[FIX] small fixes in createDefaultStatsModel.m, getAcquisitionTime.m …

…& bidsResults.m (#1248)

* changed condition to check compatibility of sliceOrder and acquisitionTime

* fixed conditional statement defining bm.Nodes.GroupBy

* Update function bidsResultsSubject: identification of run level contrasts

* fixed spelling

* update citation.cff

* update citation.cff

* add test getAcquisitionTime

* adapt test data for bids stats model

* extract regex

* add tests

* revert

---------

Co-authored-by: Remi Gau <remi_gau@hotmail.com>

CITATION.cff

@@ -93,6 +93,10 @@ authors:
   affiliation: "University of Gent"
   orcid: "https://orcid.org/0000-0001-8279-6118"
 
+- family-names: Huber
+  given-names:  Daniel
+  affiliation: University of Innsbruck
+
 - family-names: "Van Audenhaege"
   given-names:  "Alice"
   affiliation: "Université catholique de Louvain"

src/bids_model/createDefaultStatsModel.m

@@ -106,7 +106,7 @@
 
     if strcmp(levelsToUpdate{i}, 'subject')
       bm.Nodes{idx}.GroupBy = {'subject', 'contrast'};
-    elseif strcmp(levelsToUpdate{i}, 'subject')
+    elseif strcmp(levelsToUpdate{i}, 'dataset')
       bm.Nodes{idx}.GroupBy = {'contrast'};
     end
 

src/preproc/utils/getAcquisitionTime.m

@@ -18,8 +18,8 @@
 
   acquisitionTime = computeAcquisitionTime(sliceOrder, repetitionTime);
 
-  % ceil to avoid making this too brittle
-  if any(sliceOrder > ceil(acquisitionTime * 100) / 100)
+  % add small time buffer (0.01 s) to avoid making this too brittle
+  if any(sliceOrder > acquisitionTime + 0.01)
     sliceOrder = bids.internal.create_unordered_list(num2str(sliceOrder));
     msg = sprintf(['Acquisition time cannot be < to any slice timing value:\n\n', ...
                    'Current values:', ...

src/stats/utils/endsWithRunNumber.m

@@ -0,0 +1,15 @@
+function value = endsWithRunNumber(contrastName)
+  %
+  % USAGE::
+  %
+  %   endsWithRunNumber(contrastName)
+  %
+  %
+  % Returns true if the contrast name ends with an underscore
+  % followed by some number.
+  %
+
+  % (C) Copyright 2024 bidspm developers
+  result = regexp(contrastName, '_[0-9]+\${0,1}$', 'match');
+  value =  ~isempty(result);
+  return

src/workflows/stats/bidsResults.m

@@ -361,16 +361,14 @@
       %
       % Only necessary
       % if the user did not specify the run number in result.name
-      % by adding an "_[0-9]*" to indicate the run number to get this contrast
+      % by adding an "_[0-9]+" to indicate the run number to get this contrast
       % for example
       %
       %  opt.result.name = 'listening_1'
       %
 
-      endsWithRunNumber = regexp(contrastName, '_[0-9]*\${0,1}$', 'match');
-      if isempty(endsWithRunNumber)
-        tmp.name = [contrastName '_[0-9]*'];
-      else
+      tmp.name = [contrastName '_[0-9]+'];
+      if ~endsWithRunNumber(contrastName)
         tmp.name = contrastName;
       end
 
@@ -392,21 +390,18 @@
 
     contrastNb = getContrastNb(tmp, opt, SPM);
 
-    constrastsNamesList = {SPM.xCon(contrastNb).name}';
+    contrastsNamesList = {SPM.xCon(contrastNb).name}';
 
-    for j = 1:numel(constrastsNamesList)
+    for j = 1:numel(contrastsNamesList)
 
       result = opt.results(iRes);
 
-      result.name = constrastsNamesList{j};
+      result.name = contrastsNamesList{j};
 
