Merge pull request #496 from bids-standard/rel/1.4.0

REL: v1.4.0
bids-standard · Jun 11, 2020 · 24b8505 · 24b8505
2 parents 3a16c89 + cd52415
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diff --git a/mkdocs.yml b/mkdocs.yml
@@ -1,4 +1,4 @@
-site_name: Brain Imaging Data Structure v1.3.1-dev
+site_name: Brain Imaging Data Structure v1.4.0
 theme:
     name: material
     custom_dir: theme_customizations/

diff --git a/src/99-appendices/01-contributors.md b/src/99-appendices/01-contributors.md
@@ -34,6 +34,7 @@ your name is not listed, please add it.
 -   Stefan Appelhoff 📖💬🤔🐛💡💻👀⚠️📢✅🔧🔌📝
 -   Tibor Auer 💬📖💡🔧📢
 -   Sylvain Baillet 📖🔍
+-   Arshitha Basavaraj 📖🚇💻
 -   Stephan Bickel 📖
 -   Elizabeth Bock 📖💡
 -   Kristofer Bouchard 📖
@@ -159,4 +160,3 @@ your name is not listed, please add it.
 -   Gaël Varoquaux 📖
 -   Tal Yarkoni 💻📖🤔🔍🔌👀📢🐛🎨
 -   Lyuba Zehl 📖
--   Sébastien Tourbier 🤔👀📢
diff --git a/src/CHANGES.md b/src/CHANGES.md
@@ -1,6 +1,6 @@
 # Changelog
 
-## [Unreleased](https://github.com/bids-standard/bids-specification/tree/HEAD)
+## [v1.4.0](https://bids-specification.readthedocs.io/en/v1.4.0/) (2020-06-11)
 
 -   \[FIX] Clarify language on unsetting a key/value pair [#495](https://github.com/bids-standard/bids-specification/pull/495) ([nicholst](https://github.com/nicholst))
 -   ENH: Add RECOMMENDED DatasetType key to dataset description [#494](https://github.com/bids-standard/bids-specification/pull/494) ([effigies](https://github.com/effigies))
@@ -19,21 +19,19 @@
 -   \[FIX] Add reference to PDF on front page of specification [#452](https://github.com/bids-standard/bids-specification/pull/452) ([nicholst](https://github.com/nicholst))
 -   \[INFRA] Add conditional for link-checking releases [#451](https://github.com/bids-standard/bids-specification/pull/451) ([franklin-feingold](https://github.com/franklin-feingold))
 -   \[FIX] unordered list formatting in BEP018 [#449](https://github.com/bids-standard/bids-specification/pull/449) ([sappelhoff](https://github.com/sappelhoff))
--   REL: 1.3.1-dev [#448](https://github.com/bids-standard/bids-specification/pull/448) ([franklin-feingold](https://github.com/franklin-feingold))
 -   \[FIX] fix inconsistencies for task label between sections [#446](https://github.com/bids-standard/bids-specification/pull/446) ([Remi-Gau](https://github.com/Remi-Gau))
 -   \[FIX] update DECISION-MAKING.md document with new governance [#441](https://github.com/bids-standard/bids-specification/pull/441) ([sappelhoff](https://github.com/sappelhoff))
 -   \[ENH] Add `res` and `den` keywords to indicate resolution of resampled data [#301](https://github.com/bids-standard/bids-specification/pull/301) ([oesteban](https://github.com/oesteban))
 -   \[ENH] BEP 003: Common Derivatives [#265](https://github.com/bids-standard/bids-specification/pull/265) ([effigies](https://github.com/effigies))
 -   \[ENH] Add Glossary of terms/abbreviations used in the specification [#152](https://github.com/bids-standard/bids-specification/pull/152) ([yarikoptic](https://github.com/yarikoptic))
 
-## [v1.3.0](https://github.com/bids-standard/bids-specification/tree/v1.3.0) (2020-04-14)
+## [v1.3.0](https://bids-specification.readthedocs.io/en/v1.3.0/) (2020-04-14)
 
