Thanks a bit lot, Cico. The screensaver thing blew my mind.
We need to move these tools into python to avoid this type of problems.
In the meantime:  Andrew, do you have any ideas?
Cheers,
/Eugenio

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

On Aug 12, 2021, at 12:58, Francesco Cardinale <cico1965@icloud.com> wrote:

        External Email - Use Caution        


Hello FreeSurfer Developers,

I'm attempting to compute hippocampal, thalamus and brainstem subfields on my laptop (MacBook Pro, MacOS Big Sur, Freesurfer 7.1.1 or 7.2.0) with segmentHA_T1.sh, segmentThalamicNuclei.sh and segmentBS.sh scripts, respectively. All the three pipelines fail because of a Matlab Crash Dump. You can find the error logged in the bash console text reported in the last part of this email. I also attached the file brainstem-substructures-T1.log

Please, note that everything works fine with previous versions of MacOS, including Mojave. All the updates of Big Sur didn’t solve the problem.
Is it possible to use these tools with an updated Matlab Runtime?

Another note, probably helpful to somebody else: sometimes these tools fail also in previous version of MacOS, but I discovered that it happens for a different Matlab Crash Dump due to some screen savers. Avoiding the use of screen savers solved the problem under Mojave (but not under Big Sur).

Best regards

Cico Cardinale

------------------------------------------------------------------------
       Segmentation violation detected at Thu Aug  5 00:29:40 2021
------------------------------------------------------------------------

Configuration:
  Crash Decoding     : Disabled
  Current Visual     : Quartz
  Default Encoding   : US-ASCII
  MATLAB Architecture: maci64
  MATLAB Root        : /Applications/freesurfer/MCRv84
  MATLAB Version     : 8.4.0.150421 (R2014b)
  Operating System   : Darwin 20.5.0 Darwin Kernel Version 20.5.0: Sat May  8 05:10:33 PDT 2021; root:xnu-7195.121.3~9/RELEASE_X86_64 x86_64
  Processor ID       : x86 Family 6 Model 78 Stepping 3, 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 = 0000700008d9bd00  R13 = 00007fff205294bd
  R14 = 00007fff87277d38  R15 = 0000700008d9bda0

  RIP = 0000000000003002  RFL = 00007f8b5b737b30

   CS = 0000000000000000   FS = 0000000000000000   GS = 000000010c5bb560

Stack Trace (from fault):
[  0] 0x000000010c208e64 /Applications/freesurfer/MCRv84/bin/maci64/libmwfl.dylib+00028260 _ZN2fl4diag15stacktrace_base7captureERKNS0_14thread_contextEm+00000052
[  1] 0x000000010c20ca2a /Applications/freesurfer/MCRv84/bin/maci64/libmwfl.dylib+00043562 _ZN2fl4test17terminate_handledEv+00000906
[  2] 0x000000010c20c477 /Applications/freesurfer/MCRv84/bin/maci64/libmwfl.dylib+00042103 _ZN2fl4diag13terminate_logEPKcPK17__darwin_ucontext+00000119
[  3] 0x0000000111b3db7a /Applications/freesurfer/MCRv84/bin/maci64/libmwmcr.dylib+00387962 _Z32mnRunPathDependentInitializationv+00003146
[  4] 0x0000000111b3de58 /Applications/freesurfer/MCRv84/bin/maci64/libmwmcr.dylib+00388696 _Z32mnRunPathDependentInitializationv+00003880
[  5] 0x0000000111b3b733 /Applications/freesurfer/MCRv84/bin/maci64/libmwmcr.dylib+00378675 mnFatalSignalHandler+00000275
[  6] 0x00007fff205a9d7d           /usr/lib/system/libsystem_platform.dylib+00015741 _sigtramp+00000029
[  7] 0x0000000000000000                                   <unknown-module>+00000000
[  8] 0x0000000109c546ca /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:
    MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be http://www.mathworks.com/support/contact_us/

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/cico/matlab_crash_dump.19318-1 **


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

------------------------------------------------------------------------
          std::terminate() detected at Thu Aug  5 00:29:40 2021
------------------------------------------------------------------------

