brainprep: update URLs.

AGrigis · AGrigis · commit 0d4b43fb083a · 2026-04-01T14:08:51.000+02:00
diff --git a/README.rst b/README.rst
@@ -14,28 +14,28 @@
 
 **Development**
 
-.. image:: https://coveralls.io/repos/neurospin-deepinsight/brainprep/badge.svg?branch=dev&service=github
-    :target: https://coveralls.io/github/neurospin-deepinsight/brainprep
+.. image:: https://coveralls.io/repos/brainprepdesk/brainprep/badge.svg?branch=dev&service=github
+    :target: https://coveralls.io/github/brainprepdesk/brainprep
     :alt: Coveralls
 
-.. image:: https://github.com/neurospin-deepinsight/brainprep/actions/workflows/testing.yml/badge.svg?branch=dev
-    :target: https://github.com/neurospin-deepinsight/brainprep/actions
+.. image:: https://github.com/brainprepdesk/brainprep/actions/workflows/testing.yml/badge.svg?branch=dev
+    :target: https://github.com/brainprepdesk/brainprep/actions
     :alt: Testing Status
 
-.. image:: https://github.com/neurospin-deepinsight/brainprep/actions/workflows/pycodestyle.yml/badge.svg?branch=dev
-    :target: https://github.com/neurospin-deepinsight/brainprep/actions
+.. image:: https://github.com/brainprepdesk/brainprep/actions/workflows/pycodestyle.yml/badge.svg?branch=dev
+    :target: https://github.com/brainprepdesk/brainprep/actions
     :alt: PyCodeStyle
 
-.. image:: https://github.com/neurospin-deepinsight/brainprep/actions/workflows/ruff.yml/badge.svg?branch=dev
-    :target: https://github.com/neurospin-deepinsight/brainprep/actions
+.. image:: https://github.com/brainprepdesk/brainprep/actions/workflows/ruff.yml/badge.svg?branch=dev
+    :target: https://github.com/brainprepdesk/brainprep/actions
     :alt: Ruff Linter
 
-.. image:: https://github.com/neurospin-deepinsight/brainprep/actions/workflows/pydoclint.yml/badge.svg?branch=dev
-    :target: https://github.com/neurospin-deepinsight/brainprep/actions
+.. image:: https://github.com/brainprepdesk/brainprep/actions/workflows/pydoclint.yml/badge.svg?branch=dev
+    :target: https://github.com/brainprepdesk/brainprep/actions
     :alt: PyDocLint
 
-.. image:: https://github.com/neurospin-deepinsight/brainprep/actions/workflows/documentation.yml/badge.svg?branch=dev
-    :target: https://neurospin-deepinsight.github.io/brainprep
+.. image:: https://github.com/brainprepdesk/brainprep/actions/workflows/documentation.yml/badge.svg?branch=dev
+    :target: https://brainprepdesk.github.io/brainprep
     :alt: Documentation Status
 
 **Release**
@@ -96,9 +96,9 @@ scalable, and reproducible foundation to accelerate your research.
 Important Links
 ===============
 
-- Official source code repo: https://github.com/neurospin-deepinsight/brainprep
-- HTML documentation (stable release): https://neurospin-deepinsight.github.io/brainprep/stable
-- HTML documentation (dev): https://neurospin-deepinsight.github.io/brainprep/dev
+- Official source code repo: https://github.com/brainprepdesk/brainprep
+- HTML documentation (stable release): https://brainprepdesk.github.io/brainprep/stable
+- HTML documentation (dev): https://brainprepdesk.github.io/brainprep/dev
 
 
 Install
@@ -156,7 +156,7 @@ Dependencies
 ============
 
 The required dependencies to use the software are listed
-in the file `pyproject.toml <https://github.com/neurospin-deepinsight/brainprep/blob/main/pyproject.toml>`_.
+in the file `pyproject.toml <https://github.com/brainprepdesk/brainprep/blob/main/pyproject.toml>`_.
 
