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bids-standard / bids-validator

Validator for the Brain Imaging Data Structure
https://bids-standard.github.io/bids-validator/
MIT License
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`chunk` entity not covered by validator? #1582

Closed jcohenadad closed 1 week ago

jcohenadad commented 1 year ago

Hello! I have a dataset that contains the chunk entity, which is valid in v1.8.0 (see here). However, I am getting a bids-validator error: test_bids_errors.txt

Dummy dataset for testing: test_bids.zip

Is it because the BIDS validator is not (yet) covering this entity? Or did I do something stupid with my naming?

Thanks!

Remi-Gau commented 1 year ago

It is just not an anat entity:

https://bids-specification.readthedocs.io/en/stable/04-modality-specific-files/01-magnetic-resonance-imaging-data.html#anatomy-imaging-data

jcohenadad commented 1 year ago

Thank you for the insights @Remi-Gau !

How do people refer to various FOV chunks, which is pretty common in MRI

Remi-Gau commented 1 year ago

The acquisition label ? Really not sure. But this would be my first response from the top of my head.

jcohenadad commented 1 year ago

Hum, that’s too bad because the definition of chunk is much closer to that of acq for describing different FOVs acquired on the same subject in the same imaging session:

Definition: The chunk- key/value pair is used to distinguish between different regions, 2D images or 3D volumes files, of the same physical sample with different fields of view acquired in the same imaging experiment.

Maybe there is already a BEP that plans to make a wiser use of chunk? @mariehbourget @SylvainTakerkart do you know by any chance?

Remi-Gau commented 1 year ago

In theory we could add an entity from one datatype to an another existing datatype without needing a whole bep. Maybe open an issue in the specification describing your use case and motivations.

Sent from Outlook for Androidhttps://aka.ms/AAb9ysg

From: Julien Cohen-Adad @.> Sent: Thursday, January 12, 2023 11:01:15 PM To: bids-standard/bids-validator @.> Cc: Remi Gau @.>; Mention @.> Subject: Re: [bids-standard/bids-validator] chunk entity not covered by validator? (Issue #1582)

Hum, that’s too bad because the definition of chunk is much closer to that of acq for describing different FOVs acquired on the same subject in the same imaging session:

Definition: The chunk- key/value pair is used to distinguish between different regions, 2D images or 3D volumes files, of the same physical sample with different fields of view acquired in the same imaging experiment.

Maybe there is already a BEP that plans to make a wiser use of chunk? @mariehbourgethttps://github.com/mariehbourget @SylvainTakerkarthttps://github.com/SylvainTakerkart do you know by any chance?

— Reply to this email directly, view it on GitHubhttps://github.com/bids-standard/bids-validator/issues/1582#issuecomment-1381041469, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ABVDQIN64LMFTYGM6G3Z7DDWSB5KXANCNFSM6AAAAAATYWUQRE. You are receiving this because you were mentioned.Message ID: @.***>

jcohenadad commented 1 year ago

In theory we could add an entity from one datatype to an another existing datatype without needing a whole bep. Maybe open an issue in the specification describing your use case and motivations.

👍 https://github.com/bids-standard/bids-specification/issues/1382

SylvainTakerkart commented 1 year ago

this would make sense to me, this indeed would be consistent with the BIDS microscopy chunking...