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It has stalled on the fixing of topological defects. My guess is that it trying to fix a large topo defect. It may eventually fix it or it may time out. If the later, you'll have to fix it yourself by editing the wm.mgz or filled.mgz. See for example MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TopologicalDefect_freeview
Look for places where the skull stripping did not work and it is trying to place the surface around a part of the skull that is left; or maybe the cerebellum.


On 7/5/2023 4:14 AM, Rona Haker wrote:

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Hello FreeSurfer Developers,

 I'm attempting to do a full brain segmentation for a subject in my study using recon-all but after hours of running it did not reach the final step of creating aparc+aseg (the file I need), even though no error was printed. The last file that was created was 14 hours ago (till I stopped the run manually just now).

my command is: recon-all -s ./00_FSseg -i ./8_t1_mp2rage_sag_p3_iso_UNI_Images/004933_t1_mp2rage_sag_p3_iso_UNI_Images_1.dcm -openmp 8 -all

Attached is the log report of the run.

By the way, this is a subject I have tried 3 times already to segment with no success, although most subjects in my study succeeded on the first try.

 recon-all -version command outputs this:

freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c

Thank you,

Rona Haker


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