From 2bdb4a6f8c686d07549d037a95cdff0b501d50c4 Mon Sep 17 00:00:00 2001 From: Chris Markiewicz Date: Fri, 6 Sep 2024 07:20:11 -0400 Subject: [PATCH] REL: v1.10.0 (#1914) --- .all-contributorsrc | 43 ++++++++++++++-- .tributors | 59 ++++++++++++++++++++-- CITATION.cff | 37 +++++++++++--- mkdocs.yml | 2 +- src/CHANGES.md | 102 ++++++++++++++++++++------------------ src/schema/BIDS_VERSION | 2 +- src/schema/SCHEMA_VERSION | 2 +- tools/make_changelog.py | 94 +++++++++++++++++++++++++++++++++++ 8 files changed, 276 insertions(+), 65 deletions(-) create mode 100755 tools/make_changelog.py diff --git a/.all-contributorsrc b/.all-contributorsrc index 7d85506d8a..9ba497aeb7 100644 --- a/.all-contributorsrc +++ b/.all-contributorsrc @@ -274,6 +274,14 @@ "name": "Anthony Galassi", "profile": "https://github.com/bendhouseart" }, + { + "contributions": [ + "doc" + ], + "login": "arianna_sala", + "name": "Arianna Sala", + "profile": "https://www.coma.uliege.be/people/arianna-sala/" + }, { "avatar_url": [ "https://avatars.githubusercontent.com/u/118582?v=4" @@ -383,10 +391,13 @@ }, { "contributions": [ - "doc" + "doc", + "code", + "test" ], "login": "benjamin_dichter", - "name": "Benjamin Dichter" + "name": "Benjamin Dichter", + "profile": "https://bendichter.com/" }, { "contributions": [ @@ -1999,11 +2010,14 @@ { "avatar_url": "https://avatars.githubusercontent.com/u/6051303?v=4", "contributions": [ - "doc" + "doc", + "code", + "data", + "review" ], "login": "markmikkelsen", "name": "Mark Mikkelsen", - "profile": "https://vivo.weill.cornell.edu/display/cwid-mam4041" + "profile": "https://mikkelsenlab.weill.cornell.edu/" }, { "contributions": [ @@ -2303,6 +2317,13 @@ "login": "nicole_c_swann", "name": "Nicole C. Swann" }, + { + "contributions": [ + "doc" + ], + "login": "nbeliy", + "name": "Nikita Beliy" + }, { "contributions": [ "doc" @@ -2636,6 +2657,13 @@ "login": "samuel_garcia", "name": "Samuel Garcia" }, + { + "contributions": [ + "doc" + ], + "login": "SamGuay", + "name": "Samuel Guay" + }, { "avatar_url": [ "https://avatars.githubusercontent.com/u/3496566?v=4" @@ -3079,6 +3107,13 @@ "login": "viacovella", "name": "Vittorio Iacovella" }, + { + "contributions": [ + "doc" + ], + "login": "viviana_siless", + "name": "Viviana Siless" + }, { "contributions": [ "doc" diff --git a/.tributors b/.tributors index fa5b1a18f2..a220ce484f 100644 --- a/.tributors +++ b/.tributors @@ -244,6 +244,16 @@ "name": "Anthony Galassi", "orcid": "0000-0001-6550-4574" }, + "arianna_sala": { + "affiliation": "université de Liège, Belgium", + "blog": "https://www.coma.uliege.be/people/arianna-sala/", + "contributions": [ + "doc" + ], + "email": "arianna.sala@uliege.be", + "name": "Arianna Sala", + "orcid": "0000-0001-8121-0891" + }, "arokem": { "affiliation": "University of Washington, Psychology, Seattle, WA, 98107, United States of America", "blog": "https://arokem.org/", @@ -348,10 +358,17 @@ "publish_email": true }, "benjamin_dichter": { + "affiliation": "CatalystNeuro", + "blog": "https://bendichter.com/", "contributions": [ - "doc" + "doc", + "code", + "test" ], - "name": "Benjamin Dichter" + "email": "ben.dichter@catalystneuro.com", + "github": "bendichter", + "name": "Benjamin Dichter", + "orcid": "0000-0001-5725-6910" }, "benjamin_gagl": { "affiliation": "University of Vienna", @@ -1941,12 +1958,16 @@ "name": "Marie-Hélène Bourget" }, "markmikkelsen": { - "affiliation": "Weill Cornell Medicine, Department of Radiology, New York, NY, 10021, USA", - "blog": "https://vivo.weill.cornell.edu/display/cwid-mam4041", + "affiliation": "Weill