from the real part of frequency-domain
-data. — recon_imag • Spectroscopy Analysis Tools (spant) Reconstruct complex time-domain data from the real part of frequency-domain data. — recon_imag • Spectroscopy Analysis Tools (spant) Reconstruct complex time-domain data from the real part of frequency-domain
-data. — recon_imag_vec • Spectroscopy Analysis Tools (spant) Reconstruct complex time-domain data from the real part of frequency-domain data. — recon_imag_vec • Spectroscopy Analysis Tools (spant) Reconstruct 2D MRSI data from a twix file loaded with read_mrs. — recon_twix_2d_mrsi • Spectroscopy Analysis Tools (spant) Reconstruct 2D MRSI data from a twix file loaded with read_mrs. — recon_twix_2d_mrsi • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/rectangular_mask.html b/docs/reference/rectangular_mask.html
index a2117283..6e469bc9 100644
--- a/docs/reference/rectangular_mask.html
+++ b/docs/reference/rectangular_mask.html
@@ -1,5 +1,5 @@
-Create a rectangular mask stored as a matrix of logical values. — rectangular_mask • Spectroscopy Analysis Tools (spant) Create a rectangular mask stored as a matrix of logical values. — rectangular_mask • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -130,7 +130,7 @@ Value
diff --git a/docs/reference/reexports.html b/docs/reference/reexports.html
index 694a75d1..a59e8379 100644
--- a/docs/reference/reexports.html
+++ b/docs/reference/reexports.html
@@ -1,5 +1,5 @@
-Objects exported from other packages — reexports • Spectroscopy Analysis Tools (spant) Objects exported from other packages — reexports • Spectroscopy Analysis Tools (spant)
Spectroscopy Analysis Tools (spant)
- 2.21.0
+ 2.22.0
@@ -103,7 +103,7 @@ Objects exported from other packages
diff --git a/docs/reference/rep_array_dim.html b/docs/reference/rep_array_dim.html
index b9c49b4a..48c0a5ed 100644
--- a/docs/reference/rep_array_dim.html
+++ b/docs/reference/rep_array_dim.html
@@ -1,5 +1,5 @@
-Repeat an array over a given dimension. — rep_array_dim • Spectroscopy Analysis Tools (spant) Repeat an array over a given dimension. — rep_array_dim • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/rep_dyn.html b/docs/reference/rep_dyn.html
index 6bbfb0ef..89a4bb9b 100644
--- a/docs/reference/rep_dyn.html
+++ b/docs/reference/rep_dyn.html
@@ -1,5 +1,5 @@
-Replicate a scan in the dynamic dimension. — rep_dyn • Spectroscopy Analysis Tools (spant) Replicate a scan in the dynamic dimension. — rep_dyn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/rep_mrs.html b/docs/reference/rep_mrs.html
index 67730b5c..becb8f00 100644
--- a/docs/reference/rep_mrs.html
+++ b/docs/reference/rep_mrs.html
@@ -1,5 +1,5 @@
-Replicate a scan over a given dimension. — rep_mrs • Spectroscopy Analysis Tools (spant) Replicate a scan over a given dimension. — rep_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -138,7 +138,7 @@ Value
diff --git a/docs/reference/resample_basis.html b/docs/reference/resample_basis.html
index b0f2ab17..c7a6222a 100644
--- a/docs/reference/resample_basis.html
+++ b/docs/reference/resample_basis.html
@@ -1,5 +1,5 @@
-Resample a basis-set to match a mrs_data acquisition. — resample_basis • Spectroscopy Analysis Tools (spant) Resample a basis-set to match a mrs_data acquisition. — resample_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -116,7 +116,7 @@ Value
diff --git a/docs/reference/resample_img.html b/docs/reference/resample_img.html
index f1e7beaf..b0cc8f71 100644
--- a/docs/reference/resample_img.html
+++ b/docs/reference/resample_img.html
@@ -1,5 +1,5 @@
-Resample an image to match a target image space. — resample_img • Spectroscopy Analysis Tools (spant) Resample an image to match a target image space. — resample_img • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/resample_voi.html b/docs/reference/resample_voi.html
index 8fbfa836..a29ab096 100644
--- a/docs/reference/resample_voi.html
+++ b/docs/reference/resample_voi.html
@@ -1,7 +1,5 @@
-Resample a VOI to match a target image space using nearest-neighbour
-interpolation. — resample_voi • Spectroscopy Analysis Tools (spant) Resample a VOI to match a target image space using nearest-neighbour interpolation. — resample_voi • Spectroscopy Analysis Tools (spant) Reslice a nifti object to match the orientation of mrs data. — reslice_to_mrs • Spectroscopy Analysis Tools (spant) Reslice a nifti object to match the orientation of mrs data. — reslice_to_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/reson_table2mrs_data.html b/docs/reference/reson_table2mrs_data.html
index d75579ee..c5a2167a 100644
--- a/docs/reference/reson_table2mrs_data.html
+++ b/docs/reference/reson_table2mrs_data.html
@@ -1,5 +1,5 @@
-Generate mrs_data from a table of single Lorentzian resonances. — reson_table2mrs_data • Spectroscopy Analysis Tools (spant) Generate mrs_data from a table of single Lorentzian resonances. — reson_table2mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -119,7 +119,7 @@ Value
diff --git a/docs/reference/rm_dyns.html b/docs/reference/rm_dyns.html
index 5d5ef692..573e1f51 100644
--- a/docs/reference/rm_dyns.html
+++ b/docs/reference/rm_dyns.html
@@ -1,5 +1,5 @@
-Remove a subset of dynamic scans. — rm_dyns • Spectroscopy Analysis Tools (spant) Remove a subset of dynamic scans. — rm_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/scale_amp_molal.html b/docs/reference/scale_amp_molal.html
index aaeee1f2..7acb8cb0 100644
--- a/docs/reference/scale_amp_molal.html
+++ b/docs/reference/scale_amp_molal.html
@@ -1,7 +1,5 @@
-Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water). — scale_amp_molal • Spectroscopy Analysis Tools (spant) Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / kg of tissue water). — scale_amp_molal • Spectroscopy Analysis Tools (spant)
Spectroscopy Analysis Tools (spant)
- 2.21.0
+ 2.22.0
@@ -76,8 +74,7 @@
- Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water).
+ Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / kg of tissue water).
Source: R/amp_scaling.R
scale_amp_molal.Rd
@@ -163,7 +160,7 @@ Value
diff --git a/docs/reference/scale_amp_molal_pvc.html b/docs/reference/scale_amp_molal_pvc.html
index 962d6afc..4d194abd 100644
--- a/docs/reference/scale_amp_molal_pvc.html
+++ b/docs/reference/scale_amp_molal_pvc.html
@@ -1,7 +1,5 @@
-Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water). — scale_amp_molal_pvc • Spectroscopy Analysis Tools (spant)
@@ -75,8 +73,7 @@
- Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water).
+ Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / kg of tissue water).
Source: R/amp_scaling.R
scale_amp_molal_pvc.Rd
@@ -141,7 +138,7 @@ Value
diff --git a/docs/reference/scale_amp_molar.html b/docs/reference/scale_amp_molar.html
index 02358d91..dc87a338 100644
--- a/docs/reference/scale_amp_molar.html
+++ b/docs/reference/scale_amp_molar.html
@@ -1,7 +1,5 @@
-Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / Litre of tissue). — scale_amp_molar • Spectroscopy Analysis Tools (spant) Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / Litre of tissue). — scale_amp_molar • Spectroscopy Analysis Tools (spant) Convert default LCM/TARQUIN concentration scaling to molal units with partial
-volume correction. — scale_amp_molar2molal_pvc • Spectroscopy Analysis Tools (spant) Convert default LCM/TARQUIN concentration scaling to molal units with partial volume correction. — scale_amp_molar2molal_pvc • Spectroscopy Analysis Tools (spant) Scale fitted amplitudes to a ratio of signal amplitude. — scale_amp_ratio • Spectroscopy Analysis Tools (spant) Scale fitted amplitudes to a ratio of signal amplitude. — scale_amp_ratio • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -116,7 +116,7 @@ Value
diff --git a/docs/reference/scale_amp_ratio_value.html b/docs/reference/scale_amp_ratio_value.html
index 2036837a..6af8ac51 100644
--- a/docs/reference/scale_amp_ratio_value.html
+++ b/docs/reference/scale_amp_ratio_value.html
@@ -1,5 +1,5 @@
-Scale fitted amplitudes to a ratio of signal amplitude. — scale_amp_ratio_value • Spectroscopy Analysis Tools (spant) Scale fitted amplitudes to a ratio of signal amplitude. — scale_amp_ratio_value • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/scale_amp_water_ratio.html b/docs/reference/scale_amp_water_ratio.html
index 5b25e884..35a76b00 100644
--- a/docs/reference/scale_amp_water_ratio.html
+++ b/docs/reference/scale_amp_water_ratio.html
@@ -1,5 +1,5 @@
-Scale metabolite amplitudes as a ratio to the unsuppressed water amplitude. — scale_amp_water_ratio • Spectroscopy Analysis Tools (spant) Scale metabolite amplitudes as a ratio to the unsuppressed water amplitude. — scale_amp_water_ratio • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/scale_basis_amp.html b/docs/reference/scale_basis_amp.html
index 9401c3f1..5a58b5e5 100644
--- a/docs/reference/scale_basis_amp.html
+++ b/docs/reference/scale_basis_amp.html
@@ -1,5 +1,5 @@
-Scale a basis object by a scalar. — scale_basis_amp • Spectroscopy Analysis Tools (spant) Scale a basis object by a scalar. — scale_basis_amp • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/scale_basis_from_singlet.html b/docs/reference/scale_basis_from_singlet.html
index 0d542bc8..c9a19e77 100644
--- a/docs/reference/scale_basis_from_singlet.html
+++ b/docs/reference/scale_basis_from_singlet.html
@@ -1,5 +1,5 @@
-Scale a basis-set to be consistent with spant assumptions for water scaling. — scale_basis_from_singlet • Spectroscopy Analysis Tools (spant) Scale a basis-set to be consistent with spant assumptions for water scaling. — scale_basis_from_singlet • Spectroscopy Analysis Tools (spant)
Spectroscopy Analysis Tools (spant)
- 2.21.0
+ 2.22.0
@@ -127,7 +127,7 @@ Value
diff --git a/docs/reference/scale_mrs_amp.html b/docs/reference/scale_mrs_amp.html
index b5501a0d..990f058a 100644
--- a/docs/reference/scale_mrs_amp.html
+++ b/docs/reference/scale_mrs_amp.html
@@ -1,5 +1,5 @@
-Scale an mrs_data object by a scalar or vector or amplitudes. — scale_mrs_amp • Spectroscopy Analysis Tools (spant) Scale an mrs_data object by a scalar or vector or amplitudes. — scale_mrs_amp • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/scale_spec.html b/docs/reference/scale_spec.html
index 4f6ea835..6b3ddba4 100644
--- a/docs/reference/scale_spec.html
+++ b/docs/reference/scale_spec.html
@@ -1,5 +1,5 @@
-Scale mrs_data to a spectral region. — scale_spec • Spectroscopy Analysis Tools (spant) Scale mrs_data to a spectral region. — scale_spec • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -141,7 +141,7 @@ Value
diff --git a/docs/reference/sd.html b/docs/reference/sd.html
index ea1eec9f..3ae4dfd4 100644
--- a/docs/reference/sd.html
+++ b/docs/reference/sd.html
@@ -1,5 +1,5 @@
-Calculate the standard deviation spectrum from an mrs_data object. — sd • Spectroscopy Analysis Tools (spant) Calculate the standard deviation spectrum from an mrs_data object. — sd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/sd.mrs_data.html b/docs/reference/sd.mrs_data.html
index 3f92a49f..13bdda85 100644
--- a/docs/reference/sd.mrs_data.html
+++ b/docs/reference/sd.mrs_data.html
@@ -1,5 +1,5 @@
-Calculate the standard deviation spectrum from an mrs_data object. — sd.mrs_data • Spectroscopy Analysis Tools (spant) Calculate the standard deviation spectrum from an mrs_data object. — sd.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/seconds.html b/docs/reference/seconds.html
index b34d6627..467ee17f 100644
--- a/docs/reference/seconds.html
+++ b/docs/reference/seconds.html
@@ -1,5 +1,5 @@
-Return a time scale vector to match the FID of an MRS data object. — seconds • Spectroscopy Analysis Tools (spant) Return a time scale vector to match the FID of an MRS data object. — seconds • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/seq_cpmg_ideal.html b/docs/reference/seq_cpmg_ideal.html
index 547e96ab..45727c86 100644
--- a/docs/reference/seq_cpmg_ideal.html
+++ b/docs/reference/seq_cpmg_ideal.html
@@ -1,5 +1,5 @@
-CPMG style sequence with ideal pulses. — seq_cpmg_ideal • Spectroscopy Analysis Tools (spant) CPMG style sequence with ideal pulses. — seq_cpmg_ideal • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/seq_mega_press_ideal.html b/docs/reference/seq_mega_press_ideal.html
index 0769b8b4..a9cd7fa0 100644
--- a/docs/reference/seq_mega_press_ideal.html
+++ b/docs/reference/seq_mega_press_ideal.html
@@ -1,7 +1,5 @@
-MEGA-PRESS sequence with ideal localisation pulses and Gaussian shaped
-editing pulse. — seq_mega_press_ideal • Spectroscopy Analysis Tools (spant) MEGA-PRESS sequence with ideal localisation pulses and Gaussian shaped editing pulse. — seq_mega_press_ideal • Spectroscopy Analysis Tools (spant) PRESS sequence with shaped refocusing pulses. — seq_press_2d_shaped • Spectroscopy Analysis Tools (spant) PRESS sequence with shaped refocusing pulses. — seq_press_2d_shaped • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -165,7 +165,7 @@ Value
diff --git a/docs/reference/seq_press_ideal.html b/docs/reference/seq_press_ideal.html
index 8c976856..72c3af3d 100644
--- a/docs/reference/seq_press_ideal.html
+++ b/docs/reference/seq_press_ideal.html
@@ -1,5 +1,5 @@
-PRESS sequence with ideal pulses. — seq_press_ideal • Spectroscopy Analysis Tools (spant) PRESS sequence with ideal pulses. — seq_press_ideal • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/seq_pulse_acquire.html b/docs/reference/seq_pulse_acquire.html
index 4a88fc64..ad80571e 100644
--- a/docs/reference/seq_pulse_acquire.html
+++ b/docs/reference/seq_pulse_acquire.html
@@ -1,5 +1,5 @@
-Simple pulse and acquire sequence with ideal pulses. — seq_pulse_acquire • Spectroscopy Analysis Tools (spant) Simple pulse and acquire sequence with ideal pulses. — seq_pulse_acquire • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/seq_slaser_ideal.html b/docs/reference/seq_slaser_ideal.html
index 74688f4d..eb83e8e3 100644
--- a/docs/reference/seq_slaser_ideal.html
+++ b/docs/reference/seq_slaser_ideal.html
@@ -1,5 +1,5 @@
-sLASER sequence with ideal pulses. — seq_slaser_ideal • Spectroscopy Analysis Tools (spant) sLASER sequence with ideal pulses. — seq_slaser_ideal • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -126,7 +126,7 @@ Value
diff --git a/docs/reference/seq_spin_echo_ideal.html b/docs/reference/seq_spin_echo_ideal.html
index e23271de..4248716f 100644
--- a/docs/reference/seq_spin_echo_ideal.html
+++ b/docs/reference/seq_spin_echo_ideal.html
@@ -1,5 +1,5 @@
-Spin echo sequence with ideal pulses. — seq_spin_echo_ideal • Spectroscopy Analysis Tools (spant) Spin echo sequence with ideal pulses. — seq_spin_echo_ideal • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/seq_steam_ideal.html b/docs/reference/seq_steam_ideal.html
index a60685a8..1c8115d7 100644
--- a/docs/reference/seq_steam_ideal.html
+++ b/docs/reference/seq_steam_ideal.html
@@ -1,5 +1,5 @@
-STEAM sequence with ideal pulses. — seq_steam_ideal • Spectroscopy Analysis Tools (spant) STEAM sequence with ideal pulses. — seq_steam_ideal • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -128,7 +128,7 @@ Value
diff --git a/docs/reference/seq_steam_ideal_cof.html b/docs/reference/seq_steam_ideal_cof.html
index 8f225740..cba7af91 100644
--- a/docs/reference/seq_steam_ideal_cof.html
+++ b/docs/reference/seq_steam_ideal_cof.html
@@ -1,7 +1,5 @@
-STEAM sequence with ideal pulses and coherence order filtering to simulate
-gradient crushers. — seq_steam_ideal_cof • Spectroscopy Analysis Tools (spant) STEAM sequence with ideal pulses and coherence order filtering to simulate gradient crushers. — seq_steam_ideal_cof • Spectroscopy Analysis Tools (spant) STEAM sequence with ideal pulses using the z-rotation gradient simulation
-method described by Young et al JMR 140, 146-152 (1999). — seq_steam_ideal_young • Spectroscopy Analysis Tools (spant) STEAM sequence with ideal pulses using the z-rotation gradient simulation method described by Young et al JMR 140, 146-152 (1999). — seq_steam_ideal_young • Spectroscopy Analysis Tools (spant) Set the number of transients for an mrs_data object. — set_Ntrans • Spectroscopy Analysis Tools (spant) Set the number of transients for an mrs_data object. — set_Ntrans • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/set_def_acq_paras.html b/docs/reference/set_def_acq_paras.html
index 3e1b4004..cc2ada9c 100644
--- a/docs/reference/set_def_acq_paras.html
+++ b/docs/reference/set_def_acq_paras.html
@@ -1,5 +1,5 @@
-Set the default acquisition parameters. — set_def_acq_paras • Spectroscopy Analysis Tools (spant) Set the default acquisition parameters. — set_def_acq_paras • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Arguments
diff --git a/docs/reference/set_lcm_cmd.html b/docs/reference/set_lcm_cmd.html
index 2056ed01..42bb2f24 100644
--- a/docs/reference/set_lcm_cmd.html
+++ b/docs/reference/set_lcm_cmd.html
@@ -1,5 +1,5 @@
-Set the command to run the LCModel command-line program. — set_lcm_cmd • Spectroscopy Analysis Tools (spant) Set the command to run the LCModel command-line program. — set_lcm_cmd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/set_lw.html b/docs/reference/set_lw.html
index b64ec851..bb176c62 100644
--- a/docs/reference/set_lw.html
+++ b/docs/reference/set_lw.html
@@ -1,5 +1,5 @@
-Apply line-broadening to an mrs_data object to achieve a specified linewidth. — set_lw • Spectroscopy Analysis Tools (spant) Apply line-broadening to an mrs_data object to achieve a specified linewidth. — set_lw • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -123,7 +123,7 @@ Value
diff --git a/docs/reference/set_mask_xy_mat.html b/docs/reference/set_mask_xy_mat.html
index 49dc5d4e..52c4b617 100644
--- a/docs/reference/set_mask_xy_mat.html
+++ b/docs/reference/set_mask_xy_mat.html
@@ -1,5 +1,5 @@
-Set the masked voxels in a 2D MRSI dataset to given spectrum. — set_mask_xy_mat • Spectroscopy Analysis Tools (spant) Set the masked voxels in a 2D MRSI dataset to given spectrum. — set_mask_xy_mat • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Value
diff --git a/docs/reference/set_precomp_mode.html b/docs/reference/set_precomp_mode.html
index f44bd5d3..47c28e3b 100644
--- a/docs/reference/set_precomp_mode.html
+++ b/docs/reference/set_precomp_mode.html
@@ -1,5 +1,5 @@
-Set the precompute mode. — set_precomp_mode • Spectroscopy Analysis Tools (spant) Set the precompute mode. — set_precomp_mode • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/set_precomp_verbose.html b/docs/reference/set_precomp_verbose.html
index 1453a231..9c613505 100644
--- a/docs/reference/set_precomp_verbose.html
+++ b/docs/reference/set_precomp_verbose.html
@@ -1,5 +1,5 @@
-Set the verbosity of the precompute function. — set_precomp_verbose • Spectroscopy Analysis Tools (spant) Set the verbosity of the precompute function. — set_precomp_verbose • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/set_ref.html b/docs/reference/set_ref.html
index 8953fa50..5436dfa2 100644
--- a/docs/reference/set_ref.html
+++ b/docs/reference/set_ref.html
@@ -1,5 +1,5 @@
-Set the ppm reference value (eg ppm value at 0Hz). — set_ref • Spectroscopy Analysis Tools (spant) Set the ppm reference value (eg ppm value at 0Hz). — set_ref • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/set_td_pts.html b/docs/reference/set_td_pts.html
index 8a80d42a..586459ff 100644
--- a/docs/reference/set_td_pts.html
+++ b/docs/reference/set_td_pts.html
@@ -1,7 +1,5 @@
-Set the number of time-domain data points, truncating or zero-filling as
-appropriate. — set_td_pts • Spectroscopy Analysis Tools (spant) Set the number of time-domain data points, truncating or zero-filling as appropriate. — set_td_pts • Spectroscopy Analysis Tools (spant) Set the command to run the TARQUIN command-line program. — set_tqn_cmd • Spectroscopy Analysis Tools (spant) Set the command to run the TARQUIN command-line program. — set_tqn_cmd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/set_tr.html b/docs/reference/set_tr.html
index b2109ab0..65c9df5f 100644
--- a/docs/reference/set_tr.html
+++ b/docs/reference/set_tr.html
@@ -1,5 +1,5 @@
-Set the repetition time of an MRS dataset. — set_tr • Spectroscopy Analysis Tools (spant) Set the repetition time of an MRS dataset. — set_tr • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/shift.html b/docs/reference/shift.html
index ab0fe724..034591d0 100644
--- a/docs/reference/shift.html
+++ b/docs/reference/shift.html
@@ -1,5 +1,5 @@
-Apply a frequency shift to MRS data. — shift • Spectroscopy Analysis Tools (spant) Apply a frequency shift to MRS data. — shift • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/shift_basis.html b/docs/reference/shift_basis.html
index 2884be19..f55a65e0 100644
--- a/docs/reference/shift_basis.html
+++ b/docs/reference/shift_basis.html
@@ -1,5 +1,5 @@
-Apply frequency shifts to basis set signals. — shift_basis • Spectroscopy Analysis Tools (spant) Apply frequency shifts to basis set signals. — shift_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Value
diff --git a/docs/reference/sim_basis.html b/docs/reference/sim_basis.html
index c7838c46..bb5fefc6 100644
--- a/docs/reference/sim_basis.html
+++ b/docs/reference/sim_basis.html
@@ -1,5 +1,5 @@
-Simulate a basis set object. — sim_basis • Spectroscopy Analysis Tools (spant) Simulate a basis set object. — sim_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -136,7 +136,7 @@ Value
diff --git a/docs/reference/sim_basis_1h_brain.html b/docs/reference/sim_basis_1h_brain.html
index 62ed7389..f71ffa0b 100644
--- a/docs/reference/sim_basis_1h_brain.html
+++ b/docs/reference/sim_basis_1h_brain.html
@@ -1,7 +1,5 @@
-Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS
-sequence. Note, ideal pulses are assumed. — sim_basis_1h_brain • Spectroscopy Analysis Tools (spant) Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS sequence. Note, ideal pulses are assumed. — sim_basis_1h_brain • Spectroscopy Analysis Tools (spant) Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS
-sequence. Note, ideal pulses are assumed. — sim_basis_1h_brain_press • Spectroscopy Analysis Tools (spant) Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS sequence. Note, ideal pulses are assumed. — sim_basis_1h_brain_press • Spectroscopy Analysis Tools (spant) Simulate a macromolecular and lipid basis-set suitable for 1H brain MRS
-analysis. — sim_basis_mm_lip_lcm • Spectroscopy Analysis Tools (spant) Simulate a macromolecular and lipid basis-set suitable for 1H brain MRS analysis. — sim_basis_mm_lip_lcm • Spectroscopy Analysis Tools (spant) Simulate a basis file using TARQUIN. — sim_basis_tqn • Spectroscopy Analysis Tools (spant) Simulate a basis file using TARQUIN. — sim_basis_tqn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -129,7 +129,7 @@ Examples
diff --git a/docs/reference/sim_brain_1h.html b/docs/reference/sim_brain_1h.html
index 2044cf1a..717ee289 100644
--- a/docs/reference/sim_brain_1h.html
+++ b/docs/reference/sim_brain_1h.html
@@ -1,5 +1,5 @@
-Simulate MRS data with a similar appearance to normal brain (by default). — sim_brain_1h • Spectroscopy Analysis Tools (spant) Simulate MRS data with a similar appearance to normal brain (by default). — sim_brain_1h • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -159,7 +159,7 @@ Value
diff --git a/docs/reference/sim_mol.html b/docs/reference/sim_mol.html
index 23bcef50..77f76a50 100644
--- a/docs/reference/sim_mol.html
+++ b/docs/reference/sim_mol.html
@@ -1,5 +1,5 @@
-Simulate a mol_parameter object. — sim_mol • Spectroscopy Analysis Tools (spant) Simulate a mol_parameter object. — sim_mol • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -143,7 +143,7 @@ Value
diff --git a/docs/reference/sim_noise.html b/docs/reference/sim_noise.html
index 23875f79..a71477d4 100644
--- a/docs/reference/sim_noise.html
+++ b/docs/reference/sim_noise.html
@@ -1,5 +1,5 @@
-Simulate an mrs_data object containing simulated Gaussian noise. — sim_noise • Spectroscopy Analysis Tools (spant) Simulate an mrs_data object containing simulated Gaussian noise. — sim_noise • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -84,6 +84,7 @@ Simulate an mrs_data object containing simulated Gaussian noise.
ft = def_ft(),
N = def_N(),
ref = def_ref(),
+ nuc = def_nuc(),
dyns = 1,
fd = TRUE
)
@@ -111,6 +112,10 @@ Arguments
reference value for ppm scale.
nuc
+resonant nucleus.
dyns
number of dynamic scans to generate.
Value
diff --git a/docs/reference/sim_resonances.html b/docs/reference/sim_resonances.html
index 19e9a8a4..d4f8d7c0 100644
--- a/docs/reference/sim_resonances.html
+++ b/docs/reference/sim_resonances.html
@@ -1,5 +1,5 @@
-Simulate a MRS data object containing a set of simulated resonances. — sim_resonances • Spectroscopy Analysis Tools (spant) Simulate a MRS data object containing a set of simulated resonances. — sim_resonances • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -161,7 +161,7 @@ Examples
diff --git a/docs/reference/sim_th_excit_profile.html b/docs/reference/sim_th_excit_profile.html
index 5535c5ef..e781cab1 100644
--- a/docs/reference/sim_th_excit_profile.html
+++ b/docs/reference/sim_th_excit_profile.html
@@ -1,7 +1,5 @@
-Simulate an ideal pulse excitation profile by smoothing a top-hat function
-with a Gaussian. — sim_th_excit_profile • Spectroscopy Analysis Tools (spant) Simulate an ideal pulse excitation profile by smoothing a top-hat function with a Gaussian. — sim_th_excit_profile • Spectroscopy Analysis Tools (spant) Simulate an mrs_data object containing complex zero valued samples. — sim_zero • Spectroscopy Analysis Tools (spant) Simulate an mrs_data object containing complex zero valued samples. — sim_zero • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -78,7 +78,14 @@ Simulate an mrs_data object containing complex zero valued samples.
-
+
@@ -99,6 +106,10 @@ Arguments
reference value for ppm scale.
nuc
+resonant nucleus.
dyns
number of dynamic scans to generate.
Value
diff --git a/docs/reference/smooth_dyns.html b/docs/reference/smooth_dyns.html
index 4cc8da50..accf3a51 100644
--- a/docs/reference/smooth_dyns.html
+++ b/docs/reference/smooth_dyns.html
@@ -1,5 +1,5 @@
-Smooth data across the dynamic dimension with a Gaussian kernel. — smooth_dyns • Spectroscopy Analysis Tools (spant) Smooth data across the dynamic dimension with a Gaussian kernel. — smooth_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/sort_basis.html b/docs/reference/sort_basis.html
index 6a676ea2..d25cc006 100644
--- a/docs/reference/sort_basis.html
+++ b/docs/reference/sort_basis.html
@@ -1,5 +1,5 @@
-Sort the basis-set elements alphabetically. — sort_basis • Spectroscopy Analysis Tools (spant) Sort the basis-set elements alphabetically. — sort_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/spant-package.html b/docs/reference/spant-package.html
index b3dd8e21..90f19ec3 100644
--- a/docs/reference/spant-package.html
+++ b/docs/reference/spant-package.html
@@ -1,5 +1,5 @@
-spant: spectroscopy analysis tools. — spant-package • Spectroscopy Analysis Tools (spant) spant: spectroscopy analysis tools. — spant-package • Spectroscopy Analysis Tools (spant) Simulate and fit some spectra with ABfit for benchmarking purposes. Basic
-timing and performance metrics will be printed. — spant_abfit_benchmark • Spectroscopy Analysis Tools (spant) Simulate and fit some spectra with ABfit for benchmarking purposes. Basic timing and performance metrics will be printed. — spant_abfit_benchmark • Spectroscopy Analysis Tools (spant) Example MEGA-PRESS data with significant B0 drift. — spant_mpress_drift • Spectroscopy Analysis Tools (spant) Example MEGA-PRESS data with significant B0 drift. — spant_mpress_drift • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -83,7 +83,7 @@ Example MEGA-PRESS data with significant B0 drift.
Format
- An object of class mrs_data of length 13.
+ An object of class mrs_data of dimension 1 x 1 x 1 x 1 x 40 x 1 x 1024.
@@ -98,7 +98,7 @@ Format
diff --git a/docs/reference/spant_sim_fmrs_dataset.html b/docs/reference/spant_sim_fmrs_dataset.html
new file mode 100644
index 00000000..00e48b56
--- /dev/null
+++ b/docs/reference/spant_sim_fmrs_dataset.html
@@ -0,0 +1,117 @@
+
+Simulate an example fMRS dataset for a block design fMRS experiment and export a BIDS structure. — spant_sim_fmrs_dataset • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Simulate an example fMRS dataset for a block design fMRS experiment and export a BIDS structure.
+ Source: R/fmrs.R
+ spant_sim_fmrs_dataset.Rd
+
+
+
+ Simulate an example fMRS dataset for a block design fMRS experiment and
+export a BIDS structure.
+
+
+
+ spant_sim_fmrs_dataset(output_dir = NULL)
+
+
+
+ Arguments
+ - output_dir
+output directory for the BIDS data. Defaults to :
+"HOME/sim_fmrs_dataset/data".
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/spant_simulation_benchmark.html b/docs/reference/spant_simulation_benchmark.html
index 32daa8bf..d8cc6841 100644
--- a/docs/reference/spant_simulation_benchmark.html
+++ b/docs/reference/spant_simulation_benchmark.html
@@ -1,7 +1,5 @@
-Simulate a typical metabolite basis set for benchmarking. Timing metrics will
-be printed on completion. — spant_simulation_benchmark • Spectroscopy Analysis Tools (spant) Simulate a typical metabolite basis set for benchmarking. Timing metrics will be printed on completion. — spant_simulation_benchmark • Spectroscopy Analysis Tools (spant) Decompose an mrs_data object into white and gray matter spectra. — spec_decomp • Spectroscopy Analysis Tools (spant) Perform a mathematical operation on a spectral region. — spec_op • Spectroscopy Analysis Tools (spant) Perform a mathematical operation on a spectral region. — spec_op • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -98,8 +98,8 @@ Arguments
operator
-can be "sum" (default), "mean", "l2", "max", "min" or
-"max-min".
can be "sum" (default), "mean", "l2", "max", "max_cplx,
+"min" or "max-min".
freq_scale
@@ -129,7 +129,7 @@ Value
diff --git a/docs/reference/spin_sys.html b/docs/reference/spin_sys.html
index 853423a4..1eaa9e76 100644
--- a/docs/reference/spin_sys.html
+++ b/docs/reference/spin_sys.html
@@ -1,5 +1,5 @@
-Create a spin system object for pulse sequence simulation. — spin_sys • Spectroscopy Analysis Tools (spant) Create a spin system object for pulse sequence simulation. — spin_sys • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/spm_pve2categorical.html b/docs/reference/spm_pve2categorical.html
index 23a1bad9..70f10729 100644
--- a/docs/reference/spm_pve2categorical.html
+++ b/docs/reference/spm_pve2categorical.html
@@ -1,7 +1,5 @@
-Convert SPM style segmentation files to a single categorical image where
-the numerical values map as: 0) Other, 1) CSF, 2) GM and 3) WM. — spm_pve2categorical • Spectroscopy Analysis Tools (spant) Convert SPM style segmentation files to a single categorical image where the numerical values map as: 0) Other, 1) CSF, 2) GM and 3) WM. — spm_pve2categorical • Spectroscopy Analysis Tools (spant) Signal space projection method for lipid suppression. — ssp • Spectroscopy Analysis Tools (spant) Signal space projection method for lipid suppression. — ssp • Spectroscopy Analysis Tools (spant) Plot the fitting results of an object of class fit_result with
-individual basis set components shown. — stackplot.fit_result • Spectroscopy Analysis Tools (spant) Plot the fitting results of an object of class fit_result with individual basis set components shown. — stackplot.fit_result • Spectroscopy Analysis Tools (spant) Produce a plot with multiple traces. — stackplot • Spectroscopy Analysis Tools (spant) Produce a plot with multiple traces. — stackplot • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/stackplot.mrs_data.html b/docs/reference/stackplot.mrs_data.html
index 17ff5648..64eea445 100644
--- a/docs/reference/stackplot.mrs_data.html
+++ b/docs/reference/stackplot.mrs_data.html
@@ -1,5 +1,5 @@
-Stackplot plotting method for objects of class mrs_data. — stackplot.mrs_data • Spectroscopy Analysis Tools (spant) Stackplot plotting method for objects of class mrs_data. — stackplot.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -255,7 +255,7 @@ Arguments
diff --git a/docs/reference/sub_first_dyn.html b/docs/reference/sub_first_dyn.html
index dbd7f831..493b7242 100644
--- a/docs/reference/sub_first_dyn.html
+++ b/docs/reference/sub_first_dyn.html
@@ -1,5 +1,5 @@
-Subtract the first dynamic spectrum from a dynamic series. — sub_first_dyn • Spectroscopy Analysis Tools (spant) Subtract the first dynamic spectrum from a dynamic series. — sub_first_dyn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/sub_mean_dyns.html b/docs/reference/sub_mean_dyns.html
index 6e3bb2df..221bd0c1 100644
--- a/docs/reference/sub_mean_dyns.html
+++ b/docs/reference/sub_mean_dyns.html
@@ -1,5 +1,5 @@
-Subtract the mean dynamic spectrum from a dynamic series. — sub_mean_dyns • Spectroscopy Analysis Tools (spant) Subtract the mean dynamic spectrum from a dynamic series. — sub_mean_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/sub_median_dyns.html b/docs/reference/sub_median_dyns.html
index 134c495d..1e834f14 100644
--- a/docs/reference/sub_median_dyns.html
+++ b/docs/reference/sub_median_dyns.html
@@ -1,5 +1,5 @@
-Subtract the median dynamic spectrum from a dynamic series. — sub_median_dyns • Spectroscopy Analysis Tools (spant) Subtract the median dynamic spectrum from a dynamic series. — sub_median_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/sum_coils.html b/docs/reference/sum_coils.html
index 7bf559f2..e1ab3cc0 100644
--- a/docs/reference/sum_coils.html
+++ b/docs/reference/sum_coils.html
@@ -1,5 +1,5 @@
-Calculate the sum across receiver coil elements. — sum_coils • Spectroscopy Analysis Tools (spant) Calculate the sum across receiver coil elements. — sum_coils • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/sum_dyns.html b/docs/reference/sum_dyns.html
index a0be19d3..bbda2ffc 100644
--- a/docs/reference/sum_dyns.html
+++ b/docs/reference/sum_dyns.html
@@ -1,5 +1,5 @@
-Calculate the sum of data dynamics. — sum_dyns • Spectroscopy Analysis Tools (spant) Calculate the sum of data dynamics. — sum_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/sum_mrs.html b/docs/reference/sum_mrs.html
index a22f215b..3cc3ab9e 100644
--- a/docs/reference/sum_mrs.html
+++ b/docs/reference/sum_mrs.html
@@ -1,5 +1,5 @@
-Sum two mrs_data objects. — sum_mrs • Spectroscopy Analysis Tools (spant) Sum two mrs_data objects. — sum_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Value
diff --git a/docs/reference/sum_mrs_list.html b/docs/reference/sum_mrs_list.html
index f4e09aea..c3584348 100644
--- a/docs/reference/sum_mrs_list.html
+++ b/docs/reference/sum_mrs_list.html
@@ -1,5 +1,5 @@
-Return the sum of a list of mrs_data objects. — sum_mrs_list • Spectroscopy Analysis Tools (spant) Return the sum of a list of mrs_data objects. — sum_mrs_list • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/svs_1h_brain_analysis.html b/docs/reference/svs_1h_brain_analysis.html
index 8ce514db..dff0ef7d 100644
--- a/docs/reference/svs_1h_brain_analysis.html
+++ b/docs/reference/svs_1h_brain_analysis.html
@@ -1,5 +1,5 @@
-Standard SVS 1H brain analysis pipeline. — svs_1h_brain_analysis • Spectroscopy Analysis Tools (spant) Standard SVS 1H brain analysis pipeline. — svs_1h_brain_analysis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -199,7 +199,7 @@ Value
diff --git a/docs/reference/svs_1h_brain_analysis_dev.html b/docs/reference/svs_1h_brain_analysis_dev.html
index d70a14d3..d71bfea2 100644
--- a/docs/reference/svs_1h_brain_analysis_dev.html
+++ b/docs/reference/svs_1h_brain_analysis_dev.html
@@ -1,5 +1,5 @@
-Standard SVS 1H brain analysis pipeline. — svs_1h_brain_analysis_dev • Spectroscopy Analysis Tools (spant) Standard SVS 1H brain analysis pipeline. — svs_1h_brain_analysis_dev • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -193,7 +193,7 @@ Examples
diff --git a/docs/reference/svs_1h_brain_batch_analysis.html b/docs/reference/svs_1h_brain_batch_analysis.html
index 5631e8cc..15f7223e 100644
--- a/docs/reference/svs_1h_brain_batch_analysis.html
+++ b/docs/reference/svs_1h_brain_batch_analysis.html
@@ -1,5 +1,5 @@
-Batch interface to the standard SVS 1H brain analysis pipeline. — svs_1h_brain_batch_analysis • Spectroscopy Analysis Tools (spant) Batch interface to the standard SVS 1H brain analysis pipeline. — svs_1h_brain_batch_analysis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -144,7 +144,7 @@ Value
diff --git a/docs/reference/t_test_spec.html b/docs/reference/t_test_spec.html
new file mode 100644
index 00000000..56a7ea1b
--- /dev/null
+++ b/docs/reference/t_test_spec.html
@@ -0,0 +1,124 @@
+
+Perform a t-test on spectral data points. — t_test_spec • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+
+
+ Perform a t-test on spectral data points.
+
+
+
+ t_test_spec(mrs_data, group)
+
+
+
+ Arguments
+ - mrs_data
+an mrs_data object with spectra in the dynamic dimension.
- group
+vector describing the group membership of each dynamic spectrum.
+
+ Value
+
+
+a list of statistical results.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/td2fd.html b/docs/reference/td2fd.html
index 6748a6a8..f31ed524 100644
--- a/docs/reference/td2fd.html
+++ b/docs/reference/td2fd.html
@@ -1,5 +1,5 @@
-Transform time-domain data to the frequency-domain. — td2fd • Spectroscopy Analysis Tools (spant) Transform time-domain data to the frequency-domain. — td2fd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/td_conv_filt.html b/docs/reference/td_conv_filt.html
index a9f340c3..106b9b00 100644
--- a/docs/reference/td_conv_filt.html
+++ b/docs/reference/td_conv_filt.html
@@ -1,5 +1,5 @@
-Time-domain convolution based filter. — td_conv_filt • Spectroscopy Analysis Tools (spant) Time-domain convolution based filter. — td_conv_filt • Spectroscopy Analysis Tools (spant) Time-domain spectral registration. — tdsr • Spectroscopy Analysis Tools (spant) Time-domain spectral registration. — tdsr • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -121,7 +121,7 @@ Value
diff --git a/docs/reference/te.html b/docs/reference/te.html
index 010361b1..4a65711d 100644
--- a/docs/reference/te.html
+++ b/docs/reference/te.html
@@ -1,5 +1,5 @@
-Return the echo time of an MRS dataset. — te • Spectroscopy Analysis Tools (spant) Return the echo time of an MRS dataset. — te • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/tr.html b/docs/reference/tr.html
index 0c0bd63b..2e749e02 100644
--- a/docs/reference/tr.html
+++ b/docs/reference/tr.html
@@ -1,5 +1,5 @@
-Return the repetition time of an MRS dataset. — tr • Spectroscopy Analysis Tools (spant) Return the repetition time of an MRS dataset. — tr • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/varpro_3_para_opts.html b/docs/reference/varpro_3_para_opts.html
index c2270a16..52d7cd84 100644
--- a/docs/reference/varpro_3_para_opts.html
+++ b/docs/reference/varpro_3_para_opts.html
@@ -1,5 +1,5 @@
-Return a list of options for VARPRO based fitting with 3 free parameters. — varpro_3_para_opts • Spectroscopy Analysis Tools (spant) Return a list of options for VARPRO based fitting with 3 free parameters. — varpro_3_para_opts • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -141,7 +141,7 @@ Value
diff --git a/docs/reference/varpro_basic_opts.html b/docs/reference/varpro_basic_opts.html
index 32c86d22..c5104891 100644
--- a/docs/reference/varpro_basic_opts.html
+++ b/docs/reference/varpro_basic_opts.html
@@ -1,5 +1,5 @@
-Return a list of options for a basic VARPRO analysis. — varpro_basic_opts • Spectroscopy Analysis Tools (spant) Return a list of options for a basic VARPRO analysis. — varpro_basic_opts • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -118,7 +118,7 @@ Value
diff --git a/docs/reference/varpro_opts.html b/docs/reference/varpro_opts.html
index 2aabf11d..6332f730 100644
--- a/docs/reference/varpro_opts.html
+++ b/docs/reference/varpro_opts.html
@@ -1,5 +1,5 @@
-Return a list of options for VARPRO based fitting. — varpro_opts • Spectroscopy Analysis Tools (spant) Return a list of options for VARPRO based fitting. — varpro_opts • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -177,7 +177,7 @@ Examples
diff --git a/docs/reference/vec2mrs_data.html b/docs/reference/vec2mrs_data.html
index 0cccd73b..f0d58bf0 100644
--- a/docs/reference/vec2mrs_data.html
+++ b/docs/reference/vec2mrs_data.html
@@ -1,5 +1,5 @@
-Convert a vector into a mrs_data object. — vec2mrs_data • Spectroscopy Analysis Tools (spant) Convert a vector into a mrs_data object. — vec2mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -80,10 +80,11 @@ Convert a vector into a mrs_data object.
vec2mrs_data(
vec,
- fs = def_fs(),
- ft = def_ft(),
- ref = def_ref(),
- nuc = def_nuc(),
+ mrs_data = NULL,
+ fs = NULL,
+ ft = NULL,
+ ref = NULL,
+ nuc = NULL,
dyns = 1,
fd = FALSE
)
@@ -95,6 +96,10 @@ Arguments
the data vector.
mrs_data
+example data to copy acquisition parameters from.
fs
sampling frequency in Hz.
Arguments
fd
-flag to indicate if the matrix is in the frequency domain (logical).
flag to indicate if the vector is in the frequency domain (logical).
Value
diff --git a/docs/reference/write_basis.html b/docs/reference/write_basis.html
index b6e27cbd..94c5e021 100644
--- a/docs/reference/write_basis.html
+++ b/docs/reference/write_basis.html
@@ -1,5 +1,5 @@
-Write a basis object to an LCModel .basis formatted file. — write_basis • Spectroscopy Analysis Tools (spant) Write a basis object to an LCModel .basis formatted file. — write_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -108,7 +108,7 @@ Arguments
diff --git a/docs/reference/write_basis_tqn.html b/docs/reference/write_basis_tqn.html
index 6aa51c1d..116c73ec 100644
--- a/docs/reference/write_basis_tqn.html
+++ b/docs/reference/write_basis_tqn.html
@@ -1,5 +1,5 @@
-Generate a basis file using TARQUIN. — write_basis_tqn • Spectroscopy Analysis Tools (spant) Generate a basis file using TARQUIN. — write_basis_tqn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Examples
diff --git a/docs/reference/write_mrs.html b/docs/reference/write_mrs.html
index fff25f15..124b9dc4 100644
--- a/docs/reference/write_mrs.html
+++ b/docs/reference/write_mrs.html
@@ -1,5 +1,5 @@
-Write MRS data object to file. — write_mrs • Spectroscopy Analysis Tools (spant) Write MRS data object to file. — write_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Arguments
diff --git a/docs/reference/write_mrs_nifti.html b/docs/reference/write_mrs_nifti.html
index f4bf1921..bd3ed4b7 100644
--- a/docs/reference/write_mrs_nifti.html
+++ b/docs/reference/write_mrs_nifti.html
@@ -1,5 +1,5 @@
-Write MRS data object to file in NIFTI format. — write_mrs_nifti • Spectroscopy Analysis Tools (spant) Write MRS data object to file in NIFTI format. — write_mrs_nifti • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/write_pulse_ascii.html b/docs/reference/write_pulse_ascii.html
index 067ae086..221f8ebb 100644
--- a/docs/reference/write_pulse_ascii.html
+++ b/docs/reference/write_pulse_ascii.html
@@ -1,5 +1,5 @@
-Write an ASCII formatted pulse file. — write_pulse_ascii • Spectroscopy Analysis Tools (spant) Write an ASCII formatted pulse file. — write_pulse_ascii • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/zero_fade_spec.html b/docs/reference/zero_fade_spec.html
index c703745c..c8b572c3 100644
--- a/docs/reference/zero_fade_spec.html
+++ b/docs/reference/zero_fade_spec.html
@@ -1,7 +1,5 @@
-Fade a spectrum to zero by frequency domain multiplication with a tanh
-function. Note this operation distorts data points at the end of the FID. — zero_fade_spec • Spectroscopy Analysis Tools (spant) Fade a spectrum to zero by frequency domain multiplication with a tanh function. Note this operation distorts data points at the end of the FID. — zero_fade_spec • Spectroscopy Analysis Tools (spant) Zero all coherences including and above a given order. — zero_higher_orders • Spectroscopy Analysis Tools (spant) Zero all coherences including and above a given order. — zero_higher_orders • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Value
diff --git a/docs/reference/zero_td_pts_end.html b/docs/reference/zero_td_pts_end.html
index 8c1123c8..71d24ebb 100644
--- a/docs/reference/zero_td_pts_end.html
+++ b/docs/reference/zero_td_pts_end.html
@@ -1,5 +1,5 @@
-Set mrs_data object data points at the end of the FID to zero. — zero_td_pts_end • Spectroscopy Analysis Tools (spant) Set mrs_data object data points at the end of the FID to zero. — zero_td_pts_end • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/zf.html b/docs/reference/zf.html
index 85e2013c..baf50256 100644
--- a/docs/reference/zf.html
+++ b/docs/reference/zf.html
@@ -1,5 +1,5 @@
-Zero-fill MRS data in the time domain. — zf • Spectroscopy Analysis Tools (spant) Zero-fill MRS data in the time domain. — zf • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -125,7 +125,7 @@ Value
diff --git a/docs/reference/zf_xy.html b/docs/reference/zf_xy.html
index ebca3999..c4104a74 100644
--- a/docs/reference/zf_xy.html
+++ b/docs/reference/zf_xy.html
@@ -1,5 +1,5 @@
-Zero-fill MRSI data in the k-space x-y direction. — zf_xy • Spectroscopy Analysis Tools (spant) Zero-fill MRSI data in the k-space x-y direction. — zf_xy • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -113,7 +113,7 @@ Value
diff --git a/docs/sitemap.xml b/docs/sitemap.xml
index e2139f71..4c39f515 100644
--- a/docs/sitemap.xml
+++ b/docs/sitemap.xml
@@ -216,6 +216,12 @@
https://martin3141.github.io/spant/reference/comb_coils_fp_pc.html
+
+ https://martin3141.github.io/spant/reference/comb_coils_mrsi_gls.html
+
+
+ https://martin3141.github.io/spant/reference/comb_coils_svs_gls.html
+
https://martin3141.github.io/spant/reference/comb_csv_results.html
@@ -411,6 +417,9 @@
https://martin3141.github.io/spant/reference/gen_conv_reg.html
+
+ https://martin3141.github.io/spant/reference/gen_group_reg.html
+
https://martin3141.github.io/spant/reference/gen_impulse_reg.html
@@ -555,6 +564,15 @@
https://martin3141.github.io/spant/reference/glm_spec.html
+
+ https://martin3141.github.io/spant/reference/glm_spec_fmrs_fl.html
+
+
+ https://martin3141.github.io/spant/reference/glm_spec_fmrs_group.html
+
+
+ https://martin3141.github.io/spant/reference/glm_spec_group_linhyp.html
+
https://martin3141.github.io/spant/reference/grid_shift_xy.html
@@ -690,9 +708,15 @@
https://martin3141.github.io/spant/reference/mrs_data2basis.html
+
+ https://martin3141.github.io/spant/reference/mrs_data2bids.html
+
https://martin3141.github.io/spant/reference/mrs_data2mat.html
+
+ https://martin3141.github.io/spant/reference/mrs_data2spec_mat.html
+
https://martin3141.github.io/spant/reference/mrs_data2vec.html
@@ -741,6 +765,9 @@
https://martin3141.github.io/spant/reference/phase.html
+
+ https://martin3141.github.io/spant/reference/phase_ref_1h_brain.html
+
https://martin3141.github.io/spant/reference/plot.fit_result.html
@@ -780,6 +807,12 @@
https://martin3141.github.io/spant/reference/precomp.html
+
+ https://martin3141.github.io/spant/reference/preproc_svs.html
+
+
+ https://martin3141.github.io/spant/reference/preproc_svs_dataset.html
+
https://martin3141.github.io/spant/reference/print.fit_result.html
@@ -1050,6 +1083,9 @@
https://martin3141.github.io/spant/reference/spant_mpress_drift.html
+
+ https://martin3141.github.io/spant/reference/spant_sim_fmrs_dataset.html
+
https://martin3141.github.io/spant/reference/spant_simulation_benchmark.html
@@ -1107,6 +1143,9 @@
https://martin3141.github.io/spant/reference/svs_1h_brain_batch_analysis.html
+
+ https://martin3141.github.io/spant/reference/t_test_spec.html
+
https://martin3141.github.io/spant/reference/td2fd.html
Set the number of time-domain data points, truncating or zero-filling as -appropriate.
Set the number of time-domain data points, truncating or zero-filling as appropriate.
All functions
- Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS
-sequence. Note, ideal pulses are assumed.
Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS sequence. Note, ideal pulses are assumed.
- Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS
-sequence. Note, ideal pulses are assumed.
Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS sequence. Note, ideal pulses are assumed.
- Simulate a macromolecular and lipid basis-set suitable for 1H brain MRS
-analysis.
Simulate a macromolecular and lipid basis-set suitable for 1H brain MRS analysis.
@@ -1353,8 +1326,7 @@ All functions
- Simulate an ideal pulse excitation profile by smoothing a top-hat function
-with a Gaussian.
Simulate an ideal pulse excitation profile by smoothing a top-hat function with a Gaussian.
@@ -1374,17 +1346,19 @@ All functions
- Simulate and fit some spectra with ABfit for benchmarking purposes. Basic
-timing and performance metrics will be printed.
Simulate and fit some spectra with ABfit for benchmarking purposes. Basic timing and performance metrics will be printed.
Example MEGA-PRESS data with significant B0 drift.
+
+
+ Simulate an example fMRS dataset for a block design fMRS experiment and export a BIDS structure.
- Simulate a typical metabolite basis set for benchmarking. Timing metrics will
-be printed on completion.
Simulate a typical metabolite basis set for benchmarking. Timing metrics will be printed on completion.
@@ -1400,8 +1374,7 @@ All functions
- Convert SPM style segmentation files to a single categorical image where
-the numerical values map as: 0) Other, 1) CSF, 2) GM and 3) WM.
Convert SPM style segmentation files to a single categorical image where the numerical values map as: 0) Other, 1) CSF, 2) GM and 3) WM.
@@ -1413,8 +1386,7 @@ All functions
- Plot the fitting results of an object of class fit_result with
-individual basis set components shown.
Plot the fitting results of an object of class fit_result with individual basis set components shown.
@@ -1459,6 +1431,10 @@ All functions svs_1h_brain_batch_analysis()
Batch interface to the standard SVS 1H brain analysis pipeline.
+
+
+ Perform a t-test on spectral data points.
@@ -1518,8 +1494,7 @@ All functions
- Fade a spectrum to zero by frequency domain multiplication with a tanh
-function. Note this operation distorts data points at the end of the FID.
Fade a spectrum to zero by frequency domain multiplication with a tanh function. Note this operation distorts data points at the end of the FID.
@@ -1549,7 +1524,7 @@ All functions
diff --git a/docs/reference/int_spec.html b/docs/reference/int_spec.html
index c7060fe7..783325a8 100644
--- a/docs/reference/int_spec.html
+++ b/docs/reference/int_spec.html
@@ -1,5 +1,5 @@
-Integrate a spectral region. — int_spec • Spectroscopy Analysis Tools (spant) Integrate a spectral region. — int_spec • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -118,7 +118,7 @@ Value
diff --git a/docs/reference/interleave_dyns.html b/docs/reference/interleave_dyns.html
index effe5543..441eff27 100644
--- a/docs/reference/interleave_dyns.html
+++ b/docs/reference/interleave_dyns.html
@@ -1,5 +1,5 @@
-Interleave the first and second half of a dynamic series. — interleave_dyns • Spectroscopy Analysis Tools (spant) Interleave the first and second half of a dynamic series. — interleave_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/inv_even_dyns.html b/docs/reference/inv_even_dyns.html
index 9f9d4fff..dcb781dc 100644
--- a/docs/reference/inv_even_dyns.html
+++ b/docs/reference/inv_even_dyns.html
@@ -1,5 +1,5 @@
-Invert even numbered dynamic scans starting from 1 (2,4,6...). — inv_even_dyns • Spectroscopy Analysis Tools (spant) Invert even numbered dynamic scans starting from 1 (2,4,6...). — inv_even_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/inv_odd_dyns.html b/docs/reference/inv_odd_dyns.html
index 26212e2b..78d64660 100644
--- a/docs/reference/inv_odd_dyns.html
+++ b/docs/reference/inv_odd_dyns.html
@@ -1,5 +1,5 @@
-Invert odd numbered dynamic scans starting from 1 (1,3,5...). — inv_odd_dyns • Spectroscopy Analysis Tools (spant) Invert odd numbered dynamic scans starting from 1 (1,3,5...). — inv_odd_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/is.def.html b/docs/reference/is.def.html
index f196ffd0..a67b9eba 100644
--- a/docs/reference/is.def.html
+++ b/docs/reference/is.def.html
@@ -1,5 +1,5 @@
-Check if an object is defined, which is the same as being not NULL. — is.def • Spectroscopy Analysis Tools (spant) Check if an object is defined, which is the same as being not NULL. — is.def • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/is_fd.html b/docs/reference/is_fd.html
index 3b0ca165..18a193aa 100644
--- a/docs/reference/is_fd.html
+++ b/docs/reference/is_fd.html
@@ -1,7 +1,5 @@
-Check if the chemical shift dimension of an MRS data object is in the
-frequency domain. — is_fd • Spectroscopy Analysis Tools (spant) Check if the chemical shift dimension of an MRS data object is in the frequency domain. — is_fd • Spectroscopy Analysis Tools (spant) Transform 2D MRSI data from k-space to image space in the x-y direction. — kspace2img_xy • Spectroscopy Analysis Tools (spant) Transform 2D MRSI data from k-space to image space in the x-y direction. — kspace2img_xy • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/l2_reg.html b/docs/reference/l2_reg.html
index 3d781d80..21aa9849 100644
--- a/docs/reference/l2_reg.html
+++ b/docs/reference/l2_reg.html
@@ -1,5 +1,5 @@
-Perform l2 regularisation artefact suppression. — l2_reg • Spectroscopy Analysis Tools (spant) Perform l2 regularisation artefact suppression. — l2_reg • Spectroscopy Analysis Tools (spant) Apply line-broadening (apodisation) to MRS data or basis object. — lb • Spectroscopy Analysis Tools (spant) Apply line-broadening (apodisation) to MRS data or basis object. — lb • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -123,7 +123,7 @@ Value
diff --git a/docs/reference/lofdc.html b/docs/reference/lofdc.html
index 5419b1ec..31347a25 100644
--- a/docs/reference/lofdc.html
+++ b/docs/reference/lofdc.html
@@ -1,5 +1,5 @@
-Correct linear frequency drift. — lofdc • Spectroscopy Analysis Tools (spant) Correct linear frequency drift. — lofdc • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -138,7 +138,7 @@ Value
diff --git a/docs/reference/lw2alpha.html b/docs/reference/lw2alpha.html
index b83db682..25da229b 100644
--- a/docs/reference/lw2alpha.html
+++ b/docs/reference/lw2alpha.html
@@ -1,7 +1,5 @@
-Covert a linewidth in Hz to an equivalent alpha value in the time-domain ie:
-x * exp(-t * alpha). — lw2alpha • Spectroscopy Analysis Tools (spant) Covert a linewidth in Hz to an equivalent alpha value in the time-domain ie: x * exp(-t * alpha). — lw2alpha • Spectroscopy Analysis Tools (spant) Covert a linewidth in Hz to an equivalent beta value in the time-domain ie:
-x * exp(-t * t * beta). — lw2beta • Spectroscopy Analysis Tools (spant) Covert a linewidth in Hz to an equivalent beta value in the time-domain ie: x * exp(-t * t * beta). — lw2beta • Spectroscopy Analysis Tools (spant) Make a basis-set object from a directory containing LCModel formatted RAW
-files. — make_basis_from_raw • Spectroscopy Analysis Tools (spant) Make a basis-set object from a directory containing LCModel formatted RAW files. — make_basis_from_raw • Spectroscopy Analysis Tools (spant) Mask an MRS dataset in the dynamic dimension. — mask_dyns • Spectroscopy Analysis Tools (spant) Mask an MRS dataset in the dynamic dimension. — mask_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/mask_fit_res.html b/docs/reference/mask_fit_res.html
index 97baaa3f..ebd91a99 100644
--- a/docs/reference/mask_fit_res.html
+++ b/docs/reference/mask_fit_res.html
@@ -1,5 +1,5 @@
-Mask fit result spectra depending on a vector of bool values. — mask_fit_res • Spectroscopy Analysis Tools (spant) Mask fit result spectra depending on a vector of bool values. — mask_fit_res • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -116,7 +116,7 @@ Value
diff --git a/docs/reference/mask_xy.html b/docs/reference/mask_xy.html
index 11bb577c..b0d38619 100644
--- a/docs/reference/mask_xy.html
+++ b/docs/reference/mask_xy.html
@@ -1,5 +1,5 @@
-Mask an MRSI dataset in the x-y direction — mask_xy • Spectroscopy Analysis Tools (spant) Mask an MRSI dataset in the x-y direction — mask_xy • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/mask_xy_corners.html b/docs/reference/mask_xy_corners.html
index 09b16cd2..2d13839d 100644
--- a/docs/reference/mask_xy_corners.html
+++ b/docs/reference/mask_xy_corners.html
@@ -1,5 +1,5 @@
-Mask the four corners of an MRSI dataset in the x-y plane. — mask_xy_corners • Spectroscopy Analysis Tools (spant) Mask the four corners of an MRSI dataset in the x-y plane. — mask_xy_corners • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/mask_xy_ellipse.html b/docs/reference/mask_xy_ellipse.html
index 1d8b02e4..e2e749ef 100644
--- a/docs/reference/mask_xy_ellipse.html
+++ b/docs/reference/mask_xy_ellipse.html
@@ -1,7 +1,5 @@
-Mask the voxels outside an elliptical region spanning the MRSI dataset in the
-x-y plane. — mask_xy_ellipse • Spectroscopy Analysis Tools (spant) Mask the voxels outside an elliptical region spanning the MRSI dataset in the x-y plane. — mask_xy_ellipse • Spectroscopy Analysis Tools (spant) Mask a 2D MRSI dataset in the x-y dimension. — mask_xy_mat • Spectroscopy Analysis Tools (spant) Mask a 2D MRSI dataset in the x-y dimension. — mask_xy_mat • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Value
diff --git a/docs/reference/mat2mrs_data.html b/docs/reference/mat2mrs_data.html
index 2e2895f3..ae55665f 100644
--- a/docs/reference/mat2mrs_data.html
+++ b/docs/reference/mat2mrs_data.html
@@ -1,7 +1,5 @@
-Convert a matrix (with spectral points in the column dimension and dynamics
-in the row dimensions) into a mrs_data object. — mat2mrs_data • Spectroscopy Analysis Tools (spant) Convert a matrix (with spectral points in the column dimension and dynamics in the row dimensions) into a mrs_data object. — mat2mrs_data • Spectroscopy Analysis Tools (spant) Matrix exponential function taken from complexplus package to reduce the
-number of spant dependencies. — matexp • Spectroscopy Analysis Tools (spant) Matrix exponential function taken from complexplus package to reduce the number of spant dependencies. — matexp • Spectroscopy Analysis Tools (spant) Apply the max operator to an MRS dataset. — max_mrs • Spectroscopy Analysis Tools (spant) Apply the max operator to an MRS dataset. — max_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/max_mrs_interp.html b/docs/reference/max_mrs_interp.html
index e4474764..52e63f3e 100644
--- a/docs/reference/max_mrs_interp.html
+++ b/docs/reference/max_mrs_interp.html
@@ -1,5 +1,5 @@
-Apply the max operator to an interpolated MRS dataset. — max_mrs_interp • Spectroscopy Analysis Tools (spant) Apply the max operator to an interpolated MRS dataset. — max_mrs_interp • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/mean.list.html b/docs/reference/mean.list.html
index b8eb3463..048306fd 100644
--- a/docs/reference/mean.list.html
+++ b/docs/reference/mean.list.html
@@ -1,5 +1,5 @@
-Calculate the mean spectrum from an mrs_data object. — mean.list • Spectroscopy Analysis Tools (spant) Calculate the mean spectrum from an mrs_data object. — mean.list • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/mean.mrs_data.html b/docs/reference/mean.mrs_data.html
index 5531a28d..79515014 100644
--- a/docs/reference/mean.mrs_data.html
+++ b/docs/reference/mean.mrs_data.html
@@ -1,5 +1,5 @@
-Calculate the mean spectrum from an mrs_data object. — mean.mrs_data • Spectroscopy Analysis Tools (spant) Calculate the mean spectrum from an mrs_data object. — mean.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/mean_dyn_blocks.html b/docs/reference/mean_dyn_blocks.html
index 10467098..4c042448 100644
--- a/docs/reference/mean_dyn_blocks.html
+++ b/docs/reference/mean_dyn_blocks.html
@@ -1,5 +1,5 @@
-Calculate the mean of adjacent dynamic scans. — mean_dyn_blocks • Spectroscopy Analysis Tools (spant) Calculate the mean of adjacent dynamic scans. — mean_dyn_blocks • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/mean_dyn_pairs.html b/docs/reference/mean_dyn_pairs.html
index 63e909ea..1a241126 100644
--- a/docs/reference/mean_dyn_pairs.html
+++ b/docs/reference/mean_dyn_pairs.html
@@ -1,5 +1,5 @@
-Calculate the pairwise means across a dynamic data set. — mean_dyn_pairs • Spectroscopy Analysis Tools (spant) Calculate the pairwise means across a dynamic data set. — mean_dyn_pairs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/mean_dyns.html b/docs/reference/mean_dyns.html
index 73fdbfa7..0daa27df 100644
--- a/docs/reference/mean_dyns.html
+++ b/docs/reference/mean_dyns.html
@@ -1,5 +1,5 @@
-Calculate the mean dynamic data. — mean_dyns • Spectroscopy Analysis Tools (spant) Calculate the mean dynamic data. — mean_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/mean_mrs_list.html b/docs/reference/mean_mrs_list.html
index 808b6c50..10d842c0 100644
--- a/docs/reference/mean_mrs_list.html
+++ b/docs/reference/mean_mrs_list.html
@@ -1,5 +1,5 @@
-Return the mean of a list of mrs_data objects. — mean_mrs_list • Spectroscopy Analysis Tools (spant) Return the mean of a list of mrs_data objects. — mean_mrs_list • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/mean_vec_blocks.html b/docs/reference/mean_vec_blocks.html
index 8fc92eaa..dd78b122 100644
--- a/docs/reference/mean_vec_blocks.html
+++ b/docs/reference/mean_vec_blocks.html
@@ -1,5 +1,5 @@
-Calculate the mean of adjacent blocks in a vector. — mean_vec_blocks • Spectroscopy Analysis Tools (spant) Calculate the mean of adjacent blocks in a vector. — mean_vec_blocks • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/median_dyns.html b/docs/reference/median_dyns.html
index 1039d4b5..9a085b10 100644
--- a/docs/reference/median_dyns.html
+++ b/docs/reference/median_dyns.html
@@ -1,5 +1,5 @@
-Calculate the median dynamic data. — median_dyns • Spectroscopy Analysis Tools (spant) Calculate the median dynamic data. — median_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/mod_td.html b/docs/reference/mod_td.html
index 76ad0a40..141ef09e 100644
--- a/docs/reference/mod_td.html
+++ b/docs/reference/mod_td.html
@@ -1,5 +1,5 @@
-Apply the Modulus operator to the time-domain MRS signal. — mod_td • Spectroscopy Analysis Tools (spant) Apply the Modulus operator to the time-domain MRS signal. — mod_td • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/mrs_data2basis.html b/docs/reference/mrs_data2basis.html
index 62f7d749..11797b91 100644
--- a/docs/reference/mrs_data2basis.html
+++ b/docs/reference/mrs_data2basis.html
@@ -1,7 +1,5 @@
-Convert an mrs_data object to basis object - where basis signals are spread
-across the dynamic dimension in the MRS data. — mrs_data2basis • Spectroscopy Analysis Tools (spant) Convert an mrs_data object to basis object - where basis signals are spread across the dynamic dimension in the MRS data. — mrs_data2basis • Spectroscopy Analysis Tools (spant) Create a BIDS file structure from a vector of MRS data paths or list of mrs_data objects. — mrs_data2bids • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Create a BIDS file structure from a vector of MRS data paths or list of mrs_data objects.
+ Source: R/fmrs.R
+ mrs_data2bids.Rd
+
+
+
+ Create a BIDS file structure from a vector of MRS data paths or list of
+mrs_data objects.
+
+
+
+ mrs_data2bids(
+ mrs_data,
+ output_dir,
+ suffix = NULL,
+ sub = NULL,
+ ses = NULL,
+ task = NULL,
+ acq = NULL,
+ nuc = NULL,
+ voi = NULL,
+ rec = NULL,
+ run = NULL,
+ echo = NULL,
+ inv = NULL,
+ skip_existing = TRUE
+)
+
+
+
+ Arguments
+ - mrs_data
+vector of MRS data paths or list of mrs_data objects.
- output_dir
+the base directory to create the BIDS structure.
- suffix
+optional vector of file suffixes. Default behaviour is to
+automatically determine these from the input data, however it is recommended
+that they are specified to allow more efficient skipping of existing data.
- sub
+optional vector of subject labels. If not specified, these will be
+automatically generated as a series of increasing zero-padded integer values
+corresponding to the mrs_data input indices.
- ses
+optional vector of session labels.
- task
+optional vector of task labels.
- acq
+optional vector of acquisition labels.
- nuc
+optional vector of nucleus labels.
- voi
+optional vector of volume of interest labels.
- rec
+optional vector of reconstruction labels.
- run
+optional vector of run indices.
- echo
+optional vector of echo time indices.
- inv
+optional vector of inversion indices.
- skip_existing
+skip any data files that have already been converted.
+Defaults to TRUE, set to FALSE to force an overwrite of any existing data
+files.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/mrs_data2mat.html b/docs/reference/mrs_data2mat.html
index cf5ff28c..9e47688a 100644
--- a/docs/reference/mrs_data2mat.html
+++ b/docs/reference/mrs_data2mat.html
@@ -1,7 +1,5 @@
-Convert mrs_data object to a matrix, with spectral points in the column
-dimension and dynamics in the row dimension. — mrs_data2mat • Spectroscopy Analysis Tools (spant) Convert mrs_data object to a matrix, with spectral points in the column dimension and dynamics in the row dimension. — mrs_data2mat • Spectroscopy Analysis Tools (spant) Convert mrs_data object to a matrix, with spectral points in the column dimension and dynamics in the row dimension. — mrs_data2spec_mat • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Convert mrs_data object to a matrix, with spectral points in the column dimension and dynamics in the row dimension.
+ Source: R/mrs_data_proc.R
+ mrs_data2spec_mat.Rd
+
+
+
+ Convert mrs_data object to a matrix, with spectral points in the column
+dimension and dynamics in the row dimension.
+
+
+
+ mrs_data2spec_mat(mrs_data, collapse = TRUE)
+
+
+
+ Arguments
+ - mrs_data
+MRS data object or list of MRS data objects.
- collapse
+collapse all other dimensions along the dynamic dimension, eg
+a 16x16 MRSI grid would be first collapsed across 256 dynamic scans.
+
+ Value
+
+
+MRS data matrix.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/mrs_data2vec.html b/docs/reference/mrs_data2vec.html
index fb172d68..a1fd654d 100644
--- a/docs/reference/mrs_data2vec.html
+++ b/docs/reference/mrs_data2vec.html
@@ -1,5 +1,5 @@
-Convert mrs_data object to a vector. — mrs_data2vec • Spectroscopy Analysis Tools (spant) Convert mrs_data object to a vector. — mrs_data2vec • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -126,7 +126,7 @@ Value
diff --git a/docs/reference/mvfftshift.html b/docs/reference/mvfftshift.html
index 92b0841b..976b3410 100644
--- a/docs/reference/mvfftshift.html
+++ b/docs/reference/mvfftshift.html
@@ -1,7 +1,5 @@
-Perform a fftshift on a matrix, with each column replaced by its shifted
-result. — mvfftshift • Spectroscopy Analysis Tools (spant) Perform a fftshift on a matrix, with each column replaced by its shifted result. — mvfftshift • Spectroscopy Analysis Tools (spant) Perform an ifftshift on a matrix, with each column replaced by its shifted
-result. — mvifftshift • Spectroscopy Analysis Tools (spant) Perform an ifftshift on a matrix, with each column replaced by its shifted result. — mvifftshift • Spectroscopy Analysis Tools (spant) Print fit coordinates from a single index. — n2coord • Spectroscopy Analysis Tools (spant) Print fit coordinates from a single index. — n2coord • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/nifti_flip_lr.html b/docs/reference/nifti_flip_lr.html
index 730abe3c..19860b3c 100644
--- a/docs/reference/nifti_flip_lr.html
+++ b/docs/reference/nifti_flip_lr.html
@@ -1,9 +1,5 @@
-Flip the x data dimension order of a nifti image. This corresponds to
-flipping MRI data in the left-right direction, assuming the data in save in
-neurological format (can check with fslorient program). — nifti_flip_lr • Spectroscopy Analysis Tools (spant) Flip the x data dimension order of a nifti image. This corresponds to flipping MRI data in the left-right direction, assuming the data in save in neurological format (can check with fslorient program). — nifti_flip_lr • Spectroscopy Analysis Tools (spant) Export a one-page pdf of a single fit result — one_page_pdf • Spectroscopy Analysis Tools (spant) Export a one-page pdf of a single fit result — one_page_pdf • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -108,7 +108,7 @@ Arguments
diff --git a/docs/reference/ortho3.html b/docs/reference/ortho3.html
index 13ade97d..5d7dd2fd 100644
--- a/docs/reference/ortho3.html
+++ b/docs/reference/ortho3.html
@@ -1,5 +1,5 @@
-Display an orthographic projection plot of a nifti object. — ortho3 • Spectroscopy Analysis Tools (spant) Display an orthographic projection plot of a nifti object. — ortho3 • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -172,7 +172,7 @@ Arguments
diff --git a/docs/reference/ortho3_inter.html b/docs/reference/ortho3_inter.html
index 090cc5e5..15948899 100644
--- a/docs/reference/ortho3_inter.html
+++ b/docs/reference/ortho3_inter.html
@@ -1,5 +1,5 @@
-Display an interactive orthographic projection plot of a nifti object. — ortho3_inter • Spectroscopy Analysis Tools (spant) Display an interactive orthographic projection plot of a nifti object. — ortho3_inter • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -132,7 +132,7 @@ Arguments
diff --git a/docs/reference/peak_info.html b/docs/reference/peak_info.html
index 09058bd8..41c8ffaf 100644
--- a/docs/reference/peak_info.html
+++ b/docs/reference/peak_info.html
@@ -1,7 +1,5 @@
-Search for the highest peak in a spectral region and return the frequency,
-height and FWHM. — peak_info • Spectroscopy Analysis Tools (spant) Search for the highest peak in a spectral region and return the frequency, height and FWHM. — peak_info • Spectroscopy Analysis Tools (spant) Papoulis-Gerchberg (PG) algorithm method for k-space extrapolation. — pg_extrap_xy • Spectroscopy Analysis Tools (spant) Papoulis-Gerchberg (PG) algorithm method for k-space extrapolation. — pg_extrap_xy • Spectroscopy Analysis Tools (spant) Apply phasing parameters to MRS data. — phase • Spectroscopy Analysis Tools (spant) Apply phasing parameters to MRS data. — phase • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/phase_ref_1h_brain.html b/docs/reference/phase_ref_1h_brain.html
new file mode 100644
index 00000000..8707a74a
--- /dev/null
+++ b/docs/reference/phase_ref_1h_brain.html
@@ -0,0 +1,131 @@
+
+Corrected zero order phase and chemical shift offset in 1H MRS data from the brain. — phase_ref_1h_brain • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Corrected zero order phase and chemical shift offset in 1H MRS data from the brain.
+ Source: R/rats.R
+ phase_ref_1h_brain.Rd
+
+
+
+ Corrected zero order phase and chemical shift offset in 1H MRS data from the
+brain.
+
+
+
+ phase_ref_1h_brain(mrs_data, mean_ref = FALSE, ret_corr_only = TRUE)
+
+
+
+ Arguments
+ - mrs_data
+MRS data to be corrected.
- mean_ref
+apply the phase and offset of the mean spectrum to all
+others. Default is FALSE.
- ret_corr_only
+return the corrected data only.
+
+ Value
+
+
+corrected MRS data.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/plot.fit_result.html b/docs/reference/plot.fit_result.html
index e54d3bc1..836a53ee 100644
--- a/docs/reference/plot.fit_result.html
+++ b/docs/reference/plot.fit_result.html
@@ -1,5 +1,5 @@
-Plot the fitting results of an object of class fit_result. — plot.fit_result • Spectroscopy Analysis Tools (spant) Plot the fitting results of an object of class fit_result. — plot.fit_result • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -207,7 +207,7 @@ Arguments
diff --git a/docs/reference/plot.mrs_data.html b/docs/reference/plot.mrs_data.html
index fabcc35b..bb2ec651 100644
--- a/docs/reference/plot.mrs_data.html
+++ b/docs/reference/plot.mrs_data.html
@@ -1,5 +1,5 @@
-Plotting method for objects of class mrs_data. — plot.mrs_data • Spectroscopy Analysis Tools (spant) Plotting method for objects of class mrs_data. — plot.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -287,7 +287,7 @@ Arguments
diff --git a/docs/reference/plot_bc.html b/docs/reference/plot_bc.html
index 4f8309b4..b48142cc 100644
--- a/docs/reference/plot_bc.html
+++ b/docs/reference/plot_bc.html
@@ -1,5 +1,5 @@
-Convenience function to plot a baseline estimate with the original data. — plot_bc • Spectroscopy Analysis Tools (spant) Convenience function to plot a baseline estimate with the original data. — plot_bc • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -108,7 +108,7 @@ Arguments
diff --git a/docs/reference/plot_reg.html b/docs/reference/plot_reg.html
index ae1acbe7..2addb2f6 100644
--- a/docs/reference/plot_reg.html
+++ b/docs/reference/plot_reg.html
@@ -1,5 +1,5 @@
-Plot regressors as an image. — plot_reg • Spectroscopy Analysis Tools (spant) Plot regressors as an image. — plot_reg • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/plot_slice_fit.html b/docs/reference/plot_slice_fit.html
index fbc7b560..57f1af8a 100644
--- a/docs/reference/plot_slice_fit.html
+++ b/docs/reference/plot_slice_fit.html
@@ -1,5 +1,5 @@
-Plot a 2D slice from an MRSI fit result object. — plot_slice_fit • Spectroscopy Analysis Tools (spant) Plot a 2D slice from an MRSI fit result object. — plot_slice_fit • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -129,7 +129,7 @@ Arguments
diff --git a/docs/reference/plot_slice_fit_inter.html b/docs/reference/plot_slice_fit_inter.html
index 4eed104a..da105a7d 100644
--- a/docs/reference/plot_slice_fit_inter.html
+++ b/docs/reference/plot_slice_fit_inter.html
@@ -1,5 +1,5 @@
-Plot a 2D slice from an MRSI fit result object. — plot_slice_fit_inter • Spectroscopy Analysis Tools (spant) Plot a 2D slice from an MRSI fit result object. — plot_slice_fit_inter • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -134,7 +134,7 @@ Arguments
diff --git a/docs/reference/plot_slice_map.html b/docs/reference/plot_slice_map.html
index 553e9ac8..ffb2a134 100644
--- a/docs/reference/plot_slice_map.html
+++ b/docs/reference/plot_slice_map.html
@@ -1,5 +1,5 @@
-Plot a slice from a 7 dimensional array. — plot_slice_map • Spectroscopy Analysis Tools (spant) Plot a slice from a 7 dimensional array. — plot_slice_map • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -153,7 +153,7 @@ Arguments
diff --git a/docs/reference/plot_slice_map_inter.html b/docs/reference/plot_slice_map_inter.html
index 40d33b42..90968f66 100644
--- a/docs/reference/plot_slice_map_inter.html
+++ b/docs/reference/plot_slice_map_inter.html
@@ -1,7 +1,5 @@
-Plot an interactive slice map from a data array where voxels can be selected
-to display a corresponding spectrum. — plot_slice_map_inter • Spectroscopy Analysis Tools (spant) Plot an interactive slice map from a data array where voxels can be selected to display a corresponding spectrum. — plot_slice_map_inter • Spectroscopy Analysis Tools (spant) Plot the spectral standard deviation. — plot_spec_sd • Spectroscopy Analysis Tools (spant) Plot the spectral standard deviation. — plot_spec_sd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Arguments
diff --git a/docs/reference/plot_voi_overlay.html b/docs/reference/plot_voi_overlay.html
index 9a782e88..bbbbf35e 100644
--- a/docs/reference/plot_voi_overlay.html
+++ b/docs/reference/plot_voi_overlay.html
@@ -1,5 +1,5 @@
-Plot a volume as an image overlay. — plot_voi_overlay • Spectroscopy Analysis Tools (spant) Plot a volume as an image overlay. — plot_voi_overlay • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -116,7 +116,7 @@ Arguments
diff --git a/docs/reference/plot_voi_overlay_seg.html b/docs/reference/plot_voi_overlay_seg.html
index 3d4e74ff..0e800ff2 100644
--- a/docs/reference/plot_voi_overlay_seg.html
+++ b/docs/reference/plot_voi_overlay_seg.html
@@ -1,5 +1,5 @@
-Plot a volume as an overlay on a segmented brain volume. — plot_voi_overlay_seg • Spectroscopy Analysis Tools (spant) Plot a volume as an overlay on a segmented brain volume. — plot_voi_overlay_seg • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Arguments
diff --git a/docs/reference/ppm.html b/docs/reference/ppm.html
index c352327a..ee4696e2 100644
--- a/docs/reference/ppm.html
+++ b/docs/reference/ppm.html
@@ -1,5 +1,5 @@
-Return the ppm scale of an MRS dataset or fit result. — ppm • Spectroscopy Analysis Tools (spant) Return the ppm scale of an MRS dataset or fit result. — ppm • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -132,7 +132,7 @@ Value
diff --git a/docs/reference/precomp.html b/docs/reference/precomp.html
index 822d7336..df3d2c6c 100644
--- a/docs/reference/precomp.html
+++ b/docs/reference/precomp.html
@@ -1,7 +1,5 @@
-Save function results to file and load on subsequent calls to avoid repeat
-computation. — precomp • Spectroscopy Analysis Tools (spant) Save function results to file and load on subsequent calls to avoid repeat computation. — precomp • Spectroscopy Analysis Tools (spant) Preprocess and perform quality assessment of a single SVS data set. — preproc_svs • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Preprocess and perform quality assessment of a single SVS data set.
+ Source: R/fmrs.R
+ preproc_svs.Rd
+
+
+
+ Preprocess and perform quality assessment of a single SVS data set.
+
+
+
+ preproc_svs(path, label = NULL, output_dir = NULL, ref_inds = NULL)
+
+
+
+ Arguments
+ - path
+path to the fMRS data file or IMA directory.
- label
+a label to describe the data set.
- output_dir
+output directory.
- ref_inds
+a vector of 1-based indices for any water reference dynamic
+scans.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/preproc_svs_dataset.html b/docs/reference/preproc_svs_dataset.html
new file mode 100644
index 00000000..07c3a29b
--- /dev/null
+++ b/docs/reference/preproc_svs_dataset.html
@@ -0,0 +1,148 @@
+
+Preprocess and perform quality assessment of one or more SVS data sets. — preproc_svs_dataset • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Preprocess and perform quality assessment of one or more SVS data sets.
+ Source: R/fmrs.R
+ preproc_svs_dataset.Rd
+
+
+
+ Preprocess and perform quality assessment of one or more SVS data sets.
+
+
+
+ preproc_svs_dataset(
+ paths,
+ labels = NULL,
+ output_dir = "spant_analysis",
+ exclude_labels = NULL,
+ overwrite = FALSE,
+ ref_inds = NULL,
+ return_results = FALSE
+)
+
+
+
+ Arguments
+ - paths
+paths to the fMRS data file or IMA directory.
- labels
+labels to describe each data set.
- output_dir
+output directory.
- exclude_labels
+vector of labels of scans to exclude, eg poor quality
+data.
- overwrite
+overwrite saved results, defaults to FALSE.
- ref_inds
+a vector of 1-based indices for any water reference dynamic
+scans.
- return_results
+function will return key outputs, defaults to FALSE.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/print.fit_result.html b/docs/reference/print.fit_result.html
index 297f28dc..5f434e57 100644
--- a/docs/reference/print.fit_result.html
+++ b/docs/reference/print.fit_result.html
@@ -1,5 +1,5 @@
-Print a summary of an object of class fit_result. — print.fit_result • Spectroscopy Analysis Tools (spant) Print a summary of an object of class fit_result. — print.fit_result • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -105,7 +105,7 @@ Arguments
diff --git a/docs/reference/print.mrs_data.html b/docs/reference/print.mrs_data.html
index 51199017..e1561eb2 100644
--- a/docs/reference/print.mrs_data.html
+++ b/docs/reference/print.mrs_data.html
@@ -1,5 +1,5 @@
-Print a summary of mrs_data parameters. — print.mrs_data • Spectroscopy Analysis Tools (spant) Print a summary of mrs_data parameters. — print.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -109,7 +109,7 @@ Arguments
diff --git a/docs/reference/qn_states.html b/docs/reference/qn_states.html
index 0f42f2f9..d7aa6715 100644
--- a/docs/reference/qn_states.html
+++ b/docs/reference/qn_states.html
@@ -1,5 +1,5 @@
-Get the quantum coherence matrix for a spin system. — qn_states • Spectroscopy Analysis Tools (spant) Get the quantum coherence matrix for a spin system. — qn_states • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/rats.html b/docs/reference/rats.html
index 5a39a396..93585e08 100644
--- a/docs/reference/rats.html
+++ b/docs/reference/rats.html
@@ -1,5 +1,5 @@
-Robust Alignment to a Target Spectrum (RATS). — rats • Spectroscopy Analysis Tools (spant) Robust Alignment to a Target Spectrum (RATS). — rats • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -207,7 +207,7 @@ Value
diff --git a/docs/reference/re_weighting.html b/docs/reference/re_weighting.html
index d21caf21..8b0b070a 100644
--- a/docs/reference/re_weighting.html
+++ b/docs/reference/re_weighting.html
@@ -1,5 +1,5 @@
-Apply a weighting to the FID to enhance spectral resolution. — re_weighting • Spectroscopy Analysis Tools (spant) Apply a weighting to the FID to enhance spectral resolution. — re_weighting • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/read_basis.html b/docs/reference/read_basis.html
index da9b94af..eb6f8557 100644
--- a/docs/reference/read_basis.html
+++ b/docs/reference/read_basis.html
@@ -1,5 +1,5 @@
-Read a basis file in LCModel .basis format. — read_basis • Spectroscopy Analysis Tools (spant) Read a basis file in LCModel .basis format. — read_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/read_ima_coil_dir.html b/docs/reference/read_ima_coil_dir.html
index 28c02de0..4f073cd8 100644
--- a/docs/reference/read_ima_coil_dir.html
+++ b/docs/reference/read_ima_coil_dir.html
@@ -1,9 +1,5 @@
-Read a directory containing Siemens MRS IMA files and combine along the coil
-dimension. Note that the coil ID is inferred from the sorted file name and
-should be checked when consistency is required between two directories. — read_ima_coil_dir • Spectroscopy Analysis Tools (spant) Read a directory containing Siemens MRS IMA files and combine along the coil dimension. Note that the coil ID is inferred from the sorted file name and should be checked when consistency is required between two directories. — read_ima_coil_dir • Spectroscopy Analysis Tools (spant) Read a directory containing Siemens MRS IMA files and combine along the
-dynamic dimension. Note that the coil ID is inferred from the sorted file
-name and should be checked when consistency is required. — read_ima_dyn_dir • Spectroscopy Analysis Tools (spant) Read a directory containing Siemens MRS IMA files and combine along the dynamic dimension. Note that the coil ID is inferred from the sorted file name and should be checked when consistency is required. — read_ima_dyn_dir • Spectroscopy Analysis Tools (spant) Read an LCModel formatted coord file containing fit information. — read_lcm_coord • Spectroscopy Analysis Tools (spant) Read an LCModel formatted coord file containing fit information. — read_lcm_coord • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -107,7 +107,7 @@ Value
diff --git a/docs/reference/read_mrs.html b/docs/reference/read_mrs.html
index 3ac2a36b..2cf36b20 100644
--- a/docs/reference/read_mrs.html
+++ b/docs/reference/read_mrs.html
@@ -1,5 +1,5 @@
-Read MRS data from a file. — read_mrs • Spectroscopy Analysis Tools (spant) Read MRS data from a file. — read_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -88,7 +88,8 @@ Read MRS data from a file.
full_fid = FALSE,
omit_svs_ref_scans = TRUE,
verbose = FALSE,
- extra = NULL
+ extra = NULL,
+ fid_filt_dist = NULL
)
@@ -140,6 +141,13 @@ Arguments
an optional data frame to provide additional variables for use
in subsequent analysis steps, eg id or grouping variables.
fid_filt_dist
+indicate if the data has a distorted FID due to a
+brick-wall filter being used to downsample the data. Default is to auto
+detect this from the data, but TRUE or FALSE options can be given to override
+detection.
