for cc find a slice in which the callosum is disconnected in a saggital view.

for pons find a slice above the cerebellar peduncles in which the brainstem is disconnected in a horizontal view.

And make sure to use "Volume RAS" coords (or Talairach coords if you have them). The manual is incorrect!

Bruce

On Tue, 4 Jan 2005, Joongnam Yang wrote:

Hi all,

recon-all -stage1 gives me an error on "could not find corpus callosum". So, I used Tkmedit to find xyz talairach coordinates of the two structures and ran stage1 again, many times with different coordinates. "surfaces" are twisted and "filled" volume didn't look like a brain.

How can I find correct coordinates? The way I did: I loaded T1 volume and aux volume and picked the approximate center of each structure.

Any wise words? Thanks.

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