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_freeview

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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