misc

bids-standard · Apr 24, 2024 · 41bdbe8 · 41bdbe8
1 parent b953e51
commit 41bdbe8
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diff --git a/docs/assets/img/BIDS-minder.svg b/docs/assets/img/BIDS-minder.svg
diff --git a/docs/assets/img/BIDS.minder b/docs/assets/img/BIDS.minder
diff --git a/docs/blog/posts/2021-04-29-steering-group-minutes.md b/docs/blog/posts/2021-04-29-steering-group-minutes.md
@@ -25,10 +25,8 @@ The Steering Group began the meeting by discussing a new potential BEP and meeti
 -   Very modality dependent
 -   Wait and see
 -   BIDS authorship
-
 -   Adding transparency to the paper writing process
 -   Add to the BEP submission process guidelines on the [bids-specification wiki](<https://github.com/bids-standard/bids-specification/wiki/BIDS-Extension-Proposal-(BEP)-submission-process>)
-
 -   Monthly update
 -   Important components: what are we working on and the obstacles we are facing
 -   Reports are informative

diff --git a/docs/blog/posts/2023-06-15-steering-group-minutes.md b/docs/blog/posts/2023-06-15-steering-group-minutes.md
@@ -192,13 +192,9 @@ Imaging Neuroscience Response from Steve Smith
 -   Getting started for:
 
     -   Users
-
     -   tools developers,
-
     -   reviewers,
-
     -   funding agencies
-
     -   Institute directors
 
 -   Should this be in the form of a

diff --git a/docs/blog/posts/2023-07-27-steering-group-minutes.md b/docs/blog/posts/2023-07-27-steering-group-minutes.md
@@ -97,11 +97,8 @@ Ray
 ### BIDS Badges
 
 -   Ariel will follow up with Guy Jones
-
 -   Others to reach out to:
-
 -   Renzo Huber @ Aperture - and how can BIDS help Aperture? - Kim will invite them for Sept 7th meeting
-
 -   [Neurolibre](https://github.com/neurolibre/neurolibre) to add a BIDS tag?
 
 ### BIDS Derivatives
@@ -129,18 +126,11 @@ Ray
 ### BIDS 2.0 : (also feedback from the town hall)
 
 -   _Aka BIDS 1.0 with enhancements_
-
 -   How can we take advantage of ontologies in this version?
-
 -   How can new enhancements allow more flexibility for BIDS? for example use of dashes in file names
-
 -   Work on the schema may facilitate or inhibit the transition to BIDS 2.0
-
 -   How/When do we know when BIDS 2.0 is ready?
-
--   Anthony says that the [[schema is
-complete]](https://imgflip.com/i/7txwm7)
-
+-   Anthony says that the [[schema is complete]](https://imgflip.com/i/7txwm7)
 -   New BIDS issue for BIDS 2.0 specification & [project board](https://github.com/orgs/bids-standard/projects/10/views/1?layout=board).
 
 ### Neuro Open Science Prize

diff --git a/docs/blog/posts/2023-11-09-steering-group-minutes.md b/docs/blog/posts/2023-11-09-steering-group-minutes.md
@@ -169,39 +169,25 @@ consolidated.
 Here is a list to get started with:
 
 -   bids.neuroimaging.io (to go under bids-standard.org)
-
 -   apps.neuroimaging.io
-
 -   Starter kit
-
 -   Specification (now on RTD)
-
 -   Extension guidelines (now on RTD)
-
 -   Awesome BIDS list
-
 -   Governance documents that are now as a google doc
-
 -   ...
 
 Things not to merge but to link
 
 -   Google docs with draft BEPs
-
 -   Github organization, issues and workflow
-
 -   Support channels (google group, neurostars)
-
 -   Announcement channels (mattermost, twitter)
-
 -   Merchandize
-
 -   ...
 
 Things that are not for public display
 
 -   Maintainers folder on Google Drive
-
 -   Slack
-
 -   Meeting notes (at least some are not for public display)
diff --git a/docs/blog/posts/2024-02-01-steering-group-minutes.md b/docs/blog/posts/2024-02-01-steering-group-minutes.md
@@ -237,10 +237,15 @@ Yaroslav Halchenko, Rémi Gau
     file to help browse the google drive
 
 -   What?
+
 -   What was achieved by steering in past 2-3 years
+
 -   Current projects in progress in the steering group.
+
 -   A view of typical \"tasks\"/topics the steering is working on.
+
 -   ACTION: Rémi set up a meeting to populate the onboarding docs above
+
 -   ACTION: Kim added bookmark linking the BIDS Maintainers google drive
     in the BIDS steering group slack channel for easier access
 
@@ -251,10 +256,12 @@ Yaroslav Halchenko, Rémi Gau
     not following BEP protocols.
 
