BEP038: Atlas examples #501
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@oesteban Notes on
Otherwise, this needs very little adjustment to the validator. |
I don't think this should be a problem.
Gotcha, will give them content.
desc then? |
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Sounds good to me. |
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tsalo
reviewed
Oct 30, 2025
tsalo
reviewed
Oct 30, 2025
| { | ||
| "Name": "Harvard-Oxford Subcortical Probabilistic Atlas", | ||
| "SampleSize": 200, | ||
| "SpatialReference": "", |
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I have this empty because the SpatialReference depends on the resolution and this atlas is available in res-01 and res-02. Also, the SpatialReference should be present in the individual sidecar JSONs.
tsalo
reviewed
Oct 31, 2025
tsalo
reviewed
Oct 31, 2025
| "https://github.com/PennLINC/AtlasPack" | ||
| ], | ||
| "SampleSize": "n/a", | ||
| "SourceAtlases": { |
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This isn't in the BEP or the spec, but it seems like we should have something like it.
Add seven atlas examples following BEP038 specification: - atlas-AAL - atlas-Destrieux - atlas-DiFuMo (two different scales) - atlas-HarvardOxford (probseg and dseg) - atlas-Juelich (probseg and dseg) - atlas-Schaefer (two different scales) - atlas-Talairach These examples demonstrate various atlas structures and can be used for testing and validation of BEP038 implementations. However, they are most likely not fully compliant yet as some of the metadata might be missing/inaccurate and some files might have to be re-arranged.
This commit updates the existing examples based on the reviews and adds a few new ones to outline different options.
This commit aims at addressing the validation errors occurred for the last version of the examples. This refers to: - samplesize is required - funding needs to be list - resolution missing from json - tpl skullstripped or not - naming pattern re seg and scale
tsalo
reviewed
Nov 3, 2025
atlas-4S/sourcedata/atlas-4S/tpl-fsLR/anat/tpl-fsLR_atlas-4S_scale-156_den-91k_dseg.dlabel.nii
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The previous versions of Harvard Oxford, Juelich and Talairach missed the SampleSize field.
Use LabelMap JSON field instead.
Add BEP038-compliant atlas examples of commonly used publicly available atlases
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This branch implements examples according to bids-standard/bids-specification#1714 (rendered: https://bids-specification--1714.org.readthedocs.build/en/1714/).
Please make PRs against the
bep038branch, and we will merge this PR as a part of merging BEP038.xref bids-standard/bids-validator#288