Re: [Freesurfer] error in hippocampal subfields and nuclei of amygdala segmentation

External Email - Use Caution

Hi again, Could you please try unsetting your DYLD_LIBRARY_PATH with the following command?

export DYLD_LIBRARY_PATH=

-- Juan Eugenio Iglesias Centre for Medical Image Computing (CMIC) Department of Medical Physics and Biomedical Engineering University College London http://www.jeiglesias.com

From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of 오진영 jinyoung.oh555@gmail.com Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Tuesday, 30 October 2018 at 08:00 To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] error in hippocampal subfields and nuclei of amygdala segmentation

External Email - Use Caution Dear Eugenio

I have 8GB 2400 MHz DDR4. I am not sure this might be a problem cause now I run only freesurfer to segment hippocampal subfields and nuclei of amygdala with mac. I already updated the freesurfer to the latest version and installed matlab runtime(2014b) properly and I cannot figure it out which is the problem. Do I need to update software of the macOS?

Thank you for your help.

Jinyoung

2018년 10월 30일 (화) 오후 4:41, Iglesias Gonzalez, Eugenio <e.iglesias@ucl.ac.ukmailto:e.iglesias@ucl.ac.uk>님이 작성:

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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of 오진영 <jinyoung.oh555@gmail.commailto:jinyoung.oh555@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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer