Thanks! But can you please share the full log, please? I’d like to see what happens before the error ;-)
Cheers,
/Eugenio

Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://www.jeiglesias.com 

On Nov 22, 2021, at 00:15, Lab of Autism and Developmental Neuroscience, Lab of Autism and Developmental Neuroscience <ladn@email.gwu.edu> wrote:

        External Email - Use Caution        


Hello Eugenio, 

Thank you so much for your response. Here is a large section of the error message I got while running hippocampal subfields. Please let me know if more details are needed! 


------------------------------------------------------------------------
       Segmentation violation detected at Fri Nov 12 14:26:43 2021
------------------------------------------------------------------------

Configuration:
  Crash Decoding     : Disabled
  Current Visual     : Quartz
  Default Encoding   : ISO-8859-1
  MATLAB Architecture: maci64
  MATLAB Root        : /Applications/freesurfer/MCRv84
  MATLAB Version     : 8.4.0.150421 (R2014b)
  Operating System   : Darwin 20.6.0 Darwin Kernel Version 20.6.0: Mon Aug 30 06:12:21 PDT 2021; root:xnu-7195.141.6~3/RELEASE_X86_64 x86_64
  Processor ID       : x86 Family 6 Model 85 Stepping 4, 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 = 000070000c6edd00  R13 = 00007fff203e54bd
  R14 = 00007fff87147d38  R15 = 000070000c6edda0

  RIP = 0000000000003002  RFL = 00007f9f5ca7bc80

   CS = 0000000000000000   FS = 0000000000000000   GS = 000000010a6d1560

Stack Trace (from fault):
[  0] 0x000000010a320e64 /Applications/freesurfer/MCRv84/bin/maci64/libmwfl.dylib+00028260 _ZN2fl4diag15stacktrace_base7captureERKNS0_14thread_contextEm+00000052
[  1] 0x000000010a324a2a /Applications/freesurfer/MCRv84/bin/maci64/libmwfl.dylib+00043562 _ZN2fl4test17terminate_handledEv+00000906
[  2] 0x000000010a324477 /Applications/freesurfer/MCRv84/bin/maci64/libmwfl.dylib+00042103 _ZN2fl4diag13terminate_logEPKcPK17__darwin_ucontext+00000119
[  3] 0x000000010dcd9b7a /Applications/freesurfer/MCRv84/bin/maci64/libmwmcr.dylib+00387962 _Z32mnRunPathDependentInitializationv+00003146
[  4] 0x000000010dcd9e58 /Applications/freesurfer/MCRv84/bin/maci64/libmwmcr.dylib+00388696 _Z32mnRunPathDependentInitializationv+00003880
[  5] 0x000000010dcd7733 /Applications/freesurfer/MCRv84/bin/maci64/libmwmcr.dylib+00378675 mnFatalSignalHandler+00000275
[  6] 0x00007fff20465d7d           /usr/lib/system/libsystem_platform.dylib+00015741 _sigtramp+00000029
[  7] 0x0000000000000000                                   <unknown-module>+00000000
[  8] 0x0000000107d7e6ca /Applications/freesurfer/lib/gcc/lib/libstdc++.6.dylib+00063178 _ZNK10__cxxabiv121__vmi_class_type_info11__do_upcastEPKNS_17__class_type_infoEPKvRNS1_15__upcast_resultE+00000186


If this problem is reproducible, please submit a Service Request via:

A technical support engineer might contact you with further information.

Thank you for your help.** This crash report has been saved to disk as /Users/ajobsaid/matlab_crash_dump.7498-1 **


Caught "std::exception" Exception message is:
FatalException

------------------------------------------------------------------------
          std::terminate() detected at Fri Nov 12 14:26:43 2021
------------------------------------------------------------------------

Configuration:
  Crash Decoding     : Disabled
  Current Visual     : Quartz
  Default Encoding   : ISO-8859-1
  MATLAB Architecture: maci64
  MATLAB Root        : /Applications/freesurfer/MCRv84
  MATLAB Version     : 8.4.0.150421 (R2014b)
  Operating System   : Darwin 20.6.0 Darwin Kernel Version 20.6.0: Mon Aug 30 06:12:21 PDT 2021; root:xnu-7195.141.6~3/RELEASE_X86_64 x86_64
  Processor ID       : x86 Family 6 Model 85 Stepping 4, 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 = 000070000c6edd00  R13 = 00007fff203e54bd
  R14 = 00007fff87147d38  R15 = 000070000c6edda0

