External Email - Use Caution
I have installed matlab 2018b and removed 2014b.
When I run segmentHA_T1.sh the error reported below occurs:
MATLAB is exiting because of fatal error
/Applications/freesurfer/bin/run_segmentSubjectT1_autoEstimateAlveusML.sh: line 37:3955 Killed: 9 "${exe_dir}"/segmentSubjectT1_autoEstimateAlveusML.app/Contents/MacOS/segmentSubjectT1_autoEstimateAlveusML $args
Darwin iMac-di-Stefano.local 17.7.0 Darwin Kernel Version 17.7.0: Wed Apr 24 21:17:24 PDT 2019; root:xnu-4570.71.45~1/RELEASE_X86_64 x86_64
T1 hippocampal subfields exited with ERRORS at Tue Jun4 00:55:25 CEST 2019
For more details, see the log file /Applications/freesurfer/subjects/subj/scripts/hippocampal-subfields-T1.log
Please also take in account
segmentation violation detected at Tue Jun4 00:57:53 2019
------------------------------------------------------------------------
Configuration:
Crash Decoding : Disabled
Current Visual : Quartz
Default Encoding : ISO-8859-1
MATLAB Architecture: maci64
MATLAB Root: /Applications/freesurfer/MCRv84
MATLAB Version : 8.4.0.150421 (R2014b)
MATLAB Version : 8.4.0.150421 (R2014b)
Why it does not find 2018 version?
I have follow the guidelines at https://surfer.nmr.mgh.harvard.edu/fswiki/MatlabRuntime
Thanks
Stefano
External Email - Use Caution
I have reinstalled 2014 and runtime
the error persists:
Segmentation violation detected at Fri Jun7 11:59:05 2019
------------------------------------------------------------------------
Configuration:
Crash Decoding : Disabled
Current Visual : Quartz
Default Encoding : ISO-8859-1
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: Wed Apr 24 21:17:24 PDT 2019; root:xnu-4570.71.45~1/RELEASE_X86_64 x86_64
Processor ID : x86 Family 6 Model 58 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 = 00007fa9f08bc000RBX = 00007fa9f08bc000
RCX = 000070000d4db2d0RDX = 000000011493697e
RSP = 00007fa9f08bc000RBP = 00009b630d4db2d0
RSI = 00007fa9f238f940RDI = 0000000000000000
R8 = 00007fa9f0912e70 R9 = 00007fa9f08bc000
R10 = 000000012000976aR11 = 0000000000000000
R12 = 000070000d4db330R13 = 00000001147843c7
R14 = 000070000d4db3a0R15 = 0000000120009777
RIP = 000000011a3b1f40RFL = 00007fa9f0912e70
CS = 00009b6300305bc3 FS = 000000012000976a GS = 00007fa9f08bc1e8
Stack Trace (from fault):
[0] 0x000000010a6efe64 /Applications/freesurfer/MCRv84//bin/maci64/libmwfl.dylib+00028260 _ZN2fl4diag15stacktrace_base7captureERKNS0_14thread_contextEm+00000052
[1] 0x000000010a6f3a2a /Applications/freesurfer/MCRv84//bin/maci64/libmwfl.dylib+00043562 _ZN2fl4test17terminate_handledEv+00000906
[2] 0x000000010a6f3477 /Applications/freesurfer/MCRv84//bin/maci64/libmwfl.dylib+00042103 _ZN2fl4diag13terminate_logEPKcPK17__darwin_ucontext+00000119
[3] 0x000000011013db7a /Applications/freesurfer/MCRv84//bin/maci64/libmwmcr.dylib+00387962 _Z32mnRunPathDependentInitializationv+00003146
