Hi Chemda
Usually that means something big has gone wrong in the segmentation or skull stripping (like the cerebellum is still attached to a cortical hemisphere in the wm.mgz or the skull is or something like that).
More generally this happens when there is a topological defect that is too big to automatically correct in a reasonable amount of time. You can visualize the defects following the instructions here:
cheers
Bruce
From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu>
On Behalf Of chemda wiener
Sent: Sunday, December 1, 2024 5:41 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Fwd: recon-all command stuck before creating pial files
External Email - Use Caution
Hi,
My name is Chemda Wiener. I am a PhD student in a Neuro-Engineering lab. We are working with MRI scans of patients with epilepsy and I am attempting to use freesurfer to create the mesh .pial files. When I run the freesurfer recon-all command,
the command gets stuck at "correcting defects" with the last file it creates being the "lh.defect_chull". It has been stuck for a few days on this part until I finally killed the process. I tried running autorecon2 afterwards on this patient to see if it can
pick up from where it stopped but it gets stuck again at the same place.
I would appreciate any help in the matter.
Thank you in advance for your time and your software!
Chemda