BIDS validator: ASL filename error

1

I’m getting an error with the BIDS validator for an ASL dataset.

Could anyone tell me please if they can spot the problem with the following filenames?

sub-01/ses-01/perf/sub-01_ses-01_task-rest_acq-philips2d_asl.json
sub-01/ses-01/perf/sub-01_ses-01_task-rest_acq-philips2d_asl.nii.gz
sub-01/ses-01/perf/sub-01_ses-01_task-rest_acq-philips2d_aslcontext.tsv

I’m getting the generic NOT_INCLUDED error message and can’t work out which bit is invalid. Is the *_asllabeling image compulsory?

(the dataset has multiple subjects, sessions and modalities)

2

Can you share the full error message?

EDIT: Oh whoops I just realized what’s wrong. Behavioral tasks aren’t supported for ASL data yet. If you remove the task-rest entity, that should help.

3

Thanks tsalo, and thats a nasty bug given the specs doc suggests it is valid: Magnetic Resonance Imaging - Brain Imaging Data Structure v1.9.0

Do you know if its just the validator that doesn’t support it, or is it pybids as well?

4

Seems like using BIDSLayout(path, validate=False) will be the solution for now.

5

seems the spec says task is allowed for physio and stim file that go with ASL but not for ASL files themselves

this sounds like a but in the spec

let me check

6

yeah apparently this got introduced but task are not supported for ASL and diffusion data but it seems that this got lost when we added support for physio files for ASL and diffusion

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7

opened a bug report: [BUG] tiemseries files support task entity for ASL and DWI · Issue #1701 · bids-standard/bids-specification · GitHub

skipping validation seems like the way to go for pybids and you may have to bidsignore those files for the validator

I also recommend you open an issue on the bids specification so that we can start tracking “requests” for supporting task data for ASL in BIDS

8

Just dropping the task entity would make the dataset compliant with the current version though. Especially since the task is “rest”.

9

@tsalo True, but unfortunately the dataset has task state and resting state data!

@Remi-Gau are you suggesting opening another issue besides the one you’ve now opened? If so, where?

Thanks.

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10

I would suggest opening another issue on the bids specification repo.

I had done so for microscopy a while back.

We can then ping the people who were originally invovled in the ASL extension to BIDS, so they can chime in on the pros and cons.