When trying to run the segmentHA_T1_long.sh command on my data I get the following error log posted below (I ran several versions of a for loop and got issues with all of them). I closed out the matlab browsers and am retrying the code again to see if it is reproducible and so afar it is running. I just wanted to get an idea if this is a known problem.

Best,

Daniel

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

       Segmentation violation detected at Sat Mar 23 18:31:18 2019

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

Configuration:

  Crash Decoding     : Disabled

  Current Visual     : Quartz

  Default Encoding   : ISO-8859-1

  MATLAB Architecture: maci64

  MATLAB Root        : /Applications/freesurfer_dev/MCRv84

  MATLAB Version     : 8.4.0.150421 (R2014b)

  Operating System   : Darwin 16.7.0 Darwin Kernel Version 16.7.0: Wed Oct 10 20:06:00 PDT 2018; root:xnu-3789.73.24~1/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 = 00007f9c4806f000  RBX = 00007f9c4806f000

  RCX = 0000700009ab52d0  RDX = 000000011392e97e

  RSP = 00007f9c4806f000  RBP = 00009b6309ab52d0

  RSI = 00007f9c47637ba0  RDI = 0000000000000000

   R8 = 00007f9c4a0a3270   R9 = 00007f9c4806f000

  R10 = 000000011e59176a  R11 = 0000000000000000

  R12 = 0000700009ab5330  R13 = 000000011377c3c7

  R14 = 0000700009ab53a0  R15 = 000000011e591777

  RIP = 00000001188c5f40  RFL = 00007f9c4a0a3270

   CS = 00009b6300305bc3   FS = 000000011e59176a   GS = 00007f9c4806f1e8

Stack Trace (from fault):

[  0] 0x00000001075f6e64 /Applications/freesurfer_dev/MCRv84//bin/maci64/libmwfl.dylib+00028260 _ZN2fl4diag15stacktrace_base7captureERKNS0_14thread_contextEm+00000052

[  1] 0x00000001075faa2a /Applications/freesurfer_dev/MCRv84//bin/maci64/libmwfl.dylib+00043562 _ZN2fl4test17terminate_handledEv+00000906

[  2] 0x00000001075fa477 /Applications/freesurfer_dev/MCRv84//bin/maci64/libmwfl.dylib+00042103 _ZN2fl4diag13terminate_logEPKcPK17__darwin_ucontext+00000119

[  3] 0x000000010c443b7a /Applications/freesurfer_dev/MCRv84//bin/maci64/libmwmcr.dylib+00387962 _Z32mnRunPathDependentInitializationv+00003146

[  4] 0x000000010c443e58 /Applications/freesurfer_dev/MCRv84//bin/maci64/libmwmcr.dylib+00388696 _Z32mnRunPathDependentInitializationv+00003880

[  5] 0x000000010c441733 /Applications/freesurfer_dev/MCRv84//bin/maci64/libmwmcr.dylib+00378675 mnFatalSignalHandler+00000275

[  6] 0x00007fffbac1cb3a           /usr/lib/system/libsystem_platform.dylib+00011066 _sigtramp+00000026

[  7] 0x000000011377d6f8 /Applications/freesurfer_dev/MCRv84/sys/java/jre/maci64/jre//lib/server/libjvm.dylib+03192568 _ZN23JNI_ArgumentPusherVaArg7iterateEy+00000000

[  8] 0x000000011376dd67 /Applications/freesurfer_dev/MCRv84/sys/java/jre/maci64/jre//lib/server/libjvm.dylib+03128679 jni_GetMethodID+00000126

[  9] 0x000000010f8ca271 /Applications/freesurfer_dev/MCRv84//bin/maci64/libmwjmi.dylib+00160369 _Z12mljGetMethodP7_jclassPKcS2_+00000049

[ 10] 0x000000011ddec366 /Applications/freesurfer_dev/MCRv84//bin/maci64/libmwhg.dylib+00598886 _ZN2ui14JavaScreenData20getPrimaryScreenRectEv+00000150