Configuration:
  Crash Decoding     : Disabled
  Current Visual     : Quartz
  Default Encoding   : US-ASCII
  MATLAB Architecture: maci64
  MATLAB Root        : /Applications/freesurfer/MCRv84
  MATLAB Version     : 8.4.0.150421 (R2014b)
  Operating System   : Darwin 20.5.0 Darwin Kernel Version 20.5.0: Sat May  8 05:10:33 PDT 2021; root:xnu-7195.121.3~9/RELEASE_X86_64 x86_64
  Processor ID       : x86 Family 6 Model 78 Stepping 3, 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 = 0000700008d9bd00  R13 = 00007fff205294bd
  R14 = 00007fff87277d38  R15 = 0000700008d9bda0

  RIP = 0000000000003002  RFL = 00007f8b5b737b30

   CS = 0000000000000000   FS = 0000000000000000   GS = 000000010c5bb560

Stack Trace (from fault):
[  0] 0x000000010c208e64 /Applications/freesurfer/MCRv84/bin/maci64/libmwfl.dylib+00028260 _ZN2fl4diag15stacktrace_base7captureERKNS0_14thread_contextEm+00000052
[  1] 0x000000010c20ca2a /Applications/freesurfer/MCRv84/bin/maci64/libmwfl.dylib+00043562 _ZN2fl4test17terminate_handledEv+00000906
[  2] 0x000000010c20c477 /Applications/freesurfer/MCRv84/bin/maci64/libmwfl.dylib+00042103 _ZN2fl4diag13terminate_logEPKcPK17__darwin_ucontext+00000119
[  3] 0x0000000111b3db7a /Applications/freesurfer/MCRv84/bin/maci64/libmwmcr.dylib+00387962 _Z32mnRunPathDependentInitializationv+00003146
[  4] 0x0000000111b3de58 /Applications/freesurfer/MCRv84/bin/maci64/libmwmcr.dylib+00388696 _Z32mnRunPathDependentInitializationv+00003880
[  5] 0x0000000111b3b733 /Applications/freesurfer/MCRv84/bin/maci64/libmwmcr.dylib+00378675 mnFatalSignalHandler+00000275
[  6] 0x00007fff205a9d7d           /usr/lib/system/libsystem_platform.dylib+00015741 _sigtramp+00000029
[  7] 0x0000000000000000                                   <unknown-module>+00000000
[  8] 0x0000000109c546ca /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 = 0000700008da1578
  RCX = 0000000000000000  RDX = 0000000000000000
  RSP = 0000700008da0e10  RBP = 0000700008da1130
  RSI = 0000000000000000  RDI = 0000000000000000

   R8 = 0000000000000000   R9 = 0000000000000000
  R10 = 0000000000000000  R11 = 0000000000000000
  R12 = 0000700008da1d00  R13 = 0000000000000000
  R14 = 00007fff8085dcf0  R15 = 0000000000000000

