I've got following problem: to bake the polypaint from high poly to low poly, I must have both models in the same size and position. Unfortunately, my polypaint in ZBrush was done before I properly scaled and oriented the model in Maya. It seems imposiible to import the high poly into Maya and still have its polypainting. Is there any way around this problem?
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Alternatively, if it does have some lower subdivision levels, you could try and give the highpoly a temporary set of UVs. Then you dont have to worry about polypaint information being retained as it's now on a texture. Decimate, export, resize as needed, and bake.
Or you could take them both into zbrush and try Tool: Deformation: Unify. This would change the scale (and using the rotation deforms would change the orientation of the low res mesh back), but if you work on a copy of the lowpoly I don't see it being a problem. Bake with that, then apply the result to the properly scaled mesh.