Sarah, When I have seen this 'sliver' problem in the tksurfer in the past, upgrading the NVidia Linux driver fixed the problem. But that was on a native Linux system (with NVidia graphics), so I don't know what to suggest here, since a virtual Linux machine is a very different beast.
I suppose you should at least make sure your current graphics driver is up-to-date against the graphic card manufacturers website (do this at your own risk!). Nick On Thu, 2007-11-29 at 17:48 -0500, Paul Raines wrote: > Well, I don't know if there is a different video driver for you to > try. Frankly, I just think the video of a virtual machine is just > not going to cut it. For proper graphics, you really need a full, "real" > Linux machine. > > On Thu, 29 Nov 2007, Sarah Andersen wrote: > > > When I run dypyinfo, it lists both GLX and SGI-GLX. Does this mean that I > > still need to install a X11 video driver? Or is it a different problem? > > > > > > > > Thanks again, > > > > sarah > > > > > > > > From: Doug Greve [mailto:[EMAIL PROTECTED] > > Sent: Wednesday, November 28, 2007 3:26 PM > > To: Sarah Andersen > > Cc: 'Paul Raines'; freesurfer@nmr.mgh.harvard.edu > > Subject: Re: [Freesurfer] problem viewing in tksurfer > > > > > > > > It should have been xdpyinfo, not xdpyino (note the 'f'). > > > > Sarah Andersen wrote: > > > > Thank you. > > > > When I run 'xdpyino | grep GL' it says "xdpyino: Command not found" (this is > > in the tcsh shell) > > > > I am running it on VMware Player version 2.0.2 and using the FSL_vm5_32 > > virtual machine from the FSL website. If this helps and you can give me > > further instructions, I would greatly appreciate it. Otherwise, thank you > > for the help that you have already given. > > > > --sarah > > > > -----Original Message----- > > From: Paul Raines [mailto:[EMAIL PROTECTED] > > Sent: Wednesday, November 28, 2007 10:27 AM > > To: Sarah Andersen > > Cc: freesurfer@nmr.mgh.harvard.edu > > Subject: Re: [Freesurfer] problem viewing in tksurfer > > > > Your X server on your virtual Linux image does not appear to have GLX > > support. If you run 'xdpyino | grep GL' do you see GLX listed? > > > > If not, I am not sure what to say as I don't know what virtual machine > > program you are using. But you need to read up in its docs about > > how to properly install a X11 video driver for it. > > > > > > On Wed, 28 Nov 2007, Sarah Andersen wrote: > > > > > > > > Dear FreeSurfers, > > > > > > > > I am having a problem viewing in tksurfer: I can only see a sliver of the > > brain. This sliver will rotate and do everything that tksurfer is supposed > > to do, but I can't view any more of the brain than a tiny piece of the > > occipital lobe. I have tried this with several different files, and had > > > > > > the > > > > > > same issue for each of them. Tkmedit, on the other hand, works fine. > > > > > > > > I am using FreeSurfer stable release v4.0.1 on Windows Vista using a > > virtual machine. > > > > FREESURFER_HOME: /usr/local/freesurfer > > > > > > > > Build stamp: freesurfer-Linux-centos4-stable-pub-v4.0.1 > > > > > > > > RedHat release: CentOS release 5 (Final) > > > > > > > > Kernel info: Linux 2.6.18-8.1.15.el5 i686 > > > > > > > > I am working through the on-line tutorial and followed the directions to > > > > > > set > > > > > > my environment to /buckner_data/tutorial_subjs I also set SUBJECTS_DIR to > > $TUTORIAL_DATA . I am working in $SUBJECTS_DIR. The "which" command gives > > > > > > me > > > > > > /usr/local/freesurfer/bin/tksurfer > > > > > > > > I ran the command "tksurfer good_output lh inflated". The following is > > > > > > the > > > > > > resulting message. > > > > > > > > surfer: current subjects dir: > > > > > > > > /usr/local/freesurfer/subjects/freesurfer_tutorial/buckner_data/tutorial_sub > > > > > > js > > > > surfer: not in "scripts" dir ==> using cwd for session root > > > > surfer: session root data dir ($session) set to: > > > > surfer: > > > > > > > > /usr/local/freesurfer/subjects/freesurfer_tutorial/buckner_data/tutorial_sub > > > > > > js > > > > surfer: Reading header info from > > > > > > > > /usr/local/freesurfer/subjects/freesurfer_tutorial/buckner_data/tutorial_sub > > > > > > js/good_output/mri/T1.mgz > > > > surfer: vertices=125352, faces=250700 > > > > Loading /usr/local/freesurfer/surface_labels.txt > > > > surfer: ### redraw failed: no gl window open > > > > surfer: single buffered window > > > > surfer: using interface /usr/local/freesurfer/lib/tcl/tksurfer.tcl > > > > Reading /usr/local/freesurfer/lib/tcl/tkm_common.tcl > > > > Reading /usr/local/freesurfer/lib/tcl/tkm_wrappers.tcl > > > > Reading /usr/local/freesurfer/lib/tcl/fsgdfPlot.tcl > > > > Reading /usr/local/freesurfer/lib/tcl/tkUtils.tcl > > > > Successfully parsed tksurfer.tcl > > > > reading white matter vertex locations... > > > > > > > > In the email archives I have seen a response that mentioned the NVidia > > graphics card. I checked and my machine does have an NVidia graphics card. > > > > > > > > Thanks in advance for the help! > > > > Sarah > > > > > > > > > > > > Sarah Andersen > > > > Research Specialist > > > > Dept. of Neurology > > > > Dept. of Speech, Language, and Hearing Sciences > > > > (520) 621-9878 > > > > [EMAIL PROTECTED] > > > > > > > > > > > > > > > > > > > > > > > > > > > > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
