Interactive non-uniformity correction (NC) and interactive intensity standardization (IS) require sample tissue regions to be specified for several different types of tissues. Interactive NC estimates the degree of non-uniformity at each voxel in a given image, builds a global function for non-uniformity correction, and then corrects the image to improve quality. Interactive IS includes two steps: a calibration step and a transformation step. In the first step, tissue intensity signatures of each tissue from a few subjects are utilized to set up key landmarks in a standardized intensity space. In the second step, a piecewise linear intensity mapping function is built between the same tissue signatures derived from the given image and those in the standardized intensity space to transform the intensity of the given image into standardized intensity. Interactive IS for MR images combined with interactive NC can substantially improve numeric characterization of tissues.