 -   Could probably be PR?
+
 -   In any case, we should point them to the bids BEP guidelines:
     [[https://bids-extensions.readthedocs.io/en/latest/guide/#when-and-how-to-start-a-bids-extension-proposal]](https://bids-extensions.readthedocs.io/en/latest/guide/#when-and-how-to-start-a-bids-extension-proposal)
 
 -   BEP guidelines may require too high of a level of understanding of BIDS for a novice user
+
 -   ACTION: Rémi to point to BEP guidelines, mention that it is probably
     not needed to go for a BEP but a PR should be enough. Mention that a
     PR plus example should be enough.
@@ -270,16 +277,21 @@ Yaroslav Halchenko, Rémi Gau
 ### Train the trainers
 
 -   Goal is to make BIDS more accessible and increase impact
+
 -   Similar to data carpentries:
     [[https://carpentries.org/become-instructor/]](https://carpentries.org/become-instructor/)
 
 -   Repronim fellowship:
     [[https://www.repronim.org/fellowship]](https://www.repronim.org/fellowship)
 
 -   This is more geared to help fellows create material for their own training
+
 -   List "certified BIDS trainers" on the BIDS website
+
 -   Having a way to "certify" trainers
+
 -   Who will be the (meta)trainer to train the trainers?
+
 -   Data carpentry BIDS "courses" in the carpentry incubator (**for
     users not trainers**):
     [[https://github.com/bids-standard/bids-starter-kit/issues/136#issue-666838055]](https://github.com/bids-standard/bids-starter-kit/issues/136#issue-666838055)

diff --git a/docs/collaboration/governance.md b/docs/collaboration/governance.md
@@ -156,10 +156,10 @@ standard.
 This group is responsible for maintaining the [BIDS specification on
 GitHub](https://github.com/bids-standard/bids-specification). The Lead
 Maintainer and the Maintainers Group will determine how they organize
-their work, detailed in the [BIDS Maintainers
-guide](https://docs.google.com/document/d/11U43QmYVZUVdCxpJeezmYpkHf4sbzWjjN2EIjbk4Pfo/edit) and in accordance with the BIDS Code of Conduct. The maintainers guide is subject to Steering Group approval and amendment.
-BIDS contributors may self-nominate to become maintainers, with approval
-by a majority vote of current maintainers.
+their work, detailed in the [BIDS Maintainers guide](https://docs.google.com/document/d/11U43QmYVZUVdCxpJeezmYpkHf4sbzWjjN2EIjbk4Pfo/edit) and in accordance with the BIDS Code of Conduct.
+The maintainers guide is subject to Steering Group approval and amendment.
+BIDS contributors may self-nominate to become maintainers,
+with approval by a majority vote of current maintainers.
 
 This group submits
 [monthly status summaries](https://github.com/bids-standard/bids-specification/wiki/BIDS-Maintainers-Documents#bids-maintainers-reports)

diff --git a/docs/contact.md b/docs/contact.md
@@ -19,22 +19,21 @@ just post what you have so far and we will be able to point you in the right dir
 Some example questions that have already been answered include:
 
 -   [BIDS file naming specifications](https://neurostars.org/t/bids-beginner-convert-data-to-bids-format/1364)
-
 -   [BIDS beginner - convert data to BIDS format](https://neurostars.org/t/bids-beginner-convert-data-to-bids-format/1364)
 
 ---
 
 <div class="grid cards" markdown>
 
--   :simple-mattermost:{ .lg .middle } __Mattermost__
+-   :simple-mattermost:{ .lg .middle } **Mattermost**
 
     ---
 
     [:simple-mattermost: Chat on mattermost](https://mattermost.brainhack.org/brainhack/channels/bids_general){ .md-button }
 
     You can also come chat on the [Brainhack mattermost](https://mattermost.brainhack.org/) on the `~bids_general` channel.
 
--   :simple-google:{ .lg .middle } __Mailing list__
+-   :simple-google:{ .lg .middle } **Mailing list**
 
     ---
 
@@ -43,29 +42,27 @@ Some example questions that have already been answered include:
     We'd love for you to join the mailing list.
     You might find some helpful answers and discussions there.
 
--   :email:{ .lg .middle } __Email__
+-   :email:{ .lg .middle } **Email**
 
     ---
 
     [:fontawesome-solid-paper-plane: Email the maintainers](mailto:bids.maintenance+question@gmail.com){ .md-button }
 
     If you have very specific questions you can email the BIDS maintainers.
 
