Maybe you could let us know what version of freesurfer you are running, what version of Linux or Mac OS your machine is running, and how much memory the machine has. The recon-all.log could also be useful to send along. A machine lacking resources like memory, disk space, etc., could hang.

- R.

On Dec 1, 2024, at 05:41, chemda wiener <chemda10@gmail.com> wrote:

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
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer