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: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Douglas N. Greve <dgreve@mgh.harvard.edu>
Sent: Monday, March 30, 2020 11:55 AM
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
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

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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