Update to v3.2.1

Author: markmikkelsen

AlignSubSpectra.m

@@ -67,8 +67,6 @@
                 case 'GE'
                     if strcmpi(MRS_struct.p.seqorig,'Lythgoe')
                         subSpecInd = [3 2 4 1];
-                    elseif strcmpi(MRS_struct.p.seqorig,'Noeske')
-                        subSpecInd = [2 1 3 4];
                     else
                         subSpecInd = [3 2 1 4];
                     end

CoRegStandAlone/CoRegStandAlone.m

@@ -43,8 +43,8 @@
 %   1. Pre-initialise
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 
-MRS_struct.version.Gannet = '3.2.1-rc';
-MRS_struct.version.load = '220526';
+MRS_struct.version.Gannet = '3.2.1';
+MRS_struct.version.load = '220607';
 MRS_struct.ii = 0;
 if size(metabfile,2) == 1
     metabfile = metabfile';
@@ -53,7 +53,8 @@
 MRS_struct.p.HERMES = 0;
 
 % Flags
-MRS_struct.p.mat = 1; % Save results in *.mat output structure? (0 = NO, 1 = YES (default)).
+MRS_struct.p.mat = 1; % Save results in *.mat file? (0 = NO, 1 = YES (default)).
+MRS_struct.p.csv = 1; % Save results in *.csv file? (0 = NO, 1 = YES (default)).
 MRS_struct.p.vox = {'vox1'}; % Name of the voxel
 MRS_struct.p.target = {'GABAGlx'}; % Name of the target metabolite
 
@@ -69,37 +70,37 @@
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 
 for ii = 1:length(metabfile) % Loop over all files in the batch (from metabfile)
-    
+
     MRS_struct.ii = ii;
-    
+
     switch MRS_struct.p.vendor
-        
+
         case 'GE'
             MRS_struct = GERead(MRS_struct, metabfile{ii});
-            
+
         case 'Siemens_twix'
             MRS_struct = SiemensTwixRead(MRS_struct, metabfile{ii});
-            
+
         case 'Siemens_dicom'
             MRS_struct = SiemensDICOMRead(MRS_struct, metabfile{ii});
-            
+
         case 'dicom'
             MRS_struct = DICOMRead(MRS_struct, metabfile{ii});
-            
+
         case 'Siemens_rda'
             MRS_struct = SiemensRead(MRS_struct, metabfile{ii}, metabfile{ii});
-            
+
         case 'Philips'
             MRS_struct = PhilipsRead(MRS_struct, metabfile{ii});
-            
+
         case 'Philips_data'
             MRS_struct = PhilipsRead_data(MRS_struct, metabfile{ii});
-            
+
         case 'Philips_raw'
             MRS_struct = PhilipsRawLoad(MRS_struct, metabfile{ii}, 3, 0);
-            
+
     end
-    
+
 end
 
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%
@@ -124,6 +125,35 @@
     save(fullfile(pwd, 'MRS_struct_CoRegStandAlone.mat'), 'MRS_struct', '-v7.3');
 end
 
+% Export MRS_struct fields into csv file
+if MRS_struct.p.csv
+    csv_name = fullfile(pwd, 'MRS_struct.csv');
+    if exist(csv_name, 'file')
+        fprintf('\nUpdating results in %s\n\n', 'MRS_struct.csv...');
+    else
+        fprintf('\nExporting results to %s\n\n', 'MRS_struct.csv...');
+    end
+
+    if strcmp(MRS_struct.p.vendor, 'Siemens_rda')
+        filename = MRS_struct.metabfile(:,1:2:end)';
+    else
+        filename = MRS_struct.metabfile';
+    end
+    for ii = 1:length(filename)
+        [~,b,c] = fileparts(filename{ii});
+        out.filename(ii,1) = cellstr([b c]);
+    end
+
+    out.fGM  = MRS_struct.out.vox1.tissue.fGM(:);
+    out.fWM  = MRS_struct.out.vox1.tissue.fWM(:);
+    out.fCSF = MRS_struct.out.vox1.tissue.fCSF(:);
+
+    round2 = @(x) round(x*1e3)/1e3;
+    T = table(out.filename, round2(out.fGM), round2(out.fWM), round2(out.fCSF), ...
+        'VariableNames', {'Filename', 'fGM', 'fWM', 'fCSF'});
+    writetable(T, csv_name);
+end
+
 end
 
 

CoRegStandAlone/Seg.m

@@ -11,7 +11,7 @@
 % This is useful if only the tissue segmentation information is supposed to
 % be obtained.
 
