[ENH] use contrast number in contrast filename (#1347)

* [ENH] use contrast number in contrast filename

* adapt test

* fix

* add comment

* fix

* fix

Author: Remi-Gau

CHANGELOG.md

@@ -25,6 +25,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Changed
 
+* [ENH] Add SPM's contrast number in filename of each contrasts output filename #1347 by @Remi-Gau
+
 ### Deprecated
 
 ### Removed

demos/openneuro/models/model-ds000114_desc-testRetestVerbal_smdl.json

@@ -76,7 +76,44 @@
         "X": [
           1
         ],
-        "Type": "glm"
+        "Type": "glm",
+        "Software": {
+          "bidspm": {
+            "Results": [
+              {
+                "name": [
+                  "Task"
+                ],
+                "p": 0.05,
+                "MC": "FWE",
+                "png": true,
+                "binary": true,
+                "threshSpm": true,
+                "nidm": true,
+                "montage": {
+                  "do": true,
+                  "orientation": "axial",
+                  "slices": [
+                    -26,
+                    -22,
+                    -18,
+                    -14,
+                    -10,
+                    -6,
+                    -2,
+                    2,
+                    6
+                  ],
+                  "background": {
+                    "suffix": "T1w",
+                    "desc": "preproc",
+                    "modality": "anat"
+                  }
+                }
+              }
+            ]
+          }
+        }
       },
       "DummyContrasts": {
         "Test": "t"

docs/source/output/outputs.md

@@ -109,7 +109,7 @@ bidspm-stats
 │       ├── spmT_0001.nii           |
 │       ├── spmT_*.nii     ----------
 │       |
-│       ├── sub-blnd01_task-taskName_space-space_desc-contrastName_label-0039_p-0pt050_k-10_MC-FWE_montage.png
+│       ├── sub-blnd01_task-taskName_space-space_label-0039_desc-contrastName_p-0pt050_k-10_MC-FWE_montage.png
 │       |
 │       ├── sub-blnd01_task-taskName_space-space_desc-afterEstimation_designmatrix.png
 │       ├── sub-blnd01_task-taskName_space-space_desc-beforeEstimation_designmatrix.png

src/stats/results/renameOutputResults.m

@@ -16,14 +16,20 @@ function renameOutputResults(opt, result, subLabel)
   end
 
   if result.nidm
+    % TODO currently name of nidm file does not include
+    %   the label of the contrast that was used to generate it.
     renameNidm(opt, result, subLabel);
   end
 
   if result.png
+    % TODO currently name of PNG file does not include
+    %   the label of the contrast that was used to generate it.
     renamePngCsvResults(opt, result, '.png', subLabel);
   end
 
   if result.csv
+    % TODO currently name of CSV file does not include
+    %   the label of the contrast that was used to generate it.
 
     renamePngCsvResults(opt, result, '.csv', subLabel);
 

src/stats/results/returnResultNameSpec.m

@@ -7,6 +7,9 @@
   nameSpec.entities.sub = result.label;
   nameSpec.entities.task = strjoin(opt.taskName, '');
   nameSpec.entities.space = result.space{1};
+  if isfield(result, 'contrastNb')
+    nameSpec.entities.label = sprintf('%04.0f', result.contrastNb);
+  end
   nameSpec.entities.desc = result.name;
   nameSpec.entities.p = convertPvalueToString(result.p);
   nameSpec.entities.k = num2str(result.k);

src/workflows/stats/bidsResults.m

@@ -226,7 +226,7 @@
 
           for iBatch = 1:numel(matlabbatch)
             batch{1} = struct('spm', matlabbatch{iBatch}.spm);
-            status = saveAndRunWorkflow(batch, batchName, opt, subLabel);
+            status = saveAndRunWorkflow(batch, [batchName, '_', num2str(iBatch)], opt, subLabel);
 
             if status && isfield(matlabbatch{iBatch}, 'result')
               renameOutputResults(opt, matlabbatch{iBatch}.result, subLabel);

tests/tests_batches/stats/test_setBatchResults.m

@@ -67,9 +67,9 @@ function test_setBatchResults_export()
   export{1}.png = true;
   export{2}.csv = true;
   export{3}.tspm.basename = ...
-      'sub-01_task-test_space-individual_desc-test_p-0pt050_k-0_MC-FDR_spmT';
+      'sub-01_task-test_space-individual_label-0001_desc-test_p-0pt050_k-0_MC-FDR_spmT';
   export{4}.binary.basename = ...
-      'sub-01_task-test_space-individual_desc-test_p-0pt050_k-0_MC-FDR_mask';
+      'sub-01_task-test_space-individual_label-0001_desc-test_p-0pt050_k-0_MC-FDR_mask';
 
   export{5}.nidm.modality = 'FMRI';
   export{end}.nidm.refspace = 'subject';

tests/tests_slow/tests_workflows/stats/test_bidsResults.m

@@ -48,6 +48,7 @@ function test_bidsResults_subject_lvl()
   assertEqual(matlabbatch{1}.spm.stats.results.conspec, expected);
 
   rootBasename = ['sub-ctrl01_task-vislocalizer_space-IXI549Space', ...
+                  '_label-0003',  ...
                   '_desc-VisMotGtVisStat_p-0pt050_k-5_MC-FWE'];
   expected = {struct('png', true), ...
               struct('csv', true), ...