Functional connectivity - using fMRIPrep preprocessed data with CPAC

Do you have any ideas on how to modify the YAML pipeline config files in C-PAC to use FMRIPREP output, rather than C-PAC doing the pre-processing? I am using C-PAC BIDS in a docker container.
Any information greatly appreciated. Thank you.


It’s been a long time since I last used CPAC, but I believe it allows you to place the specific files at specific locations of the input tree so that it doesn’t run all the steps through that point of preprocessing.

I would suggest you post this question in their repo an ask them to reply here to reach a broader audience.

As regards how to interpret fMRIPrep outputs and reuse them, our latest preprint might be of help.

Hi, the latest C-PAC version (after v1.8.0) can take BIDS-derivatives outputs, including fMRIPrep outputs, and run downstream analysis directly. You should be able to process fMRIPrep outputs by specifying your fMRIPrep output folder when you run C-PAC. You’ll also need to turn off minimal preprocessing in your pipeline config file. Please let us know if you hit into any issues.

I tried to create an fmriprep+cpac combo pipeline (converted it a to txt so that I can upload it here) and run it in Singularity via, but I’m getting in error when it comes to confound-regression.

Is CPAC designed to process and work with confounds_timeseries.tsv that fmriprep generates?
fmriprep_wcpac.txt (21.8 KB)


CPAC is currently in a phase of transition towards a more full interoperability with other pipelines and tools. It can currently ingress preprocessed data from BIDS directories; however, due to the highly variable nature of software pipelines, there is still work to do towards making it more seamless.

If you share the error, we can help find out where the disconnect is and make it easier and help get you running.

Steve G.