Updated the manual and made minor changes to function headers for new…

… release of FID-A, Version 1.0-beta.

exampleRunScripts/run_megapressproc.m

@@ -14,10 +14,15 @@
 % filestring         = String variable for the name of the directory containing
 %                     the water suppressed .dat file.  Water unsuppressed
 %                     .dat file should be contained in [filestring '_w/'];
+% coilcombos         = (Optional).  A structure obtained by running the
+%                      op_getcoilcombos function.  This allows the user to 
+%                      specify the coil phases and amplitudes as an input, 
+%                      rather calculating these from the input data by default.  
 % avgAlignDomain     = (Optional) Perform the spectral registration (drift correction) using
 %                     the full spectrum ('t'), or only a limited frequency
 %                     range ('f').  Default is 'f'.
-% alignSS            = 0 - Do not align the edit-on and edit-off subspectra.
+% alignSS            = (Optional)
+%                     0 - Do not align the edit-on and edit-off subspectra (default).
 %                     2 - Perform manual alignment of edit-on and edit-off subspectra.
 % 
 % OUTPUTS:

inputOutput/io_readlcmraw.m

@@ -5,7 +5,7 @@
 % out=io_readlcmraw(filename,type);
 % 
 % DESCRIPTION:
-% Reads LCModel .RAW format into the FID-A data structure format in MATLAB.
+% Reads LCModel raw data format into the FID-A data structure format in MATLAB.
 % 
 % INPUTS:
 % filename   = filename of LCModel raw file.

inputOutput/io_readlcmraw_dotraw.m

@@ -5,7 +5,7 @@
 % out=io_readlcmraw_dotraw(filename);
 % 
 % DESCRIPTION:
-% Reads LCModel .raw model spectrum file into the FID-A data structure format in MATLAB.
+% Reads LCModel .RAW model spectrum file into the FID-A data structure format in MATLAB.
 % 
 % INPUTS:
 % filename   = filename of LCModel raw file.

simulationTools/sim_gradSpoil.m

@@ -5,7 +5,8 @@
 % d_out = sim_gradSpoil(d_in,H,gradVect,dur,posVect)
 % 
 % DESCRIPTION:
-% This function simulates the effect of a spoiler gradient.
+% This function simulates the effect of a rectangular spoiler gradient 
+% with a given amplitude, direction and duration.  
 % 
 % INPUTS:
 % d_in      = input density matrix structure.

simulationTools/sim_onepulse_shaped.m

@@ -7,7 +7,7 @@
 % DESCRIPTION:
 % %This function simulates the effect of a frequency selective or slice 
 % selective excitation, followed immediately by the acquisition window.  
-% This is mainly an excercise to see if I can get slice selective 
+% This is mainly an exercise to see if I can get slice selective 
 % excitation working.
 % 
 % Note that when simulating a frequency selective pulse, it is okay to
@@ -23,7 +23,7 @@
 % sys       = spin system definition structure
 % RF        = radiofrequency pulse array [N x 3].  Phase, Amplitude, Duration.
 % tp        = RF pulse duration in [ms]
-% phCyc     = Phase of excitation rf pulse.
+% phCyc     = Phase of excitation rf pulse in [degrees].
 % dfdx      = if simulating a frequency selective pulse, this argument 
 %             should be the frequency offset [Hz].  If simulating a slice
 %             selective pulse, this argument should be the position offset [cm].

simulationTools/sim_shapedRF.m

@@ -7,7 +7,7 @@
 % 
 % DESCRIPTION:
 % This function simulates the effect of a shaped rf pulse on the density
-% matrix.  The temporal shape of the refocussing pulses is modelled as a 
+% matrix.  The temporal shape of the refocusing pulses is modelled as a 
 % series of N instantaneous rotations about the effective RF field, where N 
 % is the number of time points in the RF waveform.  The instantaneous 
 % effective RF field can be an arbitrary vector, and can be represented in 

simulationTools/sim_steam_gradSim.m

@@ -17,39 +17,43 @@
 % N             = Number of 'phase cycles'
 
 % *********INPUT VARIABLES***********
-spinsys='Lac';  %Spin system.
-TE=0.020;  %Echo time.
-TM=0.005;  %Mixing time.
-N=32;      %Number of 'phase cycles'
+spinsys='Lac';      %Spin system.
+TE=0.020;           %Echo time.
+TM=0.005;           %Mixing time.
+N=32;               %Number of 'phase cycles'
+n=2048;             %Number of spectral points
+sw=2000;            %Spectral width
+B0=3;               %Magnetic Field Strength
+lw=2;               %Linewidth
 % ***********************************
 
 eval(['load ' spinsys]);
-eval(['J=j' spinsys ';']);
-eval(['shifts=shifts' spinsys ';']);
+eval(['J=sys' spinsys '.J;']);
+eval(['shifts=sys' spinsys '.shifts;']);
 sys.J=J;
 sys.shifts=shifts;
 
-steam=sim_steam(2048,2000,3,2,sys,TE,TM,0);
+steam=sim_steam(n,sw,B0,lw,sys,TE,TM,0);
 figure;
 hold;
-plot(steam.ppm,steam.specs);
+plot(steam.ppm,real(steam.specs));
 
 for spoil=360/N:360/N:(360)-(360/N)
-    steam_temp=sim_steam(2048,2000,3,2,sys,TE,TM,spoil);
-    plot(steam_temp.ppm,steam_temp.specs);
+    steam_temp=sim_steam(n,sw,B0,lw,sys,TE,TM,spoil);
+    %plot(steam_temp.ppm,steam_temp.specs);
     steam=op_addScans(steam,steam_temp);
 end
 
 steam=op_ampScale(steam,1/N);
 
-press=sim_press(2048,2000,3,2,sys,TE/2,TE/2);
+press=sim_press(n,sw,B0,lw,sys,TE/2,TE/2);
 
 figure;
-plot(steam.ppm,steam.specs,press.ppm,press.specs);
+plot(steam.ppm,real(steam.specs),press.ppm,real(press.specs));
 set(gca,'XDir','reverse');
 xlim([1 5]);
 
-%legend('press','steam');
+legend('press','steam');