afni.nimh.nih.gov

Can you please copy+paste the full align_epi_anat.py command that you are typing/using?

Note that often with FMRI processing, align_epi_anat.py would be run within an afni_proc.py command. While it can be useful to test EPI-anatomical alignment options separately, putting those options for afni_proc.py to use is nice because then that alignment step gets properly concatenated within the full processing stream for each subject.

Also, it would be nice to see the version of AFNI you are using.

--pt