afni.nimh.nih.gov

The problem seems to be your EPI to anatomical alignment. It looks like it starts out okay but then goes wrong. Try removing "-cmass cmass -align_centers yes " from the afni_proc.py "-align_opts_aea" line. The alignment may need a different cost function depending on the quality of the EPI data, and you can try "-cost lpa" or "-cost nmi" .