Hi Tanja, Sorry if I missed something but was the cortex stripped off even before you made any edits. If so, it's probably skull strip error. Please refer to this wiki for instructions to correct the error.
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/SkullStripFix But if part of the brain is missing only after you added control points and ran -autorecon2-cp -autorecon3, then please check if any of the control points were placed in GM or really close to GM. Sita. On Wed, 7 Mar 2012, Tetiana Dadakova wrote: > Dear FS list, > > We started using FS 5.1 and encountered a problem with control points. > After first recon-all some of the cortex (in occipital part) was > missing, so we added control points and re-ran -autorecon2-cp > -atorecon3. > After that, the part of the brain with control points was removed from > brainmask.mgz (Fig1). > > I never had this problem in 5.0, therefore I assume that something has > been changed in 5.1 regarding cp. Could you please suggest what can be > the problem and if it is described somewhere? > > Thank you, > Tanja. > _______________________________________________ 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.
