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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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