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30083 discussions

longitudinal hippocampal subfield
by Shizuka Hayashi 23 Mar '21

23 Mar '21

External Email - Use Caution Dear Freesurfer team, I'm studying in longitudinal hippocampal changes. Currently I have output from recon-all with T1 and T2-FLAIR across each subject for each time point and output from the longitudinal pipeline for each subject. Now, I want to run the longitudinal hippocampal subfield but the documentation states that it is for T1 scans only. Can I run segmentHA_T1_long.sh with above output or do I need to rerun all above process with only T1 scans. Thank you. Best regards, Shizuka

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Hippocampal Suubfields Segmentation Violation
by WON JONG CHWA 23 Mar '21

23 Mar '21

External Email - Use Caution Dear FreeSurfer experts, I am trying to compute hippocampal subfields with https://secure-web.cisco.com/1f2QJwnqjis6w0KTpz2gk4AyWSMQmrO3JmYGqPPbxpD5Jm…. I have tried this with multiple subjects multiple times but the following error persists. Any help would be greatly appreciated. Thank you. ------ Fitting mesh to image data took 959.4679 seconds Transforming points Transforming points Wrote image to file image.mgz Constructing image-to-world transform from header information (asmr1.mgz) Constructing image-to-world transform from header information (/Users/rajilab/Documents/CHS_IMAGING_DATA/97-2002/03638/FS/tmp/hippoSF_T1_v21_left/imageDump.mgz) Wrote image to file asmr2.mgz This file does not contain MRI parameters Caught unexpected exception of unknown type. ------------------------------------------------------------------------ Segmentation violation detected at Mon Mar 22 21:39:10 2021 ------------------------------------------------------------------------ Configuration: Crash Decoding : Disabled Current Visual : Quartz Default Encoding : ISO-8859-1 MATLAB Architecture: maci64 MATLAB Root : /Applications/freesurfer/7.1.1/MCRv84 MATLAB Version : 8.4.0.150421 (R2014b) Operating System : Darwin 20.3.0 Darwin Kernel Version 20.3.0: Thu Jan 21 00:07:06 PST 2021; root:xnu-7195.81.3~1/RELEASE_X86_64 x86_64 Processor ID : x86 Family 6 Model 85 Stepping 4, GenuineIntel Software OpenGL : 0 Virtual Machine : Java 1.7.0_55-b13 with Oracle Corporation Java HotSpot(TM) 64-Bit Server VM mixed mode Window System : Quartz Fault Count: 1 Abnormal termination: Segmentation violation Register State (from fault): RAX = 0000000000000003 RBX = 000000010a71e080 RCX = 00007fea4a200000 RDX = 0000700001207180 RSP = 00007fea4a200000 RBP = 00007fff2030195e RSI = 0000700000000000 RDI = 00007fff203031f9 R8 = 000000004a9295e0 R9 = 0000700001207180 R10 = 00007fff202f0002 R11 = 00007fea4a2d9e60 R12 = 0000700001207498 R13 = 0000000000000000 R14 = 0000000124484d9b R15 = 0000000000000060 RIP = 0000700001207498 RFL = 00007000012071e0 CS = 000000012431b27b FS = 00007000012071c0 GS = 0000000000000001 Stack Trace (from fault): [ 0] 0x000000010c970e64 /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwfl.dylib+00028260 _ZN2fl4diag15stacktrace_base7captureERKNS0_14thread_contextEm+00000052 [ 1] 0x000000010c974a2a /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwfl.dylib+00043562 _ZN2fl4test17terminate_handledEv+00000906 [ 2] 0x000000010c974477 /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwfl.dylib+00042103 _ZN2fl4diag13terminate_logEPKcPK17__darwin_ucontext+00000119 [ 3] 0x000000012405eb7a /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwmcr.dylib+00387962 _Z32mnRunPathDependentInitializationv+00003146 [ 4] 0x000000012405ee58 /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwmcr.dylib+00388696 _Z32mnRunPathDependentInitializationv+00003880 [ 5] 0x000000012405c733 /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwmcr.dylib+00378675 mnFatalSignalHandler+00000275 [ 6] 0x00007fff2051cd7d /usr/lib/system/libsystem_platform.dylib+00015741 _sigtramp+00000029 [ 7] 0x0000000000000000 <unknown-module>+00000000 [ 8] 0x000000012431b27b /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwm_interpreter.dylib+01782395 _Z10inRunMfileiPP11mxArray_tagiS1_P6Mfh_mpP15inWorkSpace_tag+00010667 [ 9] 0x0000000124274a17 /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwm_interpreter.dylib+01100311 _Z15inRunFinalizers7opcodesPS_Pi+00000119 [ 10] 0x000000012431929d /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwm_interpreter.dylib+01774237 _Z10inRunMfileiPP11mxArray_tagiS1_P6Mfh_mpP15inWorkSpace_tag+00002509 [ 11] 0x0000000124edec55 /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwm_dispatcher.dylib+00400469 _ZN8Mfh_file11dispatch_fhEiPP11mxArray_tagiS2_+00000645 [ 12] 0x00000001242bc48b /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwm_interpreter.dylib+01393803 _Z23inEvalPcodeHeaderToWordP15_memory_contextiPP11mxArray_tagP12_pcodeheaderP6Mfh_mpj+00000219 [ 13] 0x000000012426ef4b /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwm_interpreter.dylib+01077067 _Z25in_local_call_with_setjmpIN5boost3_bi6bind_tIvPFvP15_memory_contextPiPP11mxArray_tagP12_pcodeheaderjENS1_5list5INS1_5valueIS4_EENS0_3argILi1EEENSG_ILi2EEENSE_ISA_EENSE_IiEEEEEEEN6mlutil14cmddistributor17inExecutionStatusET_S5_S8_b+00000171 [ 14] 0x000000012426a221 /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwm_interpreter.dylib+01057313 _Z12inEvalStringP15_memory_contextRKSbItSt11char_traitsItESaItEE8EvalTypeiPP11mxArray_tag12inDebugCheckP12_pcodeheaderPib+00002769 [ 15] 0x000000012426a7cd /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwm_interpreter.dylib+01058765 _ZN12InterpBridge22EvalCmdWithLocalReturnERKSbItSt11char_traitsItESaItEEPibb+00000141 [ 16] 0x000000012426aa62 /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwm_interpreter.dylib+01059426 _ZN12InterpBridge33EvalCmdWithLocalReturnInDesiredWSERKSbItSt11char_traitsItESaItEEPibbP15inWorkSpace_tag+00000066 [ 17] 0x00000001241ca2de /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwm_interpreter.dylib+00402142 _Z51inEvalCmdWithLocalReturnInDesiredWSAndPublishEventsRKSbItSt11char_traitsItESaItEEPibbP15inWorkSpace_tag+00000062 [ 18] 0x0000000124d1893e /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwiqm.dylib+00227646 _ZNK3iqm18InternalEvalPlugin24inEvalCmdWithLocalReturnERKSbItSt11char_traitsItESaItEEP15inWorkSpace_tag+00000094 [ 19] 0x0000000124d17df4 /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwiqm.dylib+00224756 _ZN3iqm18InternalEvalPlugin7executeEP15inWorkSpace_tagRN5boost10shared_ptrIN14cmddistributor17IIPCompletedEventEEE+00000132 [ 20] 0x0000000124033358 /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwmcr.dylib+00209752 _ZN3mcr3mvm27McrSwappingIqmPluginAdapterIN3iqm18InternalEvalPluginEE7executeEP15inWorkSpace_tagRN5boost10shared_ptrIN14cmddistributor17IIPCompletedEventEEE+00000600 [ 21] 0x0000000124d08418 /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwiqm.dylib+00160792 _ZNK3iqm17DefaultPacketInfo7executeEP15inWorkSpace_tag+00000296 [ 22] 0x0000000124cf37f1 /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwiqm.dylib+00075761 _ZN3iqm3Iqm15setupIqmFcnPtrsEv+00004945 [ 23] 0x000000010a750005 /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwservices.dylib+00196613 _ZN10eventqueue18UserEventQueueImpl5flushEv+00001205 [ 24] 0x00000001256d3a65 /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwuix.dylib+00043621 _Z25isHandleUserEventCallbackPFvPvE+00000501 [ 25] 0x000000010a81fa45 /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwservices.dylib+01047109 _Z21svWS_ProcessCallbacksv+00016693 [ 26] 0x000000010a81b152 /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwservices.dylib+01028434 _Z25svWS_ProcessPendingEventsiib+00000834 [ 27] 0x000000010a81ae5e /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwservices.dylib+01027678 _Z25svWS_ProcessPendingEventsiib+00000078 [ 28] 0x000000012401d18f /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwmcr.dylib+00119183 _ZN3mcr7runtime17InterpreterThread4Impl14process_eventsERKN5boost10shared_ptrIS2_EE+00000095 [ 29] 0x000000012401d49f /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwmcr.dylib+00119967 _ZN3mcr7runtime17InterpreterThread4Impl3runERKN5boost10shared_ptrIS2_EEPNS2_12init_contextE+00000335 [ 30] 0x0000000124003d1b /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwmcr.dylib+00015643 _Z26run_init_and_handle_eventsPv+00000059 [ 31] 0x00007fff204d8950 /usr/lib/system/libsystem_pthread.dylib+00026960 _pthread_start+00000224 [ 32] 0x00007fff204d447b /usr/lib/system/libsystem_pthread.dylib+00009339 thread_start+00000015 If this problem is reproducible, please submit a Service Request via: http://secure-web.cisco.com/1yGaPYerP8LvBirUd2S_1Mjp8Ku8p6JR3rbHsnT1WKQjFwv… A technical support engineer might contact you with further information. Thank you for your help.** This crash report has been saved to disk as /Users/rajilab/matlab_crash_dump.8238-1 ** MATLAB is exiting because of fatal error /Applications/freesurfer/7.1.1/bin/run_segmentSubjectT1_autoEstimateAlveusML.sh: line 33: 8238 Killed: 9 /Applications/freesurfer/7.1.1/bin/segmentSubjectT1_autoEstimateAlveusML.app/Contents/MacOS/segmentSubjectT1_autoEstimateAlveusML FS /Users/rajilab/Documents/CHS_IMAGING_DATA/97-2002/03638 0.333333333333333333333333333333333333 /Applications/freesurfer/7.1.1/average/HippoSF/atlas/AtlasMesh.gz /Applications/freesurfer/7.1.1/average/HippoSF/atlas/AtlasDump.mgz /Applications/freesurfer/7.1.1/average/HippoSF/atlas/compressionLookupTable.txt 0.05 left L-BFGS v21 '/Applications/freesurfer/7.1.1/bin/fs_run_from_mcr /Applications/freesurfer/7.1.1/bin/' 0 Darwin Cyruss-MBP-2 20.3.0 Darwin Kernel Version 20.3.0: Thu Jan 21 00:07:06 PST 2021; root:xnu-7195.81.3~1/RELEASE_X86_64 x86_64 T1 hippocampal subfields exited with ERRORS at Mon Mar 22 21:39:10 CDT 2021

