New subject: Hippocampal Subfields Segmentation Violation-error

26 Mar 2021


      External Email - Use Caution
I was looking again at the stack trace that starts with,
Bus error detected at Wed Mar 24 00:59:58 2021------------------------------------------------------------------------&nbsp;Configuration:&nbsp;&nbsp;Crash Decoding&nbsp;&nbsp; &nbsp;&nbsp;: Disabled&nbsp;&nbsp;Current Visual&nbsp;&nbsp; &nbsp;&nbsp;: Quartz&nbsp;&nbsp;Default Encoding&nbsp;&nbsp;&nbsp;: ISO-8859-1&nbsp;&nbsp;MATLAB Architecture: maci64&nbsp;&nbsp;MATLAB Root&nbsp; &nbsp; &nbsp; &nbsp;&nbsp;: /Applications/freesurfer/7.1.1/MCRv84&nbsp;&nbsp;MATLAB Version&nbsp;&nbsp; &nbsp;&nbsp;: 8.4.0.150421 (R2014b)&nbsp;&nbsp;Operating System&nbsp;&nbsp;&nbsp;: Darwin 20.3.0 Darwin Kernel Version 20.3.0: Thu Jan 21 00:07:06 PST 2021; root:xnu-7195..81.3~1/RELEASE_X86_64 x86_64&nbsp;&nbsp;Processor ID&nbsp;&nbsp; &nbsp; &nbsp;&nbsp;: x86 Family 6 Model 158 Stepping 10, GenuineIntel&nbsp;&nbsp;Software OpenGL&nbsp; &nbsp;&nbsp;: 0&nbsp;&nbsp;Virtual Machine&nbsp; &nbsp;&nbsp;: Java 1.7.0_55-b13 with Oracle Corporation Java HotSpot(TM) 64-Bit Server VM mixed mode&nbsp;&nbsp;Window System&nbsp; &nbsp; &nbsp;&nbsp;: Quartz&nbsp;Fault Count: 1Further on down, lines 5, 6 and 7 list,[&nbsp;&nbsp;5] 0x000000010ec39733 /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwmcr.dylib+00378675 mnFatalSignalHandler+00000275[&nbsp;&nbsp;6] 0x00007fff20498d7d&nbsp;&nbsp; &nbsp; &nbsp; &nbsp; &nbsp;&nbsp;/usr/lib/system/libsystem_platform.dylib+00015741&nbsp;_sigtramp+00000029[&nbsp;&nbsp;7] 0x0000000000000000&nbsp;&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;&nbsp;&lt;unknown-module&gt;+00000000At line 5, some kind of signal was received by The Mathworks library fatal signal handler. &nbsp;It looks like the handler tried to process the signal and crashed falling back to the system _sigtramp which is the “user space signal trampoline”. &nbsp; &nbsp;But can’t really tell what the signal was without a more detailed stack trace, e.g., like a segmentation fault (SIGSEGV).
This bug/crash report on The Mathworks web site looks similar (see lines 5,6,7 as well)https://secure-web.cisco.com/1JQhmxBxqZzsKf_5bE2K3e0nFFjhcK2dlWpIT8XeSKRmfKJ...
In this case the culprit is supposedly a file in the Matlab application bundle installed on the machine.
This crash can be traced to the following file being missing or corrupted:/Applications/MATLAB_R2017b.app/settings/src/settingscore/settings.xsdTo correct this issue, reinstall MATLAB on your machine. You will also want to remove or rename the /Users/$USER/Downloads/MathWorks folder on your machine to ensure that complete installation files are downloaded, and to rule out any potential problems caused by corrupted installation files.
But that file also exists under the runtime environment, i.e., if you installed it under the freesurfer tree
/Applications/freesurfer/7..1.1/MCRv84&gt; lsContents/&nbsp; &nbsp; &nbsp; &nbsp;&nbsp;bin/&nbsp;&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;&nbsp;help/&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;&nbsp;mcr/&nbsp;&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;&nbsp;remote/&nbsp; &nbsp; &nbsp; &nbsp; &nbsp;&nbsp;runtime/&nbsp;&nbsp; &nbsp; &nbsp; &nbsp;&nbsp;toolbox/MCR_license.txt&nbsp;&nbsp;etc/&nbsp;&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;&nbsp;java/&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;&nbsp;patents.txt&nbsp; &nbsp; &nbsp;&nbsp;resources/&nbsp;&nbsp; &nbsp; &nbsp;&nbsp;simulink/&nbsp; &nbsp; &nbsp; &nbsp;&nbsp;trademarks.txtappdata/&nbsp;&nbsp; &nbsp; &nbsp; &nbsp;&nbsp;extern/&nbsp; &nbsp; &nbsp; &nbsp; &nbsp;&nbsp;license.txt&nbsp; &nbsp; &nbsp;&nbsp;polyspace/&nbsp;&nbsp; &nbsp; &nbsp;&nbsp;rtw/&nbsp;&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;&nbsp;sys/
/Applications/freesurfer/dev/MCRv84&gt; find . -name "settings.xsd"./toolbox/matlab/configtools/settings.xsd
I don’t know how to tell if that file is corrupted or not. &nbsp;But maybe another way to test that is to try installing the latest and greatest matlab runtime environment using the actual Mathworks pkg installer. &nbsp; That would be version R2021a (https://secure-web.cisco.com/1MljBF-xENfCJNIAKmAXBqz8Y90j_CUs1fKhVdvW8mdPjvR...)
