External Email - Use Caution
Hello Bruce,
Thank you again for offering helps regarding the Topological defect of one of our subjects. we just wanted to know whether you were able to run the SUBJECT034 file from the drive. Knowing that it takes several hours to run, and there's also other people asking questions, we are willing to try any suggestions and test it on our computers.
Thank you, Kong
On Tue, Dec 10, 2019 at 1:24 PM Kong Chuizheng kong@neurotechcenter.org wrote:
That sounds good to me! The file is about 100MB so I got a sharing link here.
https://drive.google.com/file/d/15IfN6EzZj_wAW1y0v8USIs2tthfpdH95/view?usp=s...
On Tue, Dec 10, 2019 at 12:46 PM Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
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 CautionHello 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 youtrying
to achieve? And are the holes/handles due to the tumor? Can yousend 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 tumoursubject. The recon-all.log showed
that the > program froze at Correction of the Topology with "XL defectdetected." I followed the
procedure of the > online tutorial page (https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TopologicalDefect_freev... )
> and found that there's lots of "holes" and sharp abnormalshapes in the
lh/rh.smoothwm.nofix file. It > will be very hard to fix this by hand, and we wonder if you cangive 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
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