On 27 Aug 2022, at 10:47 am, Yann Quidé <yannquide@gmail.com> wrote:

Hi team,

I have been having troubles with processing my scans for thalamic subnuclei.

In my previous post, I mentioned I was using FS7.3.2, but indeed realised that this version was not fully compatible with my OS (OSX 10.13). So I instead installed FS 7.2.0.

However, I still have issues with the matlab runtime. I installed MCRv84, but received the  error 

Setting ITK threads to 1

#--------------------------------------------

#@# Thalamic Nuclei processing Fri 26 Aug 2022 20:51:42 AEST

------------------------------------------

Setting up environment variables

---

DYLD_LIBRARY_PATH is .:/Applications/freesurfer/7.2.0/MCRv84//runtime/maci64:/Applications/freesurfer/7.2.0/MCRv84//bin/maci64:/Applications/freesurfer/7.2.0/MCRv84//sys/os/maci64:/Applications/freesurfer/7.2.0/lib/gcc/lib:

PostVMInit failed to initialize com.mathworks.mwswing.MJStartupForDesktop

------------------------------------------------------------------------

       Segmentation violation detected at Fri Aug 26 20:51:49 2022

------------------------------------------------------------------------

Configuration:

  Crash Decoding     : Disabled

  Current Visual     : Quartz

  Default Encoding   : ISO-8859-1

  MATLAB Architecture: maci64

  MATLAB Root        : /Applications/freesurfer/7.2.0/MCRv84

  MATLAB Version     : 8.4.0.150421 (R2014b)

  Operating System   : Darwin 17.7.0 Darwin Kernel Version 17.7.0: Fri Oct 30 13:34:27 PDT 2020; root:xnu-4570.71.82.8~1/RELEASE_X86_64 x86_64

  Processor ID       : x86 Family 6 Model 44 Stepping 2, 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: 1

Abnormal termination:

Segmentation violation

Register State (from fault):

  RAX = 00007ffa7100c000  RBX = 00007ffa7100c000

  RCX = 0000700006c942d0  RDX = 00000001142b897e

  RSP = 00007ffa7100c000  RBP = 00009b6306c942d0

  RSI = 00007ffa70548690  RDI = 0000000000000000

   R8 = 00007ffa73834870   R9 = 00007ffa7100c000

  R10 = 000000011e85f76a  R11 = 0000000000000000

  R12 = 0000700006c94330  R13 = 00000001141063c7

  R14 = 0000700006c943a0  R15 = 000000011e85f777

  RIP = 00000001192a4f40  RFL = 00007ffa73834870

   CS = 00009b6300305bc3   FS = 000000011e85f76a   GS = 00007ffa7100c1e8

Stack Trace (from fault):

[  0] 0x0000000107349e64 /Applications/freesurfer/7.2.0/MCRv84//bin/maci64/libmwfl.dylib+00028260 _ZN2fl4diag15stacktrace_base7captureERKNS0_14thread_contextEm+00000052

[  1] 0x000000010734da2a /Applications/freesurfer/7.2.0/MCRv84//bin/maci64/libmwfl.dylib+00043562 _ZN2fl4test17terminate_handledEv+00000906

[  2] 0x000000010734d477 /Applications/freesurfer/7.2.0/MCRv84//bin/maci64/libmwfl.dylib+00042103 _ZN2fl4diag13terminate_logEPKcPK17__darwin_ucontext+00000119

[  3] 0x000000010f5cbb7a /Applications/freesurfer/7.2.0/MCRv84//bin/maci64/libmwmcr.dylib+00387962 _Z32mnRunPathDependentInitializationv+00003146

[  4] 0x000000010f5cbe58 /Applications/freesurfer/7.2.0/MCRv84//bin/maci64/libmwmcr.dylib+00388696 _Z32mnRunPathDependentInitializationv+00003880

[  5] 0x000000010f5c9733 /Applications/freesurfer/7.2.0/MCRv84//bin/maci64/libmwmcr.dylib+00378675 mnFatalSignalHandler+00000275