I installed it on a Mac running 10.15.7, taking all the defaults in the installer application including letting it make modifications to Java.&nbsp; I ended up with the install under /Applications/MATLAB/MATLAB_runtime/v910 &nbsp;which looks like,
/Applications/MATLAB/MATLAB_runtime/v910&gt; lsMCR_license.txt&nbsp;&nbsp;bin/&nbsp;&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;&nbsp;help/&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;&nbsp;mcr/&nbsp;&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;&nbsp;remote/&nbsp; &nbsp; &nbsp; &nbsp; &nbsp;&nbsp;simulink/&nbsp; &nbsp; &nbsp; &nbsp;&nbsp;trademarks.txtVersionInfo.xml&nbsp;&nbsp;derived/&nbsp;&nbsp; &nbsp; &nbsp; &nbsp;&nbsp;interprocess/&nbsp; &nbsp;&nbsp;patents.txt&nbsp; &nbsp; &nbsp;&nbsp;resources/&nbsp;&nbsp; &nbsp; &nbsp;&nbsp;sys/&nbsp;&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;&nbsp;ui/appdata/&nbsp;&nbsp; &nbsp; &nbsp; &nbsp;&nbsp;extern/&nbsp; &nbsp; &nbsp; &nbsp; &nbsp;&nbsp;java/&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;&nbsp;polyspace/&nbsp;&nbsp; &nbsp; &nbsp;&nbsp;runtime/&nbsp;&nbsp; &nbsp; &nbsp; &nbsp;&nbsp;toolbox/
/Applications/MATLAB/MATLAB_runtime/v910&gt; find . -name "settings.xsd"./toolbox/matlab/settings/settings.xsd
So you could move aside the older copy of the runtime environment under the Freesurfer tree and make a soft link to try out the newer version,
$ cd /Applications/freesurfer/7.1.1$ sudo mv MCRv84 &nbsp;old_MCRv84$ sudo ln -s &nbsp;/Applications/MATLAB/MATLAB_Runtime/v910 &nbsp;MCRv84$ ls -l MCRv84lrwxr-xr-x&nbsp;&nbsp;1 root&nbsp;&nbsp;wheel&nbsp;&nbsp;40 Mar 26 01:27&nbsp;MCRv84@ -&gt; /Applications/MATLAB/MATLAB_Runtime/v910
… then try running your commands again.
… to put it back the way it was,
$ cd /Applications/freesurfer/7.1.1$ sudo rm MCRv84$ sudo mv old_MCRv84 &nbsp;MCRv84
I've attached a screenshots from my installation.&nbsp; Setting DYLD_LIBRARY_PATH to the actual paths listed in the installer window should work.
Once you set DYLD_LIBRARY_PATH, you could also try setting DYLD_FALLBACK_LIBRARY_PATH to the same value.
$ export&nbsp; DYLD_FALLBACK_LIBRARY_PATH=$DYLD_LIBRARY_PATH
- R.
On Mar 25, 2021, at 19:19, Ramtilak Gattu &lt;rgatt@med.wayne.edu&gt; wrote:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;External Email - Use Caution&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;External Email - Use Caution&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Hi 'E' / 'R',I even tried changing the resolution to 1.0 with no success ruling put memory issues.&nbsp;Just wondering if its time to give up and wait for your python build to successfully finish the job in mac. I wonder if any other user with a similar MacBook pro configuration as mine&nbsp;Hardware Overview:&nbsp;&nbsp;Model Name:&nbsp;MacBook Pro&nbsp;&nbsp;Model Identifier:&nbsp;MacBookPro16,1&nbsp;&nbsp;Processor Name:&nbsp;6-Core Intel Core i7&nbsp;&nbsp;Processor Speed:&nbsp;2.6 GHz&nbsp;&nbsp;Number of Processors:&nbsp;1&nbsp;&nbsp;Total Number of Cores:&nbsp;6&nbsp;&nbsp;L2 Cache (per Core):&nbsp;256 KB&nbsp;&nbsp;L3 Cache:&nbsp;12 MB&nbsp;&nbsp;Hyper-Threading Technology:&nbsp;Enabled&nbsp;&nbsp;Memory:&nbsp;16 GB&nbsp;&nbsp;System Firmware Version:&nbsp;1554.80.3.0.0 (iBridge: 18.16.14347.0.0,0)&nbsp;&nbsp;Serial Number (system):&nbsp;C02DPB3BMD6M&nbsp;&nbsp;Hardware UUID:&nbsp;D313516B-A3B9-500F-9303-EB0F4D4946A4&nbsp;&nbsp;Provisioning UDID:&nbsp;D313516B-A3B9-500F-9303-EB0F4D4946A4&nbsp;&nbsp;Activation Lock Status:&nbsp;Enabledhad successfully finished the processing or encountered the same issue and later fixed it to successfully run the segmentation. Is there a way to bypass that step and run the program till the end?&nbsp;&nbsp;I think some Compatability issues with 'MCR' holding back the processing at that stage.&nbsp;Again, thanks a lot for all your help in this regards.RegardsTilakFrom:&nbsp;Ramtilak Gattu &lt;rgatt@med.wayne.edu&gt;Sent:&nbsp;Wednesday, March 24, 2021 8:32 PMTo:&nbsp;fsbuild &lt;fsbuild@contbay.com&gt;;&nbsp;freesurfer@nmr.mgh.harvard.edu&nbsp;&lt;freesurfer@nmr.mgh.harvard.edu&gt;Subject:&nbsp;Re: [Freesurfer] Hippocampal Subfields Segmentation Violation-error&nbsp;First let me thank you 'R' and 'E' for being so patient and working with me to resolve this issue.&nbsp;As suggested by 'R' I monitored the activity monitored but unfortunately, the memory pressure graph remained green throughout the process. When the program was running memory usage jumped from 6.25gb to 7.85 gb.As suggeted by 'E" I even tried to run the code by changing the parameters in the code for&nbsp;set RESOLUTION="0.333333333333333333333333333333333333".
