BIDS validator: Full list of issues and warnings?

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1

Hello,

I am trying to work on getting a study to be BIDS-compliant. I just installed the most recent, stable version of the BIDS validator using Pip (v 1.9.7). I am currently running this through Jupyter notebook and used the example from the GitHub page (GitHub - bids-standard/bids-validator: Validator for the Brain Imaging Data Structure). All I have managed to produce thus far is “False”.

I am not sure if the validator is encountering its first error and then stopping, or?

Is there a way to get, essentially, an itemized list of all the issues that it is running into so that I can start to tease out the issues (i.e. for T1w, is it the naming that is the issue, the json file, something with the directory structure, or)?

In a previous post (BIDS Help - Validator (anat data and quantifying # of issues)) it looks like the version that is part of the Flywheel heudiconv gives such a list of errors, but I am not sure how to get that accomplished through the python version.

Any advice?

Please let me know and thank you!

Anthony

2

Hello,

I am not sure how to get this in Python, but the command line BIDS validator should output this for you. You can use the bids validator on Dockerhub, for example.

Best,
Steven

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The Python bids-validator is not fully-featured and only validates filenames. See https://bids-standard.github.io/bids-validator for the full validator.