several fixes

docs/source/API.rst

@@ -93,8 +93,8 @@ stats
 .. autofunction:: src.batches.stats.setBatchContrasts
 .. autofunction:: src.batches.stats.setBatchEstimateModel
 .. autofunction:: src.batches.stats.setBatchFactorialDesign
+.. autofunction:: src.batches.stats.setBatchFactorialDesignGlobalCalcAndNorm
 .. autofunction:: src.batches.stats.setBatchFactorialDesignImplicitMasking
-.. autofunction:: src.batches.stats.setBatchFatorialDesignGlobalCalcAndNorm
 .. autofunction:: src.batches.stats.setBatchGoodnessOfFit
 .. autofunction:: src.batches.stats.setBatchGroupLevelContrasts
 .. autofunction:: src.batches.stats.setBatchGroupLevelResults
@@ -173,6 +173,7 @@ bids
 .. autofunction:: src.bids.getAnatFilename
 .. autofunction:: src.bids.getAndCheckRepetitionTime
 .. autofunction:: src.bids.getAndCheckSliceOrder
+.. autofunction:: src.bids.getAvailableGroups
 .. autofunction:: src.bids.getBoldFilename
 .. autofunction:: src.bids.getInfo
 .. autofunction:: src.bids.getMeanFuncFilename
@@ -188,7 +189,6 @@ bids
 bids_model
 ==========
 .. autofunction:: src.bids_model.checkContrast
-.. autofunction:: src.bids_model.checkGroupBy
 .. autofunction:: src.bids_model.createDefaultStatsModel
 .. autofunction:: src.bids_model.createModelFamilies
 .. autofunction:: src.bids_model.getContrastsFromParentNode
@@ -198,6 +198,12 @@ bids_model
 .. autofunction:: src.bids_model.getDummyContrastsList
 .. autofunction:: src.bids_model.getInclusiveMask
 
+bidspm
+======
+
+data
+----
+
 cli
 ===
 .. autofunction:: src.cli.baseInputParser
@@ -220,6 +226,7 @@ cli
 
 constants
 =========
+.. autofunction:: src.constants.bidsAppsActions
 .. autofunction:: src.constants.lowLevelActions
 
 defaults
@@ -262,7 +269,6 @@ messages
 .. autofunction:: src.messages.errorHandling
 .. autofunction:: src.messages.logger
 .. autofunction:: src.messages.noRoiFound
-.. autofunction:: src.messages.noSPMmat
 .. autofunction:: src.messages.notImplemented
 .. autofunction:: src.messages.printAvailableContrasts
 .. autofunction:: src.messages.printBatchName
@@ -339,7 +345,6 @@ subject_level
 .. autofunction:: src.stats.subject_level.getSessionForRegressorNb
 .. autofunction:: src.stats.subject_level.newContrast
 .. autofunction:: src.stats.subject_level.orderAndPadCounfoundMatFile
-.. autofunction:: src.stats.subject_level.removeIntercept
 .. autofunction:: src.stats.subject_level.reorderCounfounds
 .. autofunction:: src.stats.subject_level.sanitizeConfounds
 .. autofunction:: src.stats.subject_level.saveRoiGlmSummaryTable
@@ -354,10 +359,10 @@ group_level
 .. autofunction:: src.stats.group_level.computeCumulativeFwhm
 .. autofunction:: src.stats.group_level.findSubjectConImage
 .. autofunction:: src.stats.group_level.getRFXdir
-.. autofunction:: src.stats.group_level.groupLevelGlmType
 
 utils
 -----
+.. autofunction:: src.stats.utils.checkSpmMat
 .. autofunction:: src.stats.utils.createGlmDirName
 .. autofunction:: src.stats.utils.designMatrixFigureName
 .. autofunction:: src.stats.utils.endsWithRunNumber
@@ -366,6 +371,7 @@ utils
 .. autofunction:: src.stats.utils.getRegressorIdx
 .. autofunction:: src.stats.utils.labelActivations
 .. autofunction:: src.stats.utils.labelSpmSessWithBidsSesAndRun
+.. autofunction:: src.stats.utils.removeIntercept
 .. autofunction:: src.stats.utils.returnContrastImageFile
 .. autofunction:: src.stats.utils.returnNumberScrubbedTimePoints
 .. autofunction:: src.stats.utils.validateContrasts

src/batches/stats/setBatchGroupLevelContrasts.m

@@ -122,14 +122,8 @@
 
     case 'two_sample_t_test'
 
