nipreps · oesteban · Sep 4, 2025 · Sep 2, 2025 · Sep 3, 2025 · Sep 3, 2025
diff --git a/.github/workflows/linkcheck.yml b/.github/workflows/linkcheck.yml
@@ -28,8 +28,16 @@ jobs:
         uses: actions/setup-python@v5
         with:
           python-version: 3.12
+      - name: Install MkDocs
+        run: pip install -r requirements.txt
 
-      - uses: tcort/github-action-markdown-link-check@v1
+      - name: Build site
+        run: mkdocs build
+
+      - name: Check links
+        uses: tcort/github-action-markdown-link-check@v1
         with:
           use-quiet-mode: yes
-          # use-verbose-mode: no
+          config-file: .markdown-link-check.json
+          folder-path: site
+          file-extension: .html
diff --git a/.markdown-link-check.json b/.markdown-link-check.json
@@ -0,0 +1,11 @@
+{
+  "ignorePatterns": [
+    {"pattern": "^http://127\\.0\\.0\\.1:8445"},
+    {"pattern": "^http://192\\.168\\.99\\.100:8445"},
+    {"pattern": "biorxiv\\.org"},
+    {"pattern": "doi\\.org"},
+    {"pattern": "toptal\\.com"},
+    {"pattern": "nbirn\\.net"},
+    {"pattern": "^/"}
+  ]
+}
diff --git a/docs/apps/docker.md b/docs/apps/docker.md
@@ -292,7 +292,7 @@ Once the *Docker Engine* arguments are written, the remainder of the
 command line follows the interface defined by the specific
 *BIDS App* (for instance,
 [*fMRIPrep*](https://fmriprep.readthedocs.io/en/latest/usage.html)
-or [*MRIQC*](https://mriqc.readthedocs.io/en/latest/running.html#command-line-interface)).
+or [*MRIQC*](https://mriqc.readthedocs.io/en/latest/usage.html#a-bids-apps-command-line-interface)).
 
 The first section of a call consists of arguments specific to *Docker*,
 which configure the execution of the container:

