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Draft some more stuff.
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tsalo committed Mar 21, 2024
1 parent 62a0208 commit 39e8e06
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2 changes: 2 additions & 0 deletions src/atlas.md
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Expand Up @@ -81,6 +81,8 @@ such files are the non-altered/original atlases or within a given directory unde
In the second case, atlases are altered,
derived or applied and thus multiple use cases have to be distinguished as indicated further below.

{{ MACROS___make_filename_template("atlas", suffixes=["dseg", "probseg", "mask"]) }}

### Representing an atlas as a dataset

The first option refers to atlases that were not altered, for example,
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49 changes: 47 additions & 2 deletions src/schema/rules/files/atlas/atlas.yaml
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@@ -1,12 +1,57 @@
---
atlas:
volumetric:
suffixes:
- dseg
- probseg
- mask
extensions:
- .nii.gz
- .nii
- .nii.gz
- .tsv
- .json
entities:
atlas: required
space: optional
resolution: optional
description: optional

surface:
suffixes:
- dseg
- probseg
- mask
extensions:
- .label.gii
- .label.gii.gz
- .tsv
- .json
entities:
atlas: required
space: optional
density: optional
description: optional

cifti_probseg:
suffixes:
- probseg
extensions:
- .dscalar.nii
- .tsv
- .json
entities:
atlas: required
space: optional
resolution: optional
density: optional
description: optional

cifti_dseg:
suffixes:
- dseg
- mask
extensions:
- .dlabel.nii
- .tsv
- .json
entities:
atlas: required
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2 changes: 1 addition & 1 deletion tools/schemacode/bidsschematools/render/text.py
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Expand Up @@ -248,7 +248,7 @@ def make_filename_template(
Parameters
----------
dstype : "raw" or "deriv"
dstype : "raw" or "deriv" or "atlas"
The type of files being rendered; determines if rules are found in rules.files.raw
or rules.files.deriv
schema : dict
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