[FIX] Missing trial_types are not added to a model specification / fixes #197

src/subject_level/convertOnsetTsvToMat.m

@@ -2,27 +2,23 @@
 
 function fullpathOnsetFileName = convertOnsetTsvToMat(opt, tsvFile)
   %
-  % Short description of what the function does goes here.
+  % Converts an  events.tsv file to an onset file suitable for SPM subject level
+  % analysis.
+  % The scripts extracts the trial type, onsets, and durations, and
+  % converts them and stores them in a mat file.
   %
   % USAGE::
   %
-  %   [argout1, argout2] = templateFunction(argin1, [argin2 == default,] [argin3])
+  %   fullpathOnsetFileName = convertOnsetTsvToMat(opt, tsvFile)
   %
-  % :param argin1: (dimension) obligatory argument. Lorem ipsum dolor sit amet,
-  %                consectetur adipiscing elit. Ut congue nec est ac lacinia.
-  % :type argin1: type
-  % :param argin2: optional argument and its default value. And some of the
-  %               options can be shown in litteral like ``this`` or ``that``.
-  % :type argin2: string
-  % :param argin3: (dimension) optional argument
+  % :param opt:
+  % :type opt: structure
+  % :param tsvFile:
+  % :type tsvFile: string
   %
-  % :returns: - :argout1: (type) (dimension)
-  %           - :argout2: (type) (dimension)
+  % :returns: - :fullpathOnsetFileName: (string) name of the output `.mat` file.
   %
-  % Converts a tsv file to an onset file suitable for SPM ffx analysis
-  % The scripts extracts the conditions' names, onsets, and durations, and
-  % converts them to TRs (time unit) and saves the onset file to be used for
-  % SPM
+
   %
   [pth, file, ext] = spm_fileparts(tsvFile);
   tsvFile = validationInputFile(pth, [file, ext]);
@@ -59,6 +55,11 @@
 
   isTrialType = strfind(step.Model.X, 'trial_type.');
 
+  % create empty cell to be filled in according to the conditions present in each run
+  names = {};
+  onsets = {};
+  durations = {};
+
   % for each condition
   for iCond = 1:numel(isTrialType)
 
@@ -72,10 +73,14 @@
       % each line in the tsv files
       idx = find(strcmp(conditionName, conds));
 
-      % Get the onset and duration of each condition
-      names{1, iCond} = conditionName;
-      onsets{1, iCond} = t.onset(idx)'; %#ok<*AGROW,*NASGU>
-      durations{1, iCond} = t.duration(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
   end

src/subject_level/createAndReturnOnsetFile.m

@@ -2,28 +2,27 @@
 
 function onsetFileName = createAndReturnOnsetFile(opt, subID, tsvFile, funcFWHM)
   %
-  % Short description of what the function does goes here.
+  % For a given events.tsv file it creates a .mat file that can directly be used
+  % for the GLM specification of a subject level model. The file is moved
+  % directly into the folder of the GLM.
   %
   % USAGE::
   %
-  %   [argout1, argout2] = templateFunction(argin1, [argin2 == default,] [argin3])
+  %   onsetFileName = createAndReturnOnsetFile(opt, subID, tsvFile, funcFWHM)
   %
-  % :param argin1: (dimension) obligatory argument. Lorem ipsum dolor sit amet,
-  %                consectetur adipiscing elit. Ut congue nec est ac lacinia.
-  % :type argin1: type
-  % :param argin2: optional argument and its default value. And some of the
-  %               options can be shown in litteral like ``this`` or ``that``.
-  % :type argin2: string
-  % :param argin3: (dimension) optional argument
+  % :param opt:
+  % :type opt: structure
+  % :param subID:
+  % :type subID: string
+  % :param tsvFile: fullpath name of the tsv file.
+  % :type tsvFile: string
+  % :param funcFWHM: size of the FWHM gaussian kernel used to the subject level
+  %                  GLM. Necessary for the GLM directory.
+  % :type funcFWHM: float
   %
-  % :returns: - :argout1: (type) (dimension)
-  %           - :argout2: (type) (dimension)
+  % :returns: - :onsetFileName: (string) fullpath name of the file created.
+  %                             Removes any prefix.
   %
-  % onsetFileName = createAndReturnOnsetFile(opt, boldFileName, prefix, isMVPA)
-  %
-  % gets the tsv onset file based on the bold file name (removes any prefix)
-  %
-  % convert the tsv files to a mat file to be used by SPM
 
   onsetFileName = convertOnsetTsvToMat(opt, tsvFile);
 

tests/dummyData/models/model-vislocalizer_smdl.json

@@ -9,7 +9,7 @@
       "Level": "run",
       "Model": {
         "X": [
-          "trial_type.VisMot", "trial_type.VisStat",
+          "trial_type.VisMot", "trial_type.VisStat", "trial_type.missing_condition",
           "trans_x", "trans_y", "trans_z", "rot_x", "rot_y", "rot_z"
         ]
       },