Value
@@ -183,7 +191,7 @@ Examples
diff --git a/docs/reference/read_mrs_tqn.html b/docs/reference/read_mrs_tqn.html
index 5766362f..84bdaf3a 100644
--- a/docs/reference/read_mrs_tqn.html
+++ b/docs/reference/read_mrs_tqn.html
@@ -1,5 +1,5 @@
-Read MRS data using the TARQUIN software package. — read_mrs_tqn • Spectroscopy Analysis Tools (spant) Read MRS data using the TARQUIN software package. — read_mrs_tqn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -131,7 +131,7 @@ Examples
diff --git a/docs/reference/read_pulse_ascii.html b/docs/reference/read_pulse_ascii.html
index c9e0d43c..ab11c9cc 100644
--- a/docs/reference/read_pulse_ascii.html
+++ b/docs/reference/read_pulse_ascii.html
@@ -1,5 +1,5 @@
-Read an ASCII formatted pulse file. — read_pulse_ascii • Spectroscopy Analysis Tools (spant) Read an ASCII formatted pulse file. — read_pulse_ascii • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/read_pulse_bruker.html b/docs/reference/read_pulse_bruker.html
index c92bf76a..dbe9073b 100644
--- a/docs/reference/read_pulse_bruker.html
+++ b/docs/reference/read_pulse_bruker.html
@@ -1,5 +1,5 @@
-Read a Bruker formatted pulse file — read_pulse_bruker • Spectroscopy Analysis Tools (spant) Read a Bruker formatted pulse file — read_pulse_bruker • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/read_pulse_pta.html b/docs/reference/read_pulse_pta.html
index 72e1b6d4..a0fac3c3 100644
--- a/docs/reference/read_pulse_pta.html
+++ b/docs/reference/read_pulse_pta.html
@@ -1,5 +1,5 @@
-Read a .pta formatted pulse file compatible with Siemens PulseTool. — read_pulse_pta • Spectroscopy Analysis Tools (spant) Read a .pta formatted pulse file compatible with Siemens PulseTool. — read_pulse_pta • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/read_siemens_txt_hdr.html b/docs/reference/read_siemens_txt_hdr.html
index 23fb8c70..3a17d87c 100644
--- a/docs/reference/read_siemens_txt_hdr.html
+++ b/docs/reference/read_siemens_txt_hdr.html
@@ -1,5 +1,5 @@
-Read the text format header found in Siemens IMA and TWIX data files. — read_siemens_txt_hdr • Spectroscopy Analysis Tools (spant) Read the text format header found in Siemens IMA and TWIX data files. — read_siemens_txt_hdr • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -78,7 +78,7 @@ Read the text format header found in Siemens IMA and TWIX data files.
- read_siemens_txt_hdr(input, version = "vd", verbose, offset = 0)
+ read_siemens_txt_hdr(input, version = "vd", verbose = FALSE, offset = 0)
@@ -118,7 +118,7 @@ Value
diff --git a/docs/reference/read_tqn_fit.html b/docs/reference/read_tqn_fit.html
index 4da6c25e..a1630420 100644
--- a/docs/reference/read_tqn_fit.html
+++ b/docs/reference/read_tqn_fit.html
@@ -1,5 +1,5 @@
-Reader for csv fit results generated by TARQUIN. — read_tqn_fit • Spectroscopy Analysis Tools (spant) Reader for csv fit results generated by TARQUIN. — read_tqn_fit • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -113,7 +113,7 @@ Examples
diff --git a/docs/reference/read_tqn_result.html b/docs/reference/read_tqn_result.html
index 36659714..68a3e98c 100644
--- a/docs/reference/read_tqn_result.html
+++ b/docs/reference/read_tqn_result.html
@@ -1,5 +1,5 @@
-Reader for csv results generated by TARQUIN. — read_tqn_result • Spectroscopy Analysis Tools (spant) Reader for csv results generated by TARQUIN. — read_tqn_result • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -117,7 +117,7 @@ Examples
diff --git a/docs/reference/recon_imag.html b/docs/reference/recon_imag.html
index d2a72225..5bc3b1eb 100644
--- a/docs/reference/recon_imag.html
+++ b/docs/reference/recon_imag.html
@@ -1,7 +1,5 @@
-Reconstruct complex time-domain data from the real part of frequency-domain
-data. — recon_imag • Spectroscopy Analysis Tools (spant) Reconstruct complex time-domain data from the real part of frequency-domain data. — recon_imag • Spectroscopy Analysis Tools (spant) Reconstruct complex time-domain data from the real part of frequency-domain
-data. — recon_imag_vec • Spectroscopy Analysis Tools (spant) Reconstruct complex time-domain data from the real part of frequency-domain data. — recon_imag_vec • Spectroscopy Analysis Tools (spant) Reconstruct 2D MRSI data from a twix file loaded with read_mrs. — recon_twix_2d_mrsi • Spectroscopy Analysis Tools (spant) Reconstruct 2D MRSI data from a twix file loaded with read_mrs. — recon_twix_2d_mrsi • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/rectangular_mask.html b/docs/reference/rectangular_mask.html
index a2117283..6e469bc9 100644
--- a/docs/reference/rectangular_mask.html
+++ b/docs/reference/rectangular_mask.html
@@ -1,5 +1,5 @@
-Create a rectangular mask stored as a matrix of logical values. — rectangular_mask • Spectroscopy Analysis Tools (spant) Create a rectangular mask stored as a matrix of logical values. — rectangular_mask • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -130,7 +130,7 @@ Value
diff --git a/docs/reference/reexports.html b/docs/reference/reexports.html
index 694a75d1..a59e8379 100644
--- a/docs/reference/reexports.html
+++ b/docs/reference/reexports.html
@@ -1,5 +1,5 @@
-Objects exported from other packages — reexports • Spectroscopy Analysis Tools (spant) Objects exported from other packages — reexports • Spectroscopy Analysis Tools (spant)
Spectroscopy Analysis Tools (spant)
- 2.21.0
+ 2.22.0
@@ -103,7 +103,7 @@ Objects exported from other packages
diff --git a/docs/reference/rep_array_dim.html b/docs/reference/rep_array_dim.html
index b9c49b4a..48c0a5ed 100644
--- a/docs/reference/rep_array_dim.html
+++ b/docs/reference/rep_array_dim.html
@@ -1,5 +1,5 @@
-Repeat an array over a given dimension. — rep_array_dim • Spectroscopy Analysis Tools (spant) Repeat an array over a given dimension. — rep_array_dim • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/rep_dyn.html b/docs/reference/rep_dyn.html
index 6bbfb0ef..89a4bb9b 100644
--- a/docs/reference/rep_dyn.html
+++ b/docs/reference/rep_dyn.html
@@ -1,5 +1,5 @@
-Replicate a scan in the dynamic dimension. — rep_dyn • Spectroscopy Analysis Tools (spant) Replicate a scan in the dynamic dimension. — rep_dyn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/rep_mrs.html b/docs/reference/rep_mrs.html
index 67730b5c..becb8f00 100644
--- a/docs/reference/rep_mrs.html
+++ b/docs/reference/rep_mrs.html
@@ -1,5 +1,5 @@
-Replicate a scan over a given dimension. — rep_mrs • Spectroscopy Analysis Tools (spant) Replicate a scan over a given dimension. — rep_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -138,7 +138,7 @@ Value
diff --git a/docs/reference/resample_basis.html b/docs/reference/resample_basis.html
index b0f2ab17..c7a6222a 100644
--- a/docs/reference/resample_basis.html
+++ b/docs/reference/resample_basis.html
@@ -1,5 +1,5 @@
-Resample a basis-set to match a mrs_data acquisition. — resample_basis • Spectroscopy Analysis Tools (spant) Resample a basis-set to match a mrs_data acquisition. — resample_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -116,7 +116,7 @@ Value
diff --git a/docs/reference/resample_img.html b/docs/reference/resample_img.html
index f1e7beaf..b0cc8f71 100644
--- a/docs/reference/resample_img.html
+++ b/docs/reference/resample_img.html
@@ -1,5 +1,5 @@
-Resample an image to match a target image space. — resample_img • Spectroscopy Analysis Tools (spant) Resample an image to match a target image space. — resample_img • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/resample_voi.html b/docs/reference/resample_voi.html
index 8fbfa836..a29ab096 100644
--- a/docs/reference/resample_voi.html
+++ b/docs/reference/resample_voi.html
@@ -1,7 +1,5 @@
-Resample a VOI to match a target image space using nearest-neighbour
-interpolation. — resample_voi • Spectroscopy Analysis Tools (spant) Resample a VOI to match a target image space using nearest-neighbour interpolation. — resample_voi • Spectroscopy Analysis Tools (spant) Reslice a nifti object to match the orientation of mrs data. — reslice_to_mrs • Spectroscopy Analysis Tools (spant) Reslice a nifti object to match the orientation of mrs data. — reslice_to_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/reson_table2mrs_data.html b/docs/reference/reson_table2mrs_data.html
index d75579ee..c5a2167a 100644
--- a/docs/reference/reson_table2mrs_data.html
+++ b/docs/reference/reson_table2mrs_data.html
@@ -1,5 +1,5 @@
-Generate mrs_data from a table of single Lorentzian resonances. — reson_table2mrs_data • Spectroscopy Analysis Tools (spant) Generate mrs_data from a table of single Lorentzian resonances. — reson_table2mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -119,7 +119,7 @@ Value
diff --git a/docs/reference/rm_dyns.html b/docs/reference/rm_dyns.html
index 5d5ef692..573e1f51 100644
--- a/docs/reference/rm_dyns.html
+++ b/docs/reference/rm_dyns.html
@@ -1,5 +1,5 @@
-Remove a subset of dynamic scans. — rm_dyns • Spectroscopy Analysis Tools (spant) Remove a subset of dynamic scans. — rm_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/scale_amp_molal.html b/docs/reference/scale_amp_molal.html
index aaeee1f2..7acb8cb0 100644
--- a/docs/reference/scale_amp_molal.html
+++ b/docs/reference/scale_amp_molal.html
@@ -1,7 +1,5 @@
-Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water). — scale_amp_molal • Spectroscopy Analysis Tools (spant) Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / kg of tissue water). — scale_amp_molal • Spectroscopy Analysis Tools (spant)
Spectroscopy Analysis Tools (spant)
- 2.21.0
+ 2.22.0
@@ -76,8 +74,7 @@
- Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water).
+ Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / kg of tissue water).
Source: R/amp_scaling.R
scale_amp_molal.Rd
@@ -163,7 +160,7 @@ Value
diff --git a/docs/reference/scale_amp_molal_pvc.html b/docs/reference/scale_amp_molal_pvc.html
index 962d6afc..4d194abd 100644
--- a/docs/reference/scale_amp_molal_pvc.html
+++ b/docs/reference/scale_amp_molal_pvc.html
@@ -1,7 +1,5 @@
-Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water). — scale_amp_molal_pvc • Spectroscopy Analysis Tools (spant)
@@ -75,8 +73,7 @@
- Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water).
+ Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / kg of tissue water).
Source: R/amp_scaling.R
scale_amp_molal_pvc.Rd
@@ -141,7 +138,7 @@ Value
diff --git a/docs/reference/scale_amp_molar.html b/docs/reference/scale_amp_molar.html
index 02358d91..dc87a338 100644
--- a/docs/reference/scale_amp_molar.html
+++ b/docs/reference/scale_amp_molar.html
@@ -1,7 +1,5 @@
-Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / Litre of tissue). — scale_amp_molar • Spectroscopy Analysis Tools (spant) Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / Litre of tissue). — scale_amp_molar • Spectroscopy Analysis Tools (spant) Convert default LCM/TARQUIN concentration scaling to molal units with partial
-volume correction. — scale_amp_molar2molal_pvc • Spectroscopy Analysis Tools (spant) Convert default LCM/TARQUIN concentration scaling to molal units with partial volume correction. — scale_amp_molar2molal_pvc • Spectroscopy Analysis Tools (spant) Scale fitted amplitudes to a ratio of signal amplitude. — scale_amp_ratio • Spectroscopy Analysis Tools (spant) Scale fitted amplitudes to a ratio of signal amplitude. — scale_amp_ratio • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -116,7 +116,7 @@ Value
diff --git a/docs/reference/scale_amp_ratio_value.html b/docs/reference/scale_amp_ratio_value.html
index 2036837a..6af8ac51 100644
--- a/docs/reference/scale_amp_ratio_value.html
+++ b/docs/reference/scale_amp_ratio_value.html
@@ -1,5 +1,5 @@
-Scale fitted amplitudes to a ratio of signal amplitude. — scale_amp_ratio_value • Spectroscopy Analysis Tools (spant) Scale fitted amplitudes to a ratio of signal amplitude. — scale_amp_ratio_value • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/scale_amp_water_ratio.html b/docs/reference/scale_amp_water_ratio.html
index 5b25e884..35a76b00 100644
--- a/docs/reference/scale_amp_water_ratio.html
+++ b/docs/reference/scale_amp_water_ratio.html
@@ -1,5 +1,5 @@
-Scale metabolite amplitudes as a ratio to the unsuppressed water amplitude. — scale_amp_water_ratio • Spectroscopy Analysis Tools (spant) Scale metabolite amplitudes as a ratio to the unsuppressed water amplitude. — scale_amp_water_ratio • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/scale_basis_amp.html b/docs/reference/scale_basis_amp.html
index 9401c3f1..5a58b5e5 100644
--- a/docs/reference/scale_basis_amp.html
+++ b/docs/reference/scale_basis_amp.html
@@ -1,5 +1,5 @@
-Scale a basis object by a scalar. — scale_basis_amp • Spectroscopy Analysis Tools (spant) Scale a basis object by a scalar. — scale_basis_amp • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/scale_basis_from_singlet.html b/docs/reference/scale_basis_from_singlet.html
index 0d542bc8..c9a19e77 100644
--- a/docs/reference/scale_basis_from_singlet.html
+++ b/docs/reference/scale_basis_from_singlet.html
@@ -1,5 +1,5 @@
-Scale a basis-set to be consistent with spant assumptions for water scaling. — scale_basis_from_singlet • Spectroscopy Analysis Tools (spant) Scale a basis-set to be consistent with spant assumptions for water scaling. — scale_basis_from_singlet • Spectroscopy Analysis Tools (spant)
Spectroscopy Analysis Tools (spant)
- 2.21.0
+ 2.22.0
@@ -127,7 +127,7 @@ Value
diff --git a/docs/reference/scale_mrs_amp.html b/docs/reference/scale_mrs_amp.html
index b5501a0d..990f058a 100644
--- a/docs/reference/scale_mrs_amp.html
+++ b/docs/reference/scale_mrs_amp.html
@@ -1,5 +1,5 @@
-Scale an mrs_data object by a scalar or vector or amplitudes. — scale_mrs_amp • Spectroscopy Analysis Tools (spant) Scale an mrs_data object by a scalar or vector or amplitudes. — scale_mrs_amp • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/scale_spec.html b/docs/reference/scale_spec.html
index 4f6ea835..6b3ddba4 100644
--- a/docs/reference/scale_spec.html
+++ b/docs/reference/scale_spec.html
@@ -1,5 +1,5 @@
-Scale mrs_data to a spectral region. — scale_spec • Spectroscopy Analysis Tools (spant) Scale mrs_data to a spectral region. — scale_spec • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -141,7 +141,7 @@ Value
diff --git a/docs/reference/sd.html b/docs/reference/sd.html
index ea1eec9f..3ae4dfd4 100644
--- a/docs/reference/sd.html
+++ b/docs/reference/sd.html
@@ -1,5 +1,5 @@
-Calculate the standard deviation spectrum from an mrs_data object. — sd • Spectroscopy Analysis Tools (spant) Calculate the standard deviation spectrum from an mrs_data object. — sd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/sd.mrs_data.html b/docs/reference/sd.mrs_data.html
index 3f92a49f..13bdda85 100644
--- a/docs/reference/sd.mrs_data.html
+++ b/docs/reference/sd.mrs_data.html
@@ -1,5 +1,5 @@
-Calculate the standard deviation spectrum from an mrs_data object. — sd.mrs_data • Spectroscopy Analysis Tools (spant) Calculate the standard deviation spectrum from an mrs_data object. — sd.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/seconds.html b/docs/reference/seconds.html
index b34d6627..467ee17f 100644
--- a/docs/reference/seconds.html
+++ b/docs/reference/seconds.html
@@ -1,5 +1,5 @@
-Return a time scale vector to match the FID of an MRS data object. — seconds • Spectroscopy Analysis Tools (spant) Return a time scale vector to match the FID of an MRS data object. — seconds • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/seq_cpmg_ideal.html b/docs/reference/seq_cpmg_ideal.html
index 547e96ab..45727c86 100644
--- a/docs/reference/seq_cpmg_ideal.html
+++ b/docs/reference/seq_cpmg_ideal.html
@@ -1,5 +1,5 @@
-CPMG style sequence with ideal pulses. — seq_cpmg_ideal • Spectroscopy Analysis Tools (spant) CPMG style sequence with ideal pulses. — seq_cpmg_ideal • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/seq_mega_press_ideal.html b/docs/reference/seq_mega_press_ideal.html
index 0769b8b4..a9cd7fa0 100644
--- a/docs/reference/seq_mega_press_ideal.html
+++ b/docs/reference/seq_mega_press_ideal.html
@@ -1,7 +1,5 @@
-MEGA-PRESS sequence with ideal localisation pulses and Gaussian shaped
-editing pulse. — seq_mega_press_ideal • Spectroscopy Analysis Tools (spant) MEGA-PRESS sequence with ideal localisation pulses and Gaussian shaped editing pulse. — seq_mega_press_ideal • Spectroscopy Analysis Tools (spant) PRESS sequence with shaped refocusing pulses. — seq_press_2d_shaped • Spectroscopy Analysis Tools (spant) PRESS sequence with shaped refocusing pulses. — seq_press_2d_shaped • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -165,7 +165,7 @@ Value
diff --git a/docs/reference/seq_press_ideal.html b/docs/reference/seq_press_ideal.html
index 8c976856..72c3af3d 100644
--- a/docs/reference/seq_press_ideal.html
+++ b/docs/reference/seq_press_ideal.html
@@ -1,5 +1,5 @@
-PRESS sequence with ideal pulses. — seq_press_ideal • Spectroscopy Analysis Tools (spant) PRESS sequence with ideal pulses. — seq_press_ideal • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/seq_pulse_acquire.html b/docs/reference/seq_pulse_acquire.html
index 4a88fc64..ad80571e 100644
--- a/docs/reference/seq_pulse_acquire.html
+++ b/docs/reference/seq_pulse_acquire.html
@@ -1,5 +1,5 @@
-Simple pulse and acquire sequence with ideal pulses. — seq_pulse_acquire • Spectroscopy Analysis Tools (spant) Simple pulse and acquire sequence with ideal pulses. — seq_pulse_acquire • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/seq_slaser_ideal.html b/docs/reference/seq_slaser_ideal.html
index 74688f4d..eb83e8e3 100644
--- a/docs/reference/seq_slaser_ideal.html
+++ b/docs/reference/seq_slaser_ideal.html
@@ -1,5 +1,5 @@
-sLASER sequence with ideal pulses. — seq_slaser_ideal • Spectroscopy Analysis Tools (spant) sLASER sequence with ideal pulses. — seq_slaser_ideal • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -126,7 +126,7 @@ Value
diff --git a/docs/reference/seq_spin_echo_ideal.html b/docs/reference/seq_spin_echo_ideal.html
index e23271de..4248716f 100644
--- a/docs/reference/seq_spin_echo_ideal.html
+++ b/docs/reference/seq_spin_echo_ideal.html
@@ -1,5 +1,5 @@
-Spin echo sequence with ideal pulses. — seq_spin_echo_ideal • Spectroscopy Analysis Tools (spant) Spin echo sequence with ideal pulses. — seq_spin_echo_ideal • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/seq_steam_ideal.html b/docs/reference/seq_steam_ideal.html
index a60685a8..1c8115d7 100644
--- a/docs/reference/seq_steam_ideal.html
+++ b/docs/reference/seq_steam_ideal.html
@@ -1,5 +1,5 @@
-STEAM sequence with ideal pulses. — seq_steam_ideal • Spectroscopy Analysis Tools (spant) STEAM sequence with ideal pulses. — seq_steam_ideal • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -128,7 +128,7 @@ Value
diff --git a/docs/reference/seq_steam_ideal_cof.html b/docs/reference/seq_steam_ideal_cof.html
index 8f225740..cba7af91 100644
--- a/docs/reference/seq_steam_ideal_cof.html
+++ b/docs/reference/seq_steam_ideal_cof.html
@@ -1,7 +1,5 @@
-STEAM sequence with ideal pulses and coherence order filtering to simulate
-gradient crushers. — seq_steam_ideal_cof • Spectroscopy Analysis Tools (spant) STEAM sequence with ideal pulses and coherence order filtering to simulate gradient crushers. — seq_steam_ideal_cof • Spectroscopy Analysis Tools (spant) STEAM sequence with ideal pulses using the z-rotation gradient simulation
-method described by Young et al JMR 140, 146-152 (1999). — seq_steam_ideal_young • Spectroscopy Analysis Tools (spant) STEAM sequence with ideal pulses using the z-rotation gradient simulation method described by Young et al JMR 140, 146-152 (1999). — seq_steam_ideal_young • Spectroscopy Analysis Tools (spant) Set the number of transients for an mrs_data object. — set_Ntrans • Spectroscopy Analysis Tools (spant) Set the number of transients for an mrs_data object. — set_Ntrans • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/set_def_acq_paras.html b/docs/reference/set_def_acq_paras.html
index 3e1b4004..cc2ada9c 100644
--- a/docs/reference/set_def_acq_paras.html
+++ b/docs/reference/set_def_acq_paras.html
@@ -1,5 +1,5 @@
-Set the default acquisition parameters. — set_def_acq_paras • Spectroscopy Analysis Tools (spant) Set the default acquisition parameters. — set_def_acq_paras • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Arguments
diff --git a/docs/reference/set_lcm_cmd.html b/docs/reference/set_lcm_cmd.html
index 2056ed01..42bb2f24 100644
--- a/docs/reference/set_lcm_cmd.html
+++ b/docs/reference/set_lcm_cmd.html
@@ -1,5 +1,5 @@
-Set the command to run the LCModel command-line program. — set_lcm_cmd • Spectroscopy Analysis Tools (spant) Set the command to run the LCModel command-line program. — set_lcm_cmd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/set_lw.html b/docs/reference/set_lw.html
index b64ec851..bb176c62 100644
--- a/docs/reference/set_lw.html
+++ b/docs/reference/set_lw.html
@@ -1,5 +1,5 @@
-Apply line-broadening to an mrs_data object to achieve a specified linewidth. — set_lw • Spectroscopy Analysis Tools (spant) Apply line-broadening to an mrs_data object to achieve a specified linewidth. — set_lw • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -123,7 +123,7 @@ Value
diff --git a/docs/reference/set_mask_xy_mat.html b/docs/reference/set_mask_xy_mat.html
index 49dc5d4e..52c4b617 100644
--- a/docs/reference/set_mask_xy_mat.html
+++ b/docs/reference/set_mask_xy_mat.html
@@ -1,5 +1,5 @@
-Set the masked voxels in a 2D MRSI dataset to given spectrum. — set_mask_xy_mat • Spectroscopy Analysis Tools (spant) Set the masked voxels in a 2D MRSI dataset to given spectrum. — set_mask_xy_mat • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Value
diff --git a/docs/reference/set_precomp_mode.html b/docs/reference/set_precomp_mode.html
index f44bd5d3..47c28e3b 100644
--- a/docs/reference/set_precomp_mode.html
+++ b/docs/reference/set_precomp_mode.html
@@ -1,5 +1,5 @@
-Set the precompute mode. — set_precomp_mode • Spectroscopy Analysis Tools (spant) Set the precompute mode. — set_precomp_mode • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/set_precomp_verbose.html b/docs/reference/set_precomp_verbose.html
index 1453a231..9c613505 100644
--- a/docs/reference/set_precomp_verbose.html
+++ b/docs/reference/set_precomp_verbose.html
@@ -1,5 +1,5 @@
-Set the verbosity of the precompute function. — set_precomp_verbose • Spectroscopy Analysis Tools (spant) Set the verbosity of the precompute function. — set_precomp_verbose • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/set_ref.html b/docs/reference/set_ref.html
index 8953fa50..5436dfa2 100644
--- a/docs/reference/set_ref.html
+++ b/docs/reference/set_ref.html
@@ -1,5 +1,5 @@
-Set the ppm reference value (eg ppm value at 0Hz). — set_ref • Spectroscopy Analysis Tools (spant) Set the ppm reference value (eg ppm value at 0Hz). — set_ref • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/set_td_pts.html b/docs/reference/set_td_pts.html
index 8a80d42a..586459ff 100644
--- a/docs/reference/set_td_pts.html
+++ b/docs/reference/set_td_pts.html
@@ -1,7 +1,5 @@
-Set the number of time-domain data points, truncating or zero-filling as
-appropriate. — set_td_pts • Spectroscopy Analysis Tools (spant) Set the number of time-domain data points, truncating or zero-filling as appropriate. — set_td_pts • Spectroscopy Analysis Tools (spant) Set the command to run the TARQUIN command-line program. — set_tqn_cmd • Spectroscopy Analysis Tools (spant) Set the command to run the TARQUIN command-line program. — set_tqn_cmd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/set_tr.html b/docs/reference/set_tr.html
index b2109ab0..65c9df5f 100644
--- a/docs/reference/set_tr.html
+++ b/docs/reference/set_tr.html
@@ -1,5 +1,5 @@
-Set the repetition time of an MRS dataset. — set_tr • Spectroscopy Analysis Tools (spant) Set the repetition time of an MRS dataset. — set_tr • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/shift.html b/docs/reference/shift.html
index ab0fe724..034591d0 100644
--- a/docs/reference/shift.html
+++ b/docs/reference/shift.html
@@ -1,5 +1,5 @@
-Apply a frequency shift to MRS data. — shift • Spectroscopy Analysis Tools (spant) Apply a frequency shift to MRS data. — shift • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/shift_basis.html b/docs/reference/shift_basis.html
index 2884be19..f55a65e0 100644
--- a/docs/reference/shift_basis.html
+++ b/docs/reference/shift_basis.html
@@ -1,5 +1,5 @@
-Apply frequency shifts to basis set signals. — shift_basis • Spectroscopy Analysis Tools (spant) Apply frequency shifts to basis set signals. — shift_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Value
diff --git a/docs/reference/sim_basis.html b/docs/reference/sim_basis.html
index c7838c46..bb5fefc6 100644
--- a/docs/reference/sim_basis.html
+++ b/docs/reference/sim_basis.html
@@ -1,5 +1,5 @@
-Simulate a basis set object. — sim_basis • Spectroscopy Analysis Tools (spant) Simulate a basis set object. — sim_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -136,7 +136,7 @@ Value
diff --git a/docs/reference/sim_basis_1h_brain.html b/docs/reference/sim_basis_1h_brain.html
index 62ed7389..f71ffa0b 100644
--- a/docs/reference/sim_basis_1h_brain.html
+++ b/docs/reference/sim_basis_1h_brain.html
@@ -1,7 +1,5 @@
-Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS
-sequence. Note, ideal pulses are assumed. — sim_basis_1h_brain • Spectroscopy Analysis Tools (spant) Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS sequence. Note, ideal pulses are assumed. — sim_basis_1h_brain • Spectroscopy Analysis Tools (spant) Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS
-sequence. Note, ideal pulses are assumed. — sim_basis_1h_brain_press • Spectroscopy Analysis Tools (spant) Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS sequence. Note, ideal pulses are assumed. — sim_basis_1h_brain_press • Spectroscopy Analysis Tools (spant) Simulate a macromolecular and lipid basis-set suitable for 1H brain MRS
-analysis. — sim_basis_mm_lip_lcm • Spectroscopy Analysis Tools (spant) Simulate a macromolecular and lipid basis-set suitable for 1H brain MRS analysis. — sim_basis_mm_lip_lcm • Spectroscopy Analysis Tools (spant) Simulate a basis file using TARQUIN. — sim_basis_tqn • Spectroscopy Analysis Tools (spant) Simulate a basis file using TARQUIN. — sim_basis_tqn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -129,7 +129,7 @@ Examples
diff --git a/docs/reference/sim_brain_1h.html b/docs/reference/sim_brain_1h.html
index 2044cf1a..717ee289 100644
--- a/docs/reference/sim_brain_1h.html
+++ b/docs/reference/sim_brain_1h.html
@@ -1,5 +1,5 @@
-Simulate MRS data with a similar appearance to normal brain (by default). — sim_brain_1h • Spectroscopy Analysis Tools (spant) Simulate MRS data with a similar appearance to normal brain (by default). — sim_brain_1h • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -159,7 +159,7 @@ Value
diff --git a/docs/reference/sim_mol.html b/docs/reference/sim_mol.html
index 23bcef50..77f76a50 100644
--- a/docs/reference/sim_mol.html
+++ b/docs/reference/sim_mol.html
@@ -1,5 +1,5 @@
-Simulate a mol_parameter object. — sim_mol • Spectroscopy Analysis Tools (spant) Simulate a mol_parameter object. — sim_mol • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -143,7 +143,7 @@ Value
diff --git a/docs/reference/sim_noise.html b/docs/reference/sim_noise.html
index 23875f79..a71477d4 100644
--- a/docs/reference/sim_noise.html
+++ b/docs/reference/sim_noise.html
@@ -1,5 +1,5 @@
-Simulate an mrs_data object containing simulated Gaussian noise. — sim_noise • Spectroscopy Analysis Tools (spant) Simulate an mrs_data object containing simulated Gaussian noise. — sim_noise • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -84,6 +84,7 @@ Simulate an mrs_data object containing simulated Gaussian noise.
ft = def_ft(),
N = def_N(),
ref = def_ref(),
+ nuc = def_nuc(),
dyns = 1,
fd = TRUE
)
@@ -111,6 +112,10 @@ Arguments
reference value for ppm scale.
nuc
+resonant nucleus.
dyns
number of dynamic scans to generate.
Value
diff --git a/docs/reference/sim_resonances.html b/docs/reference/sim_resonances.html
index 19e9a8a4..d4f8d7c0 100644
--- a/docs/reference/sim_resonances.html
+++ b/docs/reference/sim_resonances.html
@@ -1,5 +1,5 @@
-Simulate a MRS data object containing a set of simulated resonances. — sim_resonances • Spectroscopy Analysis Tools (spant) Simulate a MRS data object containing a set of simulated resonances. — sim_resonances • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -161,7 +161,7 @@ Examples
diff --git a/docs/reference/sim_th_excit_profile.html b/docs/reference/sim_th_excit_profile.html
index 5535c5ef..e781cab1 100644
--- a/docs/reference/sim_th_excit_profile.html
+++ b/docs/reference/sim_th_excit_profile.html
@@ -1,7 +1,5 @@
-Simulate an ideal pulse excitation profile by smoothing a top-hat function
-with a Gaussian. — sim_th_excit_profile • Spectroscopy Analysis Tools (spant) Simulate an ideal pulse excitation profile by smoothing a top-hat function with a Gaussian. — sim_th_excit_profile • Spectroscopy Analysis Tools (spant) Simulate an mrs_data object containing complex zero valued samples. — sim_zero • Spectroscopy Analysis Tools (spant) Simulate an mrs_data object containing complex zero valued samples. — sim_zero • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -78,7 +78,14 @@ Simulate an mrs_data object containing complex zero valued samples.
-
+
@@ -99,6 +106,10 @@ Arguments
reference value for ppm scale.
nuc
+resonant nucleus.
dyns
number of dynamic scans to generate.
Value
diff --git a/docs/reference/smooth_dyns.html b/docs/reference/smooth_dyns.html
index 4cc8da50..accf3a51 100644
--- a/docs/reference/smooth_dyns.html
+++ b/docs/reference/smooth_dyns.html
@@ -1,5 +1,5 @@
-Smooth data across the dynamic dimension with a Gaussian kernel. — smooth_dyns • Spectroscopy Analysis Tools (spant) Smooth data across the dynamic dimension with a Gaussian kernel. — smooth_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/sort_basis.html b/docs/reference/sort_basis.html
index 6a676ea2..d25cc006 100644
--- a/docs/reference/sort_basis.html
+++ b/docs/reference/sort_basis.html
@@ -1,5 +1,5 @@
-Sort the basis-set elements alphabetically. — sort_basis • Spectroscopy Analysis Tools (spant) Sort the basis-set elements alphabetically. — sort_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/spant-package.html b/docs/reference/spant-package.html
index b3dd8e21..90f19ec3 100644
--- a/docs/reference/spant-package.html
+++ b/docs/reference/spant-package.html
@@ -1,5 +1,5 @@
-spant: spectroscopy analysis tools. — spant-package • Spectroscopy Analysis Tools (spant) spant: spectroscopy analysis tools. — spant-package • Spectroscopy Analysis Tools (spant) Simulate and fit some spectra with ABfit for benchmarking purposes. Basic
-timing and performance metrics will be printed. — spant_abfit_benchmark • Spectroscopy Analysis Tools (spant) Simulate and fit some spectra with ABfit for benchmarking purposes. Basic timing and performance metrics will be printed. — spant_abfit_benchmark • Spectroscopy Analysis Tools (spant) Example MEGA-PRESS data with significant B0 drift. — spant_mpress_drift • Spectroscopy Analysis Tools (spant) Example MEGA-PRESS data with significant B0 drift. — spant_mpress_drift • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -83,7 +83,7 @@ Example MEGA-PRESS data with significant B0 drift.
Format
- An object of class mrs_data of length 13.
+ An object of class mrs_data of dimension 1 x 1 x 1 x 1 x 40 x 1 x 1024.
@@ -98,7 +98,7 @@ Format
diff --git a/docs/reference/spant_sim_fmrs_dataset.html b/docs/reference/spant_sim_fmrs_dataset.html
new file mode 100644
index 00000000..00e48b56
--- /dev/null
+++ b/docs/reference/spant_sim_fmrs_dataset.html
@@ -0,0 +1,117 @@
+
+Simulate an example fMRS dataset for a block design fMRS experiment and export a BIDS structure. — spant_sim_fmrs_dataset • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Simulate an example fMRS dataset for a block design fMRS experiment and export a BIDS structure.
+ Source: R/fmrs.R
+ spant_sim_fmrs_dataset.Rd
+
+
+
+ Simulate an example fMRS dataset for a block design fMRS experiment and
+export a BIDS structure.
+
+
+
+ spant_sim_fmrs_dataset(output_dir = NULL)
+
+
+
+ Arguments
+ - output_dir
+output directory for the BIDS data. Defaults to :
+"HOME/sim_fmrs_dataset/data".
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/spant_simulation_benchmark.html b/docs/reference/spant_simulation_benchmark.html
index 32daa8bf..d8cc6841 100644
--- a/docs/reference/spant_simulation_benchmark.html
+++ b/docs/reference/spant_simulation_benchmark.html
@@ -1,7 +1,5 @@
-Simulate a typical metabolite basis set for benchmarking. Timing metrics will
-be printed on completion. — spant_simulation_benchmark • Spectroscopy Analysis Tools (spant) Simulate a typical metabolite basis set for benchmarking. Timing metrics will be printed on completion. — spant_simulation_benchmark • Spectroscopy Analysis Tools (spant) Decompose an mrs_data object into white and gray matter spectra. — spec_decomp • Spectroscopy Analysis Tools (spant) Perform a mathematical operation on a spectral region. — spec_op • Spectroscopy Analysis Tools (spant) Perform a mathematical operation on a spectral region. — spec_op • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -98,8 +98,8 @@ Arguments
operator
-can be "sum" (default), "mean", "l2", "max", "min" or
-"max-min".
can be "sum" (default), "mean", "l2", "max", "max_cplx,
+"min" or "max-min".
freq_scale
@@ -129,7 +129,7 @@ Value
diff --git a/docs/reference/spin_sys.html b/docs/reference/spin_sys.html
index 853423a4..1eaa9e76 100644
--- a/docs/reference/spin_sys.html
+++ b/docs/reference/spin_sys.html
@@ -1,5 +1,5 @@
-Create a spin system object for pulse sequence simulation. — spin_sys • Spectroscopy Analysis Tools (spant) Create a spin system object for pulse sequence simulation. — spin_sys • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/spm_pve2categorical.html b/docs/reference/spm_pve2categorical.html
index 23a1bad9..70f10729 100644
--- a/docs/reference/spm_pve2categorical.html
+++ b/docs/reference/spm_pve2categorical.html
@@ -1,7 +1,5 @@
-Convert SPM style segmentation files to a single categorical image where
-the numerical values map as: 0) Other, 1) CSF, 2) GM and 3) WM. — spm_pve2categorical • Spectroscopy Analysis Tools (spant) Convert SPM style segmentation files to a single categorical image where the numerical values map as: 0) Other, 1) CSF, 2) GM and 3) WM. — spm_pve2categorical • Spectroscopy Analysis Tools (spant) Signal space projection method for lipid suppression. — ssp • Spectroscopy Analysis Tools (spant) Signal space projection method for lipid suppression. — ssp • Spectroscopy Analysis Tools (spant) Plot the fitting results of an object of class fit_result with
-individual basis set components shown. — stackplot.fit_result • Spectroscopy Analysis Tools (spant) Plot the fitting results of an object of class fit_result with individual basis set components shown. — stackplot.fit_result • Spectroscopy Analysis Tools (spant) Produce a plot with multiple traces. — stackplot • Spectroscopy Analysis Tools (spant) Produce a plot with multiple traces. — stackplot • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/stackplot.mrs_data.html b/docs/reference/stackplot.mrs_data.html
index 17ff5648..64eea445 100644
--- a/docs/reference/stackplot.mrs_data.html
+++ b/docs/reference/stackplot.mrs_data.html
@@ -1,5 +1,5 @@
-Stackplot plotting method for objects of class mrs_data. — stackplot.mrs_data • Spectroscopy Analysis Tools (spant) Stackplot plotting method for objects of class mrs_data. — stackplot.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -255,7 +255,7 @@ Arguments
diff --git a/docs/reference/sub_first_dyn.html b/docs/reference/sub_first_dyn.html
index dbd7f831..493b7242 100644
--- a/docs/reference/sub_first_dyn.html
+++ b/docs/reference/sub_first_dyn.html
@@ -1,5 +1,5 @@
-Subtract the first dynamic spectrum from a dynamic series. — sub_first_dyn • Spectroscopy Analysis Tools (spant) Subtract the first dynamic spectrum from a dynamic series. — sub_first_dyn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/sub_mean_dyns.html b/docs/reference/sub_mean_dyns.html
index 6e3bb2df..221bd0c1 100644
--- a/docs/reference/sub_mean_dyns.html
+++ b/docs/reference/sub_mean_dyns.html
@@ -1,5 +1,5 @@
-Subtract the mean dynamic spectrum from a dynamic series. — sub_mean_dyns • Spectroscopy Analysis Tools (spant) Subtract the mean dynamic spectrum from a dynamic series. — sub_mean_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/sub_median_dyns.html b/docs/reference/sub_median_dyns.html
index 134c495d..1e834f14 100644
--- a/docs/reference/sub_median_dyns.html
+++ b/docs/reference/sub_median_dyns.html
@@ -1,5 +1,5 @@
-Subtract the median dynamic spectrum from a dynamic series. — sub_median_dyns • Spectroscopy Analysis Tools (spant) Subtract the median dynamic spectrum from a dynamic series. — sub_median_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/sum_coils.html b/docs/reference/sum_coils.html
index 7bf559f2..e1ab3cc0 100644
--- a/docs/reference/sum_coils.html
+++ b/docs/reference/sum_coils.html
@@ -1,5 +1,5 @@
-Calculate the sum across receiver coil elements. — sum_coils • Spectroscopy Analysis Tools (spant) Calculate the sum across receiver coil elements. — sum_coils • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/sum_dyns.html b/docs/reference/sum_dyns.html
index a0be19d3..bbda2ffc 100644
--- a/docs/reference/sum_dyns.html
+++ b/docs/reference/sum_dyns.html
@@ -1,5 +1,5 @@
-Calculate the sum of data dynamics. — sum_dyns • Spectroscopy Analysis Tools (spant) Calculate the sum of data dynamics. — sum_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/sum_mrs.html b/docs/reference/sum_mrs.html
index a22f215b..3cc3ab9e 100644
--- a/docs/reference/sum_mrs.html
+++ b/docs/reference/sum_mrs.html
@@ -1,5 +1,5 @@
-Sum two mrs_data objects. — sum_mrs • Spectroscopy Analysis Tools (spant) Sum two mrs_data objects. — sum_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Value
diff --git a/docs/reference/sum_mrs_list.html b/docs/reference/sum_mrs_list.html
index f4e09aea..c3584348 100644
--- a/docs/reference/sum_mrs_list.html
+++ b/docs/reference/sum_mrs_list.html
@@ -1,5 +1,5 @@
-Return the sum of a list of mrs_data objects. — sum_mrs_list • Spectroscopy Analysis Tools (spant) Return the sum of a list of mrs_data objects. — sum_mrs_list • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/svs_1h_brain_analysis.html b/docs/reference/svs_1h_brain_analysis.html
index 8ce514db..dff0ef7d 100644
--- a/docs/reference/svs_1h_brain_analysis.html
+++ b/docs/reference/svs_1h_brain_analysis.html
@@ -1,5 +1,5 @@
-Standard SVS 1H brain analysis pipeline. — svs_1h_brain_analysis • Spectroscopy Analysis Tools (spant) Standard SVS 1H brain analysis pipeline. — svs_1h_brain_analysis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -199,7 +199,7 @@ Value
diff --git a/docs/reference/svs_1h_brain_analysis_dev.html b/docs/reference/svs_1h_brain_analysis_dev.html
index d70a14d3..d71bfea2 100644
--- a/docs/reference/svs_1h_brain_analysis_dev.html
+++ b/docs/reference/svs_1h_brain_analysis_dev.html
@@ -1,5 +1,5 @@
-Standard SVS 1H brain analysis pipeline. — svs_1h_brain_analysis_dev • Spectroscopy Analysis Tools (spant) Standard SVS 1H brain analysis pipeline. — svs_1h_brain_analysis_dev • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -193,7 +193,7 @@ Examples
diff --git a/docs/reference/svs_1h_brain_batch_analysis.html b/docs/reference/svs_1h_brain_batch_analysis.html
index 5631e8cc..15f7223e 100644
--- a/docs/reference/svs_1h_brain_batch_analysis.html
+++ b/docs/reference/svs_1h_brain_batch_analysis.html
@@ -1,5 +1,5 @@
-Batch interface to the standard SVS 1H brain analysis pipeline. — svs_1h_brain_batch_analysis • Spectroscopy Analysis Tools (spant) Batch interface to the standard SVS 1H brain analysis pipeline. — svs_1h_brain_batch_analysis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -144,7 +144,7 @@ Value
diff --git a/docs/reference/t_test_spec.html b/docs/reference/t_test_spec.html
new file mode 100644
index 00000000..56a7ea1b
--- /dev/null
+++ b/docs/reference/t_test_spec.html
@@ -0,0 +1,124 @@
+
+Perform a t-test on spectral data points. — t_test_spec • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+
+
+ Perform a t-test on spectral data points.
+
+
+
+ t_test_spec(mrs_data, group)
+
+
+
+ Arguments
+ - mrs_data
+an mrs_data object with spectra in the dynamic dimension.
- group
+vector describing the group membership of each dynamic spectrum.
+
+ Value
+
+
+a list of statistical results.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/td2fd.html b/docs/reference/td2fd.html
index 6748a6a8..f31ed524 100644
--- a/docs/reference/td2fd.html
+++ b/docs/reference/td2fd.html
@@ -1,5 +1,5 @@
-Transform time-domain data to the frequency-domain. — td2fd • Spectroscopy Analysis Tools (spant) Transform time-domain data to the frequency-domain. — td2fd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/td_conv_filt.html b/docs/reference/td_conv_filt.html
index a9f340c3..106b9b00 100644
--- a/docs/reference/td_conv_filt.html
+++ b/docs/reference/td_conv_filt.html
@@ -1,5 +1,5 @@
-Time-domain convolution based filter. — td_conv_filt • Spectroscopy Analysis Tools (spant) Time-domain convolution based filter. — td_conv_filt • Spectroscopy Analysis Tools (spant) Time-domain spectral registration. — tdsr • Spectroscopy Analysis Tools (spant) Time-domain spectral registration. — tdsr • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -121,7 +121,7 @@ Value
diff --git a/docs/reference/te.html b/docs/reference/te.html
index 010361b1..4a65711d 100644
--- a/docs/reference/te.html
+++ b/docs/reference/te.html
@@ -1,5 +1,5 @@
-Return the echo time of an MRS dataset. — te • Spectroscopy Analysis Tools (spant) Return the echo time of an MRS dataset. — te • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/tr.html b/docs/reference/tr.html
index 0c0bd63b..2e749e02 100644
--- a/docs/reference/tr.html
+++ b/docs/reference/tr.html
@@ -1,5 +1,5 @@
-Return the repetition time of an MRS dataset. — tr • Spectroscopy Analysis Tools (spant) Return the repetition time of an MRS dataset. — tr • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/varpro_3_para_opts.html b/docs/reference/varpro_3_para_opts.html
index c2270a16..52d7cd84 100644
--- a/docs/reference/varpro_3_para_opts.html
+++ b/docs/reference/varpro_3_para_opts.html
@@ -1,5 +1,5 @@
-Return a list of options for VARPRO based fitting with 3 free parameters. — varpro_3_para_opts • Spectroscopy Analysis Tools (spant) Return a list of options for VARPRO based fitting with 3 free parameters. — varpro_3_para_opts • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -141,7 +141,7 @@ Value
diff --git a/docs/reference/varpro_basic_opts.html b/docs/reference/varpro_basic_opts.html
index 32c86d22..c5104891 100644
--- a/docs/reference/varpro_basic_opts.html
+++ b/docs/reference/varpro_basic_opts.html
@@ -1,5 +1,5 @@
-Return a list of options for a basic VARPRO analysis. — varpro_basic_opts • Spectroscopy Analysis Tools (spant) Return a list of options for a basic VARPRO analysis. — varpro_basic_opts • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -118,7 +118,7 @@ Value
diff --git a/docs/reference/varpro_opts.html b/docs/reference/varpro_opts.html
index 2aabf11d..6332f730 100644
--- a/docs/reference/varpro_opts.html
+++ b/docs/reference/varpro_opts.html
@@ -1,5 +1,5 @@
-Return a list of options for VARPRO based fitting. — varpro_opts • Spectroscopy Analysis Tools (spant) Return a list of options for VARPRO based fitting. — varpro_opts • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -177,7 +177,7 @@ Examples
diff --git a/docs/reference/vec2mrs_data.html b/docs/reference/vec2mrs_data.html
index 0cccd73b..f0d58bf0 100644
--- a/docs/reference/vec2mrs_data.html
+++ b/docs/reference/vec2mrs_data.html
@@ -1,5 +1,5 @@
-Convert a vector into a mrs_data object. — vec2mrs_data • Spectroscopy Analysis Tools (spant) Convert a vector into a mrs_data object. — vec2mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -80,10 +80,11 @@ Convert a vector into a mrs_data object.
vec2mrs_data(
vec,
- fs = def_fs(),
- ft = def_ft(),
- ref = def_ref(),
- nuc = def_nuc(),
+ mrs_data = NULL,
+ fs = NULL,
+ ft = NULL,
+ ref = NULL,
+ nuc = NULL,
dyns = 1,
fd = FALSE
)
@@ -95,6 +96,10 @@ Arguments
the data vector.
mrs_data
+example data to copy acquisition parameters from.
fs
sampling frequency in Hz.
Arguments
fd
-flag to indicate if the matrix is in the frequency domain (logical).
flag to indicate if the vector is in the frequency domain (logical).
Value
diff --git a/docs/reference/write_basis.html b/docs/reference/write_basis.html
index b6e27cbd..94c5e021 100644
--- a/docs/reference/write_basis.html
+++ b/docs/reference/write_basis.html
@@ -1,5 +1,5 @@
-Write a basis object to an LCModel .basis formatted file. — write_basis • Spectroscopy Analysis Tools (spant) Write a basis object to an LCModel .basis formatted file. — write_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -108,7 +108,7 @@ Arguments
diff --git a/docs/reference/write_basis_tqn.html b/docs/reference/write_basis_tqn.html
index 6aa51c1d..116c73ec 100644
--- a/docs/reference/write_basis_tqn.html
+++ b/docs/reference/write_basis_tqn.html
@@ -1,5 +1,5 @@
-Generate a basis file using TARQUIN. — write_basis_tqn • Spectroscopy Analysis Tools (spant) Generate a basis file using TARQUIN. — write_basis_tqn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Examples
diff --git a/docs/reference/write_mrs.html b/docs/reference/write_mrs.html
index fff25f15..124b9dc4 100644
--- a/docs/reference/write_mrs.html
+++ b/docs/reference/write_mrs.html
@@ -1,5 +1,5 @@
-Write MRS data object to file. — write_mrs • Spectroscopy Analysis Tools (spant) Write MRS data object to file. — write_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Arguments
diff --git a/docs/reference/write_mrs_nifti.html b/docs/reference/write_mrs_nifti.html
index f4bf1921..bd3ed4b7 100644
--- a/docs/reference/write_mrs_nifti.html
+++ b/docs/reference/write_mrs_nifti.html
@@ -1,5 +1,5 @@
-Write MRS data object to file in NIFTI format. — write_mrs_nifti • Spectroscopy Analysis Tools (spant) Write MRS data object to file in NIFTI format. — write_mrs_nifti • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/write_pulse_ascii.html b/docs/reference/write_pulse_ascii.html
index 067ae086..221f8ebb 100644
--- a/docs/reference/write_pulse_ascii.html
+++ b/docs/reference/write_pulse_ascii.html
@@ -1,5 +1,5 @@
-Write an ASCII formatted pulse file. — write_pulse_ascii • Spectroscopy Analysis Tools (spant) Write an ASCII formatted pulse file. — write_pulse_ascii • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/zero_fade_spec.html b/docs/reference/zero_fade_spec.html
index c703745c..c8b572c3 100644
--- a/docs/reference/zero_fade_spec.html
+++ b/docs/reference/zero_fade_spec.html
@@ -1,7 +1,5 @@
-Fade a spectrum to zero by frequency domain multiplication with a tanh
-function. Note this operation distorts data points at the end of the FID. — zero_fade_spec • Spectroscopy Analysis Tools (spant) Fade a spectrum to zero by frequency domain multiplication with a tanh function. Note this operation distorts data points at the end of the FID. — zero_fade_spec • Spectroscopy Analysis Tools (spant) Zero all coherences including and above a given order. — zero_higher_orders • Spectroscopy Analysis Tools (spant) Zero all coherences including and above a given order. — zero_higher_orders • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Value
diff --git a/docs/reference/zero_td_pts_end.html b/docs/reference/zero_td_pts_end.html
index 8c1123c8..71d24ebb 100644
--- a/docs/reference/zero_td_pts_end.html
+++ b/docs/reference/zero_td_pts_end.html
@@ -1,5 +1,5 @@
-Set mrs_data object data points at the end of the FID to zero. — zero_td_pts_end • Spectroscopy Analysis Tools (spant) Set mrs_data object data points at the end of the FID to zero. — zero_td_pts_end • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/zf.html b/docs/reference/zf.html
index 85e2013c..baf50256 100644
--- a/docs/reference/zf.html
+++ b/docs/reference/zf.html
@@ -1,5 +1,5 @@
-Zero-fill MRS data in the time domain. — zf • Spectroscopy Analysis Tools (spant) Zero-fill MRS data in the time domain. — zf • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -125,7 +125,7 @@ Value
diff --git a/docs/reference/zf_xy.html b/docs/reference/zf_xy.html
index ebca3999..c4104a74 100644
--- a/docs/reference/zf_xy.html
+++ b/docs/reference/zf_xy.html
@@ -1,5 +1,5 @@
-Zero-fill MRSI data in the k-space x-y direction. — zf_xy • Spectroscopy Analysis Tools (spant) Zero-fill MRSI data in the k-space x-y direction. — zf_xy • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -113,7 +113,7 @@ Value
diff --git a/docs/sitemap.xml b/docs/sitemap.xml
index e2139f71..4c39f515 100644
--- a/docs/sitemap.xml
+++ b/docs/sitemap.xml
@@ -216,6 +216,12 @@
https://martin3141.github.io/spant/reference/comb_coils_fp_pc.html
+
+ https://martin3141.github.io/spant/reference/comb_coils_mrsi_gls.html
+
+
+ https://martin3141.github.io/spant/reference/comb_coils_svs_gls.html
+
https://martin3141.github.io/spant/reference/comb_csv_results.html
@@ -411,6 +417,9 @@
https://martin3141.github.io/spant/reference/gen_conv_reg.html
+
+ https://martin3141.github.io/spant/reference/gen_group_reg.html
+
https://martin3141.github.io/spant/reference/gen_impulse_reg.html
@@ -555,6 +564,15 @@
https://martin3141.github.io/spant/reference/glm_spec.html
+
+ https://martin3141.github.io/spant/reference/glm_spec_fmrs_fl.html
+
+
+ https://martin3141.github.io/spant/reference/glm_spec_fmrs_group.html
+
+
+ https://martin3141.github.io/spant/reference/glm_spec_group_linhyp.html
+
https://martin3141.github.io/spant/reference/grid_shift_xy.html
@@ -690,9 +708,15 @@
https://martin3141.github.io/spant/reference/mrs_data2basis.html
+
+ https://martin3141.github.io/spant/reference/mrs_data2bids.html
+
https://martin3141.github.io/spant/reference/mrs_data2mat.html
+
+ https://martin3141.github.io/spant/reference/mrs_data2spec_mat.html
+
https://martin3141.github.io/spant/reference/mrs_data2vec.html
@@ -741,6 +765,9 @@
https://martin3141.github.io/spant/reference/phase.html
+
+ https://martin3141.github.io/spant/reference/phase_ref_1h_brain.html
+
https://martin3141.github.io/spant/reference/plot.fit_result.html
@@ -780,6 +807,12 @@
https://martin3141.github.io/spant/reference/precomp.html
+
+ https://martin3141.github.io/spant/reference/preproc_svs.html
+
+
+ https://martin3141.github.io/spant/reference/preproc_svs_dataset.html
+
https://martin3141.github.io/spant/reference/print.fit_result.html
@@ -1050,6 +1083,9 @@
https://martin3141.github.io/spant/reference/spant_mpress_drift.html
+
+ https://martin3141.github.io/spant/reference/spant_sim_fmrs_dataset.html
+
https://martin3141.github.io/spant/reference/spant_simulation_benchmark.html
@@ -1107,6 +1143,9 @@
https://martin3141.github.io/spant/reference/svs_1h_brain_batch_analysis.html
+
+ https://martin3141.github.io/spant/reference/t_test_spec.html
+
https://martin3141.github.io/spant/reference/td2fd.html
Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS -sequence. Note, ideal pulses are assumed.
Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS sequence. Note, ideal pulses are assumed.
Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS -sequence. Note, ideal pulses are assumed.
Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS sequence. Note, ideal pulses are assumed.
Simulate a macromolecular and lipid basis-set suitable for 1H brain MRS -analysis.
Simulate a macromolecular and lipid basis-set suitable for 1H brain MRS analysis.
All functions
- Simulate an ideal pulse excitation profile by smoothing a top-hat function
-with a Gaussian.
Simulate an ideal pulse excitation profile by smoothing a top-hat function with a Gaussian.
@@ -1374,17 +1346,19 @@ All functions
- Simulate and fit some spectra with ABfit for benchmarking purposes. Basic
-timing and performance metrics will be printed.
Simulate and fit some spectra with ABfit for benchmarking purposes. Basic timing and performance metrics will be printed.
Example MEGA-PRESS data with significant B0 drift.
+
+
+ Simulate an example fMRS dataset for a block design fMRS experiment and export a BIDS structure.
- Simulate a typical metabolite basis set for benchmarking. Timing metrics will
-be printed on completion.
Simulate a typical metabolite basis set for benchmarking. Timing metrics will be printed on completion.
@@ -1400,8 +1374,7 @@ All functions
- Convert SPM style segmentation files to a single categorical image where
-the numerical values map as: 0) Other, 1) CSF, 2) GM and 3) WM.
Convert SPM style segmentation files to a single categorical image where the numerical values map as: 0) Other, 1) CSF, 2) GM and 3) WM.
@@ -1413,8 +1386,7 @@ All functions
- Plot the fitting results of an object of class fit_result with
-individual basis set components shown.
Plot the fitting results of an object of class fit_result with individual basis set components shown.
@@ -1459,6 +1431,10 @@ All functions svs_1h_brain_batch_analysis()
Batch interface to the standard SVS 1H brain analysis pipeline.
+
+
+ Perform a t-test on spectral data points.
@@ -1518,8 +1494,7 @@ All functions
- Fade a spectrum to zero by frequency domain multiplication with a tanh
-function. Note this operation distorts data points at the end of the FID.
Fade a spectrum to zero by frequency domain multiplication with a tanh function. Note this operation distorts data points at the end of the FID.
@@ -1549,7 +1524,7 @@ All functions
diff --git a/docs/reference/int_spec.html b/docs/reference/int_spec.html
index c7060fe7..783325a8 100644
--- a/docs/reference/int_spec.html
+++ b/docs/reference/int_spec.html
@@ -1,5 +1,5 @@
-Integrate a spectral region. — int_spec • Spectroscopy Analysis Tools (spant) Integrate a spectral region. — int_spec • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -118,7 +118,7 @@ Value
diff --git a/docs/reference/interleave_dyns.html b/docs/reference/interleave_dyns.html
index effe5543..441eff27 100644
--- a/docs/reference/interleave_dyns.html
+++ b/docs/reference/interleave_dyns.html
@@ -1,5 +1,5 @@
-Interleave the first and second half of a dynamic series. — interleave_dyns • Spectroscopy Analysis Tools (spant) Interleave the first and second half of a dynamic series. — interleave_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/inv_even_dyns.html b/docs/reference/inv_even_dyns.html
index 9f9d4fff..dcb781dc 100644
--- a/docs/reference/inv_even_dyns.html
+++ b/docs/reference/inv_even_dyns.html
@@ -1,5 +1,5 @@
-Invert even numbered dynamic scans starting from 1 (2,4,6...). — inv_even_dyns • Spectroscopy Analysis Tools (spant) Invert even numbered dynamic scans starting from 1 (2,4,6...). — inv_even_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/inv_odd_dyns.html b/docs/reference/inv_odd_dyns.html
index 26212e2b..78d64660 100644
--- a/docs/reference/inv_odd_dyns.html
+++ b/docs/reference/inv_odd_dyns.html
@@ -1,5 +1,5 @@
-Invert odd numbered dynamic scans starting from 1 (1,3,5...). — inv_odd_dyns • Spectroscopy Analysis Tools (spant) Invert odd numbered dynamic scans starting from 1 (1,3,5...). — inv_odd_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/is.def.html b/docs/reference/is.def.html
index f196ffd0..a67b9eba 100644
--- a/docs/reference/is.def.html
+++ b/docs/reference/is.def.html
@@ -1,5 +1,5 @@
-Check if an object is defined, which is the same as being not NULL. — is.def • Spectroscopy Analysis Tools (spant) Check if an object is defined, which is the same as being not NULL. — is.def • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/is_fd.html b/docs/reference/is_fd.html
index 3b0ca165..18a193aa 100644
--- a/docs/reference/is_fd.html
+++ b/docs/reference/is_fd.html
@@ -1,7 +1,5 @@
-Check if the chemical shift dimension of an MRS data object is in the
-frequency domain. — is_fd • Spectroscopy Analysis Tools (spant) Check if the chemical shift dimension of an MRS data object is in the frequency domain. — is_fd • Spectroscopy Analysis Tools (spant) Transform 2D MRSI data from k-space to image space in the x-y direction. — kspace2img_xy • Spectroscopy Analysis Tools (spant) Transform 2D MRSI data from k-space to image space in the x-y direction. — kspace2img_xy • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/l2_reg.html b/docs/reference/l2_reg.html
index 3d781d80..21aa9849 100644
--- a/docs/reference/l2_reg.html
+++ b/docs/reference/l2_reg.html
@@ -1,5 +1,5 @@
-Perform l2 regularisation artefact suppression. — l2_reg • Spectroscopy Analysis Tools (spant) Perform l2 regularisation artefact suppression. — l2_reg • Spectroscopy Analysis Tools (spant) Apply line-broadening (apodisation) to MRS data or basis object. — lb • Spectroscopy Analysis Tools (spant) Apply line-broadening (apodisation) to MRS data or basis object. — lb • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -123,7 +123,7 @@ Value
diff --git a/docs/reference/lofdc.html b/docs/reference/lofdc.html
index 5419b1ec..31347a25 100644
--- a/docs/reference/lofdc.html
+++ b/docs/reference/lofdc.html
@@ -1,5 +1,5 @@
-Correct linear frequency drift. — lofdc • Spectroscopy Analysis Tools (spant) Correct linear frequency drift. — lofdc • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -138,7 +138,7 @@ Value
diff --git a/docs/reference/lw2alpha.html b/docs/reference/lw2alpha.html
index b83db682..25da229b 100644
--- a/docs/reference/lw2alpha.html
+++ b/docs/reference/lw2alpha.html
@@ -1,7 +1,5 @@
-Covert a linewidth in Hz to an equivalent alpha value in the time-domain ie:
-x * exp(-t * alpha). — lw2alpha • Spectroscopy Analysis Tools (spant) Covert a linewidth in Hz to an equivalent alpha value in the time-domain ie: x * exp(-t * alpha). — lw2alpha • Spectroscopy Analysis Tools (spant) Covert a linewidth in Hz to an equivalent beta value in the time-domain ie:
-x * exp(-t * t * beta). — lw2beta • Spectroscopy Analysis Tools (spant) Covert a linewidth in Hz to an equivalent beta value in the time-domain ie: x * exp(-t * t * beta). — lw2beta • Spectroscopy Analysis Tools (spant) Make a basis-set object from a directory containing LCModel formatted RAW
-files. — make_basis_from_raw • Spectroscopy Analysis Tools (spant) Make a basis-set object from a directory containing LCModel formatted RAW files. — make_basis_from_raw • Spectroscopy Analysis Tools (spant) Mask an MRS dataset in the dynamic dimension. — mask_dyns • Spectroscopy Analysis Tools (spant) Mask an MRS dataset in the dynamic dimension. — mask_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/mask_fit_res.html b/docs/reference/mask_fit_res.html
index 97baaa3f..ebd91a99 100644
--- a/docs/reference/mask_fit_res.html
+++ b/docs/reference/mask_fit_res.html
@@ -1,5 +1,5 @@
-Mask fit result spectra depending on a vector of bool values. — mask_fit_res • Spectroscopy Analysis Tools (spant) Mask fit result spectra depending on a vector of bool values. — mask_fit_res • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -116,7 +116,7 @@ Value
diff --git a/docs/reference/mask_xy.html b/docs/reference/mask_xy.html
index 11bb577c..b0d38619 100644
--- a/docs/reference/mask_xy.html
+++ b/docs/reference/mask_xy.html
@@ -1,5 +1,5 @@
-Mask an MRSI dataset in the x-y direction — mask_xy • Spectroscopy Analysis Tools (spant) Mask an MRSI dataset in the x-y direction — mask_xy • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/mask_xy_corners.html b/docs/reference/mask_xy_corners.html
index 09b16cd2..2d13839d 100644
--- a/docs/reference/mask_xy_corners.html
+++ b/docs/reference/mask_xy_corners.html
@@ -1,5 +1,5 @@
-Mask the four corners of an MRSI dataset in the x-y plane. — mask_xy_corners • Spectroscopy Analysis Tools (spant) Mask the four corners of an MRSI dataset in the x-y plane. — mask_xy_corners • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/mask_xy_ellipse.html b/docs/reference/mask_xy_ellipse.html
index 1d8b02e4..e2e749ef 100644
--- a/docs/reference/mask_xy_ellipse.html
+++ b/docs/reference/mask_xy_ellipse.html
@@ -1,7 +1,5 @@
-Mask the voxels outside an elliptical region spanning the MRSI dataset in the
-x-y plane. — mask_xy_ellipse • Spectroscopy Analysis Tools (spant) Mask the voxels outside an elliptical region spanning the MRSI dataset in the x-y plane. — mask_xy_ellipse • Spectroscopy Analysis Tools (spant) Mask a 2D MRSI dataset in the x-y dimension. — mask_xy_mat • Spectroscopy Analysis Tools (spant) Mask a 2D MRSI dataset in the x-y dimension. — mask_xy_mat • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Value
diff --git a/docs/reference/mat2mrs_data.html b/docs/reference/mat2mrs_data.html
index 2e2895f3..ae55665f 100644
--- a/docs/reference/mat2mrs_data.html
+++ b/docs/reference/mat2mrs_data.html
@@ -1,7 +1,5 @@
-Convert a matrix (with spectral points in the column dimension and dynamics
-in the row dimensions) into a mrs_data object. — mat2mrs_data • Spectroscopy Analysis Tools (spant) Convert a matrix (with spectral points in the column dimension and dynamics in the row dimensions) into a mrs_data object. — mat2mrs_data • Spectroscopy Analysis Tools (spant) Matrix exponential function taken from complexplus package to reduce the
-number of spant dependencies. — matexp • Spectroscopy Analysis Tools (spant) Matrix exponential function taken from complexplus package to reduce the number of spant dependencies. — matexp • Spectroscopy Analysis Tools (spant) Apply the max operator to an MRS dataset. — max_mrs • Spectroscopy Analysis Tools (spant) Apply the max operator to an MRS dataset. — max_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/max_mrs_interp.html b/docs/reference/max_mrs_interp.html
index e4474764..52e63f3e 100644
--- a/docs/reference/max_mrs_interp.html
+++ b/docs/reference/max_mrs_interp.html
@@ -1,5 +1,5 @@
-Apply the max operator to an interpolated MRS dataset. — max_mrs_interp • Spectroscopy Analysis Tools (spant) Apply the max operator to an interpolated MRS dataset. — max_mrs_interp • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/mean.list.html b/docs/reference/mean.list.html
index b8eb3463..048306fd 100644
--- a/docs/reference/mean.list.html
+++ b/docs/reference/mean.list.html
@@ -1,5 +1,5 @@
-Calculate the mean spectrum from an mrs_data object. — mean.list • Spectroscopy Analysis Tools (spant) Calculate the mean spectrum from an mrs_data object. — mean.list • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/mean.mrs_data.html b/docs/reference/mean.mrs_data.html
index 5531a28d..79515014 100644
--- a/docs/reference/mean.mrs_data.html
+++ b/docs/reference/mean.mrs_data.html
@@ -1,5 +1,5 @@
-Calculate the mean spectrum from an mrs_data object. — mean.mrs_data • Spectroscopy Analysis Tools (spant) Calculate the mean spectrum from an mrs_data object. — mean.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/mean_dyn_blocks.html b/docs/reference/mean_dyn_blocks.html
index 10467098..4c042448 100644
--- a/docs/reference/mean_dyn_blocks.html
+++ b/docs/reference/mean_dyn_blocks.html
@@ -1,5 +1,5 @@
-Calculate the mean of adjacent dynamic scans. — mean_dyn_blocks • Spectroscopy Analysis Tools (spant) Calculate the mean of adjacent dynamic scans. — mean_dyn_blocks • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/mean_dyn_pairs.html b/docs/reference/mean_dyn_pairs.html
index 63e909ea..1a241126 100644
--- a/docs/reference/mean_dyn_pairs.html
+++ b/docs/reference/mean_dyn_pairs.html
@@ -1,5 +1,5 @@
-Calculate the pairwise means across a dynamic data set. — mean_dyn_pairs • Spectroscopy Analysis Tools (spant) Calculate the pairwise means across a dynamic data set. — mean_dyn_pairs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/mean_dyns.html b/docs/reference/mean_dyns.html
index 73fdbfa7..0daa27df 100644
--- a/docs/reference/mean_dyns.html
+++ b/docs/reference/mean_dyns.html
@@ -1,5 +1,5 @@
-Calculate the mean dynamic data. — mean_dyns • Spectroscopy Analysis Tools (spant) Calculate the mean dynamic data. — mean_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/mean_mrs_list.html b/docs/reference/mean_mrs_list.html
index 808b6c50..10d842c0 100644
--- a/docs/reference/mean_mrs_list.html
+++ b/docs/reference/mean_mrs_list.html
@@ -1,5 +1,5 @@
-Return the mean of a list of mrs_data objects. — mean_mrs_list • Spectroscopy Analysis Tools (spant) Return the mean of a list of mrs_data objects. — mean_mrs_list • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/mean_vec_blocks.html b/docs/reference/mean_vec_blocks.html
index 8fc92eaa..dd78b122 100644
--- a/docs/reference/mean_vec_blocks.html
+++ b/docs/reference/mean_vec_blocks.html
@@ -1,5 +1,5 @@
-Calculate the mean of adjacent blocks in a vector. — mean_vec_blocks • Spectroscopy Analysis Tools (spant) Calculate the mean of adjacent blocks in a vector. — mean_vec_blocks • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/median_dyns.html b/docs/reference/median_dyns.html
index 1039d4b5..9a085b10 100644
--- a/docs/reference/median_dyns.html
+++ b/docs/reference/median_dyns.html
@@ -1,5 +1,5 @@
-Calculate the median dynamic data. — median_dyns • Spectroscopy Analysis Tools (spant) Calculate the median dynamic data. — median_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/mod_td.html b/docs/reference/mod_td.html
index 76ad0a40..141ef09e 100644
--- a/docs/reference/mod_td.html
+++ b/docs/reference/mod_td.html
@@ -1,5 +1,5 @@
-Apply the Modulus operator to the time-domain MRS signal. — mod_td • Spectroscopy Analysis Tools (spant) Apply the Modulus operator to the time-domain MRS signal. — mod_td • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/mrs_data2basis.html b/docs/reference/mrs_data2basis.html
index 62f7d749..11797b91 100644
--- a/docs/reference/mrs_data2basis.html
+++ b/docs/reference/mrs_data2basis.html
@@ -1,7 +1,5 @@
-Convert an mrs_data object to basis object - where basis signals are spread
-across the dynamic dimension in the MRS data. — mrs_data2basis • Spectroscopy Analysis Tools (spant) Convert an mrs_data object to basis object - where basis signals are spread across the dynamic dimension in the MRS data. — mrs_data2basis • Spectroscopy Analysis Tools (spant) Create a BIDS file structure from a vector of MRS data paths or list of mrs_data objects. — mrs_data2bids • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Create a BIDS file structure from a vector of MRS data paths or list of mrs_data objects.
+ Source: R/fmrs.R
+ mrs_data2bids.Rd
+
+
+
+ Create a BIDS file structure from a vector of MRS data paths or list of
+mrs_data objects.
+
+
+
+ mrs_data2bids(
+ mrs_data,
+ output_dir,
+ suffix = NULL,
+ sub = NULL,
+ ses = NULL,
+ task = NULL,
+ acq = NULL,
+ nuc = NULL,
+ voi = NULL,
+ rec = NULL,
+ run = NULL,
+ echo = NULL,
+ inv = NULL,
+ skip_existing = TRUE
+)
+
+
+
+ Arguments
+ - mrs_data
+vector of MRS data paths or list of mrs_data objects.
- output_dir
+the base directory to create the BIDS structure.
- suffix
+optional vector of file suffixes. Default behaviour is to
+automatically determine these from the input data, however it is recommended
+that they are specified to allow more efficient skipping of existing data.
- sub
+optional vector of subject labels. If not specified, these will be
+automatically generated as a series of increasing zero-padded integer values
+corresponding to the mrs_data input indices.
- ses
+optional vector of session labels.
- task
+optional vector of task labels.
- acq
+optional vector of acquisition labels.
- nuc
+optional vector of nucleus labels.
- voi
+optional vector of volume of interest labels.
- rec
+optional vector of reconstruction labels.
- run
+optional vector of run indices.
- echo
+optional vector of echo time indices.
- inv
+optional vector of inversion indices.
- skip_existing
+skip any data files that have already been converted.
+Defaults to TRUE, set to FALSE to force an overwrite of any existing data
+files.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/mrs_data2mat.html b/docs/reference/mrs_data2mat.html
index cf5ff28c..9e47688a 100644
--- a/docs/reference/mrs_data2mat.html
+++ b/docs/reference/mrs_data2mat.html
@@ -1,7 +1,5 @@
-Convert mrs_data object to a matrix, with spectral points in the column
-dimension and dynamics in the row dimension. — mrs_data2mat • Spectroscopy Analysis Tools (spant) Convert mrs_data object to a matrix, with spectral points in the column dimension and dynamics in the row dimension. — mrs_data2mat • Spectroscopy Analysis Tools (spant) Convert mrs_data object to a matrix, with spectral points in the column dimension and dynamics in the row dimension. — mrs_data2spec_mat • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Convert mrs_data object to a matrix, with spectral points in the column dimension and dynamics in the row dimension.
+ Source: R/mrs_data_proc.R
+ mrs_data2spec_mat.Rd
+
+
+
+ Convert mrs_data object to a matrix, with spectral points in the column
+dimension and dynamics in the row dimension.
+
+
+
+ mrs_data2spec_mat(mrs_data, collapse = TRUE)
+
+
+
+ Arguments
+ - mrs_data
+MRS data object or list of MRS data objects.
- collapse
+collapse all other dimensions along the dynamic dimension, eg
+a 16x16 MRSI grid would be first collapsed across 256 dynamic scans.
+
+ Value
+
+
+MRS data matrix.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/mrs_data2vec.html b/docs/reference/mrs_data2vec.html
index fb172d68..a1fd654d 100644
--- a/docs/reference/mrs_data2vec.html
+++ b/docs/reference/mrs_data2vec.html
@@ -1,5 +1,5 @@
-Convert mrs_data object to a vector. — mrs_data2vec • Spectroscopy Analysis Tools (spant) Convert mrs_data object to a vector. — mrs_data2vec • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -126,7 +126,7 @@ Value
diff --git a/docs/reference/mvfftshift.html b/docs/reference/mvfftshift.html
index 92b0841b..976b3410 100644
--- a/docs/reference/mvfftshift.html
+++ b/docs/reference/mvfftshift.html
@@ -1,7 +1,5 @@
-Perform a fftshift on a matrix, with each column replaced by its shifted
-result. — mvfftshift • Spectroscopy Analysis Tools (spant) Perform a fftshift on a matrix, with each column replaced by its shifted result. — mvfftshift • Spectroscopy Analysis Tools (spant) Perform an ifftshift on a matrix, with each column replaced by its shifted
-result. — mvifftshift • Spectroscopy Analysis Tools (spant) Perform an ifftshift on a matrix, with each column replaced by its shifted result. — mvifftshift • Spectroscopy Analysis Tools (spant) Print fit coordinates from a single index. — n2coord • Spectroscopy Analysis Tools (spant) Print fit coordinates from a single index. — n2coord • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/nifti_flip_lr.html b/docs/reference/nifti_flip_lr.html
index 730abe3c..19860b3c 100644
--- a/docs/reference/nifti_flip_lr.html
+++ b/docs/reference/nifti_flip_lr.html
@@ -1,9 +1,5 @@
-Flip the x data dimension order of a nifti image. This corresponds to
-flipping MRI data in the left-right direction, assuming the data in save in
-neurological format (can check with fslorient program). — nifti_flip_lr • Spectroscopy Analysis Tools (spant) Flip the x data dimension order of a nifti image. This corresponds to flipping MRI data in the left-right direction, assuming the data in save in neurological format (can check with fslorient program). — nifti_flip_lr • Spectroscopy Analysis Tools (spant) Export a one-page pdf of a single fit result — one_page_pdf • Spectroscopy Analysis Tools (spant) Export a one-page pdf of a single fit result — one_page_pdf • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -108,7 +108,7 @@ Arguments
diff --git a/docs/reference/ortho3.html b/docs/reference/ortho3.html
index 13ade97d..5d7dd2fd 100644
--- a/docs/reference/ortho3.html
+++ b/docs/reference/ortho3.html
@@ -1,5 +1,5 @@
-Display an orthographic projection plot of a nifti object. — ortho3 • Spectroscopy Analysis Tools (spant) Display an orthographic projection plot of a nifti object. — ortho3 • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -172,7 +172,7 @@ Arguments
diff --git a/docs/reference/ortho3_inter.html b/docs/reference/ortho3_inter.html
index 090cc5e5..15948899 100644
--- a/docs/reference/ortho3_inter.html
+++ b/docs/reference/ortho3_inter.html
@@ -1,5 +1,5 @@
-Display an interactive orthographic projection plot of a nifti object. — ortho3_inter • Spectroscopy Analysis Tools (spant) Display an interactive orthographic projection plot of a nifti object. — ortho3_inter • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -132,7 +132,7 @@ Arguments
diff --git a/docs/reference/peak_info.html b/docs/reference/peak_info.html
index 09058bd8..41c8ffaf 100644
--- a/docs/reference/peak_info.html
+++ b/docs/reference/peak_info.html
@@ -1,7 +1,5 @@
-Search for the highest peak in a spectral region and return the frequency,
-height and FWHM. — peak_info • Spectroscopy Analysis Tools (spant) Search for the highest peak in a spectral region and return the frequency, height and FWHM. — peak_info • Spectroscopy Analysis Tools (spant) Papoulis-Gerchberg (PG) algorithm method for k-space extrapolation. — pg_extrap_xy • Spectroscopy Analysis Tools (spant) Papoulis-Gerchberg (PG) algorithm method for k-space extrapolation. — pg_extrap_xy • Spectroscopy Analysis Tools (spant) Apply phasing parameters to MRS data. — phase • Spectroscopy Analysis Tools (spant) Apply phasing parameters to MRS data. — phase • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/phase_ref_1h_brain.html b/docs/reference/phase_ref_1h_brain.html
new file mode 100644
index 00000000..8707a74a
--- /dev/null
+++ b/docs/reference/phase_ref_1h_brain.html
@@ -0,0 +1,131 @@
+
+Corrected zero order phase and chemical shift offset in 1H MRS data from the brain. — phase_ref_1h_brain • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Corrected zero order phase and chemical shift offset in 1H MRS data from the brain.
+ Source: R/rats.R
+ phase_ref_1h_brain.Rd
+
+
+
+ Corrected zero order phase and chemical shift offset in 1H MRS data from the
+brain.
+
+
+
+ phase_ref_1h_brain(mrs_data, mean_ref = FALSE, ret_corr_only = TRUE)
+
+
+
+ Arguments
+ - mrs_data
+MRS data to be corrected.
- mean_ref
+apply the phase and offset of the mean spectrum to all
+others. Default is FALSE.
- ret_corr_only
+return the corrected data only.
+
+ Value
+
+
+corrected MRS data.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/plot.fit_result.html b/docs/reference/plot.fit_result.html
index e54d3bc1..836a53ee 100644
--- a/docs/reference/plot.fit_result.html
+++ b/docs/reference/plot.fit_result.html
@@ -1,5 +1,5 @@
-Plot the fitting results of an object of class fit_result. — plot.fit_result • Spectroscopy Analysis Tools (spant) Plot the fitting results of an object of class fit_result. — plot.fit_result • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -207,7 +207,7 @@ Arguments
diff --git a/docs/reference/plot.mrs_data.html b/docs/reference/plot.mrs_data.html
index fabcc35b..bb2ec651 100644
--- a/docs/reference/plot.mrs_data.html
+++ b/docs/reference/plot.mrs_data.html
@@ -1,5 +1,5 @@
-Plotting method for objects of class mrs_data. — plot.mrs_data • Spectroscopy Analysis Tools (spant) Plotting method for objects of class mrs_data. — plot.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -287,7 +287,7 @@ Arguments
diff --git a/docs/reference/plot_bc.html b/docs/reference/plot_bc.html
index 4f8309b4..b48142cc 100644
--- a/docs/reference/plot_bc.html
+++ b/docs/reference/plot_bc.html
@@ -1,5 +1,5 @@
-Convenience function to plot a baseline estimate with the original data. — plot_bc • Spectroscopy Analysis Tools (spant) Convenience function to plot a baseline estimate with the original data. — plot_bc • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -108,7 +108,7 @@ Arguments
diff --git a/docs/reference/plot_reg.html b/docs/reference/plot_reg.html
index ae1acbe7..2addb2f6 100644
--- a/docs/reference/plot_reg.html
+++ b/docs/reference/plot_reg.html
@@ -1,5 +1,5 @@
-Plot regressors as an image. — plot_reg • Spectroscopy Analysis Tools (spant) Plot regressors as an image. — plot_reg • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/plot_slice_fit.html b/docs/reference/plot_slice_fit.html
index fbc7b560..57f1af8a 100644
--- a/docs/reference/plot_slice_fit.html
+++ b/docs/reference/plot_slice_fit.html
@@ -1,5 +1,5 @@
-Plot a 2D slice from an MRSI fit result object. — plot_slice_fit • Spectroscopy Analysis Tools (spant) Plot a 2D slice from an MRSI fit result object. — plot_slice_fit • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -129,7 +129,7 @@ Arguments
diff --git a/docs/reference/plot_slice_fit_inter.html b/docs/reference/plot_slice_fit_inter.html
index 4eed104a..da105a7d 100644
--- a/docs/reference/plot_slice_fit_inter.html
+++ b/docs/reference/plot_slice_fit_inter.html
@@ -1,5 +1,5 @@
-Plot a 2D slice from an MRSI fit result object. — plot_slice_fit_inter • Spectroscopy Analysis Tools (spant) Plot a 2D slice from an MRSI fit result object. — plot_slice_fit_inter • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -134,7 +134,7 @@ Arguments
diff --git a/docs/reference/plot_slice_map.html b/docs/reference/plot_slice_map.html
index 553e9ac8..ffb2a134 100644
--- a/docs/reference/plot_slice_map.html
+++ b/docs/reference/plot_slice_map.html
@@ -1,5 +1,5 @@
-Plot a slice from a 7 dimensional array. — plot_slice_map • Spectroscopy Analysis Tools (spant) Plot a slice from a 7 dimensional array. — plot_slice_map • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -153,7 +153,7 @@ Arguments
diff --git a/docs/reference/plot_slice_map_inter.html b/docs/reference/plot_slice_map_inter.html
index 40d33b42..90968f66 100644
--- a/docs/reference/plot_slice_map_inter.html
+++ b/docs/reference/plot_slice_map_inter.html
@@ -1,7 +1,5 @@
-Plot an interactive slice map from a data array where voxels can be selected
-to display a corresponding spectrum. — plot_slice_map_inter • Spectroscopy Analysis Tools (spant) Plot an interactive slice map from a data array where voxels can be selected to display a corresponding spectrum. — plot_slice_map_inter • Spectroscopy Analysis Tools (spant) Plot the spectral standard deviation. — plot_spec_sd • Spectroscopy Analysis Tools (spant) Plot the spectral standard deviation. — plot_spec_sd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Arguments
diff --git a/docs/reference/plot_voi_overlay.html b/docs/reference/plot_voi_overlay.html
index 9a782e88..bbbbf35e 100644
--- a/docs/reference/plot_voi_overlay.html
+++ b/docs/reference/plot_voi_overlay.html
@@ -1,5 +1,5 @@
-Plot a volume as an image overlay. — plot_voi_overlay • Spectroscopy Analysis Tools (spant) Plot a volume as an image overlay. — plot_voi_overlay • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -116,7 +116,7 @@ Arguments
diff --git a/docs/reference/plot_voi_overlay_seg.html b/docs/reference/plot_voi_overlay_seg.html
index 3d4e74ff..0e800ff2 100644
--- a/docs/reference/plot_voi_overlay_seg.html
+++ b/docs/reference/plot_voi_overlay_seg.html
@@ -1,5 +1,5 @@
-Plot a volume as an overlay on a segmented brain volume. — plot_voi_overlay_seg • Spectroscopy Analysis Tools (spant) Plot a volume as an overlay on a segmented brain volume. — plot_voi_overlay_seg • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Arguments
diff --git a/docs/reference/ppm.html b/docs/reference/ppm.html
index c352327a..ee4696e2 100644
--- a/docs/reference/ppm.html
+++ b/docs/reference/ppm.html
@@ -1,5 +1,5 @@
-Return the ppm scale of an MRS dataset or fit result. — ppm • Spectroscopy Analysis Tools (spant) Return the ppm scale of an MRS dataset or fit result. — ppm • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -132,7 +132,7 @@ Value
diff --git a/docs/reference/precomp.html b/docs/reference/precomp.html
index 822d7336..df3d2c6c 100644
--- a/docs/reference/precomp.html
+++ b/docs/reference/precomp.html
@@ -1,7 +1,5 @@
-Save function results to file and load on subsequent calls to avoid repeat
-computation. — precomp • Spectroscopy Analysis Tools (spant) Save function results to file and load on subsequent calls to avoid repeat computation. — precomp • Spectroscopy Analysis Tools (spant) Preprocess and perform quality assessment of a single SVS data set. — preproc_svs • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Preprocess and perform quality assessment of a single SVS data set.
+ Source: R/fmrs.R
+ preproc_svs.Rd
+
+
+
+ Preprocess and perform quality assessment of a single SVS data set.
+
+
+
+ preproc_svs(path, label = NULL, output_dir = NULL, ref_inds = NULL)
+
+
+
+ Arguments
+ - path
+path to the fMRS data file or IMA directory.
- label
+a label to describe the data set.
- output_dir
+output directory.
- ref_inds
+a vector of 1-based indices for any water reference dynamic
+scans.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/preproc_svs_dataset.html b/docs/reference/preproc_svs_dataset.html
new file mode 100644
index 00000000..07c3a29b
--- /dev/null
+++ b/docs/reference/preproc_svs_dataset.html
@@ -0,0 +1,148 @@
+
+Preprocess and perform quality assessment of one or more SVS data sets. — preproc_svs_dataset • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Preprocess and perform quality assessment of one or more SVS data sets.
+ Source: R/fmrs.R
+ preproc_svs_dataset.Rd
+
+
+
+ Preprocess and perform quality assessment of one or more SVS data sets.
+
+
+
+ preproc_svs_dataset(
+ paths,
+ labels = NULL,
+ output_dir = "spant_analysis",
+ exclude_labels = NULL,
+ overwrite = FALSE,
+ ref_inds = NULL,
+ return_results = FALSE
+)
+
+
+
+ Arguments
+ - paths
+paths to the fMRS data file or IMA directory.
- labels
+labels to describe each data set.
- output_dir
+output directory.
- exclude_labels
+vector of labels of scans to exclude, eg poor quality
+data.
- overwrite
+overwrite saved results, defaults to FALSE.
- ref_inds
+a vector of 1-based indices for any water reference dynamic
+scans.
- return_results
+function will return key outputs, defaults to FALSE.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/print.fit_result.html b/docs/reference/print.fit_result.html
index 297f28dc..5f434e57 100644
--- a/docs/reference/print.fit_result.html
+++ b/docs/reference/print.fit_result.html
@@ -1,5 +1,5 @@
-Print a summary of an object of class fit_result. — print.fit_result • Spectroscopy Analysis Tools (spant) Print a summary of an object of class fit_result. — print.fit_result • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -105,7 +105,7 @@ Arguments
diff --git a/docs/reference/print.mrs_data.html b/docs/reference/print.mrs_data.html
index 51199017..e1561eb2 100644
--- a/docs/reference/print.mrs_data.html
+++ b/docs/reference/print.mrs_data.html
@@ -1,5 +1,5 @@
-Print a summary of mrs_data parameters. — print.mrs_data • Spectroscopy Analysis Tools (spant) Print a summary of mrs_data parameters. — print.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -109,7 +109,7 @@ Arguments
diff --git a/docs/reference/qn_states.html b/docs/reference/qn_states.html
index 0f42f2f9..d7aa6715 100644
--- a/docs/reference/qn_states.html
+++ b/docs/reference/qn_states.html
@@ -1,5 +1,5 @@
-Get the quantum coherence matrix for a spin system. — qn_states • Spectroscopy Analysis Tools (spant) Get the quantum coherence matrix for a spin system. — qn_states • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/rats.html b/docs/reference/rats.html
index 5a39a396..93585e08 100644
--- a/docs/reference/rats.html
+++ b/docs/reference/rats.html
@@ -1,5 +1,5 @@
-Robust Alignment to a Target Spectrum (RATS). — rats • Spectroscopy Analysis Tools (spant) Robust Alignment to a Target Spectrum (RATS). — rats • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -207,7 +207,7 @@ Value
diff --git a/docs/reference/re_weighting.html b/docs/reference/re_weighting.html
index d21caf21..8b0b070a 100644
--- a/docs/reference/re_weighting.html
+++ b/docs/reference/re_weighting.html
@@ -1,5 +1,5 @@
-Apply a weighting to the FID to enhance spectral resolution. — re_weighting • Spectroscopy Analysis Tools (spant) Apply a weighting to the FID to enhance spectral resolution. — re_weighting • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/read_basis.html b/docs/reference/read_basis.html
index da9b94af..eb6f8557 100644
--- a/docs/reference/read_basis.html
+++ b/docs/reference/read_basis.html
@@ -1,5 +1,5 @@
-Read a basis file in LCModel .basis format. — read_basis • Spectroscopy Analysis Tools (spant) Read a basis file in LCModel .basis format. — read_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/read_ima_coil_dir.html b/docs/reference/read_ima_coil_dir.html
index 28c02de0..4f073cd8 100644
--- a/docs/reference/read_ima_coil_dir.html
+++ b/docs/reference/read_ima_coil_dir.html
@@ -1,9 +1,5 @@
-Read a directory containing Siemens MRS IMA files and combine along the coil
-dimension. Note that the coil ID is inferred from the sorted file name and
-should be checked when consistency is required between two directories. — read_ima_coil_dir • Spectroscopy Analysis Tools (spant) Read a directory containing Siemens MRS IMA files and combine along the coil dimension. Note that the coil ID is inferred from the sorted file name and should be checked when consistency is required between two directories. — read_ima_coil_dir • Spectroscopy Analysis Tools (spant) Read a directory containing Siemens MRS IMA files and combine along the
-dynamic dimension. Note that the coil ID is inferred from the sorted file
-name and should be checked when consistency is required. — read_ima_dyn_dir • Spectroscopy Analysis Tools (spant) Read a directory containing Siemens MRS IMA files and combine along the dynamic dimension. Note that the coil ID is inferred from the sorted file name and should be checked when consistency is required. — read_ima_dyn_dir • Spectroscopy Analysis Tools (spant) Read an LCModel formatted coord file containing fit information. — read_lcm_coord • Spectroscopy Analysis Tools (spant) Read an LCModel formatted coord file containing fit information. — read_lcm_coord • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -107,7 +107,7 @@ Value
diff --git a/docs/reference/read_mrs.html b/docs/reference/read_mrs.html
index 3ac2a36b..2cf36b20 100644
--- a/docs/reference/read_mrs.html
+++ b/docs/reference/read_mrs.html
@@ -1,5 +1,5 @@
-Read MRS data from a file. — read_mrs • Spectroscopy Analysis Tools (spant) Read MRS data from a file. — read_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -88,7 +88,8 @@ Read MRS data from a file.
full_fid = FALSE,
omit_svs_ref_scans = TRUE,
verbose = FALSE,
- extra = NULL
+ extra = NULL,
+ fid_filt_dist = NULL
)
@@ -140,6 +141,13 @@ Arguments
an optional data frame to provide additional variables for use
in subsequent analysis steps, eg id or grouping variables.
fid_filt_dist
+indicate if the data has a distorted FID due to a
+brick-wall filter being used to downsample the data. Default is to auto
+detect this from the data, but TRUE or FALSE options can be given to override
+detection.
Value
@@ -183,7 +191,7 @@ Examples
diff --git a/docs/reference/read_mrs_tqn.html b/docs/reference/read_mrs_tqn.html
index 5766362f..84bdaf3a 100644
--- a/docs/reference/read_mrs_tqn.html
+++ b/docs/reference/read_mrs_tqn.html
@@ -1,5 +1,5 @@
-Read MRS data using the TARQUIN software package. — read_mrs_tqn • Spectroscopy Analysis Tools (spant) Read MRS data using the TARQUIN software package. — read_mrs_tqn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -131,7 +131,7 @@ Examples
diff --git a/docs/reference/read_pulse_ascii.html b/docs/reference/read_pulse_ascii.html
index c9e0d43c..ab11c9cc 100644
--- a/docs/reference/read_pulse_ascii.html
+++ b/docs/reference/read_pulse_ascii.html
@@ -1,5 +1,5 @@
-Read an ASCII formatted pulse file. — read_pulse_ascii • Spectroscopy Analysis Tools (spant) Read an ASCII formatted pulse file. — read_pulse_ascii • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/read_pulse_bruker.html b/docs/reference/read_pulse_bruker.html
index c92bf76a..dbe9073b 100644
--- a/docs/reference/read_pulse_bruker.html
+++ b/docs/reference/read_pulse_bruker.html
@@ -1,5 +1,5 @@
-Read a Bruker formatted pulse file — read_pulse_bruker • Spectroscopy Analysis Tools (spant) Read a Bruker formatted pulse file — read_pulse_bruker • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/read_pulse_pta.html b/docs/reference/read_pulse_pta.html
index 72e1b6d4..a0fac3c3 100644
--- a/docs/reference/read_pulse_pta.html
+++ b/docs/reference/read_pulse_pta.html
@@ -1,5 +1,5 @@
-Read a .pta formatted pulse file compatible with Siemens PulseTool. — read_pulse_pta • Spectroscopy Analysis Tools (spant) Read a .pta formatted pulse file compatible with Siemens PulseTool. — read_pulse_pta • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/read_siemens_txt_hdr.html b/docs/reference/read_siemens_txt_hdr.html
index 23fb8c70..3a17d87c 100644
--- a/docs/reference/read_siemens_txt_hdr.html
+++ b/docs/reference/read_siemens_txt_hdr.html
@@ -1,5 +1,5 @@
-Read the text format header found in Siemens IMA and TWIX data files. — read_siemens_txt_hdr • Spectroscopy Analysis Tools (spant) Read the text format header found in Siemens IMA and TWIX data files. — read_siemens_txt_hdr • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -78,7 +78,7 @@ Read the text format header found in Siemens IMA and TWIX data files.
- read_siemens_txt_hdr(input, version = "vd", verbose, offset = 0)
+ read_siemens_txt_hdr(input, version = "vd", verbose = FALSE, offset = 0)
@@ -118,7 +118,7 @@ Value
diff --git a/docs/reference/read_tqn_fit.html b/docs/reference/read_tqn_fit.html
index 4da6c25e..a1630420 100644
--- a/docs/reference/read_tqn_fit.html
+++ b/docs/reference/read_tqn_fit.html
@@ -1,5 +1,5 @@
-Reader for csv fit results generated by TARQUIN. — read_tqn_fit • Spectroscopy Analysis Tools (spant) Reader for csv fit results generated by TARQUIN. — read_tqn_fit • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -113,7 +113,7 @@ Examples
diff --git a/docs/reference/read_tqn_result.html b/docs/reference/read_tqn_result.html
index 36659714..68a3e98c 100644
--- a/docs/reference/read_tqn_result.html
+++ b/docs/reference/read_tqn_result.html
@@ -1,5 +1,5 @@
-Reader for csv results generated by TARQUIN. — read_tqn_result • Spectroscopy Analysis Tools (spant) Reader for csv results generated by TARQUIN. — read_tqn_result • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -117,7 +117,7 @@ Examples
diff --git a/docs/reference/recon_imag.html b/docs/reference/recon_imag.html
index d2a72225..5bc3b1eb 100644
--- a/docs/reference/recon_imag.html
+++ b/docs/reference/recon_imag.html
@@ -1,7 +1,5 @@
-Reconstruct complex time-domain data from the real part of frequency-domain
-data. — recon_imag • Spectroscopy Analysis Tools (spant) Reconstruct complex time-domain data from the real part of frequency-domain data. — recon_imag • Spectroscopy Analysis Tools (spant) Reconstruct complex time-domain data from the real part of frequency-domain
-data. — recon_imag_vec • Spectroscopy Analysis Tools (spant) Reconstruct complex time-domain data from the real part of frequency-domain data. — recon_imag_vec • Spectroscopy Analysis Tools (spant) Reconstruct 2D MRSI data from a twix file loaded with read_mrs. — recon_twix_2d_mrsi • Spectroscopy Analysis Tools (spant) Reconstruct 2D MRSI data from a twix file loaded with read_mrs. — recon_twix_2d_mrsi • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/rectangular_mask.html b/docs/reference/rectangular_mask.html
index a2117283..6e469bc9 100644
--- a/docs/reference/rectangular_mask.html
+++ b/docs/reference/rectangular_mask.html
@@ -1,5 +1,5 @@
-Create a rectangular mask stored as a matrix of logical values. — rectangular_mask • Spectroscopy Analysis Tools (spant) Create a rectangular mask stored as a matrix of logical values. — rectangular_mask • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -130,7 +130,7 @@ Value
diff --git a/docs/reference/reexports.html b/docs/reference/reexports.html
index 694a75d1..a59e8379 100644
--- a/docs/reference/reexports.html
+++ b/docs/reference/reexports.html
@@ -1,5 +1,5 @@
-Objects exported from other packages — reexports • Spectroscopy Analysis Tools (spant) Objects exported from other packages — reexports • Spectroscopy Analysis Tools (spant)
Spectroscopy Analysis Tools (spant)
- 2.21.0
+ 2.22.0
@@ -103,7 +103,7 @@ Objects exported from other packages
diff --git a/docs/reference/rep_array_dim.html b/docs/reference/rep_array_dim.html
index b9c49b4a..48c0a5ed 100644
--- a/docs/reference/rep_array_dim.html
+++ b/docs/reference/rep_array_dim.html
@@ -1,5 +1,5 @@
-Repeat an array over a given dimension. — rep_array_dim • Spectroscopy Analysis Tools (spant) Repeat an array over a given dimension. — rep_array_dim • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/rep_dyn.html b/docs/reference/rep_dyn.html
index 6bbfb0ef..89a4bb9b 100644
--- a/docs/reference/rep_dyn.html
+++ b/docs/reference/rep_dyn.html
@@ -1,5 +1,5 @@
-Replicate a scan in the dynamic dimension. — rep_dyn • Spectroscopy Analysis Tools (spant) Replicate a scan in the dynamic dimension. — rep_dyn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/rep_mrs.html b/docs/reference/rep_mrs.html
index 67730b5c..becb8f00 100644
--- a/docs/reference/rep_mrs.html
+++ b/docs/reference/rep_mrs.html
@@ -1,5 +1,5 @@
-Replicate a scan over a given dimension. — rep_mrs • Spectroscopy Analysis Tools (spant) Replicate a scan over a given dimension. — rep_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -138,7 +138,7 @@ Value
diff --git a/docs/reference/resample_basis.html b/docs/reference/resample_basis.html
index b0f2ab17..c7a6222a 100644
--- a/docs/reference/resample_basis.html
+++ b/docs/reference/resample_basis.html
@@ -1,5 +1,5 @@
-Resample a basis-set to match a mrs_data acquisition. — resample_basis • Spectroscopy Analysis Tools (spant) Resample a basis-set to match a mrs_data acquisition. — resample_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -116,7 +116,7 @@ Value
diff --git a/docs/reference/resample_img.html b/docs/reference/resample_img.html
index f1e7beaf..b0cc8f71 100644
--- a/docs/reference/resample_img.html
+++ b/docs/reference/resample_img.html
@@ -1,5 +1,5 @@
-Resample an image to match a target image space. — resample_img • Spectroscopy Analysis Tools (spant) Resample an image to match a target image space. — resample_img • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/resample_voi.html b/docs/reference/resample_voi.html
index 8fbfa836..a29ab096 100644
--- a/docs/reference/resample_voi.html
+++ b/docs/reference/resample_voi.html
@@ -1,7 +1,5 @@
-Resample a VOI to match a target image space using nearest-neighbour
-interpolation. — resample_voi • Spectroscopy Analysis Tools (spant) Resample a VOI to match a target image space using nearest-neighbour interpolation. — resample_voi • Spectroscopy Analysis Tools (spant) Reslice a nifti object to match the orientation of mrs data. — reslice_to_mrs • Spectroscopy Analysis Tools (spant) Reslice a nifti object to match the orientation of mrs data. — reslice_to_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/reson_table2mrs_data.html b/docs/reference/reson_table2mrs_data.html
index d75579ee..c5a2167a 100644
--- a/docs/reference/reson_table2mrs_data.html
+++ b/docs/reference/reson_table2mrs_data.html
@@ -1,5 +1,5 @@
-Generate mrs_data from a table of single Lorentzian resonances. — reson_table2mrs_data • Spectroscopy Analysis Tools (spant) Generate mrs_data from a table of single Lorentzian resonances. — reson_table2mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -119,7 +119,7 @@ Value
diff --git a/docs/reference/rm_dyns.html b/docs/reference/rm_dyns.html
index 5d5ef692..573e1f51 100644
--- a/docs/reference/rm_dyns.html
+++ b/docs/reference/rm_dyns.html
@@ -1,5 +1,5 @@
-Remove a subset of dynamic scans. — rm_dyns • Spectroscopy Analysis Tools (spant) Remove a subset of dynamic scans. — rm_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/scale_amp_molal.html b/docs/reference/scale_amp_molal.html
index aaeee1f2..7acb8cb0 100644
--- a/docs/reference/scale_amp_molal.html
+++ b/docs/reference/scale_amp_molal.html
@@ -1,7 +1,5 @@
-Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water). — scale_amp_molal • Spectroscopy Analysis Tools (spant) Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / kg of tissue water). — scale_amp_molal • Spectroscopy Analysis Tools (spant)
Spectroscopy Analysis Tools (spant)
- 2.21.0
+ 2.22.0
@@ -76,8 +74,7 @@
- Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water).
+ Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / kg of tissue water).
Source: R/amp_scaling.R
scale_amp_molal.Rd
@@ -163,7 +160,7 @@ Value
diff --git a/docs/reference/scale_amp_molal_pvc.html b/docs/reference/scale_amp_molal_pvc.html
index 962d6afc..4d194abd 100644
--- a/docs/reference/scale_amp_molal_pvc.html
+++ b/docs/reference/scale_amp_molal_pvc.html
@@ -1,7 +1,5 @@
-Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water). — scale_amp_molal_pvc • Spectroscopy Analysis Tools (spant)
@@ -75,8 +73,7 @@
- Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water).
+ Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / kg of tissue water).
Source: R/amp_scaling.R
scale_amp_molal_pvc.Rd
@@ -141,7 +138,7 @@ Value
diff --git a/docs/reference/scale_amp_molar.html b/docs/reference/scale_amp_molar.html
index 02358d91..dc87a338 100644
--- a/docs/reference/scale_amp_molar.html
+++ b/docs/reference/scale_amp_molar.html
@@ -1,7 +1,5 @@
-Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / Litre of tissue). — scale_amp_molar • Spectroscopy Analysis Tools (spant) Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / Litre of tissue). — scale_amp_molar • Spectroscopy Analysis Tools (spant) Convert default LCM/TARQUIN concentration scaling to molal units with partial
-volume correction. — scale_amp_molar2molal_pvc • Spectroscopy Analysis Tools (spant) Convert default LCM/TARQUIN concentration scaling to molal units with partial volume correction. — scale_amp_molar2molal_pvc • Spectroscopy Analysis Tools (spant) Scale fitted amplitudes to a ratio of signal amplitude. — scale_amp_ratio • Spectroscopy Analysis Tools (spant) Scale fitted amplitudes to a ratio of signal amplitude. — scale_amp_ratio • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -116,7 +116,7 @@ Value
diff --git a/docs/reference/scale_amp_ratio_value.html b/docs/reference/scale_amp_ratio_value.html
index 2036837a..6af8ac51 100644
--- a/docs/reference/scale_amp_ratio_value.html
+++ b/docs/reference/scale_amp_ratio_value.html
@@ -1,5 +1,5 @@
-Scale fitted amplitudes to a ratio of signal amplitude. — scale_amp_ratio_value • Spectroscopy Analysis Tools (spant) Scale fitted amplitudes to a ratio of signal amplitude. — scale_amp_ratio_value • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/scale_amp_water_ratio.html b/docs/reference/scale_amp_water_ratio.html
index 5b25e884..35a76b00 100644
--- a/docs/reference/scale_amp_water_ratio.html
+++ b/docs/reference/scale_amp_water_ratio.html
@@ -1,5 +1,5 @@
-Scale metabolite amplitudes as a ratio to the unsuppressed water amplitude. — scale_amp_water_ratio • Spectroscopy Analysis Tools (spant) Scale metabolite amplitudes as a ratio to the unsuppressed water amplitude. — scale_amp_water_ratio • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/scale_basis_amp.html b/docs/reference/scale_basis_amp.html
index 9401c3f1..5a58b5e5 100644
--- a/docs/reference/scale_basis_amp.html
+++ b/docs/reference/scale_basis_amp.html
@@ -1,5 +1,5 @@
-Scale a basis object by a scalar. — scale_basis_amp • Spectroscopy Analysis Tools (spant) Scale a basis object by a scalar. — scale_basis_amp • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/scale_basis_from_singlet.html b/docs/reference/scale_basis_from_singlet.html
index 0d542bc8..c9a19e77 100644
--- a/docs/reference/scale_basis_from_singlet.html
+++ b/docs/reference/scale_basis_from_singlet.html
@@ -1,5 +1,5 @@
-Scale a basis-set to be consistent with spant assumptions for water scaling. — scale_basis_from_singlet • Spectroscopy Analysis Tools (spant) Scale a basis-set to be consistent with spant assumptions for water scaling. — scale_basis_from_singlet • Spectroscopy Analysis Tools (spant)
Spectroscopy Analysis Tools (spant)
- 2.21.0
+ 2.22.0
@@ -127,7 +127,7 @@ Value
diff --git a/docs/reference/scale_mrs_amp.html b/docs/reference/scale_mrs_amp.html
index b5501a0d..990f058a 100644
--- a/docs/reference/scale_mrs_amp.html
+++ b/docs/reference/scale_mrs_amp.html
@@ -1,5 +1,5 @@
-Scale an mrs_data object by a scalar or vector or amplitudes. — scale_mrs_amp • Spectroscopy Analysis Tools (spant) Scale an mrs_data object by a scalar or vector or amplitudes. — scale_mrs_amp • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/scale_spec.html b/docs/reference/scale_spec.html
index 4f6ea835..6b3ddba4 100644
--- a/docs/reference/scale_spec.html
+++ b/docs/reference/scale_spec.html
@@ -1,5 +1,5 @@
-Scale mrs_data to a spectral region. — scale_spec • Spectroscopy Analysis Tools (spant) Scale mrs_data to a spectral region. — scale_spec • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -141,7 +141,7 @@ Value
diff --git a/docs/reference/sd.html b/docs/reference/sd.html
index ea1eec9f..3ae4dfd4 100644
--- a/docs/reference/sd.html
+++ b/docs/reference/sd.html
@@ -1,5 +1,5 @@
-Calculate the standard deviation spectrum from an mrs_data object. — sd • Spectroscopy Analysis Tools (spant) Calculate the standard deviation spectrum from an mrs_data object. — sd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/sd.mrs_data.html b/docs/reference/sd.mrs_data.html
index 3f92a49f..13bdda85 100644
--- a/docs/reference/sd.mrs_data.html
+++ b/docs/reference/sd.mrs_data.html
@@ -1,5 +1,5 @@
-Calculate the standard deviation spectrum from an mrs_data object. — sd.mrs_data • Spectroscopy Analysis Tools (spant) Calculate the standard deviation spectrum from an mrs_data object. — sd.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/seconds.html b/docs/reference/seconds.html
index b34d6627..467ee17f 100644
--- a/docs/reference/seconds.html
+++ b/docs/reference/seconds.html
@@ -1,5 +1,5 @@
-Return a time scale vector to match the FID of an MRS data object. — seconds • Spectroscopy Analysis Tools (spant) Return a time scale vector to match the FID of an MRS data object. — seconds • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/seq_cpmg_ideal.html b/docs/reference/seq_cpmg_ideal.html
index 547e96ab..45727c86 100644
--- a/docs/reference/seq_cpmg_ideal.html
+++ b/docs/reference/seq_cpmg_ideal.html
@@ -1,5 +1,5 @@
-CPMG style sequence with ideal pulses. — seq_cpmg_ideal • Spectroscopy Analysis Tools (spant) CPMG style sequence with ideal pulses. — seq_cpmg_ideal • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/seq_mega_press_ideal.html b/docs/reference/seq_mega_press_ideal.html
index 0769b8b4..a9cd7fa0 100644
--- a/docs/reference/seq_mega_press_ideal.html
+++ b/docs/reference/seq_mega_press_ideal.html
@@ -1,7 +1,5 @@
-MEGA-PRESS sequence with ideal localisation pulses and Gaussian shaped
-editing pulse. — seq_mega_press_ideal • Spectroscopy Analysis Tools (spant) MEGA-PRESS sequence with ideal localisation pulses and Gaussian shaped editing pulse. — seq_mega_press_ideal • Spectroscopy Analysis Tools (spant) PRESS sequence with shaped refocusing pulses. — seq_press_2d_shaped • Spectroscopy Analysis Tools (spant) PRESS sequence with shaped refocusing pulses. — seq_press_2d_shaped • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -165,7 +165,7 @@ Value
diff --git a/docs/reference/seq_press_ideal.html b/docs/reference/seq_press_ideal.html
index 8c976856..72c3af3d 100644
--- a/docs/reference/seq_press_ideal.html
+++ b/docs/reference/seq_press_ideal.html
@@ -1,5 +1,5 @@
-PRESS sequence with ideal pulses. — seq_press_ideal • Spectroscopy Analysis Tools (spant) PRESS sequence with ideal pulses. — seq_press_ideal • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/seq_pulse_acquire.html b/docs/reference/seq_pulse_acquire.html
index 4a88fc64..ad80571e 100644
--- a/docs/reference/seq_pulse_acquire.html
+++ b/docs/reference/seq_pulse_acquire.html
@@ -1,5 +1,5 @@
-Simple pulse and acquire sequence with ideal pulses. — seq_pulse_acquire • Spectroscopy Analysis Tools (spant) Simple pulse and acquire sequence with ideal pulses. — seq_pulse_acquire • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/seq_slaser_ideal.html b/docs/reference/seq_slaser_ideal.html
index 74688f4d..eb83e8e3 100644
--- a/docs/reference/seq_slaser_ideal.html
+++ b/docs/reference/seq_slaser_ideal.html
@@ -1,5 +1,5 @@
-sLASER sequence with ideal pulses. — seq_slaser_ideal • Spectroscopy Analysis Tools (spant) sLASER sequence with ideal pulses. — seq_slaser_ideal • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -126,7 +126,7 @@ Value
diff --git a/docs/reference/seq_spin_echo_ideal.html b/docs/reference/seq_spin_echo_ideal.html
index e23271de..4248716f 100644
--- a/docs/reference/seq_spin_echo_ideal.html
+++ b/docs/reference/seq_spin_echo_ideal.html
@@ -1,5 +1,5 @@
-Spin echo sequence with ideal pulses. — seq_spin_echo_ideal • Spectroscopy Analysis Tools (spant) Spin echo sequence with ideal pulses. — seq_spin_echo_ideal • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/seq_steam_ideal.html b/docs/reference/seq_steam_ideal.html
index a60685a8..1c8115d7 100644
--- a/docs/reference/seq_steam_ideal.html
+++ b/docs/reference/seq_steam_ideal.html
@@ -1,5 +1,5 @@
-STEAM sequence with ideal pulses. — seq_steam_ideal • Spectroscopy Analysis Tools (spant) STEAM sequence with ideal pulses. — seq_steam_ideal • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -128,7 +128,7 @@ Value
diff --git a/docs/reference/seq_steam_ideal_cof.html b/docs/reference/seq_steam_ideal_cof.html
index 8f225740..cba7af91 100644
--- a/docs/reference/seq_steam_ideal_cof.html
+++ b/docs/reference/seq_steam_ideal_cof.html
@@ -1,7 +1,5 @@
-STEAM sequence with ideal pulses and coherence order filtering to simulate
-gradient crushers. — seq_steam_ideal_cof • Spectroscopy Analysis Tools (spant) STEAM sequence with ideal pulses and coherence order filtering to simulate gradient crushers. — seq_steam_ideal_cof • Spectroscopy Analysis Tools (spant) STEAM sequence with ideal pulses using the z-rotation gradient simulation
-method described by Young et al JMR 140, 146-152 (1999). — seq_steam_ideal_young • Spectroscopy Analysis Tools (spant) STEAM sequence with ideal pulses using the z-rotation gradient simulation method described by Young et al JMR 140, 146-152 (1999). — seq_steam_ideal_young • Spectroscopy Analysis Tools (spant) Set the number of transients for an mrs_data object. — set_Ntrans • Spectroscopy Analysis Tools (spant) Set the number of transients for an mrs_data object. — set_Ntrans • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/set_def_acq_paras.html b/docs/reference/set_def_acq_paras.html
index 3e1b4004..cc2ada9c 100644
--- a/docs/reference/set_def_acq_paras.html
+++ b/docs/reference/set_def_acq_paras.html
@@ -1,5 +1,5 @@
-Set the default acquisition parameters. — set_def_acq_paras • Spectroscopy Analysis Tools (spant) Set the default acquisition parameters. — set_def_acq_paras • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Arguments
diff --git a/docs/reference/set_lcm_cmd.html b/docs/reference/set_lcm_cmd.html
index 2056ed01..42bb2f24 100644
--- a/docs/reference/set_lcm_cmd.html
+++ b/docs/reference/set_lcm_cmd.html
@@ -1,5 +1,5 @@
-Set the command to run the LCModel command-line program. — set_lcm_cmd • Spectroscopy Analysis Tools (spant) Set the command to run the LCModel command-line program. — set_lcm_cmd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/set_lw.html b/docs/reference/set_lw.html
index b64ec851..bb176c62 100644
--- a/docs/reference/set_lw.html
+++ b/docs/reference/set_lw.html
@@ -1,5 +1,5 @@
-Apply line-broadening to an mrs_data object to achieve a specified linewidth. — set_lw • Spectroscopy Analysis Tools (spant) Apply line-broadening to an mrs_data object to achieve a specified linewidth. — set_lw • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -123,7 +123,7 @@ Value
diff --git a/docs/reference/set_mask_xy_mat.html b/docs/reference/set_mask_xy_mat.html
index 49dc5d4e..52c4b617 100644
--- a/docs/reference/set_mask_xy_mat.html
+++ b/docs/reference/set_mask_xy_mat.html
@@ -1,5 +1,5 @@
-Set the masked voxels in a 2D MRSI dataset to given spectrum. — set_mask_xy_mat • Spectroscopy Analysis Tools (spant) Set the masked voxels in a 2D MRSI dataset to given spectrum. — set_mask_xy_mat • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Value
diff --git a/docs/reference/set_precomp_mode.html b/docs/reference/set_precomp_mode.html
index f44bd5d3..47c28e3b 100644
--- a/docs/reference/set_precomp_mode.html
+++ b/docs/reference/set_precomp_mode.html
@@ -1,5 +1,5 @@
-Set the precompute mode. — set_precomp_mode • Spectroscopy Analysis Tools (spant) Set the precompute mode. — set_precomp_mode • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/set_precomp_verbose.html b/docs/reference/set_precomp_verbose.html
index 1453a231..9c613505 100644
--- a/docs/reference/set_precomp_verbose.html
+++ b/docs/reference/set_precomp_verbose.html
@@ -1,5 +1,5 @@
-Set the verbosity of the precompute function. — set_precomp_verbose • Spectroscopy Analysis Tools (spant) Set the verbosity of the precompute function. — set_precomp_verbose • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/set_ref.html b/docs/reference/set_ref.html
index 8953fa50..5436dfa2 100644
--- a/docs/reference/set_ref.html
+++ b/docs/reference/set_ref.html
@@ -1,5 +1,5 @@
-Set the ppm reference value (eg ppm value at 0Hz). — set_ref • Spectroscopy Analysis Tools (spant) Set the ppm reference value (eg ppm value at 0Hz). — set_ref • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/set_td_pts.html b/docs/reference/set_td_pts.html
index 8a80d42a..586459ff 100644
--- a/docs/reference/set_td_pts.html
+++ b/docs/reference/set_td_pts.html
@@ -1,7 +1,5 @@
-Set the number of time-domain data points, truncating or zero-filling as
-appropriate. — set_td_pts • Spectroscopy Analysis Tools (spant) Set the number of time-domain data points, truncating or zero-filling as appropriate. — set_td_pts • Spectroscopy Analysis Tools (spant) Set the command to run the TARQUIN command-line program. — set_tqn_cmd • Spectroscopy Analysis Tools (spant) Set the command to run the TARQUIN command-line program. — set_tqn_cmd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/set_tr.html b/docs/reference/set_tr.html
index b2109ab0..65c9df5f 100644
--- a/docs/reference/set_tr.html
+++ b/docs/reference/set_tr.html
@@ -1,5 +1,5 @@
-Set the repetition time of an MRS dataset. — set_tr • Spectroscopy Analysis Tools (spant) Set the repetition time of an MRS dataset. — set_tr • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/shift.html b/docs/reference/shift.html
index ab0fe724..034591d0 100644
--- a/docs/reference/shift.html
+++ b/docs/reference/shift.html
@@ -1,5 +1,5 @@
-Apply a frequency shift to MRS data. — shift • Spectroscopy Analysis Tools (spant) Apply a frequency shift to MRS data. — shift • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/shift_basis.html b/docs/reference/shift_basis.html
index 2884be19..f55a65e0 100644
--- a/docs/reference/shift_basis.html
+++ b/docs/reference/shift_basis.html
@@ -1,5 +1,5 @@
-Apply frequency shifts to basis set signals. — shift_basis • Spectroscopy Analysis Tools (spant) Apply frequency shifts to basis set signals. — shift_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Value
diff --git a/docs/reference/sim_basis.html b/docs/reference/sim_basis.html
index c7838c46..bb5fefc6 100644
--- a/docs/reference/sim_basis.html
+++ b/docs/reference/sim_basis.html
@@ -1,5 +1,5 @@
-Simulate a basis set object. — sim_basis • Spectroscopy Analysis Tools (spant) Simulate a basis set object. — sim_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -136,7 +136,7 @@ Value
diff --git a/docs/reference/sim_basis_1h_brain.html b/docs/reference/sim_basis_1h_brain.html
index 62ed7389..f71ffa0b 100644
--- a/docs/reference/sim_basis_1h_brain.html
+++ b/docs/reference/sim_basis_1h_brain.html
@@ -1,7 +1,5 @@
-Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS
-sequence. Note, ideal pulses are assumed. — sim_basis_1h_brain • Spectroscopy Analysis Tools (spant) Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS sequence. Note, ideal pulses are assumed. — sim_basis_1h_brain • Spectroscopy Analysis Tools (spant) Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS
-sequence. Note, ideal pulses are assumed. — sim_basis_1h_brain_press • Spectroscopy Analysis Tools (spant) Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS sequence. Note, ideal pulses are assumed. — sim_basis_1h_brain_press • Spectroscopy Analysis Tools (spant) Simulate a macromolecular and lipid basis-set suitable for 1H brain MRS
-analysis. — sim_basis_mm_lip_lcm • Spectroscopy Analysis Tools (spant) Simulate a macromolecular and lipid basis-set suitable for 1H brain MRS analysis. — sim_basis_mm_lip_lcm • Spectroscopy Analysis Tools (spant) Simulate a basis file using TARQUIN. — sim_basis_tqn • Spectroscopy Analysis Tools (spant) Simulate a basis file using TARQUIN. — sim_basis_tqn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -129,7 +129,7 @@ Examples
diff --git a/docs/reference/sim_brain_1h.html b/docs/reference/sim_brain_1h.html
index 2044cf1a..717ee289 100644
--- a/docs/reference/sim_brain_1h.html
+++ b/docs/reference/sim_brain_1h.html
@@ -1,5 +1,5 @@
-Simulate MRS data with a similar appearance to normal brain (by default). — sim_brain_1h • Spectroscopy Analysis Tools (spant) Simulate MRS data with a similar appearance to normal brain (by default). — sim_brain_1h • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -159,7 +159,7 @@ Value
diff --git a/docs/reference/sim_mol.html b/docs/reference/sim_mol.html
index 23bcef50..77f76a50 100644
--- a/docs/reference/sim_mol.html
+++ b/docs/reference/sim_mol.html
@@ -1,5 +1,5 @@
-Simulate a mol_parameter object. — sim_mol • Spectroscopy Analysis Tools (spant) Simulate a mol_parameter object. — sim_mol • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -143,7 +143,7 @@ Value
diff --git a/docs/reference/sim_noise.html b/docs/reference/sim_noise.html
index 23875f79..a71477d4 100644
--- a/docs/reference/sim_noise.html
+++ b/docs/reference/sim_noise.html
@@ -1,5 +1,5 @@
-Simulate an mrs_data object containing simulated Gaussian noise. — sim_noise • Spectroscopy Analysis Tools (spant) Simulate an mrs_data object containing simulated Gaussian noise. — sim_noise • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -84,6 +84,7 @@ Simulate an mrs_data object containing simulated Gaussian noise.
ft = def_ft(),
N = def_N(),
ref = def_ref(),
+ nuc = def_nuc(),
dyns = 1,
fd = TRUE
)
@@ -111,6 +112,10 @@ Arguments
reference value for ppm scale.
nuc
+resonant nucleus.
dyns
number of dynamic scans to generate.
Value
diff --git a/docs/reference/sim_resonances.html b/docs/reference/sim_resonances.html
index 19e9a8a4..d4f8d7c0 100644
--- a/docs/reference/sim_resonances.html
+++ b/docs/reference/sim_resonances.html
@@ -1,5 +1,5 @@
-Simulate a MRS data object containing a set of simulated resonances. — sim_resonances • Spectroscopy Analysis Tools (spant) Simulate a MRS data object containing a set of simulated resonances. — sim_resonances • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -161,7 +161,7 @@ Examples
diff --git a/docs/reference/sim_th_excit_profile.html b/docs/reference/sim_th_excit_profile.html
index 5535c5ef..e781cab1 100644
--- a/docs/reference/sim_th_excit_profile.html
+++ b/docs/reference/sim_th_excit_profile.html
@@ -1,7 +1,5 @@
-Simulate an ideal pulse excitation profile by smoothing a top-hat function
-with a Gaussian. — sim_th_excit_profile • Spectroscopy Analysis Tools (spant) Simulate an ideal pulse excitation profile by smoothing a top-hat function with a Gaussian. — sim_th_excit_profile • Spectroscopy Analysis Tools (spant) Simulate an mrs_data object containing complex zero valued samples. — sim_zero • Spectroscopy Analysis Tools (spant) Simulate an mrs_data object containing complex zero valued samples. — sim_zero • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -78,7 +78,14 @@ Simulate an mrs_data object containing complex zero valued samples.
-
+
@@ -99,6 +106,10 @@ Arguments
reference value for ppm scale.
nuc
+resonant nucleus.
dyns
number of dynamic scans to generate.
Value
diff --git a/docs/reference/smooth_dyns.html b/docs/reference/smooth_dyns.html
index 4cc8da50..accf3a51 100644
--- a/docs/reference/smooth_dyns.html
+++ b/docs/reference/smooth_dyns.html
@@ -1,5 +1,5 @@
-Smooth data across the dynamic dimension with a Gaussian kernel. — smooth_dyns • Spectroscopy Analysis Tools (spant) Smooth data across the dynamic dimension with a Gaussian kernel. — smooth_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/sort_basis.html b/docs/reference/sort_basis.html
index 6a676ea2..d25cc006 100644
--- a/docs/reference/sort_basis.html
+++ b/docs/reference/sort_basis.html
@@ -1,5 +1,5 @@
-Sort the basis-set elements alphabetically. — sort_basis • Spectroscopy Analysis Tools (spant) Sort the basis-set elements alphabetically. — sort_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/spant-package.html b/docs/reference/spant-package.html
index b3dd8e21..90f19ec3 100644
--- a/docs/reference/spant-package.html
+++ b/docs/reference/spant-package.html
@@ -1,5 +1,5 @@
-spant: spectroscopy analysis tools. — spant-package • Spectroscopy Analysis Tools (spant) spant: spectroscopy analysis tools. — spant-package • Spectroscopy Analysis Tools (spant) Simulate and fit some spectra with ABfit for benchmarking purposes. Basic
-timing and performance metrics will be printed. — spant_abfit_benchmark • Spectroscopy Analysis Tools (spant) Simulate and fit some spectra with ABfit for benchmarking purposes. Basic timing and performance metrics will be printed. — spant_abfit_benchmark • Spectroscopy Analysis Tools (spant) Example MEGA-PRESS data with significant B0 drift. — spant_mpress_drift • Spectroscopy Analysis Tools (spant) Example MEGA-PRESS data with significant B0 drift. — spant_mpress_drift • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -83,7 +83,7 @@ Example MEGA-PRESS data with significant B0 drift.
Format
- An object of class mrs_data of length 13.
+ An object of class mrs_data of dimension 1 x 1 x 1 x 1 x 40 x 1 x 1024.
@@ -98,7 +98,7 @@ Format
diff --git a/docs/reference/spant_sim_fmrs_dataset.html b/docs/reference/spant_sim_fmrs_dataset.html
new file mode 100644
index 00000000..00e48b56
--- /dev/null
+++ b/docs/reference/spant_sim_fmrs_dataset.html
@@ -0,0 +1,117 @@
+
+Simulate an example fMRS dataset for a block design fMRS experiment and export a BIDS structure. — spant_sim_fmrs_dataset • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Simulate an example fMRS dataset for a block design fMRS experiment and export a BIDS structure.
+ Source: R/fmrs.R
+ spant_sim_fmrs_dataset.Rd
+
+
+
+ Simulate an example fMRS dataset for a block design fMRS experiment and
+export a BIDS structure.
+
+
+
+ spant_sim_fmrs_dataset(output_dir = NULL)
+
+
+
+ Arguments
+ - output_dir
+output directory for the BIDS data. Defaults to :
+"HOME/sim_fmrs_dataset/data".
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/spant_simulation_benchmark.html b/docs/reference/spant_simulation_benchmark.html
index 32daa8bf..d8cc6841 100644
--- a/docs/reference/spant_simulation_benchmark.html
+++ b/docs/reference/spant_simulation_benchmark.html
@@ -1,7 +1,5 @@
-Simulate a typical metabolite basis set for benchmarking. Timing metrics will
-be printed on completion. — spant_simulation_benchmark • Spectroscopy Analysis Tools (spant) Simulate a typical metabolite basis set for benchmarking. Timing metrics will be printed on completion. — spant_simulation_benchmark • Spectroscopy Analysis Tools (spant) Decompose an mrs_data object into white and gray matter spectra. — spec_decomp • Spectroscopy Analysis Tools (spant) Perform a mathematical operation on a spectral region. — spec_op • Spectroscopy Analysis Tools (spant) Perform a mathematical operation on a spectral region. — spec_op • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -98,8 +98,8 @@ Arguments
operator
-can be "sum" (default), "mean", "l2", "max", "min" or
-"max-min".
can be "sum" (default), "mean", "l2", "max", "max_cplx,
+"min" or "max-min".
freq_scale
@@ -129,7 +129,7 @@ Value
diff --git a/docs/reference/spin_sys.html b/docs/reference/spin_sys.html
index 853423a4..1eaa9e76 100644
--- a/docs/reference/spin_sys.html
+++ b/docs/reference/spin_sys.html
@@ -1,5 +1,5 @@
-Create a spin system object for pulse sequence simulation. — spin_sys • Spectroscopy Analysis Tools (spant) Create a spin system object for pulse sequence simulation. — spin_sys • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/spm_pve2categorical.html b/docs/reference/spm_pve2categorical.html
index 23a1bad9..70f10729 100644
--- a/docs/reference/spm_pve2categorical.html
+++ b/docs/reference/spm_pve2categorical.html
@@ -1,7 +1,5 @@
-Convert SPM style segmentation files to a single categorical image where
-the numerical values map as: 0) Other, 1) CSF, 2) GM and 3) WM. — spm_pve2categorical • Spectroscopy Analysis Tools (spant) Convert SPM style segmentation files to a single categorical image where the numerical values map as: 0) Other, 1) CSF, 2) GM and 3) WM. — spm_pve2categorical • Spectroscopy Analysis Tools (spant) Signal space projection method for lipid suppression. — ssp • Spectroscopy Analysis Tools (spant) Signal space projection method for lipid suppression. — ssp • Spectroscopy Analysis Tools (spant) Plot the fitting results of an object of class fit_result with
-individual basis set components shown. — stackplot.fit_result • Spectroscopy Analysis Tools (spant) Plot the fitting results of an object of class fit_result with individual basis set components shown. — stackplot.fit_result • Spectroscopy Analysis Tools (spant) Produce a plot with multiple traces. — stackplot • Spectroscopy Analysis Tools (spant) Produce a plot with multiple traces. — stackplot • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/stackplot.mrs_data.html b/docs/reference/stackplot.mrs_data.html
index 17ff5648..64eea445 100644
--- a/docs/reference/stackplot.mrs_data.html
+++ b/docs/reference/stackplot.mrs_data.html
@@ -1,5 +1,5 @@
-Stackplot plotting method for objects of class mrs_data. — stackplot.mrs_data • Spectroscopy Analysis Tools (spant) Stackplot plotting method for objects of class mrs_data. — stackplot.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -255,7 +255,7 @@ Arguments
diff --git a/docs/reference/sub_first_dyn.html b/docs/reference/sub_first_dyn.html
index dbd7f831..493b7242 100644
--- a/docs/reference/sub_first_dyn.html
+++ b/docs/reference/sub_first_dyn.html
@@ -1,5 +1,5 @@
-Subtract the first dynamic spectrum from a dynamic series. — sub_first_dyn • Spectroscopy Analysis Tools (spant) Subtract the first dynamic spectrum from a dynamic series. — sub_first_dyn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/sub_mean_dyns.html b/docs/reference/sub_mean_dyns.html
index 6e3bb2df..221bd0c1 100644
--- a/docs/reference/sub_mean_dyns.html
+++ b/docs/reference/sub_mean_dyns.html
@@ -1,5 +1,5 @@
-Subtract the mean dynamic spectrum from a dynamic series. — sub_mean_dyns • Spectroscopy Analysis Tools (spant) Subtract the mean dynamic spectrum from a dynamic series. — sub_mean_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/sub_median_dyns.html b/docs/reference/sub_median_dyns.html
index 134c495d..1e834f14 100644
--- a/docs/reference/sub_median_dyns.html
+++ b/docs/reference/sub_median_dyns.html
@@ -1,5 +1,5 @@
-Subtract the median dynamic spectrum from a dynamic series. — sub_median_dyns • Spectroscopy Analysis Tools (spant) Subtract the median dynamic spectrum from a dynamic series. — sub_median_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/sum_coils.html b/docs/reference/sum_coils.html
index 7bf559f2..e1ab3cc0 100644
--- a/docs/reference/sum_coils.html
+++ b/docs/reference/sum_coils.html
@@ -1,5 +1,5 @@
-Calculate the sum across receiver coil elements. — sum_coils • Spectroscopy Analysis Tools (spant) Calculate the sum across receiver coil elements. — sum_coils • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/sum_dyns.html b/docs/reference/sum_dyns.html
index a0be19d3..bbda2ffc 100644
--- a/docs/reference/sum_dyns.html
+++ b/docs/reference/sum_dyns.html
@@ -1,5 +1,5 @@
-Calculate the sum of data dynamics. — sum_dyns • Spectroscopy Analysis Tools (spant) Calculate the sum of data dynamics. — sum_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/sum_mrs.html b/docs/reference/sum_mrs.html
index a22f215b..3cc3ab9e 100644
--- a/docs/reference/sum_mrs.html
+++ b/docs/reference/sum_mrs.html
@@ -1,5 +1,5 @@
-Sum two mrs_data objects. — sum_mrs • Spectroscopy Analysis Tools (spant) Sum two mrs_data objects. — sum_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Value
diff --git a/docs/reference/sum_mrs_list.html b/docs/reference/sum_mrs_list.html
index f4e09aea..c3584348 100644
--- a/docs/reference/sum_mrs_list.html
+++ b/docs/reference/sum_mrs_list.html
@@ -1,5 +1,5 @@
-Return the sum of a list of mrs_data objects. — sum_mrs_list • Spectroscopy Analysis Tools (spant) Return the sum of a list of mrs_data objects. — sum_mrs_list • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/svs_1h_brain_analysis.html b/docs/reference/svs_1h_brain_analysis.html
index 8ce514db..dff0ef7d 100644
--- a/docs/reference/svs_1h_brain_analysis.html
+++ b/docs/reference/svs_1h_brain_analysis.html
@@ -1,5 +1,5 @@
-Standard SVS 1H brain analysis pipeline. — svs_1h_brain_analysis • Spectroscopy Analysis Tools (spant) Standard SVS 1H brain analysis pipeline. — svs_1h_brain_analysis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -199,7 +199,7 @@ Value
diff --git a/docs/reference/svs_1h_brain_analysis_dev.html b/docs/reference/svs_1h_brain_analysis_dev.html
index d70a14d3..d71bfea2 100644
--- a/docs/reference/svs_1h_brain_analysis_dev.html
+++ b/docs/reference/svs_1h_brain_analysis_dev.html
@@ -1,5 +1,5 @@
-Standard SVS 1H brain analysis pipeline. — svs_1h_brain_analysis_dev • Spectroscopy Analysis Tools (spant) Standard SVS 1H brain analysis pipeline. — svs_1h_brain_analysis_dev • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -193,7 +193,7 @@ Examples
diff --git a/docs/reference/svs_1h_brain_batch_analysis.html b/docs/reference/svs_1h_brain_batch_analysis.html
index 5631e8cc..15f7223e 100644
--- a/docs/reference/svs_1h_brain_batch_analysis.html
+++ b/docs/reference/svs_1h_brain_batch_analysis.html
@@ -1,5 +1,5 @@
-Batch interface to the standard SVS 1H brain analysis pipeline. — svs_1h_brain_batch_analysis • Spectroscopy Analysis Tools (spant) Batch interface to the standard SVS 1H brain analysis pipeline. — svs_1h_brain_batch_analysis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -144,7 +144,7 @@ Value
diff --git a/docs/reference/t_test_spec.html b/docs/reference/t_test_spec.html
new file mode 100644
index 00000000..56a7ea1b
--- /dev/null
+++ b/docs/reference/t_test_spec.html
@@ -0,0 +1,124 @@
+
+Perform a t-test on spectral data points. — t_test_spec • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+
+
+ Perform a t-test on spectral data points.
+
+
+
+ t_test_spec(mrs_data, group)
+
+
+
+ Arguments
+ - mrs_data
+an mrs_data object with spectra in the dynamic dimension.
- group
+vector describing the group membership of each dynamic spectrum.
+
+ Value
+
+
+a list of statistical results.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/td2fd.html b/docs/reference/td2fd.html
index 6748a6a8..f31ed524 100644
--- a/docs/reference/td2fd.html
+++ b/docs/reference/td2fd.html
@@ -1,5 +1,5 @@
-Transform time-domain data to the frequency-domain. — td2fd • Spectroscopy Analysis Tools (spant) Transform time-domain data to the frequency-domain. — td2fd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/td_conv_filt.html b/docs/reference/td_conv_filt.html
index a9f340c3..106b9b00 100644
--- a/docs/reference/td_conv_filt.html
+++ b/docs/reference/td_conv_filt.html
@@ -1,5 +1,5 @@
-Time-domain convolution based filter. — td_conv_filt • Spectroscopy Analysis Tools (spant) Time-domain convolution based filter. — td_conv_filt • Spectroscopy Analysis Tools (spant) Time-domain spectral registration. — tdsr • Spectroscopy Analysis Tools (spant) Time-domain spectral registration. — tdsr • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -121,7 +121,7 @@ Value
diff --git a/docs/reference/te.html b/docs/reference/te.html
index 010361b1..4a65711d 100644
--- a/docs/reference/te.html
+++ b/docs/reference/te.html
@@ -1,5 +1,5 @@
-Return the echo time of an MRS dataset. — te • Spectroscopy Analysis Tools (spant) Return the echo time of an MRS dataset. — te • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/tr.html b/docs/reference/tr.html
index 0c0bd63b..2e749e02 100644
--- a/docs/reference/tr.html
+++ b/docs/reference/tr.html
@@ -1,5 +1,5 @@
-Return the repetition time of an MRS dataset. — tr • Spectroscopy Analysis Tools (spant) Return the repetition time of an MRS dataset. — tr • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/varpro_3_para_opts.html b/docs/reference/varpro_3_para_opts.html
index c2270a16..52d7cd84 100644
--- a/docs/reference/varpro_3_para_opts.html
+++ b/docs/reference/varpro_3_para_opts.html
@@ -1,5 +1,5 @@
-Return a list of options for VARPRO based fitting with 3 free parameters. — varpro_3_para_opts • Spectroscopy Analysis Tools (spant) Return a list of options for VARPRO based fitting with 3 free parameters. — varpro_3_para_opts • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -141,7 +141,7 @@ Value
diff --git a/docs/reference/varpro_basic_opts.html b/docs/reference/varpro_basic_opts.html
index 32c86d22..c5104891 100644
--- a/docs/reference/varpro_basic_opts.html
+++ b/docs/reference/varpro_basic_opts.html
@@ -1,5 +1,5 @@
-Return a list of options for a basic VARPRO analysis. — varpro_basic_opts • Spectroscopy Analysis Tools (spant) Return a list of options for a basic VARPRO analysis. — varpro_basic_opts • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -118,7 +118,7 @@ Value
diff --git a/docs/reference/varpro_opts.html b/docs/reference/varpro_opts.html
index 2aabf11d..6332f730 100644
--- a/docs/reference/varpro_opts.html
+++ b/docs/reference/varpro_opts.html
@@ -1,5 +1,5 @@
-Return a list of options for VARPRO based fitting. — varpro_opts • Spectroscopy Analysis Tools (spant) Return a list of options for VARPRO based fitting. — varpro_opts • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -177,7 +177,7 @@ Examples
diff --git a/docs/reference/vec2mrs_data.html b/docs/reference/vec2mrs_data.html
index 0cccd73b..f0d58bf0 100644
--- a/docs/reference/vec2mrs_data.html
+++ b/docs/reference/vec2mrs_data.html
@@ -1,5 +1,5 @@
-Convert a vector into a mrs_data object. — vec2mrs_data • Spectroscopy Analysis Tools (spant) Convert a vector into a mrs_data object. — vec2mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -80,10 +80,11 @@ Convert a vector into a mrs_data object.
vec2mrs_data(
vec,
- fs = def_fs(),
- ft = def_ft(),
- ref = def_ref(),
- nuc = def_nuc(),
+ mrs_data = NULL,
+ fs = NULL,
+ ft = NULL,
+ ref = NULL,
+ nuc = NULL,
dyns = 1,
fd = FALSE
)
@@ -95,6 +96,10 @@ Arguments
the data vector.
mrs_data
+example data to copy acquisition parameters from.
fs
sampling frequency in Hz.
Arguments
fd
-flag to indicate if the matrix is in the frequency domain (logical).
flag to indicate if the vector is in the frequency domain (logical).
Value
diff --git a/docs/reference/write_basis.html b/docs/reference/write_basis.html
index b6e27cbd..94c5e021 100644
--- a/docs/reference/write_basis.html
+++ b/docs/reference/write_basis.html
@@ -1,5 +1,5 @@
-Write a basis object to an LCModel .basis formatted file. — write_basis • Spectroscopy Analysis Tools (spant) Write a basis object to an LCModel .basis formatted file. — write_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -108,7 +108,7 @@ Arguments
diff --git a/docs/reference/write_basis_tqn.html b/docs/reference/write_basis_tqn.html
index 6aa51c1d..116c73ec 100644
--- a/docs/reference/write_basis_tqn.html
+++ b/docs/reference/write_basis_tqn.html
@@ -1,5 +1,5 @@
-Generate a basis file using TARQUIN. — write_basis_tqn • Spectroscopy Analysis Tools (spant) Generate a basis file using TARQUIN. — write_basis_tqn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Examples
diff --git a/docs/reference/write_mrs.html b/docs/reference/write_mrs.html
index fff25f15..124b9dc4 100644
--- a/docs/reference/write_mrs.html
+++ b/docs/reference/write_mrs.html
@@ -1,5 +1,5 @@
-Write MRS data object to file. — write_mrs • Spectroscopy Analysis Tools (spant) Write MRS data object to file. — write_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Arguments
diff --git a/docs/reference/write_mrs_nifti.html b/docs/reference/write_mrs_nifti.html
index f4bf1921..bd3ed4b7 100644
--- a/docs/reference/write_mrs_nifti.html
+++ b/docs/reference/write_mrs_nifti.html
@@ -1,5 +1,5 @@
-Write MRS data object to file in NIFTI format. — write_mrs_nifti • Spectroscopy Analysis Tools (spant) Write MRS data object to file in NIFTI format. — write_mrs_nifti • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/write_pulse_ascii.html b/docs/reference/write_pulse_ascii.html
index 067ae086..221f8ebb 100644
--- a/docs/reference/write_pulse_ascii.html
+++ b/docs/reference/write_pulse_ascii.html
@@ -1,5 +1,5 @@
-Write an ASCII formatted pulse file. — write_pulse_ascii • Spectroscopy Analysis Tools (spant) Write an ASCII formatted pulse file. — write_pulse_ascii • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/zero_fade_spec.html b/docs/reference/zero_fade_spec.html
index c703745c..c8b572c3 100644
--- a/docs/reference/zero_fade_spec.html
+++ b/docs/reference/zero_fade_spec.html
@@ -1,7 +1,5 @@
-Fade a spectrum to zero by frequency domain multiplication with a tanh
-function. Note this operation distorts data points at the end of the FID. — zero_fade_spec • Spectroscopy Analysis Tools (spant) Fade a spectrum to zero by frequency domain multiplication with a tanh function. Note this operation distorts data points at the end of the FID. — zero_fade_spec • Spectroscopy Analysis Tools (spant) Zero all coherences including and above a given order. — zero_higher_orders • Spectroscopy Analysis Tools (spant) Zero all coherences including and above a given order. — zero_higher_orders • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Value
diff --git a/docs/reference/zero_td_pts_end.html b/docs/reference/zero_td_pts_end.html
index 8c1123c8..71d24ebb 100644
--- a/docs/reference/zero_td_pts_end.html
+++ b/docs/reference/zero_td_pts_end.html
@@ -1,5 +1,5 @@
-Set mrs_data object data points at the end of the FID to zero. — zero_td_pts_end • Spectroscopy Analysis Tools (spant) Set mrs_data object data points at the end of the FID to zero. — zero_td_pts_end • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/zf.html b/docs/reference/zf.html
index 85e2013c..baf50256 100644
--- a/docs/reference/zf.html
+++ b/docs/reference/zf.html
@@ -1,5 +1,5 @@
-Zero-fill MRS data in the time domain. — zf • Spectroscopy Analysis Tools (spant) Zero-fill MRS data in the time domain. — zf • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -125,7 +125,7 @@ Value
diff --git a/docs/reference/zf_xy.html b/docs/reference/zf_xy.html
index ebca3999..c4104a74 100644
--- a/docs/reference/zf_xy.html
+++ b/docs/reference/zf_xy.html
@@ -1,5 +1,5 @@
-Zero-fill MRSI data in the k-space x-y direction. — zf_xy • Spectroscopy Analysis Tools (spant) Zero-fill MRSI data in the k-space x-y direction. — zf_xy • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -113,7 +113,7 @@ Value
diff --git a/docs/sitemap.xml b/docs/sitemap.xml
index e2139f71..4c39f515 100644
--- a/docs/sitemap.xml
+++ b/docs/sitemap.xml
@@ -216,6 +216,12 @@
https://martin3141.github.io/spant/reference/comb_coils_fp_pc.html
+
+ https://martin3141.github.io/spant/reference/comb_coils_mrsi_gls.html
+
+
+ https://martin3141.github.io/spant/reference/comb_coils_svs_gls.html
+
https://martin3141.github.io/spant/reference/comb_csv_results.html
@@ -411,6 +417,9 @@
https://martin3141.github.io/spant/reference/gen_conv_reg.html
+
+ https://martin3141.github.io/spant/reference/gen_group_reg.html
+
https://martin3141.github.io/spant/reference/gen_impulse_reg.html
@@ -555,6 +564,15 @@
https://martin3141.github.io/spant/reference/glm_spec.html
+
+ https://martin3141.github.io/spant/reference/glm_spec_fmrs_fl.html
+
+
+ https://martin3141.github.io/spant/reference/glm_spec_fmrs_group.html
+
+
+ https://martin3141.github.io/spant/reference/glm_spec_group_linhyp.html
+
https://martin3141.github.io/spant/reference/grid_shift_xy.html
@@ -690,9 +708,15 @@
https://martin3141.github.io/spant/reference/mrs_data2basis.html
+
+ https://martin3141.github.io/spant/reference/mrs_data2bids.html
+
https://martin3141.github.io/spant/reference/mrs_data2mat.html
+
+ https://martin3141.github.io/spant/reference/mrs_data2spec_mat.html
+
https://martin3141.github.io/spant/reference/mrs_data2vec.html
@@ -741,6 +765,9 @@
https://martin3141.github.io/spant/reference/phase.html
+
+ https://martin3141.github.io/spant/reference/phase_ref_1h_brain.html
+
https://martin3141.github.io/spant/reference/plot.fit_result.html
@@ -780,6 +807,12 @@
https://martin3141.github.io/spant/reference/precomp.html
+
+ https://martin3141.github.io/spant/reference/preproc_svs.html
+
+
+ https://martin3141.github.io/spant/reference/preproc_svs_dataset.html
+
https://martin3141.github.io/spant/reference/print.fit_result.html
@@ -1050,6 +1083,9 @@
https://martin3141.github.io/spant/reference/spant_mpress_drift.html
+
+ https://martin3141.github.io/spant/reference/spant_sim_fmrs_dataset.html
+
https://martin3141.github.io/spant/reference/spant_simulation_benchmark.html
@@ -1107,6 +1143,9 @@
https://martin3141.github.io/spant/reference/svs_1h_brain_batch_analysis.html
+
+ https://martin3141.github.io/spant/reference/t_test_spec.html
+
https://martin3141.github.io/spant/reference/td2fd.html
Simulate an ideal pulse excitation profile by smoothing a top-hat function -with a Gaussian.
Simulate an ideal pulse excitation profile by smoothing a top-hat function with a Gaussian.
All functions
- Simulate and fit some spectra with ABfit for benchmarking purposes. Basic
-timing and performance metrics will be printed.
Simulate and fit some spectra with ABfit for benchmarking purposes. Basic timing and performance metrics will be printed.
Example MEGA-PRESS data with significant B0 drift.
+
+
+ Simulate an example fMRS dataset for a block design fMRS experiment and export a BIDS structure.
- Simulate a typical metabolite basis set for benchmarking. Timing metrics will
-be printed on completion.
Simulate a typical metabolite basis set for benchmarking. Timing metrics will be printed on completion.
@@ -1400,8 +1374,7 @@ All functions
- Convert SPM style segmentation files to a single categorical image where
-the numerical values map as: 0) Other, 1) CSF, 2) GM and 3) WM.
Convert SPM style segmentation files to a single categorical image where the numerical values map as: 0) Other, 1) CSF, 2) GM and 3) WM.
@@ -1413,8 +1386,7 @@ All functions
- Plot the fitting results of an object of class fit_result with
-individual basis set components shown.
Plot the fitting results of an object of class fit_result with individual basis set components shown.
@@ -1459,6 +1431,10 @@ All functions svs_1h_brain_batch_analysis()
Batch interface to the standard SVS 1H brain analysis pipeline.
+
+
+ Perform a t-test on spectral data points.
@@ -1518,8 +1494,7 @@ All functions
- Fade a spectrum to zero by frequency domain multiplication with a tanh
-function. Note this operation distorts data points at the end of the FID.
Fade a spectrum to zero by frequency domain multiplication with a tanh function. Note this operation distorts data points at the end of the FID.
@@ -1549,7 +1524,7 @@ All functions
diff --git a/docs/reference/int_spec.html b/docs/reference/int_spec.html
index c7060fe7..783325a8 100644
--- a/docs/reference/int_spec.html
+++ b/docs/reference/int_spec.html
@@ -1,5 +1,5 @@
-Integrate a spectral region. — int_spec • Spectroscopy Analysis Tools (spant) Integrate a spectral region. — int_spec • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -118,7 +118,7 @@ Value
diff --git a/docs/reference/interleave_dyns.html b/docs/reference/interleave_dyns.html
index effe5543..441eff27 100644
--- a/docs/reference/interleave_dyns.html
+++ b/docs/reference/interleave_dyns.html
@@ -1,5 +1,5 @@
-Interleave the first and second half of a dynamic series. — interleave_dyns • Spectroscopy Analysis Tools (spant) Interleave the first and second half of a dynamic series. — interleave_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/inv_even_dyns.html b/docs/reference/inv_even_dyns.html
index 9f9d4fff..dcb781dc 100644
--- a/docs/reference/inv_even_dyns.html
+++ b/docs/reference/inv_even_dyns.html
@@ -1,5 +1,5 @@
-Invert even numbered dynamic scans starting from 1 (2,4,6...). — inv_even_dyns • Spectroscopy Analysis Tools (spant) Invert even numbered dynamic scans starting from 1 (2,4,6...). — inv_even_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/inv_odd_dyns.html b/docs/reference/inv_odd_dyns.html
index 26212e2b..78d64660 100644
--- a/docs/reference/inv_odd_dyns.html
+++ b/docs/reference/inv_odd_dyns.html
@@ -1,5 +1,5 @@
-Invert odd numbered dynamic scans starting from 1 (1,3,5...). — inv_odd_dyns • Spectroscopy Analysis Tools (spant) Invert odd numbered dynamic scans starting from 1 (1,3,5...). — inv_odd_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/is.def.html b/docs/reference/is.def.html
index f196ffd0..a67b9eba 100644
--- a/docs/reference/is.def.html
+++ b/docs/reference/is.def.html
@@ -1,5 +1,5 @@
-Check if an object is defined, which is the same as being not NULL. — is.def • Spectroscopy Analysis Tools (spant) Check if an object is defined, which is the same as being not NULL. — is.def • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/is_fd.html b/docs/reference/is_fd.html
index 3b0ca165..18a193aa 100644
--- a/docs/reference/is_fd.html
+++ b/docs/reference/is_fd.html
@@ -1,7 +1,5 @@
-Check if the chemical shift dimension of an MRS data object is in the
-frequency domain. — is_fd • Spectroscopy Analysis Tools (spant) Check if the chemical shift dimension of an MRS data object is in the frequency domain. — is_fd • Spectroscopy Analysis Tools (spant) Transform 2D MRSI data from k-space to image space in the x-y direction. — kspace2img_xy • Spectroscopy Analysis Tools (spant) Transform 2D MRSI data from k-space to image space in the x-y direction. — kspace2img_xy • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/l2_reg.html b/docs/reference/l2_reg.html
index 3d781d80..21aa9849 100644
--- a/docs/reference/l2_reg.html
+++ b/docs/reference/l2_reg.html
@@ -1,5 +1,5 @@
-Perform l2 regularisation artefact suppression. — l2_reg • Spectroscopy Analysis Tools (spant) Perform l2 regularisation artefact suppression. — l2_reg • Spectroscopy Analysis Tools (spant) Apply line-broadening (apodisation) to MRS data or basis object. — lb • Spectroscopy Analysis Tools (spant) Apply line-broadening (apodisation) to MRS data or basis object. — lb • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -123,7 +123,7 @@ Value
diff --git a/docs/reference/lofdc.html b/docs/reference/lofdc.html
index 5419b1ec..31347a25 100644
--- a/docs/reference/lofdc.html
+++ b/docs/reference/lofdc.html
@@ -1,5 +1,5 @@
-Correct linear frequency drift. — lofdc • Spectroscopy Analysis Tools (spant) Correct linear frequency drift. — lofdc • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -138,7 +138,7 @@ Value
diff --git a/docs/reference/lw2alpha.html b/docs/reference/lw2alpha.html
index b83db682..25da229b 100644
--- a/docs/reference/lw2alpha.html
+++ b/docs/reference/lw2alpha.html
@@ -1,7 +1,5 @@
-Covert a linewidth in Hz to an equivalent alpha value in the time-domain ie:
-x * exp(-t * alpha). — lw2alpha • Spectroscopy Analysis Tools (spant) Covert a linewidth in Hz to an equivalent alpha value in the time-domain ie: x * exp(-t * alpha). — lw2alpha • Spectroscopy Analysis Tools (spant) Covert a linewidth in Hz to an equivalent beta value in the time-domain ie:
-x * exp(-t * t * beta). — lw2beta • Spectroscopy Analysis Tools (spant) Covert a linewidth in Hz to an equivalent beta value in the time-domain ie: x * exp(-t * t * beta). — lw2beta • Spectroscopy Analysis Tools (spant) Make a basis-set object from a directory containing LCModel formatted RAW
-files. — make_basis_from_raw • Spectroscopy Analysis Tools (spant) Make a basis-set object from a directory containing LCModel formatted RAW files. — make_basis_from_raw • Spectroscopy Analysis Tools (spant) Mask an MRS dataset in the dynamic dimension. — mask_dyns • Spectroscopy Analysis Tools (spant) Mask an MRS dataset in the dynamic dimension. — mask_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/mask_fit_res.html b/docs/reference/mask_fit_res.html
index 97baaa3f..ebd91a99 100644
--- a/docs/reference/mask_fit_res.html
+++ b/docs/reference/mask_fit_res.html
@@ -1,5 +1,5 @@
-Mask fit result spectra depending on a vector of bool values. — mask_fit_res • Spectroscopy Analysis Tools (spant) Mask fit result spectra depending on a vector of bool values. — mask_fit_res • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -116,7 +116,7 @@ Value
diff --git a/docs/reference/mask_xy.html b/docs/reference/mask_xy.html
index 11bb577c..b0d38619 100644
--- a/docs/reference/mask_xy.html
+++ b/docs/reference/mask_xy.html
@@ -1,5 +1,5 @@
-Mask an MRSI dataset in the x-y direction — mask_xy • Spectroscopy Analysis Tools (spant) Mask an MRSI dataset in the x-y direction — mask_xy • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/mask_xy_corners.html b/docs/reference/mask_xy_corners.html
index 09b16cd2..2d13839d 100644
--- a/docs/reference/mask_xy_corners.html
+++ b/docs/reference/mask_xy_corners.html
@@ -1,5 +1,5 @@
-Mask the four corners of an MRSI dataset in the x-y plane. — mask_xy_corners • Spectroscopy Analysis Tools (spant) Mask the four corners of an MRSI dataset in the x-y plane. — mask_xy_corners • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/mask_xy_ellipse.html b/docs/reference/mask_xy_ellipse.html
index 1d8b02e4..e2e749ef 100644
--- a/docs/reference/mask_xy_ellipse.html
+++ b/docs/reference/mask_xy_ellipse.html
@@ -1,7 +1,5 @@
-Mask the voxels outside an elliptical region spanning the MRSI dataset in the
-x-y plane. — mask_xy_ellipse • Spectroscopy Analysis Tools (spant) Mask the voxels outside an elliptical region spanning the MRSI dataset in the x-y plane. — mask_xy_ellipse • Spectroscopy Analysis Tools (spant) Mask a 2D MRSI dataset in the x-y dimension. — mask_xy_mat • Spectroscopy Analysis Tools (spant) Mask a 2D MRSI dataset in the x-y dimension. — mask_xy_mat • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Value
diff --git a/docs/reference/mat2mrs_data.html b/docs/reference/mat2mrs_data.html
index 2e2895f3..ae55665f 100644
--- a/docs/reference/mat2mrs_data.html
+++ b/docs/reference/mat2mrs_data.html
@@ -1,7 +1,5 @@
-Convert a matrix (with spectral points in the column dimension and dynamics
-in the row dimensions) into a mrs_data object. — mat2mrs_data • Spectroscopy Analysis Tools (spant) Convert a matrix (with spectral points in the column dimension and dynamics in the row dimensions) into a mrs_data object. — mat2mrs_data • Spectroscopy Analysis Tools (spant) Matrix exponential function taken from complexplus package to reduce the
-number of spant dependencies. — matexp • Spectroscopy Analysis Tools (spant) Matrix exponential function taken from complexplus package to reduce the number of spant dependencies. — matexp • Spectroscopy Analysis Tools (spant) Apply the max operator to an MRS dataset. — max_mrs • Spectroscopy Analysis Tools (spant) Apply the max operator to an MRS dataset. — max_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/max_mrs_interp.html b/docs/reference/max_mrs_interp.html
index e4474764..52e63f3e 100644
--- a/docs/reference/max_mrs_interp.html
+++ b/docs/reference/max_mrs_interp.html
@@ -1,5 +1,5 @@
-Apply the max operator to an interpolated MRS dataset. — max_mrs_interp • Spectroscopy Analysis Tools (spant) Apply the max operator to an interpolated MRS dataset. — max_mrs_interp • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/mean.list.html b/docs/reference/mean.list.html
index b8eb3463..048306fd 100644
--- a/docs/reference/mean.list.html
+++ b/docs/reference/mean.list.html
@@ -1,5 +1,5 @@
-Calculate the mean spectrum from an mrs_data object. — mean.list • Spectroscopy Analysis Tools (spant) Calculate the mean spectrum from an mrs_data object. — mean.list • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/mean.mrs_data.html b/docs/reference/mean.mrs_data.html
index 5531a28d..79515014 100644
--- a/docs/reference/mean.mrs_data.html
+++ b/docs/reference/mean.mrs_data.html
@@ -1,5 +1,5 @@
-Calculate the mean spectrum from an mrs_data object. — mean.mrs_data • Spectroscopy Analysis Tools (spant) Calculate the mean spectrum from an mrs_data object. — mean.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/mean_dyn_blocks.html b/docs/reference/mean_dyn_blocks.html
index 10467098..4c042448 100644
--- a/docs/reference/mean_dyn_blocks.html
+++ b/docs/reference/mean_dyn_blocks.html
@@ -1,5 +1,5 @@
-Calculate the mean of adjacent dynamic scans. — mean_dyn_blocks • Spectroscopy Analysis Tools (spant) Calculate the mean of adjacent dynamic scans. — mean_dyn_blocks • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/mean_dyn_pairs.html b/docs/reference/mean_dyn_pairs.html
index 63e909ea..1a241126 100644
--- a/docs/reference/mean_dyn_pairs.html
+++ b/docs/reference/mean_dyn_pairs.html
@@ -1,5 +1,5 @@
-Calculate the pairwise means across a dynamic data set. — mean_dyn_pairs • Spectroscopy Analysis Tools (spant) Calculate the pairwise means across a dynamic data set. — mean_dyn_pairs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/mean_dyns.html b/docs/reference/mean_dyns.html
index 73fdbfa7..0daa27df 100644
--- a/docs/reference/mean_dyns.html
+++ b/docs/reference/mean_dyns.html
@@ -1,5 +1,5 @@
-Calculate the mean dynamic data. — mean_dyns • Spectroscopy Analysis Tools (spant) Calculate the mean dynamic data. — mean_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/mean_mrs_list.html b/docs/reference/mean_mrs_list.html
index 808b6c50..10d842c0 100644
--- a/docs/reference/mean_mrs_list.html
+++ b/docs/reference/mean_mrs_list.html
@@ -1,5 +1,5 @@
-Return the mean of a list of mrs_data objects. — mean_mrs_list • Spectroscopy Analysis Tools (spant) Return the mean of a list of mrs_data objects. — mean_mrs_list • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/mean_vec_blocks.html b/docs/reference/mean_vec_blocks.html
index 8fc92eaa..dd78b122 100644
--- a/docs/reference/mean_vec_blocks.html
+++ b/docs/reference/mean_vec_blocks.html
@@ -1,5 +1,5 @@
-Calculate the mean of adjacent blocks in a vector. — mean_vec_blocks • Spectroscopy Analysis Tools (spant) Calculate the mean of adjacent blocks in a vector. — mean_vec_blocks • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/median_dyns.html b/docs/reference/median_dyns.html
index 1039d4b5..9a085b10 100644
--- a/docs/reference/median_dyns.html
+++ b/docs/reference/median_dyns.html
@@ -1,5 +1,5 @@
-Calculate the median dynamic data. — median_dyns • Spectroscopy Analysis Tools (spant) Calculate the median dynamic data. — median_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/mod_td.html b/docs/reference/mod_td.html
index 76ad0a40..141ef09e 100644
--- a/docs/reference/mod_td.html
+++ b/docs/reference/mod_td.html
@@ -1,5 +1,5 @@
-Apply the Modulus operator to the time-domain MRS signal. — mod_td • Spectroscopy Analysis Tools (spant) Apply the Modulus operator to the time-domain MRS signal. — mod_td • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/mrs_data2basis.html b/docs/reference/mrs_data2basis.html
index 62f7d749..11797b91 100644
--- a/docs/reference/mrs_data2basis.html
+++ b/docs/reference/mrs_data2basis.html
@@ -1,7 +1,5 @@
-Convert an mrs_data object to basis object - where basis signals are spread
-across the dynamic dimension in the MRS data. — mrs_data2basis • Spectroscopy Analysis Tools (spant) Convert an mrs_data object to basis object - where basis signals are spread across the dynamic dimension in the MRS data. — mrs_data2basis • Spectroscopy Analysis Tools (spant) Create a BIDS file structure from a vector of MRS data paths or list of mrs_data objects. — mrs_data2bids • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Create a BIDS file structure from a vector of MRS data paths or list of mrs_data objects.
+ Source: R/fmrs.R
+ mrs_data2bids.Rd
+
+
+
+ Create a BIDS file structure from a vector of MRS data paths or list of
+mrs_data objects.
+
+
+
+ mrs_data2bids(
+ mrs_data,
+ output_dir,
+ suffix = NULL,
+ sub = NULL,
+ ses = NULL,
+ task = NULL,
+ acq = NULL,
+ nuc = NULL,
+ voi = NULL,
+ rec = NULL,
+ run = NULL,
+ echo = NULL,
+ inv = NULL,
+ skip_existing = TRUE
+)
+
+
+
+ Arguments
+ - mrs_data
+vector of MRS data paths or list of mrs_data objects.
- output_dir
+the base directory to create the BIDS structure.
- suffix
+optional vector of file suffixes. Default behaviour is to
+automatically determine these from the input data, however it is recommended
+that they are specified to allow more efficient skipping of existing data.
- sub
+optional vector of subject labels. If not specified, these will be
+automatically generated as a series of increasing zero-padded integer values
+corresponding to the mrs_data input indices.
- ses
+optional vector of session labels.
- task
+optional vector of task labels.
- acq
+optional vector of acquisition labels.
- nuc
+optional vector of nucleus labels.
- voi
+optional vector of volume of interest labels.
- rec
+optional vector of reconstruction labels.
- run
+optional vector of run indices.
- echo
+optional vector of echo time indices.
- inv
+optional vector of inversion indices.
- skip_existing
+skip any data files that have already been converted.
+Defaults to TRUE, set to FALSE to force an overwrite of any existing data
+files.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/mrs_data2mat.html b/docs/reference/mrs_data2mat.html
index cf5ff28c..9e47688a 100644
--- a/docs/reference/mrs_data2mat.html
+++ b/docs/reference/mrs_data2mat.html
@@ -1,7 +1,5 @@
-Convert mrs_data object to a matrix, with spectral points in the column
-dimension and dynamics in the row dimension. — mrs_data2mat • Spectroscopy Analysis Tools (spant) Convert mrs_data object to a matrix, with spectral points in the column dimension and dynamics in the row dimension. — mrs_data2mat • Spectroscopy Analysis Tools (spant) Convert mrs_data object to a matrix, with spectral points in the column dimension and dynamics in the row dimension. — mrs_data2spec_mat • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Convert mrs_data object to a matrix, with spectral points in the column dimension and dynamics in the row dimension.
+ Source: R/mrs_data_proc.R
+ mrs_data2spec_mat.Rd
+
+
+
+ Convert mrs_data object to a matrix, with spectral points in the column
+dimension and dynamics in the row dimension.
+
+
+
+ mrs_data2spec_mat(mrs_data, collapse = TRUE)
+
+
+
+ Arguments
+ - mrs_data
+MRS data object or list of MRS data objects.
- collapse
+collapse all other dimensions along the dynamic dimension, eg
+a 16x16 MRSI grid would be first collapsed across 256 dynamic scans.
+
+ Value
+
+
+MRS data matrix.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/mrs_data2vec.html b/docs/reference/mrs_data2vec.html
index fb172d68..a1fd654d 100644
--- a/docs/reference/mrs_data2vec.html
+++ b/docs/reference/mrs_data2vec.html
@@ -1,5 +1,5 @@
-Convert mrs_data object to a vector. — mrs_data2vec • Spectroscopy Analysis Tools (spant) Convert mrs_data object to a vector. — mrs_data2vec • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -126,7 +126,7 @@ Value
diff --git a/docs/reference/mvfftshift.html b/docs/reference/mvfftshift.html
index 92b0841b..976b3410 100644
--- a/docs/reference/mvfftshift.html
+++ b/docs/reference/mvfftshift.html
@@ -1,7 +1,5 @@
-Perform a fftshift on a matrix, with each column replaced by its shifted
-result. — mvfftshift • Spectroscopy Analysis Tools (spant) Perform a fftshift on a matrix, with each column replaced by its shifted result. — mvfftshift • Spectroscopy Analysis Tools (spant) Perform an ifftshift on a matrix, with each column replaced by its shifted
-result. — mvifftshift • Spectroscopy Analysis Tools (spant) Perform an ifftshift on a matrix, with each column replaced by its shifted result. — mvifftshift • Spectroscopy Analysis Tools (spant) Print fit coordinates from a single index. — n2coord • Spectroscopy Analysis Tools (spant) Print fit coordinates from a single index. — n2coord • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/nifti_flip_lr.html b/docs/reference/nifti_flip_lr.html
index 730abe3c..19860b3c 100644
--- a/docs/reference/nifti_flip_lr.html
+++ b/docs/reference/nifti_flip_lr.html
@@ -1,9 +1,5 @@
-Flip the x data dimension order of a nifti image. This corresponds to
-flipping MRI data in the left-right direction, assuming the data in save in
-neurological format (can check with fslorient program). — nifti_flip_lr • Spectroscopy Analysis Tools (spant) Flip the x data dimension order of a nifti image. This corresponds to flipping MRI data in the left-right direction, assuming the data in save in neurological format (can check with fslorient program). — nifti_flip_lr • Spectroscopy Analysis Tools (spant) Export a one-page pdf of a single fit result — one_page_pdf • Spectroscopy Analysis Tools (spant) Export a one-page pdf of a single fit result — one_page_pdf • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -108,7 +108,7 @@ Arguments
diff --git a/docs/reference/ortho3.html b/docs/reference/ortho3.html
index 13ade97d..5d7dd2fd 100644
--- a/docs/reference/ortho3.html
+++ b/docs/reference/ortho3.html
@@ -1,5 +1,5 @@
-Display an orthographic projection plot of a nifti object. — ortho3 • Spectroscopy Analysis Tools (spant) Display an orthographic projection plot of a nifti object. — ortho3 • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -172,7 +172,7 @@ Arguments
diff --git a/docs/reference/ortho3_inter.html b/docs/reference/ortho3_inter.html
index 090cc5e5..15948899 100644
--- a/docs/reference/ortho3_inter.html
+++ b/docs/reference/ortho3_inter.html
@@ -1,5 +1,5 @@
-Display an interactive orthographic projection plot of a nifti object. — ortho3_inter • Spectroscopy Analysis Tools (spant) Display an interactive orthographic projection plot of a nifti object. — ortho3_inter • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -132,7 +132,7 @@ Arguments
diff --git a/docs/reference/peak_info.html b/docs/reference/peak_info.html
index 09058bd8..41c8ffaf 100644
--- a/docs/reference/peak_info.html
+++ b/docs/reference/peak_info.html
@@ -1,7 +1,5 @@
-Search for the highest peak in a spectral region and return the frequency,
-height and FWHM. — peak_info • Spectroscopy Analysis Tools (spant) Search for the highest peak in a spectral region and return the frequency, height and FWHM. — peak_info • Spectroscopy Analysis Tools (spant) Papoulis-Gerchberg (PG) algorithm method for k-space extrapolation. — pg_extrap_xy • Spectroscopy Analysis Tools (spant) Papoulis-Gerchberg (PG) algorithm method for k-space extrapolation. — pg_extrap_xy • Spectroscopy Analysis Tools (spant) Apply phasing parameters to MRS data. — phase • Spectroscopy Analysis Tools (spant) Apply phasing parameters to MRS data. — phase • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/phase_ref_1h_brain.html b/docs/reference/phase_ref_1h_brain.html
new file mode 100644
index 00000000..8707a74a
--- /dev/null
+++ b/docs/reference/phase_ref_1h_brain.html
@@ -0,0 +1,131 @@
+
+Corrected zero order phase and chemical shift offset in 1H MRS data from the brain. — phase_ref_1h_brain • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Corrected zero order phase and chemical shift offset in 1H MRS data from the brain.
+ Source: R/rats.R
+ phase_ref_1h_brain.Rd
+
+
+
+ Corrected zero order phase and chemical shift offset in 1H MRS data from the
+brain.
+
+
+
+ phase_ref_1h_brain(mrs_data, mean_ref = FALSE, ret_corr_only = TRUE)
+
+
+
+ Arguments
+ - mrs_data
+MRS data to be corrected.
- mean_ref
+apply the phase and offset of the mean spectrum to all
+others. Default is FALSE.
- ret_corr_only
+return the corrected data only.
