Hi Ken

If it is hanging trying to correct a defect it usually means the defect is large. This is typically the case when something else has gone wrong (skull stripping left stuff around, aseg failure, or pathology in the brain). There is a tutorial on checking for defects on our wiki

https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TopologicalDefect_tktools

but you should also load the ?h.defect_labels overlay on the ?h.inflated.nofix surface to localize the big defect

cheers

Bruce

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of KennethSPrice
Sent: Monday, June 15, 2020 4:32 AM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] recon-all hanging, how to examine defect

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Hello freesurfers,

I am running recon-all on one of my subjects and it is hanging on a defect. How do I examine the reason it is hanging? Freeview the defect? Any help would be appreciated.

Thanks,

Ken

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