Add JSON Keys Automatically During Conversion

[karl-koschutnig]

Hi Marcel,

Apologies for bringing up more issues – and thank you for all your hard work on this amazing tool!

As you’re likely aware, the BIDS Validator has been completely redesigned. For many BIDS Apps, the validator is the first step in the workflow. At our MRI Lab, where I’m the head, we rely on ensuring BIDS validity across all our studies – which currently amounts to over 140 datasets. Your tool has been an absolute game-changer for us.

With the new validator, I was wondering if there’s a way to automatically add specific JSON keys during the conversion process? While we’re not encountering many errors with the updated validator, we are seeing a substantial number of warnings.

I’ve attached an example of a validator output (generated via bidscoiner) for reference:
karl_validator_output.txt

Thanks again for your support and for maintaining this fantastic tool!

Best regards,
Karl

[mateuszpawlik]

I remember a comment in the BIDS Validator project, which I can't find anymore, saying that they would like to suppress the warnings for recommended JSON sidecar keys.

[marcelzwiers]

Of course, with the GUI this is done by adding it to the meta table, but you are asking about an automatic way. So the JSON keys need to be available on disk so BIDScoin can read them and add it to the JSON output file. It happens that such a mechanism has existed already for quite a while, but I never used it myself. I named it "extended attributes", which works by putting a JSON sidecar file with your custom key-value pairs, next to the raw data. See item 3:

https://bidscoin.readthedocs.io/en/stable/bidsmap.html#structure-and-content

[marcelzwiers]

Btw, if the keys are available in the DICOM header, then it is as simple as adding it to the meta table of the template bidsmap....

[marcelzwiers]

But I see you are dealing with a lot of SJON keys here (which is actually something that dcm2niix should fix)