by:
set RESOLUTION="0.5";still, the error persists.&nbsp;It works fine on my Linux centos system(8gb ram) but fails on both the macs. surprisingly, it's the same exact error.Does running the routine after installing full matlab instead of just mcr8.4 would help? just a thought.&nbsp;ThanksRegardsTilakFrom:&nbsp;fsbuild &lt;fsbuild@contbay.com&gt;Sent:&nbsp;Wednesday, March 24, 2021 5:09 AMTo:&nbsp;freesurfer@nmr.mgh.harvard.edu&nbsp;&lt;freesurfer@nmr.mgh.harvard.edu&gt;Cc:&nbsp;Ramtilak Gattu &lt;rgatt@med.wayne.edu&gt;Subject:&nbsp;Re: [Freesurfer] Hippocampal Subfields Segmentation Violation-error&nbsp;I don’t see anything in your output showing say code 01 with Bus Error. &nbsp;But code 01 could indicate a memory issue, e.g., not enough RAM.You could bring up the Activity Monitor program and click on the memory tab to profile memory during the command run.&nbsp; But the "memory pressure" graph does not go back very far in time, so you would need to be able to see it close to the time the command exits. See&nbsp;&nbsp;https://secure-web.cisco.com/1tkr30obhmK2iOZliaWCRbke2W5CF6bmoVt191DHffCRfze... R.On Mar 24, 2021, at 04:26, Ramtilak Gattu &lt;rgatt@med.wayne.edu&gt; wrote:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;External Email - Use Caution&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;External Email - Use Caution&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Yes it says enabled.[tilak:~] tilak% csrutil statusSystem Integrity Protection status: enabled.ThanksRegards,TilakFrom:&nbsp;fsbuild &lt;fsbuild@contbay.com&gt;Sent:&nbsp;Wednesday, March 24, 2021 4:22 AMTo:&nbsp;freesurfer@nmr.mgh.harvard.edu&nbsp;&lt;freesurfer@nmr.mgh.harvard.edu&gt;Cc:&nbsp;Ramtilak Gattu &lt;rgatt@med.wayne.edu&gt;Subject:&nbsp;Re: [Freesurfer] Hippocampal Subfields Segmentation Violation-error&nbsp;Maybe you could let us know if the system integrity protection feature is turned on the Mac (which is the default). &nbsp;The following command will report if it is enabled or disabled, e.g., when enabled,$ csrutil statusSystem Integrity Protection status: enabled.- R.On Mar 24, 2021, at 01:48, Ramtilak Gattu &lt;rgatt@med.wayne.edu&gt; wrote:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;External Email - Use Caution&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;External Email - Use Caution&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Hi,Earlier I didnt have a full matlab verion but I installed mcr by running "fs_install_mcr R2014b" as suggested in FSwiki.&nbsp;I updated java to version "1.8.0_281" (Java(TM) SE Runtime Environment (build 1.8.0_281-b09)&nbsp;Java HotSpot(TM) 64-Bit Server VM (build 25.281-b09, mixed mode)&nbsp;and reinstalled or overwritten mcrv8.4 by running the same command again "fs_install_mcr R2014b" but still it ended after running for a whileand exited with errors again. But this time it says "Bus error detected instead of segmentation violation error.Bus error detected at Wed Mar 24 00:59:58 2021------------------------------------------------------------------------Configuration:&nbsp;&nbsp;Crash Decoding&nbsp;&nbsp; &nbsp;&nbsp;: Disabled&nbsp;&nbsp;Current Visual&nbsp;&nbsp; &nbsp;&nbsp;: Quartz&nbsp;&nbsp;Default Encoding&nbsp;&nbsp;&nbsp;: ISO-8859-1&nbsp;&nbsp;MATLAB Architecture: maci64&nbsp;&nbsp;MATLAB Root&nbsp; &nbsp; &nbsp; &nbsp;&nbsp;: /Applications/freesurfer/7.1.1/MCRv84&nbsp;&nbsp;MATLAB Version&nbsp;&nbsp; &nbsp;&nbsp;: 8.4.0.150421 (R2014b)&nbsp;&nbsp;Operating System&nbsp;&nbsp;&nbsp;: Darwin 20.3.0 Darwin Kernel Version 20.3.0: Thu Jan 21 00:07:06 PST 2021; root:xnu-7195.81.3~1/RELEASE_X86_64 x86_64&nbsp;&nbsp;Processor ID&nbsp;&nbsp; &nbsp; &nbsp;&nbsp;: x86 Family 6 Model 158 Stepping 10, GenuineIntel&nbsp;&nbsp;Software OpenGL&nbsp; &nbsp;&nbsp;: 0&nbsp;&nbsp;Virtual Machine&nbsp; &nbsp;&nbsp;: Java 1.7.0_55-b13 with Oracle Corporation Java HotSpot(TM) 64-Bit Server VM mixed mode&nbsp;&nbsp;Window System&nbsp; &nbsp; &nbsp;&nbsp;: QuartzFault Count: 1Abnormal