Matlab R2014b exits while executing segmentThalamicNuclei.sh in FS v7.1.1 under OS Big Sur
External Email - Use Caution
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 0Darwin 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
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
External Email - Use Caution
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
External Email - Use Caution
Andrew, many thanks for reply. The issue has been fixed by downgrading the OSX. Best Joe
On May 25, 2021, at 4:57 PM, Hoopes, Andrew AHOOPES@mgh.harvard.edu wrote:
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
External Email - Use CautionAs 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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1FP2_U6sD_AY014YYrjxjdK18J34bupMoat5cAaf-rfkJaW... The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at http://secure-web.cisco.com/1hqpa6atwA5IM4TIOjrO7QN_d5p40Bvd5MHzZSDh5F3ZTmy7... . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.
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Hoopes, Andrew -
Xin Qiao