Thank you both! On Linux, 8GB is insufficient, and 16GB is normally sufficient; I wonder if the requirements are a bit higher on MAC?
Could you please try the following?
1. Edit $FREESURFER_HOME/bin/segmentHA_T1.sh (might require sudo) 2. Replace the line: set RESOLUTION="0.333333333333333333333333333333333333"; by: set RESOLUTION="0.5"; 3. Rerunning the code, and see if it runs to completion? Cheers, /E
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: Tuesday, March 23, 2021 at 17:46 To: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Hippocampal Subfields Segmentation Violation-error
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