Freesurfer June 2020

freesurfer@nmr.mgh.harvard.edu

91 participants
130 discussions

Extract single time frame
by Rockers, Elijah D. 16 Oct '22

16 Oct '22

Hello again, I have a large time series in dicom or .nii format. I am interested in extracting a single time frame from it. I did this before, I believe with freesurfer, but I have somehow forgot the name of the command, and I can't seem to find it. I believe it could be used to specify particular regions of the volume, as well as time. I need the entire volume, still, but only one frame. Thanks in advance! Eli Houston Methodist. Leading Medicine. Ranked by U.S.News & World Report as one of America's "Best Hospitals" in 11 specialties. Named to FORTUNE® Magazine's "100 Best Companies to Work For®" list 10 years in a row. Designated as a Magnet hospital for excellence in nursing. Visit us at houstonmethodist.org. Follow us at twitter.com/MethodistHosp and www.facebook.com/HoustonMethodist. ***CONFIDENTIALITY NOTICE*** This e-mail is the property of Houston Methodist Hospital and/or its relevant affiliates and may contain restricted and privileged material for the sole use of the intended recipient(s). Any review, use, distribution or disclosure by others is strictly prohibited. If you are not the intended recipient (or authorized to receive for the recipient), please contact the sender and delete all copies of the message. Thank you.

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Job ad: MRI physicist
by Keith Schneider 07 May '21

07 May '21

External Email - Use Caution The Center for Biomedical and Brain Imaging (CBBI) is a core imaging facility at the University of Delaware dedicated to scientific research. It is equipped with a Siemens Prisma 3T MRI scanner, Bruker 9.4T small bore MRI scanner, TMS, and MRI-compatible EEG. It supports a wide range of scientific investigations through imaging of humans, animals and materials. Under general direction of the CBBI Manager, the MRI Physicist is responsible for supporting the operations of the Siemens and Bruker MRI scanners. The MRI Physicist is expected to contribute to both research and training efforts that will include pulse sequence programming, parameter and image quality optimization, protocol design, scanner operation, technical support and user training. The candidate will be expected to maintain a broad knowledge of state-of-the-art MRI technology and equipment. The incumbent must have excellent communication and organizational skills, the ability to positively interact with a diverse group of MRI users, and a strong motivation to learn new MRI techniques. MAJOR RESPONSIBILITIES: • Pulse sequence programming on Bruker 9.4T and Siemens 3T MRI scanners • Assist users on appropriate choice and use of coils • Technical liaison for obtaining sequences or protocols for non-standard imaging (e.g. cardiac, musculoskeletal) from Siemens and other sites • File reports as needed for WIP sequences and Siemens MRA • Ensure data quality from the viewpoint of machine fundamentals • Technical support 9.4T and 3T scanners • Protocol design and testing for 9.4T scanner, including imaging of live animals and awake animals; as-needed for 3T • Routine quality assurance for 9.4T and 3T MRI scanners • Train users, including students, on use of 9.4T and 3T MRI scanners • Help users optimize pulse sequence parameters to maximize SNR and avoid imaging artifacts • Consult on image analysis, as needed • Review journals and abstracts to keep abreast of new developments • Collaborate with ongoing research as needed; may have independent research projects if desired • Consult users about imaging details for manuscript preparation and grant applications, as needed • Perform miscellaneous job-related duties as assigned QUALIFICATIONS: • PhD in MR physics or MS with equivalent experience • expert understanding of MR physics, image acquisition, signal processing, imaging processing and image reconstruction • MR pulse sequence programming • Experience with Bruker and Siemens MRI scanners • MRI scanning experience with both humans and animals—willing to handle animals • Ability to design experiments, optimize MRI protocols, troubleshoot image artifacts, analyze data, and interpret results • Knowledge of functional MRI, DTI, MRS, T1/T2 relaxation and perfusion • Siemens IDEA and ICE certification (or ability to obtain) http://careers.udel.edu/cw/en-us/job/493998/mri-physicist-research-office <http://careers.udel.edu/cw/en-us/job/493998/mri-physicist-research-office> For further information, contact me. keith ----- Keith Schneider Director, Center for Biomedical and Brain Imaging Associate Professor Department of Psychological and Brain Sciences University of Delaware

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Parcellation Error Pre-Post Central Gyrus R but not L Hemisphere
by Fraser Smith 26 Apr '21

26 Apr '21

External Email - Use Caution Hi there I have a clear parcellation error with one participant who does look to have an atypical structure around the right post-central gyrus (looks split in two). Both the pre and post central gyri are shifted significantly backwards – but only for the right not the left hemisphere. I see this has been mentioned before in the archives – but I have been unable to find a fix for this. Could you provide any tips on what to try? I am using v6.0.0. Best wishes Fraser Smith

