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-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@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
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