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> From: freesurfer-boun...@nmr.mgh.harvard.edu
> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of
Bruce Fischl
> > Sent: Monday, October 22, 2018 3:30 PM
> > To: Freesurfer support list
> > Subject: Re: [Freesur
> -Lisa Krishnamurthy
> > >
> > > -Original Message-
> > > From: freesurfer-boun...@nmr.mgh.harvard.edu
> > [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of
> Bruce Fischl
> > > Sent: Monday, October
surfer support list
> Subject: Re: [Freesurfer] Stuck in "CORRECTING DEFECT"
>
> Hi Rosaila
>
> usually when you have a defect that large (>30,000) vertices, which is
about 1/4 of
the total surface more or less, something is dramatically wrong
t; -Original Message-
> > From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:
> freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl
> > Sent: Monday, October 22, 2018 3:30 PM
> > To: Freesurfer support list
> > Subject: Re: [Freesurfer] Stuck in "CORR
...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl
Sent: Monday, October 22, 2018 3:35 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Stuck in "CORRECTING DEFECT"
Hi Lisa
no, likely you have to identify and correct the source of the giant defect,
typically be either fixing the skull
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl
Sent: Monday, October 22, 2018 3:30 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Stuck in "CORRECTING DEFECT"
Hi Rosaila
usually when you have a defect that large (>30,000) vertices, which is about
1/4
-
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl
Sent: Monday, October 22, 2018 3:30 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Stuck in "CORRECTING DEFECT"
Hi Rosaila
usually when you have a defect
Hi Rosaila
usually when you have a defect that large (>30,000) vertices, which is
about 1/4 of the total surface more or less, something is dramatically
wrong and it is not worth waiting for it to finish (it might take days or
weeks). Examine the ?h.orig.nofix and ?h.inflated.nofix surfaces
External Email - Use Caution
Dear FreeSurfer team,
I Have run -autorecon1 in my sample and the report.log was "finished
without errors"
Now, running recon-all -all I have seen that a participant is stuck in
CORRECTING DEFECT 0 (vertices=31977, convex hull=5359, v0=0) for more
Hi Bruce,
Thanks for the tips. I tried playing around with the files for a bit
but didn’t make much progress.
Here’s a link to the full tar/gz’ed subject dir:
http://gate.nmr.mgh.harvard.edu/filedrop2/?p=4ej948sa49s
Thanks!
Dan
On Fri Jun 24 22:22:17 EDT 2016, Bruce Fischl
Hi Dan
that defect is too big, there must be something wrong. Check to see if the
surface is connected to dura or across the hemis or something. You can look
at the lh.inflated.nofix and/or the lh.orig.nofix to see where the defects
are. Then you'll need to correct something once you've
Hi all,
I have been trying to run freesurfer on a case for awhile now. After
receiving multiple errors when using the skull stripped nifti (nii.gz)
file, I tried to use the original dicoms as the input. While I haven't run
into any errors, the process seems to have frozen at CORRECTING DEFECT
Hi Eli
I think that defect is simply too big (it would take forever to fix). It's
more than half of the size of a typical cortical hemisphere model. Did you
check the skull stripping? And send us images (medial and lateral) of the
?h.inflated.nofix in tksurfer
cheers
Bruce
On Thu, 28 Feb
I think you are right, the auto skull stripping probably didn't quite do
the job. We are working on trying to skull strip the dicoms manually before
starting over again. In the meantime, I uploaded the lh-inflated (that
seems to be the only one in the subjects/[SUBJECT]/surf/ folder).
Thanks
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