[4] 0x000000011013de58 /Applications/freesurfer/MCRv84//bin/maci64/libmwmcr.dylib+00388696 _Z32mnRunPathDependentInitializationv+00003880
[5] 0x000000011013b733 /Applications/freesurfer/MCRv84//bin/maci64/libmwmcr.dylib+00378675 mnFatalSignalHandler+00000275
[6] 0x00007fff552c8f5a /usr/lib/system/libsystem_platform.dylib+00008026 _sigtramp+00000026
[7] 0x00000001147856f8 /Applications/freesurfer/MCRv84/sys/java/jre/maci64/jre//lib/server/libjvm.dylib+03192568 _ZN23JNI_ArgumentPusherVaArg7iterateEy+00000000
[8] 0x0000000114775d67 /Applications/freesurfer/MCRv84/sys/java/jre/maci64/jre//lib/server/libjvm.dylib+03128679 jni_GetMethodID+00000126
[9] 0x000000011356e271 /Applications/freesurfer/MCRv84//bin/maci64/libmwjmi.dylib+00160369 _Z12mljGetMethodP7_jclassPKcS2_+00000049
[ 10] 0x000000011f864366 /Applications/freesurfer/MCRv84//bin/maci64/libmwhg.dylib+00598886 _ZN2ui14JavaScreenData20getPrimaryScreenRectEv+00000150
[ 11] 0x000000011f869ef4 /Applications/freesurfer/MCRv84//bin/maci64/libmwhg.dylib+00622324 _ZN10ScreenImpl13getScreenSizeEv+00000036
[ 12] 0x000000011f8682e2 /Applications/freesurfer/MCRv84//bin/maci64/libmwhg.dylib+00615138 _ZNK2ui24RootScreenAndPointerImpl13getScreenSizeEv+00000018
[ 13] 0x000000011f86cf58 /Applications/freesurfer/MCRv84//bin/maci64/libmwhg.dylib+00634712 _ZN2ui4Root17getScreenSizeImplEPN4mcos11COSPropInfoEPNS1_9COSClientEPNS1_12COSInterfaceE+00000040
[ 14] 0x000000011fca3d13 /Applications/freesurfer/MCRv84//bin/maci64/libmwhg.dylib+05053715 _ZN7hgutils6StubPIIN2ui4RootENS_15PropertyStorageIN8graphics8datatype8PositionENS_6NoModeENS_21NoSerializableStorageEEEE8getValueEPN4mcos12COSInterfaceE+00000099
[ 15] 0x000000011118da6e /Applications/freesurfer/MCRv84//bin/maci64/libmwmcos.dylib+00371310 _ZN4mcos13COSInterfaceI18igetDirectInternalEPNS_12COSInterfaceE+00000110
[ 16] 0x0000000111183c80 /Applications/freesurfer/MCRv84//bin/maci64/libmwmcos.dylib+00330880 _ZN4mcos13COSInterfaceI10igetDirectEPKNS_9COSClientEPNS_12COSInterfaceE+00000128
[ 17] 0x00000001111f312b /Applications/freesurfer/MCRv84//bin/maci64/libmwmcos.dylib+00786731 _ZN4mcos28getValueOfKnownClassPropertyEP11mxArray_tagmPKS0_NS_15COSInterfacePtrEPKNS_9COSClientE+00000411
[ 18] 0x00000001111f4070 /Applications/freesurfer/MCRv84//bin/maci64/libmwmcos.dylib+00790640 _ZN4mcos16getPropertyValueEPKNS_9COSClientEPNS_8COSClassEPK11mxArray_tagPKcmPS5_+00000416
[ 19] 0x00000001111f4483 /Applications/freesurfer/MCRv84//bin/maci64/libmwmcos.dylib+00791683 _ZNK4mcos5GetMI6invokeEPKNS_9COSClientERiPNS_8COSValueEiPKS5_+00000355
[ 20] 0x00000001111dc1f2 /Applications/freesurfer/MCRv84//bin/maci64/libmwmcos.dylib+00692722 _ZN24OpaqueMethodCallMetaData11callCMethodEPN4mcos13COSMethodInfoEPP11mxArray_tagPKNS0_9COSClientE+00000466
