Merge pull request #723 from cpp-lln-lab/add_resize

Remi-Gau · web-flow · commit a0bff0699574 · 2022-07-19T17:58:45.000+02:00
[FIX] fix ALI toolbox issues
diff --git a/.all-contributorsrc b/.all-contributorsrc
@@ -145,6 +145,15 @@
       "contributions": [
         "bug"
       ]
+    },
+    {
+      "login": "christine0903",
+      "name": "Christine Chouinard-Leclaire",
+      "avatar_url": "https://avatars.githubusercontent.com/u/70207207?v=4",
+      "profile": "https://github.com/christine0903",
+      "contributions": [
+        "ideas"
+      ]
     }
   ],
   "contributorsPerLine": 7,
diff --git a/.github/workflows/validate_cff.yml b/.github/workflows/validate_cff.yml
@@ -35,4 +35,4 @@ jobs:
         pip3 install cffconvert
 
     - name: Validate CITATION.cff
-      run: cffconvert --validate
+      run: make validate_cff
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -55,6 +55,6 @@ repos:
   - id: black
 
 - repo: https://github.com/asottile/reorder_python_imports
-  rev: v3.3.0
+  rev: v3.8.1
   hooks:
   - id: reorder-python-imports
diff --git a/CITATION.cff b/CITATION.cff
@@ -80,6 +80,11 @@ authors:
   orcid: "https://orcid.org/0000-0001-8681-5267"
   affiliation: "Université catholique de Louvain"
 
+- family-names: "Chouinard-Leclaire"
+  given-names: "Christine"
+  orcid: "https://orcid.org/0000-0002-1066-6266"
+  affiliation: "Université de Montréal"
+
 license: GPL-3.0
 
 keywords:
diff --git a/Makefile b/Makefile
@@ -48,6 +48,9 @@ fix_submodule: ## Fix any submodules that would not be checked out
 version.txt: CITATION.cff
 	grep -w "^version" CITATION.cff | sed "s/version: /v/g" > version.txt
 
+validate_cff: ## Validate the citation file
+	cffconvert --validate
+
 
 ################################################################################
 #   doc
diff --git a/README.md b/README.md
@@ -11,7 +11,7 @@
 [![pre-commit](https://img.shields.io/badge/pre--commit-enabled-brightgreen?logo=pre-commit&logoColor=white)](https://github.com/pre-commit/pre-commit)
 [![codecov](https://codecov.io/gh/cpp-lln-lab/CPP_SPM/branch/main/graph/badge.svg?token=PMQYH0DIPX)](https://codecov.io/gh/cpp-lln-lab/CPP_SPM)
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.3554331.svg)](https://doi.org/10.5281/zenodo.3554331)
-[![All Contributors](https://img.shields.io/badge/all_contributors-12-orange.svg?style=flat-square)](https://github.com/cpp-lln-lab/CPP_SPM#contributors)
+[![All Contributors](https://img.shields.io/badge/all_contributors-13-orange.svg?style=flat-square)](https://github.com/cpp-lln-lab/CPP_SPM#contributors)
 