+
+ Value
+
+
+corrected MRS data.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/plot.fit_result.html b/docs/reference/plot.fit_result.html
index e54d3bc1..836a53ee 100644
--- a/docs/reference/plot.fit_result.html
+++ b/docs/reference/plot.fit_result.html
@@ -1,5 +1,5 @@
-Plot the fitting results of an object of class fit_result. — plot.fit_result • Spectroscopy Analysis Tools (spant) Plot the fitting results of an object of class fit_result. — plot.fit_result • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -207,7 +207,7 @@ Arguments
diff --git a/docs/reference/plot.mrs_data.html b/docs/reference/plot.mrs_data.html
index fabcc35b..bb2ec651 100644
--- a/docs/reference/plot.mrs_data.html
+++ b/docs/reference/plot.mrs_data.html
@@ -1,5 +1,5 @@
-Plotting method for objects of class mrs_data. — plot.mrs_data • Spectroscopy Analysis Tools (spant) Plotting method for objects of class mrs_data. — plot.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -287,7 +287,7 @@ Arguments
diff --git a/docs/reference/plot_bc.html b/docs/reference/plot_bc.html
index 4f8309b4..b48142cc 100644
--- a/docs/reference/plot_bc.html
+++ b/docs/reference/plot_bc.html
@@ -1,5 +1,5 @@
-Convenience function to plot a baseline estimate with the original data. — plot_bc • Spectroscopy Analysis Tools (spant) Convenience function to plot a baseline estimate with the original data. — plot_bc • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -108,7 +108,7 @@ Arguments
diff --git a/docs/reference/plot_reg.html b/docs/reference/plot_reg.html
index ae1acbe7..2addb2f6 100644
--- a/docs/reference/plot_reg.html
+++ b/docs/reference/plot_reg.html
@@ -1,5 +1,5 @@
-Plot regressors as an image. — plot_reg • Spectroscopy Analysis Tools (spant) Plot regressors as an image. — plot_reg • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/plot_slice_fit.html b/docs/reference/plot_slice_fit.html
index fbc7b560..57f1af8a 100644
--- a/docs/reference/plot_slice_fit.html
+++ b/docs/reference/plot_slice_fit.html
@@ -1,5 +1,5 @@
-Plot a 2D slice from an MRSI fit result object. — plot_slice_fit • Spectroscopy Analysis Tools (spant) Plot a 2D slice from an MRSI fit result object. — plot_slice_fit • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -129,7 +129,7 @@ Arguments
diff --git a/docs/reference/plot_slice_fit_inter.html b/docs/reference/plot_slice_fit_inter.html
index 4eed104a..da105a7d 100644
--- a/docs/reference/plot_slice_fit_inter.html
+++ b/docs/reference/plot_slice_fit_inter.html
@@ -1,5 +1,5 @@
-Plot a 2D slice from an MRSI fit result object. — plot_slice_fit_inter • Spectroscopy Analysis Tools (spant) Plot a 2D slice from an MRSI fit result object. — plot_slice_fit_inter • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -134,7 +134,7 @@ Arguments
diff --git a/docs/reference/plot_slice_map.html b/docs/reference/plot_slice_map.html
index 553e9ac8..ffb2a134 100644
--- a/docs/reference/plot_slice_map.html
+++ b/docs/reference/plot_slice_map.html
@@ -1,5 +1,5 @@
-Plot a slice from a 7 dimensional array. — plot_slice_map • Spectroscopy Analysis Tools (spant) Plot a slice from a 7 dimensional array. — plot_slice_map • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -153,7 +153,7 @@ Arguments
diff --git a/docs/reference/plot_slice_map_inter.html b/docs/reference/plot_slice_map_inter.html
index 40d33b42..90968f66 100644
--- a/docs/reference/plot_slice_map_inter.html
+++ b/docs/reference/plot_slice_map_inter.html
@@ -1,7 +1,5 @@
-Plot an interactive slice map from a data array where voxels can be selected
-to display a corresponding spectrum. — plot_slice_map_inter • Spectroscopy Analysis Tools (spant) Plot an interactive slice map from a data array where voxels can be selected to display a corresponding spectrum. — plot_slice_map_inter • Spectroscopy Analysis Tools (spant) Plot the spectral standard deviation. — plot_spec_sd • Spectroscopy Analysis Tools (spant) Plot the spectral standard deviation. — plot_spec_sd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Arguments
diff --git a/docs/reference/plot_voi_overlay.html b/docs/reference/plot_voi_overlay.html
index 9a782e88..bbbbf35e 100644
--- a/docs/reference/plot_voi_overlay.html
+++ b/docs/reference/plot_voi_overlay.html
@@ -1,5 +1,5 @@
-Plot a volume as an image overlay. — plot_voi_overlay • Spectroscopy Analysis Tools (spant) Plot a volume as an image overlay. — plot_voi_overlay • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -116,7 +116,7 @@ Arguments
diff --git a/docs/reference/plot_voi_overlay_seg.html b/docs/reference/plot_voi_overlay_seg.html
index 3d4e74ff..0e800ff2 100644
--- a/docs/reference/plot_voi_overlay_seg.html
+++ b/docs/reference/plot_voi_overlay_seg.html
@@ -1,5 +1,5 @@
-Plot a volume as an overlay on a segmented brain volume. — plot_voi_overlay_seg • Spectroscopy Analysis Tools (spant) Plot a volume as an overlay on a segmented brain volume. — plot_voi_overlay_seg • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Arguments
diff --git a/docs/reference/ppm.html b/docs/reference/ppm.html
index c352327a..ee4696e2 100644
--- a/docs/reference/ppm.html
+++ b/docs/reference/ppm.html
@@ -1,5 +1,5 @@
-Return the ppm scale of an MRS dataset or fit result. — ppm • Spectroscopy Analysis Tools (spant) Return the ppm scale of an MRS dataset or fit result. — ppm • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -132,7 +132,7 @@ Value
diff --git a/docs/reference/precomp.html b/docs/reference/precomp.html
index 822d7336..df3d2c6c 100644
--- a/docs/reference/precomp.html
+++ b/docs/reference/precomp.html
@@ -1,7 +1,5 @@
-Save function results to file and load on subsequent calls to avoid repeat
-computation. — precomp • Spectroscopy Analysis Tools (spant) Save function results to file and load on subsequent calls to avoid repeat computation. — precomp • Spectroscopy Analysis Tools (spant) Preprocess and perform quality assessment of a single SVS data set. — preproc_svs • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Preprocess and perform quality assessment of a single SVS data set.
+ Source: R/fmrs.R
+ preproc_svs.Rd
+
+
+
+ Preprocess and perform quality assessment of a single SVS data set.
+
+
+
+ preproc_svs(path, label = NULL, output_dir = NULL, ref_inds = NULL)
+
+
+
+ Arguments
+ - path
+path to the fMRS data file or IMA directory.
- label
+a label to describe the data set.
- output_dir
+output directory.
- ref_inds
+a vector of 1-based indices for any water reference dynamic
+scans.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/preproc_svs_dataset.html b/docs/reference/preproc_svs_dataset.html
new file mode 100644
index 00000000..07c3a29b
--- /dev/null
+++ b/docs/reference/preproc_svs_dataset.html
@@ -0,0 +1,148 @@
+
+Preprocess and perform quality assessment of one or more SVS data sets. — preproc_svs_dataset • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Preprocess and perform quality assessment of one or more SVS data sets.
+ Source: R/fmrs.R
+ preproc_svs_dataset.Rd
+
+
+
+ Preprocess and perform quality assessment of one or more SVS data sets.
+
+
+
+ preproc_svs_dataset(
+ paths,
+ labels = NULL,
+ output_dir = "spant_analysis",
+ exclude_labels = NULL,
+ overwrite = FALSE,
+ ref_inds = NULL,
+ return_results = FALSE
+)
+
+
+
+ Arguments
+ - paths
+paths to the fMRS data file or IMA directory.
- labels
+labels to describe each data set.
- output_dir
+output directory.
- exclude_labels
+vector of labels of scans to exclude, eg poor quality
+data.
- overwrite
+overwrite saved results, defaults to FALSE.
- ref_inds
+a vector of 1-based indices for any water reference dynamic
+scans.
- return_results
+function will return key outputs, defaults to FALSE.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/print.fit_result.html b/docs/reference/print.fit_result.html
index 297f28dc..5f434e57 100644
--- a/docs/reference/print.fit_result.html
+++ b/docs/reference/print.fit_result.html
@@ -1,5 +1,5 @@
-Print a summary of an object of class fit_result. — print.fit_result • Spectroscopy Analysis Tools (spant) Print a summary of an object of class fit_result. — print.fit_result • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -105,7 +105,7 @@ Arguments
diff --git a/docs/reference/print.mrs_data.html b/docs/reference/print.mrs_data.html
index 51199017..e1561eb2 100644
--- a/docs/reference/print.mrs_data.html
+++ b/docs/reference/print.mrs_data.html
@@ -1,5 +1,5 @@
-Print a summary of mrs_data parameters. — print.mrs_data • Spectroscopy Analysis Tools (spant) Print a summary of mrs_data parameters. — print.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -109,7 +109,7 @@ Arguments
diff --git a/docs/reference/qn_states.html b/docs/reference/qn_states.html
index 0f42f2f9..d7aa6715 100644
--- a/docs/reference/qn_states.html
+++ b/docs/reference/qn_states.html
@@ -1,5 +1,5 @@
-Get the quantum coherence matrix for a spin system. — qn_states • Spectroscopy Analysis Tools (spant) Get the quantum coherence matrix for a spin system. — qn_states • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/rats.html b/docs/reference/rats.html
index 5a39a396..93585e08 100644
--- a/docs/reference/rats.html
+++ b/docs/reference/rats.html
@@ -1,5 +1,5 @@
-Robust Alignment to a Target Spectrum (RATS). — rats • Spectroscopy Analysis Tools (spant) Robust Alignment to a Target Spectrum (RATS). — rats • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -207,7 +207,7 @@ Value
diff --git a/docs/reference/re_weighting.html b/docs/reference/re_weighting.html
index d21caf21..8b0b070a 100644
--- a/docs/reference/re_weighting.html
+++ b/docs/reference/re_weighting.html
@@ -1,5 +1,5 @@
-Apply a weighting to the FID to enhance spectral resolution. — re_weighting • Spectroscopy Analysis Tools (spant) Apply a weighting to the FID to enhance spectral resolution. — re_weighting • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/read_basis.html b/docs/reference/read_basis.html
index da9b94af..eb6f8557 100644
--- a/docs/reference/read_basis.html
+++ b/docs/reference/read_basis.html
@@ -1,5 +1,5 @@
-Read a basis file in LCModel .basis format. — read_basis • Spectroscopy Analysis Tools (spant) Read a basis file in LCModel .basis format. — read_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/read_ima_coil_dir.html b/docs/reference/read_ima_coil_dir.html
index 28c02de0..4f073cd8 100644
--- a/docs/reference/read_ima_coil_dir.html
+++ b/docs/reference/read_ima_coil_dir.html
@@ -1,9 +1,5 @@
-Read a directory containing Siemens MRS IMA files and combine along the coil
-dimension. Note that the coil ID is inferred from the sorted file name and
-should be checked when consistency is required between two directories. — read_ima_coil_dir • Spectroscopy Analysis Tools (spant) Read a directory containing Siemens MRS IMA files and combine along the coil dimension. Note that the coil ID is inferred from the sorted file name and should be checked when consistency is required between two directories. — read_ima_coil_dir • Spectroscopy Analysis Tools (spant) Read a directory containing Siemens MRS IMA files and combine along the
-dynamic dimension. Note that the coil ID is inferred from the sorted file
-name and should be checked when consistency is required. — read_ima_dyn_dir • Spectroscopy Analysis Tools (spant) Read a directory containing Siemens MRS IMA files and combine along the dynamic dimension. Note that the coil ID is inferred from the sorted file name and should be checked when consistency is required. — read_ima_dyn_dir • Spectroscopy Analysis Tools (spant) Read an LCModel formatted coord file containing fit information. — read_lcm_coord • Spectroscopy Analysis Tools (spant) Read an LCModel formatted coord file containing fit information. — read_lcm_coord • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -107,7 +107,7 @@ Value
diff --git a/docs/reference/read_mrs.html b/docs/reference/read_mrs.html
index 3ac2a36b..2cf36b20 100644
--- a/docs/reference/read_mrs.html
+++ b/docs/reference/read_mrs.html
@@ -1,5 +1,5 @@
-Read MRS data from a file. — read_mrs • Spectroscopy Analysis Tools (spant) Read MRS data from a file. — read_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -88,7 +88,8 @@ Read MRS data from a file.
full_fid = FALSE,
omit_svs_ref_scans = TRUE,
verbose = FALSE,
- extra = NULL
+ extra = NULL,
+ fid_filt_dist = NULL
)
@@ -140,6 +141,13 @@ Arguments
an optional data frame to provide additional variables for use
in subsequent analysis steps, eg id or grouping variables.
fid_filt_dist
+indicate if the data has a distorted FID due to a
+brick-wall filter being used to downsample the data. Default is to auto
+detect this from the data, but TRUE or FALSE options can be given to override
+detection.
Value
@@ -183,7 +191,7 @@ Examples
diff --git a/docs/reference/read_mrs_tqn.html b/docs/reference/read_mrs_tqn.html
index 5766362f..84bdaf3a 100644
--- a/docs/reference/read_mrs_tqn.html
+++ b/docs/reference/read_mrs_tqn.html
@@ -1,5 +1,5 @@
-Read MRS data using the TARQUIN software package. — read_mrs_tqn • Spectroscopy Analysis Tools (spant) Read MRS data using the TARQUIN software package. — read_mrs_tqn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -131,7 +131,7 @@ Examples
diff --git a/docs/reference/read_pulse_ascii.html b/docs/reference/read_pulse_ascii.html
index c9e0d43c..ab11c9cc 100644
--- a/docs/reference/read_pulse_ascii.html
+++ b/docs/reference/read_pulse_ascii.html
@@ -1,5 +1,5 @@
-Read an ASCII formatted pulse file. — read_pulse_ascii • Spectroscopy Analysis Tools (spant) Read an ASCII formatted pulse file. — read_pulse_ascii • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/read_pulse_bruker.html b/docs/reference/read_pulse_bruker.html
index c92bf76a..dbe9073b 100644
--- a/docs/reference/read_pulse_bruker.html
+++ b/docs/reference/read_pulse_bruker.html
@@ -1,5 +1,5 @@
-Read a Bruker formatted pulse file — read_pulse_bruker • Spectroscopy Analysis Tools (spant) Read a Bruker formatted pulse file — read_pulse_bruker • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/read_pulse_pta.html b/docs/reference/read_pulse_pta.html
index 72e1b6d4..a0fac3c3 100644
--- a/docs/reference/read_pulse_pta.html
+++ b/docs/reference/read_pulse_pta.html
@@ -1,5 +1,5 @@
-Read a .pta formatted pulse file compatible with Siemens PulseTool. — read_pulse_pta • Spectroscopy Analysis Tools (spant) Read a .pta formatted pulse file compatible with Siemens PulseTool. — read_pulse_pta • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/read_siemens_txt_hdr.html b/docs/reference/read_siemens_txt_hdr.html
index 23fb8c70..3a17d87c 100644
--- a/docs/reference/read_siemens_txt_hdr.html
+++ b/docs/reference/read_siemens_txt_hdr.html
@@ -1,5 +1,5 @@
-Read the text format header found in Siemens IMA and TWIX data files. — read_siemens_txt_hdr • Spectroscopy Analysis Tools (spant) Read the text format header found in Siemens IMA and TWIX data files. — read_siemens_txt_hdr • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -78,7 +78,7 @@ Read the text format header found in Siemens IMA and TWIX data files.
- read_siemens_txt_hdr(input, version = "vd", verbose, offset = 0)
+ read_siemens_txt_hdr(input, version = "vd", verbose = FALSE, offset = 0)
@@ -118,7 +118,7 @@ Value
diff --git a/docs/reference/read_tqn_fit.html b/docs/reference/read_tqn_fit.html
index 4da6c25e..a1630420 100644
--- a/docs/reference/read_tqn_fit.html
+++ b/docs/reference/read_tqn_fit.html
@@ -1,5 +1,5 @@
-Reader for csv fit results generated by TARQUIN. — read_tqn_fit • Spectroscopy Analysis Tools (spant) Reader for csv fit results generated by TARQUIN. — read_tqn_fit • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -113,7 +113,7 @@ Examples
diff --git a/docs/reference/read_tqn_result.html b/docs/reference/read_tqn_result.html
index 36659714..68a3e98c 100644
--- a/docs/reference/read_tqn_result.html
+++ b/docs/reference/read_tqn_result.html
@@ -1,5 +1,5 @@
-Reader for csv results generated by TARQUIN. — read_tqn_result • Spectroscopy Analysis Tools (spant) Reader for csv results generated by TARQUIN. — read_tqn_result • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -117,7 +117,7 @@ Examples
diff --git a/docs/reference/recon_imag.html b/docs/reference/recon_imag.html
index d2a72225..5bc3b1eb 100644
--- a/docs/reference/recon_imag.html
+++ b/docs/reference/recon_imag.html
@@ -1,7 +1,5 @@
-Reconstruct complex time-domain data from the real part of frequency-domain
-data. — recon_imag • Spectroscopy Analysis Tools (spant) Reconstruct complex time-domain data from the real part of frequency-domain data. — recon_imag • Spectroscopy Analysis Tools (spant) Reconstruct complex time-domain data from the real part of frequency-domain
-data. — recon_imag_vec • Spectroscopy Analysis Tools (spant) Reconstruct complex time-domain data from the real part of frequency-domain data. — recon_imag_vec • Spectroscopy Analysis Tools (spant) Reconstruct 2D MRSI data from a twix file loaded with read_mrs. — recon_twix_2d_mrsi • Spectroscopy Analysis Tools (spant) Reconstruct 2D MRSI data from a twix file loaded with read_mrs. — recon_twix_2d_mrsi • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/rectangular_mask.html b/docs/reference/rectangular_mask.html
index a2117283..6e469bc9 100644
--- a/docs/reference/rectangular_mask.html
+++ b/docs/reference/rectangular_mask.html
@@ -1,5 +1,5 @@
-Create a rectangular mask stored as a matrix of logical values. — rectangular_mask • Spectroscopy Analysis Tools (spant) Create a rectangular mask stored as a matrix of logical values. — rectangular_mask • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -130,7 +130,7 @@ Value
diff --git a/docs/reference/reexports.html b/docs/reference/reexports.html
index 694a75d1..a59e8379 100644
--- a/docs/reference/reexports.html
+++ b/docs/reference/reexports.html
@@ -1,5 +1,5 @@
-Objects exported from other packages — reexports • Spectroscopy Analysis Tools (spant) Objects exported from other packages — reexports • Spectroscopy Analysis Tools (spant)
Spectroscopy Analysis Tools (spant)
- 2.21.0
+ 2.22.0
@@ -103,7 +103,7 @@ Objects exported from other packages
diff --git a/docs/reference/rep_array_dim.html b/docs/reference/rep_array_dim.html
index b9c49b4a..48c0a5ed 100644
--- a/docs/reference/rep_array_dim.html
+++ b/docs/reference/rep_array_dim.html
@@ -1,5 +1,5 @@
-Repeat an array over a given dimension. — rep_array_dim • Spectroscopy Analysis Tools (spant) Repeat an array over a given dimension. — rep_array_dim • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/rep_dyn.html b/docs/reference/rep_dyn.html
index 6bbfb0ef..89a4bb9b 100644
--- a/docs/reference/rep_dyn.html
+++ b/docs/reference/rep_dyn.html
@@ -1,5 +1,5 @@
-Replicate a scan in the dynamic dimension. — rep_dyn • Spectroscopy Analysis Tools (spant) Replicate a scan in the dynamic dimension. — rep_dyn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/rep_mrs.html b/docs/reference/rep_mrs.html
index 67730b5c..becb8f00 100644
--- a/docs/reference/rep_mrs.html
+++ b/docs/reference/rep_mrs.html
@@ -1,5 +1,5 @@
-Replicate a scan over a given dimension. — rep_mrs • Spectroscopy Analysis Tools (spant) Replicate a scan over a given dimension. — rep_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -138,7 +138,7 @@ Value
diff --git a/docs/reference/resample_basis.html b/docs/reference/resample_basis.html
index b0f2ab17..c7a6222a 100644
--- a/docs/reference/resample_basis.html
+++ b/docs/reference/resample_basis.html
@@ -1,5 +1,5 @@
-Resample a basis-set to match a mrs_data acquisition. — resample_basis • Spectroscopy Analysis Tools (spant) Resample a basis-set to match a mrs_data acquisition. — resample_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -116,7 +116,7 @@ Value
diff --git a/docs/reference/resample_img.html b/docs/reference/resample_img.html
index f1e7beaf..b0cc8f71 100644
--- a/docs/reference/resample_img.html
+++ b/docs/reference/resample_img.html
@@ -1,5 +1,5 @@
-Resample an image to match a target image space. — resample_img • Spectroscopy Analysis Tools (spant) Resample an image to match a target image space. — resample_img • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/resample_voi.html b/docs/reference/resample_voi.html
index 8fbfa836..a29ab096 100644
--- a/docs/reference/resample_voi.html
+++ b/docs/reference/resample_voi.html
@@ -1,7 +1,5 @@
-Resample a VOI to match a target image space using nearest-neighbour
-interpolation. — resample_voi • Spectroscopy Analysis Tools (spant) Resample a VOI to match a target image space using nearest-neighbour interpolation. — resample_voi • Spectroscopy Analysis Tools (spant) Reslice a nifti object to match the orientation of mrs data. — reslice_to_mrs • Spectroscopy Analysis Tools (spant) Reslice a nifti object to match the orientation of mrs data. — reslice_to_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/reson_table2mrs_data.html b/docs/reference/reson_table2mrs_data.html
index d75579ee..c5a2167a 100644
--- a/docs/reference/reson_table2mrs_data.html
+++ b/docs/reference/reson_table2mrs_data.html
@@ -1,5 +1,5 @@
-Generate mrs_data from a table of single Lorentzian resonances. — reson_table2mrs_data • Spectroscopy Analysis Tools (spant) Generate mrs_data from a table of single Lorentzian resonances. — reson_table2mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -119,7 +119,7 @@ Value
diff --git a/docs/reference/rm_dyns.html b/docs/reference/rm_dyns.html
index 5d5ef692..573e1f51 100644
--- a/docs/reference/rm_dyns.html
+++ b/docs/reference/rm_dyns.html
@@ -1,5 +1,5 @@
-Remove a subset of dynamic scans. — rm_dyns • Spectroscopy Analysis Tools (spant) Remove a subset of dynamic scans. — rm_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/scale_amp_molal.html b/docs/reference/scale_amp_molal.html
index aaeee1f2..7acb8cb0 100644
--- a/docs/reference/scale_amp_molal.html
+++ b/docs/reference/scale_amp_molal.html
@@ -1,7 +1,5 @@
-Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water). — scale_amp_molal • Spectroscopy Analysis Tools (spant) Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / kg of tissue water). — scale_amp_molal • Spectroscopy Analysis Tools (spant)
Spectroscopy Analysis Tools (spant)
- 2.21.0
+ 2.22.0
@@ -76,8 +74,7 @@
- Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water).
+ Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / kg of tissue water).
Source: R/amp_scaling.R
scale_amp_molal.Rd
@@ -163,7 +160,7 @@ Value
diff --git a/docs/reference/scale_amp_molal_pvc.html b/docs/reference/scale_amp_molal_pvc.html
index 962d6afc..4d194abd 100644
--- a/docs/reference/scale_amp_molal_pvc.html
+++ b/docs/reference/scale_amp_molal_pvc.html
@@ -1,7 +1,5 @@
-Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water). — scale_amp_molal_pvc • Spectroscopy Analysis Tools (spant)
@@ -75,8 +73,7 @@
- Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water).
+ Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / kg of tissue water).
Source: R/amp_scaling.R
scale_amp_molal_pvc.Rd
@@ -141,7 +138,7 @@ Value
diff --git a/docs/reference/scale_amp_molar.html b/docs/reference/scale_amp_molar.html
index 02358d91..dc87a338 100644
--- a/docs/reference/scale_amp_molar.html
+++ b/docs/reference/scale_amp_molar.html
@@ -1,7 +1,5 @@
-Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / Litre of tissue). — scale_amp_molar • Spectroscopy Analysis Tools (spant) Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / Litre of tissue). — scale_amp_molar • Spectroscopy Analysis Tools (spant) Convert default LCM/TARQUIN concentration scaling to molal units with partial
-volume correction. — scale_amp_molar2molal_pvc • Spectroscopy Analysis Tools (spant) Convert default LCM/TARQUIN concentration scaling to molal units with partial volume correction. — scale_amp_molar2molal_pvc • Spectroscopy Analysis Tools (spant) Scale fitted amplitudes to a ratio of signal amplitude. — scale_amp_ratio • Spectroscopy Analysis Tools (spant) Scale fitted amplitudes to a ratio of signal amplitude. — scale_amp_ratio • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -116,7 +116,7 @@ Value
diff --git a/docs/reference/scale_amp_ratio_value.html b/docs/reference/scale_amp_ratio_value.html
index 2036837a..6af8ac51 100644
--- a/docs/reference/scale_amp_ratio_value.html
+++ b/docs/reference/scale_amp_ratio_value.html
@@ -1,5 +1,5 @@
-Scale fitted amplitudes to a ratio of signal amplitude. — scale_amp_ratio_value • Spectroscopy Analysis Tools (spant) Scale fitted amplitudes to a ratio of signal amplitude. — scale_amp_ratio_value • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/scale_amp_water_ratio.html b/docs/reference/scale_amp_water_ratio.html
index 5b25e884..35a76b00 100644
--- a/docs/reference/scale_amp_water_ratio.html
+++ b/docs/reference/scale_amp_water_ratio.html
@@ -1,5 +1,5 @@
-Scale metabolite amplitudes as a ratio to the unsuppressed water amplitude. — scale_amp_water_ratio • Spectroscopy Analysis Tools (spant) Scale metabolite amplitudes as a ratio to the unsuppressed water amplitude. — scale_amp_water_ratio • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/scale_basis_amp.html b/docs/reference/scale_basis_amp.html
index 9401c3f1..5a58b5e5 100644
--- a/docs/reference/scale_basis_amp.html
+++ b/docs/reference/scale_basis_amp.html
@@ -1,5 +1,5 @@
-Scale a basis object by a scalar. — scale_basis_amp • Spectroscopy Analysis Tools (spant) Scale a basis object by a scalar. — scale_basis_amp • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/scale_basis_from_singlet.html b/docs/reference/scale_basis_from_singlet.html
index 0d542bc8..c9a19e77 100644
--- a/docs/reference/scale_basis_from_singlet.html
+++ b/docs/reference/scale_basis_from_singlet.html
@@ -1,5 +1,5 @@
-Scale a basis-set to be consistent with spant assumptions for water scaling. — scale_basis_from_singlet • Spectroscopy Analysis Tools (spant) Scale a basis-set to be consistent with spant assumptions for water scaling. — scale_basis_from_singlet • Spectroscopy Analysis Tools (spant)
Spectroscopy Analysis Tools (spant)
- 2.21.0
+ 2.22.0
@@ -127,7 +127,7 @@ Value
diff --git a/docs/reference/scale_mrs_amp.html b/docs/reference/scale_mrs_amp.html
index b5501a0d..990f058a 100644
--- a/docs/reference/scale_mrs_amp.html
+++ b/docs/reference/scale_mrs_amp.html
@@ -1,5 +1,5 @@
-Scale an mrs_data object by a scalar or vector or amplitudes. — scale_mrs_amp • Spectroscopy Analysis Tools (spant) Scale an mrs_data object by a scalar or vector or amplitudes. — scale_mrs_amp • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/scale_spec.html b/docs/reference/scale_spec.html
index 4f6ea835..6b3ddba4 100644
--- a/docs/reference/scale_spec.html
+++ b/docs/reference/scale_spec.html
@@ -1,5 +1,5 @@
-Scale mrs_data to a spectral region. — scale_spec • Spectroscopy Analysis Tools (spant) Scale mrs_data to a spectral region. — scale_spec • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -141,7 +141,7 @@ Value
diff --git a/docs/reference/sd.html b/docs/reference/sd.html
index ea1eec9f..3ae4dfd4 100644
--- a/docs/reference/sd.html
+++ b/docs/reference/sd.html
@@ -1,5 +1,5 @@
-Calculate the standard deviation spectrum from an mrs_data object. — sd • Spectroscopy Analysis Tools (spant) Calculate the standard deviation spectrum from an mrs_data object. — sd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/sd.mrs_data.html b/docs/reference/sd.mrs_data.html
index 3f92a49f..13bdda85 100644
--- a/docs/reference/sd.mrs_data.html
+++ b/docs/reference/sd.mrs_data.html
@@ -1,5 +1,5 @@
-Calculate the standard deviation spectrum from an mrs_data object. — sd.mrs_data • Spectroscopy Analysis Tools (spant) Calculate the standard deviation spectrum from an mrs_data object. — sd.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/seconds.html b/docs/reference/seconds.html
index b34d6627..467ee17f 100644
--- a/docs/reference/seconds.html
+++ b/docs/reference/seconds.html
@@ -1,5 +1,5 @@
-Return a time scale vector to match the FID of an MRS data object. — seconds • Spectroscopy Analysis Tools (spant) Return a time scale vector to match the FID of an MRS data object. — seconds • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/seq_cpmg_ideal.html b/docs/reference/seq_cpmg_ideal.html
index 547e96ab..45727c86 100644
--- a/docs/reference/seq_cpmg_ideal.html
+++ b/docs/reference/seq_cpmg_ideal.html
@@ -1,5 +1,5 @@
-CPMG style sequence with ideal pulses. — seq_cpmg_ideal • Spectroscopy Analysis Tools (spant) CPMG style sequence with ideal pulses. — seq_cpmg_ideal • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/seq_mega_press_ideal.html b/docs/reference/seq_mega_press_ideal.html
index 0769b8b4..a9cd7fa0 100644
--- a/docs/reference/seq_mega_press_ideal.html
+++ b/docs/reference/seq_mega_press_ideal.html
@@ -1,7 +1,5 @@
-MEGA-PRESS sequence with ideal localisation pulses and Gaussian shaped
-editing pulse. — seq_mega_press_ideal • Spectroscopy Analysis Tools (spant) MEGA-PRESS sequence with ideal localisation pulses and Gaussian shaped editing pulse. — seq_mega_press_ideal • Spectroscopy Analysis Tools (spant) PRESS sequence with shaped refocusing pulses. — seq_press_2d_shaped • Spectroscopy Analysis Tools (spant) PRESS sequence with shaped refocusing pulses. — seq_press_2d_shaped • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -165,7 +165,7 @@ Value
diff --git a/docs/reference/seq_press_ideal.html b/docs/reference/seq_press_ideal.html
index 8c976856..72c3af3d 100644
--- a/docs/reference/seq_press_ideal.html
+++ b/docs/reference/seq_press_ideal.html
@@ -1,5 +1,5 @@
-PRESS sequence with ideal pulses. — seq_press_ideal • Spectroscopy Analysis Tools (spant) PRESS sequence with ideal pulses. — seq_press_ideal • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/seq_pulse_acquire.html b/docs/reference/seq_pulse_acquire.html
index 4a88fc64..ad80571e 100644
--- a/docs/reference/seq_pulse_acquire.html
+++ b/docs/reference/seq_pulse_acquire.html
@@ -1,5 +1,5 @@
-Simple pulse and acquire sequence with ideal pulses. — seq_pulse_acquire • Spectroscopy Analysis Tools (spant) Simple pulse and acquire sequence with ideal pulses. — seq_pulse_acquire • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/seq_slaser_ideal.html b/docs/reference/seq_slaser_ideal.html
index 74688f4d..eb83e8e3 100644
--- a/docs/reference/seq_slaser_ideal.html
+++ b/docs/reference/seq_slaser_ideal.html
@@ -1,5 +1,5 @@
-sLASER sequence with ideal pulses. — seq_slaser_ideal • Spectroscopy Analysis Tools (spant) sLASER sequence with ideal pulses. — seq_slaser_ideal • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -126,7 +126,7 @@ Value
diff --git a/docs/reference/seq_spin_echo_ideal.html b/docs/reference/seq_spin_echo_ideal.html
index e23271de..4248716f 100644
--- a/docs/reference/seq_spin_echo_ideal.html
+++ b/docs/reference/seq_spin_echo_ideal.html
@@ -1,5 +1,5 @@
-Spin echo sequence with ideal pulses. — seq_spin_echo_ideal • Spectroscopy Analysis Tools (spant) Spin echo sequence with ideal pulses. — seq_spin_echo_ideal • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/seq_steam_ideal.html b/docs/reference/seq_steam_ideal.html
index a60685a8..1c8115d7 100644
--- a/docs/reference/seq_steam_ideal.html
+++ b/docs/reference/seq_steam_ideal.html
@@ -1,5 +1,5 @@
-STEAM sequence with ideal pulses. — seq_steam_ideal • Spectroscopy Analysis Tools (spant) STEAM sequence with ideal pulses. — seq_steam_ideal • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -128,7 +128,7 @@ Value
diff --git a/docs/reference/seq_steam_ideal_cof.html b/docs/reference/seq_steam_ideal_cof.html
index 8f225740..cba7af91 100644
--- a/docs/reference/seq_steam_ideal_cof.html
+++ b/docs/reference/seq_steam_ideal_cof.html
@@ -1,7 +1,5 @@
-STEAM sequence with ideal pulses and coherence order filtering to simulate
-gradient crushers. — seq_steam_ideal_cof • Spectroscopy Analysis Tools (spant) STEAM sequence with ideal pulses and coherence order filtering to simulate gradient crushers. — seq_steam_ideal_cof • Spectroscopy Analysis Tools (spant) STEAM sequence with ideal pulses using the z-rotation gradient simulation
-method described by Young et al JMR 140, 146-152 (1999). — seq_steam_ideal_young • Spectroscopy Analysis Tools (spant) STEAM sequence with ideal pulses using the z-rotation gradient simulation method described by Young et al JMR 140, 146-152 (1999). — seq_steam_ideal_young • Spectroscopy Analysis Tools (spant) Set the number of transients for an mrs_data object. — set_Ntrans • Spectroscopy Analysis Tools (spant) Set the number of transients for an mrs_data object. — set_Ntrans • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/set_def_acq_paras.html b/docs/reference/set_def_acq_paras.html
index 3e1b4004..cc2ada9c 100644
--- a/docs/reference/set_def_acq_paras.html
+++ b/docs/reference/set_def_acq_paras.html
@@ -1,5 +1,5 @@
-Set the default acquisition parameters. — set_def_acq_paras • Spectroscopy Analysis Tools (spant) Set the default acquisition parameters. — set_def_acq_paras • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Arguments
diff --git a/docs/reference/set_lcm_cmd.html b/docs/reference/set_lcm_cmd.html
index 2056ed01..42bb2f24 100644
--- a/docs/reference/set_lcm_cmd.html
+++ b/docs/reference/set_lcm_cmd.html
@@ -1,5 +1,5 @@
-Set the command to run the LCModel command-line program. — set_lcm_cmd • Spectroscopy Analysis Tools (spant) Set the command to run the LCModel command-line program. — set_lcm_cmd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/set_lw.html b/docs/reference/set_lw.html
index b64ec851..bb176c62 100644
--- a/docs/reference/set_lw.html
+++ b/docs/reference/set_lw.html
@@ -1,5 +1,5 @@
-Apply line-broadening to an mrs_data object to achieve a specified linewidth. — set_lw • Spectroscopy Analysis Tools (spant) Apply line-broadening to an mrs_data object to achieve a specified linewidth. — set_lw • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -123,7 +123,7 @@ Value
diff --git a/docs/reference/set_mask_xy_mat.html b/docs/reference/set_mask_xy_mat.html
index 49dc5d4e..52c4b617 100644
--- a/docs/reference/set_mask_xy_mat.html
+++ b/docs/reference/set_mask_xy_mat.html
@@ -1,5 +1,5 @@
-Set the masked voxels in a 2D MRSI dataset to given spectrum. — set_mask_xy_mat • Spectroscopy Analysis Tools (spant) Set the masked voxels in a 2D MRSI dataset to given spectrum. — set_mask_xy_mat • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Value
diff --git a/docs/reference/set_precomp_mode.html b/docs/reference/set_precomp_mode.html
index f44bd5d3..47c28e3b 100644
--- a/docs/reference/set_precomp_mode.html
+++ b/docs/reference/set_precomp_mode.html
@@ -1,5 +1,5 @@
-Set the precompute mode. — set_precomp_mode • Spectroscopy Analysis Tools (spant) Set the precompute mode. — set_precomp_mode • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/set_precomp_verbose.html b/docs/reference/set_precomp_verbose.html
index 1453a231..9c613505 100644
--- a/docs/reference/set_precomp_verbose.html
+++ b/docs/reference/set_precomp_verbose.html
@@ -1,5 +1,5 @@
-Set the verbosity of the precompute function. — set_precomp_verbose • Spectroscopy Analysis Tools (spant) Set the verbosity of the precompute function. — set_precomp_verbose • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/set_ref.html b/docs/reference/set_ref.html
index 8953fa50..5436dfa2 100644
--- a/docs/reference/set_ref.html
+++ b/docs/reference/set_ref.html
@@ -1,5 +1,5 @@
-Set the ppm reference value (eg ppm value at 0Hz). — set_ref • Spectroscopy Analysis Tools (spant) Set the ppm reference value (eg ppm value at 0Hz). — set_ref • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/set_td_pts.html b/docs/reference/set_td_pts.html
index 8a80d42a..586459ff 100644
--- a/docs/reference/set_td_pts.html
+++ b/docs/reference/set_td_pts.html
@@ -1,7 +1,5 @@
-Set the number of time-domain data points, truncating or zero-filling as
-appropriate. — set_td_pts • Spectroscopy Analysis Tools (spant) Set the number of time-domain data points, truncating or zero-filling as appropriate. — set_td_pts • Spectroscopy Analysis Tools (spant) Set the command to run the TARQUIN command-line program. — set_tqn_cmd • Spectroscopy Analysis Tools (spant) Set the command to run the TARQUIN command-line program. — set_tqn_cmd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/set_tr.html b/docs/reference/set_tr.html
index b2109ab0..65c9df5f 100644
--- a/docs/reference/set_tr.html
+++ b/docs/reference/set_tr.html
@@ -1,5 +1,5 @@
-Set the repetition time of an MRS dataset. — set_tr • Spectroscopy Analysis Tools (spant) Set the repetition time of an MRS dataset. — set_tr • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/shift.html b/docs/reference/shift.html
index ab0fe724..034591d0 100644
--- a/docs/reference/shift.html
+++ b/docs/reference/shift.html
@@ -1,5 +1,5 @@
-Apply a frequency shift to MRS data. — shift • Spectroscopy Analysis Tools (spant) Apply a frequency shift to MRS data. — shift • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/shift_basis.html b/docs/reference/shift_basis.html
index 2884be19..f55a65e0 100644
--- a/docs/reference/shift_basis.html
+++ b/docs/reference/shift_basis.html
@@ -1,5 +1,5 @@
-Apply frequency shifts to basis set signals. — shift_basis • Spectroscopy Analysis Tools (spant) Apply frequency shifts to basis set signals. — shift_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Value
diff --git a/docs/reference/sim_basis.html b/docs/reference/sim_basis.html
index c7838c46..bb5fefc6 100644
--- a/docs/reference/sim_basis.html
+++ b/docs/reference/sim_basis.html
@@ -1,5 +1,5 @@
-Simulate a basis set object. — sim_basis • Spectroscopy Analysis Tools (spant) Simulate a basis set object. — sim_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -136,7 +136,7 @@ Value
diff --git a/docs/reference/sim_basis_1h_brain.html b/docs/reference/sim_basis_1h_brain.html
index 62ed7389..f71ffa0b 100644
--- a/docs/reference/sim_basis_1h_brain.html
+++ b/docs/reference/sim_basis_1h_brain.html
@@ -1,7 +1,5 @@
-Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS
-sequence. Note, ideal pulses are assumed. — sim_basis_1h_brain • Spectroscopy Analysis Tools (spant) Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS sequence. Note, ideal pulses are assumed. — sim_basis_1h_brain • Spectroscopy Analysis Tools (spant) Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS
-sequence. Note, ideal pulses are assumed. — sim_basis_1h_brain_press • Spectroscopy Analysis Tools (spant) Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS sequence. Note, ideal pulses are assumed. — sim_basis_1h_brain_press • Spectroscopy Analysis Tools (spant) Simulate a macromolecular and lipid basis-set suitable for 1H brain MRS
-analysis. — sim_basis_mm_lip_lcm • Spectroscopy Analysis Tools (spant) Simulate a macromolecular and lipid basis-set suitable for 1H brain MRS analysis. — sim_basis_mm_lip_lcm • Spectroscopy Analysis Tools (spant) Simulate a basis file using TARQUIN. — sim_basis_tqn • Spectroscopy Analysis Tools (spant) Simulate a basis file using TARQUIN. — sim_basis_tqn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -129,7 +129,7 @@ Examples
diff --git a/docs/reference/sim_brain_1h.html b/docs/reference/sim_brain_1h.html
index 2044cf1a..717ee289 100644
--- a/docs/reference/sim_brain_1h.html
+++ b/docs/reference/sim_brain_1h.html
@@ -1,5 +1,5 @@
-Simulate MRS data with a similar appearance to normal brain (by default). — sim_brain_1h • Spectroscopy Analysis Tools (spant) Simulate MRS data with a similar appearance to normal brain (by default). — sim_brain_1h • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -159,7 +159,7 @@ Value
diff --git a/docs/reference/sim_mol.html b/docs/reference/sim_mol.html
index 23bcef50..77f76a50 100644
--- a/docs/reference/sim_mol.html
+++ b/docs/reference/sim_mol.html
@@ -1,5 +1,5 @@
-Simulate a mol_parameter object. — sim_mol • Spectroscopy Analysis Tools (spant) Simulate a mol_parameter object. — sim_mol • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -143,7 +143,7 @@ Value
diff --git a/docs/reference/sim_noise.html b/docs/reference/sim_noise.html
index 23875f79..a71477d4 100644
--- a/docs/reference/sim_noise.html
+++ b/docs/reference/sim_noise.html
@@ -1,5 +1,5 @@
-Simulate an mrs_data object containing simulated Gaussian noise. — sim_noise • Spectroscopy Analysis Tools (spant) Simulate an mrs_data object containing simulated Gaussian noise. — sim_noise • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -84,6 +84,7 @@ Simulate an mrs_data object containing simulated Gaussian noise.
ft = def_ft(),
N = def_N(),
ref = def_ref(),
+ nuc = def_nuc(),
dyns = 1,
fd = TRUE
)
@@ -111,6 +112,10 @@ Arguments
reference value for ppm scale.
nuc
+resonant nucleus.
dyns
number of dynamic scans to generate.
Value
diff --git a/docs/reference/sim_resonances.html b/docs/reference/sim_resonances.html
index 19e9a8a4..d4f8d7c0 100644
--- a/docs/reference/sim_resonances.html
+++ b/docs/reference/sim_resonances.html
@@ -1,5 +1,5 @@
-Simulate a MRS data object containing a set of simulated resonances. — sim_resonances • Spectroscopy Analysis Tools (spant) Simulate a MRS data object containing a set of simulated resonances. — sim_resonances • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -161,7 +161,7 @@ Examples
diff --git a/docs/reference/sim_th_excit_profile.html b/docs/reference/sim_th_excit_profile.html
index 5535c5ef..e781cab1 100644
--- a/docs/reference/sim_th_excit_profile.html
+++ b/docs/reference/sim_th_excit_profile.html
@@ -1,7 +1,5 @@
-Simulate an ideal pulse excitation profile by smoothing a top-hat function
-with a Gaussian. — sim_th_excit_profile • Spectroscopy Analysis Tools (spant) Simulate an ideal pulse excitation profile by smoothing a top-hat function with a Gaussian. — sim_th_excit_profile • Spectroscopy Analysis Tools (spant) Simulate an mrs_data object containing complex zero valued samples. — sim_zero • Spectroscopy Analysis Tools (spant) Simulate an mrs_data object containing complex zero valued samples. — sim_zero • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -78,7 +78,14 @@ Simulate an mrs_data object containing complex zero valued samples.
-
+
@@ -99,6 +106,10 @@ Arguments
reference value for ppm scale.
nuc
+resonant nucleus.
dyns
number of dynamic scans to generate.
Value
diff --git a/docs/reference/smooth_dyns.html b/docs/reference/smooth_dyns.html
index 4cc8da50..accf3a51 100644
--- a/docs/reference/smooth_dyns.html
+++ b/docs/reference/smooth_dyns.html
@@ -1,5 +1,5 @@
-Smooth data across the dynamic dimension with a Gaussian kernel. — smooth_dyns • Spectroscopy Analysis Tools (spant) Smooth data across the dynamic dimension with a Gaussian kernel. — smooth_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/sort_basis.html b/docs/reference/sort_basis.html
index 6a676ea2..d25cc006 100644
--- a/docs/reference/sort_basis.html
+++ b/docs/reference/sort_basis.html
@@ -1,5 +1,5 @@
-Sort the basis-set elements alphabetically. — sort_basis • Spectroscopy Analysis Tools (spant) Sort the basis-set elements alphabetically. — sort_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/spant-package.html b/docs/reference/spant-package.html
index b3dd8e21..90f19ec3 100644
--- a/docs/reference/spant-package.html
+++ b/docs/reference/spant-package.html
@@ -1,5 +1,5 @@
-spant: spectroscopy analysis tools. — spant-package • Spectroscopy Analysis Tools (spant) spant: spectroscopy analysis tools. — spant-package • Spectroscopy Analysis Tools (spant) Simulate and fit some spectra with ABfit for benchmarking purposes. Basic
-timing and performance metrics will be printed. — spant_abfit_benchmark • Spectroscopy Analysis Tools (spant) Simulate and fit some spectra with ABfit for benchmarking purposes. Basic timing and performance metrics will be printed. — spant_abfit_benchmark • Spectroscopy Analysis Tools (spant) Example MEGA-PRESS data with significant B0 drift. — spant_mpress_drift • Spectroscopy Analysis Tools (spant) Example MEGA-PRESS data with significant B0 drift. — spant_mpress_drift • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -83,7 +83,7 @@ Example MEGA-PRESS data with significant B0 drift.
Format
- An object of class mrs_data of length 13.
+ An object of class mrs_data of dimension 1 x 1 x 1 x 1 x 40 x 1 x 1024.
@@ -98,7 +98,7 @@ Format
diff --git a/docs/reference/spant_sim_fmrs_dataset.html b/docs/reference/spant_sim_fmrs_dataset.html
new file mode 100644
index 00000000..00e48b56
--- /dev/null
+++ b/docs/reference/spant_sim_fmrs_dataset.html
@@ -0,0 +1,117 @@
+
+Simulate an example fMRS dataset for a block design fMRS experiment and export a BIDS structure. — spant_sim_fmrs_dataset • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Simulate an example fMRS dataset for a block design fMRS experiment and export a BIDS structure.
+ Source: R/fmrs.R
+ spant_sim_fmrs_dataset.Rd
+
+
+
+ Simulate an example fMRS dataset for a block design fMRS experiment and
+export a BIDS structure.
+
+
+
+ spant_sim_fmrs_dataset(output_dir = NULL)
+
+
+
+ Arguments
+ - output_dir
+output directory for the BIDS data. Defaults to :
+"HOME/sim_fmrs_dataset/data".
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/spant_simulation_benchmark.html b/docs/reference/spant_simulation_benchmark.html
index 32daa8bf..d8cc6841 100644
--- a/docs/reference/spant_simulation_benchmark.html
+++ b/docs/reference/spant_simulation_benchmark.html
@@ -1,7 +1,5 @@
-Simulate a typical metabolite basis set for benchmarking. Timing metrics will
-be printed on completion. — spant_simulation_benchmark • Spectroscopy Analysis Tools (spant) Simulate a typical metabolite basis set for benchmarking. Timing metrics will be printed on completion. — spant_simulation_benchmark • Spectroscopy Analysis Tools (spant) Decompose an mrs_data object into white and gray matter spectra. — spec_decomp • Spectroscopy Analysis Tools (spant) Perform a mathematical operation on a spectral region. — spec_op • Spectroscopy Analysis Tools (spant) Perform a mathematical operation on a spectral region. — spec_op • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -98,8 +98,8 @@ Arguments
operator
-can be "sum" (default), "mean", "l2", "max", "min" or
-"max-min".
can be "sum" (default), "mean", "l2", "max", "max_cplx,
+"min" or "max-min".
freq_scale
@@ -129,7 +129,7 @@ Value
diff --git a/docs/reference/spin_sys.html b/docs/reference/spin_sys.html
index 853423a4..1eaa9e76 100644
--- a/docs/reference/spin_sys.html
+++ b/docs/reference/spin_sys.html
@@ -1,5 +1,5 @@
-Create a spin system object for pulse sequence simulation. — spin_sys • Spectroscopy Analysis Tools (spant) Create a spin system object for pulse sequence simulation. — spin_sys • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/spm_pve2categorical.html b/docs/reference/spm_pve2categorical.html
index 23a1bad9..70f10729 100644
--- a/docs/reference/spm_pve2categorical.html
+++ b/docs/reference/spm_pve2categorical.html
@@ -1,7 +1,5 @@
-Convert SPM style segmentation files to a single categorical image where
-the numerical values map as: 0) Other, 1) CSF, 2) GM and 3) WM. — spm_pve2categorical • Spectroscopy Analysis Tools (spant) Convert SPM style segmentation files to a single categorical image where the numerical values map as: 0) Other, 1) CSF, 2) GM and 3) WM. — spm_pve2categorical • Spectroscopy Analysis Tools (spant) Signal space projection method for lipid suppression. — ssp • Spectroscopy Analysis Tools (spant) Signal space projection method for lipid suppression. — ssp • Spectroscopy Analysis Tools (spant) Plot the fitting results of an object of class fit_result with
-individual basis set components shown. — stackplot.fit_result • Spectroscopy Analysis Tools (spant) Plot the fitting results of an object of class fit_result with individual basis set components shown. — stackplot.fit_result • Spectroscopy Analysis Tools (spant) Produce a plot with multiple traces. — stackplot • Spectroscopy Analysis Tools (spant) Produce a plot with multiple traces. — stackplot • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/stackplot.mrs_data.html b/docs/reference/stackplot.mrs_data.html
index 17ff5648..64eea445 100644
--- a/docs/reference/stackplot.mrs_data.html
+++ b/docs/reference/stackplot.mrs_data.html
@@ -1,5 +1,5 @@
-Stackplot plotting method for objects of class mrs_data. — stackplot.mrs_data • Spectroscopy Analysis Tools (spant) Stackplot plotting method for objects of class mrs_data. — stackplot.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -255,7 +255,7 @@ Arguments
diff --git a/docs/reference/sub_first_dyn.html b/docs/reference/sub_first_dyn.html
index dbd7f831..493b7242 100644
--- a/docs/reference/sub_first_dyn.html
+++ b/docs/reference/sub_first_dyn.html
@@ -1,5 +1,5 @@
-Subtract the first dynamic spectrum from a dynamic series. — sub_first_dyn • Spectroscopy Analysis Tools (spant) Subtract the first dynamic spectrum from a dynamic series. — sub_first_dyn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/sub_mean_dyns.html b/docs/reference/sub_mean_dyns.html
index 6e3bb2df..221bd0c1 100644
--- a/docs/reference/sub_mean_dyns.html
+++ b/docs/reference/sub_mean_dyns.html
@@ -1,5 +1,5 @@
-Subtract the mean dynamic spectrum from a dynamic series. — sub_mean_dyns • Spectroscopy Analysis Tools (spant) Subtract the mean dynamic spectrum from a dynamic series. — sub_mean_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/sub_median_dyns.html b/docs/reference/sub_median_dyns.html
index 134c495d..1e834f14 100644
--- a/docs/reference/sub_median_dyns.html
+++ b/docs/reference/sub_median_dyns.html
@@ -1,5 +1,5 @@
-Subtract the median dynamic spectrum from a dynamic series. — sub_median_dyns • Spectroscopy Analysis Tools (spant) Subtract the median dynamic spectrum from a dynamic series. — sub_median_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/sum_coils.html b/docs/reference/sum_coils.html
index 7bf559f2..e1ab3cc0 100644
--- a/docs/reference/sum_coils.html
+++ b/docs/reference/sum_coils.html
@@ -1,5 +1,5 @@
-Calculate the sum across receiver coil elements. — sum_coils • Spectroscopy Analysis Tools (spant) Calculate the sum across receiver coil elements. — sum_coils • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/sum_dyns.html b/docs/reference/sum_dyns.html
index a0be19d3..bbda2ffc 100644
--- a/docs/reference/sum_dyns.html
+++ b/docs/reference/sum_dyns.html
@@ -1,5 +1,5 @@
-Calculate the sum of data dynamics. — sum_dyns • Spectroscopy Analysis Tools (spant) Calculate the sum of data dynamics. — sum_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/sum_mrs.html b/docs/reference/sum_mrs.html
index a22f215b..3cc3ab9e 100644
--- a/docs/reference/sum_mrs.html
+++ b/docs/reference/sum_mrs.html
@@ -1,5 +1,5 @@
-Sum two mrs_data objects. — sum_mrs • Spectroscopy Analysis Tools (spant) Sum two mrs_data objects. — sum_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Value
diff --git a/docs/reference/sum_mrs_list.html b/docs/reference/sum_mrs_list.html
index f4e09aea..c3584348 100644
--- a/docs/reference/sum_mrs_list.html
+++ b/docs/reference/sum_mrs_list.html
@@ -1,5 +1,5 @@
-Return the sum of a list of mrs_data objects. — sum_mrs_list • Spectroscopy Analysis Tools (spant) Return the sum of a list of mrs_data objects. — sum_mrs_list • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/svs_1h_brain_analysis.html b/docs/reference/svs_1h_brain_analysis.html
index 8ce514db..dff0ef7d 100644
--- a/docs/reference/svs_1h_brain_analysis.html
+++ b/docs/reference/svs_1h_brain_analysis.html
@@ -1,5 +1,5 @@
-Standard SVS 1H brain analysis pipeline. — svs_1h_brain_analysis • Spectroscopy Analysis Tools (spant) Standard SVS 1H brain analysis pipeline. — svs_1h_brain_analysis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -199,7 +199,7 @@ Value
diff --git a/docs/reference/svs_1h_brain_analysis_dev.html b/docs/reference/svs_1h_brain_analysis_dev.html
index d70a14d3..d71bfea2 100644
--- a/docs/reference/svs_1h_brain_analysis_dev.html
+++ b/docs/reference/svs_1h_brain_analysis_dev.html
@@ -1,5 +1,5 @@
-Standard SVS 1H brain analysis pipeline. — svs_1h_brain_analysis_dev • Spectroscopy Analysis Tools (spant) Standard SVS 1H brain analysis pipeline. — svs_1h_brain_analysis_dev • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -193,7 +193,7 @@ Examples
diff --git a/docs/reference/svs_1h_brain_batch_analysis.html b/docs/reference/svs_1h_brain_batch_analysis.html
index 5631e8cc..15f7223e 100644
--- a/docs/reference/svs_1h_brain_batch_analysis.html
+++ b/docs/reference/svs_1h_brain_batch_analysis.html
@@ -1,5 +1,5 @@
-Batch interface to the standard SVS 1H brain analysis pipeline. — svs_1h_brain_batch_analysis • Spectroscopy Analysis Tools (spant) Batch interface to the standard SVS 1H brain analysis pipeline. — svs_1h_brain_batch_analysis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -144,7 +144,7 @@ Value
diff --git a/docs/reference/t_test_spec.html b/docs/reference/t_test_spec.html
new file mode 100644
index 00000000..56a7ea1b
--- /dev/null
+++ b/docs/reference/t_test_spec.html
@@ -0,0 +1,124 @@
+
+Perform a t-test on spectral data points. — t_test_spec • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+
+
+ Perform a t-test on spectral data points.
+
+
+
+ t_test_spec(mrs_data, group)
+
+
+
+ Arguments
+ - mrs_data
+an mrs_data object with spectra in the dynamic dimension.
- group
+vector describing the group membership of each dynamic spectrum.
+
+ Value
+
+
+a list of statistical results.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/td2fd.html b/docs/reference/td2fd.html
index 6748a6a8..f31ed524 100644
--- a/docs/reference/td2fd.html
+++ b/docs/reference/td2fd.html
@@ -1,5 +1,5 @@
-Transform time-domain data to the frequency-domain. — td2fd • Spectroscopy Analysis Tools (spant) Transform time-domain data to the frequency-domain. — td2fd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/td_conv_filt.html b/docs/reference/td_conv_filt.html
index a9f340c3..106b9b00 100644
--- a/docs/reference/td_conv_filt.html
+++ b/docs/reference/td_conv_filt.html
@@ -1,5 +1,5 @@
-Time-domain convolution based filter. — td_conv_filt • Spectroscopy Analysis Tools (spant) Time-domain convolution based filter. — td_conv_filt • Spectroscopy Analysis Tools (spant) Time-domain spectral registration. — tdsr • Spectroscopy Analysis Tools (spant) Time-domain spectral registration. — tdsr • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -121,7 +121,7 @@ Value
diff --git a/docs/reference/te.html b/docs/reference/te.html
index 010361b1..4a65711d 100644
--- a/docs/reference/te.html
+++ b/docs/reference/te.html
@@ -1,5 +1,5 @@
-Return the echo time of an MRS dataset. — te • Spectroscopy Analysis Tools (spant) Return the echo time of an MRS dataset. — te • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/tr.html b/docs/reference/tr.html
index 0c0bd63b..2e749e02 100644
--- a/docs/reference/tr.html
+++ b/docs/reference/tr.html
@@ -1,5 +1,5 @@
-Return the repetition time of an MRS dataset. — tr • Spectroscopy Analysis Tools (spant) Return the repetition time of an MRS dataset. — tr • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/varpro_3_para_opts.html b/docs/reference/varpro_3_para_opts.html
index c2270a16..52d7cd84 100644
--- a/docs/reference/varpro_3_para_opts.html
+++ b/docs/reference/varpro_3_para_opts.html
@@ -1,5 +1,5 @@
-Return a list of options for VARPRO based fitting with 3 free parameters. — varpro_3_para_opts • Spectroscopy Analysis Tools (spant) Return a list of options for VARPRO based fitting with 3 free parameters. — varpro_3_para_opts • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -141,7 +141,7 @@ Value
diff --git a/docs/reference/varpro_basic_opts.html b/docs/reference/varpro_basic_opts.html
index 32c86d22..c5104891 100644
--- a/docs/reference/varpro_basic_opts.html
+++ b/docs/reference/varpro_basic_opts.html
@@ -1,5 +1,5 @@
-Return a list of options for a basic VARPRO analysis. — varpro_basic_opts • Spectroscopy Analysis Tools (spant) Return a list of options for a basic VARPRO analysis. — varpro_basic_opts • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -118,7 +118,7 @@ Value
diff --git a/docs/reference/varpro_opts.html b/docs/reference/varpro_opts.html
index 2aabf11d..6332f730 100644
--- a/docs/reference/varpro_opts.html
+++ b/docs/reference/varpro_opts.html
@@ -1,5 +1,5 @@
-Return a list of options for VARPRO based fitting. — varpro_opts • Spectroscopy Analysis Tools (spant) Return a list of options for VARPRO based fitting. — varpro_opts • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -177,7 +177,7 @@ Examples
diff --git a/docs/reference/vec2mrs_data.html b/docs/reference/vec2mrs_data.html
index 0cccd73b..f0d58bf0 100644
--- a/docs/reference/vec2mrs_data.html
+++ b/docs/reference/vec2mrs_data.html
@@ -1,5 +1,5 @@
-Convert a vector into a mrs_data object. — vec2mrs_data • Spectroscopy Analysis Tools (spant) Convert a vector into a mrs_data object. — vec2mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -80,10 +80,11 @@ Convert a vector into a mrs_data object.
vec2mrs_data(
vec,
- fs = def_fs(),
- ft = def_ft(),
- ref = def_ref(),
- nuc = def_nuc(),
+ mrs_data = NULL,
+ fs = NULL,
+ ft = NULL,
+ ref = NULL,
+ nuc = NULL,
dyns = 1,
fd = FALSE
)
@@ -95,6 +96,10 @@ Arguments
the data vector.
mrs_data
+example data to copy acquisition parameters from.
fs
sampling frequency in Hz.
Arguments
fd
-flag to indicate if the matrix is in the frequency domain (logical).
flag to indicate if the vector is in the frequency domain (logical).
Value
diff --git a/docs/reference/write_basis.html b/docs/reference/write_basis.html
index b6e27cbd..94c5e021 100644
--- a/docs/reference/write_basis.html
+++ b/docs/reference/write_basis.html
@@ -1,5 +1,5 @@
-Write a basis object to an LCModel .basis formatted file. — write_basis • Spectroscopy Analysis Tools (spant) Write a basis object to an LCModel .basis formatted file. — write_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -108,7 +108,7 @@ Arguments
diff --git a/docs/reference/write_basis_tqn.html b/docs/reference/write_basis_tqn.html
index 6aa51c1d..116c73ec 100644
--- a/docs/reference/write_basis_tqn.html
+++ b/docs/reference/write_basis_tqn.html
@@ -1,5 +1,5 @@
-Generate a basis file using TARQUIN. — write_basis_tqn • Spectroscopy Analysis Tools (spant) Generate a basis file using TARQUIN. — write_basis_tqn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Examples
diff --git a/docs/reference/write_mrs.html b/docs/reference/write_mrs.html
index fff25f15..124b9dc4 100644
--- a/docs/reference/write_mrs.html
+++ b/docs/reference/write_mrs.html
@@ -1,5 +1,5 @@
-Write MRS data object to file. — write_mrs • Spectroscopy Analysis Tools (spant) Write MRS data object to file. — write_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Arguments
diff --git a/docs/reference/write_mrs_nifti.html b/docs/reference/write_mrs_nifti.html
index f4bf1921..bd3ed4b7 100644
--- a/docs/reference/write_mrs_nifti.html
+++ b/docs/reference/write_mrs_nifti.html
@@ -1,5 +1,5 @@
-Write MRS data object to file in NIFTI format. — write_mrs_nifti • Spectroscopy Analysis Tools (spant) Write MRS data object to file in NIFTI format. — write_mrs_nifti • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/write_pulse_ascii.html b/docs/reference/write_pulse_ascii.html
index 067ae086..221f8ebb 100644
--- a/docs/reference/write_pulse_ascii.html
+++ b/docs/reference/write_pulse_ascii.html
@@ -1,5 +1,5 @@
-Write an ASCII formatted pulse file. — write_pulse_ascii • Spectroscopy Analysis Tools (spant) Write an ASCII formatted pulse file. — write_pulse_ascii • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/zero_fade_spec.html b/docs/reference/zero_fade_spec.html
index c703745c..c8b572c3 100644
--- a/docs/reference/zero_fade_spec.html
+++ b/docs/reference/zero_fade_spec.html
@@ -1,7 +1,5 @@
-Fade a spectrum to zero by frequency domain multiplication with a tanh
-function. Note this operation distorts data points at the end of the FID. — zero_fade_spec • Spectroscopy Analysis Tools (spant) Fade a spectrum to zero by frequency domain multiplication with a tanh function. Note this operation distorts data points at the end of the FID. — zero_fade_spec • Spectroscopy Analysis Tools (spant) Zero all coherences including and above a given order. — zero_higher_orders • Spectroscopy Analysis Tools (spant) Zero all coherences including and above a given order. — zero_higher_orders • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Value
diff --git a/docs/reference/zero_td_pts_end.html b/docs/reference/zero_td_pts_end.html
index 8c1123c8..71d24ebb 100644
--- a/docs/reference/zero_td_pts_end.html
+++ b/docs/reference/zero_td_pts_end.html
@@ -1,5 +1,5 @@
-Set mrs_data object data points at the end of the FID to zero. — zero_td_pts_end • Spectroscopy Analysis Tools (spant) Set mrs_data object data points at the end of the FID to zero. — zero_td_pts_end • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/zf.html b/docs/reference/zf.html
index 85e2013c..baf50256 100644
--- a/docs/reference/zf.html
+++ b/docs/reference/zf.html
@@ -1,5 +1,5 @@
-Zero-fill MRS data in the time domain. — zf • Spectroscopy Analysis Tools (spant) Zero-fill MRS data in the time domain. — zf • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -125,7 +125,7 @@ Value
diff --git a/docs/reference/zf_xy.html b/docs/reference/zf_xy.html
index ebca3999..c4104a74 100644
--- a/docs/reference/zf_xy.html
+++ b/docs/reference/zf_xy.html
@@ -1,5 +1,5 @@
-Zero-fill MRSI data in the k-space x-y direction. — zf_xy • Spectroscopy Analysis Tools (spant) Zero-fill MRSI data in the k-space x-y direction. — zf_xy • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -113,7 +113,7 @@ Value
diff --git a/docs/sitemap.xml b/docs/sitemap.xml
index e2139f71..4c39f515 100644
--- a/docs/sitemap.xml
+++ b/docs/sitemap.xml
@@ -216,6 +216,12 @@
https://martin3141.github.io/spant/reference/comb_coils_fp_pc.html
+
+ https://martin3141.github.io/spant/reference/comb_coils_mrsi_gls.html
+
+
+ https://martin3141.github.io/spant/reference/comb_coils_svs_gls.html
+
https://martin3141.github.io/spant/reference/comb_csv_results.html
@@ -411,6 +417,9 @@
https://martin3141.github.io/spant/reference/gen_conv_reg.html
+
+ https://martin3141.github.io/spant/reference/gen_group_reg.html
+
https://martin3141.github.io/spant/reference/gen_impulse_reg.html
@@ -555,6 +564,15 @@
https://martin3141.github.io/spant/reference/glm_spec.html
+
+ https://martin3141.github.io/spant/reference/glm_spec_fmrs_fl.html
+
+
+ https://martin3141.github.io/spant/reference/glm_spec_fmrs_group.html
+
+
+ https://martin3141.github.io/spant/reference/glm_spec_group_linhyp.html
+
https://martin3141.github.io/spant/reference/grid_shift_xy.html
@@ -690,9 +708,15 @@
https://martin3141.github.io/spant/reference/mrs_data2basis.html
+
+ https://martin3141.github.io/spant/reference/mrs_data2bids.html
+
https://martin3141.github.io/spant/reference/mrs_data2mat.html
+
+ https://martin3141.github.io/spant/reference/mrs_data2spec_mat.html
+
https://martin3141.github.io/spant/reference/mrs_data2vec.html
@@ -741,6 +765,9 @@
https://martin3141.github.io/spant/reference/phase.html
+
+ https://martin3141.github.io/spant/reference/phase_ref_1h_brain.html
+
https://martin3141.github.io/spant/reference/plot.fit_result.html
@@ -780,6 +807,12 @@
https://martin3141.github.io/spant/reference/precomp.html
+
+ https://martin3141.github.io/spant/reference/preproc_svs.html
+
+
+ https://martin3141.github.io/spant/reference/preproc_svs_dataset.html
+
https://martin3141.github.io/spant/reference/print.fit_result.html
@@ -1050,6 +1083,9 @@
https://martin3141.github.io/spant/reference/spant_mpress_drift.html
+
+ https://martin3141.github.io/spant/reference/spant_sim_fmrs_dataset.html
+
https://martin3141.github.io/spant/reference/spant_simulation_benchmark.html
@@ -1107,6 +1143,9 @@
https://martin3141.github.io/spant/reference/svs_1h_brain_batch_analysis.html
+
+ https://martin3141.github.io/spant/reference/t_test_spec.html
+
https://martin3141.github.io/spant/reference/td2fd.html
Simulate and fit some spectra with ABfit for benchmarking purposes. Basic -timing and performance metrics will be printed.
Simulate and fit some spectra with ABfit for benchmarking purposes. Basic timing and performance metrics will be printed.
Example MEGA-PRESS data with significant B0 drift.
Simulate an example fMRS dataset for a block design fMRS experiment and export a BIDS structure.
Simulate a typical metabolite basis set for benchmarking. Timing metrics will -be printed on completion.
Simulate a typical metabolite basis set for benchmarking. Timing metrics will be printed on completion.
All functions
- Convert SPM style segmentation files to a single categorical image where
-the numerical values map as: 0) Other, 1) CSF, 2) GM and 3) WM.
Convert SPM style segmentation files to a single categorical image where the numerical values map as: 0) Other, 1) CSF, 2) GM and 3) WM.
@@ -1413,8 +1386,7 @@ All functions
- Plot the fitting results of an object of class fit_result with
-individual basis set components shown.
Plot the fitting results of an object of class fit_result with individual basis set components shown.
@@ -1459,6 +1431,10 @@ All functions svs_1h_brain_batch_analysis()
Batch interface to the standard SVS 1H brain analysis pipeline.
+
+
+ Perform a t-test on spectral data points.
@@ -1518,8 +1494,7 @@ All functions
- Fade a spectrum to zero by frequency domain multiplication with a tanh
-function. Note this operation distorts data points at the end of the FID.
Fade a spectrum to zero by frequency domain multiplication with a tanh function. Note this operation distorts data points at the end of the FID.
@@ -1549,7 +1524,7 @@ All functions
diff --git a/docs/reference/int_spec.html b/docs/reference/int_spec.html
index c7060fe7..783325a8 100644
--- a/docs/reference/int_spec.html
+++ b/docs/reference/int_spec.html
@@ -1,5 +1,5 @@
-Integrate a spectral region. — int_spec • Spectroscopy Analysis Tools (spant) Integrate a spectral region. — int_spec • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -118,7 +118,7 @@ Value
diff --git a/docs/reference/interleave_dyns.html b/docs/reference/interleave_dyns.html
index effe5543..441eff27 100644
--- a/docs/reference/interleave_dyns.html
+++ b/docs/reference/interleave_dyns.html
@@ -1,5 +1,5 @@
-Interleave the first and second half of a dynamic series. — interleave_dyns • Spectroscopy Analysis Tools (spant) Interleave the first and second half of a dynamic series. — interleave_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/inv_even_dyns.html b/docs/reference/inv_even_dyns.html
index 9f9d4fff..dcb781dc 100644
--- a/docs/reference/inv_even_dyns.html
+++ b/docs/reference/inv_even_dyns.html
@@ -1,5 +1,5 @@
-Invert even numbered dynamic scans starting from 1 (2,4,6...). — inv_even_dyns • Spectroscopy Analysis Tools (spant) Invert even numbered dynamic scans starting from 1 (2,4,6...). — inv_even_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/inv_odd_dyns.html b/docs/reference/inv_odd_dyns.html
index 26212e2b..78d64660 100644
--- a/docs/reference/inv_odd_dyns.html
+++ b/docs/reference/inv_odd_dyns.html
@@ -1,5 +1,5 @@
-Invert odd numbered dynamic scans starting from 1 (1,3,5...). — inv_odd_dyns • Spectroscopy Analysis Tools (spant) Invert odd numbered dynamic scans starting from 1 (1,3,5...). — inv_odd_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/is.def.html b/docs/reference/is.def.html
index f196ffd0..a67b9eba 100644
--- a/docs/reference/is.def.html
+++ b/docs/reference/is.def.html
@@ -1,5 +1,5 @@
-Check if an object is defined, which is the same as being not NULL. — is.def • Spectroscopy Analysis Tools (spant) Check if an object is defined, which is the same as being not NULL. — is.def • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/is_fd.html b/docs/reference/is_fd.html
index 3b0ca165..18a193aa 100644
--- a/docs/reference/is_fd.html
+++ b/docs/reference/is_fd.html
@@ -1,7 +1,5 @@
-Check if the chemical shift dimension of an MRS data object is in the
-frequency domain. — is_fd • Spectroscopy Analysis Tools (spant) Check if the chemical shift dimension of an MRS data object is in the frequency domain. — is_fd • Spectroscopy Analysis Tools (spant) Transform 2D MRSI data from k-space to image space in the x-y direction. — kspace2img_xy • Spectroscopy Analysis Tools (spant) Transform 2D MRSI data from k-space to image space in the x-y direction. — kspace2img_xy • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/l2_reg.html b/docs/reference/l2_reg.html
index 3d781d80..21aa9849 100644
--- a/docs/reference/l2_reg.html
+++ b/docs/reference/l2_reg.html
@@ -1,5 +1,5 @@
-Perform l2 regularisation artefact suppression. — l2_reg • Spectroscopy Analysis Tools (spant) Perform l2 regularisation artefact suppression. — l2_reg • Spectroscopy Analysis Tools (spant) Apply line-broadening (apodisation) to MRS data or basis object. — lb • Spectroscopy Analysis Tools (spant) Apply line-broadening (apodisation) to MRS data or basis object. — lb • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -123,7 +123,7 @@ Value
diff --git a/docs/reference/lofdc.html b/docs/reference/lofdc.html
index 5419b1ec..31347a25 100644
--- a/docs/reference/lofdc.html
+++ b/docs/reference/lofdc.html
@@ -1,5 +1,5 @@
-Correct linear frequency drift. — lofdc • Spectroscopy Analysis Tools (spant) Correct linear frequency drift. — lofdc • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -138,7 +138,7 @@ Value
diff --git a/docs/reference/lw2alpha.html b/docs/reference/lw2alpha.html
index b83db682..25da229b 100644
--- a/docs/reference/lw2alpha.html
+++ b/docs/reference/lw2alpha.html
@@ -1,7 +1,5 @@
-Covert a linewidth in Hz to an equivalent alpha value in the time-domain ie:
-x * exp(-t * alpha). — lw2alpha • Spectroscopy Analysis Tools (spant) Covert a linewidth in Hz to an equivalent alpha value in the time-domain ie: x * exp(-t * alpha). — lw2alpha • Spectroscopy Analysis Tools (spant) Covert a linewidth in Hz to an equivalent beta value in the time-domain ie:
-x * exp(-t * t * beta). — lw2beta • Spectroscopy Analysis Tools (spant) Covert a linewidth in Hz to an equivalent beta value in the time-domain ie: x * exp(-t * t * beta). — lw2beta • Spectroscopy Analysis Tools (spant) Make a basis-set object from a directory containing LCModel formatted RAW
-files. — make_basis_from_raw • Spectroscopy Analysis Tools (spant) Make a basis-set object from a directory containing LCModel formatted RAW files. — make_basis_from_raw • Spectroscopy Analysis Tools (spant) Mask an MRS dataset in the dynamic dimension. — mask_dyns • Spectroscopy Analysis Tools (spant) Mask an MRS dataset in the dynamic dimension. — mask_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/mask_fit_res.html b/docs/reference/mask_fit_res.html
index 97baaa3f..ebd91a99 100644
--- a/docs/reference/mask_fit_res.html
+++ b/docs/reference/mask_fit_res.html
@@ -1,5 +1,5 @@
-Mask fit result spectra depending on a vector of bool values. — mask_fit_res • Spectroscopy Analysis Tools (spant) Mask fit result spectra depending on a vector of bool values. — mask_fit_res • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -116,7 +116,7 @@ Value
diff --git a/docs/reference/mask_xy.html b/docs/reference/mask_xy.html
index 11bb577c..b0d38619 100644
--- a/docs/reference/mask_xy.html
+++ b/docs/reference/mask_xy.html
@@ -1,5 +1,5 @@
-Mask an MRSI dataset in the x-y direction — mask_xy • Spectroscopy Analysis Tools (spant) Mask an MRSI dataset in the x-y direction — mask_xy • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/mask_xy_corners.html b/docs/reference/mask_xy_corners.html
index 09b16cd2..2d13839d 100644
--- a/docs/reference/mask_xy_corners.html
+++ b/docs/reference/mask_xy_corners.html
@@ -1,5 +1,5 @@
-Mask the four corners of an MRSI dataset in the x-y plane. — mask_xy_corners • Spectroscopy Analysis Tools (spant) Mask the four corners of an MRSI dataset in the x-y plane. — mask_xy_corners • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/mask_xy_ellipse.html b/docs/reference/mask_xy_ellipse.html
index 1d8b02e4..e2e749ef 100644
--- a/docs/reference/mask_xy_ellipse.html
+++ b/docs/reference/mask_xy_ellipse.html
@@ -1,7 +1,5 @@
-Mask the voxels outside an elliptical region spanning the MRSI dataset in the
-x-y plane. — mask_xy_ellipse • Spectroscopy Analysis Tools (spant) Mask the voxels outside an elliptical region spanning the MRSI dataset in the x-y plane. — mask_xy_ellipse • Spectroscopy Analysis Tools (spant) Mask a 2D MRSI dataset in the x-y dimension. — mask_xy_mat • Spectroscopy Analysis Tools (spant) Mask a 2D MRSI dataset in the x-y dimension. — mask_xy_mat • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Value
diff --git a/docs/reference/mat2mrs_data.html b/docs/reference/mat2mrs_data.html
index 2e2895f3..ae55665f 100644
--- a/docs/reference/mat2mrs_data.html
+++ b/docs/reference/mat2mrs_data.html
@@ -1,7 +1,5 @@
-Convert a matrix (with spectral points in the column dimension and dynamics
-in the row dimensions) into a mrs_data object. — mat2mrs_data • Spectroscopy Analysis Tools (spant) Convert a matrix (with spectral points in the column dimension and dynamics in the row dimensions) into a mrs_data object. — mat2mrs_data • Spectroscopy Analysis Tools (spant) Matrix exponential function taken from complexplus package to reduce the
-number of spant dependencies. — matexp • Spectroscopy Analysis Tools (spant) Matrix exponential function taken from complexplus package to reduce the number of spant dependencies. — matexp • Spectroscopy Analysis Tools (spant) Apply the max operator to an MRS dataset. — max_mrs • Spectroscopy Analysis Tools (spant) Apply the max operator to an MRS dataset. — max_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/max_mrs_interp.html b/docs/reference/max_mrs_interp.html
index e4474764..52e63f3e 100644
--- a/docs/reference/max_mrs_interp.html
+++ b/docs/reference/max_mrs_interp.html
@@ -1,5 +1,5 @@
-Apply the max operator to an interpolated MRS dataset. — max_mrs_interp • Spectroscopy Analysis Tools (spant) Apply the max operator to an interpolated MRS dataset. — max_mrs_interp • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/mean.list.html b/docs/reference/mean.list.html
index b8eb3463..048306fd 100644
--- a/docs/reference/mean.list.html
+++ b/docs/reference/mean.list.html
@@ -1,5 +1,5 @@
-Calculate the mean spectrum from an mrs_data object. — mean.list • Spectroscopy Analysis Tools (spant) Calculate the mean spectrum from an mrs_data object. — mean.list • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/mean.mrs_data.html b/docs/reference/mean.mrs_data.html
index 5531a28d..79515014 100644
--- a/docs/reference/mean.mrs_data.html
+++ b/docs/reference/mean.mrs_data.html
@@ -1,5 +1,5 @@
-Calculate the mean spectrum from an mrs_data object. — mean.mrs_data • Spectroscopy Analysis Tools (spant) Calculate the mean spectrum from an mrs_data object. — mean.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/mean_dyn_blocks.html b/docs/reference/mean_dyn_blocks.html
index 10467098..4c042448 100644
--- a/docs/reference/mean_dyn_blocks.html
+++ b/docs/reference/mean_dyn_blocks.html
@@ -1,5 +1,5 @@
-Calculate the mean of adjacent dynamic scans. — mean_dyn_blocks • Spectroscopy Analysis Tools (spant) Calculate the mean of adjacent dynamic scans. — mean_dyn_blocks • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/mean_dyn_pairs.html b/docs/reference/mean_dyn_pairs.html
index 63e909ea..1a241126 100644
--- a/docs/reference/mean_dyn_pairs.html
+++ b/docs/reference/mean_dyn_pairs.html
@@ -1,5 +1,5 @@
-Calculate the pairwise means across a dynamic data set. — mean_dyn_pairs • Spectroscopy Analysis Tools (spant) Calculate the pairwise means across a dynamic data set. — mean_dyn_pairs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/mean_dyns.html b/docs/reference/mean_dyns.html
index 73fdbfa7..0daa27df 100644
--- a/docs/reference/mean_dyns.html
+++ b/docs/reference/mean_dyns.html
@@ -1,5 +1,5 @@
-Calculate the mean dynamic data. — mean_dyns • Spectroscopy Analysis Tools (spant) Calculate the mean dynamic data. — mean_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/mean_mrs_list.html b/docs/reference/mean_mrs_list.html
index 808b6c50..10d842c0 100644
--- a/docs/reference/mean_mrs_list.html
+++ b/docs/reference/mean_mrs_list.html
@@ -1,5 +1,5 @@
-Return the mean of a list of mrs_data objects. — mean_mrs_list • Spectroscopy Analysis Tools (spant) Return the mean of a list of mrs_data objects. — mean_mrs_list • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/mean_vec_blocks.html b/docs/reference/mean_vec_blocks.html
index 8fc92eaa..dd78b122 100644
--- a/docs/reference/mean_vec_blocks.html
+++ b/docs/reference/mean_vec_blocks.html
@@ -1,5 +1,5 @@
-Calculate the mean of adjacent blocks in a vector. — mean_vec_blocks • Spectroscopy Analysis Tools (spant) Calculate the mean of adjacent blocks in a vector. — mean_vec_blocks • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/median_dyns.html b/docs/reference/median_dyns.html
index 1039d4b5..9a085b10 100644
--- a/docs/reference/median_dyns.html
+++ b/docs/reference/median_dyns.html
@@ -1,5 +1,5 @@
-Calculate the median dynamic data. — median_dyns • Spectroscopy Analysis Tools (spant) Calculate the median dynamic data. — median_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/mod_td.html b/docs/reference/mod_td.html
index 76ad0a40..141ef09e 100644
--- a/docs/reference/mod_td.html
+++ b/docs/reference/mod_td.html
@@ -1,5 +1,5 @@
-Apply the Modulus operator to the time-domain MRS signal. — mod_td • Spectroscopy Analysis Tools (spant) Apply the Modulus operator to the time-domain MRS signal. — mod_td • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/mrs_data2basis.html b/docs/reference/mrs_data2basis.html
index 62f7d749..11797b91 100644
--- a/docs/reference/mrs_data2basis.html
+++ b/docs/reference/mrs_data2basis.html
@@ -1,7 +1,5 @@
-Convert an mrs_data object to basis object - where basis signals are spread
-across the dynamic dimension in the MRS data. — mrs_data2basis • Spectroscopy Analysis Tools (spant) Convert an mrs_data object to basis object - where basis signals are spread across the dynamic dimension in the MRS data. — mrs_data2basis • Spectroscopy Analysis Tools (spant) Create a BIDS file structure from a vector of MRS data paths or list of mrs_data objects. — mrs_data2bids • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Create a BIDS file structure from a vector of MRS data paths or list of mrs_data objects.
+ Source: R/fmrs.R
+ mrs_data2bids.Rd
+
+
+
+ Create a BIDS file structure from a vector of MRS data paths or list of
+mrs_data objects.
+
+
+
+ mrs_data2bids(
+ mrs_data,
+ output_dir,
+ suffix = NULL,
+ sub = NULL,
+ ses = NULL,
+ task = NULL,
+ acq = NULL,
+ nuc = NULL,
+ voi = NULL,
+ rec = NULL,
+ run = NULL,
+ echo = NULL,
+ inv = NULL,
+ skip_existing = TRUE
+)
+
+
+
+ Arguments
+ - mrs_data
+vector of MRS data paths or list of mrs_data objects.
- output_dir
+the base directory to create the BIDS structure.
- suffix
+optional vector of file suffixes. Default behaviour is to
+automatically determine these from the input data, however it is recommended
+that they are specified to allow more efficient skipping of existing data.
- sub
+optional vector of subject labels. If not specified, these will be
+automatically generated as a series of increasing zero-padded integer values
+corresponding to the mrs_data input indices.
- ses
+optional vector of session labels.
- task
+optional vector of task labels.
- acq
+optional vector of acquisition labels.
- nuc
+optional vector of nucleus labels.
- voi
+optional vector of volume of interest labels.
- rec
+optional vector of reconstruction labels.
- run
+optional vector of run indices.
- echo
+optional vector of echo time indices.
- inv
+optional vector of inversion indices.
- skip_existing
+skip any data files that have already been converted.
+Defaults to TRUE, set to FALSE to force an overwrite of any existing data
+files.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/mrs_data2mat.html b/docs/reference/mrs_data2mat.html
index cf5ff28c..9e47688a 100644
--- a/docs/reference/mrs_data2mat.html
+++ b/docs/reference/mrs_data2mat.html
@@ -1,7 +1,5 @@
-Convert mrs_data object to a matrix, with spectral points in the column
-dimension and dynamics in the row dimension. — mrs_data2mat • Spectroscopy Analysis Tools (spant) Convert mrs_data object to a matrix, with spectral points in the column dimension and dynamics in the row dimension. — mrs_data2mat • Spectroscopy Analysis Tools (spant) Convert mrs_data object to a matrix, with spectral points in the column dimension and dynamics in the row dimension. — mrs_data2spec_mat • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Convert mrs_data object to a matrix, with spectral points in the column dimension and dynamics in the row dimension.
+ Source: R/mrs_data_proc.R
+ mrs_data2spec_mat.Rd
+
+
+
+ Convert mrs_data object to a matrix, with spectral points in the column
+dimension and dynamics in the row dimension.
+
+
+
+ mrs_data2spec_mat(mrs_data, collapse = TRUE)
+
+
+
+ Arguments
+ - mrs_data
+MRS data object or list of MRS data objects.
- collapse
+collapse all other dimensions along the dynamic dimension, eg
+a 16x16 MRSI grid would be first collapsed across 256 dynamic scans.
+
+ Value
+
+
+MRS data matrix.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/mrs_data2vec.html b/docs/reference/mrs_data2vec.html
index fb172d68..a1fd654d 100644
--- a/docs/reference/mrs_data2vec.html
+++ b/docs/reference/mrs_data2vec.html
@@ -1,5 +1,5 @@
-Convert mrs_data object to a vector. — mrs_data2vec • Spectroscopy Analysis Tools (spant) Convert mrs_data object to a vector. — mrs_data2vec • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -126,7 +126,7 @@ Value
diff --git a/docs/reference/mvfftshift.html b/docs/reference/mvfftshift.html
index 92b0841b..976b3410 100644
--- a/docs/reference/mvfftshift.html
+++ b/docs/reference/mvfftshift.html
@@ -1,7 +1,5 @@
-Perform a fftshift on a matrix, with each column replaced by its shifted
-result. — mvfftshift • Spectroscopy Analysis Tools (spant) Perform a fftshift on a matrix, with each column replaced by its shifted result. — mvfftshift • Spectroscopy Analysis Tools (spant) Perform an ifftshift on a matrix, with each column replaced by its shifted
-result. — mvifftshift • Spectroscopy Analysis Tools (spant) Perform an ifftshift on a matrix, with each column replaced by its shifted result. — mvifftshift • Spectroscopy Analysis Tools (spant) Print fit coordinates from a single index. — n2coord • Spectroscopy Analysis Tools (spant) Print fit coordinates from a single index. — n2coord • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/nifti_flip_lr.html b/docs/reference/nifti_flip_lr.html
index 730abe3c..19860b3c 100644
--- a/docs/reference/nifti_flip_lr.html
+++ b/docs/reference/nifti_flip_lr.html
@@ -1,9 +1,5 @@
-Flip the x data dimension order of a nifti image. This corresponds to
-flipping MRI data in the left-right direction, assuming the data in save in
-neurological format (can check with fslorient program). — nifti_flip_lr • Spectroscopy Analysis Tools (spant) Flip the x data dimension order of a nifti image. This corresponds to flipping MRI data in the left-right direction, assuming the data in save in neurological format (can check with fslorient program). — nifti_flip_lr • Spectroscopy Analysis Tools (spant) Export a one-page pdf of a single fit result — one_page_pdf • Spectroscopy Analysis Tools (spant) Export a one-page pdf of a single fit result — one_page_pdf • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -108,7 +108,7 @@ Arguments
diff --git a/docs/reference/ortho3.html b/docs/reference/ortho3.html
index 13ade97d..5d7dd2fd 100644
--- a/docs/reference/ortho3.html
+++ b/docs/reference/ortho3.html
@@ -1,5 +1,5 @@
-Display an orthographic projection plot of a nifti object. — ortho3 • Spectroscopy Analysis Tools (spant) Display an orthographic projection plot of a nifti object. — ortho3 • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -172,7 +172,7 @@ Arguments
diff --git a/docs/reference/ortho3_inter.html b/docs/reference/ortho3_inter.html
index 090cc5e5..15948899 100644
--- a/docs/reference/ortho3_inter.html
+++ b/docs/reference/ortho3_inter.html
@@ -1,5 +1,5 @@
-Display an interactive orthographic projection plot of a nifti object. — ortho3_inter • Spectroscopy Analysis Tools (spant) Display an interactive orthographic projection plot of a nifti object. — ortho3_inter • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -132,7 +132,7 @@ Arguments
diff --git a/docs/reference/peak_info.html b/docs/reference/peak_info.html
index 09058bd8..41c8ffaf 100644
--- a/docs/reference/peak_info.html
+++ b/docs/reference/peak_info.html
@@ -1,7 +1,5 @@
-Search for the highest peak in a spectral region and return the frequency,
-height and FWHM. — peak_info • Spectroscopy Analysis Tools (spant) Search for the highest peak in a spectral region and return the frequency, height and FWHM. — peak_info • Spectroscopy Analysis Tools (spant) Papoulis-Gerchberg (PG) algorithm method for k-space extrapolation. — pg_extrap_xy • Spectroscopy Analysis Tools (spant) Papoulis-Gerchberg (PG) algorithm method for k-space extrapolation. — pg_extrap_xy • Spectroscopy Analysis Tools (spant) Apply phasing parameters to MRS data. — phase • Spectroscopy Analysis Tools (spant) Apply phasing parameters to MRS data. — phase • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/phase_ref_1h_brain.html b/docs/reference/phase_ref_1h_brain.html
new file mode 100644
index 00000000..8707a74a
--- /dev/null
+++ b/docs/reference/phase_ref_1h_brain.html
@@ -0,0 +1,131 @@
+
+Corrected zero order phase and chemical shift offset in 1H MRS data from the brain. — phase_ref_1h_brain • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Corrected zero order phase and chemical shift offset in 1H MRS data from the brain.