[ 11] 0x000000011ddf1ef4 /Applications/freesurfer_dev/MCRv84//bin/maci64/libmwhg.dylib+00622324 _ZN10ScreenImpl13getScreenSizeEv+00000036

[ 12] 0x000000011ddf02e2 /Applications/freesurfer_dev/MCRv84//bin/maci64/libmwhg.dylib+00615138 _ZNK2ui24RootScreenAndPointerImpl13getScreenSizeEv+00000018

[ 13] 0x000000011ddf4f58 /Applications/freesurfer_dev/MCRv84//bin/maci64/libmwhg.dylib+00634712 _ZN2ui4Root17getScreenSizeImplEPN4mcos11COSPropInfoEPNS1_9COSClientEPNS1_12COSInterfaceE+00000040

[ 14] 0x000000011e22bd13 /Applications/freesurfer_dev/MCRv84//bin/maci64/libmwhg.dylib+05053715 _ZN7hgutils6StubPIIN2ui4RootENS_15PropertyStorageIN8graphics8datatype8PositionENS_6NoModeENS_21NoSerializableStorageEEEE8getValueEPN4mcos12COSInterfaceE+00000099

[ 15] 0x000000010d4e9a6e /Applications/freesurfer_dev/MCRv84//bin/maci64/libmwmcos.dylib+00371310 _ZN4mcos13COSInterfaceI18igetDirectInternalEPNS_12COSInterfaceE+00000110

[ 16] 0x000000010d4dfc80 /Applications/freesurfer_dev/MCRv84//bin/maci64/libmwmcos.dylib+00330880 _ZN4mcos13COSInterfaceI10igetDirectEPKNS_9COSClientEPNS_12COSInterfaceE+00000128

[ 17] 0x000000010d54f12b /Applications/freesurfer_dev/MCRv84//bin/maci64/libmwmcos.dylib+00786731 _ZN4mcos28getValueOfKnownClassPropertyEP11mxArray_tagmPKS0_NS_15COSInterfacePtrEPKNS_9COSClientE+00000411

[ 18] 0x000000010d550070 /Applications/freesurfer_dev/MCRv84//bin/maci64/libmwmcos.dylib+00790640 _ZN4mcos16getPropertyValueEPKNS_9COSClientEPNS_8COSClassEPK11mxArray_tagPKcmPS5_+00000416

[ 19] 0x000000010d550483 /Applications/freesurfer_dev/MCRv84//bin/maci64/libmwmcos.dylib+00791683 _ZNK4mcos5GetMI6invokeEPKNS_9COSClientERiPNS_8COSValueEiPKS5_+00000355

[ 20] 0x000000010d5381f2 /Applications/freesurfer_dev/MCRv84//bin/maci64/libmwmcos.dylib+00692722 _ZN24OpaqueMethodCallMetaData11callCMethodEPN4mcos13COSMethodInfoEPP11mxArray_tagPKNS0_9COSClientE+00000466

[ 21] 0x000000010d53af4e /Applications/freesurfer_dev/MCRv84//bin/maci64/libmwmcos.dylib+00704334 _ZN24OpaqueMethodCallMetaData23callMethodOrConstructorEP11mxArray_tagbiPS1_iPPKS0_bPKN4mcos9COSClientEPS9_PPNS6_13COSMethodInfoE+00000494

[ 22] 0x000000010d538b3e /Applications/freesurfer_dev/MCRv84//bin/maci64/libmwmcos.dylib+00695102 _Z18mcosCallMethodImplN4mcos9COSNameIDES0_PKNS_9COSClientEiPP11mxArray_tagiPPKS4_bb+00000286

[ 23] 0x000000010d539a82 /Applications/freesurfer_dev/MCRv84//bin/maci64/libmwmcos.dylib+00699010 _Z12omCallMethodN4mcos9COSNameIDES0_PKNS_9COSClientEiPP11mxArray_tagiPPKS4_b+00000114

