On Wed, Apr 27, 2011 at 5:38 PM, Bruce Fischl
<fischl@nmr.mgh.harvard.edu> wrote:
so tksurfer has never worked for you on any dataset? Have you tried it on one of the ones that we distribute? If it hasn't worked, we'll need to know about your environment (what OS, what video card, are you running in a virtual box, etc...)
cheers
Bruce
On Wed, 27 Apr 2011, jim kroger wrote:
No, I don't see anything, just black.
Thanks,
Jim
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On Wed, Apr 27, 2011 at 4:52 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu>wrote:
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...
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On Mon, Apr 25, 2011 at 12:03 PM, Bruce Fischl
<fischl@nmr.mgh.harvard.edu>wrote:
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
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