afni.nimh.nih.gov

Your NIFTI file has the sform_code set to 2, which means "aligned" to something. AFNI determines what to do with that using an environment variable, AFNI_NIFTI_VIEW. Check your .afnirc file, and see if your AFNI_NIFTI_VIEW is set to tlrc or orig. See this previous posting too:

http://afni.nimh.nih.gov/afni/community/board/read.php?1,90114,91155#msg-91155