Hello AFNI team,

I would like to "classically" co-registrate a BOLD image to a template using the movement parameters of the anatomical image, in a primate, with afni_proc.py.
for a typical command please see:
[afni.nimh.nih.gov]

I would like to know if there is a way to modify the "3dSkullStrip or "3dAutomask" parameters in -epi_strip of afni_proc.py?
For example, if I would like to add "-monkey" to 3dSkullStrip. Is it possible?

Also,
Is there a way to provide an external EPI mask?

It seems to me that having a bad SkullStrip generates lots of problems for the co-registration?
This problem seems to be recurrent for primates or mammalian BOLD images with no homogenous BOLD signal.

Thank you for your help!
Clem



Edited 1 time(s). Last edit at 06/14/2021 09:00PM by Doughboys.