New subject: [Freesurfer] can´t open an image in Freeview {Disarmed}

23 Oct 2019


      External Email - Use Caution
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 an image from the freesurfer distribution directly from the command line to see if the graphics look any different.
$ freeview $FRESURFER_HOME/subjects/bert/mri/brain.mgz
The grey boxes could be from the VM not having enough CPU or video memory resources allocated to it and so the graphics refresh is slow. &nbsp;You could try running some other graphics applications in the VM to see if you get the same greyed out effect.
If you run freeview from the command line with no args,&nbsp;$ freeview
- then you should get an empty window with just some icons at the top. &nbsp;Is it sluggish trying to drag around the empty freesurfer window? &nbsp;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 &lt;adam.rytina@outlook.cz&gt; wrote:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;External Email - Use Caution&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Hello,thanks for your answer. Please see attached the screenshot.I typed "$ which freeview.bin" --&gt; the output: "/usr/local/freesurfer/bin/freeview.bin"I typed "$ ldd `which freeview..bin` | grep not" --&gt; 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:&nbsp;Reading package lists... DoneBuilding dependency treeReading state information... DoneE: Unable to locate package libvtkverdict.so.5.6E: 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 helpRegardsAdamOd:&nbsp;fsbuild &lt;fsbuild@contbay.com&gt;Odesláno:&nbsp;pondělí 21. října 2019 4:28Komu:&nbsp;freesurfer@nmr.mgh.harvard.edu&nbsp;&lt;freesurfer@nmr.mgh.harvard.edu&gt;Kopie:&nbsp;adam.rytina@outlook.cz&nbsp;&lt;adam.rytina@outlook.cz&gt;Předmět:&nbsp;Re: [Freesurfer] can´t open an image in Freeview&nbsp;Hello Adam,Please check if you have a “freeview.bin” program.$ which freeview.binIf 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 &lt;adam.rytina@outlook.cz&gt; wrote:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;External Email - Use Caution&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;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/DownloadAndInstallPlease, could you help me?Thanks a lotAdamOd:&nbsp;fsbuild &lt;fsbuild@contbay.com&gt;Odesláno:&nbsp;pátek 18.. října 2019 22:05Komu:&nbsp;freesurfer@nmr.mgh.harvard.edu&nbsp;&lt;freesurfer@nmr.mgh.harvard.edu&gt;Kopie:&nbsp;adam.rytina@outlook.cz&nbsp;&lt;adam.rytina@outlook.cz&gt;Předmět:&nbsp;Re: [Freesurfer] can´t open an image in Freeview&nbsp;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 notAdam Rytina&nbsp;&nbsp;&nbsp;October 18, 2019 at 14:31&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;External Email - Use Caution&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;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 lotAdamBez virů.&nbsp;www.avast.com_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer________________... mailing listFreesurfer@nmr.mgh..harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer%3Cfreeview.png%... mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] can´t open an image in Freeview {Disarmed}