Freesurfer

freesurfer@nmr.mgh.harvard.edu

17 participants
30086 discussions

bbregister using freesurfer v7
by Ellen Ji 08 Jul '20

08 Jul '20

External Email - Use Caution Dear experts, I am running bbregister and have a couple questions: 1) I am using freesurfer version 7. My understanding is that I do not need any --init argument anymore, and without it, by default it uses init-coreg. Could you confirm this? (I tested the below and it seemed fine) bbregister --s subject1 --mov $dtipath/subject1/data.nii.gz --dti --reg mri/register.dat 2) A colleague performed recon-all using freesurfer v6. Is it ok if I use bbregister on these subjects using freesurfer v7 or should I install v6? Many thanks for your input! Ellen Ji, PhD Postdoctoral researcher ***** Individual Differences in Psychosis (IDP) Lab Psychiatric University Hospital University of Zürich ellen.ji(a)bli.uzh.ch

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Problem with skull strip & general beginner questions
by Nils Böer 07 Jul '20

07 Jul '20

External Email - Use Caution Hello everyone, I hope you can help me with my little problem I encountered after manually editing the skull strip. Because my internet provider crashed I'm unable to upload the log file right now and writing this from my phone. For context: I'm analyzing data with freesurfer 6.0 because the data sets already went through the recon-all process some months ago with freesurfer 6.0. I just got the data sets and my first step was to manually edit bad skull strips using tkmedit. This worked fine but after I finished and saved the data set I wanted to run: recon-all -autorecon-pial -subjid P_01 This stopped with errors and at the bott of the log i found this note which probably led to the crash: MghRead(/usr/local/freesurfer/subjects/P_01/MRI/../MRI/asset.presurf.mgz, -1): could not open file I looked into the folder and can't even find this file. Did I miss a step I have to do before or can this be due to getting the data after running recon-all on a different PC? My pre-processing pipeline looks like this (keep in mind I already get the data after recon-all was completed): 1. Skull Strip (either manually or using gcut depending on data quality) 2. Checking surfaces visually and talairach transforms if needed 3. White matter intensity normalization. Do I need to change the order here or am I missing something completely? I'm new to freesurfer and have to get into it myself. The broad tutorials online help but it's hard to check what I have to do in which order and how. If you have other guides I can check this would be an incredible help. Thanks for the help and sorry for the long email, I really appreciate every tip. Best regards, Nils

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The European Neuroscience Institute in Göttingen (ENI-G) Germany announces positions for Group Leaders (m/f/d)
by Caspar M. Schwiedrzik 07 Jul '20

07 Jul '20

External Email - Use Caution The European Neuroscience Institute in Göttingen (ENI-G) Germany announces positions for Group Leaders (m/f/d) - Limitation: fixed-term - Working period: full-time - Tariff: salary according to TV-L - Announcement published on 06.07.2020 - Vacancy from 01.01.2021 - Application deadline: 31.08.2020 The ENI-G, a joint initiative between the University Medical Center Göttingen and the Max-Planck-Society, provides an exceptional environment for excellent young researchers in the neurosciences. *We seek:* Applicants with an outstanding record of research in neuroscience. Topics range from molecular and cellular physiology, neuronal circuit analysis, imaging (at all scales), to computational and cognitive neuroscience. Current work at the ENI-G focuses on physiology, sensory processing and plasticity in multiple species, from invertebrates to humans. Research that complements these already established topics, including computational approaches at the ENI-G is also welcome. *We offer:* Group leaders a maximal amount of independence while also providing the support necessary to build up a new research program. ENI-G will provide office and laboratory space as well as a generous start-up. State of the art equipment, including dedicated microscopy infrastructure, animal facilities, a precision workshop, IT and administrative support are available in house. Unparalleled opportunities for scientific collaboration and interaction exist within the Göttingen Research Campus, including the University of Göttingen and its Medical School, three Max Planck Institutes (Biophysical Chemistry, Experimental Medicine, and Dynamics and Self Organization), the German Primate Center and the Bernstein Center for Computational Neuroscience. We will work closely with the recently established Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells (https://mbexc.de/en/)" as well as the newly starting Heart and Brain Center Göttingen. In addition to the excellent research environment that ENI-G provides, its independent group leaders can benefit from the resources and funding opportunities offered by the Collaborative Research Centers (CRC / SFB) within the Göttingen Neuroscience community. The ENI-G also houses the distinguished graduate program ‘IMPRS Neurosciences’, facilitating interactions with excellent students and providing opportunities for teaching. You will have an experienced mentor by your side, receive broad administrative support, professional leadership training, and help with relocation and establishing a life in Germany, including visa application, housing, schooling, and day-care. Successful group leaders will have the opportunity to obtain a permanent position after a two step internal and external evaluation. *We look forward to:* Applications from outstanding researchers who are enthusiastic about pursuing an independent research program in an environment that supports cutting edge research. The successful candidate is expected to develop a vigorous research program with a Ph.D. received within the last five years. Relevant research training and outstanding research reflected by high-impact publications are a prerequisite for consideration. The applicant is expected to acquire competitive third-party funding, and eligibility for ERC Starting Grant / DFG Emmy Noether level funding (or comparable) is a requirement. Details about funding opportunities can be found at http://www.eni-g.de/career/group-leader. Interested candidates should submit their curriculum vitae and record of publications highlighting their 3-5 most significant publications, as well as a research statement (3-5 pages), and a copy of their PhD degree, preferably in one pdf. Application deadline: 31 August 2020. Women are especially encouraged to apply. Applicants with disabilities and equal qualifications will be given preferential treatment. We look forward to receiving your application by *31.08.2020*: University Medical Center Göttingen European Neuroscience Institute Göttingen Christiane Becker Administration Manager Grisebachstr. 5 37077 Göttingen Tel.: 0551/39-61300 Fax: 0551/39-61399 E-Mail: c.becker(a)eni-g.de Web: http://www.eni-g.de/index.php?id=groupleader Please send your application only via e-mail as a PDF-file. Travel and application fees cannot be refunded or transferred. https://www.umg.eu/karriere/stellenangebote/stellenanzeigen-detail/?jobId=3…