+ Source: R/rats.R
+ phase_ref_1h_brain.Rd
+
+
+
+ Corrected zero order phase and chemical shift offset in 1H MRS data from the
+brain.
+
+
+
+ phase_ref_1h_brain(mrs_data, mean_ref = FALSE, ret_corr_only = TRUE)
+
+
+
+ Arguments
+ - mrs_data
+MRS data to be corrected.
- mean_ref
+apply the phase and offset of the mean spectrum to all
+others. Default is FALSE.
- ret_corr_only
+return the corrected data only.
+
+ Value
+
+
+corrected MRS data.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/plot.fit_result.html b/docs/reference/plot.fit_result.html
index e54d3bc1..836a53ee 100644
--- a/docs/reference/plot.fit_result.html
+++ b/docs/reference/plot.fit_result.html
@@ -1,5 +1,5 @@
-Plot the fitting results of an object of class fit_result. — plot.fit_result • Spectroscopy Analysis Tools (spant) Plot the fitting results of an object of class fit_result. — plot.fit_result • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -207,7 +207,7 @@ Arguments
diff --git a/docs/reference/plot.mrs_data.html b/docs/reference/plot.mrs_data.html
index fabcc35b..bb2ec651 100644
--- a/docs/reference/plot.mrs_data.html
+++ b/docs/reference/plot.mrs_data.html
@@ -1,5 +1,5 @@
-Plotting method for objects of class mrs_data. — plot.mrs_data • Spectroscopy Analysis Tools (spant) Plotting method for objects of class mrs_data. — plot.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -287,7 +287,7 @@ Arguments
diff --git a/docs/reference/plot_bc.html b/docs/reference/plot_bc.html
index 4f8309b4..b48142cc 100644
--- a/docs/reference/plot_bc.html
+++ b/docs/reference/plot_bc.html
@@ -1,5 +1,5 @@
-Convenience function to plot a baseline estimate with the original data. — plot_bc • Spectroscopy Analysis Tools (spant) Convenience function to plot a baseline estimate with the original data. — plot_bc • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -108,7 +108,7 @@ Arguments
diff --git a/docs/reference/plot_reg.html b/docs/reference/plot_reg.html
index ae1acbe7..2addb2f6 100644
--- a/docs/reference/plot_reg.html
+++ b/docs/reference/plot_reg.html
@@ -1,5 +1,5 @@
-Plot regressors as an image. — plot_reg • Spectroscopy Analysis Tools (spant) Plot regressors as an image. — plot_reg • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/plot_slice_fit.html b/docs/reference/plot_slice_fit.html
index fbc7b560..57f1af8a 100644
--- a/docs/reference/plot_slice_fit.html
+++ b/docs/reference/plot_slice_fit.html
@@ -1,5 +1,5 @@
-Plot a 2D slice from an MRSI fit result object. — plot_slice_fit • Spectroscopy Analysis Tools (spant) Plot a 2D slice from an MRSI fit result object. — plot_slice_fit • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -129,7 +129,7 @@ Arguments
diff --git a/docs/reference/plot_slice_fit_inter.html b/docs/reference/plot_slice_fit_inter.html
index 4eed104a..da105a7d 100644
--- a/docs/reference/plot_slice_fit_inter.html
+++ b/docs/reference/plot_slice_fit_inter.html
@@ -1,5 +1,5 @@
-Plot a 2D slice from an MRSI fit result object. — plot_slice_fit_inter • Spectroscopy Analysis Tools (spant) Plot a 2D slice from an MRSI fit result object. — plot_slice_fit_inter • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -134,7 +134,7 @@ Arguments
diff --git a/docs/reference/plot_slice_map.html b/docs/reference/plot_slice_map.html
index 553e9ac8..ffb2a134 100644
--- a/docs/reference/plot_slice_map.html
+++ b/docs/reference/plot_slice_map.html
@@ -1,5 +1,5 @@
-Plot a slice from a 7 dimensional array. — plot_slice_map • Spectroscopy Analysis Tools (spant) Plot a slice from a 7 dimensional array. — plot_slice_map • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -153,7 +153,7 @@ Arguments
diff --git a/docs/reference/plot_slice_map_inter.html b/docs/reference/plot_slice_map_inter.html
index 40d33b42..90968f66 100644
--- a/docs/reference/plot_slice_map_inter.html
+++ b/docs/reference/plot_slice_map_inter.html
@@ -1,7 +1,5 @@
-Plot an interactive slice map from a data array where voxels can be selected
-to display a corresponding spectrum. — plot_slice_map_inter • Spectroscopy Analysis Tools (spant) Plot an interactive slice map from a data array where voxels can be selected to display a corresponding spectrum. — plot_slice_map_inter • Spectroscopy Analysis Tools (spant) Plot the spectral standard deviation. — plot_spec_sd • Spectroscopy Analysis Tools (spant) Plot the spectral standard deviation. — plot_spec_sd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Arguments
diff --git a/docs/reference/plot_voi_overlay.html b/docs/reference/plot_voi_overlay.html
index 9a782e88..bbbbf35e 100644
--- a/docs/reference/plot_voi_overlay.html
+++ b/docs/reference/plot_voi_overlay.html
@@ -1,5 +1,5 @@
-Plot a volume as an image overlay. — plot_voi_overlay • Spectroscopy Analysis Tools (spant) Plot a volume as an image overlay. — plot_voi_overlay • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -116,7 +116,7 @@ Arguments
diff --git a/docs/reference/plot_voi_overlay_seg.html b/docs/reference/plot_voi_overlay_seg.html
index 3d4e74ff..0e800ff2 100644
--- a/docs/reference/plot_voi_overlay_seg.html
+++ b/docs/reference/plot_voi_overlay_seg.html
@@ -1,5 +1,5 @@
-Plot a volume as an overlay on a segmented brain volume. — plot_voi_overlay_seg • Spectroscopy Analysis Tools (spant) Plot a volume as an overlay on a segmented brain volume. — plot_voi_overlay_seg • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Arguments
diff --git a/docs/reference/ppm.html b/docs/reference/ppm.html
index c352327a..ee4696e2 100644
--- a/docs/reference/ppm.html
+++ b/docs/reference/ppm.html
@@ -1,5 +1,5 @@
-Return the ppm scale of an MRS dataset or fit result. — ppm • Spectroscopy Analysis Tools (spant) Return the ppm scale of an MRS dataset or fit result. — ppm • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -132,7 +132,7 @@ Value
diff --git a/docs/reference/precomp.html b/docs/reference/precomp.html
index 822d7336..df3d2c6c 100644
--- a/docs/reference/precomp.html
+++ b/docs/reference/precomp.html
@@ -1,7 +1,5 @@
-Save function results to file and load on subsequent calls to avoid repeat
-computation. — precomp • Spectroscopy Analysis Tools (spant) Save function results to file and load on subsequent calls to avoid repeat computation. — precomp • Spectroscopy Analysis Tools (spant) Preprocess and perform quality assessment of a single SVS data set. — preproc_svs • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Preprocess and perform quality assessment of a single SVS data set.
+ Source: R/fmrs.R
+ preproc_svs.Rd
+
+
+
+ Preprocess and perform quality assessment of a single SVS data set.
+
+
+
+ preproc_svs(path, label = NULL, output_dir = NULL, ref_inds = NULL)
+
+
+
+ Arguments
+ - path
+path to the fMRS data file or IMA directory.
- label
+a label to describe the data set.
- output_dir
+output directory.
- ref_inds
+a vector of 1-based indices for any water reference dynamic
+scans.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/preproc_svs_dataset.html b/docs/reference/preproc_svs_dataset.html
new file mode 100644
index 00000000..07c3a29b
--- /dev/null
+++ b/docs/reference/preproc_svs_dataset.html
@@ -0,0 +1,148 @@
+
+Preprocess and perform quality assessment of one or more SVS data sets. — preproc_svs_dataset • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Preprocess and perform quality assessment of one or more SVS data sets.
+ Source: R/fmrs.R
+ preproc_svs_dataset.Rd
+
+
+
+ Preprocess and perform quality assessment of one or more SVS data sets.
+
+
+
+ preproc_svs_dataset(
+ paths,
+ labels = NULL,
+ output_dir = "spant_analysis",
+ exclude_labels = NULL,
+ overwrite = FALSE,
+ ref_inds = NULL,
+ return_results = FALSE
+)
+
+
+
+ Arguments
+ - paths
+paths to the fMRS data file or IMA directory.
- labels
+labels to describe each data set.
- output_dir
+output directory.
- exclude_labels
+vector of labels of scans to exclude, eg poor quality
+data.
- overwrite
+overwrite saved results, defaults to FALSE.
- ref_inds
+a vector of 1-based indices for any water reference dynamic
+scans.
- return_results
+function will return key outputs, defaults to FALSE.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/print.fit_result.html b/docs/reference/print.fit_result.html
index 297f28dc..5f434e57 100644
--- a/docs/reference/print.fit_result.html
+++ b/docs/reference/print.fit_result.html
@@ -1,5 +1,5 @@
-Print a summary of an object of class fit_result. — print.fit_result • Spectroscopy Analysis Tools (spant) Print a summary of an object of class fit_result. — print.fit_result • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -105,7 +105,7 @@ Arguments
diff --git a/docs/reference/print.mrs_data.html b/docs/reference/print.mrs_data.html
index 51199017..e1561eb2 100644
--- a/docs/reference/print.mrs_data.html
+++ b/docs/reference/print.mrs_data.html
@@ -1,5 +1,5 @@
-Print a summary of mrs_data parameters. — print.mrs_data • Spectroscopy Analysis Tools (spant) Print a summary of mrs_data parameters. — print.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -109,7 +109,7 @@ Arguments
diff --git a/docs/reference/qn_states.html b/docs/reference/qn_states.html
index 0f42f2f9..d7aa6715 100644
--- a/docs/reference/qn_states.html
+++ b/docs/reference/qn_states.html
@@ -1,5 +1,5 @@
-Get the quantum coherence matrix for a spin system. — qn_states • Spectroscopy Analysis Tools (spant) Get the quantum coherence matrix for a spin system. — qn_states • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/rats.html b/docs/reference/rats.html
index 5a39a396..93585e08 100644
--- a/docs/reference/rats.html
+++ b/docs/reference/rats.html
@@ -1,5 +1,5 @@
-Robust Alignment to a Target Spectrum (RATS). — rats • Spectroscopy Analysis Tools (spant) Robust Alignment to a Target Spectrum (RATS). — rats • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -207,7 +207,7 @@ Value
diff --git a/docs/reference/re_weighting.html b/docs/reference/re_weighting.html
index d21caf21..8b0b070a 100644
--- a/docs/reference/re_weighting.html
+++ b/docs/reference/re_weighting.html
@@ -1,5 +1,5 @@
-Apply a weighting to the FID to enhance spectral resolution. — re_weighting • Spectroscopy Analysis Tools (spant) Apply a weighting to the FID to enhance spectral resolution. — re_weighting • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/read_basis.html b/docs/reference/read_basis.html
index da9b94af..eb6f8557 100644
--- a/docs/reference/read_basis.html
+++ b/docs/reference/read_basis.html
@@ -1,5 +1,5 @@
-Read a basis file in LCModel .basis format. — read_basis • Spectroscopy Analysis Tools (spant) Read a basis file in LCModel .basis format. — read_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/read_ima_coil_dir.html b/docs/reference/read_ima_coil_dir.html
index 28c02de0..4f073cd8 100644
--- a/docs/reference/read_ima_coil_dir.html
+++ b/docs/reference/read_ima_coil_dir.html
@@ -1,9 +1,5 @@
-Read a directory containing Siemens MRS IMA files and combine along the coil
-dimension. Note that the coil ID is inferred from the sorted file name and
-should be checked when consistency is required between two directories. — read_ima_coil_dir • Spectroscopy Analysis Tools (spant) Read a directory containing Siemens MRS IMA files and combine along the coil dimension. Note that the coil ID is inferred from the sorted file name and should be checked when consistency is required between two directories. — read_ima_coil_dir • Spectroscopy Analysis Tools (spant) Read a directory containing Siemens MRS IMA files and combine along the
-dynamic dimension. Note that the coil ID is inferred from the sorted file
-name and should be checked when consistency is required. — read_ima_dyn_dir • Spectroscopy Analysis Tools (spant) Read a directory containing Siemens MRS IMA files and combine along the dynamic dimension. Note that the coil ID is inferred from the sorted file name and should be checked when consistency is required. — read_ima_dyn_dir • Spectroscopy Analysis Tools (spant) Read an LCModel formatted coord file containing fit information. — read_lcm_coord • Spectroscopy Analysis Tools (spant) Read an LCModel formatted coord file containing fit information. — read_lcm_coord • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -107,7 +107,7 @@ Value
diff --git a/docs/reference/read_mrs.html b/docs/reference/read_mrs.html
index 3ac2a36b..2cf36b20 100644
--- a/docs/reference/read_mrs.html
+++ b/docs/reference/read_mrs.html
@@ -1,5 +1,5 @@
-Read MRS data from a file. — read_mrs • Spectroscopy Analysis Tools (spant) Read MRS data from a file. — read_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -88,7 +88,8 @@ Read MRS data from a file.
full_fid = FALSE,
omit_svs_ref_scans = TRUE,
verbose = FALSE,
- extra = NULL
+ extra = NULL,
+ fid_filt_dist = NULL
)
@@ -140,6 +141,13 @@ Arguments
an optional data frame to provide additional variables for use
in subsequent analysis steps, eg id or grouping variables.
fid_filt_dist
+indicate if the data has a distorted FID due to a
+brick-wall filter being used to downsample the data. Default is to auto
+detect this from the data, but TRUE or FALSE options can be given to override
+detection.
Value
@@ -183,7 +191,7 @@ Examples
diff --git a/docs/reference/read_mrs_tqn.html b/docs/reference/read_mrs_tqn.html
index 5766362f..84bdaf3a 100644
--- a/docs/reference/read_mrs_tqn.html
+++ b/docs/reference/read_mrs_tqn.html
@@ -1,5 +1,5 @@
-Read MRS data using the TARQUIN software package. — read_mrs_tqn • Spectroscopy Analysis Tools (spant) Read MRS data using the TARQUIN software package. — read_mrs_tqn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -131,7 +131,7 @@ Examples
diff --git a/docs/reference/read_pulse_ascii.html b/docs/reference/read_pulse_ascii.html
index c9e0d43c..ab11c9cc 100644
--- a/docs/reference/read_pulse_ascii.html
+++ b/docs/reference/read_pulse_ascii.html
@@ -1,5 +1,5 @@
-Read an ASCII formatted pulse file. — read_pulse_ascii • Spectroscopy Analysis Tools (spant) Read an ASCII formatted pulse file. — read_pulse_ascii • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/read_pulse_bruker.html b/docs/reference/read_pulse_bruker.html
index c92bf76a..dbe9073b 100644
--- a/docs/reference/read_pulse_bruker.html
+++ b/docs/reference/read_pulse_bruker.html
@@ -1,5 +1,5 @@
-Read a Bruker formatted pulse file — read_pulse_bruker • Spectroscopy Analysis Tools (spant) Read a Bruker formatted pulse file — read_pulse_bruker • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/read_pulse_pta.html b/docs/reference/read_pulse_pta.html
index 72e1b6d4..a0fac3c3 100644
--- a/docs/reference/read_pulse_pta.html
+++ b/docs/reference/read_pulse_pta.html
@@ -1,5 +1,5 @@
-Read a .pta formatted pulse file compatible with Siemens PulseTool. — read_pulse_pta • Spectroscopy Analysis Tools (spant) Read a .pta formatted pulse file compatible with Siemens PulseTool. — read_pulse_pta • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/read_siemens_txt_hdr.html b/docs/reference/read_siemens_txt_hdr.html
index 23fb8c70..3a17d87c 100644
--- a/docs/reference/read_siemens_txt_hdr.html
+++ b/docs/reference/read_siemens_txt_hdr.html
@@ -1,5 +1,5 @@
-Read the text format header found in Siemens IMA and TWIX data files. — read_siemens_txt_hdr • Spectroscopy Analysis Tools (spant) Read the text format header found in Siemens IMA and TWIX data files. — read_siemens_txt_hdr • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -78,7 +78,7 @@ Read the text format header found in Siemens IMA and TWIX data files.
- read_siemens_txt_hdr(input, version = "vd", verbose, offset = 0)
+ read_siemens_txt_hdr(input, version = "vd", verbose = FALSE, offset = 0)
@@ -118,7 +118,7 @@ Value
diff --git a/docs/reference/read_tqn_fit.html b/docs/reference/read_tqn_fit.html
index 4da6c25e..a1630420 100644
--- a/docs/reference/read_tqn_fit.html
+++ b/docs/reference/read_tqn_fit.html
@@ -1,5 +1,5 @@
-Reader for csv fit results generated by TARQUIN. — read_tqn_fit • Spectroscopy Analysis Tools (spant) Reader for csv fit results generated by TARQUIN. — read_tqn_fit • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -113,7 +113,7 @@ Examples
diff --git a/docs/reference/read_tqn_result.html b/docs/reference/read_tqn_result.html
index 36659714..68a3e98c 100644
--- a/docs/reference/read_tqn_result.html
+++ b/docs/reference/read_tqn_result.html
@@ -1,5 +1,5 @@
-Reader for csv results generated by TARQUIN. — read_tqn_result • Spectroscopy Analysis Tools (spant) Reader for csv results generated by TARQUIN. — read_tqn_result • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -117,7 +117,7 @@ Examples
diff --git a/docs/reference/recon_imag.html b/docs/reference/recon_imag.html
index d2a72225..5bc3b1eb 100644
--- a/docs/reference/recon_imag.html
+++ b/docs/reference/recon_imag.html
@@ -1,7 +1,5 @@
-Reconstruct complex time-domain data from the real part of frequency-domain
-data. — recon_imag • Spectroscopy Analysis Tools (spant) Reconstruct complex time-domain data from the real part of frequency-domain data. — recon_imag • Spectroscopy Analysis Tools (spant) Reconstruct complex time-domain data from the real part of frequency-domain
-data. — recon_imag_vec • Spectroscopy Analysis Tools (spant) Reconstruct complex time-domain data from the real part of frequency-domain data. — recon_imag_vec • Spectroscopy Analysis Tools (spant) Reconstruct 2D MRSI data from a twix file loaded with read_mrs. — recon_twix_2d_mrsi • Spectroscopy Analysis Tools (spant) Reconstruct 2D MRSI data from a twix file loaded with read_mrs. — recon_twix_2d_mrsi • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/rectangular_mask.html b/docs/reference/rectangular_mask.html
index a2117283..6e469bc9 100644
--- a/docs/reference/rectangular_mask.html
+++ b/docs/reference/rectangular_mask.html
@@ -1,5 +1,5 @@
-Create a rectangular mask stored as a matrix of logical values. — rectangular_mask • Spectroscopy Analysis Tools (spant) Create a rectangular mask stored as a matrix of logical values. — rectangular_mask • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -130,7 +130,7 @@ Value
diff --git a/docs/reference/reexports.html b/docs/reference/reexports.html
index 694a75d1..a59e8379 100644
--- a/docs/reference/reexports.html
+++ b/docs/reference/reexports.html
@@ -1,5 +1,5 @@
-Objects exported from other packages — reexports • Spectroscopy Analysis Tools (spant) Objects exported from other packages — reexports • Spectroscopy Analysis Tools (spant)
Spectroscopy Analysis Tools (spant)
- 2.21.0
+ 2.22.0
@@ -103,7 +103,7 @@ Objects exported from other packages
diff --git a/docs/reference/rep_array_dim.html b/docs/reference/rep_array_dim.html
index b9c49b4a..48c0a5ed 100644
--- a/docs/reference/rep_array_dim.html
+++ b/docs/reference/rep_array_dim.html
@@ -1,5 +1,5 @@
-Repeat an array over a given dimension. — rep_array_dim • Spectroscopy Analysis Tools (spant) Repeat an array over a given dimension. — rep_array_dim • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/rep_dyn.html b/docs/reference/rep_dyn.html
index 6bbfb0ef..89a4bb9b 100644
--- a/docs/reference/rep_dyn.html
+++ b/docs/reference/rep_dyn.html
@@ -1,5 +1,5 @@
-Replicate a scan in the dynamic dimension. — rep_dyn • Spectroscopy Analysis Tools (spant) Replicate a scan in the dynamic dimension. — rep_dyn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/rep_mrs.html b/docs/reference/rep_mrs.html
index 67730b5c..becb8f00 100644
--- a/docs/reference/rep_mrs.html
+++ b/docs/reference/rep_mrs.html
@@ -1,5 +1,5 @@
-Replicate a scan over a given dimension. — rep_mrs • Spectroscopy Analysis Tools (spant) Replicate a scan over a given dimension. — rep_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -138,7 +138,7 @@ Value
diff --git a/docs/reference/resample_basis.html b/docs/reference/resample_basis.html
index b0f2ab17..c7a6222a 100644
--- a/docs/reference/resample_basis.html
+++ b/docs/reference/resample_basis.html
@@ -1,5 +1,5 @@
-Resample a basis-set to match a mrs_data acquisition. — resample_basis • Spectroscopy Analysis Tools (spant) Resample a basis-set to match a mrs_data acquisition. — resample_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -116,7 +116,7 @@ Value
diff --git a/docs/reference/resample_img.html b/docs/reference/resample_img.html
index f1e7beaf..b0cc8f71 100644
--- a/docs/reference/resample_img.html
+++ b/docs/reference/resample_img.html
@@ -1,5 +1,5 @@
-Resample an image to match a target image space. — resample_img • Spectroscopy Analysis Tools (spant) Resample an image to match a target image space. — resample_img • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/resample_voi.html b/docs/reference/resample_voi.html
index 8fbfa836..a29ab096 100644
--- a/docs/reference/resample_voi.html
+++ b/docs/reference/resample_voi.html
@@ -1,7 +1,5 @@
-Resample a VOI to match a target image space using nearest-neighbour
-interpolation. — resample_voi • Spectroscopy Analysis Tools (spant) Resample a VOI to match a target image space using nearest-neighbour interpolation. — resample_voi • Spectroscopy Analysis Tools (spant) Reslice a nifti object to match the orientation of mrs data. — reslice_to_mrs • Spectroscopy Analysis Tools (spant) Reslice a nifti object to match the orientation of mrs data. — reslice_to_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/reson_table2mrs_data.html b/docs/reference/reson_table2mrs_data.html
index d75579ee..c5a2167a 100644
--- a/docs/reference/reson_table2mrs_data.html
+++ b/docs/reference/reson_table2mrs_data.html
@@ -1,5 +1,5 @@
-Generate mrs_data from a table of single Lorentzian resonances. — reson_table2mrs_data • Spectroscopy Analysis Tools (spant) Generate mrs_data from a table of single Lorentzian resonances. — reson_table2mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -119,7 +119,7 @@ Value
diff --git a/docs/reference/rm_dyns.html b/docs/reference/rm_dyns.html
index 5d5ef692..573e1f51 100644
--- a/docs/reference/rm_dyns.html
+++ b/docs/reference/rm_dyns.html
@@ -1,5 +1,5 @@
-Remove a subset of dynamic scans. — rm_dyns • Spectroscopy Analysis Tools (spant) Remove a subset of dynamic scans. — rm_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/scale_amp_molal.html b/docs/reference/scale_amp_molal.html
index aaeee1f2..7acb8cb0 100644
--- a/docs/reference/scale_amp_molal.html
+++ b/docs/reference/scale_amp_molal.html
@@ -1,7 +1,5 @@
-Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water). — scale_amp_molal • Spectroscopy Analysis Tools (spant) Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / kg of tissue water). — scale_amp_molal • Spectroscopy Analysis Tools (spant)
Spectroscopy Analysis Tools (spant)
- 2.21.0
+ 2.22.0
@@ -76,8 +74,7 @@
- Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water).
+ Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / kg of tissue water).
Source: R/amp_scaling.R
scale_amp_molal.Rd
@@ -163,7 +160,7 @@ Value
diff --git a/docs/reference/scale_amp_molal_pvc.html b/docs/reference/scale_amp_molal_pvc.html
index 962d6afc..4d194abd 100644
--- a/docs/reference/scale_amp_molal_pvc.html
+++ b/docs/reference/scale_amp_molal_pvc.html
@@ -1,7 +1,5 @@
-Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water). — scale_amp_molal_pvc • Spectroscopy Analysis Tools (spant)
@@ -75,8 +73,7 @@
- Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water).
+ Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / kg of tissue water).
Source: R/amp_scaling.R
scale_amp_molal_pvc.Rd
@@ -141,7 +138,7 @@ Value
diff --git a/docs/reference/scale_amp_molar.html b/docs/reference/scale_amp_molar.html
index 02358d91..dc87a338 100644
--- a/docs/reference/scale_amp_molar.html
+++ b/docs/reference/scale_amp_molar.html
@@ -1,7 +1,5 @@
-Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / Litre of tissue). — scale_amp_molar • Spectroscopy Analysis Tools (spant) Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / Litre of tissue). — scale_amp_molar • Spectroscopy Analysis Tools (spant) Convert default LCM/TARQUIN concentration scaling to molal units with partial
-volume correction. — scale_amp_molar2molal_pvc • Spectroscopy Analysis Tools (spant) Convert default LCM/TARQUIN concentration scaling to molal units with partial volume correction. — scale_amp_molar2molal_pvc • Spectroscopy Analysis Tools (spant) Scale fitted amplitudes to a ratio of signal amplitude. — scale_amp_ratio • Spectroscopy Analysis Tools (spant) Scale fitted amplitudes to a ratio of signal amplitude. — scale_amp_ratio • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -116,7 +116,7 @@ Value
diff --git a/docs/reference/scale_amp_ratio_value.html b/docs/reference/scale_amp_ratio_value.html
index 2036837a..6af8ac51 100644
--- a/docs/reference/scale_amp_ratio_value.html
+++ b/docs/reference/scale_amp_ratio_value.html
@@ -1,5 +1,5 @@
-Scale fitted amplitudes to a ratio of signal amplitude. — scale_amp_ratio_value • Spectroscopy Analysis Tools (spant) Scale fitted amplitudes to a ratio of signal amplitude. — scale_amp_ratio_value • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/scale_amp_water_ratio.html b/docs/reference/scale_amp_water_ratio.html
index 5b25e884..35a76b00 100644
--- a/docs/reference/scale_amp_water_ratio.html
+++ b/docs/reference/scale_amp_water_ratio.html
@@ -1,5 +1,5 @@
-Scale metabolite amplitudes as a ratio to the unsuppressed water amplitude. — scale_amp_water_ratio • Spectroscopy Analysis Tools (spant) Scale metabolite amplitudes as a ratio to the unsuppressed water amplitude. — scale_amp_water_ratio • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/scale_basis_amp.html b/docs/reference/scale_basis_amp.html
index 9401c3f1..5a58b5e5 100644
--- a/docs/reference/scale_basis_amp.html
+++ b/docs/reference/scale_basis_amp.html
@@ -1,5 +1,5 @@
-Scale a basis object by a scalar. — scale_basis_amp • Spectroscopy Analysis Tools (spant) Scale a basis object by a scalar. — scale_basis_amp • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/scale_basis_from_singlet.html b/docs/reference/scale_basis_from_singlet.html
index 0d542bc8..c9a19e77 100644
--- a/docs/reference/scale_basis_from_singlet.html
+++ b/docs/reference/scale_basis_from_singlet.html
@@ -1,5 +1,5 @@
-Scale a basis-set to be consistent with spant assumptions for water scaling. — scale_basis_from_singlet • Spectroscopy Analysis Tools (spant) Scale a basis-set to be consistent with spant assumptions for water scaling. — scale_basis_from_singlet • Spectroscopy Analysis Tools (spant)
Spectroscopy Analysis Tools (spant)
- 2.21.0
+ 2.22.0
@@ -127,7 +127,7 @@ Value
diff --git a/docs/reference/scale_mrs_amp.html b/docs/reference/scale_mrs_amp.html
index b5501a0d..990f058a 100644
--- a/docs/reference/scale_mrs_amp.html
+++ b/docs/reference/scale_mrs_amp.html
@@ -1,5 +1,5 @@
-Scale an mrs_data object by a scalar or vector or amplitudes. — scale_mrs_amp • Spectroscopy Analysis Tools (spant) Scale an mrs_data object by a scalar or vector or amplitudes. — scale_mrs_amp • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/scale_spec.html b/docs/reference/scale_spec.html
index 4f6ea835..6b3ddba4 100644
--- a/docs/reference/scale_spec.html
+++ b/docs/reference/scale_spec.html
@@ -1,5 +1,5 @@
-Scale mrs_data to a spectral region. — scale_spec • Spectroscopy Analysis Tools (spant) Scale mrs_data to a spectral region. — scale_spec • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -141,7 +141,7 @@ Value
diff --git a/docs/reference/sd.html b/docs/reference/sd.html
index ea1eec9f..3ae4dfd4 100644
--- a/docs/reference/sd.html
+++ b/docs/reference/sd.html
@@ -1,5 +1,5 @@
-Calculate the standard deviation spectrum from an mrs_data object. — sd • Spectroscopy Analysis Tools (spant) Calculate the standard deviation spectrum from an mrs_data object. — sd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/sd.mrs_data.html b/docs/reference/sd.mrs_data.html
index 3f92a49f..13bdda85 100644
--- a/docs/reference/sd.mrs_data.html
+++ b/docs/reference/sd.mrs_data.html
@@ -1,5 +1,5 @@
-Calculate the standard deviation spectrum from an mrs_data object. — sd.mrs_data • Spectroscopy Analysis Tools (spant) Calculate the standard deviation spectrum from an mrs_data object. — sd.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/seconds.html b/docs/reference/seconds.html
index b34d6627..467ee17f 100644
--- a/docs/reference/seconds.html
+++ b/docs/reference/seconds.html
@@ -1,5 +1,5 @@
-Return a time scale vector to match the FID of an MRS data object. — seconds • Spectroscopy Analysis Tools (spant) Return a time scale vector to match the FID of an MRS data object. — seconds • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/seq_cpmg_ideal.html b/docs/reference/seq_cpmg_ideal.html
index 547e96ab..45727c86 100644
--- a/docs/reference/seq_cpmg_ideal.html
+++ b/docs/reference/seq_cpmg_ideal.html
@@ -1,5 +1,5 @@
-CPMG style sequence with ideal pulses. — seq_cpmg_ideal • Spectroscopy Analysis Tools (spant) CPMG style sequence with ideal pulses. — seq_cpmg_ideal • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/seq_mega_press_ideal.html b/docs/reference/seq_mega_press_ideal.html
index 0769b8b4..a9cd7fa0 100644
--- a/docs/reference/seq_mega_press_ideal.html
+++ b/docs/reference/seq_mega_press_ideal.html
@@ -1,7 +1,5 @@
-MEGA-PRESS sequence with ideal localisation pulses and Gaussian shaped
-editing pulse. — seq_mega_press_ideal • Spectroscopy Analysis Tools (spant) MEGA-PRESS sequence with ideal localisation pulses and Gaussian shaped editing pulse. — seq_mega_press_ideal • Spectroscopy Analysis Tools (spant) PRESS sequence with shaped refocusing pulses. — seq_press_2d_shaped • Spectroscopy Analysis Tools (spant) PRESS sequence with shaped refocusing pulses. — seq_press_2d_shaped • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -165,7 +165,7 @@ Value
diff --git a/docs/reference/seq_press_ideal.html b/docs/reference/seq_press_ideal.html
index 8c976856..72c3af3d 100644
--- a/docs/reference/seq_press_ideal.html
+++ b/docs/reference/seq_press_ideal.html
@@ -1,5 +1,5 @@
-PRESS sequence with ideal pulses. — seq_press_ideal • Spectroscopy Analysis Tools (spant) PRESS sequence with ideal pulses. — seq_press_ideal • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/seq_pulse_acquire.html b/docs/reference/seq_pulse_acquire.html
index 4a88fc64..ad80571e 100644
--- a/docs/reference/seq_pulse_acquire.html
+++ b/docs/reference/seq_pulse_acquire.html
@@ -1,5 +1,5 @@
-Simple pulse and acquire sequence with ideal pulses. — seq_pulse_acquire • Spectroscopy Analysis Tools (spant) Simple pulse and acquire sequence with ideal pulses. — seq_pulse_acquire • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/seq_slaser_ideal.html b/docs/reference/seq_slaser_ideal.html
index 74688f4d..eb83e8e3 100644
--- a/docs/reference/seq_slaser_ideal.html
+++ b/docs/reference/seq_slaser_ideal.html
@@ -1,5 +1,5 @@
-sLASER sequence with ideal pulses. — seq_slaser_ideal • Spectroscopy Analysis Tools (spant) sLASER sequence with ideal pulses. — seq_slaser_ideal • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -126,7 +126,7 @@ Value
diff --git a/docs/reference/seq_spin_echo_ideal.html b/docs/reference/seq_spin_echo_ideal.html
index e23271de..4248716f 100644
--- a/docs/reference/seq_spin_echo_ideal.html
+++ b/docs/reference/seq_spin_echo_ideal.html
@@ -1,5 +1,5 @@
-Spin echo sequence with ideal pulses. — seq_spin_echo_ideal • Spectroscopy Analysis Tools (spant) Spin echo sequence with ideal pulses. — seq_spin_echo_ideal • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/seq_steam_ideal.html b/docs/reference/seq_steam_ideal.html
index a60685a8..1c8115d7 100644
--- a/docs/reference/seq_steam_ideal.html
+++ b/docs/reference/seq_steam_ideal.html
@@ -1,5 +1,5 @@
-STEAM sequence with ideal pulses. — seq_steam_ideal • Spectroscopy Analysis Tools (spant) STEAM sequence with ideal pulses. — seq_steam_ideal • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -128,7 +128,7 @@ Value
diff --git a/docs/reference/seq_steam_ideal_cof.html b/docs/reference/seq_steam_ideal_cof.html
index 8f225740..cba7af91 100644
--- a/docs/reference/seq_steam_ideal_cof.html
+++ b/docs/reference/seq_steam_ideal_cof.html
@@ -1,7 +1,5 @@
-STEAM sequence with ideal pulses and coherence order filtering to simulate
-gradient crushers. — seq_steam_ideal_cof • Spectroscopy Analysis Tools (spant) STEAM sequence with ideal pulses and coherence order filtering to simulate gradient crushers. — seq_steam_ideal_cof • Spectroscopy Analysis Tools (spant) STEAM sequence with ideal pulses using the z-rotation gradient simulation
-method described by Young et al JMR 140, 146-152 (1999). — seq_steam_ideal_young • Spectroscopy Analysis Tools (spant) STEAM sequence with ideal pulses using the z-rotation gradient simulation method described by Young et al JMR 140, 146-152 (1999). — seq_steam_ideal_young • Spectroscopy Analysis Tools (spant) Set the number of transients for an mrs_data object. — set_Ntrans • Spectroscopy Analysis Tools (spant) Set the number of transients for an mrs_data object. — set_Ntrans • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/set_def_acq_paras.html b/docs/reference/set_def_acq_paras.html
index 3e1b4004..cc2ada9c 100644
--- a/docs/reference/set_def_acq_paras.html
+++ b/docs/reference/set_def_acq_paras.html
@@ -1,5 +1,5 @@
-Set the default acquisition parameters. — set_def_acq_paras • Spectroscopy Analysis Tools (spant) Set the default acquisition parameters. — set_def_acq_paras • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Arguments
diff --git a/docs/reference/set_lcm_cmd.html b/docs/reference/set_lcm_cmd.html
index 2056ed01..42bb2f24 100644
--- a/docs/reference/set_lcm_cmd.html
+++ b/docs/reference/set_lcm_cmd.html
@@ -1,5 +1,5 @@
-Set the command to run the LCModel command-line program. — set_lcm_cmd • Spectroscopy Analysis Tools (spant) Set the command to run the LCModel command-line program. — set_lcm_cmd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/set_lw.html b/docs/reference/set_lw.html
index b64ec851..bb176c62 100644
--- a/docs/reference/set_lw.html
+++ b/docs/reference/set_lw.html
@@ -1,5 +1,5 @@
-Apply line-broadening to an mrs_data object to achieve a specified linewidth. — set_lw • Spectroscopy Analysis Tools (spant) Apply line-broadening to an mrs_data object to achieve a specified linewidth. — set_lw • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -123,7 +123,7 @@ Value
diff --git a/docs/reference/set_mask_xy_mat.html b/docs/reference/set_mask_xy_mat.html
index 49dc5d4e..52c4b617 100644
--- a/docs/reference/set_mask_xy_mat.html
+++ b/docs/reference/set_mask_xy_mat.html
@@ -1,5 +1,5 @@
-Set the masked voxels in a 2D MRSI dataset to given spectrum. — set_mask_xy_mat • Spectroscopy Analysis Tools (spant) Set the masked voxels in a 2D MRSI dataset to given spectrum. — set_mask_xy_mat • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Value
diff --git a/docs/reference/set_precomp_mode.html b/docs/reference/set_precomp_mode.html
index f44bd5d3..47c28e3b 100644
--- a/docs/reference/set_precomp_mode.html
+++ b/docs/reference/set_precomp_mode.html
@@ -1,5 +1,5 @@
-Set the precompute mode. — set_precomp_mode • Spectroscopy Analysis Tools (spant) Set the precompute mode. — set_precomp_mode • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/set_precomp_verbose.html b/docs/reference/set_precomp_verbose.html
index 1453a231..9c613505 100644
--- a/docs/reference/set_precomp_verbose.html
+++ b/docs/reference/set_precomp_verbose.html
@@ -1,5 +1,5 @@
-Set the verbosity of the precompute function. — set_precomp_verbose • Spectroscopy Analysis Tools (spant) Set the verbosity of the precompute function. — set_precomp_verbose • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/set_ref.html b/docs/reference/set_ref.html
index 8953fa50..5436dfa2 100644
--- a/docs/reference/set_ref.html
+++ b/docs/reference/set_ref.html
@@ -1,5 +1,5 @@
-Set the ppm reference value (eg ppm value at 0Hz). — set_ref • Spectroscopy Analysis Tools (spant) Set the ppm reference value (eg ppm value at 0Hz). — set_ref • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/set_td_pts.html b/docs/reference/set_td_pts.html
index 8a80d42a..586459ff 100644
--- a/docs/reference/set_td_pts.html
+++ b/docs/reference/set_td_pts.html
@@ -1,7 +1,5 @@
-Set the number of time-domain data points, truncating or zero-filling as
-appropriate. — set_td_pts • Spectroscopy Analysis Tools (spant) Set the number of time-domain data points, truncating or zero-filling as appropriate. — set_td_pts • Spectroscopy Analysis Tools (spant) Set the command to run the TARQUIN command-line program. — set_tqn_cmd • Spectroscopy Analysis Tools (spant) Set the command to run the TARQUIN command-line program. — set_tqn_cmd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/set_tr.html b/docs/reference/set_tr.html
index b2109ab0..65c9df5f 100644
--- a/docs/reference/set_tr.html
+++ b/docs/reference/set_tr.html
@@ -1,5 +1,5 @@
-Set the repetition time of an MRS dataset. — set_tr • Spectroscopy Analysis Tools (spant) Set the repetition time of an MRS dataset. — set_tr • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/shift.html b/docs/reference/shift.html
index ab0fe724..034591d0 100644
--- a/docs/reference/shift.html
+++ b/docs/reference/shift.html
@@ -1,5 +1,5 @@
-Apply a frequency shift to MRS data. — shift • Spectroscopy Analysis Tools (spant) Apply a frequency shift to MRS data. — shift • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/shift_basis.html b/docs/reference/shift_basis.html
index 2884be19..f55a65e0 100644
--- a/docs/reference/shift_basis.html
+++ b/docs/reference/shift_basis.html
@@ -1,5 +1,5 @@
-Apply frequency shifts to basis set signals. — shift_basis • Spectroscopy Analysis Tools (spant) Apply frequency shifts to basis set signals. — shift_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Value
diff --git a/docs/reference/sim_basis.html b/docs/reference/sim_basis.html
index c7838c46..bb5fefc6 100644
--- a/docs/reference/sim_basis.html
+++ b/docs/reference/sim_basis.html
@@ -1,5 +1,5 @@
-Simulate a basis set object. — sim_basis • Spectroscopy Analysis Tools (spant) Simulate a basis set object. — sim_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -136,7 +136,7 @@ Value
diff --git a/docs/reference/sim_basis_1h_brain.html b/docs/reference/sim_basis_1h_brain.html
index 62ed7389..f71ffa0b 100644
--- a/docs/reference/sim_basis_1h_brain.html
+++ b/docs/reference/sim_basis_1h_brain.html
@@ -1,7 +1,5 @@
-Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS
-sequence. Note, ideal pulses are assumed. — sim_basis_1h_brain • Spectroscopy Analysis Tools (spant) Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS sequence. Note, ideal pulses are assumed. — sim_basis_1h_brain • Spectroscopy Analysis Tools (spant) Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS
-sequence. Note, ideal pulses are assumed. — sim_basis_1h_brain_press • Spectroscopy Analysis Tools (spant) Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS sequence. Note, ideal pulses are assumed. — sim_basis_1h_brain_press • Spectroscopy Analysis Tools (spant) Simulate a macromolecular and lipid basis-set suitable for 1H brain MRS
-analysis. — sim_basis_mm_lip_lcm • Spectroscopy Analysis Tools (spant) Simulate a macromolecular and lipid basis-set suitable for 1H brain MRS analysis. — sim_basis_mm_lip_lcm • Spectroscopy Analysis Tools (spant) Simulate a basis file using TARQUIN. — sim_basis_tqn • Spectroscopy Analysis Tools (spant) Simulate a basis file using TARQUIN. — sim_basis_tqn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -129,7 +129,7 @@ Examples
diff --git a/docs/reference/sim_brain_1h.html b/docs/reference/sim_brain_1h.html
index 2044cf1a..717ee289 100644
--- a/docs/reference/sim_brain_1h.html
+++ b/docs/reference/sim_brain_1h.html
@@ -1,5 +1,5 @@
-Simulate MRS data with a similar appearance to normal brain (by default). — sim_brain_1h • Spectroscopy Analysis Tools (spant) Simulate MRS data with a similar appearance to normal brain (by default). — sim_brain_1h • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -159,7 +159,7 @@ Value
diff --git a/docs/reference/sim_mol.html b/docs/reference/sim_mol.html
index 23bcef50..77f76a50 100644
--- a/docs/reference/sim_mol.html
+++ b/docs/reference/sim_mol.html
@@ -1,5 +1,5 @@
-Simulate a mol_parameter object. — sim_mol • Spectroscopy Analysis Tools (spant) Simulate a mol_parameter object. — sim_mol • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -143,7 +143,7 @@ Value
diff --git a/docs/reference/sim_noise.html b/docs/reference/sim_noise.html
index 23875f79..a71477d4 100644
--- a/docs/reference/sim_noise.html
+++ b/docs/reference/sim_noise.html
@@ -1,5 +1,5 @@
-Simulate an mrs_data object containing simulated Gaussian noise. — sim_noise • Spectroscopy Analysis Tools (spant) Simulate an mrs_data object containing simulated Gaussian noise. — sim_noise • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -84,6 +84,7 @@ Simulate an mrs_data object containing simulated Gaussian noise.
ft = def_ft(),
N = def_N(),
ref = def_ref(),
+ nuc = def_nuc(),
dyns = 1,
fd = TRUE
)
@@ -111,6 +112,10 @@ Arguments
reference value for ppm scale.
nuc
+resonant nucleus.
dyns
number of dynamic scans to generate.
Value
diff --git a/docs/reference/sim_resonances.html b/docs/reference/sim_resonances.html
index 19e9a8a4..d4f8d7c0 100644
--- a/docs/reference/sim_resonances.html
+++ b/docs/reference/sim_resonances.html
@@ -1,5 +1,5 @@
-Simulate a MRS data object containing a set of simulated resonances. — sim_resonances • Spectroscopy Analysis Tools (spant) Simulate a MRS data object containing a set of simulated resonances. — sim_resonances • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -161,7 +161,7 @@ Examples
diff --git a/docs/reference/sim_th_excit_profile.html b/docs/reference/sim_th_excit_profile.html
index 5535c5ef..e781cab1 100644
--- a/docs/reference/sim_th_excit_profile.html
+++ b/docs/reference/sim_th_excit_profile.html
@@ -1,7 +1,5 @@
-Simulate an ideal pulse excitation profile by smoothing a top-hat function
-with a Gaussian. — sim_th_excit_profile • Spectroscopy Analysis Tools (spant) Simulate an ideal pulse excitation profile by smoothing a top-hat function with a Gaussian. — sim_th_excit_profile • Spectroscopy Analysis Tools (spant) Simulate an mrs_data object containing complex zero valued samples. — sim_zero • Spectroscopy Analysis Tools (spant) Simulate an mrs_data object containing complex zero valued samples. — sim_zero • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -78,7 +78,14 @@ Simulate an mrs_data object containing complex zero valued samples.
-
+
@@ -99,6 +106,10 @@ Arguments
reference value for ppm scale.
nuc
+resonant nucleus.
dyns
number of dynamic scans to generate.
Value
diff --git a/docs/reference/smooth_dyns.html b/docs/reference/smooth_dyns.html
index 4cc8da50..accf3a51 100644
--- a/docs/reference/smooth_dyns.html
+++ b/docs/reference/smooth_dyns.html
@@ -1,5 +1,5 @@
-Smooth data across the dynamic dimension with a Gaussian kernel. — smooth_dyns • Spectroscopy Analysis Tools (spant) Smooth data across the dynamic dimension with a Gaussian kernel. — smooth_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/sort_basis.html b/docs/reference/sort_basis.html
index 6a676ea2..d25cc006 100644
--- a/docs/reference/sort_basis.html
+++ b/docs/reference/sort_basis.html
@@ -1,5 +1,5 @@
-Sort the basis-set elements alphabetically. — sort_basis • Spectroscopy Analysis Tools (spant) Sort the basis-set elements alphabetically. — sort_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/spant-package.html b/docs/reference/spant-package.html
index b3dd8e21..90f19ec3 100644
--- a/docs/reference/spant-package.html
+++ b/docs/reference/spant-package.html
@@ -1,5 +1,5 @@
-spant: spectroscopy analysis tools. — spant-package • Spectroscopy Analysis Tools (spant) spant: spectroscopy analysis tools. — spant-package • Spectroscopy Analysis Tools (spant) Simulate and fit some spectra with ABfit for benchmarking purposes. Basic
-timing and performance metrics will be printed. — spant_abfit_benchmark • Spectroscopy Analysis Tools (spant) Simulate and fit some spectra with ABfit for benchmarking purposes. Basic timing and performance metrics will be printed. — spant_abfit_benchmark • Spectroscopy Analysis Tools (spant) Example MEGA-PRESS data with significant B0 drift. — spant_mpress_drift • Spectroscopy Analysis Tools (spant) Example MEGA-PRESS data with significant B0 drift. — spant_mpress_drift • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -83,7 +83,7 @@ Example MEGA-PRESS data with significant B0 drift.
Format
- An object of class mrs_data of length 13.
+ An object of class mrs_data of dimension 1 x 1 x 1 x 1 x 40 x 1 x 1024.
@@ -98,7 +98,7 @@ Format
diff --git a/docs/reference/spant_sim_fmrs_dataset.html b/docs/reference/spant_sim_fmrs_dataset.html
new file mode 100644
index 00000000..00e48b56
--- /dev/null
+++ b/docs/reference/spant_sim_fmrs_dataset.html
@@ -0,0 +1,117 @@
+
+Simulate an example fMRS dataset for a block design fMRS experiment and export a BIDS structure. — spant_sim_fmrs_dataset • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Simulate an example fMRS dataset for a block design fMRS experiment and export a BIDS structure.
+ Source: R/fmrs.R
+ spant_sim_fmrs_dataset.Rd
+
+
+
+ Simulate an example fMRS dataset for a block design fMRS experiment and
+export a BIDS structure.
+
+
+
+ spant_sim_fmrs_dataset(output_dir = NULL)
+
+
+
+ Arguments
+ - output_dir
+output directory for the BIDS data. Defaults to :
+"HOME/sim_fmrs_dataset/data".
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/spant_simulation_benchmark.html b/docs/reference/spant_simulation_benchmark.html
index 32daa8bf..d8cc6841 100644
--- a/docs/reference/spant_simulation_benchmark.html
+++ b/docs/reference/spant_simulation_benchmark.html
@@ -1,7 +1,5 @@
-Simulate a typical metabolite basis set for benchmarking. Timing metrics will
-be printed on completion. — spant_simulation_benchmark • Spectroscopy Analysis Tools (spant) Simulate a typical metabolite basis set for benchmarking. Timing metrics will be printed on completion. — spant_simulation_benchmark • Spectroscopy Analysis Tools (spant) Decompose an mrs_data object into white and gray matter spectra. — spec_decomp • Spectroscopy Analysis Tools (spant) Perform a mathematical operation on a spectral region. — spec_op • Spectroscopy Analysis Tools (spant) Perform a mathematical operation on a spectral region. — spec_op • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -98,8 +98,8 @@ Arguments
operator
-can be "sum" (default), "mean", "l2", "max", "min" or
-"max-min".
can be "sum" (default), "mean", "l2", "max", "max_cplx,
+"min" or "max-min".
freq_scale
@@ -129,7 +129,7 @@ Value
diff --git a/docs/reference/spin_sys.html b/docs/reference/spin_sys.html
index 853423a4..1eaa9e76 100644
--- a/docs/reference/spin_sys.html
+++ b/docs/reference/spin_sys.html
@@ -1,5 +1,5 @@
-Create a spin system object for pulse sequence simulation. — spin_sys • Spectroscopy Analysis Tools (spant) Create a spin system object for pulse sequence simulation. — spin_sys • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/spm_pve2categorical.html b/docs/reference/spm_pve2categorical.html
index 23a1bad9..70f10729 100644
--- a/docs/reference/spm_pve2categorical.html
+++ b/docs/reference/spm_pve2categorical.html
@@ -1,7 +1,5 @@
-Convert SPM style segmentation files to a single categorical image where
-the numerical values map as: 0) Other, 1) CSF, 2) GM and 3) WM. — spm_pve2categorical • Spectroscopy Analysis Tools (spant) Convert SPM style segmentation files to a single categorical image where the numerical values map as: 0) Other, 1) CSF, 2) GM and 3) WM. — spm_pve2categorical • Spectroscopy Analysis Tools (spant) Signal space projection method for lipid suppression. — ssp • Spectroscopy Analysis Tools (spant) Signal space projection method for lipid suppression. — ssp • Spectroscopy Analysis Tools (spant) Plot the fitting results of an object of class fit_result with
-individual basis set components shown. — stackplot.fit_result • Spectroscopy Analysis Tools (spant) Plot the fitting results of an object of class fit_result with individual basis set components shown. — stackplot.fit_result • Spectroscopy Analysis Tools (spant) Produce a plot with multiple traces. — stackplot • Spectroscopy Analysis Tools (spant) Produce a plot with multiple traces. — stackplot • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/stackplot.mrs_data.html b/docs/reference/stackplot.mrs_data.html
index 17ff5648..64eea445 100644
--- a/docs/reference/stackplot.mrs_data.html
+++ b/docs/reference/stackplot.mrs_data.html
@@ -1,5 +1,5 @@
-Stackplot plotting method for objects of class mrs_data. — stackplot.mrs_data • Spectroscopy Analysis Tools (spant) Stackplot plotting method for objects of class mrs_data. — stackplot.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -255,7 +255,7 @@ Arguments
diff --git a/docs/reference/sub_first_dyn.html b/docs/reference/sub_first_dyn.html
index dbd7f831..493b7242 100644
--- a/docs/reference/sub_first_dyn.html
+++ b/docs/reference/sub_first_dyn.html
@@ -1,5 +1,5 @@
-Subtract the first dynamic spectrum from a dynamic series. — sub_first_dyn • Spectroscopy Analysis Tools (spant) Subtract the first dynamic spectrum from a dynamic series. — sub_first_dyn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/sub_mean_dyns.html b/docs/reference/sub_mean_dyns.html
index 6e3bb2df..221bd0c1 100644
--- a/docs/reference/sub_mean_dyns.html
+++ b/docs/reference/sub_mean_dyns.html
@@ -1,5 +1,5 @@
-Subtract the mean dynamic spectrum from a dynamic series. — sub_mean_dyns • Spectroscopy Analysis Tools (spant) Subtract the mean dynamic spectrum from a dynamic series. — sub_mean_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/sub_median_dyns.html b/docs/reference/sub_median_dyns.html
index 134c495d..1e834f14 100644
--- a/docs/reference/sub_median_dyns.html
+++ b/docs/reference/sub_median_dyns.html
@@ -1,5 +1,5 @@
-Subtract the median dynamic spectrum from a dynamic series. — sub_median_dyns • Spectroscopy Analysis Tools (spant) Subtract the median dynamic spectrum from a dynamic series. — sub_median_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/sum_coils.html b/docs/reference/sum_coils.html
index 7bf559f2..e1ab3cc0 100644
--- a/docs/reference/sum_coils.html
+++ b/docs/reference/sum_coils.html
@@ -1,5 +1,5 @@
-Calculate the sum across receiver coil elements. — sum_coils • Spectroscopy Analysis Tools (spant) Calculate the sum across receiver coil elements. — sum_coils • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/sum_dyns.html b/docs/reference/sum_dyns.html
index a0be19d3..bbda2ffc 100644
--- a/docs/reference/sum_dyns.html
+++ b/docs/reference/sum_dyns.html
@@ -1,5 +1,5 @@
-Calculate the sum of data dynamics. — sum_dyns • Spectroscopy Analysis Tools (spant) Calculate the sum of data dynamics. — sum_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/sum_mrs.html b/docs/reference/sum_mrs.html
index a22f215b..3cc3ab9e 100644
--- a/docs/reference/sum_mrs.html
+++ b/docs/reference/sum_mrs.html
@@ -1,5 +1,5 @@
-Sum two mrs_data objects. — sum_mrs • Spectroscopy Analysis Tools (spant) Sum two mrs_data objects. — sum_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Value
diff --git a/docs/reference/sum_mrs_list.html b/docs/reference/sum_mrs_list.html
index f4e09aea..c3584348 100644
--- a/docs/reference/sum_mrs_list.html
+++ b/docs/reference/sum_mrs_list.html
@@ -1,5 +1,5 @@
-Return the sum of a list of mrs_data objects. — sum_mrs_list • Spectroscopy Analysis Tools (spant) Return the sum of a list of mrs_data objects. — sum_mrs_list • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/svs_1h_brain_analysis.html b/docs/reference/svs_1h_brain_analysis.html
index 8ce514db..dff0ef7d 100644
--- a/docs/reference/svs_1h_brain_analysis.html
+++ b/docs/reference/svs_1h_brain_analysis.html
@@ -1,5 +1,5 @@
-Standard SVS 1H brain analysis pipeline. — svs_1h_brain_analysis • Spectroscopy Analysis Tools (spant) Standard SVS 1H brain analysis pipeline. — svs_1h_brain_analysis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -199,7 +199,7 @@ Value
diff --git a/docs/reference/svs_1h_brain_analysis_dev.html b/docs/reference/svs_1h_brain_analysis_dev.html
index d70a14d3..d71bfea2 100644
--- a/docs/reference/svs_1h_brain_analysis_dev.html
+++ b/docs/reference/svs_1h_brain_analysis_dev.html
@@ -1,5 +1,5 @@
-Standard SVS 1H brain analysis pipeline. — svs_1h_brain_analysis_dev • Spectroscopy Analysis Tools (spant) Standard SVS 1H brain analysis pipeline. — svs_1h_brain_analysis_dev • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -193,7 +193,7 @@ Examples
diff --git a/docs/reference/svs_1h_brain_batch_analysis.html b/docs/reference/svs_1h_brain_batch_analysis.html
index 5631e8cc..15f7223e 100644
--- a/docs/reference/svs_1h_brain_batch_analysis.html
+++ b/docs/reference/svs_1h_brain_batch_analysis.html
@@ -1,5 +1,5 @@
-Batch interface to the standard SVS 1H brain analysis pipeline. — svs_1h_brain_batch_analysis • Spectroscopy Analysis Tools (spant) Batch interface to the standard SVS 1H brain analysis pipeline. — svs_1h_brain_batch_analysis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -144,7 +144,7 @@ Value
diff --git a/docs/reference/t_test_spec.html b/docs/reference/t_test_spec.html
new file mode 100644
index 00000000..56a7ea1b
--- /dev/null
+++ b/docs/reference/t_test_spec.html
@@ -0,0 +1,124 @@
+
+Perform a t-test on spectral data points. — t_test_spec • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+
+
+ Perform a t-test on spectral data points.
+
+
+
+ t_test_spec(mrs_data, group)
+
+
+
+ Arguments
+ - mrs_data
+an mrs_data object with spectra in the dynamic dimension.
- group
+vector describing the group membership of each dynamic spectrum.
+
+ Value
+
+
+a list of statistical results.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/td2fd.html b/docs/reference/td2fd.html
index 6748a6a8..f31ed524 100644
--- a/docs/reference/td2fd.html
+++ b/docs/reference/td2fd.html
@@ -1,5 +1,5 @@
-Transform time-domain data to the frequency-domain. — td2fd • Spectroscopy Analysis Tools (spant) Transform time-domain data to the frequency-domain. — td2fd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/td_conv_filt.html b/docs/reference/td_conv_filt.html
index a9f340c3..106b9b00 100644
--- a/docs/reference/td_conv_filt.html
+++ b/docs/reference/td_conv_filt.html
@@ -1,5 +1,5 @@
-Time-domain convolution based filter. — td_conv_filt • Spectroscopy Analysis Tools (spant) Time-domain convolution based filter. — td_conv_filt • Spectroscopy Analysis Tools (spant) Time-domain spectral registration. — tdsr • Spectroscopy Analysis Tools (spant) Time-domain spectral registration. — tdsr • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -121,7 +121,7 @@ Value
diff --git a/docs/reference/te.html b/docs/reference/te.html
index 010361b1..4a65711d 100644
--- a/docs/reference/te.html
+++ b/docs/reference/te.html
@@ -1,5 +1,5 @@
-Return the echo time of an MRS dataset. — te • Spectroscopy Analysis Tools (spant) Return the echo time of an MRS dataset. — te • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/tr.html b/docs/reference/tr.html
index 0c0bd63b..2e749e02 100644
--- a/docs/reference/tr.html
+++ b/docs/reference/tr.html
@@ -1,5 +1,5 @@
-Return the repetition time of an MRS dataset. — tr • Spectroscopy Analysis Tools (spant) Return the repetition time of an MRS dataset. — tr • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/varpro_3_para_opts.html b/docs/reference/varpro_3_para_opts.html
index c2270a16..52d7cd84 100644
--- a/docs/reference/varpro_3_para_opts.html
+++ b/docs/reference/varpro_3_para_opts.html
@@ -1,5 +1,5 @@
-Return a list of options for VARPRO based fitting with 3 free parameters. — varpro_3_para_opts • Spectroscopy Analysis Tools (spant) Return a list of options for VARPRO based fitting with 3 free parameters. — varpro_3_para_opts • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -141,7 +141,7 @@ Value
diff --git a/docs/reference/varpro_basic_opts.html b/docs/reference/varpro_basic_opts.html
index 32c86d22..c5104891 100644
--- a/docs/reference/varpro_basic_opts.html
+++ b/docs/reference/varpro_basic_opts.html
@@ -1,5 +1,5 @@
-Return a list of options for a basic VARPRO analysis. — varpro_basic_opts • Spectroscopy Analysis Tools (spant) Return a list of options for a basic VARPRO analysis. — varpro_basic_opts • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -118,7 +118,7 @@ Value
diff --git a/docs/reference/varpro_opts.html b/docs/reference/varpro_opts.html
index 2aabf11d..6332f730 100644
--- a/docs/reference/varpro_opts.html
+++ b/docs/reference/varpro_opts.html
@@ -1,5 +1,5 @@
-Return a list of options for VARPRO based fitting. — varpro_opts • Spectroscopy Analysis Tools (spant) Return a list of options for VARPRO based fitting. — varpro_opts • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -177,7 +177,7 @@ Examples
diff --git a/docs/reference/vec2mrs_data.html b/docs/reference/vec2mrs_data.html
index 0cccd73b..f0d58bf0 100644
--- a/docs/reference/vec2mrs_data.html
+++ b/docs/reference/vec2mrs_data.html
@@ -1,5 +1,5 @@
-Convert a vector into a mrs_data object. — vec2mrs_data • Spectroscopy Analysis Tools (spant) Convert a vector into a mrs_data object. — vec2mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -80,10 +80,11 @@ Convert a vector into a mrs_data object.
vec2mrs_data(
vec,
- fs = def_fs(),
- ft = def_ft(),
- ref = def_ref(),
- nuc = def_nuc(),
+ mrs_data = NULL,
+ fs = NULL,
+ ft = NULL,
+ ref = NULL,
+ nuc = NULL,
dyns = 1,
fd = FALSE
)
@@ -95,6 +96,10 @@ Arguments
the data vector.
mrs_data
+example data to copy acquisition parameters from.
fs
sampling frequency in Hz.
Arguments
fd
-flag to indicate if the matrix is in the frequency domain (logical).
flag to indicate if the vector is in the frequency domain (logical).
Value
diff --git a/docs/reference/write_basis.html b/docs/reference/write_basis.html
index b6e27cbd..94c5e021 100644
--- a/docs/reference/write_basis.html
+++ b/docs/reference/write_basis.html
@@ -1,5 +1,5 @@
-Write a basis object to an LCModel .basis formatted file. — write_basis • Spectroscopy Analysis Tools (spant) Write a basis object to an LCModel .basis formatted file. — write_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -108,7 +108,7 @@ Arguments
diff --git a/docs/reference/write_basis_tqn.html b/docs/reference/write_basis_tqn.html
index 6aa51c1d..116c73ec 100644
--- a/docs/reference/write_basis_tqn.html
+++ b/docs/reference/write_basis_tqn.html
@@ -1,5 +1,5 @@
-Generate a basis file using TARQUIN. — write_basis_tqn • Spectroscopy Analysis Tools (spant) Generate a basis file using TARQUIN. — write_basis_tqn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Examples
diff --git a/docs/reference/write_mrs.html b/docs/reference/write_mrs.html
index fff25f15..124b9dc4 100644
--- a/docs/reference/write_mrs.html
+++ b/docs/reference/write_mrs.html
@@ -1,5 +1,5 @@
-Write MRS data object to file. — write_mrs • Spectroscopy Analysis Tools (spant) Write MRS data object to file. — write_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Arguments
diff --git a/docs/reference/write_mrs_nifti.html b/docs/reference/write_mrs_nifti.html
index f4bf1921..bd3ed4b7 100644
--- a/docs/reference/write_mrs_nifti.html
+++ b/docs/reference/write_mrs_nifti.html
@@ -1,5 +1,5 @@
-Write MRS data object to file in NIFTI format. — write_mrs_nifti • Spectroscopy Analysis Tools (spant) Write MRS data object to file in NIFTI format. — write_mrs_nifti • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/write_pulse_ascii.html b/docs/reference/write_pulse_ascii.html
index 067ae086..221f8ebb 100644
--- a/docs/reference/write_pulse_ascii.html
+++ b/docs/reference/write_pulse_ascii.html
@@ -1,5 +1,5 @@
-Write an ASCII formatted pulse file. — write_pulse_ascii • Spectroscopy Analysis Tools (spant) Write an ASCII formatted pulse file. — write_pulse_ascii • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/zero_fade_spec.html b/docs/reference/zero_fade_spec.html
index c703745c..c8b572c3 100644
--- a/docs/reference/zero_fade_spec.html
+++ b/docs/reference/zero_fade_spec.html
@@ -1,7 +1,5 @@
-Fade a spectrum to zero by frequency domain multiplication with a tanh
-function. Note this operation distorts data points at the end of the FID. — zero_fade_spec • Spectroscopy Analysis Tools (spant) Fade a spectrum to zero by frequency domain multiplication with a tanh function. Note this operation distorts data points at the end of the FID. — zero_fade_spec • Spectroscopy Analysis Tools (spant) Zero all coherences including and above a given order. — zero_higher_orders • Spectroscopy Analysis Tools (spant) Zero all coherences including and above a given order. — zero_higher_orders • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Value
diff --git a/docs/reference/zero_td_pts_end.html b/docs/reference/zero_td_pts_end.html
index 8c1123c8..71d24ebb 100644
--- a/docs/reference/zero_td_pts_end.html
+++ b/docs/reference/zero_td_pts_end.html
@@ -1,5 +1,5 @@
-Set mrs_data object data points at the end of the FID to zero. — zero_td_pts_end • Spectroscopy Analysis Tools (spant) Set mrs_data object data points at the end of the FID to zero. — zero_td_pts_end • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/zf.html b/docs/reference/zf.html
index 85e2013c..baf50256 100644
--- a/docs/reference/zf.html
+++ b/docs/reference/zf.html
@@ -1,5 +1,5 @@
-Zero-fill MRS data in the time domain. — zf • Spectroscopy Analysis Tools (spant) Zero-fill MRS data in the time domain. — zf • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -125,7 +125,7 @@ Value
diff --git a/docs/reference/zf_xy.html b/docs/reference/zf_xy.html
index ebca3999..c4104a74 100644
--- a/docs/reference/zf_xy.html
+++ b/docs/reference/zf_xy.html
@@ -1,5 +1,5 @@
-Zero-fill MRSI data in the k-space x-y direction. — zf_xy • Spectroscopy Analysis Tools (spant) Zero-fill MRSI data in the k-space x-y direction. — zf_xy • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -113,7 +113,7 @@ Value
diff --git a/docs/sitemap.xml b/docs/sitemap.xml
index e2139f71..4c39f515 100644
--- a/docs/sitemap.xml
+++ b/docs/sitemap.xml
@@ -216,6 +216,12 @@
https://martin3141.github.io/spant/reference/comb_coils_fp_pc.html
+
+ https://martin3141.github.io/spant/reference/comb_coils_mrsi_gls.html
+
+
+ https://martin3141.github.io/spant/reference/comb_coils_svs_gls.html
+
https://martin3141.github.io/spant/reference/comb_csv_results.html
@@ -411,6 +417,9 @@
https://martin3141.github.io/spant/reference/gen_conv_reg.html
+
+ https://martin3141.github.io/spant/reference/gen_group_reg.html
+
https://martin3141.github.io/spant/reference/gen_impulse_reg.html
@@ -555,6 +564,15 @@
https://martin3141.github.io/spant/reference/glm_spec.html
+
+ https://martin3141.github.io/spant/reference/glm_spec_fmrs_fl.html
+
+
+ https://martin3141.github.io/spant/reference/glm_spec_fmrs_group.html
+
+
+ https://martin3141.github.io/spant/reference/glm_spec_group_linhyp.html
+
https://martin3141.github.io/spant/reference/grid_shift_xy.html
@@ -690,9 +708,15 @@
https://martin3141.github.io/spant/reference/mrs_data2basis.html
+
+ https://martin3141.github.io/spant/reference/mrs_data2bids.html
+
https://martin3141.github.io/spant/reference/mrs_data2mat.html
+
+ https://martin3141.github.io/spant/reference/mrs_data2spec_mat.html
+
https://martin3141.github.io/spant/reference/mrs_data2vec.html
@@ -741,6 +765,9 @@
https://martin3141.github.io/spant/reference/phase.html
+
+ https://martin3141.github.io/spant/reference/phase_ref_1h_brain.html
+
https://martin3141.github.io/spant/reference/plot.fit_result.html
@@ -780,6 +807,12 @@
https://martin3141.github.io/spant/reference/precomp.html
+
+ https://martin3141.github.io/spant/reference/preproc_svs.html
+
+
+ https://martin3141.github.io/spant/reference/preproc_svs_dataset.html
+
https://martin3141.github.io/spant/reference/print.fit_result.html
@@ -1050,6 +1083,9 @@
https://martin3141.github.io/spant/reference/spant_mpress_drift.html
+
+ https://martin3141.github.io/spant/reference/spant_sim_fmrs_dataset.html
+
https://martin3141.github.io/spant/reference/spant_simulation_benchmark.html
@@ -1107,6 +1143,9 @@
https://martin3141.github.io/spant/reference/svs_1h_brain_batch_analysis.html
+
+ https://martin3141.github.io/spant/reference/t_test_spec.html
+
https://martin3141.github.io/spant/reference/td2fd.html
Convert SPM style segmentation files to a single categorical image where -the numerical values map as: 0) Other, 1) CSF, 2) GM and 3) WM.
Convert SPM style segmentation files to a single categorical image where the numerical values map as: 0) Other, 1) CSF, 2) GM and 3) WM.
All functions
- Plot the fitting results of an object of class fit_result with
-individual basis set components shown.
Plot the fitting results of an object of class fit_result with individual basis set components shown.
@@ -1459,6 +1431,10 @@ All functions svs_1h_brain_batch_analysis()
Batch interface to the standard SVS 1H brain analysis pipeline.
+
+
+ Perform a t-test on spectral data points.
@@ -1518,8 +1494,7 @@ All functions
- Fade a spectrum to zero by frequency domain multiplication with a tanh
-function. Note this operation distorts data points at the end of the FID.
Fade a spectrum to zero by frequency domain multiplication with a tanh function. Note this operation distorts data points at the end of the FID.
@@ -1549,7 +1524,7 @@ All functions
diff --git a/docs/reference/int_spec.html b/docs/reference/int_spec.html
index c7060fe7..783325a8 100644
--- a/docs/reference/int_spec.html
+++ b/docs/reference/int_spec.html
@@ -1,5 +1,5 @@
-Integrate a spectral region. — int_spec • Spectroscopy Analysis Tools (spant) Integrate a spectral region. — int_spec • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -118,7 +118,7 @@ Value
diff --git a/docs/reference/interleave_dyns.html b/docs/reference/interleave_dyns.html
index effe5543..441eff27 100644
--- a/docs/reference/interleave_dyns.html
+++ b/docs/reference/interleave_dyns.html
@@ -1,5 +1,5 @@
-Interleave the first and second half of a dynamic series. — interleave_dyns • Spectroscopy Analysis Tools (spant) Interleave the first and second half of a dynamic series. — interleave_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/inv_even_dyns.html b/docs/reference/inv_even_dyns.html
index 9f9d4fff..dcb781dc 100644
--- a/docs/reference/inv_even_dyns.html
+++ b/docs/reference/inv_even_dyns.html
@@ -1,5 +1,5 @@
-Invert even numbered dynamic scans starting from 1 (2,4,6...). — inv_even_dyns • Spectroscopy Analysis Tools (spant) Invert even numbered dynamic scans starting from 1 (2,4,6...). — inv_even_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/inv_odd_dyns.html b/docs/reference/inv_odd_dyns.html
index 26212e2b..78d64660 100644
--- a/docs/reference/inv_odd_dyns.html
+++ b/docs/reference/inv_odd_dyns.html
@@ -1,5 +1,5 @@
-Invert odd numbered dynamic scans starting from 1 (1,3,5...). — inv_odd_dyns • Spectroscopy Analysis Tools (spant) Invert odd numbered dynamic scans starting from 1 (1,3,5...). — inv_odd_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/is.def.html b/docs/reference/is.def.html
index f196ffd0..a67b9eba 100644
--- a/docs/reference/is.def.html
+++ b/docs/reference/is.def.html
@@ -1,5 +1,5 @@
-Check if an object is defined, which is the same as being not NULL. — is.def • Spectroscopy Analysis Tools (spant) Check if an object is defined, which is the same as being not NULL. — is.def • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/is_fd.html b/docs/reference/is_fd.html
index 3b0ca165..18a193aa 100644
--- a/docs/reference/is_fd.html
+++ b/docs/reference/is_fd.html
@@ -1,7 +1,5 @@
-Check if the chemical shift dimension of an MRS data object is in the
-frequency domain. — is_fd • Spectroscopy Analysis Tools (spant) Check if the chemical shift dimension of an MRS data object is in the frequency domain. — is_fd • Spectroscopy Analysis Tools (spant) Transform 2D MRSI data from k-space to image space in the x-y direction. — kspace2img_xy • Spectroscopy Analysis Tools (spant) Transform 2D MRSI data from k-space to image space in the x-y direction. — kspace2img_xy • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/l2_reg.html b/docs/reference/l2_reg.html
index 3d781d80..21aa9849 100644
--- a/docs/reference/l2_reg.html
+++ b/docs/reference/l2_reg.html
@@ -1,5 +1,5 @@
-Perform l2 regularisation artefact suppression. — l2_reg • Spectroscopy Analysis Tools (spant) Perform l2 regularisation artefact suppression. — l2_reg • Spectroscopy Analysis Tools (spant) Apply line-broadening (apodisation) to MRS data or basis object. — lb • Spectroscopy Analysis Tools (spant) Apply line-broadening (apodisation) to MRS data or basis object. — lb • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -123,7 +123,7 @@ Value
diff --git a/docs/reference/lofdc.html b/docs/reference/lofdc.html
index 5419b1ec..31347a25 100644
--- a/docs/reference/lofdc.html
+++ b/docs/reference/lofdc.html
@@ -1,5 +1,5 @@
-Correct linear frequency drift. — lofdc • Spectroscopy Analysis Tools (spant) Correct linear frequency drift. — lofdc • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -138,7 +138,7 @@ Value
diff --git a/docs/reference/lw2alpha.html b/docs/reference/lw2alpha.html
index b83db682..25da229b 100644
--- a/docs/reference/lw2alpha.html
+++ b/docs/reference/lw2alpha.html
@@ -1,7 +1,5 @@
-Covert a linewidth in Hz to an equivalent alpha value in the time-domain ie:
-x * exp(-t * alpha). — lw2alpha • Spectroscopy Analysis Tools (spant) Covert a linewidth in Hz to an equivalent alpha value in the time-domain ie: x * exp(-t * alpha). — lw2alpha • Spectroscopy Analysis Tools (spant) Covert a linewidth in Hz to an equivalent beta value in the time-domain ie:
-x * exp(-t * t * beta). — lw2beta • Spectroscopy Analysis Tools (spant) Covert a linewidth in Hz to an equivalent beta value in the time-domain ie: x * exp(-t * t * beta). — lw2beta • Spectroscopy Analysis Tools (spant) Make a basis-set object from a directory containing LCModel formatted RAW
-files. — make_basis_from_raw • Spectroscopy Analysis Tools (spant) Make a basis-set object from a directory containing LCModel formatted RAW files. — make_basis_from_raw • Spectroscopy Analysis Tools (spant) Mask an MRS dataset in the dynamic dimension. — mask_dyns • Spectroscopy Analysis Tools (spant) Mask an MRS dataset in the dynamic dimension. — mask_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/mask_fit_res.html b/docs/reference/mask_fit_res.html
index 97baaa3f..ebd91a99 100644
--- a/docs/reference/mask_fit_res.html
+++ b/docs/reference/mask_fit_res.html
@@ -1,5 +1,5 @@
-Mask fit result spectra depending on a vector of bool values. — mask_fit_res • Spectroscopy Analysis Tools (spant) Mask fit result spectra depending on a vector of bool values. — mask_fit_res • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -116,7 +116,7 @@ Value
diff --git a/docs/reference/mask_xy.html b/docs/reference/mask_xy.html
index 11bb577c..b0d38619 100644
--- a/docs/reference/mask_xy.html
+++ b/docs/reference/mask_xy.html
@@ -1,5 +1,5 @@
-Mask an MRSI dataset in the x-y direction — mask_xy • Spectroscopy Analysis Tools (spant) Mask an MRSI dataset in the x-y direction — mask_xy • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/mask_xy_corners.html b/docs/reference/mask_xy_corners.html
index 09b16cd2..2d13839d 100644
--- a/docs/reference/mask_xy_corners.html
+++ b/docs/reference/mask_xy_corners.html
@@ -1,5 +1,5 @@
-Mask the four corners of an MRSI dataset in the x-y plane. — mask_xy_corners • Spectroscopy Analysis Tools (spant) Mask the four corners of an MRSI dataset in the x-y plane. — mask_xy_corners • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/mask_xy_ellipse.html b/docs/reference/mask_xy_ellipse.html
index 1d8b02e4..e2e749ef 100644
--- a/docs/reference/mask_xy_ellipse.html
+++ b/docs/reference/mask_xy_ellipse.html
@@ -1,7 +1,5 @@
-Mask the voxels outside an elliptical region spanning the MRSI dataset in the
-x-y plane. — mask_xy_ellipse • Spectroscopy Analysis Tools (spant) Mask the voxels outside an elliptical region spanning the MRSI dataset in the x-y plane. — mask_xy_ellipse • Spectroscopy Analysis Tools (spant) Mask a 2D MRSI dataset in the x-y dimension. — mask_xy_mat • Spectroscopy Analysis Tools (spant) Mask a 2D MRSI dataset in the x-y dimension. — mask_xy_mat • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Value
diff --git a/docs/reference/mat2mrs_data.html b/docs/reference/mat2mrs_data.html
index 2e2895f3..ae55665f 100644
--- a/docs/reference/mat2mrs_data.html
+++ b/docs/reference/mat2mrs_data.html
@@ -1,7 +1,5 @@
-Convert a matrix (with spectral points in the column dimension and dynamics
-in the row dimensions) into a mrs_data object. — mat2mrs_data • Spectroscopy Analysis Tools (spant) Convert a matrix (with spectral points in the column dimension and dynamics in the row dimensions) into a mrs_data object. — mat2mrs_data • Spectroscopy Analysis Tools (spant) Matrix exponential function taken from complexplus package to reduce the
-number of spant dependencies. — matexp • Spectroscopy Analysis Tools (spant) Matrix exponential function taken from complexplus package to reduce the number of spant dependencies. — matexp • Spectroscopy Analysis Tools (spant) Apply the max operator to an MRS dataset. — max_mrs • Spectroscopy Analysis Tools (spant) Apply the max operator to an MRS dataset. — max_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/max_mrs_interp.html b/docs/reference/max_mrs_interp.html
index e4474764..52e63f3e 100644
--- a/docs/reference/max_mrs_interp.html
+++ b/docs/reference/max_mrs_interp.html
@@ -1,5 +1,5 @@
-Apply the max operator to an interpolated MRS dataset. — max_mrs_interp • Spectroscopy Analysis Tools (spant) Apply the max operator to an interpolated MRS dataset. — max_mrs_interp • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/mean.list.html b/docs/reference/mean.list.html
index b8eb3463..048306fd 100644
--- a/docs/reference/mean.list.html
+++ b/docs/reference/mean.list.html
@@ -1,5 +1,5 @@
-Calculate the mean spectrum from an mrs_data object. — mean.list • Spectroscopy Analysis Tools (spant) Calculate the mean spectrum from an mrs_data object. — mean.list • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/mean.mrs_data.html b/docs/reference/mean.mrs_data.html
index 5531a28d..79515014 100644
--- a/docs/reference/mean.mrs_data.html
+++ b/docs/reference/mean.mrs_data.html
@@ -1,5 +1,5 @@
-Calculate the mean spectrum from an mrs_data object. — mean.mrs_data • Spectroscopy Analysis Tools (spant) Calculate the mean spectrum from an mrs_data object. — mean.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/mean_dyn_blocks.html b/docs/reference/mean_dyn_blocks.html
index 10467098..4c042448 100644
--- a/docs/reference/mean_dyn_blocks.html
+++ b/docs/reference/mean_dyn_blocks.html
@@ -1,5 +1,5 @@
-Calculate the mean of adjacent dynamic scans. — mean_dyn_blocks • Spectroscopy Analysis Tools (spant) Calculate the mean of adjacent dynamic scans. — mean_dyn_blocks • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/mean_dyn_pairs.html b/docs/reference/mean_dyn_pairs.html
index 63e909ea..1a241126 100644
--- a/docs/reference/mean_dyn_pairs.html
+++ b/docs/reference/mean_dyn_pairs.html
@@ -1,5 +1,5 @@
-Calculate the pairwise means across a dynamic data set. — mean_dyn_pairs • Spectroscopy Analysis Tools (spant) Calculate the pairwise means across a dynamic data set. — mean_dyn_pairs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/mean_dyns.html b/docs/reference/mean_dyns.html
index 73fdbfa7..0daa27df 100644
--- a/docs/reference/mean_dyns.html
+++ b/docs/reference/mean_dyns.html
@@ -1,5 +1,5 @@
-Calculate the mean dynamic data. — mean_dyns • Spectroscopy Analysis Tools (spant) Calculate the mean dynamic data. — mean_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/mean_mrs_list.html b/docs/reference/mean_mrs_list.html
index 808b6c50..10d842c0 100644
--- a/docs/reference/mean_mrs_list.html
+++ b/docs/reference/mean_mrs_list.html
@@ -1,5 +1,5 @@
-Return the mean of a list of mrs_data objects. — mean_mrs_list • Spectroscopy Analysis Tools (spant) Return the mean of a list of mrs_data objects. — mean_mrs_list • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/mean_vec_blocks.html b/docs/reference/mean_vec_blocks.html
index 8fc92eaa..dd78b122 100644
--- a/docs/reference/mean_vec_blocks.html
+++ b/docs/reference/mean_vec_blocks.html
@@ -1,5 +1,5 @@
-Calculate the mean of adjacent blocks in a vector. — mean_vec_blocks • Spectroscopy Analysis Tools (spant) Calculate the mean of adjacent blocks in a vector. — mean_vec_blocks • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/median_dyns.html b/docs/reference/median_dyns.html
index 1039d4b5..9a085b10 100644
--- a/docs/reference/median_dyns.html
+++ b/docs/reference/median_dyns.html
@@ -1,5 +1,5 @@
-Calculate the median dynamic data. — median_dyns • Spectroscopy Analysis Tools (spant) Calculate the median dynamic data. — median_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/mod_td.html b/docs/reference/mod_td.html
index 76ad0a40..141ef09e 100644
--- a/docs/reference/mod_td.html
+++ b/docs/reference/mod_td.html
@@ -1,5 +1,5 @@
-Apply the Modulus operator to the time-domain MRS signal. — mod_td • Spectroscopy Analysis Tools (spant) Apply the Modulus operator to the time-domain MRS signal. — mod_td • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/mrs_data2basis.html b/docs/reference/mrs_data2basis.html
index 62f7d749..11797b91 100644
--- a/docs/reference/mrs_data2basis.html
+++ b/docs/reference/mrs_data2basis.html
@@ -1,7 +1,5 @@
-Convert an mrs_data object to basis object - where basis signals are spread
-across the dynamic dimension in the MRS data. — mrs_data2basis • Spectroscopy Analysis Tools (spant) Convert an mrs_data object to basis object - where basis signals are spread across the dynamic dimension in the MRS data. — mrs_data2basis • Spectroscopy Analysis Tools (spant) Create a BIDS file structure from a vector of MRS data paths or list of mrs_data objects. — mrs_data2bids • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Create a BIDS file structure from a vector of MRS data paths or list of mrs_data objects.
+ Source: R/fmrs.R
+ mrs_data2bids.Rd
+
+
+
+ Create a BIDS file structure from a vector of MRS data paths or list of
+mrs_data objects.
+
+
+
+ mrs_data2bids(
+ mrs_data,
+ output_dir,
+ suffix = NULL,
+ sub = NULL,
+ ses = NULL,
+ task = NULL,
+ acq = NULL,
+ nuc = NULL,
+ voi = NULL,
+ rec = NULL,
+ run = NULL,
+ echo = NULL,
+ inv = NULL,
+ skip_existing = TRUE
+)
+
+
+
+ Arguments
+ - mrs_data
+vector of MRS data paths or list of mrs_data objects.
- output_dir
+the base directory to create the BIDS structure.
- suffix
+optional vector of file suffixes. Default behaviour is to
+automatically determine these from the input data, however it is recommended
+that they are specified to allow more efficient skipping of existing data.
- sub
+optional vector of subject labels. If not specified, these will be
+automatically generated as a series of increasing zero-padded integer values
+corresponding to the mrs_data input indices.
- ses
+optional vector of session labels.
- task
+optional vector of task labels.
- acq
+optional vector of acquisition labels.
- nuc
+optional vector of nucleus labels.
- voi
+optional vector of volume of interest labels.
- rec
+optional vector of reconstruction labels.
- run
+optional vector of run indices.
- echo
+optional vector of echo time indices.
- inv
+optional vector of inversion indices.
- skip_existing
+skip any data files that have already been converted.
+Defaults to TRUE, set to FALSE to force an overwrite of any existing data
+files.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/mrs_data2mat.html b/docs/reference/mrs_data2mat.html
index cf5ff28c..9e47688a 100644
--- a/docs/reference/mrs_data2mat.html
+++ b/docs/reference/mrs_data2mat.html
@@ -1,7 +1,5 @@
-Convert mrs_data object to a matrix, with spectral points in the column
-dimension and dynamics in the row dimension. — mrs_data2mat • Spectroscopy Analysis Tools (spant) Convert mrs_data object to a matrix, with spectral points in the column dimension and dynamics in the row dimension. — mrs_data2mat • Spectroscopy Analysis Tools (spant) Convert mrs_data object to a matrix, with spectral points in the column dimension and dynamics in the row dimension. — mrs_data2spec_mat • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Convert mrs_data object to a matrix, with spectral points in the column dimension and dynamics in the row dimension.
+ Source: R/mrs_data_proc.R
+ mrs_data2spec_mat.Rd
+
+
+
+ Convert mrs_data object to a matrix, with spectral points in the column
+dimension and dynamics in the row dimension.
+
+
+
+ mrs_data2spec_mat(mrs_data, collapse = TRUE)
+
+
+
+ Arguments
+ - mrs_data
+MRS data object or list of MRS data objects.
- collapse
+collapse all other dimensions along the dynamic dimension, eg
+a 16x16 MRSI grid would be first collapsed across 256 dynamic scans.
