Freesurfer September 2019

freesurfer@nmr.mgh.harvard.edu

93 participants
143 discussions

Re: [Freesurfer] Hippocampal-subfields-T1 interruption (Bruce Fischl)
by 3 6 13 Sep '19

13 Sep '19

External Email - Use Caution Hi Bruce, I checked the alias, I really aliased mv to “mv -i”, and it worked automatically, after I unaliased. Thanks for your help. Best regards, Guodong > 在 2019年9月13日，上午12:00，freesurfer-request@nmr.mgh.harvard.edu 写道： > > Re: Hippocampal-subfields-T1 interruption (Bruce Fischl)

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c_ras for HCP compatibility
by Robert Austin Bruce Benn 13 Sep '19

13 Sep '19

External Email - Use Caution Hi Y’all, I was wondering if Y’all could tell me how c_ras is calculated in the x_form matrix for orig.mgz? I’ve been using some animal brains, and the pipeline works very well at creating surfaces and aligning them to their coresponding image for freeview. Post pipeline I’ve been applying the cras matix as derived from the orig.mgz to remove the offset for use in wb_view. The commands for applying the transforms work fine. However I end up getting a surface that is either inverted, or perpendicular to the nifti volume in wb_view. The animal image does have a large field of view, with a relatively small brain. I think the cras matrix isn’t getting calculated correctly, but that the images I’m using may not have a standered cras so I may need to hack around that. Could you explain to me how c_ras is calculated? Also if I need to edit c_ras how would I go about doing it? is it derived from the q and s forms? thanks! austin *************** AVISO LEGAL *************** Este mensaje va dirigido, de manera exclusiva, a su destinatario y contiene información confidencial y sujeta al secreto profesional, cuya divulgación no está permitida por la ley. En caso de haber recibido este mensaje por error, le rogamos que, de forma inmediata, nos lo comunique mediante correo electrónico remitido a nuestra atención o a través del teléfono (+34 914531200) y proceda a su eliminación, así como a la de cualquier documento adjunto al mismo. Asimismo, le comunicamos que la distribución, copia o utilización de este mensaje, o de cualquier documento adjunto al mismo, cualquiera que fuera su finalidad, están prohibidas por la ley. Le informamos, como destinatario de este mensaje, que el correo electrónico y las comunicaciones por medio de Internet no permiten asegurar ni garantizar la confidencialidad de los mensajes transmitidos, así como tampoco su integridad o su correcta recepción, por lo que el CNIC no asume responsabilidad alguna por tales circunstancias. Si no consintiese la utilización del correo electrónico o de las comunicaciones vía Internet le rogamos nos lo comunique y ponga en nuestro conocimiento de manera inmediata. *************** LEGAL NOTICE ************** This message is intended exclusively for the person to whom it is addressed and contains privileged and confidential information protected from disclosure by law. If you are not the addressee indicated in this message, you should immediately delete it and any attachments and notify the sender by reply e-mail or by phone (+34 914531200). In such case, you are hereby notified that any dissemination, distribution, copying or use of this message or any attachments, for any purpose, is strictly prohibited by law. We hereby inform you, as addressee of this message, that e-mail and Internet do not guarantee the confidentiality, nor the completeness or proper reception of the messages sent and, thus, CNIC does not assume any liability for those circumstances. Should you not agree to the use of e-mail or to communications via Internet, you are kindly requested to notify us immediately.

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Hippocampal-subfields-T1 interruption
by 3 6 12 Sep '19

12 Sep '19

External Email - Use Caution Hello FreeSurfer Developers, I'm attempting to analyze hippocampal subfields for T1 scan, but when I run the command recon-all -s subjects -hippocampal-subfields-T1, I always get interrupted by the warning : mv: overwrite ‘imageDump.mgz’? It keep running only when I type Y or N. I've searched the list and no similar request have been submitted. Does anyone have any thoughts on how to make it automatically running? Also, I’ve attached the hippocampal-subfields-T1.log in case it's of any use. 1) FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0 2) Platform: CentOS release 7 3) recon-all.log: see attached Best regards, Guodong