-
--   :handshake_tone1_tone5:{ .lg .middle } __Social media__
+-   :handshake_tone1_tone5:{ .lg .middle } **Social media**
 
     ---
 
     -   [:simple-bluesky: Bluesky](https://bsky.app/profile/bidsstandard.bsky.social/)
     -   [:simple-mastodon: Mastodon](https://fosstodon.org/@bidsstandard/)
-    -   [:simple-x: Twitter/ X ](https://x.com/BIDSstandard)
+    -   [:simple-x: Twitter/ X](https://x.com/BIDSstandard)
     -   [:simple-youtube: YouTube](https://www.youtube.com/embed/-c4PUhTwmz4)
     -   Listen to our [podcast](https://anchor.fm/bids-maintenance)
 
     If you are interested in receiving occasional updates around BIDS,
     feel free to join one of the communication channels that we use regularly.
 
-
 </div>
 
 <!--

diff --git a/docs/FAQ/apps.md → docs/faq/apps.md b/docs/FAQ/apps.md → docs/faq/apps.md
diff --git a/docs/FAQ/bep.md → docs/faq/bep.md b/docs/FAQ/bep.md → docs/faq/bep.md
diff --git a/docs/FAQ/eeg.md → docs/faq/eeg.md b/docs/FAQ/eeg.md → docs/faq/eeg.md
diff --git a/docs/FAQ/general.md → docs/faq/general.md b/docs/FAQ/general.md → docs/faq/general.md
diff --git a/docs/FAQ/index.md → docs/faq/index.md b/docs/FAQ/index.md → docs/faq/index.md
diff --git a/docs/FAQ/mri.md → docs/faq/mri.md b/docs/FAQ/mri.md → docs/faq/mri.md
diff --git a/docs/FAQ/pheno.md → docs/faq/pheno.md b/docs/FAQ/pheno.md → docs/faq/pheno.md
diff --git a/docs/grant_writing_kit.md → docs/grant-writing-kit.md b/docs/grant_writing_kit.md → docs/grant-writing-kit.md
@@ -106,7 +106,7 @@ we have over 300 credited contributors.
 
 #### Gender of contributors
 
-Guessed with: https://pypi.org/project/gender-guesser/
+Guessed with [gender-guesser](https://pypi.org/project/gender-guesser/)
 
 -   male: 177
 -   female: 47

diff --git a/docs/index.md b/docs/index.md
@@ -24,15 +24,24 @@ to reflect current lab practices and make it accessible to a wide range of scien
 
 ## BIDS is a community effort
 
-BIDS is developed by the community for the community and everybody can [become a part of the community](https://bids.neuroimaging.io/get_involved.html).
+BIDS is developed by the community for the community
+and everybody can [become a part of the community](https://bids.neuroimaging.io/get_involved.html).
+
+The most important part of BIDS are the users:
+if more people use it, more data will be shared and the more powerful it will become.
+
+<strong>We want to make it easy to learn</strong> and more adopted.
+
+Since BIDS is platform independent
+and still an adapting, growing tool, the greater the community, the better it will be.
 
 ## Specification vs. Ecosystem
 
 Since the inception of the BIDS specification that documents how to organize neuroimaging data,
 a large ecosystem of tools and resources has evolved around BIDS.
 
 A few of the key elements of this ecosystem are the [BIDS specification](http://bids-specification.readthedocs.io/)
-with the nitty-gritty details, the [BIDS starter kit](https://bids-standard.github.io/bids-starter-kit/)
+with the nitty-gritty details, the [starter kit](./bids-starter-kit/src/index.md)
 with a simple explanation how to work with it, the [BIDS validator](https://github.com/bids-standard/bids-validator)
 to automatically check datasets for adherence to the specification, [BIDS Apps](https://doi.org/10.1371/journal.pcbi.1005209),
 a collection of portable neuroimaging pipelines that understand BIDS datasets, and [OpenNeuro](https://openneuro.org/),
@@ -44,8 +53,41 @@ With the ongoing development of new tools and resources it is important to keep
 that the [BIDS specification](http://bids-specification.readthedocs.io/) remains
 the standard according to which the entire ecosystem must adhere.
 
+## Philosophy
+
+Another part is that BIDS is striving to not reinventing other standards and metadata ontologies but reuse them:
+
+![BIDS-minder](./assets/img/BIDS-minder.svg)
+
 ## Benefits
 
+<div class="grid cards" markdown>
+
+-   :material-account-group:{ .lg .middle } **For the public good**
+
+    ---
+
+    -   Lowers scientific waste
+    -   Gives opportunity to less-funded researchers
+    -   Improves efficiency
+    -   Spurs innovation
+
+-   :recycle:{ .lg .middle } **For yourself**
+
+    ---
+
+    -   You are likely the future user of the data and data analysis pipelines you’ve developed
+
+    -   Enables and simplifies collaboration
+
+    -   Reviewers and funding agencies like to see reproducible results
+
+    -   Open-science based funding opportunities and awards available
+        (for instance: OHBM Replication Award, Mozilla Open Science Fellowship,
+        Google Summer of Code, and so on.)
+
+</div>
+
 By using this standard you will benefit in the following ways:
 
