Merge branch 'master' of https://github.com/markmikkelsen/bids-specification

Author: markmikkelsen

.github/workflows/publish_schema.yml

@@ -0,0 +1,91 @@
+name: "Publish schema"
+
+on:
+  push:
+    branches:
+      - "master"
+    tags:
+      - "schema-*"
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+defaults:
+  run:
+    shell: bash
+
+env:
+  GIT_AUTHOR_NAME: BIDS CI
+  GIT_AUTHOR_EMAIL: [email protected]
+  GIT_COMMITTER_NAME: BIDS CI
+  GIT_COMMITTER_EMAIL: [email protected]
+
+permissions:
+  contents: write
+  id-token: write
+
+jobs:
+  publish:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+          filter: "blob:none"
+      - uses: actions/setup-python@v5
+        with:
+          python-version: 3
+      - name: Install bidsschematools
+        run: |
+          pip install --upgrade tools/schemacode
+          git clean -fxd tools/schemacode
+      - name: Checkout jsr-dist
+        run: |
+          git checkout -t origin/jsr-dist
+      - name: Regenerate schema
+        run: bst export > schema.json
+      - name: Regenerate context types
+        run: |
+          jq .meta.context schema.json \
+          | npx quicktype --src-lang schema --lang ts -t Context --just-types \
+          > context.ts
+      - name: Regenerate metaschema types
+        run: |
+          # Name the file schema so the type will be named Schema
+          bst export-metaschema > /tmp/schema.json
+          npx --package=json-schema-to-typescript json2ts --unknownAny /tmp/schema.json > metaschema.ts
+      - name: Determine next version
+        run: |
+          BASE=$( jq -r .schema_version schema.json )
+          if [[ "$BASE" =~ ^[0-9]*.[0-9]*.[0-9]*$ ]]; then
+            # Release, so unconditionally update version
+            VERSION=$BASE
+            jq ".version = \"$VERSION\"" jsr.json > tmp.json && mv tmp.json jsr.json
+          else
+            DENOVER=$( jq -r .version jsr.json )
+            # Get the reference of the latest commit to touch the schema directory
+            HASH=$( git log -n 1 --pretty=%h $REF -- src/schema )
+            if [[ $DENOVER =~ ^"$BASE".[0-9] ]]; then
+              PREFIX=${DENOVER%+*}
+              let SERIAL=1+${PREFIX#$BASE.}
+            else
+              SERIAL=1
+            fi
+            VERSION="$BASE.$SERIAL+$HASH"
+          fi
+          echo VERSION=$VERSION | tee -a $GITHUB_ENV
+        env:
+          REF: ${{ github.ref }}
+      - name: Check for changes, set version and commit
+        run: |
+          if ! git diff -s --exit-code; then
+            jq ".version = \"$VERSION\"" jsr.json > tmp.json && mv tmp.json jsr.json
+            git add jsr.json schema.json context.ts metaschema.ts
+            git commit -m "Update schema JSR distribution"
+            git push
+          fi
+      - name: Publish to JSR
+        if: success()
+        run: |
+          npx jsr publish

.pre-commit-config.yaml

@@ -15,7 +15,7 @@ repos:
       - id: check-added-large-files
       - id: check-case-conflict
   - repo: https://github.com/python-jsonschema/check-jsonschema
-    rev: 0.29.1
+    rev: 0.29.2
     hooks:
       - id: check-dependabot
       - id: check-github-workflows
@@ -67,7 +67,7 @@ repos:
       - id: codespell
         args: ["--config=.codespellrc", "--dictionary=-", "--dictionary=.codespell_dict"]
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.11.1
+    rev: v1.11.2
     hooks:
       - id: mypy
         # Sync with project.optional-dependencies.typing

README.md

@@ -30,6 +30,7 @@ BIDS currently supports the following data modalities with more to come in the f
 - microscopy
 - NIRS
 - motion
+- MRS
 
 # Formatting your data with BIDS
 

mkdocs.yml

@@ -19,6 +19,7 @@ nav:
           - Microscopy: modality-specific-files/microscopy.md
           - Near-Infrared Spectroscopy: modality-specific-files/near-infrared-spectroscopy.md
           - Motion: modality-specific-files/motion.md
+          - Magnetic Resonance Spectroscopy: modality-specific-files/magnetic-resonance-spectroscopy.md
       - Derivatives:
           - BIDS Derivatives: derivatives/introduction.md
           - Common data types and metadata: derivatives/common-data-types.md

src/appendices/cross-modality-correspondence.md

@@ -12,3 +12,10 @@ The reason for this is that the MRI needs to be corrected for nonlinear gradient
 in order to fit the accompanying PET scans for co-registration
 (Knudsen et al. 2020, [doi:10.1177/0271678X20905433](https://doi.org/10.1177/0271678X20905433);
 Norgaard et al. 2019, [doi:10.1016/j.neuroimage.2019.05.055](https://doi.org/10.1016/j.neuroimage.2019.05.055)).
+
+## MRS-MRI correspondence
+
+It is typical to acquire high-resolution 3D anatomical MR images alongside MRS data for
+voxel/slab placement, co-registration, and partial-volume tissue correction of metabolite concentrations.
+To avoid incorrectly matching an MRS dataset with a corresponding anatomical MR image,
+it is RECOMMENDED that the field `AnatomicalImage` be included in the MRS sidecar JSON files.

src/introduction.md

@@ -184,6 +184,10 @@ For example:
      PsyArXiv.
      [doi:10.31234/osf.io/w6z79](https://doi.org/10.31234/osf.io/w6z79)
 
+#### MRS
+
+-   (publication forthcoming)
+
 ### Research Resource Identifier (RRID)
 
 BIDS has also a