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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