External Email - Use Caution
Dear J
How much RAM memory do you have?
Andrew: do you think this might be the problem?
Cheers
E
Sent from my phone, please excuse brevity and typos
________________________________
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of 오진영
<jinyoung.oh...@gmail.com>
Sent: Tuesday, October 30, 2018 5:51:22 AM
To: Freesurfer support list
Subject: [Freesurfer] error in hippocampal subfields and nuclei of amygdala
segmentation
External Email - Use Caution
Dear freesurfer experts,
I'm trying to run segmentation of hippocampal subfields and nuclei of amygdala
with segmentHA_T1.sh command.
I already run segmentation of hippocampal subfields and nuclei of amygdala
several times, however, after segment nuclei of amygdala in left hemisphere and
before segment nuclei of amygdala in right hemisphere, there appears same error
"MATLAB is exiting because of fatal error" and hippocampal subfields
segmentation stops.
Ignoring and Trying the same command few more times, I can make it to segment
subfields of amygdala, but I am still wondering if I can run segmentHA_T1.sh
without any error.
Following is the repeated error with the few lines:
#--------------------------------------------
#@# Hippocampal Subfields processing (T1) right 2018년 10월 30일 화요일 14시 07분 17초
KST
------------------------------------------
Setting up environment variables
---
DYLD_LIBRARY_PATH is
.:/Applications/freesurfer/MCRv84//runtime/maci64:/Applications/freesurfer/MCRv84//bin/maci64:/Applications/freesurfer/MCRv84//sys/os/maci64:/Applications/freesurfer/lib/gcc/lib:
PostVMInit failed to initialize com.mathworks.mwswing.MJStartupForDesktop
------------------------------------------------------------------------
Segmentation violation detected at Tue Oct 30 14:07:20 2018
------------------------------------------------------------------------
Configuration:
Crash Decoding : Disabled
Current Visual : Quartz
Default Encoding : US-ASCII
MATLAB Architecture: maci64
MATLAB Root : /Applications/freesurfer/MCRv84
MATLAB Version : 8.4.0.150421 (R2014b)
Operating System : Darwin 17.7.0 Darwin Kernel Version 17.7.0: Thu Jun 21
22:53:14 PDT 2018; root:xnu-4570.71.2~1/RELEASE_X86_64 x86_64
Processor ID : x86 Family 6 Model 158 Stepping 9, GenuineIntel
Software OpenGL : 0
Virtual Machine : Java 1.7.0_55-b13 with Oracle Corporation Java
HotSpot(TM) 64-Bit Server VM mixed mode
Window System : Quartz
Fault Count: 2
Abnormal termination:
Segmentation violation
Register State (from fault):
RAX = 00007fafcba4f000 RBX = 00007fafcba4f000
RCX = 000070000cdf72d0 RDX = 0000000111cba97e
RSP = 00007fafcba4f000 RBP = 00009b630cdf72d0
RSI = 00007fafcdb8a9b0 RDI = 0000000000000000
R8 = 00007fafcc2dc270 R9 = 00007fafcba4f000
R10 = 000000011bd1f76a R11 = 0000000000000000
R12 = 000070000cdf7330 R13 = 0000000111b083c7
