BEP-038: Atlases #1714
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BEP-038: Atlases #1714
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I made a first draft of the atlas BEP based on the Google doc
Added atlas content
All the content of the BEP038 Google document has been ported to the atlas.md file. Additionally atlas and a definition of what of means was added as an entity. There are still smaller things to fix as some links, references and the tables still need to be inserted.
Fixed details such as linking to entities and suffixes as well as clarified some of the example text. The tables need still to be fixed.
[BEP038] Style and similar cleanups
Collaborator
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@erdalkaraca @tsalo this has passed the review period now, can this be checked and merged? thx |
Collaborator
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I'm working on a review. Please hold on. |
Collaborator
Author
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I also have not finished my review/proposed changes. I am unlikely to get to it before the meeting next week as I am traveling for another meeting this week. |
Collaborator
Author
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This BEP currently needs:
I'm converting this to draft to reflect this status. I'm going to temporarily restrict comments, pending synchronous discussion. |
…irement for tpl entity
mguaypaq
reviewed
Nov 12, 2025
mguaypaq
reviewed
Nov 12, 2025
Co-authored-by: Mathieu Guay-Paquet <[email protected]>
Co-authored-by: Mathieu Guay-Paquet <[email protected]>
mguaypaq
reviewed
Nov 13, 2025
Co-authored-by: Mathieu Guay-Paquet <[email protected]>
effigies
commented
Nov 17, 2025
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| AtlasSampleSize: required | ||
| Description: recommended | ||
| Authors: recommended | ||
| Curators: optional | ||
| Funding: optional | ||
| ReferencesAndLinks: optional | ||
| Species: optional |
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The consensus in #2250 (comment) appears to be:
Suggested change
| AtlasSampleSize: required | |
| Description: recommended | |
| Authors: recommended | |
| Curators: optional | |
| Funding: optional | |
| ReferencesAndLinks: optional | |
| Species: optional | |
| Description: recommended | |
| Authors: recommended | |
| Curators: optional | |
| Funding: optional | |
| ReferencesAndLinks: optional | |
| Species: optional | |
| AtlasSampleSize: optional |
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| Segmentations and parcellations MAY or MAY NOT be associated with | ||
| [atlases](SPEC_ROOT/common-principles.md#definitions), | ||
| Therefore, `seg-<label>` SHOULD NOT be used to designate | ||
| [atlases](SPEC_ROOT/common-principles.md#definitions), | ||
| please refer to the [template and atlas section](SPEC_ROOT/derivatives/atlas.md) | ||
| for detailed specifications on their combined use. |
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Suggested change
| Segmentations and parcellations MAY or MAY NOT be associated with | |
| [atlases](SPEC_ROOT/common-principles.md#definitions), | |
| Therefore, `seg-<label>` SHOULD NOT be used to designate | |
| [atlases](SPEC_ROOT/common-principles.md#definitions), | |
| please refer to the [template and atlas section](SPEC_ROOT/derivatives/atlas.md) | |
| for detailed specifications on their combined use. | |
| Segmentations and parcellations MAY or MAY NOT be associated with | |
| [atlases](SPEC_ROOT/common-principles.md#definitions). | |
| Therefore, `seg-<label>` SHOULD NOT be used to designate | |
| [atlases](SPEC_ROOT/common-principles.md#definitions). | |
| Please refer to the [template and atlas section](SPEC_ROOT/derivatives/atlas.md) | |
| for detailed specifications on their combined use. |
| [atlases](SPEC_ROOT/common-principles.md#definitions), | ||
| please refer to the [template and atlas section](SPEC_ROOT/derivatives/atlas.md) | ||
| for detailed specifications on their combined use. | ||
| When a segmentation *is a realization* of an atlas' segmentation or parcellation, |
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Suggested change
| When a segmentation *is a realization* of an atlas' segmentation or parcellation, | |
| When a segmentation is a *realization* of an atlas' segmentation or parcellation, |
| type: string | ||
| AtlasSampleSize: | ||
| name: SampleSize | ||
| display_name: Atlas' sample size |
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Suggested change
| display_name: Atlas' sample size | |
| display_name: The sample size of the reference dataset used to generate the atlas |
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| Number of items (typically, independent participants, | ||
| although it could also refer, for example, to sessions) | ||
| that employed to create the corresponding atlas. |
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Suggested change
| Number of items (typically, independent participants, | |
| although it could also refer, for example, to sessions) | |
| that employed to create the corresponding atlas. | |
| Number of items (typically, independent participants; | |
| although it could also refer to, for example, sessions) | |
| that were employed to create the corresponding atlas. |
| name: DerivedFrom | ||
| display_name: DerivedFrom | ||
| description: | | ||
| Indicate what data modality the atlas was derived from, for example, "cytoarchitecture", "resting-state", "task". |
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Suggested change
| Indicate what data modality the atlas was derived from, for example, "cytoarchitecture", "resting-state", "task". | |
| Indicate what data modality the atlas was derived from; for example, "cytoarchitecture", "resting-state", or "task". |
| name: LevelType | ||
| display_name: LevelType | ||
| description: | | ||
| Indicate what analysis level the atlas was derived from, for example, "group", "individual". |
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Suggested change
| Indicate what analysis level the atlas was derived from, for example, "group", "individual". | |
| Indicate what analysis level the atlas was derived from; for example, "group" or "individual". |
| name: Species | ||
| display_name: Species | ||
| description: | | ||
| The species the atlas was derived from. For example, could be Human, Macaque, Rat, or Mouse. |
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Suggested change
| The species the atlas was derived from. For example, could be Human, Macaque, Rat, or Mouse. | |
| The species from which the atlas was derived. For example, "human", "macaque", "rat", or "mouse". |
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This PR proposes the inclusion of BEP-038 into the BIDS specification.
The BEP is hosted on its own branch in the main repository, and BEP leads have been given write permissions to the branch. If you are a BEP lead and having issues writing to the branch, please let a maintainer know and we can make sure you have access.
At present this is a starting point, and I anticipate significant rewriting and reorganization before final merge. There is extensive discussion in #1281 that needs to be turned into concrete proposals. I would suggest keeping the discussion on this PR minimal so that newcomers can follow the thread. When opening PRs against this branch, please include a reference to this PR (
#1714) so that it shows up in the thread.Rendered draft
https://bids-specification--1714.org.readthedocs.build/en/1714/derivatives/atlas.html
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