An option to produce BIDS sidecar .json files to accompany .nii{.gz}

[yarikoptic]

@wtclarke , thanks for chiming in on nipy/heudiconv#381 (comment)! I've decided to proceed with specific question here since pertains more to spec2nii than to heudiconv ;)

Are you familiar with BIDS?
I wonder if similarly to -b option of dcm2niix by @neurolabusc for DICOM to NIfTI conversion, spec2cli could also produce a side car .json files filling up "interesting" fields as being harmonized in the BIDS Enhancement proposal for MRS: BEP022?

[wtclarke]

Hi @yarikoptic,

Apols for the delay in responding. NIfTI MRS uses json to encode metadata in a NIfTI header extension already. This can be generated as an additional sidecar file by spec2nii by either using the -j, --json Create json sidecar option at conversion time, or by using spec2nii extract after conversion.

The fields that are defined for this JSON are in the NIfTI-MRS specification. I'd be up for helping someone to create a small program which then takes this file and adds the extra BIDs specified info.

[yarikoptic]

Thanks @wtclarke ! Great to hear that there is already extraction of metadata! FWIW

• I barely ever relied/used extensions within niftis since AFAIK they were never standardized across tools and thus always required a specific tool to be capable of understanding them
• so it is great that spec2nii extract can already extract it into a separate json file (didn't try yet)
• Great to discover NIfTI-MRS specification and closing the "loop" for ignorant myself since BIDS MRS BEP022 (3.1) already mentions NIfTI-MRS and you already had brief comments exchange with Mark Mikkelsen which I joined to now ;)
• I found centralization of such extractions/conversions in the tool which does initial extraction (i.e. in our case dcm2niix) very beneficial since avoids breeding of half-breed solutions. May be it could be just an option to spec2nii extract --bids or alike?
• But may be it all could be avoided at large? I am yet to get basic understanding of difference in sidecar info of NIfTI-MRS and BIDS BEP022 to see why they couldn't be "compatible". Any specific example/pointer would be appreciated