Freesurfer

freesurfer@nmr.mgh.harvard.edu

16 participants
30084 discussions

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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Difference between vox2ras and vox2ras-tkr for subject-specific T1w through FreeSurfer
by Adam Li 25 Mar '21

25 Mar '21

External Email - Use Caution Hi, I am a bit noob on FreeSurfer and coordinate systems and I had a few questions. I am wondering if I have the T1.mgz file of FreeSurfer after running recon-all and this is the 256^3 image re-scaled and re-oriented from your orig.mgz file, then how does one define the fsnative (volume RAS) vs surface RAS (tkras in FreeSurfer)? Assuming there was no preprocessing done on the original scanner nifti, I run the following commands: (base) workstation$ mri_info ~/bids/derivatives/freesurfer/la02/mri/T1.mgz --vox2ras -1.00000 0.00000 0.00000 126.81799 0.00000 -0.00000 1.00000 -121.57332 0.00000 -1.00000 0.00000 159.64563 0.00000 0.00000 0.00000 1.00000 (base) workstation$ mri_info ~/bids/derivatives/freesurfer/la02/mri/T1.mgz --vox2ras-tkr -1.00000 0.00000 0.00000 128.00000 0.00000 0.00000 1.00000 -128.00000 0.00000 -1.00000 0.00000 128.00000 0.00000 0.00000 0.00000 1.00000 *Questions:* 1. Applying the `vox2ras` to any voxel, I would get RAS xyz coordinates right? 2. If I apply `vox2ras-tkr` to any voxel, I would also get RAS xyz coordinates? 3. So what is the difference exactly between these two transforms? Is there anything special / consistent in terms of the definition of the origin and orientation? E.g. Orientation is always RAS, and origin is always... estimated center of the patient's brain? Or is the origin somewhere special like the AC? 3. When would I use one transform over the other? I've searched online and read through the following, but I feel like there is not explicit discussion of the above questions: - https://secure-web.cisco.com/1sKe3PERttYdO2z94AST1tBVsT1X0Q84dpaG1N3eU1eJEW… - http://secure-web.cisco.com/1fnkHZ6-zCUMYrDAnGdeklCU8ErX4aX7Dumo0EB8QRqeu1t… -- Best Regards, Adam Li (he/him) PhD Student in Biomedical Engineering Johns Hopkins University & School of Medicine

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Re: [Freesurfer] Missing 'brainstemSsLabels.v10.mgz' file
by Iglesias Gonzalez, Juan E. 24 Mar '21

24 Mar '21

Dear Lisa, Maybe the brainstem module failed for some reason? If you send us the log files, we can take a look. Cheers, /Eugenio Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://www.jeiglesias.com From: <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of "Taylor, Lisa Marie" <ltaylor2(a)hs.uci.edu> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Date: Tuesday, March 23, 2021 at 15:32 To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> Subject: [Freesurfer] Missing 'brainstemSsLabels.v10.mgz' file 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.

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Re: [Freesurfer] Some brain area missing after running recon-all
by Stef Meliss 24 Mar '21

24 Mar '21

External Email - Use Caution Hi Bruce, Thanks so much for your quick reply. Indeed, the area is still present in the ?h.orig.nofix but not in the ?h.orig. Most of the wm.mgz voxels that are included in ?h.orig.nofix, but not in ?h.orig have intensities above 100, but some are as low as 86. Additionally, it also looks to me as if wm.mgz is also missing some voxels. What kind of intervention would you recommend? Many thanks, Stef 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: Monday, 22 March 2021 at 17:16 To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Some brain area missing after running recon-all Hi Stef This is usually the result of a incorrectly fixed topological defect. You can confirm this if the area is present in the ?h.orig.nofix and not in the ?h.orig. The fix depends on the source of the defect. It might be as simple as drawing a single voxel back into the wm.mgz, but might need more. Look at the wm and see if it is mostly accurate or not and whether the intensities in the white matter are near where they should be (target is 110, so ideally mostly above 100) Cheers Bruce From: freesurfer-bounces(a)nmr.mgh.harvard.edu <freesurfer-bounces(a)nmr.mgh.harvard.edu> On Behalf Of Stef Meliss Sent: Monday, March 22, 2021 10:37 AM To: freesurfer(a)nmr.mgh.harvard.edu Subject: [Freesurfer] Some brain area missing after running recon-all External Email - Use Caution External Email - Use Caution Dear FreeSurfer Experts I am using FreeSurfer on my anatomical data to use segmentations and parcellations in my fMRI analyses in AFNI. After reviewing the output from recon-all -all (FreeSurfer version 6.0.0), I noticed that one subject is missing some occipital areas in the output (e.g. aparc+aseg.mgz). Please see attached for a screenshot of the output from freeview -v mri/brainmask.mgz \ mri/wm.mgz:colormap=heat:opacity=0.4 \ -f surf/lh.white:edgecolor=yellow \ surf/lh.pial:edgecolor=red \ surf/rh.white:edgecolor=yellow \ surf/rh.pial:edgecolor=red \ surf/rh.inflated:visible=0 \ surf/lh.inflated:visible=0 From what I read in the information on troubleshooting the output, I understand that manual editing is necessary to fix this – is this correct? I have verified that the missing areas are included in the brainmask as well as aseg.presurf. I am not sure though how to determine whether I am dealing with a segmentation error or a normalization error or maybe even a combination of both. If you could give me some pointers on which steps to take, that would be highly appreciated. Many thanks in advance for your help. Best regards, Stef

