diff --git a/.github/workflows/validation.yml b/.github/workflows/validation.yml index aea69e6e93..c039058bbc 100644 --- a/.github/workflows/validation.yml +++ b/.github/workflows/validation.yml @@ -24,7 +24,7 @@ jobs: runs-on: ubuntu-latest steps: - uses: actions/checkout@v4 - - uses: actions/setup-node@v3 + - uses: actions/setup-node@v4 with: node-version: 14 - name: Install dependencies diff --git a/.lgtm.yml b/.lgtm.yml deleted file mode 100644 index 0734210407..0000000000 --- a/.lgtm.yml +++ /dev/null @@ -1,8 +0,0 @@ ---- -# This file contains configuration for the LGTM tool: https://lgtm.com/ -# The bids-specification repository is continuously scanned by the LGTM tool -# for any security and/or code vulnerabilities. You can find the alert here: -# https://lgtm.com/projects/g/bids-standard/bids-specification/ -queries: - # https://lgtm.com/rules/6770079/ - - exclude: py/unused-import diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 178ebb0f1e..37311c71f3 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -13,7 +13,7 @@ repos: - id: check-added-large-files - id: check-case-conflict - repo: https://github.com/psf/black - rev: 23.10.0 + rev: 23.10.1 hooks: - id: black files: ^tools/(?!schemacode) diff --git a/src/CHANGES.md b/src/CHANGES.md index 5190da2f23..2b2836b02a 100644 --- a/src/CHANGES.md +++ b/src/CHANGES.md @@ -2,9 +2,15 @@ ## [Unreleased](https://github.com/bids-standard/bids-specification/tree/HEAD) +- \[ENH] add `ElectricalStimulation` and `\*Parameters` metadata to MEEG jsons [#1638](https://github.com/bids-standard/bids-specification/pull/1638) ([sappelhoff](https://github.com/sappelhoff)) +- Fix years and degrees Units and unit to be singular to match the rest [#1631](https://github.com/bids-standard/bids-specification/pull/1631) ([yarikoptic](https://github.com/yarikoptic)) +- \[FIX] Hierarchical Event Descriptors (HED) page update [#1623](https://github.com/bids-standard/bids-specification/pull/1623) ([effigies](https://github.com/effigies)) - FIX: Do not require notch frequencies to be parsed as numbers, accommodating multiples [#1605](https://github.com/bids-standard/bids-specification/pull/1605) ([effigies](https://github.com/effigies)) - \[ENH] Allow Levels field of column descriptions to be objects with TermURLs for each level [#1603](https://github.com/bids-standard/bids-specification/pull/1603) ([Remi-Gau](https://github.com/Remi-Gau)) - \[ENH] Add optional low_cutoff and high_cutoff columns for fnirs channels.tsv [#1597](https://github.com/bids-standard/bids-specification/pull/1597) ([Remi-Gau](https://github.com/Remi-Gau)) +- Recommend SliceTiming if MRAcquisitionType is "2D" [#1594](https://github.com/bids-standard/bids-specification/pull/1594) ([tsalo](https://github.com/tsalo)) +- \[ENH] Add Level objects to channels.json for motion [#1591](https://github.com/bids-standard/bids-specification/pull/1591) ([effigies](https://github.com/effigies)) +- \[ENH] Add "chunk" entity to MRI datatype [#1586](https://github.com/bids-standard/bids-specification/pull/1586) ([valosekj](https://github.com/valosekj)) - \[SCHEMA]\[ENH] Remove atlas entity and replace it with seg in prep of BEP038 [#1579](https://github.com/bids-standard/bids-specification/pull/1579) ([melanieganz](https://github.com/melanieganz)) - \[FIX] improve longitudinal example [#1576](https://github.com/bids-standard/bids-specification/pull/1576) ([Remi-Gau](https://github.com/Remi-Gau)) - Adds Kim Ray as maintainer. [#1571](https://github.com/bids-standard/bids-specification/pull/1571) ([arokem](https://github.com/arokem)) @@ -494,7 +500,7 @@ - \[ENH] add `ce-\` for fmri data [#70](https://github.com/bids-standard/bids-specification/pull/70) ([dasturge](https://github.com/dasturge)) - \[INFRA] pin