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_freev...) 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
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_freev...) 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
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 CautionHello 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_freev... )
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
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
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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 abnormal shapesin 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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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 CautionHello 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_freev... )
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
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:
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 [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 > >_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
I was looking at this page (https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TopologicalDefect_freev...) 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:
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 [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 > >_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
yes. It is hard to predict the effects of tumors on the topology of the surface. It might be fine or it might need fixing. And I expect the program isn't actually frozen. The time to fix a defect is quadratic in the number of vertices in the (convex hull) of the defect, so for small ones it is quiite fast, but for huge ones it can take forever. It also probably won't do what you want it to on defects that are that big
On Tue, 10 Dec 2019, Kong Chuizheng wrote:
External Email - Use Caution
I was looking at this page (https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TopologicalDefect_freev...) 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: 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 [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 > >_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
Kong Chuizheng