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[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 <[email protected]>
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‎CITATION.cff‎

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

‎src/bids_model/createDefaultStatsModel.m‎

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

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

‎src/stats/utils/endsWithRunNumber.m‎

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

‎src/workflows/stats/bidsResults.m‎

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

‎tests/data/models/model-default_smdl.json‎

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

‎tests/tests_bids_model/test_createDefaultStatsModel.m‎

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

‎tests/tests_preproc/utils/test_getAcquisitionTime.m‎

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

‎tests/tests_stats/utils/test_endsWithRunNumber.m‎

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function test_suite = test_endsWithRunNumber %#ok<*STOUT>
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% (C) Copyright 2022 bidspm developers
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try % assignment of 'localfunctions' is necessary in Matlab >= 2016
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test_functions = localfunctions(); %#ok<*NASGU>
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catch % no problem; early Matlab versions can use initTestSuite fine
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end
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initTestSuite;
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end
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function test_endsWithRunNumber_basic()
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assertEqual(endsWithRunNumber('foo_1'), true);
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assertEqual(endsWithRunNumber('foo_1_'), false);
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assertEqual(endsWithRunNumber('foo_1_a'), false);
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assertEqual(endsWithRunNumber('foo_'), false);
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assertEqual(endsWithRunNumber('foo'), false);
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assertEqual(endsWithRunNumber('foo1'), false);
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end

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