Abstract: A method and apparatus for radiation therapy using functional measurements of branching structures. The method includes determining a location of each voxel of a plurality of voxels in a reference frame of a radiation device. The method further includes obtaining measurements that indicate a tissue type at each voxel. The method further includes determining a subset of the voxels based on an anatomical parameter of a respective branching structure of a set of branching structures indicated by the measurements. The method further includes determining a subset of the voxels that enclose an organ-at-risk (OAR) volume. The method further includes determining a value of a utility measure at each voxel. The method further includes determining a series of beam shapes and intensities which minimize a value of an objective function based on a computed dose delivered to each voxel and the utility measure for that voxel summed over all voxels.