Dear FreeSurfer community,
I have a newly installed version of FreeSurfer:
freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
running on Red Hat Enterprise Linux 6.4. When I load a surface in tksurfer, eg:
tksurfer fsaverage5 lh smoothwm
the wrong hemisphere loads and the surface is upside down (see attached image). Further, when I try to select a vertex on the surface, there is no alignment between the pointer and the vertex ultimately selected. For instance, as seen in the attached image, when I click on STG, the vertex highlighted is in the central sulcus. Terminal output is below. I get similar behavior for other surfaces and other pre-installed subjects. The only error message I am getting is:
libGL error: failed to load driver: nouveau libGL error: Try again with LIBGL_DEBUG=verbose for more details.
Nouveau appears to be installed:
[31] /sbin/lspci -v -s `/sbin/lspci | awk '/VGA/{print $1}'` 05:00.0 VGA compatible controller: NVIDIA Corporation GF116 [GeForce GTX 550 Ti] (rev a1) (prog-if 00 [VGA controller]) Subsystem: eVga.com. Corp. Device 1559 Flags: bus master, fast devsel, latency 0, IRQ 30 Memory at f8000000 (32-bit, non-prefetchable) [size=32M] Memory at d8000000 (64-bit, prefetchable) [size=128M] Memory at d4000000 (64-bit, prefetchable) [size=64M] I/O ports at ec00 [size=128] Expansion ROM at f7f80000 [disabled] [size=512K] Capabilities: <access denied> Kernel driver in use: nouveau Kernel modules: nouveau, nvidiafb
Any thoughts on what else I should check or what might be going wrong?
cheers Iain
[20] tksurfer fsaverage5 lh smoothwm subject is fsaverage5 hemi is lh surface is smoothwm surfer: current subjects dir: /home/dewitt/mrdata/freesurfer/subjects surfer: not in "scripts" dir ==> using cwd for session root surfer: session root data dir ($session) set to: surfer: /home/dewitt checking for nofix files in 'smoothwm' Reading image info (/home/dewitt/mrdata/freesurfer/subjects/fsaverage5) Reading /home/dewitt/mrdata/freesurfer/subjects/fsaverage5/mri/orig.mgz surfer: Reading header info from /home/dewitt/mrdata/freesurfer/subjects/fsaverage5/mri/orig.mgz surfer: vertices=10242, faces=20480 surfer: single buffered window surfer: tkoInitWindow(fsaverage5) libGL error: failed to load driver: nouveau libGL error: Try again with LIBGL_DEBUG=verbose for more details. surfer: using interface /home/dewitt/apps/freesurfer/tktools/tksurfer.tcl Reading /home/dewitt/apps/freesurfer/tktools/tkm_common.tcl Reading /home/dewitt/apps/freesurfer/tktools/tkm_wrappers.tcl Reading /home/dewitt/apps/freesurfer/lib/tcl/fsgdfPlot.tcl Reading /home/dewitt/apps/freesurfer/tktools/tkUtils.tcl Successfully parsed tksurfer.tcl reading white matter vertex locations... % ----------------------------------- selected vertex 6123 out of 10242 current -47.84 -8.78 45.57 orig -49.76 -9.85 46.75 pial 0.00 0.00 0.00 white -49.73 -9.60 46.90 inflated 0.00 0.00 0.00 normals -0.68 -0.66 0.32 nneighbors 6 ripflag 0 surfer: dmin=1.2521, vno=6123, x=-47.8367, y=-8.7830, z=45.5727 surfer: curv=0.000000, fs=0.000000 surfer: val=0.000000, val2=0.000000 surfer: amp=0.000000, angle=0.000000 deg (0.000000) surfer: vertex 6123 marked (curv=0.000000, stat=0.000000) x = (-47.8, -8.8, 45.6), n = (-0.7, -0.7, 0.3).
