diff --git a/Figures/Figure1.png b/Figures/Figure1.png index 96476e8..4f78028 100644 Binary files a/Figures/Figure1.png and b/Figures/Figure1.png differ diff --git a/Figures/Figure3.png b/Figures/Figure3.png index 83f4b92..aa106e2 100644 Binary files a/Figures/Figure3.png and b/Figures/Figure3.png differ diff --git a/Figures/Figure4.png b/Figures/Figure4.png index c2ee967..eca68be 100644 Binary files a/Figures/Figure4.png and b/Figures/Figure4.png differ diff --git a/Figures/Figure5.png b/Figures/Figure5.png index 57d4950..869fb2a 100644 Binary files a/Figures/Figure5.png and b/Figures/Figure5.png differ diff --git a/Figures/Figure6.png b/Figures/Figure6.png index 7375771..5696260 100644 Binary files a/Figures/Figure6.png and b/Figures/Figure6.png differ diff --git a/Figures/Figure7.png b/Figures/Figure7.png index 4f7cd8d..748dcbd 100644 Binary files a/Figures/Figure7.png and b/Figures/Figure7.png differ diff --git a/Figures/Figure8.png b/Figures/Figure8.png new file mode 100644 index 0000000..76a009d Binary files /dev/null and b/Figures/Figure8.png differ diff --git a/Figures/Figure9.png b/Figures/Figure9.png new file mode 100644 index 0000000..53e0b03 Binary files /dev/null and b/Figures/Figure9.png differ diff --git a/Manuscript.md b/Manuscript.md index a496b67..790bc45 100644 --- a/Manuscript.md +++ b/Manuscript.md @@ -1,6 +1,5 @@ ---- -title: "Advances in Spiral fMRI: A High-resolution Study with Single-shot Acquisition" ---- +Advances in Spiral fMRI: A High-resolution Study with Single-shot Acquisition +============================================================================= Lars Kasper1,2,†, Maria Engel1, Jakob Heinzle2, Matthias Mueller-Schrader2, Nadine N. Graedel1,3, Jonas Reber1, Thomas Schmid1, Christoph Barmet1, Bertram @@ -24,6 +23,7 @@ J. Wilm1, Klaas Enno Stephan2,4,5, Klaas P. Pruessmann1 †Current Address: Techna Institute, University Health Network Toronto, Canada Highlights +---------- - This work reports the first fMRI study at 7T with high-resolution spiral readout gradient waveforms. @@ -41,6 +41,7 @@ Highlights providing two images per shot (1.5 mm resolution). Abstract +-------- Spiral fMRI has been put forward as a viable alternative to rectilinear echo-planar imaging, in particular due to its enhanced average k-space speed and @@ -1139,8 +1140,6 @@ Figures [Figure 1](Figures/Figure1.png) ------------------------------- -![](media/7bd18961ee4c4ca63ab8a36adad83f5e.tif) - Utilized 2D single-shot spiral acquisitions (R=4 undersampling): High-resolution single-shot spiral-out (nominal resolution 0.8 mm, black) and spiral in/out trajectory (1.5 mm resolution, blue). Depicted are the gradient waveforms @@ -1152,8 +1151,6 @@ start a few milliseconds before the spiral readout gradient waveforms. [Figure 2](Figures/Figure2.png) ------------------------------- -![](media/d6bffbfb0d818bde29b2b7157c36e82d.tif) - Overview of image quality for high-resolution (0.8 mm) single-shot spiral-out acquisition. (A) 8 oblique-transverse slices (of 36) depicting the time-series magnitude mean of one functional run (subject S7, 100 volumes). (B) @@ -1164,8 +1161,6 @@ corresponding to lower row of (A). [Figure 3](Figures/Figure3.png) ------------------------------- -![](media/083043f4a1ebb3c5caaf35238a6e2c47.tif) - Characterization of image time series fluctuations over 1 spiral-out run (95 volumes, discarding first five). (A) Signal-to-Noise Fluctuation Ratio (SFNR) image for same slices as in Fig 2. Rather homogeneous, exhibiting sufficient @@ -1179,8 +1174,6 @@ internal capsule, due to its reduced average signal level. [Figure 4](Figures/Figure4.png) ------------------------------- -![](media/cbe4a3f5c6deb69ae1fb8ba529a2fccb.tif) - Image quality and geometric accuracy of spiral images, reconstructed with the expanded signal model. (A) Anatomical Reference: Mean multi-echo (ME) spin-warp image (1 mm resolution) (B) High-resolution (0.8 mm) spiral-out; (C) In-part of @@ -1195,10 +1188,8 @@ geometric incongruence by through-plane dephasing (white) or incomplete B0 mapping and correction (yellow) in the spiral-out, which are reduced in the out-part and absent in the in-part of the spiral-in/out sequence. -Figure 5 --------- - -![C:\\Users\\kasperla\\polybox\\Papers\\SpiralFmri7T\\Submission\\Revision1\\Figure5_HighRes.tif](media/d0c81df5d13f62cdec3cd985751b3f79.tiff) +[Figure 5](Figures/Figure5.png) +-------------------------------- Quantification of spatial specificity in spiral images via contour distance mapping. @@ -1218,11 +1209,9 @@ contour voxels in all subjects were strictly overlapping, with $$76 \pm 7\ \%$$ at most 1 voxel apart and only $$11 \pm 5\ \%$$ exceeding a distance of 2 voxels (1.6 mm). -[Figure 6](Figures/Figure5.png) +[Figure 6](Figures/Figure6.png) -------------------------------- -![](media/7aa19932ca25ab701710314e846fd9d1.tif) - Visual Activation Maps of high-resolution (0.8 mm) spiral-out fMRI for a single subject (S2). Representative stimuli of both conditions (ULLR and URLL) are displayed at the top. (A) Overlay of differential t-contrast maps (p\<0.001 @@ -1234,11 +1223,9 @@ maps in different orientations: transverse (top), coronal (middle) and sagittal conditions (blue: ULLR, yellow: URLL), showing more widespread activation and high spatial specificity, i.e., little spatial overlap (green). -[Figure 7](Figures/Figure5.png) +[Figure 7](Figures/Figure7.png) ------------------------------- -![](media/628728a19dad854bd7fe6f1f1dacd22d.tif) - Mean spiral images and activation maps over subjects (S2-S7) for high-resolution spiral-out fMRI. For each subject, the following 4 sections are displayed, with the mean ME image as anatomical underlay: transverse, coronal and sagittal slice @@ -1248,10 +1235,8 @@ uncorrected). To assess raw spiral data quality, the corresponding mean functional image is displayed side-by-side to the anatomical transverse slice as an alternative underlay. -Figure 8 --------- - -![C:\\Users\\kasperla\\Documents\\Projects\\SPIFI\\Results\\Summary\\Pipeline02\\Figures\\Figure22\\smoothed_tissue_threshold_60_percent_clusterFWE\\Histogram_Stacked_Barplot_Activation_Tissue_Overlap_per_Subject_legendbelow.png](media/8668a18de46f1a9c68f6a4088eafb32f.png) +[Figure 8](Figures/Figure8.png) +-------------------------------- Spatial specificity of functional activation for high-resolution spiral-out fMRI. Percentage of significant voxels over both differential t-contrasts (+/- @@ -1264,10 +1249,8 @@ Surface). On average, the majority (75 %) of activation was contained in gray matter or adjacent surfaces, with 6 % and 13 % residing in majority white matter and CSF voxels, respectively. -Figure 9 --------- - -![](media/19f8ce80da864227d69809c762bac2dd.tif) +[Figure 9](Figures/Figure9.png) +-------------------------------- Visual Activation Maps of spiral in/out (1.5mm) fMRI run for a single subject (S2, as in Fig. 6). (A-C) Displayed are the differential t-contrast maps @@ -1296,7 +1279,7 @@ i.e., the one reported in the sub-table directly above. Since resolutions differ between spiral-out (0.8 mm) and spiral in/out (1.5 mm), we compare activated volume instead of voxel count. -| | **Subjects** | **Gain vs** | | | | | | | | | +| | **Subjects** | | | | | | | | **Gain vs** | | |--------------------------------|--------------|-------------|-------|-------|-------|-------|---------|------|-------------------|-----------------------| | *Measure* | *S2* | *S3* | *S4* | *S5* | *S6* | *S7* | *Mean* | *SD* | *previous spiral* | *high-res spiral out* | | **high-resolution spiral out** | | | | | | | | | | | @@ -1327,7 +1310,7 @@ volume instead of voxel count. Supplementary Material ====================== -Figure SM 1 +Figure SM 1 ----------- Figure collection of high-resolution (0.8 mm) spiral fMRI data. For every @@ -1346,7 +1329,7 @@ Magnitude-mean spiral fMRI image, overlaid with edges of anatomical reference (p\<0.001 uncorrected) on transverse slices of mean spiral image (hot colormap: URLL-ULLR, cool colormap: ULLR-URLL, display range t=3.2-8). -Figure SM 2 +Figure SM 2 ----------- Figure collection of spiral in/out fMRI data (1.5 mm resolution). For every @@ -1366,7 +1349,7 @@ Magnitude-mean spiral fMRI image, overlaid with edges of anatomical reference (p\<0.001 uncorrected) on transverse slices of mean spiral image (hot colormap: URLL-ULLR, cool colormap: ULLR-URLL, display range t=3.2-8). -Table SM 3 +Table SM 3 ---------- Comparison of acquisition efficiency in published 2D spiral fMRI studies. @@ -1393,7 +1376,7 @@ efficiency. | (Singh et al., 2018) | 1.2 | 1.2 | 192 | 14 | 160 | 12 | 3 | 1.0 | 3 | 102 | | *This study* | 0.8 | 0.9 | 230 | 32 | 288 | 36 | 1 | 3.3 | 3.3 | 902 | -Figure SM 4 +Figure SM 4 ----------- Impact of readout duration and spatial smoothing on activation maps in diff --git a/README.md b/README.md index 88455bd..54ba149 100644 --- a/README.md +++ b/README.md @@ -1,5 +1,5 @@ -Spiral Fmri 7T Paper -==================== +Paper Advances in Spiral fMRI +============================= Summary -------