Merge remote-tracking branch 'upstream/main' into slice

Author: Remi-Gau

.github/workflows/run_tests_notebooks.yml

@@ -30,7 +30,7 @@ jobs:
                 sudo apt-get -y install unzip wget tree
 
         -   name: Install MATLAB
-            uses: matlab-actions/[email protected].0
+            uses: matlab-actions/[email protected].1
             with:
           # MATLAB release to set up R2020a
                 release: R2023a

.github/workflows/tests.yml

@@ -108,7 +108,7 @@ jobs:
                 git clone https://github.com/MOcov/MOcov.git --depth 1
 
         -   name: Install MATLAB
-            uses: matlab-actions/[email protected].0
+            uses: matlab-actions/[email protected].1
             with:
                 release: ${{ matrix.matlab }}
 
@@ -203,7 +203,7 @@ jobs:
                 git clone https://github.com/MOcov/MOcov.git --depth 1
 
         -   name: Install MATLAB
-            uses: matlab-actions/[email protected].0
+            uses: matlab-actions/[email protected].1
             with:
                 release: ${{ matrix.matlab }}
 
@@ -299,7 +299,7 @@ jobs:
             run: make -C demos/bayes data_ds000114
 
         -   name: Install MATLAB
-            uses: matlab-actions/[email protected].0
+            uses: matlab-actions/[email protected].1
             with:
                 release: ${{ matrix.matlab }}
 

.github/workflows/tests_windows.yml

@@ -107,7 +107,7 @@ jobs:
                 git clone https://github.com/MOcov/MOcov.git --depth 1
 
         -   name: Install MATLAB
-            uses: matlab-actions/[email protected].0
+            uses: matlab-actions/[email protected].1
             with:
                 release: ${{ matrix.matlab }}
 

.pre-commit-config.yaml

@@ -66,7 +66,7 @@ repos:
     -   id: rst-inline-touching-normal
 
 -   repo: https://github.com/pycqa/isort
-    rev: 6.0.0
+    rev: 6.0.1
     hooks:
     -   id: isort
         args: [--profile, black]

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

lib/octache

@@ -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/renameOutputResults.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);