Having (x,y,z)=(0,0,0) in a reasonably central location should pretty much always be a good idea. Having pretty good alignment between the EPI and anatomical is generally helpful, too. Getting rid of obliquity considerations at the same time... priceless (well, at least it is mildly helpful).
This should accomplish the above for the dset you shared, methinks:
#!/bin/tcsh
set dset_orig = DSET_ANAT
set dset_new = anat_ctr.nii
3dcopy $dset_orig $dset_new
3dCM -set 0 0 0 $dset_new
set dset_orig = DSET_EPI
set dset_new = epi_ctr.nii
set dset_mask = epi_mask.nii
# get a mask well-approximating where the brain is in the EPI
3dAutomask \
-prefix $dset_mask \
$dset_orig
3dcopy $dset_orig $dset_new
3dCM -mask $dset_mask -set 0 0 0 $dset_new
--pt
