cpp-lln-lab · Remi-Gau · Mar 10, 2021 · Mar 9, 2021 · Mar 9, 2021 · Mar 9, 2021
diff --git a/.github/workflows/run_system_tests.yml b/.github/workflows/run_system_tests.yml
@@ -58,8 +58,7 @@ jobs:
 
     - name: Update octave path
       run: |
-        octave $OCTFLAGS --eval "addpath(genpath(fullfile(pwd, 'lib'))); savepath();"
-        octave $OCTFLAGS --eval "addpath(genpath(fullfile(pwd, 'src'))); savepath();"        
+        octave $OCTFLAGS --eval "initCppSpm; savepath();"       
 
     - name: Prepare data
       run: |

diff --git a/.github/workflows/run_tests.yml b/.github/workflows/run_tests.yml
@@ -62,8 +62,8 @@ jobs:
 
     - name: Update octave path
       run: |
-        octave $OCTFLAGS --eval "addpath(genpath(fullfile(pwd, 'lib'))); savepath();"
-        octave $OCTFLAGS --eval "addpath(genpath(fullfile(pwd, 'src'))); savepath();"        
+        octave $OCTFLAGS --eval "initCppSpm; savepath();"
+        octave $OCTFLAGS --eval "addpath(fullfile(pwd, 'tests', 'utils')); savepath();"        
 
     - name: Prepare data
       run: |

diff --git a/demos/openneuro/ds000001_run.m b/demos/openneuro/ds000001_run.m
@@ -9,12 +9,7 @@
 FWHM = 6;
 conFWHM = 6;
 
-% directory with this script becomes the current directory
-WD = fileparts(mfilename('fullpath'));
-
-% we add all the subfunctions that are in the sub directories
-addpath(genpath(fullfile(WD, '..', '..', 'src')));
-addpath(genpath(fullfile(WD, '..', '..', 'lib')));
+initCppSpm();
 
 %% Set options
 opt = ds000001_getOption();

diff --git a/demos/openneuro/ds000114_run.m b/demos/openneuro/ds000114_run.m
@@ -9,12 +9,7 @@
 FWHM = 6;
 conFWHM = 6;
 
-% directory with this script becomes the current directory
-WD = fileparts(mfilename('fullpath'));
-
-% we add all the subfunctions that are in the sub directories
-addpath(genpath(fullfile(WD, '..', '..', 'src')));
-addpath(genpath(fullfile(WD, '..', '..', 'lib')));
+initCppSpm();
 
 %% Set options
 opt = ds000114_getOption();

diff --git a/demos/openneuro/ds001168_run.m b/demos/openneuro/ds001168_run.m
@@ -8,12 +8,7 @@
 % Smoothing to apply
 FWHM = 6;
 
-% directory with this script becomes the current directory
-WD = fileparts(mfilename('fullpath'));
-
-% we add all the subfunctions that are in the sub directories
-addpath(genpath(fullfile(WD, '..', '..', 'src')));
-addpath(genpath(fullfile(WD, '..', '..', 'lib')));
+initCppSpm();
 
 %% Set options
 opt = ds001168_getOption();

diff --git a/demos/spm_face_rep/face_rep_run.m b/demos/spm_face_rep/face_rep_run.m
@@ -26,9 +26,7 @@
 % directory with this script becomes the current directory
 WD = fileparts(mfilename('fullpath'));
 
-% we add all the subfunctions that are in the sub directories
-addpath(genpath(fullfile(WD, '..', '..', 'src')));
-addpath(genpath(fullfile(WD, '..', '..', 'lib')));
+initCppSpm();
 
 %% Set options
 opt = FaceRep_getOption();

diff --git a/initCppSpm.m b/initCppSpm.m
@@ -7,6 +7,11 @@ function initCppSpm()
 
   % we add all the subfunctions that are in the sub directories
   addpath(genpath(fullfile(WD, 'src')));
-  addpath(genpath(fullfile(WD, 'lib')));
+  addpath(genpath(fullfile(WD, 'lib', 'mancoreg')));
+  addpath(genpath(fullfile(WD, 'lib', 'NiftiTools')));
+  addpath(genpath(fullfile(WD, 'lib', 'spmup')));
+  addpath(genpath(fullfile(WD, 'lib', 'utils')));
+
+  addpath(fullfile(WD, 'lib', 'bids-matlab'));
 
 end
diff --git a/src/QA/anatomicalQA.m b/src/QA/anatomicalQA.m
@@ -23,43 +23,37 @@ function anatomicalQA(opt)
   end
   opt = loadAndCheckOptions(opt);
 