termination:Bus errorRegister State (from fault):&nbsp;&nbsp;RAX = 0000000000000003&nbsp;&nbsp;RBX = 000000010145d080&nbsp;&nbsp;RCX = 00007fdc9c700000&nbsp;&nbsp;RDX = 000070000959f180&nbsp;&nbsp;RSP = 00007fdc9c700000&nbsp;&nbsp;RBP = 00007fff2027d95e&nbsp;&nbsp;RSI = 0000700000000000&nbsp;&nbsp;RDI = 00007fff2027f1f9&nbsp;&nbsp;&nbsp;R8 = 0000000070c054b0&nbsp;&nbsp;&nbsp;R9 = 000070000959f180&nbsp;&nbsp;R10 = 00007fff20270002&nbsp;&nbsp;R11 = 00007fdc9c7429e0&nbsp;&nbsp;R12 = 000070000959f498&nbsp;&nbsp;R13 = 0000000000000000&nbsp;&nbsp;R14 = 000000010f061d9b&nbsp;&nbsp;R15 = 0000000000000060&nbsp;&nbsp;RIP = 000070000959f498&nbsp;&nbsp;RFL = 000070000959f1e0&nbsp;&nbsp;&nbsp;CS = 000000010eef827b&nbsp;&nbsp;&nbsp;FS = 000070000959f1c0&nbsp;&nbsp;&nbsp;GS = 0000000000000001Stack Trace (from fault):[&nbsp;&nbsp;0] 0x00000001036a0e64 /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwfl.dylib+00028260 _ZN2fl4diag15stacktrace_base7captureERKNS0_14thread_contextEm+00000052[&nbsp;&nbsp;1] 0x00000001036a4a2a /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwfl.dylib+00043562 _ZN2fl4test17terminate_handledEv+00000906[&nbsp;&nbsp;2] 0x00000001036a4477 /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwfl.dylib+00042103 _ZN2fl4diag13terminate_logEPKcPK17__darwin_ucontext+00000119[&nbsp;&nbsp;3] 0x000000010ec3bb7a /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwmcr.dylib+00387962 _Z32mnRunPathDependentInitializationv+00003146[&nbsp;&nbsp;4] 0x000000010ec3be58 /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwmcr.dylib+00388696 _Z32mnRunPathDependentInitializationv+00003880[&nbsp;&nbsp;5] 0x000000010ec39733 /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwmcr.dylib+00378675 mnFatalSignalHandler+00000275[&nbsp;&nbsp;6] 0x00007fff20498d7d&nbsp;&nbsp; &nbsp; &nbsp; &nbsp; &nbsp;&nbsp;/usr/lib/system/libsystem_platform.dylib+00015741 _sigtramp+00000029[&nbsp;&nbsp;7] 0x0000000000000000&nbsp;&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;&nbsp;&lt;unknown-module&gt;+00000000[&nbsp;&nbsp;8] 0x000000010eef827b /Applications/freesurfer/7.1..1/MCRv84/bin/maci64/libmwm_interpreter.dylib+01782395 _Z10inRunMfileiPP11mxArray_tagiS1_P6Mfh_mpP15inWorkSpace_tag+00010667[&nbsp;&nbsp;9] 0x000000010ee51a17 /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwm_interpreter.dylib+01100311 _Z15inRunFinalizers7opcodesPS_Pi+00000119[ 10] 0x000000010eef629d /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwm_interpreter.dylib+01774237 _Z10inRunMfileiPP11mxArray_tagiS1_P6Mfh_mpP15inWorkSpace_tag+00002509[ 11] 0x000000010fc74c55 /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwm_dispatcher.dylib+00400469 _ZN8Mfh_file11dispatch_fhEiPP11mxArray_tagiS2_+00000645[ 12] 0x000000010ee9948b /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwm_interpreter.dylib+01393803 _Z23inEvalPcodeHeaderToWordP15_memory_contextiPP11mxArray_tagP12_pcodeheaderP6Mfh_mpj+00000219[ 13] 0x000000010ee4bf4b /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwm_interpreter.dylib+01077067 _Z25in_local_call_with_setjmpIN5boost3_bi6bind_tIvPFvP15_memory_contextPiPP11mxArray_tagP12_pcodeheaderjENS1_5list5INS1_5valueIS4_EENS0_3argILi1EEENSG_ILi2EEENSE_ISA_EENSE_IiEEEEEEEN6mlutil14cmddistributor17inExecutionStatusET_S5_S8_b+00000171[ 14] 0x000000010ee47221 /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwm_interpreter.dylib+01057313 _Z12inEvalStringP15_memory_contextRKSbItSt11char_traitsItESaItEE8EvalTypeiPP11mxArray_tag12inDebugCheckP12_pcodeheaderPib+00002769[ 15] 0x000000010ee477cd /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwm_interpreter.dylib+01058765 _ZN12InterpBridge22EvalCmdWithLocalReturnERKSbItSt11char_traitsItESaItEEPibb+00000141[ 16] 0x000000010ee47a62 /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwm_interpreter.dylib+01059426 _ZN12InterpBridge33EvalCmdWithLocalReturnInDesiredWSERKSbItSt11char_traitsItESaItEEPibbP15inWorkSpace_tag+00000066[ 17] 0x000000010eda72de /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwm_interpreter.dylib+00402142 _Z51inEvalCmdWithLocalReturnInDesiredWSAndPublishEventsRKSbItSt11char_traitsItESaItEEPibbP15inWorkSpace_tag+00000062[ 18] 0x000000010f8f593e /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwiqm.dylib+00227646 _ZNK3iqm18InternalEvalPlugin24inEvalCmdWithLocalReturnERKSbItSt11char_traitsItESaItEEP15inWorkSpace_tag+00000094[ 19] 0x000000010f8f4df4 /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwiqm.dylib+00224756 _ZN3iqm18InternalEvalPlugin7executeEP15inWorkSpace_tagRN5boost10shared_ptrIN14cmddistributor17IIPCompletedEventEEE+00000132[ 20] 0x000000010ec10358 /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwmcr.dylib+00209752 _ZN3mcr3mvm27McrSwappingIqmPluginAdapterIN3iqm18InternalEvalPluginEE7executeEP15inWorkSpace_tagRN5boost10shared_ptrIN14cmddistributor17IIPCompletedEventEEE+00000600[ 21] 0x000000010f8e5418 /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwiqm.dylib+00160792 _ZNK3iqm17DefaultPacketInfo7executeEP15inWorkSpace_tag+00000296[ 22] 0x000000010f8d07f1 /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwiqm.dylib+00075761 _ZN3iqm3Iqm15setupIqmFcnPtrsEv+00004945[ 23] 0x000000010148e005 /Applications/freesurfer/7.1..1/MCRv84/bin/maci64/libmwservices.dylib+00196613 _ZN10eventqueue18UserEventQueueImpl5flushEv+00001205[ 24] 0x000000010fa83a65 /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwuix.dylib+00043621 _Z25isHandleUserEventCallbackPFvPvE+00000501[ 25] 0x000000010155da45 /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwservices.dylib+01047109 _Z21svWS_ProcessCallbacksv+00016693[ 26] 0x0000000101559152 /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwservices.dylib+01028434 _Z25svWS_ProcessPendingEventsiib+00000834[ 27] 0x0000000101558e5e /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwservices.dylib+01027678 _Z25svWS_ProcessPendingEventsiib+00000078[ 28] 0x000000010ebfa18f /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwmcr.dylib+00119183 _ZN3mcr7runtime17InterpreterThread4Impl14process_eventsERKN5boost10shared_ptrIS2_EE+00000095[ 29] 0x000000010ebfa49f /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwmcr.dylib+00119967 _ZN3mcr7runtime17InterpreterThread4Impl3runERKN5boost10shared_ptrIS2_EEPNS2_12init_contextE+00000335[ 30] 0x000000010ebe0d1b /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwmcr.dylib+00015643 _Z26run_init_and_handle_eventsPv+00000059[ 31] 0x00007fff20454950&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;&nbsp;/usr/lib/system/libsystem_pthread.dylib+00026960 _pthread_start+00000224[ 32] 0x00007fff2045047b&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;&nbsp;/usr/lib/system/libsystem_pthread.dylib+00009339 thread_start+00000015If this problem is reproducible, please submit a Service Request via:&nbsp; &nbsp;&nbsp;http://secure-web.cisco.com/1eidi0IlCiU-mTvwSttFoSKPGF30rZgh0SZHeFxbmGnq8-0T... technical support engineer might contact you with further information.Thank you for your help.** This crash report has been saved to disk as /Users/tilak/matlab_crash_dump.2179-1 **MATLAB is exiting because of fatal error/Applications/freesurfer/7.1.1/bin/run_segmentSubjectT1_autoEstimateAlveusML.sh: line 33:&nbsp;&nbsp;2179 Killed: 9&nbsp;&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;&nbsp;/Applications/freesurfer/7.1.1/bin/segmentSubjectT1_autoEstimateAlveusML.app/Contents/MacOS/segmentSubjectT1_autoEstimateAlveusML Amy_Damboise /Users/tilak/Desktop/Work/CNS_cases/Hipps 0.333333333333333333333333333333333333 /Applications/freesurfer/7.1.1/average/HippoSF/atlas/AtlasMesh.gz /Applications/freesurfer/7.1.1/average/HippoSF/atlas/AtlasDump.mgz /Applications/freesurfer/7.1.1/average/HippoSF/atlas/compressionLookupTable.txt 0.05 left L-BFGS v21 '/Applications/freesurfer/7.1.1/bin/fs_run_from_mcr /Applications/freesurfer/7.1.1/bin/' 0Darwin tilak.lan 20.3.0 Darwin Kernel Version 20.3.0: Thu Jan 21 00:07:06 PST 2021; root:xnu-7195.81.3~1/RELEASE_X86_64 x86_64T1 hippocampal subfields exited