Merge pull request #530 from Remi-Gau/glm_checks

[ENH] add checks and more verbose ouput for subject level GLM specification

Author: Remi-Gau

demos/face_repetition/face_rep_func.m

@@ -8,8 +8,6 @@
 % instead of AR(1), motion regressors added)
 %
 % TODO
-% - add derivatives to the model
-% - compute the relevant contrasts
 % - compute motion effect
 % - run parametric model
 %
@@ -46,7 +44,7 @@
 bidsResliceTpmToFunc(opt);
 
 % DEBUG
-% functionalQA(opt);
+functionalQA(opt);
 
 bidsSmoothing(FWHM, opt);
 

src/batches/setBatchSubjectLevelGLMSpec.m

@@ -100,6 +100,10 @@
 
     for iRun = 1:nbRuns
 
+      if ~strcmp(runs{iRun}, '')
+        fprintf(1, 'Processing run %s\n', runs{iRun});
+      end
+
       % get functional files
       [fullpathBoldFileName, prefix]  = ...
           getBoldFilenameForFFX(BIDS, opt, subLabel, funcFWHM, iSes, iRun);

src/subject_level/convertOnsetTsvToMat.m

@@ -26,9 +26,29 @@
   tsvFile = validationInputFile(pth, [file, ext]);
 
   % Read the tsv file
-  fprintf('reading the tsv file : %s \n', tsvFile);
+  fprintf(' Reading the tsv file : %s \n', tsvFile);
   t = spm_load(tsvFile);
 
+  if ~all(isnumeric(t.onset))
+
+    errorStruct.identifier = 'convertOnsetTsvToMat:onsetsNotNumeric';
+    errorStruct.message = sprintf('%s\n%s', ...
+                                  'Onset column contains non numeric values in this file:', ...
+                                  tsvFile);
+    error(errorStruct);
+
+  end
+
+  if ~all(isnumeric(t.duration))
+
+    errorStruct.identifier = 'convertOnsetTsvToMat:durationsNotNumeric';
+    errorStruct.message = sprintf('%s\n%s', ...
+                                  'Duration column contains non numeric values in this file:', ...
+                                  tsvFile);
+    error(errorStruct);
+
+  end
+
   if ~isfield(t, 'trial_type')
 
     errorStruct.identifier = 'convertOnsetTsvToMat:noTrialType';
@@ -76,13 +96,17 @@
       % each line in the tsv files
       idx = find(strcmp(conditionName, conds));
 
+      fprintf('  Condition %s: %i trials found.\n', conditionName, numel(idx));
+
       if ~isempty(idx)
         % Get the onset and duration of each condition
         names{1, end + 1} = conditionName;
         onsets{1, end + 1} = t.onset(idx)'; %#ok<*AGROW,*NASGU>
         durations{1, end + 1} = t.duration(idx)';
+
       else
         warning('No trial found for trial type %s in \n%s', conditionName, tsvFile);
+
       end
 
     end