[REF] centralize and update links

README.md

@@ -32,7 +32,7 @@ The specification is hosted on [https://bids-specification.readthedocs.io](https
 To contribute to the specification,
 please submit an [issue](https://github.com/bids-standard/bids-specification/issues)
 or send a [pull request](https://github.com/bids-standard/bids-specification/pulls)
-on the [bids-specification](https://github.com/bids-standard/bids-specification) repository.
+on the [bids-specification][specification_gh] repository.
 
 ## Asking questions about BIDS
 

docs/blog/posts/2020-03-12-steering-group-minutes.md

@@ -21,7 +21,7 @@ We discussed generating an example slide deck that community members can use (or
 We discussed considerations for when to open a repository under the BIDS standard organization on GitHub.
 Previously, community members have opened repositories under the BIDS
 [GitHub organization](https://docs.github.com/en/organizations/collaborating-with-groups-in-organizations/about-organizations)
-named [`bids-standard`](https://github.com/bids-standard).
+named [`bids-standard`][bids_standard].
 We want to codify guidelines to govern this.
 The plan is that there should be multiple people committed to the repository (otherwise it is better under the personal GitHub account), the maintainers should be clearly identifiable (for example, as a
 [CODEOWNERS file](https://docs.github.com/en/repositories/managing-your-repositorys-settings-and-features/customizing-your-repository/about-code-owners#about-code-owners)

docs/blog/posts/2020-03-23-steering-group-minutes.md

@@ -19,17 +19,17 @@ to pilot at NRM and OHBM in June.
 
 We also have a [list of channels](https://docs.google.com/spreadsheets/d/16SAGK3zG93WM2EWuoZDcRIC7ygPc5b7PDNGpFyC3obA/edit#gid=0)
 to share BIDS related information on. The have a plan for handling non-BIDS related information on our channels
-is to share on our [google group](https://groups.google.com/forum/#!forum/bids-discussion).
+is to share on our [google group][bids_google_group].
 
 The attending members of the Steering Group gave approval for moving forward
 with completing the [Genetic Information BEP](https://github.com/bids-standard/bids-specification/pull/395).
 This will solidify the process for incorporating BEPs moving forward.
 
 The process will be:
 
-1.  merging in the BEP constructed examples to [BIDS-examples](https://github.com/bids-standard/bids-examples)
+1.  merging in the BEP constructed examples to [BIDS-examples][bids_examples_gh]
 1.  merge the validator extension into [BIDS-validator](https://github.com/bids-standard/bids-validator), and
-1.  merge the BEP into [BIDS-specification](https://github.com/bids-standard/bids-specification)
+1.  merge the BEP into [BIDS-specification][specification_gh]
 
 The Steering Group gave direction on handling author lists on Zenodo - make it a single author:
 “BIDS Contributors Group” as defined in the [governance document](https://docs.google.com/document/d/1R-J2lL9V_wIkYhye4zH-feyl4P4J8NyO40rIYyY141o/edit).
@@ -65,10 +65,10 @@ The Steering Group gave direction on handling author lists on Zenodo - make it a
 
 -   Attending Steering Group members gave approval to move forward with finalizing the [Genetic Information extension](https://github.com/bids-standard/bids-specification/pull/395) and merging into the specification. This will trigger a [v1.3.0 release](https://github.com/bids-standard/bids-specification/pull/435) (according to our [release guidelines](https://github.com/bids-standard/bids-specification/blob/master/Release_Guideline.md)).
 
--   For future BEPs, they will submit their examples to [BIDS-examples](https://github.com/bids-standard/bids-examples)
+-   For future BEPs, they will submit their examples to [BIDS-examples][bids_examples_gh]
     for review by the Steering Group and confirm the [validator](https://github.com/bids-standard/bids-validator) has been extended properly.
     The BEP leads can leave it as a draft PR.
-    It was determined that opening the PR from a branch of the [BIDS specification repository](https://github.com/bids-standard/bids-specification)
+    It was determined that opening the PR from a branch of the [BIDS specification repository][specification_gh]
     should be done allowing us to render the extension via ReadTheDocs.
 
     -   Genetic Information was in the BEP lead's fork of BIDS-examples (after the meeting a [PR was opened](https://github.com/bids-standard/bids-examples/pull/178)).
@@ -79,7 +79,7 @@ The Steering Group gave direction on handling author lists on Zenodo - make it a
 
 -   The Steering Group discussed where to share non-BIDS related information.
 
--   The consensus was to share on the [bids-discussion](https://groups.google.com/forum/#!forum/bids-discussion) Google group channel.
+-   The consensus was to share on the [bids-discussion][bids_google_group] Google group channel.
 
