Update export_fig to v3.15; some cosmetic changes

Author: markmikkelsen

CoRegStandAlone/CoReg.m

@@ -2,25 +2,25 @@
 
 % Coregistration of MRS voxel volumes to imaging datasets, based on headers.
 
-MRS_struct.version.coreg = '201204';
+MRS_struct.version.coreg = '210701';
 
 warning('off'); % temporarily suppress warning messages
 
 % First check if SPM12 is installed and on the search path
-spmversion = fileparts(which('spm'));
-if isempty(spmversion)
+spm_version = fileparts(which('spm'));
+if isempty(spm_version)
     msg = 'SPM not found! Please install SPM12 and make sure it is in your search path.';
     msg = hyperlink('https://www.fil.ion.ucl.ac.uk/spm/software/spm12', 'SPM12', msg);
     error(msg);
-elseif strcmpi(spmversion(end-3:end),'spm8')
+elseif strcmpi(spm_version(end-3:end),'spm8')
     msg = ['SPM8 detected. Gannet no longer supports SPM8. ' ...
            'Please install SPM12 and make sure it is in your search path.'];
     msg = hyperlink('https://www.fil.ion.ucl.ac.uk/spm/software/spm12', 'SPM12', msg);
     error(msg);
 end
 
 if MRS_struct.ii ~= length(struc)
-    error('The number of nifti files does not match the number of MRS files processed by CoRegStandAlone.');
+    error('The number of NIfTI files does not match the number of MRS files processed by CoRegStandAlone.');
 end
 
 numscans = numel(MRS_struct.metabfile);
@@ -151,9 +151,7 @@
         colormap('gray');
         img = MRS_struct.mask.(vox{kk}).img{ii}(:);
         caxis([0 mean(img(img > 0.01)) + 3*std(img(img > 0.01))]);
-        axis equal;
-        axis tight;
-        axis off;
+        axis equal tight off;
         text(10, size(MRS_struct.mask.(vox{kk}).img{ii},1)/2, 'L', 'Color', [1 1 1], 'FontSize', 20);
         text(size(MRS_struct.mask.(vox{kk}).img{ii},2) - 20, size(MRS_struct.mask.(vox{kk}).img{ii},1)/2, 'R', 'Color', [1 1 1], 'FontSize', 20);
         set(ha,'pos',[0 0.15 1 1]);
@@ -165,15 +163,13 @@
         axes('Position', [0.825, 0.05, 0.125, 0.125]);
         imshow(I);
         text(0.9, 0, MRS_struct.version.Gannet, 'Units', 'normalized', 'FontName', 'Arial', 'FontSize', 14, 'FontWeight', 'bold', 'HorizontalAlignment', 'left');
-        axis off;
-        axis square;
+        axis off square;
 
         % Gannet documentation
         axes('Position', [(1-0.9)/2, 0.025, 0.9, 0.15]);
         str = 'For complete documentation, please visit: https://markmikkelsen.github.io/Gannet-docs';
         text(0.5, 0, str, 'FontName', 'Arial', 'FontSize', 11, 'HorizontalAlignment', 'center');
-        axis off;
-        axis square;
+        axis off square;
 
         % For Philips .data
         if strcmpi(MRS_struct.p.vendor,'Philips_data')
@@ -207,7 +203,6 @@
         end
         saveas(gcf, pdfname);
 
-        
     end
 
 end

CoRegStandAlone/CoRegStandAlone.m

@@ -43,7 +43,7 @@
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 
 MRS_struct.version.Gannet = '3.2.0';
-MRS_struct.version.load = '210624';
+MRS_struct.version.load = '210730';
 MRS_struct.ii = 0;
 if size(metabfile,2) == 1
     metabfile = metabfile';

CoRegStandAlone/Seg.m

@@ -11,30 +11,30 @@
 % This is useful if only the tissue segmentation information is supposed to
 % be obtained.
 
-MRS_struct.version.segment = '201204';
+MRS_struct.version.segment = '210331';
 vox = MRS_struct.p.vox(1);
 
 warning('off'); % temporarily suppress warning messages
 
 % First check if SPM12 is installed and on the search path
-spmversion = fileparts(which('spm'));
-if isempty(spmversion)
+spm_version = fileparts(which('spm'));
+if isempty(spm_version)
     msg = 'SPM not found! Please install SPM12 and make sure it is in your search path.';
     msg = hyperlink('https://www.fil.ion.ucl.ac.uk/spm/software/spm12', 'SPM12', msg);
     error(msg);
-elseif strcmpi(spmversion(end-3:end),'spm8')
+elseif strcmpi(spm_version(end-3:end),'spm8')
     msg = ['SPM8 detected. Gannet no longer supports SPM8. ' ...
            'Please install SPM12 and make sure it is in your search path.'];
     msg = hyperlink('https://www.fil.ion.ucl.ac.uk/spm/software/spm12', 'SPM12', msg);
     error(msg);
 end
 
 kk = 1;
-setupSPM = 1;
+setup_spm = 1;
 
 for ii = 1:length(MRS_struct.metabfile)
 
