Gggrrr that rules out the memory problems - you can try 1.0 instead of 0.5 but that shouldn’t be it, as (0.5/0.33)^3 is already a reduction by a factor of 3 in memory requirements… It is weird because it runs almost the whole way to completion… R, any further ideas? Cheers, /E PS: our plan is to port the subregion modules to Python in the near future, to avoid all these problems…

Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://www.jeiglesias.com

From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Ramtilak Gattu rgatt@med.wayne.edu Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Wednesday, March 24, 2021 at 20:33 To: fsbuild fsbuild@contbay.com, "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Hippocampal Subfields Segmentation Violation-error

External Email - Use Caution

External Email - Use Caution First let me thank you 'R' and 'E' for being so patient and working with me to resolve this issue.

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

set RESOLUTION="0.333333333333333333333333333333333333".

by:

set RESOLUTION="0.5";

still, the error persists.

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.

Thanks

Regards Tilak

________________________________ From: fsbuild fsbuild@contbay.com Sent: Wednesday, March 24, 2021 5:09 AM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Cc: Ramtilak Gattu rgatt@med.wayne.edu Subject: Re: [Freesurfer] Hippocampal Subfields Segmentation Violation-error

I don’t see anything in your output showing say code 01 with Bus Error. 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. 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 https://www.lifewire.com/use-activity-monitor-to-track-mac-memory-usage-2260...

- R.

On Mar 24, 2021, at 04:26, Ramtilak Gattu rgatt@med.wayne.edu wrote:

External Email - Use Caution External Email - Use Caution Yes it says enabled.

[tilak:~] tilak% csrutil status System Integrity Protection status: enabled.

Thanks

Regards, Tilak ________________________________ From: fsbuild <fsbuild@contbay.commailto:fsbuild@contbay.com> Sent: Wednesday, March 24, 2021 4:22 AM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Cc: Ramtilak Gattu <rgatt@med.wayne.edumailto:rgatt@med.wayne.edu> Subject: Re: [Freesurfer] Hippocampal Subfields Segmentation Violation-error

Maybe you could let us know if the system integrity protection feature is turned on the Mac (which is the default). The following command will report if it is enabled or disabled, e.g., when enabled,

$ csrutil status System Integrity Protection status: enabled. - R.

On Mar 24, 2021, at 01:48, Ramtilak Gattu rgatt@med.wayne.edu wrote:

External Email - Use Caution External Email - Use Caution Hi,

Earlier I didnt have a full matlab verion but I installed mcr by running "fs_install_mcr R2014b" as suggested in FSwiki.

I updated java to version "1.8.0_281" (Java(TM) SE Runtime Environment (build 1.8.0_281-b09) Java HotSpot(TM) 64-Bit Server VM (build 25.281-b09, mixed mode) 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: Crash Decoding : Disabled Current Visual : Quartz Default Encoding : ISO-8859-1 MATLAB Architecture: maci64 MATLAB Root : /Applications/freesurfer/7.1.1/MCRv84 MATLAB Version : 8.4.0.150421 (R2014b) Operating System : 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 Processor ID : x86 Family 6 Model 158 Stepping 10, 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: Bus error

Register State (from fault): RAX = 0000000000000003 RBX = 000000010145d080 RCX = 00007fdc9c700000 RDX = 000070000959f180 RSP = 00007fdc9c700000 RBP = 00007fff2027d95e RSI = 0000700000000000 RDI = 00007fff2027f1f9

R8 = 0000000070c054b0 R9 = 000070000959f180 R10 = 00007fff20270002 R11 = 00007fdc9c7429e0 R12 = 000070000959f498 R13 = 0000000000000000 R14 = 000000010f061d9b R15 = 0000000000000060

