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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
https://secure-web.cisco.com/19E3rIjqpc70fHmEHToyw2VjL4giqi0PVTvYU058m8nuTFYLrbpj4F-S2oOIlwvDHVvYzO5r-86GBnDFot4dKd0HrVam8i9PxOVdG8x2l1Ark_2qtHh5RvV98PAmIRrybABZcDYsPmKDvYlXl-k2uYA0MhLwFZOOMjmwbHZt7nebfHOa6xmhD26IFmZSGgrM8LBFyVFVERHM3EzU2CzCJ2qBdqnYY643pNCyD7j_Fh45KXJs4jUJPlJTxxgEoNpObdbeVIX9Kg_CwSvFTgMTWoA/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FTopologicalDefect_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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