[  6] 0x00007fff5aad3f5a           /usr/lib/system/libsystem_platform.dylib+00008026 _sigtramp+00000026

[  7] 0x0000700006c9ffff                                   <unknown-module>+00000000

[  8] 0x00000001140f7d67 /Applications/freesurfer/7.2.0/MCRv84/sys/java/jre/maci64/jre//lib/server/libjvm.dylib+03128679 jni_GetMethodID+00000126

[  9] 0x0000000112ab5271 /Applications/freesurfer/7.2.0/MCRv84//bin/maci64/libmwjmi.dylib+00160369 _Z12mljGetMethodP7_jclassPKcS2_+00000049

[ 10] 0x000000011e0ba366 /Applications/freesurfer/7.2.0/MCRv84//bin/maci64/libmwhg.dylib+00598886 _ZN2ui14JavaScreenData20getPrimaryScreenRectEv+00000150

[ 11] 0x000000011e0bfef4 /Applications/freesurfer/7.2.0/MCRv84//bin/maci64/libmwhg.dylib+00622324 _ZN10ScreenImpl13getScreenSizeEv+00000036

[ 12] 0x000000011e0be2e2 /Applications/freesurfer/7.2.0/MCRv84//bin/maci64/libmwhg.dylib+00615138 _ZNK2ui24RootScreenAndPointerImpl13getScreenSizeEv+00000018

[ 13] 0x000000011e0c2f58 /Applications/freesurfer/7.2.0/MCRv84//bin/maci64/libmwhg.dylib+00634712 _ZN2ui4Root17getScreenSizeImplEPN4mcos11COSPropInfoEPNS1_9COSClientEPNS1_12COSInterfaceE+00000040

[ 14] 0x000000011e4f9d13 /Applications/freesurfer/7.2.0/MCRv84//bin/maci64/libmwhg.dylib+05053715 _ZN7hgutils6StubPIIN2ui4RootENS_15PropertyStorageIN8graphics8datatype8PositionENS_6NoModeENS_21NoSerializableStorageEEEE8getValueEPN4mcos12COSInterfaceE+00000099

[ 15] 0x0000000110632a6e /Applications/freesurfer/7.2.0/MCRv84//bin/maci64/libmwmcos.dylib+00371310 _ZN4mcos13COSInterfaceI18igetDirectInternalEPNS_12COSInterfaceE+00000110

[ 16] 0x0000000110628c80 /Applications/freesurfer/7.2.0/MCRv84//bin/maci64/libmwmcos.dylib+00330880 _ZN4mcos13COSInterfaceI10igetDirectEPKNS_9COSClientEPNS_12COSInterfaceE+00000128

[ 17] 0x000000011069812b /Applications/freesurfer/7.2.0/MCRv84//bin/maci64/libmwmcos.dylib+00786731 _ZN4mcos28getValueOfKnownClassPropertyEP11mxArray_tagmPKS0_NS_15COSInterfacePtrEPKNS_9COSClientE+00000411

[ 18] 0x0000000110699070 /Applications/freesurfer/7.2.0/MCRv84//bin/maci64/libmwmcos.dylib+00790640 _ZN4mcos16getPropertyValueEPKNS_9COSClientEPNS_8COSClassEPK11mxArray_tagPKcmPS5_+00000416

[ 19] 0x0000000110699483 /Applications/freesurfer/7.2.0/MCRv84//bin/maci64/libmwmcos.dylib+00791683 _ZNK4mcos5GetMI6invokeEPKNS_9COSClientERiPNS_8COSValueEiPKS5_+00000355

[ 20] 0x00000001106811f2 /Applications/freesurfer/7.2.0/MCRv84//bin/maci64/libmwmcos.dylib+00692722 _ZN24OpaqueMethodCallMetaData11callCMethodEPN4mcos13COSMethodInfoEPP11mxArray_tagPKNS0_9COSClientE+00000466

