Freesurfer June 2020

freesurfer@nmr.mgh.harvard.edu

91 participants
130 discussions

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

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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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Re: [Freesurfer] lGI permutation and monte-carlo
by Avi Gharehgazlou 12 Jun '20

12 Jun '20

External Email - Use Caution Thank you so much for your input, it was very helpful and I really appreciate it. Regarding your question with relation to my 4th question, when I run the below command line to visualize my results after correcting for multiple comparisons using monte-carlo at 1.3 significance level in this example, I assumed the clusters that appear on freeview are only my significant clusters (clusters that survived monte carlo correction) since I put " cache.th13.abs.sig.cluster.mgh" and then as overlay " cache.th13.abs.sig.ocn.annot " in my command line. If not, will you please tell me how I can see only clusters that are significant after correction for multiple comparisons (at 1.3 sig level in this case)? Also, in my command line, I can put either lh.pial or lh.inflated to see the results//clusters on the pial or inflated surface, respectively. Correct? vglrun freeview -f $SUBJECTS_DIR/fsaverage/surf/lh.pial:overlay=lh.lgi.TD_PTSD_age_SA_IQ_FWHM0.glmdir/group.diff/cache.th13.abs.sig.cluster.mgh:overlay_threshold=1.3,5:annot=lh.lgi.TD_PTSD_age_SA_IQ_FWHM0.glmdir/group.diff/cache.th13.abs.sig.ocn.annot -viewport 3d Thank you so much, Avi

2 1

Matlab runtime installation error for Freesurfer v7.1.0
by Yann Quidé 11 Jun '20

11 Jun '20

External Email - Use Caution Hi team, I am trying to install fs_install_mcr R2014b, but encounter an error just at the end of it: mv: rename /var/folders/1f/4_zl7p9n795c2yq1dgb3hvt40000gq/T/tmp.Xvv7Ku4d/install-target/v84 to /Applications/freesurfer/7.1.0/MCRv84: Permission denied Any idea how I can fix this to finalise the installation? I should have the admin rights on the machine. Thanks, Yann

2 2

Re: [Freesurfer] Regarding installation in CentOS7
by fsbuild 11 Jun '20

11 Jun '20

External Email - Use Caution Hello Rahul, Did you try following the instructions on the wiki pages about how to do an install with the tar archive or RPM ?  Please see links to Linux and/or Mac install and setup, https://surfer.nmr..mgh.harvard.edu/fswiki/rel7downloads -R. On Jun 11, 2020, at 16:25, Rahul Sharma <sharmarahul.26dec(a)gmail.com> wrote:        External Email - Use Caution        Unable to perform installation. Please help me out regarding the same.Regards:Rahul SharmaResearch ScholarNIT Silchar (Assam)9827834360_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

2 1

Regarding installation in CentOS7
by Rahul Sharma 11 Jun '20

11 Jun '20

External Email - Use Caution Unable to perform installation. Please help me out regarding the same. Regards: Rahul Sharma Research Scholar NIT Silchar (Assam) 9827834360

1 0

Final result of monkey make_averge_subject
by Pam Garcia 11 Jun '20

11 Jun '20

External Email - Use Caution Hi FS developers, I have some questions related to make_average_subject I followed the steps describe here https://surfer.nmr.mgh.harvard.edu/fswiki/SurfaceRegAndTemplates to 1. build a monkey curvature pattern 2. build FS monkey average using 40 subjects I've finished the surface and volume average, but the anatomy of the prefrontal lobe looks rounded and the size of the brain was adjusted to the human MNI. I suppose that this is due to the affine registration. My questions are the follows: 1. Is there some way to avoid the affine registration or only use 3 DOF for registration when the average is built? All the images were previously registered to MNI monkey space 2. In the case that the affine registration can´t be avoided is it correct to use a surface gotten from the template image and next use this as average in mris_preproc?

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Freesurfer June 2020