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[ENH] Add volspace entity for CIFTI files #1900

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[ENH] Add volspace entity for CIFTI files #1900

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a75882c
Add volspace entity.
tsalo Aug 21, 2024
53ee0d4
Remove self from schema CODEOWNERS.
tsalo Aug 21, 2024
0a52d88
Update imaging.yaml
tsalo Aug 21, 2024
60248c3
Update entities.yaml
tsalo Aug 21, 2024
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4 changes: 2 additions & 2 deletions CODEOWNERS
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Validating CODEOWNERS rules …
Original file line number Diff line number Diff line change
Expand Up @@ -16,5 +16,5 @@
/src/derivatives/diffusion-derivatives.md @francopestilli @oesteban @Lestropie

# The schema
/src/schema/ @tsalo @erdalkaraca
/tools/schemacode/ @tsalo @erdalkaraca
/src/schema/ @erdalkaraca
/tools/schemacode/ @erdalkaraca
19 changes: 10 additions & 9 deletions src/derivatives/imaging.md
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Original file line number Diff line number Diff line change
Expand Up @@ -11,7 +11,7 @@ Template:
<pipeline_name>/
sub-<label>/
<datatype>/
<source_entities>[_space-<space>][_res-<label>][_den-<label>][_desc-<label>]_<suffix>.<extension>
<source_entities>[_space-<space>][_volspace-<space>][_res-<label>][_den-<label>][_desc-<label>]_<suffix>.<extension>
```

Volumetric preprocessing does not modify the number of dimensions, and so
Expand Down Expand Up @@ -113,11 +113,11 @@ A guide for using macros can be found at
"pipeline1": {
"sub-001": {
"func": {
"sub-001_task-rest_run-1_space-fsLR_res-1_den-10k_bold.dtseries.nii": "",
"sub-001_task-rest_run-1_space-fsLR_res-1_den-41k_bold.dtseries.nii": "",
"sub-001_task-rest_run-1_space-fsLR_res-2_den-10k_bold.dtseries.nii": "",
"sub-001_task-rest_run-1_space-fsLR_res-2_den-41k_bold.dtseries.nii": "",
"sub-001_task-rest_run-1_space-fsLR_bold.json": "",
"sub-001_task-rest_run-1_space-fsLR_volspace-MNI152NLin6Asym_res-1_den-10k_bold.dtseries.nii": "",
"sub-001_task-rest_run-1_space-fsLR_volspace-MNI152NLin6Asym_res-1_den-41k_bold.dtseries.nii": "",
"sub-001_task-rest_run-1_space-fsLR_volspace-MNI152NLin6Asym_res-2_den-10k_bold.dtseries.nii": "",
"sub-001_task-rest_run-1_space-fsLR_volspace-MNI152NLin6Asym_res-2_den-41k_bold.dtseries.nii": "",
"sub-001_task-rest_run-1_space-fsLR_volspace-MNI152NLin6Asym_bold.json": "",
},
},
}
Expand Down Expand Up @@ -265,7 +265,7 @@ Template:
<pipeline_name>/
sub-<label>/
anat|func|dwi/
<source_entities>[_space-<space>][_seg-<label>][_res-<label>][_den-<label>]_dseg.nii.gz
<source_entities>[_space-<space>][_seg-<label>][_res-<label>]_dseg.nii.gz
```

Example:
Expand Down Expand Up @@ -329,7 +329,7 @@ Template:
<pipeline_name>/
sub-<label>/
func|anat|dwi/
<source_entities>[_space-<space>][_seg-<label>][_res-<label>][_den-<label>][_label-<label>]_probseg.nii.gz
<source_entities>[_space-<space>][_seg-<label>][_res-<label>][_label-<label>]_probseg.nii.gz
```

Example:
Expand Down Expand Up @@ -403,7 +403,8 @@ Template:
<pipeline_name>/
sub-<label>/
anat/
<source_entities>[_hemi-{L|R}][_space-<space>][_seg-<label>][_res-<label>][_den-<label>]_dseg.{label.gii|dlabel.nii}
<source_entities>[_hemi-{L|R}][_space-<space>][_seg-<label>][_den-<label>]_dseg.{label.gii}
<source_entities>[_hemi-{L|R}][_space-<space>][_volspace-<space>][_seg-<label>][_res-<label>][_den-<label>]_dseg.{dlabel.nii}
```

The [`hemi-<label>`](../appendices/entities.md#hemi) entity is REQUIRED for GIFTI files storing information about
Expand Down
11 changes: 11 additions & 0 deletions src/schema/objects/entities.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -422,3 +422,14 @@ tracksys:
may be longer and more human readable.
type: string
format: label
volspace:
name: volspace
display_name: Volumetric Space
description: |
The `volspace-<label>` entity can be used to indicate the spatial reference to which
the volumetric component of a combined surface-volume file (for example, a CIFTI file)
has been aligned.
The `<label>` MUST be taken from one of the modality specific lists in the
[Coordinate Systems Appendix](SPEC_ROOT/appendices/coordinate-systems.md).
type: string
format: label
19 changes: 19 additions & 0 deletions src/schema/rules/files/deriv/imaging.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -4,6 +4,7 @@ anat_parametric_volumetric:
entities:
$ref: rules.files.raw.anat.parametric.entities
space: optional
volspace: optional
resolution: optional
density: optional
description: optional
Expand All @@ -13,6 +14,7 @@ anat_nonparametric_volumetric:
entities:
$ref: rules.files.raw.anat.nonparametric.entities
space: optional
volspace: optional
resolution: optional
density: optional
description: optional
Expand All @@ -22,6 +24,7 @@ dwi_volumetric:
entities:
$ref: rules.files.raw.dwi.dwi.entities
space: optional
volspace: optional
resolution: optional
density: optional
description: optional
Expand All @@ -31,6 +34,7 @@ dwi_isotropic:
entities:
$ref: rules.files.raw.dwi.isotropic.entities
space: optional
volspace: optional
resolution: optional
density: optional
description: optional
Expand All @@ -40,6 +44,7 @@ func_volumetric:
entities:
$ref: rules.files.raw.func.func.entities
space: optional
volspace: optional
resolution: optional
density: optional
description: optional
Expand All @@ -51,6 +56,7 @@ anat_parametric_mask:
entities:
$ref: rules.files.raw.anat.parametric.entities
space: optional
volspace: optional
resolution: optional
density: optional
label: optional
Expand All @@ -63,6 +69,7 @@ anat_nonparametric_mask:
entities:
$ref: rules.files.raw.anat.nonparametric.entities
space: optional
volspace: optional
resolution: optional
density: optional
label: optional
Expand All @@ -75,6 +82,7 @@ dwi_mask:
entities:
$ref: rules.files.raw.dwi.dwi.entities
space: optional
volspace: optional
resolution: optional
density: optional
label: optional
Expand All @@ -87,6 +95,7 @@ func_mask:
entities:
$ref: rules.files.raw.func.func.entities
space: optional
volspace: optional
resolution: optional
density: optional
label: optional
Expand All @@ -99,6 +108,7 @@ anat_parametric_discrete_segmentation:
entities:
$ref: rules.files.raw.anat.parametric.entities
space: optional
volspace: optional
resolution: optional
density: optional
description: optional
Expand All @@ -115,6 +125,7 @@ anat_nonparametric_discrete_segmentation:
entities:
$ref: rules.files.raw.anat.nonparametric.entities
space: optional
volspace: optional
resolution: optional
density: optional
description: optional
Expand All @@ -131,6 +142,7 @@ func_discrete_segmentation:
entities:
$ref: rules.files.raw.func.func.entities
space: optional
volspace: optional
resolution: optional
density: optional
description: optional
Expand All @@ -142,6 +154,7 @@ dwi_discrete_segmentation:
entities:
$ref: rules.files.raw.dwi.dwi.entities
space: optional
volspace: optional
resolution: optional
density: optional
description: optional
Expand All @@ -153,6 +166,7 @@ anat_parametric_probabilistic_segmentation:
entities:
$ref: rules.files.raw.anat.parametric.entities
space: optional
volspace: optional
resolution: optional
density: optional
label: optional
Expand All @@ -165,6 +179,7 @@ anat_nonparametric_probabilistic_segmentation:
entities:
$ref: rules.files.raw.anat.nonparametric.entities
space: optional
volspace: optional
resolution: optional
density: optional
label: optional
Expand All @@ -177,6 +192,7 @@ func_probabilistic_segmentation:
entities:
$ref: rules.files.raw.func.func.entities
space: optional
volspace: optional
resolution: optional
density: optional
label: optional
Expand All @@ -189,6 +205,7 @@ dwi_probabilistic_segmentation:
entities:
$ref: rules.files.raw.dwi.dwi.entities
space: optional
volspace: optional
resolution: optional
density: optional
label: optional
Expand All @@ -207,6 +224,7 @@ anat_parametic_discrete_surface:
$ref: rules.files.raw.anat.parametric.entities
hemisphere: optional
space: optional
volspace: optional
resolution: optional
density: optional
description: optional
Expand All @@ -224,6 +242,7 @@ anat_nonparametic_discrete_surface:
$ref: rules.files.raw.anat.nonparametric.entities
hemisphere: optional
space: optional
volspace: optional
resolution: optional
density: optional
description: optional