[FIX] exclude late events (#1060)

* exclude late onsets

* update changelog

Author: Remi-Gau

CHANGELOG.md

@@ -57,6 +57,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Fixed
 
+* [FIX] Exclude from GLM specification events with onsets longer than the run duration (#1060) @Remi-Gau
 * [FIX] remove dummies from preproc dataset and not raw dataset when using CLI (#1057) @Remi-Gau
 * [FIX] skip smoothing when running bidspm prepoc in dryRun (#1054) @Remi-Gau
 * [FIX] handle phase entity in filename (#1034) @Remi-Gau

src/batches/stats/setBatchSubjectLevelGLMSpec.m

@@ -110,11 +110,15 @@
 
         spmSess(spmSessCounter).scans = getBoldFilenameForFFX(BIDS, opt, subLabel, iSes, iRun);
 
+        runDuration = getRunDuration(opt, spmSess(spmSessCounter).scans, TR);
+
+        spec = struct('sub', subLabel, ...
+                      'ses', sessions{iSes}, ...
+                      'task', opt.taskName{iTask}, ...
+                      'run', runs{iRun});
         onsetFilename = returnOnsetsFile(BIDS, opt, ...
-                                         subLabel, ...
-                                         sessions{iSes}, ...
-                                         opt.taskName{iTask}, ...
-                                         runs{iRun});
+                                         spec, ...
+                                         runDuration);
         spmSess(spmSessCounter).onsetsFile = onsetFilename;
 
         % get confounds
@@ -234,20 +238,49 @@
 
 end
 
-function fmriSpec = setScans(opt, fullpathBoldFilename, fmriSpec, spmSessCounter)
+function runDuration = getRunDuration(opt, fullpathBoldFilename, TR)
 
-  if opt.model.designOnly
+  nvVols = getNbVols(opt, fullpathBoldFilename);
+  runDuration = nvVols * TR;
+
+end
 
+function nbVols = getNbVols(opt, fullpathBoldFilename)
+  if opt.glm.maxNbVols == Inf && isempty(opt.funcVolToSelect)
     try
       hdr = spm_vol(fullpathBoldFilename);
+      nbVols = numel(hdr);
     catch
+      nbVols = nan;
+    end
+    return
+  end
+
+  if opt.glm.maxNbVols ~= Inf
+    nbVols = opt.glm.maxNbVols;
+    return
+  end
+
+  if ~isempty(opt.funcVolToSelect)
+    nbVols = numel(opt.funcVolToSelect);
+    return
+  end
+  error('WTF');
+end
+
+function fmriSpec = setScans(opt, fullpathBoldFilename, fmriSpec, spmSessCounter)
+
+  if opt.model.designOnly
+
+    nbVols = getNbVols(opt, fullpathBoldFilename);
+    if isnan(nbVols)
       warning('Could not open %s.\nExpected during testing.', fullpathBoldFilename);
       % TODO a value should be passed by user for this
       % hard coded value for test
-      hdr = ones(200, 1);
+      nbVols = 200;
     end
 
-    fmriSpec.sess(spmSessCounter).nscan = numel(hdr);
+    fmriSpec.sess(spmSessCounter).nscan = nbVols;
 
   else
 
@@ -257,14 +290,14 @@
 
 end
 
-function onsetFilename = returnOnsetsFile(BIDS, opt, subLabel, session, task, run)
+function onsetFilename = returnOnsetsFile(BIDS, opt, spec, runDuration)
 
   % get events file from raw data set and convert it to a onsets.mat file
   % store in the subject level GLM directory
-  filter = fileFilterForBold(opt, subLabel, 'events');
-  filter.ses = session;
-  filter.run = run;
-  filter.task = task;
+  filter = fileFilterForBold(opt, spec.sub, 'events');
+  filter.ses = spec.ses;
+  filter.run = spec.run;
+  filter.task = spec.task;
 
   tsvFile = bids.query(BIDS.raw, 'data', filter);
 
@@ -282,6 +315,7 @@
   end
 
   onsetFilename = createAndReturnOnsetFile(opt, ...
-                                           subLabel, ...
-                                           tsvFile);
+                                           spec.sub, ...
+                                           tsvFile, ...
+                                           runDuration);
 end

src/stats/subject_level/convertOnsetTsvToMat.m

@@ -1,4 +1,4 @@
-function fullpathOnsetFilename = convertOnsetTsvToMat(opt, tsvFile)
+function fullpathOnsetFilename = convertOnsetTsvToMat(opt, tsvFile, runDuration)
   %
   % Converts an events.tsv file to an onset file suitable for SPM subject level analysis.
   %
@@ -13,6 +13,10 @@
   % :param tsvFile:
   % :type  tsvFile: char
   %
+  % :param runDuration: Total duration of the run (in seconds). Optional.
+  %                     Events occurring later than this will be excluded.
+  % :type  runDuration: numeric
+  %
   % Use a BIDS stats model specified in a JSON file to:
   %
   % - loads events.tsv and apply the ``Node.Transformations`` to its content
@@ -51,12 +55,24 @@
 
