Get "turnkey" bids2nidm container (or ideally a BIDS-app)

OpenNeuroDatasets-JSONLD / .github

Interesting things to be said about augmented OpenNeuro datasets

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Get "turnkey" bids2nidm container (or ideally a BIDS-app) #6

Open yarikoptic opened 3 years ago

yarikoptic commented 3 years ago

should be as simple as

docker run -it -v $PWD nidm/bids2nidm $PWD

to get nidm.jsonld (ideally, but could be option to direct which serializations to produce, e.g. -f jsonld,ttl)

yarikoptic commented 1 year ago

@dbkeator Echoing our brief discussion yesterday, would you be open to work on this component which would need

[ ] tune up to the code of bids2nidm to allow for an option to error out instead of asking for input if some new information is needed
[ ] providing a "bids-app" interface and wrapping it into a container to be included/shipped among other bids-apps (then it would become available through https://github.com/ReproNim/containers/ and we could reuse that collection of containers)
- might need a separate repo (not sure what is the best workflow for maintaining bids-app on top of another project code)

surchs commented 1 year ago

hey @yarikoptic, since you mentioned this in #5.

You should be able to run

docker run -v $(pwd):$(pwd) neurobagel/bagelcli pheno --pheno $(pwd)/participants.tsv --dictionary $(pwd)/participants.json --output $(pwd) --name $ds

from the cli image. There are a couple of issues open to fix some of the things participants.json can do that we didn't think of yet, but I think those should be fixed early next week.

surchs commented 1 year ago

providing a "bids-app" interface and wrapping it into a container to be included/shipped among other bids-apps

I also think this would be pretty cool. We're currently rethinking the interface for this CLI/container, maybe we could make it look (more) like a BIDS app