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
>       >
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