Hi Abeoseh

You need to take a look at the output and see what is causing the large defect. It is usually something like a big piece of skull left around.

Cheers

Bruce

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Flemister, Abeoseh B.
Sent: Thursday, January 25, 2024 10:33 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Extra Large Defect T1

        External Email - Use Caution        

Hi Freesurfer team,

I have gotten this error message on a successful run before:

An extra large defect has been detected...

This often happens because cerebellum or dura has not been removed from wm.mgz.

This may cause recon-all to run very slowly or crash.

if so, see MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TopologicalDefect_freeview

Try following those instructions

while running recon-all on a T1.nii.gz structural scan. I read the link and it seems I have to use the wm.mgz file I get from the freesurfer run, but I was wondering if there is any preprocessing I can do to the T1 scan to prevent it? 

Thanks,

Abeoseh Flemister