R14 = 000070000cdf73a0 R15 = 000000011bd1f777
RIP = 0000000116ca6f40 RFL = 00007fafcc2dc270
CS = 00009b6300305bc3 FS = 000000011bd1f76a GS = 00007fafcba4f1e8
Stack Trace (from fault):
[ 0] 0x0000000105f76e64
/Applications/freesurfer/MCRv84//bin/maci64/libmwfl.dylib+00028260
_ZN2fl4diag15stacktrace_base7captureERKNS0_14thread_contextEm+00000052
[ 1] 0x0000000105f7aa2a
/Applications/freesurfer/MCRv84//bin/maci64/libmwfl.dylib+00043562
_ZN2fl4test17terminate_handledEv+00000906
[ 2] 0x0000000105f7a477
/Applications/freesurfer/MCRv84//bin/maci64/libmwfl.dylib+00042103
_ZN2fl4diag13terminate_logEPKcPK17__darwin_ucontext+00000119
[ 3] 0x000000010d041b7a
/Applications/freesurfer/MCRv84//bin/maci64/libmwmcr.dylib+00387962
_Z32mnRunPathDependentInitializationv+00003146
[ 4] 0x000000010d041e58
/Applications/freesurfer/MCRv84//bin/maci64/libmwmcr.dylib+00388696
_Z32mnRunPathDependentInitializationv+00003880
[ 5] 0x000000010d03f733
/Applications/freesurfer/MCRv84//bin/maci64/libmwmcr.dylib+00378675
mnFatalSignalHandler+00000275
[ 6] 0x00007fff74b75f5a
/usr/lib/system/libsystem_platform.dylib+00008026 _sigtramp+00000026
[ 7] 0x0000000111b096f8
/Applications/freesurfer/MCRv84/sys/java/jre/maci64/jre//lib/server/libjvm.dylib+03192568
_ZN23JNI_ArgumentPusherVaArg7iterateEy+00000000
[ 8] 0x0000000111af9d67
/Applications/freesurfer/MCRv84/sys/java/jre/maci64/jre//lib/server/libjvm.dylib+03128679
jni_GetMethodID+00000126
[ 9] 0x00000001104dd271
/Applications/freesurfer/MCRv84//bin/maci64/libmwjmi.dylib+00160369
_Z12mljGetMethodP7_jclassPKcS2_+00000049
[ 10] 0x000000011b57a366
/Applications/freesurfer/MCRv84//bin/maci64/libmwhg.dylib+00598886
_ZN2ui14JavaScreenData20getPrimaryScreenRectEv+00000150
[ 11] 0x000000011b57fef4
/Applications/freesurfer/MCRv84//bin/maci64/libmwhg.dylib+00622324
_ZN10ScreenImpl13getScreenSizeEv+00000036
[ 12] 0x000000011b57e2e2
/Applications/freesurfer/MCRv84//bin/maci64/libmwhg.dylib+00615138
_ZNK2ui24RootScreenAndPointerImpl13getScreenSizeEv+00000018
[ 13] 0x000000011b582f58
/Applications/freesurfer/MCRv84//bin/maci64/libmwhg.dylib+00634712
_ZN2ui4Root17getScreenSizeImplEPN4mcos11COSPropInfoEPNS1_9COSClientEPNS1_12COSInterfaceE+00000040
[ 14] 0x000000011b9b9d13
/Applications/freesurfer/MCRv84//bin/maci64/libmwhg.dylib+05053715
_ZN7hgutils6StubPIIN2ui4RootENS_15PropertyStorageIN8graphics8datatype8PositionENS_6NoModeENS_21NoSerializableStorageEEEE8getValueEPN4mcos12COSInterfaceE+00000099
[ 15] 0x000000010e0e7a6e
/Applications/freesurfer/MCRv84//bin/maci64/libmwmcos.dylib+00371310
_ZN4mcos13COSInterfaceI18igetDirectInternalEPNS_12COSInterfaceE+00000110
[ 16] 0x000000010e0ddc80
/Applications/freesurfer/MCRv84//bin/maci64/libmwmcos.dylib+00330880
_ZN4mcos13COSInterfaceI10igetDirectEPKNS_9COSClientEPNS_12COSInterfaceE+00000128
[ 17] 0x000000010e14d12b
/Applications/freesurfer/MCRv84//bin/maci64/libmwmcos.dylib+00786731
