Merge branch 'master' into pheno_dir

.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

.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)

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-\<label\>` 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))

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:
+
+<!-- This block generates a metadata table.
+These tables are defined in
+  src/schema/rules/sidecars
+The definitions of the fields specified in these tables may be found in
+  src/schema/objects/metadata.yaml
+A guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
+{{ MACROS___make_sidecar_table("eeg.EEGOptional") }}
+
 #### Hardware information
 
 <!-- This block generates a metadata table.

src/modality-specific-files/magnetoencephalography.md

@@ -135,6 +135,18 @@ A guide for using macros can be found at
 -->
 {{ MACROS___make_sidecar_table("meg.MEGRecommended") }}
 
+These fields MAY be present:
+
+<!-- This block generates a metadata table.
+These tables are defined in
+  src/schema/rules/sidecars
+The definitions of the fields specified in these tables may be found in
+  src/schema/objects/metadata.yaml
+A guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
+{{ MACROS___make_sidecar_table("meg.MEGOptional") }}
+
 #### Hardware information
 
 <!-- This block generates a metadata table.

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:

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<<T1) and a small flip angle.
   unit: arbitrary
 PLI:
   value: PLI

src/schema/rules/sidecars/eeg.yaml

@@ -43,6 +43,7 @@ EEGInstitutionInformation:
     InstitutionAddress: recommended
     InstitutionalDepartmentName: recommended
 
+# Specific EEG fields MUST be present
 EEGRequired:
   selectors:
     - datatype == "eeg"
@@ -57,6 +58,7 @@ EEGRequired:
     PowerLineFrequency: required
     SoftwareFilters: required
 
+# Specific EEG fields SHOULD be present
 EEGRecommended:
   selectors:
     - datatype == "eeg"
@@ -79,6 +81,15 @@ EEGRecommended:
     HardwareFilters: recommended
     SubjectArtefactDescription: recommended
 
+# Specific EEG fields MAY be present
+EEGOptional:
+  selectors:
+    - datatype == "eeg"
+    - suffix == "eeg"
+  fields:
+    ElectricalStimulation: optional
+    ElectricalStimulationParameters: optional
+
 # General fields
 EEGCoordsystemGeneral:
   selectors:

src/schema/rules/sidecars/meg.yaml

@@ -107,6 +107,15 @@ MEGRecommended:
     AssociatedEmptyRoom: recommended
     HardwareFilters: recommended
 
+# Specific MEG fields MAY be present
+MEGOptional:
+  selectors:
+    - datatype == "meg"
+    - suffix == "meg"
+  fields:
+    ElectricalStimulation: optional
+    ElectricalStimulationParameters: optional
+
 # Specific EEG fields
 # NOTE: I'm not sure if "EEG is present" is enough to indicate simultaneous EEG/MEG.
 MEGwithEEG: