Community Review: BEP038 - Atlases and Templates #2250
Replies: 11 comments 49 replies
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I think we should remove the I would like to avoid having to switch between |
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I don't think the |
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I'm puzzled about the "License" field in
I'm also surprised that "SampleSize" is marked as REQUIRED, especially since it doesn't even appear in the accompanying example. My proposal would be to:
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I don't think it is currently clear how to create multiple templates with different spatial references. For example, given the SUIT example, the data from 20 subjects are spatially normalized to MNI, and then averaged to create tpl-SUIT_T1w.nii.gz. The corresponding json file should include the 'SpatialReference', which is 'https://templateflow.s3.amazonaws.com/tpl-MNI152NLin6Asym_res-02_T1w.nii.gz' in this case. However, if I now wanted to create the template with a new spatial reference e.g. MNI152NLin2009Asym, how should this be structured, so I don't end up with two files with the same name? Can I use the 'space' entity to distinguish these? I would suggest to allow for that. |
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I think it would be nice to also include a surface example using fsaverage. Given that the fsaverage spatial reference also appears https://bids-specification.readthedocs.io/en/stable/appendices/coordinate-systems.html and with the template here (https://www.templateflow.org/browse/), I would suggest to create a BIDS example using this, to also represent surfaces where the data spans multiple files (i.e. left and right hemispheres), where it is necessary to include the ‘hemi’ entity. This would probably also require to add more notation on surface-based templates and file names/extensions (such as *surf.gii?). |
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what happened to the 3D mean SUVR PET template (bids-standard/bids-examples@e463def#diff-7abfb299aa45ecdaa05d7609e65095cc9c09f3ecec58aaeceb98dde1396bac50) ? is that the _pet vs _petmap issue related @melanieganz @mnoergaard |
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To test out this BEP, I'm trying to BIDSify the PAM50 spinal cord template, and I have some questions. The atlas folder contains several probabilistic segmentations, with one structure per file.
In short: where should one describe the values of the label entity for probsegs? |
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In trying to BIDSify the PAM50 template, I'm also running into some missing suffixes (other than
For the number of axons, it's an integer, but it's not really a dseg. Is there a recommended suffix to use for this kind of data file? |
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Minor error spotted in the example: |
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This is out of scope for this BEP, but I am curious how other BEPs (especially BEP 017: Relationship matrix data schema and others that describe parcellated data, such as BEP011 and BEP012) will work around the As an example, using Schaefer (since that includes atlas, seg, and scale entities): @PeerHerholz @jdkent is this taken into account in BEP017? I just want to make sure that the proposed entities can be inherited and do not need to be modified for downstream outputs. For example, I'd like to make sure that |
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Judging by the three votes and ongoing discussions, the questions have not been resolved. Can we schedule a call for this week or next to see if we can come to a consensus? We've been doing 10-11am EST (4pm CET) on Tuesdays, if that works for people. I will also ping the email thread. |
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We are pleased to announce the community review period for BIDS Extension Proposal (BEP) 038!
BEP038 extends the BIDS standard to describe BIDS Derivatives datasets that are intended to be distributed as atlases and/or templates. It introduces new organizational and metadata features, but it does not introduce new data file types.
The draft specification may be found at: https://bids-specification.readthedocs.io/en/bep038/, with the most significant changes in Derivatives - Template and Atlases and Derivatives - Imaging data types - Derivatives from atlases.
The proposed changes may be found at #1714. To view the source difference, click the Files changed tab.
Example datasets may be found at:
Procedure
Review period
Community review is open from November 10 - November 21, 2025.
Voting
This discussion is a poll, which you can vote in once and cannot change your response. Therefore, please vote once you are satisfied that your answer will not change.
If you vote "No", you may create a thread to explain your reasoning or send a private email to bids.maintenance [at] gmail.com so that your position can be fully understood.
How to review
Use threads in this discussion to request clarification or changes to the BEP. Each independent topic or proposed change should have its own thread. Please review existing threads and consider adding comments to those, if your topics are already being discussed. If your concerns are adequately represented by an existing comment or comments, consider using the 👍🏻 reaction button to indicate agreement in place of extending the discussion.
Where possible, propose the specific text you would like to see added or removed.
For minor issues, such as typos, feel free to make code suggestions only, using the suggest feature on the BEP038 pull request. These suggestions may be accepted or rejected without discussion, so do not make substantial proposals in this way.
Finalization
Once the review period is finished, the BEP leads and maintainers will consider the entire discussion, identify outstanding points to be resolved, and work toward finalizing the BEP. Community members may be asked to participate in this process to provide the necessary expertise.
Before being merged, the BEP will be integrated into the BIDS validator, and the examples must pass the validator.
A BIDS 1.11.0 release is anticipated in December 2025/January 2026, regardless of the conclusion of this specific BEP.
If, for any reason, a critical issue is found after the BEP is merged, the BEP will be reverted while the issues are addressed. At the discretion of the BIDS steering group and maintainers group, depending on the scope of changes, a new community review period may be opened.
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