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TRACULA path error
by David Ziegler 26 Mar '21

26 Mar '21

External Email - Use Caution Hey Freesurfer folks, I'm running into a strange error with the TRACULA longitudinal stream, whereby all of the steps run "without error" but the final merged paths look like a collection of single voxels (see screenshot below). The individual paths typically show up as single or a few voxels as well. This seems to be happening on all/most of my subjects. I've checked the outputs from trac-all -prep and the FA volumes look right. I've also QAed all of the cortical surface recons and they look good. Also, the individual tract streamlines (the .trk files) look pretty reasonable (see second screenshot). So, I'm assuming that this is an issue at -path step when converting the .trk files to volumes, but am unsure how to troubleshoot it. I'm assuming that the path stats that are output are derived from the volumes and not the streamlines, so this is probably an important step to correct, right? Just FYI, I'm running freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b on Ubuntu 18.04.4 LTS and FSL v4 (FSL v5.0 won't work with the trac-all -prep commands for me) and I run bedpost directly on the dmri folder (I have an SGE cluster). Any chance you've seen this error before? Thanks in advance for any advice! David merged path volumes: several of the streamline files from the same subject:

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Re: [Freesurfer] Hippocampal Subfields Segmentation Violation-error
by fsbuild 26 Mar '21

26 Mar '21

External Email - Use Caution I was looking again at the stack trace that starts with, 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: 1Further on down, lines 5, 6 and 7 list,[  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>+00000000At line 5, some kind of signal was received by The Mathworks library fatal signal handler.  It looks like the handler tried to process the signal and crashed falling back to the system _sigtramp which is the “user space signal trampoline”.    But can’t really tell what the signal was without a more detailed stack trace, e.g., like a segmentation fault (SIGSEGV). This bug/crash report on The Mathworks web site looks similar (see lines 5,6,7 as well)https://secure-web.cisco.com/1JQhmxBxqZzsKf_5bE2K3e0nFFjhcK2dlWpIT8XeS… In this case the culprit is supposedly a file in the Matlab application bundle installed on the machine. This crash can be traced to the following file being missing or corrupted:/Applications/MATLAB_R2017b.app/settings/src/settingscore/settings.xsdTo correct this issue, reinstall MATLAB on your machine. You will also want to remove or rename the /Users/$USER/Downloads/MathWorks folder on your machine to ensure that complete installation files are downloaded, and to rule out any potential problems caused by corrupted installation files. But that file also exists under the runtime environment, i.e., if you installed it under the freesurfer tree /Applications/freesurfer/7..1.1/MCRv84> lsContents/        bin/             help/            mcr/             remote/          runtime/         toolbox/MCR_license.txt  etc/             java/            patents.txt      resources/       simulink/        trademarks.txtappdata/         extern/          license.txt      polyspace/       rtw/             sys/ /Applications/freesurfer/dev/MCRv84> find . -name "settings.xsd"./toolbox/matlab/configtools/settings.xsd I don’t know how to tell if that file is corrupted or not.  But maybe another way to test that is to try installing the latest and greatest matlab runtime environment using the actual Mathworks pkg installer.   That would be version R2021a (https://secure-web.cisco.com/1MljBF-xENfCJNIAKmAXBqz8Y90j_CUs1fKhVdvW8mdPjv…) I installed it on a Mac running 10.15.7, taking all the defaults in the installer application including letting it make modifications to Java.  I ended up with the install under /Applications/MATLAB/MATLAB_runtime/v910  which looks like, /Applications/MATLAB/MATLAB_runtime/v910> lsMCR_license.txt  bin/             help/            mcr/             remote/          simulink/        trademarks.txtVersionInfo.xml  derived/         interprocess/    patents.txt      resources/       sys/             ui/appdata/         extern/          java/            polyspace/       runtime/         toolbox/ /Applications/MATLAB/MATLAB_runtime/v910> find . -name "settings.xsd"./toolbox/matlab/settings/settings.xsd So you could move aside the older copy of the runtime environment under the Freesurfer tree and make a soft link to try out the newer version, $ cd /Applications/freesurfer/7.1.1$ sudo mv MCRv84  old_MCRv84$ sudo ln -s  /Applications/MATLAB/MATLAB_Runtime/v910  MCRv84$ ls -l MCRv84lrwxr-xr-x  1 root  wheel  40 Mar 26 01:27 MCRv84@ -> /Applications/MATLAB/MATLAB_Runtime/v910 … then try running your commands again. … to put it back the way it was, $ cd /Applications/freesurfer/7.1.1$ sudo rm MCRv84$ sudo mv old_MCRv84  MCRv84 I've attached a screenshots from my installation.  