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 accomplishing this. Save the wm volume, then rerun the fill and inflation as usual.

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 Jan 2005, Joongnam Yang wrote:

...

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?

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