-      designMatrix = removeIntercept(designMatrix);
-
-      if any(ismember(designMatrix, fieldnames(participants)))
-        % TODO will this ignore the contrasts define at other levels
-        % and not passed through the filter ?
-        edge = bm.get_edge('Destination', nodeName);
-        contrastsList = edge.Filter.contrast;
-      end
+      edge = bm.get_edge('Destination', nodeName);
+      contrastsList = edge.Filter.contrast;
 
       for j = 1:numel(contrastsList)
 

src/batches/stats/setBatchSubjectLevelContrasts.m

@@ -27,10 +27,10 @@
 
   printBatchName('subject level contrasts specification', opt);
 
-  spmMatFile = fullfile(getFFXdir(subLabel, opt), 'SPM.mat');
-  if ~checkSpmMat(dir, opt)
+  if ~checkSpmMat(getFFXdir(subLabel, opt), opt)
     return
   end
+  spmMatFile = fullfile(getFFXdir(subLabel, opt), 'SPM.mat');
 
   load(spmMatFile, 'SPM');
 

src/batches/stats/setBatchSubjectLevelGLMSpec.m

@@ -185,7 +185,7 @@
     matlabbatch{end + 1}.spm.stats.fmri_design = fmri_spec;
 
   else
-    node = model.get_root_node();
+    node = bm.get_root_node();
 
     fmri_spec.mask = {getInclusiveMask(opt, node.Name, BIDS, subLabel)};
     matlabbatch{end + 1}.spm.stats.fmri_spec = fmri_spec;

src/bids/getAvailableGroups.m

@@ -1,6 +1,11 @@
 function availableGroups = getAvailableGroups(opt, groupColumnHdr)
 
   % (C) Copyright 2024 bidspm developers
+  if isempty(groupColumnHdr)
+    availableGroups = {};
+    return
+  end
+
   tsvFile = fullfile(opt.dir.raw, 'participants.tsv');
 
   assert(exist(tsvFile, 'file') == 2);

src/bids_model/getContrastsList.m

@@ -48,7 +48,7 @@
         % TODO relax those assumptions
 
         % assumptions
-        assert(model.validateGroupBy(node.Name participants));
+        assert(model.validateGroupBy(node.Name, participants));
         assert(node.Model.X == 1);
 
         contrastsList = getContrastsFromParentNode(model, node);

src/bids_model/getContrastsListForFactorialDesign.m

@@ -41,7 +41,7 @@
       % if no specific dummy contrasts mentioned also include all contrasts from previous levels
       % or if contrasts are mentioned we grab them
       if ~isfield(node.DummyContrasts, 'Contrasts') || isfield(node, 'Contrasts')
-        tmp = getContrastsList(bm, nodeName, columns);
+        tmp = getContrastsList(bm, nodeName, participants);
         for i = 1:numel(tmp)
           contrastsList{end + 1} = tmp{i}.Name;
         end

src/stats/subject_level/specifyContrasts.m

@@ -113,7 +113,7 @@
     return
   end
 
-  if isempty(model.Edges)
+  if isempty(bm.Edges)
     bm = bm.get_edges_from_nodes();
   end
 

src/workflows/roi/bidsRoiBasedGLM.m

@@ -79,11 +79,11 @@
     if ~checkSpmMat(outputDir, opt, strict)
       continue
     end
-    spmFile = fullfile(outputDir, 'SPM.mat');
-    load(spmFile, 'SPM');
+    spmMatFile = fullfile(outputDir, 'SPM.mat');
+    load(spmMatFile, 'SPM');
     model = mardo(SPM);
 