 
 Citation
@@ -171,5 +171,5 @@ repository. Thank you.
     @misc{brainprep,
         title = {{BrainPrep source code (Version 1.0.0)}},
         author = {Grigis, Antoine and Victor, Julie and Dorval, Loic and Duchesnay, Edouard},
-        url = {https://github.com/neurospin-deepinsight/brainprep},
+        url = {https://github.com/brainprepdesk/brainprep},
     }
diff --git a/brainprep/decorators.py b/brainprep/decorators.py
@@ -485,7 +485,7 @@ def before_call(
                     {
                         "Name": "brainprep",
                         "Version": __version__,
-                        "CodeURL": ("https://github.com/neurospin-deepinsight/"
+                        "CodeURL": ("https://github.com/brainprepdesk/"
                                     "brainprep"),
                     }
                 ],
diff --git a/brainprep/reporting/data/base.html b/brainprep/reporting/data/base.html
@@ -33,7 +33,7 @@
     <link
       rel="icon"
       type="image/x-icon"
-      href="https://raw.githubusercontent.com/neurospin-deepinsight/brainprep/refs/heads/dev/doc/logos/favicon.ico"
+      href="https://raw.githubusercontent.com/brainprepdesk/brainprep/refs/heads/dev/doc/logos/favicon.ico"
     />
   </head>
   <body>
@@ -62,7 +62,7 @@
             </div>
             <div class="col-6 text-right">
               <div class="mr-auto">
-                <a href="https://github.com/neurospin-deepinsight/brainprep" class="p-2 pl-0"><i class="fa fa-github"></i></a>
+                <a href="https://github.com/brainprepdesk/brainprep" class="p-2 pl-0"><i class="fa fa-github"></i></a>
               </div>
               
             </div>
diff --git a/brainprep/reporting/data/body.html b/brainprep/reporting/data/body.html
@@ -22,7 +22,7 @@
 
