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-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Xin Qiao
<qiaox2...@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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