I’m not sure what the cause of this would be, unfortunately. The matlab runtime
library errors become very difficult to track down. One thing you could do is
try to run this in a singularity or docker container, if available on your
cluster. You could use centos7 as the base image, and mount the paths to your
freesurfer installation and your input/output data.
Andrew
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Caitlin R Bowman
<bowm...@uwm.edu>
Date: Wednesday, March 9, 2022 at 12:57 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Hippocampal segmentation Matlab crash
External Email - Use Caution
Tried it, but I still get the same error.
--
Caitlin Bowman, Ph.D.
Assistant Professor of Psychology
University of Wisconsin-Milwaukee
From: <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of "Hoopes, Andrew"
<ahoo...@mgh.harvard.edu>
Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date: Tuesday, March 8, 2022 at 3:18 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Hippocampal segmentation Matlab crash
Hi Cait,
Before running the command, can you try unsetting the LD_LIBRARY_PATH variable?
You can do this in bash with:
unset LD_LIBRARY_PATH
or in cshell with:
unsetenv LD_LIBRARY_PATH
best,
Andrew
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Caitlin R Bowman
<bowm...@uwm.edu>
Date: Tuesday, March 8, 2022 at 3:14 PM
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] Hippocampal segmentation Matlab crash
External Email - Use Caution
Hello,
I am trying to run the hippocampal segmentation used in freesurfer 7. I have
tried with both 7.1.1 and 7.2 and have run into an issue at the same spot. I am
running on a computing cluster, not locally. The same code works fine on my
local computer. The managers of the computing cluster have tried to help but
are stuck themselves. Find the command that I run below followed by the full
error log.
Best,
Cait
Command:
segmentHA_T2.sh sub-110033 $ANATDIR/sub-110033_T2w.nii.gz T2 0
Error log:
------------------------------
USER bowman2
HOST compute-081.mortimer
PROCESSID 11325
PROCESSOR x86_64
OS Linux
Linux compute-081.mortimer 3.10.0-1160.49.1.el7.x86_64 #1 SMP Tue Nov 30
15:51:32 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux
------------------------------
#--------------------------------------------
#@# Hippocampal Subfields processing (T2) left Thu Feb 24 14:14:35 CST 2022
------------------------------------------
Setting up environment variables
---
LD_LIBRARY_PATH is
.:/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84//runtime/glnxa64:/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84//bin/glnxa64:/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84//sys/os/glnxa64:/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/server:/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/client:/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64:/sharedapps/LS/psych_imaging/fsl/6.0.4/lib:/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84/sys/os/glnxa64::/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84/bin/glnxa64:/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84/runtime/glnxa64:/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/lib/vtk/lib/vtk-5.6/:/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/lib/tcltktixblt/lib/:/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/lib/KWWidgets/lib/KWWidgets:/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/mni/lib:/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/lib
------------------------------------------------------------------------
std::terminate() detected at Thu Feb 24 14:14:37 2022
------------------------------------------------------------------------
Configuration:
Crash Decoding : Disabled
Default Encoding : UTF-8
GNU C Library : 2.17 stable
MATLAB Architecture: glnxa64
MATLAB Root :
/raid-07/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84
MATLAB Version : 8.4.0.150421 (R2014b)
Operating System : Linux 3.10.0-1160.49.1.el7.x86_64 #1 SMP Tue Nov 30
15:51:32 UTC 2021 x86_64
Processor ID : x86 Family 6 Model 63 Stepping 2, GenuineIntel
Fault Count: 1
Abnormal termination:
std::terminate()
Register State (captured):
RAX = 0000000000000000 RBX = 00002baa657204e8
RCX = 0000000000000000 RDX = 00002baa6570f758
RSP = 00002baa93ffb0b0 RBP = 00002baa93ffb470
RSI = 00002baa654c3fb3 RDI = 00002baa93ffb0c0
R8 = 0000000000000000 R9 = 00002baa60271f90
R10 = 0000000000000000 R11 = 0000000000000000
R12 = 00002baa65730520 R13 = 00002baa93ffc0b0
R14 = 00002baa93ffc090 R15 = 00002baa93ffc470
RIP = 00002baa65422f4e EFL = 0000000000000000
CS = 0000 FS = 0000 GS = 0000
Stack Trace (captured):
[ 0] 0x00002baa65422f4e
/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84//bin/glnxa64/libmwfl.so+00966478
_ZN2fl4diag5linux12context_base12capture_dataEv+00000030
[ 1] 0x00002baa65420424
/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84//bin/glnxa64/libmwfl.so+00955428
[ 2] 0x00002baa740ef0f5
/raid-07/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84/bin/glnxa64/libmwmcr.so+00868597
[ 3] 0x00002baa740f12ca
/raid-07/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84/bin/glnxa64/libmwmcr.so+00877258
[ 4] 0x00002baa740f13c1
/raid-07/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84/bin/glnxa64/libmwmcr.so+00877505
[ 5] 0x00002baa740f1743
/raid-07/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84/bin/glnxa64/libmwmcr.so+00878403
[ 6] 0x00002baa740f17b3
/raid-07/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84/bin/glnxa64/libmwmcr.so+00878515
[ 7] 0x00002baa5ffe4a06
/lib64/libstdc++.so.6+00387590
[ 8] 0x00002baa5ffe4a33
/lib64/libstdc++.so.6+00387635
[ 9] 0x00002baa5ffe4c53
/lib64/libstdc++.so.6+00388179
[ 10] 0x00002baa60fe3822
/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84//bin/glnxa64/libmwi18n.so+00325666
_ZN2fl4i18n14MessageCatalog17GetMessageCatalogERKNS0_9CatalogIDERKNS0_8MwLocaleE+00001186
[ 11] 0x00002baa60fe4113
/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84//bin/glnxa64/libmwi18n.so+00327955
_ZN2fl4i18n14MessageCatalog11get_messageERKN13resource_core9BaseMsgIDERKNS0_8MwLocaleE+00000051
[ 12] 0x00002baa6589bf57
/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84//bin/glnxa64/libmx.so+01482583
[ 13] 0x00002baa6589ae6f
/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84//bin/glnxa64/libmx.so+01478255
[ 14] 0x00002baa65832a44
/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84//bin/glnxa64/libmx.so+01051204
_Z14mxWarningMsgIdRKN13resource_core9BaseMsgIDE+00000052
[ 15] 0x00002baa74443a95
/raid-07/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84/bin/glnxa64/libmwjmi.so+01100437
[ 16] 0x00002baa74443d2f
/raid-07/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84/bin/glnxa64/libmwjmi.so+01101103
_Z50mljInitFirstCrackSignalHandlerIfJavaAlreadyStartedv+00000015
[ 17] 0x00002baa740c5855
/raid-07/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84/bin/glnxa64/libmwmcr.so+00698453
[ 18] 0x00002baa740b64ec
