[Freesurfer] problem with skullstrip- shoulders and neck remaining

Hi there,

I am having difficulties with one of my images. On first inspection, freesurfer had performed a bad skull strip, leaving the base of the skull plus what looked to be the shoulders and neck. I decreased the watershed to 5, and the shoulders/neck still appeared, so i decreased to 2 and now sections of the brain have disappeared (see attached), do you know how i can fix this?

Many thanks ,

Julia Hill Research Assistant School of Psychiatry University of New South Wales

Previously Prince of Wales Medical Research Institute www.NeuRA.edu.au Barker Street Randwick Sydney NSW 2031 Australia PO Box 1165 Randwick Sydney NSW 2031 Australia T +61 2 9399 1268