Re: [Freesurfer] two questions

2005-01-12 Thread evelina
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

Re: [Freesurfer] two questions

2005-01-12 Thread Bruce Fischl
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

Re: [Freesurfer] two questions

2005-01-12 Thread Joongnam Yang
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. __

Re: [Freesurfer] Question about symmetry of registered spheres

2005-01-12 Thread Bruce Fischl
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

[Freesurfer] Question about symmetry of registered spheres

2005-01-12 Thread XJ Kang
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

Re: [Freesurfer] talairach coords on TkMedit

2005-01-12 Thread Bruce Fischl
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

[Freesurfer] talairach coords on TkMedit

2005-01-12 Thread Joongnam Yang
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. _

Re: [Freesurfer] loading curvature

2005-01-12 Thread Kevin Teich
[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

Re: [Freesurfer] loading curvature

2005-01-12 Thread Brian T. Quinn
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

Re: [Freesurfer] loading curvature

2005-01-12 Thread Brendan Connell
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

[Freesurfer] loading curvature

2005-01-12 Thread Goldman, Aaron (NIH/NIMH)
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

Re: [Freesurfer] normalization failed

2005-01-12 Thread Joongnam Yang
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