 -   \[INFRA] add zenodo badge to README [#447](https://github.com/bids-standard/bids-specification/pull/447) ([sappelhoff](https://github.com/sappelhoff))
 -   Added contributors from VisLab [#444](https://github.com/bids-standard/bids-specification/pull/444) ([VisLab](https://github.com/VisLab))
 -   FIX: Clarify  snake_case+CamelCase in TSV+JSON [#442](https://github.com/bids-standard/bids-specification/pull/442) ([sappelhoff](https://github.com/sappelhoff))
 -   \[FIX] Eliminate web/online-specific language [#437](https://github.com/bids-standard/bids-specification/pull/437) ([nicholst](https://github.com/nicholst))
 -   \[INFRA] ensure build_docs_pdf CircleCI job runs last [#436](https://github.com/bids-standard/bids-specification/pull/436) ([sappelhoff](https://github.com/sappelhoff))
--   REL: v1.3.0 [#435](https://github.com/bids-standard/bids-specification/pull/435) ([franklin-feingold](https://github.com/franklin-feingold))
 -   \[INFRA] Add issue templates for GitHub [#434](https://github.com/bids-standard/bids-specification/pull/434) ([sappelhoff](https://github.com/sappelhoff))
 -   \[INFRA] Get latest PDF build from CircleCI artifacts [#433](https://github.com/bids-standard/bids-specification/pull/433) ([sappelhoff](https://github.com/sappelhoff))
 -   \[INFRA] Update release protocol [#432](https://github.com/bids-standard/bids-specification/pull/432) ([franklin-feingold](https://github.com/franklin-feingold))
@@ -43,16 +41,14 @@
 -   \[FIX] Unify section titles and table-of-contents entries [#422](https://github.com/bids-standard/bids-specification/pull/422) ([nicholst](https://github.com/nicholst))
 -   \[INFRA] add # before heading in CHANGES [#419](https://github.com/bids-standard/bids-specification/pull/419) ([sappelhoff](https://github.com/sappelhoff))
 -   \[INFRA] fix heading of auto changelog to be a markdown header [#417](https://github.com/bids-standard/bids-specification/pull/417) ([sappelhoff](https://github.com/sappelhoff))
--   REL: 1.3.0-dev [#413](https://github.com/bids-standard/bids-specification/pull/413) ([franklin-feingold](https://github.com/franklin-feingold))
 -   ENH: Add OPTIONAL EthicsApprovals field to dataset description [#412](https://github.com/bids-standard/bids-specification/pull/412) ([effigies](https://github.com/effigies))
 -   \[ENH] BEP 018 - Genetic Information [#395](https://github.com/bids-standard/bids-specification/pull/395) ([effigies](https://github.com/effigies))
 
-## [v1.2.2](https://github.com/bids-standard/bids-specification/tree/v1.2.2) (2020-02-12)
+## [v1.2.2](https://bids-specification.readthedocs.io/en/v1.2.2/) (2020-02-12)
 
 -   \[FIX] improve wording on data dictionaries [#410](https://github.com/bids-standard/bids-specification/pull/410) ([sappelhoff](https://github.com/sappelhoff))
 -   \[MISC] update contributions by CPernet [#409](https://github.com/bids-standard/bids-specification/pull/409) ([CPernet](https://github.com/CPernet))
 -   Units2ascii [#408](https://github.com/bids-standard/bids-specification/pull/408) ([satra](https://github.com/satra))
--   REL: v1.2.2 [#405](https://github.com/bids-standard/bids-specification/pull/405) ([franklin-feingold](https://github.com/franklin-feingold))
 -   \[FIX] Fix typos and formatting [#404](https://github.com/bids-standard/bids-specification/pull/404) ([alexandreroutier](https://github.com/alexandreroutier))
 -   BEP 18 suggestions [#398](https://github.com/bids-standard/bids-specification/pull/398) ([effigies](https://github.com/effigies))
 -   \[MISC] Add Sébastien Tourbier to contributors [#394](https://github.com/bids-standard/bids-specification/pull/394) ([sebastientourbier](https://github.com/sebastientourbier))
@@ -89,18 +85,15 @@
 -   \[FIX] Revise template-generated coordinate systems [#307](https://github.com/bids-standard/bids-specification/pull/307) ([oesteban](https://github.com/oesteban))
 -   \[FIX] Normalization of template-generated standard spaces [#306](https://github.com/bids-standard/bids-specification/pull/306) ([oesteban](https://github.com/oesteban))
 -   \[ENH] Release protocol notes [#304](https://github.com/bids-standard/bids-specification/pull/304) ([franklin-feingold](https://github.com/franklin-feingold))
--   REL: 1.3.0-dev [#303](https://github.com/bids-standard/bids-specification/pull/303) ([franklin-feingold](https://github.com/franklin-feingold))
 -   \[INFRA] Adding contributor appendix sentence to PR template  [#299](https://github.com/bids-standard/bids-specification/pull/299) ([franklin-feingold](https://github.com/franklin-feingold))
 -   \[ENH] Added discontinuous datatype for EEG and iEEG [#286](https://github.com/bids-standard/bids-specification/pull/286) ([wouterpotters](https://github.com/wouterpotters))
 -   \[FIX] Clarify paragraph about custom data types [#264](https://github.com/bids-standard/bids-specification/pull/264) ([effigies](https://github.com/effigies))
 
