HI Afni Experts,
Regarding question 2 I came across a previous post by Bob which may answer this :
[afni.nimh.nih.gov]

I am testing to see if I use 3dTcorr1D with a mask first (mni brainmask x MNI-warped EPI brainmask for overlap), prior to 3dttest++. This may remove some of the outliers and non-brain regions per subject (along with typically using a mask in 3dttest++). I will also add the -zskip option since the coverage for each person's MNI warped brain will not be the same (especially cerebellum or part of the cortex).

In addition to my first question in the previous post, Is it recommended to use -resid flag with -clustsim?

Thanks,
Ajay