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Command failed in QDEC
by James Karantonis 11 Sep '19

11 Sep '19

External Email - Use Caution Hi there, In QDEC, I have successfully imported my data tables, generated stats, and when I go to analyse, I get the following error: “Error in Analyze: command failed mri_glmfit –y…”. It seems this error only occurs when I use the two variables of age and ICV. Whenever I remove one of those variables, or add any additional variables, it appears to work. Specifically, this is for two comparisons, between bipolar patients and healthy controls, bipolar and schizophrenia patients, but it works for schizophrenia and healthy control comparisons. I’m working on an iMac running High Sierra and Freesurfer v.6. Any information on how to resolve this error would be greatly appreciated! I’ve attached a screenshot for reference. Kind regards, James

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neuroimaging postdoc position available
by Keith Schneider 11 Sep '19

11 Sep '19

External Email - Use Caution A post-doctoral position is available with Keith Schneider at the University of Delaware http://keith.psych.udel.edu <http://keith.psych.udel.edu/>. The position is funded by NEI/NIH to study the subcortical mechanisms of vision, audition, attention and dyslexia. The successful candidate will join a thriving neuroimaging community at the University of Delaware. The Center for Biomedical & Brain Imaging includes a Siemens Prisma 3T MRI scanner, simultaneous EEG, TMS, eye-tracking, and a Bruker 9.4 T scanner for small animals. I am looking for a scientist who: * has experience with fMRI * has programming experience (e.g. Matlab or Python) * has an interest in attention, sensory systems, reading and/or neuroimaging methods development (acquisition or analysis) This position is initially for one year but can be renewed as mutually agreed. The start date is flexible but can begin immediately. To inquire, e-mail your CV and a PDF of a first-authored journal article to keithas(a)udel.edu. The University of Delaware is located in Newark, Delaware, a small college town, located along the Northeast Corridor, within 2 hours of New York and Washington, DC, and within an hour of Philadelphia and Baltimore. ----- Keith Schneider Director, Center for Biomedical & Brain Imaging Associate Professor, Department of Psychological & Brain Sciences University of Delaware

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Re: [Freesurfer] Additional scans in hippocampal subfields segmentation
by Rovai Antonin 11 Sep '19

11 Sep '19

External Email - Use Caution I’m resending this request as I really would like to know what you think :-) Best Antonin Hôpital Erasme - ULB Cliniques universitaires de Bruxelles Route de Lennik 808 - B - 1070 Bruxelles S www.erasme.ulb.ac.be Disclaimer : http://www.erasme.ulb.ac.be/email-disclaimer > On 30 Aug 2019, at 11:00, Rovai Antonin <Antonin.Rovai(a)erasme.ulb.ac.be> wrote: > > Hello > > I’d like to know if there is any advantage in having a T2 FLAIR as additional scan (in addition to our 1mm isotropic T1 scans) when using the hippocampal subfield segmentation tool. We do not have T2 nor PD available. > > Thanks for you help > > Antonin Rovai

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-qcache recon-all exciting with error
by Swanson,Clayton 10 Sep '19

10 Sep '19

External Email - Use Caution Hello FreeSurfer Developers, I am attempting to run -qcache on a cohort (55) of participants and two of them excited with error. It’s worth noting I am running recon-all -qcache after initial recon-all then correcting for errors and re-processing again. The error I am receiving is ERROR: number of vertices in /Users/claytonswanson/Desktop/Studies/Current_Studies/MS_Study/MRS_MRI/FreeSurfer/Subject_Dir_T1/Subj_010_T1/surf/lh.thickness does not match surface (154775,154624) ERROR: reading curvature file ERROR: number of vertices in /Users/claytonswanson/Desktop/Studies/Current_Studies/MS_Study/MRS_MRI/FreeSurfer/Subject_Dir_T1/Subj_008_T1/surf/lh.thickness does not match surface (141413,141431) ERROR: reading curvature file I have not been able to find anything in the mail archive to answer this particular question. I have attached the recon-all.log file if its of use. Thanks for your help, Clayton ________________________________ Clayton Swanson MS Graduate Research Assistant & PhD Student Sensorimotor Neuroimaging Laboratory Colorado State University Office: (970) 491-6160 Clayton.Swanson(a)colostate.edu