-## [v1.2.1](https://github.com/bids-standard/bids-specification/tree/v1.2.1) (2019-08-14)
+## [v1.2.1](https://bids-specification.readthedocs.io/en/v1.2.1/) (2019-08-14)
 
--   Sync rel/1.2.1 to master [#302](https://github.com/bids-standard/bids-specification/pull/302) ([franklin-feingold](https://github.com/franklin-feingold))
 -   FIX: repair link in anatomical MRI table [#297](https://github.com/bids-standard/bids-specification/pull/297) ([sappelhoff](https://github.com/sappelhoff))
 -   \[ENH] Clarify requirements in Release Protocol [#294](https://github.com/bids-standard/bids-specification/pull/294) ([franklin-feingold](https://github.com/franklin-feingold))
 -   \[INFRA+FIX] Use linkchecker (from a dedicated docker image) to check all URLs [#293](https://github.com/bids-standard/bids-specification/pull/293) ([yarikoptic](https://github.com/yarikoptic))
--   REL: v1.2.1 [#291](https://github.com/bids-standard/bids-specification/pull/291) ([franklin-feingold](https://github.com/franklin-feingold))
 -   \[ENH] Adding Contributors and updating contributions [#284](https://github.com/bids-standard/bids-specification/pull/284) ([franklin-feingold](https://github.com/franklin-feingold))
 -   \[MISC] update Code of Conduct contact [#281](https://github.com/bids-standard/bids-specification/pull/281) ([franklin-feingold](https://github.com/franklin-feingold))
 -   \[ENH] Update contributing guide and README to make discussion forums easy to find [#279](https://github.com/bids-standard/bids-specification/pull/279) ([emdupre](https://github.com/emdupre))
@@ -121,7 +114,6 @@
 -   \[MISC] Document BEPs that are not active anymore, but have not been merged [#240](https://github.com/bids-standard/bids-specification/pull/240) ([sappelhoff](https://github.com/sappelhoff))
 -   \[FIX] remove ManufacturersAmplifierModelName (again) [#236](https://github.com/bids-standard/bids-specification/pull/236) ([robertoostenveld](https://github.com/robertoostenveld))
 -   \[INFRA] Update release protocol [#235](https://github.com/bids-standard/bids-specification/pull/235) ([effigies](https://github.com/effigies))
--   REL: 1.3.0-dev [#234](https://github.com/bids-standard/bids-specification/pull/234) ([effigies](https://github.com/effigies))
 -   \[INFRA] Enable version panel for quickly finding previous versions [#232](https://github.com/bids-standard/bids-specification/pull/232) ([effigies](https://github.com/effigies))
 -   \[FIX] use \\&lt;label> for \_desc- - not some \\&lt;value> + clarify \\&lt;value> [#224](https://github.com/bids-standard/bids-specification/pull/224) ([yarikoptic](https://github.com/yarikoptic))
 -   \[FIX] Clarify Appendix II: The list of licenses only lists examples [#222](https://github.com/bids-standard/bids-specification/pull/222) ([sappelhoff](https://github.com/sappelhoff))
@@ -154,9 +146,8 @@
 -   \[FIX] Specify marker file names for KIT data (MEG) [#62](https://github.com/bids-standard/bids-specification/pull/62) ([monkeyman192](https://github.com/monkeyman192))
 -   \[FIX] Remove father-level for meg filetypes other than BTi/4D data [#19](https://github.com/bids-standard/bids-specification/pull/19) ([teonbrooks](https://github.com/teonbrooks))
 
-## [v1.2.0](https://github.com/bids-standard/bids-specification/tree/v1.2.0) (2019-03-04)
+## [v1.2.0](https://bids-specification.readthedocs.io/en/v1.2.0/) (2019-03-04)
 
--   REL: v1.2.0 [#161](https://github.com/bids-standard/bids-specification/pull/161) ([chrisgorgo](https://github.com/chrisgorgo))
 -   \[MISC] Adding Dimitri Papadopoulos Orfanos to the list of contributors [#157](https://github.com/bids-standard/bids-specification/pull/157) ([DimitriPapadopoulos](https://github.com/DimitriPapadopoulos))
 -   RF: use "specification" not "protocol" to refer to BIDS [#156](https://github.com/bids-standard/bids-specification/pull/156) ([yarikoptic](https://github.com/yarikoptic))
 -   Fix example misalignment [#155](https://github.com/bids-standard/bids-specification/pull/155) ([DimitriPapadopoulos](https://github.com/DimitriPapadopoulos))
@@ -172,9 +163,8 @@
 -   Adding formal decision-making rules [#104](https://github.com/bids-standard/bids-specification/pull/104) ([chrisgorgo](https://github.com/chrisgorgo))
 -   \[MRG] number of small corrections to the specification [#98](https://github.com/bids-standard/bids-specification/pull/98) ([robertoostenveld](https://github.com/robertoostenveld))
 
