hmmm, if you tar and gzip that subject and upload it to our ftp site we
will see if we can replicate the problem
On Mon, 29 May 2017, Jens Offenbach
wrote:
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
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The information in this e-mail is intended only for the person to whom it is
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contains patient information, please contact the Partners Compliance HelpLine at
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