The medical image registration apparatus includes: a frequency distribution acquisition unit that acquires the frequency distribution of the density value of at least one of first and second medical images obtained by imaging the same subject; a gradation processing unit that performs gradation processing for increasing the frequency distribution in a density range where the number of pixels included in the unit density width is relatively large, of the acquired frequency distribution, and reducing the frequency distribution in a density range where the number of pixels included in the unit density width is relatively small, of the acquired frequency distribution, for at least the one medical image; and a registration processing unit that performs registration processing for matching the anatomical position of the subject included in the first medical image with the anatomical position of the subject included in the second medical image for the first and second medical images.
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