RIP = 000070000959f498 RFL = 000070000959f1e0

CS = 000000010eef827b FS = 000070000959f1c0 GS = 0000000000000001

Stack Trace (from fault): [ 0] 0x00000001036a0e64 /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwfl.dylib+00028260 _ZN2fl4diag15stacktrace_base7captureERKNS0_14thread_contextEm+00000052 [ 1] 0x00000001036a4a2a /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwfl.dylib+00043562 _ZN2fl4test17terminate_handledEv+00000906 [ 2] 0x00000001036a4477 /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwfl.dylib+00042103 _ZN2fl4diag13terminate_logEPKcPK17__darwin_ucontext+00000119 [ 3] 0x000000010ec3bb7a /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwmcr.dylib+00387962 _Z32mnRunPathDependentInitializationv+00003146 [ 4] 0x000000010ec3be58 /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwmcr.dylib+00388696 _Z32mnRunPathDependentInitializationv+00003880 [ 5] 0x000000010ec39733 /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwmcr.dylib+00378675 mnFatalSignalHandler+00000275 [ 6] 0x00007fff20498d7d /usr/lib/system/libsystem_platform.dylib+00015741 _sigtramp+00000029 [ 7] 0x0000000000000000 <unknown-module>+00000000 [ 8] 0x000000010eef827b /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwm_interpreter.dylib+01782395 _Z10inRunMfileiPP11mxArray_tagiS1_P6Mfh_mpP15inWorkSpace_tag+00010667 [ 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 /usr/lib/system/libsystem_pthread.dylib+00026960 _pthread_start+00000224 [ 32] 0x00007fff2045047b /usr/lib/system/libsystem_pthread.dylib+00009339 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/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: 2179 Killed: 9 /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/' 0 Darwin 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_64

T1 hippocampal subfields exited with ERRORS at Wed Mar 24 00:59:59 EDT 2021

For more details, see the log file /Users/tilak/Desktop/Work/CNS_cases/Hipps/Amy_Damboise/scripts/hippocampal-subfields-T1..log

tilak@tilak Hipps %

________________________________ From: fsbuild <fsbuild@contbay.commailto:fsbuild@contbay.com> Sent: Tuesday, March 23, 2021 11:00 PM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Cc: Ramtilak Gattu <rgatt@med.wayne.edumailto:rgatt@med.wayne.edu> Subject: Re: [Freesurfer] Hippocampal Subfields Segmentation Violation-error

[EXTERNAL] I”m wondering if this is an issue with the version of Java installed on the machine and Matlab. I’ve seen the latest MCR Matlab installer try to make changes to java installed on a Mac. So maybe updating or re-installing the Matlab software on your machine could force a java update. 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 <rgatt@med.wayne.edumailto:rgatt@med.wayne.edu> wrote:

External Email - Use Caution External Email - Use Caution 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 details

Hardware Overview:

Model Name: MacBook Pro Model Identifier: MacBookPro16,1 Processor Name: 6-Core Intel Core i7 Processor Speed: 2.6 GHz Number of Processors: 1 Total Number of Cores: 6 L2 Cache (per Core): 256 KB L3 Cache: 12 MB Hyper-Threading Technology: Enabled Memory: 16 GB System Firmware Version: 1554.80.3.0.0 (iBridge: 18.16.14347.0.0,0) Serial Number (system): C02DPB3BMD6M Hardware UUID: D313516B-A3B9-500F-9303-EB0F4D4946A4 Provisioning UDID: D313516B-A3B9-500F-9303-EB0F4D4946A4 Activation Lock Status: Enabled

Here is the log for segmentation violation error *************************************************** Fitting mesh to image data took 742.9022 seconds Transforming points Transforming points Wrote image to file image.mgz Constructing 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.mgz This file does not contain MRI parameters Caught unexpected exception of unknown type.

------------------------------------------------------------------------ Segmentation violation detected at Tue Mar 23 15:53:07 2021 ------------------------------------------------------------------------

Configuration: Crash Decoding : Disabled Current Visual : Quartz Default Encoding : ISO-8859-1 MATLAB Architecture: maci64 MATLAB Root : /Applications/freesurfer/7.1.1/MCRv84 MATLAB Version : 8.4..0.150421 (R2014b) Operating System : 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 Processor ID : x86 Family 6 Model 158 Stepping 10, 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 = 0000000000000003 RBX = 0000000102cde080 RCX = 00007ff4ce000000 RDX = 000070000624c180 RSP = 00007ff4ce000000 RBP = 00007fff2041595e RSI = 0000700000000000 RDI = 00007fff204171f9

R8 = 00000000660333a0 R9 = 000070000624c180 R10 = 00007fff20410002 R11 = 00007ff4ce05b4e0 R12 = 000070000624c498 R13 = 0000000000000000 R14 = 000000010e5fbd9b R15 = 0000000000000060

RIP = 000070000624c498 RFL = 000070000624c1e0

CS = 000000010e49227b FS = 000070000624c1c0 GS = 0000000000000001

Stack Trace (from fault): [ 0] 0x00000001048a9e64 /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwfl.dylib+00028260 _ZN2fl4diag15stacktrace_base7captureERKNS0_14thread_contextEm+00000052 [ 1] 0x00000001048ada2a /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwfl.dylib+00043562 _ZN2fl4test17terminate_handledEv+00000906 [ 2] 0x00000001048ad477 /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwfl.dylib+00042103 _ZN2fl4diag13terminate_logEPKcPK17__darwin_ucontext+00000119 [ 3] 0x0000000107e39b7a /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwmcr.dylib+00387962 _Z32mnRunPathDependentInitializationv+00003146 [ 4] 0x0000000107e39e58 /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwmcr.dylib+00388696 _Z32mnRunPathDependentInitializationv+00003880 [ 5] 0x0000000107e37733 /Applications/freesurfer/7.1..1/MCRv84/bin/maci64/libmwmcr.dylib+00378675 mnFatalSignalHandler+00000275 [ 6] 0x00007fff20630d7d /usr/lib/system/libsystem_platform.dylib+00015741 _sigtramp+00000029 [ 7] 0x0000000000000000 <unknown-module>+00000000 [ 8] 0x000000010e49227b /Applications/freesurfer/7.1..1/MCRv84/bin/maci64/libmwm_interpreter.dylib+01782395 _Z10inRunMfileiPP11mxArray_tagiS1_P6Mfh_mpP15inWorkSpace_tag+00010667 [ 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 /usr/lib/system/libsystem_pthread.dylib+00026960 _pthread_start+00000224 [ 32] 0x00007fff205e847b /usr/lib/system/libsystem_pthread.dylib+00009339 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/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 /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/' 0 Darwin 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_64

T1 hippocampal subfields exited with ERRORS at Tue Mar 23 15:53:07 EDT 2021

Thanks

Regards Tilak

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​

Matt (cc’d) has recently posted a similar error on the last. Unfortunately, these mac MCR errors are difficult to debug. You could wait for the python subfield port to get released, but that might be a few months down the line. If you want to get things running immediately, one thing to try is to download the 7.1 docker container from https://hub.docker.com/r/freesurfer/freesurfer and run FS through that. That should fix any system-specific problems.

Best Andrew

From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Ramtilak Gattu rgatt@med.wayne.edu Date: Thursday, March 25, 2021 at 7:20 PM To: fsbuild fsbuild@contbay.com, freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Hippocampal Subfields Segmentation Violation-error

External Email - Use Caution

External Email - Use Caution Hi 'E' / 'R',

I even tried changing the resolution to 1.0 with no success ruling put memory issues.

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 Hardware Overview:

Model Name: MacBook Pro Model Identifier: MacBookPro16,1 Processor Name: 6-Core Intel Core i7 Processor Speed: 2.6 GHz Number of Processors: 1 Total Number of Cores: 6 L2 Cache (per Core): 256 KB L3 Cache: 12 MB Hyper-Threading Technology: Enabled Memory: 16 GB System Firmware Version: 1554.80.3.0.0 (iBridge: 18.16.14347.0.0,0) Serial Number (system): C02DPB3BMD6M Hardware UUID: D313516B-A3B9-500F-9303-EB0F4D4946A4 Provisioning UDID: D313516B-A3B9-500F-9303-EB0F4D4946A4 Activation Lock Status: Enabled

had 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?

I think some Compatability issues with 'MCR' holding back the processing at that stage.

Again, thanks a lot for all your help in this regards.

Regards Tilak ________________________________ From: Ramtilak Gattu rgatt@med.wayne.edu Sent: Wednesday, March 24, 2021 8:32 PM To: fsbuild fsbuild@contbay.com; freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Hippocampal Subfields Segmentation Violation-error

First let me thank you 'R' and 'E' for being so patient and working with me to resolve this issue.

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

set RESOLUTION="0.333333333333333333333333333333333333".

by:

set RESOLUTION="0.5";

still, the error persists.

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.

Thanks

Regards Tilak

________________________________ From: fsbuild fsbuild@contbay.com Sent: Wednesday, March 24, 2021 5:09 AM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Cc: Ramtilak Gattu rgatt@med.wayne.edu Subject: Re: [Freesurfer] Hippocampal Subfields Segmentation Violation-error

I don’t see anything in your output showing say code 01 with Bus Error. 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. 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 https://www.lifewire.com/use-activity-monitor-to-track-mac-memory-usage-2260...

- R.

On Mar 24, 2021, at 04:26, Ramtilak Gattu rgatt@med.wayne.edu wrote:

External Email - Use Caution External Email - Use Caution Yes it says enabled.

[tilak:~] tilak% csrutil status System Integrity Protection status: enabled.

