fix models

CHANGELOG.md

@@ -24,6 +24,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Added
 
+* [ENH] add support for one-way ANOVA across groups at the group level #1296 by @Remi-Gau
+* [ENH] allow for 2 sample T-Test, within group T-Test and one-way ANOVA to ne more flexible with respect to what praticipants.tsv column to use to allocate subjects in each group #1296 by @Remi-Gau
 * [ENH] make `addConfoundsToDesignMatrix` a method of `BidsModel` #1294 by @Remi-Gau
 * [ENH] add Apptainer definition #1254 by @Remi-Gau and @monique2208
 * [ENH] allow to copy anat only on raw datasets #1181 by @Remi-Gau
@@ -43,7 +45,6 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Changed
 
-
 * [ENH] align specification of F contrasts on the BIDS stats model: they should now be specified as a 2D matrix and not a 1D vector. #1276 @Remi-Gau
 * [DOC] change theme and structure of the documentation #1256 @Remi-Gau
 * [REF] Refactor and update CLI in #1096 @Remi-Gau

src/batches/stats/setBatchFactorialDesign.m

@@ -32,8 +32,6 @@
     return
   end
 
-  [~, opt] = getData(opt, opt.dir.preproc);
-
   printBatchName(sprintf('specify group level fmri model for node "%s"', nodeName), opt);
 
   % now we fetch the contrast for each subject and allocate them in the batch

src/workflows/stats/bidsRFX.m

@@ -90,6 +90,8 @@
 
     case 'rfx'
 
+      [~, opt] = getData(opt, opt.dir.preproc);
+
       participants = bids.util.tsvread(fullfile(opt.dir.raw, 'participants.tsv'));
 
       matlabbatch = {};

tests/data/models/model-vislocalizerSeveralDatasetLevels_smdl.json

@@ -171,5 +171,19 @@
         ]
       }
     }
+  ],
+  "Edges": [
+    {
+      "Source": "run_level",
+      "Destination": "subject_level"
+    },
+    {
+      "Source": "subject_level",
+      "Destination": "simple contrast"
+    },
+    {
+      "Source": "subject_level",
+      "Destination": "complex contrast"
+    }
   ]
 }

tests/data/models/model-vismotionNoOverWrite_smdl.json

@@ -227,5 +227,27 @@
         }
       ]
     }
+  ],
+  "Edges": [
+    {
+      "Source": "run_level",
+      "Destination": "subject_level"
+    },
+    {
+      "Source": "subject_level",
+      "Destination": "simple contrast"
+    },
+    {
+      "Source": "subject_level",
+      "Destination": "complex contrast"
+    },
+    {
+      "Source": "subject_level",
+      "Destination": "within_group"
+    },
+    {
+      "Source": "subject_level",
+      "Destination": "between_groups"
+    }
   ]
 }

tests/data/models/model-vismotionSeveralDatasetLevel_smdl.json

@@ -160,5 +160,19 @@
         ]
       }
     }
+  ],
+  "Edges": [
+    {
+      "Source": "run_level",
+      "Destination": "subject_level"
+    },
+    {
+      "Source": "subject_level",
+      "Destination": "simple contrast"
+    },
+    {
+      "Source": "subject_level",
+      "Destination": "complex contrast"
+    }
   ]
 }

tests/tests_slow/tests_batches/stats/test_setBatchFactorialDesign.m

@@ -8,12 +8,45 @@
   initTestSuite;
 end
 
+function test_setBatchFactorialDesign_complex_alone()
+
+  markTestAs('slow');
+
+  opt = setOptions('vismotion', {'^01'}, 'pipelineType', 'stats');
+
+  [~, opt] = getData(opt, opt.dir.preproc);
+
+  opt.model.file = spm_file(opt.model.file, ...
+                            'basename', ...
+                            'model-vismotionSeveralDatasetLevel_smdl');
+
+  opt.model.bm = BidsModel('file', opt.model.file);
+
+  datasetNode = opt.model.bm.get_nodes('Name', 'complex contrast');
+
+  matlabbatch = {};
+  matlabbatch = setBatchFactorialDesign(matlabbatch, opt, datasetNode.Name);
+
+  % (1 contrasts) specified at the dataset level * 2
+  % batches (design specification + figure design matrix)
+  assertEqual(numel(matlabbatch), 2);
+
+  % check that directory name contains:
+  % desc-Node(dataset).name_contrast_contrastName
+  [~, dir] = fileparts(matlabbatch{1}.spm.stats.factorial_design.dir{1});
+  assertEqual(dir, ...
+              [basedirName 'node-complexContrast_contrast-VisMotGtVisStat']);
+
+end
+
 function test_setBatchFactorialDesign_within_group()
 
   markTestAs('slow');
 
   opt = setOptions('vislocalizer', '', 'pipelineType', 'stats');
 
+  [~, opt] = getData(opt, opt.dir.preproc);
+
   opt.model.file = spm_file(opt.model.file, ...
                             'basename', ...
                             'model-vislocalizerWithinGroup_smdl');
@@ -37,6 +70,8 @@ function test_setBatchFactorialDesign_complex()
 
   opt = setOptions('vismotion', {'^01'}, 'pipelineType', 'stats');
 
+  [~, opt] = getData(opt, opt.dir.preproc);
+
   opt.model.file = spm_file(opt.model.file, ...
                             'basename', ...
                             'model-vismotionSeveralDatasetLevel_smdl');
@@ -83,6 +118,8 @@ function test_setBatchFactorialDesign_basic()
 
   opt = setOptions('vismotion', {'01' 'ctrl01'}, 'pipelineType', 'stats');
 
+  [~, opt] = getData(opt, opt.dir.preproc);
+
   datasetNode = opt.model.bm.get_nodes('Level', 'dataset');
 
   opt.model.bm.Nodes{3}.Model.Options = rmfield(opt.model.bm.Nodes{3}.Model.Options, ...

tests/tests_slow/tests_batches/stats/test_setBatchFactorialDesign_3_groups.m

@@ -13,6 +13,8 @@ function test_setBatchFactorialDesign_between_3_groups()
   opt = setOptions('3_groups', '', 'pipelineType', 'stats');
   opt.verbosity = 0;
 
+  [~, opt] = getData(opt, opt.dir.preproc);
+
   matlabbatch = {};
   [matlabbatch, ~, ~] = setBatchFactorialDesign(matlabbatch, ...
                                                 opt, ...

tests/tests_workflows/stats/test_bidsRFX_3_groups.m

@@ -27,6 +27,8 @@ function test_bidsRFX_one_way_anova_contrast()
 
   opt = setOptions('3_groups', '', 'pipelineType', 'stats');
 
+  [~, opt] = getData(opt, opt.dir.preproc);
+
   opt.model.bm = BidsModel('file', opt.model.file);
   opt.verbosity = 0;