No, I don't see anything, just black. Thanks, Jim
-- Cell: 575-571-8274 Email: jkk251@gmail.com
On Wed, Apr 27, 2011 at 4:52 PM, Bruce Fischl fischl@nmr.mgh.harvard.eduwrote:
and do you see a hemisphere properly rendered or not?
On Wed, 27 Apr 2011, jim kroger wrote:
Hi Bruce, this is my first attempt to see something in tksurfer. It's a
step in the making edits to white matter. I will go through the tksurfer tutorial, but I noticed that when I start tksurfer, there may be an error. Here's the output, think this might be it? (I am using red hat on a 32 gig Ram pretty fast machine, the drivers should be updated regularly along with all other updates)
tksurfer heinrick rh inflated subject is heinrick hemi is rh surface is inflated surfer: current subjects dir: /usr/local/freesurfer/subjects/ surfer: not in "scripts" dir ==> using cwd for session root surfer: session root data dir ($session) set to: surfer: /usr/local/freesurfer/subjects Reading image info (/usr/local/freesurfer/subjects//heinrick) Reading /usr/local/freesurfer/subjects//heinrick/mri/orig.mgz surfer: Reading header info from /usr/local/freesurfer/subjects//heinrick/mri/orig.mgz surfer: vertices=159373, faces=318742
mrisReadTriangleFile(/usr/local/freesurfer/subjects//heinrick/surf/rh.sphere.reg): surface doesn't match /usr/local/freesurfer/subjects//heinrick/surf/rh.inflated
mrisReadTriangleFile failed.
surfer: single buffered window surfer: tkoInitWindow(heinrick) 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...
-- Cell: 575-571-8274 Email: jkk251@gmail.com
On Mon, Apr 25, 2011 at 12:03 PM, Bruce Fischl fischl@nmr.mgh.harvard.eduwrote:
is this in tksurfer? There have been issues with video card drivers, so
make sure your's are up to date. Have you been able to view any surfaces in tksurfer?
On Mon, 25 Apr 2011, jim kroger wrote:
HI Bruce, thanks so much for the reply. All of the surfaces we have needed
to view to fix the Talairach (was OK), white matter, etc., have been there. It's only when I tried to look at the inflated brain during the WhiteMatterEdits step that something seemed to be missing. I will look at tkmedit and tkregister2 documentation to see if there are different ways to look for the inflated brain, but if anybody has suggestions on why I'm seeing only a tiny fraction it would be great. It sort of seems like a thresholding issue, but I have no idea why on little 2 square inch or so section of cortex is there and the rest is not, or I can't see it. The edges of what I see are very sharp and defined.
Jim
On Sat, Apr 23, 2011 at 9:16 PM, Bruce Fischl < fischl@nmr.mgh.harvard.edu
wrote:
Hi Jim
Have you been able to view other surfaces in tksurfer? The situation you describe sounds normal except for the display issue (e.g. The thalamus should be interior to the white surface) Cheers Bruce
On Apr 22, 2011, at 12:28 PM, jim kroger jkk251@gmail.com wrote:
Hello, I am following the sequence in the "FreeSurfer Troubleshooting Reconstruction Work Flow" instructions, and am at step 8, FsTutorial/WhiteMatterEdits. It looks like the thalamus and corpus callosum are included as white matter, and the pial surface surrounds some subcortical structures. Assuming this is not correct, I decided to look at the inflated surface as suggested in the referenced page " Making Edits to the White Matter." Unfortunately when I issue:
tksurfer wm1_edits_before rh inflated
I only see what looks like a very small fraction of an egg shell for the rh, and nothing for lh. Can I check somehow to see why I have almost no inflated brain?
Thanks, Jim
-- Cell: 575-571-8274 Email: jkk251@gmail.comjkk251@gmail.com
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