Cornell Medicine", + "blog": "https://mikkelsenlab.weill.cornell.edu/", "contributions": [ - "doc" + "doc", + "code", + "data", + "review" ], "email": "mam4041@med.cornell.edu", + "github": "markmikkelsen", "name": "Mark Mikkelsen", "orcid": "0000-0002-0349-3782", "publish_email": true @@ -2241,6 +2262,16 @@ ], "name": "Nicole C. Swann" }, + "nbeliy": { + "affiliation": "University of Liege (Liege, Belgium)", + "contributions": [ + "doc" + ], + "email": "nikita.beliy@uliege.be", + "github": "nbeliy", + "name": "Nikita Beliy", + "orcid": "0009-0002-0830-3279" + }, "nima_bigdely_shamlo": { "contributions": [ "doc" @@ -2556,6 +2587,16 @@ ], "name": "Samuel Garcia" }, + "SamGuay": { + "affiliation": "Université de Montréal, Montreal, Québec, CA", + "contributions": [ + "doc" + ], + "email": "samuel.guay@umontreal.ca", + "github": "SamGuay", + "name": "Samuel Guay", + "orcid": "0000-0001-6990-839X" + }, "snastase": { "affiliation": "Princeton University", "blog": "https://snastase.github.io/", @@ -3005,6 +3046,14 @@ "name": "Vittorio Iacovella", "orcid": "0000-0002-0853-1573" }, + "viviana_siless": { + "affiliation": "Business School, Universidad Torcuato di Tella", + "contributions": [ + "doc" + ], + "email": "viviana.siless@utdt.edu", + "name": "Viviana Siless" + }, "vladimir_litvak": { "affiliation": "UCL Queen Square Institute of Neurology", "contributions": [ diff --git a/CITATION.cff b/CITATION.cff index 23f53ad4bd..98daeabda6 100644 --- a/CITATION.cff +++ b/CITATION.cff @@ -5,9 +5,10 @@ cff-version: 1.2.0 title: The Brain Imaging Data Structure (BIDS) Specification abstract: >- - The Brain Imaging Data Structure (BIDS) is a simple and intuitive way to organize and describe data. + The Brain Imaging Data Structure (BIDS) is a simple and intuitive way to organize + and describe data. -version: 1.10.0-dev +version: 1.10.0 license: CC-BY-4.0 @@ -142,6 +143,12 @@ authors: family-names: Galassi website: https://github.com/bendhouseart orcid: https://orcid.org/0000-0001-6550-4574 + - given-names: Arianna + family-names: Sala + website: https://www.coma.uliege.be/people/arianna-sala/ + orcid: https://orcid.org/0000-0001-8121-0891 + affiliation: université de Liège, Belgium + email: arianna.sala@uliege.be - given-names: Ariel family-names: Rokem website: https://arokem.org/ @@ -189,6 +196,10 @@ authors: website: https://github.com/musicinmybrain - given-names: Benjamin family-names: Dichter + website: https://bendichter.com/ + orcid: https://orcid.org/0000-0001-5725-6910 + affiliation: CatalystNeuro + email: ben.dichter@catalystneuro.com - given-names: Benjamin family-names: Gagl orcid: https://orcid.org/0000-0002-2339-6293 @@ -872,10 +883,9 @@ authors: website: https://github.com/mariehbourget - given-names: Mark family-names: Mikkelsen - website: https://vivo.weill.cornell.edu/display/cwid-mam4041 + website: https://mikkelsenlab.weill.cornell.edu/ orcid: https://orcid.org/0000-0002-0349-3782 - affiliation: Weill Cornell Medicine, Department of Radiology, New York, NY, 10021, - USA + affiliation: Weill Cornell Medicine email: mam4041@med.cornell.edu - given-names: Markus family-names: Morawski @@ -993,6 +1003,11 @@ authors: family-names: Ramsey - given-names: Nicole C. family-names: Swann + - given-names: Nikita + family-names: Beliy + orcid: https://orcid.org/0009-0002-0830-3279 + affiliation: University of Liege (Liege, Belgium) + email: nikita.beliy@uliege.be - given-names: Nima family-names: Bigdely Shamlo orcid: https://orcid.org/0000-0001-6403-892X @@ -1077,7 +1092,8 @@ authors: email: Rik.Henson@mrc-cbu.cam.ac.uk - given-names: Robert B. family-names: Innis - website: https://www.nimh.nih.gov/research/research-conducted-at-nimh/research-areas/clinics-and-labs/mib/molecular-imaging-branch-mib + website: + https://www.nimh.nih.gov/research/research-conducted-at-nimh/research-areas/clinics-and-labs/mib/molecular-imaging-branch-mib orcid: https://orcid.org/0000-0003-1238-7209 affiliation: NIMH Intramural Research Program, Bethesda, MD 20850 USA, MD 20892 USA email: robert.innis@nih.gov @@ -1121,6 +1137,11 @@ authors: website: https://github.com/samirdas - given-names: Samuel family-names: Garcia + - given-names: Samuel + family-names: Guay + orcid: https://orcid.org/0000-0001-6990-839X + affiliation: Université de Montréal, Montreal, Québec, CA + email: samuel.guay@umontreal.ca - given-names: Samuel family-names: Nastase website: https://snastase.github.io/ @@ -1312,6 +1333,10 @@ authors: - given-names: Vittorio family-names: Iacovella orcid: https://orcid.org/0000-0002-0853-1573 + - given-names: Viviana + family-names: Siless + affiliation: Business School, Universidad Torcuato di Tella + email: viviana.siless@utdt.edu - given-names: Vladimir family-names: Litvak orcid: https://orcid.org/0000-0001-8535-7452 diff --git a/mkdocs.yml b/mkdocs.yml index cfbdba2a49..b48801bcc5 100644 --- a/mkdocs.yml +++ b/mkdocs.yml @@ -1,4 +1,4 @@ -site_name: Brain Imaging Data Structure 1.10.0-dev +site_name: Brain Imaging Data Structure 1.10.0 site_url: https://bids-specification.readthedocs.io/en/stable/ repo_url: https://github.com/bids-standard/bids-specification nav: diff --git a/src/CHANGES.md b/src/CHANGES.md index 106f7e1aa0..1a8d02b31c 100644 --- a/src/CHANGES.md +++ b/src/CHANGES.md @@ -1,39 +1,47 @@ # Changelog -## [Unreleased](https://github.com/bids-standard/bids-specification/tree/HEAD) - -- \[ENH] Add use of session entity as example of encoding multi-site studies in a single dataset [#1803](https://github.com/bids-standard/bids-specification/pull/1803) ([yarikoptic](https://github.com/yarikoptic)) -- \[ENH] Describe Inheritance Principle in Common Principles [#1807](https://github.com/bids-standard/bids-specification/pull/1807) ([Lestropie](https://github.com/Lestropie)) -- \[ENH] Use deidentification consistently in place of anonymization [#1799](https://github.com/bids-standard/bids-specification/pull/1799) ([DimitriPapadopoulos](https://github.com/DimitriPapadopoulos)) -- \[INFRA] Introduce metaschema [#1787](https://github.com/bids-standard/bids-specification/pull/1787) ([bendichter](https://github.com/bendichter)) -- \[ENH] Add warning about deidentification when sharing sourcedata [#1769](https://github.com/bids-standard/bids-specification/pull/1769) ([Remi-Gau](https://github.com/Remi-Gau)) -- ENH: Use "Tag XXXX, YYYY" not "Tag (XXXX,YYYY)" for DICOM Tags [#1758](https://github.com/bids-standard/bids-specification/pull/1758) ([yarikoptic](https://github.com/yarikoptic)) -- \[ENH]\[SCHEMA] Allow .bval and .bvec files for pepolar fmaps [#1754](https://github.com/bids-standard/bids-specification/pull/1754) ([mattcieslak](https://github.com/mattcieslak)) -- FIX: Move `\_stim.