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... 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 AHOOPES@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 komnenicd@gmail.com *Date: *Tuesday, April 17, 2018 at 11:35 AM *To: *"Hoopes, Andrew" AHOOPES@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: #
- /home/lisak/Desktop/freesurfer/bin/freeview
- /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 AHOOPES@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-bounces@nmr.mgh.harvard.edu on behalf of Darko Komnenić komnenicd@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
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