Merge pull request #425 from CerenB/cer-bidsConcatFix

bidsConcatBetaTmaps. fix

Author: Remi-Gau

src/workflows/bidsConcatBetaTmaps.m

@@ -9,9 +9,9 @@ function bidsConcatBetaTmaps(opt, funcFWHM, deleteIndBeta, deleteIndTmaps)
   % :param funcFWHM: smoothing (FWHM) applied to the the normalized EPI
   % :type funcFWHM: (scalar)
   % :param deleteIndBeta: decide to delete beta-maps
-  % :type funcFWHM: (boolean)
+  % :type deleteIndBeta: (boolean)
   % :param deleteIndTmaps: decide to delete t-maps
-  % :type funcFWHM: (boolean)
+  % :type deleteIndTmaps: (boolean)
   %
   % When concatenating betamaps:
   %
@@ -22,12 +22,21 @@ function bidsConcatBetaTmaps(opt, funcFWHM, deleteIndBeta, deleteIndTmaps)
   %
   % (C) Copyright 2019 CPP_SPM developers
 
-  if nargin < 3
-    deleteIndBeta = 1;
-    deleteIndTmaps = 1;
+  [~, opt] = setUpWorkflow(opt, 'merge beta images and t-maps');
+
+  % TODO temporary check: will be removed on the dev branch
+  if ~isfield(opt, 'dryRun')
+    opt.dryRun = false;
   end
 
-  [~, opt] = setUpWorkflow(opt, 'merge beta images and t-maps');
+  if nargin < 3
+    deleteIndBeta = true;
+    deleteIndTmaps = true;
+  end
+  if opt.dryRun
+    deleteIndBeta = false;
+    deleteIndTmaps = false;
+  end
 
   RT = 0;
 
@@ -41,21 +50,25 @@ function bidsConcatBetaTmaps(opt, funcFWHM, deleteIndBeta, deleteIndTmaps)
 
     load(fullfile(ffxDir, 'SPM.mat'));
 
-    contrasts = specifyContrasts(ffxDir, opt.taskName, opt);
+    model = spm_jsonread(opt.model.file);
+
+    contrasts = specifyContrasts(SPM, opt.taskName, model);
 
     beta_maps = cell(length(contrasts), 1);
     t_maps = cell(length(contrasts), 1);
 
     % path to beta and t-map files.
+    fprintf(1, '\nConcatenating the following contrasts:');
     for iContrast = 1:length(beta_maps)
 
+      fprintf(1, '\n\t%s', contrasts(iContrast).name);
       betasIndices = find(contrasts(iContrast).C);
 
       if numel(betasIndices) > 1
         error('Supposed to concatenate one beta image per contrast.');
       end
 
-      % for this beta iamge we identify
+      % for this beta image we identify
       % - which run it came from
       % - the exact condition name stored in the SPM.mat
       % so they can be saved in a tsv for for "label" and "fold" for MVPA
@@ -70,7 +83,6 @@ function bidsConcatBetaTmaps(opt, funcFWHM, deleteIndBeta, deleteIndTmaps)
       fileName = validationInputFile(ffxDir, fileName);
       beta_maps{iContrast, 1} = [fileName, ',1'];
 
-      % while the contrastes (t-maps) are not from the index. They were created
       fileName = sprintf('spmT_%04d.nii', iContrast);
       fileName = validationInputFile(ffxDir, fileName);
       t_maps{iContrast, 1} = [fileName, ',1'];
@@ -81,15 +93,17 @@ function bidsConcatBetaTmaps(opt, funcFWHM, deleteIndBeta, deleteIndTmaps)
     nameStructure = struct( ...
                            'ext', '.tsv', ...
                            'suffix', 'labelfold', ...
-                           'entities' struct('sub', subLabel, ...
-                                             'task', opt.taskName, ...
-                                             'space', opt.space));
+                           'entities', struct('sub', subLabel, ...
+                                              'task', opt.taskName, ...
+                                              'space', opt.space));
+    nameStructure.use_schema = false;
     tsvName = bids.create_filename(nameStructure);
 
     tsvContent = struct('folds', runs, 'labels', {conditions});
 
     spm_save(fullfile(ffxDir, tsvName), tsvContent);
 
