Hi all,
I'm having trouble using freesurfer's tksurfer program (I only get a sliver of the brain). Here is the error info I get:
[ghidra: subjects]$ tksurfer 77059 lh pial
surfer: current subjects dir: /home/freesurfer/subjects
surfer: not in "scripts" dir ==> using cwd for session root
surfer: session root data dir ($session) set to:
surfer: /home/freesurfer/subjects
surfer: Reading header info from /home/freesurfer/subjects/77059/mri/T1.mgz
surfer: vertices=184362, faces=368720
Loading /home/freesurfer/surface_labels.txt
surfer: ### redraw failed: no gl window open
surfer: single buffered window
surfer: tkoInitWindow(77059)
surfer: using interface /home/freesurfer/lib/tcl/tksurfer.tcl
Reading /home/freesurfer/lib/tcl/tkm_common.tcl
Reading /home/freesurfer/lib/tcl/tkm_wrappers.tcl
Reading /home/freesurfer/lib/tcl/fsgdfPlot.tcl
Reading /home/freesurfer/lib/tcl/tkUtils.tcl
Successfully parsed tksurfer.tcl
reading white matter vertex locations...
The driver info (from /etc/X11/xorg.conf) is:
Section "Device"
BoardName "ES1000 515E"
BusID "14:13:0"
Driver "radeon"
Identifier "Device[0]"
Option "GARTSize" "32"
Option "usevnc" "yes"
Section "DRI"
Group "video"
Mode 0660
EndSection
I'm have an onboard ATI ES1000 515E graphics chip.
Any ideas??
Matthew J. Hoptman, PhD Research Scientist V Nathan S. Kline Institute for Psychiatric Research
Research Associate Professor in Psychiatry NYU School of Medicine
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Hi Matthew,
This is the typical symptom of either not having the right OpenGL libraries and/or not having a driver that supports the 3d stuff. That particular chip (ES1000) seems to be an orphan as far as Linux support goes - I haven't found a driver installation package on the ATI/AMD site that purports to support it. I'd be interested in hearing which linux distro you are using and which flavor radeon driver you're using.
Is this a Dell PowerEdge server? I have a bunch of them that I can't run tksurfer on for the same reason. So far I've been using a workstation that has an Nvidia card, which works properly with the NVidia proprietary driver installed.
mjp
On Sep 8, 2008, at 9:14 AM, Hoptman, Matthew wrote:
Hi all, I’m having trouble using freesurfer’s tksurfer program (I only get a sliver of the brain). Here is the error info I get:
[ghidra: subjects]$ tksurfer 77059 lh pial surfer: current subjects dir: /home/freesurfer/subjects surfer: not in "scripts" dir ==> using cwd for session root surfer: session root data dir ($session) set to: surfer: /home/freesurfer/subjects surfer: Reading header info from /home/freesurfer/subjects/77059/mri/ T1.mgz surfer: vertices=184362, faces=368720 Loading /home/freesurfer/surface_labels.txt surfer: ### redraw failed: no gl window open surfer: single buffered window surfer: tkoInitWindow(77059) surfer: using interface /home/freesurfer/lib/tcl/tksurfer.tcl Reading /home/freesurfer/lib/tcl/tkm_common.tcl Reading /home/freesurfer/lib/tcl/tkm_wrappers.tcl Reading /home/freesurfer/lib/tcl/fsgdfPlot.tcl Reading /home/freesurfer/lib/tcl/tkUtils.tcl Successfully parsed tksurfer.tcl reading white matter vertex locations...
The driver info (from /etc/X11/xorg.conf) is: Section "Device" BoardName "ES1000 515E" BusID "14:13:0" Driver "radeon" Identifier "Device[0]" Option "GARTSize" "32" Option "usevnc" "yes"
Section "DRI" Group "video" Mode 0660 EndSection
I’m have an onboard ATI ES1000 515E graphics chip.
Any ideas?? Matthew J. Hoptman, PhD Research Scientist V Nathan S. Kline Institute for Psychiatric Research Research Associate Professor in Psychiatry NYU School of Medicine
IMPORTANT NOTICE: This e-mail is meant only for the use of the intended recipient. It may contain confidential information which is legally privileged or otherwise protected by law. If you received this e-mail in error or from someone who was not authorized to send it to you, you are strictly prohibited from reviewing, using, disseminating, distributing or copying the e- mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for your cooperation.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi all,
FYI, this same problem has been bugging me for several months. Most ATI chipsets have a nice driver installer bundle that, once installed, will let you run tksurfer without a problem. However, this particular chipset, the ES1000, which is the chipset on Dell PowerEdge servers, is unsupported and seems to have been abandoned by ATI/AMD/whoever they are this week.
If you happen to be unlucky enough to have Dell PowerEdge servers with this chipset and the need to run tksurfer, you're out of luck, until you put a slightly "better" graphics card in. I just managed to install an nVidia 8400GS (the x1 PCI-e version - the poweredge PCI-e bus is x8, which means it won't work with any of the most recent cards, but will work with slightly older x1 cards) and tksurfer works fine now. I can provide the gory details if you're in this boat.
mjp
On Sep 8, 2008, at 9:14 AM, Hoptman, Matthew wrote:
Hi all, I’m having trouble using freesurfer’s tksurfer program (I only get a sliver of the brain). Here is the error info I get:
[ghidra: subjects]$ tksurfer 77059 lh pial surfer: current subjects dir: /home/freesurfer/subjects surfer: not in "scripts" dir ==> using cwd for session root surfer: session root data dir ($session) set to: surfer: /home/freesurfer/subjects surfer: Reading header info from /home/freesurfer/subjects/77059/mri/ T1.mgz surfer: vertices=184362, faces=368720 Loading /home/freesurfer/surface_labels.txt surfer: ### redraw failed: no gl window open surfer: single buffered window surfer: tkoInitWindow(77059) surfer: using interface /home/freesurfer/lib/tcl/tksurfer.tcl Reading /home/freesurfer/lib/tcl/tkm_common.tcl Reading /home/freesurfer/lib/tcl/tkm_wrappers.tcl Reading /home/freesurfer/lib/tcl/fsgdfPlot.tcl Reading /home/freesurfer/lib/tcl/tkUtils.tcl Successfully parsed tksurfer.tcl reading white matter vertex locations...
The driver info (from /etc/X11/xorg.conf) is: Section "Device" BoardName "ES1000 515E" BusID "14:13:0" Driver "radeon" Identifier "Device[0]" Option "GARTSize" "32" Option "usevnc" "yes"
Section "DRI" Group "video" Mode 0660 EndSection
I’m have an onboard ATI ES1000 515E graphics chip.
Any ideas?? Matthew J. Hoptman, PhD Research Scientist V Nathan S. Kline Institute for Psychiatric Research Research Associate Professor in Psychiatry NYU School of Medicine
IMPORTANT NOTICE: This e-mail is meant only for the use of the intended recipient. It may contain confidential information which is legally privileged or otherwise protected by law. If you received this e-mail in error or from someone who was not authorized to send it to you, you are strictly prohibited from reviewing, using, disseminating, distributing or copying the e- mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for your cooperation.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Hoptman, Matthew -
Mark J. Pearrow