If you have an up-to-date version of AFNI (less than a month old), you can try this first
3dUnifize -input ANAT+orig -prefix ANATuni
This will (approximately) unshade the T1-weighted volume, and then you can try 3dSkullStrip on the ANATuni+orig dataset.
All this is assuming the original volume is at about 1x1x1 mm resolution, which is what we are used to.