Hi again,
The centers being out of alignment is not the problem. The problem is that the EPI are not aligned with the Anatomicals to begin with. So if Xa is the transform that takes the Anatomicals to TLRC space then you cannot apply Xa to the EPI and expect them to be in TLRC space also.
I don't know why your Anatomicals and EPI do not lineup to begin with. But that is through no fault of your own, then you can just warp the EPI to tlrc space using an EPI template.
To align anatomicals:
@auto_tlrc -base TT_avg152T1+tlrc -input Anat+orig -suffix NONE
To align EPI:
@auto_tlrc -base TT_EPI+tlrc -input EPI+orig -suffix NONE
-ziad