-  [group, opt, BIDS] = getData(opt);
+  [BIDS, opt] = getData(opt);
 
   fprintf(1, ' ANATOMICAL: QUALITY CONTROL\n\n');
 
-  %% Loop through the groups, subjects, and sessions
-  for iGroup = 1:length(group)
+  parfor iSub = 1:numel(opt.subjects)
 
-    groupName = group(iGroup).name;
+    subID = opt.subjects{iSub};
 
-    parfor iSub = 1:group(iGroup).numSub
+    printProcessingSubject(iSub, subID);
 
-      subID = group(iGroup).subNumber{iSub};
+    [anatImage, anatDataDir] = getAnatFilename(BIDS, subID, opt);
 
-      printProcessingSubject(groupName, iSub, subID);
+    % get grey and white matter tissue probability maps
+    TPMs = validationInputFile(anatDataDir, anatImage, 'c[12]');
 
-      [anatImage, anatDataDir] = getAnatFilename(BIDS, subID, opt);
+    % sanity check that all images are in the same space.
+    anatImage = fullfile(anatDataDir, anatImage);
+    volumesToCheck = {anatImage; TPMs(1, :); TPMs(2, :)};
+    spm_check_orientations(spm_vol(char(volumesToCheck)));
 
-      % get grey and white matter tissue probability maps
-      TPMs = validationInputFile(anatDataDir, anatImage, 'c[12]');
+    % Basic QA for anatomical data is to get SNR, CNR, FBER and Entropy
+    % This is useful to check coregistration worked fine
+    anatQA = spmup_anatQA(anatImage, TPMs(1, :), TPMs(2, :)); %#ok<*NASGU>
 
-      % sanity check that all images are in the same space.
-      anatImage = fullfile(anatDataDir, anatImage);
-      volumesToCheck = {anatImage; TPMs(1, :); TPMs(2, :)};
-      spm_check_orientations(spm_vol(char(volumesToCheck)));
+    anatQA.avgDistToSurf = spmup_comp_dist2surf(anatImage);
 
-      % Basic QA for anatomical data is to get SNR, CNR, FBER and Entropy
-      % This is useful to check coregistration worked fine
-      anatQA = spmup_anatQA(anatImage, TPMs(1, :), TPMs(2, :)); %#ok<*NASGU>
+    spm_jsonwrite( ...
+                  strrep(anatImage, '.nii', '_qa.json'), ...
+                  anatQA, ...
+                  struct('indent', '   '));
 
-      anatQA.avgDistToSurf = spmup_comp_dist2surf(anatImage);
-
-      spm_jsonwrite( ...
-                    strrep(anatImage, '.nii', '_qa.json'), ...
-                    anatQA, ...
-                    struct('indent', '   '));
-
-    end
   end
 
 end
diff --git a/src/QA/functionalQA.m b/src/QA/functionalQA.m
@@ -35,106 +35,99 @@ function functionalQA(opt)
   end
   opt = loadAndCheckOptions(opt);
 
-  [group, opt, BIDS] = getData(opt);
+  [BIDS, opt] = getData(opt);
 
   fprintf(1, ' FUNCTIONAL: QUALITY CONTROL\n\n');
 
-  %% Loop through the groups, subjects, and sessions
-  for iGroup = 1:length(group)
+  for iSub = 1:numel(opt.subjects)
 
-    groupName = group(iGroup).name;
+    subID = opt.subjects{iSub};
 
-    for iSub = 1:group(iGroup).numSub
+    printProcessingSubject(iSub, subID);
 
-      subID = group(iGroup).subNumber{iSub};
+    % get grey and white matter and csf tissue probability maps
+    [anatImage, anatDataDir] = getAnatFilename(BIDS, subID, opt);
+    TPMs = validationInputFile(anatDataDir, anatImage, 'rc[123]');
 
-      printProcessingSubject(groupName, iSub, subID);
+    % load metrics from anat QA
+    anatQA = spm_jsonread( ...
+                          fullfile( ...
+                                   anatDataDir,  ...
+                                   strrep(anatImage, '.nii', '_qa.json')));
 
-      % get grey and white matter and csf tissue probability maps
-      [anatImage, anatDataDir] = getAnatFilename(BIDS, subID, opt);
-      TPMs = validationInputFile(anatDataDir, anatImage, 'rc[123]');
+    [sessions, nbSessions] = getInfo(BIDS, subID, opt, 'Sessions');
 