     <section id="workflow-details-{{ uuid }}">
       <h3>Description</h3>
-        Data were analyzed using <a href="https://neurospin-deepinsight/brainprep">BrainPrep</a>
+        Data were analyzed using <a href="https://brainprepdesk/brainprep">BrainPrep</a>
         (version={{ version }}).
         <br/><br/>
         <pre><code class="language-html">
diff --git a/containers/Dockerfile.defacing b/containers/Dockerfile.defacing
@@ -81,7 +81,7 @@ LABEL org.opencontainers.image.title="BrainPrep Defacing" \
       org.opencontainers.image.version="v2" \
       org.opencontainers.image.licenses="CeCILL-B" \
       org.opencontainers.image.authors="CEA/NeuroSpin/GAIA" \
-      org.opencontainers.image.documentation="https://neurospin-deepinsight.github.io/brainprep/stable" \
-      org.opencontainers.image.source="https://github.com/neurospin-deepinsight/brainprep" \
+      org.opencontainers.image.documentation="https://brainprepdesk.github.io/brainprep/stable" \
+      org.opencontainers.image.source="https://github.com/brainprepdesk/brainprep" \
       org.opencontainers.image.created="2025-01-15" \
       com.brainprep.fsl.version="${FSL_VERSION}"
diff --git a/containers/Dockerfile.fmriprep b/containers/Dockerfile.fmriprep
@@ -34,7 +34,7 @@ LABEL org.opencontainers.image.title="BrainPrep functional MRI preprocessings" \
       org.opencontainers.image.version="v2" \
       org.opencontainers.image.licenses="CeCILL-B" \
       org.opencontainers.image.authors="CEA/NeuroSpin/GAIA" \
-      org.opencontainers.image.documentation="https://neurospin-deepinsight.github.io/brainprep/stable" \
-      org.opencontainers.image.source="https://github.com/neurospin-deepinsight/brainprep" \
+      org.opencontainers.image.documentation="https://brainprepdesk.github.io/brainprep/stable" \
+      org.opencontainers.image.source="https://github.com/brainprepdesk/brainprep" \
       org.opencontainers.image.created="2025-01-15" \
       com.brainprep.fmriprep.version="25.2.4"
diff --git a/containers/Dockerfile.quality_assurance b/containers/Dockerfile.quality_assurance
@@ -34,7 +34,7 @@ LABEL org.opencontainers.image.title="BrainPrep Defacing" \
       org.opencontainers.image.version="v2" \
       org.opencontainers.image.licenses="CeCILL-B" \
       org.opencontainers.image.authors="CEA/NeuroSpin/GAIA" \
-      org.opencontainers.image.documentation="https://neurospin-deepinsight.github.io/brainprep/stable" \
-      org.opencontainers.image.source="https://github.com/neurospin-deepinsight/brainprep" \
+      org.opencontainers.image.documentation="https://brainprepdesk.github.io/brainprep/stable" \
+      org.opencontainers.image.source="https://github.com/brainprepdesk/brainprep" \
       org.opencontainers.image.created="2025-01-15" \
       com.brainprep.mriqc.version="24.0.2"
diff --git a/containers/Dockerfile.quasiraw b/containers/Dockerfile.quasiraw
@@ -206,8 +206,8 @@ LABEL org.opencontainers.image.title="BrainPrep Quasi-Raw" \
       org.opencontainers.image.version="v2" \
       org.opencontainers.image.licenses="CeCILL-B" \
       org.opencontainers.image.authors="CEA/NeuroSpin/GAIA" \
-      org.opencontainers.image.documentation="https://neurospin-deepinsight.github.io/brainprep/stable" \
-      org.opencontainers.image.source="https://github.com/neurospin-deepinsight/brainprep" \
+      org.opencontainers.image.documentation="https://brainprepdesk.github.io/brainprep/stable" \
+      org.opencontainers.image.source="https://github.com/brainprepdesk/brainprep" \
       org.opencontainers.image.created="2025-01-15" \
       com.brainprep.fsl.version="${FSL_VERSION}" \
       com.brainprep.freesurfer.version="${FS_VERSION}" \
diff --git a/containers/Dockerfile.sbm b/containers/Dockerfile.sbm
@@ -169,7 +169,7 @@ LABEL org.opencontainers.image.title="BrainPrep SBM" \
       org.opencontainers.image.version="v2" \
       org.opencontainers.image.licenses="CeCILL-B" \
       org.opencontainers.image.authors="CEA/NeuroSpin/GAIA" \
-      org.opencontainers.image.documentation="https://neurospin-deepinsight.github.io/brainprep/stable" \
-      org.opencontainers.image.source="https://github.com/neurospin-deepinsight/brainprep" \
+      org.opencontainers.image.documentation="https://brainprepdesk.github.io/brainprep/stable" \
+      org.opencontainers.image.source="https://github.com/brainprepdesk/brainprep" \
       org.opencontainers.image.created="2025-01-15" \
       com.brainprep.freesurfer.version="$FS_VERSION"
diff --git a/containers/Dockerfile.vbm b/containers/Dockerfile.vbm
@@ -98,8 +98,8 @@ LABEL org.opencontainers.image.title="BrainPrep VBM" \
       org.opencontainers.image.version="v2" \
       org.opencontainers.image.licenses="CeCILL-B" \
       org.opencontainers.image.authors="CEA/NeuroSpin/GAIA" \
-      org.opencontainers.image.documentation="https://neurospin-deepinsight.github.io/brainprep/stable" \
-      org.opencontainers.image.source="https://github.com/neurospin-deepinsight/brainprep" \
+      org.opencontainers.image.documentation="https://brainprepdesk.github.io/brainprep/stable" \
+      org.opencontainers.image.source="https://github.com/brainprepdesk/brainprep" \
       org.opencontainers.image.created="2025-01-15" \
       com.brainprep.mcr.version="$MCR_VERSION" \
       com.brainprep.cat12.version="$CAT12_VERSION $CAT12_TAG" \
diff --git a/containers/README.rst b/containers/README.rst
@@ -25,7 +25,7 @@ Then, generate the new recipies (one per workflow type):
         --label description="brainprep quality assesssment" version="2.0" \
         --yes \
         --entrypoint python3 \
-        --run-bash "pip install git+https://github.com/neurospin-deepinsight/brainprep.git@dev" \
+        --run-bash "pip install git+https://github.com/brainprepdesk/brainprep.git@dev" \
         > Dockerfile.qa
 