-    eventSpec = getEventSpecificationRoiGlm(spmFile, opt.model.file);
+    eventSpec = getEventSpecificationRoiGlm(spmMatFile, opt.model.file);
 
     subTempDir = fullfile(tempDir, ['sub-' subLabel]);
     spm_mkdir(subTempDir);

tests/tests_batches/preproc/test_setBatchGenerateT1map.m

@@ -48,7 +48,7 @@ function test_setBatchGenerateT1map_warning()
   BIDS = getLayout(opt);
 
   matlabbatch = {};
-  opt.verbosity = 2;
+  opt.verbosity = 1;
   assertWarning(@() setBatchGenerateT1map(matlabbatch, BIDS, opt, subLabel), ...
                 'setBatchGenerateT1map:missingNonBIDSMetadata');
 

tests/tests_bids/test_fileFilterForBold.m

@@ -13,7 +13,7 @@
 function test_fileFilterForBold_events()
 
   opt.bidsFilterFile.bold = struct('modality', 'func', 'suffix', 'bold');
-  opt.verbosity = 2;
+  opt.verbosity = 0;
   opt.taskName = 'foo';
   opt.fwhm.func = 6;
   opt.space = {'IXI549Space'};
@@ -38,7 +38,7 @@ function test_fileFilterForBold_events_aroma()
   opt.bidsFilterFile.bold = struct('modality', 'func', ...
                                    'suffix', 'bold', ...
                                    'desc', {'smoothAROMAnonaggr'});
-  opt.verbosity = 2;
+  opt.verbosity = 0;
   opt.taskName = 'foo';
   opt.fwhm.func = 6;
   opt.space = {'MNI152NLin6Asym'};
@@ -61,7 +61,7 @@ function test_fileFilterForBold_events_aroma()
 function test_fileFilterForBold_confounds()
 
   opt.bidsFilterFile.bold = struct('modality', 'func', 'suffix', 'bold');
-  opt.verbosity = 2;
+  opt.verbosity = 0;
   opt.taskName = 'foo';
   opt.fwhm.func = 6;
   opt.space = {'IXI549Space'};
@@ -84,7 +84,7 @@ function test_fileFilterForBold_confounds()
 function test_fileFilterForBold_basic()
 
   opt.bidsFilterFile.bold = struct('modality', 'func', 'suffix', 'bold');
-  opt.verbosity = 2;
+  opt.verbosity = 0;
   opt.taskName = 'foo';
   opt.fwhm.func = 6;
   opt.space = {'IXI549Space'};
@@ -111,7 +111,7 @@ function test_fileFilterForBold_desc()
   opt.bidsFilterFile.bold = struct('modality', 'func', ...
                                    'suffix', 'bold', ...
                                    'desc', {'smoothAROMAnonaggr'});
-  opt.verbosity = 2;
+  opt.verbosity = 0;
   opt.taskName = 'foo';
   opt.fwhm.func = 6;
   opt.space = {'MNI152NLin6Asym'};
@@ -138,7 +138,7 @@ function test_fileFilterForBold_desc()
 function test_fileFilterForBold_no_smooth()
 
   opt.bidsFilterFile.bold = struct('modality', 'func', 'suffix', 'bold');
-  opt.verbosity = 2;
+  opt.verbosity = 0;
   opt.taskName = 'foo';
   opt.fwhm.func = 0;
   opt.space = {'IXI549Space'};
@@ -163,7 +163,7 @@ function test_fileFilterForBold_no_smooth()
 function test_fileFilterForBold_stc()
 
   opt.bidsFilterFile.bold = struct('modality', 'func', 'suffix', 'bold');
-  opt.verbosity = 2;
+  opt.verbosity = 0;
   opt.taskName = 'foo';
   opt.fwhm.func = 0;
   opt.space = {'IXI549Space'};

tests/tests_bids_model/test_getOptionsFromModel.m

@@ -27,7 +27,7 @@ function test_getOptionsFromModel_no_model()
   opt.pipeline.type = 'stats';
   opt.model.file = '';
   opt.tolerant = true;
-  opt.verbosity = 3;
+  opt.verbosity = 1;
   opt.pipeline.isBms = false;
 
   assertExceptionThrown(@() getOptionsFromModel(opt), 'getOptionsFromModel:modelFileMissing');
@@ -79,7 +79,7 @@ function test_getOptionsFromModel_task()
 
