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-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@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<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
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Please note that this e-mail is not secure (encrypted). If you do not wish to
continue communication over unencrypted e-mail, please notify the sender of
this message immediately. Continuing to send or respond to e-mail after
receiving this message means you understand and accept this risk and wish to
continue to communicate over unencrypted e-mail.