+
+ Value
+
+
+MRS data matrix.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/mrs_data2vec.html b/docs/reference/mrs_data2vec.html
index fb172d68..a1fd654d 100644
--- a/docs/reference/mrs_data2vec.html
+++ b/docs/reference/mrs_data2vec.html
@@ -1,5 +1,5 @@
-Convert mrs_data object to a vector. — mrs_data2vec • Spectroscopy Analysis Tools (spant) Convert mrs_data object to a vector. — mrs_data2vec • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -126,7 +126,7 @@ Value
diff --git a/docs/reference/mvfftshift.html b/docs/reference/mvfftshift.html
index 92b0841b..976b3410 100644
--- a/docs/reference/mvfftshift.html
+++ b/docs/reference/mvfftshift.html
@@ -1,7 +1,5 @@
-Perform a fftshift on a matrix, with each column replaced by its shifted
-result. — mvfftshift • Spectroscopy Analysis Tools (spant) Perform a fftshift on a matrix, with each column replaced by its shifted result. — mvfftshift • Spectroscopy Analysis Tools (spant) Perform an ifftshift on a matrix, with each column replaced by its shifted
-result. — mvifftshift • Spectroscopy Analysis Tools (spant) Perform an ifftshift on a matrix, with each column replaced by its shifted result. — mvifftshift • Spectroscopy Analysis Tools (spant) Print fit coordinates from a single index. — n2coord • Spectroscopy Analysis Tools (spant) Print fit coordinates from a single index. — n2coord • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/nifti_flip_lr.html b/docs/reference/nifti_flip_lr.html
index 730abe3c..19860b3c 100644
--- a/docs/reference/nifti_flip_lr.html
+++ b/docs/reference/nifti_flip_lr.html
@@ -1,9 +1,5 @@
-Flip the x data dimension order of a nifti image. This corresponds to
-flipping MRI data in the left-right direction, assuming the data in save in
-neurological format (can check with fslorient program). — nifti_flip_lr • Spectroscopy Analysis Tools (spant) Flip the x data dimension order of a nifti image. This corresponds to flipping MRI data in the left-right direction, assuming the data in save in neurological format (can check with fslorient program). — nifti_flip_lr • Spectroscopy Analysis Tools (spant) Export a one-page pdf of a single fit result — one_page_pdf • Spectroscopy Analysis Tools (spant) Export a one-page pdf of a single fit result — one_page_pdf • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -108,7 +108,7 @@ Arguments
diff --git a/docs/reference/ortho3.html b/docs/reference/ortho3.html
index 13ade97d..5d7dd2fd 100644
--- a/docs/reference/ortho3.html
+++ b/docs/reference/ortho3.html
@@ -1,5 +1,5 @@
-Display an orthographic projection plot of a nifti object. — ortho3 • Spectroscopy Analysis Tools (spant) Display an orthographic projection plot of a nifti object. — ortho3 • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -172,7 +172,7 @@ Arguments
diff --git a/docs/reference/ortho3_inter.html b/docs/reference/ortho3_inter.html
index 090cc5e5..15948899 100644
--- a/docs/reference/ortho3_inter.html
+++ b/docs/reference/ortho3_inter.html
@@ -1,5 +1,5 @@
-Display an interactive orthographic projection plot of a nifti object. — ortho3_inter • Spectroscopy Analysis Tools (spant) Display an interactive orthographic projection plot of a nifti object. — ortho3_inter • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -132,7 +132,7 @@ Arguments
diff --git a/docs/reference/peak_info.html b/docs/reference/peak_info.html
index 09058bd8..41c8ffaf 100644
--- a/docs/reference/peak_info.html
+++ b/docs/reference/peak_info.html
@@ -1,7 +1,5 @@
-Search for the highest peak in a spectral region and return the frequency,
-height and FWHM. — peak_info • Spectroscopy Analysis Tools (spant) Search for the highest peak in a spectral region and return the frequency, height and FWHM. — peak_info • Spectroscopy Analysis Tools (spant) Papoulis-Gerchberg (PG) algorithm method for k-space extrapolation. — pg_extrap_xy • Spectroscopy Analysis Tools (spant) Papoulis-Gerchberg (PG) algorithm method for k-space extrapolation. — pg_extrap_xy • Spectroscopy Analysis Tools (spant) Apply phasing parameters to MRS data. — phase • Spectroscopy Analysis Tools (spant) Apply phasing parameters to MRS data. — phase • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/phase_ref_1h_brain.html b/docs/reference/phase_ref_1h_brain.html
new file mode 100644
index 00000000..8707a74a
--- /dev/null
+++ b/docs/reference/phase_ref_1h_brain.html
@@ -0,0 +1,131 @@
+
+Corrected zero order phase and chemical shift offset in 1H MRS data from the brain. — phase_ref_1h_brain • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Corrected zero order phase and chemical shift offset in 1H MRS data from the brain.
+ Source: R/rats.R
+ phase_ref_1h_brain.Rd
+
+
+
+ Corrected zero order phase and chemical shift offset in 1H MRS data from the
+brain.
+
+
+
+ phase_ref_1h_brain(mrs_data, mean_ref = FALSE, ret_corr_only = TRUE)
+
+
+
+ Arguments
+ - mrs_data
+MRS data to be corrected.
- mean_ref
+apply the phase and offset of the mean spectrum to all
+others. Default is FALSE.
- ret_corr_only
+return the corrected data only.
+
+ Value
+
+
+corrected MRS data.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/plot.fit_result.html b/docs/reference/plot.fit_result.html
index e54d3bc1..836a53ee 100644
--- a/docs/reference/plot.fit_result.html
+++ b/docs/reference/plot.fit_result.html
@@ -1,5 +1,5 @@
-Plot the fitting results of an object of class fit_result. — plot.fit_result • Spectroscopy Analysis Tools (spant) Plot the fitting results of an object of class fit_result. — plot.fit_result • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -207,7 +207,7 @@ Arguments
diff --git a/docs/reference/plot.mrs_data.html b/docs/reference/plot.mrs_data.html
index fabcc35b..bb2ec651 100644
--- a/docs/reference/plot.mrs_data.html
+++ b/docs/reference/plot.mrs_data.html
@@ -1,5 +1,5 @@
-Plotting method for objects of class mrs_data. — plot.mrs_data • Spectroscopy Analysis Tools (spant) Plotting method for objects of class mrs_data. — plot.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -287,7 +287,7 @@ Arguments
diff --git a/docs/reference/plot_bc.html b/docs/reference/plot_bc.html
index 4f8309b4..b48142cc 100644
--- a/docs/reference/plot_bc.html
+++ b/docs/reference/plot_bc.html
@@ -1,5 +1,5 @@
-Convenience function to plot a baseline estimate with the original data. — plot_bc • Spectroscopy Analysis Tools (spant) Convenience function to plot a baseline estimate with the original data. — plot_bc • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -108,7 +108,7 @@ Arguments
diff --git a/docs/reference/plot_reg.html b/docs/reference/plot_reg.html
index ae1acbe7..2addb2f6 100644
--- a/docs/reference/plot_reg.html
+++ b/docs/reference/plot_reg.html
@@ -1,5 +1,5 @@
-Plot regressors as an image. — plot_reg • Spectroscopy Analysis Tools (spant) Plot regressors as an image. — plot_reg • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/plot_slice_fit.html b/docs/reference/plot_slice_fit.html
index fbc7b560..57f1af8a 100644
--- a/docs/reference/plot_slice_fit.html
+++ b/docs/reference/plot_slice_fit.html
@@ -1,5 +1,5 @@
-Plot a 2D slice from an MRSI fit result object. — plot_slice_fit • Spectroscopy Analysis Tools (spant) Plot a 2D slice from an MRSI fit result object. — plot_slice_fit • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -129,7 +129,7 @@ Arguments
diff --git a/docs/reference/plot_slice_fit_inter.html b/docs/reference/plot_slice_fit_inter.html
index 4eed104a..da105a7d 100644
--- a/docs/reference/plot_slice_fit_inter.html
+++ b/docs/reference/plot_slice_fit_inter.html
@@ -1,5 +1,5 @@
-Plot a 2D slice from an MRSI fit result object. — plot_slice_fit_inter • Spectroscopy Analysis Tools (spant) Plot a 2D slice from an MRSI fit result object. — plot_slice_fit_inter • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -134,7 +134,7 @@ Arguments
diff --git a/docs/reference/plot_slice_map.html b/docs/reference/plot_slice_map.html
index 553e9ac8..ffb2a134 100644
--- a/docs/reference/plot_slice_map.html
+++ b/docs/reference/plot_slice_map.html
@@ -1,5 +1,5 @@
-Plot a slice from a 7 dimensional array. — plot_slice_map • Spectroscopy Analysis Tools (spant) Plot a slice from a 7 dimensional array. — plot_slice_map • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -153,7 +153,7 @@ Arguments
diff --git a/docs/reference/plot_slice_map_inter.html b/docs/reference/plot_slice_map_inter.html
index 40d33b42..90968f66 100644
--- a/docs/reference/plot_slice_map_inter.html
+++ b/docs/reference/plot_slice_map_inter.html
@@ -1,7 +1,5 @@
-Plot an interactive slice map from a data array where voxels can be selected
-to display a corresponding spectrum. — plot_slice_map_inter • Spectroscopy Analysis Tools (spant) Plot an interactive slice map from a data array where voxels can be selected to display a corresponding spectrum. — plot_slice_map_inter • Spectroscopy Analysis Tools (spant) Plot the spectral standard deviation. — plot_spec_sd • Spectroscopy Analysis Tools (spant) Plot the spectral standard deviation. — plot_spec_sd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Arguments
diff --git a/docs/reference/plot_voi_overlay.html b/docs/reference/plot_voi_overlay.html
index 9a782e88..bbbbf35e 100644
--- a/docs/reference/plot_voi_overlay.html
+++ b/docs/reference/plot_voi_overlay.html
@@ -1,5 +1,5 @@
-Plot a volume as an image overlay. — plot_voi_overlay • Spectroscopy Analysis Tools (spant) Plot a volume as an image overlay. — plot_voi_overlay • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -116,7 +116,7 @@ Arguments
diff --git a/docs/reference/plot_voi_overlay_seg.html b/docs/reference/plot_voi_overlay_seg.html
index 3d4e74ff..0e800ff2 100644
--- a/docs/reference/plot_voi_overlay_seg.html
+++ b/docs/reference/plot_voi_overlay_seg.html
@@ -1,5 +1,5 @@
-Plot a volume as an overlay on a segmented brain volume. — plot_voi_overlay_seg • Spectroscopy Analysis Tools (spant) Plot a volume as an overlay on a segmented brain volume. — plot_voi_overlay_seg • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Arguments
diff --git a/docs/reference/ppm.html b/docs/reference/ppm.html
index c352327a..ee4696e2 100644
--- a/docs/reference/ppm.html
+++ b/docs/reference/ppm.html
@@ -1,5 +1,5 @@
-Return the ppm scale of an MRS dataset or fit result. — ppm • Spectroscopy Analysis Tools (spant) Return the ppm scale of an MRS dataset or fit result. — ppm • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -132,7 +132,7 @@ Value
diff --git a/docs/reference/precomp.html b/docs/reference/precomp.html
index 822d7336..df3d2c6c 100644
--- a/docs/reference/precomp.html
+++ b/docs/reference/precomp.html
@@ -1,7 +1,5 @@
-Save function results to file and load on subsequent calls to avoid repeat
-computation. — precomp • Spectroscopy Analysis Tools (spant) Save function results to file and load on subsequent calls to avoid repeat computation. — precomp • Spectroscopy Analysis Tools (spant) Preprocess and perform quality assessment of a single SVS data set. — preproc_svs • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Preprocess and perform quality assessment of a single SVS data set.
+ Source: R/fmrs.R
+ preproc_svs.Rd
+
+
+
+ Preprocess and perform quality assessment of a single SVS data set.
+
+
+
+ preproc_svs(path, label = NULL, output_dir = NULL, ref_inds = NULL)
+
+
+
+ Arguments
+ - path
+path to the fMRS data file or IMA directory.
- label
+a label to describe the data set.
- output_dir
+output directory.
- ref_inds
+a vector of 1-based indices for any water reference dynamic
+scans.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/preproc_svs_dataset.html b/docs/reference/preproc_svs_dataset.html
new file mode 100644
index 00000000..07c3a29b
--- /dev/null
+++ b/docs/reference/preproc_svs_dataset.html
@@ -0,0 +1,148 @@
+
+Preprocess and perform quality assessment of one or more SVS data sets. — preproc_svs_dataset • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Preprocess and perform quality assessment of one or more SVS data sets.
+ Source: R/fmrs.R
+ preproc_svs_dataset.Rd
+
+
+
+ Preprocess and perform quality assessment of one or more SVS data sets.
+
+
+
+ preproc_svs_dataset(
+ paths,
+ labels = NULL,
+ output_dir = "spant_analysis",
+ exclude_labels = NULL,
+ overwrite = FALSE,
+ ref_inds = NULL,
+ return_results = FALSE
+)
+
+
+
+ Arguments
+ - paths
+paths to the fMRS data file or IMA directory.
- labels
+labels to describe each data set.
- output_dir
+output directory.
- exclude_labels
+vector of labels of scans to exclude, eg poor quality
+data.
- overwrite
+overwrite saved results, defaults to FALSE.
- ref_inds
+a vector of 1-based indices for any water reference dynamic
+scans.
- return_results
+function will return key outputs, defaults to FALSE.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/print.fit_result.html b/docs/reference/print.fit_result.html
index 297f28dc..5f434e57 100644
--- a/docs/reference/print.fit_result.html
+++ b/docs/reference/print.fit_result.html
@@ -1,5 +1,5 @@
-Print a summary of an object of class fit_result. — print.fit_result • Spectroscopy Analysis Tools (spant) Print a summary of an object of class fit_result. — print.fit_result • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -105,7 +105,7 @@ Arguments
diff --git a/docs/reference/print.mrs_data.html b/docs/reference/print.mrs_data.html
index 51199017..e1561eb2 100644
--- a/docs/reference/print.mrs_data.html
+++ b/docs/reference/print.mrs_data.html
@@ -1,5 +1,5 @@
-Print a summary of mrs_data parameters. — print.mrs_data • Spectroscopy Analysis Tools (spant) Print a summary of mrs_data parameters. — print.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -109,7 +109,7 @@ Arguments
diff --git a/docs/reference/qn_states.html b/docs/reference/qn_states.html
index 0f42f2f9..d7aa6715 100644
--- a/docs/reference/qn_states.html
+++ b/docs/reference/qn_states.html
@@ -1,5 +1,5 @@
-Get the quantum coherence matrix for a spin system. — qn_states • Spectroscopy Analysis Tools (spant) Get the quantum coherence matrix for a spin system. — qn_states • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/rats.html b/docs/reference/rats.html
index 5a39a396..93585e08 100644
--- a/docs/reference/rats.html
+++ b/docs/reference/rats.html
@@ -1,5 +1,5 @@
-Robust Alignment to a Target Spectrum (RATS). — rats • Spectroscopy Analysis Tools (spant) Robust Alignment to a Target Spectrum (RATS). — rats • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -207,7 +207,7 @@ Value
diff --git a/docs/reference/re_weighting.html b/docs/reference/re_weighting.html
index d21caf21..8b0b070a 100644
--- a/docs/reference/re_weighting.html
+++ b/docs/reference/re_weighting.html
@@ -1,5 +1,5 @@
-Apply a weighting to the FID to enhance spectral resolution. — re_weighting • Spectroscopy Analysis Tools (spant) Apply a weighting to the FID to enhance spectral resolution. — re_weighting • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/read_basis.html b/docs/reference/read_basis.html
index da9b94af..eb6f8557 100644
--- a/docs/reference/read_basis.html
+++ b/docs/reference/read_basis.html
@@ -1,5 +1,5 @@
-Read a basis file in LCModel .basis format. — read_basis • Spectroscopy Analysis Tools (spant) Read a basis file in LCModel .basis format. — read_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/read_ima_coil_dir.html b/docs/reference/read_ima_coil_dir.html
index 28c02de0..4f073cd8 100644
--- a/docs/reference/read_ima_coil_dir.html
+++ b/docs/reference/read_ima_coil_dir.html
@@ -1,9 +1,5 @@
-Read a directory containing Siemens MRS IMA files and combine along the coil
-dimension. Note that the coil ID is inferred from the sorted file name and
-should be checked when consistency is required between two directories. — read_ima_coil_dir • Spectroscopy Analysis Tools (spant) Read a directory containing Siemens MRS IMA files and combine along the coil dimension. Note that the coil ID is inferred from the sorted file name and should be checked when consistency is required between two directories. — read_ima_coil_dir • Spectroscopy Analysis Tools (spant) Read a directory containing Siemens MRS IMA files and combine along the
-dynamic dimension. Note that the coil ID is inferred from the sorted file
-name and should be checked when consistency is required. — read_ima_dyn_dir • Spectroscopy Analysis Tools (spant) Read a directory containing Siemens MRS IMA files and combine along the dynamic dimension. Note that the coil ID is inferred from the sorted file name and should be checked when consistency is required. — read_ima_dyn_dir • Spectroscopy Analysis Tools (spant) Read an LCModel formatted coord file containing fit information. — read_lcm_coord • Spectroscopy Analysis Tools (spant) Read an LCModel formatted coord file containing fit information. — read_lcm_coord • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -107,7 +107,7 @@ Value
diff --git a/docs/reference/read_mrs.html b/docs/reference/read_mrs.html
index 3ac2a36b..2cf36b20 100644
--- a/docs/reference/read_mrs.html
+++ b/docs/reference/read_mrs.html
@@ -1,5 +1,5 @@
-Read MRS data from a file. — read_mrs • Spectroscopy Analysis Tools (spant) Read MRS data from a file. — read_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -88,7 +88,8 @@ Read MRS data from a file.
full_fid = FALSE,
omit_svs_ref_scans = TRUE,
verbose = FALSE,
- extra = NULL
+ extra = NULL,
+ fid_filt_dist = NULL
)
@@ -140,6 +141,13 @@ Arguments
an optional data frame to provide additional variables for use
in subsequent analysis steps, eg id or grouping variables.
fid_filt_dist
+indicate if the data has a distorted FID due to a
+brick-wall filter being used to downsample the data. Default is to auto
+detect this from the data, but TRUE or FALSE options can be given to override
+detection.
Value
@@ -183,7 +191,7 @@ Examples
diff --git a/docs/reference/read_mrs_tqn.html b/docs/reference/read_mrs_tqn.html
index 5766362f..84bdaf3a 100644
--- a/docs/reference/read_mrs_tqn.html
+++ b/docs/reference/read_mrs_tqn.html
@@ -1,5 +1,5 @@
-Read MRS data using the TARQUIN software package. — read_mrs_tqn • Spectroscopy Analysis Tools (spant) Read MRS data using the TARQUIN software package. — read_mrs_tqn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -131,7 +131,7 @@ Examples
diff --git a/docs/reference/read_pulse_ascii.html b/docs/reference/read_pulse_ascii.html
index c9e0d43c..ab11c9cc 100644
--- a/docs/reference/read_pulse_ascii.html
+++ b/docs/reference/read_pulse_ascii.html
@@ -1,5 +1,5 @@
-Read an ASCII formatted pulse file. — read_pulse_ascii • Spectroscopy Analysis Tools (spant) Read an ASCII formatted pulse file. — read_pulse_ascii • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/read_pulse_bruker.html b/docs/reference/read_pulse_bruker.html
index c92bf76a..dbe9073b 100644
--- a/docs/reference/read_pulse_bruker.html
+++ b/docs/reference/read_pulse_bruker.html
@@ -1,5 +1,5 @@
-Read a Bruker formatted pulse file — read_pulse_bruker • Spectroscopy Analysis Tools (spant) Read a Bruker formatted pulse file — read_pulse_bruker • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/read_pulse_pta.html b/docs/reference/read_pulse_pta.html
index 72e1b6d4..a0fac3c3 100644
--- a/docs/reference/read_pulse_pta.html
+++ b/docs/reference/read_pulse_pta.html
@@ -1,5 +1,5 @@
-Read a .pta formatted pulse file compatible with Siemens PulseTool. — read_pulse_pta • Spectroscopy Analysis Tools (spant) Read a .pta formatted pulse file compatible with Siemens PulseTool. — read_pulse_pta • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/read_siemens_txt_hdr.html b/docs/reference/read_siemens_txt_hdr.html
index 23fb8c70..3a17d87c 100644
--- a/docs/reference/read_siemens_txt_hdr.html
+++ b/docs/reference/read_siemens_txt_hdr.html
@@ -1,5 +1,5 @@
-Read the text format header found in Siemens IMA and TWIX data files. — read_siemens_txt_hdr • Spectroscopy Analysis Tools (spant) Read the text format header found in Siemens IMA and TWIX data files. — read_siemens_txt_hdr • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -78,7 +78,7 @@ Read the text format header found in Siemens IMA and TWIX data files.
- read_siemens_txt_hdr(input, version = "vd", verbose, offset = 0)
+ read_siemens_txt_hdr(input, version = "vd", verbose = FALSE, offset = 0)
@@ -118,7 +118,7 @@ Value
diff --git a/docs/reference/read_tqn_fit.html b/docs/reference/read_tqn_fit.html
index 4da6c25e..a1630420 100644
--- a/docs/reference/read_tqn_fit.html
+++ b/docs/reference/read_tqn_fit.html
@@ -1,5 +1,5 @@
-Reader for csv fit results generated by TARQUIN. — read_tqn_fit • Spectroscopy Analysis Tools (spant) Reader for csv fit results generated by TARQUIN. — read_tqn_fit • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -113,7 +113,7 @@ Examples
diff --git a/docs/reference/read_tqn_result.html b/docs/reference/read_tqn_result.html
index 36659714..68a3e98c 100644
--- a/docs/reference/read_tqn_result.html
+++ b/docs/reference/read_tqn_result.html
@@ -1,5 +1,5 @@
-Reader for csv results generated by TARQUIN. — read_tqn_result • Spectroscopy Analysis Tools (spant) Reader for csv results generated by TARQUIN. — read_tqn_result • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -117,7 +117,7 @@ Examples
diff --git a/docs/reference/recon_imag.html b/docs/reference/recon_imag.html
index d2a72225..5bc3b1eb 100644
--- a/docs/reference/recon_imag.html
+++ b/docs/reference/recon_imag.html
@@ -1,7 +1,5 @@
-Reconstruct complex time-domain data from the real part of frequency-domain
-data. — recon_imag • Spectroscopy Analysis Tools (spant) Reconstruct complex time-domain data from the real part of frequency-domain data. — recon_imag • Spectroscopy Analysis Tools (spant) Reconstruct complex time-domain data from the real part of frequency-domain
-data. — recon_imag_vec • Spectroscopy Analysis Tools (spant) Reconstruct complex time-domain data from the real part of frequency-domain data. — recon_imag_vec • Spectroscopy Analysis Tools (spant) Reconstruct 2D MRSI data from a twix file loaded with read_mrs. — recon_twix_2d_mrsi • Spectroscopy Analysis Tools (spant) Reconstruct 2D MRSI data from a twix file loaded with read_mrs. — recon_twix_2d_mrsi • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/rectangular_mask.html b/docs/reference/rectangular_mask.html
index a2117283..6e469bc9 100644
--- a/docs/reference/rectangular_mask.html
+++ b/docs/reference/rectangular_mask.html
@@ -1,5 +1,5 @@
-Create a rectangular mask stored as a matrix of logical values. — rectangular_mask • Spectroscopy Analysis Tools (spant) Create a rectangular mask stored as a matrix of logical values. — rectangular_mask • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -130,7 +130,7 @@ Value
diff --git a/docs/reference/reexports.html b/docs/reference/reexports.html
index 694a75d1..a59e8379 100644
--- a/docs/reference/reexports.html
+++ b/docs/reference/reexports.html
@@ -1,5 +1,5 @@
-Objects exported from other packages — reexports • Spectroscopy Analysis Tools (spant) Objects exported from other packages — reexports • Spectroscopy Analysis Tools (spant)
Spectroscopy Analysis Tools (spant)
- 2.21.0
+ 2.22.0
@@ -103,7 +103,7 @@ Objects exported from other packages
diff --git a/docs/reference/rep_array_dim.html b/docs/reference/rep_array_dim.html
index b9c49b4a..48c0a5ed 100644
--- a/docs/reference/rep_array_dim.html
+++ b/docs/reference/rep_array_dim.html
@@ -1,5 +1,5 @@
-Repeat an array over a given dimension. — rep_array_dim • Spectroscopy Analysis Tools (spant) Repeat an array over a given dimension. — rep_array_dim • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/rep_dyn.html b/docs/reference/rep_dyn.html
index 6bbfb0ef..89a4bb9b 100644
--- a/docs/reference/rep_dyn.html
+++ b/docs/reference/rep_dyn.html
@@ -1,5 +1,5 @@
-Replicate a scan in the dynamic dimension. — rep_dyn • Spectroscopy Analysis Tools (spant) Replicate a scan in the dynamic dimension. — rep_dyn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/rep_mrs.html b/docs/reference/rep_mrs.html
index 67730b5c..becb8f00 100644
--- a/docs/reference/rep_mrs.html
+++ b/docs/reference/rep_mrs.html
@@ -1,5 +1,5 @@
-Replicate a scan over a given dimension. — rep_mrs • Spectroscopy Analysis Tools (spant) Replicate a scan over a given dimension. — rep_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -138,7 +138,7 @@ Value
diff --git a/docs/reference/resample_basis.html b/docs/reference/resample_basis.html
index b0f2ab17..c7a6222a 100644
--- a/docs/reference/resample_basis.html
+++ b/docs/reference/resample_basis.html
@@ -1,5 +1,5 @@
-Resample a basis-set to match a mrs_data acquisition. — resample_basis • Spectroscopy Analysis Tools (spant) Resample a basis-set to match a mrs_data acquisition. — resample_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -116,7 +116,7 @@ Value
diff --git a/docs/reference/resample_img.html b/docs/reference/resample_img.html
index f1e7beaf..b0cc8f71 100644
--- a/docs/reference/resample_img.html
+++ b/docs/reference/resample_img.html
@@ -1,5 +1,5 @@
-Resample an image to match a target image space. — resample_img • Spectroscopy Analysis Tools (spant) Resample an image to match a target image space. — resample_img • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/resample_voi.html b/docs/reference/resample_voi.html
index 8fbfa836..a29ab096 100644
--- a/docs/reference/resample_voi.html
+++ b/docs/reference/resample_voi.html
@@ -1,7 +1,5 @@
-Resample a VOI to match a target image space using nearest-neighbour
-interpolation. — resample_voi • Spectroscopy Analysis Tools (spant) Resample a VOI to match a target image space using nearest-neighbour interpolation. — resample_voi • Spectroscopy Analysis Tools (spant) Reslice a nifti object to match the orientation of mrs data. — reslice_to_mrs • Spectroscopy Analysis Tools (spant) Reslice a nifti object to match the orientation of mrs data. — reslice_to_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/reson_table2mrs_data.html b/docs/reference/reson_table2mrs_data.html
index d75579ee..c5a2167a 100644
--- a/docs/reference/reson_table2mrs_data.html
+++ b/docs/reference/reson_table2mrs_data.html
@@ -1,5 +1,5 @@
-Generate mrs_data from a table of single Lorentzian resonances. — reson_table2mrs_data • Spectroscopy Analysis Tools (spant) Generate mrs_data from a table of single Lorentzian resonances. — reson_table2mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -119,7 +119,7 @@ Value
diff --git a/docs/reference/rm_dyns.html b/docs/reference/rm_dyns.html
index 5d5ef692..573e1f51 100644
--- a/docs/reference/rm_dyns.html
+++ b/docs/reference/rm_dyns.html
@@ -1,5 +1,5 @@
-Remove a subset of dynamic scans. — rm_dyns • Spectroscopy Analysis Tools (spant) Remove a subset of dynamic scans. — rm_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/scale_amp_molal.html b/docs/reference/scale_amp_molal.html
index aaeee1f2..7acb8cb0 100644
--- a/docs/reference/scale_amp_molal.html
+++ b/docs/reference/scale_amp_molal.html
@@ -1,7 +1,5 @@
-Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water). — scale_amp_molal • Spectroscopy Analysis Tools (spant) Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / kg of tissue water). — scale_amp_molal • Spectroscopy Analysis Tools (spant)
Spectroscopy Analysis Tools (spant)
- 2.21.0
+ 2.22.0
@@ -76,8 +74,7 @@
- Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water).
+ Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / kg of tissue water).
Source: R/amp_scaling.R
scale_amp_molal.Rd
@@ -163,7 +160,7 @@ Value
diff --git a/docs/reference/scale_amp_molal_pvc.html b/docs/reference/scale_amp_molal_pvc.html
index 962d6afc..4d194abd 100644
--- a/docs/reference/scale_amp_molal_pvc.html
+++ b/docs/reference/scale_amp_molal_pvc.html
@@ -1,7 +1,5 @@
-Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water). — scale_amp_molal_pvc • Spectroscopy Analysis Tools (spant)
@@ -75,8 +73,7 @@
- Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water).
+ Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / kg of tissue water).
Source: R/amp_scaling.R
scale_amp_molal_pvc.Rd
@@ -141,7 +138,7 @@ Value
diff --git a/docs/reference/scale_amp_molar.html b/docs/reference/scale_amp_molar.html
index 02358d91..dc87a338 100644
--- a/docs/reference/scale_amp_molar.html
+++ b/docs/reference/scale_amp_molar.html
@@ -1,7 +1,5 @@
-Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / Litre of tissue). — scale_amp_molar • Spectroscopy Analysis Tools (spant) Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / Litre of tissue). — scale_amp_molar • Spectroscopy Analysis Tools (spant) Convert default LCM/TARQUIN concentration scaling to molal units with partial
-volume correction. — scale_amp_molar2molal_pvc • Spectroscopy Analysis Tools (spant) Convert default LCM/TARQUIN concentration scaling to molal units with partial volume correction. — scale_amp_molar2molal_pvc • Spectroscopy Analysis Tools (spant) Scale fitted amplitudes to a ratio of signal amplitude. — scale_amp_ratio • Spectroscopy Analysis Tools (spant) Scale fitted amplitudes to a ratio of signal amplitude. — scale_amp_ratio • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -116,7 +116,7 @@ Value
diff --git a/docs/reference/scale_amp_ratio_value.html b/docs/reference/scale_amp_ratio_value.html
index 2036837a..6af8ac51 100644
--- a/docs/reference/scale_amp_ratio_value.html
+++ b/docs/reference/scale_amp_ratio_value.html
@@ -1,5 +1,5 @@
-Scale fitted amplitudes to a ratio of signal amplitude. — scale_amp_ratio_value • Spectroscopy Analysis Tools (spant) Scale fitted amplitudes to a ratio of signal amplitude. — scale_amp_ratio_value • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/scale_amp_water_ratio.html b/docs/reference/scale_amp_water_ratio.html
index 5b25e884..35a76b00 100644
--- a/docs/reference/scale_amp_water_ratio.html
+++ b/docs/reference/scale_amp_water_ratio.html
@@ -1,5 +1,5 @@
-Scale metabolite amplitudes as a ratio to the unsuppressed water amplitude. — scale_amp_water_ratio • Spectroscopy Analysis Tools (spant) Scale metabolite amplitudes as a ratio to the unsuppressed water amplitude. — scale_amp_water_ratio • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/scale_basis_amp.html b/docs/reference/scale_basis_amp.html
index 9401c3f1..5a58b5e5 100644
--- a/docs/reference/scale_basis_amp.html
+++ b/docs/reference/scale_basis_amp.html
@@ -1,5 +1,5 @@
-Scale a basis object by a scalar. — scale_basis_amp • Spectroscopy Analysis Tools (spant) Scale a basis object by a scalar. — scale_basis_amp • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/scale_basis_from_singlet.html b/docs/reference/scale_basis_from_singlet.html
index 0d542bc8..c9a19e77 100644
--- a/docs/reference/scale_basis_from_singlet.html
+++ b/docs/reference/scale_basis_from_singlet.html
@@ -1,5 +1,5 @@
-Scale a basis-set to be consistent with spant assumptions for water scaling. — scale_basis_from_singlet • Spectroscopy Analysis Tools (spant) Scale a basis-set to be consistent with spant assumptions for water scaling. — scale_basis_from_singlet • Spectroscopy Analysis Tools (spant)
Spectroscopy Analysis Tools (spant)
- 2.21.0
+ 2.22.0
@@ -127,7 +127,7 @@ Value
diff --git a/docs/reference/scale_mrs_amp.html b/docs/reference/scale_mrs_amp.html
index b5501a0d..990f058a 100644
--- a/docs/reference/scale_mrs_amp.html
+++ b/docs/reference/scale_mrs_amp.html
@@ -1,5 +1,5 @@
-Scale an mrs_data object by a scalar or vector or amplitudes. — scale_mrs_amp • Spectroscopy Analysis Tools (spant) Scale an mrs_data object by a scalar or vector or amplitudes. — scale_mrs_amp • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/scale_spec.html b/docs/reference/scale_spec.html
index 4f6ea835..6b3ddba4 100644
--- a/docs/reference/scale_spec.html
+++ b/docs/reference/scale_spec.html
@@ -1,5 +1,5 @@
-Scale mrs_data to a spectral region. — scale_spec • Spectroscopy Analysis Tools (spant) Scale mrs_data to a spectral region. — scale_spec • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -141,7 +141,7 @@ Value
diff --git a/docs/reference/sd.html b/docs/reference/sd.html
index ea1eec9f..3ae4dfd4 100644
--- a/docs/reference/sd.html
+++ b/docs/reference/sd.html
@@ -1,5 +1,5 @@
-Calculate the standard deviation spectrum from an mrs_data object. — sd • Spectroscopy Analysis Tools (spant) Calculate the standard deviation spectrum from an mrs_data object. — sd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/sd.mrs_data.html b/docs/reference/sd.mrs_data.html
index 3f92a49f..13bdda85 100644
--- a/docs/reference/sd.mrs_data.html
+++ b/docs/reference/sd.mrs_data.html
@@ -1,5 +1,5 @@
-Calculate the standard deviation spectrum from an mrs_data object. — sd.mrs_data • Spectroscopy Analysis Tools (spant) Calculate the standard deviation spectrum from an mrs_data object. — sd.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/seconds.html b/docs/reference/seconds.html
index b34d6627..467ee17f 100644
--- a/docs/reference/seconds.html
+++ b/docs/reference/seconds.html
@@ -1,5 +1,5 @@
-Return a time scale vector to match the FID of an MRS data object. — seconds • Spectroscopy Analysis Tools (spant) Return a time scale vector to match the FID of an MRS data object. — seconds • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/seq_cpmg_ideal.html b/docs/reference/seq_cpmg_ideal.html
index 547e96ab..45727c86 100644
--- a/docs/reference/seq_cpmg_ideal.html
+++ b/docs/reference/seq_cpmg_ideal.html
@@ -1,5 +1,5 @@
-CPMG style sequence with ideal pulses. — seq_cpmg_ideal • Spectroscopy Analysis Tools (spant) CPMG style sequence with ideal pulses. — seq_cpmg_ideal • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/seq_mega_press_ideal.html b/docs/reference/seq_mega_press_ideal.html
index 0769b8b4..a9cd7fa0 100644
--- a/docs/reference/seq_mega_press_ideal.html
+++ b/docs/reference/seq_mega_press_ideal.html
@@ -1,7 +1,5 @@
-MEGA-PRESS sequence with ideal localisation pulses and Gaussian shaped
-editing pulse. — seq_mega_press_ideal • Spectroscopy Analysis Tools (spant) MEGA-PRESS sequence with ideal localisation pulses and Gaussian shaped editing pulse. — seq_mega_press_ideal • Spectroscopy Analysis Tools (spant) PRESS sequence with shaped refocusing pulses. — seq_press_2d_shaped • Spectroscopy Analysis Tools (spant) PRESS sequence with shaped refocusing pulses. — seq_press_2d_shaped • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -165,7 +165,7 @@ Value
diff --git a/docs/reference/seq_press_ideal.html b/docs/reference/seq_press_ideal.html
index 8c976856..72c3af3d 100644
--- a/docs/reference/seq_press_ideal.html
+++ b/docs/reference/seq_press_ideal.html
@@ -1,5 +1,5 @@
-PRESS sequence with ideal pulses. — seq_press_ideal • Spectroscopy Analysis Tools (spant) PRESS sequence with ideal pulses. — seq_press_ideal • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/seq_pulse_acquire.html b/docs/reference/seq_pulse_acquire.html
index 4a88fc64..ad80571e 100644
--- a/docs/reference/seq_pulse_acquire.html
+++ b/docs/reference/seq_pulse_acquire.html
@@ -1,5 +1,5 @@
-Simple pulse and acquire sequence with ideal pulses. — seq_pulse_acquire • Spectroscopy Analysis Tools (spant) Simple pulse and acquire sequence with ideal pulses. — seq_pulse_acquire • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/seq_slaser_ideal.html b/docs/reference/seq_slaser_ideal.html
index 74688f4d..eb83e8e3 100644
--- a/docs/reference/seq_slaser_ideal.html
+++ b/docs/reference/seq_slaser_ideal.html
@@ -1,5 +1,5 @@
-sLASER sequence with ideal pulses. — seq_slaser_ideal • Spectroscopy Analysis Tools (spant) sLASER sequence with ideal pulses. — seq_slaser_ideal • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -126,7 +126,7 @@ Value
diff --git a/docs/reference/seq_spin_echo_ideal.html b/docs/reference/seq_spin_echo_ideal.html
index e23271de..4248716f 100644
--- a/docs/reference/seq_spin_echo_ideal.html
+++ b/docs/reference/seq_spin_echo_ideal.html
@@ -1,5 +1,5 @@
-Spin echo sequence with ideal pulses. — seq_spin_echo_ideal • Spectroscopy Analysis Tools (spant) Spin echo sequence with ideal pulses. — seq_spin_echo_ideal • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/seq_steam_ideal.html b/docs/reference/seq_steam_ideal.html
index a60685a8..1c8115d7 100644
--- a/docs/reference/seq_steam_ideal.html
+++ b/docs/reference/seq_steam_ideal.html
@@ -1,5 +1,5 @@
-STEAM sequence with ideal pulses. — seq_steam_ideal • Spectroscopy Analysis Tools (spant) STEAM sequence with ideal pulses. — seq_steam_ideal • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -128,7 +128,7 @@ Value
diff --git a/docs/reference/seq_steam_ideal_cof.html b/docs/reference/seq_steam_ideal_cof.html
index 8f225740..cba7af91 100644
--- a/docs/reference/seq_steam_ideal_cof.html
+++ b/docs/reference/seq_steam_ideal_cof.html
@@ -1,7 +1,5 @@
-STEAM sequence with ideal pulses and coherence order filtering to simulate
-gradient crushers. — seq_steam_ideal_cof • Spectroscopy Analysis Tools (spant) STEAM sequence with ideal pulses and coherence order filtering to simulate gradient crushers. — seq_steam_ideal_cof • Spectroscopy Analysis Tools (spant) STEAM sequence with ideal pulses using the z-rotation gradient simulation
-method described by Young et al JMR 140, 146-152 (1999). — seq_steam_ideal_young • Spectroscopy Analysis Tools (spant) STEAM sequence with ideal pulses using the z-rotation gradient simulation method described by Young et al JMR 140, 146-152 (1999). — seq_steam_ideal_young • Spectroscopy Analysis Tools (spant) Set the number of transients for an mrs_data object. — set_Ntrans • Spectroscopy Analysis Tools (spant) Set the number of transients for an mrs_data object. — set_Ntrans • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/set_def_acq_paras.html b/docs/reference/set_def_acq_paras.html
index 3e1b4004..cc2ada9c 100644
--- a/docs/reference/set_def_acq_paras.html
+++ b/docs/reference/set_def_acq_paras.html
@@ -1,5 +1,5 @@
-Set the default acquisition parameters. — set_def_acq_paras • Spectroscopy Analysis Tools (spant) Set the default acquisition parameters. — set_def_acq_paras • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Arguments
diff --git a/docs/reference/set_lcm_cmd.html b/docs/reference/set_lcm_cmd.html
index 2056ed01..42bb2f24 100644
--- a/docs/reference/set_lcm_cmd.html
+++ b/docs/reference/set_lcm_cmd.html
@@ -1,5 +1,5 @@
-Set the command to run the LCModel command-line program. — set_lcm_cmd • Spectroscopy Analysis Tools (spant) Set the command to run the LCModel command-line program. — set_lcm_cmd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/set_lw.html b/docs/reference/set_lw.html
index b64ec851..bb176c62 100644
--- a/docs/reference/set_lw.html
+++ b/docs/reference/set_lw.html
@@ -1,5 +1,5 @@
-Apply line-broadening to an mrs_data object to achieve a specified linewidth. — set_lw • Spectroscopy Analysis Tools (spant) Apply line-broadening to an mrs_data object to achieve a specified linewidth. — set_lw • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -123,7 +123,7 @@ Value
diff --git a/docs/reference/set_mask_xy_mat.html b/docs/reference/set_mask_xy_mat.html
index 49dc5d4e..52c4b617 100644
--- a/docs/reference/set_mask_xy_mat.html
+++ b/docs/reference/set_mask_xy_mat.html
@@ -1,5 +1,5 @@
-Set the masked voxels in a 2D MRSI dataset to given spectrum. — set_mask_xy_mat • Spectroscopy Analysis Tools (spant) Set the masked voxels in a 2D MRSI dataset to given spectrum. — set_mask_xy_mat • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Value
diff --git a/docs/reference/set_precomp_mode.html b/docs/reference/set_precomp_mode.html
index f44bd5d3..47c28e3b 100644
--- a/docs/reference/set_precomp_mode.html
+++ b/docs/reference/set_precomp_mode.html
@@ -1,5 +1,5 @@
-Set the precompute mode. — set_precomp_mode • Spectroscopy Analysis Tools (spant) Set the precompute mode. — set_precomp_mode • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/set_precomp_verbose.html b/docs/reference/set_precomp_verbose.html
index 1453a231..9c613505 100644
--- a/docs/reference/set_precomp_verbose.html
+++ b/docs/reference/set_precomp_verbose.html
@@ -1,5 +1,5 @@
-Set the verbosity of the precompute function. — set_precomp_verbose • Spectroscopy Analysis Tools (spant) Set the verbosity of the precompute function. — set_precomp_verbose • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/set_ref.html b/docs/reference/set_ref.html
index 8953fa50..5436dfa2 100644
--- a/docs/reference/set_ref.html
+++ b/docs/reference/set_ref.html
@@ -1,5 +1,5 @@
-Set the ppm reference value (eg ppm value at 0Hz). — set_ref • Spectroscopy Analysis Tools (spant) Set the ppm reference value (eg ppm value at 0Hz). — set_ref • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/set_td_pts.html b/docs/reference/set_td_pts.html
index 8a80d42a..586459ff 100644
--- a/docs/reference/set_td_pts.html
+++ b/docs/reference/set_td_pts.html
@@ -1,7 +1,5 @@
-Set the number of time-domain data points, truncating or zero-filling as
-appropriate. — set_td_pts • Spectroscopy Analysis Tools (spant) Set the number of time-domain data points, truncating or zero-filling as appropriate. — set_td_pts • Spectroscopy Analysis Tools (spant) Set the command to run the TARQUIN command-line program. — set_tqn_cmd • Spectroscopy Analysis Tools (spant) Set the command to run the TARQUIN command-line program. — set_tqn_cmd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/set_tr.html b/docs/reference/set_tr.html
index b2109ab0..65c9df5f 100644
--- a/docs/reference/set_tr.html
+++ b/docs/reference/set_tr.html
@@ -1,5 +1,5 @@
-Set the repetition time of an MRS dataset. — set_tr • Spectroscopy Analysis Tools (spant) Set the repetition time of an MRS dataset. — set_tr • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/shift.html b/docs/reference/shift.html
index ab0fe724..034591d0 100644
--- a/docs/reference/shift.html
+++ b/docs/reference/shift.html
@@ -1,5 +1,5 @@
-Apply a frequency shift to MRS data. — shift • Spectroscopy Analysis Tools (spant) Apply a frequency shift to MRS data. — shift • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/shift_basis.html b/docs/reference/shift_basis.html
index 2884be19..f55a65e0 100644
--- a/docs/reference/shift_basis.html
+++ b/docs/reference/shift_basis.html
@@ -1,5 +1,5 @@
-Apply frequency shifts to basis set signals. — shift_basis • Spectroscopy Analysis Tools (spant) Apply frequency shifts to basis set signals. — shift_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Value
diff --git a/docs/reference/sim_basis.html b/docs/reference/sim_basis.html
index c7838c46..bb5fefc6 100644
--- a/docs/reference/sim_basis.html
+++ b/docs/reference/sim_basis.html
@@ -1,5 +1,5 @@
-Simulate a basis set object. — sim_basis • Spectroscopy Analysis Tools (spant) Simulate a basis set object. — sim_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -136,7 +136,7 @@ Value
diff --git a/docs/reference/sim_basis_1h_brain.html b/docs/reference/sim_basis_1h_brain.html
index 62ed7389..f71ffa0b 100644
--- a/docs/reference/sim_basis_1h_brain.html
+++ b/docs/reference/sim_basis_1h_brain.html
@@ -1,7 +1,5 @@
-Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS
-sequence. Note, ideal pulses are assumed. — sim_basis_1h_brain • Spectroscopy Analysis Tools (spant) Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS sequence. Note, ideal pulses are assumed. — sim_basis_1h_brain • Spectroscopy Analysis Tools (spant) Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS
-sequence. Note, ideal pulses are assumed. — sim_basis_1h_brain_press • Spectroscopy Analysis Tools (spant) Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS sequence. Note, ideal pulses are assumed. — sim_basis_1h_brain_press • Spectroscopy Analysis Tools (spant) Simulate a macromolecular and lipid basis-set suitable for 1H brain MRS
-analysis. — sim_basis_mm_lip_lcm • Spectroscopy Analysis Tools (spant) Simulate a macromolecular and lipid basis-set suitable for 1H brain MRS analysis. — sim_basis_mm_lip_lcm • Spectroscopy Analysis Tools (spant) Simulate a basis file using TARQUIN. — sim_basis_tqn • Spectroscopy Analysis Tools (spant) Simulate a basis file using TARQUIN. — sim_basis_tqn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -129,7 +129,7 @@ Examples
diff --git a/docs/reference/sim_brain_1h.html b/docs/reference/sim_brain_1h.html
index 2044cf1a..717ee289 100644
--- a/docs/reference/sim_brain_1h.html
+++ b/docs/reference/sim_brain_1h.html
@@ -1,5 +1,5 @@
-Simulate MRS data with a similar appearance to normal brain (by default). — sim_brain_1h • Spectroscopy Analysis Tools (spant) Simulate MRS data with a similar appearance to normal brain (by default). — sim_brain_1h • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -159,7 +159,7 @@ Value
diff --git a/docs/reference/sim_mol.html b/docs/reference/sim_mol.html
index 23bcef50..77f76a50 100644
--- a/docs/reference/sim_mol.html
+++ b/docs/reference/sim_mol.html
@@ -1,5 +1,5 @@
-Simulate a mol_parameter object. — sim_mol • Spectroscopy Analysis Tools (spant) Simulate a mol_parameter object. — sim_mol • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -143,7 +143,7 @@ Value
diff --git a/docs/reference/sim_noise.html b/docs/reference/sim_noise.html
index 23875f79..a71477d4 100644
--- a/docs/reference/sim_noise.html
+++ b/docs/reference/sim_noise.html
@@ -1,5 +1,5 @@
-Simulate an mrs_data object containing simulated Gaussian noise. — sim_noise • Spectroscopy Analysis Tools (spant) Simulate an mrs_data object containing simulated Gaussian noise. — sim_noise • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -84,6 +84,7 @@ Simulate an mrs_data object containing simulated Gaussian noise.
ft = def_ft(),
N = def_N(),
ref = def_ref(),
+ nuc = def_nuc(),
dyns = 1,
fd = TRUE
)
@@ -111,6 +112,10 @@ Arguments
reference value for ppm scale.
nuc
+resonant nucleus.
dyns
number of dynamic scans to generate.
Value
diff --git a/docs/reference/sim_resonances.html b/docs/reference/sim_resonances.html
index 19e9a8a4..d4f8d7c0 100644
--- a/docs/reference/sim_resonances.html
+++ b/docs/reference/sim_resonances.html
@@ -1,5 +1,5 @@
-Simulate a MRS data object containing a set of simulated resonances. — sim_resonances • Spectroscopy Analysis Tools (spant) Simulate a MRS data object containing a set of simulated resonances. — sim_resonances • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -161,7 +161,7 @@ Examples
diff --git a/docs/reference/sim_th_excit_profile.html b/docs/reference/sim_th_excit_profile.html
index 5535c5ef..e781cab1 100644
--- a/docs/reference/sim_th_excit_profile.html
+++ b/docs/reference/sim_th_excit_profile.html
@@ -1,7 +1,5 @@
-Simulate an ideal pulse excitation profile by smoothing a top-hat function
-with a Gaussian. — sim_th_excit_profile • Spectroscopy Analysis Tools (spant) Simulate an ideal pulse excitation profile by smoothing a top-hat function with a Gaussian. — sim_th_excit_profile • Spectroscopy Analysis Tools (spant) Simulate an mrs_data object containing complex zero valued samples. — sim_zero • Spectroscopy Analysis Tools (spant) Simulate an mrs_data object containing complex zero valued samples. — sim_zero • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -78,7 +78,14 @@ Simulate an mrs_data object containing complex zero valued samples.
-
+
@@ -99,6 +106,10 @@ Arguments
reference value for ppm scale.
nuc
+resonant nucleus.
dyns
number of dynamic scans to generate.
Value
diff --git a/docs/reference/smooth_dyns.html b/docs/reference/smooth_dyns.html
index 4cc8da50..accf3a51 100644
--- a/docs/reference/smooth_dyns.html
+++ b/docs/reference/smooth_dyns.html
@@ -1,5 +1,5 @@
-Smooth data across the dynamic dimension with a Gaussian kernel. — smooth_dyns • Spectroscopy Analysis Tools (spant) Smooth data across the dynamic dimension with a Gaussian kernel. — smooth_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/sort_basis.html b/docs/reference/sort_basis.html
index 6a676ea2..d25cc006 100644
--- a/docs/reference/sort_basis.html
+++ b/docs/reference/sort_basis.html
@@ -1,5 +1,5 @@
-Sort the basis-set elements alphabetically. — sort_basis • Spectroscopy Analysis Tools (spant) Sort the basis-set elements alphabetically. — sort_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/spant-package.html b/docs/reference/spant-package.html
index b3dd8e21..90f19ec3 100644
--- a/docs/reference/spant-package.html
+++ b/docs/reference/spant-package.html
@@ -1,5 +1,5 @@
-spant: spectroscopy analysis tools. — spant-package • Spectroscopy Analysis Tools (spant) spant: spectroscopy analysis tools. — spant-package • Spectroscopy Analysis Tools (spant) Simulate and fit some spectra with ABfit for benchmarking purposes. Basic
-timing and performance metrics will be printed. — spant_abfit_benchmark • Spectroscopy Analysis Tools (spant) Simulate and fit some spectra with ABfit for benchmarking purposes. Basic timing and performance metrics will be printed. — spant_abfit_benchmark • Spectroscopy Analysis Tools (spant) Example MEGA-PRESS data with significant B0 drift. — spant_mpress_drift • Spectroscopy Analysis Tools (spant) Example MEGA-PRESS data with significant B0 drift. — spant_mpress_drift • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -83,7 +83,7 @@ Example MEGA-PRESS data with significant B0 drift.
Format
- An object of class mrs_data of length 13.
+ An object of class mrs_data of dimension 1 x 1 x 1 x 1 x 40 x 1 x 1024.
@@ -98,7 +98,7 @@ Format
diff --git a/docs/reference/spant_sim_fmrs_dataset.html b/docs/reference/spant_sim_fmrs_dataset.html
new file mode 100644
index 00000000..00e48b56
--- /dev/null
+++ b/docs/reference/spant_sim_fmrs_dataset.html
@@ -0,0 +1,117 @@
+
+Simulate an example fMRS dataset for a block design fMRS experiment and export a BIDS structure. — spant_sim_fmrs_dataset • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Simulate an example fMRS dataset for a block design fMRS experiment and export a BIDS structure.
+ Source: R/fmrs.R
+ spant_sim_fmrs_dataset.Rd
+
+
+
+ Simulate an example fMRS dataset for a block design fMRS experiment and
+export a BIDS structure.
+
+
+
+ spant_sim_fmrs_dataset(output_dir = NULL)
+
+
+
+ Arguments
+ - output_dir
+output directory for the BIDS data. Defaults to :
+"HOME/sim_fmrs_dataset/data".
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/spant_simulation_benchmark.html b/docs/reference/spant_simulation_benchmark.html
index 32daa8bf..d8cc6841 100644
--- a/docs/reference/spant_simulation_benchmark.html
+++ b/docs/reference/spant_simulation_benchmark.html
@@ -1,7 +1,5 @@
-Simulate a typical metabolite basis set for benchmarking. Timing metrics will
-be printed on completion. — spant_simulation_benchmark • Spectroscopy Analysis Tools (spant) Simulate a typical metabolite basis set for benchmarking. Timing metrics will be printed on completion. — spant_simulation_benchmark • Spectroscopy Analysis Tools (spant) Decompose an mrs_data object into white and gray matter spectra. — spec_decomp • Spectroscopy Analysis Tools (spant) Perform a mathematical operation on a spectral region. — spec_op • Spectroscopy Analysis Tools (spant) Perform a mathematical operation on a spectral region. — spec_op • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -98,8 +98,8 @@ Arguments
operator
-can be "sum" (default), "mean", "l2", "max", "min" or
-"max-min".
can be "sum" (default), "mean", "l2", "max", "max_cplx,
+"min" or "max-min".
freq_scale
@@ -129,7 +129,7 @@ Value
diff --git a/docs/reference/spin_sys.html b/docs/reference/spin_sys.html
index 853423a4..1eaa9e76 100644
--- a/docs/reference/spin_sys.html
+++ b/docs/reference/spin_sys.html
@@ -1,5 +1,5 @@
-Create a spin system object for pulse sequence simulation. — spin_sys • Spectroscopy Analysis Tools (spant) Create a spin system object for pulse sequence simulation. — spin_sys • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/spm_pve2categorical.html b/docs/reference/spm_pve2categorical.html
index 23a1bad9..70f10729 100644
--- a/docs/reference/spm_pve2categorical.html
+++ b/docs/reference/spm_pve2categorical.html
@@ -1,7 +1,5 @@
-Convert SPM style segmentation files to a single categorical image where
-the numerical values map as: 0) Other, 1) CSF, 2) GM and 3) WM. — spm_pve2categorical • Spectroscopy Analysis Tools (spant) Convert SPM style segmentation files to a single categorical image where the numerical values map as: 0) Other, 1) CSF, 2) GM and 3) WM. — spm_pve2categorical • Spectroscopy Analysis Tools (spant) Signal space projection method for lipid suppression. — ssp • Spectroscopy Analysis Tools (spant) Signal space projection method for lipid suppression. — ssp • Spectroscopy Analysis Tools (spant) Plot the fitting results of an object of class fit_result with
-individual basis set components shown. — stackplot.fit_result • Spectroscopy Analysis Tools (spant) Plot the fitting results of an object of class fit_result with individual basis set components shown. — stackplot.fit_result • Spectroscopy Analysis Tools (spant) Produce a plot with multiple traces. — stackplot • Spectroscopy Analysis Tools (spant) Produce a plot with multiple traces. — stackplot • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/stackplot.mrs_data.html b/docs/reference/stackplot.mrs_data.html
index 17ff5648..64eea445 100644
--- a/docs/reference/stackplot.mrs_data.html
+++ b/docs/reference/stackplot.mrs_data.html
@@ -1,5 +1,5 @@
-Stackplot plotting method for objects of class mrs_data. — stackplot.mrs_data • Spectroscopy Analysis Tools (spant) Stackplot plotting method for objects of class mrs_data. — stackplot.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -255,7 +255,7 @@ Arguments
diff --git a/docs/reference/sub_first_dyn.html b/docs/reference/sub_first_dyn.html
index dbd7f831..493b7242 100644
--- a/docs/reference/sub_first_dyn.html
+++ b/docs/reference/sub_first_dyn.html
@@ -1,5 +1,5 @@
-Subtract the first dynamic spectrum from a dynamic series. — sub_first_dyn • Spectroscopy Analysis Tools (spant) Subtract the first dynamic spectrum from a dynamic series. — sub_first_dyn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/sub_mean_dyns.html b/docs/reference/sub_mean_dyns.html
index 6e3bb2df..221bd0c1 100644
--- a/docs/reference/sub_mean_dyns.html
+++ b/docs/reference/sub_mean_dyns.html
@@ -1,5 +1,5 @@
-Subtract the mean dynamic spectrum from a dynamic series. — sub_mean_dyns • Spectroscopy Analysis Tools (spant) Subtract the mean dynamic spectrum from a dynamic series. — sub_mean_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/sub_median_dyns.html b/docs/reference/sub_median_dyns.html
index 134c495d..1e834f14 100644
--- a/docs/reference/sub_median_dyns.html
+++ b/docs/reference/sub_median_dyns.html
@@ -1,5 +1,5 @@
-Subtract the median dynamic spectrum from a dynamic series. — sub_median_dyns • Spectroscopy Analysis Tools (spant) Subtract the median dynamic spectrum from a dynamic series. — sub_median_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/sum_coils.html b/docs/reference/sum_coils.html
index 7bf559f2..e1ab3cc0 100644
--- a/docs/reference/sum_coils.html
+++ b/docs/reference/sum_coils.html
@@ -1,5 +1,5 @@
-Calculate the sum across receiver coil elements. — sum_coils • Spectroscopy Analysis Tools (spant) Calculate the sum across receiver coil elements. — sum_coils • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/sum_dyns.html b/docs/reference/sum_dyns.html
index a0be19d3..bbda2ffc 100644
--- a/docs/reference/sum_dyns.html
+++ b/docs/reference/sum_dyns.html
@@ -1,5 +1,5 @@
-Calculate the sum of data dynamics. — sum_dyns • Spectroscopy Analysis Tools (spant) Calculate the sum of data dynamics. — sum_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/sum_mrs.html b/docs/reference/sum_mrs.html
index a22f215b..3cc3ab9e 100644
--- a/docs/reference/sum_mrs.html
+++ b/docs/reference/sum_mrs.html
@@ -1,5 +1,5 @@
-Sum two mrs_data objects. — sum_mrs • Spectroscopy Analysis Tools (spant) Sum two mrs_data objects. — sum_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Value
diff --git a/docs/reference/sum_mrs_list.html b/docs/reference/sum_mrs_list.html
index f4e09aea..c3584348 100644
--- a/docs/reference/sum_mrs_list.html
+++ b/docs/reference/sum_mrs_list.html
@@ -1,5 +1,5 @@
-Return the sum of a list of mrs_data objects. — sum_mrs_list • Spectroscopy Analysis Tools (spant) Return the sum of a list of mrs_data objects. — sum_mrs_list • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/svs_1h_brain_analysis.html b/docs/reference/svs_1h_brain_analysis.html
index 8ce514db..dff0ef7d 100644
--- a/docs/reference/svs_1h_brain_analysis.html
+++ b/docs/reference/svs_1h_brain_analysis.html
@@ -1,5 +1,5 @@
-Standard SVS 1H brain analysis pipeline. — svs_1h_brain_analysis • Spectroscopy Analysis Tools (spant) Standard SVS 1H brain analysis pipeline. — svs_1h_brain_analysis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -199,7 +199,7 @@ Value
diff --git a/docs/reference/svs_1h_brain_analysis_dev.html b/docs/reference/svs_1h_brain_analysis_dev.html
index d70a14d3..d71bfea2 100644
--- a/docs/reference/svs_1h_brain_analysis_dev.html
+++ b/docs/reference/svs_1h_brain_analysis_dev.html
@@ -1,5 +1,5 @@
-Standard SVS 1H brain analysis pipeline. — svs_1h_brain_analysis_dev • Spectroscopy Analysis Tools (spant) Standard SVS 1H brain analysis pipeline. — svs_1h_brain_analysis_dev • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -193,7 +193,7 @@ Examples
diff --git a/docs/reference/svs_1h_brain_batch_analysis.html b/docs/reference/svs_1h_brain_batch_analysis.html
index 5631e8cc..15f7223e 100644
--- a/docs/reference/svs_1h_brain_batch_analysis.html
+++ b/docs/reference/svs_1h_brain_batch_analysis.html
@@ -1,5 +1,5 @@
-Batch interface to the standard SVS 1H brain analysis pipeline. — svs_1h_brain_batch_analysis • Spectroscopy Analysis Tools (spant) Batch interface to the standard SVS 1H brain analysis pipeline. — svs_1h_brain_batch_analysis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -144,7 +144,7 @@ Value
diff --git a/docs/reference/t_test_spec.html b/docs/reference/t_test_spec.html
new file mode 100644
index 00000000..56a7ea1b
--- /dev/null
+++ b/docs/reference/t_test_spec.html
@@ -0,0 +1,124 @@
+
+Perform a t-test on spectral data points. — t_test_spec • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+
+
+ Perform a t-test on spectral data points.
+
+
+
+ t_test_spec(mrs_data, group)
+
+
+
+ Arguments
+ - mrs_data
+an mrs_data object with spectra in the dynamic dimension.
- group
+vector describing the group membership of each dynamic spectrum.
+
+ Value
+
+
+a list of statistical results.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/td2fd.html b/docs/reference/td2fd.html
index 6748a6a8..f31ed524 100644
--- a/docs/reference/td2fd.html
+++ b/docs/reference/td2fd.html
@@ -1,5 +1,5 @@
-Transform time-domain data to the frequency-domain. — td2fd • Spectroscopy Analysis Tools (spant) Transform time-domain data to the frequency-domain. — td2fd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/td_conv_filt.html b/docs/reference/td_conv_filt.html
index a9f340c3..106b9b00 100644
--- a/docs/reference/td_conv_filt.html
+++ b/docs/reference/td_conv_filt.html
@@ -1,5 +1,5 @@
-Time-domain convolution based filter. — td_conv_filt • Spectroscopy Analysis Tools (spant) Time-domain convolution based filter. — td_conv_filt • Spectroscopy Analysis Tools (spant) Time-domain spectral registration. — tdsr • Spectroscopy Analysis Tools (spant) Time-domain spectral registration. — tdsr • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -121,7 +121,7 @@ Value
diff --git a/docs/reference/te.html b/docs/reference/te.html
index 010361b1..4a65711d 100644
--- a/docs/reference/te.html
+++ b/docs/reference/te.html
@@ -1,5 +1,5 @@
-Return the echo time of an MRS dataset. — te • Spectroscopy Analysis Tools (spant) Return the echo time of an MRS dataset. — te • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/tr.html b/docs/reference/tr.html
index 0c0bd63b..2e749e02 100644
--- a/docs/reference/tr.html
+++ b/docs/reference/tr.html
@@ -1,5 +1,5 @@
-Return the repetition time of an MRS dataset. — tr • Spectroscopy Analysis Tools (spant) Return the repetition time of an MRS dataset. — tr • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/varpro_3_para_opts.html b/docs/reference/varpro_3_para_opts.html
index c2270a16..52d7cd84 100644
--- a/docs/reference/varpro_3_para_opts.html
+++ b/docs/reference/varpro_3_para_opts.html
@@ -1,5 +1,5 @@
-Return a list of options for VARPRO based fitting with 3 free parameters. — varpro_3_para_opts • Spectroscopy Analysis Tools (spant) Return a list of options for VARPRO based fitting with 3 free parameters. — varpro_3_para_opts • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -141,7 +141,7 @@ Value
diff --git a/docs/reference/varpro_basic_opts.html b/docs/reference/varpro_basic_opts.html
index 32c86d22..c5104891 100644
--- a/docs/reference/varpro_basic_opts.html
+++ b/docs/reference/varpro_basic_opts.html
@@ -1,5 +1,5 @@
-Return a list of options for a basic VARPRO analysis. — varpro_basic_opts • Spectroscopy Analysis Tools (spant) Return a list of options for a basic VARPRO analysis. — varpro_basic_opts • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -118,7 +118,7 @@ Value
diff --git a/docs/reference/varpro_opts.html b/docs/reference/varpro_opts.html
index 2aabf11d..6332f730 100644
--- a/docs/reference/varpro_opts.html
+++ b/docs/reference/varpro_opts.html
@@ -1,5 +1,5 @@
-Return a list of options for VARPRO based fitting. — varpro_opts • Spectroscopy Analysis Tools (spant) Return a list of options for VARPRO based fitting. — varpro_opts • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -177,7 +177,7 @@ Examples
diff --git a/docs/reference/vec2mrs_data.html b/docs/reference/vec2mrs_data.html
index 0cccd73b..f0d58bf0 100644
--- a/docs/reference/vec2mrs_data.html
+++ b/docs/reference/vec2mrs_data.html
@@ -1,5 +1,5 @@
-Convert a vector into a mrs_data object. — vec2mrs_data • Spectroscopy Analysis Tools (spant) Convert a vector into a mrs_data object. — vec2mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -80,10 +80,11 @@ Convert a vector into a mrs_data object.
vec2mrs_data(
vec,
- fs = def_fs(),
- ft = def_ft(),
- ref = def_ref(),
- nuc = def_nuc(),
+ mrs_data = NULL,
+ fs = NULL,
+ ft = NULL,
+ ref = NULL,
+ nuc = NULL,
dyns = 1,
fd = FALSE
)
@@ -95,6 +96,10 @@ Arguments
the data vector.
mrs_data
+example data to copy acquisition parameters from.
fs
sampling frequency in Hz.
Arguments
fd
-flag to indicate if the matrix is in the frequency domain (logical).
flag to indicate if the vector is in the frequency domain (logical).
Value
diff --git a/docs/reference/write_basis.html b/docs/reference/write_basis.html
index b6e27cbd..94c5e021 100644
--- a/docs/reference/write_basis.html
+++ b/docs/reference/write_basis.html
@@ -1,5 +1,5 @@
-Write a basis object to an LCModel .basis formatted file. — write_basis • Spectroscopy Analysis Tools (spant) Write a basis object to an LCModel .basis formatted file. — write_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -108,7 +108,7 @@ Arguments
diff --git a/docs/reference/write_basis_tqn.html b/docs/reference/write_basis_tqn.html
index 6aa51c1d..116c73ec 100644
--- a/docs/reference/write_basis_tqn.html
+++ b/docs/reference/write_basis_tqn.html
@@ -1,5 +1,5 @@
-Generate a basis file using TARQUIN. — write_basis_tqn • Spectroscopy Analysis Tools (spant) Generate a basis file using TARQUIN. — write_basis_tqn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Examples
diff --git a/docs/reference/write_mrs.html b/docs/reference/write_mrs.html
index fff25f15..124b9dc4 100644
--- a/docs/reference/write_mrs.html
+++ b/docs/reference/write_mrs.html
@@ -1,5 +1,5 @@
-Write MRS data object to file. — write_mrs • Spectroscopy Analysis Tools (spant) Write MRS data object to file. — write_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Arguments
diff --git a/docs/reference/write_mrs_nifti.html b/docs/reference/write_mrs_nifti.html
index f4bf1921..bd3ed4b7 100644
--- a/docs/reference/write_mrs_nifti.html
+++ b/docs/reference/write_mrs_nifti.html
@@ -1,5 +1,5 @@
-Write MRS data object to file in NIFTI format. — write_mrs_nifti • Spectroscopy Analysis Tools (spant) Write MRS data object to file in NIFTI format. — write_mrs_nifti • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/write_pulse_ascii.html b/docs/reference/write_pulse_ascii.html
index 067ae086..221f8ebb 100644
--- a/docs/reference/write_pulse_ascii.html
+++ b/docs/reference/write_pulse_ascii.html
@@ -1,5 +1,5 @@
-Write an ASCII formatted pulse file. — write_pulse_ascii • Spectroscopy Analysis Tools (spant) Write an ASCII formatted pulse file. — write_pulse_ascii • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/zero_fade_spec.html b/docs/reference/zero_fade_spec.html
index c703745c..c8b572c3 100644
--- a/docs/reference/zero_fade_spec.html
+++ b/docs/reference/zero_fade_spec.html
@@ -1,7 +1,5 @@
-Fade a spectrum to zero by frequency domain multiplication with a tanh
-function. Note this operation distorts data points at the end of the FID. — zero_fade_spec • Spectroscopy Analysis Tools (spant) Fade a spectrum to zero by frequency domain multiplication with a tanh function. Note this operation distorts data points at the end of the FID. — zero_fade_spec • Spectroscopy Analysis Tools (spant) Zero all coherences including and above a given order. — zero_higher_orders • Spectroscopy Analysis Tools (spant) Zero all coherences including and above a given order. — zero_higher_orders • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Value
diff --git a/docs/reference/zero_td_pts_end.html b/docs/reference/zero_td_pts_end.html
index 8c1123c8..71d24ebb 100644
--- a/docs/reference/zero_td_pts_end.html
+++ b/docs/reference/zero_td_pts_end.html
@@ -1,5 +1,5 @@
-Set mrs_data object data points at the end of the FID to zero. — zero_td_pts_end • Spectroscopy Analysis Tools (spant) Set mrs_data object data points at the end of the FID to zero. — zero_td_pts_end • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/zf.html b/docs/reference/zf.html
index 85e2013c..baf50256 100644
--- a/docs/reference/zf.html
+++ b/docs/reference/zf.html
@@ -1,5 +1,5 @@
-Zero-fill MRS data in the time domain. — zf • Spectroscopy Analysis Tools (spant) Zero-fill MRS data in the time domain. — zf • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -125,7 +125,7 @@ Value
diff --git a/docs/reference/zf_xy.html b/docs/reference/zf_xy.html
index ebca3999..c4104a74 100644
--- a/docs/reference/zf_xy.html
+++ b/docs/reference/zf_xy.html
@@ -1,5 +1,5 @@
-Zero-fill MRSI data in the k-space x-y direction. — zf_xy • Spectroscopy Analysis Tools (spant) Zero-fill MRSI data in the k-space x-y direction. — zf_xy • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -113,7 +113,7 @@ Value
diff --git a/docs/sitemap.xml b/docs/sitemap.xml
index e2139f71..4c39f515 100644
--- a/docs/sitemap.xml
+++ b/docs/sitemap.xml
@@ -216,6 +216,12 @@
https://martin3141.github.io/spant/reference/comb_coils_fp_pc.html
+
+ https://martin3141.github.io/spant/reference/comb_coils_mrsi_gls.html
+
+
+ https://martin3141.github.io/spant/reference/comb_coils_svs_gls.html
+
https://martin3141.github.io/spant/reference/comb_csv_results.html
@@ -411,6 +417,9 @@
https://martin3141.github.io/spant/reference/gen_conv_reg.html
+
+ https://martin3141.github.io/spant/reference/gen_group_reg.html
+
https://martin3141.github.io/spant/reference/gen_impulse_reg.html
@@ -555,6 +564,15 @@
https://martin3141.github.io/spant/reference/glm_spec.html
+
+ https://martin3141.github.io/spant/reference/glm_spec_fmrs_fl.html
+
+
+ https://martin3141.github.io/spant/reference/glm_spec_fmrs_group.html
+
+
+ https://martin3141.github.io/spant/reference/glm_spec_group_linhyp.html
+
https://martin3141.github.io/spant/reference/grid_shift_xy.html
@@ -690,9 +708,15 @@
https://martin3141.github.io/spant/reference/mrs_data2basis.html
+
+ https://martin3141.github.io/spant/reference/mrs_data2bids.html
+
https://martin3141.github.io/spant/reference/mrs_data2mat.html
+
+ https://martin3141.github.io/spant/reference/mrs_data2spec_mat.html
+
https://martin3141.github.io/spant/reference/mrs_data2vec.html
@@ -741,6 +765,9 @@
https://martin3141.github.io/spant/reference/phase.html
+
+ https://martin3141.github.io/spant/reference/phase_ref_1h_brain.html
+
https://martin3141.github.io/spant/reference/plot.fit_result.html
@@ -780,6 +807,12 @@
https://martin3141.github.io/spant/reference/precomp.html
+
+ https://martin3141.github.io/spant/reference/preproc_svs.html
+
+
+ https://martin3141.github.io/spant/reference/preproc_svs_dataset.html
+
https://martin3141.github.io/spant/reference/print.fit_result.html
@@ -1050,6 +1083,9 @@
https://martin3141.github.io/spant/reference/spant_mpress_drift.html
+
+ https://martin3141.github.io/spant/reference/spant_sim_fmrs_dataset.html
+
https://martin3141.github.io/spant/reference/spant_simulation_benchmark.html
@@ -1107,6 +1143,9 @@
https://martin3141.github.io/spant/reference/svs_1h_brain_batch_analysis.html
+
+ https://martin3141.github.io/spant/reference/t_test_spec.html
+
https://martin3141.github.io/spant/reference/td2fd.html
Plot the fitting results of an object of class fit_result with
-individual basis set components shown.
Plot the fitting results of an object of class fit_result with individual basis set components shown.
All functions svs_1h_brain_batch_analysis()
Batch interface to the standard SVS 1H brain analysis pipeline.
Batch interface to the standard SVS 1H brain analysis pipeline.
Perform a t-test on spectral data points.
All functions
- Fade a spectrum to zero by frequency domain multiplication with a tanh
-function. Note this operation distorts data points at the end of the FID.
Fade a spectrum to zero by frequency domain multiplication with a tanh function. Note this operation distorts data points at the end of the FID.
@@ -1549,7 +1524,7 @@ All functions
diff --git a/docs/reference/int_spec.html b/docs/reference/int_spec.html
index c7060fe7..783325a8 100644
--- a/docs/reference/int_spec.html
+++ b/docs/reference/int_spec.html
@@ -1,5 +1,5 @@
-Integrate a spectral region. — int_spec • Spectroscopy Analysis Tools (spant) Integrate a spectral region. — int_spec • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -118,7 +118,7 @@ Value
diff --git a/docs/reference/interleave_dyns.html b/docs/reference/interleave_dyns.html
index effe5543..441eff27 100644
--- a/docs/reference/interleave_dyns.html
+++ b/docs/reference/interleave_dyns.html
@@ -1,5 +1,5 @@
-Interleave the first and second half of a dynamic series. — interleave_dyns • Spectroscopy Analysis Tools (spant) Interleave the first and second half of a dynamic series. — interleave_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/inv_even_dyns.html b/docs/reference/inv_even_dyns.html
index 9f9d4fff..dcb781dc 100644
--- a/docs/reference/inv_even_dyns.html
+++ b/docs/reference/inv_even_dyns.html
@@ -1,5 +1,5 @@
-Invert even numbered dynamic scans starting from 1 (2,4,6...). — inv_even_dyns • Spectroscopy Analysis Tools (spant) Invert even numbered dynamic scans starting from 1 (2,4,6...). — inv_even_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/inv_odd_dyns.html b/docs/reference/inv_odd_dyns.html
index 26212e2b..78d64660 100644
--- a/docs/reference/inv_odd_dyns.html
+++ b/docs/reference/inv_odd_dyns.html
@@ -1,5 +1,5 @@
-Invert odd numbered dynamic scans starting from 1 (1,3,5...). — inv_odd_dyns • Spectroscopy Analysis Tools (spant) Invert odd numbered dynamic scans starting from 1 (1,3,5...). — inv_odd_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/is.def.html b/docs/reference/is.def.html
index f196ffd0..a67b9eba 100644
--- a/docs/reference/is.def.html
+++ b/docs/reference/is.def.html
@@ -1,5 +1,5 @@
-Check if an object is defined, which is the same as being not NULL. — is.def • Spectroscopy Analysis Tools (spant) Check if an object is defined, which is the same as being not NULL. — is.def • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/is_fd.html b/docs/reference/is_fd.html
index 3b0ca165..18a193aa 100644
--- a/docs/reference/is_fd.html
+++ b/docs/reference/is_fd.html
@@ -1,7 +1,5 @@
-Check if the chemical shift dimension of an MRS data object is in the
-frequency domain. — is_fd • Spectroscopy Analysis Tools (spant) Check if the chemical shift dimension of an MRS data object is in the frequency domain. — is_fd • Spectroscopy Analysis Tools (spant) Transform 2D MRSI data from k-space to image space in the x-y direction. — kspace2img_xy • Spectroscopy Analysis Tools (spant) Transform 2D MRSI data from k-space to image space in the x-y direction. — kspace2img_xy • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/l2_reg.html b/docs/reference/l2_reg.html
index 3d781d80..21aa9849 100644
--- a/docs/reference/l2_reg.html
+++ b/docs/reference/l2_reg.html
@@ -1,5 +1,5 @@
-Perform l2 regularisation artefact suppression. — l2_reg • Spectroscopy Analysis Tools (spant) Perform l2 regularisation artefact suppression. — l2_reg • Spectroscopy Analysis Tools (spant) Apply line-broadening (apodisation) to MRS data or basis object. — lb • Spectroscopy Analysis Tools (spant) Apply line-broadening (apodisation) to MRS data or basis object. — lb • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -123,7 +123,7 @@ Value
diff --git a/docs/reference/lofdc.html b/docs/reference/lofdc.html
index 5419b1ec..31347a25 100644
--- a/docs/reference/lofdc.html
+++ b/docs/reference/lofdc.html
@@ -1,5 +1,5 @@
-Correct linear frequency drift. — lofdc • Spectroscopy Analysis Tools (spant) Correct linear frequency drift. — lofdc • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -138,7 +138,7 @@ Value
diff --git a/docs/reference/lw2alpha.html b/docs/reference/lw2alpha.html
index b83db682..25da229b 100644
--- a/docs/reference/lw2alpha.html
+++ b/docs/reference/lw2alpha.html
@@ -1,7 +1,5 @@
-Covert a linewidth in Hz to an equivalent alpha value in the time-domain ie:
-x * exp(-t * alpha). — lw2alpha • Spectroscopy Analysis Tools (spant) Covert a linewidth in Hz to an equivalent alpha value in the time-domain ie: x * exp(-t * alpha). — lw2alpha • Spectroscopy Analysis Tools (spant) Covert a linewidth in Hz to an equivalent beta value in the time-domain ie:
-x * exp(-t * t * beta). — lw2beta • Spectroscopy Analysis Tools (spant) Covert a linewidth in Hz to an equivalent beta value in the time-domain ie: x * exp(-t * t * beta). — lw2beta • Spectroscopy Analysis Tools (spant) Make a basis-set object from a directory containing LCModel formatted RAW
-files. — make_basis_from_raw • Spectroscopy Analysis Tools (spant) Make a basis-set object from a directory containing LCModel formatted RAW files. — make_basis_from_raw • Spectroscopy Analysis Tools (spant) Mask an MRS dataset in the dynamic dimension. — mask_dyns • Spectroscopy Analysis Tools (spant) Mask an MRS dataset in the dynamic dimension. — mask_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/mask_fit_res.html b/docs/reference/mask_fit_res.html
index 97baaa3f..ebd91a99 100644
--- a/docs/reference/mask_fit_res.html
+++ b/docs/reference/mask_fit_res.html
@@ -1,5 +1,5 @@
-Mask fit result spectra depending on a vector of bool values. — mask_fit_res • Spectroscopy Analysis Tools (spant) Mask fit result spectra depending on a vector of bool values. — mask_fit_res • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -116,7 +116,7 @@ Value
diff --git a/docs/reference/mask_xy.html b/docs/reference/mask_xy.html
index 11bb577c..b0d38619 100644
--- a/docs/reference/mask_xy.html
+++ b/docs/reference/mask_xy.html
@@ -1,5 +1,5 @@
-Mask an MRSI dataset in the x-y direction — mask_xy • Spectroscopy Analysis Tools (spant) Mask an MRSI dataset in the x-y direction — mask_xy • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/mask_xy_corners.html b/docs/reference/mask_xy_corners.html
index 09b16cd2..2d13839d 100644
--- a/docs/reference/mask_xy_corners.html
+++ b/docs/reference/mask_xy_corners.html
@@ -1,5 +1,5 @@
-Mask the four corners of an MRSI dataset in the x-y plane. — mask_xy_corners • Spectroscopy Analysis Tools (spant) Mask the four corners of an MRSI dataset in the x-y plane. — mask_xy_corners • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/mask_xy_ellipse.html b/docs/reference/mask_xy_ellipse.html
index 1d8b02e4..e2e749ef 100644
--- a/docs/reference/mask_xy_ellipse.html
+++ b/docs/reference/mask_xy_ellipse.html
@@ -1,7 +1,5 @@
-Mask the voxels outside an elliptical region spanning the MRSI dataset in the
-x-y plane. — mask_xy_ellipse • Spectroscopy Analysis Tools (spant) Mask the voxels outside an elliptical region spanning the MRSI dataset in the x-y plane. — mask_xy_ellipse • Spectroscopy Analysis Tools (spant) Mask a 2D MRSI dataset in the x-y dimension. — mask_xy_mat • Spectroscopy Analysis Tools (spant) Mask a 2D MRSI dataset in the x-y dimension. — mask_xy_mat • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Value
diff --git a/docs/reference/mat2mrs_data.html b/docs/reference/mat2mrs_data.html
index 2e2895f3..ae55665f 100644
--- a/docs/reference/mat2mrs_data.html
+++ b/docs/reference/mat2mrs_data.html
@@ -1,7 +1,5 @@
-Convert a matrix (with spectral points in the column dimension and dynamics
-in the row dimensions) into a mrs_data object. — mat2mrs_data • Spectroscopy Analysis Tools (spant) Convert a matrix (with spectral points in the column dimension and dynamics in the row dimensions) into a mrs_data object. — mat2mrs_data • Spectroscopy Analysis Tools (spant) Matrix exponential function taken from complexplus package to reduce the
-number of spant dependencies. — matexp • Spectroscopy Analysis Tools (spant) Matrix exponential function taken from complexplus package to reduce the number of spant dependencies. — matexp • Spectroscopy Analysis Tools (spant) Apply the max operator to an MRS dataset. — max_mrs • Spectroscopy Analysis Tools (spant) Apply the max operator to an MRS dataset. — max_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/max_mrs_interp.html b/docs/reference/max_mrs_interp.html
index e4474764..52e63f3e 100644
--- a/docs/reference/max_mrs_interp.html
+++ b/docs/reference/max_mrs_interp.html
@@ -1,5 +1,5 @@
-Apply the max operator to an interpolated MRS dataset. — max_mrs_interp • Spectroscopy Analysis Tools (spant) Apply the max operator to an interpolated MRS dataset. — max_mrs_interp • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/mean.list.html b/docs/reference/mean.list.html
index b8eb3463..048306fd 100644
--- a/docs/reference/mean.list.html
+++ b/docs/reference/mean.list.html
@@ -1,5 +1,5 @@
-Calculate the mean spectrum from an mrs_data object. — mean.list • Spectroscopy Analysis Tools (spant) Calculate the mean spectrum from an mrs_data object. — mean.list • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/mean.mrs_data.html b/docs/reference/mean.mrs_data.html
index 5531a28d..79515014 100644
--- a/docs/reference/mean.mrs_data.html
+++ b/docs/reference/mean.mrs_data.html
@@ -1,5 +1,5 @@
-Calculate the mean spectrum from an mrs_data object. — mean.mrs_data • Spectroscopy Analysis Tools (spant) Calculate the mean spectrum from an mrs_data object. — mean.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/mean_dyn_blocks.html b/docs/reference/mean_dyn_blocks.html
index 10467098..4c042448 100644
--- a/docs/reference/mean_dyn_blocks.html
+++ b/docs/reference/mean_dyn_blocks.html
@@ -1,5 +1,5 @@
-Calculate the mean of adjacent dynamic scans. — mean_dyn_blocks • Spectroscopy Analysis Tools (spant) Calculate the mean of adjacent dynamic scans. — mean_dyn_blocks • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/mean_dyn_pairs.html b/docs/reference/mean_dyn_pairs.html
index 63e909ea..1a241126 100644
--- a/docs/reference/mean_dyn_pairs.html
+++ b/docs/reference/mean_dyn_pairs.html
@@ -1,5 +1,5 @@
-Calculate the pairwise means across a dynamic data set. — mean_dyn_pairs • Spectroscopy Analysis Tools (spant) Calculate the pairwise means across a dynamic data set. — mean_dyn_pairs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/mean_dyns.html b/docs/reference/mean_dyns.html
index 73fdbfa7..0daa27df 100644
--- a/docs/reference/mean_dyns.html
+++ b/docs/reference/mean_dyns.html
@@ -1,5 +1,5 @@
-Calculate the mean dynamic data. — mean_dyns • Spectroscopy Analysis Tools (spant) Calculate the mean dynamic data. — mean_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/mean_mrs_list.html b/docs/reference/mean_mrs_list.html
index 808b6c50..10d842c0 100644
--- a/docs/reference/mean_mrs_list.html
+++ b/docs/reference/mean_mrs_list.html
@@ -1,5 +1,5 @@
-Return the mean of a list of mrs_data objects. — mean_mrs_list • Spectroscopy Analysis Tools (spant) Return the mean of a list of mrs_data objects. — mean_mrs_list • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/mean_vec_blocks.html b/docs/reference/mean_vec_blocks.html
index 8fc92eaa..dd78b122 100644
--- a/docs/reference/mean_vec_blocks.html
+++ b/docs/reference/mean_vec_blocks.html
@@ -1,5 +1,5 @@
-Calculate the mean of adjacent blocks in a vector. — mean_vec_blocks • Spectroscopy Analysis Tools (spant) Calculate the mean of adjacent blocks in a vector. — mean_vec_blocks • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/median_dyns.html b/docs/reference/median_dyns.html
index 1039d4b5..9a085b10 100644
--- a/docs/reference/median_dyns.html
+++ b/docs/reference/median_dyns.html
@@ -1,5 +1,5 @@
-Calculate the median dynamic data. — median_dyns • Spectroscopy Analysis Tools (spant) Calculate the median dynamic data. — median_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/mod_td.html b/docs/reference/mod_td.html
index 76ad0a40..141ef09e 100644
--- a/docs/reference/mod_td.html
+++ b/docs/reference/mod_td.html
@@ -1,5 +1,5 @@
-Apply the Modulus operator to the time-domain MRS signal. — mod_td • Spectroscopy Analysis Tools (spant) Apply the Modulus operator to the time-domain MRS signal. — mod_td • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/mrs_data2basis.html b/docs/reference/mrs_data2basis.html
index 62f7d749..11797b91 100644
--- a/docs/reference/mrs_data2basis.html
+++ b/docs/reference/mrs_data2basis.html
@@ -1,7 +1,5 @@
-Convert an mrs_data object to basis object - where basis signals are spread
-across the dynamic dimension in the MRS data. — mrs_data2basis • Spectroscopy Analysis Tools (spant) Convert an mrs_data object to basis object - where basis signals are spread across the dynamic dimension in the MRS data. — mrs_data2basis • Spectroscopy Analysis Tools (spant) Create a BIDS file structure from a vector of MRS data paths or list of mrs_data objects. — mrs_data2bids • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Create a BIDS file structure from a vector of MRS data paths or list of mrs_data objects.
+ Source: R/fmrs.R
+ mrs_data2bids.Rd
+
+
+
+ Create a BIDS file structure from a vector of MRS data paths or list of
+mrs_data objects.
