Thanks! Sorry, this got buried and I did not see this response. I am going through Freesurfer right now as per the tutorial.
Btw, I was wondering: is the aligned functional volume stored anywhere in the output of uber_subject.py? I was assuming that this was in the all_runs.Imag_anat2epi+tlrc. files but this seems to be something else (the images are too noisy and do not appear to have any definition at all).
Many thanks again, and best wishes,
Ranjan