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, > > 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 > > > _______________________________________________ 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.