_ZN4mcos28getValueOfKnownClassPropertyEP11mxArray_tagmPKS0_NS_15COSInterfacePtrEPKNS_9COSClientE+00000411
[ 18] 0x000000010e14e070
/Applications/freesurfer/MCRv84//bin/maci64/libmwmcos.dylib+00790640
_ZN4mcos16getPropertyValueEPKNS_9COSClientEPNS_8COSClassEPK11mxArray_tagPKcmPS5_+00000416
[ 19] 0x000000010e14e483
/Applications/freesurfer/MCRv84//bin/maci64/libmwmcos.dylib+00791683
_ZNK4mcos5GetMI6invokeEPKNS_9COSClientERiPNS_8COSValueEiPKS5_+00000355
[ 20] 0x000000010e1361f2
/Applications/freesurfer/MCRv84//bin/maci64/libmwmcos.dylib+00692722
_ZN24OpaqueMethodCallMetaData11callCMethodEPN4mcos13COSMethodInfoEPP11mxArray_tagPKNS0_9COSClientE+00000466
[ 21] 0x000000010e138f4e
/Applications/freesurfer/MCRv84//bin/maci64/libmwmcos.dylib+00704334
_ZN24OpaqueMethodCallMetaData23callMethodOrConstructorEP11mxArray_tagbiPS1_iPPKS0_bPKN4mcos9COSClientEPS9_PPNS6_13COSMethodInfoE+00000494
[ 22] 0x000000010e136b3e
/Applications/freesurfer/MCRv84//bin/maci64/libmwmcos.dylib+00695102
_Z18mcosCallMethodImplN4mcos9COSNameIDES0_PKNS_9COSClientEiPP11mxArray_tagiPPKS4_bb+00000286
[ 23] 0x000000010e137a82
/Applications/freesurfer/MCRv84//bin/maci64/libmwmcos.dylib+00699010
_Z12omCallMethodN4mcos9COSNameIDES0_PKNS_9COSClientEiPP11mxArray_tagiPPKS4_b+00000114
[ 24] 0x000000011cd286c2
/Applications/freesurfer/MCRv84//bin/maci64/libmwhgutils.dylib+00440002
_ZN7hgutils17MCOSMethodInvoker6invokeEPKN4mcos9COSClientERiPNS1_8COSValueEiPKS6_+00000866
[ 25] 0x000000011cd28220
/Applications/freesurfer/MCRv84//bin/maci64/libmwhgutils.dylib+00438816
_ZN7hgutils14callMCOSMethodERKN4mcos9COSNameIDERKNS0_12MemberAccessEPNS0_8COSClassEPKNS0_9COSClientERiPNS0_8COSValueEiPKSD_+00000112
[ 26] 0x000000011cd281a7
/Applications/freesurfer/MCRv84//bin/maci64/libmwhgutils.dylib+00438695
_ZN7hgutils14callMCOSMethodERKN4mcos9COSNameIDEPNS0_8COSClassEPKNS0_9COSClientERiPNS0_8COSValueEiPKSA_+00000055
[ 27] 0x000000011cd0e292
/Applications/freesurfer/MCRv84//bin/maci64/libmwhgutils.dylib+00332434
_ZThn8_NK7hgutils22HGPropHandlerClassInfo16areChildrenSavedEv+00029170
[ 28] 0x000000010e1361f2
/Applications/freesurfer/MCRv84//bin/maci64/libmwmcos.dylib+00692722
_ZN24OpaqueMethodCallMetaData11callCMethodEPN4mcos13COSMethodInfoEPP11mxArray_tagPKNS0_9COSClientE+00000466
[ 29] 0x000000010e138f4e
/Applications/freesurfer/MCRv84//bin/maci64/libmwmcos.dylib+00704334
_ZN24OpaqueMethodCallMetaData23callMethodOrConstructorEP11mxArray_tagbiPS1_iPPKS0_bPKN4mcos9COSClientEPS9_PPNS6_13COSMethodInfoE+00000494
[ 30] 0x000000010e137d41
/Applications/freesurfer/MCRv84//bin/maci64/libmwmcos.dylib+00699713
_Z22omCallMethodWithClientP11mxArray_tagbS0_iPS0_iPPKS_PKN4mcos9COSClientEPS8_PPNS5_13COSMethodInfoE+00000417
[ 31] 0x000000010e1c3930
/Applications/freesurfer/MCRv84//bin/maci64/libmwmcos.dylib+01272112
_Z18omCallOpaqueMethodP11mxArray_tagS0_iPS0_iPPKS_+00000112
[ 32] 0x000000011adc9353
/Applications/freesurfer/MCRv84//bin/maci64/libmwhgbuiltins.dylib+00193363
hgGetWrapper+00000435
[ 33] 0x000000010df6ecc6
/Applications/freesurfer/MCRv84//bin/maci64/libmwm_dispatcher.dylib+00117958
_ZN11Mfh_builtin11dispatch_mfEiPP11mxArray_tagiS2_+00000086
[ 34] 0x000000010df5712d
/Applications/freesurfer/MCRv84//bin/maci64/libmwm_dispatcher.dylib+00020781
_ZN13Mfh_MATLAB_fn11dispatch_fhEiPP11mxArray_tagiS2_+00000333
[ 35] 0x000000010d314d62
/Applications/freesurfer/MCRv84//bin/maci64/libmwm_interpreter.dylib+01523042
_Z19inDispatchFromStackiPKcii+00001650
[ 36] 0x000000010d2b6dd8
/Applications/freesurfer/MCRv84//bin/maci64/libmwm_interpreter.dylib+01138136
inPcodeWalker+00022552
[ 37] 0x000000010d2b3917
/Applications/freesurfer/MCRv84//bin/maci64/libmwm_interpreter.dylib+01124631
inPcodeWalker+00009047
[ 38] 0x000000010d2aefb7
/Applications/freesurfer/MCRv84//bin/maci64/libmwm_interpreter.dylib+01105847
inInterPcode+00000935
[ 39] 0x000000010d2b01c6
/Applications/freesurfer/MCRv84//bin/maci64/libmwm_interpreter.dylib+01110470
_Z26inExecuteMFunctionOrScriptP6Mfh_mpb+00000886
[ 40] 0x000000010d3521f1
/Applications/freesurfer/MCRv84//bin/maci64/libmwm_interpreter.dylib+01774065
_Z10inRunMfileiPP11mxArray_tagiS1_P6Mfh_mpP15inWorkSpace_tag+00002337
[ 41] 0x000000010dfb3c28
/Applications/freesurfer/MCRv84//bin/maci64/libmwm_dispatcher.dylib+00400424
_ZN8Mfh_file11dispatch_fhEiPP11mxArray_tagiS2_+00000600
[ 42] 0x000000010e197e8e
/Applications/freesurfer/MCRv84//bin/maci64/libmwmcos.dylib+01093262
_ZNK4mcos17MScopedMethodInfo6invokeEPKNS_9COSClientERiPNS_8COSValueEiPKS5_+00000606
[ 43] 0x000000010e135597
/Applications/freesurfer/MCRv84//bin/maci64/libmwmcos.dylib+00689559
_ZN24OpaqueMethodCallMetaData11callMMethodEPN4mcos13COSMethodInfoEPP11mxArray_tagPKNS0_9COSClientE+00000359
[ 44] 0x000000010e138e63
/Applications/freesurfer/MCRv84//bin/maci64/libmwmcos.dylib+00704099
_ZN24OpaqueMethodCallMetaData23callMethodOrConstructorEP11mxArray_tagbiPS1_iPPKS0_bPKN4mcos9COSClientEPS9_PPNS6_13COSMethodInfoE+00000259
[ 45] 0x000000010e137d41
/Applications/freesurfer/MCRv84//bin/maci64/libmwmcos.dylib+00699713
_Z22omCallMethodWithClientP11mxArray_tagbS0_iPS0_iPPKS_PKN4mcos9COSClientEPS8_PPNS5_13COSMethodInfoE+00000417
[ 46] 0x000000010e1c3ee8
/Applications/freesurfer/MCRv84//bin/maci64/libmwmcos.dylib+01273576
_Z18omCallStaticMethodP11mxArray_tagiPS0_iPPKS_+00000088
[ 47] 0x000000010e24ce64
/Applications/freesurfer/MCRv84//bin/maci64/libmwmcos.dylib+01834596
_ZN17Mfh_opaque_static11dispatch_mfEiPP11mxArray_tagiS2_+00000116
[ 48] 0x000000010df5712d
/Applications/freesurfer/MCRv84//bin/maci64/libmwm_dispatcher.dylib+00020781
_ZN13Mfh_MATLAB_fn11dispatch_fhEiPP11mxArray_tagiS2_+00000333
[ 49] 0x000000010e249acc
/Applications/freesurfer/MCRv84//bin/maci64/libmwmcos.dylib+01821388
_ZN10Mfh_opaque11dispatch_fhEiPP11mxArray_tagiS2_+00000028
[ 50] 0x000000010d314d62
/Applications/freesurfer/MCRv84//bin/maci64/libmwm_interpreter.dylib+01523042
_Z19inDispatchFromStackiPKcii+00001650
[ 51] 0x000000010d26a59e
/Applications/freesurfer/MCRv84//bin/maci64/libmwm_interpreter.dylib+00824734
inCallFcnFromReference+00000110
[ 52] 0x000000010d2b3003
/Applications/freesurfer/MCRv84//bin/maci64/libmwm_interpreter.dylib+01122307
inPcodeWalker+00006723
[ 53] 0x000000010d2aefb7
/Applications/freesurfer/MCRv84//bin/maci64/libmwm_interpreter.dylib+01105847
inInterPcode+00000935
[ 54] 0x000000010d2b01c6
/Applications/freesurfer/MCRv84//bin/maci64/libmwm_interpreter.dylib+01110470
_Z26inExecuteMFunctionOrScriptP6Mfh_mpb+00000886
[ 55] 0x000000010d3521f1
/Applications/freesurfer/MCRv84//bin/maci64/libmwm_interpreter.dylib+01774065
_Z10inRunMfileiPP11mxArray_tagiS1_P6Mfh_mpP15inWorkSpace_tag+00002337
[ 56] 0x000000010dfb3c55
/Applications/freesurfer/MCRv84//bin/maci64/libmwm_dispatcher.dylib+00400469
_ZN8Mfh_file11dispatch_fhEiPP11mxArray_tagiS2_+00000645
[ 57] 0x000000010d314d62
/Applications/freesurfer/MCRv84//bin/maci64/libmwm_interpreter.dylib+01523042
_Z19inDispatchFromStackiPKcii+00001650
[ 58] 0x000000010d2b6dd8
/Applications/freesurfer/MCRv84//bin/maci64/libmwm_interpreter.dylib+01138136
inPcodeWalker+00022552
[ 59] 0x000000010d2b3702
/Applications/freesurfer/MCRv84//bin/maci64/libmwm_interpreter.dylib+01124098
inPcodeWalker+00008514
[ 60] 0x000000010d2aefb7
/Applications/freesurfer/MCRv84//bin/maci64/libmwm_interpreter.dylib+01105847
inInterPcode+00000935
[ 61] 0x000000010d2aecad
/Applications/freesurfer/MCRv84//bin/maci64/libmwm_interpreter.dylib+01105069
inInterPcode+00000157
[ 62] 0x000000010d2a5b9f
/Applications/freesurfer/MCRv84//bin/maci64/libmwm_interpreter.dylib+01067935
_ZN12InterpBridge33DoMatlabFcnCallInDesiredWorkspaceEiPP11mxArray_tagiPPKS0_P13Mfh_MATLAB_fnP15inWorkSpace_tag+00004015
[ 63] 0x000000010d2a7a79
/Applications/freesurfer/MCRv84//bin/maci64/libmwm_interpreter.dylib+01075833
_Z25in_local_call_with_setjmpIN5boost3_bi6bind_tIvPFvPiP12_pcodeheaderS3_PP11mxArray_tag12inDebugCheckENS1_5list5INS1_5valueIS3_EENSD_IS5_EENS0_3argILi1EEENSG_ILi2EEENSD_IS9_EEEEEEEN6mlutil14cmddistributor17inExecutionStatusET_S3_S8_b+00000073
[ 64] 0x000000010d2a328d
/Applications/freesurfer/MCRv84//bin/maci64/libmwm_interpreter.dylib+01057421
_Z12inEvalStringP15_memory_contextRKSbItSt11char_traitsItESaItEE8EvalTypeiPP11mxArray_tag12inDebugCheckP12_pcodeheaderPib+00002877
[ 65] 0x000000010d2a37cd
/Applications/freesurfer/MCRv84//bin/maci64/libmwm_interpreter.dylib+01058765
_ZN12InterpBridge22EvalCmdWithLocalReturnERKSbItSt11char_traitsItESaItEEPibb+00000141
[ 66] 0x000000010d2a3c05
/Applications/freesurfer/MCRv84//bin/maci64/libmwm_interpreter.dylib+01059845