Thanks

Regards, Tilak ________________________________ From: fsbuild <fsbuild@contbay.commailto:fsbuild@contbay.com> Sent: Wednesday, March 24, 2021 4:22 AM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Cc: Ramtilak Gattu <rgatt@med.wayne.edumailto:rgatt@med.wayne.edu> Subject: Re: [Freesurfer] Hippocampal Subfields Segmentation Violation-error

Maybe you could let us know if the system integrity protection feature is turned on the Mac (which is the default). The following command will report if it is enabled or disabled, e.g., when enabled,

$ csrutil status System Integrity Protection status: enabled. - R.

On Mar 24, 2021, at 01:48, Ramtilak Gattu rgatt@med.wayne.edu wrote:

External Email - Use Caution External Email - Use Caution Hi,

Earlier I didnt have a full matlab verion but I installed mcr by running "fs_install_mcr R2014b" as suggested in FSwiki.

I updated java to version "1.8.0_281" (Java(TM) SE Runtime Environment (build 1.8.0_281-b09) Java HotSpot(TM) 64-Bit Server VM (build 25.281-b09, mixed mode) 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: Crash Decoding : Disabled Current Visual : Quartz Default Encoding : ISO-8859-1 MATLAB Architecture: maci64 MATLAB Root : /Applications/freesurfer/7.1.1/MCRv84 MATLAB Version : 8.4.0.150421 (R2014b) Operating System : 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 Processor ID : x86 Family 6 Model 158 Stepping 10, 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: Bus error

Register State (from fault): RAX = 0000000000000003 RBX = 000000010145d080 RCX = 00007fdc9c700000 RDX = 000070000959f180 RSP = 00007fdc9c700000 RBP = 00007fff2027d95e RSI = 0000700000000000 RDI = 00007fff2027f1f9

R8 = 0000000070c054b0 R9 = 000070000959f180 R10 = 00007fff20270002 R11 = 00007fdc9c7429e0 R12 = 000070000959f498 R13 = 0000000000000000 R14 = 000000010f061d9b R15 = 0000000000000060

RIP = 000070000959f498 RFL = 000070000959f1e0

CS = 000000010eef827b FS = 000070000959f1c0 GS = 0000000000000001

Stack Trace (from fault): [ 0] 0x00000001036a0e64 /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwfl.dylib+00028260 _ZN2fl4diag15stacktrace_base7captureERKNS0_14thread_contextEm+00000052 [ 1] 0x00000001036a4a2a /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwfl.dylib+00043562 _ZN2fl4test17terminate_handledEv+00000906 [ 2] 0x00000001036a4477 /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwfl.dylib+00042103 _ZN2fl4diag13terminate_logEPKcPK17__darwin_ucontext+00000119 [ 3] 0x000000010ec3bb7a /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwmcr.dylib+00387962 _Z32mnRunPathDependentInitializationv+00003146 [ 4] 0x000000010ec3be58 /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwmcr.dylib+00388696 _Z32mnRunPathDependentInitializationv+00003880 [ 5] 0x000000010ec39733 /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwmcr.dylib+00378675 mnFatalSignalHandler+00000275 [ 6] 0x00007fff20498d7d /usr/lib/system/libsystem_platform.dylib+00015741 _sigtramp+00000029 [ 7] 0x0000000000000000 <unknown-module>+00000000 [ 8] 0x000000010eef827b /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwm_interpreter.dylib+01782395 _Z10inRunMfileiPP11mxArray_tagiS1_P6Mfh_mpP15inWorkSpace_tag+00010667 [ 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 /usr/lib/system/libsystem_pthread.dylib+00026960 _pthread_start+00000224 [ 32] 0x00007fff2045047b /usr/lib/system/libsystem_pthread.dylib+00009339 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/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: 2179 Killed: 9 /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/' 0 Darwin 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_64

T1 hippocampal subfields exited with ERRORS at Wed Mar 24 00:59:59 EDT 2021

For more details, see the log file /Users/tilak/Desktop/Work/CNS_cases/Hipps/Amy_Damboise/scripts/hippocampal-subfields-T1..log

tilak@tilak Hipps %

________________________________ From: fsbuild <fsbuild@contbay.commailto:fsbuild@contbay.com> Sent: Tuesday, March 23, 2021 11:00 PM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Cc: Ramtilak Gattu <rgatt@med.wayne.edumailto:rgatt@med.wayne.edu> Subject: Re: [Freesurfer] Hippocampal Subfields Segmentation Violation-error

