----- Forwarded message from William Ary <[email protected]> -----
Date: Wed, 13 Mar 2013 17:25:31 -0400
From: William Ary <[email protected]>
Reply-To: William Ary <[email protected]>
Subject: Software for landmarks
To: [email protected]
Hello, everyone-
My lab is using segmented high-resolution CT images to generate models
for geometric morphometrics. I am having problems doing the following:
1. Finding homologous landmarks for smooth bones that have no
intersections with other bones. This forces us to use less repeatable
things like ridges and prominences that are harder to place landmarks
on in a consistent manner. I plan to use a sliding semilandmark method
to solve this problem, possibly a 3-D version as I have heard that the
Geomorph package in R handles 3D semilandmarks. Other packages like
SPHARM, MorphoJ, Morphologika etc. are in the running if they can
solve my landmark issue.
2. Picking a software for placing landmarks that works with our large
high-resolution models with millions of elements. I have sampled the
vast array of programs to some degree, having tried Paraview, Meshlab,
MiniMagics, and our segmentation software, Analyze. I have encountered
problems with all of them as follows:
Paraview- Doesn't record points, cannot find way to place multiple
points, doesn't record Cartesian 3-space coordinates.
Meshlab- Looked great but bogs down or crashes when placing points,
likely due to model complexity
MiniMagics- Could not figure out how to place multiple landmarks/model
size issues. Investigating if MIMICS is better.
Analyze- Points disappear on the topology of the model and are hard to
see once the model is moved.
After all this, I welcome any suggestions you may have on which
programs allow picking landmarks/semilandmarks on high resolution
models and how to generate landmarks on our smooth bones. We are
hoping there is an alternative to coarsening our models. I would be
especially grateful to know how to go about placing a series of
sliding semilandmarks. I have read some papers on this, but suggested
reading is always appreciated!
Many thanks!
Will Ary
Master's candidate
San Diego State University
[email protected]
----- End forwarded message -----
