Merge branch 'dev' of https://github.com/cpp-lln-lab/CPP_ROI into dev

Remi-Gau · Remi-Gau · commit 1defdfb5229d · 2022-06-18T08:56:21.000+02:00
diff --git a/.github/workflows/validate_cff.yml b/.github/workflows/validate_cff.yml
@@ -0,0 +1,38 @@
+name: validate CITATION.cff
+
+on:
+  push:
+    branches: ['*']
+    paths:
+      - 'CITATION.cff'
+      - '.github/workflows/validate_cff.yml'
+  pull_request:
+    branches: ['*']
+    paths:
+      - 'CITATION.cff'
+      - '.github/workflows/validate_cff.yml'
+
+jobs:
+
+  validate_cff:
+
+    runs-on: ubuntu-latest
+
+    steps:
+
+    - uses: actions/checkout@v3
+      with:
+        fetch-depth: 1
+
+    - name: Set up Python
+      uses: actions/setup-python@v3
+      with:
+        python-version: 3.9
+
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip setuptools
+        pip3 install cffconvert
+
+    - name: Validate CITATION.cff
+      run: cffconvert --validate
diff --git a/.tributors b/.tributors
@@ -1,11 +1,14 @@
 {
     "marcobarilari": {
         "name": "Marco Barilari",
-        "blog": "https://github.com/marcobarilari"
+        "blog": "https://github.com/marcobarilari",
+        "orcid": "0000-0002-3313-3120"
     },
     "Remi-Gau": {
         "name": "Remi Gau",
-        "blog": "https://github.com/Remi-Gau"
+        "blog": "https://github.com/Remi-Gau",
+        "orcid": "0000-0002-1535-9767",
+        "affiliation": "Université catholique de Louvain"
     },
     "JeanneCaronGuyon ": {
         "name": "Jeanne Caron-Guyon ",
@@ -17,10 +20,14 @@
     },
     "fedefalag": {
         "name": "Federica Falagiarda",
-        "blog": "https://github.com/fedefalag"
+        "blog": "https://github.com/fedefalag",
+        "orcid": "0000-0001-7844-1605",
+        "affiliation": "Université catholique de Louvain"
     },
     "CerenB": {
         "name": "Ceren Battal",
-        "blog": "https://github.com/CerenB"
+        "blog": "https://github.com/CerenB",
+        "orcid": "0000-0002-9844-7630",
+        "affiliation": "Université catholique de Louvain"
     }
 }
diff --git a/CITATION.cff b/CITATION.cff
@@ -2,7 +2,7 @@ cff-version: 1.2.0
 
 title: "CPP ROI"
 
-version: 0.2.0dev
+version: 0.3.0
 
 abstract: Set of Octave and Matlab functions, demos and scripts to help manage ROIs and to play nice with BIDS datasets.
 
@@ -37,6 +37,11 @@ authors:
   orcid: "https://orcid.org/0000-0001-7844-1605"
   affiliation: "Université catholique de Louvain"
 
+- family-names: "Caron-Guyon"
+  given-names: "Jeanne"
+  orcid: "https://orcid.org/0000-0001-8681-5267"
+  affiliation: "Université catholique de Louvain"
+
 license: GPL-3.0
 
 keywords:
diff --git a/README.md b/README.md
@@ -64,18 +64,9 @@ as a submodule, and intitialized when running `initCppSpm`.
     -   the SPM Anatomy toolbox (INSERT URL)
     -   the SPM neuromorphometric atlas
     -   neurosynth probabilty maps
-    -   the probabilistic maps of visual topography in human cortex:
+    -   the probabilistic maps of visual topography in human cortex [@wang2014]
         -   https://scholar.princeton.edu/napl/resources
-        -   Wang, L., Mruczek, R. E., Arcaro, M. J., & Kastner, S. (2015).
-            Probabilistic Maps of Visual Topography in Human Cortex. Cerebral
-            cortex (New York, N.Y. : 1991), 25(10), 3911–3931.
-            https://doi.org/10.1093/cercor/bhu277
-    -   the probabilistic functional atlas of human occipito-temporal visual
-        cortex
-        -   Rosenke, M., van Hoof, R., van den Hurk, J., Grill-Spector, K., &
-            Goebel, R. (2021). A Probabilistic Functional Atlas of Human
-            Occipito-Temporal Visual Cortex. Cerebral cortex (New York, N.Y. :
-            1991), 31(1), 603–619. https://doi.org/10.1093/cercor/bhaa246
+    -   the probabilistic functional atlas of human occipito-temporal visual cortex [@rosenke2020]
 