[ 21] 0x0000000110683f4e /Applications/freesurfer/7.2.0/MCRv84//bin/maci64/libmwmcos.dylib+00704334 _ZN24OpaqueMethodCallMetaData23callMethodOrConstructorEP11mxArray_tagbiPS1_iPPKS0_bPKN4mcos9COSClientEPS9_PPNS6_13COSMethodInfoE+00000494

[ 22] 0x0000000110681b3e /Applications/freesurfer/7.2.0/MCRv84//bin/maci64/libmwmcos.dylib+00695102 _Z18mcosCallMethodImplN4mcos9COSNameIDES0_PKNS_9COSClientEiPP11mxArray_tagiPPKS4_bb+00000286

[ 23] 0x0000000110682a82 /Applications/freesurfer/7.2.0/MCRv84//bin/maci64/libmwmcos.dylib+00699010 _Z12omCallMethodN4mcos9COSNameIDES0_PKNS_9COSClientEiPP11mxArray_tagiPPKS4_b+00000114

[ 24] 0x000000011f8686c2 /Applications/freesurfer/7.2.0/MCRv84//bin/maci64/libmwhgutils.dylib+00440002 _ZN7hgutils17MCOSMethodInvoker6invokeEPKN4mcos9COSClientERiPNS1_8COSValueEiPKS6_+00000866

[ 25] 0x000000011f868220 /Applications/freesurfer/7.2.0/MCRv84//bin/maci64/libmwhgutils.dylib+00438816 _ZN7hgutils14callMCOSMethodERKN4mcos9COSNameIDERKNS0_12MemberAccessEPNS0_8COSClassEPKNS0_9COSClientERiPNS0_8COSValueEiPKSD_+00000112

[ 26] 0x000000011f8681a7 /Applications/freesurfer/7.2.0/MCRv84//bin/maci64/libmwhgutils.dylib+00438695 _ZN7hgutils14callMCOSMethodERKN4mcos9COSNameIDEPNS0_8COSClassEPKNS0_9COSClientERiPNS0_8COSValueEiPKSA_+00000055

[ 27] 0x000000011f84e292 /Applications/freesurfer/7.2.0/MCRv84//bin/maci64/libmwhgutils.dylib+00332434 _ZThn8_NK7hgutils22HGPropHandlerClassInfo16areChildrenSavedEv+00029170

[ 28] 0x00000001106811f2 /Applications/freesurfer/7.2.0/MCRv84//bin/maci64/libmwmcos.dylib+00692722 _ZN24OpaqueMethodCallMetaData11callCMethodEPN4mcos13COSMethodInfoEPP11mxArray_tagPKNS0_9COSClientE+00000466

[ 29] 0x0000000110683f4e /Applications/freesurfer/7.2.0/MCRv84//bin/maci64/libmwmcos.dylib+00704334 _ZN24OpaqueMethodCallMetaData23callMethodOrConstructorEP11mxArray_tagbiPS1_iPPKS0_bPKN4mcos9COSClientEPS9_PPNS6_13COSMethodInfoE+00000494

[ 30] 0x0000000110682d41 /Applications/freesurfer/7.2.0/MCRv84//bin/maci64/libmwmcos.dylib+00699713 _Z22omCallMethodWithClientP11mxArray_tagbS0_iPS0_iPPKS_PKN4mcos9COSClientEPS8_PPNS5_13COSMethodInfoE+00000417

[ 31] 0x000000011070e930 /Applications/freesurfer/7.2.0/MCRv84//bin/maci64/libmwmcos.dylib+01272112 _Z18omCallOpaqueMethodP11mxArray_tagS0_iPS0_iPPKS_+00000112

[ 32] 0x000000011d909353 /Applications/freesurfer/7.2.0/MCRv84//bin/maci64/libmwhgbuiltins.dylib+00193363 hgGetWrapper+00000435

[ 33] 0x00000001104b9cc6 /Applications/freesurfer/7.2.0/MCRv84//bin/maci64/libmwm_dispatcher.dylib+00117958 _ZN11Mfh_builtin11dispatch_mfEiPP11mxArray_tagiS2_+00000086

