tksurfer display broken: fixed - Freesurfer

30 May 2008


      Not exactly sure how or what happened...but did manage to "fix" my tksurfer display problem.
Since others on the list had reported similar problems, I thought I'd post what I did to "fix" the problem. Since I'm not a Linux guru, my "fix" is probably just a "bandaid"...but it did work...and hopefully the info provides some assistance to others.
Just to note the following particulars of my system:
RHEL5 (DELL Precision 690n box went live April 16, 2008)
Linux_x86_64 architecture
2 kernels: 
drwxr-xr-x 18 root root 4096 May  9 13:50 2.6.18-53.1.19.el5-x86_64
drwxr-xr-x 18 root root 4096 May 27 15:02 2.6.18-92.el5-x86_64
NVIDIA Quadro Fx 3450/4000 SDI
Driver Version 1.0-9746
"Friendly" software also installed on the same box=fslv404
MATLAB r2008a is also installed (currently running -lgi on bert...I'll update on the outcome of this "friendliness" test)
As of yesterday, had several possible scenarios outlined:
1) rpm -e dell-nvidia-rhel5-169.12-1dkms.x86_64.rpm
   rpm -ivh dell-nvidia-9746-7dkms.x86_64.rpm
--> should return to a well-behaved (albeit "older") nvidia
driver...same as "out of the box"
2) restore original "out of the box" settings for entire system via
/usr/var/dell/reinstall.sh
--> should return ALL system settings to original "out of the box"...good for freesurfer and fsl apps but not so good for matlab...
3) boot into older kernel (I apparently have a total of 2 listed in
/usr/src/kernels)
[root@localhost kernels]# ls -l
total 16
drwxr-xr-x 18 root root 4096 May  9 13:50 2.6.18-53.1.19.el5-x86_64
drwxr-xr-x 18 root root 4096 May 27 15:02 2.6.18-92.el5-x86_64
I attempted (1) first. However, the driver was not well-behaved for bert (tkmedit or tksurfer).
I attempted (3) second. However, no change in behavior.
While tarballing to prepare for (3)...since everything worked perfectly fine right out of the box -- before Matlab and before any package updates...I found my *original* /etc/X11/xorg.conf file (from April 16) and cp it into /etc/X11/xorg.conf & rebooted.
RESULTS:
Was *very* happy to see tksurfer & tkmedit behave properly for bert.
Proper behavior for tksurfer & tkmedit was observed in both kernels (after the xorg.conf file replacement).
Still waiting to see if matlab behaves for bert's -lgi.
I diff'd the "original" xorg.conf with the "broken" one and the following lines were returned:
Hope this helps others find their "bandaid" solution to get them up and running again.
Cheers,
Jenifer
[root@localhost X11]# diff xorg.conf.backup.OLD xorg.conf.backup
1,4c1,2
< 
< # nvidia-xconfig: X configuration file generated by nvidia-xconfig
< # nvidia-xconfig:  version 1.0  (buildmeister@builder26)  Fri Dec 15 10:40:27 PST 2006
< # Xorg configuration created by system-config-display
---
...
# nvidia-settings: X configuration file generated by nvidia-settings
# nvidia-settings:  version 1.0  (buildmeister@builder26)  Fri Dec 15 10:40:57 PST 2006
7,10c5,8
<       Identifier     "Default Layout"
<       Screen      0  "Screen0" 0 0
<       InputDevice    "Mouse0" "CorePointer"
<       InputDevice    "Keyboard0" "CoreKeyboard"
---
...
Identifier     "Layout0"
Screen      0  "Screen0" 0 0
InputDevice    "Keyboard0" "CoreKeyboard"
InputDevice    "Mouse0" "CorePointer"

13a12,13
...
RgbPath         "/usr/lib64/X11/rgb"
FontPath        "unix/:7100"

17c17,21
<       Load  "glx"
---
...
Load           "dbe"
Load           "extmod"
Load           "type1"
Load           "freetype"
Load           "glx"

21c25
<       Option      "AllowMouseOpenFail" "yes"
---
...
Option         "Xinerama" "0"

25d28
< 
27,32c30,35
<       Identifier  "Mouse0"
<       Driver      "mouse"
<       Option      "Protocol" "auto"
<       Option      "Device" "/dev/input/mice"
<       Option      "Emulate3Buttons" "no"
<       Option      "ZAxisMapping" "4 5"
---
...
Identifier     "Mouse0"
Driver         "mouse"
Option         "Protocol" "auto"
Option         "Device" "/dev/input/mice"
Option         "Emulate3Buttons" "no"
Option         "ZAxisMapping" "4 5"

36,39c39,43
<       Identifier  "Keyboard0"
<       Driver      "kbd"
<       Option      "XkbModel" "pc105"
<       Option      "XkbLayout" "us"
---
...
# generated from data in "/etc/sysconfig/keyboard"
Identifier     "Keyboard0"
Driver         "kbd"
Option         "XkbLayout" "us"
Option         "XkbModel" "pc105"

43,49c47,53
<       Identifier   "Monitor0"
<       VendorName   "Unknown"
<       ModelName    "Unknown"
<  ### Comment all HorizSync and VertSync values to use DDC:
<       HorizSync    30.0 - 110.0
<       VertRefresh  50.0 - 150.0
<       Option      "DPMS"
---
...
# HorizSync source: edid, VertRefresh source: edid
Identifier     "Monitor0"
VendorName     "Unknown"
ModelName      "DELL 2007WFP"
HorizSync       30.0 - 83.0
VertRefresh     56.0 - 76.0
Option         "DPMS"

53,55c57,60
<       Identifier  "Videocard0"
<       Driver      "nvidia"
<       BoardName   "NVIDIA PCI-Express Quadro FX 3450"
---
...
Identifier     "Videocard0"
Driver         "nvidia"
VendorName     "NVIDIA Corporation"
BoardName      "Quadro FX 3450/4000 SDI"

59,71c64,72
<       Identifier "Screen0"
<       Device     "Videocard0"
<       Monitor    "Monitor0"
<       DefaultDepth     16
<       SubSection "Display"
<               Viewport   0 0
<               Depth     24
<       EndSubSection
<       SubSection "Display"
<               Viewport   0 0
<               Depth     16
<               Modes    "1024x768" "800x600" "640x480"
<       EndSubSection
---
...
Identifier     "Screen0"
Device         "Videocard0"
Monitor        "Monitor0"
DefaultDepth    16
Option         "metamodes" "1024x768 +0+0; 1600x1024 +0+0; 800x600 +0+0; 640x480 +0+0; 1280x1024 +0+0"
SubSection     "Display"
    Depth       16
    Modes      "1600x1200" "1280x1024" "1024x768" "800x600" "640x480"
EndSubSection

[root@localhost X11]#