External Email - Use Caution
Hi Freesurfer Support,
One of my colleagues receives the following error after running a recon:
exited with errors: "excessive topologic defect encountered: could not allocate 289309485 edges for retessellation"
I checked the inflated view and there does appear to be significant portions of the brain missing (however I cannot see this in 2D). I've attached a screenshot of the inflated view.
How would I go about fixing the error?
Thank you!
Laurel Quinlan Associate Research Specialist Center for Healthy Minds University of Wisconsin-Madison
Look at the lh.orig.nofix and see if you can find the defect. Also, look at it in the volume and the surface views. Might be cerebellum
On 12/3/2019 11:30 AM, Laurel Quinlan wrote:
External Email - Use Caution
Hi Freesurfer Support,
One of my colleagues receives the following error after running a recon:
exited with errors: "excessive topologic defect encountered: could not allocate 289309485 edges for retessellation"
I checked the inflated view and there does appear to be significant portions of the brain missing (however I cannot see this in 2D). I've attached a screenshot of the inflated view.
How would I go about fixing the error?
Thank you!
Laurel Quinlan Associate Research Specialist Center for Healthy Minds University of Wisconsin-Madison
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
it might also be the hemispheres not being separated, hard to tell (although that almost never happens). You can look at the filled.mgz to check this (the hemis should have different labels) On Tue, 3 Dec 2019, Greve, Douglas N.,Ph.D. wrote:
Look at the lh.orig.nofix and see if you can find the defect. Also, look at it in the volume and the surface views. Might be cerebellum
On 12/3/2019 11:30 AM, Laurel Quinlan wrote:
External Email - Use Caution Hi Freesurfer Support,One of my colleagues receives the following error after running a recon:
exited with errors: "excessive topologic defect encountered: could not allocate 289309485 edges for retessellation"
I checked the inflated view and there does appear to be significant portions of the brain missing (however I cannot see this in 2D). I've attached a screenshot of the inflated view.
How would I go about fixing the error?
Thank you!
Laurel Quinlan Associate Research Specialist Center for Healthy Minds University of Wisconsin-Madison
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
Thank you!
Attached are two screenshots of the filled.mgz view and the lh.orig.nofix view. The cerebellum doesn't seem to be the problem, and both hemispheres are distinguished. Additionally, the brainmask does not show this defect. All of the brain is included in the brainmask.
How can I get FS to recognize that the missing portion of brain is gray/white matter that should be included in the pial line?
Thanks!
-Laurel
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Bruce Fischl fischl@nmr.mgh.harvard.edu Sent: Tuesday, December 3, 2019 11:57 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] topological defect error
it might also be the hemispheres not being separated, hard to tell (although that almost never happens). You can look at the filled.mgz to check this (the hemis should have different labels) On Tue, 3 Dec 2019, Greve, Douglas N.,Ph.D. wrote:
Look at the lh.orig.nofix and see if you can find the defect. Also, look at it in the volume and the surface views. Might be cerebellum
On 12/3/2019 11:30 AM, Laurel Quinlan wrote:
External Email - Use Caution Hi Freesurfer Support,One of my colleagues receives the following error after running a recon:
exited with errors: "excessive topologic defect encountered: could not allocate 289309485 edges for retessellation"
I checked the inflated view and there does appear to be significant portions of the brain missing (however I cannot see this in 2D). I've attached a screenshot of the inflated view.
How would I go about fixing the error?
Thank you!
Laurel Quinlan Associate Research Specialist Center for Healthy Minds University of Wisconsin-Madison
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Laurel
do you want to upload this subject to our ftp site and we can take a look? Alternatively you can overlay the wm.mgz as a heatmap on top of the brain.mgz with the ?h.orig surface overlaid so you can see where it is missing stuff and why Bruce
On Thu, 5 Dec 2019, Laurel Quinlan wrote:
External Email - Use Caution
Thank you!
Attached are two screenshots of the filled.mgz view and the lh.orig.nofix view. The cerebellum doesn't seem to be the problem, and both hemispheres are distinguished. Additionally, the brainmask does not show this defect. All of the brain is included in the brainmask.
How can I get FS to recognize that the missing portion of brain is gray/white matter that should be included in the pial line?
Thanks!
-Laurel
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Bruce Fischl fischl@nmr.mgh.harvard.edu Sent: Tuesday, December 3, 2019 11:57 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] topological defect error it might also be the hemispheres not being separated, hard to tell (although that almost never happens). You can look at the filled.mgz to check this (the hemis should have different labels) On Tue, 3 Dec 2019, Greve, Douglas N.,Ph.D. wrote:
Look at the lh.orig.nofix and see if you can find the defect. Also, look at it in the volume and the surface views. Might be cerebellum
On 12/3/2019 11:30 AM, Laurel Quinlan wrote:
External Email - Use Caution
Hi Freesurfer Support,
One of my colleagues receives the following error after running a recon:
exited with errors: "excessive topologic defect encountered: could not allocate 289309485 edges for retessellation"
I checked the inflated view and there does appear to be significant portions of the brain missing (however I cannot see this in 2D). I've attached a screenshot of the inflated view.
