[ENH] BEP022 - Magnetic Resonance Spectroscopy

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/schema/meta/context.yaml

@@ -328,6 +328,10 @@ 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/objects/common_principles.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/datatypes.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/entities.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/enums.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