Honestly, I’m not sure. Without tracebacks it’s getting very difficult to debug these matlab runtime errors. It seems like Big Sur is the common culprit here, but we really don’t know why. Hopefully we can release the python port soon... Cico, could you try running freesurfer through a docker container instead?

https://hub.docker.com/r/freesurfer/freesurfer

Best Andrew

From: Iglesias Gonzalez, Juan E. JIGLESIASGONZALEZ@mgh.harvard.edu Date: Thursday, August 12, 2021 at 2:57 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Cc: Hoopes, Andrew AHOOPES@mgh.harvard.edu Subject: Re: [Freesurfer] Hippocampal, thalamus and brainstem subfields: Matlab crash bump on macOS Big Sur 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.commailto: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/http://secure-web.cisco.com/1r6MICtmf5EwCmlXokWPh6xbfJIxsDgSIeH9_RH4qZaI_YbFVNDWvvWAAJRVGPrP1U6moLoZyP0wk5rVM1JDyfMpmpXqyPaMmL5K8SaQoqFwrVgkdrh--yPxYFPa0s1Repf7-3gT2TwNlIaVsHZWiN4SYMS-8lM3FRrbSXXEDenawR8kW1PGuP010K8apqdcBxNZaixfgenCCld1AvYFxsQ-WAg_8ryWQAFf26dsJ1WljZtL_NJntqlnW1NvMJ6D1ooj8qc0NDF5c5q6s5TXbHg/http%3A%2F%2Fwww.mathworks.com%2Fsupport%2Fcontact_us%2F

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" Piazza dell'Ospedale Maggiore, 3 - 20162 - Milano - Italia phone + 39 02 64442867 fax +39 02 64442868 e-mail francesco.cardinale@ospedaleniguarda.itmailto:francesco.cardinale@ospedaleniguarda.it

<brainstem-substructures-T1.log>