I'm getting started on my first Freesurfer project (previously using SPM and FSL only). I'm working via the jalapeno cluster at FMRIB (University of Oxford) which runs, I believe, the latest version of FreeSurfer. I've run into a number of early problems, including whilst working on the tutorial data. I will describe what I hope is a basic problem.
I cannot get tkmedit to work, and see the error message GLUT: Fatal Error in tkmedit.bin: OpenGL GLX extension not supported by display: :7.0 (my display number for my VNC connection is 7)
I have, I think, launched FreeSurfer correctly in the terminal before running the tkmedit command, using either
. $FREESURFER_HOME/SetUpFreeSurfer.sh SUBJECTS_DIRecho SUBJECTS
Or
tcsh source . $FREESURFER_HOME/SetUpFreeSurfer.csh setenv SUBJECTS_DIR $TUTORIAL_DATA/buckner_data/tutorial_subjs
So, I can see previous threads suggesting I have not launched FreeSurfer correctly but I suspect FreeSurfer is indeed launched, or perhaps because I need to be using X11/xming. But of course I am unsure. Any tips?
Dr. Amy Bilderbeck University of Oxford, Dept of Psychiatry Warneford Hospital, OX3 7JX
Hello Amy,
Is your VNC connection from a Windows client to the cluster? Have you ever been able to display graphical interfaces from the cluster onto your PC over that VNC connection? And lastly, what happens if you type 'glxgears' while connected to the cluster,,, does a graphical interface with spinning 3D gears appear?
Getting the various freesurfer GUIs to display over a VNC connection with completely different operating systems at the server and client side is fraught with a multitude of potential issues, not necessarily freesurfer related. I would suggest researching various X Window Servers for Windows in conjuction with something like PuTTY. See the following link for additional information:
https://cc.jlab.org/windows/X11onWindows
-Zeke
On 08/02/2013 11:19 AM, Amy Bilderbeck wrote:
I’m getting started on my first Freesurfer project (previously using SPM and FSL only). I’m working via the jalapeno cluster at FMRIB (University of Oxford) which runs, I believe, the latest version of FreeSurfer. I’ve run into a number of early problems, including whilst working on the tutorial data. I will describe what I hope is a basic problem.
I cannot get tkmedit to work, and see the error message
GLUT: Fatal Error in tkmedit.bin: OpenGL GLX extension not supported by display: :7.0
(my display number for my VNC connection is 7)
I have, I think, launched FreeSurfer correctly in the terminal before running the tkmedit command, using either
. $FREESURFER_HOME/SetUpFreeSurfer.sh SUBJECTS_DIRecho SUBJECTS
Or
tcsh
source . $FREESURFER_HOME/SetUpFreeSurfer.csh
setenv SUBJECTS_DIR $TUTORIAL_DATA/buckner_data/tutorial_subjs
So, I can see previous threads suggesting I have not launched FreeSurfer correctly but I suspect FreeSurfer is indeed launched, or perhaps because I need to be using X11/xming. But of course I am unsure. Any tips?
Dr. Amy Bilderbeck
University of Oxford, Dept of Psychiatry
Warneford Hospital, OX3 7JX
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
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Amy Bilderbeck -
Z K