 Also includes:
 
@@ -87,10 +78,12 @@ Also includes:
 <!-- markdownlint-disable -->
 <table>
   <tr>
-    <td align="center"><a href="https://github.com/marcobarilari"><img src="https://avatars.githubusercontent.com/u/38101692?v=4?s=100" width="100px;" alt=""/><br /><sub><b>Marco Barilari</b></sub></a><br /><a href="https://github.com/cpp-lln-lab/CPP_ROI/commits?author=marcobarilari" title="Code">💻</a></td>
-    <td align="center"><a href="https://github.com/Remi-Gau"><img src="https://avatars.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_ROI/commits?author=Remi-Gau" title="Code">💻</a></td>
+    <td align="center"><a href="https://github.com/marcobarilari"><img src="https://avatars.githubusercontent.com/u/38101692?v=4?s=100" width="100px;" alt=""/><br /><sub><b>Marco Barilari</b></sub></a><br /><a href="https://github.com/cpp-lln-lab/CPP_ROI/commits?author=marcobarilari" title="Code">💻</a> <a href="https://github.com/cpp-lln-lab/CPP_ROI/commits?author=marcobarilari" title="Documentation">📖</a> <a href="#ideas-marcobarilari" title="Ideas, Planning, & Feedback">🤔</a></td>
+    <td align="center"><a href="https://github.com/Remi-Gau"><img src="https://avatars.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_ROI/commits?author=Remi-Gau" title="Code">💻</a> <a href="https://github.com/cpp-lln-lab/CPP_ROI/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_ROI/pulls?q=is%3Apr+reviewed-by%3ARemi-Gau" title="Reviewed Pull Requests">👀</a> <a href="https://github.com/cpp-lln-lab/CPP_ROI/issues?q=author%3ARemi-Gau" title="Bug reports">🐛</a> <a href="https://github.com/cpp-lln-lab/CPP_ROI/commits?author=Remi-Gau" title="Tests">⚠️</a></td>
+    <td align="center"><a href="https://github.com/JeanneCaronGuyon"><img src="https://avatars.githubusercontent.com/u/8718798?v=4?s=100" width="100px;" alt=""/><br /><sub><b>Jeanne Caron-Guyon </b></sub></a><br /><a href="#ideas-JeanneCaronGuyon " title="Ideas, Planning, & Feedback">🤔</a> <a href="#userTesting-JeanneCaronGuyon " title="User Testing">📓</a></td>
+    <td align="center"><a href="https://github.com/iqrashahzad14"><img src="https://avatars.githubusercontent.com/u/75671348?v=4?s=100" width="100px;" alt=""/><br /><sub><b>Iqra Shahzad</b></sub></a><br /><a href="#userTesting-iqrashahzad14" title="User Testing">📓</a></td>
     <td align="center"><a href="https://github.com/fedefalag"><img src="https://avatars2.githubusercontent.com/u/50373329?v=4?s=100" width="100px;" alt=""/><br /><sub><b>Federica Falagiarda</b></sub></a><br /><a href="https://github.com/cpp-lln-lab/CPP_ROI/issues?q=author%3Afedefalag" title="Bug reports">🐛</a> <a href="#userTesting-fedefalag" title="User Testing">📓</a></td>
-    <td align="center"><a href="https://github.com/CerenB"><img src="https://avatars.githubusercontent.com/u/10451654?v=4?s=100" width="100px;" alt=""/><br /><sub><b>Ceren Battal</b></sub></a><br /><a href="https://github.com/cpp-lln-lab/CPP_ROI/commits?author=CerenB" title="Code">💻</a></td>
+    <td align="center"><a href="https://github.com/CerenB"><img src="https://avatars.githubusercontent.com/u/10451654?v=4?s=100" width="100px;" alt=""/><br /><sub><b>Ceren Battal</b></sub></a><br /><a href="https://github.com/cpp-lln-lab/CPP_ROI/commits?author=CerenB" title="Code">💻</a> <a href="https://github.com/cpp-lln-lab/CPP_ROI/pulls?q=is%3Apr+reviewed-by%3ACerenB" title="Reviewed Pull Requests">👀</a> <a href="#userTesting-CerenB" title="User Testing">📓</a></td>
   </tr>
 </table>
 