diff --git a/docs/apps/framework.md b/docs/apps/framework.md
@@ -5,7 +5,7 @@
 brain datasets, including MRI.
 The common naming convention and folder structure allow researchers to easily reuse BIDS datasets, re-apply analysis protocols, and run standardized automatic data preprocessing pipelines (and particularly, BIDS Apps).
 The [BIDS starter-kit](https://github.com/bids-standard/bids-starter-kit) contains a wide collection of educational resources.
-Validity of the structure can be assessed with the online [BIDS-Validator](https://bids-standard.github.io/bidsvalidator/).
+Validity of the structure can be assessed with the online [BIDS-Validator](https://bids-standard.github.io/bids-validator/).
 The tree of a typical, valid (*BIDS-compliant*) dataset is shown below:
 
 ```

diff --git a/docs/apps/singularity.md b/docs/apps/singularity.md
@@ -72,7 +72,7 @@ $ singularity run --cleanenv fmriprep.simg \
 
 ## Handling environment variables
 
-Singularity by default [exposes all environment variables from the host inside the container](https://github.com/singularityware/singularity/issues/445).
+Singularity by default [exposes all environment variables from the host inside the container](https://github.com/apptainer/singularity/issues/445).
 Because of this, your host libraries (e.g., [NiPype](https://nipype.readthedocs.io) or a Python environment) could be accidentally used instead of the ones inside the
 container. To avoid such a situation, we strongly **recommend** using the
 `--cleanenv` argument in all scenarios. For example:

diff --git a/docs/assets/ORN-Workshop/index.html b/docs/assets/ORN-Workshop/index.html
@@ -259,7 +259,7 @@
           highlightLines: true,
           countIncrementalSlides: false,
           highlightSpans: true,
-          sourceUrl: 'https://raw.githubusercontent.com/nipreps/nipreps.github.io/mkdocs/docs/assets/ORN-Workshop/presentation.md',
+          sourceUrl: 'presentation.md',
           ratio: '16:9'
       });
     </script>

diff --git a/docs/assets/ORN-Workshop/presentation.md b/docs/assets/ORN-Workshop/presentation.md
@@ -53,7 +53,7 @@ class: section-separator
 <br />
 
 <p align="center">
-<img src="../nipreps-qr.svg" width="70%" />
+<object type="text/xml+svg" data="https://raw.githubusercontent.com/nipreps/identity/refs/heads/main/nipreps-general/qr-code.svg" style="width: 70%"></object>
 </p>
 <br />
 <p align="center">
@@ -77,7 +77,7 @@ layout: true
 <br />
 
 <p align="center">
-<img src="../nipreps-qr.svg" width="70%" />
+<object type="text/xml+svg" data="https://raw.githubusercontent.com/nipreps/identity/refs/heads/main/nipreps-general/qr-code.svg" style="width: 70%"></object>
 </p>
 <br />
 <p align="center">
@@ -125,7 +125,7 @@ template: sidebar
 ## The garden of forking paths
 
 <p align="center">
-<img src="assets/narps.png" width="800px" alt="NARPS Paper" />
+<img src="../assets/narps.png" width="800px" alt="NARPS Paper" />
 </p>
 
 (Botvinik-Nezer et al., 2020)
@@ -139,7 +139,7 @@ Around 50% of teams used fMRIPrep'ed inputs.
 ### fMRIPrep produces analysis-ready data from diverse data
 * minimal requirements ([BIDS-compliant](https://bids-standard.github.io/bids-validator/));
 * *agnostic* to downstream steps of the workflow
-  * produces [BIDS-Derivatives](https://bids-specification.readthedocs.io/en/derivatives/05-derivatives/01-introduction.html);
+  * produces [BIDS-Derivatives](https://bids-specification.readthedocs.io/en/stable/derivatives/introduction.html);
 * robust against inhomogeneity of data across studies
 
 ???
@@ -227,7 +227,7 @@ to fmriprep.org, which is the documentation website.
 ## Key aspect: credit all direct contributors
 
 <p align="center">
-<img src="assets/fmriprep-authors.png" width="700px" alt="fMRIPrep authors" />
+<img src="../assets/fmriprep-authors.png" width="700px" alt="fMRIPrep authors" />
 </p>
 
 --

diff --git a/docs/assets/bhd2020/index.html b/docs/assets/bhd2020/index.html
@@ -259,7 +259,7 @@
           highlightLines: true,
           countIncrementalSlides: false,
           highlightSpans: true,
-          sourceUrl: 'https://raw.githubusercontent.com/nipreps/nipreps.github.io/mkdocs/docs/assets/bhd2020/presentation.md',
+          sourceUrl: 'presentation.md',
           ratio: '16:9'
       });
     </script>

diff --git a/docs/assets/bhd2020/presentation.md b/docs/assets/bhd2020/presentation.md
@@ -53,7 +53,7 @@ class: section-separator
 <br />
 
 <p align="center">
-<img src="../nipreps-qr.svg" width="70%" />
+<object type="text/xml+svg" data="https://raw.githubusercontent.com/nipreps/identity/refs/heads/main/nipreps-general/qr-code.svg" style="width: 70%"></object>
 </p>
 <br />
 <p align="center">
@@ -77,7 +77,7 @@ layout: true
 <br />
 
 <p align="center">
-<img src="../nipreps-qr.svg" width="70%" />
+<object type="text/xml+svg" data="https://raw.githubusercontent.com/nipreps/identity/refs/heads/main/nipreps-general/qr-code.svg" style="width: 70%"></object>
 </p>
 <br />
 <p align="center">
@@ -196,7 +196,7 @@ Around 50% of teams used *fMRIPrep*'ed inputs.
 ### fMRIPrep produces analysis-ready data from diverse data
 * minimal requirements ([BIDS-compliant](https://bids-standard.github.io/bids-validator/));
 * *agnostic* to downstream steps of the workflow
-  * produces [BIDS-Derivatives](https://bids-specification.readthedocs.io/en/derivatives/05-derivatives/01-introduction.html);
+  * produces [BIDS-Derivatives](https://bids-specification.readthedocs.io/en/stable/derivatives/introduction.html);
 * robust against inhomogeneity of data across studies
 
 ???

diff --git a/docs/assets/torw2020/presentation.md b/docs/assets/torw2020/presentation.md
@@ -1,3 +1,4 @@
+<!-- markdown-link-check-disable -->
 name: title
 layout: true
 class: center
@@ -103,7 +104,7 @@ template: sidebar
 ### fMRIPrep produces analysis-ready data from acquired (fMRI) data
 * minimal requirements ([BIDS-compliant](https://bids-standard.github.io/bids-validator/));
 * *agnostic* to downstream steps of the workflow
-  * produces [BIDS-Derivatives](https://bids-specification.readthedocs.io/en/derivatives/05-derivatives/01-introduction.html);
+  * produces [BIDS-Derivatives](https://bids-specification.readthedocs.io/en/stable/derivatives/introduction.html);
 
 ???
 
@@ -1200,3 +1201,4 @@ layout: false
 
 ## Questions?
 ]
+<!-- markdown-link-check-enable -->
diff --git a/docs/community/CONTRIBUTING.md b/docs/community/CONTRIBUTING.md
@@ -389,7 +389,7 @@ You're awesome. :wave::smiley:
 [link_stemmrolemodels]: https://github.com/KirstieJane/STEMMRoleModels
 [link_zenodo]: https://github.com/nipreps/fmriprep/blob/master/.zenodo.json
 [link_update_script]: https://github.com/nipreps/fmriprep/blob/master/.maint/update_authors.py
-[link_devel]: https://fmriprep.readthedocs.io/en/latest/contributors.html
+[link_devel]: ../devs/devenv.md
 [link_fmriprep]: http://fmriprep.org
 [link_bidsapps]: https://bids-apps.neuroimaging.io
 [link_mattermost]: https://mattermost.brainhack.org/brainhack/channels/fmriprep

diff --git a/docs/community/features.md b/docs/community/features.md
@@ -75,7 +75,7 @@ as the *NiPreps* maintainers will consider them:
     > Especially when the CLI is affected, and yet another option is added,
     > that makes the tool more complex to use.
     >
-    > -- <cite>Alejandro ([source](https://github.com/nipreps/fmriprep/    issues/1963#issuecomment-582174814))</cite>.
+    > -- <cite>Alejandro ([source](https://github.com/nipreps/fmriprep/issues/1963#issuecomment-582174814))</cite>.
 
   * Does the new feature substantially **increase the internal complexity**?
     Maintainers and developers will attempt to consolidate tools and lower the internal

diff --git a/docs/community/members.md b/docs/community/members.md
@@ -16,15 +16,15 @@ section.
 
 Developers are members of a wonderful team _driving the project_.
 Names and contacts of all developers are included in the
-[`.maint/developers.json` file](https://github.com/nipreps/fmriprep/blob/master/.maint/developers.json) of each project.
+[`.maint/MAINTAINERS.md` file](https://github.com/nipreps/fmriprep/blob/master/.maint/MAINTAINERS.md) of each project.
 Examples of steering activities that _drive the project_ are: actively participating in the
 follow-up meetings, leading documentation sprints, helping in the design of the tool and definition of the roadmap,
 providing resources (in the broad sense, including funding), code-review, etc.
 
 ### Contributors
 
 Contributors enlisted in the
-[`.maint/contributors.json` file](https://github.com/nipreps/fmriprep/blob/master/.maint/contributors.json) of each project
+[`.maint/CONTRIBUTORS.md` file](https://github.com/nipreps/fmriprep/blob/master/.maint/CONTRIBUTORS.md) of each project
 actively help or have previously helped the project in a broad sense: writing code, writing documentation,
 benchmarking modules of the tool, proposing new features, helping improve the scientific
 rigor of implementations, giving out support on the different communication
@@ -37,7 +37,7 @@ Before every release, unlisted contributors will be invited again to add their n
 
 Contributors who have contributed at some point to the project but were required or they wished to
 disconnect from the project's updates and to drop-out from publications and other dissemination activities,
-are listed in the [`.maint/former.json` file](https://github.com/nipreps/fmriprep/blob/master/.maint/former.json).
+are listed in the [`.maint/FORMER.md` file](https://github.com/nipreps/fmriprep/blob/master/.maint/FORMER.md).
 
 
-[link_neurostars]: https://neurostars.org
+[link_neurostars]: https://neurostars.org
diff --git a/docs/devs/devenv.md b/docs/devs/devenv.md
@@ -154,7 +154,7 @@ INFO    - No authentication
 INFO    - Not serving HTTPS
 ```
 
