diff --git a/src/atlas.md b/src/atlas.md index 6a2297b97f..1bd73dba15 100644 --- a/src/atlas.md +++ b/src/atlas.md @@ -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, diff --git a/src/schema/rules/files/atlas/atlas.yaml b/src/schema/rules/files/atlas/atlas.yaml index c457df7111..2b3dc620a8 100644 --- a/src/schema/rules/files/atlas/atlas.yaml +++ b/src/schema/rules/files/atlas/atlas.yaml @@ -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 diff --git a/tools/schemacode/bidsschematools/render/text.py b/tools/schemacode/bidsschematools/render/text.py index 1106e17185..08aec10485 100644 --- a/tools/schemacode/bidsschematools/render/text.py +++ b/tools/schemacode/bidsschematools/render/text.py @@ -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