-MRS_struct.version.segment = '210331';
+MRS_struct.version.segment = '220607';
 vox = MRS_struct.p.vox(1);
 
 warning('off'); % temporarily suppress warning messages
@@ -94,18 +94,18 @@
     airvol_thresh = airvol_tmp .* T1_tmp;
     airvol_thresh = airvol_thresh(:);
 
-    MRS_struct.out.tissue.CV_WM(ii) = std(WMvol_thresh, 'omitnan') / mean(WMvol_thresh, 'omitnan');
-    MRS_struct.out.tissue.CV_GM(ii) = std(GMvol_thresh, 'omitnan') / mean(GMvol_thresh, 'omitnan');
-    MRS_struct.out.tissue.CJV(ii)   = (std(WMvol_thresh, 'omitnan') + std(GMvol_thresh, 'omitnan')) ...
+    MRS_struct.out.QA.CV_WM(ii) = std(WMvol_thresh, 'omitnan') / mean(WMvol_thresh, 'omitnan');
+    MRS_struct.out.QA.CV_GM(ii) = std(GMvol_thresh, 'omitnan') / mean(GMvol_thresh, 'omitnan');
+    MRS_struct.out.QA.CJV(ii)   = (std(WMvol_thresh, 'omitnan') + std(GMvol_thresh, 'omitnan')) ...
                                       / abs(mean(WMvol_thresh, 'omitnan') - mean(GMvol_thresh, 'omitnan'));
-    MRS_struct.out.tissue.CNR(ii)   = abs(mean(WMvol_thresh, 'omitnan') - mean(GMvol_thresh, 'omitnan')) / ...
+    MRS_struct.out.QA.CNR(ii)   = abs(mean(WMvol_thresh, 'omitnan') - mean(GMvol_thresh, 'omitnan')) / ...
                                       sqrt(var(airvol_thresh, 'omitnan') + var(WMvol_thresh, 'omitnan') + var(GMvol_thresh, 'omitnan'));
 
     T1_tmp  = T1_tmp(:);
     n_vox   = numel(T1_tmp);
     efc_max = n_vox * (1/sqrt(n_vox)) * log(1/sqrt(n_vox));
     b_max   = sqrt(sum(T1_tmp.^2));
-    MRS_struct.out.tissue.EFC(ii) = (1/efc_max) .* sum((T1_tmp ./ b_max) .* log((T1_tmp + eps) ./ b_max));
+    MRS_struct.out.QA.EFC(ii) = (1/efc_max) .* sum((T1_tmp ./ b_max) .* log((T1_tmp + eps) ./ b_max));
 
     % Loop over voxels if PRIAM
     for kk = 1:length(vox)

GannetLoad.m

@@ -13,8 +13,8 @@
 %   6. Build GannetLoad output
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 
-MRS_struct.version.Gannet = '3.2.1-rc';
-MRS_struct.version.load   = '220526';
+MRS_struct.version.Gannet = '3.2.1';
+MRS_struct.version.load   = '220607';
 VersionCheck(0, MRS_struct.version.Gannet);
 ToolboxCheck;
 

GannetPreInitialise.m

@@ -12,7 +12,7 @@
                                        %   and MEGA-PRESS: {'GABA'}, {'Glx'}, {'GSH'}, {'Lac'}, or {'EtOH'}
                                        %   and HERMES: {'GABA','GSH'}, {'Glx','GSH'}, {'Lac','GSH'}, or {'EtOH','GABA','GSH'}
     MRS_struct.p.seqorig = 'JHU'; % Origin of Philips MEGA-PRESS or GE HERMES sequences;
-                                  % options are 'JHU' or 'Philips' if Philips, or 'Lythgoe' or 'Noeske' if GE (HERMES only)
+                                  % options are 'JHU' or 'Philips' if Philips, or 'Lythgoe' if GE (HERMES only)
 
