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.