From 5b835b0b182b50aa27ead6dffeb727e59322d1fe Mon Sep 17 00:00:00 2001 From: Mark Mikkelsen Date: Wed, 28 Feb 2024 14:36:50 -0500 Subject: [PATCH 1/5] [FIX] Missing word in `genetic-descriptor.md` (#1715) --- src/modality-specific-files/genetic-descriptor.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/modality-specific-files/genetic-descriptor.md b/src/modality-specific-files/genetic-descriptor.md index 304359ed45..e50994bbee 100644 --- a/src/modality-specific-files/genetic-descriptor.md +++ b/src/modality-specific-files/genetic-descriptor.md @@ -1,6 +1,6 @@ # Genetic Descriptor -Support genetic descriptors was developed as a +Support for genetic descriptors was developed as a [BIDS Extension Proposal](../extensions.md#bids-extension-proposals). Please see [Citing BIDS](../introduction.md#citing-bids) on how to appropriately credit this extension when referring to it in the From a8c93a87b45c5cb1c34444d74cd14e3f65038d15 Mon Sep 17 00:00:00 2001 From: Remi Gau Date: Thu, 29 Feb 2024 10:31:07 +0100 Subject: [PATCH 2/5] [FIX] Add misssing files in filename template for NIRS --- src/modality-specific-files/near-infrared-spectroscopy.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/modality-specific-files/near-infrared-spectroscopy.md b/src/modality-specific-files/near-infrared-spectroscopy.md index 1947836c17..03e4ad5685 100644 --- a/src/modality-specific-files/near-infrared-spectroscopy.md +++ b/src/modality-specific-files/near-infrared-spectroscopy.md @@ -22,7 +22,7 @@ and a guide for using macros can be found at {{ MACROS___make_filename_template( "raw", datatypes=["nirs"], - suffixes=["nirs", "events", "physio", "stim"]) + suffixes=["nirs", "events", "channels", "optodes", "coordsystem", "physio", "stim"]) }} Only the *Shared Near Infrared Spectroscopy Format* ([SNIRF](https://github.com/fNIRS/snirf)) From 327bece13c60b8c565805f0935fd4c79809bfa23 Mon Sep 17 00:00:00 2001 From: Yaroslav Halchenko Date: Thu, 7 Mar 2024 14:24:48 -0500 Subject: [PATCH 3/5] [DATALAD RUNCMD] Fix typo in SpatialAxes === Do not change lines below === { "chain": [], "cmd": "git-sedi SpatialAxis SpatialAxes", "exit": 0, "extra_inputs": [], "inputs": [], "outputs": [], "pwd": "." } ^^^ Do not change lines above ^^^ --- src/schema/objects/columns.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/schema/objects/columns.yaml b/src/schema/objects/columns.yaml index ba9f86ba31..bc11e7def7 100644 --- a/src/schema/objects/columns.yaml +++ b/src/schema/objects/columns.yaml @@ -397,7 +397,7 @@ reference_frame: description: | Specification of a reference frame in which the motion data are to be interpreted. The description of the levels in `*_channels.json` SHOULD use `RotationRule`, - `RotationOrder`, and `SpatialAxis`, and MAY use `Description` for the specification. + `RotationOrder`, and `SpatialAxes`, and MAY use `Description` for the specification. anyOf: - type: string - type: string From 19f80784e6c73a526b6915fbf311464d22f5a94d Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ya=C3=ABl=20Balbastre?= Date: Mon, 11 Mar 2024 15:19:03 +0000 Subject: [PATCH 4/5] [ENH] Add support for HiP-CT (#1686) * microscopy: add "hipCT" suffix * suffixes.yaml: add "hipCT" suffix * files/micr.yaml: add "hipCT" suffix * Update src/modality-specific-files/microscopy.md --------- Co-authored-by: Satrajit Ghosh Co-authored-by: Chris Markiewicz --- src/modality-specific-files/microscopy.md | 3 ++- src/schema/objects/suffixes.yaml | 5 +++++ src/schema/rules/files/raw/micr.yaml | 1 + 3 files changed, 8 insertions(+), 1 deletion(-) diff --git a/src/modality-specific-files/microscopy.md b/src/modality-specific-files/microscopy.md index 5d08f79377..7e3108c13f 100644 --- a/src/modality-specific-files/microscopy.md +++ b/src/modality-specific-files/microscopy.md @@ -26,7 +26,7 @@ and a guide for using macros can be found at