Oh, and regarding how to tell afni_proc.py to tell align_epi_anat.py to use 3dSkullStrip on the EPI, Daniel has provided The Right Answer (as we knew he would).
It should be entered via this AP option:
-align_epi_strip_method METHOD : specify EPI skull strip method in AEA
e.g. -align_epi_strip_method 3dSkullStrip
default: 3dAutomask (changed from 3dSkullStrip, 20 Aug, 2013)
When align_epi_anat.py is used to align the EPI and anatomy, it
uses 3dSkullStrip to remove non-brain tissue from the EPI dataset.
However afni_proc.py changes that to 3dAutomask by default (as of
August 20, 2013). This option can be used to specify which method
to use, one of 3dSkullStrip, 3dAutomask or None.
This option assumes the 'align' processing block is used.
So, your afni_proc.py command could contain this:
-align_epi_strip_method 3dSkullStrip \
-align_opts_aea -cost lpc+ZZ -giant_move \
-skullstrip_opts -monkey \
.... and that passes everything along correctly.
-pt