[ 24] 0x000000011f59a6c2 /Applications/freesurfer_dev/MCRv84//bin/maci64/libmwhgutils.dylib+00440002 _ZN7hgutils17MCOSMethodInvoker6invokeEPKN4mcos9COSClientERiPNS1_8COSValueEiPKS6_+00000866

[ 25] 0x000000011f59a220 /Applications/freesurfer_dev/MCRv84//bin/maci64/libmwhgutils.dylib+00438816 _ZN7hgutils14callMCOSMethodERKN4mcos9COSNameIDERKNS0_12MemberAccessEPNS0_8COSClassEPKNS0_9COSClientERiPNS0_8COSValueEiPKSD_+00000112

[ 26] 0x000000011f59a1a7 /Applications/freesurfer_dev/MCRv84//bin/maci64/libmwhgutils.dylib+00438695 _ZN7hgutils14callMCOSMethodERKN4mcos9COSNameIDEPNS0_8COSClassEPKNS0_9COSClientERiPNS0_8COSValueEiPKSA_+00000055

[ 27] 0x000000011f580292 /Applications/freesurfer_dev/MCRv84//bin/maci64/libmwhgutils.dylib+00332434 _ZThn8_NK7hgutils22HGPropHandlerClassInfo16areChildrenSavedEv+00029170

[ 28] 0x000000010d5381f2 /Applications/freesurfer_dev/MCRv84//bin/maci64/libmwmcos.dylib+00692722 _ZN24OpaqueMethodCallMetaData11callCMethodEPN4mcos13COSMethodInfoEPP11mxArray_tagPKNS0_9COSClientE+00000466

[ 29] 0x000000010d53af4e /Applications/freesurfer_dev/MCRv84//bin/maci64/libmwmcos.dylib+00704334 _ZN24OpaqueMethodCallMetaData23callMethodOrConstructorEP11mxArray_tagbiPS1_iPPKS0_bPKN4mcos9COSClientEPS9_PPNS6_13COSMethodInfoE+00000494

[ 30] 0x000000010d539d41 /Applications/freesurfer_dev/MCRv84//bin/maci64/libmwmcos.dylib+00699713 _Z22omCallMethodWithClientP11mxArray_tagbS0_iPS0_iPPKS_PKN4mcos9COSClientEPS8_PPNS5_13COSMethodInfoE+00000417

[ 31] 0x000000010d5c5930 /Applications/freesurfer_dev/MCRv84//bin/maci64/libmwmcos.dylib+01272112 _Z18omCallOpaqueMethodP11mxArray_tagS0_iPS0_iPPKS_+00000112

[ 32] 0x000000011d63b353 /Applications/freesurfer_dev/MCRv84//bin/maci64/libmwhgbuiltins.dylib+00193363 hgGetWrapper+00000435

[ 33] 0x000000010d370cc6 /Applications/freesurfer_dev/MCRv84//bin/maci64/libmwm_dispatcher.dylib+00117958 _ZN11Mfh_builtin11dispatch_mfEiPP11mxArray_tagiS2_+00000086

[ 34] 0x000000010d35912d /Applications/freesurfer_dev/MCRv84//bin/maci64/libmwm_dispatcher.dylib+00020781 _ZN13Mfh_MATLAB_fn11dispatch_fhEiPP11mxArray_tagiS2_+00000333

[ 35] 0x000000010c716d62 /Applications/freesurfer_dev/MCRv84//bin/maci64/libmwm_interpreter.dylib+01523042 _Z19inDispatchFromStackiPKcii+00001650

[ 36] 0x000000010c6b8dd8 /Applications/freesurfer_dev/MCRv84//bin/maci64/libmwm_interpreter.dylib+01138136 inPcodeWalker+00022552

[ 37] 0x000000010c6b5917 /Applications/freesurfer_dev/MCRv84//bin/maci64/libmwm_interpreter.dylib+01124631 inPcodeWalker+00009047

