Hi AFNI experts,

I am working on using 3dQwarp within AFNI_proc.py and noticed not-so-great registration with a template I am using. I am guessing this is due to the problem from skull-stripping where it is not removing skull and non-brain matter very effectively. When I overlay the template on top of my Qwarped brains, it looks like the warp included the non-brain matter.

I am wondering if it is possible within the Qwarp command options to allow a non-skull-stripped template to be used at the non-linear step? So, essentially use the skull-stripped template for the affine warp, then use a non-skull-stripped template and a mask (brain only) for non-linear step? Then apply this warp to the EPI. I believe this is how FSL's FNIRT command works and was curious whether this is a possibility within Qwarp.

Thanks,

Danny