Hi Julia,
After the skull strip was corrected, you should run:
recon-all -autorecon2 -autorecon3 -s Subject_name
this will create new surfaces based on new skull strip.
Tanja.
On Mon, Aug 22, 2011 at 6:47 AM, Julia Hill julia.hill@neura.edu.au wrote:
Hi Bruce
I am new to freesurfer and im having a few issues with a number of my scans. The cerebellum and sections of the occipital lobe seems to be cut off on a number of subjects, so i went in and altered the skull stripping by increasing the watershed threshold to 35 and using -no-wsgcaatlas. When i review the scans afterwards, the pial and WM surfaces haven't included the original missing sections of the scans. How do i go back and include these missing sections?
I have attached a screenshots.
Thank you kindly
Julia
Julia Hill Research Assistant
School of Psychiatry
University of New South Wales
Previously Prince of Wales Medical Research Institute
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