[ 21] 0x00000001111def4e /Applications/freesurfer/MCRv84//bin/maci64/libmwmcos.dylib+00704334 _ZN24OpaqueMethodCallMetaData23callMethodOrConstructorEP11mxArray_tagbiPS1_iPPKS0_bPKN4mcos9COSClientEPS9_PPNS6_13COSMethodInfoE+00000494
[ 22] 0x00000001111dcb3e /Applications/freesurfer/MCRv84//bin/maci64/libmwmcos.dylib+00695102 _Z18mcosCallMethodImplN4mcos9COSNameIDES0_PKNS_9COSClientEiPP11mxArray_tagiPPKS4_bb+00000286
[ 23] 0x00000001111dda82 /Applications/freesurfer/MCRv84//bin/maci64/libmwmcos.dylib+00699010 _Z12omCallMethodN4mcos9COSNameIDES0_PKNS_9COSClientEiPP11mxArray_tagiPPKS4_b+00000114
[ 24] 0x00000001210126c2 /Applications/freesurfer/MCRv84//bin/maci64/libmwhgutils.dylib+00440002 _ZN7hgutils17MCOSMethodInvoker6invokeEPKN4mcos9COSClientERiPNS1_8COSValueEiPKS6_+00000866
[ 25] 0x0000000121012220 /Applications/freesurfer/MCRv84//bin/maci64/libmwhgutils.dylib+00438816 _ZN7hgutils14callMCOSMethodERKN4mcos9COSNameIDERKNS0_12MemberAccessEPNS0_8COSClassEPKNS0_9COSClientERiPNS0_8COSValueEiPKSD_+00000112
[ 26] 0x00000001210121a7 /Applications/freesurfer/MCRv84//bin/maci64/libmwhgutils.dylib+00438695 _ZN7hgutils14callMCOSMethodERKN4mcos9COSNameIDEPNS0_8COSClassEPKNS0_9COSClientERiPNS0_8COSValueEiPKSA_+00000055
[ 27] 0x0000000120ff8292 /Applications/freesurfer/MCRv84//bin/maci64/libmwhgutils.dylib+00332434 _ZThn8_NK7hgutils22HGPropHandlerClassInfo16areChildrenSavedEv+00029170
[ 28] 0x00000001111dc1f2 /Applications/freesurfer/MCRv84//bin/maci64/libmwmcos.dylib+00692722 _ZN24OpaqueMethodCallMetaData11callCMethodEPN4mcos13COSMethodInfoEPP11mxArray_tagPKNS0_9COSClientE+00000466
[ 29] 0x00000001111def4e /Applications/freesurfer/MCRv84//bin/maci64/libmwmcos.dylib+00704334 _ZN24OpaqueMethodCallMetaData23callMethodOrConstructorEP11mxArray_tagbiPS1_iPPKS0_bPKN4mcos9COSClientEPS9_PPNS6_13COSMethodInfoE+00000494
[ 30] 0x00000001111ddd41 /Applications/freesurfer/MCRv84//bin/maci64/libmwmcos.dylib+00699713 _Z22omCallMethodWithClientP11mxArray_tagbS0_iPS0_iPPKS_PKN4mcos9COSClientEPS8_PPNS5_13COSMethodInfoE+00000417
[ 31] 0x0000000111269930 /Applications/freesurfer/MCRv84//bin/maci64/libmwmcos.dylib+01272112 _Z18omCallOpaqueMethodP11mxArray_tagS0_iPS0_iPPKS_+00000112
[ 32] 0x000000011f0b3353 /Applications/freesurfer/MCRv84//bin/maci64/libmwhgbuiltins.dylib+00193363 hgGetWrapper+00000435
[ 33] 0x0000000111014cc6 /Applications/freesurfer/MCRv84//bin/maci64/libmwm_dispatcher.dylib+00117958 _ZN11Mfh_builtin11dispatch_mfEiPP11mxArray_tagiS2_+00000086
[ 34] 0x0000000110ffd12d /Applications/freesurfer/MCRv84//bin/maci64/libmwm_dispatcher.dylib+00020781 _ZN13Mfh_MATLAB_fn11dispatch_fhEiPP11mxArray_tagiS2_+00000333
[ 35] 0x00000001103bad62 /Applications/freesurfer/MCRv84//bin/maci64/libmwm_interpreter.dylib+01523042 _Z19inDispatchFromStackiPKcii+00001650
[ 36] 0x000000011035cdd8 /Applications/freesurfer/MCRv84//bin/maci64/libmwm_interpreter.dylib+01138136 inPcodeWalker+00022552
[ 37] 0x0000000110359917 /Applications/freesurfer/MCRv84//bin/maci64/libmwm_interpreter.dylib+01124631 inPcodeWalker+00009047
[ 38] 0x0000000110354fb7 /Applications/freesurfer/MCRv84//bin/maci64/libmwm_interpreter.dylib+01105847 inInterPcode+00000935
[ 39] 0x00000001103561c6 /Applications/freesurfer/MCRv84//bin/maci64/libmwm_interpreter.dylib+01110470 _Z26inExecuteMFunctionOrScriptP6Mfh_mpb+00000886
[ 40] 0x00000001103f81f1 /Applications/freesurfer/MCRv84//bin/maci64/libmwm_interpreter.dylib+01774065 _Z10inRunMfileiPP11mxArray_tagiS1_P6Mfh_mpP15inWorkSpace_tag+00002337
[ 41] 0x0000000111059c28 /Applications/freesurfer/MCRv84//bin/maci64/libmwm_dispatcher.dylib+00400424 _ZN8Mfh_file11dispatch_fhEiPP11mxArray_tagiS2_+00000600
[ 42] 0x000000011123de8e /Applications/freesurfer/MCRv84//bin/maci64/libmwmcos.dylib+01093262 _ZNK4mcos17MScopedMethodInfo6invokeEPKNS_9COSClientERiPNS_8COSValueEiPKS5_+00000606
[ 43] 0x00000001111db597 /Applications/freesurfer/MCRv84//bin/maci64/libmwmcos.dylib+00689559 _ZN24OpaqueMethodCallMetaData11callMMethodEPN4mcos13COSMethodInfoEPP11mxArray_tagPKNS0_9COSClientE+00000359
[ 44] 0x00000001111dee63 /Applications/freesurfer/MCRv84//bin/maci64/libmwmcos.dylib+00704099 _ZN24OpaqueMethodCallMetaData23callMethodOrConstructorEP11mxArray_tagbiPS1_iPPKS0_bPKN4mcos9COSClientEPS9_PPNS6_13COSMethodInfoE+00000259
[ 45] 0x00000001111ddd41 /Applications/freesurfer/MCRv84//bin/maci64/libmwmcos.dylib+00699713 _Z22omCallMethodWithClientP11mxArray_tagbS0_iPS0_iPPKS_PKN4mcos9COSClientEPS8_PPNS5_13COSMethodInfoE+00000417
[ 46] 0x0000000111269ee8 /Applications/freesurfer/MCRv84//bin/maci64/libmwmcos.dylib+01273576 _Z18omCallStaticMethodP11mxArray_tagiPS0_iPPKS_+00000088
[ 47] 0x00000001112f2e64 /Applications/freesurfer/MCRv84//bin/maci64/libmwmcos.dylib+01834596 _ZN17Mfh_opaque_static11dispatch_mfEiPP11mxArray_tagiS2_+00000116
[ 48] 0x0000000110ffd12d /Applications/freesurfer/MCRv84//bin/maci64/libmwm_dispatcher.dylib+00020781 _ZN13Mfh_MATLAB_fn11dispatch_fhEiPP11mxArray_tagiS2_+00000333
[ 49] 0x00000001112efacc /Applications/freesurfer/MCRv84//bin/maci64/libmwmcos.dylib+01821388 _ZN10Mfh_opaque11dispatch_fhEiPP11mxArray_tagiS2_+00000028
[ 50] 0x00000001103bad62 /Applications/freesurfer/MCRv84//bin/maci64/libmwm_interpreter.dylib+01523042 _Z19inDispatchFromStackiPKcii+00001650
[ 51] 0x000000011031059e /Applications/freesurfer/MCRv84//bin/maci64/libmwm_interpreter.dylib+00824734 inCallFcnFromReference+00000110
[ 52] 0x0000000110359003 /Applications/freesurfer/MCRv84//bin/maci64/libmwm_interpreter.dylib+01122307 inPcodeWalker+00006723
[ 53] 0x0000000110354fb7 /Applications/freesurfer/MCRv84//bin/maci64/libmwm_interpreter.dylib+01105847 inInterPcode+00000935
[ 54] 0x00000001103561c6 /Applications/freesurfer/MCRv84//bin/maci64/libmwm_interpreter.dylib+01110470 _Z26inExecuteMFunctionOrScriptP6Mfh_mpb+00000886
