Merge branch 'main' into blog/SG_20240808

bids-standard · Oct 19, 2024 · d816c78 · d816c78
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diff --git a/docs/blog/posts/2023-05-25-steering-group-minutes.md b/docs/blog/posts/2023-05-25-steering-group-minutes.md
@@ -135,8 +135,7 @@ Add a list of BIDS ignore files:
 Should we reach out to the new **Imaging Neuroscience** journal while
 they are still developing their platform?
 
-Potentially reach out to someone on their [[editorial
-board]](https://janeway.imaging-neuroscience.org/editorialteam/)
+Potentially reach out to someone on their [editorial board](https://direct.mit.edu/imag/pages/editorial-info)
 
 -   possible Thomas Yeo, Damian Fair
 

diff --git a/docs/blog/posts/bids-news-september-2024.md b/docs/blog/posts/bids-news-september-2024.md
@@ -47,7 +47,7 @@ You can find more [about BIDS governance](https://bids-website.readthedocs.io/en
 
 ## Recent venues BIDS presented
 
-BIDS continues to be featured in different venues. Our very own maintainer extraordinaire, Rémi Gau, was recently featured in a yet-to-be-released podcast. The BIDS Town Hall was featured at OHBM again this year in June. For a full recount refer to [this blog post](https://bids-website.readthedocs.io/en/latest/blog/2024/07/01/BIDS%20Town%20Hall%202024%3A%20summary.html).
+BIDS continues to be featured in different venues. Our very own maintainer extraordinaire, Rémi Gau, was recently featured in a yet-to-be-released podcast. The BIDS Town Hall was featured at OHBM again this year in June. For a full recount refer to [this blog post](./town-hall-2024-debrief.md).
 
 ## BIDS Extension Proposals (BEPs)
 

diff --git a/docs/extensions/beps.md b/docs/extensions/beps.md
@@ -17,6 +17,10 @@ Below is a table of BEPs that have been merged.
 The references of the final publication for those BEPS
 can be found in the BIDS [specification](https://bids-specification.readthedocs.io/en/latest/01-introduction.html#datatype-specific-publications).
 
+<!-- use snippet to include a file
+https://facelessuser.github.io/pymdown-extensions/extensions/snippets/#snippets-notation
+-->
+
 --8<-- "tmp/bids_timeline.html"
 
 {{ MACROS___generate_beps_table(file="beps_completed.yml", type="completed") }}

diff --git a/docs/extensions/general-guidelines.md b/docs/extensions/general-guidelines.md
diff --git a/docs/getting_started/resources/talks.md b/docs/getting_started/resources/talks.md
@@ -20,20 +20,20 @@ Two great resources for curated lists of talks and slides are:
 
