I successfully completed the semi-landmark acquisition process on a sample model using the PseudoLMGenerator plugin. However, I only performed it for one sample.
Now, I want to apply the same number and equally spaced semi-landmarks to all my other models. For PCA analysis, the coordinates of all models must be consistent with each other.
How can I apply this process to all models in the most accurate and automated way?
The idea behind PseudoLMGenerator is to use one sample as a representative of a population of samples to represent their geometry and then transfer this template set of points onto new samples by other means. You can do this in two ways:
If you have set of sparse anatomical landmarks on all your samples, you can use SlicerMorph→Utilities→ProjectSemiLMs, which uses a combination of TPS deformation and point projection to move points to the target models. Note that if your manual landmarks are too sparse you may not get good results.
You can use ALPACA for a totally automated process: Tutorials/ALPACA at main · SlicerMorph/Tutorials · GitHub . It is default settings are usually OK for most samples, but you do want to experiment to improve the deformation and point correspondences.