[ 38] 0x000000010c6b0fb7 /Applications/freesurfer_dev/MCRv84//bin/maci64/libmwm_interpreter.dylib+01105847 inInterPcode+00000935

[ 39] 0x000000010c6b21c6 /Applications/freesurfer_dev/MCRv84//bin/maci64/libmwm_interpreter.dylib+01110470 _Z26inExecuteMFunctionOrScriptP6Mfh_mpb+00000886

[ 40] 0x000000010c7541f1 /Applications/freesurfer_dev/MCRv84//bin/maci64/libmwm_interpreter.dylib+01774065 _Z10inRunMfileiPP11mxArray_tagiS1_P6Mfh_mpP15inWorkSpace_tag+00002337

[ 41] 0x000000010d3b5c28 /Applications/freesurfer_dev/MCRv84//bin/maci64/libmwm_dispatcher.dylib+00400424 _ZN8Mfh_file11dispatch_fhEiPP11mxArray_tagiS2_+00000600

[ 42] 0x000000010d599e8e /Applications/freesurfer_dev/MCRv84//bin/maci64/libmwmcos.dylib+01093262 _ZNK4mcos17MScopedMethodInfo6invokeEPKNS_9COSClientERiPNS_8COSValueEiPKS5_+00000606

[ 43] 0x000000010d537597 /Applications/freesurfer_dev/MCRv84//bin/maci64/libmwmcos.dylib+00689559 _ZN24OpaqueMethodCallMetaData11callMMethodEPN4mcos13COSMethodInfoEPP11mxArray_tagPKNS0_9COSClientE+00000359

[ 44] 0x000000010d53ae63 /Applications/freesurfer_dev/MCRv84//bin/maci64/libmwmcos.dylib+00704099 _ZN24OpaqueMethodCallMetaData23callMethodOrConstructorEP11mxArray_tagbiPS1_iPPKS0_bPKN4mcos9COSClientEPS9_PPNS6_13COSMethodInfoE+00000259

[ 45] 0x000000010d539d41 /Applications/freesurfer_dev/MCRv84//bin/maci64/libmwmcos.dylib+00699713 _Z22omCallMethodWithClientP11mxArray_tagbS0_iPS0_iPPKS_PKN4mcos9COSClientEPS8_PPNS5_13COSMethodInfoE+00000417

[ 46] 0x000000010d5c5ee8 /Applications/freesurfer_dev/MCRv84//bin/maci64/libmwmcos.dylib+01273576 _Z18omCallStaticMethodP11mxArray_tagiPS0_iPPKS_+00000088

[ 47] 0x000000010d64ee64 /Applications/freesurfer_dev/MCRv84//bin/maci64/libmwmcos.dylib+01834596 _ZN17Mfh_opaque_static11dispatch_mfEiPP11mxArray_tagiS2_+00000116

[ 48] 0x000000010d35912d /Applications/freesurfer_dev/MCRv84//bin/maci64/libmwm_dispatcher.dylib+00020781 _ZN13Mfh_MATLAB_fn11dispatch_fhEiPP11mxArray_tagiS2_+00000333

[ 49] 0x000000010d64bacc /Applications/freesurfer_dev/MCRv84//bin/maci64/libmwmcos.dylib+01821388 _ZN10Mfh_opaque11dispatch_fhEiPP11mxArray_tagiS2_+00000028

[ 50] 0x000000010c716d62 /Applications/freesurfer_dev/MCRv84//bin/maci64/libmwm_interpreter.dylib+01523042 _Z19inDispatchFromStackiPKcii+00001650

[ 51] 0x000000010c66c59e /Applications/freesurfer_dev/MCRv84//bin/maci64/libmwm_interpreter.dylib+00824734 inCallFcnFromReference+00000110

[ 52] 0x000000010c6b5003 /Applications/freesurfer_dev/MCRv84//bin/maci64/libmwm_interpreter.dylib+01122307 inPcodeWalker+00006723

[ 53] 0x000000010c6b0fb7 /Applications/freesurfer_dev/MCRv84//bin/maci64/libmwm_interpreter.dylib+01105847 inInterPcode+00000935