   % (C) Copyright 2019 bidspm developers
 
+  if nargin < 3
+    runDuration = nan;
+  end
+
   REQUIRED_COLUMNS = {'onset', 'duration'};
 
   [pth, file, ext] = spm_fileparts(tsvFile);
   tsv.file = validationInputFile(pth, [file, ext]);
   tsv.content = bids.util.tsvread(tsv.file);
 
+  if ~isnan(runDuration)
+    eventsToExclude = tsv.content.onset >= runDuration;
+    columns = fieldnames(tsv.content);
+    for iCol = 1:numel(columns)
+      tsv.content.(columns{iCol})(eventsToExclude) = [];
+    end
+  end
+
   for i = 1:numel(REQUIRED_COLUMNS)
     if ~isfield(tsv.content, REQUIRED_COLUMNS{i})
       msg = sprintf(['''%s'' column is missing from file: %s', ...

src/stats/subject_level/createAndReturnOnsetFile.m

@@ -1,4 +1,4 @@
-function onsetFilename = createAndReturnOnsetFile(opt, subLabel, tsvFile)
+function onsetFilename = createAndReturnOnsetFile(opt, subLabel, tsvFile, runDuration)
   %
   % For a given ``_events.tsv`` file and ``_model.json``,
   % it creates a  ``_onset.mat`` file that can directly be used
@@ -20,6 +20,10 @@
   % :param tsvFile: fullpath name of the tsv file.
   % :type  tsvFile: char
   %
+  % :param runDuration: Total duration of the run (in seconds). Optional.
+  %                     Events occurring later than this will be excluded.
+  % :type  runDuration: numeric
+  %
   % :returns: :onsetFilename: (path) fullpath name of the file created.
   %
   % See also: convertOnsetTsvToMat
@@ -35,7 +39,7 @@
   msg = sprintf('\n  Reading the tsv file : %s \n', pathToPrint(tsvFile));
   logger('INFO', msg, 'options', opt, 'filename', mfilename());
 
-  onsetFilename = convertOnsetTsvToMat(opt, tsvFile);
+  onsetFilename = convertOnsetTsvToMat(opt, tsvFile, runDuration);
 
   % move file into the FFX directory
   [~, filename, ext] = spm_fileparts(onsetFilename);

tests/tests_stats/subject_level/test_convertOnsetTsvToMat.m

@@ -12,6 +12,36 @@
 
 end
 
+function test_convertOnsetTsvToMat_exclude_late_events()
+
+  % GIVEN
+  tsvFile = fullfile(getTestDataDir(), ...
+                     'tsv_files', ...
+                     'sub-01_task-vismotion_events.tsv');
+  opt = setOptions('vismotion');
+  opt.model.bm = BidsModel('file', opt.model.file);
+
+  % WHEN
+  runDuration = 3;
+  fullpathOnsetFilename = convertOnsetTsvToMat(opt, tsvFile, runDuration);
+
+  % THEN
+  assertEqual(fullfile(getTestDataDir(), ...
+                       'tsv_files', ...
+                       'sub-01_task-vismotion_onsets.mat'), ...
+              fullpathOnsetFilename);
+  assertEqual(exist(fullpathOnsetFilename, 'file'), 2);
+
+  load(fullpathOnsetFilename);
+
+  assertEqual(names, {'VisMot'});
+  assertEqual(onsets, {2});
+  assertEqual(durations, {2});
+
+  cleanUp(fullpathOnsetFilename);
+
+end
+
 function test_convertOnsetTsvToMat_parametric_modulation()
 
   % GIVEN

tests/tests_stats/subject_level/test_createAndReturnOnsetFile.m

@@ -30,7 +30,9 @@ function test_createAndReturnOnsetFile_basic()
                   'extension', '.tsv');
   tsvFile = bids.query(BIDS, 'data', filter);
 
-  onsetFilename = createAndReturnOnsetFile(opt, subLabel, tsvFile);
+  runDuration = nan;
+
+  onsetFilename = createAndReturnOnsetFile(opt, subLabel, tsvFile, runDuration);
 
   expectedFilename = fullfile(getTestDataDir('stats'), 'sub-01', ...
                               'task-vislocalizer_space-IXI549Space_FWHM-6', ...