Dear WJC, This is a very weird one, but if I was wondering if it could simply be an out-of-memory error? How much RAM does your (virtual) machine have? Cheers, /Eugenio
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 WON JONG CHWA williamchwa@ucla.edu Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Monday, March 22, 2021 at 23:19 To: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Hippocampal Suubfields Segmentation Violation
External Email - Use Caution Dear FreeSurfer experts,
I am trying to compute hippocampal subfields with MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldsAndNucleiOfAmy...https://secure-web.cisco.com/1f2QJwnqjis6w0KTpz2gk4AyWSMQmrO3JmYGqPPbxpD5JmmDwbJUxZvvKKZq6qt2Y3hoFg8_CcTB_QmP5hdXEqByKvJoyiipEKvwvEhB1aLd1_SovZI6F7-sjY9ZMjQxIGngrN1ZEtMTF9y2YNZbAr0nNvcskDaNW803jSZ1y3CFGTbRdm8MnVa6zDdc-DRz-982-ay8UM0Nv5zKpFqHzvNzFn0X-R-xuf3nNYTxWe2mSo_3dRDrKI_abtuVjWSmZJNlJ3R8JwY2gsSF5XqaT4w/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FHippocampalSubfieldsAndNucleiOfAmygdala. I have tried this with multiple subjects multiple times but the following error persists. Any help would be greatly appreciated. Thank you.
------ Fitting mesh to image data took 959.4679 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/rajilab/Documents/CHS_IMAGING_DATA/97-2002/03638/FS/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 Mon Mar 22 21:39:10 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 85 Stepping 4, GenuineIntel Software OpenGL : 0 Virtual Machine : Java 1.7.0_55-b13 with Oracle Corporation Java HotSpot(TM) 64-Bit Server VM mixed mode Window System : Quartz
Fault Count: 1
Abnormal termination: Segmentation violation
Register State (from fault): RAX = 0000000000000003 RBX = 000000010a71e080 RCX = 00007fea4a200000 RDX = 0000700001207180 RSP = 00007fea4a200000 RBP = 00007fff2030195e RSI = 0000700000000000 RDI = 00007fff203031f9
R8 = 000000004a9295e0 R9 = 0000700001207180 R10 = 00007fff202f0002 R11 = 00007fea4a2d9e60 R12 = 0000700001207498 R13 = 0000000000000000 R14 = 0000000124484d9b R15 = 0000000000000060
RIP = 0000700001207498 RFL = 00007000012071e0
CS = 000000012431b27b FS = 00007000012071c0 GS = 0000000000000001
Stack Trace (from fault): [ 0] 0x000000010c970e64 /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwfl.dylib+00028260 _ZN2fl4diag15stacktrace_base7captureERKNS0_14thread_contextEm+00000052 [ 1] 0x000000010c974a2a /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwfl.dylib+00043562 _ZN2fl4test17terminate_handledEv+00000906 [ 2] 0x000000010c974477 /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwfl.dylib+00042103 _ZN2fl4diag13terminate_logEPKcPK17__darwin_ucontext+00000119 [ 3] 0x000000012405eb7a /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwmcr.dylib+00387962 _Z32mnRunPathDependentInitializationv+00003146 [ 4] 0x000000012405ee58 /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwmcr.dylib+00388696 _Z32mnRunPathDependentInitializationv+00003880 [ 5] 0x000000012405c733 /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwmcr.dylib+00378675 mnFatalSignalHandler+00000275 [ 6] 0x00007fff2051cd7d /usr/lib/system/libsystem_platform.dylib+00015741 _sigtramp+00000029 [ 7] 0x0000000000000000 <unknown-module>+00000000 [ 8] 0x000000012431b27b /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwm_interpreter.dylib+01782395 _Z10inRunMfileiPP11mxArray_tagiS1_P6Mfh_mpP15inWorkSpace_tag+00010667 [ 9] 0x0000000124274a17 /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwm_interpreter.dylib+01100311 _Z15inRunFinalizers7opcodesPS_Pi+00000119 [ 10] 0x000000012431929d /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwm_interpreter.dylib+01774237 _Z10inRunMfileiPP11mxArray_tagiS1_P6Mfh_mpP15inWorkSpace_tag+00002509 [ 11] 0x0000000124edec55 /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwm_dispatcher.dylib+00400469 _ZN8Mfh_file11dispatch_fhEiPP11mxArray_tagiS2_+00000645 [ 12] 0x00000001242bc48b /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwm_interpreter.dylib+01393803 _Z23inEvalPcodeHeaderToWordP15_memory_contextiPP11mxArray_tagP12_pcodeheaderP6Mfh_mpj+00000219 [ 13] 0x000000012426ef4b /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] 0x000000012426a221 /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwm_interpreter.dylib+01057313 _Z12inEvalStringP15_memory_contextRKSbItSt11char_traitsItESaItEE8EvalTypeiPP11mxArray_tag12inDebugCheckP12_pcodeheaderPib+00002769 [ 15] 0x000000012426a7cd /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwm_interpreter.dylib+01058765 _ZN12InterpBridge22EvalCmdWithLocalReturnERKSbItSt11char_traitsItESaItEEPibb+00000141 [ 16] 0x000000012426aa62 /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwm_interpreter.dylib+01059426 _ZN12InterpBridge33EvalCmdWithLocalReturnInDesiredWSERKSbItSt11char_traitsItESaItEEPibbP15inWorkSpace_tag+00000066 [ 17] 0x00000001241ca2de /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwm_interpreter.dylib+00402142 _Z51inEvalCmdWithLocalReturnInDesiredWSAndPublishEventsRKSbItSt11char_traitsItESaItEEPibbP15inWorkSpace_tag+00000062 [ 18] 0x0000000124d1893e /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwiqm.dylib+00227646 _ZNK3iqm18InternalEvalPlugin24inEvalCmdWithLocalReturnERKSbItSt11char_traitsItESaItEEP15inWorkSpace_tag+00000094 [ 19] 0x0000000124d17df4 /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwiqm.dylib+00224756 _ZN3iqm18InternalEvalPlugin7executeEP15inWorkSpace_tagRN5boost10shared_ptrIN14cmddistributor17IIPCompletedEventEEE+00000132 [ 20] 0x0000000124033358 /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwmcr.dylib+00209752 _ZN3mcr3mvm27McrSwappingIqmPluginAdapterIN3iqm18InternalEvalPluginEE7executeEP15inWorkSpace_tagRN5boost10shared_ptrIN14cmddistributor17IIPCompletedEventEEE+00000600 [ 21] 0x0000000124d08418 /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwiqm.dylib+00160792 _ZNK3iqm17DefaultPacketInfo7executeEP15inWorkSpace_tag+00000296 [ 22] 0x0000000124cf37f1 /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwiqm.dylib+00075761 _ZN3iqm3Iqm15setupIqmFcnPtrsEv+00004945 [ 23] 0x000000010a750005 /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwservices.dylib+00196613 _ZN10eventqueue18UserEventQueueImpl5flushEv+00001205 [ 24] 0x00000001256d3a65 /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwuix.dylib+00043621 _Z25isHandleUserEventCallbackPFvPvE+00000501 [ 25] 0x000000010a81fa45 /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwservices.dylib+01047109 _Z21svWS_ProcessCallbacksv+00016693 [ 26] 0x000000010a81b152 /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwservices.dylib+01028434 _Z25svWS_ProcessPendingEventsiib+00000834 [ 27] 0x000000010a81ae5e /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwservices.dylib+01027678 _Z25svWS_ProcessPendingEventsiib+00000078 [ 28] 0x000000012401d18f /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwmcr.dylib+00119183 _ZN3mcr7runtime17InterpreterThread4Impl14process_eventsERKN5boost10shared_ptrIS2_EE+00000095 [ 29] 0x000000012401d49f /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwmcr.dylib+00119967 _ZN3mcr7runtime17InterpreterThread4Impl3runERKN5boost10shared_ptrIS2_EEPNS2_12init_contextE+00000335 [ 30] 0x0000000124003d1b /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwmcr.dylib+00015643 _Z26run_init_and_handle_eventsPv+00000059 [ 31] 0x00007fff204d8950 /usr/lib/system/libsystem_pthread.dylib+00026960 _pthread_start+00000224 [ 32] 0x00007fff204d447b /usr/lib/system/libsystem_pthread.dylib+00009339 thread_start+00000015
If this problem is reproducible, please submit a Service Request via: MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be http://www.mathworks.com/support/contact_us/http://secure-web.cisco.com/1yGaPYerP8LvBirUd2S_1Mjp8Ku8p6JR3rbHsnT1WKQjFwvHfIJvlgqYb4hRD_9QnlRPTv2Cr14LV91gThHvNHZ6uyC_SzFAYQaOuxumRsmPGeRgkMMCQvDmU8sVTbRbEnBogEp6KvqcOmsLyks868AFwMTcaL5-H4Tf8BGyDKn-Cu7hzgX5H5KoA-tWXrlcG4DBDg3_mTbgRpgXJp48eHwX5IYeati-cHM3Jj98c_fsNSX2UH-xy34ecLHz1gVDLXlkXygvcR0jLFSr-L3iJaQ/http%3A%2F%2Fwww.mathworks.com%2Fsupport%2Fcontact_us%2F
A technical support engineer might contact you with further information.
Thank you for your help.** This crash report has been saved to disk as /Users/rajilab/matlab_crash_dump.8238-1 **
MATLAB is exiting because of fatal error /Applications/freesurfer/7.1.1/bin/run_segmentSubjectT1_autoEstimateAlveusML.sh: line 33: 8238 Killed: 9 /Applications/freesurfer/7.1.1/bin/segmentSubjectT1_autoEstimateAlveusML.app/Contents/MacOS/segmentSubjectT1_autoEstimateAlveusML FS /Users/rajilab/Documents/CHS_IMAGING_DATA/97-2002/03638 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 Cyruss-MBP-2 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 Mon Mar 22 21:39:10 CDT 2021