   %%
   opt.taskName = {'foo'};
-  opt.verbosity = 2;
+  opt.verbosity = 1;
   opt.tolerant = true;
 
   assertWarning(@() getOptionsFromModel(opt), 'getOptionsFromModel:modelOverridesOptions');
@@ -104,7 +104,7 @@ function test_getOptionsFromModel_subject()
 
   %%
   opt.subjects = '02';
-  opt.verbosity = 2;
+  opt.verbosity = 1;
 
   assertWarning(@() getOptionsFromModel(opt), 'getOptionsFromModel:modelOverridesOptions');
 
@@ -147,7 +147,7 @@ function test_getOptionsFromModel_query()
 
   %%
   opt.query.acq = 'foo';
-  opt.verbosity = 2;
+  opt.verbosity = 1;
 
   assertWarning(@() getOptionsFromModel(opt), 'getOptionsFromModel:modelOverridesOptions');
 

tests/tests_bids_model/test_validateGroupBy.m

@@ -38,7 +38,7 @@ function test_validateGroupBy_subject()
   assertWarning(@()bm.validateGroupBy(nodeName), 'BidsModel:notImplemented');
 end
 
-function test_checkGroupBy_dataset()
+function test_validateGroupBy_dataset()
 
   opt = setOptions('vismotion', {'01' 'ctrl01'}, 'pipelineType', 'stats');
 
@@ -62,7 +62,7 @@ function test_checkGroupBy_dataset()
 
 end
 
-function test_checkGroupBy_dataset_group_from_participant()
+function test_validateGroupBy_dataset_group_from_participant()
 
   opt = setOptions('vismotion', {'01' 'ctrl01'}, 'pipelineType', 'stats');
 
@@ -71,6 +71,6 @@ function test_checkGroupBy_dataset_group_from_participant()
   nodeName = bm.Nodes{3}.Name;
 
   bm.Nodes{3}.GroupBy = {'contrast', 'diagnostic'};
-  bm.validateGroupBy(nodeName, {'diagnostic'});
+  bm.validateGroupBy(nodeName, struct('diagnostic', {{'foo', 'bar'}}));
 
 end

tests/tests_slow/tests_workflows/stats/test_bidsResults.m

@@ -15,7 +15,7 @@ function test_bidsResults_no_results()
   skipIfOctave('mixed-string-concat warning thrown');
 
   opt = setOptions('vismotion', '', 'pipelineType', 'stats');
-  opt.verbosity = 2;
+  opt.verbosity = 1;
 
   opt = rmfield(opt, 'results');
 

tests/tests_slow/tests_workflows/test_renameSegmentParameter.m

@@ -30,7 +30,7 @@ function test_renameSegmentParameter_basic()
                      'index_dependencies', false);
 
   opt.dryRun = false;
-  opt.verbosity = 2;
+  opt.verbosity = 0;
 
   segParamFiles = spm_select('FPListRec', tmpDir, '^.*_T1w_seg8.mat$');
   assertEqual(size(segParamFiles, 1), 1);

tests/tests_slow/tests_workflows/test_renameUnwarpParameter.m

@@ -25,7 +25,7 @@ function test_renameUnwarpParameter_basic()
                      'index_dependencies', false);
 
   opt.dryRun = false;
-  opt.verbosity = 2;
+  opt.verbosity = 0;
 
   unwarpParamFiles = spm_select('FPListRec', tmpDir, '^.*_bold_uw.mat$');
   assertEqual(size(unwarpParamFiles, 1), 1);

tests/tests_stats/unit_tests/test_getInclusiveMask.m

@@ -15,7 +15,7 @@ function test_getInclusiveMask_too_many()
 
   opt = setOptions('vismotion', '01', 'useTempDir', true);
 
-  opt.verbosity = 2;
+  opt.verbosity = 1;
 
   opt.model.bm = BidsModel('file', opt.model.file);
 
@@ -63,7 +63,7 @@ function test_getInclusiveMask_no_image()
 
   opt = setOptions('vismotion', '01');
 
-  opt.verbosity = 2;
+  opt.verbosity = 1;
 
   opt.model.bm = BidsModel('file', opt.model.file);