HI Chemda
The “nofix” files are surfaces prior to topology correction, so they will have
defects in them. The defect_labels files are *not* surfaces, they are scalar
fields over the surface (like curvature files), so load them that way
Cheers
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> On Behalf Of chemda wiener
Sent: Monday, December 2, 2024 4:19 AM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Fwd: recon-all command stuck before creating pial
files
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Thanks Bruce! Unfortunately when I try to open the lh.defect_labels it quits
freeview. The lh.orig.nofix loads okay, but I was wondering if it was a problem
that this file is even called "nofix", does that mean it was not able to
correct for defects?
On Sun, Dec 1, 2024 at 5:49 PM Fischl, Bruce R.,PHD
<bfis...@mgh.harvard.edu<mailto:bfis...@mgh.harvard.edu>> wrote:
Hi Chemda
Usually that means something big has gone wrong in the segmentation or skull
stripping (like the cerebellum is still attached to a cortical hemisphere in
the wm.mgz or the skull is or something like that). More generally this happens
when there is a topological defect that is too big to automatically correct in
a reasonable amount of time. You can visualize the defects following the
instructions here:
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cheers
Bruce
From:
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
On Behalf Of chemda wiener
Sent: Sunday, December 1, 2024 5:41 AM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] Fwd: recon-all command stuck before creating pial files
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Hi,
My name is Chemda Wiener. I am a PhD student in a Neuro-Engineering lab. We are
working with MRI scans of patients with epilepsy and I am attempting to use
freesurfer to create the mesh .pial files. When I run the freesurfer recon-all
command, the command gets stuck at "correcting defects" with the last file it
creates being the "lh.defect_chull". It has been stuck for a few days on this
part until I finally killed the process. I tried running autorecon2 afterwards
on this patient to see if it can pick up from where it stopped but it gets
stuck again at the same place.
I would appreciate any help in the matter.
Thank you in advance for your time and your software!
Chemda
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