Hi Stephan

I think there has always been topology fixing. The ?h.orig should be created prior to the fixing then corrected I believe, but if you have big topological defects you probably want to figure out why and correct them. Have you visualize the ?h.inflated.nofix or the ?h.orig.nofix? If they are taking forever it means something big went wrong like the cerebellum or large pieces of the skull are attached.

Cheers Bruce

From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Stephan Wunderlich Sent: Tuesday, April 20, 2021 2:46 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] -nofix topology command

External Email - Use Caution Dear all,

I want to run recon-all with the -nofix command, so that no fix of the topology is done, because it takes too much time or never finishes. Especially these commands in the recon-all.log file never finish.

PIDs (232383 232386)…

But sometimes when I run recon-all with -nofix the surf/xh.orig files are not created since this is done by the fix topology command. Is there way to still create these files without fixing the topology of the brain so that recon-all finished successfully?

I remember that in older version of freesurfer there was not fix topology and it worked as well.

Best, Stephan