MATLAB Answers

Segmentation violation when using freesurfer 7.1.1 with MCR 8.4

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Natalie Jenkins
Natalie Jenkins on 18 Dec 2020
Answered: Saurav Chaudhary on 21 Dec 2020
Using MacOS 11.1 each time I try to run freesurfer 7.0 with MCR 8.4 I receieve a segementation violation error with the following crash dump report:
Segmentation violation detected at Fri Dec 18 18:04:54 2020
------------------------------------------------------------------------
Configuration:
Crash Decoding : Disabled
Current Visual : Quartz
Default Encoding : ISO-8859-1
MATLAB Architecture: maci64
MATLAB Root : /Applications/freesurfer/7.1.1/MCRv84
MATLAB Version : 8.4.0.150421 (R2014b)
Operating System : Darwin 20.2.0 Darwin Kernel Version 20.2.0: Wed Dec 2 20:39:59 PST 2020; root:xnu-7195.60.75~1/RELEASE_X86_64 x86_64
Processor ID : x86 Family 6 Model 142 Stepping 10, 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 = 0000000000000003 RBX = 0000000102a1b080
RCX = 00007fe7f0c00000 RDX = 000070000dcc4180
RSP = 00007fe7f0c00000 RBP = 00007fff2019095e
RSI = 0000700000000000 RDI = 00007fff201921f9
R8 = 00000000f4970f10 R9 = 000070000dcc4180
R10 = 00007fff20180002 R11 = 00007fe7f0cf5920
R12 = 000070000dcc4498 R13 = 0000000000000000
R14 = 000000010e6f2d9b R15 = 0000000000000060
RIP = 000070000dcc4498 RFL = 000070000dcc41e0
CS = 000000010e58927b FS = 000070000dcc41c0 GS = 0000000000000001
Stack Trace (from fault):
[ 0] 0x0000000104c5de64 /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwfl.dylib+00028260 _ZN2fl4diag15stacktrace_base7captureERKNS0_14thread_contextEm+00000052
[ 1] 0x0000000104c61a2a /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwfl.dylib+00043562 _ZN2fl4test17terminate_handledEv+00000906
[ 2] 0x0000000104c61477 /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwfl.dylib+00042103 _ZN2fl4diag13terminate_logEPKcPK17__darwin_ucontext+00000119
[ 3] 0x000000010e276b7a /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwmcr.dylib+00387962 _Z32mnRunPathDependentInitializationv+00003146
[ 4] 0x000000010e276e58 /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwmcr.dylib+00388696 _Z32mnRunPathDependentInitializationv+00003880
[ 5] 0x000000010e274733 /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwmcr.dylib+00378675 mnFatalSignalHandler+00000275
[ 6] 0x00007fff203abd7d /usr/lib/system/libsystem_platform.dylib+00015741 _sigtramp+00000029
[ 7] 0x0000000000000000 <unknown-module>+00000000
[ 8] 0x000000010e58927b /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwm_interpreter.dylib+01782395 _Z10inRunMfileiPP11mxArray_tagiS1_P6Mfh_mpP15inWorkSpace_tag+00010667
[ 9] 0x000000010e4e2a17 /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwm_interpreter.dylib+01100311 _Z15inRunFinalizers7opcodesPS_Pi+00000119
[ 10] 0x000000010e58729d /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwm_interpreter.dylib+01774237 _Z10inRunMfileiPP11mxArray_tagiS1_P6Mfh_mpP15inWorkSpace_tag+00002509
[ 11] 0x000000010f1e8c55 /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwm_dispatcher.dylib+00400469 _ZN8Mfh_file11dispatch_fhEiPP11mxArray_tagiS2_+00000645
[ 12] 0x000000010e52a48b /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwm_interpreter.dylib+01393803 _Z23inEvalPcodeHeaderToWordP15_memory_contextiPP11mxArray_tagP12_pcodeheaderP6Mfh_mpj+00000219
[ 13] 0x000000010e4dcf4b /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwm_interpreter.dylib+01077067 _Z25in_local_call_with_setjmpIN5boost3_bi6bind_tIvPFvP15_memory_contextPiPP11mxArray_tagP12_pcodeheaderjENS1_5list5INS1_5valueIS4_EENS0_3argILi1EEENSG_ILi2EEENSE_ISA_EENSE_IiEEEEEEEN6mlutil14cmddistributor17inExecutionStatusET_S5_S8_b+00000171
[ 14] 0x000000010e4d8221 /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwm_interpreter.dylib+01057313 _Z12inEvalStringP15_memory_contextRKSbItSt11char_traitsItESaItEE8EvalTypeiPP11mxArray_tag12inDebugCheckP12_pcodeheaderPib+00002769
[ 15] 0x000000010e4d87cd /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwm_interpreter.dylib+01058765 _ZN12InterpBridge22EvalCmdWithLocalReturnERKSbItSt11char_traitsItESaItEEPibb+00000141
[ 16] 0x000000010e4d8a62 /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwm_interpreter.dylib+01059426 _ZN12InterpBridge33EvalCmdWithLocalReturnInDesiredWSERKSbItSt11char_traitsItESaItEEPibbP15inWorkSpace_tag+00000066
[ 17] 0x000000010e4382de /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwm_interpreter.dylib+00402142 _Z51inEvalCmdWithLocalReturnInDesiredWSAndPublishEventsRKSbItSt11char_traitsItESaItEEPibbP15inWorkSpace_tag+00000062
[ 18] 0x000000010ef8693e /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwiqm.dylib+00227646 _ZNK3iqm18InternalEvalPlugin24inEvalCmdWithLocalReturnERKSbItSt11char_traitsItESaItEEP15inWorkSpace_tag+00000094
[ 19] 0x000000010ef85df4 /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwiqm.dylib+00224756 _ZN3iqm18InternalEvalPlugin7executeEP15inWorkSpace_tagRN5boost10shared_ptrIN14cmddistributor17IIPCompletedEventEEE+00000132
[ 20] 0x000000010e24b358 /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwmcr.dylib+00209752 _ZN3mcr3mvm27McrSwappingIqmPluginAdapterIN3iqm18InternalEvalPluginEE7executeEP15inWorkSpace_tagRN5boost10shared_ptrIN14cmddistributor17IIPCompletedEventEEE+00000600
[ 21] 0x000000010ef76418 /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwiqm.dylib+00160792 _ZNK3iqm17DefaultPacketInfo7executeEP15inWorkSpace_tag+00000296
[ 22] 0x000000010ef617f1 /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwiqm.dylib+00075761 _ZN3iqm3Iqm15setupIqmFcnPtrsEv+00004945
[ 23] 0x0000000102a4d005 /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwservices.dylib+00196613 _ZN10eventqueue18UserEventQueueImpl5flushEv+00001205
[ 24] 0x000000010fa1ea65 /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwuix.dylib+00043621 _Z25isHandleUserEventCallbackPFvPvE+00000501
[ 25] 0x0000000102b1ca45 /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwservices.dylib+01047109 _Z21svWS_ProcessCallbacksv+00016693
[ 26] 0x0000000102b18152 /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwservices.dylib+01028434 _Z25svWS_ProcessPendingEventsiib+00000834
[ 27] 0x0000000102b17e5e /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwservices.dylib+01027678 _Z25svWS_ProcessPendingEventsiib+00000078
[ 28] 0x000000010e23518f /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwmcr.dylib+00119183 _ZN3mcr7runtime17InterpreterThread4Impl14process_eventsERKN5boost10shared_ptrIS2_EE+00000095
[ 29] 0x000000010e23549f /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwmcr.dylib+00119967 _ZN3mcr7runtime17InterpreterThread4Impl3runERKN5boost10shared_ptrIS2_EEPNS2_12init_contextE+00000335
[ 30] 0x000000010e21bd1b /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwmcr.dylib+00015643 _Z26run_init_and_handle_eventsPv+00000059
[ 31] 0x00007fff20367950 /usr/lib/system/libsystem_pthread.dylib+00026960 _pthread_start+00000224
[ 32] 0x00007fff2036347b /usr/lib/system/libsystem_pthread.dylib+00009339 thread_start+00000015
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.

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Answers (1)

Saurav Chaudhary
Saurav Chaudhary on 21 Dec 2020
Try the workaround provided in this Bug report. Also refer this MATLAB answer for more information.

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