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Correct for sulcuses & ventricles size
by John Anderson 13 Dec '20

13 Dec '20

External Email - Use Caution Dear Freesurfer experts, I have two groups of subjects (healthy and patients). The patients have different degrees of atrophy. Looking into the individual scans, the subjects are largely different in the space between the sulcuses and the size of ventricles. My questions are: 1. Is there any way to correct for these differences in the surface based analysis? 2. Including eTIV covariate does it help in this case? 3. Does the resampling to "fsaverage" overcome the challenge of these differences between the subjects? I appreciate any advice, John

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Visualizing significant clusters, monte-carlo and permutation
by Avi Gharehgazlou 27 Aug '20

27 Aug '20

External Email - Use Caution Hi experts, I am a bit confused with visualizing my significant clusters after having corrected my results for multiple comparisons. after running mri_glmfit, I corrected with monte carlo and permutation as explained below, will you please confirm my understanding below is correct ? 1. I ran monte carlo simulation (1.3 sig level). My understanding is that "cache.th13.abs.sig.cluster.summary" shows the clusters that are significant after correction for multiple comparisons. I have 1 cluster listed in this file. Thus, I am interpreting this as having 1 significant cluster after correction at p<0.05, is this correct? When I want to visualize my corrected results I use the command line below. I am assuming this command line displays only the significant clusters that survived multiple comparison correction because only the cluster that is listed in my "cache.th13.abs.sig.cluster.summary" file appears on the brain here, and because I have put " cache.th13.abs.sig.cluster.mgh" and as overlay " cache.th13.abs.sig.ocn.annot" and set the threshold to 1.3 in my command line. Is it correct that the cluster that appears when running the below command line is my significant cluster surviving multiple comparisons correction at p<0.05? vglrun freeview -f $SUBJECTS_DIR/fsaverage/surf/lh.inflated :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 also, how can I get the clusters to look their appropriate colours when I am vieweing them with the command line above? all my clusters appear gray (regardless of whether they have positive or negative max values, in which case they should be yellow and blue, respectively) 2. I then ran permutation testing. My "perm.th13.abs.sig.cluster.summary" file is blank. I interpret this as no clusters having survived multiple comparison correction with permutation testing. Am I correct? When I use the below command line to visualize my result I see a blank brain (with no clusters coloured). Which makes sense to me because my "perm.th13.abs.sig.cluster.summary" also showed no significant clusters. is this interpretation and the command line I am using below correct? vglrun freeview -f $SUBJECTS_DIR/fsaverage/surf/lh.inflated:overlay=lh.lgi.TD_PTSD_age_SA_IQ_FWHM0.glmdir/group.diff/perm.th13.abs.sig.cluster.mgh:overlay_threshold=1.3,5:annot=lh.lgi.TD_PTSD_age_SA_IQ_FWHM0.glmdir/group.diff/perm.th13.abs.sig.ocn.annot -viewport 3d -layout 1 I think my understanding is correct, but I am confused because the FreeSurfer instructions state that the above command lines will display "all clusters, regardless of significance"... but using the above command lines seems to only display my significant clusters. I am assuming this is because I set my threshold to 1.3 (the same threshold I used to correct for multiple comparisons in 1 and 2 above). But wanted to make sure I am correct before proceeding. Thank you so much for your support, Avi

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LGI and Global GI
by Alexopoulos, Dimitrios 07 Aug '20

07 Aug '20

External Email - Use Caution HI, I have generated the LGI for a group of pediatric subjects. Is there a way to compute a single Global gyrification index measure for each subject? Jim, ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

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Error in Trac-All Pre-Processing step
by Jocelyn Ra 28 Jul '20

28 Jul '20

External Email - Use Caution Hi all, After running the trac-all command in the pre-processing step in the official TRACULA tutorial, I ran into the following error: WARN: Could not find satisfactory control point fit - try 4718 Writing output files to /home1/jr2359/diffusion_tutorial_april2018/diffusion_tutorial/elmo.2005/dlabel/mni/rh.cst_AS_avg33_mni_bbr_* Writing spline volume to /home1/jr2359/diffusion_tutorial_april2018/diffusion_tutorial/elmo.2005/dlabel/mni/rh.cst_AS_avg33_mni_bbr_cpts_6.nii.gz Segmentation fault The "WARN" message repeated several times before this final message, making me believe the issue is with the control points. For reference, I am using the tutorial data set, "set ncpts = (6 6 5 5 5 5 7 5 5 5 5 5 4 4 5 5 5 5)" for the control points, and LINUX. Has anyone else run into this error, and could someone please help me with this issue? Thank you in advance! Sincerely, Jocelyn

