Freesurfer

freesurfer@nmr.mgh.harvard.edu

30132 discussions

mri_glmfit error
by 邓刊 16 Jun '20

16 Jun '20

External Email - Use Caution Hello Freesurfer Experts! I met the mri_glmfit error: matrix is ill-conditioned or badly scaled, condno = 1e+08.I am trying to run a 8 group 3 variables analysis: with diagnosis being my variable of interest and trying to regress out the effects of gender,background,age,education and seizure. 1. Command line: mris_preproc --fsgd qdec/group.fsgd --cache-in thickness.fwhm10.fsaverage --target fsaverage --hemi lh --out lh.thickness.fwhm10.groups.mgh mri_glmfit --y lh.thickness.fwhm10.groups.mgh --fsgd group.fsgd dods --C Difference.group.mtx --surf fsaverage lh --cortex --glmdir fwhm10.thickness.glmdir 2. The FSGD file (see attached) 3. And the design matrix: 1 1 1 1 -1 -1 -1 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 (or see attached) I encounter this error. I have no idea how to proceed.Is all this because I have too many covariates? I am looking forward to your response! Thanks, Kan

2 1

Re-register functional volume rotation issue
by Paul Soulos 15 Jun '20

15 Jun '20

External Email - Use Caution Hello, I am trying to solve an issue with reregistering functional images onto a new anatomical. Let’s say I have two anatomical images from sub01-ses01/orig.mgz and sub01-ses02/orig.mgz, as well as functional files each registered to their corresponding anatomical sub01-ses01/fmcpr.nii.gz and sub01-ses02/fmcpr.nii.gz. My goal is to reregister Dsub01-ses01/fmcpr.nii.gz onto the sub01-ses02 anatomical. Screenshots of my issue are available at: https://imgur.com/a/9GDm9yp To create a mapping between the two anatomical images, I first run: $ mri_cvs_register --mov sub01-ses01 --template sub-01-ses-02 When I view the output of the mri_cvs_register command, everything is lined up and looks good: https://i.imgur.com/SvjPVHX.png Next, I reregister sub01-ses01/fmcpr.nii.gz using the mapping created with mri_cvs_register: $ mri_vol2vol --noDefM3zPath --mov sub01-ses01/fmcpr.nii.gz --m3z $SUBECTS/sub01-ses01/cvs/final_CVSmorph_to-sub01-ses02.m3z --o sub01-ses01/fmcpr.ses02space.nii.gz --nearest --targ sub01-ses02/orig.mgz When I view sub01-ses01/fmcpr.ses02space.nii.gz over sub01-ses02/orig.mgz, the functional image is off by 90 degrees. This is unexpected: https://i.imgur.com/CpGtKyM.png If I manually rotate the functional image in Freeview by 90 degrees, it looks good: https://i.imgur.com/SkDNzuK.png mri_vol2vol has a --rot argument, so I tried to use this to perform the rotation automatically. Rather than 90 degrees, I now have to specify -90 degrees. Unfortunately, the output when I specify the rotation in mri_vol2vol does not line up well with the anatomical. https://i.imgur.com/vjxV6rv.png Does anyone know why this is happening? Please let me know if you have any suggestions. Thank you! Paul

2 5

BIDS Common Derivatives released
by Franklin Feingold 15 Jun '20

15 Jun '20

External Email - Use Caution Hello! The BIDS community is proud to announce the release of Common Derivatives! Derivatives are the outputs of preprocessing pipelines, capturing data and meta-data sufficient for a researcher to understand and (critically) reuse those outputs in subsequent pipelines. This specification can be found at: https://bids-specification.readthedocs.io/en/stable/05-derivatives/01-intro… Common principles for derivative datasets: * Derivative datasets describe the contents of the dataset, the methods by which it was generated, and the original dataset(s) that were used to generate it. This metadata is mandatory at the dataset level and optional at the file level. * Derivative files must be distinguishable from raw files. A generic description (desc-) entity allows this if no other entity applies. * The spatial interpretation of data, if applicable, can be specified with a space entity and SpatialReference metadata. Releasing the common principles for derivative datasets will enable further progress into our modality specific derivative initiatives such as, electrophysiological<https://github.com/bids-standard/bep021>, PET, and diffusion MRI<https://github.com/bids-standard/bids-bep016>. Our immediate attention will shift to focus on specifying anatomical and functional derivatives (Look out for the pull requests soon!). BEP 028: (provenance)<https://github.com/bids-standard/bids-specification/pull/487> is a closely related effort that we hope to see progress quickly as well! We would like to thank our incredible community of contributors and members that helped push this extension over the finish line! Thank you, Chris and Franklin - BIDS Maintainers

