afni.nimh.nih.gov

That script does not yet support NIFTI data input. Try copying to AFNI format first with 3dcopy. You may need to use the "-giant_move" option too if data is not close to start. Also take a look at this example written several years ago for alignment across two sessions.

http://afni.nimh.nih.gov/sscc/dglen/alignmentacross2sessions