also, not sure if this info will be useful, but libvtkverdict.so.5.6 exists on my computer in /home/lisak/Desktop/freesurfer/lib/vtk/lib/vtk-5.6 subfolder, but from the error message above it seems as if Freesurfer expects the file to be located in lib/vtk/*bin *subfolder.
On Tue, Apr 17, 2018 at 6:36 PM, Darko Komnenić <komnen...@gmail.com> wrote: > Hi Andrew, > thanks for getting back so quickly. > Here are the outputs: > “tcsh --version” gives a "tcsh 6.18.01 (Astron) 2012-02-14 > (x86_64-unknown-linux) options wide,nls,dl,al,kan,rh,nd,color,filec" > > I added echo $PATH right before the “freeview.bin $argv” line in the > freeview script, and the output to > "freeview" is now: > "/home/lisak/Desktop/freesurfer/lib/qt/bin:/home/ > lisak/Desktop/freesurfer/lib/vtk/bin:$FS_TCL_HOME/bin:$PATH > freeview.bin: Command not found." > > So it seems it has something to do with libraries. > If I type freeview.bin instead of just freeview, I get: > "freeview.bin: error while loading shared libraries: libvtkverdict.so.5.6: > cannot open shared object file: No such file or directory" > > There seems to be a similar entry in the mailing list already, but from > what I see, it hasn't been solved. This is the link to the old question: > https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/ > 2017-September/053992.html > Unlike the original poster, i don't get the "Abort" feedback, though. > > Thanks a lot! > Best, > Darko > > On Tue, Apr 17, 2018 at 6:26 PM, Hoopes, Andrew <ahoo...@mgh.harvard.edu> > wrote: > >> Do you have tcsh properly installed? You can check by running the command >> “tcsh --version”. >> >> >> >> If it is installed, I’m not quite sure why you’re experiencing this >> problem, but I would suggest modifying the freeview script at >> /home/lisak/Desktop/freesurfer/bin/freeview to debug. Try adding the >> following line right before the call to “freeview.bin $argv”: >> >> >> >> echo $PATH >> >> >> >> and send the output over. >> >> >> >> best >> >> Andrew >> >> >> >> >> >> *From: *Darko Komnenić <komnen...@gmail.com> >> *Date: *Tuesday, April 17, 2018 at 11:35 AM >> *To: *"Hoopes, Andrew" <ahoo...@mgh.harvard.edu> >> *Cc: *FS Help <freesurfer@nmr.mgh.harvard.edu> >> *Subject: *Re: [Freesurfer] unable to open freeview >> >> >> >> Hi Andrew, >> >> FreeSurfer is being sourced automatically each time I open the terminal, >> and I see the usual lines: >> >> Setting up environment for FreeSurfer/FS-FAST (and FSL) >> FREESURFER_HOME /home/lisak/Desktop/freesurfer >> FSFAST_HOME /home/lisak/Desktop/freesurfer/fsfast >> FSF_OUTPUT_FORMAT nii.gz >> SUBJECTS_DIR /home/lisak/Desktop/freesurfer/subjects >> MNI_DIR /home/lisak/Desktop/freesurfer/mni >> FSL_DIR /home/lisak/Desktop/fsl >> >> The outputs of which freeview and which freeview.bin are, respectively: # >> 1. /home/lisak/Desktop/freesurfer/bin/freeview >> 2. /home/lisak/Desktop/freesurfer/bin/freeview.bin >> >> These are actual locations of the file, so all seems good until that >> point. I typed "freeview" again, after doing the "which freeview" commands, >> and I got the "freeview.bin: Command not found." again. >> >> Any further suggestions are appreciated! >> >> Thanks in advance, >> >> Darko >> >> >> >> >> >> >> >> On Tue, Apr 17, 2018 at 5:28 PM, Hoopes, Andrew <ahoo...@mgh.harvard.edu> >> wrote: >> >> Hi Darko, how are you sourcing freesurfer? And what is the output of >> running “which freeview” and “which freeview.bin”? >> >> >> >> best, >> >> Andrew >> >> >> >> *From: *<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Darko >> Komnenić <komnen...@gmail.com> >> *Reply-To: *FS Help <freesurfer@nmr.mgh.harvard.edu> >> *Date: *Tuesday, April 17, 2018 at 11:17 AM >> *To: *FS Help <freesurfer@nmr.mgh.harvard.edu> >> *Subject: *[Freesurfer] unable to open freeview >> >> >> >> Dear experts, >> >> I encountered a problem when trying to open freeview. I am using >> FreeSurfer v.5.3.0-HCP, and after sourcing it, I tried typing simply >> freeview in the terminal, as described in this link: >> http://freesurfer.net/fswiki/FreeviewGuide/FreeviewGeneralUs >> age/FreeviewQuickStart >> >> but the feedback I get is: freeview.bin: Command not found. >> >> Am I missing something? When searching for freeview on my computer, >> "freesurfer" and "freesurfer.bin" appear in my bin subfolder, but for some >> reason they seem not to be recognized. >> >> Any help is appreciated! >> >> Best, >> >> Darko >> >> The information in this e-mail is intended only for the person to whom it >> is >> addressed. If you believe this e-mail was sent to you in error and the >> e-mail >> contains patient information, please contact the Partners Compliance >> HelpLine at >> http://www.partners.org/complianceline . If the e-mail was sent to you >> in error >> but does not contain patient information, please contact the sender and >> properly >> dispose of the e-mail. >> >> >> > >
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