 <!-- markdown-link-check-enable -->
 
@@ -180,6 +180,7 @@ Thanks goes to these wonderful people
     <td align="center"><a href="https://github.com/mcgnunes"><img src="https://avatars.githubusercontent.com/u/98760858?v=4?s=100" width="100px;" alt=""/><br /><sub><b>Márcia Nunes</b></sub></a><br /><a href="https://github.com/cpp-lln-lab/CPP_SPM/issues?q=author%3Amcgnunes" title="Bug reports">🐛</a></td>
     <td align="center"><a href="https://cpplab.be"><img src="https://avatars0.githubusercontent.com/u/55407947?v=4?s=100" width="100px;" alt=""/><br /><sub><b>Olivier Collignon</b></sub></a><br /><a href="https://github.com/cpp-lln-lab/CPP_SPM/commits?author=OliColli" title="Code">💻</a> <a href="#design-OliColli" title="Design">🎨</a> <a href="https://github.com/cpp-lln-lab/CPP_SPM/commits?author=OliColli" title="Documentation">📖</a></td>
     <td align="center"><a href="https://remi-gau.github.io/"><img src="https://avatars3.githubusercontent.com/u/6961185?v=4?s=100" width="100px;" alt=""/><br /><sub><b>Remi Gau</b></sub></a><br /><a href="https://github.com/cpp-lln-lab/CPP_SPM/commits?author=Remi-Gau" title="Code">💻</a> <a href="https://github.com/cpp-lln-lab/CPP_SPM/commits?author=Remi-Gau" title="Documentation">📖</a> <a href="#infra-Remi-Gau" title="Infrastructure (Hosting, Build-Tools, etc)">🚇</a> <a href="#design-Remi-Gau" title="Design">🎨</a> <a href="https://github.com/cpp-lln-lab/CPP_SPM/pulls?q=is%3Apr+reviewed-by%3ARemi-Gau" title="Reviewed Pull Requests">👀</a> <a href="https://github.com/cpp-lln-lab/CPP_SPM/issues?q=author%3ARemi-Gau" title="Bug reports">🐛</a> <a href="https://github.com/cpp-lln-lab/CPP_SPM/commits?author=Remi-Gau" title="Tests">⚠️</a></td>
+    <td align="center"><a href="https://github.com/christine0903"><img src="https://avatars.githubusercontent.com/u/70207207?v=4?s=100" width="100px;" alt=""/><br /><sub><b>Christine Chouinard-Leclaire</b></sub></a><br /><a href="#ideas-christine0903" title="Ideas, Planning, & Feedback">🤔</a></td>
   </tr>
 </table>
 
diff --git a/src/batches/lesion/setBatchLesionSegmentation.m b/src/batches/lesion/setBatchLesionSegmentation.m
@@ -21,10 +21,16 @@
 
   [anatImage, anatDataDir] = getAnatFilename(BIDS, opt, subLabel);
 
-  hdr = spm_vol(fullfile(anatDataDir, anatImage));
-  voxRes = diag(hdr.mat);
-  voxRes = min(voxRes(1:3));
-  unified_segmentation.step1vox = abs(voxRes);
+  % TODO
+  % this needs to be changed
+  % - to be consistent across subject
+  % - to reslice the size of the mask that is then used for lesion detection
+  %
+  %   hdr = spm_vol(fullfile(anatDataDir, anatImage));
+  %   voxRes = diag(hdr.mat);
+  %   voxRes = min(voxRes(1:3));
+  %   unified_segmentation.step1vox = abs(voxRes);
+
   unified_segmentation.step1data{1} = fullfile(anatDataDir, anatImage);
 
   matlabbatch{end + 1}.spm.tools.ali.unified_segmentation = unified_segmentation;
diff --git a/src/defaults/ALI_my_defaults.m b/src/defaults/ALI_my_defaults.m
@@ -52,8 +52,11 @@
   defaults.toolbox.ALI.outliers_detection.step3tissue.step3Lambda = -4;
 
   % specify lesion mask
-  defaults.toolbox.ALI.lesionMask = fullfile(spmDir, 'toolbox', 'ALI', ...
-                                             'Mask_image', 'mask_controls_vox2mm.nii');
+  defaults.toolbox.ALI.outliers_detection.step3mask{1} = fullfile(spmDir, ...
+                                                                  'toolbox', ...
+                                                                  'ALI', ...
+                                                                  'Mask_image', ...
+                                                                  'mask_controls_vox2mm.nii');
 
   % threshold for the mask
   defaults.toolbox.ALI.outliers_detection.step3mask_thr = 0;
diff --git a/src/workflows/lesion/bidsLesionAbnormalitiesDetection.m b/src/workflows/lesion/bidsLesionAbnormalitiesDetection.m
@@ -80,6 +80,6 @@ function bidsLesionAbnormalitiesDetection(opt)
   matlabbatch = {};
   matlabbatch = setBatchLesionAbnormalitiesDetection(matlabbatch, opt, images);
 
-  saveAndRunWorkflow(matlabbatch, 'LesionAbnormalitiesDetection', opt, subLabel);
+  saveAndRunWorkflow(matlabbatch, 'LesionAbnormalitiesDetection', opt);
 
 end
