Attenuation coefficients of tissue must be known to accurately model dose in radiation therapy. MR-guided radiation therapy better visualizes soft tissue, but it does not inherently contain attenuation information in the same way as CT images. CT and MR images can be registered to pool information, but the bones can become severely distorted. This work applies a rigidity penalty to bones segmented in CT, such that the soft tissue is allowed to deform while the bones remain rigid during CT to MRI registration. We show that this technique improves the registration, making the deformations more anatomically feasible.