Hi Teo, Yes it does, but you can use the -no-wsgcaatlas flag. You can also try using gcut which doesn't use an atlas (almost certain).

Link with skullstripping info: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/SkullStripFix_freeview

-Louis

On Fri, 27 Jun 2014, Teo Gelles wrote:

Hi Everyone,

I am trying to skullstrip an mri image without using an atlas.  Does the following command use an atlas at any point?  If so, is there a way to run the skullstripping algorithm without using information from an atlas?

recon-all -s bert/ -clean-bm -skullstrip

Thanks.

Teo Gelles