-    % 1 - Take nifti from GannetCoRegister and segment it in SPM
+    % 1. Take NIfTI from GannetCoRegister and segment it in SPM
 
     [T1dir, T1name, T1ext] = fileparts(MRS_struct.mask.(vox{kk}).T1image{ii});
     struc = MRS_struct.mask.(vox{kk}).T1image{ii};
@@ -49,16 +49,16 @@
         filesExist(jj) = exist(tmp{jj}, 'file'); %#ok<AGROW>
     end
     if ~all(filesExist)
-        if setupSPM
-            % Set up SPM for batch processing (do it once and only when needed)
+        if setup_spm
+            % Set up SPM for batch processing (do it once per batch)
             spm('defaults','fmri');
             spm_jobman('initcfg');
-            setupSPM = 0;
+            setup_spm = 0;
         end
         CallSPM12segmentation(struc);
     end
 
-    % 2 - Determine GM, WM and CSF fractions for each voxel
+    % 2. Calculate QC metrics and GM, WM, and CSF fractions for each voxel
 
     if strcmp(T1dir,'')
         T1dir = '.';
@@ -73,40 +73,40 @@
     WMvol  = spm_vol(WM);
     CSFvol = spm_vol(CSF);
     airvol = spm_vol(air);
-
+    
     % Segmentation quality metrics (Chua et al. JMRI, 2009; Ganzetti et
     % al. Front. Neuroinform., 2016; Esteban et al. PLOS One, 2017)
     T1     = spm_vol(struc);
     T1_tmp = T1.private.dat(:,:,:);
-
+    
     WMvol_tmp = WMvol.private.dat(:,:,:);
     WMvol_tmp(WMvol_tmp < 0.9) = NaN;
     WMvol_thresh = WMvol_tmp .* T1_tmp;
     WMvol_thresh = WMvol_thresh(:);
-
+    
     GMvol_tmp = GMvol.private.dat(:,:,:);
     GMvol_tmp(GMvol_tmp < 0.9) = NaN;
     GMvol_thresh = GMvol_tmp .* T1_tmp;
     GMvol_thresh = GMvol_thresh(:);
-
+    
     airvol_tmp = airvol.private.dat(:,:,:);
     airvol_tmp(airvol_tmp < 0.9) = NaN;
     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')) ...
-                                      / abs(mean(WMvol_thresh,'omitnan') - mean(GMvol_thresh,'omitnan'));
-    MRS_struct.out.tissue.CNR(ii)   = abs(mean(WMvol_thresh,'omitnan') - mean(GMvol_thresh,'omitnan')) / ...
-                                      sqrt(var(airvol_thresh,'omitnan') + var(WMvol_thresh,'omitnan') + var(GMvol_thresh,'omitnan'));
+    
+    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')) ...
+                                      / abs(mean(WMvol_thresh, 'omitnan') - mean(GMvol_thresh, 'omitnan'));
+    MRS_struct.out.tissue.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));
-
+    
     % Loop over voxels if PRIAM
     for kk = 1:length(vox)
 
@@ -115,7 +115,7 @@
 
         % GM
         O_GMvox.fname = fullfile(a, [b '_GM' c]);
-        O_GMvox.descrip = 'GMmasked_MRS_Voxel_Mask';
+        O_GMvox.descrip = 'MRS_voxel_mask_GM';
         O_GMvox.dim = voxmaskvol.dim;
         O_GMvox.dt = voxmaskvol.dt;
         O_GMvox.mat = voxmaskvol.mat;
@@ -124,7 +124,7 @@
 
         % WM
         O_WMvox.fname = fullfile(a, [b '_WM' c]);
-        O_WMvox.descrip = 'WMmasked_MRS_Voxel_Mask';
+        O_WMvox.descrip = 'MRS_voxel_mask_WM';
         O_WMvox.dim = voxmaskvol.dim;
         O_WMvox.dt = voxmaskvol.dt;
         O_WMvox.mat = voxmaskvol.mat;
@@ -133,14 +133,14 @@
 
         % CSF
         O_CSFvox.fname = fullfile(a, [b '_CSF' c]);
-        O_CSFvox.descrip = 'CSFmasked_MRS_Voxel_Mask';
+        O_CSFvox.descrip = 'MRS_voxel_mask_CSF';
         O_CSFvox.dim = voxmaskvol.dim;
         O_CSFvox.dt = voxmaskvol.dt;
         O_CSFvox.mat = voxmaskvol.mat;
         CSF_voxmask_vol = CSFvol.private.dat(:,:,:) .* voxmaskvol.private.dat(:,:,:);
         O_CSFvox = spm_write_vol(O_CSFvox, CSF_voxmask_vol);
 