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Re: [Freesurfer] freeview crash -- petsc error when opening volume
by fsbuild 10 Sep '19

10 Sep '19

External Email - Use Caution Hello Tristan, Please check to see that what is listed in the makefile.wiki under the section for Ubuntu is installed on your machine.   I would also try building with the instructions in the makefile if you have not already done so; that works on my Ubuntu 18.04 system, although I am not running the server distribution, e.g., type “make -f makefile.wiki help”.   The makefile based build will also save logs for the cmake command, build and install pass, so you could send me those directly - look for ./freesurfer/{cmake.log, make.log, install.log} - R. On Sep 10, 2019, at 13:52, TRISTAN J PAUTSCH <tpautsch(a)wisc.edu> wrote:        External Email - Use Caution        Thank you so much again for the detailed reply. I attempted your suggestion, following the instructions from the wiki to a T and compiled everything from scratch, and I still get the same PETSC error from my first post. To be thorough, I again tested on multiple machines, experiencing the same error on each.I also realized I've never posted the specs of the system on which I've been attempting all of this, so in case it's relevant to anyone else, here they are:OS: Ubuntu 18.04 ServerCPU: 4x Xeon Platinum 8164RAM: 512GB DDR4 ECC (16x32GB DIMMs)From: TRISTAN J PAUTSCH <tpautsch@wisc.edu>Sent: Thursday, August 29, 2019 10:27 AMTo: fsbuild <fsbuild@contbay.com>Cc: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>Subject: Re: [Freesurfer] freeview crash -- petsc error when opening volume Thank you for the reply, I will try this when time permits!TristanFrom: fsbuild <fsbuild@contbay.com>Sent: Tuesday, August 27, 2019 4:25 PMTo: TRISTAN J PAUTSCH <tpautsch@wisc.edu>Cc: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>Subject: Re: [Freesurfer] freeview crash -- petsc error when opening volume Hello Tristan,Please try rebuilding the dev branch on your Ubuntu 18 machine using the makefile listed from the wiki, (wiki page, https://surfer.nmr.mgh.harvard.edu/fswiki/CMake) where the download link to makefile is https://drive.google.com/file/d/1IMEWQty_7zjsglbErQOlu_KpXb8Lmgmv/v… should go in the same subdirectory that contains the ./freesurfer treeThere are some comments in there which recommend the following be installed for Ubuntu, so please check these are installed before building,      # sudo apt-get install build-essential      # sudo apt-get install libgl1-mesa-dev freeglut3-dev mesa-common-dev      # sudo apt-get install libblas-dev liblapack-dev      # sudo apt-get install ocl-icd-opencl-dev      # sudo apt-get install libxmu-dev libxi-dev      # sudo apt-get install libopencv-dev       # Ubuntu 16: sudo apt-get install gcc-4.9 g++-4.9 gfortran-4.9      # Ubuntu 18: sudo apt-get install gcc-4.8 g++-4.8 gfortran-4.8 <----      # sudo apt-get install xorg xorg-dev libx11-dev      # sudo apt-get install tcl tcl-dev tk tk-dev      # sudo apt-get install qt5-default qtcreator      # sudo apt-get install libqt5x11extras5-dev      # sudo apt-get install git-annex       # sudo apt-get install python3-devI’ve attached an archive containing that makefile along with the cmake output/build logs from my Ubuntu 18.04 machine so you can see what it looks like for me, see cmake_make_install_ubuntu18.tgzI’ve run all the freeview tutorial commands using the 6.0.0 release on my Ubuntu 18.04 machine, but have not been able to reproduce a petsc error so far.- R.On Aug 27, 2019, at 11:27, TRISTAN J PAUTSCH <tpautsch(a)wisc.edu> wrote:        External Email - Use Caution        Some final bits of troubleshooting information for future readers, since I'm assuming this issue will now get lost in the sauce...I'll probably try compiling everything from scratch at some point, but my hopes aren't particularly highI manually compiled the missing libs to get the CentOS7 version of FS-dev freeview running on Ubuntu 18, and ultimately the same errors occur. As well, I replicated this behavior on a separate Ubuntu 18 machine in the environment, this time using a different lab's T1/brainmask/surface files. It would definitely seem like there is some sort of hard incompatibility with newer versions of freeview and loading surface files on top of volumes in Ubuntu 18. For what it's worth, it's not evident that any other part of FS has an issue; all CLI tools seem to work just fine.TristanFrom: TRISTAN J PAUTSCH <tpautsch@wisc.edu>Sent: Friday, August 23, 2019 11:38 AMTo: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>Subject: Re: [Freesurfer] freeview crash -- petsc error when opening volume Good morning Ruopeng, thank you for your continued assistance!Unfortunately, I get the same error using the CentOS6 dev version.. I tried the CentOS7 dev version, however this led to a series of library errors, the majority of which are unsolvable on Ubuntu 18 without individually compiling each necessary library (sym-linking newer libraries does not work).I wanted to ensure I provide the most details possible, so I also installed FS 5.3.0 and tested the files...interestingly, they opened just fine, no errors at all.This leads me to believe there is some strange incompatibility between Ubuntu 18 and the 6.x/dev version of FS (at least when it comes to surface files), specifically related to PETSC. Is there anything else I can do to help troubleshoot?TristanFrom: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of Ruopeng Wang <rpwang@nmr.mgh.harvard.edu>Sent: Thursday, August 22, 2019 5:00 PMTo: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>Subject: Re: [Freesurfer] freeview crash -- petsc error when opening volume Hi Tristan,Thanks for the files. I have no problem loading them with the latest dev build and stable 6..0 build. I do not have an Ubuntu system, though. If I’m not mistaken you use dev version of freeview binary along with stable 6.0 FS binary. Is that correct? Is there any chance you can try installing the whole FS dev package?RuopengOn Aug 22, 2019, at 12:20 PM, TRISTAN J PAUTSCH <tpautsch(a)wisc.edu> wrote:        External Email - Use Caution        Ruopeng,I've uploaded the files to the FTP drop (transfer/incoming/freesurfer_data.tar.gz). The command my user is running against these files is:freeview -v brainmask.mgz T1.mgz -f lh.white:edgecolor=yellow lh.pial:edgecolor=magenta rh.white:edgecolor=yellow rh.pial:edgecolor=magentaWe can also replicate the error by opening freeview and opening all the above files sequentially through the GUI.Thank you!TristanFrom: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Ruopeng Wang <rpwang@nmr.mgh.harvard.edu>Sent: Thursday, August 22, 2019 8:16 AMTo: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>Subject: Re: [Freesurfer] freeview crash -- petsc error when opening volume Hi Tristan,Would it be possible to send us the files and the command-line you run? Best,RuopengOn Aug 21, 2019, at 12:18 PM, TRISTAN J PAUTSCH <tpautsch(a)wisc.edu> wrote:        External Email - Use Caution        Adding more details provided by my