Hi Joe,
Is this the full command output from start to finish? There is usually some helpful information preceding the “Segmentation violation detected” error.
Best Andrew
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Xin Qiao qiaox2000@yahoo.com Date: Thursday, May 20, 2021 at 12:44 AM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Matlab R2014b exits while executing segmentThalamicNuclei.sh in FS v7.1.1 under OS Big Sur
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As mentioned, recon-all function with T1 MRI data works well with no problem at all. With results from recon-all, while trying to run segmentThalamicNuclei.sh, MATLAB quit with message as follows:
------------------------------------------------------------------------ Segmentation violation detected at Wed May 19 19:42:08 2021 ------------------------------------------------------------------------
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 20.4.0 Darwin Kernel Version 20.4.0: Thu Apr 22 21:46:47 PDT 2021; root:xnu-7195.101.2~1/RELEASE_X86_64 x86_64 Processor ID : x86 Family 6 Model 69 Stepping 1, 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 = 0000000000000000 RBX = 0000000000000000 RCX = 0000000000000000 RDX = 0000000000000000 RSP = 0000000000000000 RBP = 0000000000000000 RSI = 0000000000000000 RDI = 0000000000000000
R8 = 0000000000000000 R9 = 0000000000000000 R10 = 0000000000000000 R11 = 0000000000000000 R12 = 00007000029b8d00 R13 = 00007fff2041d4bd R14 = 00007fff87147cf8 R15 = 00007000029b8da0
RIP = 0000000000003002 RFL = 00007fa5bda93250
CS = 0000000000000000 FS = 0000000000000000 GS = 000000010f288560
Stack Trace (from fault): [ 0] 0x000000010eedce64 /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwfl.dylib+00028260 _ZN2fl4diag15stacktrace_base7captureERKNS0_14thread_contextEm+00000052 [ 1] 0x000000010eee0a2a /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwfl.dylib+00043562 _ZN2fl4test17terminate_handledEv+00000906 [ 2] 0x000000010eee0477 /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwfl.dylib+00042103 _ZN2fl4diag13terminate_logEPKcPK17__darwin_ucontext+00000119 [ 3] 0x0000000117c5fb7a /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwmcr.dylib+00387962 _Z32mnRunPathDependentInitializationv+00003146 [ 4] 0x0000000117c5fe58 /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwmcr.dylib+00388696 _Z32mnRunPathDependentInitializationv+00003880 [ 5] 0x0000000117c5d733 /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwmcr.dylib+00378675 mnFatalSignalHandler+00000275 [ 6] 0x00007fff2049dd7d /usr/lib/system/libsystem_platform.dylib+00015741 _sigtramp+00000029 [ 7] 0x0000000000000000 <unknown-module>+00000000 [ 8] 0x000000010df9a6ca /Applications/freesurfer/7.1.1/lib/gcc/lib/libstdc++.6.dylib+00063178 _ZNK10__cxxabiv121__vmi_class_type_info11__do_upcastEPKNS_17__class_type_infoEPKvRNS1_15__upcast_resultE+00000186
This crash report has been saved to disk as /Users/transmri/matlab_crash_dump.9882-1 **
Caught "std::exception" Exception message is: FatalException
------------------------------------------------------------------------ std::terminate() detected at Wed May 19 19:42:10 2021 ------------------------------------------------------------------------
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 20.4.0 Darwin Kernel Version 20.4.0: Thu Apr 22 21:46:47 PDT 2021; root:xnu-7195.101.2~1/RELEASE_X86_64 x86_64 Processor ID : x86 Family 6 Model 69 Stepping 1, 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 = 0000000000000000 RBX = 0000000000000000 RCX = 0000000000000000 RDX = 0000000000000000 RSP = 0000000000000000 RBP = 0000000000000000 RSI = 0000000000000000 RDI = 0000000000000000
R8 = 0000000000000000 R9 = 0000000000000000 R10 = 0000000000000000 R11 = 0000000000000000 R12 = 00007000029b8d00 R13 = 00007fff2041d4bd R14 = 00007fff87147cf8 R15 = 00007000029b8da0
RIP = 0000000000003002 RFL = 00007fa5bda93250
CS = 0000000000000000 FS = 0000000000000000 GS = 000000010f288560
Stack Trace (from fault): [ 0] 0x000000010eedce64 /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwfl.dylib+00028260 _ZN2fl4diag15stacktrace_base7captureERKNS0_14thread_contextEm+00000052 [ 1] 0x000000010eee0a2a /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwfl.dylib+00043562 _ZN2fl4test17terminate_handledEv+00000906 [ 2] 0x000000010eee0477 /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwfl.dylib+00042103 _ZN2fl4diag13terminate_logEPKcPK17__darwin_ucontext+00000119 [ 3] 0x0000000117c5fb7a /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwmcr.dylib+00387962 _Z32mnRunPathDependentInitializationv+00003146 [ 4] 0x0000000117c5fe58 /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwmcr.dylib+00388696 _Z32mnRunPathDependentInitializationv+00003880 [ 5] 0x0000000117c5d733 /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwmcr.dylib+00378675 mnFatalSignalHandler+00000275 [ 6] 0x00007fff2049dd7d /usr/lib/system/libsystem_platform.dylib+00015741 _sigtramp+00000029 [ 7] 0x0000000000000000 <unknown-module>+00000000 [ 8] 0x000000010df9a6ca /Applications/freesurfer/7.1.1/lib/gcc/lib/libstdc++.6.dylib+00063178 _ZNK10__cxxabiv121__vmi_class_type_info11__do_upcastEPKNS_17__class_type_infoEPKvRNS1_15__upcast_resultE+00000186