  RIP = 0000000000003002  RFL = 00007f9f5ca7bc80

   CS = 0000000000000000   FS = 0000000000000000   GS = 000000010a6d1560

Stack Trace (from fault):
[  0] 0x000000010a320e64 /Applications/freesurfer/MCRv84/bin/maci64/libmwfl.dylib+00028260 _ZN2fl4diag15stacktrace_base7captureERKNS0_14thread_contextEm+00000052
[  1] 0x000000010a324a2a /Applications/freesurfer/MCRv84/bin/maci64/libmwfl.dylib+00043562 _ZN2fl4test17terminate_handledEv+00000906
[  2] 0x000000010a324477 /Applications/freesurfer/MCRv84/bin/maci64/libmwfl.dylib+00042103 _ZN2fl4diag13terminate_logEPKcPK17__darwin_ucontext+00000119
[  3] 0x000000010dcd9b7a /Applications/freesurfer/MCRv84/bin/maci64/libmwmcr.dylib+00387962 _Z32mnRunPathDependentInitializationv+00003146
[  4] 0x000000010dcd9e58 /Applications/freesurfer/MCRv84/bin/maci64/libmwmcr.dylib+00388696 _Z32mnRunPathDependentInitializationv+00003880
[  5] 0x000000010dcd7733 /Applications/freesurfer/MCRv84/bin/maci64/libmwmcr.dylib+00378675 mnFatalSignalHandler+00000275
[  6] 0x00007fff20465d7d           /usr/lib/system/libsystem_platform.dylib+00015741 _sigtramp+00000029
[  7] 0x0000000000000000                                   <unknown-module>+00000000
[  8] 0x0000000107d7e6ca /Applications/freesurfer/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 = 000070000c6f3578
  RCX = 0000000000000000  RDX = 0000000000000000
  RSP = 000070000c6f2e10  RBP = 000070000c6f3130
  RSI = 0000000000000000  RDI = 0000000000000000

   R8 = 0000000000000000   R9 = 0000000000000000
  R10 = 0000000000000000  R11 = 0000000000000000
  R12 = 000070000c6f3d00  R13 = 0000000000000000
  R14 = 00007fff80719d70  R15 = 0000000000000000