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Postdoc position - Functional connectomics in glioma - CIMeC - University of Trento
by Jovicich, Jorge 24 Mar '21

24 Mar '21

External Email - Use Caution Apologies for the multiple posting A postdoctoral position in *functional brain connectomics in glioma* will be available towards the end of 2021 to work with Dr. Silvio Sarubbo (Neurosurgery Unit, "S. Chiara" Hospital, Trento, Italy) and Prof. Jorge Jovicich (Center for Mind/Brain Sciences, University of Trento, Italy). For more information: https://secure-web.cisco.com/1xoZqsnhBBxXbYFohlAErnlMyWXQJ_4A3AOb4aNgirjKRC…. Thanks, Jorge -- Jorge Jovicich, Ph.D. Center for Mind/Brain Sciences University of Trento, Via delle Regole, 101 38100 Mattarello (TN) Italy Telephone: +39-0461-28 3064 Fax: +39-0461-28-3066 Email: jorge.jovicich(a)unitn.it MRI Methods Group: http://secure-web.cisco.com/1oo6NimY-2hpj-cpDfN0FxxBTMfombqbvNDmT6tUAfmtd5t… CIMEC: http://secure-web.cisco.com/17e8diJzu-3lHswjNzmQwRotmhQxVMDrJ4i5jl7UqtGE_H5…

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Re: [Freesurfer] Hippocampal Subfields Segmentation Violation-error
by Iglesias Gonzalez, Juan E. 24 Mar '21

24 Mar '21

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(a)nmr.mgh.harvard.edu> on behalf of Ramtilak Gattu <rgatt(a)med.wayne.edu> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Date: Tuesday, March 23, 2021 at 17:46 To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)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

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Re: [Freesurfer] Hippocampal Subfields Segmentation Violation-error
by fsbuild 24 Mar '21

24 Mar '21

External Email - Use Caution 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 <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/1VXNlaPSDpyVyn99uzU-nnvtrM7e9mrXcEfiGMaaVKXFdjYhZDFyLjaVzfXE3m5W4-v_BYIDQCI1YujdbT0EwuX_CuBErnGN-70qx6qpNsr4LA1ZXP9ygc_YZVj9wkpFFIpg-P45dPGyTnp9RwHnY11v-6ntXmbbkupdDvuEb_eh7HFkFmU9-WQifdcGDbvY2yr6Nf9i2Z-WP2NILWKbRVuDO31llfKFIqC_A0dc68Skvd_2Etg5f1Gn3CFaSvaqMRbJdMjUy36sCZB6F9a50Ew/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/1VXNlaPSDpyVyn99uzU-nnvtrM7e9mrXcEfiGMaaVKXFdjYhZDFyLjaVzfXE3m5W4-v_BYIDQCI1YujdbT0EwuX_CuBErnGN-70qx6qpNsr4LA1ZXP9ygc_YZVj9wkpFFIpg-P45dPGyTnp9RwHnY11v-6ntXmbbkupdDvuEb_eh7HFkFmU9-WQifdcGDbvY2yr6Nf9i2Z-WP2NILWKbRVuDO31llfKFIqC_A0dc68Skvd_2Etg5f1Gn3CFaSvaqMRbJdMjUy36sCZB6F9a50Ew/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

2 1

Re: [Freesurfer] Hippocampal Subfields Segmentation Violation-error
by fsbuild 24 Mar '21

24 Mar '21

External Email - Use Caution 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@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/1N3nL92CZgUrP1ZwPLnEIXfH5-KxmzioguLGs8239n4uxDMkEULOp_UkNbAWtYsUKEt5zN5vzR3cZrFCjD4n-l5_uZPibIV5c1RAO9wOfFKCqIeHCHPeWpUsupYEyhzb51THpTkPkkYWz5S47JR_P7GEJtwiUuIVYefF-s20i7PfipD7_tIr7xq7RKONGx2Fo68YXdy_zb4_Se2xVpvj02M7MXhc2OeXqFCHLjzHrl07H5nbTieQ2PfC7RfhuIp81HQq-fCR9O_a6T7COHtXdXA/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

2 1

Hippocampal Subfields Segmentation Violation-error
by Ramtilak Gattu 23 Mar '21

23 Mar '21

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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Matlab Runtime error line 334
by Cleary, Matthew 23 Mar '21

23 Mar '21

External Email - Use Caution Hi team, I’m wondering if I could please ask for help - I am trying to install fs_install_mcr R2014b on a 2020 M1 chip MacBook. I’m encountering an error at the end, that goes as follows; inflating: sys/java/jre/maci64/jre/THIRDPARTYLICENSEREADME.txt inflating: sys/java/jre/maci64/jre/Welcome.html inflating: trademarks.txt ./install: line 334: /var/folders/2f/fyngt3b52mn39mcc6_419q8h0000gn/T/tmp.rt0pgVdq/bin/unknown/install_unix: No such file or directory ls: /var/folders/2f/fyngt3b52mn39mcc6_419q8h0000gn/T/tmp.rt0pgVdq/install-target/v*: No such file or directory Do you have any idea how I can fix this? Any help would be massively appreciated. Kindest regards, Matt

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