Hi Rosalia,
> If my T1 images have to be or not to be skull stripped.
They do not need to be brain extracted (if for some reason you want to use brain extracted images, you can pass the -b option to run_first_all).
> How restrict the analysis, from the very beginning, to the entire amygdala only.
You can pass -s L_Amyg,R_Amyg to run_first_all.
> If I have problem with the "automatic registration"...how to manage
The run_first_all script should do all the registration steps for you. Are you running into a specific problem?
Hope that helps!
Cheers,
Eelke
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