Hi Ana you might need to fix the labeling in the aseg. If you can't get this to work feel free to upload and we will take a look
cheers Bruce On Mon, 5 Oct 2015, Anastasia Klimovich-Smith wrote: > Dear freesurfer experts, > > I have an issue with -autorecon2-wm stage results (freesurfer v.5.3.0). > Sometimes the ventricles are not fully filled and the white matter is > localized within the remaining gaps. After manually filling the gaps in > the wm.mgz (following the wiki - Fixing Common Geometric Inaccuracies in > White Matter Surfaces) and rerunning (-autorecon2-wm) I still have the > wm surface following the ventricle holes, even though I can see they are > filled on wm.mgz. I used freesurfer v.5.1.0 before and didn't have these > issues. How would you recommend fixing this? > > Thanks a lot, > Ana > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ 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.
