Hi Mengxing,
No, you are correct, but it is okay, and not so obvious why.
In the anat block, the anat is always aligned to the EPI. However, due to that e2a option, the inverse of that (a2e) transformation is applied to the EPI (via the cat_matvec command using -I). That transformation is concatenated with the volreg one to prevent multiple interpolation steps.
Does that seem reasonable?
- rick