I’m working some some sclerites that lack obvious landmarks that lend themselves to conventional landmarking and want to attempt to use the ALPACA module. I have surface meshes (.ply), with segmentations performed in a different program. I’ve used PseudoLMGenerator on my template specimen, using the ellipse geometry and the midline/sagittal plane. I’m not as concerned with the number of landmarks for now - I just want it working before making those decisions. I will note that, as it is bilaterally symmetrical, I am following a protocol for other sclerites where I perform a GPA on all points then use only half for downstream analyses to avoid midline artifacts. In the image, we are looking at the right side of the structure.
I exported the SymmetricPseudoLandmarks file as a fiducial csv to be used in ALPACA. I have chosen a target mesh for a single alignment that is not too different from the template (but some differ considerably).
I see from the Porto et al preprint that the two meshes do not have to be oriented in the same way. In the tutorial, it notes the ‘Select Subsampling Voxel Size’ is important but I don’t have it on my interface.
Anyway, I perform the subsampling and alignment, and the result is below. The two structures do not seem aligned to me. I also selected another target, with similar results (third image).
Am I missing some step, or need to change some options? Here are my questions to try to make this work:
1 - Do I need to manually change the registration for each sclerite such that they are oriented with anterior being anterior, dorsal being dorsal, etc for this to work? And if so, how do I do that?
2 - If that is not the case, do options do you recommend toggling in the ALPACA advanced parameter settings?
3 - Something else I’m not thinking of?