1. A visualization apparatus, comprising: a memory; and a processor coupled to the memory and configured to: calculate, for each brightness value for voxels included in a predetermined Region Of Interest (ROI) in three-dimensional volume data, an appearance frequency of the brightness value, wherein the brightness value is a normalized value representing a gray-scale brightness of a voxel for which the brightness value is set; calculate, for each brightness value for the voxels included in the predetermined ROI, an appearance probability that the brightness value appears in the voxels included in the predetermined ROI, based on distribution of the calculated appearance frequencies; set, for each brightness value for the voxels included in the predetermined ROI, opacity so that a voxel that has a brightness value of a higher appearance probability becomes more transparent and a voxel that has a brightness value of a lower appearance probability becomes more opaque; generate three-dimensional image data for a portion on and under a cross section that is set for the three-dimensional volume data, by using the opacity of each brightness value and color data that corresponds to a brightness value of each voxel included in the predetermined ROI; synthesize a cross section image generated from data of voxels on the cross section and the three-dimensional image data by using a transparency value that is set for the cross section image; and display an image obtained by the synthesizing.