[ 55] 0x00000001103f81f1 /Applications/freesurfer/MCRv84//bin/maci64/libmwm_interpreter.dylib+01774065 _Z10inRunMfileiPP11mxArray_tagiS1_P6Mfh_mpP15inWorkSpace_tag+00002337
[ 56] 0x0000000111059c55 /Applications/freesurfer/MCRv84//bin/maci64/libmwm_dispatcher.dylib+00400469 _ZN8Mfh_file11dispatch_fhEiPP11mxArray_tagiS2_+00000645
[ 57] 0x00000001103bad62 /Applications/freesurfer/MCRv84//bin/maci64/libmwm_interpreter.dylib+01523042 _Z19inDispatchFromStackiPKcii+00001650
[ 58] 0x000000011035cdd8 /Applications/freesurfer/MCRv84//bin/maci64/libmwm_interpreter.dylib+01138136 inPcodeWalker+00022552
[ 59] 0x0000000110359702 /Applications/freesurfer/MCRv84//bin/maci64/libmwm_interpreter.dylib+01124098 inPcodeWalker+00008514
[ 60] 0x0000000110354fb7 /Applications/freesurfer/MCRv84//bin/maci64/libmwm_interpreter.dylib+01105847 inInterPcode+00000935
[ 61] 0x0000000110354cad /Applications/freesurfer/MCRv84//bin/maci64/libmwm_interpreter.dylib+01105069 inInterPcode+00000157
[ 62] 0x000000011034bb9f /Applications/freesurfer/MCRv84//bin/maci64/libmwm_interpreter.dylib+01067935 _ZN12InterpBridge33DoMatlabFcnCallInDesiredWorkspaceEiPP11mxArray_tagiPPKS0_P13Mfh_MATLAB_fnP15inWorkSpace_tag+00004015
[ 63] 0x000000011034da79 /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] 0x000000011034928d /Applications/freesurfer/MCRv84//bin/maci64/libmwm_interpreter.dylib+01057421 _Z12inEvalStringP15_memory_contextRKSbItSt11char_traitsItESaItEE8EvalTypeiPP11mxArray_tag12inDebugCheckP12_pcodeheaderPib+00002877
[ 65] 0x00000001103497cd /Applications/freesurfer/MCRv84//bin/maci64/libmwm_interpreter.dylib+01058765 _ZN12InterpBridge22EvalCmdWithLocalReturnERKSbItSt11char_traitsItESaItEEPibb+00000141
[ 66] 0x0000000110349c05 /Applications/freesurfer/MCRv84//bin/maci64/libmwm_interpreter.dylib+01059845 _ZN12InterpBridge7EvalCmdERKSbItSt11char_traitsItESaItEEb+00000021
[ 67] 0x00000001102a7347 /Applications/freesurfer/MCRv84//bin/maci64/libmwm_interpreter.dylib+00394055 inEvalCmd+00000119
[ 68] 0x00000001101157fa /Applications/freesurfer/MCRv84//bin/maci64/libmwmcr.dylib+00223226 _Z16mnRunLoginScriptv+00000586
[ 69] 0x000000011013cf63 /Applications/freesurfer/MCRv84//bin/maci64/libmwmcr.dylib+00384867 _Z32mnRunPathDependentInitializationv+00000051
[ 70] 0x000000011012380c /Applications/freesurfer/MCRv84//bin/maci64/libmwmcr.dylib+00280588 _ZN11mcrInstance26init_on_interpreter_threadEP11MfileReaderP13MexFileReader+00000988
[ 71] 0x0000000110131fb8 /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] 0x0000000110130dc1 /Applications/freesurfer/MCRv84//bin/maci64/libmwmcr.dylib+00335297 _ZN3mcr7runtime17InterpreterThread4Impl22TypedInvocationRequestIbE29doNotRethrowMxArrayExceptionsERKN5boost8functionIFbvEEE+00000033