Setting DYLD_LIBRARY_PATH to the actual paths listed in the installer window should work. Once you set DYLD_LIBRARY_PATH, you could also try setting DYLD_FALLBACK_LIBRARY_PATH to the same value. $ export  DYLD_FALLBACK_LIBRARY_PATH=$DYLD_LIBRARY_PATH - R. On Mar 25, 2021, at 19:19, Ramtilak Gattu <rgatt(a)med.wayne.edu> wrote:        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: Enabledhad 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.RegardsTilakFrom: Ramtilak Gattu <rgatt@med.wayne.edu>Sent: Wednesday, March 24, 2021 8:32 PMTo: 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. ThanksRegardsTilakFrom: fsbuild <fsbuild@contbay.com>Sent: Wednesday, March 24, 2021 5:09 AMTo: 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://secure-web.cisco.com/1tkr30obhmK2iOZliaWCRbke2W5CF6b… R.On Mar 24, 2021, at 04:26, Ramtilak Gattu <rgatt(a)med.wayne.edu> wrote:        External Email - Use Caution                External Email - Use Caution        Yes it says enabled.[tilak:~] tilak% csrutil statusSystem Integrity Protection status: enabled.ThanksRegards,TilakFrom: fsbuild <fsbuild@contbay.com>Sent: Wednesday, March 24, 2021 4:22 AMTo: 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 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 statusSystem Integrity Protection status: enabled.- R.On Mar 24, 2021, at 01:48, Ramtilak Gattu <rgatt(a)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      : QuartzFault Count: 1Abnormal termination:Bus errorRegister 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 = 0000000000000001Stack 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+00000015If this problem is reproducible, please submit a Service Request via:    http://secure-web.cisco.com/1eidi0IlCiU-mTvwSttFoSKPGF30rZgh0SZHeFxbmGnq8-0Tll5s9m7NhTOt72razRV5JLt5yGlSQIFDNG5oQ_9_ED2JUXtBgM8RjQDlzYzvz0jJJdQGZy8jWVCC3P8zsrCxywlkH5Zv-7Pv7MFezz5EJM_rR5IkrKtWtyAtb7s4tU06DYdz6Ex8kO_o72ewWNDys8NeqtuAyf8nFT33oTteNq44VvNczlyKkdoUyk6DD__a-I-KjGXr1nqq-TXIx66tzEYCkrZOX2QWVMLGQFg/http%3A%2F%2Fwww.mathworks.com%2Fsupport%2Fcontact_us%2FA 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/' 0Darwin 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_64T1 hippocampal subfields exited with ERRORS at Wed Mar 24 00:59:59 EDT 2021For more details, see the log file /Users/tilak/Desktop/Work/CNS_cases/Hipps/Amy_Damboise/scripts/hippocampal-subfields-T1..logtilak@tilak Hipps %             From: fsbuild <fsbuild@contbay.com>Sent: Tuesday, March 23, 2021 11:00 PMTo: 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 [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(a)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 detailsHardware 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: EnabledHere is the log for segmentation violation error***************************************************Fitting mesh to image data took 742.9022 secondsTransforming pointsTransforming pointsWrote image to file image.mgzConstructing 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.mgzThis file does not contain MRI parametersCaught 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      : QuartzFault Count: 1Abnormal termination:Segmentation violationRegister 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 = 0000000000000001Stack 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+00000015If this problem is reproducible, please submit a Service Request via:    http://secure-web.cisco.com/1eidi0IlCiU-mTvwSttFoSKPGF30rZgh0SZHeFxbmGnq8-0Tll5s9m7NhTOt72razRV5JLt5yGlSQIFDNG5oQ_9_ED2JUXtBgM8RjQDlzYzvz0jJJdQGZy8jWVCC3P8zsrCxywlkH5Zv-7Pv7MFezz5EJM_rR5IkrKtWtyAtb7s4tU06DYdz6Ex8kO_o72ewWNDys8NeqtuAyf8nFT33oTteNq44VvNczlyKkdoUyk6DD__a-I-KjGXr1nqq-TXIx66tzEYCkrZOX2QWVMLGQFg/http%3A%2F%2Fwww.mathworks.com%2Fsupport%2Fcontact_us%2FA 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/' 0Darwin 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_64T1 hippocampal subfields exited with ERRORS at Tue Mar 23 15:53:07 EDT 2021ThanksRegardsTilak_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh..harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

2 1

Can FS use the recon all command to automatically divide it into DKT32 areas?
by 1248742467 26 Mar '21

26 Mar '21

External Email - Use Caution Hello, Fs I saw an article that gave the Dice coefficient and ACC of Freesurfer's automatic segmentation, so I am curious, can Fs automatically divide it into 32 regions?