-Now you can switch to your favorite browser and go to: [127.0.0.1:8445](http://127.0.0.1:8445) (or [192.168.99.100:8445](http://192.168.99.100:8445) for Docker Toolbox).
+Now you can switch to your favorite browser and go to: `http://127.0.0.1:8445` (or `http://192.168.99.100:8445` for Docker Toolbox).
 
 **3. Copy `fmriprep.egg-info` into your `fmriprep/` project directory**
 `fmriprep.egg-info` makes the package executable inside the docker container.

diff --git a/docs/users/educational.md b/docs/users/educational.md
@@ -13,12 +13,12 @@
 
 ## Online books
 
-- [QC-Book, member-initiated tutorial at ISMRM 2022](../../qc-book)
-- [NiPreps Book, developing processing tools for dMRI, ISBI 2021](../../nipreps-book)
+- [QC-Book, member-initiated tutorial at ISMRM 2022](https://www.nipreps.org/qc-book)
+- [NiPreps Book, developing processing tools for dMRI, ISBI 2021](https://www.nipreps.org/nipreps-book/)
 
 ## QC protocols and Standard Operating Procedures
 
-- [SOPs-cookiecutter, a template repository for version-controlled SOPs](https//github.com/nipreps/sops-cookiecutter). The example template is rendered [here](/sops-cookiecutter/)
+- [SOPs-cookiecutter, a template repository for version-controlled SOPs](https://github.com/nipreps/sops-cookiecutter). The example template is rendered [here](/sops-cookiecutter/)
 
 ## Presentation
 - [Educational Talk at OHBM 2023 - Quality Control in fMRI studies with MRIQC and fMRIPrep](../../assets/OHBM2023/QCTalkOHBM23CelineProvins.pdf)