  RIP = 000000010a325e8b  RFL = 0000000000000000

   CS = 0000000100000001   FS = fffffffffffffff8   GS = 0000000000000000

Stack Trace (captured):
[  0] 0x000000010a320e64 /Applications/freesurfer/MCRv84/bin/maci64/libmwfl.dylib+00028260 _ZN2fl4diag15stacktrace_base7captureERKNS0_14thread_contextEm+00000052
[  1] 0x000000010a324a2a /Applications/freesurfer/MCRv84/bin/maci64/libmwfl.dylib+00043562 _ZN2fl4test17terminate_handledEv+00000906
[  2] 0x000000010a324477 /Applications/freesurfer/MCRv84/bin/maci64/libmwfl.dylib+00042103 _ZN2fl4diag13terminate_logEPKcPK17__darwin_ucontext+00000119
[  3] 0x000000010dcd9b7a /Applications/freesurfer/MCRv84/bin/maci64/libmwmcr.dylib+00387962 _Z32mnRunPathDependentInitializationv+00003146
[  4] 0x000000010dcd9e58 /Applications/freesurfer/MCRv84/bin/maci64/libmwmcr.dylib+00388696 _Z32mnRunPathDependentInitializationv+00003880
[  5] 0x000000010dcd93a0 /Applications/freesurfer/MCRv84/bin/maci64/libmwmcr.dylib+00385952 _Z32mnRunPathDependentInitializationv+00001136
[  6] 0x000000010dcd8e54 /Applications/freesurfer/MCRv84/bin/maci64/libmwmcr.dylib+00384596 _Z22mnInstallCrashHandlersv+00000420
[  7] 0x0000000107d7c698 /Applications/freesurfer/lib/gcc/lib/libstdc++.6.dylib+00054936 _ZN10__cxxabiv111__terminateEPFvvE+00000008
[  8] 0x000000010de4b7f1 /Applications/freesurfer/MCRv84/bin/maci64/libmwiqm.dylib+00075761 _ZN3iqm3Iqm15setupIqmFcnPtrsEv+00004945
[  9] 0x0000000108119005 /Applications/freesurfer/MCRv84/bin/maci64/libmwservices.dylib+00196613 _ZN10eventqueue18UserEventQueueImpl5flushEv+00001205
[ 10] 0x000000011b343a65 /Applications/freesurfer/MCRv84/bin/maci64/libmwuix.dylib+00043621 _Z25isHandleUserEventCallbackPFvPvE+00000501
[ 11] 0x00000001081e8a45 /Applications/freesurfer/MCRv84/bin/maci64/libmwservices.dylib+01047109 _Z21svWS_ProcessCallbacksv+00016693
[ 12] 0x00000001081e4152 /Applications/freesurfer/MCRv84/bin/maci64/libmwservices.dylib+01028434 _Z25svWS_ProcessPendingEventsiib+00000834
[ 13] 0x00000001081e3e5e /Applications/freesurfer/MCRv84/bin/maci64/libmwservices.dylib+01027678 _Z25svWS_ProcessPendingEventsiib+00000078
[ 14] 0x000000010dc9818f /Applications/freesurfer/MCRv84/bin/maci64/libmwmcr.dylib+00119183 _ZN3mcr7runtime17InterpreterThread4Impl14process_eventsERKN5boost10shared_ptrIS2_EE+00000095
[ 15] 0x000000010dc9849f /Applications/freesurfer/MCRv84/bin/maci64/libmwmcr.dylib+00119967 _ZN3mcr7runtime17InterpreterThread4Impl3runERKN5boost10shared_ptrIS2_EEPNS2_12init_contextE+00000335
[ 16] 0x000000010dc7ed1b /Applications/freesurfer/MCRv84/bin/maci64/libmwmcr.dylib+00015643 _Z26run_init_and_handle_eventsPv+00000059
[ 17] 0x00007fff204208fc            /usr/lib/system/libsystem_pthread.dylib+00026876 _pthread_start+00000224
[ 18] 0x00007fff2041c443            /usr/lib/system/libsystem_pthread.dylib+00009283 thread_start+00000015


If this problem is reproducible, please submit a Service Request via:

A technical support engineer might contact you with further information.

Thank you for your help.** This crash report has been saved to disk as /Users/ajobsaid/matlab_crash_dump.7498-2 **

MATLAB is exiting because of fatal error
/Applications/freesurfer/bin/run_segmentSubjectT1_autoEstimateAlveusML.sh: line 37:  7498 Killed: 9               "${exe_dir}"/segmentSubjectT1_autoEstimateAlveusML.app/Contents/MacOS/segmentSubjectT1_autoEstimateAlveusML $args
Darwin CCAPSY-0GYM0XV 20.6.0 Darwin Kernel Version 20.6.0: Mon Aug 30 06:12:21 PDT 2021; root:xnu-7195.141.6~3/RELEASE_X86_64 x86_64

T1 hippocampal subfields exited with ERRORS at Fri Nov 12 14:26:43 EST 2021

Thanks! 
Alex

On Tue, Nov 16, 2021 at 12:05 PM Iglesias Gonzalez, Juan E. <JIGLESIASGONZALEZ@mgh.harvard.edu> wrote:
Dear Alex,
Can you please send us the full output?
Cheers,
/Eugenio

Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be http://www.jeiglesias.com



On 12 Nov 2021, at 23:39, Lab of Autism and Developmental Neuroscience, Lab of Autism and Developmental Neuroscience <ladn@email.gwu.edu> wrote:

        External Email - Use Caution        


Hello Freesurfer experts! 

Hope that you are all well. I am having errors when running hippocampal subfields and thalamic subfields. When in the error log for the hippocampal pipeline, this is part of the error that I got: 

MATLAB is exiting because of fatal error
/Applications/freesurfer/bin/run_segmentSubjectT1_autoEstimateAlveusML.sh: line 37:  7498 Killed: 9               "${exe_dir}"/segmentSubjectT1_autoEstimateAlveusML.app/Contents/MacOS/segmentSubjectT1_autoEstimateAlveusML $args
Darwin CCAPSY-0GYM0XV 20.6.0 Darwin Kernel Version 20.6.0: Mon Aug 30 06:12:21 PDT 2021; root:xnu-7195.141.6~3/RELEASE_X86_64 x86_64

T1 hippocampal subfields exited with ERRORS at Fri Nov 12 14:26:43 EST 2021

Please let me know if additional info is needed. 

Thank you so much, 
Alex
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