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Add volspace entity.
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@tsalo
tsalo committed Aug 21, 2024
1 parent 9377b20 commit a75882c
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Showing 3 changed files with 38 additions and 9 deletions.
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
9 changes: 9 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 +422,12 @@ 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).
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

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