[ 34] 0x00000001104a212d /Applications/freesurfer/7.2.0/MCRv84//bin/maci64/libmwm_dispatcher.dylib+00020781 _ZN13Mfh_MATLAB_fn11dispatch_fhEiPP11mxArray_tagiS2_+00000333

[ 35] 0x000000010f85fd62 /Applications/freesurfer/7.2.0/MCRv84//bin/maci64/libmwm_interpreter.dylib+01523042 _Z19inDispatchFromStackiPKcii+00001650

[ 36] 0x000000010f801dd8 /Applications/freesurfer/7.2.0/MCRv84//bin/maci64/libmwm_interpreter.dylib+01138136 inPcodeWalker+00022552

[ 37] 0x000000010f7fe917 /Applications/freesurfer/7.2.0/MCRv84//bin/maci64/libmwm_interpreter.dylib+01124631 inPcodeWalker+00009047

[ 38] 0x000000010f7f9fb7 /Applications/freesurfer/7.2.0/MCRv84//bin/maci64/libmwm_interpreter.dylib+01105847 inInterPcode+00000935

[ 39] 0x000000010f7fb1c6 /Applications/freesurfer/7.2.0/MCRv84//bin/maci64/libmwm_interpreter.dylib+01110470 _Z26inExecuteMFunctionOrScriptP6Mfh_mpb+00000886

[ 40] 0x000000010f89d1f1 /Applications/freesurfer/7.2.0/MCRv84//bin/maci64/libmwm_interpreter.dylib+01774065 _Z10inRunMfileiPP11mxArray_tagiS1_P6Mfh_mpP15inWorkSpace_tag+00002337

[ 41] 0x00000001104fec28 /Applications/freesurfer/7.2.0/MCRv84//bin/maci64/libmwm_dispatcher.dylib+00400424 _ZN8Mfh_file11dispatch_fhEiPP11mxArray_tagiS2_+00000600

[ 42] 0x00000001106e2e8e /Applications/freesurfer/7.2.0/MCRv84//bin/maci64/libmwmcos.dylib+01093262 _ZNK4mcos17MScopedMethodInfo6invokeEPKNS_9COSClientERiPNS_8COSValueEiPKS5_+00000606

[ 43] 0x0000000110680597 /Applications/freesurfer/7.2.0/MCRv84//bin/maci64/libmwmcos.dylib+00689559 _ZN24OpaqueMethodCallMetaData11callMMethodEPN4mcos13COSMethodInfoEPP11mxArray_tagPKNS0_9COSClientE+00000359

[ 44] 0x0000000110683e63 /Applications/freesurfer/7.2.0/MCRv84//bin/maci64/libmwmcos.dylib+00704099 _ZN24OpaqueMethodCallMetaData23callMethodOrConstructorEP11mxArray_tagbiPS1_iPPKS0_bPKN4mcos9COSClientEPS9_PPNS6_13COSMethodInfoE+00000259

[ 45] 0x0000000110682d41 /Applications/freesurfer/7.2.0/MCRv84//bin/maci64/libmwmcos.dylib+00699713 _Z22omCallMethodWithClientP11mxArray_tagbS0_iPS0_iPPKS_PKN4mcos9COSClientEPS8_PPNS5_13COSMethodInfoE+00000417

[ 46] 0x000000011070eee8 /Applications/freesurfer/7.2.0/MCRv84//bin/maci64/libmwmcos.dylib+01273576 _Z18omCallStaticMethodP11mxArray_tagiPS0_iPPKS_+00000088

[ 47] 0x0000000110797e64 /Applications/freesurfer/7.2.0/MCRv84//bin/maci64/libmwmcos.dylib+01834596 _ZN17Mfh_opaque_static11dispatch_mfEiPP11mxArray_tagiS2_+00000116

[ 48] 0x00000001104a212d /Applications/freesurfer/7.2.0/MCRv84//bin/maci64/libmwm_dispatcher.dylib+00020781 _ZN13Mfh_MATLAB_fn11dispatch_fhEiPP11mxArray_tagiS2_+00000333