-      if ~isRunLevel
-        % skip contrast with name ending in _[0-9]* as they are run level
-        % contrasts
-        endsWithRunNumber = regexp(result.name, '_[0-9]*$', 'match');
-        if ~isempty(endsWithRunNumber)
-          continue
-        end
+      % skip contrast with name ending in _[0-9]+
+      % as they are run level contrasts
+      if ~isRunLevel && endsWithRunNumber(result.name)
+        continue
       end
 
       result.space = opt.space;

tests/data/models/model-default_smdl.json

@@ -1,7 +1,7 @@
 {
-  "Name": "default_rest_vislocalizer_vismotion_model",
+  "Name": "default_vislocalizer_model",
   "BIDSModelVersion": "1.0.0",
-  "Description": "default BIDS stats model for rest/vislocalizer/vismotion task",
+  "Description": "default BIDS stats model for vislocalizer task",
   "Input": {
     "task": [
       "vislocalizer"
@@ -61,8 +61,8 @@
         },
         "Software": {
           "SPM": {
-            "InclusiveMaskingThreshold": 0.8,
-            "SerialCorrelation": "FAST"
+            "SerialCorrelation": "FAST",
+            "InclusiveMaskingThreshold": 0.8
           }
         }
       },
@@ -107,7 +107,7 @@
       "Level": "Dataset",
       "Name": "dataset",
       "GroupBy": [
-        ""
+        "contrast"
       ],
       "Model": {
         "X": [

tests/tests_bids_model/test_createDefaultStatsModel.m

@@ -14,6 +14,7 @@ function test_createDefaultStatsModel_basic()
 
   BIDS = getLayout(opt);
 
+  %   opt.dir.derivatives = pwd;
   opt.dir.derivatives = tempName();
   opt.space = {'IXI549Space'};
   opt.taskName = {'vislocalizer'};

tests/tests_preproc/utils/test_getAcquisitionTime.m

@@ -77,3 +77,52 @@ function test_getAcquisitionTime_bug_967()
   getAcquisitionTime(sliceOrder, repetitionTime);
 
 end
+
+function test_openneuro_ds000224()
+  %  test a less brittle version of getAcquisitionTime
+
+  repetitionTime =  2.2;
+
+  sliceOrder = [
+                1.105, ...
+                0, ...
+                1.1675, ...
+                0.0625, ...
+                1.2275, ...
+                0.1225, ...
+                1.29, ...
+                0.185, ...
+                1.35, ...
+                0.245, ...
+                1.4125, ...
+                0.3075, ...
+                1.4725, ...
+                0.37, ...
+                1.535, ...
+                0.43, ...
+                1.595, ...
+                0.4925, ...
+                1.6575, ...
+                0.5525, ...
+                1.7175, ...
+                0.615, ...
+                1.78, ...
+                0.675, ...
+                1.84, ...
+                0.7375, ...
+                1.9025, ...
+                0.7975, ...
+                1.965, ...
+                0.86, ...
+                2.025, ...
+                0.92, ...
+                2.0875, ...
+                0.9825, ...
+                2.1475, ...
+                1.0425];
+
+  acquisitionTime = getAcquisitionTime(sliceOrder, repetitionTime);
+
+  assertElementsAlmostEqual(acquisitionTime, 2.1389, 'absolute', 1e-4);
+
+end

tests/tests_stats/utils/test_endsWithRunNumber.m

@@ -0,0 +1,19 @@
+function test_suite = test_endsWithRunNumber %#ok<*STOUT>
+  % (C) Copyright 2022 bidspm 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_endsWithRunNumber_basic()
+
+  assertEqual(endsWithRunNumber('foo_1'), true);
+  assertEqual(endsWithRunNumber('foo_1_'), false);
+  assertEqual(endsWithRunNumber('foo_1_a'), false);
+  assertEqual(endsWithRunNumber('foo_'), false);
+  assertEqual(endsWithRunNumber('foo'), false);
+  assertEqual(endsWithRunNumber('foo1'), false);
+
+end