  RIP = 000000010c20de8b  RFL = 0000000000000000

   CS = 0000000100000001   FS = fffffffffffffff8   GS = 0000000000000000

Stack Trace (captured):
[  0] 0x000000010c208e64 /Applications/freesurfer/MCRv84/bin/maci64/libmwfl.dylib+00028260 _ZN2fl4diag15stacktrace_base7captureERKNS0_14thread_contextEm+00000052
[  1] 0x000000010c20ca2a /Applications/freesurfer/MCRv84/bin/maci64/libmwfl.dylib+00043562 _ZN2fl4test17terminate_handledEv+00000906
[  2] 0x000000010c20c477 /Applications/freesurfer/MCRv84/bin/maci64/libmwfl.dylib+00042103 _ZN2fl4diag13terminate_logEPKcPK17__darwin_ucontext+00000119
[  3] 0x0000000111b3db7a /Applications/freesurfer/MCRv84/bin/maci64/libmwmcr.dylib+00387962 _Z32mnRunPathDependentInitializationv+00003146
[  4] 0x0000000111b3de58 /Applications/freesurfer/MCRv84/bin/maci64/libmwmcr.dylib+00388696 _Z32mnRunPathDependentInitializationv+00003880
[  5] 0x0000000111b3d3a0 /Applications/freesurfer/MCRv84/bin/maci64/libmwmcr.dylib+00385952 _Z32mnRunPathDependentInitializationv+00001136
[  6] 0x0000000111b3ce54 /Applications/freesurfer/MCRv84/bin/maci64/libmwmcr.dylib+00384596 _Z22mnInstallCrashHandlersv+00000420
[  7] 0x0000000109c52698 /Applications/freesurfer/lib/gcc/lib/libstdc++.6.dylib+00054936 _ZN10__cxxabiv111__terminateEPFvvE+00000008
[  8] 0x00000001127d27f1 /Applications/freesurfer/MCRv84/bin/maci64/libmwiqm.dylib+00075761 _ZN3iqm3Iqm15setupIqmFcnPtrsEv+00004945
[  9] 0x0000000109ff2005 /Applications/freesurfer/MCRv84/bin/maci64/libmwservices.dylib+00196613 _ZN10eventqueue18UserEventQueueImpl5flushEv+00001205
[ 10] 0x0000000112cb9a65 /Applications/freesurfer/MCRv84/bin/maci64/libmwuix.dylib+00043621 _Z25isHandleUserEventCallbackPFvPvE+00000501
[ 11] 0x000000010a0c1a45 /Applications/freesurfer/MCRv84/bin/maci64/libmwservices.dylib+01047109 _Z21svWS_ProcessCallbacksv+00016693
[ 12] 0x000000010a0bd152 /Applications/freesurfer/MCRv84/bin/maci64/libmwservices.dylib+01028434 _Z25svWS_ProcessPendingEventsiib+00000834
[ 13] 0x000000010a0bce5e /Applications/freesurfer/MCRv84/bin/maci64/libmwservices.dylib+01027678 _Z25svWS_ProcessPendingEventsiib+00000078
[ 14] 0x0000000111afc18f /Applications/freesurfer/MCRv84/bin/maci64/libmwmcr.dylib+00119183 _ZN3mcr7runtime17InterpreterThread4Impl14process_eventsERKN5boost10shared_ptrIS2_EE+00000095
[ 15] 0x0000000111afc49f /Applications/freesurfer/MCRv84/bin/maci64/libmwmcr.dylib+00119967 _ZN3mcr7runtime17InterpreterThread4Impl3runERKN5boost10shared_ptrIS2_EEPNS2_12init_contextE+00000335
[ 16] 0x0000000111ae2d1b /Applications/freesurfer/MCRv84/bin/maci64/libmwmcr.dylib+00015643 _Z26run_init_and_handle_eventsPv+00000059
[ 17] 0x00007fff205648fc            /usr/lib/system/libsystem_pthread.dylib+00026876 _pthread_start+00000224
[ 18] 0x00007fff20560443            /usr/lib/system/libsystem_pthread.dylib+00009283 thread_start+00000015


If this problem is reproducible, please submit a Service Request via:
    http://www.mathworks.com/support/contact_us/

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/cico/matlab_crash_dump.19318-2 **



MATLAB is exiting because of fatal error
/Applications/freesurfer/bin/run_SegmentSubject.sh: line 33: 84854 Killed: 9               /Applications/freesurfer/bin/segmentSubject.app/Contents/MacOS/segmentSubject ctrl16_paola_01 /Users/cico/Documents/subjects_fs 0.5 /Applications/freesurfer/average/BrainstemSS/atlas/AtlasMesh.gz /Applications/freesurfer/average/BrainstemSS/atlas/AtlasDump.mgz /Applications/freesurfer/average/BrainstemSS/atlas/compressionLookupTable.txt 0.05 L-BFGS v12 '/Applications/freesurfer/bin/fs_run_from_mcr /Applications/freesurfer/bin/'
Darwin CicoPro17.local 20.5.0 Darwin Kernel Version 20.5.0: Sat May  8 05:10:33 PDT 2021; root:xnu-7195.121.3~9/RELEASE_X86_64 x86_64

T1 Brainstem Substructures exited with ERRORS at Gio  5 Ago 2021 00:29:40 CEST

Francesco Cardinale, MD

Neurosurgeon
"Claudio Munari" Centre for Epilepsy and Parkinson Surgery
ASST GOM Niguarda "Ca' Granda"
phone + 39 02 64442867
fax +39 02 64442868

<brainstem-substructures-T1.log>