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 <komnenicd@gmail.com>
Date: Tuesday, April 17, 2018 at 12:36 PM
To: "Hoopes, Andrew" <AHOOPES@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

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: #
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 <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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