pip version [#68](https://github.com/bids-standard/bids-specification/pull/68) ([chrisgorgo](https://github.com/chrisgorgo)) - \[MISC] Fix link in index [#46](https://github.com/bids-standard/bids-specification/pull/46) ([chrisgorgo](https://github.com/chrisgorgo)) -- \[MISC] edit contributing guide [#44](https://github.com/bids-standard/bids-specification/pull/44) ([Park-Patrick](https://github.com/Park-Patrick)) +- \[MISC] edit contributing guide [#44](https://github.com/bids-standard/bids-specification/pull/44) ([patrick-g-h](https://github.com/patrick-g-h)) - \[INFRA] Mkdocs configuration and RTD setup [#42](https://github.com/bids-standard/bids-specification/pull/42) ([choldgraf](https://github.com/choldgraf)) - \[MISC] Move definitions, compulsory, and raw/derivatives sections to principles [#40](https://github.com/bids-standard/bids-specification/pull/40) ([chrisgorgo](https://github.com/chrisgorgo)) - \[MISC] Remove duplicate section [#39](https://github.com/bids-standard/bids-specification/pull/39) ([chrisgorgo](https://github.com/chrisgorgo)) diff --git a/src/modality-specific-files/electroencephalography.md b/src/modality-specific-files/electroencephalography.md index 46ffce2921..e38f2236ef 100644 --- a/src/modality-specific-files/electroencephalography.md +++ b/src/modality-specific-files/electroencephalography.md @@ -113,6 +113,18 @@ A guide for using macros can be found at --> {{ MACROS___make_sidecar_table("eeg.EEGRecommended") }} +These fields MAY be present: + + +{{ MACROS___make_sidecar_table("eeg.EEGOptional") }} + #### Hardware information {{ MACROS___make_sidecar_table("meg.MEGRecommended") }} +These fields MAY be present: + + +{{ MACROS___make_sidecar_table("meg.MEGOptional") }} + #### Hardware information + +[object]: https://www.json.org/json-en.html + +[string]: https://www.w3schools.com/js/js_json_datatypes.asp diff --git a/src/schema/objects/columns.yaml b/src/schema/objects/columns.yaml index b52da751fe..89d28a5f09 100644 --- a/src/schema/objects/columns.yaml +++ b/src/schema/objects/columns.yaml @@ -378,6 +378,18 @@ reference__ieeg: - type: string enum: - n/a +reference_frame: + name: reference_frame + display_name: 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. + anyOf: + - type: string + - type: string + enum: + - n/a respiratory: name: respiratory display_name: Respiratory measurement diff --git a/src/schema/objects/metadata.yaml b/src/schema/objects/metadata.yaml index d0fa480198..2f8d26d33e 100644 --- a/src/schema/objects/metadata.yaml +++ b/src/schema/objects/metadata.yaml @@ -901,7 +901,7 @@ ElectricalStimulationParameters: display_name: Electrical Stimulation Parameters description: | Free form description of stimulation parameters, such as frequency or shape. - Specific onsets can be specified in the events.tsv file. + Specific onsets can be specified in the `events.tsv` file. Specific shapes can be described here in freeform text. type: string ElectrodeManufacturer: diff --git a/src/schema/objects/suffixes.yaml b/src/schema/objects/suffixes.yaml index caa943ee7c..16e410c70d 100644 --- a/src/schema/objects/suffixes.yaml +++ b/src/schema/objects/suffixes.yaml @@ -228,10 +228,8 @@ PDw: In arbitrary units (arbitrary). The contrast of these images is mainly determined by spatial variations in the spin density (1H) of the imaged specimen. - In spin-echo sequences this contrast is achieved at short repetition and long - echo times. - In a gradient-echo acquisition, PD weighting dominates the contrast at long - repetition and short echo times, and at small flip angles. + This contrast is achieved at short echo times and long repetition times; + for gradient echo, this weighting is also possible with a short TR (TR<