New subject: mri_convert: Segmentation fault (core dumped) synthsr scan

16 Sep 2023


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Hello Ken,
The output from your linux shell limits in the log show the following,
cputime&nbsp; &nbsp; &nbsp; unlimitedfilesize&nbsp; &nbsp; &nbsp;unlimiteddatasize&nbsp; &nbsp; &nbsp;unlimitedstacksize&nbsp; &nbsp; 8192 kbytescoredumpsize 0 kbytesmemoryuse&nbsp; &nbsp; unlimitedvmemoryuse&nbsp; &nbsp;unlimiteddescriptors&nbsp; 1024&nbsp;memorylocked 64 kbytesmaxproc&nbsp; &nbsp; &nbsp; 7823&nbsp;maxlocks&nbsp; &nbsp; &nbsp;unlimitedmaxsignal&nbsp; &nbsp; 7823&nbsp;maxmessage&nbsp; &nbsp;819200&nbsp;maxnice&nbsp; &nbsp; &nbsp; 0&nbsp;maxrtprio&nbsp; &nbsp; 0&nbsp;maxrttime&nbsp; &nbsp; unlimited
I would set at least coredumpsize to something non-zero so you can at least get a core file saved that could be looked at.&nbsp; &nbsp;By default the limits on my Ubuntu 22 system are:
$ ulimit -areal-time non-blocking time&nbsp; (microseconds, -R) unlimitedcore file size&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; (blocks, -c) unlimiteddata seg size &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; (kbytes, -d) unlimitedscheduling priority &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; (-e) 0file size &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; (blocks, -f) unlimitedpending signals &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; (-i) 378881max locked memory &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; (kbytes, -l) 64max memory size &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; (kbytes, -m) unlimitedopen files&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; (-n) 1048576pipe size&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; (512 bytes, -p) 8POSIX message queues &nbsp; &nbsp; &nbsp; &nbsp; (bytes, -q) 819200real-time priority&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; (-r) 0stack size&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; (kbytes, -s) 8192cpu time &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; (seconds, -t) unlimitedmax user processes&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; (-u) unlimitedvirtual memory&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; (kbytes, -v) unlimitedfile locks&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; (-x) unlimited
You can try setting the core file size to unlimited with,
$ ulimit -c unlimited... then check the value was changed to something &gt; 0 ...$ ulimit -a
You could increase memory size (and as many shell limits as possible) to unlimited to get the max size allowed by the system in the script you use to run recon-all, and then try running recon-all&nbsp; again to see if you can retrieve a core dump file.
- R.
On Sep 16, 2023, at 09:55, KennethSPrice &lt;KennethSPrice@protonmail.com&gt; wrote:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;External Email - Use Caution&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;OK, I've attached the log file.&nbsp;------- Original Message -------On Friday, September 15th, 2023 at 2:59 PM, fsbuild &lt;fsbuild@contbay.com&gt; wrote:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;External Email - Use Caution&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;It might help if you could send along the crash report as an attachment..-R.On Sep 15, 2023, at 14:36, KennethSPrice &lt;KennethSPrice@protonmail.com&gt; wrote:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;External Email - Use Caution&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Update: I tried running recon-all (5.1, ubuntu 18) on a sample MPRAGE scan and got the "mri_convert: segmentation fault (core dumped)" error again. Any clarity on this issue would be appreciated.&nbsp;Thanks,K------- Original Message -------On Thursday, September 14th, 2023 at 10:41 PM, KennethSPrice &lt;KennethSPrice@protonmail.com&gt; wrote:Howdy yall,I ran a subject through synthsr (freesurfer 7.4) and am trying to run the output through the freesurfer 5.1 pipeline (the rest of my dataset was processed with 5.1). I am getting the error "Segmentation fault (core dumped)" during the mri_convert step. Any suggestions?&nbsp;Thanks,Ken_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer%3Crecon-all.log... mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] mri_convert: Segmentation fault (core dumped) synthsr scan