I had a similar problem with very noisy data acquired on a 3T scanner. I ended up having to clip as much of the non-head regions of the T1 images so that the noise would not pull the mask outside the head. I used @clip_volume to zero this out. In the AFNI viewer, load in your T1 and make a note of the six x, y, z planes that get you as close to the head as possible and then create, possibly multiple, @clip_volume commands to implement the clipping. You'd do this clipping before running @SSwarper. It's a somewhat tedious process but it worked wonders for noisy T1s in this particular dataset.