 -   We brainstormed what may be the related initiatives to keep aware of. FF contacted INCF to see if they have information regarding this. Please see the [INCF blog](https://www.incf.org/blogs-list).
 

docs/blog/posts/2020-03-30-steering-group-minutes.md

@@ -12,7 +12,7 @@ categories:
 
 We discussed how to move forward with implementing the author lists on [Zenodo](https://zenodo.org/record/3686062) from our pdf specification.
 We want to provide guidance on how we landed on our decision: a single author “BIDS Contributing Group”.
-This will be opened as a proposal with a request for comments (RFC) on the [BIDS-Specification repository](https://github.com/bids-standard/bids-specification).
+This will be opened as a proposal with a request for comments (RFC) on the [BIDS-Specification repository][specification_gh].
 This is important to deploy with the community’s approval. This may give way for a stronger contributor tracking system.
 
 We clarified the format and points for the monthly Maintainers update.

docs/blog/posts/2020-06-18-steering-group-minutes.md

@@ -10,7 +10,7 @@ categories:
 
 ## Executive Summary
 
-We discussed and decided on utilizing the [BrainHack Mattermost platform](https://mattermost.brainhack.org/) for our instant messaging solution. This fits nicely into where our community has been informally organized.
+We discussed and decided on utilizing the [BrainHack Mattermost platform][brainhack_mattermost] for our instant messaging solution. This fits nicely into where our community has been informally organized.
 
 We went over our BIDS presentations occurring in the [Open Science Room](https://ohbm.github.io/osr2020/schedule/) at [OHBM](https://www.humanbrainmapping.org/i4a/pages/index.cfm?pageID=3885). We are sharing on the website [all the BIDS presentations and posters](https://bids.neuroimaging.io/2020/06/19/BIDS-OHBM-OSR-2020.html) happening at OHBM. There are many BIDS-aware tools being developed, but an emphasis should be put on generating the associated documentation.
 

docs/blog/posts/2021-02-25-steering-group-minutes.md

@@ -36,7 +36,7 @@ The Steering Group spent the rest of the meeting with the [BEP031: Microscopy](h
 -   Addressing in vivo and ex vivo
 -   There are other types of standards and data structures
 -   [Recent preprint on bioarxiv](https://www.biorxiv.org/content/10.1101/2021.02.10.430563v2) from the SPARC group
--   Detail level questions can be opened as issues in the [bids-specification repository](https://github.com/bids-standard/bids-specification) to get Maintainers thoughts
+-   Detail level questions can be opened as issues in the [bids-specification repository][specification_gh] to get Maintainers thoughts
 -   The [Neuroscience Data Structure](https://github.com/INCF/neuroscience-data-structure/issues) group is another team thinking about this
 -   Considering species, formats, and experiments
 -   Microscopy could be split into microscopy and mouse/animal

docs/blog/posts/community-review-pet.md

@@ -12,8 +12,11 @@ The BIDS community is preparing to merge the PET (Positron Emission Tomography)
 
 1/19 PET community review update: We have extended the community review period to Friday, February 12 at 11:59pm (pacific time).
 
-We are happy to announce that the Positron emission tomography BIDS extension is finally nearing it’s completion. Hence, we are seeking final community feedback for the PET BIDS standard. We are looking for feedback on GitHub and specifically to the [BIDS-PET extension proposal](https://github.com/bids-standard/bids-specification/pull/633). We have also developed an extension for the [validator](https://github.com/bids-standard/legacy-validator/pull/1088) and added [PET examples into BIDS examples](https://github.com/bids-standard/bids-examples/).
+We are happy to announce that the Positron emission tomography BIDS extension is finally nearing it’s completion. Hence, we are seeking final community feedback for the PET BIDS standard.
+We are looking for feedback on GitHub and specifically to the [BIDS-PET extension proposal](https://github.com/bids-standard/bids-specification/pull/633).
+We have also developed an extension for the [validator](https://github.com/bids-standard/legacy-validator/pull/1088) and added [PET examples into BIDS examples][bids_examples_gh].
 
-This BIDS extension seeks to establish how PET data and additional metadata are organized within the BIDS structure. This encompasses the recent guidelines for brain PET data in publications and in archives provided in the consensus paper ([Knudsen et al. 2020](https://doi.org/10.1177/0271678X20905433)), including blood and metabolite data.
+This BIDS extension seeks to establish how PET data and additional metadata are organized within the BIDS structure.
+This encompasses the recent guidelines for brain PET data in publications and in archives provided in the consensus paper ([Knudsen et al. 2020](https://doi.org/10.1177/0271678X20905433)), including blood and metabolite data.
 
 The final review entails a two week period for public commenting, with a possibility of extension for unresolved discussion. Once public comments are concluded, there will be a one week freeze, during which only critical issues will be considered. (Please see our [release protocol](https://github.com/bids-standard/bids-specification/blob/master/Release_Protocol.md) for more details)

docs/blog/posts/join-the-bids-community-on-the-brainhack-mattermost.md

@@ -4,11 +4,11 @@ slug: Join the BIDS community on the BrainHack Mattermost
 author: Franklin Feingold
 ---
 
-BIDS is joining the [BrainHack Mattermost](https://mattermost.brainhack.org/)!
+BIDS is joining the [BrainHack Mattermost][brainhack_mattermost]!
 