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Re: [Freesurfer] Freeview on Mac not starting due PETSC error {Disarmed}
by fsbuild 15 Jun '20

15 Jun '20

External Email - Use Caution Hello Alex, Did you try the install with the 7.1.0 release using the .pkg file installer from https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/7.1.0/free… If you did not go thru all the security exemptions (not related to your firewall settings) on Catalina, then something may be blocked from running.  The install procedure to follow using the .pkg installer is under,https://surfer.nmr.mgh.harvard.edu/fswiki//FS7_mac I did this on my mac running Catalina and had no issues running freeview. - R.. On Jun 14, 2020, at 17:45, Alex White <alexander.l.white(a)gmail.com> wrote:        External Email - Use Caution        Hi Ruopeng I tried deleting that .plist file, but it did not work, even after restarting the machine. The same PETSC crash occurred when I try to start Freeview either through the terminal or clicking on the icon. Thanks for your continued help, AlexOn Jun 14, 2020, at 2:29 PM, Wang, Ruopeng <RWANG4(a)mgh.harvard.edu> wrote:Can you delete this file and wait for a minute and then try starting freeview again?/Users/USERNAME/Library/Preferences/edu.harvard.mgh.nmr.FreeView.plistReplace USERNAME with your actual username. On Jun 14, 2020, at 1:47 PM, Alex White <alexander.l.white(a)gmail.com> wrote:        External Email - Use Caution        Hello Ruopeng, Thanks for the quick reply! I tried launching Freeview by double-clicking on the app icon, and I tried installing the latest build. The same crash occurs (full output copied again below. Also, I do have XQuartz 2.7.11 and it can run xeyes. And yes, FREESURFER_HOME and SetUpFreesurfer.sh both reference the current version 7.1.0. I didn’t see any LD_LIBRARY_PATH in my shell init file. Here’s what’s in my .bashrc file: % cat .bashrc#set freesurfer directories and set up scriptexport FREESURFER_HOME=/Applications/freesurfer/7.1.0export SUBJECTS_DIR=$FREESURFER_HOME/subjectssource $FREESURFER_HOME/SetUpFreeSurfer.shAny other ideas? Thanks, AlexCrash output:  ~ % freeview[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 16, Tue Sep 23 10:02:49 CDT 2008 HG revision: 31306062cd1a6f6a2496fccb4878f485c9b91760[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 darwin15. named gse7359200.local by alexlw Sun Jun 14 10:46:00 2020[0]PETSC ERROR: Libraries linked from /autofs/cluster/pubsw/arch/MacOS10.11/packages/petsc/2.3.3/src/petsc/lib/darwin15.6.0-c-opt[0]PETSC ERROR: Configure run at Mon Apr 22 13:14:02 2019[0]PETSC ERROR: Configure options --with-debugging=no --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 0On Jun 14, 2020, at 6:56 AM, Wang, Ruopeng <RWANG4(a)mgh.harvard.edu> wrote:HI Alex,Have you tried launching freeview by double-clicking freeview.app bundle? Can you also try the latest build from here?https://surfer.nmr.mgh.harvard.edu/fswiki/UpdateFreeviewBest,RuopengOn Jun 14, 2020, at 12:07 AM, Alex White <alexander.l.white(a)gmail.com> wrote:        External Email - Use Caution        Hello freesurfer team! I can’t get Freeview to start up on my Mac (Catalina v 10.15.15). It worked intermittently earlier this year, then stopped working. I updated Freeview, and then all of freesurfer, and still have the same problem. So now I have this version of freesurfer:  freesurfer-darwin-macOS-7.1.0-20200511-813297bTyping “freeview” into the terminal generates the following error: [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 16, Tue Sep 23 10:02:49 CDT 2008 HG revision: 31306062cd1a6f6a2496fccb4878f485c9b91760[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 darwin15. named gse7359200.local by alexlw Sat Jun 13 20:58:43 2020[0]PETSC ERROR: Libraries linked from /autofs/cluster/pubsw/arch/MacOS10.11/packages/petsc/2..3.3/src/petsc/lib/darwin15.6.0-c-opt[0]PETSC ERROR: Configure run at Mon Apr 22 13:14:02 2019[0]PETSC ERROR: Configure options --with-debugging=no --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 0I searched through the log of previous emails and found several others with “PETSC errors” but could not discern a common solution. Help? Thank you, Alex White PS: I also can’t get Freeview to launch on a linux machine, and will send a report on that in a separate email. _______________________________________________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_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

