I have been working off this example by @ChrisGorgolewski which has been extremely helpful in generating a first-level model from my fMRIPrep outputs. I now need to add a second level / fixed-effects level to merge runs for each participant. In another post @nataliavelez adapted and reworked Chris’ script as a Nipype workflow. I prefer not to do that since I am new to Nipype and FSL, and would rather to add to the Chris’ example script.
I have run the first-level workflow on a few participants (each with 2 runs). I now have all my outputs (copes, varcopes, etc.) for both runs for each participant. I understand that fixed-effects is more-or-less an averaging of the copes for each participant’s runs. Does anyone have any suggestions on how to do so? Can I apply something like this to Chris’ example? Is that the correct use? If so, how do I apply this Nipype code to Chris’ example, since it’s structured/worded slightly differently? At what point would I apply
Thank you for the help.