I received a helpful reply from Murat Maga that I wanted to share here for anyone having the same issue (I haven't tried yet, but looks promising!)
I am not sure how IDAV does it, but you can use R/Morpho to achieve an > average in a manner like this: You need to read your all your landmarks, do > a Procrustes fit without scaling, then provide a sample as reference. This > sample is typically the sample that is closest the Procrustes mean . > > > > > > gpa=procSym(LM, scale = FALSE, CSinit = FALSE) > > #LM is the array of all your landmarks > > > > sample.mean = tps3d (refmat = reference.lm, tarmat = gpa$mshape, x = > reference.mesh) > > #reference.mesh is the ply file of the sample closest to the Procrustes > mean > > #reference.lm is landmark set associated with the mesh above. > > > > Then you can write your sample mean with command > > Rvcg::vcgPlyWrite(mesh = sample.mean, filename = …) > > > On Monday, November 12, 2018 at 4:00:17 PM UTC-5, Grace Capshaw wrote: > > > Hi all, > > I am currently using Landmark IDAV to place landmarks onto .ply mesh > files, but when I try to compute a species average from several meshes the > software crashes. This happens even when I reduce the number of mesh files > to be averaged, and when I use the "Low Resolution" output option. Has > anyone run into this issue (and ideally, figured out how to fix it)? If > not, can anyone recommend a (free) software or R package that can compute a > species average from a set of landmarks? > > Thanks very much for your help! > > Best, > Grace > -- MORPHMET may be accessed via its webpage at http://www.morphometrics.org --- You received this message because you are subscribed to the Google Groups "MORPHMET" group. To unsubscribe from this group and stop receiving emails from it, send an email to morphmet+unsubscr...@morphometrics.org.