3 2

recon-all hanging, how to examine defect
by KennethSPrice 15 Jun '20

15 Jun '20

External Email - Use Caution Hello freesurfers, I am running recon-all on one of my subjects and it is hanging on a defect. How do I examine the reason it is hanging? Freeview the defect? Any help would be appreciated. Thanks, Ken Sent with [ProtonMail](https://protonmail.com) Secure Email.

3 2

MGN and LGN in ThalamicNuclei segmentation
by julienbesle 15 Jun '20

15 Jun '20

External Email - Use Caution Hello, I'm interested in locating the MGN and LGN using segmentationThalamicNuclei, but there seems to be a mismatch between the location I obtain in the discrete segmentation and the underlying probability maps obtained by setting environment variable WRITE_POSTERIORS to 1. While the LGN segmentation (orange and dark blue below) has many voxels within the corresponding area of maximum probability (superimposed hot color scale thresholded at p>0.2 below), the MGN is almost absent from the discrete segmentation (or way too lateral/posterior/superior relative to its area of max probability to be seen in the screen shot below). Any reason why this could be happening? Is there anything I can do (parameters I can change) to fix this? The defaut Freesurfer segmentation ("thalamus proper", shown in white below) is generally larger than the segmentation output by segmentThalamicNuclei, except in the area of the LGN, where the thalamic segmentation extends more laterally/inferiorly, as if it had been extended in order to include the LGN (although imperfectly). However, this does not seem to be happening for the MGN (which is my primary area of interest). (Note that I'm using T1-weighted MPRAGE data at a resolution of 0.7 mm isotropic)

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Re: [Freesurfer] Freeview on Mac not starting due PETSC error
by fsbuild 14 Jun '20