_ZN12InterpBridge7EvalCmdERKSbItSt11char_traitsItESaItEEb+00000021
[ 67] 0x000000010d201347
/Applications/freesurfer/MCRv84//bin/maci64/libmwm_interpreter.dylib+00394055
inEvalCmd+00000119
[ 68] 0x000000010d0197fa
/Applications/freesurfer/MCRv84//bin/maci64/libmwmcr.dylib+00223226
_Z16mnRunLoginScriptv+00000586
[ 69] 0x000000010d040f63
/Applications/freesurfer/MCRv84//bin/maci64/libmwmcr.dylib+00384867
_Z32mnRunPathDependentInitializationv+00000051
[ 70] 0x000000010d02780c
/Applications/freesurfer/MCRv84//bin/maci64/libmwmcr.dylib+00280588
_ZN11mcrInstance26init_on_interpreter_threadEP11MfileReaderP13MexFileReader+00000988
[ 71] 0x000000010d035fb8
/Applications/freesurfer/MCRv84//bin/maci64/libmwmcr.dylib+00339896
_ZN5boost6detail8function21function_obj_invoker0INS_3_bi6bind_tIbNS_4_mfi3mf2Ib11mcrInstanceP11MfileReaderP13MexFileReaderEENS3_5list3INS3_5valueIPS7_EENSE_IS9_EENSE_ISB_EEEEEEbE6invokeERNS1_15function_bufferE+00000040
[ 72] 0x000000010d034dc1
/Applications/freesurfer/MCRv84//bin/maci64/libmwmcr.dylib+00335297
_ZN3mcr7runtime17InterpreterThread4Impl22TypedInvocationRequestIbE29doNotRethrowMxArrayExceptionsERKN5boost8functionIFbvEEE+00000033
[ 73] 0x000000010d035bd9
/Applications/freesurfer/MCRv84//bin/maci64/libmwmcr.dylib+00338905
_ZN5boost6detail11task_objectIbNS_3_bi6bind_tIbPFbRKNS_8functionIFbvEEEENS2_5list1INS2_5valueIS6_EEEEEEE6do_runEv+00000025
[ 74] 0x000000010d035276
/Applications/freesurfer/MCRv84//bin/maci64/libmwmcr.dylib+00336502
_ZN5boost6detail9task_baseIbE3runEv+00000166
[ 75] 0x000000010d035067
/Applications/freesurfer/MCRv84//bin/maci64/libmwmcr.dylib+00335975
_ZN3mcr7runtime17InterpreterThread4Impl22TypedInvocationRequestIbE3runEv+00000023
[ 76] 0x000000010cffff90
/Applications/freesurfer/MCRv84//bin/maci64/libmwmcr.dylib+00118672
_ZN3mcr7runtime17InterpreterThread4Impl26invocation_request_handlerEl+00000032
[ 77] 0x00000001053fd005
/Applications/freesurfer/MCRv84//bin/maci64/libmwservices.dylib+00196613
_ZN10eventqueue18UserEventQueueImpl5flushEv+00001205
[ 78] 0x000000010e7e9a65
/Applications/freesurfer/MCRv84//bin/maci64/libmwuix.dylib+00043621
_Z25isHandleUserEventCallbackPFvPvE+00000501
[ 79] 0x00000001054cca45
/Applications/freesurfer/MCRv84//bin/maci64/libmwservices.dylib+01047109
_Z21svWS_ProcessCallbacksv+00016693
[ 80] 0x00000001054c8152
/Applications/freesurfer/MCRv84//bin/maci64/libmwservices.dylib+01028434
_Z25svWS_ProcessPendingEventsiib+00000834
[ 81] 0x00000001054c7e5e
/Applications/freesurfer/MCRv84//bin/maci64/libmwservices.dylib+01027678
_Z25svWS_ProcessPendingEventsiib+00000078
[ 82] 0x000000010d00018f
/Applications/freesurfer/MCRv84//bin/maci64/libmwmcr.dylib+00119183
_ZN3mcr7runtime17InterpreterThread4Impl14process_eventsERKN5boost10shared_ptrIS2_EE+00000095
[ 83] 0x000000010d00049f
