External Email - Use Caution 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,https://secure-web.cisco.com/1cphCEkfouFma1YYMWmPUTPpDCt3HnegC93vKeXgpXkYopaRmrIFAOX5SsTtI6kXwY57rQFCzCky19jtT-4kLesJXahLsC0dpNHkWy95k1whjdSQIL25rYQTwYN5GqmohnATiCOl3zc0iNbjFqu_1GG674YhHdBYM71d8D0WvsPlqT47FNblY-U2xxXfcogMV8EB_aZXY5lzxSMUsQqK_Gm_EyYoxPeyS0tq4_qT5joqonK1Hd5O-IPookdc4hztXvq7Kufv6wm4j3NICs58RMrcnTR644b2VW43sg_31wMfxVN9TXnBcP61uW1gNDJvUjN0UlZCiJlg3j5A4WAXC_qWVNGGyXAn_uCKuns3eKf8/https%3A%2F%2Fssd.mathworks.com%2Fsupportfiles%2Fdownloads%2FR2017b%2Fdeployment_files%2FR2017b%2Finstallers%2Fmaci64%2FMCR_R2017b_maci64_installer.dmg.zip 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 <[email protected]> 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 : QuartzFault Count: 1Abnormal termination:Segmentation violationRegister 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 = 000000010a6d1560Stack 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+00000186If 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://secure-web.cisco.com/1YLRLijXwFNY_9s31qpWP7OijPJA7VNOM42hUT_vx98hGLggSgtzgX7LhEbnB2ZOlK-Iso9XFNPc4nnYwa4SluhNyOMVBpEiT1JwoDVdDcZACpoVnU-RACC2t844xLY3wPe136KnMc3VYOJ-CtduTX72WXPTVJDO66YqY71HDu0U3zCDARdZUkleovwrgDz7JtSefaQzS0ZqlDZIVann7ETzYXUCrL5UPgBPNG2dinbiBx1GVpo-LDM_MnvCOhE9F2oGFX3-smwvot45yTnAWiwTId-YFh858AASUqyRnwnDaojOO6kw14f0dqJ_qXoBVBu_O5z0jJFn-gdOlFrf-2NgoC3EnYuw4Yhn-KpocduM/http%3A%2F%2Fwww.mathworks.com%2Fsupport%2Fcontact_us%2FA 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 : QuartzFault Count: 2Abnormal termination:Segmentation violationRegister 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 = 000000010a6d1560Stack 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+00000186Abnormal 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 = 0000000000000000Stack 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+00000015If 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://secure-web.cisco.com/1YLRLijXwFNY_9s31qpWP7OijPJA7VNOM42hUT_vx98hGLggSgtzgX7LhEbnB2ZOlK-Iso9XFNPc4nnYwa4SluhNyOMVBpEiT1JwoDVdDcZACpoVnU-RACC2t844xLY3wPe136KnMc3VYOJ-CtduTX72WXPTVJDO66YqY71HDu0U3zCDARdZUkleovwrgDz7JtSefaQzS0ZqlDZIVann7ETzYXUCrL5UPgBPNG2dinbiBx1GVpo-LDM_MnvCOhE9F2oGFX3-smwvot45yTnAWiwTId-YFh858AASUqyRnwnDaojOO6kw14f0dqJ_qXoBVBu_O5z0jJFn-gdOlFrf-2NgoC3EnYuw4Yhn-KpocduM/http%3A%2F%2Fwww.mathworks.com%2Fsupport%2Fcontact_us%2FA 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 $argsDarwin CCAPSY-0GYM0XV 20.6.0 Darwin Kernel Version 20.6.0: Mon Aug 30 06:12:21 PDT 2021; root:xnu-7195.141.6~3/RELEASE_X86_64 x86_64T1 hippocampal subfields exited with ERRORS at Fri Nov 12 14:26:43 EST 2021Thanks! AlexOn Tue, Nov 16, 2021 at 12:05 PM Iglesias Gonzalez, Juan E. <[email protected]> wrote:Dear Alex,Can you please send us the full output?Cheers,/EugenioJuan Eugenio IglesiasSenior research fellowCMIC (UCL), MGH (HMS) and CSAIL (MIT)MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be