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.edumailto: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: 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/1sFp6ev4em_EM8c3cbPoUE6trXNZE7Efoemg6n7hk6C5IFGAsAMrbbI93SRSR8goYyCUFBY68NYUCsB2ph7cj5aHUrjym28U5j03Gc9dH1qdpLKkKkTVKbZ0E3qVZh9N7uZnkk6meV4_HRjZYlsfzCPOW28OcmRDRsqp_jlQVoJSNMFJACs9sJU6zytyTlb2wQYtDc5vOylv5fqJpLgVgRfBV3RmkgQoO7Rsh8PFHHrJ3oiXFc8OSZfFyOmbJfqyMYh0z1EsxQjZjbDinL21loMrMtfRUYB5ATo6Zo5zQW81mGOqsL0ff8TBFoUk5iEiS53q7767J0edrOObAVLjtNj-uXtcriQ3BOeUlYHY9sxE/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/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: 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/1sFp6ev4em_EM8c3cbPoUE6trXNZE7Efoemg6n7hk6C5IFGAsAMrbbI93SRSR8goYyCUFBY68NYUCsB2ph7cj5aHUrjym28U5j03Gc9dH1qdpLKkKkTVKbZ0E3qVZh9N7uZnkk6meV4_HRjZYlsfzCPOW28OcmRDRsqp_jlQVoJSNMFJACs9sJU6zytyTlb2wQYtDc5vOylv5fqJpLgVgRfBV3RmkgQoO7Rsh8PFHHrJ3oiXFc8OSZfFyOmbJfqyMYh0z1EsxQjZjbDinL21loMrMtfRUYB5ATo6Zo5zQW81mGOqsL0ff8TBFoUk5iEiS53q7767J0edrOObAVLjtNj-uXtcriQ3BOeUlYHY9sxE/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/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 $args Darwin CCAPSY-0GYM0XV 20.6.0 Darwin Kernel Version 20.6.0: Mon Aug 30 06:12:21 PDT 2021; root:xnu-7195.141.6~3/RELEASE_X86_64 x86_64
T1 hippocampal subfields exited with ERRORS at Fri Nov 12 14:26:43 EST 2021
Thanks! Alex
On Tue, Nov 16, 2021 at 12:05 PM Iglesias Gonzalez, Juan E. <JIGLESIASGONZALEZ@mgh.harvard.edumailto:JIGLESIASGONZALEZ@mgh.harvard.edu> wrote: Dear Alex, Can you please send us the full output? Cheers, /Eugenio
Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be http://www.jeiglesias.comhttp://secure-web.cisco.com/1TeCpgrxvt8bIkbdkgpN2XezPTkU9wu3kj7LRtXKjfpCH4FAr1qZOYEySIAtfRiAMln0GtQGZNhkn1BYM1QpBk6OnKYzZONWNgjoaNAucvOavgMVCBoALN7YhYXsPKMEj_555pJQYmhPui4CWnFZXnG8H4B8oNtiaSTTEMT9XGkEOUtM3DGGEBB83ASaZxQ0igRdn7yiC5T5r4E2cD9i7B6Je-g7MFMcwX1LieEwRIBN_G5lcE9GwDGR1gnKLISyPtxUguq65_LCB90hChNZisuw5Hc0D3l3UI8yQ9uEGnGShpVf64uODg3P9SFmKKl4-cK_J_nCFZwG04as-0wwsECMTka4Wqc4teLruG-ySa90/http%3A%2F%2Fwww.jeiglesias.com
On 12 Nov 2021, at 23:39, Lab of Autism and Developmental Neuroscience, Lab of Autism and Developmental Neuroscience <ladn@email.gwu.edumailto:ladn@email.gwu.edu> wrote:
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Hello Freesurfer experts!
Hope that you are all well. I am having errors when running hippocampal subfields and thalamic subfields. When in the error log for the hippocampal pipeline, this is part of the error that I got:
MATLAB is exiting because of fatal error /Applications/freesurfer/bin/run_segmentSubjectT1_autoEstimateAlveusML.sh: line 37: 7498 Killed: 9 "${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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurferhttps://secure-web.cisco.com/1wJaTkHwn-VkpF_lNXS_GbWO108NU97mb4KPById3DE3cFcM77Y1ssbd6coJ_io-Q38JKIloIvwOFIRm8GS_9mV1dyghTvzZoanxM34WrKsveQUlbcnfRC_Z_djTFqvxEBdam0HD3Xv0mIM6c7ZFUHqx2-gGClQRCVvkaGyheSpDb8HOAvX-3tva5URaaOJe2YFSIQTTQQk3eUdtAxqiqFmsnQPXO9qSk15yefVdjJx_g622F9aRZa0OAGBb0mIqd4OilACfMxrtPiIc-knzLZDU9WB2AlCuYQNPaHrKbFnh45Na9Ba_f-xqff6WYTctsi4ZgG099Rd6te_Newj21ryM5V-yBWBg2TAxoreWL2S4/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
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