Merge pull request #1377 from bids-standard/bep022

[ENH] BEP022 - Magnetic Resonance Spectroscopy

Author: effigies

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

src/modality-specific-files/magnetic-resonance-spectroscopy.md

@@ -405,6 +405,10 @@ properties:
         name: 'sform code'
         description: 'Use of the affine fields.'
         type: integer
+      mrs:
+        name: 'NIfTI-MRS extension'
+        description: 'NIfTI-MRS JSON fields'
+        type: object
   ome:
     name: 'Open Microscopy Environment fields'
     description: 'Parsed contents of OME-XML header, which may be found in OME-TIFF or OME-ZARR files'

src/schema/meta/context.yaml

@@ -41,6 +41,9 @@ data_type:
         12. `nirs` (near infrared spectroscopy)
 
         13. `motion` (motion)
+
+        14. `mrs` (magnetic resonance spectroscopy)
+
 dataset:
   display_name: Dataset
   description: |

src/schema/objects/common_principles.yaml

@@ -47,6 +47,10 @@ motion:
   value: motion
   display_name: Motion
   description: Motion data from a tracking system
+mrs:
+  value: mrs
+  display_name: Magnetic Resonance Spectroscopy
+  description: Magnetic resonance spectroscopy data
 perf:
   value: perf
   display_name: Perfusion imaging

src/schema/objects/datatypes.yaml

@@ -179,6 +179,17 @@ mtransfer:
   enum:
     - $ref: objects.enums.on__mtransfer.value
     - $ref: objects.enums.off__mtransfer.value
+nucleus:
+  name: nuc
+  display_name: Nucleus
+  description: |
+    The `nuc-<label>` entity can be used to distinguish acquisitions tuned
+    to detect different nuclei.
+    The label is the name of the nucleus or nuclei, which corresponds to DICOM Tag `0018, 9100`.
+    If present in the filename, `"ResonantNucleus"` MUST also be included in
+    the associated metadata.
+  type: string
+  format: label
 part:
   name: part
   display_name: Part
@@ -408,9 +419,19 @@ tracer:
     Please note that the `<label>` does not need to match the actual value of the field.
   type: string
   format: label
+volume:
+  name: voi
+  display_name: Volume of Interest
+  description: |
+    The `voi-<label>` entity can be used to distinguish acquisitions localized to different regions.
+    The label SHOULD be the name of the body region or part scanned.
+    If used, the fields `"BodyPart"` and `"BodyPartDetails"` MUST be defined in the JSON file.
+    `BodyPartDetailsOntology` is OPTIONAL to also include.
+  type: string
+  format: label
 tracksys:
   name: tracksys
-  display_name: Tracking system
+  display_name: Tracking System
   description: |
     The `tracksys-<label>` entity can be used as a key-value pair
     to label *_motion.tsv and *_motion.json files.

src/schema/objects/entities.yaml

@@ -120,6 +120,11 @@ Absent:
   display_name: Absent
   description: |
     No specific M0 information is present.
+OneD:
+  value: 1D
+  display_name: One-dimensional
+  description: |
+    One-dimensional MR acquisition.
 TwoD:
   value: 2D
   display_name: Two-dimensional