     neurodocker generate docker \
@@ -35,7 +35,7 @@ Then, generate the new recipies (one per workflow type):
         --entrypoint python3 \
         --fsl version=6.0.7.18 \
           install_path=/opt/fsl-6.0.7.18 \
-        --run-bash "pip install git+https://github.com/neurospin-deepinsight/brainprep.git@dev" \
+        --run-bash "pip install git+https://github.com/brainprepdesk/brainprep.git@dev" \
         > Dockerfile.defacing
 
     neurodocker generate docker \
@@ -49,7 +49,7 @@ Then, generate the new recipies (one per workflow type):
           install_path=/opt/freesurfer-7.4.1 \
           exclude_paths="average/mult-comp-cor lib/cuda lib/qt subjects/V1_average subjects/bert subjects/cvs_avg35 subjects/cvs_avg35_inMNI152 subjects/fsaverage3 subjects/fsaverage4 subjects/fsaverage5 subjects/fsaverage6 subjects/fsaverage_sym trctrain" \
         --ants version=2.6.2 \
-        --run-bash "pip install git+https://github.com/neurospin-deepinsight/brainprep.git@dev" \
+        --run-bash "pip install git+https://github.com/brainprepdesk/brainprep.git@dev" \
         > Dockerfile.quasiraw
 
     neurodocker generate docker \
@@ -60,7 +60,7 @@ Then, generate the new recipies (one per workflow type):
         --matlabmcr version=2023b \
         --cat12 version=12.9_R2023b \
           install_path=/opt/cat12-12.9_R2023b \
-        --run-bash "pip install git+https://github.com/neurospin-deepinsight/brainprep.git@dev" \
+        --run-bash "pip install git+https://github.com/brainprepdesk/brainprep.git@dev" \
         > Dockerfile.vbm
 
     neurodocker generate docker \
@@ -71,7 +71,7 @@ Then, generate the new recipies (one per workflow type):
         --freesurfer version=7.4.1 \
           install_path=/opt/freesurfer-7.4.1 \
           exclude_paths="diffusion docs fsfast average/mult-comp-cor lib/cuda lib/qt subjects/V1_average subjects/bert subjects/cvs_avg35 subjects/cvs_avg35_inMNI152 subjects/fsaverage3 subjects/fsaverage4 subjects/fsaverage5 subjects/fsaverage6 subjects/fsaverage_sym trctrain" \
-        --run-bash "pip install git+https://github.com/neurospin-deepinsight/brainprep.git@dev" \
+        --run-bash "pip install git+https://github.com/brainprepdesk/brainprep.git@dev" \
         > Dockerfile.brainparc
 
     neurodocker generate docker \
@@ -81,23 +81,23 @@ Then, generate the new recipies (one per workflow type):
         --entrypoint python3 \
         --fsl version=6.0.7.18 \
           install_path=/opt/fsl-6.0.7.18 \
-        --run-bash "pip install git+https://github.com/neurospin-deepinsight/brainprep.git@dev" \
+        --run-bash "pip install git+https://github.com/brainprepdesk/brainprep.git@dev" \
         > Dockerfile.tbss
 
     neurodocker generate docker \
         --base-image nipreps/fmriprep:25.2.3 \
         --pkg-manager apt \
         --yes \
         --entrypoint python3 \
-        --run-bash "pip install git+https://github.com/neurospin-deepinsight/brainprep.git@dev" \
+        --run-bash "pip install git+https://github.com/brainprepdesk/brainprep.git@dev" \
         > Dockerfile.fmriprep
 
     neurodocker generate docker \
         --base-image pennlinc/qsiprep:1.0.2 \
         --pkg-manager apt \
         --yes \
         --entrypoint python3 \
-        --run-bash "pip install git+https://github.com/neurospin-deepinsight/brainprep.git@dev" \
+        --run-bash "pip install git+https://github.com/brainprepdesk/brainprep.git@dev" \
         > Dockerfile.dmriprep
 
 .. note::
diff --git a/containers/resources/entrypoint.sh b/containers/resources/entrypoint.sh
@@ -10,7 +10,7 @@ cat <<EOF
 
   Version : 2
   License : CeCILL-B
-  Source  : https://github.com/neurospin-deepinsight/brainprep
+  Source  : https://github.com/brainprepdesk/brainprep
 
   Container started at : $START_TIME
 
diff --git a/containers/resources/pixi.toml b/containers/resources/pixi.toml
@@ -8,5 +8,5 @@ platforms = ["linux-64"]
 python = "==3.12"
 
 [pypi-dependencies]
-brainprep = { git = "https://github.com/neurospin-deepinsight/brainprep.git", branch = "dev" }
+brainprep = { git = "https://github.com/brainprepdesk/brainprep.git", branch = "main" }
 
diff --git a/examples/tools/plot_html_reporting.py b/examples/tools/plot_html_reporting.py
@@ -26,12 +26,12 @@
 
 
 git_download(
-    url=("https://raw.githubusercontent.com/neurospin-deepinsight/brainprep/"
+    url=("https://raw.githubusercontent.com/brainprepdesk/brainprep/"
          "dev/doc/logos/brainprep.png"),
     destination=working_dir / "im1.png",
 )
 git_download(
-    url=("https://raw.githubusercontent.com/neurospin-deepinsight/brainprep/"
+    url=("https://raw.githubusercontent.com/brainprepdesk/brainprep/"
          "dev/doc/logos/brainprep.png"),
     destination=working_dir / "im2.png",
 )
diff --git a/pyproject.toml b/pyproject.toml
@@ -62,9 +62,9 @@ doc = [
 ]
 
 [project.urls]
-Development = "https://github.com/neurospin-deepinsight/brainprep"
-issues = "https://github.com/neurospin-deepinsight/brainprep/issues"
-homepage = "https://neurospin-deepinsight.github.io/brainprep/stable"
+Development = "https://github.com/brainprepdesk/brainprep"
+issues = "https://github.com/brainprepdesk/brainprep/issues"
+homepage = "https://brainprepdesk.github.io/brainprep/stable"
 
 [tool.setuptools]
 include-package-data = true
diff --git a/references.bib b/references.bib
@@ -1,8 +1,8 @@
 @misc{brainprep-source,
-  title      = "neurospin-deepinsight/brainprep: v1.0.0",
+  title      = "brainprepdesk/brainprep: v1.0.0",
   author     = "Grigis, Antoine and Victor, Julie and Dorval, Loic and
                 Duchesnay, Edouard",
-  url        = "https://github.com/neurospin-deepinsight/brainprep",
+  url        = "https://github.com/brainprepdesk/brainprep",
   year       = 2025,
 }
 
@@ -180,7 +180,7 @@ @article{bischoff2007deface
 @misc{gulban2009deface,
   title      = "poldracklab/pydeface: v2.0.0",
   author     = "Gulban, O. F. and Nielson D. and Poldrack R.",
-  url        = "https://github.com/neurospin-deepinsight/brainprep",
+  url        = "https://zenodo.org/records/3524401",
   year       = 2009,
 }
 
@@ -528,6 +528,15 @@ @article{reuter2012freesurferlong
 }
 
 
+@article{fischer2012morphologist,
+    title   = "Morphologist 2012: the new morphological pipeline of BrainVISA",
+    author  = "Fischer, C. and Operto, Grégory and Laguitton, S. and
+               Perrot, Matthieu and Denghien, I. and Rivière, D.",
+    year    = 2012,
+    journal = "Proceedings of the 18th HBM Scientific Meeting}
+}
+
+
 
 
 

Original file line number	Diff line number	Diff line change
`@@ -485,7 +485,7 @@ def before_call(`
`485`	`485`	`{`
`486`	`486`	`"Name": "brainprep",`
`487`	`487`	`"Version": __version__,`
`488`		`- "CodeURL": ("https://github.com/neurospin-deepinsight/"`
	`488`	`+ "CodeURL": ("https://github.com/brainprepdesk/"`
`489`	`489`	`"brainprep"),`
`490`	`490`	`}`
`491`	`491`	`],`