-## [v1.1.2](https://github.com/bids-standard/bids-specification/tree/v1.1.2) (2019-01-10)
+## [v1.1.2](https://bids-specification.readthedocs.io/en/v1.1.2/) (2019-01-10)
 
--   REL: v.1.1.2 [#121](https://github.com/bids-standard/bids-specification/pull/121) ([chrisgorgo](https://github.com/chrisgorgo))
 -   Update 01-contributors.md [#120](https://github.com/bids-standard/bids-specification/pull/120) ([oesteban](https://github.com/oesteban))
 -   Global fields in data dictionaries [#117](https://github.com/bids-standard/bids-specification/pull/117) ([chrisgorgo](https://github.com/chrisgorgo))
 -   Propose BEP026 MER [#116](https://github.com/bids-standard/bids-specification/pull/116) ([greydongilmore](https://github.com/greydongilmore))
@@ -274,8 +264,8 @@
     NumberOfVolumesDiscardedByScanner field \[[4.1 Task (including
     resting state) imaging data](04-modality-specific-files/01-magnetic-resonance-imaging-data.md#task-including-resting-state-imaging-data)].
 
--   Added TotalReadoutTime to functional images metadata list
-     \[[4.1 Task (including resting state) imaging
+-   Added TotalReadoutTime to functional images metadata list
+     \[[4.1 Task (including resting state) imaging
     data](04-modality-specific-files/01-magnetic-resonance-imaging-data.md#task-including-resting-state-imaging-data)].
 
 ## 1.0.1-rc1
@@ -290,16 +280,16 @@
 
 -   Added SoftwareVersions
 
--   Added run-&lt;run_index> to the phase encoding
+-   Added run-&lt;run_index> to the phase encoding
     maps. Improved the description.
 
--   Added InversionTime metadata key.
+-   Added InversionTime metadata key.
 
 -   Clarification on the source vs raw language.
 
--   Added trial_type column to the event files.
+-   Added trial_type column to the event files.
 
--   Added missing sub-&lt;participant_label> in
+-   Added missing sub-&lt;participant_label> in
     behavioral data file names
 
 -   Added ability to store stimuli files.
@@ -330,10 +320,10 @@
 
 ## 1.0.0-rc3
 
--   Renamed PhaseEncodingDirection values from “x”, “y”,
+-   Renamed PhaseEncodingDirection values from “x”, “y”,
     “z” to “i”, “j”, “k” to avoid confusion with FSL parameters
 
--   Renamed SliceEncodingDirection values from “x”, “y”,
+-   Renamed SliceEncodingDirection values from “x”, “y”,
     “z” to “i”, “j”, “k”
 
 ## 1.0.0-rc2
@@ -346,39 +336,39 @@
 
 -   Make support for uncompressed .nii files more explicit.
 
--   Added BIDSVersion to dataset.json
+-   Added BIDSVersion to dataset.json
 
--   Remove the statement that SliceEncodingDirection is
+-   Remove the statement that SliceEncodingDirection is
     necessary for slice time correction
 
 -   Change dicom converter recommendation from dcmstack to dcm2nii and
     dicm2nii following interactions with the community (see
-    <https://github.com/moloney/dcmstack/issues/39> and
+    <https://github.com/moloney/dcmstack/issues/39> and
     <https://github.com/neurolabusc/dcm2niix/issues/4>).
 
 -   Added section on behavioral experiments with no accompanying MRI
     acquisition
 
--   Add \_magnitude.nii\[.gz] image for GE type
+-   Add \_magnitude.nii\[.gz] image for GE type
     fieldmaps.
 
--   Replaced EchoTimeDifference with
-    EchoTime1 and EchoTime2 (SPM toolbox
+-   Replaced EchoTimeDifference with
+    EchoTime1 and EchoTime2 (SPM toolbox
     requires this input).
 
 -   Added support for single band reference image for DWI.
 
--   Added DatasetDOI field in the dataset
+-   Added DatasetDOI field in the dataset
     description.
 
 -   Added description of more metadata fields relevant to DWI fieldmap
     correction.
 
--   PhaseEncodingDirection is now expressed in “x”, “y” etc. instead of “PA”
+-   PhaseEncodingDirection is now expressed in “x”, “y” etc. instead of “PA”
     “RL” for DWI scans
     (so it’s the same as BOLD scans)
 
--   Added rec-&lt;label> flag to BOLD files to
+-   Added rec-&lt;label> flag to BOLD files to
     distinguish
     between different reconstruction algorithms
     (analogous to anatomical scans).