/Applications/freesurfer/MCRv84//bin/maci64/libmwmcr.dylib+00119967
_ZN3mcr7runtime17InterpreterThread4Impl3runERKN5boost10shared_ptrIS2_EEPNS2_12init_contextE+00000335
[ 84] 0x000000010cfe6d1b
/Applications/freesurfer/MCRv84//bin/maci64/libmwmcr.dylib+00015643
_Z26run_init_and_handle_eventsPv+00000059
[ 85] 0x00007fff74b7f661
/usr/lib/system/libsystem_pthread.dylib+00013921 _pthread_body+00000340
[ 86] 0x00007fff74b7f50d
/usr/lib/system/libsystem_pthread.dylib+00013581 _pthread_body+00000000
[ 87] 0x00007fff74b7ebf9
/usr/lib/system/libsystem_pthread.dylib+00011257 thread_start+00000013
Abnormal termination:
Segmentation violation
Register State (from fault):
RAX = 00007fafcba4f000 RBX = 00007fafcba4f000
RCX = 000070000cdff9e0 RDX = 0000000111cba97e
RSP = 00007fafcba4f000 RBP = 00009b630cdff9e0
RSI = 00007fafcdb8a9b0 RDI = 0000000000000000
R8 = 00007fafcc2dc270 R9 = 00007fafcba4f000
R10 = 000000011bd1f76a R11 = 0000000000000000
R12 = 000070000cdffa40 R13 = 0000000111b083c7
R14 = 000070000cdffab0 R15 = 000000011bd1f777
RIP = 0000000116ca6f40 RFL = 00007fafcc2dc270
CS = 00009b6300305bc3 FS = 000000011bd1f76a GS = 00007fafcba4f1e8
Stack Trace (from fault):
[ 0] 0x0000000105f76e64
/Applications/freesurfer/MCRv84//bin/maci64/libmwfl.dylib+00028260
_ZN2fl4diag15stacktrace_base7captureERKNS0_14thread_contextEm+00000052
[ 1] 0x0000000105f7aa2a
/Applications/freesurfer/MCRv84//bin/maci64/libmwfl.dylib+00043562
_ZN2fl4test17terminate_handledEv+00000906
[ 2] 0x0000000105f7a477
/Applications/freesurfer/MCRv84//bin/maci64/libmwfl.dylib+00042103
_ZN2fl4diag13terminate_logEPKcPK17__darwin_ucontext+00000119
[ 3] 0x000000010d041b7a
/Applications/freesurfer/MCRv84//bin/maci64/libmwmcr.dylib+00387962
_Z32mnRunPathDependentInitializationv+00003146
[ 4] 0x000000010d041e58
/Applications/freesurfer/MCRv84//bin/maci64/libmwmcr.dylib+00388696
_Z32mnRunPathDependentInitializationv+00003880
[ 5] 0x000000010d03f733
/Applications/freesurfer/MCRv84//bin/maci64/libmwmcr.dylib+00378675
mnFatalSignalHandler+00000275
[ 6] 0x00007fff74b75f5a
/usr/lib/system/libsystem_platform.dylib+00008026 _sigtramp+00000026
[ 7] 0x0000000111b096f8
/Applications/freesurfer/MCRv84/sys/java/jre/maci64/jre//lib/server/libjvm.dylib+03192568
_ZN23JNI_ArgumentPusherVaArg7iterateEy+00000000
[ 8] 0x0000000111af9d67
/Applications/freesurfer/MCRv84/sys/java/jre/maci64/jre//lib/server/libjvm.dylib+03128679
jni_GetMethodID+00000126
[ 9] 0x00000001104dd271
/Applications/freesurfer/MCRv84//bin/maci64/libmwjmi.dylib+00160369
_Z12mljGetMethodP7_jclassPKcS2_+00000049
[ 10] 0x000000011b57a366
/Applications/freesurfer/MCRv84//bin/maci64/libmwhg.dylib+00598886
_ZN2ui14JavaScreenData20getPrimaryScreenRectEv+00000150
[ 11] 0x000000011b57f23a
/Applications/freesurfer/MCRv84//bin/maci64/libmwhg.dylib+00619066
_ZN10gbtobjects10ScreenData14getScreenWidthEv+00000010
