Hi Isa,
Since your EPIs are across sessions, you should probably
align them within a session, and then each session to the
same anatomy. This is not optimal though.
Given that, it might be good to use @auto_tlrc and then
align_epi_anat.py yourself, and then have afni_proc.py
finish it off.
Otherwise, you could take the proc script, add a second
align_epi_anat.py command (for the second EPI base),
and modify it to catentate transformations for each EPI
base. Hmmm, maybe that is getting dangerous. Running
AEA.py before AP.py might be easier.
- rick