-      % load metrics from anat QA
-      anatQA = spm_jsonread( ...
-                            fullfile( ...
-                                     anatDataDir,  ...
-                                     strrep(anatImage, '.nii', '_qa.json')));
+    for iSes = 1:nbSessions
 
-      [sessions, nbSessions] = getInfo(BIDS, subID, opt, 'Sessions');
+      % get all runs for that subject across all sessions
+      [runs, nbRuns] = getInfo(BIDS, subID, opt, 'Runs', sessions{iSes});
 
-      for iSes = 1:nbSessions
+      for iRun = 1:nbRuns
 
-        % get all runs for that subject across all sessions
-        [runs, nbRuns] = getInfo(BIDS, subID, opt, 'Runs', sessions{iSes});
+        % get the filename for this bold run for this task
+        [fileName, subFuncDataDir] = getBoldFilename( ...
+                                                     BIDS, ...
+                                                     subID, ...
+                                                     sessions{iSes}, ...
+                                                     runs{iRun}, ...
+                                                     opt);
 
-        for iRun = 1:nbRuns
+        prefix = getPrefix('funcQA', opt);
+        funcImage = validationInputFile(subFuncDataDir, fileName, prefix);
 
-          % get the filename for this bold run for this task
-          [fileName, subFuncDataDir] = getBoldFilename( ...
-                                                       BIDS, ...
-                                                       subID, ...
-                                                       sessions{iSes}, ...
-                                                       runs{iRun}, ...
-                                                       opt);
+        % sanity check that all images are in the same space.
+        volumesToCheck = {funcImage; TPMs(1, :); TPMs(2, :); TPMs(3, :)};
+        spm_check_orientations(spm_vol(char(volumesToCheck)));
 
-          prefix = getPrefix('funcQA', opt);
-          funcImage = validationInputFile(subFuncDataDir, fileName, prefix);
+        fMRIQA = computeFuncQAMetrics(funcImage, TPMs, anatQA.avgDistToSurf, opt);
 
-          % sanity check that all images are in the same space.
-          volumesToCheck = {funcImage; TPMs(1, :); TPMs(2, :); TPMs(3, :)};
-          spm_check_orientations(spm_vol(char(volumesToCheck)));
+        % TODO
+        % find an ouput format that is leaner than a 3 Gb json file!!!
+        %           spm_jsonwrite( ...
+        %                         fullfile( ...
+        %                                  subFuncDataDir, ...
+        %                                  strrep(fileName, '.nii',  '_qa.json')), ...
+        %                         fMRIQA, ...
+        %                         struct('indent', '   '));
+        %           save( ...
+        %                fullfile( ...
+        %                         subFuncDataDir, ...
+        %                         strrep(fileName, '.nii',  '_qa.mat')), ...
+        %                'fMRIQA');
 
-          fMRIQA = computeFuncQAMetrics(funcImage, TPMs, anatQA.avgDistToSurf, opt);
+        outputFiles = spmup_first_level_qa( ...
+                                           funcImage, ...
+                                           'Voltera', 'on', ...
+                                           'Radius', anatQA.avgDistToSurf);
 
-          % TODO
-          % find an ouput format that is leaner than a 3 Gb json file!!!
-          %           spm_jsonwrite( ...
-          %                         fullfile( ...
-          %                                  subFuncDataDir, ...
-          %                                  strrep(fileName, '.nii',  '_qa.json')), ...
-          %                         fMRIQA, ...
-          %                         struct('indent', '   '));
-          %           save( ...
-          %                fullfile( ...
-          %                         subFuncDataDir, ...
-          %                         strrep(fileName, '.nii',  '_qa.mat')), ...
-          %                'fMRIQA');
+        movefile( ...
+                 fullfile(subFuncDataDir, 'spmup_QC.ps'), ...
+                 fullfile(subFuncDataDir, strrep(fileName, '.nii',  '_qa.ps')));
 
-          outputFiles = spmup_first_level_qa( ...
-                                             funcImage, ...
-                                             'Voltera', 'on', ...
-                                             'Radius', anatQA.avgDistToSurf);
+        confounds = load(outputFiles.design);
 
-          movefile( ...
-                   fullfile(subFuncDataDir, 'spmup_QC.ps'), ...
-                   fullfile(subFuncDataDir, strrep(fileName, '.nii',  '_qa.ps')));
+        spm_save( ...
+                 fullfile( ...
+                          subFuncDataDir, ...
+                          strrep(fileName, ...
+                                 '_bold.nii',  ...
+                                 '_desc-confounds_regressors.tsv')), ...
+                 confounds);
 
-          confounds = load(outputFiles.design);
+        delete(outputFiles.design);
 
-          spm_save( ...
-                   fullfile( ...
-                            subFuncDataDir, ...
-                            strrep(fileName, ...
-                                   '_bold.nii',  ...
-                                   '_desc-confounds_regressors.tsv')), ...
-                   confounds);
+        createDataDictionary(subFuncDataDir, fileName, size(confounds, 2));
 
-          delete(outputFiles.design);
-
-          createDataDictionary(subFuncDataDir, fileName, size(confounds, 2));
-
-          % create carpet plot
-
-          % horrible hack to prevent the "abrupt" way spmup_volumecorr crashes
-          % if nansum is not there
-          if exist('nansum', 'file') == 2
-            spmup_timeseriesplot(funcImage, TPMs(1, :), TPMs(2, :), TPMs(3, :), ...
-                                 'motion', 'on', ...
-                                 'nuisances', 'on', ...
-                                 'correlation', 'on', ...
-                                 'makefig', 'on');
-          end
+        % create carpet plot
 
+        % horrible hack to prevent the "abrupt" way spmup_volumecorr crashes
+        % if nansum is not there
+        if exist('nansum', 'file') == 2
+          spmup_timeseriesplot(funcImage, TPMs(1, :), TPMs(2, :), TPMs(3, :), ...
+                               'motion', 'on', ...
+                               'nuisances', 'on', ...
+                               'correlation', 'on', ...
+                               'makefig', 'on');
         end
 
       end

diff --git a/src/batches/setBatchCoregistrationFmap.m b/src/batches/setBatchCoregistrationFmap.m
@@ -1,20 +1,20 @@
 % (C) Copyright 2020 CPP BIDS SPM-pipeline developers
 
-function matlabbatch = setBatchCoregistrationFmap(matlabbatch, BIDS, opt, subID)
+function matlabbatch = setBatchCoregistrationFmap(matlabbatch, BIDS, opt, subLabel)
   %
   % Set the batch for the coregistration of field maps
   %
   % USAGE::
   %
-  %   matlabbatch = setBatchCoregistrationFmap(matlabbatch, BIDS, opt, subID)
+  %   matlabbatch = setBatchCoregistrationFmap(matlabbatch, BIDS, opt, subLabel)
   %
   % :param BIDS: BIDS layout returned by ``getData``.
   % :type BIDS: structure
   % :param opt: structure or json filename containing the options. See
   %             ``checkOptions()`` and ``loadAndCheckOptions()``.
   % :type opt: structure
-  % :param subID: subject ID
-  % :type subID: string
+  % :param subLabel:
+  % :type subLabel: string
   %
   % :returns: - :matlabbatch: (structure) The matlabbatch ready to run the spm job
   %
@@ -26,31 +26,31 @@
 
   % Use a rough mean of the 1rst run to improve SNR for coregistration
   % created by spmup
-  [sessions, nbSessions] = getInfo(BIDS, subID, opt, 'Sessions');
-  runs = getInfo(BIDS, subID, opt, 'Runs', sessions{1});
-  [fileName, subFuncDataDir] = getBoldFilename(BIDS, subID, sessions{1}, runs{1}, opt);
+  [sessions, nbSessions] = getInfo(BIDS, subLabel, opt, 'Sessions');
+  runs = getInfo(BIDS, subLabel, opt, 'Runs', sessions{1});
+  [fileName, subFuncDataDir] = getBoldFilename(BIDS, subLabel, sessions{1}, runs{1}, opt);
   refImage = validationInputFile(subFuncDataDir, fileName, 'mean_');
 
   for iSes = 1:nbSessions
 
     runs = bids.query(BIDS, 'runs', ...
                       'modality', 'fmap', ...
-                      'sub', subID, ...
+                      'sub', subLabel, ...
                       'ses', sessions{iSes});
 
     for iRun = 1:numel(runs)
 
       metadata = bids.query(BIDS, 'metadata', ...
                             'modality', 'fmap', ...
-                            'sub', subID, ...
+                            'sub', subLabel, ...
                             'ses', sessions{iSes}, ...
                             'run', runs{iRun});
 
       if strfind(metadata.IntendedFor, opt.taskName)
 
         fmapFiles = bids.query(BIDS, 'data', ...
                                'modality', 'fmap', ...
-                               'sub', subID, ...
+                               'sub', subLabel, ...
                                'ses', sessions{iSes}, ...
                                'run', runs{iRun});