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The Matlab MCRv84 release used by Freesurfer is too old to be supported on MacOS 11 Big Sur by The Mathworks (looks like you are running MacOS 11.5 beta 2 release).

There are also error reports similar to yours with old versions of Matlab on different versions of MacOS.  From what I read on The Mathworks web site, it looks like a fix was made in R2017b, but I don’t if that release will work with freesurfer or MacOS 11.

If you want to try that release, you could do the following.

Download R2017b from,
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After downloading, double click on the zip archive to get the dmg archive.  Then double click on the dmg archive to see the installer pkg.

When you double click on the installer pkg to run it and go thru the steps you will get to a window showing the install path.  Type in the path /Applications/freesurfer in the installer window and then click on Next.

Then when the installer finishes you should have a subdirectory /Applications/freesurfer/v93

The new v93 subdirectory needs to look like it has the MCRv84 distribution name.  So save the MCRv84 distribution by just moving it aside as something with a different name like WAS_MCRv84

$ sudo cd /Applications/freesurfer
$ sudo mv  MCRv84  WAS_MCRv84

Use a soft link to allow the new v93 directory to be accessed with the old MCRv84 directory name ...

$ sudo ln  -s  v93 MCRv84

Now when you ls /Applications/freesurfer/MCRv84 you will really see the newer R2017b matlab release under the v93 subdirectory.

The Matlab installer will probably say to set the environment variable DYLD_LIBRARY_PATH and show paths with /Applications/freesurfer/v93   I think that is OK since now there is both the real subdirectory /Applications/freesurfer/v93 and also the soft link MCRv84 that points to it.

If you want to put everything back to the way it was then,

$ sudo cd /Applications/freesurfer/7.2.0
$ sudo rm MCRv84
$ sudo mv  WAS_MCRv84  MCRv84

- R.


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

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

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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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