http://secure-web.cisco.com/15Cdhj3LNq_RwvAkNk-hat1i8c0CX7qVDA2sbNIWQQIH7SqdSq1bCcP4_fmh3Wb_L7--xxIrYShoPrWfgbSlSsnzYWJfaimdT728oo7G2LT2AKmTUNmAHYYvFMLuKPKdgybTWZImlL3KDNyLXsgL-AH--DroNOtZN5hqEJHW3ZsqRTVrvCfMAamOCkxgdhA6TXblO7meC4kTJ6SBE3jjDaB5XeyFLJCHR508soXHHBUkzlrk53HItn48DJd1ibCWyaSwvWXpa9EpVMQ_jHvTvaS2aBQ_1voi325ezJe6PocYyafHRmhf_QJQE-Ao3G9-v6By42DITehQg73_gc8A2c6bKoJWe918fzPc3dSrqES4/http%3A%2F%2Fwww.jeiglesias.comOn 12 Nov 2021, at 23:39, Lab of Autism and Developmental Neuroscience, Lab of Autism and Developmental Neuroscience <[email protected]> wrote: External Email - Use Caution Hello Freesurfer experts! Hope that you are all well. I am having errors when running hippocampal subfields and thalamic subfields. When in the error log for the hippocampal pipeline, this is part of the error that I got: MATLAB is exiting because of fatal error/Applications/freesurfer/bin/run_segmentSubjectT1_autoEstimateAlveusML.sh: line 37: 7498 Killed: 9 "${exe_dir}"/segmentSubjectT1_autoEstimateAlveusML.app/Contents/MacOS/segmentSubjectT1_autoEstimateAlveusML $argsDarwin 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_64T1 hippocampal subfields exited with ERRORS at Fri Nov 12 14:26:43 EST 2021Please let me know if additional info is needed. Thank you so much, Alex_______________________________________________Freesurfer mailing [email protected] has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1qlSMaH5lwydIo7lfolBJmu5uEEfo93ZBD9Ai7f_zkiw-hoRGqD7T-39x2T96vRHt17xOZXS55NfnXyX-nO2wgLNwo1kqHffJi-IKX1cPJVtGgyF3CPQc2RoJ5dsT-A71fqXd7rBtgPzmIfmAk-syR07RebH8WIDrc6DkRgV-2Y4ZtMQ48NgfJY9C3I-B4q_pDbFWWL_QsolDDWgPDRejrH1vIsFZNAvdUNcvpKEuQH51QZgD97592t8m74juH6bisryss1diQzfCZd8B8bpExnK4XOVtgmKMBv2m0SLUVNbdhi1O-j_vu8w5PnctkC4vBQZSrFJ_YJZPIYi4vj_HGVdqq4p8-3b_utzLjJpVG0A/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer_______________________________________________Freesurfer mailing [email protected] has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1qnXBMbD40ZVLX3RwULANcZQDif3uUyu5MINeIGKgmC7tbvYFplok-hlUWWwuHFE5eubBHi9JxX3_RZw-_JMJ4UmSKGVhZ_P_BC6aiakcQ435deRCokgGKLwKVnk5zggUrwyQ8zRQ2Wi1ZHidV8vhjftxnsqfmeqnWbcKB0hoFhCwAczw9KrBx8HkVYOxdtOHJV7qdGjxHyO2zd8eb7pBxNM_t7hpBeBYjhQamejPLqq6N_p0IxNiLCM2XyPx0cTijJV_XsP8Gam1Es4fz3e2Y7LIBO8BL-sJEBdLnmuMeRDpu1d9TUv5hhY0NkEXjyOxEozAHhmQMwVVZ5PWdZaaoWG5JDvhmBJo1FJEyYYORHI/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2FfreesurferThe information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be http://secure-web.cisco.com/1KdkqTsFrq4x5-8J0JkQZkrfQUJL1hlCw5kHzDnIrtSmayGbNBPcOek8yv4SDkF0iTL0geq2e_WGxpGPAMAZKvxWDGJgOz_smwLSpxnCB0EBAfl63Xynp9SsxVAyxrXPVgBG7SUHnxJkq7NJ6p73HzlhuwGorctIyTHCdv9EDNaN1z27mV6JhPRti3HmoW0z00__Pq72WKlhQirPEcjLH_7BRhddnXlf6Fpd6w_3rJKKbZCvWUPrvoHTo1ODCWMSPzZRy1sNlD6-vy_3vF7NskwNPqUhqNlRz7p80nXMRvKkqxWrxDcAaor25rEk6b7ELi-SLSuQ5z_IG24FXGA8sKqa9FMHU2ZbRg6X4K72zAtE/http%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline%C2%A0 If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail. _______________________________________________Freesurfer mailing [email protected]https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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