user:The crash only happens when loading surface files, either via the -f flag from the CLI or directly through the GUI. Could this be an issue with the surface files or the manner in which they are created?From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard..edu> on behalf of TRISTAN J PAUTSCH <freesurfer-bounces@nmr.mgh.harvard.edu>Sent: Tuesday, August 20, 2019 2:35 PMTo: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>Subject: [Freesurfer] freeview crash -- petsc error when opening volume         External Email - Use Caution        Greetings all, I'll try to keep this succinct. I'm attempting to deploy FreeSurfer on Ubuntu 18.04 servers here at the lab. I used the stable 6.0/CentOS 6 download, in addition to the dev version of freeview per the .../fswiki/UpdateFreeview instructions. All dependencies have ostensibly been satisfied, all libs from 'ldd freeview.bin' installed. Freeview launches fine and stays open when launched alone, however attempting to open a volume (either through the GUI or directly via the CLI) causes a crash and the following error about 5-8 seconds after launching (brain images begin to populate, then crash):---[0]PETSC ERROR: ------------------------------------------------------------------------[0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably memory access out of range[0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger[0]PETSC ERROR: or see http://www.mcs.anl.gov/petsc/petsc-as/documentation/troubleshootin…: or try http://valgrind.org on linux or man libgmalloc on Apple to find memory corruption errors[0]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and run [0]PETSC ERROR: to get more information on the crash.[0]PETSC ERROR: --------------------- Error Message ------------------------------------[0]PETSC ERROR: Signal received![0]PETSC ERROR: ------------------------------------------------------------------------[0]PETSC ERROR: Petsc Release Version 2.3.3, Patch 13, Thu May 15 17:29:26 CDT 2008 HG revision: 4466c6289a0922df26e20626fd4a0b4dd03c8124[0]PETSC ERROR: See docs/changes/index.html for recent updates.[0]PETSC ERROR: See docs/faq.html for hints about trouble shooting.[0]PETSC ERROR: See docs/index.html for manual pages.[0]PETSC ERROR: ------------------------------------------------------------------------[0]PETSC ERROR: Unknown Name on a linux-gnu named xxxxxxx by xxxxxxx Tue Aug 20 13:44:15 2019[0]PETSC ERROR: Libraries linked from /autofs/space/lyon_006/pubsw/Linux2-2.3-x86_64/packages/petsc/2.3.3-p13/src/petsc-2.3.3-p13/lib/linux-gnu-c-opt[0]PETSC ERROR: Configure run at Tue Aug 10 15:01:59 2010[0]PETSC ERROR: Configure options --with-debugging=no --with-cc=gcc --with-fc=g77 --download-f-blas-lapack=0 --download-mpich=1 --with-mpi=1 --with-x=0 --with-gnu-copyright-code=0 --with-shared=0 COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3[0]PETSC ERROR: ------------------------------------------------------------------------[0]PETSC ERROR: User provided function() line 0 in unknown directory unknown file[unset]: aborting job:application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0Segmentation fault (core dumped)---I've seen a number of other posts on the mailing list about this, but all of them I could find either end abruptly without a solution or with an unanswered request for more info. Happy to provide any additional information or anything that may aid in the resolution of this issue. Thanks everyone,~T_______________________________________________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