[ 73] 0x0000000110131bd9 /Applications/freesurfer/MCRv84//bin/maci64/libmwmcr.dylib+00338905 _ZN5boost6detail11task_objectIbNS_3_bi6bind_tIbPFbRKNS_8functionIFbvEEEENS2_5list1INS2_5valueIS6_EEEEEEE6do_runEv+00000025
[ 74] 0x0000000110131276 /Applications/freesurfer/MCRv84//bin/maci64/libmwmcr.dylib+00336502 _ZN5boost6detail9task_baseIbE3runEv+00000166
[ 75] 0x0000000110131067 /Applications/freesurfer/MCRv84//bin/maci64/libmwmcr.dylib+00335975 _ZN3mcr7runtime17InterpreterThread4Impl22TypedInvocationRequestIbE3runEv+00000023
[ 76] 0x00000001100fbf90 /Applications/freesurfer/MCRv84//bin/maci64/libmwmcr.dylib+00118672 _ZN3mcr7runtime17InterpreterThread4Impl26invocation_request_handlerEl+00000032
[ 77] 0x00000001084d6005 /Applications/freesurfer/MCRv84//bin/maci64/libmwservices.dylib+00196613 _ZN10eventqueue18UserEventQueueImpl5flushEv+00001205
[ 78] 0x000000011188fa65 /Applications/freesurfer/MCRv84//bin/maci64/libmwuix.dylib+00043621 _Z25isHandleUserEventCallbackPFvPvE+00000501
[ 79] 0x00000001085a5a45 /Applications/freesurfer/MCRv84//bin/maci64/libmwservices.dylib+01047109 _Z21svWS_ProcessCallbacksv+00016693
[ 80] 0x00000001085a1152 /Applications/freesurfer/MCRv84//bin/maci64/libmwservices.dylib+01028434 _Z25svWS_ProcessPendingEventsiib+00000834
[ 81] 0x00000001085a0e5e /Applications/freesurfer/MCRv84//bin/maci64/libmwservices.dylib+01027678 _Z25svWS_ProcessPendingEventsiib+00000078
[ 82] 0x00000001100fc18f /Applications/freesurfer/MCRv84//bin/maci64/libmwmcr.dylib+00119183 _ZN3mcr7runtime17InterpreterThread4Impl14process_eventsERKN5boost10shared_ptrIS2_EE+00000095
[ 83] 0x00000001100fc49f /Applications/freesurfer/MCRv84//bin/maci64/libmwmcr.dylib+00119967 _ZN3mcr7runtime17InterpreterThread4Impl3runERKN5boost10shared_ptrIS2_EEPNS2_12init_contextE+00000335
[ 84] 0x00000001100e2d1b /Applications/freesurfer/MCRv84//bin/maci64/libmwmcr.dylib+00015643 _Z26run_init_and_handle_eventsPv+00000059
[ 85] 0x00007fff552d2661/usr/lib/system/libsystem_pthread.dylib+00013921 _pthread_body+00000340
[ 86] 0x00007fff552d250d/usr/lib/system/libsystem_pthread.dylib+00013581 _pthread_body+00000000
[ 87] 0x00007fff552d1bf9/usr/lib/system/libsystem_pthread.dylib+00011257 thread_start+00000013
Abnormal termination:
Segmentation violation
Register State (from fault):
RAX = 00007fa9f08bc000RBX = 00007fa9f08bc000
RCX = 000070000d4e39e0RDX = 000000011493697e
RSP = 00007fa9f08bc000RBP = 00009b630d4e39e0
RSI = 00007fa9f238f940RDI = 0000000000000000
R8 = 00007fa9f0912e70 R9 = 00007fa9f08bc000
R10 = 000000012000976aR11 = 0000000000000000
R12 = 000070000d4e3a40R13 = 00000001147843c7
R14 = 000070000d4e3ab0R15 = 0000000120009777
RIP = 000000011a3b1f40RFL = 00007fa9f0912e70
CS = 00009b6300305bc3 FS = 000000012000976a GS = 00007fa9f08bc1e8
Stack Trace (from fault):
