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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 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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