the topology fixing output should let you find the defect that is so big and figure out how to fix it. If you want to tar/gzip the entire subject dir and send it to us we will be happy to help
cheers Bruce On Tue, 10 Dec 2019, Kong Chuizheng wrote:
External Email - Use Caution
Hello Bruce, We are trying to get the pial surface file for both hemisphere. However, freesurfer would freeze after a while at a XL defect. Since the hemisphere without tumor also has little holes, I thought this might have other reasons.
Best, Chuizheng Kong
On Tue, Dec 10, 2019 at 8:58 AM Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Does your 3D model need to be topologically correct? What are you trying to achieve? And are the holes/handles due to the tumor? Can you send us some images?
cheers Bruce On Tue, 10 Dec 2019, Kong Chuizheng wrote: > > External Email - Use Caution > > Hello Freesurfer Developers, > > > > We are trying to construct a 3D cortex model of a tumour subject. The recon-all.log showed that the > program froze at Correction of the Topology with "XL defect detected." I followed the procedure of the > online tutorial page ( https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TopologicalDefect_freeview) > and found that there's lots of "holes" and sharp abnormal shapes in the lh/rh.smoothwm.nofix file. It > will be very hard to fix this by hand, and we wonder if you can give us some advice. > > > > Sincerely, > > Chuizheng Kong > > > > Chuizheng Kong > >_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer