Howdy-
I think the best way to go would be to paste your current afni_proc.py (AP) command here, and we can recommend tweaking options from there. The PyQt4 dependencies are really difficult nowadays. We have let uber_subject.py lapse because, in general, working with the AP script directly is clearly and easier to discuss, particularly on the Message Board here. (All uber_subject.py did was wrap around filling in fields within the AP command anyways---when writing back and forth, simply adjusting text is most straightforward.)
Some things that should help diagnose issues, as well, are the automatically created QC HTML by afni_proc.py, too. That will even make images of initial EPI-anatomical overlap, which might suggest how to add options.
It would be good to verify that you have a current/modern AFNI version, too. What is your "afni -ver"? You can always run "@update.afni.binaries -d" to update it, if you are using a binary distribution.
--pt
