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. > > 1) FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0 > > 2) Platform: CentOS release 6.8 (Final) > > 3) 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 > > 4) 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 -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
