[INFRA] add integration test roi based glm

.github/workflows/run_tests_matlab.yml

@@ -46,6 +46,14 @@ jobs:
       - name: Install validators
         run: make install
 
+      - name: Get moae fmriprep data from OSF
+        run: |
+          mkdir -p demos/MoAE/inputs/
+          cd demos/MoAE/inputs/
+          wget https://osf.io/vufjs/download
+          unzip download
+          mv moae_fmriprep fmriprep
+
       - name: Install SPM
         run: |
           git clone https://github.com/spm/spm12.git --depth 1

.github/workflows/run_tests_octave.yml

@@ -56,6 +56,14 @@ jobs:
     - name: Install validators
       run: make install
 
+    - name: Get moae fmriprep data from OSF
+      run: |
+        mkdir -p demos/MoAE/inputs/
+        cd demos/MoAE/inputs/
+        wget https://osf.io/vufjs/download
+        unzip download
+        mv moae_fmriprep fmriprep
+
     - name: Install SPM
       run: |
         git clone https://github.com/spm/spm12.git --depth 1

README.md

@@ -12,9 +12,10 @@
   [![codecov](https://codecov.io/gh/cpp-lln-lab/bidspm/branch/main/graph/badge.svg?token=PMQYH0DIPX)](https://codecov.io/gh/cpp-lln-lab/bidspm)
   [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.3554331.svg)](https://doi.org/10.5281/zenodo.3554331)
   [![GitHub last commit](https://img.shields.io/github/last-commit/cpp-lln-lab/bidspm)](https://github.com/cpp-lln-lab/bidspm.git)
-  [![HitCount](https://hits.dwyl.com/cpp-lln-lab/bidspm.svg?style=flat-square&show=unique)](http://hits.dwyl.com/cpp-lln-lab/bidspm)
   [![All Contributors](https://img.shields.io/badge/all_contributors-14-orange.svg?style=flat-square)](https://github.com/cpp-lln-lab/bidspm#contributors)
 
+<!-- [![HitCount](https://hits.dwyl.com/cpp-lln-lab/bidspm.svg?style=flat-square&show=unique)](http://hits.dwyl.com/cpp-lln-lab/bidspm) -->
+
 
 # bidspm
 

demos/face_repetition/face_rep_03_roi_analysis.m

@@ -39,6 +39,7 @@
 preproc_dir = fullfile(opt.dir.derivatives, 'bidspm-preproc');
 
 opt.bidsFilterFile.roi.space = 'individual';
+opt.bidsFilterFile.roi.label = 'V1d';
 
 model_file = fullfile(this_dir, 'models', 'model-faceRepetition_smdl.json');
 
@@ -52,3 +53,19 @@
        'options', opt, ...
        'fwhm', 0, ...
        'skip_validation', skip_validation);
+
+opt.bidsFilterFile.roi.space = 'individual';
+opt.bidsFilterFile.roi.label = 'V1v';
+
+return
+
+bidspm(bids_dir, output_dir, 'subject', ...
+       'action', 'stats', ...
+       'participant_label', {'01'}, ...
+       'preproc_dir', preproc_dir, ...
+       'model_file', model_file, ...
+       'roi_based', true, ...
+       'space', {'individual'}, ...
+       'options', opt, ...
+       'fwhm', 0, ...
+       'skip_validation', skip_validation);

src/QA/plotRoiTimeCourse.m

@@ -43,6 +43,11 @@
 
   tsvFile = args.Results.tsvFile;
   timeCourse = bids.util.tsvread(tsvFile);
+  if ~isstruct(timeCourse)
+    tmp = struct('this_condition', timeCourse);
+    timeCourse = tmp;
+    clear tmp;
+  end
   conditionNames = fieldnames(timeCourse);
 
   visible = 'off';

src/bids/getROIs.m

@@ -71,9 +71,8 @@
       errorHandling(mfilename(), 'noSubject', msg, false, opt.verbosity > 0);
     end
 
-    filter = struct('sub', regexify(subLabel), ...
-                    'space', space, ...
-                    'suffix', 'mask');
+    filter = opt.bidsFilterFile.roi;
+    filter.sub = regexify(subLabel);
 
     if ~isempty(roiNames)
       if iscell(roiNames)

src/workflows/roi/bidsRoiBasedGLM.m

@@ -154,7 +154,7 @@
 
       timeCourse = {};
       dt = [];
-      percentSignalChange = [];
+      percentSignalChange = struct('absMax', [], 'max', []);
 
       for iCon = 1:numel(eventSpec)
 

tests/tests_workflows/stats/test_bidsRoiBasedGLM.m

@@ -17,3 +17,60 @@ function test_bidsRoiBasedGLM_checks()
   assertExceptionThrown(@() bidsRoiBasedGLM(opt), 'bidsRoiBasedGLM:roiBasedAnalysis');
 
 end
+
+function test_bidsRoiBasedGLM_run()
+  %
+  % integration test:
+  %  - also makes sure that previous results are not deleted
+  %
+
+  opt = setOptions('MoAE-fmriprep', '01');
+
+  opt.query.space = opt.space;
+
+  opt.dir.input = opt.dir.fmriprep;
+
+  opt.versbosity = 0;
+
+  bidsCopyInputFolder(opt, 'unzip', true);
+
+  opt.model.file = fullfile(getMoaeDir(), ...
+                            'models', ...
+                            'model-MoAE_smdl.json');
+
+  opt.model.bm = BidsModel('file', opt.model.file);
+  opt.model.bm.Input.space = opt.space;
+
+  opt.glm.roibased.do = true;
+  opt.dryRun = false;
+  opt.fwhm.func = 0;
+
+  bidsFFX('specify', opt);
+
+  % rmdir(fullfile(pwd, 'options'), 's');
+
+  opt.dir.roi = fullfile(opt.dir.derivatives, 'bidspm-roi');
+
+  opt.roi.atlas = 'wang';
+  opt.roi.name = {'V1v', 'V1d'};
+  opt.roi.space = opt.space;
+
+  opt.bidsFilterFile.roi.space = 'MNI';
+
+  bidsCreateROI(opt);
+
+  opt.roi.name = {'.*V1v'};
+
+  bidsRoiBasedGLM(opt);
+
+  opt.roi.name = {'.*V1d'};
+
+  bidsRoiBasedGLM(opt);
+
+  timecourseFiles = spm_select('FPListRec', opt.dir.stats, '^.*timecourse.tsv$');
+
+  assertEqual(size(timecourseFiles, 1), 4);
+
+  delete('skipped_roi_*.tsv');
+
+end

tests/utils/setOptions.m

@@ -50,6 +50,17 @@
     opt.results(1).name = 'listening';
     opt.results(2).name = 'listening_inf_baseline';
 
+  elseif strcmp(task, 'MoAE-fmriprep')
+
+    task = {'auditory'};
+
+    opt.space = {'MNI152NLin6Asym'};
+
+    opt.dir.raw = fullfile(getMoaeDir(), 'inputs', 'raw');
+    opt.dir.fmriprep = fullfile(getMoaeDir(), 'inputs', 'fmriprep');
+    opt.dir.derivatives = fullfile(getMoaeDir(), 'outputs', 'derivatives');
+    opt.dir.stats = fullfile(opt.dir.derivatives, 'bidspm-stats');
+
   elseif strcmp(task, 'MoAE-preproc')
 
     task = {'auditory'};