+    % TODO in the dev branch make those output filenames "BIDS derivatives" compliant
     % beta maps
     outputName = ['4D_beta_', num2str(funcFWHM), '.nii'];
 
@@ -101,7 +115,10 @@ function bidsConcatBetaTmaps(opt, funcFWHM, deleteIndBeta, deleteIndTmaps)
 
     matlabbatch = setBatch3Dto4D(matlabbatch, t_maps, RT, outputName);
 
-    saveAndRunWorkflow(matlabbatch, 'concat_betaImg_tMaps', opt, subLabel);
+    % TODO temporary: remove on dev branch
+    if ~opt.dryRun
+      saveAndRunWorkflow(matlabbatch, 'concat_betaImg_tMaps', opt, subLabel);
+    end
 
     removeBetaImgTmaps(t_maps, deleteIndBeta, deleteIndTmaps, ffxDir);
 
@@ -136,6 +153,7 @@ function removeBetaImgTmaps(t_maps, deleteIndBeta, deleteIndTmaps, ffxDir)
       delete(t_maps{iTmap}(1:end - 2));
     end
     fprintf('Done. \n\n\n ');
+
   end
 
 end

tests/createDummyDataSet.sh

@@ -110,7 +110,14 @@ do
 		touch $ThisDir/mask.nii
 
 		touch $ThisDir/spmT_0001.nii
-		touch $ThisDir/spmT_0002.nii		
+		touch $ThisDir/spmT_0002.nii	
+		touch $ThisDir/spmT_0003.nii
+		touch $ThisDir/spmT_0004.nii		
+
+		touch $ThisDir/beta_0001.nii
+		touch $ThisDir/beta_0002.nii
+		touch $ThisDir/beta_0003.nii
+		touch $ThisDir/beta_0004.nii			
 
 		touch $ThisDir/con_0001.nii
 		touch $ThisDir/con_0002.nii

tests/dummyData/models/model-vismotionMVPA_smdl.json

@@ -0,0 +1,16 @@
+{
+  "Name": "vismotion",
+  "Description": "This model only has simple contrasts for MVPA",
+  "Input": {
+    "task": "vismotion"
+  },
+  "Steps": [
+    {
+      "Level": "subject",
+      "AutoContrasts": [
+        "trial_type.VisMot",
+        "trial_type.VisStat"
+      ]
+    }
+  ]
+}

tests/test_bidsConcatBetaTmaps.m

@@ -0,0 +1,33 @@
+function test_suite = test_bidsConcatBetaTmaps %#ok<*STOUT>
+  %
+  % (C) Copyright 2019 CPP_SPM developers
+  try % assignment of 'localfunctions' is necessary in Matlab >= 2016
+    test_functions = localfunctions(); %#ok<*NASGU>
+  catch % no problem; early Matlab versions can use initTestSuite fine
+  end
+  initTestSuite;
+end
+
+function test_bidsConcatBetaTmapsBasic()
+
+  subLabel = '01';
+  funcFWHM = 6;
+
+  opt = setOptions('vismotion', subLabel);
+  opt.dryRun = true;
+
+  opt.model.file = spm_file(opt.model.file, 'filename', 'model-vismotionMVPA_smdl.json');
+
+  bidsConcatBetaTmaps(opt, funcFWHM);
+
+  ffxDir = getFFXdir(subLabel, funcFWHM, opt);
+  content = bids.util.tsvread(fullfile(ffxDir, ...
+                                       'sub-01_task-vismotion_space-MNI_labelfold.tsv'));
+
+  expectedContent = struct('labels', {{'VisMot*bf(1)'; 'VisStat*bf(1)'}}, 'folds', [1; 1]);
+
+  assertEqual(content, expectedContent);
+
+  delete(fullfile(ffxDir, 'sub-01_task-vismotion_space-MNI_labelfold.tsv'));
+
+end

version.txt

@@ -1 +1 @@
-v1.1.2
+v1.1.3