Originally posted by Konflict
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the plugin uses an analytical approach to perfectly match the poses of the skeletons and we do few adjustments to compensate some "structural" differences (e.g. the Head bones are oriented differently, if you align them the resulting UE4 skeleton will face-up too much). Note that small errors in the retarget base pose produce big errors in the final animations (e.g. your fingers, in our tests we have better results).
But the problem you pointed out is mostly due to the different meshes of the models: e.g. the chest and arm dimensions of your source Mixamo model are smaller that the UE4 mannequin one, so when you apply the "Mixamo" rotation to the arm it will inevitably intersecate the bigger chest of the UE4 mannequin. This is a problem inherent to all animations retargeting when the meshes are different, not only with Mixamo. The proper solution would require modifications to the animation, not only the skeleton.
Anyway the end result of our plugin can be manually tuned to help minimizing this sort of issues: you can tune the analytically computed "retarget base pose" to counteract the differences between the meshes if/when needed. E.g. slightly rotating "backward" the arms could avoid the intersection with the chest (well, not having tested it it's only an opinion

Cheers.
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