+
+
+
+ mrs_data2bids(
+ mrs_data,
+ output_dir,
+ suffix = NULL,
+ sub = NULL,
+ ses = NULL,
+ task = NULL,
+ acq = NULL,
+ nuc = NULL,
+ voi = NULL,
+ rec = NULL,
+ run = NULL,
+ echo = NULL,
+ inv = NULL,
+ skip_existing = TRUE
+)
+
+
+
+ Arguments
+ - mrs_data
+vector of MRS data paths or list of mrs_data objects.
- output_dir
+the base directory to create the BIDS structure.
- suffix
+optional vector of file suffixes. Default behaviour is to
+automatically determine these from the input data, however it is recommended
+that they are specified to allow more efficient skipping of existing data.
- sub
+optional vector of subject labels. If not specified, these will be
+automatically generated as a series of increasing zero-padded integer values
+corresponding to the mrs_data input indices.
- ses
+optional vector of session labels.
- task
+optional vector of task labels.
- acq
+optional vector of acquisition labels.
- nuc
+optional vector of nucleus labels.
- voi
+optional vector of volume of interest labels.
- rec
+optional vector of reconstruction labels.
- run
+optional vector of run indices.
- echo
+optional vector of echo time indices.
- inv
+optional vector of inversion indices.
- skip_existing
+skip any data files that have already been converted.
+Defaults to TRUE, set to FALSE to force an overwrite of any existing data
+files.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/mrs_data2mat.html b/docs/reference/mrs_data2mat.html
index cf5ff28c..9e47688a 100644
--- a/docs/reference/mrs_data2mat.html
+++ b/docs/reference/mrs_data2mat.html
@@ -1,7 +1,5 @@
-Convert mrs_data object to a matrix, with spectral points in the column
-dimension and dynamics in the row dimension. — mrs_data2mat • Spectroscopy Analysis Tools (spant) Convert mrs_data object to a matrix, with spectral points in the column dimension and dynamics in the row dimension. — mrs_data2mat • Spectroscopy Analysis Tools (spant) Convert mrs_data object to a matrix, with spectral points in the column dimension and dynamics in the row dimension. — mrs_data2spec_mat • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Convert mrs_data object to a matrix, with spectral points in the column dimension and dynamics in the row dimension.
+ Source: R/mrs_data_proc.R
+ mrs_data2spec_mat.Rd
+
+
+
+ Convert mrs_data object to a matrix, with spectral points in the column
+dimension and dynamics in the row dimension.
+
+
+
+ mrs_data2spec_mat(mrs_data, collapse = TRUE)
+
+
+
+ Arguments
+ - mrs_data
+MRS data object or list of MRS data objects.
- collapse
+collapse all other dimensions along the dynamic dimension, eg
+a 16x16 MRSI grid would be first collapsed across 256 dynamic scans.
+
+ Value
+
+
+MRS data matrix.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/mrs_data2vec.html b/docs/reference/mrs_data2vec.html
index fb172d68..a1fd654d 100644
--- a/docs/reference/mrs_data2vec.html
+++ b/docs/reference/mrs_data2vec.html
@@ -1,5 +1,5 @@
-Convert mrs_data object to a vector. — mrs_data2vec • Spectroscopy Analysis Tools (spant) Convert mrs_data object to a vector. — mrs_data2vec • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -126,7 +126,7 @@ Value
diff --git a/docs/reference/mvfftshift.html b/docs/reference/mvfftshift.html
index 92b0841b..976b3410 100644
--- a/docs/reference/mvfftshift.html
+++ b/docs/reference/mvfftshift.html
@@ -1,7 +1,5 @@
-Perform a fftshift on a matrix, with each column replaced by its shifted
-result. — mvfftshift • Spectroscopy Analysis Tools (spant) Perform a fftshift on a matrix, with each column replaced by its shifted result. — mvfftshift • Spectroscopy Analysis Tools (spant) Perform an ifftshift on a matrix, with each column replaced by its shifted
-result. — mvifftshift • Spectroscopy Analysis Tools (spant) Perform an ifftshift on a matrix, with each column replaced by its shifted result. — mvifftshift • Spectroscopy Analysis Tools (spant) Print fit coordinates from a single index. — n2coord • Spectroscopy Analysis Tools (spant) Print fit coordinates from a single index. — n2coord • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/nifti_flip_lr.html b/docs/reference/nifti_flip_lr.html
index 730abe3c..19860b3c 100644
--- a/docs/reference/nifti_flip_lr.html
+++ b/docs/reference/nifti_flip_lr.html
@@ -1,9 +1,5 @@
-Flip the x data dimension order of a nifti image. This corresponds to
-flipping MRI data in the left-right direction, assuming the data in save in
-neurological format (can check with fslorient program). — nifti_flip_lr • Spectroscopy Analysis Tools (spant) Flip the x data dimension order of a nifti image. This corresponds to flipping MRI data in the left-right direction, assuming the data in save in neurological format (can check with fslorient program). — nifti_flip_lr • Spectroscopy Analysis Tools (spant) Export a one-page pdf of a single fit result — one_page_pdf • Spectroscopy Analysis Tools (spant) Export a one-page pdf of a single fit result — one_page_pdf • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -108,7 +108,7 @@ Arguments
diff --git a/docs/reference/ortho3.html b/docs/reference/ortho3.html
index 13ade97d..5d7dd2fd 100644
--- a/docs/reference/ortho3.html
+++ b/docs/reference/ortho3.html
@@ -1,5 +1,5 @@
-Display an orthographic projection plot of a nifti object. — ortho3 • Spectroscopy Analysis Tools (spant) Display an orthographic projection plot of a nifti object. — ortho3 • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -172,7 +172,7 @@ Arguments
diff --git a/docs/reference/ortho3_inter.html b/docs/reference/ortho3_inter.html
index 090cc5e5..15948899 100644
--- a/docs/reference/ortho3_inter.html
+++ b/docs/reference/ortho3_inter.html
@@ -1,5 +1,5 @@
-Display an interactive orthographic projection plot of a nifti object. — ortho3_inter • Spectroscopy Analysis Tools (spant) Display an interactive orthographic projection plot of a nifti object. — ortho3_inter • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -132,7 +132,7 @@ Arguments
diff --git a/docs/reference/peak_info.html b/docs/reference/peak_info.html
index 09058bd8..41c8ffaf 100644
--- a/docs/reference/peak_info.html
+++ b/docs/reference/peak_info.html
@@ -1,7 +1,5 @@
-Search for the highest peak in a spectral region and return the frequency,
-height and FWHM. — peak_info • Spectroscopy Analysis Tools (spant) Search for the highest peak in a spectral region and return the frequency, height and FWHM. — peak_info • Spectroscopy Analysis Tools (spant) Papoulis-Gerchberg (PG) algorithm method for k-space extrapolation. — pg_extrap_xy • Spectroscopy Analysis Tools (spant) Papoulis-Gerchberg (PG) algorithm method for k-space extrapolation. — pg_extrap_xy • Spectroscopy Analysis Tools (spant) Apply phasing parameters to MRS data. — phase • Spectroscopy Analysis Tools (spant) Apply phasing parameters to MRS data. — phase • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/phase_ref_1h_brain.html b/docs/reference/phase_ref_1h_brain.html
new file mode 100644
index 00000000..8707a74a
--- /dev/null
+++ b/docs/reference/phase_ref_1h_brain.html
@@ -0,0 +1,131 @@
+
+Corrected zero order phase and chemical shift offset in 1H MRS data from the brain. — phase_ref_1h_brain • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Corrected zero order phase and chemical shift offset in 1H MRS data from the brain.
+ Source: R/rats.R
+ phase_ref_1h_brain.Rd
+
+
+
+ Corrected zero order phase and chemical shift offset in 1H MRS data from the
+brain.
+
+
+
+ phase_ref_1h_brain(mrs_data, mean_ref = FALSE, ret_corr_only = TRUE)
+
+
+
+ Arguments
+ - mrs_data
+MRS data to be corrected.
- mean_ref
+apply the phase and offset of the mean spectrum to all
+others. Default is FALSE.
- ret_corr_only
+return the corrected data only.
+
+ Value
+
+
+corrected MRS data.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/plot.fit_result.html b/docs/reference/plot.fit_result.html
index e54d3bc1..836a53ee 100644
--- a/docs/reference/plot.fit_result.html
+++ b/docs/reference/plot.fit_result.html
@@ -1,5 +1,5 @@
-Plot the fitting results of an object of class fit_result. — plot.fit_result • Spectroscopy Analysis Tools (spant) Plot the fitting results of an object of class fit_result. — plot.fit_result • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -207,7 +207,7 @@ Arguments
diff --git a/docs/reference/plot.mrs_data.html b/docs/reference/plot.mrs_data.html
index fabcc35b..bb2ec651 100644
--- a/docs/reference/plot.mrs_data.html
+++ b/docs/reference/plot.mrs_data.html
@@ -1,5 +1,5 @@
-Plotting method for objects of class mrs_data. — plot.mrs_data • Spectroscopy Analysis Tools (spant) Plotting method for objects of class mrs_data. — plot.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -287,7 +287,7 @@ Arguments
diff --git a/docs/reference/plot_bc.html b/docs/reference/plot_bc.html
index 4f8309b4..b48142cc 100644
--- a/docs/reference/plot_bc.html
+++ b/docs/reference/plot_bc.html
@@ -1,5 +1,5 @@
-Convenience function to plot a baseline estimate with the original data. — plot_bc • Spectroscopy Analysis Tools (spant) Convenience function to plot a baseline estimate with the original data. — plot_bc • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -108,7 +108,7 @@ Arguments
diff --git a/docs/reference/plot_reg.html b/docs/reference/plot_reg.html
index ae1acbe7..2addb2f6 100644
--- a/docs/reference/plot_reg.html
+++ b/docs/reference/plot_reg.html
@@ -1,5 +1,5 @@
-Plot regressors as an image. — plot_reg • Spectroscopy Analysis Tools (spant) Plot regressors as an image. — plot_reg • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/plot_slice_fit.html b/docs/reference/plot_slice_fit.html
index fbc7b560..57f1af8a 100644
--- a/docs/reference/plot_slice_fit.html
+++ b/docs/reference/plot_slice_fit.html
@@ -1,5 +1,5 @@
-Plot a 2D slice from an MRSI fit result object. — plot_slice_fit • Spectroscopy Analysis Tools (spant) Plot a 2D slice from an MRSI fit result object. — plot_slice_fit • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -129,7 +129,7 @@ Arguments
diff --git a/docs/reference/plot_slice_fit_inter.html b/docs/reference/plot_slice_fit_inter.html
index 4eed104a..da105a7d 100644
--- a/docs/reference/plot_slice_fit_inter.html
+++ b/docs/reference/plot_slice_fit_inter.html
@@ -1,5 +1,5 @@
-Plot a 2D slice from an MRSI fit result object. — plot_slice_fit_inter • Spectroscopy Analysis Tools (spant) Plot a 2D slice from an MRSI fit result object. — plot_slice_fit_inter • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -134,7 +134,7 @@ Arguments
diff --git a/docs/reference/plot_slice_map.html b/docs/reference/plot_slice_map.html
index 553e9ac8..ffb2a134 100644
--- a/docs/reference/plot_slice_map.html
+++ b/docs/reference/plot_slice_map.html
@@ -1,5 +1,5 @@
-Plot a slice from a 7 dimensional array. — plot_slice_map • Spectroscopy Analysis Tools (spant) Plot a slice from a 7 dimensional array. — plot_slice_map • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -153,7 +153,7 @@ Arguments
diff --git a/docs/reference/plot_slice_map_inter.html b/docs/reference/plot_slice_map_inter.html
index 40d33b42..90968f66 100644
--- a/docs/reference/plot_slice_map_inter.html
+++ b/docs/reference/plot_slice_map_inter.html
@@ -1,7 +1,5 @@
-Plot an interactive slice map from a data array where voxels can be selected
-to display a corresponding spectrum. — plot_slice_map_inter • Spectroscopy Analysis Tools (spant) Plot an interactive slice map from a data array where voxels can be selected to display a corresponding spectrum. — plot_slice_map_inter • Spectroscopy Analysis Tools (spant) Plot the spectral standard deviation. — plot_spec_sd • Spectroscopy Analysis Tools (spant) Plot the spectral standard deviation. — plot_spec_sd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Arguments
diff --git a/docs/reference/plot_voi_overlay.html b/docs/reference/plot_voi_overlay.html
index 9a782e88..bbbbf35e 100644
--- a/docs/reference/plot_voi_overlay.html
+++ b/docs/reference/plot_voi_overlay.html
@@ -1,5 +1,5 @@
-Plot a volume as an image overlay. — plot_voi_overlay • Spectroscopy Analysis Tools (spant) Plot a volume as an image overlay. — plot_voi_overlay • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -116,7 +116,7 @@ Arguments
diff --git a/docs/reference/plot_voi_overlay_seg.html b/docs/reference/plot_voi_overlay_seg.html
index 3d4e74ff..0e800ff2 100644
--- a/docs/reference/plot_voi_overlay_seg.html
+++ b/docs/reference/plot_voi_overlay_seg.html
@@ -1,5 +1,5 @@
-Plot a volume as an overlay on a segmented brain volume. — plot_voi_overlay_seg • Spectroscopy Analysis Tools (spant) Plot a volume as an overlay on a segmented brain volume. — plot_voi_overlay_seg • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Arguments
diff --git a/docs/reference/ppm.html b/docs/reference/ppm.html
index c352327a..ee4696e2 100644
--- a/docs/reference/ppm.html
+++ b/docs/reference/ppm.html
@@ -1,5 +1,5 @@
-Return the ppm scale of an MRS dataset or fit result. — ppm • Spectroscopy Analysis Tools (spant) Return the ppm scale of an MRS dataset or fit result. — ppm • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -132,7 +132,7 @@ Value
diff --git a/docs/reference/precomp.html b/docs/reference/precomp.html
index 822d7336..df3d2c6c 100644
--- a/docs/reference/precomp.html
+++ b/docs/reference/precomp.html
@@ -1,7 +1,5 @@
-Save function results to file and load on subsequent calls to avoid repeat
-computation. — precomp • Spectroscopy Analysis Tools (spant) Save function results to file and load on subsequent calls to avoid repeat computation. — precomp • Spectroscopy Analysis Tools (spant) Preprocess and perform quality assessment of a single SVS data set. — preproc_svs • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Preprocess and perform quality assessment of a single SVS data set.
+ Source: R/fmrs.R
+ preproc_svs.Rd
+
+
+
+ Preprocess and perform quality assessment of a single SVS data set.
+
+
+
+ preproc_svs(path, label = NULL, output_dir = NULL, ref_inds = NULL)
+
+
+
+ Arguments
+ - path
+path to the fMRS data file or IMA directory.
- label
+a label to describe the data set.
- output_dir
+output directory.
- ref_inds
+a vector of 1-based indices for any water reference dynamic
+scans.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/preproc_svs_dataset.html b/docs/reference/preproc_svs_dataset.html
new file mode 100644
index 00000000..07c3a29b
--- /dev/null
+++ b/docs/reference/preproc_svs_dataset.html
@@ -0,0 +1,148 @@
+
+Preprocess and perform quality assessment of one or more SVS data sets. — preproc_svs_dataset • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Preprocess and perform quality assessment of one or more SVS data sets.
+ Source: R/fmrs.R
+ preproc_svs_dataset.Rd
+
+
+
+ Preprocess and perform quality assessment of one or more SVS data sets.
+
+
+
+ preproc_svs_dataset(
+ paths,
+ labels = NULL,
+ output_dir = "spant_analysis",
+ exclude_labels = NULL,
+ overwrite = FALSE,
+ ref_inds = NULL,
+ return_results = FALSE
+)
+
+
+
+ Arguments
+ - paths
+paths to the fMRS data file or IMA directory.
- labels
+labels to describe each data set.
- output_dir
+output directory.
- exclude_labels
+vector of labels of scans to exclude, eg poor quality
+data.
- overwrite
+overwrite saved results, defaults to FALSE.
- ref_inds
+a vector of 1-based indices for any water reference dynamic
+scans.
- return_results
+function will return key outputs, defaults to FALSE.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/print.fit_result.html b/docs/reference/print.fit_result.html
index 297f28dc..5f434e57 100644
--- a/docs/reference/print.fit_result.html
+++ b/docs/reference/print.fit_result.html
@@ -1,5 +1,5 @@
-Print a summary of an object of class fit_result. — print.fit_result • Spectroscopy Analysis Tools (spant) Print a summary of an object of class fit_result. — print.fit_result • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -105,7 +105,7 @@ Arguments
diff --git a/docs/reference/print.mrs_data.html b/docs/reference/print.mrs_data.html
index 51199017..e1561eb2 100644
--- a/docs/reference/print.mrs_data.html
+++ b/docs/reference/print.mrs_data.html
@@ -1,5 +1,5 @@
-Print a summary of mrs_data parameters. — print.mrs_data • Spectroscopy Analysis Tools (spant) Print a summary of mrs_data parameters. — print.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -109,7 +109,7 @@ Arguments
diff --git a/docs/reference/qn_states.html b/docs/reference/qn_states.html
index 0f42f2f9..d7aa6715 100644
--- a/docs/reference/qn_states.html
+++ b/docs/reference/qn_states.html
@@ -1,5 +1,5 @@
-Get the quantum coherence matrix for a spin system. — qn_states • Spectroscopy Analysis Tools (spant) Get the quantum coherence matrix for a spin system. — qn_states • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/rats.html b/docs/reference/rats.html
index 5a39a396..93585e08 100644
--- a/docs/reference/rats.html
+++ b/docs/reference/rats.html
@@ -1,5 +1,5 @@
-Robust Alignment to a Target Spectrum (RATS). — rats • Spectroscopy Analysis Tools (spant) Robust Alignment to a Target Spectrum (RATS). — rats • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -207,7 +207,7 @@ Value
diff --git a/docs/reference/re_weighting.html b/docs/reference/re_weighting.html
index d21caf21..8b0b070a 100644
--- a/docs/reference/re_weighting.html
+++ b/docs/reference/re_weighting.html
@@ -1,5 +1,5 @@
-Apply a weighting to the FID to enhance spectral resolution. — re_weighting • Spectroscopy Analysis Tools (spant) Apply a weighting to the FID to enhance spectral resolution. — re_weighting • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/read_basis.html b/docs/reference/read_basis.html
index da9b94af..eb6f8557 100644
--- a/docs/reference/read_basis.html
+++ b/docs/reference/read_basis.html
@@ -1,5 +1,5 @@
-Read a basis file in LCModel .basis format. — read_basis • Spectroscopy Analysis Tools (spant) Read a basis file in LCModel .basis format. — read_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/read_ima_coil_dir.html b/docs/reference/read_ima_coil_dir.html
index 28c02de0..4f073cd8 100644
--- a/docs/reference/read_ima_coil_dir.html
+++ b/docs/reference/read_ima_coil_dir.html
@@ -1,9 +1,5 @@
-Read a directory containing Siemens MRS IMA files and combine along the coil
-dimension. Note that the coil ID is inferred from the sorted file name and
-should be checked when consistency is required between two directories. — read_ima_coil_dir • Spectroscopy Analysis Tools (spant) Read a directory containing Siemens MRS IMA files and combine along the coil dimension. Note that the coil ID is inferred from the sorted file name and should be checked when consistency is required between two directories. — read_ima_coil_dir • Spectroscopy Analysis Tools (spant) Read a directory containing Siemens MRS IMA files and combine along the
-dynamic dimension. Note that the coil ID is inferred from the sorted file
-name and should be checked when consistency is required. — read_ima_dyn_dir • Spectroscopy Analysis Tools (spant) Read a directory containing Siemens MRS IMA files and combine along the dynamic dimension. Note that the coil ID is inferred from the sorted file name and should be checked when consistency is required. — read_ima_dyn_dir • Spectroscopy Analysis Tools (spant) Read an LCModel formatted coord file containing fit information. — read_lcm_coord • Spectroscopy Analysis Tools (spant) Read an LCModel formatted coord file containing fit information. — read_lcm_coord • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -107,7 +107,7 @@ Value
diff --git a/docs/reference/read_mrs.html b/docs/reference/read_mrs.html
index 3ac2a36b..2cf36b20 100644
--- a/docs/reference/read_mrs.html
+++ b/docs/reference/read_mrs.html
@@ -1,5 +1,5 @@
-Read MRS data from a file. — read_mrs • Spectroscopy Analysis Tools (spant) Read MRS data from a file. — read_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -88,7 +88,8 @@ Read MRS data from a file.
full_fid = FALSE,
omit_svs_ref_scans = TRUE,
verbose = FALSE,
- extra = NULL
+ extra = NULL,
+ fid_filt_dist = NULL
)
@@ -140,6 +141,13 @@ Arguments
an optional data frame to provide additional variables for use
in subsequent analysis steps, eg id or grouping variables.
fid_filt_dist
+indicate if the data has a distorted FID due to a
+brick-wall filter being used to downsample the data. Default is to auto
+detect this from the data, but TRUE or FALSE options can be given to override
+detection.
Value
@@ -183,7 +191,7 @@ Examples
diff --git a/docs/reference/read_mrs_tqn.html b/docs/reference/read_mrs_tqn.html
index 5766362f..84bdaf3a 100644
--- a/docs/reference/read_mrs_tqn.html
+++ b/docs/reference/read_mrs_tqn.html
@@ -1,5 +1,5 @@
-Read MRS data using the TARQUIN software package. — read_mrs_tqn • Spectroscopy Analysis Tools (spant) Read MRS data using the TARQUIN software package. — read_mrs_tqn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -131,7 +131,7 @@ Examples
diff --git a/docs/reference/read_pulse_ascii.html b/docs/reference/read_pulse_ascii.html
index c9e0d43c..ab11c9cc 100644
--- a/docs/reference/read_pulse_ascii.html
+++ b/docs/reference/read_pulse_ascii.html
@@ -1,5 +1,5 @@
-Read an ASCII formatted pulse file. — read_pulse_ascii • Spectroscopy Analysis Tools (spant) Read an ASCII formatted pulse file. — read_pulse_ascii • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/read_pulse_bruker.html b/docs/reference/read_pulse_bruker.html
index c92bf76a..dbe9073b 100644
--- a/docs/reference/read_pulse_bruker.html
+++ b/docs/reference/read_pulse_bruker.html
@@ -1,5 +1,5 @@
-Read a Bruker formatted pulse file — read_pulse_bruker • Spectroscopy Analysis Tools (spant) Read a Bruker formatted pulse file — read_pulse_bruker • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/read_pulse_pta.html b/docs/reference/read_pulse_pta.html
index 72e1b6d4..a0fac3c3 100644
--- a/docs/reference/read_pulse_pta.html
+++ b/docs/reference/read_pulse_pta.html
@@ -1,5 +1,5 @@
-Read a .pta formatted pulse file compatible with Siemens PulseTool. — read_pulse_pta • Spectroscopy Analysis Tools (spant) Read a .pta formatted pulse file compatible with Siemens PulseTool. — read_pulse_pta • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/read_siemens_txt_hdr.html b/docs/reference/read_siemens_txt_hdr.html
index 23fb8c70..3a17d87c 100644
--- a/docs/reference/read_siemens_txt_hdr.html
+++ b/docs/reference/read_siemens_txt_hdr.html
@@ -1,5 +1,5 @@
-Read the text format header found in Siemens IMA and TWIX data files. — read_siemens_txt_hdr • Spectroscopy Analysis Tools (spant) Read the text format header found in Siemens IMA and TWIX data files. — read_siemens_txt_hdr • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -78,7 +78,7 @@ Read the text format header found in Siemens IMA and TWIX data files.
- read_siemens_txt_hdr(input, version = "vd", verbose, offset = 0)
+ read_siemens_txt_hdr(input, version = "vd", verbose = FALSE, offset = 0)
@@ -118,7 +118,7 @@ Value
diff --git a/docs/reference/read_tqn_fit.html b/docs/reference/read_tqn_fit.html
index 4da6c25e..a1630420 100644
--- a/docs/reference/read_tqn_fit.html
+++ b/docs/reference/read_tqn_fit.html
@@ -1,5 +1,5 @@
-Reader for csv fit results generated by TARQUIN. — read_tqn_fit • Spectroscopy Analysis Tools (spant) Reader for csv fit results generated by TARQUIN. — read_tqn_fit • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -113,7 +113,7 @@ Examples
diff --git a/docs/reference/read_tqn_result.html b/docs/reference/read_tqn_result.html
index 36659714..68a3e98c 100644
--- a/docs/reference/read_tqn_result.html
+++ b/docs/reference/read_tqn_result.html
@@ -1,5 +1,5 @@
-Reader for csv results generated by TARQUIN. — read_tqn_result • Spectroscopy Analysis Tools (spant) Reader for csv results generated by TARQUIN. — read_tqn_result • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -117,7 +117,7 @@ Examples
diff --git a/docs/reference/recon_imag.html b/docs/reference/recon_imag.html
index d2a72225..5bc3b1eb 100644
--- a/docs/reference/recon_imag.html
+++ b/docs/reference/recon_imag.html
@@ -1,7 +1,5 @@
-Reconstruct complex time-domain data from the real part of frequency-domain
-data. — recon_imag • Spectroscopy Analysis Tools (spant) Reconstruct complex time-domain data from the real part of frequency-domain data. — recon_imag • Spectroscopy Analysis Tools (spant) Reconstruct complex time-domain data from the real part of frequency-domain
-data. — recon_imag_vec • Spectroscopy Analysis Tools (spant) Reconstruct complex time-domain data from the real part of frequency-domain data. — recon_imag_vec • Spectroscopy Analysis Tools (spant) Reconstruct 2D MRSI data from a twix file loaded with read_mrs. — recon_twix_2d_mrsi • Spectroscopy Analysis Tools (spant) Reconstruct 2D MRSI data from a twix file loaded with read_mrs. — recon_twix_2d_mrsi • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/rectangular_mask.html b/docs/reference/rectangular_mask.html
index a2117283..6e469bc9 100644
--- a/docs/reference/rectangular_mask.html
+++ b/docs/reference/rectangular_mask.html
@@ -1,5 +1,5 @@
-Create a rectangular mask stored as a matrix of logical values. — rectangular_mask • Spectroscopy Analysis Tools (spant) Create a rectangular mask stored as a matrix of logical values. — rectangular_mask • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -130,7 +130,7 @@ Value
diff --git a/docs/reference/reexports.html b/docs/reference/reexports.html
index 694a75d1..a59e8379 100644
--- a/docs/reference/reexports.html
+++ b/docs/reference/reexports.html
@@ -1,5 +1,5 @@
-Objects exported from other packages — reexports • Spectroscopy Analysis Tools (spant) Objects exported from other packages — reexports • Spectroscopy Analysis Tools (spant)
Spectroscopy Analysis Tools (spant)
- 2.21.0
+ 2.22.0
@@ -103,7 +103,7 @@ Objects exported from other packages
diff --git a/docs/reference/rep_array_dim.html b/docs/reference/rep_array_dim.html
index b9c49b4a..48c0a5ed 100644
--- a/docs/reference/rep_array_dim.html
+++ b/docs/reference/rep_array_dim.html
@@ -1,5 +1,5 @@
-Repeat an array over a given dimension. — rep_array_dim • Spectroscopy Analysis Tools (spant) Repeat an array over a given dimension. — rep_array_dim • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/rep_dyn.html b/docs/reference/rep_dyn.html
index 6bbfb0ef..89a4bb9b 100644
--- a/docs/reference/rep_dyn.html
+++ b/docs/reference/rep_dyn.html
@@ -1,5 +1,5 @@
-Replicate a scan in the dynamic dimension. — rep_dyn • Spectroscopy Analysis Tools (spant) Replicate a scan in the dynamic dimension. — rep_dyn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/rep_mrs.html b/docs/reference/rep_mrs.html
index 67730b5c..becb8f00 100644
--- a/docs/reference/rep_mrs.html
+++ b/docs/reference/rep_mrs.html
@@ -1,5 +1,5 @@
-Replicate a scan over a given dimension. — rep_mrs • Spectroscopy Analysis Tools (spant) Replicate a scan over a given dimension. — rep_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -138,7 +138,7 @@ Value
diff --git a/docs/reference/resample_basis.html b/docs/reference/resample_basis.html
index b0f2ab17..c7a6222a 100644
--- a/docs/reference/resample_basis.html
+++ b/docs/reference/resample_basis.html
@@ -1,5 +1,5 @@
-Resample a basis-set to match a mrs_data acquisition. — resample_basis • Spectroscopy Analysis Tools (spant) Resample a basis-set to match a mrs_data acquisition. — resample_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -116,7 +116,7 @@ Value
diff --git a/docs/reference/resample_img.html b/docs/reference/resample_img.html
index f1e7beaf..b0cc8f71 100644
--- a/docs/reference/resample_img.html
+++ b/docs/reference/resample_img.html
@@ -1,5 +1,5 @@
-Resample an image to match a target image space. — resample_img • Spectroscopy Analysis Tools (spant) Resample an image to match a target image space. — resample_img • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/resample_voi.html b/docs/reference/resample_voi.html
index 8fbfa836..a29ab096 100644
--- a/docs/reference/resample_voi.html
+++ b/docs/reference/resample_voi.html
@@ -1,7 +1,5 @@
-Resample a VOI to match a target image space using nearest-neighbour
-interpolation. — resample_voi • Spectroscopy Analysis Tools (spant) Resample a VOI to match a target image space using nearest-neighbour interpolation. — resample_voi • Spectroscopy Analysis Tools (spant) Reslice a nifti object to match the orientation of mrs data. — reslice_to_mrs • Spectroscopy Analysis Tools (spant) Reslice a nifti object to match the orientation of mrs data. — reslice_to_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/reson_table2mrs_data.html b/docs/reference/reson_table2mrs_data.html
index d75579ee..c5a2167a 100644
--- a/docs/reference/reson_table2mrs_data.html
+++ b/docs/reference/reson_table2mrs_data.html
@@ -1,5 +1,5 @@
-Generate mrs_data from a table of single Lorentzian resonances. — reson_table2mrs_data • Spectroscopy Analysis Tools (spant) Generate mrs_data from a table of single Lorentzian resonances. — reson_table2mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -119,7 +119,7 @@ Value
diff --git a/docs/reference/rm_dyns.html b/docs/reference/rm_dyns.html
index 5d5ef692..573e1f51 100644
--- a/docs/reference/rm_dyns.html
+++ b/docs/reference/rm_dyns.html
@@ -1,5 +1,5 @@
-Remove a subset of dynamic scans. — rm_dyns • Spectroscopy Analysis Tools (spant) Remove a subset of dynamic scans. — rm_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/scale_amp_molal.html b/docs/reference/scale_amp_molal.html
index aaeee1f2..7acb8cb0 100644
--- a/docs/reference/scale_amp_molal.html
+++ b/docs/reference/scale_amp_molal.html
@@ -1,7 +1,5 @@
-Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water). — scale_amp_molal • Spectroscopy Analysis Tools (spant) Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / kg of tissue water). — scale_amp_molal • Spectroscopy Analysis Tools (spant)
Spectroscopy Analysis Tools (spant)
- 2.21.0
+ 2.22.0
@@ -76,8 +74,7 @@
- Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water).
+ Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / kg of tissue water).
Source: R/amp_scaling.R
scale_amp_molal.Rd
@@ -163,7 +160,7 @@ Value
diff --git a/docs/reference/scale_amp_molal_pvc.html b/docs/reference/scale_amp_molal_pvc.html
index 962d6afc..4d194abd 100644
--- a/docs/reference/scale_amp_molal_pvc.html
+++ b/docs/reference/scale_amp_molal_pvc.html
@@ -1,7 +1,5 @@
-Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water). — scale_amp_molal_pvc • Spectroscopy Analysis Tools (spant)
@@ -75,8 +73,7 @@
- Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water).
+ Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / kg of tissue water).
Source: R/amp_scaling.R
scale_amp_molal_pvc.Rd
@@ -141,7 +138,7 @@ Value
diff --git a/docs/reference/scale_amp_molar.html b/docs/reference/scale_amp_molar.html
index 02358d91..dc87a338 100644
--- a/docs/reference/scale_amp_molar.html
+++ b/docs/reference/scale_amp_molar.html
@@ -1,7 +1,5 @@
-Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / Litre of tissue). — scale_amp_molar • Spectroscopy Analysis Tools (spant) Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / Litre of tissue). — scale_amp_molar • Spectroscopy Analysis Tools (spant) Convert default LCM/TARQUIN concentration scaling to molal units with partial
-volume correction. — scale_amp_molar2molal_pvc • Spectroscopy Analysis Tools (spant) Convert default LCM/TARQUIN concentration scaling to molal units with partial volume correction. — scale_amp_molar2molal_pvc • Spectroscopy Analysis Tools (spant) Scale fitted amplitudes to a ratio of signal amplitude. — scale_amp_ratio • Spectroscopy Analysis Tools (spant) Scale fitted amplitudes to a ratio of signal amplitude. — scale_amp_ratio • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -116,7 +116,7 @@ Value
diff --git a/docs/reference/scale_amp_ratio_value.html b/docs/reference/scale_amp_ratio_value.html
index 2036837a..6af8ac51 100644
--- a/docs/reference/scale_amp_ratio_value.html
+++ b/docs/reference/scale_amp_ratio_value.html
@@ -1,5 +1,5 @@
-Scale fitted amplitudes to a ratio of signal amplitude. — scale_amp_ratio_value • Spectroscopy Analysis Tools (spant) Scale fitted amplitudes to a ratio of signal amplitude. — scale_amp_ratio_value • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/scale_amp_water_ratio.html b/docs/reference/scale_amp_water_ratio.html
index 5b25e884..35a76b00 100644
--- a/docs/reference/scale_amp_water_ratio.html
+++ b/docs/reference/scale_amp_water_ratio.html
@@ -1,5 +1,5 @@
-Scale metabolite amplitudes as a ratio to the unsuppressed water amplitude. — scale_amp_water_ratio • Spectroscopy Analysis Tools (spant) Scale metabolite amplitudes as a ratio to the unsuppressed water amplitude. — scale_amp_water_ratio • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/scale_basis_amp.html b/docs/reference/scale_basis_amp.html
index 9401c3f1..5a58b5e5 100644
--- a/docs/reference/scale_basis_amp.html
+++ b/docs/reference/scale_basis_amp.html
@@ -1,5 +1,5 @@
-Scale a basis object by a scalar. — scale_basis_amp • Spectroscopy Analysis Tools (spant) Scale a basis object by a scalar. — scale_basis_amp • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/scale_basis_from_singlet.html b/docs/reference/scale_basis_from_singlet.html
index 0d542bc8..c9a19e77 100644
--- a/docs/reference/scale_basis_from_singlet.html
+++ b/docs/reference/scale_basis_from_singlet.html
@@ -1,5 +1,5 @@
-Scale a basis-set to be consistent with spant assumptions for water scaling. — scale_basis_from_singlet • Spectroscopy Analysis Tools (spant) Scale a basis-set to be consistent with spant assumptions for water scaling. — scale_basis_from_singlet • Spectroscopy Analysis Tools (spant)
Spectroscopy Analysis Tools (spant)
- 2.21.0
+ 2.22.0
@@ -127,7 +127,7 @@ Value
diff --git a/docs/reference/scale_mrs_amp.html b/docs/reference/scale_mrs_amp.html
index b5501a0d..990f058a 100644
--- a/docs/reference/scale_mrs_amp.html
+++ b/docs/reference/scale_mrs_amp.html
@@ -1,5 +1,5 @@
-Scale an mrs_data object by a scalar or vector or amplitudes. — scale_mrs_amp • Spectroscopy Analysis Tools (spant) Scale an mrs_data object by a scalar or vector or amplitudes. — scale_mrs_amp • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/scale_spec.html b/docs/reference/scale_spec.html
index 4f6ea835..6b3ddba4 100644
--- a/docs/reference/scale_spec.html
+++ b/docs/reference/scale_spec.html
@@ -1,5 +1,5 @@
-Scale mrs_data to a spectral region. — scale_spec • Spectroscopy Analysis Tools (spant) Scale mrs_data to a spectral region. — scale_spec • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -141,7 +141,7 @@ Value
diff --git a/docs/reference/sd.html b/docs/reference/sd.html
index ea1eec9f..3ae4dfd4 100644
--- a/docs/reference/sd.html
+++ b/docs/reference/sd.html
@@ -1,5 +1,5 @@
-Calculate the standard deviation spectrum from an mrs_data object. — sd • Spectroscopy Analysis Tools (spant) Calculate the standard deviation spectrum from an mrs_data object. — sd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/sd.mrs_data.html b/docs/reference/sd.mrs_data.html
index 3f92a49f..13bdda85 100644
--- a/docs/reference/sd.mrs_data.html
+++ b/docs/reference/sd.mrs_data.html
@@ -1,5 +1,5 @@
-Calculate the standard deviation spectrum from an mrs_data object. — sd.mrs_data • Spectroscopy Analysis Tools (spant) Calculate the standard deviation spectrum from an mrs_data object. — sd.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/seconds.html b/docs/reference/seconds.html
index b34d6627..467ee17f 100644
--- a/docs/reference/seconds.html
+++ b/docs/reference/seconds.html
@@ -1,5 +1,5 @@
-Return a time scale vector to match the FID of an MRS data object. — seconds • Spectroscopy Analysis Tools (spant) Return a time scale vector to match the FID of an MRS data object. — seconds • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/seq_cpmg_ideal.html b/docs/reference/seq_cpmg_ideal.html
index 547e96ab..45727c86 100644
--- a/docs/reference/seq_cpmg_ideal.html
+++ b/docs/reference/seq_cpmg_ideal.html
@@ -1,5 +1,5 @@
-CPMG style sequence with ideal pulses. — seq_cpmg_ideal • Spectroscopy Analysis Tools (spant) CPMG style sequence with ideal pulses. — seq_cpmg_ideal • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/seq_mega_press_ideal.html b/docs/reference/seq_mega_press_ideal.html
index 0769b8b4..a9cd7fa0 100644
--- a/docs/reference/seq_mega_press_ideal.html
+++ b/docs/reference/seq_mega_press_ideal.html
@@ -1,7 +1,5 @@
-MEGA-PRESS sequence with ideal localisation pulses and Gaussian shaped
-editing pulse. — seq_mega_press_ideal • Spectroscopy Analysis Tools (spant) MEGA-PRESS sequence with ideal localisation pulses and Gaussian shaped editing pulse. — seq_mega_press_ideal • Spectroscopy Analysis Tools (spant) PRESS sequence with shaped refocusing pulses. — seq_press_2d_shaped • Spectroscopy Analysis Tools (spant) PRESS sequence with shaped refocusing pulses. — seq_press_2d_shaped • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -165,7 +165,7 @@ Value
diff --git a/docs/reference/seq_press_ideal.html b/docs/reference/seq_press_ideal.html
index 8c976856..72c3af3d 100644
--- a/docs/reference/seq_press_ideal.html
+++ b/docs/reference/seq_press_ideal.html
@@ -1,5 +1,5 @@
-PRESS sequence with ideal pulses. — seq_press_ideal • Spectroscopy Analysis Tools (spant) PRESS sequence with ideal pulses. — seq_press_ideal • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/seq_pulse_acquire.html b/docs/reference/seq_pulse_acquire.html
index 4a88fc64..ad80571e 100644
--- a/docs/reference/seq_pulse_acquire.html
+++ b/docs/reference/seq_pulse_acquire.html
@@ -1,5 +1,5 @@
-Simple pulse and acquire sequence with ideal pulses. — seq_pulse_acquire • Spectroscopy Analysis Tools (spant) Simple pulse and acquire sequence with ideal pulses. — seq_pulse_acquire • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/seq_slaser_ideal.html b/docs/reference/seq_slaser_ideal.html
index 74688f4d..eb83e8e3 100644
--- a/docs/reference/seq_slaser_ideal.html
+++ b/docs/reference/seq_slaser_ideal.html
@@ -1,5 +1,5 @@
-sLASER sequence with ideal pulses. — seq_slaser_ideal • Spectroscopy Analysis Tools (spant) sLASER sequence with ideal pulses. — seq_slaser_ideal • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -126,7 +126,7 @@ Value
diff --git a/docs/reference/seq_spin_echo_ideal.html b/docs/reference/seq_spin_echo_ideal.html
index e23271de..4248716f 100644
--- a/docs/reference/seq_spin_echo_ideal.html
+++ b/docs/reference/seq_spin_echo_ideal.html
@@ -1,5 +1,5 @@
-Spin echo sequence with ideal pulses. — seq_spin_echo_ideal • Spectroscopy Analysis Tools (spant) Spin echo sequence with ideal pulses. — seq_spin_echo_ideal • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/seq_steam_ideal.html b/docs/reference/seq_steam_ideal.html
index a60685a8..1c8115d7 100644
--- a/docs/reference/seq_steam_ideal.html
+++ b/docs/reference/seq_steam_ideal.html
@@ -1,5 +1,5 @@
-STEAM sequence with ideal pulses. — seq_steam_ideal • Spectroscopy Analysis Tools (spant) STEAM sequence with ideal pulses. — seq_steam_ideal • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -128,7 +128,7 @@ Value
diff --git a/docs/reference/seq_steam_ideal_cof.html b/docs/reference/seq_steam_ideal_cof.html
index 8f225740..cba7af91 100644
--- a/docs/reference/seq_steam_ideal_cof.html
+++ b/docs/reference/seq_steam_ideal_cof.html
@@ -1,7 +1,5 @@
-STEAM sequence with ideal pulses and coherence order filtering to simulate
-gradient crushers. — seq_steam_ideal_cof • Spectroscopy Analysis Tools (spant) STEAM sequence with ideal pulses and coherence order filtering to simulate gradient crushers. — seq_steam_ideal_cof • Spectroscopy Analysis Tools (spant) STEAM sequence with ideal pulses using the z-rotation gradient simulation
-method described by Young et al JMR 140, 146-152 (1999). — seq_steam_ideal_young • Spectroscopy Analysis Tools (spant) STEAM sequence with ideal pulses using the z-rotation gradient simulation method described by Young et al JMR 140, 146-152 (1999). — seq_steam_ideal_young • Spectroscopy Analysis Tools (spant) Set the number of transients for an mrs_data object. — set_Ntrans • Spectroscopy Analysis Tools (spant) Set the number of transients for an mrs_data object. — set_Ntrans • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/set_def_acq_paras.html b/docs/reference/set_def_acq_paras.html
index 3e1b4004..cc2ada9c 100644
--- a/docs/reference/set_def_acq_paras.html
+++ b/docs/reference/set_def_acq_paras.html
@@ -1,5 +1,5 @@
-Set the default acquisition parameters. — set_def_acq_paras • Spectroscopy Analysis Tools (spant) Set the default acquisition parameters. — set_def_acq_paras • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Arguments
diff --git a/docs/reference/set_lcm_cmd.html b/docs/reference/set_lcm_cmd.html
index 2056ed01..42bb2f24 100644
--- a/docs/reference/set_lcm_cmd.html
+++ b/docs/reference/set_lcm_cmd.html
@@ -1,5 +1,5 @@
-Set the command to run the LCModel command-line program. — set_lcm_cmd • Spectroscopy Analysis Tools (spant) Set the command to run the LCModel command-line program. — set_lcm_cmd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/set_lw.html b/docs/reference/set_lw.html
index b64ec851..bb176c62 100644
--- a/docs/reference/set_lw.html
+++ b/docs/reference/set_lw.html
@@ -1,5 +1,5 @@
-Apply line-broadening to an mrs_data object to achieve a specified linewidth. — set_lw • Spectroscopy Analysis Tools (spant) Apply line-broadening to an mrs_data object to achieve a specified linewidth. — set_lw • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -123,7 +123,7 @@ Value
diff --git a/docs/reference/set_mask_xy_mat.html b/docs/reference/set_mask_xy_mat.html
index 49dc5d4e..52c4b617 100644
--- a/docs/reference/set_mask_xy_mat.html
+++ b/docs/reference/set_mask_xy_mat.html
@@ -1,5 +1,5 @@
-Set the masked voxels in a 2D MRSI dataset to given spectrum. — set_mask_xy_mat • Spectroscopy Analysis Tools (spant) Set the masked voxels in a 2D MRSI dataset to given spectrum. — set_mask_xy_mat • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Value
diff --git a/docs/reference/set_precomp_mode.html b/docs/reference/set_precomp_mode.html
index f44bd5d3..47c28e3b 100644
--- a/docs/reference/set_precomp_mode.html
+++ b/docs/reference/set_precomp_mode.html
@@ -1,5 +1,5 @@
-Set the precompute mode. — set_precomp_mode • Spectroscopy Analysis Tools (spant) Set the precompute mode. — set_precomp_mode • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/set_precomp_verbose.html b/docs/reference/set_precomp_verbose.html
index 1453a231..9c613505 100644
--- a/docs/reference/set_precomp_verbose.html
+++ b/docs/reference/set_precomp_verbose.html
@@ -1,5 +1,5 @@
-Set the verbosity of the precompute function. — set_precomp_verbose • Spectroscopy Analysis Tools (spant) Set the verbosity of the precompute function. — set_precomp_verbose • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/set_ref.html b/docs/reference/set_ref.html
index 8953fa50..5436dfa2 100644
--- a/docs/reference/set_ref.html
+++ b/docs/reference/set_ref.html
@@ -1,5 +1,5 @@
-Set the ppm reference value (eg ppm value at 0Hz). — set_ref • Spectroscopy Analysis Tools (spant) Set the ppm reference value (eg ppm value at 0Hz). — set_ref • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/set_td_pts.html b/docs/reference/set_td_pts.html
index 8a80d42a..586459ff 100644
--- a/docs/reference/set_td_pts.html
+++ b/docs/reference/set_td_pts.html
@@ -1,7 +1,5 @@
-Set the number of time-domain data points, truncating or zero-filling as
-appropriate. — set_td_pts • Spectroscopy Analysis Tools (spant) Set the number of time-domain data points, truncating or zero-filling as appropriate. — set_td_pts • Spectroscopy Analysis Tools (spant) Set the command to run the TARQUIN command-line program. — set_tqn_cmd • Spectroscopy Analysis Tools (spant) Set the command to run the TARQUIN command-line program. — set_tqn_cmd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/set_tr.html b/docs/reference/set_tr.html
index b2109ab0..65c9df5f 100644
--- a/docs/reference/set_tr.html
+++ b/docs/reference/set_tr.html
@@ -1,5 +1,5 @@
-Set the repetition time of an MRS dataset. — set_tr • Spectroscopy Analysis Tools (spant) Set the repetition time of an MRS dataset. — set_tr • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/shift.html b/docs/reference/shift.html
index ab0fe724..034591d0 100644
--- a/docs/reference/shift.html
+++ b/docs/reference/shift.html
@@ -1,5 +1,5 @@
-Apply a frequency shift to MRS data. — shift • Spectroscopy Analysis Tools (spant) Apply a frequency shift to MRS data. — shift • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/shift_basis.html b/docs/reference/shift_basis.html
index 2884be19..f55a65e0 100644
--- a/docs/reference/shift_basis.html
+++ b/docs/reference/shift_basis.html
@@ -1,5 +1,5 @@
-Apply frequency shifts to basis set signals. — shift_basis • Spectroscopy Analysis Tools (spant) Apply frequency shifts to basis set signals. — shift_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Value
diff --git a/docs/reference/sim_basis.html b/docs/reference/sim_basis.html
index c7838c46..bb5fefc6 100644
--- a/docs/reference/sim_basis.html
+++ b/docs/reference/sim_basis.html
@@ -1,5 +1,5 @@
-Simulate a basis set object. — sim_basis • Spectroscopy Analysis Tools (spant) Simulate a basis set object. — sim_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -136,7 +136,7 @@ Value
diff --git a/docs/reference/sim_basis_1h_brain.html b/docs/reference/sim_basis_1h_brain.html
index 62ed7389..f71ffa0b 100644
--- a/docs/reference/sim_basis_1h_brain.html
+++ b/docs/reference/sim_basis_1h_brain.html
@@ -1,7 +1,5 @@
-Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS
-sequence. Note, ideal pulses are assumed. — sim_basis_1h_brain • Spectroscopy Analysis Tools (spant) Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS sequence. Note, ideal pulses are assumed. — sim_basis_1h_brain • Spectroscopy Analysis Tools (spant) Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS
-sequence. Note, ideal pulses are assumed. — sim_basis_1h_brain_press • Spectroscopy Analysis Tools (spant) Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS sequence. Note, ideal pulses are assumed. — sim_basis_1h_brain_press • Spectroscopy Analysis Tools (spant) Simulate a macromolecular and lipid basis-set suitable for 1H brain MRS
-analysis. — sim_basis_mm_lip_lcm • Spectroscopy Analysis Tools (spant) Simulate a macromolecular and lipid basis-set suitable for 1H brain MRS analysis. — sim_basis_mm_lip_lcm • Spectroscopy Analysis Tools (spant) Simulate a basis file using TARQUIN. — sim_basis_tqn • Spectroscopy Analysis Tools (spant) Simulate a basis file using TARQUIN. — sim_basis_tqn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -129,7 +129,7 @@ Examples
diff --git a/docs/reference/sim_brain_1h.html b/docs/reference/sim_brain_1h.html
index 2044cf1a..717ee289 100644
--- a/docs/reference/sim_brain_1h.html
+++ b/docs/reference/sim_brain_1h.html
@@ -1,5 +1,5 @@
-Simulate MRS data with a similar appearance to normal brain (by default). — sim_brain_1h • Spectroscopy Analysis Tools (spant) Simulate MRS data with a similar appearance to normal brain (by default). — sim_brain_1h • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -159,7 +159,7 @@ Value
diff --git a/docs/reference/sim_mol.html b/docs/reference/sim_mol.html
index 23bcef50..77f76a50 100644
--- a/docs/reference/sim_mol.html
+++ b/docs/reference/sim_mol.html
@@ -1,5 +1,5 @@
-Simulate a mol_parameter object. — sim_mol • Spectroscopy Analysis Tools (spant) Simulate a mol_parameter object. — sim_mol • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -143,7 +143,7 @@ Value
diff --git a/docs/reference/sim_noise.html b/docs/reference/sim_noise.html
index 23875f79..a71477d4 100644
--- a/docs/reference/sim_noise.html
+++ b/docs/reference/sim_noise.html
@@ -1,5 +1,5 @@
-Simulate an mrs_data object containing simulated Gaussian noise. — sim_noise • Spectroscopy Analysis Tools (spant) Simulate an mrs_data object containing simulated Gaussian noise. — sim_noise • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -84,6 +84,7 @@ Simulate an mrs_data object containing simulated Gaussian noise.
ft = def_ft(),
N = def_N(),
ref = def_ref(),
+ nuc = def_nuc(),
dyns = 1,
fd = TRUE
)
@@ -111,6 +112,10 @@ Arguments
reference value for ppm scale.
nuc
+resonant nucleus.
dyns
number of dynamic scans to generate.
Value
diff --git a/docs/reference/sim_resonances.html b/docs/reference/sim_resonances.html
index 19e9a8a4..d4f8d7c0 100644
--- a/docs/reference/sim_resonances.html
+++ b/docs/reference/sim_resonances.html
@@ -1,5 +1,5 @@
-Simulate a MRS data object containing a set of simulated resonances. — sim_resonances • Spectroscopy Analysis Tools (spant) Simulate a MRS data object containing a set of simulated resonances. — sim_resonances • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -161,7 +161,7 @@ Examples
diff --git a/docs/reference/sim_th_excit_profile.html b/docs/reference/sim_th_excit_profile.html
index 5535c5ef..e781cab1 100644
--- a/docs/reference/sim_th_excit_profile.html
+++ b/docs/reference/sim_th_excit_profile.html
@@ -1,7 +1,5 @@
-Simulate an ideal pulse excitation profile by smoothing a top-hat function
-with a Gaussian. — sim_th_excit_profile • Spectroscopy Analysis Tools (spant) Simulate an ideal pulse excitation profile by smoothing a top-hat function with a Gaussian. — sim_th_excit_profile • Spectroscopy Analysis Tools (spant) Simulate an mrs_data object containing complex zero valued samples. — sim_zero • Spectroscopy Analysis Tools (spant) Simulate an mrs_data object containing complex zero valued samples. — sim_zero • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -78,7 +78,14 @@ Simulate an mrs_data object containing complex zero valued samples.
-
+
@@ -99,6 +106,10 @@ Arguments
reference value for ppm scale.
nuc
+resonant nucleus.
dyns
number of dynamic scans to generate.
Value
diff --git a/docs/reference/smooth_dyns.html b/docs/reference/smooth_dyns.html
index 4cc8da50..accf3a51 100644
--- a/docs/reference/smooth_dyns.html
+++ b/docs/reference/smooth_dyns.html
@@ -1,5 +1,5 @@
-Smooth data across the dynamic dimension with a Gaussian kernel. — smooth_dyns • Spectroscopy Analysis Tools (spant) Smooth data across the dynamic dimension with a Gaussian kernel. — smooth_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/sort_basis.html b/docs/reference/sort_basis.html
index 6a676ea2..d25cc006 100644
--- a/docs/reference/sort_basis.html
+++ b/docs/reference/sort_basis.html
@@ -1,5 +1,5 @@
-Sort the basis-set elements alphabetically. — sort_basis • Spectroscopy Analysis Tools (spant) Sort the basis-set elements alphabetically. — sort_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/spant-package.html b/docs/reference/spant-package.html
index b3dd8e21..90f19ec3 100644
--- a/docs/reference/spant-package.html
+++ b/docs/reference/spant-package.html
@@ -1,5 +1,5 @@
-spant: spectroscopy analysis tools. — spant-package • Spectroscopy Analysis Tools (spant) spant: spectroscopy analysis tools. — spant-package • Spectroscopy Analysis Tools (spant) Simulate and fit some spectra with ABfit for benchmarking purposes. Basic
-timing and performance metrics will be printed. — spant_abfit_benchmark • Spectroscopy Analysis Tools (spant) Simulate and fit some spectra with ABfit for benchmarking purposes. Basic timing and performance metrics will be printed. — spant_abfit_benchmark • Spectroscopy Analysis Tools (spant) Example MEGA-PRESS data with significant B0 drift. — spant_mpress_drift • Spectroscopy Analysis Tools (spant) Example MEGA-PRESS data with significant B0 drift. — spant_mpress_drift • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -83,7 +83,7 @@ Example MEGA-PRESS data with significant B0 drift.
Format
- An object of class mrs_data of length 13.
+ An object of class mrs_data of dimension 1 x 1 x 1 x 1 x 40 x 1 x 1024.
@@ -98,7 +98,7 @@ Format
diff --git a/docs/reference/spant_sim_fmrs_dataset.html b/docs/reference/spant_sim_fmrs_dataset.html
new file mode 100644
index 00000000..00e48b56
--- /dev/null
+++ b/docs/reference/spant_sim_fmrs_dataset.html
@@ -0,0 +1,117 @@
+
+Simulate an example fMRS dataset for a block design fMRS experiment and export a BIDS structure. — spant_sim_fmrs_dataset • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Simulate an example fMRS dataset for a block design fMRS experiment and export a BIDS structure.
+ Source: R/fmrs.R
+ spant_sim_fmrs_dataset.Rd
+
+
+
+ Simulate an example fMRS dataset for a block design fMRS experiment and
+export a BIDS structure.
+
+
+
+ spant_sim_fmrs_dataset(output_dir = NULL)
+
+
+
+ Arguments
+ - output_dir
+output directory for the BIDS data. Defaults to :
+"HOME/sim_fmrs_dataset/data".
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/spant_simulation_benchmark.html b/docs/reference/spant_simulation_benchmark.html
index 32daa8bf..d8cc6841 100644
--- a/docs/reference/spant_simulation_benchmark.html
+++ b/docs/reference/spant_simulation_benchmark.html
@@ -1,7 +1,5 @@
-Simulate a typical metabolite basis set for benchmarking. Timing metrics will
-be printed on completion. — spant_simulation_benchmark • Spectroscopy Analysis Tools (spant) Simulate a typical metabolite basis set for benchmarking. Timing metrics will be printed on completion. — spant_simulation_benchmark • Spectroscopy Analysis Tools (spant) Decompose an mrs_data object into white and gray matter spectra. — spec_decomp • Spectroscopy Analysis Tools (spant) Perform a mathematical operation on a spectral region. — spec_op • Spectroscopy Analysis Tools (spant) Perform a mathematical operation on a spectral region. — spec_op • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -98,8 +98,8 @@ Arguments
operator
-can be "sum" (default), "mean", "l2", "max", "min" or
-"max-min".
can be "sum" (default), "mean", "l2", "max", "max_cplx,
+"min" or "max-min".
freq_scale
@@ -129,7 +129,7 @@ Value
diff --git a/docs/reference/spin_sys.html b/docs/reference/spin_sys.html
index 853423a4..1eaa9e76 100644
--- a/docs/reference/spin_sys.html
+++ b/docs/reference/spin_sys.html
@@ -1,5 +1,5 @@
-Create a spin system object for pulse sequence simulation. — spin_sys • Spectroscopy Analysis Tools (spant) Create a spin system object for pulse sequence simulation. — spin_sys • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/spm_pve2categorical.html b/docs/reference/spm_pve2categorical.html
index 23a1bad9..70f10729 100644
--- a/docs/reference/spm_pve2categorical.html
+++ b/docs/reference/spm_pve2categorical.html
@@ -1,7 +1,5 @@
-Convert SPM style segmentation files to a single categorical image where
-the numerical values map as: 0) Other, 1) CSF, 2) GM and 3) WM. — spm_pve2categorical • Spectroscopy Analysis Tools (spant) Convert SPM style segmentation files to a single categorical image where the numerical values map as: 0) Other, 1) CSF, 2) GM and 3) WM. — spm_pve2categorical • Spectroscopy Analysis Tools (spant) Signal space projection method for lipid suppression. — ssp • Spectroscopy Analysis Tools (spant) Signal space projection method for lipid suppression. — ssp • Spectroscopy Analysis Tools (spant) Plot the fitting results of an object of class fit_result with
-individual basis set components shown. — stackplot.fit_result • Spectroscopy Analysis Tools (spant) Plot the fitting results of an object of class fit_result with individual basis set components shown. — stackplot.fit_result • Spectroscopy Analysis Tools (spant) Produce a plot with multiple traces. — stackplot • Spectroscopy Analysis Tools (spant) Produce a plot with multiple traces. — stackplot • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/stackplot.mrs_data.html b/docs/reference/stackplot.mrs_data.html
index 17ff5648..64eea445 100644
--- a/docs/reference/stackplot.mrs_data.html
+++ b/docs/reference/stackplot.mrs_data.html
@@ -1,5 +1,5 @@
-Stackplot plotting method for objects of class mrs_data. — stackplot.mrs_data • Spectroscopy Analysis Tools (spant) Stackplot plotting method for objects of class mrs_data. — stackplot.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -255,7 +255,7 @@ Arguments
diff --git a/docs/reference/sub_first_dyn.html b/docs/reference/sub_first_dyn.html
index dbd7f831..493b7242 100644
--- a/docs/reference/sub_first_dyn.html
+++ b/docs/reference/sub_first_dyn.html
@@ -1,5 +1,5 @@
-Subtract the first dynamic spectrum from a dynamic series. — sub_first_dyn • Spectroscopy Analysis Tools (spant) Subtract the first dynamic spectrum from a dynamic series. — sub_first_dyn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/sub_mean_dyns.html b/docs/reference/sub_mean_dyns.html
index 6e3bb2df..221bd0c1 100644
--- a/docs/reference/sub_mean_dyns.html
+++ b/docs/reference/sub_mean_dyns.html
@@ -1,5 +1,5 @@
-Subtract the mean dynamic spectrum from a dynamic series. — sub_mean_dyns • Spectroscopy Analysis Tools (spant) Subtract the mean dynamic spectrum from a dynamic series. — sub_mean_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/sub_median_dyns.html b/docs/reference/sub_median_dyns.html
index 134c495d..1e834f14 100644
--- a/docs/reference/sub_median_dyns.html
+++ b/docs/reference/sub_median_dyns.html
@@ -1,5 +1,5 @@
-Subtract the median dynamic spectrum from a dynamic series. — sub_median_dyns • Spectroscopy Analysis Tools (spant) Subtract the median dynamic spectrum from a dynamic series. — sub_median_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/sum_coils.html b/docs/reference/sum_coils.html
index 7bf559f2..e1ab3cc0 100644
--- a/docs/reference/sum_coils.html
+++ b/docs/reference/sum_coils.html
@@ -1,5 +1,5 @@
-Calculate the sum across receiver coil elements. — sum_coils • Spectroscopy Analysis Tools (spant) Calculate the sum across receiver coil elements. — sum_coils • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/sum_dyns.html b/docs/reference/sum_dyns.html
index a0be19d3..bbda2ffc 100644
--- a/docs/reference/sum_dyns.html
+++ b/docs/reference/sum_dyns.html
@@ -1,5 +1,5 @@
-Calculate the sum of data dynamics. — sum_dyns • Spectroscopy Analysis Tools (spant) Calculate the sum of data dynamics. — sum_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/sum_mrs.html b/docs/reference/sum_mrs.html
index a22f215b..3cc3ab9e 100644
--- a/docs/reference/sum_mrs.html
+++ b/docs/reference/sum_mrs.html
@@ -1,5 +1,5 @@
-Sum two mrs_data objects. — sum_mrs • Spectroscopy Analysis Tools (spant) Sum two mrs_data objects. — sum_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Value
diff --git a/docs/reference/sum_mrs_list.html b/docs/reference/sum_mrs_list.html
index f4e09aea..c3584348 100644
--- a/docs/reference/sum_mrs_list.html
+++ b/docs/reference/sum_mrs_list.html
@@ -1,5 +1,5 @@
-Return the sum of a list of mrs_data objects. — sum_mrs_list • Spectroscopy Analysis Tools (spant) Return the sum of a list of mrs_data objects. — sum_mrs_list • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/svs_1h_brain_analysis.html b/docs/reference/svs_1h_brain_analysis.html
index 8ce514db..dff0ef7d 100644
--- a/docs/reference/svs_1h_brain_analysis.html
+++ b/docs/reference/svs_1h_brain_analysis.html
@@ -1,5 +1,5 @@
-Standard SVS 1H brain analysis pipeline. — svs_1h_brain_analysis • Spectroscopy Analysis Tools (spant) Standard SVS 1H brain analysis pipeline. — svs_1h_brain_analysis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -199,7 +199,7 @@ Value
diff --git a/docs/reference/svs_1h_brain_analysis_dev.html b/docs/reference/svs_1h_brain_analysis_dev.html
index d70a14d3..d71bfea2 100644
--- a/docs/reference/svs_1h_brain_analysis_dev.html
+++ b/docs/reference/svs_1h_brain_analysis_dev.html
@@ -1,5 +1,5 @@
-Standard SVS 1H brain analysis pipeline. — svs_1h_brain_analysis_dev • Spectroscopy Analysis Tools (spant) Standard SVS 1H brain analysis pipeline. — svs_1h_brain_analysis_dev • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -193,7 +193,7 @@ Examples
diff --git a/docs/reference/svs_1h_brain_batch_analysis.html b/docs/reference/svs_1h_brain_batch_analysis.html
index 5631e8cc..15f7223e 100644
--- a/docs/reference/svs_1h_brain_batch_analysis.html
+++ b/docs/reference/svs_1h_brain_batch_analysis.html
@@ -1,5 +1,5 @@
-Batch interface to the standard SVS 1H brain analysis pipeline. — svs_1h_brain_batch_analysis • Spectroscopy Analysis Tools (spant) Batch interface to the standard SVS 1H brain analysis pipeline. — svs_1h_brain_batch_analysis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -144,7 +144,7 @@ Value
diff --git a/docs/reference/t_test_spec.html b/docs/reference/t_test_spec.html
new file mode 100644
index 00000000..56a7ea1b
--- /dev/null
+++ b/docs/reference/t_test_spec.html
@@ -0,0 +1,124 @@
+
+Perform a t-test on spectral data points. — t_test_spec • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+
+
+ Perform a t-test on spectral data points.
+
+
+
+ t_test_spec(mrs_data, group)
+
+
+
+ Arguments
+ - mrs_data
+an mrs_data object with spectra in the dynamic dimension.
- group
+vector describing the group membership of each dynamic spectrum.
+
+ Value
+
+
+a list of statistical results.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/td2fd.html b/docs/reference/td2fd.html
index 6748a6a8..f31ed524 100644
--- a/docs/reference/td2fd.html
+++ b/docs/reference/td2fd.html
@@ -1,5 +1,5 @@
-Transform time-domain data to the frequency-domain. — td2fd • Spectroscopy Analysis Tools (spant) Transform time-domain data to the frequency-domain. — td2fd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/td_conv_filt.html b/docs/reference/td_conv_filt.html
index a9f340c3..106b9b00 100644
--- a/docs/reference/td_conv_filt.html
+++ b/docs/reference/td_conv_filt.html
@@ -1,5 +1,5 @@
-Time-domain convolution based filter. — td_conv_filt • Spectroscopy Analysis Tools (spant) Time-domain convolution based filter. — td_conv_filt • Spectroscopy Analysis Tools (spant) Time-domain spectral registration. — tdsr • Spectroscopy Analysis Tools (spant) Time-domain spectral registration. — tdsr • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -121,7 +121,7 @@ Value
diff --git a/docs/reference/te.html b/docs/reference/te.html
index 010361b1..4a65711d 100644
--- a/docs/reference/te.html
+++ b/docs/reference/te.html
@@ -1,5 +1,5 @@
-Return the echo time of an MRS dataset. — te • Spectroscopy Analysis Tools (spant) Return the echo time of an MRS dataset. — te • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/tr.html b/docs/reference/tr.html
index 0c0bd63b..2e749e02 100644
--- a/docs/reference/tr.html
+++ b/docs/reference/tr.html
@@ -1,5 +1,5 @@
-Return the repetition time of an MRS dataset. — tr • Spectroscopy Analysis Tools (spant) Return the repetition time of an MRS dataset. — tr • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/varpro_3_para_opts.html b/docs/reference/varpro_3_para_opts.html
index c2270a16..52d7cd84 100644
--- a/docs/reference/varpro_3_para_opts.html
+++ b/docs/reference/varpro_3_para_opts.html
@@ -1,5 +1,5 @@
-Return a list of options for VARPRO based fitting with 3 free parameters. — varpro_3_para_opts • Spectroscopy Analysis Tools (spant) Return a list of options for VARPRO based fitting with 3 free parameters. — varpro_3_para_opts • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -141,7 +141,7 @@ Value
diff --git a/docs/reference/varpro_basic_opts.html b/docs/reference/varpro_basic_opts.html
index 32c86d22..c5104891 100644
--- a/docs/reference/varpro_basic_opts.html
+++ b/docs/reference/varpro_basic_opts.html
@@ -1,5 +1,5 @@
-Return a list of options for a basic VARPRO analysis. — varpro_basic_opts • Spectroscopy Analysis Tools (spant) Return a list of options for a basic VARPRO analysis. — varpro_basic_opts • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -118,7 +118,7 @@ Value
diff --git a/docs/reference/varpro_opts.html b/docs/reference/varpro_opts.html
index 2aabf11d..6332f730 100644
--- a/docs/reference/varpro_opts.html
+++ b/docs/reference/varpro_opts.html
@@ -1,5 +1,5 @@
-Return a list of options for VARPRO based fitting. — varpro_opts • Spectroscopy Analysis Tools (spant) Return a list of options for VARPRO based fitting. — varpro_opts • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -177,7 +177,7 @@ Examples
diff --git a/docs/reference/vec2mrs_data.html b/docs/reference/vec2mrs_data.html
index 0cccd73b..f0d58bf0 100644
--- a/docs/reference/vec2mrs_data.html
+++ b/docs/reference/vec2mrs_data.html
@@ -1,5 +1,5 @@
-Convert a vector into a mrs_data object. — vec2mrs_data • Spectroscopy Analysis Tools (spant) Convert a vector into a mrs_data object. — vec2mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -80,10 +80,11 @@ Convert a vector into a mrs_data object.
vec2mrs_data(
vec,
- fs = def_fs(),
- ft = def_ft(),
- ref = def_ref(),
- nuc = def_nuc(),
+ mrs_data = NULL,
+ fs = NULL,
+ ft = NULL,
+ ref = NULL,
+ nuc = NULL,
dyns = 1,
fd = FALSE
)
@@ -95,6 +96,10 @@ Arguments
the data vector.
mrs_data
+example data to copy acquisition parameters from.
fs
sampling frequency in Hz.
Arguments
fd
-flag to indicate if the matrix is in the frequency domain (logical).
flag to indicate if the vector is in the frequency domain (logical).
Value
diff --git a/docs/reference/write_basis.html b/docs/reference/write_basis.html
index b6e27cbd..94c5e021 100644
--- a/docs/reference/write_basis.html
+++ b/docs/reference/write_basis.html
@@ -1,5 +1,5 @@
-Write a basis object to an LCModel .basis formatted file. — write_basis • Spectroscopy Analysis Tools (spant) Write a basis object to an LCModel .basis formatted file. — write_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -108,7 +108,7 @@ Arguments
diff --git a/docs/reference/write_basis_tqn.html b/docs/reference/write_basis_tqn.html
index 6aa51c1d..116c73ec 100644
--- a/docs/reference/write_basis_tqn.html
+++ b/docs/reference/write_basis_tqn.html
@@ -1,5 +1,5 @@
-Generate a basis file using TARQUIN. — write_basis_tqn • Spectroscopy Analysis Tools (spant) Generate a basis file using TARQUIN. — write_basis_tqn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Examples
diff --git a/docs/reference/write_mrs.html b/docs/reference/write_mrs.html
index fff25f15..124b9dc4 100644
--- a/docs/reference/write_mrs.html
+++ b/docs/reference/write_mrs.html
@@ -1,5 +1,5 @@
-Write MRS data object to file. — write_mrs • Spectroscopy Analysis Tools (spant) Write MRS data object to file. — write_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Arguments
diff --git a/docs/reference/write_mrs_nifti.html b/docs/reference/write_mrs_nifti.html
index f4bf1921..bd3ed4b7 100644
--- a/docs/reference/write_mrs_nifti.html
+++ b/docs/reference/write_mrs_nifti.html
@@ -1,5 +1,5 @@
-Write MRS data object to file in NIFTI format. — write_mrs_nifti • Spectroscopy Analysis Tools (spant) Write MRS data object to file in NIFTI format. — write_mrs_nifti • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/write_pulse_ascii.html b/docs/reference/write_pulse_ascii.html
index 067ae086..221f8ebb 100644
--- a/docs/reference/write_pulse_ascii.html
+++ b/docs/reference/write_pulse_ascii.html
@@ -1,5 +1,5 @@
-Write an ASCII formatted pulse file. — write_pulse_ascii • Spectroscopy Analysis Tools (spant) Write an ASCII formatted pulse file. — write_pulse_ascii • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/zero_fade_spec.html b/docs/reference/zero_fade_spec.html
index c703745c..c8b572c3 100644
--- a/docs/reference/zero_fade_spec.html
+++ b/docs/reference/zero_fade_spec.html
@@ -1,7 +1,5 @@
-Fade a spectrum to zero by frequency domain multiplication with a tanh
-function. Note this operation distorts data points at the end of the FID. — zero_fade_spec • Spectroscopy Analysis Tools (spant) Fade a spectrum to zero by frequency domain multiplication with a tanh function. Note this operation distorts data points at the end of the FID. — zero_fade_spec • Spectroscopy Analysis Tools (spant) Zero all coherences including and above a given order. — zero_higher_orders • Spectroscopy Analysis Tools (spant) Zero all coherences including and above a given order. — zero_higher_orders • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Value
diff --git a/docs/reference/zero_td_pts_end.html b/docs/reference/zero_td_pts_end.html
index 8c1123c8..71d24ebb 100644
--- a/docs/reference/zero_td_pts_end.html
+++ b/docs/reference/zero_td_pts_end.html
@@ -1,5 +1,5 @@
-Set mrs_data object data points at the end of the FID to zero. — zero_td_pts_end • Spectroscopy Analysis Tools (spant) Set mrs_data object data points at the end of the FID to zero. — zero_td_pts_end • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/zf.html b/docs/reference/zf.html
index 85e2013c..baf50256 100644
--- a/docs/reference/zf.html
+++ b/docs/reference/zf.html
@@ -1,5 +1,5 @@
-Zero-fill MRS data in the time domain. — zf • Spectroscopy Analysis Tools (spant) Zero-fill MRS data in the time domain. — zf • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -125,7 +125,7 @@ Value
diff --git a/docs/reference/zf_xy.html b/docs/reference/zf_xy.html
index ebca3999..c4104a74 100644
--- a/docs/reference/zf_xy.html
+++ b/docs/reference/zf_xy.html
@@ -1,5 +1,5 @@
-Zero-fill MRSI data in the k-space x-y direction. — zf_xy • Spectroscopy Analysis Tools (spant) Zero-fill MRSI data in the k-space x-y direction. — zf_xy • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -113,7 +113,7 @@ Value
diff --git a/docs/sitemap.xml b/docs/sitemap.xml
index e2139f71..4c39f515 100644
--- a/docs/sitemap.xml
+++ b/docs/sitemap.xml
@@ -216,6 +216,12 @@
https://martin3141.github.io/spant/reference/comb_coils_fp_pc.html
+
+ https://martin3141.github.io/spant/reference/comb_coils_mrsi_gls.html
+
+
+ https://martin3141.github.io/spant/reference/comb_coils_svs_gls.html
+
https://martin3141.github.io/spant/reference/comb_csv_results.html
@@ -411,6 +417,9 @@
https://martin3141.github.io/spant/reference/gen_conv_reg.html
+
+ https://martin3141.github.io/spant/reference/gen_group_reg.html
+
https://martin3141.github.io/spant/reference/gen_impulse_reg.html
@@ -555,6 +564,15 @@
https://martin3141.github.io/spant/reference/glm_spec.html
+
+ https://martin3141.github.io/spant/reference/glm_spec_fmrs_fl.html
+
+
+ https://martin3141.github.io/spant/reference/glm_spec_fmrs_group.html
+
+
+ https://martin3141.github.io/spant/reference/glm_spec_group_linhyp.html
+
https://martin3141.github.io/spant/reference/grid_shift_xy.html
@@ -690,9 +708,15 @@
https://martin3141.github.io/spant/reference/mrs_data2basis.html
+
+ https://martin3141.github.io/spant/reference/mrs_data2bids.html
+
https://martin3141.github.io/spant/reference/mrs_data2mat.html
+
+ https://martin3141.github.io/spant/reference/mrs_data2spec_mat.html
+
https://martin3141.github.io/spant/reference/mrs_data2vec.html
@@ -741,6 +765,9 @@
https://martin3141.github.io/spant/reference/phase.html
+
+ https://martin3141.github.io/spant/reference/phase_ref_1h_brain.html
+
https://martin3141.github.io/spant/reference/plot.fit_result.html
@@ -780,6 +807,12 @@
https://martin3141.github.io/spant/reference/precomp.html
+
+ https://martin3141.github.io/spant/reference/preproc_svs.html
+
+
+ https://martin3141.github.io/spant/reference/preproc_svs_dataset.html
+
https://martin3141.github.io/spant/reference/print.fit_result.html
@@ -1050,6 +1083,9 @@
https://martin3141.github.io/spant/reference/spant_mpress_drift.html
+
+ https://martin3141.github.io/spant/reference/spant_sim_fmrs_dataset.html
+
https://martin3141.github.io/spant/reference/spant_simulation_benchmark.html
@@ -1107,6 +1143,9 @@
https://martin3141.github.io/spant/reference/svs_1h_brain_batch_analysis.html
+
+ https://martin3141.github.io/spant/reference/t_test_spec.html
+
https://martin3141.github.io/spant/reference/td2fd.html
Fade a spectrum to zero by frequency domain multiplication with a tanh -function. Note this operation distorts data points at the end of the FID.
Fade a spectrum to zero by frequency domain multiplication with a tanh function. Note this operation distorts data points at the end of the FID.
All functions
diff --git a/docs/reference/int_spec.html b/docs/reference/int_spec.html
index c7060fe7..783325a8 100644
--- a/docs/reference/int_spec.html
+++ b/docs/reference/int_spec.html
@@ -1,5 +1,5 @@
-Integrate a spectral region. — int_spec • Spectroscopy Analysis Tools (spant) Integrate a spectral region. — int_spec • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -118,7 +118,7 @@ Value
diff --git a/docs/reference/interleave_dyns.html b/docs/reference/interleave_dyns.html
index effe5543..441eff27 100644
--- a/docs/reference/interleave_dyns.html
+++ b/docs/reference/interleave_dyns.html
@@ -1,5 +1,5 @@
-Interleave the first and second half of a dynamic series. — interleave_dyns • Spectroscopy Analysis Tools (spant) Interleave the first and second half of a dynamic series. — interleave_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/inv_even_dyns.html b/docs/reference/inv_even_dyns.html
index 9f9d4fff..dcb781dc 100644
--- a/docs/reference/inv_even_dyns.html
+++ b/docs/reference/inv_even_dyns.html
@@ -1,5 +1,5 @@
-Invert even numbered dynamic scans starting from 1 (2,4,6...). — inv_even_dyns • Spectroscopy Analysis Tools (spant) Invert even numbered dynamic scans starting from 1 (2,4,6...). — inv_even_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/inv_odd_dyns.html b/docs/reference/inv_odd_dyns.html
index 26212e2b..78d64660 100644
--- a/docs/reference/inv_odd_dyns.html
+++ b/docs/reference/inv_odd_dyns.html
@@ -1,5 +1,5 @@
-Invert odd numbered dynamic scans starting from 1 (1,3,5...). — inv_odd_dyns • Spectroscopy Analysis Tools (spant) Invert odd numbered dynamic scans starting from 1 (1,3,5...). — inv_odd_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/is.def.html b/docs/reference/is.def.html
index f196ffd0..a67b9eba 100644
--- a/docs/reference/is.def.html
+++ b/docs/reference/is.def.html
@@ -1,5 +1,5 @@
-Check if an object is defined, which is the same as being not NULL. — is.def • Spectroscopy Analysis Tools (spant) Check if an object is defined, which is the same as being not NULL. — is.def • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/is_fd.html b/docs/reference/is_fd.html
index 3b0ca165..18a193aa 100644
--- a/docs/reference/is_fd.html
+++ b/docs/reference/is_fd.html
@@ -1,7 +1,5 @@
-Check if the chemical shift dimension of an MRS data object is in the
-frequency domain. — is_fd • Spectroscopy Analysis Tools (spant) Check if the chemical shift dimension of an MRS data object is in the frequency domain. — is_fd • Spectroscopy Analysis Tools (spant) Transform 2D MRSI data from k-space to image space in the x-y direction. — kspace2img_xy • Spectroscopy Analysis Tools (spant) Transform 2D MRSI data from k-space to image space in the x-y direction. — kspace2img_xy • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/l2_reg.html b/docs/reference/l2_reg.html
index 3d781d80..21aa9849 100644
--- a/docs/reference/l2_reg.html
+++ b/docs/reference/l2_reg.html
@@ -1,5 +1,5 @@
-Perform l2 regularisation artefact suppression. — l2_reg • Spectroscopy Analysis Tools (spant) Perform l2 regularisation artefact suppression. — l2_reg • Spectroscopy Analysis Tools (spant) Apply line-broadening (apodisation) to MRS data or basis object. — lb • Spectroscopy Analysis Tools (spant) Apply line-broadening (apodisation) to MRS data or basis object. — lb • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -123,7 +123,7 @@ Value
diff --git a/docs/reference/lofdc.html b/docs/reference/lofdc.html
index 5419b1ec..31347a25 100644
--- a/docs/reference/lofdc.html
+++ b/docs/reference/lofdc.html
@@ -1,5 +1,5 @@
-Correct linear frequency drift. — lofdc • Spectroscopy Analysis Tools (spant) Correct linear frequency drift. — lofdc • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -138,7 +138,7 @@ Value
diff --git a/docs/reference/lw2alpha.html b/docs/reference/lw2alpha.html
index b83db682..25da229b 100644
--- a/docs/reference/lw2alpha.html
+++ b/docs/reference/lw2alpha.html
@@ -1,7 +1,5 @@
-Covert a linewidth in Hz to an equivalent alpha value in the time-domain ie:
-x * exp(-t * alpha). — lw2alpha • Spectroscopy Analysis Tools (spant) Covert a linewidth in Hz to an equivalent alpha value in the time-domain ie: x * exp(-t * alpha). — lw2alpha • Spectroscopy Analysis Tools (spant) Covert a linewidth in Hz to an equivalent beta value in the time-domain ie:
-x * exp(-t * t * beta). — lw2beta • Spectroscopy Analysis Tools (spant) Covert a linewidth in Hz to an equivalent beta value in the time-domain ie: x * exp(-t * t * beta). — lw2beta • Spectroscopy Analysis Tools (spant) Make a basis-set object from a directory containing LCModel formatted RAW
-files. — make_basis_from_raw • Spectroscopy Analysis Tools (spant) Make a basis-set object from a directory containing LCModel formatted RAW files. — make_basis_from_raw • Spectroscopy Analysis Tools (spant) Mask an MRS dataset in the dynamic dimension. — mask_dyns • Spectroscopy Analysis Tools (spant) Mask an MRS dataset in the dynamic dimension. — mask_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/mask_fit_res.html b/docs/reference/mask_fit_res.html
index 97baaa3f..ebd91a99 100644
--- a/docs/reference/mask_fit_res.html
+++ b/docs/reference/mask_fit_res.html
@@ -1,5 +1,5 @@
-Mask fit result spectra depending on a vector of bool values. — mask_fit_res • Spectroscopy Analysis Tools (spant) Mask fit result spectra depending on a vector of bool values. — mask_fit_res • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -116,7 +116,7 @@ Value
diff --git a/docs/reference/mask_xy.html b/docs/reference/mask_xy.html
index 11bb577c..b0d38619 100644
--- a/docs/reference/mask_xy.html
+++ b/docs/reference/mask_xy.html
@@ -1,5 +1,5 @@
-Mask an MRSI dataset in the x-y direction — mask_xy • Spectroscopy Analysis Tools (spant) Mask an MRSI dataset in the x-y direction — mask_xy • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/mask_xy_corners.html b/docs/reference/mask_xy_corners.html
index 09b16cd2..2d13839d 100644
--- a/docs/reference/mask_xy_corners.html
+++ b/docs/reference/mask_xy_corners.html
@@ -1,5 +1,5 @@
-Mask the four corners of an MRSI dataset in the x-y plane. — mask_xy_corners • Spectroscopy Analysis Tools (spant) Mask the four corners of an MRSI dataset in the x-y plane. — mask_xy_corners • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/mask_xy_ellipse.html b/docs/reference/mask_xy_ellipse.html
index 1d8b02e4..e2e749ef 100644
--- a/docs/reference/mask_xy_ellipse.html
+++ b/docs/reference/mask_xy_ellipse.html
@@ -1,7 +1,5 @@
-Mask the voxels outside an elliptical region spanning the MRSI dataset in the
-x-y plane. — mask_xy_ellipse • Spectroscopy Analysis Tools (spant) Mask the voxels outside an elliptical region spanning the MRSI dataset in the x-y plane. — mask_xy_ellipse • Spectroscopy Analysis Tools (spant) Mask a 2D MRSI dataset in the x-y dimension. — mask_xy_mat • Spectroscopy Analysis Tools (spant) Mask a 2D MRSI dataset in the x-y dimension. — mask_xy_mat • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Value
diff --git a/docs/reference/mat2mrs_data.html b/docs/reference/mat2mrs_data.html
index 2e2895f3..ae55665f 100644
--- a/docs/reference/mat2mrs_data.html
+++ b/docs/reference/mat2mrs_data.html
@@ -1,7 +1,5 @@
-Convert a matrix (with spectral points in the column dimension and dynamics
-in the row dimensions) into a mrs_data object. — mat2mrs_data • Spectroscopy Analysis Tools (spant) Convert a matrix (with spectral points in the column dimension and dynamics in the row dimensions) into a mrs_data object. — mat2mrs_data • Spectroscopy Analysis Tools (spant) Matrix exponential function taken from complexplus package to reduce the
-number of spant dependencies. — matexp • Spectroscopy Analysis Tools (spant) Matrix exponential function taken from complexplus package to reduce the number of spant dependencies. — matexp • Spectroscopy Analysis Tools (spant) Apply the max operator to an MRS dataset. — max_mrs • Spectroscopy Analysis Tools (spant) Apply the max operator to an MRS dataset. — max_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/max_mrs_interp.html b/docs/reference/max_mrs_interp.html
index e4474764..52e63f3e 100644
--- a/docs/reference/max_mrs_interp.html
+++ b/docs/reference/max_mrs_interp.html
@@ -1,5 +1,5 @@
-Apply the max operator to an interpolated MRS dataset. — max_mrs_interp • Spectroscopy Analysis Tools (spant) Apply the max operator to an interpolated MRS dataset. — max_mrs_interp • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/mean.list.html b/docs/reference/mean.list.html
index b8eb3463..048306fd 100644
--- a/docs/reference/mean.list.html
+++ b/docs/reference/mean.list.html
@@ -1,5 +1,5 @@
-Calculate the mean spectrum from an mrs_data object. — mean.list • Spectroscopy Analysis Tools (spant) Calculate the mean spectrum from an mrs_data object. — mean.list • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/mean.mrs_data.html b/docs/reference/mean.mrs_data.html
index 5531a28d..79515014 100644
--- a/docs/reference/mean.mrs_data.html
+++ b/docs/reference/mean.mrs_data.html
@@ -1,5 +1,5 @@
-Calculate the mean spectrum from an mrs_data object. — mean.mrs_data • Spectroscopy Analysis Tools (spant) Calculate the mean spectrum from an mrs_data object. — mean.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/mean_dyn_blocks.html b/docs/reference/mean_dyn_blocks.html
index 10467098..4c042448 100644
--- a/docs/reference/mean_dyn_blocks.html
+++ b/docs/reference/mean_dyn_blocks.html
@@ -1,5 +1,5 @@
-Calculate the mean of adjacent dynamic scans. — mean_dyn_blocks • Spectroscopy Analysis Tools (spant) Calculate the mean of adjacent dynamic scans. — mean_dyn_blocks • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/mean_dyn_pairs.html b/docs/reference/mean_dyn_pairs.html
index 63e909ea..1a241126 100644
--- a/docs/reference/mean_dyn_pairs.html
+++ b/docs/reference/mean_dyn_pairs.html
@@ -1,5 +1,5 @@
-Calculate the pairwise means across a dynamic data set. — mean_dyn_pairs • Spectroscopy Analysis Tools (spant) Calculate the pairwise means across a dynamic data set. — mean_dyn_pairs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/mean_dyns.html b/docs/reference/mean_dyns.html
index 73fdbfa7..0daa27df 100644
--- a/docs/reference/mean_dyns.html
+++ b/docs/reference/mean_dyns.html
@@ -1,5 +1,5 @@
-Calculate the mean dynamic data. — mean_dyns • Spectroscopy Analysis Tools (spant) Calculate the mean dynamic data. — mean_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/mean_mrs_list.html b/docs/reference/mean_mrs_list.html
index 808b6c50..10d842c0 100644
--- a/docs/reference/mean_mrs_list.html
+++ b/docs/reference/mean_mrs_list.html
@@ -1,5 +1,5 @@
-Return the mean of a list of mrs_data objects. — mean_mrs_list • Spectroscopy Analysis Tools (spant) Return the mean of a list of mrs_data objects. — mean_mrs_list • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/mean_vec_blocks.html b/docs/reference/mean_vec_blocks.html
index 8fc92eaa..dd78b122 100644
--- a/docs/reference/mean_vec_blocks.html
+++ b/docs/reference/mean_vec_blocks.html
@@ -1,5 +1,5 @@
-Calculate the mean of adjacent blocks in a vector. — mean_vec_blocks • Spectroscopy Analysis Tools (spant) Calculate the mean of adjacent blocks in a vector. — mean_vec_blocks • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/median_dyns.html b/docs/reference/median_dyns.html
index 1039d4b5..9a085b10 100644
--- a/docs/reference/median_dyns.html
+++ b/docs/reference/median_dyns.html
@@ -1,5 +1,5 @@
-Calculate the median dynamic data. — median_dyns • Spectroscopy Analysis Tools (spant) Calculate the median dynamic data. — median_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/mod_td.html b/docs/reference/mod_td.html
index 76ad0a40..141ef09e 100644
--- a/docs/reference/mod_td.html
+++ b/docs/reference/mod_td.html
@@ -1,5 +1,5 @@
-Apply the Modulus operator to the time-domain MRS signal. — mod_td • Spectroscopy Analysis Tools (spant) Apply the Modulus operator to the time-domain MRS signal. — mod_td • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/mrs_data2basis.html b/docs/reference/mrs_data2basis.html
index 62f7d749..11797b91 100644
--- a/docs/reference/mrs_data2basis.html
+++ b/docs/reference/mrs_data2basis.html
@@ -1,7 +1,5 @@
-Convert an mrs_data object to basis object - where basis signals are spread
-across the dynamic dimension in the MRS data. — mrs_data2basis • Spectroscopy Analysis Tools (spant) Convert an mrs_data object to basis object - where basis signals are spread across the dynamic dimension in the MRS data. — mrs_data2basis • Spectroscopy Analysis Tools (spant) Create a BIDS file structure from a vector of MRS data paths or list of mrs_data objects. — mrs_data2bids • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Create a BIDS file structure from a vector of MRS data paths or list of mrs_data objects.
