I was thinking of getting fmriprep to output in EPI space because I would like to do connectivity analysis using freesurfer’s ROIs on a subject level. I have read some topics about this but I’m still confused with what you would recommend. @ChrisGorgolewski here suggests using T1w space, but others appear to prefer EPI space.
What is the current recommendation in fmriprep if my aim is to conduct connectivity analysis with subject-specific ROIs? I was also wondering that if my ROIs are, originally, in freesurfer space, perhaps fsavarage would also make sense. So in your opinion what space would you recommend I do my subject-level ROI analysis in: T1w, func or fsaverage?