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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
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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