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.h...@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. > >
_______________________________________________ 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.
