From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of KennethSPrice
Sent: Sunday, September 17, 2023 11:35 AM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] mri_convert: Segmentation fault (core dumped) synthsr scan

I've set the coredumpsize to unlimited, and still get the same error. Could it be something with the installation? 

 

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------- Original Message -------
On Saturday, September 16th, 2023 at 9:49 PM, fsbuild <fsbuild@contbay.com> wrote:

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Hello Ken,

 

The output from your linux shell limits in the log show the following,

 

cputime      unlimited

filesize     unlimited

datasize     unlimited

stacksize    8192 kbytes

coredumpsize 0 kbytes

memoryuse    unlimited

vmemoryuse   unlimited

descriptors  1024 

memorylocked 64 kbytes

maxproc      7823 

maxlocks     unlimited

maxsignal    7823 

maxmessage   819200 

maxnice      0 

maxrtprio    0 

maxrttime    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.   By default the limits on my Ubuntu 22 system are:

 

$ ulimit -a

real-time non-blocking time  (microseconds, -R) unlimited

core file size              (blocks, -c) unlimited

data seg size               (kbytes, -d) unlimited

scheduling priority                 (-e) 0

file size                   (blocks, -f) unlimited

pending signals                     (-i) 378881

max locked memory           (kbytes, -l) 64

max memory size             (kbytes, -m) unlimited

open files                          (-n) 1048576

pipe size                (512 bytes, -p) 8

POSIX message queues         (bytes, -q) 819200

real-time priority                  (-r) 0

stack size                  (kbytes, -s) 8192

cpu time                   (seconds, -t) unlimited

max user processes                  (-u) unlimited

virtual memory              (kbytes, -v) unlimited

file locks                          (-x) unlimited

 

You can try setting the core file size to unlimited with,

 

$ ulimit -c unlimited

... then check the value was changed to something > 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  again to see if you can retrieve a core dump file.

 

- R.

On Sep 16, 2023, at 09:55, KennethSPrice <KennethSPrice@protonmail.com> wrote:

 

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OK, I've attached the log file. 

 

------- Original Message -------
On Friday, September 15th, 2023 at 2:59 PM, fsbuild <fsbuild@contbay.com> wrote:

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 It might help if you could send along the crash report as an attachment..

 

-R.

On Sep 15, 2023, at 14:36, KennethSPrice <KennethSPrice@protonmail.com> wrote:

 

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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. 

 

Thanks,

K

------- Original Message -------
On Thursday, September 14th, 2023 at 10:41 PM, KennethSPrice <KennethSPrice@protonmail.com> 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? 

 

Thanks,

Ken

 

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