[0] 0x000000010a6efe64 /Applications/freesurfer/MCRv84//bin/maci64/libmwfl.dylib+00028260 _ZN2fl4diag15stacktrace_base7captureERKNS0_14thread_contextEm+00000052
[1] 0x000000010a6f3a2a /Applications/freesurfer/MCRv84//bin/maci64/libmwfl.dylib+00043562 _ZN2fl4test17terminate_handledEv+00000906
[2] 0x000000010a6f3477 /Applications/freesurfer/MCRv84//bin/maci64/libmwfl.dylib+00042103 _ZN2fl4diag13terminate_logEPKcPK17__darwin_ucontext+00000119
[3] 0x000000011013db7a /Applications/freesurfer/MCRv84//bin/maci64/libmwmcr.dylib+00387962 _Z32mnRunPathDependentInitializationv+00003146
[4] 0x000000011013de58 /Applications/freesurfer/MCRv84//bin/maci64/libmwmcr.dylib+00388696 _Z32mnRunPathDependentInitializationv+00003880
[5] 0x000000011013b733 /Applications/freesurfer/MCRv84//bin/maci64/libmwmcr.dylib+00378675 mnFatalSignalHandler+00000275
[6] 0x00007fff552c8f5a /usr/lib/system/libsystem_platform.dylib+00008026 _sigtramp+00000026
[7] 0x00000001147856f8 /Applications/freesurfer/MCRv84/sys/java/jre/maci64/jre//lib/server/libjvm.dylib+03192568 _ZN23JNI_ArgumentPusherVaArg7iterateEy+00000000
[8] 0x0000000114775d67 /Applications/freesurfer/MCRv84/sys/java/jre/maci64/jre//lib/server/libjvm.dylib+03128679 jni_GetMethodID+00000126
[9] 0x000000011356e271 /Applications/freesurfer/MCRv84//bin/maci64/libmwjmi.dylib+00160369 _Z12mljGetMethodP7_jclassPKcS2_+00000049
[ 10] 0x000000011f864366 /Applications/freesurfer/MCRv84//bin/maci64/libmwhg.dylib+00598886 _ZN2ui14JavaScreenData20getPrimaryScreenRectEv+00000150
[ 11] 0x000000011f86923a /Applications/freesurfer/MCRv84//bin/maci64/libmwhg.dylib+00619066 _ZN10gbtobjects10ScreenData14getScreenWidthEv+00000010
[ 12] 0x000000011f8801a6 /Applications/freesurfer/MCRv84//bin/maci64/libmwhg.dylib+00713126 _ZN2ui9container9Container16getChildRefFrameEv+00000038
[ 13] 0x000000011f88055e /Applications/freesurfer/MCRv84//bin/maci64/libmwhg.dylib+00714078 _ZN2ui9container9Container20fillInUpdateViewInfoERN7hgutils14UpdateViewInfoE+00000046
[ 14] 0x000000011f86d4d6 /Applications/freesurfer/MCRv84//bin/maci64/libmwhg.dylib+00636118 _ZN2ui4Root20fillInUpdateViewInfoERN7hgutils14UpdateViewInfoE+00000022
[ 15] 0x000000011f86879a /Applications/freesurfer/MCRv84//bin/maci64/libmwhg.dylib+00616346 _ZN10gbtobjects13UpdateVisitor5applyERN2ui4RootE+00000218
[ 16] 0x000000011f97df9a /Applications/freesurfer/MCRv84//bin/maci64/libmwhg.dylib+01752986 _ZN10gbtobjects20CommitUpdatesManager13performUpdateEv+00000122
[ 17] 0x000000011f97e07b /Applications/freesurfer/MCRv84//bin/maci64/libmwhg.dylib+01753211 _ZN10gbtobjects20CommitUpdatesManager24commitAllDatabaseUpdatesEbb+00000027
[ 18] 0x00000001085b87c8 /Applications/freesurfer/MCRv84//bin/maci64/libmwservices.dylib+01124296 _Z26svWS_CommitDatabaseUpdates27svCommitDatabaseUpdatesType+00000152
[ 19] 0x00000001085a0e2f /Applications/freesurfer/MCRv84//bin/maci64/libmwservices.dylib+01027631 _Z25svWS_ProcessPendingEventsiib+00000031
