1. A method for directly planning a treatment based on a magnetic resonance image, the method comprising: acquiring a plurality of magnetic resonance images of a subject with different acquisition parameters; normalizing at least some magnetic resonance images of the plurality of magnetic resonance images, the normalizing comprising: for magnetic resonance images of the plurality of magnetic resonance images showing irregular intensity inhomogeneities, applying homomorphic filtering to the magnetic resonance images; and for magnetic resonance images of the plurality of magnetic resonance images showing signal decay in a caudal direction, applying a slice-wise normalization to the magnetic resonance images, the applying of the slice-wise normalization comprising dividing each transversal slice of the magnetic resonance image by a maximum intensity value; separating tissue classes in magnetic resonance images, the separating comprising: generating a multi-dimensional intensity distribution model from the plurality of magnetic resonance images, the multi-dimensional intensity distribution model representing a distribution of intensities of voxels in each magnetic resonance image of the plurality, wherein the multi-dimensional intensity distribution model is or is fitted to a joint histogram for the plurality of magnetic resonance images; identifying clusters of correlated intensities in the multi-dimensional intensity distribution model; assigning the clusters into one or more tissue classes based on the correlated intensities of each of the clusters; and creating a data model of the subject, wherein the data model is segmented into one or more regions of different tissue classes, such that voxels in each region of the one or more regions corresponds to the clusters in the multi-dimensional intensity distribution model; and calculating dose distribution for the subject based on the created data model of the subject.