From f593fbc4d534d7f53b282d9cdb4b7e4bfc4e55d1 Mon Sep 17 00:00:00 2001 From: Remi Gau Date: Thu, 12 Dec 2024 17:06:42 +0100 Subject: [PATCH 01/11] fix openneuro --- docs/blog/posts/meet-the-bids-steering-group.md | 2 +- docs/collaboration/governance.md | 2 +- docs/datasets/index.md | 2 +- docs/faq/general.md | 2 +- docs/impact/measuring.md | 2 +- docs/index.md | 4 ++-- includes/abbreviations.md | 13 +++++++++++-- 7 files changed, 18 insertions(+), 9 deletions(-) diff --git a/docs/blog/posts/meet-the-bids-steering-group.md b/docs/blog/posts/meet-the-bids-steering-group.md index 68da306b..ae753f35 100644 --- a/docs/blog/posts/meet-the-bids-steering-group.md +++ b/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? diff --git a/docs/collaboration/governance.md b/docs/collaboration/governance.md index e2c91fad..c2c26259 100644 --- a/docs/collaboration/governance.md +++ b/docs/collaboration/governance.md @@ -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. diff --git a/docs/datasets/index.md b/docs/datasets/index.md index cd16473e..42b3aa54 100644 --- a/docs/datasets/index.md +++ b/docs/datasets/index.md @@ -9,7 +9,7 @@ Many public repositories for neuroimaging data are accepting (and in some cases data submitted in BIDS format. Below is a small sample of some main resources for finding BIDS datasets that may be used in your analyses. -[OpenNeuro](https://openneuro.org/): +[OpenNeuro][openneuro]: If you're looking for full data files to run the validator on or simply compare to your own _bidsified_ data try searching here. Datasets here are (by and large) publicly available and conform to BIDS. diff --git a/docs/faq/general.md b/docs/faq/general.md index 52582134..a162e013 100644 --- a/docs/faq/general.md +++ b/docs/faq/general.md @@ -180,5 +180,5 @@ If you want to know more about what license to choose for your dataset, see the [turing way](https://the-turing-way.netlify.app/reproducible-research/licensing/licensing-data.html#data-licenses) page dedicated to this topic. -If you plan to put your dataset on [openneuro](https://openneuro.org/), +If you plan to put your dataset on [openneuro][openneuro], you should use a CC0 or a PDDL license as explained in their [FAQ](https://openneuro.org/faq). diff --git a/docs/impact/measuring.md b/docs/impact/measuring.md index 52b34539..30e4f798 100644 --- a/docs/impact/measuring.md +++ b/docs/impact/measuring.md @@ -6,7 +6,7 @@ Over the years, the number of shared datasets available to the public has greatly increased. At its heart, adoption of the BIDS standard across datasets aids in the sharing of data and collaboration of research through the standardization of descriptive files names and the organization of data. BIDS organized datasets are -available through public repositories such as [Openneuro.org](https://openneuro.org/) +available through public repositories such as [Openneuro.org][openneuro] and the number of publicly available BIDS datasets continues to grow every year. 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/) as a database for BIDS formatted datasets. +and [OpenNeuro][openneuro] as a database for BIDS formatted datasets. A non-exhaustive list of further tools can be found in the [tools](./tools/index.md) section. diff --git a/includes/abbreviations.md b/includes/abbreviations.md index 7aabfef3..d2bcc50d 100644 --- a/includes/abbreviations.md +++ b/includes/abbreviations.md @@ -1,5 +1,14 @@ - - +[openneuro]: https://openneuro.org +[bids_google_group]: https://groups.google.com/forum/#!forum/bids-discussion +[brainhack_mattermost]: https://mattermost.brainhack.org +[specification]: https://bids-specification.readthedocs.io +[specification_gh]: https://github.com/bids-standard/bids-specification +[bids_standard]: https://github.com/bids-standard +[bids_examples_gh]: https://github.com/bids-standard/bids-examples) +[bids_wesbite_gh]: https://github.com/bids-standard/bids-website + + + *[ASL]: Arterial Spin Labelling *[BEP]: BIDS Extension Proposal From 7048eed967843b6b32e59a48c9a6600511b06891 Mon Sep 17 00:00:00 2001 From: Remi Gau Date: Thu, 12 Dec 2024 17:07:38 +0100 Subject: [PATCH 02/11] fix mailing list --- docs/blog/posts/2020-03-23-steering-group-minutes.md | 4 ++-- docs/collaboration/governance.md | 6 +++--- docs/extensions/general-guidelines.md | 2 +- docs/impact/index.md | 2 +- 4 files changed, 7 insertions(+), 7 deletions(-) diff --git a/docs/blog/posts/2020-03-23-steering-group-minutes.md b/docs/blog/posts/2020-03-23-steering-group-minutes.md index d11921df..f9668f2a 100644 --- a/docs/blog/posts/2020-03-23-steering-group-minutes.md +++ b/docs/blog/posts/2020-03-23-steering-group-minutes.md @@ -19,7 +19,7 @@ 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). @@ -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). diff --git a/docs/collaboration/governance.md b/docs/collaboration/governance.md index c2c26259..d8c33d55 100644 --- a/docs/collaboration/governance.md +++ b/docs/collaboration/governance.md @@ -46,7 +46,7 @@ software tools, [examples](https://github.com/bids-standard/bids-examples), and general discussions. The relevant discussions are located in our -[Google Group](https://groups.google.com/forum/#!forum/bids-discussion), +[Google Group][bids_google_group], [GitHub organization](https://github.com/bids-standard), and public Google Documents (typically associated with an [extension proposal](../extensions/beps.md)). @@ -235,7 +235,7 @@ through an open letter via a "read-only" Google Document addressed to the BIDS S 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), +- [Google Group][bids_google_group], - and [social media channels](). This proposal will state what their group aims and goals are. @@ -434,7 +434,7 @@ 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 +list][bids_google_group], or in [GitHub issues](https://github.com/bids-standard/) within the appropriate repository. diff --git a/docs/extensions/general-guidelines.md b/docs/extensions/general-guidelines.md index fe5e7262..15f8c084 100644 --- a/docs/extensions/general-guidelines.md +++ b/docs/extensions/general-guidelines.md @@ -83,7 +83,7 @@ allowing more people to get involved. 1. Share the draft (remember to [share a link that allows anyone to comment](https://support.google.com/docs/answer/2494822?co=GENIE.Platform%3DDesktop&hl=en)) with the - [bids-discussion mailing list](https://groups.google.com/forum/#!forum/bids-discussion) + [bids-discussion mailing list][bids_google_group] and ask for comments. 1. Incorporate the feedback and strive for consensus. diff --git a/docs/impact/index.md b/docs/impact/index.md index 32761794..cd657336 100644 --- a/docs/impact/index.md +++ b/docs/impact/index.md @@ -119,7 +119,7 @@ TODO add automation to update every 6 months As of July 1, 2020, we have 183 people signed up for our [BIDS email list](https://forms.gle/JFo2aEkYbKY4EbmE6) and 412 members on our -[google group](https://groups.google.com/forum/#!forum/bids-discussion). +[google group][bids_google_group]. ## How the BIDS team can help you From caf6ab1c5d7881497077d81aa7cde8a0e2dc0eb9 Mon Sep 17 00:00:00 2001 From: Remi Gau Date: Thu, 12 Dec 2024 17:08:03 +0100 Subject: [PATCH 03/11] fix mattermost --- docs/blog/posts/2020-06-18-steering-group-minutes.md | 2 +- .../join-the-bids-community-on-the-brainhack-mattermost.md | 4 ++-- docs/contact/index.md | 2 +- 3 files changed, 4 insertions(+), 4 deletions(-) diff --git a/docs/blog/posts/2020-06-18-steering-group-minutes.md b/docs/blog/posts/2020-06-18-steering-group-minutes.md index 486932b0..bbc4fd5e 100644 --- a/docs/blog/posts/2020-06-18-steering-group-minutes.md +++ b/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. diff --git a/docs/blog/posts/join-the-bids-community-on-the-brainhack-mattermost.md b/docs/blog/posts/join-the-bids-community-on-the-brainhack-mattermost.md index 007d842b..71cdd3b6 100644 --- a/docs/blog/posts/join-the-bids-community-on-the-brainhack-mattermost.md +++ b/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]! -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: diff --git a/docs/contact/index.md b/docs/contact/index.md index 913f7505..4a3d17d7 100644 --- a/docs/contact/index.md +++ b/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** From 9eddaa29ccc72759af89df0627de9e7325310bcf Mon Sep 17 00:00:00 2001 From: Remi Gau Date: Thu, 12 Dec 2024 17:08:48 +0100 Subject: [PATCH 04/11] fix spec --- docs/collaboration/governance.md | 6 +++--- docs/getting_started/tutorials/annotation.md | 2 +- docs/impact/index.md | 4 ++-- docs/standards/bids_specification/index.md | 2 +- docs/tools/validator.md | 2 +- 5 files changed, 8 insertions(+), 8 deletions(-) diff --git a/docs/collaboration/governance.md b/docs/collaboration/governance.md index d8c33d55..46eac7c2 100644 --- a/docs/collaboration/governance.md +++ b/docs/collaboration/governance.md @@ -17,11 +17,11 @@ 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. The development edition is available in -[HTML](https://bids-specification.readthedocs.io/en/latest/). +[HTML][specification]. The specification is based in a [GitHub repository](https://github.com/bids-standard/bids-specification) and rendered with [ReadTheDocs](https://docs.readthedocs.io/en/stable/). @@ -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. diff --git a/docs/getting_started/tutorials/annotation.md b/docs/getting_started/tutorials/annotation.md index 720a9bc0..6d607adc 100644 --- a/docs/getting_started/tutorials/annotation.md +++ b/docs/getting_started/tutorials/annotation.md @@ -128,7 +128,7 @@ without having meaningful information about the dataset events. #### Additional information See [Task events](https://bids-specification.readthedocs.io/en/stable/04-modality-specific-files/05-task-events.html) and [Appendix III: Hierarchical Event Descriptors](https://bids-specification.readthedocs.io/en/stable/99-appendices/03-hed.html) -in the [BIDS specification](https://bids-specification.readthedocs.io/en/stable/) +in the [BIDS specification][specification] for an overview of events before getting started with your own annotation. The next section provides an overview of the event annotation process diff --git a/docs/impact/index.md b/docs/impact/index.md index cd657336..1aabc4aa 100644 --- a/docs/impact/index.md +++ b/docs/impact/index.md @@ -13,7 +13,7 @@ BIDS encompasses: - 100+ sample data models for BIDS specifications in the [bids-examples](../datasets/examples.md). - Read more about the [BIDS specification](https://bids-specification.readthedocs.io/en/stable/). + Read more about the [BIDS specification][specification]. - 2000 open datasets across repositories including [OpenNeuro](https://www.openneuro.org). @@ -63,7 +63,7 @@ BIDS initiatives or database can be found ### Website and Specification traffic dashboards In order to measure the volume of traffic to our website and the -[ReadTheDocs rendering of the specification](https://bids-specification.readthedocs.io/en/stable/), +[ReadTheDocs rendering of the specification][specification], we utilize Google Analytics. For visualizing our metrics, we have put together 2 dashboards: diff --git a/docs/standards/bids_specification/index.md b/docs/standards/bids_specification/index.md index 828f1fed..e1afcd97 100644 --- a/docs/standards/bids_specification/index.md +++ b/docs/standards/bids_specification/index.md @@ -1,6 +1,6 @@ # The BIDS specification -The Brain Imaging Data Structure specification can be [browsed online](https://bids-specification.readthedocs.io/en/stable/). +The Brain Imaging Data Structure specification can be [browsed online][specification]. PDF versions of the specification can be found on zenodo at [https://doi.org/10.5281/zenodo.10175845](https://doi.org/10.5281/zenodo.10175845) diff --git a/docs/tools/validator.md b/docs/tools/validator.md index fe35b688..e69e3e8f 100644 --- a/docs/tools/validator.md +++ b/docs/tools/validator.md @@ -112,7 +112,7 @@ user@host:~/bids-examples$ bids-validator pet001 As stated with