\` specification within the Task Events module [#1750](https://github.com/bids-standard/bids-specification/pull/1750) ([oesteban](https://github.com/oesteban)) -- ENH: Add compressed TSV files to the common principles [#1749](https://github.com/bids-standard/bids-specification/pull/1749) ([oesteban](https://github.com/oesteban)) -- \[MAINT] split physio metadata tables [#1746](https://github.com/bids-standard/bids-specification/pull/1746) ([Remi-Gau](https://github.com/Remi-Gau)) -- \[FIX] Move `rawdata/` into `sourcedata/raw` in alternative structure example, clarify on naming of datasets themselves [#1741](https://github.com/bids-standard/bids-specification/pull/1741) ([yarikoptic](https://github.com/yarikoptic)) -- \[FIX] Remove mentions of sourcedata in the datatype specific pages [#1737](https://github.com/bids-standard/bids-specification/pull/1737) ([Remi-Gau](https://github.com/Remi-Gau)) -- \[ENH] events.tsv should be sorted by onset values [#1732](https://github.com/bids-standard/bids-specification/pull/1732) ([Remi-Gau](https://github.com/Remi-Gau)) -- \[FIX] fix typo in motion.md [#1731](https://github.com/bids-standard/bids-specification/pull/1731) ([Remi-Gau](https://github.com/Remi-Gau)) -- \[ENH] Specify the naming of scanner-generated TRACE and ADC volumes [#1725](https://github.com/bids-standard/bids-specification/pull/1725) ([effigies](https://github.com/effigies)) -- FIX: Re-add run entity to electrodes.tsv [#1722](https://github.com/bids-standard/bids-specification/pull/1722) ([effigies](https://github.com/effigies)) -- \[FIX] Add misssing files in filename template for NIRS [#1716](https://github.com/bids-standard/bids-specification/pull/1716) ([Remi-Gau](https://github.com/Remi-Gau)) -- \[FIX] Missing word in `genetic-descriptor.md` [#1715](https://github.com/bids-standard/bids-specification/pull/1715) ([markmikkelsen](https://github.com/markmikkelsen)) -- Add `descriptions.tsv` to the schema [#1707](https://github.com/bids-standard/bids-specification/pull/1707) ([tsalo](https://github.com/tsalo)) -- \[FIX] Remove task entity from DWI and PERF time series file templates [#1703](https://github.com/bids-standard/bids-specification/pull/1703) ([Remi-Gau](https://github.com/Remi-Gau)) -- ENH: Clarify the relation of motion.tsv columns to channels.tsv rows [#1699](https://github.com/bids-standard/bids-specification/pull/1699) ([effigies](https://github.com/effigies)) -- \[STY] apply black 24.1.0 [#1688](https://github.com/bids-standard/bids-specification/pull/1688) ([Remi-Gau](https://github.com/Remi-Gau)) -- \[ENH] Describe parametric images above the suffix table, rather than below [#1687](https://github.com/bids-standard/bids-specification/pull/1687) ([CPernet](https://github.com/CPernet)) -- \[ENH] Add support for HiP-CT [#1686](https://github.com/bids-standard/bids-specification/pull/1686) ([balbasty](https://github.com/balbasty)) -- \[FIX] Add `part-` to the PEPOLAR fieldmaps [#1685](https://github.com/bids-standard/bids-specification/pull/1685) ([oesteban](https://github.com/oesteban)) -- \[MISC] Restructure MEG empty room example texts [#1677](https://github.com/bids-standard/bids-specification/pull/1677) ([guiomar](https://github.com/guiomar)) -- ENH: Add sample metadata to MRI and PET [#1593](https://github.com/bids-standard/bids-specification/pull/1593) ([effigies](https://github.com/effigies)) -- \[ENH] Add noRF suffix for MR excitation-free noise scans [#1451](https://github.com/bids-standard/bids-specification/pull/1451) ([tsalo](https://github.com/tsalo)) -- \[ENH] Add generic metadata from BEP22 to MRI [#1396](https://github.com/bids-standard/bids-specification/pull/1396) ([Remi-Gau](https://github.com/Remi-Gau)) -- \[FIX] Consistently refer to Neuromag/Elekta/MEGIN [#1310](https://github.com/bids-standard/bids-specification/pull/1310) ([sappelhoff](https://github.com/sappelhoff)) - -## [v1.9.0](https://github.com/bids-standard/bids-specification/tree/v1.9.0) (2023-11-20) +## [v1.10.0](https://bids-specification.readthedocs.io/en/v1.10.0) (2024-09-06) + +- \[ENH] Add noRF and n/a ASL volume types [1884](https://github.com/bids-standard/bids-specification/pull/1884) ([tsalo](https://github.com/tsalo)) +- \[ENH] Provide baseline definition for behavioral files [1907](https://github.com/bids-standard/bids-specification/pull/1907) ([effigies](https://github.com/effigies)) +- \[ENH] Add metadata fields for DeIdentificationMethod/CodeSequence for MRI and PET [1772](https://github.com/bids-standard/bids-specification/pull/1772) ([CGSchwarzMayo](https://github.com/CGSchwarzMayo)) +- \[ENH] Apply derivative definition to qMRI appendix [1813](https://github.com/bids-standard/bids-specification/pull/1813) ([Remi-Gau](https://github.com/Remi-Gau)) +- \[ENH] BEP022 - Magnetic Resonance Spectroscopy [1377](https://github.com/bids-standard/bids-specification/pull/1377) ([markmikkelsen](https://github.com/markmikkelsen)) +- \[ENH] MRI: Improve definition of bvec file [1811](https://github.com/bids-standard/bids-specification/pull/1811) ([Lestropie](https://github.com/Lestropie)) +- \[ENH] Add TablePosition tag to MRI [1690](https://github.com/bids-standard/bids-specification/pull/1690) ([po09i](https://github.com/po09i)) +- \[ENH] Add explicit wording on DICOM terms correspondence [1450](https://github.com/bids-standard/bids-specification/pull/1450) ([yarikoptic](https://github.com/yarikoptic)) +- \[ENH] Generalize Units definition to apply to any variable, including TSV columns [1849](https://github.com/bids-standard/bids-specification/pull/1849) ([yarikoptic](https://github.com/yarikoptic)) +- \[ENH] Add use of session entity as example of encoding multi-site studies in a single dataset [1803](https://github.com/bids-standard/bids-specification/pull/1803) ([yarikoptic](https://github.com/yarikoptic)) +- \[ENH] Describe Inheritance Principle in Common Principles [1807](https://github.com/bids-standard/bids-specification/pull/1807) ([Lestropie](https://github.com/Lestropie)) +- \[ENH] Use deidentification consistently in place of anonymization [1799](https://github.com/bids-standard/bids-specification/pull/1799) ([DimitriPapadopoulos](https://github.com/DimitriPapadopoulos)) +- \[ENH] Allow .bval and .bvec files for pepolar fmaps [1754](https://github.com/bids-standard/bids-specification/pull/1754) ([mattcieslak](https://github.com/mattcieslak)) +- \[ENH] Add noRF suffix for MR excitation-free noise scans [1451](https://github.com/bids-standard/bids-specification/pull/1451) ([tsalo](https://github.com/tsalo)) +- \[ENH] Add warning about deidentification when sharing sourcedata [1769](https://github.com/bids-standard/bids-specification/pull/1769) ([Remi-Gau](https://github.com/Remi-Gau)) +- \[ENH] Use "Tag XXXX, YYYY" not "Tag (XXXX,YYYY)" for DICOM Tags [1758](https://github.com/bids-standard/bids-specification/pull/1758) ([yarikoptic](https://github.com/yarikoptic)) +- \[ENH] Add generic metadata from BEP22 to MRI [1396](https://github.com/bids-standard/bids-specification/pull/1396) ([Remi-Gau](https://github.com/Remi-Gau)) +- \[ENH] events.tsv should be sorted by onset values [1732](https://github.com/bids-standard/bids-specification/pull/1732) ([Remi-Gau](https://github.com/Remi-Gau)) +- \[ENH] Add compressed TSV files to the common principles [1749](https://github.com/bids-standard/bids-specification/pull/1749) ([oesteban](https://github.com/oesteban)) +- \[ENH] Add support for HiP-CT [1686](https://github.com/bids-standard/bids-specification/pull/1686) ([balbasty](https://github.com/balbasty)) +- \[ENH] Add sample metadata to MRI and PET [1593](https://github.com/bids-standard/bids-specification/pull/1593) ([effigies](https://github.com/effigies)) +- \[ENH] Clarify the relation of motion.tsv columns to channels.tsv rows [1699](https://github.com/bids-standard/bids-specification/pull/1699) ([effigies](https://github.com/effigies)) +- \[ENH] Describe parametric images above the suffix table, rather than below [1687](https://github.com/bids-standard/bids-specification/pull/1687) ([CPernet](https://github.com/CPernet)) +- \[FIX] Define a metadata table for TB1EPI [1912](https://github.com/bids-standard/bids-specification/pull/1912) ([effigies](https://github.com/effigies)) +- \[FIX] Update text to reflect that BackgroundSuppressionPulseTime is recommended [1891](https://github.com/bids-standard/bids-specification/pull/1891) ([michaelf500](https://github.com/michaelf500)) +- \[FIX] Remove extra bracket [1865](https://github.com/bids-standard/bids-specification/pull/1865) ([kabilar](https://github.com/kabilar)) +- \[FIX] Change hipCT microscopy suffix to XPCT [1822](https://github.com/bids-standard/bids-specification/pull/1822) ([chourroutm](https://github.com/chourroutm)) +- \[FIX] Consistently refer to Neuromag/Elekta/MEGIN [1310](https://github.com/bids-standard/bids-specification/pull/1310) ([sappelhoff](https://github.com/sappelhoff)) +- \[FIX] Re-add run entity to electrodes.tsv [1722](https://github.com/bids-standard/bids-specification/pull/1722) ([effigies](https://github.com/effigies)) +- \[FIX] Move `rawdata/` into `sourcedata/raw` in alternative structure example, clarify on naming of datasets themselves [1741](https://github.com/bids-standard/bids-specification/pull/1741) ([yarikoptic](https://github.com/yarikoptic)) +- \[FIX] Move ``_stim.`` specification within the Task Events module [1750](https://github.com/bids-standard/bids-specification/pull/1750) ([oesteban](https://github.com/oesteban)) +- \[FIX] Remove mentions of sourcedata in the datatype specific pages [1737](https://github.com/bids-standard/bids-specification/pull/1737) ([Remi-Gau](https://github.com/Remi-Gau)) +- \[FIX] Add misssing files in filename template for NIRS [1716](https://github.com/bids-standard/bids-specification/pull/1716) ([Remi-Gau](https://github.com/Remi-Gau)) +- \[FIX] Remove task entity from DWI and PERF time series file templates [1703](https://github.com/bids-standard/bids-specification/pull/1703) ([Remi-Gau](https://github.com/Remi-Gau)) +- \[FIX] Add `part-` to the PEPOLAR fieldmaps [1685](https://github.com/bids-standard/bids-specification/pull/1685) ([oesteban](https://github.com/oesteban)) +- \[INFRA] Publish schema to Javascript Registry (https://jsr.io/@bids/schema) on changes and releases [1899](https://github.com/bids-standard/bids-specification/pull/1899) ([effigies](https://github.com/effigies)) +- \[INFRA] Introduce metaschema [1787](https://github.com/bids-standard/bids-specification/pull/1787) ([bendichter](https://github.com/bendichter)) +- \[MISC] Restructure MEG empty room example texts [1677](https://github.com/bids-standard/bids-specification/pull/1677) ([guiomar](https://github.com/guiomar)) + +## [v1.9.0](https://bids-specification.readthedocs.io/en/v1.9.0) (2023-11-20) - \[ENH] Add `descriptions.tsv` file relating to the `desc-