Hi Mingbo,
I just tested this by resampling to ASR and running
3dZcutup and it worked well. Would you please
provide your exact command, along with the output
from 3dinfo (no HISTORY is needed)?
To cut in other directions, is it good enough to
run 3dresample -orient first? That is what I just
did.
If the centers are far off, consider fixing that
by running @Align_Centers before align_epie_ana.py.
- rick