External Email - Use Caution        

Hello,

Yes sure, I checked my setup of Freesurfer enviroment - the same as the wiki 
page I guess.

I loaded an image from the freesurfer distribution directly from the command 
line - the same problem (the grey windows popping out).

The strange thing is I´m running also FSL on Ubuntu VM without any problem, 
thereby I don´t think the issue is related to the Ubuntu VM. Moreover, I 
succesfully opened some images few days ago and the program was running without 
any problem. However, it took just a while and then this issued appeared again. 
There is just a grey window popping out (choosing all options run very quickly 
without any problem).

Well, I´m totally helpless. I tried to download it again, run Freesurfer on 
Ubuntu 16. and 18. version but the problem still persists.

Regards
Adam

________________________________
Od: fsbuild <fsbu...@contbay.com>
Odesláno: středa 23. října 2019 7:30
Komu: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Kopie: adam.ryt...@outlook.cz <adam.ryt...@outlook.cz>
Předmět: Re: [Freesurfer] can´t open an image in Freeview

Hello Adam,

It’s not clear to me that the vtk libs are the issue.

Please check that you setup your FREESURFER environment as listed on the 
freesurfer help/wiki pages,
https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall

It looks like you would do (using sh or bash),

$ export FREESURFER_HOME=/usr/local/freesurfer
$ source $FREESURFER_HOME/SetUpFreeSurfer.sh
… output showing your settings ...
..
.

You could try loading
to see if the graphics look any different.

$ freeview $FRESURFER_HOME/subjects/bert/mri/brain.mgz

The grey boxes could be from the VM not having enough CPU or video memory 
resources allocated to it and so the graphics refresh is slow.  You could try 
running some other graphics applications in the VM to see if you get the same 
greyed out effect.

If you run freeview from the command line with no args,
$ freeview

- then you should get an empty window with just some icons at the top.  Is it 
sluggish trying to drag around the empty freesurfer window?  If so, I would ask 
whoever setup the VM to try and improve its performance.

You could also try setting this on the command line for the vtk libs - but it 
may not fix the graphics getting greyed out.
$ export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$FREESURFER_HOME/lib/vtk/lib/vtk5.6

- R.

On Oct 22, 2019, at 14:46, Adam Rytina <adam.ryt...@outlook.cz> wrote:

        External Email - Use Caution
Hello,

thanks for your answer. Please see attached the screenshot.

I typed "$ which freeview.bin" --> the output: 
"/usr/local/freesurfer/bin/freeview.bin"
I typed "$ ldd `which freeview.bin` | grep not" --> the output: 20 files 
"libvtk...so.5.6 are not found" Please see the attached screenshot.

While trying to install the packages (eg. "sudo apt-get install 
libvtkverdict.so.5.6"), the output is:
Reading package lists... Done
Building dependency tree
Reading state information... Done
E: Unable to locate package libvtkverdict..so.5.6
E: Couldn't find any package by glob 'libvtkverdict.so.5.6'
E: Couldn't find any package by regex 'libvtkverdict.so.5.6'

What´s wrong? Please, could you advise me? I tried to run freeview on Ubuntu 
16.04 and 18.04 as well but the problem still remains the same.

Thanks a lot for your help
Regards
Adam
________________________________
Od: fsbuild <fsbu...@contbay.com<mailto:fsbu...@contbay.com>>
Odesláno: pondělí 21. října 2019 4:28
Komu: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> 
<freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
Kopie: adam.ryt...@outlook.cz<mailto:adam.ryt...@outlook.cz> 
<adam.ryt...@outlook.cz<mailto:adam.ryt...@outlook.cz>>
Předmět: Re: [Freesurfer] can´t open an image in Freeview

Hello Adam,

Please check if you have a “freeview.bin” program.

$ which freeview.bin

If you get a path back with freeview.bin in it, e.g. something like
/usr/local/freesurfer/bin/freeview.bin

- then try the ldd command on freeview.bin,

$ ldd `which freeview.bin` | grep not

- then see if it lists that something is not found.

- R.

On Oct 19, 2019, at 03:27, Adam Rytina 
<adam.ryt...@outlook.cz<mailto:adam.ryt...@outlook.cz>> wrote:

        External Email - Use Caution
Hello,

I run the command "$ ldd `which freeview` | grep not" and the result is "not a 
dynamic executable". Do you know where the problem is?

What I read there could be the problem regarding 32bit or 64bit system I´m 
working on. I am running on Windows 10 64bit, 64 bit CPU, 64bit Ubuntu 16.04. I 
downloaded the 6.0.0. Freesurfer version from the official 
page:https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall

Please, could you help me?

Thanks a lot
Adam

________________________________
Od: fsbuild <fsbu...@contbay.com<mailto:fsbu...@contbay.com>>
Odesláno: pátek 18.. října 2019 22:05
Komu: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> 
<freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
Kopie: adam.ryt...@outlook.cz<mailto:adam.ryt...@outlook.cz> 
<adam.ryt...@outlook.cz<mailto:adam.ryt...@outlook.cz>>
Předmět: Re: [Freesurfer] can´t open an image in Freeview

Hello Adam,

See if you can run the following command, and if it reports anything is not 
found (you can cut and paste the command)

- R.

$ ldd `which freeview` | grep not

Adam Rytina<mailto:adam.ryt...@outlook.cz>

October 18, 2019 at 14:31
        External Email - Use Caution
Hello all,

I´m new to Freesurfer and I´m struggling with loading an image in FreeView.. I 
am running the Freesurfer 6.0.0. on Ubuntu 16.04. Virtual Machine. While 
opening FreeView (typing "freeview" in the shell) just some empty grey windows 
will pop out (please see attached the screenshot). Besides this, everything is 
OK, I successfully tested Freesurfer installation. I haven´t found any simmilar 
issue on the Internet. Thus, please, could you help me to address this issue?

Thanks a lot
Adam

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