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Re: [Freesurfer] error in longitudinal stream command
by Alexandru Hanganu 10 Sep '19

10 Sep '19

External Email - Use Caution Hello Martin, I was wondering - how solved the "Unmatched" error ? In our case, this error appears for both 5.3, 6.0 and dev, on 2 different clusters. All folders exist, are filled with data and reecon-all finished without error, plus hippocampus and brainstem all folders and readable: drwxrwsrwx (chmod 777 -R) In the base-tps - all time points are listed correctly. Re-running -base - did not solve the issue. Name has no underscores '_' I didn't have this error on the local installation, so, I suspect it might be linked to sourcing some libraries/folders, since we had to source the mni folder to make it work. Best, Alexandru.

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[WARNING: UNSCANNABLE EXTRACTION FAILED]Re: freeview crash -- petsc error when opening volume
by fsbuild 10 Sep '19

10 Sep '19

External Email - Use Caution Hello Tristan, Please try rebuilding the dev branch on your Ubuntu 18 machine using the makefile listed from the wiki, (wiki page, https://surfer.nmr.mgh.harvard.edu/fswiki/CMake) where the download link to makefile is https://drive.google.com/file/d/1IMEWQty_7zjsglbErQOlu_KpXb8Lmgmv/v… should go in the same subdirectory that contains the ./freesurfer tree There are some comments in there which recommend the following be installed for Ubuntu, so please check these are installed before building,       # sudo apt-get install build-essential       # sudo apt-get install libgl1-mesa-dev freeglut3-dev mesa-common-dev       # sudo apt-get install libblas-dev liblapack-dev       # sudo apt-get install ocl-icd-opencl-dev       # sudo apt-get install libxmu-dev libxi-dev       # sudo apt-get install libopencv-dev        # Ubuntu 16: sudo apt-get install gcc-4..9 g++-4.9 gfortran-4.9       # Ubuntu 18: sudo apt-get install gcc-4.8 g++-4.8 gfortran-4.8 <----       # sudo apt-get install xorg xorg-dev libx11-dev       # sudo apt-get install tcl tcl-dev tk tk-dev       # sudo apt-get install qt5-default qtcreator       # sudo apt-get install libqt5x11extras5-dev       # sudo apt-get install git-annex        # sudo apt-get install python3-dev I’ve attached an archive containing that makefile along with the cmake output/build logs from my Ubuntu 18.04 machine so you can see what it looks like for me, see cmake_make_install_ubuntu18.tgz I’ve run all the freeview tutorial commands using the 6.0.0 release on my Ubuntu 18.04 machine, but have not been able to reproduce a petsc error so far. - R. On Aug 27, 2019, at 11:27, TRISTAN J PAUTSCH <tpautsch(a)wisc.edu> wrote:        External Email - Use Caution        Some final bits of troubleshooting information for future readers, since I'm assuming this issue will now get lost in the sauce...I'll probably try compiling everything from scratch at some point, but my hopes aren't particularly highI manually compiled the missing libs to get the CentOS7 version of FS-dev freeview running on Ubuntu 18, and ultimately the same errors occur. As well, I replicated this behavior on a separate Ubuntu 18 machine in the environment, this time using a different lab's T1/brainmask/surface files. It would definitely seem like there is some sort of hard incompatibility with newer versions of freeview and loading surface files on top of volumes in Ubuntu 18. For what it's worth, it's not evident that any other part of FS has an issue; all CLI tools seem to work just fine.TristanFrom: TRISTAN J PAUTSCH <tpautsch@wisc.edu>Sent: Friday, August 23, 2019 11:38 AMTo: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>Subject: Re: [Freesurfer] freeview crash -- petsc error when opening volume Good morning Ruopeng, thank you for your continued assistance!Unfortunately, I get the same error using the CentOS6 dev version. I tried the CentOS7 dev version, however this led to a series of library errors, the majority of which are unsolvable on Ubuntu 18 without individually compiling each necessary library (sym-linking newer libraries does not work).I wanted to ensure I provide the most details possible, so I also installed FS 5.3.0 and tested the files...interestingly, they opened just fine, no errors at all.This leads me to believe there is some strange incompatibility between Ubuntu 18 and the 6.x/dev version of FS (at least when it comes to surface files), specifically related to PETSC. Is there anything else I can do to help troubleshoot?TristanFrom: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of Ruopeng Wang <rpwang@nmr.mgh.harvard.edu>Sent: Thursday, August 22, 2019 5:00 PMTo: Freesurfer support list <freesurfer@nmr..mgh.harvard.edu>Subject: Re: [Freesurfer] freeview crash -- petsc error when opening volume Hi Tristan,Thanks for the files. I have no problem loading them with the latest dev build and stable 6.0 