Thank you very much Daniel! I did try supplying an external mask (generated through doing skull-stripping in FSL) as input following the @SSwarper example 3. The voxels included in the mask are indeed included in the anatS.ID.nii output (first pass of skull-stripping) but additional voxels are being cut-off during the second pass of skull-stripping in the anatSS.ID.nii output (I attached a screenshot comparing the two outputs). Therefore, my skull-stripping problem still persists. I don't know what else I am missing...

If there is no way to skip the second-round of skull-stripping that inevitably causes a problem for skull-stripping, I will just skip the @SSwarper step, do skull-strip separately, and uses the default nonlinear warping in afni_proc.py for this particular participant? I also just want to make sure that it is okay for one participant's data to be processed slightly different than the rest of the participants.

Thank you so much again!

--Zehua