2 1

cross sectional vs longitudinal TRACULA reliability
by Carissa Nicole Weis 25 Mar '21

25 Mar '21

External Email - Use Caution Hello, I’ve run both longitudinal and cross-sectional TRACULA pipelines on the same dataset, and I’ve found surprisingly low correlations of FA measurements for several tracts (as low as r= .1 in some cases). Which measurement should be considered more reliable? I’m having a hard time deciding which set of results to carry forward to group analysis. Thanks, Carissa

2 1

Re: [Freesurfer] make_average_subject without Talairach transform
by Trisanna Sprung-Much 25 Mar '21

25 Mar '21

External Email - Use Caution Thanks Bruce for your speedy response. I am dealing with chimp scans and therefore am trying to avoid anything to do with Talairach. The surfaces have reconstructed pretty nicely using recon-all, but I’d like to create an average surface now. I will try as you suggest Trisanna Sprung-Much Research Associate McGill University MD Anderson Cancer Centre -- From: <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of "Fischl, Bruce" <BFISCHL(a)mgh.harvard.edu> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Date: Thursday, March 25, 2021 at 10:59 AM To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] make_average_subject without Talairach transform Sure, I guess you can just run mri_average. I think also if you specify the file name for the transform as identity.nofile to any binary that takes an lta file, the code will internally create an identity transform. I won’t look pretty though…. Cheers Bruce From: freesurfer-bounces(a)nmr.mgh.harvard.edu <freesurfer-bounces(a)nmr.mgh.harvard.edu> On Behalf Of Trisanna Sprung-Much Sent: Thursday, March 25, 2021 10:19 AM To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Subject: [Freesurfer] make_average_subject without Talairach transform External Email - Use Caution External Email - Use Caution Hi there I’d like to know if it is possible to create an average volume and average surface of several subjects without having to incorporate the Talairach transform and no transform at all. Thank you, Trisanna Sprung-Much Research Associate McGill University MD Anderson Cancer Centre --

2 1

read_surf surface
by Shizuka Hayashi 25 Mar '21

25 Mar '21

External Email - Use Caution Dear Freesurfer team, I have a question about the inconsistency between the vertex read from read_surf and vertex shown in Freeview. I have a volume from the hippocampal subfield pipeline and I converted it to surface mesh using mri_tessellate mri/lh.hippoAmygLabels-T1.long.v21.mgz -an surf/lh.hippoAmygLabels-T1.long.v21.surf. Then I smoothed the surface using mris_smooth surf/lh.hippoAmygLabels-T1.long.v21.surf surf/lh.hippoAmygLabels-T1.long.v21.surf Now I want to get the corresponding voxel of lh.hippoAmygLabels-T1.long.v21.mgz with the vertex. In Freeview, for example, the vertex 0 is [5.17, -19.5, 4.83]. I know how to convert this vertex to the corresponding voxel. However, when I read the surf/lh.hippoAmygLabels-T1.long.v21.surf from Matlab using read_surf, the first vertex ( vertex(1,:,:)) is equal to [165.4900,217.3600,-159.7300]. Are there any ways to solve the issue? Thank you. Regards, Shizuka

2 1

Questions regarding atlas labels
by Blanpain, Lou 25 Mar '21

25 Mar '21

External Email - Use Caution Hello, I had the following 2 general questions regarding Freesurfer: 1. Is there an extensive list of anatomical labels for each atlas used? For instance, what are all the potential labels used in wmparc.mgz? I am aware of the extensive list of labels in ‘FreeSurferColorLUT.txt’, but this list does not seem to indicate which labels are included in which atlas. 2. Do we know of Freesurfer users who have already worked on categorizing labels from such atlases? For instance, I would be interested in categorizing labels belonging to the visual system network vs the auditory system network. Thank you so much for your assistance. Warm regards, Lou Blanpain ________________________________ This e-mail message (including any attachments) is for the sole use of the intended recipient(s) and may contain confidential and privileged information. If the reader of this message is not the intended recipient, you are hereby notified that any dissemination, distribution or copying of this message (including any attachments) is strictly prohibited. If you have received this message in error, please contact the sender by reply e-mail message and destroy all copies of the original message (including attachments).