14 Jun '20

External Email - Use Caution Hello Alex, See what you get for results on your Mac with the commands listed below.  Your version of MacOS may be slightly different.  It should work to cut and paste the commands below. - R. - - - - -  buildqa-Mac:/tmp % bash The default interactive shell is now zsh.To update your account to use zsh, please run `chsh -s /bin/zsh`.For more details, please visit https://support.apple.com/kb/HT208050. buildqa-Mac:/tmp> sw_versProductName: Mac OS XProductVersion: 10.15.2BuildVersion: 19C57 buildqa-Mac:/tmp> echo $PATH | tr -s ':' '\n' /usr/local/bin/usr/bin/bin/usr/sbin/sbin/opt/X11/bin/Users/buildqa/bin buildqa-Mac:/tmp> ls /opt/X11/binX@               cvt*             freetype-config* lndir*           showrgb*         xclipboard*      xev*             xkbcomp*         xman*            xsetpointer*Xephyr*          cxpm*            fslsfonts*       luit*            smproxy*         xclock*          xeyes*           xkbevd*          xmessage*        xsetroot*Xfake*           editres*         fstobdf*         makedepend*      startx*          xcmsdb*          xfd*             xkbprint*        xmh*             xsm*Xnest*           fc-cache*        gccmakedep*      mkfontdir*       sxpm*            xcompmgr*        xfindproxy*      xkbvleds*        xmodmap*         xstdcmap*Xorg*            fc-cat*          glxgears*        mkfontscale*     twm*             xconsole*        xfontsel*        xkbwatch*        xmore*           xterm*Xquartz*         fc-list*         glxinfo*         oclock*          ucs2any*         xcursorgen*      xfs*             xkeystone*       xpr*             xvinfo*Xvfb*            fc-match*        gtf*             png-fix-itxt*    uxterm*          xcutsel*         xfsinfo*         xkill*           xprop*           xwd*appres*          fc-pattern*      iceauth*         pngfix*          viewres*         xditview*        xgamma*          xload*           xrandr*          xwininfo*atobm*           fc-query*        ico*             quartz-wm*       x11perf*         xdm*             xgc*             xlogo*           xrdb*            xwud*bdftopcf*        fc-scan*         koi8rxterm*      resize*          x11perfcomp*     xdmshell*        xhost*           xlsatoms*        xrefresh*bdftruncate*     fc-validate*     libpng-config@   sessreg*         xauth*           xdpr*            xinit*           xlsclients*      xscope*bitmap*          font_cache*      libpng16-config* setxkbmap*       xbacklight*      xdpyinfo*        xinput*          xlsfonts*        xset*bmtoa*           fonttosfnt*      listres*         showfont*        xcalc*           xedit*           xkbbell*         xmag*            xsetmode* buildqa-Mac:/tmp> export FREESURFER_HOME=/Applications/freesurfer/7.1.0buildqa-Mac:/tmp> ls $FREESURFER_HOMEASegStatsLUT.txt*              SetUpFreeSurfer.sh*            etc/                           sources.csh*DefectLUT.txt*                 Simple_surface_labels2009.txt* fsafd/                         sources.sh*FreeSurferColorLUT.txt*        WMParcStatsLUT.txt*            fsfast/                        subjects/FreeSurferEnv.csh*             average/                       lib/                           tkmeditParcColorsCMA*FreeSurferEnv.sh*              bin/                           matlab/                        trctrain/Freeview.app/                  build-stamp.txt*               mni/                           uninstall.sh*SegmentNoLUT.txt*              diffusion/                     python/SetUpFreeSurfer.csh*           docs/                          sessions/ buildqa-Mac:/tmp> source $FREESURFER_HOME/SetUpFreeSurfer..sh-------- freesurfer-darwin-macOS-7.1.0-20200511-813297b --------Setting up environment for FreeSurfer/FS-FAST (and FSL)FREESURFER_HOME   /Applications/freesurfer/7.1.0FSFAST_HOME       /Applications/freesurfer/7.1.0/fsfastFSF_OUTPUT_FORMAT nii.gzSUBJECTS_DIR      /Applications/freesurfer/7.1.0/subjectsMNI_DIR           /Applications/freesurfer/7.1.0/mni buildqa-Mac:/tmp> echo $PATH | tr -s ':' '\n'/Applications/freesurfer/7.1.0/bin/Applications/freesurfer/7.1.0/fsfast/bin/Applications/freesurfer/7.1.0/mni/bin/usr/local/bin/usr/bin/bin/usr/sbin/sbin/opt/X11/bin/Users/buildqa/bin buildqa-Mac:/tmp> open -a $FREESURFER_HOME/Freeview.app<...pop up window asking to accept network connections, then freeview should open in a separate window … then exit freeview...> buildqa-Mac:/tmp> otool -L /Applications/freesurfer/7.1.0/Freeview.app/Contents/MacOS/freeview /Applications/freesurfer/7.1.0/Freeview.app/Contents/MacOS/freeview: /System/Library/Frameworks/Cocoa.framework/Versions/A/Cocoa (compatibility version 1.0.0, current version 23.0.0) /System/Library/Frameworks/IOKit.framework/Versions/A/IOKit (compatibility version 1.0.0, current version 275.0.0) /System/Library/Frameworks/Accelerate.framework/Versions/A/Accelerate (compatibility version 1.0.0, current version 4.0.0) @rpath/QtWidgets.framework/Versions/5/QtWidgets (compatibility version 5.12.0, current version 5.12.7) /System/Library/Frameworks/OpenGL.framework/Versions/A/OpenGL (compatibility version 1.0.0, current version 1.0.0) /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1252.250.1) /System/Library/Frameworks/ApplicationServices.framework/Versions/A/ApplicationServices (compatibility version 1.0.0, current version 50.1.0) /System/Library/Frameworks/CoreServices.framework/Versions/A/CoreServices (compatibility version 1.0.0, current version 946.0.0) /usr/lib/libz.1.dylib (compatibility version 1.0.0, current version 1.2.11) @rpath/QtGui.framework/Versions/5/QtGui (compatibility version 5.12.0, current version 5.12.7) @rpath/QtCore.framework/Versions/5/QtCore (compatibility version 5.12.0, current version 5.12.7) /usr/lib/libc++.1.dylib (compatibility version 1.0.0, current version 400.9.4) /System/Library/Frameworks/AppKit.framework/Versions/C/AppKit (compatibility version 45.0.0, current version 1671.60.107) /System/Library/Frameworks/CoreFoundation..framework/Versions/A/CoreFoundation (compatibility version 150.0.0, current version 1575.17.0) /System/Library/Frameworks/CoreGraphics.framework/Versions/A/CoreGraphics (compatibility version 64.0.0, current version 1265.9.0) /System/Library/Frameworks/Foundation.framework/Versions/C/Foundation (compatibility version 300.0.0, current version 1575.17.0) /usr/lib/libobjc.A.dylib (compatibility version 1.0.0, current version 228.0..0) On Jun 14, 2020, at 18:34, fsbuild <fsbuild(a)contbay.com> wrote:        External Email - Use Caution        Hello Alex,Did you try the install with the 7.1.0 release using the .pkg file installer from https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/7.1.0/free… you did not go thru all the security exemptions (not related to your firewall settings) on Catalina, then something may be blocked from running.  The install procedure to follow using the .pkg installer is under,https://surfer.nmr.mgh.harvard.edu/fswiki//FS7_macI did this on my mac running Catalina and had no issues running freeview.- R.On Jun 14, 2020, at 17:45, Alex White <alexander.l.white(a)gmail.com> wrote:        External Email - Use Caution        Hi Ruopeng I tried deleting that .plist file, but it did not work, even after restarting the machine. The same PETSC crash occurred when I try to start Freeview either through the terminal or clicking on the icon. Thanks for your continued help, AlexOn Jun 14, 2020, at 2:29 PM, Wang, Ruopeng <RWANG4(a)mgh.harvard.edu> wrote:Can you delete this file and wait for a minute and then try starting freeview again?