I would like to use the semi-automated landmarking approach ALPACA to auto-landmark clavicles.
However, I seem to be unable to find suitable parameters for the auto-landmarking process, and I was hoping you could point me in the right direction. As far as I can tell the surface alignment operates well. However, the output of semilandmarks is not comprehensible. If I run the algorithm with the default settings, all landmarks of all surfaces culminate in one point, i.e. the output.fcsv files contain replicates of one point in 3D space.
When I check the box ‘Skip projection’, all output.fcsv files contain different landmark arrays, as one would expect. I can read those with the read.fcsv() function from the Morpho package in R, but when I perform a Procrustes fit via ProcSym(), all landmark configurations are identical. The same happens when I use the GPA module in Slicer - all specimens share one set of Procrustes coordinates.
I was hoping that this is a common mistake in my approach of the program. I looked through the Slicer Forum and FAQ, and there seems to be nothing remotely similar to my issue. I would be grateful for any help you can offer.
How do I register those landmarks in a way that they actually differ?