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:
https://surfer.nmr.mgh.harvard.edu/fswiki/FreeviewGuide/FreeviewWorkingWithData/FreeviewSurfaces?highlight=%28defect%5C_labels%29 cheers Bruce From: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@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
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