https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md --> {{ MACROS___make_filename_template("raw", datatypes=["micr"], suffixes=["TEM", "SEM", "uCT", "BF", "DF", -"PC", "DIC", "FLUO", "CONF", "PLI", "CARS", "2PE", "MPE", "SR", "NLO", "OCT", "SPIM"], n_dupes_to_combine=4) }} +"PC", "DIC", "FLUO", "CONF", "PLI", "CARS", "2PE", "MPE", "SR", "NLO", "OCT", "SPIM", "hipCT"], n_dupes_to_combine=4) }} Microscopy data MUST be stored in the `micr` directory. @@ -89,6 +89,7 @@ and a guide for using macros can be found at "NLO", "OCT", "SPIM", + "hipCT", ] ) }} diff --git a/src/schema/objects/suffixes.yaml b/src/schema/objects/suffixes.yaml index 16e410c70d..13ee57ebc5 100644 --- a/src/schema/objects/suffixes.yaml +++ b/src/schema/objects/suffixes.yaml @@ -595,6 +595,11 @@ headshape: description: | The 3-D locations of points that describe the head shape and/or electrode locations can be digitized and stored in separate files. +hipCT: + value: hipCT + display_name: HiP-CT + description: | + Hierarchical Phase-Contrast Tomography imaging data ieeg: value: ieeg display_name: Intracranial Electroencephalography diff --git a/src/schema/rules/files/raw/micr.yaml b/src/schema/rules/files/raw/micr.yaml index aba1b48352..52d1adb74f 100644 --- a/src/schema/rules/files/raw/micr.yaml +++ b/src/schema/rules/files/raw/micr.yaml @@ -18,6 +18,7 @@ microscopy: - NLO - OCT - SPIM + - hipCT extensions: - .ome.tif - .ome.btf From c9e4779092b41d6fd31146e09b3410c9ebc647bb Mon Sep 17 00:00:00 2001 From: Stefan Appelhoff Date: Mon, 11 Mar 2024 16:20:21 +0100 Subject: [PATCH 5/5] Organize BIDS communication channels (#1717) * update release protocol * keep only initial year in LICENSE see https://hynek.me/til/copyright-years/ * update twitter link to x; add instagram social link * organize BIDS communication channels * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * add youtube as social media icon --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> --- LICENSE | 2 +- README.md | 37 ++++++++++++++++++++++++++++--------- mkdocs.yml | 8 ++++++-- 3 files changed, 35 insertions(+), 12 deletions(-) diff --git a/LICENSE b/LICENSE index d591978380..22091e01bb 100644 --- a/LICENSE +++ b/LICENSE @@ -1,6 +1,6 @@ Attribution 4.0 International -Copyright (c) 2018-2022, BIDS Contributors. +Copyright (c) 2018, BIDS Contributors. ======================================================================= diff --git a/README.md b/README.md index 574659f292..6474f470a1 100644 --- a/README.md +++ b/README.md @@ -1,7 +1,7 @@ [![Validation](https://github.com/bids-standard/bids-specification/actions/workflows/validation.yml/badge.svg)](https://github.com/bids-standard/bids-specification/actions/workflows/validation.yml) [![CircleCI](https://circleci.com/gh/bids-standard/bids-specification.svg?style=shield)](https://circleci.com/gh/bids-standard/bids-specification) [![Mastodon Follow](https://img.shields.io/mastodon/follow/109520103085644521?domain=https%3A%2F%2Ffosstodon.org%2F)](https://fosstodon.org/@bidsstandard) -[![@BIDSstandard](http://img.shields.io/twitter/follow/bidsstandard.svg?style=social)](https://twitter.com/BIDSstandard) +[![@BIDSstandard](https://img.shields.io/twitter/follow/bidsstandard.svg?style=social)](https://x.com/BIDSstandard) [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.3686061.svg)](https://doi.org/10.5281/zenodo.3686061) bids-logo @@ -13,7 +13,6 @@ organization of neuroimaging data. In this repository, we develop the [BIDS specification](https://bids-specification.readthedocs.io/en/latest/). - # When to use BIDS To organize your data in BIDS, all you need is neuro data, a computer, and the @@ -44,10 +43,7 @@ The specification is provided in the form of a webpage, built using 1. Read some introductory material, most likely the very basic problems have already been addressed! - [BIDS Starter Kit](https://github.com/bids-standard/bids-starter-kit) for tutorials, wikis, templates, ... 