+ Source: R/fmrs.R
+ mrs_data2bids.Rd
+
+
+
+ Create a BIDS file structure from a vector of MRS data paths or list of
+mrs_data objects.
+
+
+
+ mrs_data2bids(
+ mrs_data,
+ output_dir,
+ suffix = NULL,
+ sub = NULL,
+ ses = NULL,
+ task = NULL,
+ acq = NULL,
+ nuc = NULL,
+ voi = NULL,
+ rec = NULL,
+ run = NULL,
+ echo = NULL,
+ inv = NULL,
+ skip_existing = TRUE
+)
+
+
+
+ Arguments
+ - mrs_data
+vector of MRS data paths or list of mrs_data objects.
- output_dir
+the base directory to create the BIDS structure.
- suffix
+optional vector of file suffixes. Default behaviour is to
+automatically determine these from the input data, however it is recommended
+that they are specified to allow more efficient skipping of existing data.
- sub
+optional vector of subject labels. If not specified, these will be
+automatically generated as a series of increasing zero-padded integer values
+corresponding to the mrs_data input indices.
- ses
+optional vector of session labels.
- task
+optional vector of task labels.
- acq
+optional vector of acquisition labels.
- nuc
+optional vector of nucleus labels.
- voi
+optional vector of volume of interest labels.
- rec
+optional vector of reconstruction labels.
- run
+optional vector of run indices.
- echo
+optional vector of echo time indices.
- inv
+optional vector of inversion indices.
- skip_existing
+skip any data files that have already been converted.
+Defaults to TRUE, set to FALSE to force an overwrite of any existing data
+files.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/mrs_data2mat.html b/docs/reference/mrs_data2mat.html
index cf5ff28c..9e47688a 100644
--- a/docs/reference/mrs_data2mat.html
+++ b/docs/reference/mrs_data2mat.html
@@ -1,7 +1,5 @@
-Convert mrs_data object to a matrix, with spectral points in the column
-dimension and dynamics in the row dimension. — mrs_data2mat • Spectroscopy Analysis Tools (spant) Convert mrs_data object to a matrix, with spectral points in the column dimension and dynamics in the row dimension. — mrs_data2mat • Spectroscopy Analysis Tools (spant) Convert mrs_data object to a matrix, with spectral points in the column dimension and dynamics in the row dimension. — mrs_data2spec_mat • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Convert mrs_data object to a matrix, with spectral points in the column dimension and dynamics in the row dimension.
+ Source: R/mrs_data_proc.R
+ mrs_data2spec_mat.Rd
+
+
+
+ Convert mrs_data object to a matrix, with spectral points in the column
+dimension and dynamics in the row dimension.
+
+
+
+ mrs_data2spec_mat(mrs_data, collapse = TRUE)
+
+
+
+ Arguments
+ - mrs_data
+MRS data object or list of MRS data objects.
- collapse
+collapse all other dimensions along the dynamic dimension, eg
+a 16x16 MRSI grid would be first collapsed across 256 dynamic scans.
+
+ Value
+
+
+MRS data matrix.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/mrs_data2vec.html b/docs/reference/mrs_data2vec.html
index fb172d68..a1fd654d 100644
--- a/docs/reference/mrs_data2vec.html
+++ b/docs/reference/mrs_data2vec.html
@@ -1,5 +1,5 @@
-Convert mrs_data object to a vector. — mrs_data2vec • Spectroscopy Analysis Tools (spant) Convert mrs_data object to a vector. — mrs_data2vec • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -126,7 +126,7 @@ Value
diff --git a/docs/reference/mvfftshift.html b/docs/reference/mvfftshift.html
index 92b0841b..976b3410 100644
--- a/docs/reference/mvfftshift.html
+++ b/docs/reference/mvfftshift.html
@@ -1,7 +1,5 @@
-Perform a fftshift on a matrix, with each column replaced by its shifted
-result. — mvfftshift • Spectroscopy Analysis Tools (spant) Perform a fftshift on a matrix, with each column replaced by its shifted result. — mvfftshift • Spectroscopy Analysis Tools (spant) Perform an ifftshift on a matrix, with each column replaced by its shifted
-result. — mvifftshift • Spectroscopy Analysis Tools (spant) Perform an ifftshift on a matrix, with each column replaced by its shifted result. — mvifftshift • Spectroscopy Analysis Tools (spant) Print fit coordinates from a single index. — n2coord • Spectroscopy Analysis Tools (spant) Print fit coordinates from a single index. — n2coord • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/nifti_flip_lr.html b/docs/reference/nifti_flip_lr.html
index 730abe3c..19860b3c 100644
--- a/docs/reference/nifti_flip_lr.html
+++ b/docs/reference/nifti_flip_lr.html
@@ -1,9 +1,5 @@
-Flip the x data dimension order of a nifti image. This corresponds to
-flipping MRI data in the left-right direction, assuming the data in save in
-neurological format (can check with fslorient program). — nifti_flip_lr • Spectroscopy Analysis Tools (spant) Flip the x data dimension order of a nifti image. This corresponds to flipping MRI data in the left-right direction, assuming the data in save in neurological format (can check with fslorient program). — nifti_flip_lr • Spectroscopy Analysis Tools (spant) Export a one-page pdf of a single fit result — one_page_pdf • Spectroscopy Analysis Tools (spant) Export a one-page pdf of a single fit result — one_page_pdf • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -108,7 +108,7 @@ Arguments
diff --git a/docs/reference/ortho3.html b/docs/reference/ortho3.html
index 13ade97d..5d7dd2fd 100644
--- a/docs/reference/ortho3.html
+++ b/docs/reference/ortho3.html
@@ -1,5 +1,5 @@
-Display an orthographic projection plot of a nifti object. — ortho3 • Spectroscopy Analysis Tools (spant) Display an orthographic projection plot of a nifti object. — ortho3 • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -172,7 +172,7 @@ Arguments
diff --git a/docs/reference/ortho3_inter.html b/docs/reference/ortho3_inter.html
index 090cc5e5..15948899 100644
--- a/docs/reference/ortho3_inter.html
+++ b/docs/reference/ortho3_inter.html
@@ -1,5 +1,5 @@
-Display an interactive orthographic projection plot of a nifti object. — ortho3_inter • Spectroscopy Analysis Tools (spant) Display an interactive orthographic projection plot of a nifti object. — ortho3_inter • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -132,7 +132,7 @@ Arguments
diff --git a/docs/reference/peak_info.html b/docs/reference/peak_info.html
index 09058bd8..41c8ffaf 100644
--- a/docs/reference/peak_info.html
+++ b/docs/reference/peak_info.html
@@ -1,7 +1,5 @@
-Search for the highest peak in a spectral region and return the frequency,
-height and FWHM. — peak_info • Spectroscopy Analysis Tools (spant) Search for the highest peak in a spectral region and return the frequency, height and FWHM. — peak_info • Spectroscopy Analysis Tools (spant) Papoulis-Gerchberg (PG) algorithm method for k-space extrapolation. — pg_extrap_xy • Spectroscopy Analysis Tools (spant) Papoulis-Gerchberg (PG) algorithm method for k-space extrapolation. — pg_extrap_xy • Spectroscopy Analysis Tools (spant) Apply phasing parameters to MRS data. — phase • Spectroscopy Analysis Tools (spant) Apply phasing parameters to MRS data. — phase • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/phase_ref_1h_brain.html b/docs/reference/phase_ref_1h_brain.html
new file mode 100644
index 00000000..8707a74a
--- /dev/null
+++ b/docs/reference/phase_ref_1h_brain.html
@@ -0,0 +1,131 @@
+
+Corrected zero order phase and chemical shift offset in 1H MRS data from the brain. — phase_ref_1h_brain • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Corrected zero order phase and chemical shift offset in 1H MRS data from the brain.
+ Source: R/rats.R
+ phase_ref_1h_brain.Rd
+
+
+
+ Corrected zero order phase and chemical shift offset in 1H MRS data from the
+brain.
+
+
+
+ phase_ref_1h_brain(mrs_data, mean_ref = FALSE, ret_corr_only = TRUE)
+
+
+
+ Arguments
+ - mrs_data
+MRS data to be corrected.
- mean_ref
+apply the phase and offset of the mean spectrum to all
+others. Default is FALSE.
- ret_corr_only
+return the corrected data only.
+
+ Value
+
+
+corrected MRS data.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/plot.fit_result.html b/docs/reference/plot.fit_result.html
index e54d3bc1..836a53ee 100644
--- a/docs/reference/plot.fit_result.html
+++ b/docs/reference/plot.fit_result.html
@@ -1,5 +1,5 @@
-Plot the fitting results of an object of class fit_result. — plot.fit_result • Spectroscopy Analysis Tools (spant) Plot the fitting results of an object of class fit_result. — plot.fit_result • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -207,7 +207,7 @@ Arguments
diff --git a/docs/reference/plot.mrs_data.html b/docs/reference/plot.mrs_data.html
index fabcc35b..bb2ec651 100644
--- a/docs/reference/plot.mrs_data.html
+++ b/docs/reference/plot.mrs_data.html
@@ -1,5 +1,5 @@
-Plotting method for objects of class mrs_data. — plot.mrs_data • Spectroscopy Analysis Tools (spant) Plotting method for objects of class mrs_data. — plot.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -287,7 +287,7 @@ Arguments
diff --git a/docs/reference/plot_bc.html b/docs/reference/plot_bc.html
index 4f8309b4..b48142cc 100644
--- a/docs/reference/plot_bc.html
+++ b/docs/reference/plot_bc.html
@@ -1,5 +1,5 @@
-Convenience function to plot a baseline estimate with the original data. — plot_bc • Spectroscopy Analysis Tools (spant) Convenience function to plot a baseline estimate with the original data. — plot_bc • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -108,7 +108,7 @@ Arguments
diff --git a/docs/reference/plot_reg.html b/docs/reference/plot_reg.html
index ae1acbe7..2addb2f6 100644
--- a/docs/reference/plot_reg.html
+++ b/docs/reference/plot_reg.html
@@ -1,5 +1,5 @@
-Plot regressors as an image. — plot_reg • Spectroscopy Analysis Tools (spant) Plot regressors as an image. — plot_reg • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/plot_slice_fit.html b/docs/reference/plot_slice_fit.html
index fbc7b560..57f1af8a 100644
--- a/docs/reference/plot_slice_fit.html
+++ b/docs/reference/plot_slice_fit.html
@@ -1,5 +1,5 @@
-Plot a 2D slice from an MRSI fit result object. — plot_slice_fit • Spectroscopy Analysis Tools (spant) Plot a 2D slice from an MRSI fit result object. — plot_slice_fit • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -129,7 +129,7 @@ Arguments
diff --git a/docs/reference/plot_slice_fit_inter.html b/docs/reference/plot_slice_fit_inter.html
index 4eed104a..da105a7d 100644
--- a/docs/reference/plot_slice_fit_inter.html
+++ b/docs/reference/plot_slice_fit_inter.html
@@ -1,5 +1,5 @@
-Plot a 2D slice from an MRSI fit result object. — plot_slice_fit_inter • Spectroscopy Analysis Tools (spant) Plot a 2D slice from an MRSI fit result object. — plot_slice_fit_inter • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -134,7 +134,7 @@ Arguments
diff --git a/docs/reference/plot_slice_map.html b/docs/reference/plot_slice_map.html
index 553e9ac8..ffb2a134 100644
--- a/docs/reference/plot_slice_map.html
+++ b/docs/reference/plot_slice_map.html
@@ -1,5 +1,5 @@
-Plot a slice from a 7 dimensional array. — plot_slice_map • Spectroscopy Analysis Tools (spant) Plot a slice from a 7 dimensional array. — plot_slice_map • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -153,7 +153,7 @@ Arguments
diff --git a/docs/reference/plot_slice_map_inter.html b/docs/reference/plot_slice_map_inter.html
index 40d33b42..90968f66 100644
--- a/docs/reference/plot_slice_map_inter.html
+++ b/docs/reference/plot_slice_map_inter.html
@@ -1,7 +1,5 @@
-Plot an interactive slice map from a data array where voxels can be selected
-to display a corresponding spectrum. — plot_slice_map_inter • Spectroscopy Analysis Tools (spant) Plot an interactive slice map from a data array where voxels can be selected to display a corresponding spectrum. — plot_slice_map_inter • Spectroscopy Analysis Tools (spant) Plot the spectral standard deviation. — plot_spec_sd • Spectroscopy Analysis Tools (spant) Plot the spectral standard deviation. — plot_spec_sd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Arguments
diff --git a/docs/reference/plot_voi_overlay.html b/docs/reference/plot_voi_overlay.html
index 9a782e88..bbbbf35e 100644
--- a/docs/reference/plot_voi_overlay.html
+++ b/docs/reference/plot_voi_overlay.html
@@ -1,5 +1,5 @@
-Plot a volume as an image overlay. — plot_voi_overlay • Spectroscopy Analysis Tools (spant) Plot a volume as an image overlay. — plot_voi_overlay • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -116,7 +116,7 @@ Arguments
diff --git a/docs/reference/plot_voi_overlay_seg.html b/docs/reference/plot_voi_overlay_seg.html
index 3d4e74ff..0e800ff2 100644
--- a/docs/reference/plot_voi_overlay_seg.html
+++ b/docs/reference/plot_voi_overlay_seg.html
@@ -1,5 +1,5 @@
-Plot a volume as an overlay on a segmented brain volume. — plot_voi_overlay_seg • Spectroscopy Analysis Tools (spant) Plot a volume as an overlay on a segmented brain volume. — plot_voi_overlay_seg • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Arguments
diff --git a/docs/reference/ppm.html b/docs/reference/ppm.html
index c352327a..ee4696e2 100644
--- a/docs/reference/ppm.html
+++ b/docs/reference/ppm.html
@@ -1,5 +1,5 @@
-Return the ppm scale of an MRS dataset or fit result. — ppm • Spectroscopy Analysis Tools (spant) Return the ppm scale of an MRS dataset or fit result. — ppm • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -132,7 +132,7 @@ Value
diff --git a/docs/reference/precomp.html b/docs/reference/precomp.html
index 822d7336..df3d2c6c 100644
--- a/docs/reference/precomp.html
+++ b/docs/reference/precomp.html
@@ -1,7 +1,5 @@
-Save function results to file and load on subsequent calls to avoid repeat
-computation. — precomp • Spectroscopy Analysis Tools (spant) Save function results to file and load on subsequent calls to avoid repeat computation. — precomp • Spectroscopy Analysis Tools (spant) Preprocess and perform quality assessment of a single SVS data set. — preproc_svs • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Preprocess and perform quality assessment of a single SVS data set.
+ Source: R/fmrs.R
+ preproc_svs.Rd
+
+
+
+ Preprocess and perform quality assessment of a single SVS data set.
+
+
+
+ preproc_svs(path, label = NULL, output_dir = NULL, ref_inds = NULL)
+
+
+
+ Arguments
+ - path
+path to the fMRS data file or IMA directory.
- label
+a label to describe the data set.
- output_dir
+output directory.
- ref_inds
+a vector of 1-based indices for any water reference dynamic
+scans.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/preproc_svs_dataset.html b/docs/reference/preproc_svs_dataset.html
new file mode 100644
index 00000000..07c3a29b
--- /dev/null
+++ b/docs/reference/preproc_svs_dataset.html
@@ -0,0 +1,148 @@
+
+Preprocess and perform quality assessment of one or more SVS data sets. — preproc_svs_dataset • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Preprocess and perform quality assessment of one or more SVS data sets.
+ Source: R/fmrs.R
+ preproc_svs_dataset.Rd
+
+
+
+ Preprocess and perform quality assessment of one or more SVS data sets.
+
+
+
+ preproc_svs_dataset(
+ paths,
+ labels = NULL,
+ output_dir = "spant_analysis",
+ exclude_labels = NULL,
+ overwrite = FALSE,
+ ref_inds = NULL,
+ return_results = FALSE
+)
+
+
+
+ Arguments
+ - paths
+paths to the fMRS data file or IMA directory.
- labels
+labels to describe each data set.
- output_dir
+output directory.
- exclude_labels
+vector of labels of scans to exclude, eg poor quality
+data.
- overwrite
+overwrite saved results, defaults to FALSE.
- ref_inds
+a vector of 1-based indices for any water reference dynamic
+scans.
- return_results
+function will return key outputs, defaults to FALSE.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/print.fit_result.html b/docs/reference/print.fit_result.html
index 297f28dc..5f434e57 100644
--- a/docs/reference/print.fit_result.html
+++ b/docs/reference/print.fit_result.html
@@ -1,5 +1,5 @@
-Print a summary of an object of class fit_result. — print.fit_result • Spectroscopy Analysis Tools (spant) Print a summary of an object of class fit_result. — print.fit_result • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -105,7 +105,7 @@ Arguments
diff --git a/docs/reference/print.mrs_data.html b/docs/reference/print.mrs_data.html
index 51199017..e1561eb2 100644
--- a/docs/reference/print.mrs_data.html
+++ b/docs/reference/print.mrs_data.html
@@ -1,5 +1,5 @@
-Print a summary of mrs_data parameters. — print.mrs_data • Spectroscopy Analysis Tools (spant) Print a summary of mrs_data parameters. — print.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -109,7 +109,7 @@ Arguments
diff --git a/docs/reference/qn_states.html b/docs/reference/qn_states.html
index 0f42f2f9..d7aa6715 100644
--- a/docs/reference/qn_states.html
+++ b/docs/reference/qn_states.html
@@ -1,5 +1,5 @@
-Get the quantum coherence matrix for a spin system. — qn_states • Spectroscopy Analysis Tools (spant) Get the quantum coherence matrix for a spin system. — qn_states • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/rats.html b/docs/reference/rats.html
index 5a39a396..93585e08 100644
--- a/docs/reference/rats.html
+++ b/docs/reference/rats.html
@@ -1,5 +1,5 @@
-Robust Alignment to a Target Spectrum (RATS). — rats • Spectroscopy Analysis Tools (spant) Robust Alignment to a Target Spectrum (RATS). — rats • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -207,7 +207,7 @@ Value
diff --git a/docs/reference/re_weighting.html b/docs/reference/re_weighting.html
index d21caf21..8b0b070a 100644
--- a/docs/reference/re_weighting.html
+++ b/docs/reference/re_weighting.html
@@ -1,5 +1,5 @@
-Apply a weighting to the FID to enhance spectral resolution. — re_weighting • Spectroscopy Analysis Tools (spant) Apply a weighting to the FID to enhance spectral resolution. — re_weighting • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/read_basis.html b/docs/reference/read_basis.html
index da9b94af..eb6f8557 100644
--- a/docs/reference/read_basis.html
+++ b/docs/reference/read_basis.html
@@ -1,5 +1,5 @@
-Read a basis file in LCModel .basis format. — read_basis • Spectroscopy Analysis Tools (spant) Read a basis file in LCModel .basis format. — read_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/read_ima_coil_dir.html b/docs/reference/read_ima_coil_dir.html
index 28c02de0..4f073cd8 100644
--- a/docs/reference/read_ima_coil_dir.html
+++ b/docs/reference/read_ima_coil_dir.html
@@ -1,9 +1,5 @@
-Read a directory containing Siemens MRS IMA files and combine along the coil
-dimension. Note that the coil ID is inferred from the sorted file name and
-should be checked when consistency is required between two directories. — read_ima_coil_dir • Spectroscopy Analysis Tools (spant) Read a directory containing Siemens MRS IMA files and combine along the coil dimension. Note that the coil ID is inferred from the sorted file name and should be checked when consistency is required between two directories. — read_ima_coil_dir • Spectroscopy Analysis Tools (spant) Read a directory containing Siemens MRS IMA files and combine along the
-dynamic dimension. Note that the coil ID is inferred from the sorted file
-name and should be checked when consistency is required. — read_ima_dyn_dir • Spectroscopy Analysis Tools (spant) Read a directory containing Siemens MRS IMA files and combine along the dynamic dimension. Note that the coil ID is inferred from the sorted file name and should be checked when consistency is required. — read_ima_dyn_dir • Spectroscopy Analysis Tools (spant) Read an LCModel formatted coord file containing fit information. — read_lcm_coord • Spectroscopy Analysis Tools (spant) Read an LCModel formatted coord file containing fit information. — read_lcm_coord • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -107,7 +107,7 @@ Value
diff --git a/docs/reference/read_mrs.html b/docs/reference/read_mrs.html
index 3ac2a36b..2cf36b20 100644
--- a/docs/reference/read_mrs.html
+++ b/docs/reference/read_mrs.html
@@ -1,5 +1,5 @@
-Read MRS data from a file. — read_mrs • Spectroscopy Analysis Tools (spant) Read MRS data from a file. — read_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -88,7 +88,8 @@ Read MRS data from a file.
full_fid = FALSE,
omit_svs_ref_scans = TRUE,
verbose = FALSE,
- extra = NULL
+ extra = NULL,
+ fid_filt_dist = NULL
)
@@ -140,6 +141,13 @@ Arguments
an optional data frame to provide additional variables for use
in subsequent analysis steps, eg id or grouping variables.
fid_filt_dist
+indicate if the data has a distorted FID due to a
+brick-wall filter being used to downsample the data. Default is to auto
+detect this from the data, but TRUE or FALSE options can be given to override
+detection.
Value
@@ -183,7 +191,7 @@ Examples
diff --git a/docs/reference/read_mrs_tqn.html b/docs/reference/read_mrs_tqn.html
index 5766362f..84bdaf3a 100644
--- a/docs/reference/read_mrs_tqn.html
+++ b/docs/reference/read_mrs_tqn.html
@@ -1,5 +1,5 @@
-Read MRS data using the TARQUIN software package. — read_mrs_tqn • Spectroscopy Analysis Tools (spant) Read MRS data using the TARQUIN software package. — read_mrs_tqn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -131,7 +131,7 @@ Examples
diff --git a/docs/reference/read_pulse_ascii.html b/docs/reference/read_pulse_ascii.html
index c9e0d43c..ab11c9cc 100644
--- a/docs/reference/read_pulse_ascii.html
+++ b/docs/reference/read_pulse_ascii.html
@@ -1,5 +1,5 @@
-Read an ASCII formatted pulse file. — read_pulse_ascii • Spectroscopy Analysis Tools (spant) Read an ASCII formatted pulse file. — read_pulse_ascii • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/read_pulse_bruker.html b/docs/reference/read_pulse_bruker.html
index c92bf76a..dbe9073b 100644
--- a/docs/reference/read_pulse_bruker.html
+++ b/docs/reference/read_pulse_bruker.html
@@ -1,5 +1,5 @@
-Read a Bruker formatted pulse file — read_pulse_bruker • Spectroscopy Analysis Tools (spant) Read a Bruker formatted pulse file — read_pulse_bruker • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/read_pulse_pta.html b/docs/reference/read_pulse_pta.html
index 72e1b6d4..a0fac3c3 100644
--- a/docs/reference/read_pulse_pta.html
+++ b/docs/reference/read_pulse_pta.html
@@ -1,5 +1,5 @@
-Read a .pta formatted pulse file compatible with Siemens PulseTool. — read_pulse_pta • Spectroscopy Analysis Tools (spant) Read a .pta formatted pulse file compatible with Siemens PulseTool. — read_pulse_pta • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/read_siemens_txt_hdr.html b/docs/reference/read_siemens_txt_hdr.html
index 23fb8c70..3a17d87c 100644
--- a/docs/reference/read_siemens_txt_hdr.html
+++ b/docs/reference/read_siemens_txt_hdr.html
@@ -1,5 +1,5 @@
-Read the text format header found in Siemens IMA and TWIX data files. — read_siemens_txt_hdr • Spectroscopy Analysis Tools (spant) Read the text format header found in Siemens IMA and TWIX data files. — read_siemens_txt_hdr • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -78,7 +78,7 @@ Read the text format header found in Siemens IMA and TWIX data files.
- read_siemens_txt_hdr(input, version = "vd", verbose, offset = 0)
+ read_siemens_txt_hdr(input, version = "vd", verbose = FALSE, offset = 0)
@@ -118,7 +118,7 @@ Value
diff --git a/docs/reference/read_tqn_fit.html b/docs/reference/read_tqn_fit.html
index 4da6c25e..a1630420 100644
--- a/docs/reference/read_tqn_fit.html
+++ b/docs/reference/read_tqn_fit.html
@@ -1,5 +1,5 @@
-Reader for csv fit results generated by TARQUIN. — read_tqn_fit • Spectroscopy Analysis Tools (spant) Reader for csv fit results generated by TARQUIN. — read_tqn_fit • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -113,7 +113,7 @@ Examples
diff --git a/docs/reference/read_tqn_result.html b/docs/reference/read_tqn_result.html
index 36659714..68a3e98c 100644
--- a/docs/reference/read_tqn_result.html
+++ b/docs/reference/read_tqn_result.html
@@ -1,5 +1,5 @@
-Reader for csv results generated by TARQUIN. — read_tqn_result • Spectroscopy Analysis Tools (spant) Reader for csv results generated by TARQUIN. — read_tqn_result • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -117,7 +117,7 @@ Examples
diff --git a/docs/reference/recon_imag.html b/docs/reference/recon_imag.html
index d2a72225..5bc3b1eb 100644
--- a/docs/reference/recon_imag.html
+++ b/docs/reference/recon_imag.html
@@ -1,7 +1,5 @@
-Reconstruct complex time-domain data from the real part of frequency-domain
-data. — recon_imag • Spectroscopy Analysis Tools (spant) Reconstruct complex time-domain data from the real part of frequency-domain data. — recon_imag • Spectroscopy Analysis Tools (spant) Reconstruct complex time-domain data from the real part of frequency-domain
-data. — recon_imag_vec • Spectroscopy Analysis Tools (spant) Reconstruct complex time-domain data from the real part of frequency-domain data. — recon_imag_vec • Spectroscopy Analysis Tools (spant) Reconstruct 2D MRSI data from a twix file loaded with read_mrs. — recon_twix_2d_mrsi • Spectroscopy Analysis Tools (spant) Reconstruct 2D MRSI data from a twix file loaded with read_mrs. — recon_twix_2d_mrsi • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/rectangular_mask.html b/docs/reference/rectangular_mask.html
index a2117283..6e469bc9 100644
--- a/docs/reference/rectangular_mask.html
+++ b/docs/reference/rectangular_mask.html
@@ -1,5 +1,5 @@
-Create a rectangular mask stored as a matrix of logical values. — rectangular_mask • Spectroscopy Analysis Tools (spant) Create a rectangular mask stored as a matrix of logical values. — rectangular_mask • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -130,7 +130,7 @@ Value
diff --git a/docs/reference/reexports.html b/docs/reference/reexports.html
index 694a75d1..a59e8379 100644
--- a/docs/reference/reexports.html
+++ b/docs/reference/reexports.html
@@ -1,5 +1,5 @@
-Objects exported from other packages — reexports • Spectroscopy Analysis Tools (spant) Objects exported from other packages — reexports • Spectroscopy Analysis Tools (spant)
Spectroscopy Analysis Tools (spant)
- 2.21.0
+ 2.22.0
@@ -103,7 +103,7 @@ Objects exported from other packages
diff --git a/docs/reference/rep_array_dim.html b/docs/reference/rep_array_dim.html
index b9c49b4a..48c0a5ed 100644
--- a/docs/reference/rep_array_dim.html
+++ b/docs/reference/rep_array_dim.html
@@ -1,5 +1,5 @@
-Repeat an array over a given dimension. — rep_array_dim • Spectroscopy Analysis Tools (spant) Repeat an array over a given dimension. — rep_array_dim • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/rep_dyn.html b/docs/reference/rep_dyn.html
index 6bbfb0ef..89a4bb9b 100644
--- a/docs/reference/rep_dyn.html
+++ b/docs/reference/rep_dyn.html
@@ -1,5 +1,5 @@
-Replicate a scan in the dynamic dimension. — rep_dyn • Spectroscopy Analysis Tools (spant) Replicate a scan in the dynamic dimension. — rep_dyn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/rep_mrs.html b/docs/reference/rep_mrs.html
index 67730b5c..becb8f00 100644
--- a/docs/reference/rep_mrs.html
+++ b/docs/reference/rep_mrs.html
@@ -1,5 +1,5 @@
-Replicate a scan over a given dimension. — rep_mrs • Spectroscopy Analysis Tools (spant) Replicate a scan over a given dimension. — rep_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -138,7 +138,7 @@ Value
diff --git a/docs/reference/resample_basis.html b/docs/reference/resample_basis.html
index b0f2ab17..c7a6222a 100644
--- a/docs/reference/resample_basis.html
+++ b/docs/reference/resample_basis.html
@@ -1,5 +1,5 @@
-Resample a basis-set to match a mrs_data acquisition. — resample_basis • Spectroscopy Analysis Tools (spant) Resample a basis-set to match a mrs_data acquisition. — resample_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -116,7 +116,7 @@ Value
diff --git a/docs/reference/resample_img.html b/docs/reference/resample_img.html
index f1e7beaf..b0cc8f71 100644
--- a/docs/reference/resample_img.html
+++ b/docs/reference/resample_img.html
@@ -1,5 +1,5 @@
-Resample an image to match a target image space. — resample_img • Spectroscopy Analysis Tools (spant) Resample an image to match a target image space. — resample_img • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/resample_voi.html b/docs/reference/resample_voi.html
index 8fbfa836..a29ab096 100644
--- a/docs/reference/resample_voi.html
+++ b/docs/reference/resample_voi.html
@@ -1,7 +1,5 @@
-Resample a VOI to match a target image space using nearest-neighbour
-interpolation. — resample_voi • Spectroscopy Analysis Tools (spant) Resample a VOI to match a target image space using nearest-neighbour interpolation. — resample_voi • Spectroscopy Analysis Tools (spant) Reslice a nifti object to match the orientation of mrs data. — reslice_to_mrs • Spectroscopy Analysis Tools (spant) Reslice a nifti object to match the orientation of mrs data. — reslice_to_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/reson_table2mrs_data.html b/docs/reference/reson_table2mrs_data.html
index d75579ee..c5a2167a 100644
--- a/docs/reference/reson_table2mrs_data.html
+++ b/docs/reference/reson_table2mrs_data.html
@@ -1,5 +1,5 @@
-Generate mrs_data from a table of single Lorentzian resonances. — reson_table2mrs_data • Spectroscopy Analysis Tools (spant) Generate mrs_data from a table of single Lorentzian resonances. — reson_table2mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -119,7 +119,7 @@ Value
diff --git a/docs/reference/rm_dyns.html b/docs/reference/rm_dyns.html
index 5d5ef692..573e1f51 100644
--- a/docs/reference/rm_dyns.html
+++ b/docs/reference/rm_dyns.html
@@ -1,5 +1,5 @@
-Remove a subset of dynamic scans. — rm_dyns • Spectroscopy Analysis Tools (spant) Remove a subset of dynamic scans. — rm_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/scale_amp_molal.html b/docs/reference/scale_amp_molal.html
index aaeee1f2..7acb8cb0 100644
--- a/docs/reference/scale_amp_molal.html
+++ b/docs/reference/scale_amp_molal.html
@@ -1,7 +1,5 @@
-Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water). — scale_amp_molal • Spectroscopy Analysis Tools (spant) Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / kg of tissue water). — scale_amp_molal • Spectroscopy Analysis Tools (spant)
Spectroscopy Analysis Tools (spant)
- 2.21.0
+ 2.22.0
@@ -76,8 +74,7 @@
- Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water).
+ Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / kg of tissue water).
Source: R/amp_scaling.R
scale_amp_molal.Rd
@@ -163,7 +160,7 @@ Value
diff --git a/docs/reference/scale_amp_molal_pvc.html b/docs/reference/scale_amp_molal_pvc.html
index 962d6afc..4d194abd 100644
--- a/docs/reference/scale_amp_molal_pvc.html
+++ b/docs/reference/scale_amp_molal_pvc.html
@@ -1,7 +1,5 @@
-Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water). — scale_amp_molal_pvc • Spectroscopy Analysis Tools (spant)
@@ -75,8 +73,7 @@
- Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / kg of tissue water).
+ Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / kg of tissue water).
Source: R/amp_scaling.R
scale_amp_molal_pvc.Rd
@@ -141,7 +138,7 @@ Value
diff --git a/docs/reference/scale_amp_molar.html b/docs/reference/scale_amp_molar.html
index 02358d91..dc87a338 100644
--- a/docs/reference/scale_amp_molar.html
+++ b/docs/reference/scale_amp_molar.html
@@ -1,7 +1,5 @@
-Apply water reference scaling to a fitting results object to yield metabolite
-quantities in millimolar (mM) units (mol / Litre of tissue). — scale_amp_molar • Spectroscopy Analysis Tools (spant) Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / Litre of tissue). — scale_amp_molar • Spectroscopy Analysis Tools (spant) Convert default LCM/TARQUIN concentration scaling to molal units with partial
-volume correction. — scale_amp_molar2molal_pvc • Spectroscopy Analysis Tools (spant) Convert default LCM/TARQUIN concentration scaling to molal units with partial volume correction. — scale_amp_molar2molal_pvc • Spectroscopy Analysis Tools (spant) Scale fitted amplitudes to a ratio of signal amplitude. — scale_amp_ratio • Spectroscopy Analysis Tools (spant) Scale fitted amplitudes to a ratio of signal amplitude. — scale_amp_ratio • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -116,7 +116,7 @@ Value
diff --git a/docs/reference/scale_amp_ratio_value.html b/docs/reference/scale_amp_ratio_value.html
index 2036837a..6af8ac51 100644
--- a/docs/reference/scale_amp_ratio_value.html
+++ b/docs/reference/scale_amp_ratio_value.html
@@ -1,5 +1,5 @@
-Scale fitted amplitudes to a ratio of signal amplitude. — scale_amp_ratio_value • Spectroscopy Analysis Tools (spant) Scale fitted amplitudes to a ratio of signal amplitude. — scale_amp_ratio_value • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/scale_amp_water_ratio.html b/docs/reference/scale_amp_water_ratio.html
index 5b25e884..35a76b00 100644
--- a/docs/reference/scale_amp_water_ratio.html
+++ b/docs/reference/scale_amp_water_ratio.html
@@ -1,5 +1,5 @@
-Scale metabolite amplitudes as a ratio to the unsuppressed water amplitude. — scale_amp_water_ratio • Spectroscopy Analysis Tools (spant) Scale metabolite amplitudes as a ratio to the unsuppressed water amplitude. — scale_amp_water_ratio • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/scale_basis_amp.html b/docs/reference/scale_basis_amp.html
index 9401c3f1..5a58b5e5 100644
--- a/docs/reference/scale_basis_amp.html
+++ b/docs/reference/scale_basis_amp.html
@@ -1,5 +1,5 @@
-Scale a basis object by a scalar. — scale_basis_amp • Spectroscopy Analysis Tools (spant) Scale a basis object by a scalar. — scale_basis_amp • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/scale_basis_from_singlet.html b/docs/reference/scale_basis_from_singlet.html
index 0d542bc8..c9a19e77 100644
--- a/docs/reference/scale_basis_from_singlet.html
+++ b/docs/reference/scale_basis_from_singlet.html
@@ -1,5 +1,5 @@
-Scale a basis-set to be consistent with spant assumptions for water scaling. — scale_basis_from_singlet • Spectroscopy Analysis Tools (spant) Scale a basis-set to be consistent with spant assumptions for water scaling. — scale_basis_from_singlet • Spectroscopy Analysis Tools (spant)
Spectroscopy Analysis Tools (spant)
- 2.21.0
+ 2.22.0
@@ -127,7 +127,7 @@ Value
diff --git a/docs/reference/scale_mrs_amp.html b/docs/reference/scale_mrs_amp.html
index b5501a0d..990f058a 100644
--- a/docs/reference/scale_mrs_amp.html
+++ b/docs/reference/scale_mrs_amp.html
@@ -1,5 +1,5 @@
-Scale an mrs_data object by a scalar or vector or amplitudes. — scale_mrs_amp • Spectroscopy Analysis Tools (spant) Scale an mrs_data object by a scalar or vector or amplitudes. — scale_mrs_amp • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/scale_spec.html b/docs/reference/scale_spec.html
index 4f6ea835..6b3ddba4 100644
--- a/docs/reference/scale_spec.html
+++ b/docs/reference/scale_spec.html
@@ -1,5 +1,5 @@
-Scale mrs_data to a spectral region. — scale_spec • Spectroscopy Analysis Tools (spant) Scale mrs_data to a spectral region. — scale_spec • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -141,7 +141,7 @@ Value
diff --git a/docs/reference/sd.html b/docs/reference/sd.html
index ea1eec9f..3ae4dfd4 100644
--- a/docs/reference/sd.html
+++ b/docs/reference/sd.html
@@ -1,5 +1,5 @@
-Calculate the standard deviation spectrum from an mrs_data object. — sd • Spectroscopy Analysis Tools (spant) Calculate the standard deviation spectrum from an mrs_data object. — sd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/sd.mrs_data.html b/docs/reference/sd.mrs_data.html
index 3f92a49f..13bdda85 100644
--- a/docs/reference/sd.mrs_data.html
+++ b/docs/reference/sd.mrs_data.html
@@ -1,5 +1,5 @@
-Calculate the standard deviation spectrum from an mrs_data object. — sd.mrs_data • Spectroscopy Analysis Tools (spant) Calculate the standard deviation spectrum from an mrs_data object. — sd.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -111,7 +111,7 @@ Value
diff --git a/docs/reference/seconds.html b/docs/reference/seconds.html
index b34d6627..467ee17f 100644
--- a/docs/reference/seconds.html
+++ b/docs/reference/seconds.html
@@ -1,5 +1,5 @@
-Return a time scale vector to match the FID of an MRS data object. — seconds • Spectroscopy Analysis Tools (spant) Return a time scale vector to match the FID of an MRS data object. — seconds • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/seq_cpmg_ideal.html b/docs/reference/seq_cpmg_ideal.html
index 547e96ab..45727c86 100644
--- a/docs/reference/seq_cpmg_ideal.html
+++ b/docs/reference/seq_cpmg_ideal.html
@@ -1,5 +1,5 @@
-CPMG style sequence with ideal pulses. — seq_cpmg_ideal • Spectroscopy Analysis Tools (spant) CPMG style sequence with ideal pulses. — seq_cpmg_ideal • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/seq_mega_press_ideal.html b/docs/reference/seq_mega_press_ideal.html
index 0769b8b4..a9cd7fa0 100644
--- a/docs/reference/seq_mega_press_ideal.html
+++ b/docs/reference/seq_mega_press_ideal.html
@@ -1,7 +1,5 @@
-MEGA-PRESS sequence with ideal localisation pulses and Gaussian shaped
-editing pulse. — seq_mega_press_ideal • Spectroscopy Analysis Tools (spant) MEGA-PRESS sequence with ideal localisation pulses and Gaussian shaped editing pulse. — seq_mega_press_ideal • Spectroscopy Analysis Tools (spant) PRESS sequence with shaped refocusing pulses. — seq_press_2d_shaped • Spectroscopy Analysis Tools (spant) PRESS sequence with shaped refocusing pulses. — seq_press_2d_shaped • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -165,7 +165,7 @@ Value
diff --git a/docs/reference/seq_press_ideal.html b/docs/reference/seq_press_ideal.html
index 8c976856..72c3af3d 100644
--- a/docs/reference/seq_press_ideal.html
+++ b/docs/reference/seq_press_ideal.html
@@ -1,5 +1,5 @@
-PRESS sequence with ideal pulses. — seq_press_ideal • Spectroscopy Analysis Tools (spant) PRESS sequence with ideal pulses. — seq_press_ideal • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/seq_pulse_acquire.html b/docs/reference/seq_pulse_acquire.html
index 4a88fc64..ad80571e 100644
--- a/docs/reference/seq_pulse_acquire.html
+++ b/docs/reference/seq_pulse_acquire.html
@@ -1,5 +1,5 @@
-Simple pulse and acquire sequence with ideal pulses. — seq_pulse_acquire • Spectroscopy Analysis Tools (spant) Simple pulse and acquire sequence with ideal pulses. — seq_pulse_acquire • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/seq_slaser_ideal.html b/docs/reference/seq_slaser_ideal.html
index 74688f4d..eb83e8e3 100644
--- a/docs/reference/seq_slaser_ideal.html
+++ b/docs/reference/seq_slaser_ideal.html
@@ -1,5 +1,5 @@
-sLASER sequence with ideal pulses. — seq_slaser_ideal • Spectroscopy Analysis Tools (spant) sLASER sequence with ideal pulses. — seq_slaser_ideal • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -126,7 +126,7 @@ Value
diff --git a/docs/reference/seq_spin_echo_ideal.html b/docs/reference/seq_spin_echo_ideal.html
index e23271de..4248716f 100644
--- a/docs/reference/seq_spin_echo_ideal.html
+++ b/docs/reference/seq_spin_echo_ideal.html
@@ -1,5 +1,5 @@
-Spin echo sequence with ideal pulses. — seq_spin_echo_ideal • Spectroscopy Analysis Tools (spant) Spin echo sequence with ideal pulses. — seq_spin_echo_ideal • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/seq_steam_ideal.html b/docs/reference/seq_steam_ideal.html
index a60685a8..1c8115d7 100644
--- a/docs/reference/seq_steam_ideal.html
+++ b/docs/reference/seq_steam_ideal.html
@@ -1,5 +1,5 @@
-STEAM sequence with ideal pulses. — seq_steam_ideal • Spectroscopy Analysis Tools (spant) STEAM sequence with ideal pulses. — seq_steam_ideal • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -128,7 +128,7 @@ Value
diff --git a/docs/reference/seq_steam_ideal_cof.html b/docs/reference/seq_steam_ideal_cof.html
index 8f225740..cba7af91 100644
--- a/docs/reference/seq_steam_ideal_cof.html
+++ b/docs/reference/seq_steam_ideal_cof.html
@@ -1,7 +1,5 @@
-STEAM sequence with ideal pulses and coherence order filtering to simulate
-gradient crushers. — seq_steam_ideal_cof • Spectroscopy Analysis Tools (spant) STEAM sequence with ideal pulses and coherence order filtering to simulate gradient crushers. — seq_steam_ideal_cof • Spectroscopy Analysis Tools (spant) STEAM sequence with ideal pulses using the z-rotation gradient simulation
-method described by Young et al JMR 140, 146-152 (1999). — seq_steam_ideal_young • Spectroscopy Analysis Tools (spant) STEAM sequence with ideal pulses using the z-rotation gradient simulation method described by Young et al JMR 140, 146-152 (1999). — seq_steam_ideal_young • Spectroscopy Analysis Tools (spant) Set the number of transients for an mrs_data object. — set_Ntrans • Spectroscopy Analysis Tools (spant) Set the number of transients for an mrs_data object. — set_Ntrans • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/set_def_acq_paras.html b/docs/reference/set_def_acq_paras.html
index 3e1b4004..cc2ada9c 100644
--- a/docs/reference/set_def_acq_paras.html
+++ b/docs/reference/set_def_acq_paras.html
@@ -1,5 +1,5 @@
-Set the default acquisition parameters. — set_def_acq_paras • Spectroscopy Analysis Tools (spant) Set the default acquisition parameters. — set_def_acq_paras • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Arguments
diff --git a/docs/reference/set_lcm_cmd.html b/docs/reference/set_lcm_cmd.html
index 2056ed01..42bb2f24 100644
--- a/docs/reference/set_lcm_cmd.html
+++ b/docs/reference/set_lcm_cmd.html
@@ -1,5 +1,5 @@
-Set the command to run the LCModel command-line program. — set_lcm_cmd • Spectroscopy Analysis Tools (spant) Set the command to run the LCModel command-line program. — set_lcm_cmd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/set_lw.html b/docs/reference/set_lw.html
index b64ec851..bb176c62 100644
--- a/docs/reference/set_lw.html
+++ b/docs/reference/set_lw.html
@@ -1,5 +1,5 @@
-Apply line-broadening to an mrs_data object to achieve a specified linewidth. — set_lw • Spectroscopy Analysis Tools (spant) Apply line-broadening to an mrs_data object to achieve a specified linewidth. — set_lw • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -123,7 +123,7 @@ Value
diff --git a/docs/reference/set_mask_xy_mat.html b/docs/reference/set_mask_xy_mat.html
index 49dc5d4e..52c4b617 100644
--- a/docs/reference/set_mask_xy_mat.html
+++ b/docs/reference/set_mask_xy_mat.html
@@ -1,5 +1,5 @@
-Set the masked voxels in a 2D MRSI dataset to given spectrum. — set_mask_xy_mat • Spectroscopy Analysis Tools (spant) Set the masked voxels in a 2D MRSI dataset to given spectrum. — set_mask_xy_mat • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Value
diff --git a/docs/reference/set_precomp_mode.html b/docs/reference/set_precomp_mode.html
index f44bd5d3..47c28e3b 100644
--- a/docs/reference/set_precomp_mode.html
+++ b/docs/reference/set_precomp_mode.html
@@ -1,5 +1,5 @@
-Set the precompute mode. — set_precomp_mode • Spectroscopy Analysis Tools (spant) Set the precompute mode. — set_precomp_mode • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/set_precomp_verbose.html b/docs/reference/set_precomp_verbose.html
index 1453a231..9c613505 100644
--- a/docs/reference/set_precomp_verbose.html
+++ b/docs/reference/set_precomp_verbose.html
@@ -1,5 +1,5 @@
-Set the verbosity of the precompute function. — set_precomp_verbose • Spectroscopy Analysis Tools (spant) Set the verbosity of the precompute function. — set_precomp_verbose • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/set_ref.html b/docs/reference/set_ref.html
index 8953fa50..5436dfa2 100644
--- a/docs/reference/set_ref.html
+++ b/docs/reference/set_ref.html
@@ -1,5 +1,5 @@
-Set the ppm reference value (eg ppm value at 0Hz). — set_ref • Spectroscopy Analysis Tools (spant) Set the ppm reference value (eg ppm value at 0Hz). — set_ref • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/set_td_pts.html b/docs/reference/set_td_pts.html
index 8a80d42a..586459ff 100644
--- a/docs/reference/set_td_pts.html
+++ b/docs/reference/set_td_pts.html
@@ -1,7 +1,5 @@
-Set the number of time-domain data points, truncating or zero-filling as
-appropriate. — set_td_pts • Spectroscopy Analysis Tools (spant) Set the number of time-domain data points, truncating or zero-filling as appropriate. — set_td_pts • Spectroscopy Analysis Tools (spant) Set the command to run the TARQUIN command-line program. — set_tqn_cmd • Spectroscopy Analysis Tools (spant) Set the command to run the TARQUIN command-line program. — set_tqn_cmd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Arguments
diff --git a/docs/reference/set_tr.html b/docs/reference/set_tr.html
index b2109ab0..65c9df5f 100644
--- a/docs/reference/set_tr.html
+++ b/docs/reference/set_tr.html
@@ -1,5 +1,5 @@
-Set the repetition time of an MRS dataset. — set_tr • Spectroscopy Analysis Tools (spant) Set the repetition time of an MRS dataset. — set_tr • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/shift.html b/docs/reference/shift.html
index ab0fe724..034591d0 100644
--- a/docs/reference/shift.html
+++ b/docs/reference/shift.html
@@ -1,5 +1,5 @@
-Apply a frequency shift to MRS data. — shift • Spectroscopy Analysis Tools (spant) Apply a frequency shift to MRS data. — shift • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/shift_basis.html b/docs/reference/shift_basis.html
index 2884be19..f55a65e0 100644
--- a/docs/reference/shift_basis.html
+++ b/docs/reference/shift_basis.html
@@ -1,5 +1,5 @@
-Apply frequency shifts to basis set signals. — shift_basis • Spectroscopy Analysis Tools (spant) Apply frequency shifts to basis set signals. — shift_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Value
diff --git a/docs/reference/sim_basis.html b/docs/reference/sim_basis.html
index c7838c46..bb5fefc6 100644
--- a/docs/reference/sim_basis.html
+++ b/docs/reference/sim_basis.html
@@ -1,5 +1,5 @@
-Simulate a basis set object. — sim_basis • Spectroscopy Analysis Tools (spant) Simulate a basis set object. — sim_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -136,7 +136,7 @@ Value
diff --git a/docs/reference/sim_basis_1h_brain.html b/docs/reference/sim_basis_1h_brain.html
index 62ed7389..f71ffa0b 100644
--- a/docs/reference/sim_basis_1h_brain.html
+++ b/docs/reference/sim_basis_1h_brain.html
@@ -1,7 +1,5 @@
-Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS
-sequence. Note, ideal pulses are assumed. — sim_basis_1h_brain • Spectroscopy Analysis Tools (spant) Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS sequence. Note, ideal pulses are assumed. — sim_basis_1h_brain • Spectroscopy Analysis Tools (spant) Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS
-sequence. Note, ideal pulses are assumed. — sim_basis_1h_brain_press • Spectroscopy Analysis Tools (spant) Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS sequence. Note, ideal pulses are assumed. — sim_basis_1h_brain_press • Spectroscopy Analysis Tools (spant) Simulate a macromolecular and lipid basis-set suitable for 1H brain MRS
-analysis. — sim_basis_mm_lip_lcm • Spectroscopy Analysis Tools (spant) Simulate a macromolecular and lipid basis-set suitable for 1H brain MRS analysis. — sim_basis_mm_lip_lcm • Spectroscopy Analysis Tools (spant) Simulate a basis file using TARQUIN. — sim_basis_tqn • Spectroscopy Analysis Tools (spant) Simulate a basis file using TARQUIN. — sim_basis_tqn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -129,7 +129,7 @@ Examples
diff --git a/docs/reference/sim_brain_1h.html b/docs/reference/sim_brain_1h.html
index 2044cf1a..717ee289 100644
--- a/docs/reference/sim_brain_1h.html
+++ b/docs/reference/sim_brain_1h.html
@@ -1,5 +1,5 @@
-Simulate MRS data with a similar appearance to normal brain (by default). — sim_brain_1h • Spectroscopy Analysis Tools (spant) Simulate MRS data with a similar appearance to normal brain (by default). — sim_brain_1h • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -159,7 +159,7 @@ Value
diff --git a/docs/reference/sim_mol.html b/docs/reference/sim_mol.html
index 23bcef50..77f76a50 100644
--- a/docs/reference/sim_mol.html
+++ b/docs/reference/sim_mol.html
@@ -1,5 +1,5 @@
-Simulate a mol_parameter object. — sim_mol • Spectroscopy Analysis Tools (spant) Simulate a mol_parameter object. — sim_mol • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -143,7 +143,7 @@ Value
diff --git a/docs/reference/sim_noise.html b/docs/reference/sim_noise.html
index 23875f79..a71477d4 100644
--- a/docs/reference/sim_noise.html
+++ b/docs/reference/sim_noise.html
@@ -1,5 +1,5 @@
-Simulate an mrs_data object containing simulated Gaussian noise. — sim_noise • Spectroscopy Analysis Tools (spant) Simulate an mrs_data object containing simulated Gaussian noise. — sim_noise • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -84,6 +84,7 @@ Simulate an mrs_data object containing simulated Gaussian noise.
ft = def_ft(),
N = def_N(),
ref = def_ref(),
+ nuc = def_nuc(),
dyns = 1,
fd = TRUE
)
@@ -111,6 +112,10 @@ Arguments
reference value for ppm scale.
nuc
+resonant nucleus.
dyns
number of dynamic scans to generate.
Value
diff --git a/docs/reference/sim_resonances.html b/docs/reference/sim_resonances.html
index 19e9a8a4..d4f8d7c0 100644
--- a/docs/reference/sim_resonances.html
+++ b/docs/reference/sim_resonances.html
@@ -1,5 +1,5 @@
-Simulate a MRS data object containing a set of simulated resonances. — sim_resonances • Spectroscopy Analysis Tools (spant) Simulate a MRS data object containing a set of simulated resonances. — sim_resonances • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -161,7 +161,7 @@ Examples
diff --git a/docs/reference/sim_th_excit_profile.html b/docs/reference/sim_th_excit_profile.html
index 5535c5ef..e781cab1 100644
--- a/docs/reference/sim_th_excit_profile.html
+++ b/docs/reference/sim_th_excit_profile.html
@@ -1,7 +1,5 @@
-Simulate an ideal pulse excitation profile by smoothing a top-hat function
-with a Gaussian. — sim_th_excit_profile • Spectroscopy Analysis Tools (spant) Simulate an ideal pulse excitation profile by smoothing a top-hat function with a Gaussian. — sim_th_excit_profile • Spectroscopy Analysis Tools (spant) Simulate an mrs_data object containing complex zero valued samples. — sim_zero • Spectroscopy Analysis Tools (spant) Simulate an mrs_data object containing complex zero valued samples. — sim_zero • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -78,7 +78,14 @@ Simulate an mrs_data object containing complex zero valued samples.
-
+
@@ -99,6 +106,10 @@ Arguments
reference value for ppm scale.
nuc
+resonant nucleus.
dyns
number of dynamic scans to generate.
Value
diff --git a/docs/reference/smooth_dyns.html b/docs/reference/smooth_dyns.html
index 4cc8da50..accf3a51 100644
--- a/docs/reference/smooth_dyns.html
+++ b/docs/reference/smooth_dyns.html
@@ -1,5 +1,5 @@
-Smooth data across the dynamic dimension with a Gaussian kernel. — smooth_dyns • Spectroscopy Analysis Tools (spant) Smooth data across the dynamic dimension with a Gaussian kernel. — smooth_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/sort_basis.html b/docs/reference/sort_basis.html
index 6a676ea2..d25cc006 100644
--- a/docs/reference/sort_basis.html
+++ b/docs/reference/sort_basis.html
@@ -1,5 +1,5 @@
-Sort the basis-set elements alphabetically. — sort_basis • Spectroscopy Analysis Tools (spant) Sort the basis-set elements alphabetically. — sort_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/spant-package.html b/docs/reference/spant-package.html
index b3dd8e21..90f19ec3 100644
--- a/docs/reference/spant-package.html
+++ b/docs/reference/spant-package.html
@@ -1,5 +1,5 @@
-spant: spectroscopy analysis tools. — spant-package • Spectroscopy Analysis Tools (spant) spant: spectroscopy analysis tools. — spant-package • Spectroscopy Analysis Tools (spant) Simulate and fit some spectra with ABfit for benchmarking purposes. Basic
-timing and performance metrics will be printed. — spant_abfit_benchmark • Spectroscopy Analysis Tools (spant) Simulate and fit some spectra with ABfit for benchmarking purposes. Basic timing and performance metrics will be printed. — spant_abfit_benchmark • Spectroscopy Analysis Tools (spant) Example MEGA-PRESS data with significant B0 drift. — spant_mpress_drift • Spectroscopy Analysis Tools (spant) Example MEGA-PRESS data with significant B0 drift. — spant_mpress_drift • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -83,7 +83,7 @@ Example MEGA-PRESS data with significant B0 drift.
Format
- An object of class mrs_data of length 13.
+ An object of class mrs_data of dimension 1 x 1 x 1 x 1 x 40 x 1 x 1024.
@@ -98,7 +98,7 @@ Format
diff --git a/docs/reference/spant_sim_fmrs_dataset.html b/docs/reference/spant_sim_fmrs_dataset.html
new file mode 100644
index 00000000..00e48b56
--- /dev/null
+++ b/docs/reference/spant_sim_fmrs_dataset.html
@@ -0,0 +1,117 @@
+
+Simulate an example fMRS dataset for a block design fMRS experiment and export a BIDS structure. — spant_sim_fmrs_dataset • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+ Simulate an example fMRS dataset for a block design fMRS experiment and export a BIDS structure.
+ Source: R/fmrs.R
+ spant_sim_fmrs_dataset.Rd
+
+
+
+ Simulate an example fMRS dataset for a block design fMRS experiment and
+export a BIDS structure.
+
+
+
+ spant_sim_fmrs_dataset(output_dir = NULL)
+
+
+
+ Arguments
+ - output_dir
+output directory for the BIDS data. Defaults to :
+"HOME/sim_fmrs_dataset/data".
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/spant_simulation_benchmark.html b/docs/reference/spant_simulation_benchmark.html
index 32daa8bf..d8cc6841 100644
--- a/docs/reference/spant_simulation_benchmark.html
+++ b/docs/reference/spant_simulation_benchmark.html
@@ -1,7 +1,5 @@
-Simulate a typical metabolite basis set for benchmarking. Timing metrics will
-be printed on completion. — spant_simulation_benchmark • Spectroscopy Analysis Tools (spant) Simulate a typical metabolite basis set for benchmarking. Timing metrics will be printed on completion. — spant_simulation_benchmark • Spectroscopy Analysis Tools (spant) Decompose an mrs_data object into white and gray matter spectra. — spec_decomp • Spectroscopy Analysis Tools (spant) Perform a mathematical operation on a spectral region. — spec_op • Spectroscopy Analysis Tools (spant) Perform a mathematical operation on a spectral region. — spec_op • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -98,8 +98,8 @@ Arguments
operator
-can be "sum" (default), "mean", "l2", "max", "min" or
-"max-min".
can be "sum" (default), "mean", "l2", "max", "max_cplx,
+"min" or "max-min".
freq_scale
@@ -129,7 +129,7 @@ Value
diff --git a/docs/reference/spin_sys.html b/docs/reference/spin_sys.html
index 853423a4..1eaa9e76 100644
--- a/docs/reference/spin_sys.html
+++ b/docs/reference/spin_sys.html
@@ -1,5 +1,5 @@
-Create a spin system object for pulse sequence simulation. — spin_sys • Spectroscopy Analysis Tools (spant) Create a spin system object for pulse sequence simulation. — spin_sys • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Value
diff --git a/docs/reference/spm_pve2categorical.html b/docs/reference/spm_pve2categorical.html
index 23a1bad9..70f10729 100644
--- a/docs/reference/spm_pve2categorical.html
+++ b/docs/reference/spm_pve2categorical.html
@@ -1,7 +1,5 @@
-Convert SPM style segmentation files to a single categorical image where
-the numerical values map as: 0) Other, 1) CSF, 2) GM and 3) WM. — spm_pve2categorical • Spectroscopy Analysis Tools (spant) Convert SPM style segmentation files to a single categorical image where the numerical values map as: 0) Other, 1) CSF, 2) GM and 3) WM. — spm_pve2categorical • Spectroscopy Analysis Tools (spant) Signal space projection method for lipid suppression. — ssp • Spectroscopy Analysis Tools (spant) Signal space projection method for lipid suppression. — ssp • Spectroscopy Analysis Tools (spant) Plot the fitting results of an object of class fit_result with
-individual basis set components shown. — stackplot.fit_result • Spectroscopy Analysis Tools (spant) Plot the fitting results of an object of class fit_result with individual basis set components shown. — stackplot.fit_result • Spectroscopy Analysis Tools (spant) Produce a plot with multiple traces. — stackplot • Spectroscopy Analysis Tools (spant) Produce a plot with multiple traces. — stackplot • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/stackplot.mrs_data.html b/docs/reference/stackplot.mrs_data.html
index 17ff5648..64eea445 100644
--- a/docs/reference/stackplot.mrs_data.html
+++ b/docs/reference/stackplot.mrs_data.html
@@ -1,5 +1,5 @@
-Stackplot plotting method for objects of class mrs_data. — stackplot.mrs_data • Spectroscopy Analysis Tools (spant) Stackplot plotting method for objects of class mrs_data. — stackplot.mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -255,7 +255,7 @@ Arguments
diff --git a/docs/reference/sub_first_dyn.html b/docs/reference/sub_first_dyn.html
index dbd7f831..493b7242 100644
--- a/docs/reference/sub_first_dyn.html
+++ b/docs/reference/sub_first_dyn.html
@@ -1,5 +1,5 @@
-Subtract the first dynamic spectrum from a dynamic series. — sub_first_dyn • Spectroscopy Analysis Tools (spant) Subtract the first dynamic spectrum from a dynamic series. — sub_first_dyn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/sub_mean_dyns.html b/docs/reference/sub_mean_dyns.html
index 6e3bb2df..221bd0c1 100644
--- a/docs/reference/sub_mean_dyns.html
+++ b/docs/reference/sub_mean_dyns.html
@@ -1,5 +1,5 @@
-Subtract the mean dynamic spectrum from a dynamic series. — sub_mean_dyns • Spectroscopy Analysis Tools (spant) Subtract the mean dynamic spectrum from a dynamic series. — sub_mean_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/sub_median_dyns.html b/docs/reference/sub_median_dyns.html
index 134c495d..1e834f14 100644
--- a/docs/reference/sub_median_dyns.html
+++ b/docs/reference/sub_median_dyns.html
@@ -1,5 +1,5 @@
-Subtract the median dynamic spectrum from a dynamic series. — sub_median_dyns • Spectroscopy Analysis Tools (spant) Subtract the median dynamic spectrum from a dynamic series. — sub_median_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/sum_coils.html b/docs/reference/sum_coils.html
index 7bf559f2..e1ab3cc0 100644
--- a/docs/reference/sum_coils.html
+++ b/docs/reference/sum_coils.html
@@ -1,5 +1,5 @@
-Calculate the sum across receiver coil elements. — sum_coils • Spectroscopy Analysis Tools (spant) Calculate the sum across receiver coil elements. — sum_coils • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/sum_dyns.html b/docs/reference/sum_dyns.html
index a0be19d3..bbda2ffc 100644
--- a/docs/reference/sum_dyns.html
+++ b/docs/reference/sum_dyns.html
@@ -1,5 +1,5 @@
-Calculate the sum of data dynamics. — sum_dyns • Spectroscopy Analysis Tools (spant) Calculate the sum of data dynamics. — sum_dyns • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/sum_mrs.html b/docs/reference/sum_mrs.html
index a22f215b..3cc3ab9e 100644
--- a/docs/reference/sum_mrs.html
+++ b/docs/reference/sum_mrs.html
@@ -1,5 +1,5 @@
-Sum two mrs_data objects. — sum_mrs • Spectroscopy Analysis Tools (spant) Sum two mrs_data objects. — sum_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Value
diff --git a/docs/reference/sum_mrs_list.html b/docs/reference/sum_mrs_list.html
index f4e09aea..c3584348 100644
--- a/docs/reference/sum_mrs_list.html
+++ b/docs/reference/sum_mrs_list.html
@@ -1,5 +1,5 @@
-Return the sum of a list of mrs_data objects. — sum_mrs_list • Spectroscopy Analysis Tools (spant) Return the sum of a list of mrs_data objects. — sum_mrs_list • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/svs_1h_brain_analysis.html b/docs/reference/svs_1h_brain_analysis.html
index 8ce514db..dff0ef7d 100644
--- a/docs/reference/svs_1h_brain_analysis.html
+++ b/docs/reference/svs_1h_brain_analysis.html
@@ -1,5 +1,5 @@
-Standard SVS 1H brain analysis pipeline. — svs_1h_brain_analysis • Spectroscopy Analysis Tools (spant) Standard SVS 1H brain analysis pipeline. — svs_1h_brain_analysis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -199,7 +199,7 @@ Value
diff --git a/docs/reference/svs_1h_brain_analysis_dev.html b/docs/reference/svs_1h_brain_analysis_dev.html
index d70a14d3..d71bfea2 100644
--- a/docs/reference/svs_1h_brain_analysis_dev.html
+++ b/docs/reference/svs_1h_brain_analysis_dev.html
@@ -1,5 +1,5 @@
-Standard SVS 1H brain analysis pipeline. — svs_1h_brain_analysis_dev • Spectroscopy Analysis Tools (spant) Standard SVS 1H brain analysis pipeline. — svs_1h_brain_analysis_dev • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -193,7 +193,7 @@ Examples
diff --git a/docs/reference/svs_1h_brain_batch_analysis.html b/docs/reference/svs_1h_brain_batch_analysis.html
index 5631e8cc..15f7223e 100644
--- a/docs/reference/svs_1h_brain_batch_analysis.html
+++ b/docs/reference/svs_1h_brain_batch_analysis.html
@@ -1,5 +1,5 @@
-Batch interface to the standard SVS 1H brain analysis pipeline. — svs_1h_brain_batch_analysis • Spectroscopy Analysis Tools (spant) Batch interface to the standard SVS 1H brain analysis pipeline. — svs_1h_brain_batch_analysis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -144,7 +144,7 @@ Value
diff --git a/docs/reference/t_test_spec.html b/docs/reference/t_test_spec.html
new file mode 100644
index 00000000..56a7ea1b
--- /dev/null
+++ b/docs/reference/t_test_spec.html
@@ -0,0 +1,124 @@
+
+Perform a t-test on spectral data points. — t_test_spec • Spectroscopy Analysis Tools (spant)
+
+
+
+
+
+
+
+
+
+
+
+
+ Perform a t-test on spectral data points.
+
+
+
+ t_test_spec(mrs_data, group)
+
+
+
+ Arguments
+ - mrs_data
+an mrs_data object with spectra in the dynamic dimension.
- group
+vector describing the group membership of each dynamic spectrum.
+
+ Value
+
+
+a list of statistical results.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/td2fd.html b/docs/reference/td2fd.html
index 6748a6a8..f31ed524 100644
--- a/docs/reference/td2fd.html
+++ b/docs/reference/td2fd.html
@@ -1,5 +1,5 @@
-Transform time-domain data to the frequency-domain. — td2fd • Spectroscopy Analysis Tools (spant) Transform time-domain data to the frequency-domain. — td2fd • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/td_conv_filt.html b/docs/reference/td_conv_filt.html
index a9f340c3..106b9b00 100644
--- a/docs/reference/td_conv_filt.html
+++ b/docs/reference/td_conv_filt.html
@@ -1,5 +1,5 @@
-Time-domain convolution based filter. — td_conv_filt • Spectroscopy Analysis Tools (spant) Time-domain convolution based filter. — td_conv_filt • Spectroscopy Analysis Tools (spant) Time-domain spectral registration. — tdsr • Spectroscopy Analysis Tools (spant) Time-domain spectral registration. — tdsr • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -121,7 +121,7 @@ Value
diff --git a/docs/reference/te.html b/docs/reference/te.html
index 010361b1..4a65711d 100644
--- a/docs/reference/te.html
+++ b/docs/reference/te.html
@@ -1,5 +1,5 @@
-Return the echo time of an MRS dataset. — te • Spectroscopy Analysis Tools (spant) Return the echo time of an MRS dataset. — te • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/tr.html b/docs/reference/tr.html
index 0c0bd63b..2e749e02 100644
--- a/docs/reference/tr.html
+++ b/docs/reference/tr.html
@@ -1,5 +1,5 @@
-Return the repetition time of an MRS dataset. — tr • Spectroscopy Analysis Tools (spant) Return the repetition time of an MRS dataset. — tr • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -106,7 +106,7 @@ Value
diff --git a/docs/reference/varpro_3_para_opts.html b/docs/reference/varpro_3_para_opts.html
index c2270a16..52d7cd84 100644
--- a/docs/reference/varpro_3_para_opts.html
+++ b/docs/reference/varpro_3_para_opts.html
@@ -1,5 +1,5 @@
-Return a list of options for VARPRO based fitting with 3 free parameters. — varpro_3_para_opts • Spectroscopy Analysis Tools (spant) Return a list of options for VARPRO based fitting with 3 free parameters. — varpro_3_para_opts • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -141,7 +141,7 @@ Value
diff --git a/docs/reference/varpro_basic_opts.html b/docs/reference/varpro_basic_opts.html
index 32c86d22..c5104891 100644
--- a/docs/reference/varpro_basic_opts.html
+++ b/docs/reference/varpro_basic_opts.html
@@ -1,5 +1,5 @@
-Return a list of options for a basic VARPRO analysis. — varpro_basic_opts • Spectroscopy Analysis Tools (spant) Return a list of options for a basic VARPRO analysis. — varpro_basic_opts • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -118,7 +118,7 @@ Value
diff --git a/docs/reference/varpro_opts.html b/docs/reference/varpro_opts.html
index 2aabf11d..6332f730 100644
--- a/docs/reference/varpro_opts.html
+++ b/docs/reference/varpro_opts.html
@@ -1,5 +1,5 @@
-Return a list of options for VARPRO based fitting. — varpro_opts • Spectroscopy Analysis Tools (spant) Return a list of options for VARPRO based fitting. — varpro_opts • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -177,7 +177,7 @@ Examples
diff --git a/docs/reference/vec2mrs_data.html b/docs/reference/vec2mrs_data.html
index 0cccd73b..f0d58bf0 100644
--- a/docs/reference/vec2mrs_data.html
+++ b/docs/reference/vec2mrs_data.html
@@ -1,5 +1,5 @@
-Convert a vector into a mrs_data object. — vec2mrs_data • Spectroscopy Analysis Tools (spant) Convert a vector into a mrs_data object. — vec2mrs_data • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -80,10 +80,11 @@ Convert a vector into a mrs_data object.
vec2mrs_data(
vec,
- fs = def_fs(),
- ft = def_ft(),
- ref = def_ref(),
- nuc = def_nuc(),
+ mrs_data = NULL,
+ fs = NULL,
+ ft = NULL,
+ ref = NULL,
+ nuc = NULL,
dyns = 1,
fd = FALSE
)
@@ -95,6 +96,10 @@ Arguments
the data vector.
mrs_data
+example data to copy acquisition parameters from.
fs
sampling frequency in Hz.
Arguments
fd
-flag to indicate if the matrix is in the frequency domain (logical).
flag to indicate if the vector is in the frequency domain (logical).
Value
diff --git a/docs/reference/write_basis.html b/docs/reference/write_basis.html
index b6e27cbd..94c5e021 100644
--- a/docs/reference/write_basis.html
+++ b/docs/reference/write_basis.html
@@ -1,5 +1,5 @@
-Write a basis object to an LCModel .basis formatted file. — write_basis • Spectroscopy Analysis Tools (spant) Write a basis object to an LCModel .basis formatted file. — write_basis • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -108,7 +108,7 @@ Arguments
diff --git a/docs/reference/write_basis_tqn.html b/docs/reference/write_basis_tqn.html
index 6aa51c1d..116c73ec 100644
--- a/docs/reference/write_basis_tqn.html
+++ b/docs/reference/write_basis_tqn.html
@@ -1,5 +1,5 @@
-Generate a basis file using TARQUIN. — write_basis_tqn • Spectroscopy Analysis Tools (spant) Generate a basis file using TARQUIN. — write_basis_tqn • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Examples
diff --git a/docs/reference/write_mrs.html b/docs/reference/write_mrs.html
index fff25f15..124b9dc4 100644
--- a/docs/reference/write_mrs.html
+++ b/docs/reference/write_mrs.html
@@ -1,5 +1,5 @@
-Write MRS data object to file. — write_mrs • Spectroscopy Analysis Tools (spant) Write MRS data object to file. — write_mrs • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Arguments
diff --git a/docs/reference/write_mrs_nifti.html b/docs/reference/write_mrs_nifti.html
index f4bf1921..bd3ed4b7 100644
--- a/docs/reference/write_mrs_nifti.html
+++ b/docs/reference/write_mrs_nifti.html
@@ -1,5 +1,5 @@
-Write MRS data object to file in NIFTI format. — write_mrs_nifti • Spectroscopy Analysis Tools (spant) Write MRS data object to file in NIFTI format. — write_mrs_nifti • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/write_pulse_ascii.html b/docs/reference/write_pulse_ascii.html
index 067ae086..221f8ebb 100644
--- a/docs/reference/write_pulse_ascii.html
+++ b/docs/reference/write_pulse_ascii.html
@@ -1,5 +1,5 @@
-Write an ASCII formatted pulse file. — write_pulse_ascii • Spectroscopy Analysis Tools (spant) Write an ASCII formatted pulse file. — write_pulse_ascii • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/zero_fade_spec.html b/docs/reference/zero_fade_spec.html
index c703745c..c8b572c3 100644
--- a/docs/reference/zero_fade_spec.html
+++ b/docs/reference/zero_fade_spec.html
@@ -1,7 +1,5 @@
-Fade a spectrum to zero by frequency domain multiplication with a tanh
-function. Note this operation distorts data points at the end of the FID. — zero_fade_spec • Spectroscopy Analysis Tools (spant) Fade a spectrum to zero by frequency domain multiplication with a tanh function. Note this operation distorts data points at the end of the FID. — zero_fade_spec • Spectroscopy Analysis Tools (spant) Zero all coherences including and above a given order. — zero_higher_orders • Spectroscopy Analysis Tools (spant) Zero all coherences including and above a given order. — zero_higher_orders • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -115,7 +115,7 @@ Value
diff --git a/docs/reference/zero_td_pts_end.html b/docs/reference/zero_td_pts_end.html
index 8c1123c8..71d24ebb 100644
--- a/docs/reference/zero_td_pts_end.html
+++ b/docs/reference/zero_td_pts_end.html
@@ -1,5 +1,5 @@
-Set mrs_data object data points at the end of the FID to zero. — zero_td_pts_end • Spectroscopy Analysis Tools (spant) Set mrs_data object data points at the end of the FID to zero. — zero_td_pts_end • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -110,7 +110,7 @@ Value
diff --git a/docs/reference/zf.html b/docs/reference/zf.html
index 85e2013c..baf50256 100644
--- a/docs/reference/zf.html
+++ b/docs/reference/zf.html
@@ -1,5 +1,5 @@
-Zero-fill MRS data in the time domain. — zf • Spectroscopy Analysis Tools (spant) Zero-fill MRS data in the time domain. — zf • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -125,7 +125,7 @@ Value
diff --git a/docs/reference/zf_xy.html b/docs/reference/zf_xy.html
index ebca3999..c4104a74 100644
--- a/docs/reference/zf_xy.html
+++ b/docs/reference/zf_xy.html
@@ -1,5 +1,5 @@
-Zero-fill MRSI data in the k-space x-y direction. — zf_xy • Spectroscopy Analysis Tools (spant) Zero-fill MRSI data in the k-space x-y direction. — zf_xy • Spectroscopy Analysis Tools (spant)
@@ -17,7 +17,7 @@
@@ -113,7 +113,7 @@ Value
diff --git a/docs/sitemap.xml b/docs/sitemap.xml
index e2139f71..4c39f515 100644
--- a/docs/sitemap.xml
+++ b/docs/sitemap.xml
@@ -216,6 +216,12 @@
https://martin3141.github.io/spant/reference/comb_coils_fp_pc.html
+
+ https://martin3141.github.io/spant/reference/comb_coils_mrsi_gls.html
+
+
+ https://martin3141.github.io/spant/reference/comb_coils_svs_gls.html
+
https://martin3141.github.io/spant/reference/comb_csv_results.html
@@ -411,6 +417,9 @@
https://martin3141.github.io/spant/reference/gen_conv_reg.html
+
+ https://martin3141.github.io/spant/reference/gen_group_reg.html
+
https://martin3141.github.io/spant/reference/gen_impulse_reg.html
@@ -555,6 +564,15 @@
https://martin3141.github.io/spant/reference/glm_spec.html
+
+ https://martin3141.github.io/spant/reference/glm_spec_fmrs_fl.html
+
+
+ https://martin3141.github.io/spant/reference/glm_spec_fmrs_group.html
+
+
+ https://martin3141.github.io/spant/reference/glm_spec_group_linhyp.html
+
https://martin3141.github.io/spant/reference/grid_shift_xy.html
@@ -690,9 +708,15 @@
https://martin3141.github.io/spant/reference/mrs_data2basis.html
+
+ https://martin3141.github.io/spant/reference/mrs_data2bids.html
+
https://martin3141.github.io/spant/reference/mrs_data2mat.html
+
+ https://martin3141.github.io/spant/reference/mrs_data2spec_mat.html
+
https://martin3141.github.io/spant/reference/mrs_data2vec.html
@@ -741,6 +765,9 @@
https://martin3141.github.io/spant/reference/phase.html
+
+ https://martin3141.github.io/spant/reference/phase_ref_1h_brain.html
+
https://martin3141.github.io/spant/reference/plot.fit_result.html
@@ -780,6 +807,12 @@
https://martin3141.github.io/spant/reference/precomp.html
+
+ https://martin3141.github.io/spant/reference/preproc_svs.html
+
+
+ https://martin3141.github.io/spant/reference/preproc_svs_dataset.html
+
https://martin3141.github.io/spant/reference/print.fit_result.html
@@ -1050,6 +1083,9 @@
https://martin3141.github.io/spant/reference/spant_mpress_drift.html
+
+ https://martin3141.github.io/spant/reference/spant_sim_fmrs_dataset.html
+
https://martin3141.github.io/spant/reference/spant_simulation_benchmark.html
@@ -1107,6 +1143,9 @@
https://martin3141.github.io/spant/reference/svs_1h_brain_batch_analysis.html
+
+ https://martin3141.github.io/spant/reference/t_test_spec.html
+
https://martin3141.github.io/spant/reference/td2fd.html
+
+
+
+
+
+
+
+
+
+
+ Create a BIDS file structure from a vector of MRS data paths or list of mrs_data objects.
+ Source:R/fmrs.R
+ mrs_data2bids.Rd
+
+
+ Create a BIDS file structure from a vector of MRS data paths or list of +mrs_data objects.
+
+
+
+
+ mrs_data2bids(
+ mrs_data,
+ output_dir,
+ suffix = NULL,
+ sub = NULL,
+ ses = NULL,
+ task = NULL,
+ acq = NULL,
+ nuc = NULL,
+ voi = NULL,
+ rec = NULL,
+ run = NULL,
+ echo = NULL,
+ inv = NULL,
+ skip_existing = TRUE
+)
+
+
+ Arguments
+- mrs_data +
vector of MRS data paths or list of mrs_data objects.
+
+
+- output_dir +
the base directory to create the BIDS structure.
+
+
+- suffix +
optional vector of file suffixes. Default behaviour is to +automatically determine these from the input data, however it is recommended +that they are specified to allow more efficient skipping of existing data.
+
+
+- sub +
optional vector of subject labels. If not specified, these will be +automatically generated as a series of increasing zero-padded integer values +corresponding to the mrs_data input indices.
+
+
+- ses +
optional vector of session labels.
+
+
+- task +
optional vector of task labels.
+
+
+- acq +
optional vector of acquisition labels.
+
+
+- nuc +
optional vector of nucleus labels.
+
+
+- voi +
optional vector of volume of interest labels.
+
+
+- rec +
optional vector of reconstruction labels.
+
+
+- run +
optional vector of run indices.
+
+
+- echo +
optional vector of echo time indices.
+
+
+- inv +
optional vector of inversion indices.
+
+
+- skip_existing +
skip any data files that have already been converted. +Defaults to TRUE, set to FALSE to force an overwrite of any existing data +files.
+
+
+
+
+
+
+
+
+
+
+
+
+ Convert mrs_data object to a matrix, with spectral points in the column dimension and dynamics in the row dimension.
+ Source:R/mrs_data_proc.R
+ mrs_data2spec_mat.Rd
+
+
+ Convert mrs_data object to a matrix, with spectral points in the column +dimension and dynamics in the row dimension.
+
+
+
+
+ mrs_data2spec_mat(mrs_data, collapse = TRUE)
+
+ Arguments
+- mrs_data +
MRS data object or list of MRS data objects.
+
+
+- collapse +
collapse all other dimensions along the dynamic dimension, eg +a 16x16 MRSI grid would be first collapsed across 256 dynamic scans.
+
+
+
+
+ Value
+ + +MRS data matrix.
+
+
+
+
+
+
+
+
+
+
+
+ Corrected zero order phase and chemical shift offset in 1H MRS data from the brain.
+ Source:R/rats.R
+ phase_ref_1h_brain.Rd
+
+
+ Corrected zero order phase and chemical shift offset in 1H MRS data from the +brain.
+
+
+
+
+ phase_ref_1h_brain(mrs_data, mean_ref = FALSE, ret_corr_only = TRUE)
+
+ Arguments
+- mrs_data +
MRS data to be corrected.
+
+
+- mean_ref +
apply the phase and offset of the mean spectrum to all +others. Default is FALSE.
+
+
+- ret_corr_only +
return the corrected data only.
+
+
+
+
+ Value
+ + +corrected MRS data.
+
+
+
+
+
+
+
+
+
+
+
+ Preprocess and perform quality assessment of a single SVS data set.
+ Source:R/fmrs.R
+ preproc_svs.Rd
+
+
+ Preprocess and perform quality assessment of a single SVS data set.
+
+
+
+
+ preproc_svs(path, label = NULL, output_dir = NULL, ref_inds = NULL)
+
+
+ Arguments
+- path +
path to the fMRS data file or IMA directory.
+
+
+- label +
a label to describe the data set.
+
+
+- output_dir +
output directory.
+
+
+- ref_inds +
a vector of 1-based indices for any water reference dynamic +scans.
+
+
+
+
+
+
+
+
+
+
+
+
+ Preprocess and perform quality assessment of one or more SVS data sets.
+ Source:R/fmrs.R
+ preproc_svs_dataset.Rd
+
+
+ Preprocess and perform quality assessment of one or more SVS data sets.
+
+
+
+
+ preproc_svs_dataset(
+ paths,
+ labels = NULL,
+ output_dir = "spant_analysis",
+ exclude_labels = NULL,
+ overwrite = FALSE,
+ ref_inds = NULL,
+ return_results = FALSE
+)
+
+
+ Arguments
+- paths +
paths to the fMRS data file or IMA directory.
+
+
+- labels +
labels to describe each data set.
+
+
+- output_dir +
output directory.
+
+
+- exclude_labels +
vector of labels of scans to exclude, eg poor quality +data.
+
+
+- overwrite +
overwrite saved results, defaults to FALSE.
+
+
+- ref_inds +
a vector of 1-based indices for any water reference dynamic +scans.
+
+
+- return_results +
function will return key outputs, defaults to FALSE.
+
+
an optional data frame to provide additional variables for use in subsequent analysis steps, eg id or grouping variables.
indicate if the data has a distorted FID due to a +brick-wall filter being used to downsample the data. Default is to auto +detect this from the data, but TRUE or FALSE options can be given to override +detection.
Value
@@ -183,7 +191,7 @@Examples
read_siemens_txt_hdr(input, version = "vd", verbose, offset = 0)read_siemens_txt_hdr(input, version = "vd", verbose = FALSE, offset = 0)Value
-
@@ -163,7 +160,7 @@ Apply water reference scaling to a fitting results object to yield metabolite -quantities in millimolar (mM) units (mol / kg of tissue water).
+Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / kg of tissue water).
Source:R/amp_scaling.R
scale_amp_molal.RdValue
-
@@ -141,7 +138,7 @@ Apply water reference scaling to a fitting results object to yield metabolite -quantities in millimolar (mM) units (mol / kg of tissue water).
+Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / kg of tissue water).
Source:R/amp_scaling.R
scale_amp_molal_pvc.RdValue
reference value for ppm scale.
resonant nucleus.
number of dynamic scans to generate.
Arguments
reference value for ppm scale.
resonant nucleus.
number of dynamic scans to generate.
Value
Format
-An object of class mrs_data of length 13.
An object of class mrs_data of dimension 1 x 1 x 1 x 1 x 40 x 1 x 1024.
+
+
+
+
+
+
+
+
+
+
+ Simulate an example fMRS dataset for a block design fMRS experiment and export a BIDS structure.
+ Source:R/fmrs.R
+ spant_sim_fmrs_dataset.Rd
+
+
+ Simulate an example fMRS dataset for a block design fMRS experiment and +export a BIDS structure.
+
+
+
+
+ spant_sim_fmrs_dataset(output_dir = NULL)
+
+
+ Arguments
+- output_dir +
output directory for the BIDS data. Defaults to : +"HOME/sim_fmrs_dataset/data".
+
+
can be "sum" (default), "mean", "l2", "max", "min" or -"max-min".
can be "sum" (default), "mean", "l2", "max", "max_cplx, +"min" or "max-min".
+
+
+
+
+
+
+
+
+
+
+
+ Perform a t-test on spectral data points.
+
+
+
+
+ t_test_spec(mrs_data, group)
+
+ Arguments
+- mrs_data +
an mrs_data object with spectra in the dynamic dimension.
+
+
+- group +
vector describing the group membership of each dynamic spectrum.
+
+
+
+
+ Value
+ + +a list of statistical results.
+vec2mrs_data(
vec,
- fs = def_fs(),
- ft = def_ft(),
- ref = def_ref(),
- nuc = def_nuc(),
+ mrs_data = NULL,
+ fs = NULL,
+ ft = NULL,
+ ref = NULL,
+ nuc = NULL,
dyns = 1,
fd = FALSE
)Arguments
the data vector.
example data to copy acquisition parameters from.
sampling frequency in Hz.
Arguments
flag to indicate if the matrix is in the frequency domain (logical).
flag to indicate if the vector is in the frequency domain (logical).