the browser version above, one may elect to ignore warnings, but the information provided via the validator should help to pinpoint where and how to resolve some of these warnings. - When in doubt consult the [BIDS specification](https://bids-specification.readthedocs.io/en/latest/) + When in doubt consult the [BIDS specification][specification] ```bash [WARNING] JSON_KEY_RECOMMENDED A JSON file is missing a key listed as recommended. From 48ad279b0fb8a36ac3e1d550ee120603e61e88bf Mon Sep 17 00:00:00 2001 From: Remi Gau Date: Thu, 12 Dec 2024 17:09:11 +0100 Subject: [PATCH 05/11] fix spec repo --- README.md | 2 +- docs/blog/posts/2020-03-23-steering-group-minutes.md | 4 ++-- docs/blog/posts/2020-03-30-steering-group-minutes.md | 2 +- docs/blog/posts/2021-02-25-steering-group-minutes.md | 2 +- docs/collaboration/governance.md | 10 +++++----- docs/collaboration/index.md | 2 +- docs/extensions/submission.md | 2 +- 7 files changed, 12 insertions(+), 12 deletions(-) diff --git a/README.md b/README.md index 810e0f90..206eb450 100644 --- a/README.md +++ b/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 diff --git a/docs/blog/posts/2020-03-23-steering-group-minutes.md b/docs/blog/posts/2020-03-23-steering-group-minutes.md index f9668f2a..a25db6da 100644 --- a/docs/blog/posts/2020-03-23-steering-group-minutes.md +++ b/docs/blog/posts/2020-03-23-steering-group-minutes.md @@ -29,7 +29,7 @@ The process will be: 1. merging in the BEP constructed examples to [BIDS-examples](https://github.com/bids-standard/bids-examples) 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). @@ -68,7 +68,7 @@ The Steering Group gave direction on handling author lists on Zenodo - make it a - For future BEPs, they will submit their examples to [BIDS-examples](https://github.com/bids-standard/bids-examples) 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)). diff --git a/docs/blog/posts/2020-03-30-steering-group-minutes.md b/docs/blog/posts/2020-03-30-steering-group-minutes.md index efcbee6e..55adf053 100644 --- a/docs/blog/posts/2020-03-30-steering-group-minutes.md +++ b/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. diff --git a/docs/blog/posts/2021-02-25-steering-group-minutes.md b/docs/blog/posts/2021-02-25-steering-group-minutes.md index b0d9d592..7d0d0b89 100644 --- a/docs/blog/posts/2021-02-25-steering-group-minutes.md +++ b/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 diff --git a/docs/collaboration/governance.md b/docs/collaboration/governance.md index 46eac7c2..534ddeb5 100644 --- a/docs/collaboration/governance.md +++ b/docs/collaboration/governance.md @@ -22,7 +22,7 @@ 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. The development edition is available in [HTML][specification]. -The specification is based in a [GitHub repository](https://github.com/bids-standard/bids-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. @@ -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. @@ -234,7 +234,7 @@ 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), +- the [BIDS-Specification GitHub repository][specification_gh], - [Google Group][bids_google_group], - and [social media channels](). @@ -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. @@ -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 diff --git a/docs/collaboration/index.md b/docs/collaboration/index.md index 44fa5ee2..adb942a6 100644 --- a/docs/collaboration/index.md +++ b/docs/collaboration/index.md @@ -27,7 +27,7 @@ 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"} diff --git a/docs/extensions/submission.md b/docs/extensions/submission.md index 01b62d7d..91a14139 100644 --- a/docs/extensions/submission.md +++ b/docs/extensions/submission.md @@ -2,7 +2,7 @@ This document conveys the process for submitting a BEP to BIDS. This process assumes the BEP is ready to be opened as a pull request to the -[`bids-specification` repository](https://github.com/bids-standard/bids-specification) +[`bids-specification` repository][specification_gh] under