Hi Jon - I suspect that the source of the problem is before the -path step, but your trac-all.log only has output from that step. Did you by any chance move the original trac-all.log file somewhere else? Typically with every new invocation of trac-all the new output is just appended at the end of the log file.

a.y

________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Whitney, Jon jon.whitney@ert.com Sent: Monday, October 29, 2018 4:59:17 PM To: freesurfer@nmr.mgh.harvard.edu Cc: Walia, Piyush Subject: Re: [Freesurfer] Segmentation fault

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I got someone to help me, and based on what they told me the trac-all.log is where the debug information gets stored (I tried using -x +x in my bash command script and it only gave me upper level debugging information), so I have attached the trac-all.log file. I also was able to get help from someone who was able to save the core dump for when the system crashed, but it is extremely large (1.7GB). I can upload the core dump file if that would be helpful. I watched the system resources while the program ran, and I noticed that the memory usage only got up to 4% while the CPU usage was 100%, so I don't think I'm running out of memory. We looked at the core dump file, and my linux expert friend suggested that it may be a memory overflow error because it references memory at 0x0000000etc.

[image.png] unfortunately, without the source code to help us interpret the core dump, I don't think I can provide much more in the way of specific information. Please let me know if there's somewhere I can upload the core dump if you want to look at it.

Thanks!

On Mon, Oct 29, 2018 at 1:32 AM fsbuild <fsbuild@contbay.commailto:fsbuild@contbay.com> wrote:

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Hello Jon,

Can you get any stack or backtrace information after the segfault occurs ?, e.g., Mac OS has the option to display the crash report with a trace. On Linux you could run thru gdb and get a back trace. This would help us to see where the code is exiting.

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Hi Jon – This log file also has output only from trac-all –path, and not from trac-all –prep. I’ll have to see the output from all steps. Thanks!

a.y

From: <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of "Whitney, Jon" <jon.whitney@ert.commailto:jon.whitney@ert.com> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Wednesday, October 31, 2018 at 9:57 AM To: "freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Segmentation fault

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Yes, here is the log file.

Thanks for your help!

-Jon

On Tue, Oct 30, 2018 at 5:34 PM Yendiki, Anastasia <AYENDIKI@mgh.harvard.edumailto:AYENDIKI@mgh.harvard.edu> wrote:

Hi Jon - I suspect that the source of the problem is before the -path step, but your trac-all.log only has output from that step. Did you by any chance move the original trac-all.log file somewhere else? Typically with every new invocation of trac-all the new output is just appended at the end of the log file.

a.y

________________________________ From:freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Whitney, Jon <jon.whitney@ert.commailto:jon.whitney@ert.com> Sent: Monday, October 29, 2018 4:59:17 PM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Cc: Walia, Piyush Subject: Re: [Freesurfer] Segmentation fault

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I got someone to help me, and based on what they told me the trac-all.log is where the debug information gets stored (I tried using -x +x in my bash command script and it only gave me upper level debugging information), so I have attached the trac-all.log file. I also was able to get help from someone who was able to save the core dump for when the system crashed, but it is extremely large (1.7GB). I can upload the core dump file if that would be helpful. I watched the system resources while the program ran, and I noticed that the memory usage only got up to 4% while the CPU usage was 100%, so I don't think I'm running out of memory. We looked at the core dump file, and my linux expert friend suggested that it may be a memory overflow error because it references memory at 0x0000000etc.

[image.png] unfortunately, without the source code to help us interpret the core dump, I don't think I can provide much more in the way of specific information. Please let me know if there's somewhere I can upload the core dump if you want to look at it.

Thanks!

On Mon, Oct 29, 2018 at 1:32 AM fsbuild <fsbuild@contbay.commailto:fsbuild@contbay.com> wrote:

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Hello Jon,

Can you get any stack or backtrace information after the segfault occurs ?, e.g., Mac OS has the option to display the crash report with a trace. On Linux you could run thru gdb and get a back trace. This would help us to see where the code is exiting.

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

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Jon Whitney Image Analysis Engineer ERT | 26801 Miles Rd | Cleveland, OH 44128 | USA ert.com

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Notice: This e-mail message, together with any attachments, contains information of ERT that may be confidential, proprietary copyrighted and/or legally privileged, and is intended solely for the use of the individual or entity named on this message. If you are not the intended recipient, and have received this message in error, please immediately return this by e-mail and then delete it. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Jon Whitney Image Analysis Engineer ERT | 26801 Miles Rd | Cleveland, OH 44128 | USA ert.com

https://www.ert.com/ [http://signature.ert.com/uc/5ae1cd7003abc93ec2b1d227/img]http://signature.ert.com/uc/5ae1cd7003abc93ec2b1d227

Notice: This e-mail message, together with any attachments, contains information of ERT that may be confidential, proprietary copyrighted and/or legally privileged, and is intended solely for the use of the individual or entity named on this message. If you are not the intended recipient, and have received this message in error, please immediately return this by e-mail and then delete it.

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Update - Segmentation fault

I think I have finally found the issue. The bvec files I uploaded actually contained only zeroes for each bvec value, and that made it impossible for Tracula to function properly. This was a result of the original files we were given having empty header data. We have been able to locate the original bvec values and it appears as though everything is working now.

Thanks for your help!!

On Wed, Oct 31, 2018 at 10:55 AM Whitney, Jon jon.whitney@ert.com wrote:

I probably deleted the log file prior to running the path step so I could focus on what was going on. I'll re-run it and give you the results when it finishes.

Thanks!