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Re: [Freesurfer] aparcstats2table error
by Devika K 15 Jul '20

15 Jul '20

External Email - Use Caution I tried doing cortical parcellation using Destrieux atlas. I ran the aparcstats2table command from the SUBJECTS_DIR directory containing all of the output from recon-all. But I got an error, PFA. Do I need to run any other commands before running aparcstats2table command, I would be grateful if anyone could help me to resolve this issue. Many thanks in advance. Regards Devika K Research Scholar, Dept of EEE e: k_devika(a)cb.students.amrita.edu Amrita Vishwa Vidyapeetham Coimbatore, India

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Re: [Freesurfer] Freeview on Mac not starting due PETSC error
by fsbuild 03 Jul '20

03 Jul '20

External Email - Use Caution Hello Alex, While I'm (fsbuild) and not Ruopeng, I don't mind being mistaken for such a smart/nice guy ;-) .  So I'm cc'ing back to the list so he and others can follow up. It looks like you already have the commands to set FREESURFER_HOME and source the setup script in your $HOME/.bashrc file - as that information is printed out to the terminal after you run bash.  So there should be no need to repeat typing those commands in the terminal window (though it should do no harm).. I guess one question would be if it works for yo to do: 1) reboot your machine 2) start a new terminal window 3) type "bash" .... see output from the freesurfer environment and then run the command ... 4) open -a $FREESURFER_HOME/Freeview.app Then try loading a simple volume in freeview. (Under the freeview File pull down menu, select load volume, then you could try navigating to this file and select it, /Applications/freesurfer/7.1.0/subjects/bert/mri/brain.mgz - see screen shot below). I think Ruopeng wanted to know if after the steps above, it also works for you to double click on Freeview.app in the Finder window and launch it (navigate with the Finder to /Applications/freesurfer/7.1.0). You could try making bash your default shell with this command in the terminal window, so you don't have to type bash in step (3). $ chsh -s /bin/bash - R. Alex White wrote: Hello again Ruopeng, I copied those commands into my terminal. To my amazement, Freeview opened successfully with the command  open -a $FREESURFER_HOME/Freeview.appIt was also able to load a volume. And then I was able to start Freeview with the simpler command “freeview.” I can’t explain that.. The FREESURFER_HOME variable didn’t change, and my shell init script had already sourced SetUpFreesurfer.sh. However, I restarted my machine and tried again, and then Freeview wouldn’t open with either command, even following the whole sequence of commands you suggested. Then I tried again, and it worked. For some reason it’s only working intermittently. In response to your other question, when I double-clicked on the app bundle to start freeview, there was no crash report generated.Below is the output to the commands you requested. Do you see anything suspicious? Thanks a million! Alexalexlw@gse7359200 ~ % bash-------- freesurfer-darwin-macOS-7.1.0-20200511-813297b --------Setting up environment for FreeSurfer/FS-FAST (and FSL)FREESURFER_HOME   /Applications/freesurfer/7.1.0FSFAST_HOME       /Applications/freesurfer/7.1.0/fsfastFSF_OUTPUT_FORMAT nii.gzSUBJECTS_DIR      /Applications/freesurfer/7.1.0/subjectsMNI_DIR           /Applications/freesurfer/7.1.0/mniThe default interactive shell is now zsh.To update your account to use zsh, please run `chsh -s /bin/zsh`.For more details, please visit https://support.apple.com/kb/HT208050.bash-3.2$ sw_versProductName: Mac OS XProductVersion: 10.15.5BuildVersion: 19F101bash-3.2$ echo $PATH | tr -s ':' '\n'/Applications/freesurfer/7.1.0/bin/Applications/freesurfer/7.1.0/fsfast/bin/Applications/freesurfer/7.1.0/mni/bin/Users/alexlw/google-cloud-sdk/bin/Library/Frameworks/Python.framework/Versions/3.8/bin/Applications/freesurfer/7.1.0/bin/Applications/freesurfer/7.1.0/fsfast/bin/Applications/freesurfer/7.1.0/mni/bin/usr/local/bin/usr/bin/bin/usr/sbin/sbin/opt/X11/bin/Users/alexlw/Library/Python/3.8/bin/Users/alexlw/Library/Python/3.8/bin/Users/alexlw/Library/Python/3.8/binbash-3.2$ ls /opt/X11/binX bmtoa font_cache libpng-config resize x11perf xditview xfsinfo xkeystone xmore xstdcmapXephyr cvt fonttosfnt libpng16-config sessreg x11perfcomp xdm xgamma xkill xpr xtermXfake cxpm freetype-config listres setxkbmap xauth xdmshell xgc xload xprop xvinfoXnest editres fslsfonts lndir showfont xbacklight xdpr xhost xlogo xrandr xwdXorg fc-cache fstobdf luit showrgb xcalc xdpyinfo xinit xlsatoms xrdb xwininfoXquartz fc-cat gccmakedep makedepend smproxy xclipboard xedit xinput xlsclients xrefresh xwudXvfb fc-list glxgears mkfontdir startx xclock xev xkbbell xlsfonts xscopeappres fc-match glxinfo mkfontscale sxpm xcmsdb xeyes xkbcomp xmag xsetatobm fc-pattern gtf oclock twm xcompmgr xfd xkbevd xman xsetmodebdftopcf fc-query iceauth png-fix-itxt ucs2any xconsole xfindproxy xkbprint xmessage xsetpointerbdftruncate fc-scan ico pngfix uxterm xcursorgen xfontsel xkbvleds xmh xsetrootbitmap fc-validate koi8rxterm quartz-wm viewres xcutsel xfs xkbwatch xmodmap xsm  bash-3.2$ export FREESURFER_HOME=/Applications/freesurfer/7.1.0  bash-3.2$ ls $FREESURFER_HOMEASegStatsLUT.txt SetUpFreeSurfer.csh diffusion matlab tkmeditParcColorsCMADefectLUT.txt SetUpFreeSurfer.sh docs mni trctrainFreeSurferColorLUT.txt Simple_surface_labels2009.txt etc python uninstall.shFreeSurferEnv.csh WMParcStatsLUT.txt fsafd sessionsFreeSurferEnv.sh average fsfast sources.cshFreeview.app bin lib sources.shSegmentNoLUT.txt build-stamp.txt license.txt subjects  bash-3.2$ source $FREESURFER_HOME/SetUpFreeSurfer.sh-------- freesurfer-darwin-macOS-7.1.0-20200511-813297b --------Setting up environment for FreeSurfer/FS-FAST (and FSL)FREESURFER_HOME   /Applications/freesurfer/7.1.0FSFAST_HOME       /Applications/freesurfer/7.1.0/fsfastFSF_OUTPUT_FORMAT nii.gzSUBJECTS_DIR      /Applications/freesurfer/7.1..0/subjectsMNI_DIR           /Applications/freesurfer/7.1.0/mni bash-3.2$ echo $PATH | tr -s ':' '\n'/Applications/freesurfer/7.1.0/bin/Applications/freesurfer/7.1.0/fsfast/bin/Applications/freesurfer/7.1.0/mni/bin/Applications/freesurfer/7.1.0/bin/Applications/freesurfer/7.1.0/fsfast/bin/Applications/freesurfer/7.1.0/mni/bin/Users/alexlw/google-cloud-sdk/bin/Library/Frameworks/Python.framework/Versions/3.8/bin/Applications/freesurfer/7.1.0/bin/Applications/freesurfer/7..1.0/fsfast/bin/Applications/freesurfer/7.1.0/mni/bin/usr/local/bin/usr/bin/bin/usr/sbin/sbin/opt/X11/bin/Users/alexlw/Library/Python/3.8/bin/Users/alexlw/Library/Python/3.8/bin/Users/alexlw/Library/Python/3.8/binbash-3.2$ open -a $FREESURFER_HOME/Freeview.app Freeview opens…sometimes bash-3.2$ 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 8:49 PM, fsbuild <fsbuild(a)contbay.com> wrote: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 % bashThe 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_versProd…: Mac OS XProductVersion: 10.15.2BuildVersion: 19C57buildqa-Mac:/tmp> echo $PATH | tr -s ':' '\n' /usr/local/bin/usr/bin/bin/usr/sbin/sbin/opt/X11/bin/Users/buildqa/binbuildqa-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/mnibuildqa-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/binbuildqa-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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Error with "recon-all -make all" following multiple manual editing
by Matthieu VANHOUTTE 03 Jul '20

03 Jul '20

External Email - Use Caution Dear Freesurfer's experts, Havng done multiple types of manual editing in two subjects, I relaunched the recon-all process (Freesurfer 6.0.1) with the flag "-make all". However, during the process, I goth for both subjects the following error message: / / /make: *** [/netapp/vol2_agewell/pro/IMAP/imap_mvh/FS6.0.1/awellv1s097/mri/aseg.presurf.mgz] Error 1/ /recon-all -s /netapp/vol2_agewell/pro/IMAP/imap_mvh/FS6.0.1/awellv3s024 -ccseg ERROR: Flag -ccseg unrecognized./ Following the troubleshooting site (https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TroubleshootingDataV6.0) I have over-writed the "recon-all.makefile" file since I use the 6.0.1 version of Freesurfer. Thanks for helping. Best, Matthieu

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Freesurfer June 2020