 % Analysis parameters
     MRS_struct.p.LB            = 3; % Exponential line-broadening (in Hz)
@@ -38,9 +38,9 @@
     MRS_struct.p.mat      = 0; % Save MRS_struct as a .mat file
     MRS_struct.p.csv      = 0; % Extract useful data from MRS_struct and export them to a .csv file (applies to GannetFit,
                                % GannetSegment and GannetQuantify)
-    MRS_struct.p.append   = 1; % Append PDF outputs into one PDF (separately for each module) (requires export_fig in the Gannet
+    MRS_struct.p.append   = 0; % Append PDF outputs into one PDF (separately for each module) (requires export_fig in the Gannet
                                % folder to be added to the search path and GhostScript to be installed)
-    MRS_struct.p.hide     = 0; % Do not dynamically display output figures
+    MRS_struct.p.hide     = 0; % Do not display output figures
 
 end
 

GannetSegment.m

@@ -7,7 +7,7 @@
 % for the GM, WM and CSF segmentations. If these files are present, they
 % are loaded and used for the voxel segmentation
 
-MRS_struct.version.segment = '210331';
+MRS_struct.version.segment = '220607';
 
 warning('off'); % temporarily suppress warning messages
 
@@ -110,18 +110,18 @@
         airvol_thresh = airvol_tmp .* T1_tmp;
         airvol_thresh = airvol_thresh(:);
 
-        MRS_struct.out.tissue.CV_WM(ii) = std(WMvol_thresh, 'omitnan') / mean(WMvol_thresh, 'omitnan');
-        MRS_struct.out.tissue.CV_GM(ii) = std(GMvol_thresh, 'omitnan') / mean(GMvol_thresh, 'omitnan');
-        MRS_struct.out.tissue.CJV(ii)   = (std(WMvol_thresh, 'omitnan') + std(GMvol_thresh, 'omitnan')) ...
+        MRS_struct.out.QA.CV_WM(ii) = std(WMvol_thresh, 'omitnan') / mean(WMvol_thresh, 'omitnan');
+        MRS_struct.out.QA.CV_GM(ii) = std(GMvol_thresh, 'omitnan') / mean(GMvol_thresh, 'omitnan');
+        MRS_struct.out.QA.CJV(ii)   = (std(WMvol_thresh, 'omitnan') + std(GMvol_thresh, 'omitnan')) ...
                                           / abs(mean(WMvol_thresh, 'omitnan') - mean(GMvol_thresh, 'omitnan'));
-        MRS_struct.out.tissue.CNR(ii)   = abs(mean(WMvol_thresh, 'omitnan') - mean(GMvol_thresh, 'omitnan')) / ...
+        MRS_struct.out.QA.CNR(ii)   = abs(mean(WMvol_thresh, 'omitnan') - mean(GMvol_thresh, 'omitnan')) / ...
                                           sqrt(var(airvol_thresh, 'omitnan') + var(WMvol_thresh, 'omitnan') + var(GMvol_thresh, 'omitnan'));
 
         T1_tmp  = T1_tmp(:);
         n_vox   = numel(T1_tmp);
         efc_max = n_vox * (1/sqrt(n_vox)) * log(1/sqrt(n_vox));
         b_max   = sqrt(sum(T1_tmp.^2));
-        MRS_struct.out.tissue.EFC(ii) = (1/efc_max) .* sum((T1_tmp ./ b_max) .* log((T1_tmp + eps) ./ b_max));
+        MRS_struct.out.QA.EFC(ii) = (1/efc_max) .* sum((T1_tmp ./ b_max) .* log((T1_tmp + eps) ./ b_max));
 
         % Voxel mask
         voxmaskvol = spm_vol(MRS_struct.mask.(vox{kk}).outfile{ii});