That is a pretty big defect. Have you looked at the images to see if the cerebellum is attached? Or perhaps a large part of the skull or dura?
On 12/21/2017 06:44 AM, Daan de Jong wrote:
Hello FreeSurfer Developers,
I'm attempting to run recon-all on a MPRAGE acquisition (just a single one), and for many subjects the process gets killed during the mris_fix_topology script. An example of the message I get:
CORRECTING DEFECT 5 (vertices=22062, convex hull=4299, v0=4005)
Killed
Linux RAD-MEMORYCL
Recon-all –s PINxxx_t0 exited with ERRORS at Tue Dec 19 07:14:34 CET 2017
I've searched the list and no similar errors have been reported. Does anyone have any thoughts on how to trouble-shoot this one? Also, I’ve attached the recon-all.log in case it's of any use.
FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0
Platform: CentOS release 6.8 (Final)
uname -a: Linux RAD-MEMORYCL004 2.6.32-642.1.1.el6.x86_64 #1 SMP
Tue May 31 21:57:07 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux
- recon-all.log: see attached
With kind regards,
*Daan de Jong, MSc*
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer