Hello,

Sorry for losing your previous message (please feel free to occasionally bump them with a tiny reply).

The anat->template image shows a blurry underlay, which I did not notice in your command. When using non-linear registration, the template should not be blurry (if it is, you might as well use affine registration). But that won't affect the original skull-stripping problems. @SSwarper should indeed do a better job with that, however it might be hindered by use of the blurry template.

Wait, you didn't use a blurry template in the @SSwarper command. So specify the @SSwarper template with the -tlrc_base option in afni_proc.py, to avoid confusion.

Cortical atrophy could certainly make this more difficult though.

Maybe Paul or Daniel will have suggestions for things you might try to improve this.

- rick