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

www.NeuRA.edu.au http://neura.edu.au/ Barker Street Randwick Sydney NSW 2031 Australia PO Box 1165 Randwick Sydney NSW 2031 Australia *T *+61 2 9399 1268

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.