with ERRORS at Wed Mar 24 00:59:59 EDT 2021For more details, see the log file /Users/tilak/Desktop/Work/CNS_cases/Hipps/Amy_Damboise/scripts/hippocampal-subfields-T1..logtilak@tilak Hipps %&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;From:&nbsp;fsbuild &lt;fsbuild@contbay.com&gt;Sent:&nbsp;Tuesday, March 23, 2021 11:00 PMTo:&nbsp;freesurfer@nmr.mgh.harvard.edu&nbsp;&lt;freesurfer@nmr.mgh.harvard.edu&gt;Cc:&nbsp;Ramtilak Gattu &lt;rgatt@med.wayne.edu&gt;Subject:&nbsp;Re: [Freesurfer] Hippocampal Subfields Segmentation Violation-error&nbsp;[EXTERNAL]I”m wondering if this is an issue with the version of Java installed on the machine and Matlab. &nbsp;I’ve seen the latest MCR Matlab installer try to make changes to java installed on a Mac. &nbsp;So maybe updating or re-installing the Matlab software on your machine could force a java update. &nbsp;You should be able to exit the installer before it makes any changes if you decide not to go thru with it.- R.On Mar 23, 2021, at 17:45, Ramtilak Gattu &lt;rgatt@med.wayne.edu&gt; wrote:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;External Email - Use Caution&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;External Email - Use Caution&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Hi,I am also encountering the same issue as WON JONG CHWA on my macbook pro (16gb ram) and I even tried the same on imac (8gb ram). I ran recon-all successfully on both systems. Here are my system detailsHardware Overview:&nbsp;&nbsp;Model Name:&nbsp;MacBook Pro&nbsp;&nbsp;Model Identifier:&nbsp;MacBookPro16,1&nbsp;&nbsp;Processor Name:&nbsp;6-Core Intel Core i7&nbsp;&nbsp;Processor Speed:&nbsp;2.6 GHz&nbsp;&nbsp;Number of Processors:&nbsp;1&nbsp;&nbsp;Total Number of Cores:&nbsp;6&nbsp;&nbsp;L2 Cache (per Core):&nbsp;256 KB&nbsp;&nbsp;L3 Cache:&nbsp;12 MB&nbsp;&nbsp;Hyper-Threading Technology:&nbsp;Enabled&nbsp;&nbsp;Memory:&nbsp;16 GB&nbsp;&nbsp;System Firmware Version:&nbsp;1554.80.3.0.0 (iBridge: 18.16.14347.0.0,0)&nbsp;&nbsp;Serial Number (system):&nbsp;C02DPB3BMD6M&nbsp;&nbsp;Hardware UUID:&nbsp;D313516B-A3B9-500F-9303-EB0F4D4946A4&nbsp;&nbsp;Provisioning UDID:&nbsp;D313516B-A3B9-500F-9303-EB0F4D4946A4&nbsp;&nbsp;Activation Lock Status:&nbsp;EnabledHere is the log for segmentation violation error***************************************************Fitting mesh to image data took 742.9022 secondsTransforming pointsTransforming pointsWrote image to file image.mgzConstructing image-to-world transform from header information (asmr1.mgz)Constructing image-to-world transform from header information (/Users/tilak/Desktop/Work/CNS_cases/Hipps/AD/tmp/hippoSF_T1_v21_left/imageDump.mgz)Wrote image to file asmr2.mgzThis file does not contain MRI parametersCaught unexpected exception of unknown type.------------------------------------------------------------------------&nbsp; &nbsp; &nbsp; &nbsp;Segmentation violation detected at Tue Mar 23 15:53:07 2021------------------------------------------------------------------------Configuration:&nbsp; Crash Decoding &nbsp; &nbsp; : Disabled&nbsp; Current Visual &nbsp; &nbsp; : Quartz&nbsp; Default Encoding &nbsp; : ISO-8859-1&nbsp; MATLAB Architecture: maci64&nbsp; MATLAB Root &nbsp; &nbsp; &nbsp; &nbsp;: /Applications/freesurfer/7.1.1/MCRv84&nbsp; MATLAB Version &nbsp; &nbsp; : 8.4..0.150421 (R2014b)&nbsp; Operating System &nbsp; : Darwin 20.3.0 Darwin Kernel Version 20.3.0: Thu Jan 21 00:07:06 PST 2021; root:xnu-7195.81.3~1/RELEASE_X86_64 x86_64&nbsp; Processor ID &nbsp; &nbsp; &nbsp; : x86 Family 6 Model 158 Stepping 10, GenuineIntel&nbsp; Software OpenGL &nbsp; &nbsp;: 0&nbsp; Virtual Machine &nbsp; &nbsp;: Java 1.7.0_55-b13 with Oracle Corporation Java HotSpot(TM) 64-Bit Server VM mixed mode&nbsp; Window System &nbsp; &nbsp; &nbsp;: QuartzFault Count: 1Abnormal termination:Segmentation violationRegister State (from fault):&nbsp; RAX = 0000000000000003 &nbsp;RBX = 0000000102cde080&nbsp; RCX = 00007ff4ce000000 &nbsp;RDX = 000070000624c180&nbsp; RSP = 00007ff4ce000000 &nbsp;RBP = 00007fff2041595e&nbsp; RSI = 0000700000000000 &nbsp;RDI = 00007fff204171f9&nbsp; &nbsp;R8 = 00000000660333a0 &nbsp; R9 = 000070000624c180&nbsp; R10 = 00007fff20410002 &nbsp;R11 = 00007ff4ce05b4e0&nbsp; R12 = 000070000624c498 &nbsp;R13 = 0000000000000000&nbsp; R14 = 000000010e5fbd9b &nbsp;R15 = 0000000000000060&nbsp; RIP = 000070000624c498 &nbsp;RFL = 000070000624c1e0&nbsp; &nbsp;CS = 000000010e49227b &nbsp; FS = 000070000624c1c0 &nbsp; GS = 0000000000000001Stack Trace (from fault):[ &nbsp;0] 0x00000001048a9e64 /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwfl.dylib+00028260 _ZN2fl4diag15stacktrace_base7captureERKNS0_14thread_contextEm+00000052[ &nbsp;1] 0x00000001048ada2a /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwfl.dylib+00043562 _ZN2fl4test17terminate_handledEv+00000906[ &nbsp;2] 0x00000001048ad477 /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwfl.dylib+00042103 _ZN2fl4diag13terminate_logEPKcPK17__darwin_ucontext+00000119[ &nbsp;3] 0x0000000107e39b7a /Applications/freesurfer/7..1.1/MCRv84/bin/maci64/libmwmcr.dylib+00387962 _Z32mnRunPathDependentInitializationv+00003146[ &nbsp;4] 0x0000000107e39e58 /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwmcr.dylib+00388696 _Z32mnRunPathDependentInitializationv+00003880[ &nbsp;5] 0x0000000107e37733 /Applications/freesurfer/7.1..1/MCRv84/bin/maci64/libmwmcr.dylib+00378675 mnFatalSignalHandler+00000275[ &nbsp;6] 0x00007fff20630d7d &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; /usr/lib/system/libsystem_platform.dylib+00015741 _sigtramp+00000029[ &nbsp;7] 0x0000000000000000 &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &lt;unknown-module&gt;+00000000[ &nbsp;8] 0x000000010e49227b /Applications/freesurfer/7.1..1/MCRv84/bin/maci64/libmwm_interpreter.dylib+01782395 _Z10inRunMfileiPP11mxArray_tagiS1_P6Mfh_mpP15inWorkSpace_tag+00010667[ &nbsp;9] 0x000000010e3eba17 /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwm_interpreter.dylib+01100311 _Z15inRunFinalizers7opcodesPS_Pi+00000119[ 10] 0x000000010e49029d /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwm_interpreter.dylib+01774237 _Z10inRunMfileiPP11mxArray_tagiS1_P6Mfh_mpP15inWorkSpace_tag+00002509[ 11] 0x000000010f0b9c55 /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwm_dispatcher.dylib+00400469 _ZN8Mfh_file11dispatch_fhEiPP11mxArray_tagiS2_+00000645[ 12] 0x000000010e43348b /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwm_interpreter.dylib+01393803 _Z23inEvalPcodeHeaderToWordP15_memory_contextiPP11mxArray_tagP12_pcodeheaderP6Mfh_mpj+00000219[ 13] 0x000000010e3e5f4b /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwm_interpreter.dylib+01077067 _Z25in_local_call_with_setjmpIN5boost3_bi6bind_tIvPFvP15_memory_contextPiPP11mxArray_tagP12_pcodeheaderjENS1_5list5INS1_5valueIS4_EENS0_3argILi1EEENSG_ILi2EEENSE_ISA_EENSE_IiEEEEEEEN6mlutil14cmddistributor17inExecutionStatusET_S5_S8_b+00000171[ 14] 0x000000010e3e1221 /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwm_interpreter.dylib+01057313 _Z12inEvalStringP15_memory_contextRKSbItSt11char_traitsItESaItEE8EvalTypeiPP11mxArray_tag12inDebugCheckP12_pcodeheaderPib+00002769[ 15] 0x000000010e3e17cd /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwm_interpreter.dylib+01058765 _ZN12InterpBridge22EvalCmdWithLocalReturnERKSbItSt11char_traitsItESaItEEPibb+00000141[ 16] 0x000000010e3e1a62 /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwm_interpreter.dylib+01059426 _ZN12InterpBridge33EvalCmdWithLocalReturnInDesiredWSERKSbItSt11char_traitsItESaItEEPibbP15inWorkSpace_tag+00000066[ 17] 0x000000010e3412de /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwm_interpreter.dylib+00402142 _Z51inEvalCmdWithLocalReturnInDesiredWSAndPublishEventsRKSbItSt11char_traitsItESaItEEPibbP15inWorkSpace_tag+00000062[ 18] 0x000000010ee8f93e /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwiqm.dylib+00227646 _ZNK3iqm18InternalEvalPlugin24inEvalCmdWithLocalReturnERKSbItSt11char_traitsItESaItEEP15inWorkSpace_tag+00000094[ 