How would I go about fixing the error?
Thank you!
Laurel Quinlan Associate Research Specialist Center for Healthy Minds University of Wisconsin-Madison
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
Thanks Bruce! I will chat with my supervisor about uploading the brain to the ftp site, but for now, I can see intensity issues on the brain.mgz volume. The area being excluded from segmentation is darker and the R frontal region is hyperintense.
Would this be a case to try mri_normalize?
-Laurel ________________________________ From: Bruce Fischl fischl@nmr.mgh.harvard.edu Sent: Thursday, December 5, 2019 3:40 PM To: Laurel Quinlan laurel.quinlan@wisc.edu Cc: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] topological defect error
Hi Laurel
do you want to upload this subject to our ftp site and we can take a look? Alternatively you can overlay the wm.mgz as a heatmap on top of the brain.mgz with the ?h.orig surface overlaid so you can see where it is missing stuff and why Bruce
On Thu, 5 Dec 2019, Laurel Quinlan wrote:
External Email - Use CautionThank you!
Attached are two screenshots of the filled.mgz view and the lh.orig.nofix view. The cerebellum doesn't seem to be the problem, and both hemispheres are distinguished. Additionally, the brainmask does not show this defect. All of the brain is included in the brainmask.
How can I get FS to recognize that the missing portion of brain is gray/white matter that should be included in the pial line?
Thanks!
-Laurel
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Bruce Fischl fischl@nmr.mgh.harvard.edu Sent: Tuesday, December 3, 2019 11:57 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] topological defect error it might also be the hemispheres not being separated, hard to tell (although that almost never happens). You can look at the filled.mgz to check this (the hemis should have different labels) On Tue, 3 Dec 2019, Greve, Douglas N.,Ph.D. wrote:
Look at the lh.orig.nofix and see if you can find the defect. Also, look at it in the volume and the surface views. Might be cerebellum
On 12/3/2019 11:30 AM, Laurel Quinlan wrote:
External Email - Use Caution Hi Freesurfer Support,One of my colleagues receives the following error after running a recon:
exited with errors: "excessive topologic defect encountered: could not allocate 289309485 edges for retessellation"
I checked the inflated view and there does appear to be significant portions of the brain missing (however I cannot see this in 2D). I've attached a screenshot of the inflated view.
How would I go about fixing the error?
Thank you!
Laurel Quinlan Associate Research Specialist Center for Healthy Minds University of Wisconsin-Madison
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
I guess I would try adding control points to the wm in the region that is darker
On Thu, 5 Dec 2019, Laurel Quinlan wrote:
External Email - Use Caution
Thanks Bruce! I will chat with my supervisor about uploading the brain to the ftp site, but for now, I can see intensity issues on the brain.mgz volume. The area being excluded from segmentation is darker and the R frontal region is hyperintense.
Would this be a case to try mri_normalize?
-Laurel
From: Bruce Fischl fischl@nmr.mgh.harvard.edu Sent: Thursday, December 5, 2019 3:40 PM To: Laurel Quinlan laurel.quinlan@wisc.edu Cc: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] topological defect error Hi Laurel
do you want to upload this subject to our ftp site and we can take a look? Alternatively you can overlay the wm.mgz as a heatmap on top of the brain.mgz with the ?h.orig surface overlaid so you can see where it is missing stuff and why Bruce
On Thu, 5 Dec 2019, Laurel Quinlan wrote:
External Email - Use Caution
Thank you!
Attached are two screenshots of the filled.mgz view and the lh.orig.nofix view. The cerebellum doesn't seem to be the problem, and both hemispheres are distinguished. Additionally, the brainmask does not show this defect. All of the brain is included in the brainmask.
How can I get FS to recognize that the missing portion of brain is gray/white matter that should be included in the pial line?
Thanks!
-Laurel
_
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of
Bruce
Fischl fischl@nmr.mgh.harvard.edu Sent: Tuesday, December 3, 2019 11:57 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] topological defect error it might also be the hemispheres not being separated, hard to tell (although that almost never happens). You can look at the filled.mgz to check this (the hemis should have different labels) On Tue, 3 Dec 2019, Greve, Douglas N.,Ph.D. wrote:
Look at the lh.orig.nofix and see if you can find the defect. Also, look at it in the volume and the surface views. Might be cerebellum
On 12/3/2019 11:30 AM, Laurel Quinlan wrote:
External Email - Use Caution
Hi Freesurfer Support,
One of my colleagues receives the following error after running a recon:
exited with errors: "excessive topologic defect encountered: could not allocate 289309485 edges for retessellation"
I checked the inflated view and there does appear to be significant portions of the brain missing (however I cannot see this in 2D). I've attached a screenshot of the inflated view.
How would I go about fixing the error?
Thank you!
Laurel Quinlan Associate Research Specialist Center for Healthy Minds University of Wisconsin-Madison
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
Greve, Douglas N.,Ph.D. -
Laurel Quinlan