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
> >
> >
> >
> >
>
>