[ENH] add csf tpm to lesion detection and update submodules

.github/dependabot.yml

@@ -2,7 +2,12 @@
 # https://docs.github.com/en/code-security/dependabot/dependabot-version-updates/configuration-options-for-the-dependabot.yml-file
 version: 2
 updates:
-  - package-ecosystem: "github-actions"
-    directory: "/"
+  - package-ecosystem: 'github-actions'
+    directory: '/'
     schedule:
-      interval: "weekly"
+      interval: 'monthly'
+
+  - package-ecosystem: 'gitsubmodule'
+    directory: '/'
+    schedule:
+      interval: 'monthly'

.github/workflows/run_system_tests_matlab.yml

@@ -66,7 +66,7 @@ jobs:
       - name: Clone bidspm
         uses: actions/checkout@v3
         with:
-          submodules: true
+          submodules: recursive
           fetch-depth: 0
 
       - name: Get moae fmriprep data from OSF

.github/workflows/run_system_tests_octave.yml

@@ -65,7 +65,7 @@ jobs:
     - name: Clone bidspm
       uses: actions/checkout@v3
       with:
-        submodules: true
+        submodules: recursive
         fetch-depth: 0
 
     - name: Get moae fmriprep data from OSF

.github/workflows/run_tests_matlab.yml

@@ -32,7 +32,7 @@ jobs:
       - name: Clone bidspm
         uses: actions/checkout@v3
         with:
-          submodules: true
+          submodules: recursive
           fetch-depth: 0
 
       - name: Install SPM

.github/workflows/run_tests_octave.yml

@@ -42,7 +42,7 @@ jobs:
     - name: Clone bidspm
       uses: actions/checkout@v3
       with:
-        submodules: true
+        submodules: recursive
         fetch-depth: 0
 
     - name: Install SPM

.gitignore

@@ -1,5 +1,7 @@
 *_report.md
 
+src/batches/cfg
+
 # General
 .DS_Store
 

.vscode/settings.json

@@ -5,5 +5,5 @@
         "url": "https://bids-standard.github.io/stats-models/BIDSStatsModel.json"
         }
     ],
-    "esbonio.sphinx.confDir": ""
+    "files.associations": {"*.m": "matlab"}
 }

bidspm.m

@@ -301,6 +301,7 @@ function preprocess(args)
   end
   bidsSpatialPrepro(opt);
   if opt.fwhm.func > 0 && ~opt.anatOnly
+    opt.query.desc = 'preproc';
     bidsSmoothing(opt);
   end
 

scripts/reslice_mid_brain.m

@@ -16,7 +16,7 @@
 
   roiFiles = bids.query(BIDSroi, 'data', 'sub', subLabel, 'label', 'V1d', 'hemi', 'R');
 
-  referenceImg bids.query(BIDS, 'data', 'space', 'individual', 'desc', 'mean', 'suffix', 'bold');
+  referenceImg = bids.query(BIDS, 'data', 'space', 'individual', 'desc', 'mean', 'suffix', 'bold');
 
   printProcessingSubject(iSub, subLabel);
 

src/IO/unzipAndReturnsFullpathName.m

@@ -27,9 +27,13 @@
     errorHandling(mfilename(), 'emptyInput', msg, false, true);
   end
 
+  if ~iscell(fullpathName)
+    fullpathName = cellstr(fullpathName);
+  end
+
   for iFile = 1:size(fullpathName, 1)
 
-    [directory, filename, ext] = spm_fileparts(fullpathName(iFile, :));
+    [directory, filename, ext] = spm_fileparts(fullpathName{iFile});
 
     if strcmp(ext, '.gz') && ~opt.dryRun
 

src/batches/preproc/setBatchSmoothing.m

@@ -31,6 +31,10 @@
 
   % (C) Copyright 2019 bidspm developers
 
+  if isempty(images)
+    return
+  end
+
   printBatchName('smoothing images', opt);
 
   matlabbatch{end + 1}.spm.spatial.smooth.data = images;

