Hi Ruopeng,
Sorry for the confusion in my initial post. The screen capture is actually a grab from one of the viewing windows in FREEVIEW; so I am actually not doing anything on the command line with tkmedit. In freeview, I am loading the original T1 volume and then loading the skin, outer skull, or inner skull surfaces from the watershed algorithm and they are obviously in different coordinates. As a matter of fact the exact same volume and surface boundary load up perfectly lined up in tkmedit. I am just wondering why the two programs do not behave in the same way, and how I can get them to behave similarly if possible. -Kambiz

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Kambiz Tavabi PhD
Institute for Learning & Brain Sciences
1715 Columbia Road N
Portage Bay Building
Box 357988
University of Washington
Seattle, WA 98195-7988
Tel: 206-685-6173
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On Wed, Oct 16, 2013 at 12:26 PM, Ruopeng Wang <rpwang@nmr.mgh.harvard.edu> wrote:
Would it be possible to send us the command line and the files that produces the screenshot?

Thanks,
Ruopeng

On Oct 16, 2013, at 2:28 PM, Kambiz Tavabi <ktavabi@uw.edu> wrote:

I would like to inspect the results of my surface boundary on the volume as per the approach in tkmedit. However in freeview the surface boundary and volume are not aligned in a common space. Why is that? How does one go about aligning the tkregRAS with the RAS? (those are apparently the two different coordinate systems according to the information panel). Thanks in advance.

<freeview.jpg>
------------------------------------------------------------
Kambiz Tavabi PhD
Institute for Learning & Brain Sciences
1715 Columbia Road N
Portage Bay Building
Box 357988
University of Washington
Seattle, WA 98195-7988
Tel: 206-685-6173
------------------------------------------------------------
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