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Missing 'brainstemSsLabels.v10.mgz' file
by Taylor, Lisa Marie 25 Mar '21

25 Mar '21

External Email - Use Caution Hi, This is the first time I have encountered this problem. I have a participant that has been through recon all, but when trying to create PET masks, the error that comes up is that the 'brainstemSsLabels.v10.mgz' file is missing in the MRI directory. I am unsure of how to have this label created when it has been created in other participants from freesurfer. Here is the command and the arguments used when running this participant (every one of our participants has had the same command): ${FREESURFER_HOME}/bin/recon-all -s /pub/ltaylor2/*PARTICIPANT* -no-isrunning -all -hippocampal-subfields-T1 -brainstem-structures -qcache Any understanding as to why this particular participant is not having this file created? Any leads would be greatly appreciated! Lisa ________________________________ This message may contain confidential information and is for the sole use of the intended recipient(s). If you are not the intended recipient, do not use, distribute, or copy this e-mail. Please notify the UC Irvine Health – Compliance and Privacy Office via email at hacompliance(a)uci.edu or by phone 888-456-7006 immediately if you have received this e-mail in error. E-mail transmission cannot be guaranteed to be secure or error-free as information could be intercepted, corrupted, lost, destroyed, arrive late or incomplete, or contain viruses. The sender therefore does not accept liability for any errors or omissions in the contents of this message, which arise as a result of e-mail transmission.

2 1

Lesion Heatmap question - follow up
by XY XY 25 Mar '21

25 Mar '21

External Email - Use Caution Thanks Douglas, "mri_convert lesionmap.mgz -at samseg.m3z lesionmap.mni152.mgz" worked fabulously after some tweaks in the command line! What would be the best approach to compare population-wise lesion heat maps between groups of subjects using the output from SAMSEG? (the full FS pipeline cannot process my data due to brain defects and time restrictions). Thanks for all the support for these fantastic tools! Stay safe! ----------------------------------------------------- David Olayinka Kamson, MD PhD Clinical and Research Fellow Joint Neuro-Oncology Program of Johns Hopkins Medicine & National Institutes of Health dkamson1(a)jhmi.edu <mailto:dkamson1@jhmi.edu>

2 1

Re: [Freesurfer] Which pial surface to trust
by Jones, Richard 25 Mar '21

25 Mar '21

External Email - Use Caution A couple of questions:- 1) Do you experience similar variability with the T2 and FLAIR options or is FLAIR more variable due to it's generally lower SNR? 2) Should the spatial resolution of the T2/FLAIR scan match that of the T1 scan? Richard Message: 8 Date: Wed, 17 Mar 2021 17:51:51 -0400 From: "Douglas N. Greve" <dgreve(a)mgh.harvard.edu> Subject: Re: [Freesurfer] Which pial surface to trust, with or without -FLAIR option To: <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <3c789103-dad7-974a-0d76-58a02cba2992(a)mgh.harvard.edu> Content-Type: text/plain; charset="utf-8" We get a lot of variable results with FLAIR. Sometimes it helps, sometimes it hurts. FLAIR scans themselves can be very variable across sites. If it is looking like it is hurting your results, then just run without it. On 3/12/2021 11:07 AM, Xiaojiang Yang wrote: > > ????????External Email - Use Caution > > Dear FS developers, > > I have run FS?s recon-all on many cases, with and without -FLAIR > options. I found the pial? surface results (?h.pial) I obtained > without -FLAIR option fit to the original image > (subjected/mri/orig.mgz) much better than those with -FLAIR option, at > least from my visual judgment. See *MailScanner has detected a > possible fraud attempt from "secure-web.cisco.com" claiming to be* > https://secure-web.cisco.com/1kdfPWDTAquCY3qAKfDNtc8TRiBI5hNHL96VYA9_mTvUn4… > <https://secure-web.cisco.com/1jL9MUfd9oLXR_SVyZl8-wPztrX70T9SJxxJaJElRv5e-D…>?for > one example. > > I know -FLAIR option was introduced to improve the quality of pial > surface segmentation. Now for many cases, my intuition is that -FLAIR > option decreases the pial quality. My questions are: > > * Is this intuition correct? > * Should I trust the pial surface that?s obtained with or without > -FLAIR option in general? > > In addition, when I use the -FLAIR option, I sometimes get failed when > running recon-all. After I did some manual edits to the brainmask > image, and re-run the recon-all: > > recon-all -autorecon-pial -subjid <subjectID> > > I can get recon-all successful. But if I run recon-all without -FLAIR > option, I can get successful results without needing to manually edit > the brainmask image. > > So my last question is: > > * Should I just run recon-all without -FLAIR option, or, with -FLAIR > option + manual edit + re-run with -autorecon-pial? Which is better? > > Thank you very much! > > John >

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