A computer based system and method of visualizing a region using multiple image data sets is provided. The method includes acquiring first volumetric image data of a region and acquiring at least second volumetric image data of the region. The first image data is generally selected such that the structural features of the region are readily visualized. At least one control point is determined in the region using an identifiable structural characteristic discernable in the first volumetric image data. The at least one control point is also located in the at least second image data of the region such that the first image data and the at least second image data can be registered to one another using the at least one control point. Once the image data sets are registered, the registered first image data and at least second image data can be fused into a common display data set. The multiple image data sets have different and complimentary information to differentiate the structures and the functions in the region such that image segmentation algorithms and user interactive editing tools can be applied to obtain 3d spatial relations of the components in the region. Methods to correct spatial inhomogeneity in MR image data is also provided.