/Users/USERNAME/Library/Preferences/edu.harvard.mgh.nmr.FreeView.plistReplace USERNAME with your actual username. On Jun 14, 2020, at 1:47 PM, Alex White <alexander.l.white(a)gmail.com> wrote:        External Email - Use Caution        Hello Ruopeng, Thanks for the quick reply! I tried launching Freeview by double-clicking on the app icon, and I tried installing the latest build. The same crash occurs (full output copied again below. Also, I do have XQuartz 2.7.11 and it can run xeyes. And yes, FREESURFER_HOME and SetUpFreesurfer.sh both reference the current version 7.1.0. I didn’t see any LD_LIBRARY_PATH in my shell init file. Here’s what’s in my .bashrc file: % cat .bashrc#set freesurfer directories and set up scriptexport FREESURFER_HOME=/Applications/freesurfer/7.1.0export SUBJECTS_DIR=$FREESURFER_HOME/subjectssource $FREESURFER_HOME/SetUpFreeSurfer.shAny other ideas? Thanks, AlexCrash output:  ~ % freeview[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 16, Tue Sep 23 10:02:49 CDT 2008 HG revision: 31306062cd1a6f6a2496fccb4878f485c9b91760[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 darwin15. named gse7359200.local by alexlw Sun Jun 14 10:46:00 2020[0]PETSC ERROR: Libraries linked from /autofs/cluster/pubsw/arch/MacOS10.11/packages/petsc/2..3.3/src/petsc/lib/darwin15.6.0-c-opt[0]PETSC ERROR: Configure run at Mon Apr 22 13:14:02 2019[0]PETSC ERROR: Configure options --with-debugging=no --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 0On Jun 14, 2020, at 6:56 AM, Wang, Ruopeng <RWANG4(a)mgh.harvard.edu> wrote:HI Alex,Have you tried launching freeview by double-clicking freeview.app bundle? Can you also try the latest build from here?https://surfer.nmr.mgh.harvard.edu/fswiki/UpdateFreeviewBest,RuopengOn Jun 14, 2020, at 12:07 AM, Alex White <alexander.l.white(a)gmail.com> wrote:        External Email - Use Caution        Hello freesurfer team! I can’t get Freeview to start up on my Mac (Catalina v 10.15.15). It worked intermittently earlier this year, then stopped working. I updated Freeview, and then all of freesurfer, and still have the same problem. So now I have this version of freesurfer:  freesurfer-darwin-macOS-7.1.0-20200511-813297bTyping “freeview” into the terminal generates the following error: [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 16, Tue Sep 23 10:02:49 CDT 2008 HG revision: 31306062cd1a6f6a2496fccb4878f485c9b91760[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 darwin15. named gse7359200.local by alexlw Sat Jun 13 20:58:43 2020[0]PETSC ERROR: Libraries linked from /autofs/cluster/pubsw/arch/MacOS10.11/packages/petsc/2.3.3/src/petsc/lib/darwin15.6.0-c-opt[0]PETSC ERROR: Configure run at Mon Apr 22 13:14:02 2019[0]PETSC ERROR: Configure options --with-debugging=no --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 0I searched through the log of previous emails and found several others with “PETSC errors” but could not discern a common solution. Help? Thank you, Alex White PS: I also can’t get Freeview to launch on a linux machine, and will send a report on that in a separate email. _______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________Freesurfer mailing listFreesurfer(a)nmr.mgh.harvard.eduMailScanner has detected a possible fraud attempt from "mail.nmr.mgh..harvard.edu" claiming to be https://mail.nmr.mgh.harvard.edu/mailman/listinfo/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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Freeview on Mac not starting due PETSC error
by Alex White 14 Jun '20