2 1

freeview crash
by 超级无敌 22 Mar '21

22 Mar '21

External Email - Use Caution To whom it may concern: I am a graduate student major in neurosurgery at Fudan University. Nowadays, I am learning to use freesurfer in order to segment brain sulci and gyri. However, in some situation, the freeview will crash. For example, when I load “lh.area” surface, the freeview crashed. The error code is “0x02000148”. The information of system is list below: OS Version: Mac OS X 10.15.5 (19F101) Report Version: 12 Bridge OS Version: 4.5 (17P5300) Model: MacBookPro15,1, 8 processors, 8-Core Intel Core i9, 2.3 GHz, 32 GB There are some other operations to the freeview will lead to the crashes. But the load of surface is a more common one. Could give me any advice in solving the problem. I look forward to hearing from you soon. Thanks so much Yusheng Tong

2 1

Re: [Freesurfer] VirtualBox Ubuntu login
by fsbuild 22 Mar '21

22 Mar '21

External Email - Use Caution Hello Sarah, I will send the information to your email shortly. - R. On Mar 22, 2021, at 22:35, Bick, Sarah <sarah.bick(a)vumc.org> wrote:        External Email - Use Caution                External Email - Use Caution        I am attempting to login to ubuntu via VirtualBox but am required to input a password for the “Developer” account. Could you please help me with what this is or how I can login?_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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VirtualBox Ubuntu login
by Bick, Sarah 22 Mar '21

22 Mar '21

External Email - Use Caution I am attempting to login to ubuntu via VirtualBox but am required to input a password for the “Developer” account. Could you please help me with what this is or how I can login?

