Howdy-
Just to note that AFNI's macaque demo (@Install_MACAQUE_DEMO) includes subjects who have MION during the EPI acquisition. Indeed, we found that using lpa+zz was the way to go for those, noting in the afni_proc.py part of the script:
# Using the lpa+zz cost func for some macaques who have MION;
# lpc+zz for the others
The align block options used there were as follows:
-align_opts_aea -cost ${cost_a2e} -giant_move \
-cmass cmass -feature_size 0.5 \
with "cost_a2e" being lpa+zz for the MION-ated macaques. Things like the need for "-giant_move" and "-cmas cmass" will be **very** dependent on how you acquire and convert your data (do you have good coords? Do you have lots of non-brain matter in the FOV? etc.). So, indeed, these kinds of things will be study-dependent.
But that makes it all the nicer to:
+ share what ideas work in what contexts, to benefit other users
+ use a program like afni_proc.py where you can relatively easily tweak/adjust these things scriptically, and save them for later and/or share them widely.
--pt
