Hi Ranjan,
The align_epi_anat.py program defaults to aligning the anat
to the EPI. If you want the EPI aligned to the anat, consider
adding -epi2anat, and maybe something like -master_epi 3.5
(note that 3.5 mm is the voxel size that afni_proc.py would
use if you were asking it to write the analysis script).
- rick
