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-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Ramtilak Gattu
<rg...@med.wayne.edu>
Date: Thursday, March 25, 2021 at 7:20 PM
To: fsbuild <fsbu...@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 <rg...@med.wayne.edu>
Sent: Wednesday, March 24, 2021 8:32 PM
To: fsbuild <fsbu...@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 <fsbu...@contbay.com>
Sent: Wednesday, March 24, 2021 5:09 AM
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Cc: Ramtilak Gattu <rg...@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-2260880
- R.
On Mar 24, 2021, at 04:26, Ramtilak Gattu <rg...@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 <fsbu...@contbay.com<mailto:fsbu...@contbay.com>>
Sent: Wednesday, March 24, 2021 4:22 AM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
<freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
Cc: Ramtilak Gattu <rg...@med.wayne.edu<mailto:rg...@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 <rg...@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 <fsbu...@contbay.com<mailto:fsbu...@contbay.com>>
Sent: Tuesday, March 23, 2021 11:00 PM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
<freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
Cc: Ramtilak Gattu <rg...@med.wayne.edu<mailto:rg...@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
<rg...@med.wayne.edu<mailto:rg...@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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Freesurfer@nmr.mgh.harvard.edu
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