 <!-- more -->
 
-We are proud to announce our home for hosting BIDS organization instant messaging: the [BrainHack Mattermost platform](https://mattermost.brainhack.org/)! In the past few years, several BIDS channels have independently been created on Mattermost by the community.
+We are proud to announce our home for hosting BIDS organization instant messaging: the [BrainHack Mattermost platform][brainhack_mattermost]! In the past few years, several BIDS channels have independently been created on Mattermost by the community.
 The Steering Group and Maintainers Group have chosen to recognize the BrainHack Mattermost as a member of our organizations's official communication suite.
 This platform will live alongside our other official communication channels:
 

docs/blog/posts/meet-the-bids-steering-group.md

@@ -126,7 +126,7 @@ Furthermore, I hope that we can extend BIDS with more raw data types, like eye-t
 
 I am a professor of psychology at Stanford.
 My main basic research interests are focused on the brain systems involved in decision making and executive function, primarily using fMRI.
-In the last decade I've become increasingly interested in meta-scientific topics focused on reproducibility and transparency, including involvement in a number of data sharing initiatives including [OpenNeuro](https://openneuro.org/), [NeuroVault](https://neurovault.org/), and [NeuroSynth](https://neurosynth.org/).
+In the last decade I've become increasingly interested in meta-scientific topics focused on reproducibility and transparency, including involvement in a number of data sharing initiatives including [OpenNeuro][openneuro], [NeuroVault](https://neurovault.org/), and [NeuroSynth](https://neurosynth.org/).
 
 #### How did you get involved in BIDS?
 

docs/blog/posts/v1.9.0-release.md

@@ -18,7 +18,7 @@ We would like to thank contributors to this BEP, led by Sein Jeung and Julius We
 
 Check out the [preprint associated with this BEP](https://osf.io/preprints/psyarxiv/w6z79/).
 
-Example datasets for motion data can be found on our [BIDS example repository](https://github.com/bids-standard/bids-examples):
+Example datasets for motion data can be found on our [BIDS example repository][bids_examples_gh]:
 
 -   [motion_dualtask](https://github.com/bids-standard/bids-examples/tree/master/motion_dualtask)
 -   [motion_spotrotation](https://github.com/bids-standard/bids-examples/tree/master/motion_spotrotation)

docs/collaboration/governance.md

@@ -17,12 +17,12 @@ The Brain Imaging Data Structure (BIDS) is a standard specifying the
 description of neuroimaging data in a filesystem hierarchy and of the
 metadata associated with the imaging data.
 The current edition of the standard is available in
-[HTML](https://bids-specification.readthedocs.io/en/stable/) with all
+[HTML][specification] with all
 the previous editions available since October 2018 (listed in the
-[Changelog](https://bids-specification.readthedocs.io/en/stable/CHANGES.html)). The pre-October 2018 specification editions can be found in this [repository](https://github.com/bids-standard/bids-website) as PDFs.
+[Changelog](https://bids-specification.readthedocs.io/en/stable/CHANGES.html)). The pre-October 2018 specification editions can be found in this [repository][bids_wesbite_gh] as PDFs.
 The development edition is available in
-[HTML](https://bids-specification.readthedocs.io/en/latest/).
-The specification is based in a [GitHub repository](https://github.com/bids-standard/bids-specification)
+[HTML][specification].
+The specification is based in a [GitHub repository][specification_gh]
 and rendered with [ReadTheDocs](https://docs.readthedocs.io/en/stable/).
 
 We strive for community consensus in decision making.
@@ -43,11 +43,11 @@ specification development and maintenance,
 [BIDS Extension Proposals (BEPs)](../extensions/beps.md),
 software tools,
 [starter kits](https://bids-standard.github.io/bids-starter-kit/),
-[examples](https://github.com/bids-standard/bids-examples),
+[examples][bids_examples_gh],
 and general discussions.
 The relevant discussions are located in our
-[Google Group](https://groups.google.com/forum/#!forum/bids-discussion),
-[GitHub organization](https://github.com/bids-standard),
+[Google Group][bids_google_group],
+[GitHub organization][bids_standard],
 and public Google Documents (typically associated with an [extension proposal](../extensions/beps.md)).
 
