ohbm / hackathon2019

Website and projects for the OHBM Hackathon in Rome 2019

https://ohbm.github.io/hackathon2019

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BIDS Execution spec / BIDS Apps 2.0 #89

Open effigies opened 5 years ago

effigies commented 5 years ago

BIDS Execution spec / BIDS Apps 2.0

Project Description

I have the start of a draft here: https://docs.google.com/document/d/104HLZedFtx0TaXEUwd7eyWvJUlc0CcSUtCzwjNgmGxE/edit#heading=h.4k1noo90gelw

It's based on some notes here: https://docs.google.com/document/d/1NQe5qP0VdfqPI5nl2cIQKzii70ndpPJEzemzK4qn6uY/edit#heading=h.usmuhelpi8fq

Skills required to participate

Reading and writing.

effigies commented 5 years ago

Discussed current spec with @adelavega, @peerherholz, @shotgunosine, with some useful interjections from @tyarkoni. The main results of this discussion:

We need to have a more defined semantics for the --<entity>-label filters.
We should output the original command line, and this would probably best happen in dataset_description.json:PipelineDescription.

PeerHerholz commented 5 years ago

There was also a comment from @emdupre on how output folders should be named. The proposal was to include the name of the BIDS-App and its version: <bidsapp>-<version>, e.g., fmriprep-0.1.

emdupre commented 5 years ago

Thanks for noting this, @PeerHerholz ! To reference specific lines, the idea was that here instead of requiring that the folder name contains PipelineDescription.Name as a substring, the string should match exactly.

For example, here, fmripreprocess-v1/ would become fmriprep-v1/.