[EXTERNAL] I”m wondering if this is an issue with the version of Java installed on the machine and Matlab. I’ve seen the latest MCR Matlab installer try to make changes to java installed on a Mac. So maybe updating or re-installing the Matlab software on your machine could force a java update. 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 <rgatt@med.wayne.edumailto:rgatt@med.wayne.edu> wrote:

External Email - Use Caution External Email - Use Caution 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 details

Hardware Overview:

Model Name: MacBook Pro Model Identifier: MacBookPro16,1 Processor Name: 6-Core Intel Core i7 Processor Speed: 2.6 GHz Number of Processors: 1 Total Number of Cores: 6 L2 Cache (per Core): 256 KB L3 Cache: 12 MB Hyper-Threading Technology: Enabled Memory: 16 GB System Firmware Version: 1554.80.3.0.0 (iBridge: 18.16.14347.0.0,0) Serial Number (system): C02DPB3BMD6M Hardware UUID: D313516B-A3B9-500F-9303-EB0F4D4946A4 Provisioning UDID: D313516B-A3B9-500F-9303-EB0F4D4946A4 Activation Lock Status: Enabled

Here is the log for segmentation violation error *************************************************** Fitting mesh to image data took 742.9022 seconds Transforming points Transforming points Wrote image to file image.mgz Constructing 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.mgz This file does not contain MRI parameters Caught unexpected exception of unknown type.

------------------------------------------------------------------------ Segmentation violation detected at Tue Mar 23 15:53:07 2021 ------------------------------------------------------------------------

Configuration: Crash Decoding : Disabled Current Visual : Quartz Default Encoding : ISO-8859-1 MATLAB Architecture: maci64 MATLAB Root : /Applications/freesurfer/7.1.1/MCRv84 MATLAB Version : 8.4..0.150421 (R2014b) Operating System : 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 Processor ID : x86 Family 6 Model 158 Stepping 10, 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 = 0000000000000003 RBX = 0000000102cde080 RCX = 00007ff4ce000000 RDX = 000070000624c180 RSP = 00007ff4ce000000 RBP = 00007fff2041595e RSI = 0000700000000000 RDI = 00007fff204171f9

R8 = 00000000660333a0 R9 = 000070000624c180 R10 = 00007fff20410002 R11 = 00007ff4ce05b4e0 R12 = 000070000624c498 R13 = 0000000000000000 R14 = 000000010e5fbd9b R15 = 0000000000000060

RIP = 000070000624c498 RFL = 000070000624c1e0

CS = 000000010e49227b FS = 000070000624c1c0 GS = 0000000000000001

Stack Trace (from fault): [ 0] 0x00000001048a9e64 /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwfl.dylib+00028260 _ZN2fl4diag15stacktrace_base7captureERKNS0_14thread_contextEm+00000052 [ 1] 0x00000001048ada2a /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwfl.dylib+00043562 _ZN2fl4test17terminate_handledEv+00000906 [ 2] 0x00000001048ad477 /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwfl.dylib+00042103 _ZN2fl4diag13terminate_logEPKcPK17__darwin_ucontext+00000119 [ 3] 0x0000000107e39b7a /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwmcr.dylib+00387962 _Z32mnRunPathDependentInitializationv+00003146 [ 4] 0x0000000107e39e58 /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwmcr.dylib+00388696 _Z32mnRunPathDependentInitializationv+00003880 [ 5] 0x0000000107e37733 /Applications/freesurfer/7.1..1/MCRv84/bin/maci64/libmwmcr.dylib+00378675 mnFatalSignalHandler+00000275 [ 6] 0x00007fff20630d7d /usr/lib/system/libsystem_platform.dylib+00015741 _sigtramp+00000029 [ 7] 0x0000000000000000 <unknown-module>+00000000 [ 8] 0x000000010e49227b /Applications/freesurfer/7.1..1/MCRv84/bin/maci64/libmwm_interpreter.dylib+01782395 _Z10inRunMfileiPP11mxArray_tagiS1_P6Mfh_mpP15inWorkSpace_tag+00010667 [ 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 /usr/lib/system/libsystem_pthread.dylib+00026960 _pthread_start+00000224 [ 32] 0x00007fff205e847b /usr/lib/system/libsystem_pthread.dylib+00009339 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/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 /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/' 0 Darwin 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_64

T1 hippocampal subfields exited with ERRORS at Tue Mar 23 15:53:07 EDT 2021

Thanks

Regards Tilak

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