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:raines@nmr.mgh.harvard.edu] 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

sander@email.arizona.edu

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:greve@nmr.mgh.harvard.edu] 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:raines@nmr.mgh.harvard.edu] 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

sander@email.arizona.edu

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:greve@nmr.mgh.harvard.edu] 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:raines@nmr.mgh.harvard.edu] 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

sander@email.arizona.edu