2. Post your question in one of several channels where BIDS members are active - - the [NeuroStars](https://neurostars.org/tags/bids) discourse forum - - the [BrainHack Mattermost](https://mattermost.brainhack.org), for instant messaging (see also this [news item](https://bids.neuroimaging.io/2020/06/24/Join-the-BIDS-community-on-the-BrainHack-Mattermost.html)) - - the [Google group](https://groups.google.com/forum/#!forum/bids-discussion), for broader discussions surrounding BIDS - - the [specification repository issue page](https://github.com/bids-standard/bids-specification/issues), if you found inconsistencies, typos, or other issues with the BIDS specification itself + - see: [BIDS communication channels](#bids-communication-channels) # Contributing to BIDS @@ -58,11 +54,34 @@ For a current list of our contributors, please see our [Contributors appendix](h When you're ready to get started, check out [our contributing guidelines](https://github.com/bids-standard/bids-specification/blob/master/CONTRIBUTING.md). -We ask that all contributions to BIDS across all project-related spaces (including but not limited to: -[GitHub](https://github.com/bids-standard), -the [Google group](https://groups.google.com/forum/#!forum/bids-discussion), and newsletter emails), +We ask that all contributions to BIDS across all project-related spaces +(including but not limited to: +[GitHub](https://github.com/bids-standard), and the +[Google group](https://groups.google.com/forum/#!forum/bids-discussion); see +[BIDS communication channels](#bids-communication-channels)) adhere to our [code of conduct](https://github.com/bids-standard/bids-specification/blob/master/CODE_OF_CONDUCT.md). +# BIDS communication channels + +## Main communication channels + + - "Issue" pages on the different GitHub repositories of the [`bids-standard` GitHub organization](https://github.com/bids-standard), + such as the [BIDS specification repository](https://github.com/bids-standard/bids-specification/issues), + for reporting problems or making suggestions + - The [NeuroStars Discourse forum](https://neurostars.org/tags/bids), for asking usage questions + - The [BrainHack Mattermost](https://mattermost.brainhack.org), for instant messaging + (see also this [news item](https://bids.neuroimaging.io/2020/06/24/Join-the-BIDS-community-on-the-BrainHack-Mattermost.html)) + - The [Google group](https://groups.google.com/forum/#!forum/bids-discussion), for broader discussions and announcements surrounding BIDS + - The [BIDS website "news"](https://bids.neuroimaging.io/news.html), similar to the Google group, for broader discussions and announcements + +## Social media channels + +- [X](https://x.com/BIDSstandard) +- [Mastodon](https://fosstodon.org/@bidsstandard) +- [Bluesky](https://bsky.app/profile/bidsstandard.bsky.social) +- [Youtube](https://www.youtube.com/channel/UCxZUcYfd_nvIVWAbzRB1tlw) +- [Instagram](https://www.instagram.com/bidsstandard/) + ## Contributors Thanks goes to these wonderful people. diff --git a/mkdocs.yml b/mkdocs.yml index 82badc4288..4ae97195be 100644 --- a/mkdocs.yml +++ b/mkdocs.yml @@ -84,12 +84,16 @@ extra: social: - icon: fontawesome/brands/github link: https://github.com/bids-standard/bids-specification/ - - icon: fontawesome/brands/twitter - link: https://twitter.com/BIDSstandard/ + - icon: fontawesome/brands/x-twitter + link: https://x.com/BIDSstandard/ - icon: fontawesome/brands/mastodon link: https://fosstodon.org/@bidsstandard - icon: fontawesome/brands/google link: https://groups.google.com/g/bids-discussion + - icon: fontawesome/brands/instagram + link: https://www.instagram.com/bidsstandard/ + - icon: fontawesome/brands/youtube + link: https://www.youtube.com/channel/UCxZUcYfd_nvIVWAbzRB1tlw extra_javascript: - js/jquery-3.6.0.min.js