[WIP] improve roi based analysis (#1086)

* try using mni rois in subject folders

* deal with unsanitize cofounds

* clean

* fixes

* do not delete GLM folder content before running roi based glm

* fix tests

Author: Remi-Gau

.github/workflows/run_tests_cli.yml

@@ -6,9 +6,9 @@ on:
   push:
     branches:
     - main
-    - dev
   pull_request:
-    branches: ['*']
+    branches:
+    - main
 
 jobs:
   tests_cli:

.github/workflows/tests.yml

@@ -21,9 +21,9 @@ concurrency:
 
 on:
   push:
-    branches: ['*']
+    branches: [main]
   pull_request:
-    branches: ['*']
+    branches: [main]
   schedule:
   - cron: 0 0 1,15 * *
 

.github/workflows/tests_octave.yml

@@ -24,9 +24,9 @@ concurrency:
 
 on:
   push:
-    branches: ['*']
+    branches: [main]
   pull_request:
-    branches: ['*']
+    branches: [main]
   schedule:
   - cron: 0 0 1,15 * *
 

.github/workflows/tests_windows.yml

@@ -21,9 +21,9 @@ concurrency:
 
 on:
   push:
-    branches: ['*']
+    branches: [main]
   pull_request:
-    branches: ['*']
+    branches: [main]
   schedule:
   - cron: 0 0 1,15 * *
 

.github/workflows/validation.yml

@@ -3,9 +3,9 @@ name: validation
 
 on:
   push:
-    branches: ['*']
+    branches: [main]
   pull_request:
-    branches: ['*']
+    branches: [main]
 
 concurrency:
   group: ${{ github.workflow }}-${{ github.ref }}

src/batches/stats/setBatchSubjectLevelGLMSpec.m

@@ -72,9 +72,19 @@
   % Create ffxDir if it does not exist
   % If it exists, issue a warning that it has been overwritten
   ffxDir = getFFXdir(subLabel, opt);
-  overwriteDir(ffxDir, opt);
+  if ~opt.glm.roibased.do
+    overwriteDir(ffxDir, opt);
+  else
+    if exist(fullfile(ffxDir, 'SPM.mat'), 'file')
+      delete(fullfile(ffxDir, 'SPM.mat'));
+    else
+      spm_mkdir(ffxDir);
+    end
+  end
+
   msg = sprintf(' output dir:\n\t%s', pathToPrint(ffxDir));
   logger('INFO', msg, 'options', opt, 'filename', mfilename());
+
   fmri_spec.dir = {ffxDir};
 
   fmri_spec.fact = struct('name', {}, 'levels', {});
@@ -188,7 +198,7 @@
   filter = fileFilterForBold(opt, subLabel);
 
   [name, version] = generatedBy(BIDS);
-  tokens = strsplit(version);
+  tokens = strsplit(version, '.');
   % TODO implement differently for fmriprep >=20.2.4
   % https://fmriprep.org/en/stable/changes.html#october-04-2021
   skip = opt.stc.skip || ...

src/bids/getROIs.m

@@ -1,9 +1,11 @@
 function [roiList, roiFolder] = getROIs(varargin)
   %
-  % Get the rois from :
+  % Get the rois depending on value of "opt.bidsFilterFile.roi.space":
   %
-  % - the group folder when running analysis in MNI space
-  % - the ``sub-*/roi/sub-subLabel`` folder when in individual space
+  % - the group folder for space: "MNI" or "IXI549Space"
+  % - the ``sub-*/roi/sub-subLabel`` folder:
+  %     - when in individual space ('T1w')
+  %     - or another MNI space
   %
   % USAGE::
   %
@@ -64,22 +66,31 @@
 
   else
 
-    % we expect ROI files to have BIDS valid names
-    BIDS_ROI = bids.layout(opt.dir.roi, 'use_schema', false);
-
     if strcmp(subLabel, '')
-      msg = sprintf('Provide a subject label amongst those:\n%s\n\n', ...
-                    bids.internal.create_unordered_list(bids.query(BIDS_ROI, 'subjects')));
+      msg = sprintf('Provide a subject label.');
       id = 'noSubject';
       logger('ERROR', msg, 'filename', mfilename(), 'id', id);
     end
 
+    % we expect ROI files to have BIDS valid names
+    clear filter;
+    filter.sub = {subLabel};
+    filter.modality = {'roi'};
+    BIDS_ROI = bids.layout(opt.dir.roi, ...
+                           'use_schema', false, ...
+                           'filter', filter, ...
+                           'verbose', opt.verbosity > 1, ...
+                           'index_dependencies', false);
+
+    clear filter;
     filter = opt.bidsFilterFile.roi;
     filter.sub = regexify(subLabel);
 
     if ~isempty(roiNames)
       if iscell(roiNames)
-        if ~(numel(roiNames) == 1 && ~strcmp(roiNames{1}, ''))
+        if numel(roiNames) > 1
+          filter.label = ['(' strjoin(opt.roi.name, '|') '){1}'];
+        elseif ~(numel(roiNames) == 1 && ~strcmp(roiNames{1}, ''))
         else
           filter.label = ['(' strjoin(opt.roi.name, '|') '){1}'];
         end
@@ -119,7 +130,8 @@
     space = {space};
   end
 
-  if any(~cellfun('isempty', regexp(space, 'MNI'))) || ismember('IXI549Space', space)
+  if ~strcmp(space{1}, 'MNI') && ~cellfun('isempty', regexp(space, 'MNI'))
+  elseif ismember(space, {'IXI549Space', 'MNI'})
     space = 'MNI';
   end
 

src/infra/checkDependencies.m

@@ -28,7 +28,7 @@ function checkDependencies(opt)
   msg = sprintf(' Using %s %s', a, b);
   logger('INFO', msg, 'options', opt, 'filename', mfilename());
 
-  if ~strcmp(a, SPM_main) || str2num(b) < 7219
+  if ~strcmp(a, SPM_main) || str2num(b) < SPM_sub
     str = sprintf('%s %s %s.\n%s', ...
                   'The current version SPM version is less than', SPM_main, SPM_sub, ...
                   'Update with: spm_update update');

src/stats/subject_level/createAndReturnCounfoundMatFile.m

@@ -47,6 +47,7 @@
   content = bids.transformers(transformers, content);
 
   [names, R] = createConfounds(content, designMatrix, opt.glm.maxNbVols); %#ok<*ASGLU>
+  [names, R] = sanitizeConfounds(names, R);
 
   % save the confounds as a matfile
   bf = bids.File(tsvFile);

src/stats/subject_level/createConfounds.m

@@ -95,7 +95,7 @@
 
     tmp(isnan(tmp)) = 0;
 
-    R(:, col) = tmp;
+    R(:, col) = tmp; %#ok<*AGROW>
 
   end