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()

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/

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