You'll have to find and remove the defect manually. It is probably cerebellum that is still attached or maybe a piece of dura or skull. There is some info on defects here http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TopologicalDefect_freevi...
You can also run defect2seg --s subject should only take a few minutes Then run tkmeditfv subject brain.finalsurfs.mgz -defect -aux wm.mgz This will load the defects as a segmentation; there will also be a point set that you can use to go from one defect to another
On 1/29/2021 12:24 PM, Paul, Rahul wrote:
*From:* Paul, Rahul *Sent:* Thursday, January 28, 2021 3:52 PM *To:* freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu *Subject:* Freesurfer recon all Hi,
I just started working on the freesurfer software. I was trying to use recon-all command but there was an output saying XL error detected, and it remained same for more than 6 hours or so.
Any idea how I can fix it? Bdw i stopped it running after 8 hours or so.
I am using a T1-MRI scan. I am using a MacBook pro (8GB RAM). I am attaching a screenshot and the command I used can be seen in the bottom of the screenshot.
Thank you,
Rahul Paul
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