 ## Other Slideshows and talk
 
-| Title                                                                            | Speaker                             | Year | Occasion                                                                                                                                              | Location                             | Video                                                                                        | Slides                                                                                                                       |
-| -------------------------------------------------------------------------------- | ----------------------------------- | ---- | ----------------------------------------------------------------------------------------------------------------------------------------------------- | ------------------------------------ | -------------------------------------------------------------------------------------------- | ---------------------------------------------------------------------------------------------------------------------------- |
-| BIDS: underlying data management principles                                      | Remi Gau                            | 2022 | [Open Research at the Wellcome Centre for Integrative Neuroimaging (WIN)](https://open.win.ox.ac.uk/pages/open-science/community/Open-WIN-Community/) | Online                               | [link](https://vimeo.com/showcase/7645853/video/668642973)                                   | [link](https://osf.io/h6gsr/)                                                                                                |
-| BIDS: a recipe for success                                                       | Patricia Clement                    | 2021 | [GlimR](https://glimr.eu/) BIDS workshop                                                                                                              |                                      | [link](https://www.youtube.com/watch?v=ukgiAP2Hn3E)                                          | [link](https://osf.io/nu24a)                                                                                                 |
-| BIDS conversion                                                                  | Remi Gau & Guiomar Niso             | 2021 | ACCS & OHBM Webinar and Workshop Series                                                                                                               | online                               | [link](https://www.youtube.com/watch?v=m7vEHGpqQIw)                                          | [link](https://remi-gau.github.io/bids_cookbook/)                                                                            |
-| The BIDS Ecosystem                                                               | Chris Markiewicz                    | 2020 | Neuro Data Science School                                                                                                                             | Online                               | n/a                                                                                          | [link](https://effigies.github.io/bids-ecosystem/)                                                                           |
-| BIDS Applications and Derivatives                                                | Chris Markiewicz                    | 2019 | BIDS Computational Models Workshop                                                                                                                    | Princeton USA                        | n/a                                                                                          | [link](https://effigies.github.io/bids-derivatives/)                                                                         |
-| BIDS Apps Metadata                                                               | Chris Markiewicz                    | 2019 | Making Open Neuroscience Infrastructure Interoperable (MONII 2.0)                                                                                     | Montreal, Canada                     | n/a                                                                                          | [link](https://effigies.github.io/bids-metadata/)                                                                            |
-| BIDS - Open Science Working Group                                                | A Shephard                          | 2018 | n/a                                                                                                                                                   | Aston University, Birmingham England | n/a                                                                                          | [link](https://github.com/bids-standard/bids-starter-kit/files/2068336/Brain.Imaging.Data.Structure.-.OSWG.pptx)             |
-| FAIR Data - BIDS datasets                                                        | Maryann Martone & Jeffrey Grethe    | 2018 | OHBM                                                                                                                                                  | Singapore                            | [link](https://www.pathlms.com/ohbm/courses/8246/sections/12542/video_presentations/115883#) | n/a                                                                                                                          |
-| ReproIn: automatic, shareable, version-controlled BIDS datasets from MR scanners | Matteo Visconti di Oleggio Castello | 2018 | OHBM                                                                                                                                                  | Singapore                            | n/a                                                                                          | [link](https://www.pathlms.com/ohbm/courses/8246/sections/12541/video_presentations/115999#)                                 |
-| OpenNeuro presentation                                                           | Krzysztof Gorgolewski               | 2017 | OHBM                                                                                                                                                  | Vancouver, Canada                    | [link](https://www.pathlms.com/ohbm/courses/5158/sections/7806/video_presentations/76062#)   | [link](https://www.slideshare.net/chrisfilo1/openneuro-a-free-online-platform-for-sharing-and-analysis-of-neuroimaging-data) |
-| fMRIprep                                                                         | Krzysztof Gorgolewski               | 2017 | n/a                                                                                                                                                   | Stanford University, Stanford USA    | n/a                                                                                          | [link](https://www.slideshare.net/chrisfilo1/fmriprep-robust-and-easy-to-use-fmri-preprocessing-pipeline)                    |
