Re: [Freesurfer] Fwd: fix topology problem

You should load that with the ?h.orig.nofix surface to see if there the surface is grabbing that part of the skull. If it is, you can edit the wm.mgz to remove those voxels. Probably there are only a few voxels that, if erased, would disconnect the skull from the rest of the brain

On 04/19/2017 02:04 PM, miracle ozzoude wrote:

Yes, part of the skull is still there. Please see screenshot. Best, Paul

Inline image 2

On Wed, Apr 19, 2017 at 1:49 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:

Did you check whether there was something else attached? Eg, a big
piece
of skull, etc.?


On 04/19/2017 01:23 PM, miracle ozzoude wrote:
> Hello Doug,
> No, the cerebellum has been removed.
> Best,
> Paul
>
> On Wed, Apr 19, 2017 at 1:13 PM, Douglas N Greve
> <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>>> wrote:
>
>     Did you check to see whether cerebellum as still attached in the
>     wm.mgz
>     file?
>
>
>     On 04/18/2017 09:06 PM, miracle ozzoude wrote:
>     >
>     > ---------- Forwarded message ----------
>     > From: *miracle ozzoude* <miracooloz@gmail.com
<mailto:miracooloz@gmail.com> <mailto:miracooloz@gmail.com
<mailto:miracooloz@gmail.com>>
>     > <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com>
<mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com>>>>
>     > Date: Mon, Apr 17, 2017 at 8:40 AM
>     > Subject: fix topology problem
>     > To: Douglas N Greve <freesurfer@nmr.mgh.harvard.edu
<mailto:freesurfer@nmr.mgh.harvard.edu>
>     <mailto:freesurfer@nmr.mgh.harvard.edu
<mailto:freesurfer@nmr.mgh.harvard.edu>>
>     > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>
>     <mailto:freesurfer@nmr.mgh.harvard.edu
<mailto:freesurfer@nmr.mgh.harvard.edu>>>>
>     >
>     >
>     > Hello freesurfer,
>     > I am running recon-all on a scan and for the past 4 days,
it hasn't
>     > finished the fix topology step of recon-all. I have
attached the
>     > recon.log in the email. Thanks
>     > Best,
>     > Paul
>     >
>     >
>     >
>     >
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>     MGH-NMR Center
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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
Phone Number: 617-724-2358 <tel:617-724-2358>
Fax: 617-726-7422 <tel:617-726-7422>

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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www.nmr.mgh.harvard.edu/facility/filedrop/index.html
<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
Outgoing:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
<ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/>

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