Or if all else seems to fail and you have time constraints, you can edit
the pons out manually in the wm volume. Use a large radius for the
brush size (about a 3 or 4) and use a square brush, then just erase
across the pons, where the cutting plane should have been. Coronal is
the best view for a
did you run the MNI talairaching? Did it work? If not, you need to use
volume scanner coords as input (you can turn them on under
view->information). Make sure it is a point in which the pons appears
disconnected in a horizontal view, and superior to the cerebellar
peduncles.
Bruce
On Wed, 12
Hi,
I collected new anatomical data with isometric voxels.
When I ran "create surface," the pons is not being removed.
I tried many different coordinates for the pons (either Volume Index or
Talairach), but the pons is still not being cut out.
Any suggestions?
Thanks
Nam.
__
sorry, I don't understand. What do you have to rotate/translate? And what
are R and C? And why do you need them to be symmetrical in the first place?
Bruce
On Wed, 12 Jan 2005, XJ Kang wrote:
Hi,
When I display the registered spheres of left and right hemispheres, they
look more or less symmetri
Hi,
When I display the registered spheres of left and right hemispheres,
they look more or less symmetrical in their default positions in the
tksurfer window. But when I convert the ?h.sphere.reg to ascii format,
extract the X, Y, Z, C values, convert them to THETA, PHI, R, C values
and display
there needs to be an xform line in the COR-.info file of the volume you
loaded that points to the talairach.xfm file
cheers,
Bruce
On Wed, 12 Jan 2005, Joongnam
Yang wrote:
Hi,
TkMedit doesn't show talairach coordinates.
I ran talairach2 -s subjid, and clicked (View->Information->talairach), bu
Hi,
TkMedit doesn't show talairach coordinates.
I ran talairach2 -s subjid, and clicked (View->Information->talairach), but
still talairach coords row comes out blank in TkMedit, no numbers, just
0,0,0.
Would someone suggest anything to make the tal coords available o nTkMedit?
Thanks.
Nam.
_
[Brian]
you can do a lot more than that with a -tcl flag, but here is what
one would need to look like for loading curvature (binary):
read_binary_curv
Minimally, you would need:
open_window
read_binary_curv
redraw
--
Kevin Teich
___
Freesurfer mailing
you can do a lot more than that with a -tcl flag, but here is what one
would need to look like for loading curvature (binary):
read_binary_curv
i've included some info you can use to load tkmedit with both volumes (wm
and T1) and both surfaces (rh and lh). also, it will load the talairach
and d
On Wed, 12 Jan 2005, Goldman, Aaron (NIH/NIMH) shaped the electrons to say:
> Hi, I'm writing a script to make manual editing a bit more convenient, and
> want to call tksurfer and tkmedit with all the parameters of csurf's "Edit
> Segmentation" option, and using T1 as the aux volume. Right now, I
Hi, I'm writing a script to make manual editing
a bit more convenient, and want to call tksurfer and tkmedit with all the parameters
of csurf's "Edit Segmentation" option, and using T1 as the
aux volume. Right now, I have:
tksurfer $s $h inflated &
tkmedit $s wm $h.orig -aux T1
How
Hi,
I am having trouble removing the pons with recon-all -stage1 -pons-xyz.
I've tried five pons coords, unsuccessfully.
When you move the mouse location in the sagittal, horizontal, and coronal
images,
the slice numbers change. When I get the talairach coords for the pons,
should the slice numbe
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