Hi Beate,
If you are warping the anat (to match the EPI), there should be
no effect on the EPI processing... unless you are then warping
to standard (+tlrc) space first, are you?
It should only affect the EPI processing if you have actually
transformed the EPI data. Are you using either -deoblique or
-oblique2card at some point?
Please post all of the 3dWarp commands that you are using. It
will make it much easier to figure out what is happening.
Also, is all of your processing in +orig space?
- rick