afni.nimh.nih.gov

Hi-

Have you looked into using @SSwarper with afni_proc.py for setting up your FMRI processing? The latter program will set up all the intermediate alignments for you; it will manage several less exciting details of processing, while allowing you to specify your processing stream in detail.

If nothing else, you can run @SSwarper + afni_proc.py to see how afni_proc.py sets up the inversions+concatenations of processing.

--pt