Hi Clem,
sorry for jumping into your thread, but I am a fellow AFNI/NHP/MION user who has been struggling with similar issues.
So you did you get it to work with 3dSkullStrip and -skullstrip_opts -monkey and cost lpa+ZZ, correct?
For me, both 3dSkullstrip and 3dAutomask always failed on a subset of session (each in its own distinct way), but I found out that no epi skullstripping and lpa (without +ZZ) worked surprisingly well for me.
But I never learned about -skullstrip_opts -monkey before, so thank you for this thread, it was educational for me and I am going to test this option on my dataset.