[ 54] 0x000000010c6b21c6 /Applications/freesurfer_dev/MCRv84//bin/maci64/libmwm_interpreter.dylib+01110470 _Z26inExecuteMFunctionOrScriptP6Mfh_mpb+00000886

[ 55] 0x000000010c7541f1 /Applications/freesurfer_dev/MCRv84//bin/maci64/libmwm_interpreter.dylib+01774065 _Z10inRunMfileiPP11mxArray_tagiS1_P6Mfh_mpP15inWorkSpace_tag+00002337

[ 56] 0x000000010d3b5c55 /Applications/freesurfer_dev/MCRv84//bin/maci64/libmwm_dispatcher.dylib+00400469 _ZN8Mfh_file11dispatch_fhEiPP11mxArray_tagiS2_+00000645

[ 57] 0x000000010c716d62 /Applications/freesurfer_dev/MCRv84//bin/maci64/libmwm_interpreter.dylib+01523042 _Z19inDispatchFromStackiPKcii+00001650

[ 58] 0x000000010c6b8dd8 /Applications/freesurfer_dev/MCRv84//bin/maci64/libmwm_interpreter.dylib+01138136 inPcodeWalker+00022552

[ 59] 0x000000010c6b5702 /Applications/freesurfer_dev/MCRv84//bin/maci64/libmwm_interpreter.dylib+01124098 inPcodeWalker+00008514

[ 60] 0x000000010c6b0fb7 /Applications/freesurfer_dev/MCRv84//bin/maci64/libmwm_interpreter.dylib+01105847 inInterPcode+00000935

[ 61] 0x000000010c6b0cad /Applications/freesurfer_dev/MCRv84//bin/maci64/libmwm_interpreter.dylib+01105069 inInterPcode+00000157

[ 62] 0x000000010c6a7b9f /Applications/freesurfer_dev/MCRv84//bin/maci64/libmwm_interpreter.dylib+01067935 _ZN12InterpBridge33DoMatlabFcnCallInDesiredWorkspaceEiPP11mxArray_tagiPPKS0_P13Mfh_MATLAB_fnP15inWorkSpace_tag+00004015

[ 63] 0x000000010c6a9a79 /Applications/freesurfer_dev/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] 0x000000010c6a528d /Applications/freesurfer_dev/MCRv84//bin/maci64/libmwm_interpreter.dylib+01057421 _Z12inEvalStringP15_memory_contextRKSbItSt11char_traitsItESaItEE8EvalTypeiPP11mxArray_tag12inDebugCheckP12_pcodeheaderPib+00002877

[ 65] 0x000000010c6a57cd /Applications/freesurfer_dev/MCRv84//bin/maci64/libmwm_interpreter.dylib+01058765 _ZN12InterpBridge22EvalCmdWithLocalReturnERKSbItSt11char_traitsItESaItEEPibb+00000141

[ 66] 0x000000010c6a5c05 /Applications/freesurfer_dev/MCRv84//bin/maci64/libmwm_interpreter.dylib+01059845 _ZN12InterpBridge7EvalCmdERKSbItSt11char_traitsItESaItEEb+00000021

[ 67] 0x000000010c603347 /Applications/freesurfer_dev/MCRv84//bin/maci64/libmwm_interpreter.dylib+00394055 inEvalCmd+00000119

[ 68] 0x000000010c41b7fa /Applications/freesurfer_dev/MCRv84//bin/maci64/libmwmcr.dylib+00223226 _Z16mnRunLoginScriptv+00000586

[ 69] 0x000000010c442f63 /Applications/freesurfer_dev/MCRv84//bin/maci64/libmwmcr.dylib+00384867 _Z32mnRunPathDependentInitializationv+00000051

[ 70] 0x000000010c42980c /Applications/freesurfer_dev/MCRv84//bin/maci64/libmwmcr.dylib+00280588 _ZN11mcrInstance26init_on_interpreter_threadEP11MfileReaderP13MexFileReader+00000988

