On Dec 20, 2006, at 1:04 PM, Julia Molony wrote:
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.
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
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
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?
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/
What values do the columns of the border projection files represent?
Department of Anatomy and Neurobiology
Washington University School of Medicine
660 S. Euclid Ave. Box 8108
St. Louis, MO 63110 USA