src/batches/preproc/setBatchSmoothingAnat.m

@@ -0,0 +1,87 @@
+function matlabbatch = setBatchSmoothingAnat(matlabbatch, BIDS, opt, subLabel)
+  %
+  % Creates a batch to smooth the anat files of a subject
+  %
+  % USAGE::
+  %
+  %   matlabbatch = setBatchSmoothingAnat(matlabbatch, BIDS, opt, subLabel)
+  %
+  % :param matlabbatch:
+  % :type  matlabbatch: structure
+  %
+  % :type  BIDS: structure
+  % :param BIDS: dataset layout.
+  %
+  % :param opt: Options chosen for the analysis.
+  %             See also: ``checkOptions()`` and ``loadAndCheckOptions()``.
+  % :type  opt: structure
+  %
+  % :param subLabel:
+  % :type  subLabel:
+  %
+  % :returns: - :matlabbatch: (structure)
+  %
+  %
+  % See also: bidsSmoothing, setBatchSmoothing
+  %
+
+  % (C) Copyright 2022 bidspm developers
+
+  printBatchName('smoothing anat images', opt);
+
+  opt.query.space = opt.space;
+  opt = mniToIxi(opt);
+
+  % identify sessions for this subject
+  [sessions, nbSessions] = getInfo(BIDS, subLabel, opt, 'Sessions');
+
+  allFiles = [];
+
+  for iSes = 1:nbSessions
+
+    [runs, nbRuns] = getInfo(BIDS, subLabel, opt, 'Runs', sessions{iSes});
+
+    for iRun = 1:nbRuns
+
+      opt.bidsFilterFile.t1w.ses = sessions{iSes};
+      opt.bidsFilterFile.t1w.run = runs{iRun};
+
+      fieldsToTransfer = {'space', 'desc', 'label', 'res'};
+      for i = 1:numel(fieldsToTransfer)
+        field = fieldsToTransfer{i};
+        if isfield(opt.query, field)
+          opt.bidsFilterFile.t1w.(field) = opt.query.(field);
+        end
+      end
+
+      tolerant = true;
+      nbImgToReturn = Inf;
+      [anatImage, anatDataDir] = getAnatFilename(BIDS, opt, subLabel, nbImgToReturn, tolerant);
+
+      if isempty(anatImage)
+        break
+      end
+
+      anatImage = cellstr(anatImage);
+      anatDataDir = cellstr(anatDataDir);
+
+      for iFile = 1:numel(anatImage)
+        files{iFile, 1} = validationInputFile(anatDataDir{iFile}, ...
+                                              anatImage{iFile}); %#ok<*AGROW>
+      end
+
+      % add the files to list
+      allFilesTemp = cellstr(char(files));
+      allFiles = [allFiles; allFilesTemp];
+
+    end
+  end
+
+  % Prefix = FWHM
+  matlabbatch = setBatchSmoothing(matlabbatch, ...
+                                  opt, ...
+                                  allFiles, ...
+                                  opt.fwhm.func, ...
+                                  [spm_get_defaults('smooth.prefix'), num2str(opt.fwhm.func)]);
+
+end

src/batches/preproc/setBatchSmoothingFunc.m

@@ -1,6 +1,6 @@
 function matlabbatch = setBatchSmoothingFunc(matlabbatch, BIDS, opt, subLabel)
   %
-  % Short description of what the function does goes here.
+  % Creates a batch to smooth the bold files of a subject
   %
   % USAGE::
   %
@@ -17,8 +17,8 @@
   %             See also: ``checkOptions()`` and ``loadAndCheckOptions()``.
   % :type  opt: structure
   %
-  % :param subLabel:
-  % :type  subLabel:
+  % :param subLabel: subject label
+  % :type  subLabel: char
   %
   % :returns: - :matlabbatch: (structure)
   %
@@ -30,7 +30,11 @@
 
   printBatchName('smoothing functional images', opt);
 
-  opt.query.desc = 'preproc';
+  desc = 'preproc';
+  if isfield(opt.query, 'desc') && ~isempty(opt.query.desc)
+    desc = opt.query.desc;
+  end
+  opt.query.desc = desc;
   opt.query.space = opt.space;
   opt = mniToIxi(opt);
 
@@ -45,8 +49,7 @@
 
     for iRun = 1:nbRuns
 
-      [fileName, subFuncDataDir] = getBoldFilename( ...
-                                                   BIDS, ...
+      [fileName, subFuncDataDir] = getBoldFilename(BIDS, ...
                                                    subLabel, sessions{iSes}, runs{iRun}, opt);
 
       % TODO remove this extra check