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[FIX] Re-align the text and the schema for filenames in derivatives #1567

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[FIX] Re-align the text and the schema for filenames in derivatives #1567

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3c1ec6e
Add desc entity to filename templates in the text
mguaypaq Jul 25, 2023
da05c04
Add session layer to filename templates in the text
mguaypaq Jul 31, 2023
1866012
Add atlas entity to the schema for segmentations
mguaypaq Jul 31, 2023
91c4bff
Merge remote-tracking branch 'bids-standard/master' into mgp/allow-de…
mguaypaq Nov 19, 2024
857bef9
Revert "Add atlas entity to the schema for segmentations"
mguaypaq Nov 19, 2024
140ceb2
Remove density from mask nifti file template
mguaypaq Nov 19, 2024
6143053
Line up text and yaml for discrete segmentations
mguaypaq Nov 19, 2024
ccf3f73
Line up text and yaml for probabilistic segmentations
mguaypaq Nov 19, 2024
84da428
Fix typo (missing 'r')
mguaypaq Nov 19, 2024
ccca8b7
Line up text and yaml for probabilistic segmentations
mguaypaq Nov 19, 2024
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5 changes: 3 additions & 2 deletions src/derivatives/common-data-types.md
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Original file line number Diff line number Diff line change
Expand Up @@ -180,8 +180,9 @@ Template:
```Text
<pipeline_name>/
sub-<label>/
<datatype>/
<source_entities>[_space-<space>][_desc-<label>]_<suffix>.<extension>
[ses-<label>/]
<datatype>/
<source_entities>[_space-<space>][_desc-<label>]_<suffix>.<extension>
```

Data is considered to be *preprocessed* or *cleaned* if the data type of the input,
Expand Down
32 changes: 22 additions & 10 deletions src/derivatives/imaging.md
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Original file line number Diff line number Diff line change
Expand Up @@ -10,8 +10,9 @@ Template:
```Text
<pipeline_name>/
sub-<label>/
<datatype>/
<source_entities>[_space-<space>][_res-<label>][_den-<label>][_desc-<label>]_<suffix>.<extension>
[ses-<label>/]
<datatype>/
<source_entities>[_space-<space>][_res-<label>][_den-<label>][_desc-<label>]_<suffix>.<extension>
```

Volumetric preprocessing does not modify the number of dimensions, and so
Expand Down Expand Up @@ -147,8 +148,10 @@ Template:
```Text
<pipeline_name>/
sub-<label>/
anat|func|dwi/
<source_entities>[_space-<space>][_res-<label>][_den-<label>][_label-<label>][_desc-<label>]_mask.nii.gz
[ses-<label>/]
anat|func|dwi/
<source_entities>[_space-<space>][_res-<label>][_label-<label>][_desc-<label>]_mask.json
<source_entities>[_space-<space>][_res-<label>][_label-<label>][_desc-<label>]_mask.nii[.gz]
```

A binary (1 - inside, 0 - outside) mask in the space defined by the [`space` entity](../appendices/entities.md#space).
Expand Down Expand Up @@ -264,8 +267,11 @@ Template:
```Text
<pipeline_name>/
sub-<label>/
anat|func|dwi/
<source_entities>[_space-<space>][_seg-<label>][_res-<label>][_den-<label>]_dseg.nii.gz
[ses-<label>/]
anat|func|dwi/
<source_entities>[_space-<space>][_seg-<label>][_res-<label>][_desc-<label>]_dseg.json
<source_entities>[_space-<space>][_seg-<label>][_res-<label>][_desc-<label>]_dseg.nii[.gz]
<source_entities>[_space-<space>][_seg-<label>][_res-<label>][_desc-<label>]_dseg.tsv
```

Example:
Expand Down Expand Up @@ -328,8 +334,10 @@ Template:
```Text
<pipeline_name>/
sub-<label>/
func|anat|dwi/
<source_entities>[_space-<space>][_seg-<label>][_res-<label>][_den-<label>][_label-<label>]_probseg.nii.gz
[ses-<label>/]
func|anat|dwi/
<source_entities>[_space-<space>][_seg-<label>][_res-<label>][_label-<label>][_desc-<label>]_probseg.json
<source_entities>[_space-<space>][_seg-<label>][_res-<label>][_label-<label>][_desc-<label>]_probseg.nii[.gz]
```

