Hi Andrew, OK, so here is what happened: After adding the echo $PATH under the first line, my output is now this: "/home/lisak/miniconda3/bin:/home/lisak/Desktop/freesurfer/b in:/home/lisak/Desktop/freesurfer/fsfast/bin:/home/lisak/ Desktop/freesurfer/tktools:/home/lisak/Desktop/fsl/bin:/ home/lisak/Desktop/freesurfer/mni/bin:/home/lisak/Desktop/fsl/bin:E: Linuxbrew directory detected, but it seems to be broken. Try to remove '/home/lisak/.linuxbrew' and try again./bin:/home/lisak/Desktop /fsl/bin:/home/lisak/bin:/home/lisak/.local/bin:/usr/ local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/ usr/games:/usr/local/games:/snap/bin /home/lisak/Desktop/freesurfer/lib/qt/bin:/home/lisak/ Desktop/freesurfer/lib/vtk/bin:$FS_TCL_HOME/bin:$PATH freeview.bin: Command not found."
Also sending attached the tcf_setup files. I guess now I know a bit more about what happened. I was running the Human Connectome Project pipelines, and had an error that included an unmatched quote. It turned out that, for some reason, my computer had an issue with single quotes in some setup files, including a tcf_setup file. For that reason, we changed the single to double quotes and that error went away. (If you're interested in more details, one of the commands performed in the FreeSurferPipeline was the tkregister2 command. After trying to run this command in isolation (having previously defined $mridir variable in the terminal), we finally got the same *Unmatched ".* error that we got initially, by running the entire pipeline. Playing with double and single quotes in that line did not do anything, and it seemed that the error arises instantaneously, without FreeSurfer having the time to even try anything. so we opened the tkregister2 file in desktop/freesurfer/bin folder. This file seemed to refer to a tcl_setup file within the same subfolder. So, we opened that one, and replaced all double quotes with single quotes, in accordance with this forum post: https://stackoverflow.com/questions/10761838/getting-unmatched -on-a-simple-csh-ssh-script Even though csh is not my default shell, I think it is still being used by some processes. (Not sure if that makes any sense, I am a beginner when it comes to using Linux.) Running the tkregister2 command then in the terminal did not return Unmatched ". error, and the Pipeline was able to be completed.) The tcf_setup file in the attachment is the file we edited, whereas the tcl_setup_backup is the original file. Would you then recommend renaming the old file to tcl_setup? That would mean then renaming them back and forth, depending on the step we are doing in the analysis, but I guess it's doable. Best, Darko On Tue, Apr 17, 2018 at 6:57 PM, Hoopes, Andrew <ahoo...@mgh.harvard.edu> wrote: > Hi Darko, the freeview wrapper script sets up libraries used by > freeview.bin, so the error you get when only calling freeview.bin is > expected. There is something odd going on with your PATH after sourcing the > TCL package. Can you send me your tcl_setup file in $FREESURFER_HOME/bin? > > > > It would also be helpful if you add another “echo $PATH” line right below > the “#!/bin/tcsh -ef” in the freeview script > > > > best > > Andrew > > > > *From: *Darko Komnenić <komnen...@gmail.com> > *Date: *Tuesday, April 17, 2018 at 12:36 PM > > *To: *"Hoopes, Andrew" <ahoo...@mgh.harvard.edu> > *Cc: *FS Help <freesurfer@nmr.mgh.harvard.edu> > *Subject: *Re: [Freesurfer] unable to open freeview > > > > 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 > <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/FreeviewGeneralUsage/ > 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. > > > > >
tcl_setup
Description: Binary data
tcl_setup_backup
Description: Binary data
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