[ 12] 0x000000011b5961a6
/Applications/freesurfer/MCRv84//bin/maci64/libmwhg.dylib+00713126
_ZN2ui9container9Container16getChildRefFrameEv+00000038
[ 13] 0x000000011b59655e
/Applications/freesurfer/MCRv84//bin/maci64/libmwhg.dylib+00714078
_ZN2ui9container9Container20fillInUpdateViewInfoERN7hgutils14UpdateViewInfoE+00000046
[ 14] 0x000000011b5834d6
/Applications/freesurfer/MCRv84//bin/maci64/libmwhg.dylib+00636118
_ZN2ui4Root20fillInUpdateViewInfoERN7hgutils14UpdateViewInfoE+00000022
[ 15] 0x000000011b57e79a
/Applications/freesurfer/MCRv84//bin/maci64/libmwhg.dylib+00616346
_ZN10gbtobjects13UpdateVisitor5applyERN2ui4RootE+00000218
[ 16] 0x000000011b693f9a
/Applications/freesurfer/MCRv84//bin/maci64/libmwhg.dylib+01752986
_ZN10gbtobjects20CommitUpdatesManager13performUpdateEv+00000122
[ 17] 0x000000011b69407b
/Applications/freesurfer/MCRv84//bin/maci64/libmwhg.dylib+01753211
_ZN10gbtobjects20CommitUpdatesManager24commitAllDatabaseUpdatesEbb+00000027
[ 18] 0x00000001054df7c8
/Applications/freesurfer/MCRv84//bin/maci64/libmwservices.dylib+01124296
_Z26svWS_CommitDatabaseUpdates27svCommitDatabaseUpdatesType+00000152
[ 19] 0x00000001054c7e2f
/Applications/freesurfer/MCRv84//bin/maci64/libmwservices.dylib+01027631
_Z25svWS_ProcessPendingEventsiib+00000031
[ 20] 0x000000010d00018f
/Applications/freesurfer/MCRv84//bin/maci64/libmwmcr.dylib+00119183
_ZN3mcr7runtime17InterpreterThread4Impl14process_eventsERKN5boost10shared_ptrIS2_EE+00000095
[ 21] 0x000000010d00049f
/Applications/freesurfer/MCRv84//bin/maci64/libmwmcr.dylib+00119967
_ZN3mcr7runtime17InterpreterThread4Impl3runERKN5boost10shared_ptrIS2_EEPNS2_12init_contextE+00000335
[ 22] 0x000000010cfe6d1b
/Applications/freesurfer/MCRv84//bin/maci64/libmwmcr.dylib+00015643
_Z26run_init_and_handle_eventsPv+00000059
[ 23] 0x00007fff74b7f661
/usr/lib/system/libsystem_pthread.dylib+00013921 _pthread_body+00000340
[ 24] 0x00007fff74b7f50d
/usr/lib/system/libsystem_pthread.dylib+00013581 _pthread_body+00000000
[ 25] 0x00007fff74b7ebf9
/usr/lib/system/libsystem_pthread.dylib+00011257 thread_start+00000013
If this problem is reproducible, please submit a Service Request via:
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
/Users/mnd_mac/matlab_crash_dump.49812-2 **
MATLAB is exiting because of fatal error
/Applications/freesurfer/bin/run_segmentSubjectT1_autoEstimateAlveusML.sh: line
37: 49812 Killed: 9
"${exe_dir}"/segmentSubjectT1_autoEstimateAlveusML.app/Contents/MacOS/segmentSubjectT1_autoEstimateAlveusML
$args
Darwin MnD-macui-iMac.local 17.7.0 Darwin Kernel Version 17.7.0: Thu Jun 21
22:53:14 PDT 2018; root:xnu-4570.71.2~1/RELEASE_X86_64 x86_64
Do I need to request to mathworks?
If you have any recommendation, please send me mail back.
Thanks a lot!
and I hope you to have a good day!
Jinyoung
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