I’m new to slicer so I apologize if this is a question driven by my ineptness. I am working on generating GPA/PCA visualizations, however when I try to generate a Mean shape visualization for the proximal and distal end of a bone (I have run into this problem running full bone analyses as well) the points will show up but the underlying model will not. I have tried running it multiple times, restarting Slicer, and updating to the latest version and reinstalling SlicerMorph. Is there something I can do to in order to get this to show up? Thanks!
Because there is no underlying model. GPA is an analysis that operates on the coordinates (landmarks) collected, not the models. You might want to read a review article about geometric morphometrics and how it is implemented.
However, you can still approximate this visualization by using a proxy. You need to select a sample, and their corresponding set of landmarks. See the tutorial: Tutorials/GPA_2 at main · SlicerMorph/Tutorials · GitHub
I’ve done this in the mean shape vis. section , picking a proxy sample from the dataset to upload, so it has all the correct points. I am thinking it may be an issue with the python code it is running or selecting the landmarks. In 3D model vis. it says I cannot use it due to the points not corresponding to the selected ones in the analysis. Is this because I am excluding points included in the proxy? Could I fix this by re-landmarking the scan used in the visualization?
Error is very clear. You do not have the exact same number of landmarks you used in your proxy and and the GPA analysis. They need to match (and be in exactly the same order).
If I understood correctly, you chose to exclude LMs in GPA. So, just make a copy of the LMs belonging to the proxy you want to use, then delete the ones you excluded in the gpa analysis and retry
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