1 0

Research Assistant Positions at Washington University School of Medicine
by Dincer, Aylin 22 Mar '21

22 Mar '21

External Email - Use Caution The Benzinger Imaging Core Laboratory<https://sites.wustl.edu/benzinger/> at Washington University School of Medicine is looking for full-time Research Assistants (multiple openings available!) to work with us on magnetic resonance imaging and positron emission tomography studies of Alzheimer disease. Your responsibilities will include: 1. Processing of imaging data using neuroimaging software toolkits (FreeSurfer, MATLAB, R, SAS, SPSS) 2. Performing QC / QA on imaging data and preliminary analyses 3. Opportunities to work on your own research projects and perform statistical analyses. 4. Assisting with research studies, collection of data, set-up and maintenance of equipment. The ideal candidate will be able to work independently, communicate with laboratory staff and investigators, and maintain complete and organized records/reports. They'll have working knowledge of computer software and a familiarity with command line interface computer processing (Linux). They are interested in psychology and/or neuroscience. Apply with one of the links below interested! RTII Posting 50550<https://jobs.wustl.edu/psc/APPLHRMS/EMPLOYEE/HRMS/c/HRS_HRAM.HRS_APP_SCHJOB…> RTII Posting 50947<https://jobs.wustl.edu/psc/APPLHRMS/EMPLOYEE/HRMS/c/HRS_HRAM.HRS_APP_SCHJOB…> All the best, Aylin Aylin Dincer, Neuroimaging Engineer Benzinger Lab | Mallinckrodt Institute of Radiology | Neuroimaging Laboratory Pronouns: she/her/hers Washington University School of Medicine 4525 Scott Ave. St. Louis, MO 63110 aylin.dincer(a)wustl.edu<mailto:aylin.dincer@wustl.edu> ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

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License Agreement for re-distribution
by Ezequiel Mikulan 22 Mar '21

22 Mar '21

External Email - Use Caution Hi All, I've developed an open-source software for MRI pseudonymization that uses Freesurfer so I wanted to check that I'm correctly handling the licenses. In Freesurfer's License Agreement it says that: "If you distribute Software (as defined below) downloaded from FreeSurfer, all of the paragraphs of Part B of this Agreement must be included with and apply to such Software". It is not clear to me if we should copy the relevant part into our license or if it is ok if we add a text file in the software with Freesurfer's license. In other words, should Part B be included inside our license or inside the software as a file? How should I proceed? Thanks, Ezequiel

2 1

Some brain area missing after running recon-all
by Stef Meliss 22 Mar '21

22 Mar '21

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

2 1

Freesurfer 6.0.0 Container & MCR
by Ursula Tooley 22 Mar '21

22 Mar '21

External Email - Use Caution Hi Freesurfer experts, I’m trying to use the official FS 6.0.0 container from Dockerhub on a new HPC (for consistency with previous pipelines), and got the error below about not finding the Matlab Compiler Runtime in the container. I have worked around it by explicitly binding the mcr on the HPC to the container with “-B /cbica/software/external/matlab/mcr/v711/:/opt/freesurfer/MCRv80”, but is this the expected behavior? Or is there some issue? My understanding was that one of the advantages of mcr was that you could include it in containers and distribute compiled code, so was surprised to find this come up. Thanks in advance, Ursula --- Ursula Tooley Ph.D. Candidate Neuroscience Graduate Group University of Pennsylvania she/her/hers utooley(a)gmail.com 202.413.5627

2 2

Freesurfer 7.1 recon-all -long exits with erros
by Yakupov, Renat /DZNE 22 Mar '21

22 Mar '21

External Email - Use Caution Dear Freesurfer developers, I am trying to run the longitudinal processing pipeline of our data on our HPC cluster (SGE based) and it crashes at the 3rd step - generating the longitudinal runs. The exact command is 'recon-all -long tp1dir basedir -all'. There is no error message on the screen, it just says that it exited with errors. The recon-all.log file has no error information either, other than the statement that it exited with errors. It seems to have stopped after mri_nu_correct.mni step and looking further it looks like it crashed at the beginning of orig_nu step, since orig_nu.log has this error message: /usr/bin/time: /dev/stdout: Not a directory Please see attached log files. Additional information: Freesurfer version: freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551 uname -a: Linux compute-0-2.local 2.6.32-504.16.2.el6.x86_64 #1 SMP Wed Apr 22 06:48:29 UTC 2015 x86_64 x86_64 x86_64 GNU/Linux lsb_release -a: LSB Version: :base-4.0-amd64:base-4.0-noarch:core-4.0-amd64:core-4.0-noarch:graphics-4.0-amd64:graphics-4.0-noarch:printing-4.0-amd64:printing-4.0-noarch Distributor ID: CentOS Description: CentOS release 6.6 (Final) Release: 6.6 Codename: Final What is interesting is that running it on the headnode directly without qsub works fine. The headnode has the same OS and tcsh versions. In my rather poorly informed opinion, it looks like fs_time is the culprit. For a quick fix, is it safe to assume that using fs_time from Freesurfer 6 wont affect the processing pipeline in any way? Thank you! Best regards, Renat.

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