Abnormal termination: std::terminate()
Register State (captured): RAX = 0000000000000000 RBX = 00007000029be578 RCX = 0000000000000000 RDX = 0000000000000000 RSP = 00007000029bde10 RBP = 00007000029be130 RSI = 0000000000000000 RDI = 0000000000000000
R8 = 0000000000000000 R9 = 0000000000000000 R10 = 0000000000000000 R11 = 0000000000000000 R12 = 00007000029bed00 R13 = 0000000000000000 R14 = 00007fff80752070 R15 = 0000000000000000
RIP = 000000010eee1e8b RFL = 0000000000000000
CS = 0000000100000001 FS = fffffffffffffff8 GS = 0000000000000000
Stack Trace (captured): [ 0] 0x000000010eedce64 /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwfl.dylib+00028260 _ZN2fl4diag15stacktrace_base7captureERKNS0_14thread_contextEm+00000052 [ 1] 0x000000010eee0a2a /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwfl.dylib+00043562 _ZN2fl4test17terminate_handledEv+00000906 [ 2] 0x000000010eee0477 /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwfl.dylib+00042103 _ZN2fl4diag13terminate_logEPKcPK17__darwin_ucontext+00000119 [ 3] 0x0000000117c5fb7a /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwmcr.dylib+00387962 _Z32mnRunPathDependentInitializationv+00003146 [ 4] 0x0000000117c5fe58 /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwmcr.dylib+00388696 _Z32mnRunPathDependentInitializationv+00003880 [ 5] 0x0000000117c5f3a0 /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwmcr.dylib+00385952 _Z32mnRunPathDependentInitializationv+00001136 [ 6] 0x0000000117c5ee54 /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwmcr.dylib+00384596 _Z22mnInstallCrashHandlersv+00000420 [ 7] 0x000000010df98698 /Applications/freesurfer/7.1.1/lib/gcc/lib/libstdc++.6.dylib+00054936 _ZN10__cxxabiv111__terminateEPFvvE+00000008 [ 8] 0x000000011890b7f1 /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwiqm.dylib+00075761 _ZN3iqm3Iqm15setupIqmFcnPtrsEv+00004945 [ 9] 0x000000010e335005 /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwservices.dylib+00196613 _ZN10eventqueue18UserEventQueueImpl5flushEv+00001205 [ 10] 0x00000001193c8a65 /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwuix.dylib+00043621 _Z25isHandleUserEventCallbackPFvPvE+00000501 [ 11] 0x000000010e404a45 /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwservices.dylib+01047109 _Z21svWS_ProcessCallbacksv+00016693 [ 12] 0x000000010e400152 /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwservices.dylib+01028434 _Z25svWS_ProcessPendingEventsiib+00000834 [ 13] 0x000000010e3ffe5e /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwservices.dylib+01027678 _Z25svWS_ProcessPendingEventsiib+00000078 [ 14] 0x0000000117c1e18f /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwmcr.dylib+00119183 _ZN3mcr7runtime17InterpreterThread4Impl14process_eventsERKN5boost10shared_ptrIS2_EE+00000095 [ 15] 0x0000000117c1e49f /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwmcr.dylib+00119967 _ZN3mcr7runtime17InterpreterThread4Impl3runERKN5boost10shared_ptrIS2_EEPNS2_12init_contextE+00000335 [ 16] 0x0000000117c04d1b /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwmcr.dylib+00015643 _Z26run_init_and_handle_eventsPv+00000059 [ 17] 0x00007fff20458954 /usr/lib/system/libsystem_pthread.dylib+00026964 _pthread_start+00000224 [ 18] 0x00007fff204544a7 /usr/lib/system/libsystem_pthread.dylib+00009383 thread_start+00000015
This crash report has been saved to disk as /Users/transmri/matlab_crash_dump.9882-2 **
MATLAB is exiting because of fatal error /Applications/freesurfer/7.1.1/bin/run_SegmentThalamicNuclei.sh: line 33: 9882 Killed: 9 /Applications/freesurfer/7.1.1/bin/SegmentThalamicNuclei.app/Contents/MacOS/SegmentThalamicNuclei Test001 /Applications/freesurfer/7.1.1/subjects/2108220/ 0.5 /Applications/freesurfer/7.1.1/average/ThalamicNuclei/atlas/AtlasMesh.gz /Applications/freesurfer/7.1.1/average/ThalamicNuclei/atlas/AtlasDump.mgz /Applications/freesurfer/7.1.1/average/ThalamicNuclei/atlas/compressionLookupTable.txt 0.05 L-BFGS v12 '/Applications/freesurfer/7.1.1/bin/fs_run_from_mcr /Applications/freesurfer/7.1.1/bin/' 1 0 Darwin TransMRIs-Mac-mini.local 20.4.0 Darwin Kernel Version 20.4.0: Thu Apr 22 21:46:47 PDT 2021; root:xnu-7195.101.2~1/RELEASE_X86_64 x86_64
Many thanks in advance for any solution or hint!
Joe