An update, in the .bash_profile file, there is a line about linuxbrew. Do you recommend that I remove it? Sending the file attached. Best, Darko
On Thu, Apr 19, 2018 at 11:59 AM, Darko Komnenić <komnen...@gmail.com> wrote: > Hi Andrew, > sorry for the delay. Attached is the hidden bashrc file from my Home > folder. It doesn't seem to specify anything about linuxbrew, so I don't > know why this error is showing up. Thanks a lot for any suggestions! > Best, > Darko > > On Tue, Apr 17, 2018 at 11:07 PM, Hoopes, Andrew <ahoo...@mgh.harvard.edu> > wrote: > >> Are you using a bash shell? If you are, there should be a file located at >> ~/.bashrc (it’s a hidden file in your home folder) >> >> Andrew >> >> >> >> >> >> *From: *Darko Komnenić <komnen...@gmail.com> >> *Date: *Tuesday, April 17, 2018 at 2:24 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 a lot for your feedback! >> >> I renamed the original fine, so it is now called just tcl_setup, and here >> is the output I got after typing "freeview" >> >> /home/lisak/miniconda3/bin:/home/lisak/Desktop/freesurfer/bi >> n:/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 >> Unmatched ". >> >> So this looks pretty much like the error I got when using Human >> Connectome Project pipelines (to answer your earlier question, the only >> time I got this error before was while running FreeSurferPipelineBatch.sh >> in HCP pipelines, specifically after the start of FreeSurferHighResWhite >> script). I don't use FreeSurfer for anything else on this computer, since >> this is the special 5.3-HCP version, and I use FS6 on a different computer. >> Also, the Unmatched quote error does not appear when running FSL or other >> programs. >> >> (Not sure if you're familiar with HCP pipelines, but they are used (among >> other things) to estimate cortical myelin content, and have 3 main >> preprocessing pipelines, PreeFS one, FS one, and PostFS one - I got the >> Unmatched ". error in the FS one. When writing to their mailing list, I was >> told that it seems like an error unique to my computer, and they have not >> encountered it before.) >> >> >> >> Anyway, the Linuxbrew error appears again now after trying to start >> freeview. >> >> I searched for bashrc on my computer and I got two locations, one in perl >> subfolder, and one in miniconda3 subfolder. The latter just has 2 lines, so >> it's probably not the one you meant. The former is quite a long file, but >> does not mention linuxbrew at any point. I am sending the file attached. >> >> I would be really very grateful if you would try helping out with this. I >> have been googling this error, but was not able to find anything. >> >> Thanks a bunch! >> >> Darko >> >> >> >> >> >> On Tue, Apr 17, 2018 at 7:52 PM, Hoopes, Andrew <ahoo...@mgh.harvard.edu> >> wrote: >> >> Hi Darko, there’s a big difference between using single vs double quotes >> in shell scripting – single quotes prevent variable expansion. Your >> modification to tcl_setup actually renders your PATH completely unusable. >> The quote syntax in the setup scripts shouldn’t cause any problems, and >> your unmatched errors indicate a more low-level issue that should probably >> get fixed directly. Are you only getting these unmatched errors with >> freesurfer tools? I can try to help you solve this, but I’m not quite sure >> I understand the initial problem. >> >> >> >> PS: At some point in your .bashrc is linuxbrew called? You don’t want >> that “Linuxbrew directory detected…” error in your PATH variable >> >> >> >> *From: *Darko Komnenić <komnen...@gmail.com> >> *Date: *Tuesday, April 17, 2018 at 1:21 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, >> >> 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/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. >> >> >> >> >> >> >> >> >> > >
.bash_profile
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_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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.