19] 0x000000010ee8edf4 /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwiqm.dylib+00224756 _ZN3iqm18InternalEvalPlugin7executeEP15inWorkSpace_tagRN5boost10shared_ptrIN14cmddistributor17IIPCompletedEventEEE+00000132[ 20] 0x0000000107e0e358 /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwmcr.dylib+00209752 _ZN3mcr3mvm27McrSwappingIqmPluginAdapterIN3iqm18InternalEvalPluginEE7executeEP15inWorkSpace_tagRN5boost10shared_ptrIN14cmddistributor17IIPCompletedEventEEE+00000600[ 21] 0x000000010ee7f418 /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwiqm.dylib+00160792 _ZNK3iqm17DefaultPacketInfo7executeEP15inWorkSpace_tag+00000296[ 22] 0x000000010ee6a7f1 /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwiqm.dylib+00075761 _ZN3iqm3Iqm15setupIqmFcnPtrsEv+00004945[ 23] 0x0000000102688005 /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwservices.dylib+00196613 _ZN10eventqueue18UserEventQueueImpl5flushEv+00001205[ 24] 0x000000010f1dea65 /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwuix.dylib+00043621 _Z25isHandleUserEventCallbackPFvPvE+00000501[ 25] 0x0000000102757a45 /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwservices.dylib+01047109 _Z21svWS_ProcessCallbacksv+00016693[ 26] 0x0000000102753152 /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwservices.dylib+01028434 _Z25svWS_ProcessPendingEventsiib+00000834[ 27] 0x0000000102752e5e /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwservices.dylib+01027678 _Z25svWS_ProcessPendingEventsiib+00000078[ 28] 0x0000000107df818f /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwmcr.dylib+00119183 _ZN3mcr7runtime17InterpreterThread4Impl14process_eventsERKN5boost10shared_ptrIS2_EE+00000095[ 29] 0x0000000107df849f /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwmcr.dylib+00119967 _ZN3mcr7runtime17InterpreterThread4Impl3runERKN5boost10shared_ptrIS2_EEPNS2_12init_contextE+00000335[ 30] 0x0000000107dded1b /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwmcr.dylib+00015643 _Z26run_init_and_handle_eventsPv+00000059[ 31] 0x00007fff205ec950 &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;/usr/lib/system/libsystem_pthread.dylib+00026960 _pthread_start+00000224[ 32] 0x00007fff205e847b &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;/usr/lib/system/libsystem_pthread.dylib+00009339 thread_start+00000015If this problem is reproducible, please submit a Service Request via:&nbsp; &nbsp;&nbsp;http://secure-web.cisco.com/1eidi0IlCiU-mTvwSttFoSKPGF30rZgh0SZHeFxbmGnq8-0T... technical support engineer might contact you with further information.Thank you for your help.** This crash report has been saved to disk as /Users/tilak/matlab_crash_dump.30147-1 **MATLAB is exiting because of fatal error/Applications/freesurfer/7.1.1/bin/run_segmentSubjectT1_autoEstimateAlveusML.sh: line 33: 95683 Killed: 9 &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; /Applications/freesurfer/7.1.1/bin/segmentSubjectT1_autoEstimateAlveusML.app/Contents/MacOS/segmentSubjectT1_autoEstimateAlveusML Amy_Damboise /Users/tilak/Desktop/Work/CNS_cases/Hipps 0.333333333333333333333333333333333333 /Applications/freesurfer/7.1.1/average/HippoSF/atlas/AtlasMesh.gz /Applications/freesurfer/7.1.1/average/HippoSF/atlas/AtlasDump.mgz /Applications/freesurfer/7.1.1/average/HippoSF/atlas/compressionLookupTable.txt 0.05 left L-BFGS v21 '/Applications/freesurfer/7.1.1/bin/fs_run_from_mcr /Applications/freesurfer/7.1.1/bin/' 0Darwin tilak.lan 20.3.0 Darwin Kernel Version 20.3.0: Thu Jan 21 00:07:06 PST 2021; root:xnu-7195.81.3~1/RELEASE_X86_64 x86_64T1 hippocampal subfields exited with ERRORS at Tue Mar 23 15:53:07 EDT 2021ThanksRegardsTilak_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer%C2%A0__________... mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer%C2%A0__________... mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer%C2%A0__________... mailing listFreesurfer@nmr.mgh..harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer