Hi Lily
that looks ok I think, although it's hard to tell for sure. The
cerebellum shouldn't be included in the surface. Are you sure you have
enough ram on your machine? It looked like half of it was in use when you
ran recon-all. If you want you can tar and gzip the whole subject dir and
ftp it to us and we will take a look, but I would try rerunning when
nothing else is taking up significant chunks of memory on your machine and
see if that fixes it
cheers
Bruce
On Mon, 30 Mar 2020, Wang, Lily wrote:
Hi Dr. Greve,
I'm not seeing any glaring issues with inclusion of cerebellum or skull in
the surfaces or the mgz. There is a bit of inclusion of the cerebellum in
the wm.mgz. However, two things that do seem strange are 1. a portion of the
subject's cerebellum is black/missing, 2. in the wm.mgz on grayscale, it
looks like the ventricles are supposed to be white, but a big portion of
this subject's ventricles are not included and it seems that it's messing up
the lh.orig.nofix surface as well. Could this possibly be an issue? Please
see attached screenshot.
Thank you,
Lily
____________________________________________________________________________
From: [email protected]
<[email protected]> on behalf of Douglas N. Greve
<[email protected]>
Sent: Monday, March 30, 2020 11:55 AM
To: [email protected] <[email protected]>
Subject: Re: [Freesurfer] Recon-all exited with errors
It looks like there might be a very large defect. Try looking at the wm.mgz
and brainmask.mgz and the lh.orig.nofix surface to see if there is a large
part of skull or cerebellum that is encompassed in the orig.nofix surface
On 3/30/2020 11:26 AM, Wang, Lily wrote:
Hi All,
I have a subject whose T1 quality is quite good but reconstruction
exited with errors so I am not sure what the issue could be. Attached
is the recon-all.log. Could it be that the subject is very old and has
a lot of degeneration?
Thank you,
Lily
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