 -   It will be easy for another researcher to work on your data.

diff --git a/docs/merch.md b/docs/merch.md
@@ -0,0 +1,11 @@
+---
+hide:
+-   toc
+-   navigation
+---
+
+See our [store](https://www.teepublic.com/user/bids)
+
+[![](./assets/img/new_merch.png)](https://www.teepublic.com/user/bids)
+
+All profits from sales are donated to the Wikimedia Foundation.
diff --git a/docs/tools/validator.md b/docs/tools/validator.md
@@ -14,45 +14,43 @@ Instructions to install and use these versions can be found
 within the [quickstart guide](https://github.com/bids-standard/bids-validator)
 at the BIDS Validator repository.
 
-**Data Privacy and Confidentiality**
+## Data Privacy and Confidentiality
 
 Please note that the web app is entirely browser(not server) based.
 As such, there is no file uploading as part of the validation.
 
 ## Browser Version
 
-1. The BIDS Validator can be found at <http://bids-standard.github.io/bids-validator/>.
-   It requires that you use the Chrome or Firefox browser,
-   since those are the only ones in which you can select a whole folder rather than individual files.
+1.  The BIDS Validator can be found at <http://bids-standard.github.io/bids-validator/>.
+    It requires that you use the Chrome or Firefox browser,
+    since those are the only ones in which you can select a whole folder rather than individual files.
 
-<!-- TODO grab that image and add to the repo -->
+    ![home](../assets/img/YD38eTE.png)
 
-![home](../assets/img/YD38eTE.png)
-
-2. You can then choose the **folder** that you wish to validate
+1.  You can then choose the **folder** that you wish to validate
 
 ### Types of Feedback
 
 !!! failure "Error"
 
-       This response indicates that your dataset is not BIDS compliant.
-       Try following the suggestions listed to make the appropriate corrections.
+    This response indicates that your dataset is not BIDS compliant.
+    Try following the suggestions listed to make the appropriate corrections.
 
-       ![Error](../assets/img//PEz9hbd.png)
+    ![Error](../assets/img//PEz9hbd.png)
 
 !!! warning
 
-       This response indicates that your dataset is BIDS compliant,
-       but there are some non-critical problems
-       (such as optional fields missing, or differences between participants).
+    This response indicates that your dataset is BIDS compliant,
+    but there are some non-critical problems
+    (such as optional fields missing, or differences between participants).
 
-       ![Warning](../assets/img//Gqwc1q9.png)
+    ![Warning](../assets/img//Gqwc1q9.png)
 
 !!! success "Success :rocket:"
 
-       This response indicates that your folder contains a valid BIDS Dataset!
+    This response indicates that your folder contains a valid BIDS Dataset!
 
-       ![Valid](../assets/img/DPFVXOR.png)
+    ![Valid](../assets/img/DPFVXOR.png)
 
 ## Command Line Version
 

diff --git a/makefile b/makefile
@@ -27,4 +27,4 @@ package.json:
 	npm install `cat npm-requirements.txt`
 
 remark: package.json
-	npx remark .faq ./docs/index.md ./docs/blog ./docs/tools ./docs/collaboration ./docs/FAQ ./docs/grant/README.md ./docs/standards --rc-path .remarkrc
+	npx remark faq ./docs/*.md ./docs/blog ./docs/tools ./docs/collaboration ./docs/FAQ ./docs/standards --rc-path .remarkrc
diff --git a/mkdocs.yml b/mkdocs.yml
@@ -38,6 +38,7 @@ exclude_docs: |
     starter_kit/src/FAQ.md
     starter_kit/src/contact.md
     starter_kit/src/tutorials/media/README.md
+    starter_kit/src/validator.md
     stats_models/README.md
     stats_models/bsmschema/README.md
     stats_models/specification/walkthrough-2.md
@@ -140,18 +141,19 @@ nav:
     -   submission: extensions/docs/submission.md
     -   macros: specification/macros_doc.md
 -   FAQ:
-    -   FAQ/index.md
-    -   general: FAQ/general.md
-    -   eeg: FAQ/eeg.md
-    -   mri: FAQ/mri.md
-    -   phenotype: FAQ/pheno.md
-    -   bids extensions: FAQ/bep.md
-    -   bids apps: FAQ/apps.md
+    -   faq/index.md
+    -   general: faq/general.md
+    -   eeg: faq/eeg.md
+    -   mri: faq/mri.md
+    -   phenotype: faq/pheno.md
+    -   bids extensions: faq/bep.md
+    -   bids apps: faq/apps.md
 -   Blog:
     -   blog/index.md
 -   Impact:
-    -   grant_writing_kit.md
+    -   grant-writing-kit.md
 -   Contact: contact.md
+-   Merch: merch.md
 
 theme:
     name: material