afni.nimh.nih.gov

My guess is that the two coordinate systems have little to do with each other. That means they may not even overlap at all. Try either using the @Align_Centers script on the input to your datasets or using the "-ginormous_move" option for align_epi_anat.py. If you do use the @Align_Centers script, then the "-giant_move" is likely to be useful here.