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_freev...https://secure-web.cisco.com/1kY22AwBCARfSQUY7cjfeplC3gw9EQSf1L_ErLh8Y6XncMttzSfui32YtKdC8yzeSGA6EvSJzqGrvVh45T_FOBdeGPtikP-NnKxpiuzQAOS5tZARwjSTPVZYPUvsVpk7ehOFT9Oj2jScxguAwyxvMsa5Ge1SkwNewJ8RW1choweXRNZRr6STkkSqSWWzUqE0t0gDEEsfue7cWQx1jxNHhXK1KtH3yVAn-tF2IrM-QJwqj3kgXKSC5pm4YF366jYShQnEX3r_BOFvobrwUavi11j2F_tlUUuEXVH0AwpDgFHpiX1UuTurUiRpLYHEKioSDNXUeFWxrtz_Kl_oCjrfr3Q/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FTopologicalDefect_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