Re: [Freesurfer] problem with skullstrip- shoulders and neck remaining

You can try running just recon-all -skullstrip first, if that doesn't fix the problem, you can try changing the wsthresh and removing the -no-wsgcaatlas flag (or add the flag if you didn't include it). Sometimes that makes a difference. -Khoa On Wed, 9 Nov 2011, Julia Hill wrote: > Hi there,

Re: [Freesurfer] problem with skullstrip- shoulders and neck remaining

 Hi JuliaDoes the stuff left around mess anything up?  You are probably fine running it that wayBruceOn Nov 8, 2011, at 9:30 PM, Julia Hill wrote:Hi there,I am having difficulties with one of my images.  On first inspection, freesurfer had performed a bad skull strip, leav