[ 49] 0x0000000110794acc /Applications/freesurfer/7.2.0/MCRv84//bin/maci64/libmwmcos.dylib+01821388 _ZN10Mfh_opaque11dispatch_fhEiPP11mxArray_tagiS2_+00000028

[ 50] 0x000000010f85fd62 /Applications/freesurfer/7.2.0/MCRv84//bin/maci64/libmwm_interpreter.dylib+01523042 _Z19inDispatchFromStackiPKcii+00001650

[ 51] 0x000000010f7b559e /Applications/freesurfer/7.2.0/MCRv84//bin/maci64/libmwm_interpreter.dylib+00824734 inCallFcnFromReference+00000110

[ 52] 0x000000010f7fe003 /Applications/freesurfer/7.2.0/MCRv84//bin/maci64/libmwm_interpreter.dylib+01122307 inPcodeWalker+00006723

[ 53] 0x000000010f7f9fb7 /Applications/freesurfer/7.2.0/MCRv84//bin/maci64/libmwm_interpreter.dylib+01105847 inInterPcode+00000935

[ 54] 0x000000010f7fb1c6 /Applications/freesurfer/7.2.0/MCRv84//bin/maci64/libmwm_interpreter.dylib+01110470 _Z26inExecuteMFunctionOrScriptP6Mfh_mpb+00000886

[ 55] 0x000000010f89d1f1 /Applications/freesurfer/7.2.0/MCRv84//bin/maci64/libmwm_interpreter.dylib+01774065 _Z10inRunMfileiPP11mxArray_tagiS1_P6Mfh_mpP15inWorkSpace_tag+00002337

[ 56] 0x00000001104fec55 /Applications/freesurfer/7.2.0/MCRv84//bin/maci64/libmwm_dispatcher.dylib+00400469 _ZN8Mfh_file11dispatch_fhEiPP11mxArray_tagiS2_+00000645

[ 57] 0x000000010f85fd62 /Applications/freesurfer/7.2.0/MCRv84//bin/maci64/libmwm_interpreter.dylib+01523042 _Z19inDispatchFromStackiPKcii+00001650

[ 58] 0x000000010f801dd8 /Applications/freesurfer/7.2.0/MCRv84//bin/maci64/libmwm_interpreter.dylib+01138136 inPcodeWalker+00022552

[ 59] 0x000000010f7fe702 /Applications/freesurfer/7.2.0/MCRv84//bin/maci64/libmwm_interpreter.dylib+01124098 inPcodeWalker+00008514

[ 60] 0x000000010f7f9fb7 /Applications/freesurfer/7.2.0/MCRv84//bin/maci64/libmwm_interpreter.dylib+01105847 inInterPcode+00000935

[ 61] 0x000000010f7f9cad /Applications/freesurfer/7.2.0/MCRv84//bin/maci64/libmwm_interpreter.dylib+01105069 inInterPcode+00000157

[ 62] 0x000000010f7f0b9f /Applications/freesurfer/7.2.0/MCRv84//bin/maci64/libmwm_interpreter.dylib+01067935 _ZN12InterpBridge33DoMatlabFcnCallInDesiredWorkspaceEiPP11mxArray_tagiPPKS0_P13Mfh_MATLAB_fnP15inWorkSpace_tag+00004015

[ 63] 0x000000010f7f2a79 /Applications/freesurfer/7.2.0/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] 0x000000010f7ee28d /Applications/freesurfer/7.2.0/MCRv84//bin/maci64/libmwm_interpreter.dylib+01057421 _Z12inEvalStringP15_memory_contextRKSbItSt11char_traitsItESaItEE8EvalTypeiPP11mxArray_tag12inDebugCheckP12_pcodeheaderPib+00002877

[ 65] 0x000000010f7ee7cd /Applications/freesurfer/7.2.0/MCRv84//bin/maci64/libmwm_interpreter.dylib+01058765 _ZN12InterpBridge22EvalCmdWithLocalReturnERKSbItSt11char_traitsItESaItEEPibb+00000141

[ 66] 0x000000010f7eec05 /Applications/freesurfer/7.2.0/MCRv84//bin/maci64/libmwm_interpreter.dylib+01059845 _ZN12InterpBridge7EvalCmdERKSbItSt11char_traitsItESaItEEb+00000021

[ 67] 0x000000010f74c347 /Applications/freesurfer/7.2.0/MCRv84//bin/maci64/libmwm_interpreter.dylib+00394055 inEvalCmd+00000119

[ 68] 0x000000010f5a37fa /Applications/freesurfer/7.2.0/MCRv84//bin/maci64/libmwmcr.dylib+00223226 _Z16mnRunLoginScriptv+00000586

[ 69] 0x000000010f5caf63 /Applications/freesurfer/7.2.0/MCRv84//bin/maci64/libmwmcr.dylib+00384867 _Z32mnRunPathDependentInitializationv+00000051

[ 70] 0x000000010f5b180c /Applications/freesurfer/7.2.0/MCRv84//bin/maci64/libmwmcr.dylib+00280588 _ZN11mcrInstance26init_on_interpreter_threadEP11MfileReaderP13MexFileReader+00000988

[ 71] 0x000000010f5bffb8 /Applications/freesurfer/7.2.0/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] 0x000000010f5bedc1 /Applications/freesurfer/7.2.0/MCRv84//bin/maci64/libmwmcr.dylib+00335297 _ZN3mcr7runtime17InterpreterThread4Impl22TypedInvocationRequestIbE29doNotRethrowMxArrayExceptionsERKN5boost8functionIFbvEEE+00000033

[ 73] 0x000000010f5bfbd9 /Applications/freesurfer/7.2.0/MCRv84//bin/maci64/libmwmcr.dylib+00338905 _ZN5boost6detail11task_objectIbNS_3_bi6bind_tIbPFbRKNS_8functionIFbvEEEENS2_5list1INS2_5valueIS6_EEEEEEE6do_runEv+00000025

[ 74] 0x000000010f5bf276 /Applications/freesurfer/7.2.0/MCRv84//bin/maci64/libmwmcr.dylib+00336502 _ZN5boost6detail9task_baseIbE3runEv+00000166

[ 75] 0x000000010f5bf067 /Applications/freesurfer/7.2.0/MCRv84//bin/maci64/libmwmcr.dylib+00335975 _ZN3mcr7runtime17InterpreterThread4Impl22TypedInvocationRequestIbE3runEv+00000023

[ 76] 0x000000010f589f90 /Applications/freesurfer/7.2.0/MCRv84//bin/maci64/libmwmcr.dylib+00118672 _ZN3mcr7runtime17InterpreterThread4Impl26invocation_request_handlerEl+00000032

[ 77] 0x0000000105132005 /Applications/freesurfer/7.2.0/MCRv84//bin/maci64/libmwservices.dylib+00196613 _ZN10eventqueue18UserEventQueueImpl5flushEv+00001205

[ 78] 0x0000000110d34a65 /Applications/freesurfer/7.2.0/MCRv84//bin/maci64/libmwuix.dylib+00043621 _Z25isHandleUserEventCallbackPFvPvE+00000501

[ 79] 0x0000000105201a45 /Applications/freesurfer/7.2.0/MCRv84//bin/maci64/libmwservices.dylib+01047109 _Z21svWS_ProcessCallbacksv+00016693

[ 80] 0x00000001051fd152 /Applications/freesurfer/7.2.0/MCRv84//bin/maci64/libmwservices.dylib+01028434 _Z25svWS_ProcessPendingEventsiib+00000834

[ 81] 0x00000001051fce5e /Applications/freesurfer/7.2.0/MCRv84//bin/maci64/libmwservices.dylib+01027678 _Z25svWS_ProcessPendingEventsiib+00000078

[ 82] 0x000000010f58a18f /Applications/freesurfer/7.2.0/MCRv84//bin/maci64/libmwmcr.dylib+00119183 _ZN3mcr7runtime17InterpreterThread4Impl14process_eventsERKN5boost10shared_ptrIS2_EE+00000095

[ 83] 0x000000010f58a49f /Applications/freesurfer/7.2.0/MCRv84//bin/maci64/libmwmcr.dylib+00119967 _ZN3mcr7runtime17InterpreterThread4Impl3runERKN5boost10shared_ptrIS2_EEPNS2_12init_contextE+00000335

[ 84] 0x000000010f570d1b /Applications/freesurfer/7.2.0/MCRv84//bin/maci64/libmwmcr.dylib+00015643 _Z26run_init_and_handle_eventsPv+00000059

[ 85] 0x00007fff5aadd661            /usr/lib/system/libsystem_pthread.dylib+00013921 _pthread_body+00000340

[ 86] 0x00007fff5aadd50d            /usr/lib/system/libsystem_pthread.dylib+00013581 _pthread_body+00000000

[ 87] 0x00007fff5aadcbf9            /usr/lib/system/libsystem_pthread.dylib+00011257 thread_start+00000013

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.

I did a bit of reading and saw this post.

I installed v93 and soft linked it as MCRv84. But no luck, I now receive this error:

Setting ITK threads to 1

#--------------------------------------------

#@# Thalamic Nuclei processing Sat 27 Aug 2022 10:28:43 AEST

------------------------------------------

Setting up environment variables

---

DYLD_LIBRARY_PATH is .:/Applications/freesurfer/7.2.0/MCRv84//runtime/maci64:/Applications/freesurfer/7.2.0/MCRv84//bin/maci64:/Applications/freesurfer/7.2.0/MCRv84//sys/os/maci64:/Applications/freesurfer/7.2.0/lib/gcc/lib:

dyld: lazy symbol binding failed: Symbol not found: __Z14standaloneMainRKSt6vectorISsSaISsEEbb

  Referenced from: /Applications/freesurfer/7.2.0/bin/SegmentThalamicNuclei.app/Contents/MacOS/SegmentThalamicNuclei

  Expected in: /Applications/freesurfer/7.2.0/MCRv84//bin/maci64/libmwlaunchermain.dylib

dyld: Symbol not found: __Z14standaloneMainRKSt6vectorISsSaISsEEbb

  Referenced from: /Applications/freesurfer/7.2.0/bin/SegmentThalamicNuclei.app/Contents/MacOS/SegmentThalamicNuclei

  Expected in: /Applications/freesurfer/7.2.0/MCRv84//bin/maci64/libmwlaunchermain.dylib

/Applications/freesurfer/7.2.0/bin/run_SegmentThalamicNuclei.sh: line 33: 83766 Abort trap: 6           /Applications/freesurfer/7.2.0/bin/SegmentThalamicNuclei.app/Contents/MacOS/SegmentThalamicNuclei sub-BA_105131 /Volumes/MacintoshHD2/mridata/ASRB/ENIGMA_SZ_Thalamic_nuclei/Subjects 0.5 /Applications/freesurfer/7.2.0/average/ThalamicNuclei/atlas/AtlasMesh.gz /Applications/freesurfer/7.2.0/average/ThalamicNuclei/atlas/AtlasDump.mgz /Applications/freesurfer/7.2.0/average/ThalamicNuclei/atlas/compressionLookupTable.txt 0.05 L-BFGS v12 '/Applications/freesurfer/7.2.0/bin/fs_run_from_mcr /Applications/freesurfer/7.2.0/bin/' 1 0

134

Darwin Ians-Mac-Pro.local 17.7.0 Darwin Kernel Version 17.7.0: Fri Oct 30 13:34:27 PDT 2020; root:xnu-4570.71.82.8~1/RELEASE_X86_64 x86_64

Thalamic nuclei exited with ERRORS at Sat 27 Aug 2022 10:28:44 AEST

It seems that FS is looking for v84 files that are missing in v93?

Does anyone have an idea of what I am doing wrong?

Thanks in advance.

