This brain activity classifier harmonization system, for harmonizing brain measurement data acquired from a plurality of institutions and achieving discrimination processing by brain function imaging, acquires, with respect to a plurality of moving examination who are under common measurement at each of a plurality of measurement sites, data from the results of measuring brain activities in a predetermined plurality of brain regions of each of the moving examination subjects, calculates, for each of the moving examination subjects, predetermined elements of a brain functional connectivity matrix representing the time correlation of brain activity for a set of the plurality of brain regions, uses a generalized linear mixed model method to calculate, for each of the predetermined elements of the functional connectivity matrix, measurement bias data 3108 serving in each of the measurement sites as a fixed effect from the mean of the elements of the plurality of measurement sites and the plurality of moving examination subjects, and executes harmonization processing.
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