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I was looking at this page (https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TopologicalDefect_freeview) on finding and fixing holes using wm.mgz. I thought that tumor might not be the primary reason that the program froze. I did have some subject models that was built successfully even with the shape of surgical removal preserved. When you mentioned fill in the tumor do you mean adding the hollow part of the brain in wm.mgz?

Best,
Chuizheng Kong

On Dec 10, 2019, at 12:07 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote:

have you looked at our tutorial on topology fixing? I would try that first. You might need to fill in the tumor in the wm.mgz. The little holes won't be a problem - it is the big ones that might be

cheers
Bruce
On Tue, 10 Dec 2019, Kong Chuizheng wrote:

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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
[cleardot.gif]
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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