Segmentation fault (core dumped) error

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Devin Sodums

26 May 2017 26 May '17

9:35 a.m.

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

Attachments:

attachment.html (text/html — 3.3 KB)
recon-all.log (application/octet-stream — 311.4 KB)

Show replies by date

Douglas Greve

26 May 26 May

9:49 a.m.

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 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Devin Sodums

9:52 a.m.

Sure thing, I'll send it in a few. Thanks, Devin

From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@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)

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.edumailto:Freesurfer@nmr.mgh.harvard.edu

https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Jens Offenbach

29 May 29 May

1:41 a.m.

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" dsodums1@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

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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer%5Bhttps://mail....] 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%5Bhttp://www.partners.org/compliancel...] . 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.

Jens Offenbach

2:02 a.m.

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" wolle5050@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

recon-all -s OAS1_0004_MR1 exited with ERRORS at Mon May 29 04:32:32 UTC 2017

Any ideas?

Regards, Jens

Sure thing, I’ll send it in a few. Thanks, Devin

_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu[mailto:Freesurfer@nmr.mgh.harvard.edu] https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer%5Bhttps://mail....] _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer%5Bhttps://mail....]] 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%5Bhttp://www.partners.org/compliancel...]] . 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.

_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer%5Bhttps://mail....]

Bruce Fischl

10:32 a.m.

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" wolle5050@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" dsodums1@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-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@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%5Bhttps://mail....] _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer%5Bhttps://mail....]] 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%5Bhttp://www.partners.org/compliancel...]] . 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.

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer%5Bhttps://mail....]

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Jens Offenbach

2:49 p.m.

I have created the archive "OAS1_0004_MR1.tar.gz" and uploaded it onto our server in the folder "transfer/incoming".

The folder "RAW" contains the original images provided by OASIS (Brains) http://www.oasis-brains.org/. I converted them via "mri_convert" to the files listed in the folder "mri". Maybe the problem is caused here?

I will try to rerun the recon-all analysis of this subject.

Thank you very much for your help!

Regards, Jens

Gesendet: Montag, 29. Mai 2017 um 16:32 Uhr Von: "Bruce Fischl" fischl@nmr.mgh.harvard.edu An: "Freesurfer support list" freesurfer@nmr.mgh.harvard.edu Betreff: Re: [Freesurfer] Segmentation fault (core dumped) error 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" wolle5050@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" dsodums1@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-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@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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participants (4)

Bruce Fischl
Devin Sodums
Douglas Greve
Jens Offenbach