-        % 3 - Calculate a CSF-corrected i.u. value and output it to the structure
+        % 3. Calculate a CSF-corrected i.u. value and output it to the structure
 
         GMsum  = sum(sum(sum(O_GMvox.private.dat(:,:,:))));
         WMsum  = sum(sum(sum(O_WMvox.private.dat(:,:,:))));
@@ -154,7 +154,7 @@
         MRS_struct.out.(vox{kk}).tissue.fWM(ii)  = fWM;
         MRS_struct.out.(vox{kk}).tissue.fCSF(ii) = fCSF;
 
-        % 4 - Build output
+        % 4. Build output
 
         if ishandle(104)
             clf(104);
@@ -296,8 +296,6 @@
 
 warning('on'); % turn warnings back on
 
-end
-
 
 function img_montage = PlotSegmentedVoxels(struc, voxoff, voxmaskvol, O_GMvox, O_WMvox, O_CSFvox)
 
@@ -368,16 +366,12 @@
 
 ha = subplot(2,3,1:3);
 imagesc(img_montage);
-axis equal;
-axis tight;
-axis off;
+axis equal tight off;
 text(floor(size(mask_t,2)/2), 20, 'Voxel', 'Color', [1 1 1], 'FontSize', 20, 'HorizontalAlignment', 'center');
 text(floor(size(mask_t,2)) + floor(size(mask_t,2)/2), 20, 'GM', 'Color', [1 1 1], 'FontSize', 20, 'HorizontalAlignment', 'center');
 text(2*floor(size(mask_t,2)) + floor(size(mask_t,2)/2), 20, 'WM', 'Color', [1 1 1], 'FontSize', 20, 'HorizontalAlignment', 'center');
 text(3*floor(size(mask_t,2)) + floor(size(mask_t,2)/2), 20, 'CSF', 'Color', [1 1 1], 'FontSize', 20, 'HorizontalAlignment', 'center');
-set(ha,'pos',[0 0.17 1 1]);
-
-end
+set(ha, 'pos', [0 0.17 1 1]);
 
 
 

GannetCoRegister.m

@@ -26,7 +26,7 @@
 end
 
 if MRS_struct.ii ~= length(struc)
-    error('The number of nifti files does not match the number of MRS files processed by GannetLoad.');
+    error('The number of NIfTI files does not match the number of MRS files processed by GannetLoad.');
 end
 
 run_count = 0;

GannetMask_Philips.m

@@ -58,7 +58,7 @@
 lr_ang  = MRS_struct.p.voxang(ii,1);
 cc_ang  = MRS_struct.p.voxang(ii,3);
 
-% We need to flip ap and lr axes to match NIFTI convention
+% We need to flip ap and lr axes to match NIfTI convention
 ap_off = -ap_off;
 lr_off = -lr_off;
 ap_ang = -ap_ang;

GannetMask_SiemensRDA.m

@@ -21,7 +21,7 @@
     ii = 1;
 end
 
-% Parse RDA filename and establish nifti voxelmask filename
+% Parse RDA filename and establish NIfTI voxelmask filename
 [path, name] = fileparts(fname);
 fidoutmask = fullfile(path,[name '_mask.nii']);
 fid = fopen(fname);
@@ -168,7 +168,7 @@
 halfpixshift(3) = -halfpixshift(3);
 XYZ = XYZ + repmat(halfpixshift, [1 size(XYZ,2)]);
 
-% We need to flip ap and lr axes to match NIFTI convention
+% We need to flip ap and lr axes to match NIfTI convention
 VoxOffs(1) = -VoxOffs(1);
 VoxOffs(2) = -VoxOffs(2);
 

GannetMask_SiemensTWIX.m

@@ -122,7 +122,7 @@
 halfpixshift(3) = -halfpixshift(3);
 XYZ = XYZ + repmat(halfpixshift, [1 size(XYZ,2)]);
 
-% We need to flip ap and lr axes to match NIFTI convention
+% We need to flip ap and lr axes to match NIfTI convention
 VoxOffs(1) = -VoxOffs(1);
 VoxOffs(2) = -VoxOffs(2);
 

GannetSegment.m

@@ -38,7 +38,7 @@
 
     for ii = 1:MRS_struct.p.numScans
 
-        % 1. Take nifti from GannetCoRegister and segment it in SPM
+        % 1. Take NIfTI from GannetCoRegister and segment it in SPM
 
         [T1dir, T1name, T1ext] = fileparts(MRS_struct.mask.(vox{kk}).T1image{ii});
         struc = MRS_struct.mask.(vox{kk}).T1image{ii};
@@ -211,19 +211,19 @@
         text_pos = 1;
 
         if strcmp(MRS_struct.p.vendor,'Siemens_rda')
-            [~,filesExist,tmp3] = fileparts(MRS_struct.metabfile{1,ii*2-1});
+            [~,tmp2,tmp3] = fileparts(MRS_struct.metabfile{1,ii*2-1});
         else
-            [~,filesExist,tmp3] = fileparts(MRS_struct.metabfile{1,ii});
+            [~,tmp2,tmp3] = fileparts(MRS_struct.metabfile{1,ii});
         end
-        fname = [filesExist tmp3];
+        fname = [tmp2 tmp3];
         if length(fname) > 30
             fname = [fname(1:12) '...' fname(end-11:end)];
         end
         text(0.5, text_pos-0.12, 'Filename: ', 'FontName', 'Arial', 'HorizontalAlignment','right', 'VerticalAlignment', 'top', 'FontSize', 13);
         text(0.5, text_pos-0.12, [' ' fname], 'FontName', 'Arial', 'VerticalAlignment', 'top', 'FontSize', 13, 'Interpreter', 'none');
 
-        [~,filesExist,tmp3] = fileparts(MRS_struct.mask.(vox{kk}).T1image{ii});
-        T1image = [filesExist tmp3];
+        [~,tmp2,tmp3] = fileparts(MRS_struct.mask.(vox{kk}).T1image{ii});
+        T1image = [tmp2 tmp3];
         if length(T1image) > 30
             T1image = [T1image(1:12) '...' T1image(end-11:end)];
         end
@@ -247,16 +247,16 @@
                 switch target{jj}
                     case 'GABA'
                         tmp1 = 'GABA+/Water (CSF-corrected): ';
-                        filesExist = sprintf(' %.2f i.u.', MRS_struct.out.(vox{kk}).GABA.ConcIU_CSFcorr(ii));
+                        tmp2 = sprintf(' %.2f i.u.', MRS_struct.out.(vox{kk}).GABA.ConcIU_CSFcorr(ii));
                     case 'Lac'
                         tmp1 = 'Lac+MM/Water (CSF-corrected): ';
-                        filesExist = sprintf(' %.2f i.u.', MRS_struct.out.(vox{kk}).Lac.ConcIU_CSFcorr(ii));
+                        tmp2 = sprintf(' %.2f i.u.', MRS_struct.out.(vox{kk}).Lac.ConcIU_CSFcorr(ii));
                     case {'Glx','GSH','EtOH'}
                         tmp1 = [target{jj} '/Water (CSF-corrected): '];
-                        filesExist = sprintf(' %.2f i.u.', MRS_struct.out.(vox{kk}).(target{jj}).ConcIU_CSFcorr(ii));
+                        tmp2 = sprintf(' %.2f i.u.', MRS_struct.out.(vox{kk}).(target{jj}).ConcIU_CSFcorr(ii));
                 end
                 text(0.5, text_pos, tmp1, 'FontName', 'Arial', 'HorizontalAlignment','right', 'VerticalAlignment', 'top', 'FontSize', 13);
-                text(0.5, text_pos, filesExist, 'FontName', 'Arial', 'VerticalAlignment', 'top', 'FontSize', 13);
+                text(0.5, text_pos, tmp2, 'FontName', 'Arial', 'VerticalAlignment', 'top', 'FontSize', 13);
             end
         end
 
@@ -286,11 +286,11 @@
         MRS_struct.mask.(vox{kk}).img_montage{ii} = PlotSegmentedVoxels(struc, voxoff, voxmaskvol, O_GMvox, O_WMvox, O_CSFvox);
 
         if strcmp(MRS_struct.p.vendor, 'Siemens_rda')
-            [~,tmp,filesExist] = fileparts(MRS_struct.metabfile{1,ii*2-1});
+            [~,tmp,tmp2] = fileparts(MRS_struct.metabfile{1,ii*2-1});
         else
-            [~,tmp,filesExist] = fileparts(MRS_struct.metabfile{1,ii});
+            [~,tmp,tmp2] = fileparts(MRS_struct.metabfile{1,ii});
         end
-        fname = [tmp filesExist];
+        fname = [tmp tmp2];
         if length(fname) > 30
             fname = [fname(1:12) '...' fname(end-11:end)];
         end

GannetVersion.m

@@ -11,4 +11,4 @@
 str = char(str(:)');
 expression = '(?<field>MRS_struct.version.Gannet = )''(?<version>.*?)''';
 out = regexp(str, expression, 'names');
-fprintf('\n   %s\n\n', out.version);
+fprintf('\nYour version of Gannet is %s\n\n', out.version);