On Dec 20, 2006, at 1:04 PM, Julia Molony wrote:

Donna,

I have been writing to you about spherical registration. I am working on implementing a landmark based registration approach and I want to use Caret to learn about the currently accepted landmark placements and deformation process. Using the tutorials, I have successfully drawn the landmarks and run the spherical deformation. During the deformation process, I get two error messages but both seem resolved.

“INFO: Border Link (0,6) in Landmark CentralSulcus does not project to a tile and has been discarded.”
“Color ??? Specified multiple times with different color components.”

Are either of these messages a problem? How can I prevent these errors?

Neither of those messages are a problem. The first has to do with projection of borders. There are instances when a border point fails to project into a surface triangle so the projection process discards the point. The second message indicates that the color named "???" (the default color) was defined multiple times with different color components. You can ignore these informational messages. However, if you were to receive more than a few of the border link message that would be a concern.

Also, I’m having trouble interpreting the deformation files and viewing the results. Why are deformed files created in both the individual’s directory and the atlas directory? Is the spec file in the atlas directory the one I want to use?

By default, the deformation process deforms data both ways, from individual to atlas and from atlas to individual. You can disable the atlas-to-individual deformation by unchecking the "Deform Indiv to Atlas and Atlas to Individual" box on the Spherical Surface Deformation Dialog's Deformation tab. The deformed spec file in the ATLAS directory list the original atlas files and the deformed individual files.

How do I know if the landmarks reach their target? Can I look at the deformed individual sphere with both the deformed landmarks I created and the original atlas landmarks, and compare these two sets of borders?

Yes. Start Caret and open the "deformed" spec file in the atlas directory. In the border/border projection files section of the Spec File Dialog will be the atlas' LANDMARK border file and the individual's "deformed" LANDMARK border file. Choose both of the files and you will see the alignment of the atlas borders and the individual's deformed borders.

What are the difference between border projection files and border files? I only have a border file for the atlas sphere. I read a note on the message board about saving the border projection files relative to the spherical surface, but this is not directed in the tutorials. Is this a step that generally applies to surface deformations?
What values do the columns of the border projection files represent?

Border files contain a three-dimensional coordinate (XYZ) for each point in a border, and, as a result, the border is for a specific surface (fiducial, spherical, flat). The border projection files use barycentric coordinates (http://mathworld.wolfram.com/ BarycentricCoordinates.html) for each of the coordinates. Essentially, in a border projection file, the border points are attached to a relative position on a surface triangle. As the triangle moves in space, the border point will follow the triangle. As a result, the border projection may be displayed on a surface and any of its geometrically altered versions. The border projection file is described at "http://brainmap.wustl.edu/caret/caret5.5_help/ file_formats/file_formats.html#borderProjection".

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John Harwell
[EMAIL PROTECTED]
314-362-3467

Department of Anatomy and Neurobiology
Washington University School of Medicine
660 S. Euclid Ave.    Box 8108
St. Louis, MO 63110   USA


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