Yes, copy all your meshes to a folder, and pass the path to it to placePatch. I 
thought I used binary stls as well, but I might be mistaken.
Make sure the Z dimname (or sample name) in the p.k.n array matches the 
filenames (minus .ply) since I think I that’s what it uses to match the LM 
array to the mesh.

M



From: morphmet@morphometrics.org [mailto:morphmet@morphometrics.org] On Behalf 
Of Pere Ibáñez
Sent: Thursday, March 10, 2016 7:38 AM
To: MORPHMET <morphmet@morphometrics.org>
Subject: [MORPHMET] placePatch in Morpho (R)

I am using the function placePatch in Morpho: placePatch(atlas, dat.array, 
path, prefix = NULL, fileext = ".ply", ray = TRUE, inflate = NULL, tol = 
inflate, relax.patch = TRUE, keep.fix = NULL, rhotol = NULL, silent = FALSE, 
mc.cores = 1). I already created the atlas using createAtlas, and I checked 
using plotAtlas and it looks fine.

In placePatch, in path, I am supposed to specify the directory where the 
surface meshes of the sample are stored. Does this mean that I have to specify 
the folder where all the 3D images are? In that case, must they be in a 
specific format? Ascii PLY maybe?

I tried specifying the folder where my images are, but it didn't work (I 
obtained a pxkxn array with only missing values -NAs-). May this occur because 
my images are Binary PLY?

Thanks in advance!

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