External Email - Use Caution Hi Andrew, I did close it and reopen it. There seem to be two different errors in this output. If I just run echo $PATH, I get: "/home/lisak/miniconda3/bin:/home/lisak/Desktop/freesurfer/bin:/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"
meaning the same error from before, but without the Unmatched ". whereas, if I cd into Desktop/freesurfer/bin and then run tcl_setup I just get the Unmatched ". I hope this helps. Best, Darko On Thu, Apr 19, 2018 at 7:17 PM, Hoopes, Andrew <ahoo...@mgh.harvard.edu> wrote: > Did you close and open a new terminal window first? Sorry, I forgot to > mention that the bash_profile needs to be re-sourced if you make changes. > After this, run “echo $PATH” to make sure that the brew error is no longer > present > > Andrew > > > > *From: *Darko Komnenić <komnen...@gmail.com> > *Date: *Thursday, April 19, 2018 at 1:08 PM > > *To: *"Hoopes, Andrew" <ahoo...@mgh.harvard.edu> > *Cc: *FS Help <freesurfer@nmr.mgh.harvard.edu> > *Subject: *Re: [Freesurfer] unable to open freeview > > > > Hi Andrew, > > I commented out the last two lines, and the same error message still > appears. Please let me know if you have any other suggestions. Thanks! > > Best, > > Darko > > > > On Thu, Apr 19, 2018 at 6:08 PM, Hoopes, Andrew <ahoo...@mgh.harvard.edu> > wrote: > > Hi Darko, try commenting out the last two lines and rerunning freeview > (it’s possible that the error message getting inserted into your PATH is > the source of these issues): > > # export PATH="$HOME/.linuxbrew/bin:$PATH" > > # export PATH="$(brew --prefix)/bin:$PATH" > > > > > > *From: *Darko Komnenić <komnen...@gmail.com> > *Date: *Thursday, April 19, 2018 at 6:54 AM > > > *To: *"Hoopes, Andrew" <ahoo...@mgh.harvard.edu> > *Cc: *FS Help <freesurfer@nmr.mgh.harvard.edu> > *Subject: *Re: [Freesurfer] unable to open freeview > > > > 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/ > bin:/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 $PATH under the first line, my output is now this: > "/home/lisak/miniconda3/bin:/home/lisak/Desktop/freesurfer/ > bin:/home/lisak/Desktop/freesurfer/fsfast/bin:/home/ > lisak/Desktop/freesurfer/tktools:/home/lisak/Desktop/ > fsl/bin:/home/lisak/Desktop/freesurfer/mni/bin:/home/lisak/Desktop/fsl/bin:E: > Linuxbrew directory detected, but it seems to be broken. Try to remove > '/home/lisak/.linuxbrew' and try again./bin:/home/lisak/ > Desktop/fsl/bin:/home/lisak/bin:/home/lisak/.local/bin:/ > usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin: > /usr/games:/usr/local/games:/snap/bin > /home/lisak/Desktop/freesurfer/lib/qt/bin:/home/ > lisak/Desktop/freesurfer/lib/vtk/bin:$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. > > > > > > > > > > > > > > >
_______________________________________________ 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.
