Bids apps on fmriprep output


I am looking for standard pipelines based on fmriprep output (e.g. GLM, rest connectivity etc). I was checking for any BIDS app that processes BIDS derivatives as well as past posts here on neurostars, but I have not found much. For example here Performing full glm analysis with fsl on the bold images preprocessed by fmriprep without re-registering the data to the MNI space people are building their own FSL “hacks” to do FEAT GLM over fmriprep output.

Could you point me to anything worth checking before I start re-inventing wheels? :slight_smile:




Thank you Chris!

Is it that these are not listed in the BIDS Apps website because they are based on BIDS derivatives which is still a draft proposal?


The non final nature of derivatives is one thing, but BIDS Apps also require specific command line interface and versioned software containers.

We should list those tools on nonetheless.

1 Like

@eglerean Don’t know if it’s a bit off topic and just in case you haven’t checked this already: the Neuroimaging Data Model (original publication in scientific data here) could also be helpful and include some pointers.

Thanks @PeerHerholz!

I’m aware of NIDM but never used it. I wonder how much the BIDS models spec (used in the fitlins link above) overlaps/complements the NIDM? The draft doesn’t mention it, ideally they are all somewhat compatible.