14 Jun '20

External Email - Use Caution Hello freesurfer team! I can’t get Freeview to start up on my Mac (Catalina v 10.15.15). It worked intermittently earlier this year, then stopped working. I updated Freeview, and then all of freesurfer, and still have the same problem. So now I have this version of freesurfer: freesurfer-darwin-macOS-7.1.0-20200511-813297b Typing “freeview” into the terminal generates the following error: [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/troubleshooting.html#Si… ERROR: 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 16, Tue Sep 23 10:02:49 CDT 2008 HG revision: 31306062cd1a6f6a2496fccb4878f485c9b91760 [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 darwin15. named gse7359200.local by alexlw Sat Jun 13 20:58:43 2020 [0]PETSC ERROR: Libraries linked from /autofs/cluster/pubsw/arch/MacOS10.11/packages/petsc/2.3.3/src/petsc/lib/darwin15.6.0-c-opt [0]PETSC ERROR: Configure run at Mon Apr 22 13:14:02 2019 [0]PETSC ERROR: Configure options --with-debugging=no --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 0 I searched through the log of previous emails and found several others with “PETSC errors” but could not discern a common solution. Help? Thank you, Alex White PS: I also can’t get Freeview to launch on a linux machine, and will send a report on that in a separate email.

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Re: [Freesurfer] Freeview on Mac not starting due PETSC error {Disarmed}
by fsbuild 14 Jun '20

14 Jun '20

External Email - Use Caution Hello Alex, Please make sure you have the latest version of Xquartz (2.7.11) installed on the Mac from, https://www.xquartz.org.  You can right click and select “Get Info” on the XQuartz.app under Applications -> Utilities in order to check the version.   Launch XQuartz, wait for it to open an X window, and in that window run xeyes or xgc to see if it displays basic graphics. If you set FREESURFER_HOME in your shell init file(s), I would check it is set to the 7.1.0 release so that you are source’ing the SetUpFreeSurfer{.sh,csh} script from 7.1.0 (and not from previous releases) .  I would also unset or comment out setting LD_LIBRARY_PATH before you source the SetUpFreeSurfer{.sh,csh} script in any shell init files or in your environment. - R. On Jun 14, 2020, at 00:07, Alex White <alexander.l.white(a)gmail.com> wrote:        External Email - Use Caution        Hello freesurfer team! I can’t get Freeview to start up on my Mac (Catalina v 10.15.15). It worked intermittently earlier this year, then stopped working. I updated Freeview, and then all of freesurfer, and still have the same problem. So now I have this version of freesurfer:  freesurfer-darwin-macOS-7.1.0-20200511-813297bTyping “freeview” into the terminal generates the following error: [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 16, Tue Sep 23 10:02:49 CDT 2008 HG revision: 31306062cd1a6f6a2496fccb4878f485c9b91760[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 darwin15. named gse7359200.local by alexlw Sat Jun 13 20:58:43 2020[0]PETSC ERROR: Libraries linked from /autofs/cluster/pubsw/arch/MacOS10.11/packages/petsc/2.3.3/src/petsc/lib/darwin15.6.0-c-opt[0]PETSC ERROR: Configure run at Mon Apr 22 13:14:02 2019[0]PETSC ERROR: Configure options --with-debugging=no --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 0I searched through the log of previous emails and found several others with “PETSC errors” but could not discern a common solution. Help? Thank you, Alex White PS: I also can’t get Freeview to launch on a linux machine, and will send a report on that in a separate email. _______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

1 0

ver 7.1: recon-all executes out of order?
by Roman Fleysher 12 Jun '20

12 Jun '20

External Email - Use Caution Dear FreeSurfer Develovers, FreeSurfer 7.1 was recently installed on our cluster. I am testing it and stumbled on the error. It is difficult for me to debug it myself (perhaps if https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllTableStableV7<https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllTableStableV6.0>.1 existed it would help me). I hope you can help. The symptom is that I run: recon-all -s FOLDER_1 -hemi lh -white -smooth2 -inflate2 -sphere -surfreg -cortparc -pial -sd FOLDER_2 Notice strange combination: -s FOLDER_1 -sd FOLDER_2 . Data is actually in FOLDER_2 where specific subject is set up in the environmental variable. The error message in recon-all.log is: mris_smooth -n 3 -nw -seed 1234 ../surf/lh.white.preaparc ../surf/lh.smoothwm smoothing for 3 iterations setting seed for random number generator to 1234 error: No such file or directory error: MRISread(../surf/lh.white.preaparc): could not open file error: No such file or directory error: mris_smooth: could not read surface file ../surf/lh.white.preaparc Indeed, file ../surf/lh.white.preaparc does not exist. It seems to indicate that -white was not actually executed before -smooth2. This command worked on version 6.0. Is this a bug in recon-all script version 7.1? Is this expected? Previous successful command on the same data was: recon-all -s FOLDER_1 -hemi lh -fix -sd FOLDER_2 General info: 1) FreeSurfer version: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b 2) Platform: likely CentOS, not sure how to tell 3) uname -a: Linux loginnode4 2.6.32-696.6.3.el6.694g0000.x86_64 #1 SMP Wed Jul 12 02:19:57 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux 4) recon-all.log: not attached because folder structure contains sensitive information that is hard to remove. Thank you, Roman

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