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mris_convert error
by Mason Wells 07 Jul '20

07 Jul '20

External Email - Use Caution Hi Experts, I am using mris_convert to convert native FreeSurfer surf files (inflated, pial and white) to GIFTI files. However, when I view them in Freeview, there seems to be a misalignment/error (attached). The commands I ran followed this structure: Mris_convert lh.inflated lh.inflated.surf.gii Any help would be great. Mason Mason T Wells, MSc PhD student School of Optometry and Vision Sciences & Cardiff University Brain Research Imaging Centre (CUBRIC), School of Psychology Cardiff University Cardiff CF24 4HQ UK Email: WellsMT1(a)cardiff.ac.uk<mailto:WellsMT1@cardiff.ac.uk> Tel: 02920 879628 Web: Cardiff University webpage<https://www.cardiff.ac.uk/people/research-students/view/974214-> Mason T Wells, MSc Myfyriwr PhD Yr Ysgol Optometreg a Gwyddorau’r Golwg & Canolfan Ymchwil Delweddu’r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr Ysgol Seicoleg Prifysgol Caerdydd Heol Maindy Caerdydd CF24 4HQ DU E-bost: WellsMT1(a)caerdydd.ac.uk<mailto:WellsMT1@caerdydd.ac.uk> Ffôn: 02920 879628

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PhD Position on the Brain, Language and Multilingualism
by Narly Golestani 06 Jul '20

06 Jul '20

External Email - Use Caution With the launch of a new ‘NCCR Evolving Language’ (http://www.snf.ch/SiteCollectionDocuments/nfs/Faktenblatt_NCCR_evolvinglang…) which involves nearly 40 different research groups from a large variety of disciplines across Switzerland, we seek to fill a PhD position for a four-year project, starting in September or October 2020. Our goal is to make progress in understanding language giftedness from cognitive, psychological and neural perspectives. To this end, we plan to carry out a set of studies involving acquisition of both behavioral measures of cognitive and language-related abilities (e.g. auditory/perceptual abilities, phonemic perception and production, inductive learning, working memory etc) and of brain imaging measures (fMRI and sMRI). The project will be supervised by Narly Golestani (University of Geneva) and Raphael Berthele (University of Fribourg), and will be done in collaboration with a postdoctoral fellow. Data will be collected with Francophone (mono- and multilingual) subjects. Applicants should hold have a background in cognitive neuroscience or psychology, with solid experience in brain functional neuroimaging (ideally fMRI), behavioral testing and strong statistics skills. Command of the French and English languages is essential. Given hiring restrictions due to Covid19, priority will be given to European applicants, at least for now. The NCCR places great emphasis on gender diversity and we particularly encourage women to apply. Applicants may send a pdf file including a cover letter, a CV, names and contact information of 3 references as well as any other relevant documents to Narly.Golestani(a)unige.ch<mailto:Narly.Golestani@unige.ch> and Raphael.berthele(a)unifr.ch<mailto:Raphael.berthele@unifr.ch>. Deadline for application: July 22nd 2020 ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Brain and Language Lab Prof. Narly GOLESTANI Department of Psychology Campus Biotech 9 Chemin des Mines, 1202 Genève +41 22 379 53 52 <https://outlook.unige.ch/owa/redir.aspx?SURL=5WTo-p-J-W9FrDydU-0WU4PdMytUGs…>http://www.brainandlanguagelab.org https://twitter.com/brain_lang_lab ----------------------------------------------------------------------------------------------------------------------------------------------------------------- <https://outlook.unige.ch/owa/redir.aspx?SURL=5WTo-p-J-W9FrDydU-0WU4PdMytUGs…>

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cortical thickness
by Nasiriavanaki, Zahra 06 Jul '20

06 Jul '20

Hi Freesurfer experts I have a question about the way FS calculates cortical thickness and I appreciate if you could please respond. I calculated the cortical thickness using read_curv script in a specific ROI in parietal lobe. The mean thickness at that area was 2.4. Does this number show the cortical thickness in millimeter? Thanks MOna

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Destrieux atlas volume based in matlab
by Gian Marco Duma 06 Jul '20

06 Jul '20

External Email - Use Caution Dear Freesurfers experts, I need to obtain in the volume and not in the surface, in MNI space with voxels of 2mm. At this moment I do not need to obtain a parcellation of a single subject, even a parcellation in the volume from the MNI template would be great. Do you have any suggestions? thanks

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Fsaverage stats
by Alina Rojas 06 Jul '20

06 Jul '20

External Email - Use Caution Hello Freesurfer Developers, I'm attempting to compare the cortical thickness values from the stats (?h.aparc.stats) of a stack of subjects and compare them with fsaverage. With aparcstats2table I did it for my subjects without problem, but the fsaverage folder doesn’t have the ?.h.aparc.stats file. I need it to compare the cortical thickness values of the different regions of the brain from the stack of subjects with fsaverage to see if we have a relevant difference. Do you have a suggestion how I can do it? Thanks in advance, Alina

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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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