[ 20] 0x00000001100fc18f /Applications/freesurfer/MCRv84//bin/maci64/libmwmcr.dylib+00119183 _ZN3mcr7runtime17InterpreterThread4Impl14process_eventsERKN5boost10shared_ptrIS2_EE+00000095
[ 21] 0x00000001100fc49f /Applications/freesurfer/MCRv84//bin/maci64/libmwmcr.dylib+00119967 _ZN3mcr7runtime17InterpreterThread4Impl3runERKN5boost10shared_ptrIS2_EEPNS2_12init_contextE+00000335
[ 22] 0x00000001100e2d1b /Applications/freesurfer/MCRv84//bin/maci64/libmwmcr.dylib+00015643 _Z26run_init_and_handle_eventsPv+00000059
[ 23] 0x00007fff552d2661/usr/lib/system/libsystem_pthread.dylib+00013921 _pthread_body+00000340
[ 24] 0x00007fff552d250d/usr/lib/system/libsystem_pthread.dylib+00013581 _pthread_body+00000000
[ 25] 0x00007fff552d1bf9/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/Stefano/matlab_crash_dump.9067-2 **
MATLAB is exiting because of fatal error
/Applications/freesurfer/bin/run_segmentSubjectT1_autoEstimateAlveusML.sh: line 37:9067 Killed: 9 "${exe_dir}"/segmentSubjectT1_autoEstimateAlveusML.app/Contents/MacOS/segmentSubjectT1_autoEstimateAlveusML $args
Darwin iMac-di-Stefano.local 17.7.0 Darwin Kernel Version 17.7.0: Wed Apr 24 21:17:24 PDT 2019; root:xnu-4570.71.45~1/RELEASE_X86_64 x86_64
T1 hippocampal subfields exited with ERRORS at Fri Jun7 11:59:05 CEST 2019
For more details, see the log file /Applications/freesurfer/subjects/subject_prova/subj/scripts/hippocampal-subfields-T1.log
Il 6 giugno 2019 alle 0.34 stdp82@virgilio.it ha scritto:
I have installed matlab 2018b and removed 2014b. When I run segmentHA_T1.sh the error reported below occurs: MATLAB is exiting because of fatal error /Applications/freesurfer/bin/run_segmentSubjectT1_autoEstimateAlveusML.sh: line 37:3955 Killed: 9 "${exe_dir}"/segmentSubjectT1_autoEstimateAlveusML.app/Contents/MacOS/segmentSubjectT1_autoEstimateAlveusML $args Darwin iMac-di-Stefano.local 17.7.0 Darwin Kernel Version 17.7.0: Wed Apr 24 21:17:24 PDT 2019; root:xnu-4570.71.45~1/RELEASE_X86_64 x86_64 T1 hippocampal subfields exited with ERRORS at Tue Jun4 00:55:25 CEST 2019 For more details, see the log file /Applications/freesurfer/subjects/subj/scripts/hippocampal-subfields-T1.log Please also take in account segmentation violation detected at Tue Jun4 00:57:53 2019 ------------------------------------------------------------------------ Configuration: Crash Decoding : Disabled Current Visual : Quartz Default Encoding : ISO-8859-1 MATLAB Architecture: maci64 MATLAB Root: /Applications/freesurfer/MCRv84 MATLAB Version : 8.4.0.150421 (R2014b) MATLAB Version : 8.4.0.150421 (R2014b) Why it does not find 2018 version? I have follow the guidelines at https://surfer.nmr.mgh.harvard.edu/fswiki/MatlabRuntime Thanks Stefano
freesurfer@nmr.mgh.harvard.edu
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stdp82＠virgilio.it