Example:
Expand Down Expand Up @@ -402,8 +410,12 @@ Template:
```Text
<pipeline_name>/
sub-<label>/
anat/
<source_entities>[_hemi-{L|R}][_space-<space>][_seg-<label>][_res-<label>][_den-<label>]_dseg.{label.gii|dlabel.nii}
[ses-<label>/]
anat/
<source_entities>[_hemi-{L|R}][_space-<space>][_seg-<label>][_res-<label>][_den-<label>][_desc-<label>]_dseg.json
<source_entities>[_hemi-{L|R}][_space-<space>][_seg-<label>][_den-<label>][_desc-<label>]_dseg.label.gii
<source_entities>[_hemi-{L|R}][_space-<space>][_seg-<label>][_res-<label>][_den-<label>][_desc-<label>]_dseg.dlabel.nii
<source_entities>[_hemi-{L|R}][_space-<space>][_seg-<label>][_res-<label>][_den-<label>][_desc-<label>]_dseg.tsv
```

The [`hemi-<label>`](../appendices/entities.md#hemi) entity is REQUIRED for GIFTI files storing information about
Expand Down
43 changes: 29 additions & 14 deletions src/schema/rules/files/deriv/imaging.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -52,7 +52,6 @@ anat_parametric_mask:
$ref: rules.files.raw.anat.parametric.entities
space: optional
resolution: optional
density: optional
label: optional
description: optional

Expand All @@ -64,19 +63,21 @@ anat_nonparametric_mask:
$ref: rules.files.raw.anat.nonparametric.entities
space: optional
resolution: optional
density: optional
label: optional
description: optional

dwi_mask:
$ref: rules.files.raw.dwi.dwi
suffixes:
- mask
extensions:
- .nii.gz
- .nii
- .json
entities:
$ref: rules.files.raw.dwi.dwi.entities
space: optional
resolution: optional
density: optional
label: optional
description: optional

Expand All @@ -88,7 +89,6 @@ func_mask:
$ref: rules.files.raw.func.func.entities
space: optional
resolution: optional
density: optional
label: optional
description: optional

Expand All @@ -99,8 +99,8 @@ anat_parametric_discrete_segmentation:
entities:
$ref: rules.files.raw.anat.parametric.entities
space: optional
segmentation: optional
resolution: optional
density: optional
description: optional
extensions:
- .nii.gz
Expand All @@ -115,8 +115,8 @@ anat_nonparametric_discrete_segmentation:
entities:
$ref: rules.files.raw.anat.nonparametric.entities
space: optional
segmentation: optional
resolution: optional
density: optional
description: optional
extensions:
- .nii.gz
Expand All @@ -131,9 +131,14 @@ func_discrete_segmentation:
entities:
$ref: rules.files.raw.func.func.entities
space: optional
segmentation: optional
resolution: optional
density: optional
description: optional
extensions:
- .nii.gz
- .nii
- .json
- .tsv

dwi_discrete_segmentation:
$ref: rules.files.raw.dwi.dwi
Expand All @@ -143,8 +148,12 @@ dwi_discrete_segmentation:
$ref: rules.files.raw.dwi.dwi.entities
space: optional
resolution: optional
density: optional
description: optional
extensions:
- .nii.gz
- .nii
- .json
- .tsv

anat_parametric_probabilistic_segmentation:
$ref: rules.files.raw.anat.parametric
Expand All @@ -153,8 +162,8 @@ anat_parametric_probabilistic_segmentation:
entities:
$ref: rules.files.raw.anat.parametric.entities
space: optional
segmentation: optional
resolution: optional
density: optional
label: optional
description: optional

Expand All @@ -165,8 +174,8 @@ anat_nonparametric_probabilistic_segmentation:
entities:
$ref: rules.files.raw.anat.nonparametric.entities
space: optional
segmentation: optional
resolution: optional
density: optional
label: optional
description: optional

Expand All @@ -177,8 +186,8 @@ func_probabilistic_segmentation:
entities:
$ref: rules.files.raw.func.func.entities
space: optional
segmentation: optional
resolution: optional
density: optional
label: optional
description: optional

Expand All @@ -189,12 +198,16 @@ dwi_probabilistic_segmentation:
entities:
$ref: rules.files.raw.dwi.dwi.entities
space: optional
segmentation: optional
resolution: optional
density: optional
label: optional
description: optional
extensions:
- .nii.gz
- .nii
- .json

anat_parametic_discrete_surface:
anat_parametric_discrete_surface:
$ref: rules.files.raw.anat.parametric
suffixes:
- dseg
Expand All @@ -207,11 +220,12 @@ anat_parametic_discrete_surface:
$ref: rules.files.raw.anat.parametric.entities
hemisphere: optional
space: optional
segmentation: optional
resolution: optional
density: optional
description: optional

anat_nonparametic_discrete_surface:
anat_nonparametric_discrete_surface:
$ref: rules.files.raw.anat.nonparametric
suffixes:
- dseg
Expand All @@ -224,6 +238,7 @@ anat_nonparametic_discrete_surface:
$ref: rules.files.raw.anat.nonparametric.entities
hemisphere: optional
space: optional
segmentation: optional
resolution: optional
density: optional
description: optional