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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 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

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