Howdy-
I think it would be muuuuch preferable to set up processing from the afni_proc.py command rather than edit scripts... Editing the script is pretty complicated (even though the afni_proc.py ones are still magically commented). I would copy your original afni_proc.py command, and adapt the copy to your current processing needs.
Can you please post your new afni_proc.py command, and we can try to recommend from here? (Likely, Rick will be better at suggesting fixes for these things than me, so I will ping him...) But it will be muuuch more stable to edit the options of the AP command, rather than dig through a script and tweak things.
--pt
