With a mask dataset as input, you would not use the -init_skullstr_off option. See the example 3 in the current @SSwarper help for how to use an external mask dataset as input. The mask provides a replacement for the initial skullstripping step. Voxels included in that mask should be included in the output datasets. The default nonlinear warping in afni_proc.py will work too, but it's a little different because of the skullstripping in @SSwarper and the default affine alignment in step.