 A key component of the BIDS initiative is the collection of associated
@@ -62,7 +62,7 @@ Python and [bids-matlab](https://github.com/bids-standard/bids-matlab)
 libraries allow querying and manipulating BIDS-compliant datasets,
 [BIDS-Apps](https://bids-website.readthedocs.io/en/latest/tools/bids-apps.html) for running portable
 pipelines on validated BIDS datasets, and platforms like
-[OpenNeuro](https://openneuro.org/) store and serve BIDS datasets. Note
+[OpenNeuro][openneuro] store and serve BIDS datasets. Note
 that the associated software does not fall under the same governance
 structure as BIDS, although the contributor and user base may largely
 overlap.
@@ -153,7 +153,7 @@ standard.
 ### BIDS Maintainers Group
 
 This group is responsible for maintaining the [BIDS specification on
-GitHub](https://github.com/bids-standard/bids-specification). The Lead
+GitHub][specification_gh]. 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.
@@ -179,7 +179,7 @@ However, you may receive a more timely response when pinging them on one of the
 
 This group consists of individuals who have contributed to the BIDS
 community. Group members are identified on the [BIDS
-contributors](https://bids-specification.readthedocs.io/en/latest/99-appendices/01-contributors.html) list,
+contributors](https://bids-specification.readthedocs.io/en/latest/appendices/contributors.html) list,
 a list that is intended to be inclusive of all forms of engagement with the BIDS community,
 and that contributors are encouraged to update via the
 [specification wiki](https://github.com/bids-standard/bids-specification/wiki/Recent-Contributors).
@@ -234,8 +234,8 @@ The working/interest group formation is formalized
 through an open letter via a "read-only" Google Document addressed to the BIDS Steering Group.
 The open letter will be posted on:
 
--   the [BIDS-Specification GitHub repository](https://github.com/bids-standard/bids-specification),
--   [Google Group](https://groups.google.com/forum/#!forum/bids-discussion),
+-   the [BIDS-Specification GitHub repository][specification_gh],
+-   [Google Group][bids_google_group],
 -   and [social media channels](<https://github.com/bids-standard/bids-specification?tab=readme-ov-file#BIDS-communication-channels>).
 
 This proposal will state what their group aims and goals are.
@@ -300,7 +300,7 @@ BEP to a Proposed BEP:
 
 Upon a successful Draft BEP review, the BEP will be converted from a
 Google document to a pull request for the
-[BIDS standard](https://github.com/bids-standard/bids-specification).
+[BIDS standard][specification_gh].
 This will enable further community feedback on the Proposed BEP. Tools
 may begin integrating the Proposed BEP specification.
 
@@ -323,7 +323,7 @@ The Steering Group evaluates:
 ### A. BEP Procedure: Key definitions
 
 **BIDS Specification** - This is the [BIDS
-specification](https://bids-specification.readthedocs.io/en/stable/).
+specification][specification].
 This covers the current raw data organization for brain MRI, MEG, EEG,
 and iEEG.
 
@@ -349,7 +349,7 @@ Proposed BEP.
 BEP, it becomes a specific addition and/or modification of BIDS, in the
 form of a Proposed BEP. At this time, the Proposed BEP will take the
 form of a pull request on the [BIDS GitHub
-repository](https://github.com/bids-standard/bids-specification).
+repository][specification_gh].
 
 **Proposed BEP review** - This review is performed by the BIDS Steering
 Group on the Proposed BEP. The review aims to ensure the community input
@@ -434,8 +434,8 @@ contains links to all the BIDS informational and help materials.
 
 We encourage questions and discussion  on [NeuroStars, under the "bids"
 tag](https://neurostars.org/tags/bids), via the [BIDS mailing
-list](https://groups.google.com/forum/#!forum/bids-discussion), or in
-[GitHub issues](https://github.com/bids-standard/) within the
+list][bids_google_group], or in
+[GitHub issues][bids_standard] within the
 appropriate repository.
 
 We prefer questions to be asked via

docs/collaboration/index.md

@@ -27,12 +27,12 @@ Below is a list of common resources where users can get involved in making the B
     and proposing changes via
     [Pull Requests](https://github.com/bids-standard/bids-specification/pulls){:target="_blank"}
     on
-    [GitHub](https://github.com/bids-standard/bids-specification){:target="_blank"}.
+    [GitHub][specification_gh]{:target="_blank"}.
 
 -   To make improvements to the website that you are reading right now, you can also open an
     [Issue](https://github.com/bids-standard/bids-website/issues){:target="_blank"}
     and propose changes via Pull Requests at the
-    [BIDS website GitHub repository](https://github.com/bids-standard/bids-website){:target="_blank"}.
+    [BIDS website GitHub repository][bids_wesbite_gh]{:target="_blank"}.
 
 <u> Become a part of the BIDS Community </u>
 

docs/contact/index.md

@@ -26,7 +26,7 @@ Some example questions that have already been answered include:
 
     [: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.
+    You can also come chat on the [Brainhack mattermost][brainhack_mattermost] on the `~bids_general` channel.
 
 -   :simple-google:{ .lg .middle } **Mailing list**