the [`bids-standard` organization](https://github.com/bids-standard). Please reach out to [the BIDS maintainers](https://github.com/bids-standard/bids-specification/blob/master/DECISION-MAKING.md#maintainers-group) From 530fe4fbef0b0c701d81c15bb3869609aa8063a1 Mon Sep 17 00:00:00 2001 From: Remi Gau Date: Thu, 12 Dec 2024 17:09:39 +0100 Subject: [PATCH 06/11] fix bids gh --- docs/blog/posts/2020-03-12-steering-group-minutes.md | 2 +- docs/collaboration/governance.md | 4 ++-- docs/extensions/submission.md | 2 +- 3 files changed, 4 insertions(+), 4 deletions(-) diff --git a/docs/blog/posts/2020-03-12-steering-group-minutes.md b/docs/blog/posts/2020-03-12-steering-group-minutes.md index 5e57848d..ee58c3c3 100644 --- a/docs/blog/posts/2020-03-12-steering-group-minutes.md +++ b/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) diff --git a/docs/collaboration/governance.md b/docs/collaboration/governance.md index 534ddeb5..6f53f715 100644 --- a/docs/collaboration/governance.md +++ b/docs/collaboration/governance.md @@ -47,7 +47,7 @@ software tools, and general discussions. The relevant discussions are located in our [Google Group][bids_google_group], -[GitHub organization](https://github.com/bids-standard), +[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 @@ -435,7 +435,7 @@ 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][bids_google_group], or in -[GitHub issues](https://github.com/bids-standard/) within the +[GitHub issues][bids_standard] within the appropriate repository. We prefer questions to be asked via diff --git a/docs/extensions/submission.md b/docs/extensions/submission.md index 91a14139..d07feba5 100644 --- a/docs/extensions/submission.md +++ b/docs/extensions/submission.md @@ -3,7 +3,7 @@ This document conveys the process for submitting a BEP to BIDS. This process assumes the BEP is ready to be opened as a pull request to the [`bids-specification` repository][specification_gh] -under the [`bids-standard` organization](https://github.com/bids-standard). +under the [`bids-standard` organization][bids_standard]. Please reach out to [the BIDS maintainers](https://github.com/bids-standard/bids-specification/blob/master/DECISION-MAKING.md#maintainers-group) to let them know you are reaching this step in the process. They will assist the From 7bcba1d0271cc84020becb39006674e15e49fed2 Mon Sep 17 00:00:00 2001 From: Remi Gau Date: Thu, 12 Dec 2024 17:10:08 +0100 Subject: [PATCH 07/11] fix bids examples gh --- docs/blog/posts/2020-03-23-steering-group-minutes.md | 4 ++-- docs/blog/posts/community-review-pet.md | 2 +- docs/blog/posts/v1.9.0-release.md | 2 +- docs/collaboration/governance.md | 2 +- docs/extensions/submission.md | 2 +- includes/abbreviations.md | 2 +- 6 files changed, 7 insertions(+), 7 deletions(-) diff --git a/docs/blog/posts/2020-03-23-steering-group-minutes.md b/docs/blog/posts/2020-03-23-steering-group-minutes.md index a25db6da..5605e63b 100644 --- a/docs/blog/posts/2020-03-23-steering-group-minutes.md +++ b/docs/blog/posts/2020-03-23-steering-group-minutes.md @@ -27,7 +27,7 @@ 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][specification_gh] @@ -65,7 +65,7 @@ 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][specification_gh] diff --git a/docs/blog/posts/community-review-pet.md b/docs/blog/posts/community-review-pet.md index 851cb7aa..8ad051d1 100644 --- a/docs/blog/posts/community-review-pet.md +++ b/docs/blog/posts/community-review-pet.md @@ -12,7 +12,7 @@ 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. diff --git a/docs/blog/posts/v1.9.0-release.md b/docs/blog/posts/v1.9.0-release.md index 28d9ebd4..32ef024d 100644 --- a/docs/blog/posts/v1.9.0-release.md +++ b/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) diff --git a/docs/collaboration/governance.md b/docs/collaboration/governance.md index 6f53f715..628d3a44 100644 --- a/docs/collaboration/governance.md +++ b/docs/collaboration/governance.md @@ -43,7 +43,7 @@ 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][bids_google_group], diff --git a/docs/extensions/submission.md b/docs/extensions/submission.md index d07feba5..22fe4589 100644 --- a/docs/extensions/submission.md +++ b/docs/extensions/submission.md @@ -18,7 +18,7 @@ merging of the BEP into the Specification. to support the BEP 1. Examples (to test the validator is working properly) added to - [`bids-examples`](https://github.com/bids-standard/bids-examples) + [`bids-examples`][bids_examples_gh] ## SUGGESTED deliverables diff --git a/includes/abbreviations.md b/includes/abbreviations.md index d2bcc50d..1673f9ec 100644 --- a/includes/abbreviations.md +++ b/includes/abbreviations.md @@ -4,7 +4,7 @@ [specification]: https://bids-specification.readthedocs.io [specification_gh]: https://github.com/bids-standard/bids-specification [bids_standard]: https://github.com/bids-standard -[bids_examples_gh]: https://github.com/bids-standard/bids-examples) +[bids_examples_gh]: https://github.com/bids-standard/bids-examples [bids_wesbite_gh]: https://github.com/bids-standard/bids-website From dec281e1b47fc799779baff6466e9ee2b9fa673e Mon Sep 17 00:00:00 2001 From: Remi Gau Date: Thu, 12 Dec 2024 17:10:33 +0100 Subject: [PATCH 08/11] fix bids website gh --- docs/collaboration/governance.md | 2 +- docs/collaboration/index.md | 2 +- docs/extensions/general-guidelines.md | 2 +- docs/extensions/submission.md | 2 +- 4 files changed, 4 insertions(+), 4 deletions(-) diff --git a/docs/collaboration/governance.md b/docs/collaboration/governance.md index 628d3a44..85eb51ce 100644 --- a/docs/collaboration/governance.md +++ b/docs/collaboration/governance.md @@ -19,7 +19,7 @@ metadata associated with the imaging data. The current edition of the standard is available in [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][specification]. The specification is based in a [GitHub repository][specification_gh] diff --git a/docs/collaboration/index.md b/docs/collaboration/index.md index adb942a6..075062c8 100644 --- a/docs/collaboration/index.md +++ b/docs/collaboration/index.md @@ -32,7 +32,7 @@ Below is a list of common resources where users can get involved in making the B - 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"}. Become a part of the BIDS Community diff --git a/docs/extensions/general-guidelines.md b/docs/extensions/general-guidelines.md index 15f8c084..a0af9341 100644 --- a/docs/extensions/general-guidelines.md +++ b/docs/extensions/general-guidelines.md @@ -71,7 +71,7 @@ allowing more people to get involved. To obtain a number for your BEP, follow the previous steps and then [open a new issue](https://github.com/bids-standard/bids-website/issues) or [submit a pull request](https://github.com/bids-standard/bids-website/pulls) to the - [website GitHub repository](https://github.com/bids-standard/bids-website/), + [website GitHub repository][bids_wesbite_gh], cross-linking to any other already existing issues. 1. Create a draft of your extension by discussing among colleagues. The diff --git a/docs/extensions/submission.md b/docs/extensions/submission.md index 22fe4589..55a75fa4 100644 --- a/docs/extensions/submission.md +++ b/docs/extensions/submission.md @@ -26,7 +26,7 @@ merging of the BEP into the Specification. writing suggestion below) 1. Press release for the - [`bids-website`](https://github.com/bids-standard/bids-website) + [`bids-website`][bids_wesbite_gh] [news section](https://github.com/bids-standard/bids-website/tree/gh-pages/_posts) ## Giving collaborators additional permissions within our `bids-standard` organization From 975b4aa7d4b5c7039f917ce05160b6ea9ce5db52 Mon Sep 17 00:00:00 2001 From: Remi Gau Date: Thu, 12 Dec 2024 17:11:18 +0100 Subject: [PATCH 09/11] sort --- includes/abbreviations.md | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/includes/abbreviations.md b/includes/abbreviations.md index 1673f9ec..02a13c5f 100644 --- a/includes/abbreviations.md +++ b/includes/abbreviations.md @@ -1,11 +1,11 @@ -[openneuro]: https://openneuro.org +[bids_examples_gh]: https://github.com/bids-standard/bids-examples [bids_google_group]: https://groups.google.com/forum/#!forum/bids-discussion +[bids_standard]: https://github.com/bids-standard +[bids_wesbite_gh]: https://github.com/bids-standard/bids-website [brainhack_mattermost]: https://mattermost.brainhack.org +[openneuro]: https://openneuro.org [specification]: https://bids-specification.readthedocs.io [specification_gh]: https://github.com/bids-standard/bids-specification -[bids_standard]: https://github.com/bids-standard -[bids_examples_gh]: https://github.com/bids-standard/bids-examples -[bids_wesbite_gh]: https://github.com/bids-standard/bids-website From 5710409290057cd2dceee53b1875807c5c594fab Mon Sep 17 00:00:00 2001 From: Remi Gau Date: Thu, 12 Dec 2024 17:12:14 +0100 Subject: [PATCH 10/11] fix appendix links --- docs/collaboration/governance.md | 2 +- docs/getting_started/resources/glossary.md | 2 +- docs/getting_started/tutorials/annotation.md | 2 +- docs/impact/measuring.md | 2 +- 4 files changed, 4 insertions(+), 4 deletions(-) diff --git a/docs/collaboration/governance.md b/docs/collaboration/governance.md index 85eb51ce..b21cfab4 100644 --- a/docs/collaboration/governance.md +++ b/docs/collaboration/governance.md @@ -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). diff --git a/docs/getting_started/resources/glossary.md b/docs/getting_started/resources/glossary.md index f0d79853..e25e2a99 100644 --- a/docs/getting_started/resources/glossary.md +++ b/docs/getting_started/resources/glossary.md @@ -3,7 +3,7 @@ ## Simple definitions for any BIDS related terms Make sure to also check the -[official glossary](https://bids-specification.readthedocs.io/en/latest/99-appendices/14-glossary.html) +[official glossary](https://bids-specification.readthedocs.io/en/latest/glossary.html) that lists all the terms of the BIDS specification. We know that when you're getting started with something new there are often jargon-y words diff --git a/docs/getting_started/tutorials/annotation.md b/docs/getting_started/tutorials/annotation.md index 6d607adc..ce6f44f5 100644 --- a/docs/getting_started/tutorials/annotation.md +++ b/docs/getting_started/tutorials/annotation.md @@ -127,7 +127,7 @@ without having meaningful information about the dataset events. #### Additional information See [Task events](https://bids-specification.readthedocs.io/en/stable/04-modality-specific-files/05-task-events.html) and -[Appendix III: Hierarchical Event Descriptors](https://bids-specification.readthedocs.io/en/stable/99-appendices/03-hed.html) +[Appendix III: Hierarchical Event Descriptors](https://bids-specification.readthedocs.io/en/stable/appendices/hed.html) in the [BIDS specification][specification] for an overview of events before getting started with your own annotation. diff --git a/docs/impact/measuring.md b/docs/impact/measuring.md index 30e4f798..8d16edda 100644 --- a/docs/impact/measuring.md +++ b/docs/impact/measuring.md @@ -62,7 +62,7 @@ For the number of docker pulls of specific BIDS apps, please check the ## Contributors Our list of contributors are captured in our -[contributor appendix](https://bids-specification.readthedocs.io/en/latest/99-appendices/01-contributors.html). +[contributor appendix](https://bids-specification.readthedocs.io/en/latest/appendices/contributors.html). We update the contributor appendix every specification release. As of July 2023, we have over 300 credited contributors. From 194a1e1fdda30579006a5bf6a2c4426fe9909952 Mon Sep 17 00:00:00 2001 From: Remi Gau Date: Thu, 12 Dec 2024 17:22:44 +0100 Subject: [PATCH 11/11] remark --- docs/blog/posts/community-review-pet.md | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/docs/blog/posts/community-review-pet.md b/docs/blog/posts/community-review-pet.md index 8ad051d1..98e5d00e 100644 --- a/docs/blog/posts/community-review-pet.md +++ b/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][bids_examples_gh]. +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)