-| BIDS                                                                             | Krzysztof Gorgolewski               | 2016 | OHBM                                                                                                                                                  | Geneva, Switzerland                  | n/a                                                                                          | [link](https://www.slideshare.net/chrisfilo1/the-brain-imaging-data-structure-ohbm-2016)                                     |
+| Title                                                                            | Speaker                             | Year | Occasion                                                                | Location                             | Video                                                                                        | Slides                                                                                                                       |
+| -------------------------------------------------------------------------------- | ----------------------------------- | ---- | ------------------------------------------------------------------------| ------------------------------------ | -------------------------------------------------------------------------------------------- | ---------------------------------------------------------------------------------------------------------------------------- |
+| BIDS: underlying data management principles                                      | Remi Gau                            | 2022 | Open Research at the Wellcome Centre for Integrative Neuroimaging (WIN) | Online                               | [link](https://vimeo.com/showcase/7645853/video/668642973)                                   | [link](https://osf.io/h6gsr/)                                                                                                |
+| BIDS: a recipe for success                                                       | Patricia Clement                    | 2021 | [GlimR](https://glimr.eu/) BIDS workshop                                |                                      | [link](https://www.youtube.com/watch?v=ukgiAP2Hn3E)                                          | [link](https://osf.io/nu24a)                                                                                                 |
+| BIDS conversion                                                                  | Remi Gau & Guiomar Niso             | 2021 | ACCS & OHBM Webinar and Workshop Series                                 | online                               | [link](https://www.youtube.com/watch?v=m7vEHGpqQIw)                                          | [link](https://remi-gau.github.io/bids_cookbook/)                                                                            |
+| The BIDS Ecosystem                                                               | Chris Markiewicz                    | 2020 | Neuro Data Science School                                               | Online                               | n/a                                                                                          | [link](https://effigies.github.io/bids-ecosystem/)                                                                           |
+| BIDS Applications and Derivatives                                                | Chris Markiewicz                    | 2019 | BIDS Computational Models Workshop                                      | Princeton USA                        | n/a                                                                                          | [link](https://effigies.github.io/bids-derivatives/)                                                                         |
+| BIDS Apps Metadata                                                               | Chris Markiewicz                    | 2019 | Making Open Neuroscience Infrastructure Interoperable (MONII 2.0)       | Montreal, Canada                     | n/a                                                                                          | [link](https://effigies.github.io/bids-metadata/)                                                                            |
+| BIDS - Open Science Working Group                                                | A Shephard                          | 2018 | n/a                                                                     | Aston University, Birmingham England | n/a                                                                                          | [link](https://github.com/bids-standard/bids-starter-kit/files/2068336/Brain.Imaging.Data.Structure.-.OSWG.pptx)             |
+| FAIR Data - BIDS datasets                                                        | Maryann Martone & Jeffrey Grethe    | 2018 | OHBM                                                                    | Singapore                            | [link](https://www.pathlms.com/ohbm/courses/8246/sections/12542/video_presentations/115883#) | n/a                                                                                                                          |
+| ReproIn: automatic, shareable, version-controlled BIDS datasets from MR scanners | Matteo Visconti di Oleggio Castello | 2018 | OHBM                                                                    | Singapore                            | n/a                                                                                          | [link](https://www.pathlms.com/ohbm/courses/8246/sections/12541/video_presentations/115999#)                                 |
+| OpenNeuro presentation                                                           | Krzysztof Gorgolewski               | 2017 | OHBM                                                                    | Vancouver, Canada                    | [link](https://www.pathlms.com/ohbm/courses/5158/sections/7806/video_presentations/76062#)   | [link](https://www.slideshare.net/chrisfilo1/openneuro-a-free-online-platform-for-sharing-and-analysis-of-neuroimaging-data) |
+| fMRIprep                                                                         | Krzysztof Gorgolewski               | 2017 | n/a                                                                     | Stanford University, Stanford USA    | n/a                                                                                          | [link](https://www.slideshare.net/chrisfilo1/fmriprep-robust-and-easy-to-use-fmri-preprocessing-pipeline)                    |
+| BIDS                                                                             | Krzysztof Gorgolewski               | 2016 | OHBM                                                                    | Geneva, Switzerland                  | n/a                                                                                          | [link](https://www.slideshare.net/chrisfilo1/the-brain-imaging-data-structure-ohbm-2016)                                     |
 
