afni.nimh.nih.gov

These didn't start off too far apart, so I just tried this with your data:

align_epi_anat.py -dset1 kodi_anatT1_ssiu.nii.gz -dset2 dti_FA_shft.nii.gz -dset1_strip None -dset2_strip None -big_move -suffix _al2FA

This seemed to work well. See if this is okay for you.