/raid-07/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84/bin/glnxa64/libmwmcr.so+00636140
[ 19] 0x00002baa740a2cdd
/raid-07/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84/bin/glnxa64/libmwmcr.so+00556253
[ 20] 0x00002baa607adea5
/lib64/libpthread.so.0+00032421
[ 21] 0x00002baa60ac0b0d
/lib64/libc.so.6+01043213 clone+00000109
If this problem is reproducible, please submit a Service Request via:
MailScanner has detected a possible fraud attempt from
"secure-web.cisco.com" claiming to be
http://www.mathworks.com/support/contact_us/<https://secure-web.cisco.com/1sWwW4ZPn37eyMEn2XV0J_7cDBgIf6OqYIkEUaQB3x0FDiNqshbYvtFDuwcDUcIose8Wg091GkCg3PkVPu0Rs9gOwF8cm6lChaBtVIS3Y1Qe471Ax485MNHwbb1wOSqpsi0-EEZeWWl6FbiCXPcQPjiLlzkcktM8kFK1Njc53ueuwl_Vcasi_q4_9Soj7P6lDUxG3RfHxKkDr5Zsm1FHAZLj2_PMeL6_Z4S80622FRNP6MGGqqUWx1U9BqsbkErXPTq5tPpX_4UsgkR0L5ztNV3HV_t-XxaZDcon2rOT6PHKvmBEYpCZNXVSjvFeOFGsqWBGEQpeExY1-Y0VAEDv_Pw/https%3A%2F%2Fnam02.safelinks.protection.outlook.com%2F%3Furl%3Dhttp%253A%252F%252Fsecure-web.cisco.com%252F1RD2fc7k7E8B1e1GuwRGzMU8V8DVzFuosUwM0pYlETnQWtEx6xRP1hZXV9KgVWbTmwwZ6rjxCui7a7Z1iml5v4TaNl4xnmf89gqHycFhq0I71youH1AF-OklX-cGCU70_6yLlyHTdS4pZFbhCHYWBJQt6X2U7ZXI3UECoW6vcvCodWKtq9E-Sxq57idxwYw11q4aezRUNuI5snvLBC2EGuLySL_fm_11CQ-9ND-3sLMGbHxFrpqGHKvtEhEI2yO3jaHOn_lHaG1qvz9dtLHB_nlwHd_HhZWFE7Cnufl25py4DZb6ZkjgkZ400ZzpsS6ntmhSWKmJ9uOlGM2lAk-YgJA%252Fhttp%25253A%25252F%25252Fwww.mathworks.com%25252Fsupport%25252Fcontact_us%25252F%26data%3D04%257C01%257Cbowman2%2540uwm.edu%257C9df12445484b4d5d9c3508da014923f3%257C0bca7ac3fcb64efd89eb6de97603cf21%257C0%257C0%257C637823710900179724%257CUnknown%257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%253D%257C3000%26sdata%3DzC2Pqg5dqmsfJaEg1%252FQGAimbmtvL%252FfXBihNRb%252Bs%252Fljw%253D%26reserved%3D0>
A technical support engineer might contact you with further information.
Thank you for your help.** This crash report has been saved to disk as
/home/bowman2/matlab_crash_dump.11396-1 **
MATLAB is exiting because of fatal error
/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/bin/run_segmentSubjectT2_autoEstimateAlveusML.sh:
line 40: 11396 Killed
/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/bin/segmentSubjectT2_autoEstimateAlveusML
sub-CC110037 /home/bowman2/Data/camcan/fs_camcan/
/raid-18/LS/bowman2/camcan/imaging/anat/sub-CC110037/sub-CC110037_T2w.nii.gz
0.333333333333333333333333333333333333
/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/average/HippoSF/atlas/AtlasMesh.gz
/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/average/HippoSF/atlas/AtlasDump.mgz
/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/average/HippoSF/atlas/compressionLookupTable.txt
0.05 left L-BFGS v21 T2
'/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/bin/fs_run_from_mcr
/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/bin/' 0 1 0
@#@FSTIME 2022:02:24:14:14:35 run_segmentSubjectT2_autoEstimateAlveusML.sh N
18 e 1.65 S 0.13 U 1.19 P 80% M 67608 F 0 R 19447 W 0 c 32 w 559 I 0 O 84720 L
5.00 5.06 4.81
@#@FSLOADPOST 2022:02:24:14:14:37 run_segmentSubjectT2_autoEstimateAlveusML.sh
N 18 5.00 5.06 4.81
Linux compute-081.mortimer 3.10.0-1160.49.1.el7.x86_64 #1 SMP Tue Nov 30
15:51:32 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux
T2 hippocampal subfields exited with ERRORS at Thu Feb 24 14:14:37 CST 2022
--
Caitlin Bowman, Ph.D.
Assistant Professor of Psychology
University of Wisconsin-Milwaukee
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