 <!-- TEMPLATE -->
 <!-- | Title    | Speaker  | Year | Occasion    | Location     | [link](video) | [link](slides)    |  -->

diff --git a/docs/getting_started/templates/index.md b/docs/getting_started/templates/index.md
@@ -0,0 +1,24 @@
+# Templates
+
+This section contains templates of different files you can find in a BIDS dataset,
+so tou can copy-paste-modity them into your own dataset.
+
+## README.md
+
+<!-- use snippet to include a file
+https://facelessuser.github.io/pymdown-extensions/extensions/snippets/#snippets-notation
+-->
+
+```markdown
+--8<-- "templates/README.md"
+```
+
+## dataset_description.json
+
+<!-- use snippet to include a file
+https://facelessuser.github.io/pymdown-extensions/extensions/snippets/#snippets-notation
+-->
+
+```json
+--8<-- "templates/dataset_description.json"
+```
diff --git a/docs/getting_started/tutorials/annotation.md b/docs/getting_started/tutorials/annotation.md
@@ -26,13 +26,13 @@ Annotations in BIDS can be done at several levels, including the dataset, subjec
 funding, and citation information.
 This file does not provide any actual description of the data.
 
-> You can fill in this blank [dataset description template](https://raw.githubusercontent.com/bids-standard/bids-starter-kit/main/templates/dataset_description.json) or use it as a guide.
+> You can fill in this blank [dataset description template](../templates/index.md#dataset_descriptionjson) or use it as a guide.
 
 ### Dataset description (`README`)
 `README` file is a top-level text file that gives the actual overview of the dataset.
 A comprehensive `README` is essential for users of your data.
 
-> You can edit the [README template](https://raw.githubusercontent.com/bids-standard/bids-starter-kit/main/templates/README.MD) with the vital information needed for others to analyze your dataset.
+> You can edit the [README template](../templates/index.md#readmemd) with the vital information needed for others to analyze your dataset.
 
 ## Subject annotations
 Annotations at the subject level can be done in the `participants.tsv` file,

diff --git a/docs/impact/index.md b/docs/impact/index.md
@@ -43,6 +43,10 @@ A listing of the previous grants can be found [here](../collaboration/acknowledg
 
 ### Datasets
 
+<!-- use snippet to include a file
+https://facelessuser.github.io/pymdown-extensions/extensions/snippets/#snippets-notation
+-->
+
 --8<-- "tmp/openneuro_data_growth.html"
 
 ### Citation Count
@@ -51,6 +55,10 @@ BIDS references are  centralized in a [zotero group](https://www.zotero.org/grou
 
 You can also find them [in the specification](https://bids-specification.readthedocs.io/en/latest/introduction.html#citing-bids)
 
+<!-- use snippet to include a file
+https://facelessuser.github.io/pymdown-extensions/extensions/snippets/#snippets-notation
+-->
+
 --8<-- "tmp/citation_per_year.html"
 
 ### GitHub stars
@@ -99,12 +107,24 @@ we have over 300 credited contributors.
 
 Guessed with [gender-guesser](https://pypi.org/project/gender-guesser/)
 
+<!-- use snippet to include a file
+https://facelessuser.github.io/pymdown-extensions/extensions/snippets/#snippets-notation
+-->
+
 --8<-- "data/people/gender.md"
 
 #### Contributors affiliations
 
+<!-- use snippet to include a file
+https://facelessuser.github.io/pymdown-extensions/extensions/snippets/#snippets-notation
+-->
+
 --8<-- "data/people/affiliations.md"
 
+<!-- use snippet to include a file
+https://facelessuser.github.io/pymdown-extensions/extensions/snippets/#snippets-notation
+-->
+
 --8<-- "tmp/affiliations.html"
 
 ### GitHub dependents

diff --git a/makefile b/makefile
@@ -54,5 +54,6 @@ lint: remark
 remark: package.json
 	npx remark \
 		./docs \
+		./templates \
 		--frail \
 		--rc-path .remarkrc
diff --git a/md_link_check_config.json b/md_link_check_config.json
@@ -14,8 +14,10 @@
     },
     {
       "pattern": "^https://www.instagram.com/bidsstandard.*"
+    },
+    {
+      "pattern": "^https://direct.mit.edu/imag/pages/editorial-info"
     }
-
   ],
   "timeout": "20s",
   "retryOn429": true

diff --git a/mkdocs.yml b/mkdocs.yml
@@ -131,6 +131,8 @@ nav:
             -   getting_started/tutorials/conversion/pet.md
     -   How to:
         -   getting_started/how_to/index.md
+    -   Templates:
+        -   getting_started/templates/index.md
 -   Tools:
     -   tools/index.md
     -   tools/validator.md
@@ -177,6 +179,7 @@ theme:
   features:
     - announce.dismiss
     - content.action.edit
+    - content.code.copy
     - content.tooltips
     - footnotes
     - header.autohide