diff --git a/references.bib b/references.bib
@@ -0,0 +1,29 @@
+@article{rosenke2020,
+  author  = {Rosenke, Mona and van Hoof, Rick and van den Hurk, Job and Grill-Spector, Kalanit and Goebel, Rainer},
+  title   = {{A Probabilistic Functional Atlas of Human Occipito-Temporal Visual Cortex}},
+  journal = {Cerebral Cortex},
+  volume  = {31},
+  number  = {1},
+  pages   = {603-619},
+  year    = {2020},
+  month   = {09},
+  issn    = {1047-3211},
+  doi     = {10.1093/cercor/bhaa246},
+  url     = {https://doi.org/10.1093/cercor/bhaa246},
+  eprint  = {https://academic.oup.com/cercor/article-pdf/31/1/603/34840143/bhaa246.pdf}
+}
+
+@article{wang2014,
+  author  = {Wang, Liang and Mruczek, Ryan E.B. and Arcaro, Michael J. and Kastner, Sabine},
+  title   = {{Probabilistic Maps of Visual Topography in Human Cortex}},
+  journal = {Cerebral Cortex},
+  volume  = {25},
+  number  = {10},
+  pages   = {3911-3931},
+  year    = {2014},
+  month   = {12},
+  issn    = {1047-3211},
+  doi     = {10.1093/cercor/bhu277},
+  url     = {https://doi.org/10.1093/cercor/bhu277},
+  eprint  = {https://academic.oup.com/cercor/article-pdf/25/10/3911/14102011/bhu277.pdf}
+}
diff --git a/src/roi/plotDataInRoi.m b/src/roi/plotDataInRoi.m
@@ -222,7 +222,11 @@ function labelAxis(roiAs, rows, cols, subplotList, roiImages, dataLabel)
       subplot(rows, cols, subplotList(1, i));
 
       bf = bids.File(roiImages{i});
-      title(sprintf('roi: %s', bf.entities.label));
+      desc = '';
+      if isfield(bf.entities, 'desc')
+        desc = sprintf('- desc: %s', bf.entities.desc);
+      end
+      title(sprintf('roi: %s%s', bf.entities.label, desc));
 
       subplot(rows, cols, subplotList(end, i));
 
diff --git a/src/roi/resliceRoiImages.m b/src/roi/resliceRoiImages.m
@@ -1,10 +1,31 @@
-% (C) Copyright 2021 CPP ROI developers
-
-function reslicedImages = resliceRoiImages(referenceImage, imagesToCheck)
+function [reslicedImages, matlabbatch] = resliceRoiImages(referenceImage, imagesToCheck, dryRun)
+  %
+  % Check if images are in the same orientation and reslice if necessarrry.
+  %
+  % USAGE::
+  %
+  %     reslicedImages = resliceRoiImages(referenceImage, imagesToCheck, dryRun)
+  %
+  % :param referenceImage:
+  % :type referenceImage: path
+  %
+  % :param imagesToCheck:
+  % :type imagesToCheck: path or cellstr
+  %
+  % :param dryRun: Returns the matlabbatch without running it.
+  % :type dryRun: logical
+  %
+  % (C) Copyright 2021 CPP ROI developers
 
   % TODO
   % - allow option to binarize output?
 
+  if nargin < 3
+    dryRun = false;
+  end
+
+  matlabbatch = {};
+
   % check if files are in the same space
   % if not we reslice the ROI to have the same resolution as the data image
   sts = checkRoiOrientation(referenceImage, imagesToCheck);
@@ -13,9 +34,11 @@
 
   else
 
-    matlabbatch = {};
     matlabbatch = setBatchReslice(matlabbatch, referenceImage, imagesToCheck);
-    spm_jobman('run', matlabbatch);
+
+    if ~dryRun
+      spm_jobman('run', matlabbatch);
+    end
 
     basename = spm_file(imagesToCheck, 'basename');
     reslicedImages = spm_file(imagesToCheck, 'basename', ...
diff --git a/version.txt b/version.txt
@@ -1 +1 @@
-v0.2.0dev
+v0.3.0