Yann

On 20 Aug 2022, at 9:42 am, Yann Quidé <yannquide@gmail.com> wrote:

Not a good news for me, but thanks!

Yann

On 20 Aug 2022, at 06:40, fsbuild <fsbuild@contbay.com> wrote:

Hello Yann,

It looks like the system library, /usr/lib/libSystem.B.dylib, is too old on your machine running MacOS (10.13) to work with the Matlab MCRv97 runtime environment.   MacOS 10.13 (High Sierra), 10.14 (Mojave) - are no longer supported by Apple.  Soon Apple will also drop support for MacOS10.15 (Catalina).  I think you would need to upgrade to Catalina to use the Matlab R2019b release as installed by the script ./freesurfer/bin/fs_install_mcr

- R.

On Aug 19, 2022, at 07:33, Yann Quidé <yannquide@gmail.com> wrote:

        External Email - Use Caution        

Hi team,

I am trying to run the thalamic nuclei pipeline with FS7.3.2, on scans processed with recon-all from FS5.3 (mac OSX10.13).

However, I receive the below error.

Any idea how I could solve this?

Thanks in advance.

Yann

------------------------------

USER yann

HOST Ians-Mac-Pro.local

PROCESSID 86082 

PROCESSOR x86_64

OS Darwin

ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS 1 

Darwin Ians-Mac-Pro.local 17.7.0 Darwin Kernel Version 17.7.0: Fri Oct 30 13:34:27 PDT 2020; root:xnu-4570.71.82.8~1/RELEASE_X86_64 x86_64

------------------------------

freesurfer-darwin-macOS-7.3.2-20220804-6354275

 

setenv SUBJECTS_DIR /Volumes/MacintoshHD2/mridata/IGP/ENIGMA_SZ_Thalamic_nuclei/Subjects

cd /Volumes/MacintoshHD2/mridata/IGP/ENIGMA_SZ_Thalamic_nuclei/ENIGMA_BARI

/Applications/freesurfer/7.3.2/bin/segmentThalamicNuclei.sh sub-BA_IGP001

#--------------------------------------------

#@# Thalamic Nuclei processing Fri 19 Aug 2022 20:10:24 AEST

------------------------------------------

Setting up environment variables

---

DYLD_LIBRARY_PATH is .:/Applications/freesurfer/7.3.2/MCRv97//runtime/maci64:/Applications/freesurfer/7.3.2/MCRv97//bin/maci64:/Applications/freesurfer/7.3.2/MCRv97//sys/os/maci64:/Applications/freesurfer/7.3.2/lib/gcc/lib:

Invalid MEX-file '/private/tmp/MCR_3324153754/.mcrCache9.7/Segmen0/Users/developer/eugenio/GEMS2.build/bin/kvlGEMSMatlab.mexmaci64': dlopen(/private/tmp/MCR_3324153754/.mcrCache9.7/Segmen0/Users/developer/eugenio/GEMS2.build/bin/kvlGEMSMatlab.mexmaci64, 6): Symbol not found: ____chkstk_darwin

  Referenced from: /private/tmp/MCR_3324153754/.mcrCache9.7/Segmen0/Users/developer/eugenio/GEMS2.build/bin/kvlGEMSMatlab.mexmaci64 (which was built for Mac OS X 10.15)

  Expected in: /usr/lib/libSystem.B.dylib

 in /private/tmp/MCR_3324153754/.mcrCache9.7/Segmen0/Users/developer/eugenio/GEMS2.build/bin/kvlGEMSMatlab.mexmaci64

Error in kvlClear (line 11)

Error in SegmentThalamicNuclei (line 139)

MATLAB:mex:ErrInvalidMEXFile

Darwin Ians-Mac-Pro.local 17.7.0 Darwin Kernel Version 17.7.0: Fri Oct 30 13:34:27 PDT 2020; root:xnu-4570.71.82.8~1/RELEASE_X86_64 x86_64

Thalamic nuclei exited with ERRORS at Fri 19 Aug 2022 20:11:24 AEST

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