This says the system's log: May 29 03:34:08 neuroimaging01 kernel: [234004.243039] mri_cc[13706]: segfault at c0 ip 00007fb197611194 sp 00007ffc908771b0 error 4 in libc-2.23.so[7fb1975c4000+1bf000] May 29 04:32:32 neuroimaging01 kernel: [237508.346011] mri_cc[13744]: segfault at c0 ip 00007f3509aa0194 sp 00007ffeee7af590 error 4 in libc-2.23.so[7f3509a53000+1bf000]
There are two more runs shortly before the problematic section. I will report, if the issue appears there, too. Regards, Jens Gesendet: Montag, 29. Mai 2017 um 07:41 Uhr Von: "Jens Offenbach" <wolle5...@gmx.de> An: freesurfer@nmr.mgh.harvard.edu Cc: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu> Betreff: Re: [Freesurfer] Segmentation fault (core dumped) error I am facing a similar issue with recon-all in FreeSurfer 6.0.0. on two subjects from OASIS-Brains. I will retry the run. This is the last log entry: mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /home/ubuntu/freesurfer/subjects/OAS1_0004_MR1/mri/transforms/cc_up.lta OAS1_0004_MR1 verbose diagnostics enabled... will read input aseg from aseg.auto_noCCseg.mgz writing aseg with cc labels to aseg.auto.mgz will write lta as /home/ubuntu/freesurfer/subjects/OAS1_0004_MR1/mri/transforms/cc_up.lta read 1 frames INFO: loaded talairach xform : /home/ubuntu/freesurfer/subjects/OAS1_0004_MR1/mri/transforms/talairach.xfm read 1 frames INFO: loaded talairach xform : /home/ubuntu/freesurfer/subjects/OAS1_0004_MR1/mri/transforms/talairach.xfm reading aseg from /home/ubuntu/freesurfer/subjects/OAS1_0004_MR1/mri/aseg.auto_noCCseg.mgz reading norm from /home/ubuntu/freesurfer/subjects/OAS1_0004_MR1/mri/norm.mgz allocating 28035 voxel indices... allocating 36016 voxel indices... 28035 voxels in left wm, 36016 in right wm, xrange [126, 133] searching rotation angles z=[-9 5], y=[-6 8] searching scale 1 Z rot -8.7 searching scale 1 Z rot -8.5 searching scale 1 Z rot -8.2 searching scale 1 Z rot -8.0 searching scale 1 Z rot -7.7 searching scale 1 Z rot -7.5 searching scale 1 Z rot -7.2 searching scale 1 Z rot -7.0 searching scale 1 Z rot -6.7 searching scale 1 Z rot -6.5 searching scale 1 Z rot -6.2 searching scale 1 Z rot -6.0 searching scale 1 Z rot -5.7 searching scale 1 Z rot -5.5 searching scale 1 Z rot -5.2 searching scale 1 Z rot -5.0 searching scale 1 Z rot -4.7 searching scale 1 Z rot -4.5 searching scale 1 Z rot -4.2 searching scale 1 Z rot -4.0 searching scale 1 Z rot -3.7 searching scale 1 Z rot -3.5 searching scale 1 Z rot -3.2 searching scale 1 Z rot -3.0 searching scale 1 Z rot -2.7 searching scale 1 Z rot -2.5 searching scale 1 Z rot -2.2 searching scale 1 Z rot -2.0 searching scale 1 Z rot -1.7 searching scale 1 Z rot -1.5 searching scale 1 Z rot -1.2 searching scale 1 Z rot -1.0 searching scale 1 Z rot -0.7 searching scale 1 Z rot -0.5 searching scale 1 Z rot -0.2 searching scale 1 Z rot 0.0 searching scale 1 Z rot 0.3 searching scale 1 Z rot 0.5 searching scale 1 Z rot 0.8 searching scale 1 Z rot 1.0 searching scale 1 Z rot 1.3 searching scale 1 Z rot 1.5 searching scale 1 Z rot 1.8 searching scale 1 Z rot 2.0 searching scale 1 Z rot 2.3 searching scale 1 Z rot 2.5 searching scale 1 Z rot 2.8 searching scale 1 Z rot 3.0 searching scale 1 Z rot 3.3 searching scale 1 Z rot 3.5 searching scale 1 Z rot 3.8 searching scale 1 Z rot 4.0 searching scale 1 Z rot 4.3 searching scale 1 Z rot 4.5 searching scale 1 Z rot 4.8 searching scale 1 Z rot 5.0 global minimum found at slice 129.6, rotations (1.35, -1.71) final transformation (x=129.6, yr=1.348, zr=-1.710): 0.99928 0.02984 0.02351 -7.33587; -0.02983 0.99955 -0.00070 14.98749; -0.02352 0.00000 0.99972 32.07550; 0.00000 0.00000 0.00000 1.00000; updating x range to be [126, 130] in xformed coordinates best xformed slice 128 cc center is found at 128 117 99 eigenvectors: 0.00099 0.00201 1.00000; -0.30008 -0.95391 0.00221; 0.95391 -0.30008 -0.00034; Segmentation fault (core dumped) Linux neuroimaging01 4.8.0-52-generic #55~16.04.1-Ubuntu SMP Fri Apr 28 14:36:29 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux recon-all -s OAS1_0004_MR1 exited with ERRORS at Mon May 29 04:32:32 UTC 2017 Any ideas? Regards, Jens Gesendet: Freitag, 26. Mai 2017 um 15:52 Uhr Von: "Devin Sodums" <dsodu...@jhmi.edu> An: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu> Betreff: Re: [Freesurfer] Segmentation fault (core dumped) error Sure thing, I’ll send it in a few. Thanks, Devin From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas Greve Sent: Friday, May 26, 2017 9:49 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Segmentation fault (core dumped) error No idea. Can you upload the subject so I can take a closer look? https://gate.nmr.mgh.harvard.edu/filedrop2 On 5/26/17 9:35 AM, Devin Sodums wrote: Hello FreeSurfer developers, I’m attempting to run recon-all on a T1 image and keep getting the same error message: Segmentation fault (core dumped) The recon-all seems to crash when running mris_volmask. I’m not sure what the problem is, as I have ran recon-all successfully on over 50 similar T1 files. I have searched for this error on the list serv and see that it can happen due to low memory. I have tried running the recon-all alone, without any other ones, and still have had the same issue. Is there any other possible fix I could look into? I have attached the recon-all.log file, and here is my operating system info from the VirtualBox Ubuntu system I am using: Linux xubuntu-VirtualBox 3.2.0-23-generic #36-Ubuntu SMP Tue Apr 10 20:41:14 UTC 2012 i686 i686 i386 GNU/Linux FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 Thank you, Devin Sodums _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu[mailto:Freesurfer@nmr.mgh.harvard.edu] https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer[https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer] _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer[https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer][https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer[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. 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