  We present a deep learning model to automatically generate computer models of
the human heart from patient imaging data with an emphasis on its capability to
generate thin-walled cardiac structures. Our method works by deforming a
template mesh to fit the cardiac structures to the given image. Compared with
prior deep learning methods that adopted this approach, our framework is
designed to minimize mesh self-penetration, which typically arises when
deforming surface meshes separated by small distances. We achieve this by using
a two-stage diffeomorphic deformation process along with a novel loss function
derived from the kinematics of motion that penalizes surface contact and
interpenetration. Our model demonstrates comparable accuracy with
state-of-the-art methods while additionally producing meshes free of
self-intersections. The resultant meshes are readily usable in physics based
simulation, minimizing the need for post-processing and cleanup.