[ 71] 0x000000010c437fb8 /Applications/freesurfer_dev/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] 0x000000010c436dc1 /Applications/freesurfer_dev/MCRv84//bin/maci64/libmwmcr.dylib+00335297 _ZN3mcr7runtime17InterpreterThread4Impl22TypedInvocationRequestIbE29doNotRethrowMxArrayExceptionsERKN5boost8functionIFbvEEE+00000033

[ 73] 0x000000010c437bd9 /Applications/freesurfer_dev/MCRv84//bin/maci64/libmwmcr.dylib+00338905 _ZN5boost6detail11task_objectIbNS_3_bi6bind_tIbPFbRKNS_8functionIFbvEEEENS2_5list1INS2_5valueIS6_EEEEEEE6do_runEv+00000025

[ 74] 0x000000010c437276 /Applications/freesurfer_dev/MCRv84//bin/maci64/libmwmcr.dylib+00336502 _ZN5boost6detail9task_baseIbE3runEv+00000166

[ 75] 0x000000010c437067 /Applications/freesurfer_dev/MCRv84//bin/maci64/libmwmcr.dylib+00335975 _ZN3mcr7runtime17InterpreterThread4Impl22TypedInvocationRequestIbE3runEv+00000023

[ 76] 0x000000010c401f90 /Applications/freesurfer_dev/MCRv84//bin/maci64/libmwmcr.dylib+00118672 _ZN3mcr7runtime17InterpreterThread4Impl26invocation_request_handlerEl+00000032

[ 77] 0x0000000105114005 /Applications/freesurfer_dev/MCRv84//bin/maci64/libmwservices.dylib+00196613 _ZN10eventqueue18UserEventQueueImpl5flushEv+00001205

[ 78] 0x000000010dbeba65 /Applications/freesurfer_dev/MCRv84//bin/maci64/libmwuix.dylib+00043621 _Z25isHandleUserEventCallbackPFvPvE+00000501

[ 79] 0x00000001051e3a45 /Applications/freesurfer_dev/MCRv84//bin/maci64/libmwservices.dylib+01047109 _Z21svWS_ProcessCallbacksv+00016693

[ 80] 0x00000001051df152 /Applications/freesurfer_dev/MCRv84//bin/maci64/libmwservices.dylib+01028434 _Z25svWS_ProcessPendingEventsiib+00000834

[ 81] 0x00000001051dee5e /Applications/freesurfer_dev/MCRv84//bin/maci64/libmwservices.dylib+01027678 _Z25svWS_ProcessPendingEventsiib+00000078

[ 82] 0x000000010c40218f /Applications/freesurfer_dev/MCRv84//bin/maci64/libmwmcr.dylib+00119183 _ZN3mcr7runtime17InterpreterThread4Impl14process_eventsERKN5boost10shared_ptrIS2_EE+00000095

[ 83] 0x000000010c40249f /Applications/freesurfer_dev/MCRv84//bin/maci64/libmwmcr.dylib+00119967 _ZN3mcr7runtime17InterpreterThread4Impl3runERKN5boost10shared_ptrIS2_EEPNS2_12init_contextE+00000335

[ 84] 0x000000010c3e8d1b /Applications/freesurfer_dev/MCRv84//bin/maci64/libmwmcr.dylib+00015643 _Z26run_init_and_handle_eventsPv+00000059

[ 85] 0x00007fffbac2693b            /usr/lib/system/libsystem_pthread.dylib+00014651 _pthread_body+00000180

[ 86] 0x00007fffbac26887            /usr/lib/system/libsystem_pthread.dylib+00014471 _pthread_body+00000000

[ 87] 0x00007fffbac2608d            /usr/lib/system/libsystem_pthread.dylib+00012429 thread_start+00000013

If this problem is reproducible, please submit a Service Request via:

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A technical support engineer might contact you with further information.

Thank you for your help.

Daniel Callow