build.. I do not have an Ubuntu system, though. If I’m not mistaken you use dev version of freeview binary along with stable 6.0 FS binary. Is that correct? Is there any chance you can try installing the whole FS dev package?RuopengOn Aug 22, 2019, at 12:20 PM, TRISTAN J PAUTSCH <tpautsch(a)wisc.edu> wrote:        External Email - Use Caution        Ruopeng,I've uploaded the files to the FTP drop (transfer/incoming/freesurfer_data.tar.gz). The command my user is running against these files is:freeview -v brainmask.mgz T1.mgz -f lh.white:edgecolor=yellow lh.pial:edgecolor=magenta rh.white:edgecolor=yellow rh.pial:edgecolor=magentaWe can also replicate the error by opening freeview and opening all the above files sequentially through the GUI.Thank you!TristanFrom: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Ruopeng Wang <rpwang@nmr.mgh..harvard.edu>Sent: Thursday, August 22, 2019 8:16 AMTo: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>Subject: Re: [Freesurfer] freeview crash -- petsc error when opening volume Hi Tristan,Would it be possible to send us the files and the command-line you run? Best,RuopengOn Aug 21, 2019, at 12:18 PM, TRISTAN J PAUTSCH <tpautsch(a)wisc.edu> wrote:        External Email - Use Caution        Adding more details provided by my user:The crash only happens when loading surface files, either via the -f flag from the CLI or directly through the GUI. Could this be an issue with the surface files or the manner in which they are created?From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of TRISTAN J PAUTSCH <freesurfer-bounces@nmr.mgh.harvard.edu>Sent: Tuesday, August 20, 2019 2:35 PMTo: freesurfer@nmr..mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>Subject: [Freesurfer] freeview crash -- petsc error when opening volume         External Email - Use Caution        Greetings all, I'll try to keep this succinct. I'm attempting to deploy FreeSurfer on Ubuntu 18.04 servers here at the lab. I used the stable 6.0/CentOS 6 download, in addition to the dev version of freeview per the .../fswiki/UpdateFreeview instructions. All dependencies have ostensibly been satisfied, all libs from 'ldd freeview.bin' installed. Freeview launches fine and stays open when launched alone, however attempting to open a volume (either through the GUI or directly via the CLI) causes a crash and the following error about 5-8 seconds after launching (brain images begin to populate, then crash):---[0]PETSC ERROR: ------------------------------------------------------------------------[0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably memory access out of range[0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger[0]PETSC ERROR: or see http://www.mcs.anl.gov/petsc/petsc-as/documentation/troubleshootin…: or try http://valgrind.org on linux or man libgmalloc on Apple to find memory corruption errors[0]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and run [0]PETSC ERROR: to get more information on the crash.[0]PETSC ERROR: --------------------- Error Message ------------------------------------[0]PETSC ERROR: Signal received![0]PETSC ERROR: ------------------------------------------------------------------------[0]PETSC ERROR: Petsc Release Version 2.3.3, Patch 13, Thu May 15 17:29:26 CDT 2008 HG revision: 4466c6289a0922df26e20626fd4a0b4dd03c8124[0]PETSC ERROR: See docs/changes/index.html for recent updates.[0]PETSC ERROR: See docs/faq.html for hints about trouble shooting.[0]PETSC ERROR: See docs/index.html for manual pages.[0]PETSC ERROR: ------------------------------------------------------------------------[0]PETSC ERROR: Unknown Name on a linux-gnu named xxxxxxx by xxxxxxx Tue Aug 20 13:44:15 2019[0]PETSC ERROR: Libraries linked from /autofs/space/lyon_006/pubsw/Linux2-2.3-x86_64/packages/petsc/2.3.3-p13/src/petsc-2.3.3-p13/lib/linux-gnu-c-opt[0]PETSC ERROR: Configure run at Tue Aug 10 15:01:59 2010[0]PETSC ERROR: Configure options --with-debugging=no --with-cc=gcc --with-fc=g77 --download-f-blas-lapack=0 --download-mpich=1 --with-mpi=1 --with-x=0 --with-gnu-copyright-code=0 --with-shared=0 COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3[0]PETSC ERROR: ------------------------------------------------------------------------[0]PETSC ERROR: User provided function() line 0 in unknown directory unknown file[unset]: aborting job:application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0Segmentation fault (core dumped)---I've seen a number of other posts on the mailing list about this, but all of them I could find either end abruptly without a solution or with an unanswered request for more info. Happy to provide any additional information or anything that may aid in the resolution of this issue. Thanks everyone,~T_______________________________________________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

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Freesurfer September 2019