External Email - Use Caution
I've set the coredumpsize to unlimited, and still get the same error. Could it
be something with the installation?
build-stamp.txt: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0
Linux DESKTOP-MRI 4.4.0-19041-Microsoft #3393-Microsoft Mon Aug 14 14:52:00 PST
2023 x86_64 x86_64 x86_64 GNU/Linux
cputime unlimited
filesize unlimited
datasize unlimited
stacksize 8192 kbytes
coredumpsize unlimited
memoryuse unlimited
vmemoryuse unlimited
descriptors 1024
memorylocked 64 kbytes
maxproc 7823
maxlocks unlimited
maxsignal 7823
maxmessage 819200
maxnice 0
maxrtprio 0
maxrttime unlimited
total used free shared buff/cache available
Mem: 16643620 4264632 12149636 17720 229352 12245256Swap: 29192228 0 29192228
------- Original Message -------
On Saturday, September 16th, 2023 at 9:49 PM, fsbuild <fsbu...@contbay.com>
wrote:
> External Email - Use Caution
>
> 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 <kennethspr...@protonmail.com>
>> wrote:
>>
>> External Email - Use Caution
>>
>> OK, I've attached the log file.
>>
>> ------- Original Message -------
>> On Friday, September 15th, 2023 at 2:59 PM, fsbuild <fsbu...@contbay.com>
>> wrote:
>>
>>> External Email - Use Caution
>>>
>>> It might help if you could send along the crash report as an attachment..
>>>
>>> -R.
>>>
>>>> On Sep 15, 2023, at 14:36, KennethSPrice <kennethspr...@protonmail.com>
>>>> wrote:
>>>>
>>>> External Email - Use Caution
>>>>
>>>> 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
>>>> <kennethspr...@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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