Just to note: in looking at the data, the contrast was a bit different than what might be expected; using the "nmi" cost function seems to sort out the EPI-anatomical alignment. So, changing:

-align_opts_aea -cost lpc+ZZ -check_flip \

to

-align_opts_aea -cost nmi -check_flip \

In most cases, starting with "lpc+ZZ" would still be recommended; but then there are alternatives that can be useful, as here.

We would also probably recommend using @SSwarper for the nonlinear alignment to template space (warping) and skullstripping (ss). This program would be run before afni_proc.py (AP), and its results provided with a couple command line options, as demonstrated here in SSW's help:
https://afni.nimh.nih.gov/pub/dist/doc/htmldoc/programs/alpha/%40SSwarper_sphx.html#using-ssw-with-afni-proc-py

--pt



Edited 1 time(s). Last edit at 11/27/2022 08:38AM by ptaylor.