Dear Surfers,
I am trying to launch tksurfer/tkmedit in the stable 5_0_0 environment in the Martinos network, but this fails with glut segmentation errors. FS version 6 tksurfer works on the same machine and data, but I need to create some figures that match version 5. We
already tried with a different user and a few years older linux box, same issues. Any suggestions would be greatly appreciated!
For example, is there a variable that we could set to point to an older OpenGL version?
(My LD_LIBRARY_PATH has not been set, and my PATH does not include anything pointing to /usr/lib or /usr/lib64)
Details:
on machine rukki (locally at terminal):
setenv USE_STABLE_5_0_0
source /usr/local/freesurfer/nmr-stable50-env
cd $MY_SUBJECTS_DIR
Checking version:
freesurfer
...
You are running this version of FreeSurfer:
freesurfer-Linux-centos4_x86_64-stable-v5.0.0-20110319
echo $FREESURFER_HOME
/usr/local/freesurfer/stable5_0_0
cp -r $FREESURFER_HOME/subjects/fsaverage $MY_SUBJECTS_DIR/.
chmod -R 777 fsaverage
[rukki:sphsm10-ffx] (nmr-stable5.0-env) tksurfer fsaverage lh inflated
subject is fsaverage
hemi is lh
surface is inflated
surfer: current subjects dir: <$MY_SUBJECTS_DIR>
surfer: not in "scripts" dir ==> using cwd for session root
surfer: session root data dir ($session) set to:
surfer: <$MY_SUBJECTS_DIR>
Reading image info <$MY_SUBJECTS_DIR>/fsaverage)
Reading <$MY_SUBJECTS_DIR>/fsaverage/mri/orig.mgz
surfer: Reading header info from /<$MY_SUBJECTS_DIR>/fsaverage/mri/orig.mgz
[rukki:sphsm10-ffx] (nmr-stable5.0-env)
... after which there is no screen output. The file xdebug_tksurfer was generated:
[rukki:sphsm10-ffx] (nmr-stable5.0-env) more .xdebug_tksurfer
Segfault
Initializing glut
xDebug stack (length: 1)
00:
00: Initializing glut
Segfault
Initializing glut
[rukki:sphsm10-ffx] (nmr-stable5.0-env)
[rukki:sphsm10-ffx] (nmr-stable5.0-env) echo $DISPLAY
:3
setenv DISPLAY :0 does not fix the issue (results in GLUT: Fatal Error in tksurfer.bin: could not open display: 0)
I also tried fsaverage4, fsaverage5, fsaverage6, and bert, copied from the same folder into my $SUBJECTS_DIR, same result.
The issue is not specific to tksurfer:
tkmedit -f fsaverage/mri/T1.mgz
===================================
ERROR: A segfault has occurred. This is not your fault,
: but is most likely an unrecoverable error and has
: made the program unstable.
:
: Please send the contents of the file .xdebug_tkmedit
: that should be in this directory to freesurfer@nmr.mgh.harvard.edu
:
: Now exiting...
:
[rukki:sphsm10-ffx] (nmr-stable5.0-env)
more .xdebug_tkmedit
tkmedit started: Wed Aug 7 16:54:21 2024
tkmedit.bin -f fsaverage/mri/T1.mgz
$Id: tkmedit.c,v 1.341.2.1 2010/08/04 20:47:28 greve Exp $ $Name: stable5_0_0 $
Set user home dir to ($MY_SUBJECTS_DIR)
Set subject home dir to fsaverage/mri/T1.mgz
Segfault
Importing volume with MRIread
xDebug stack (length: 5)
04: Volm_ImportData( this=0x3447db0, isSource=./fsaverage/mri/T1.mgz )
04: Importing volume with MRIread
03: LoadVolume( iType=0, isName=fsaverage/mri/T1.mgz, ibConform = 0 )
03: Reading data into volume
02: ParseCmdLineArgs( argc=3, argv=tkmedit.bin )
02: Loading volume fsaverage/mri/T1.mgz
01: main()
01: Parsing command line arguments
00:
00:
[rukki:sphsm10-ffx] (nmr-stable5.0-env)
My OpenGL version:
[rukki:sphsm10-ffx] (nmr-stable5.0-env) glxinfo | grep "OpenGL version"
OpenGL version string: 4.6.0 NVIDIA 550.54.14
The other machine we tried had OpenGL version 4.6.0 NVIDIA 535.54.03
Thank you!
Best regards,
Tommi
---
Tommi Raij, MD, PhD
Director, TMS Clinical Research
MGH/MIT Athinoula A. Martinos Center for Biomedical Imaging
Bldg 149, 13th st
Charlestown, MA 02129