Hi, Jenna-

As Rick pointed out, this warning-behavior is most likely where values are veeeery small, which might be ventricles and/or outside the brain. So, likely it isn't a meaningful issue at all.

One primary point of @SSwarper is the "warper" part: calculating the warp to standard space, which can then be applied in, e.g., afni_proc.py. I doubt the above affects this at all. This can be verified by checking the QC of the warping---if that looks good, then you should be all set on that front.

The other main part of the program is the "SS" part---skullstripping. You could *try* substracting the output anat*SS* image from the original input, and see where differences are large, *but* by default the output anat*SS* volume is unifized, to make the brightness levels more uniform across the volume and within tissues. So, actually, unless you have turned unifizing off, this kind of test isn't possible. And in general, I don't see why turning off unifizing would be so useful, because often that helps with EPI-anatomical alignment. So, if there aren't any visual oddities in the anat*SS* image, I would assume things are fine.

--pt