[ENH]: BEP046, diffusion tractography

mkdocs.yml

@@ -29,6 +29,7 @@ nav:
           - BIDS Derivatives: derivatives/introduction.md
           - Common data types and metadata: derivatives/common-data-types.md
           - Imaging data types: derivatives/imaging.md
+          - Diffusion MRI: derivatives/diffusion-derivatives.md
           - Templates and atlases: derivatives/atlas.md
       - Longitudinal and multi-site studies: longitudinal-and-multi-site-studies.md
       - Glossary: glossary.md
@@ -157,6 +158,7 @@ plugins:
         "05-derivatives/01-introduction.md": "derivatives/introduction.md"
         "05-derivatives/02-common-data-types.md": "derivatives/common-data-types.md"
         "05-derivatives/03-imaging.md": "derivatives/imaging.md"
+        "05-derivatives/03-diffusion.md": "derivatives/diffusion-derivatives.md"
         "06-longitudinal-and-multi-site-studies.md": "longitudinal-and-multi-site-studies.md"
         "07-extensions.md": "extensions.md"
         "99-appendices/14-glossary.md": "glossary.md"

src/derivatives/diffusion-derivatives.md

@@ -0,0 +1,31 @@
+# Diffusion derivatives
+
+## Diffusion-based tractography
+
+Tractography based on diffusion-weighted MRI data is stored as streamlines in
+the TRX file format:
+
+```Text
+<pipeline_name>/
+    sub-<label>/
+        [ses-<label>/]
+            <modality/
+                <source-entities>[space-<space>]_[tract-<tract name>]_[track-<tracking method>]_tractogram.trx
+                <source-entities>[space-<space>]_[tract-<tract name>]_[track-<tracking method>]_tractogram.json
+```
+
+Where `tract` is the anatomical/structural entity that is being imaged, and
+`track` uses as its value one of the items in a controlled vocabulary.
+
+For example:
+
+```Text
+
+AFQ/
+    sub–01/
+        dwi/
+            sub-01_space-MNI152NLin2009cAsym_tract-wholebrain_track-eudx_tractogram.trx
+            sub-01_space-MNI152NLin2009cAsym_tract-wholebrain_track-eudx_tractogram.json
+            sub-01_space-MNI152NLin2009cAsym_tract-ArcuateFasciculus_hemi-L_track-eudx_tractogram.trx
+            sub-01_space-MNI152NLin2009cAsym_tract-ArcuateFasciculus_hemi-L_track-eudx_tractogram.json
+```

src/schema/objects/entities.yaml

@@ -512,6 +512,14 @@ volume:
     `BodyPartDetailsOntology` is OPTIONAL to also include.
   type: string
   format: label
+track:
+  name: track
+  display_name: Tractography Method
+  description: |
+    The `track-<label>` entity identifies the tractography method
+    employed to reconstruct white matter fiber streamlines.
+  type: string
+  format: label
 tracksys:
   name: tracksys
   display_name: Tracking System
@@ -526,3 +534,14 @@ tracksys:
     may be longer and more human readable.
   type: string
   format: label
+tract:
+  name: tract
+  display_name: Anatomical Tract
+  description: |
+    The `tract-<label>` entity identifies the white matter fiber
+    anatomical/structural entity that is imaged through a
+    tractogram (for example, `tract-wholebrain` would correspond to a
+    whole-brain tractogram, whereas `tract-ArcuateFasciculus` would
+    correspond to a tractogram of the arcuate fasciculus).
+  type: string
+  format: label

src/schema/rules/entities.yaml

@@ -26,6 +26,8 @@
 - processing
 - hemisphere
 - space
+- tract
+- track
 - split
 - recording
 - chunk