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I had this same dilemma and found a way to overcome it. You see I have a game resolution head in max that I have already set up blendshapes for so I cannot just change the topology without having to redo morphtargets. That mesh had tris and n-gons in it so I had to find a way to get it to and from mudbox to create other heads from the same topology that would still work with my phoneme blendshapes. I couldnt just mesh smooth it and then export it because like you said the changes would not propogate back down the the base mesh. What I found to be the solution was to:
export the mesh (in obj format of course) to zbrush, then subdivide it once from there.
Export that subdivided obj from zbrush (after saving the z tool) and import the once subdivided mesh into mudbox.
Sculpt, scupt , and sculpt some more in the best thing since sliced bread that is mudbox, then page down to level 0 in mudbox then export.
Import that level 0 mesh from mudbox in the saved z tool in zbrush, (at the correct subdivision level) drop down to the subdivision level that is your base mesh, then export that back into max.
Viola, you have a mesh that you altered in mudbox in your max scene that will work with any existing blend shapes you have already created.
I have used this workflow about 6 times now and because I have been able to use mudbox, my characters have done nothing but improve visually. The workflow sounds daunting but it really is not when you go though it. Damn I wish I could show the heads I have been working on. I really am improving dramatically and I believe its due to the ease of use that comes with mudbox. I am able to think almost exclusivley about the creation process instead of how to use the damn software or what topology is needed for the end result. I hope this workflow solves you problem.
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