A brain network activity estimation system (1) includes means for obtaining brain wave measurement data (121) and functional magnetic resonance imaging measurement data (122) simultaneously measured from a subject (S), means (152) for constructing a feature estimation model (10) which receives the brain wave measurement data as input data and determining a parameter which defines the feature estimation model, means (154) for calculating a feature value for each module based on an output value from each module that is calculated when the brain wave measurement data is provided as the input data, means (158) for calculating an image feature value for each brain network based on the functional magnetic resonance imaging measurement data, and means (160) for determining one or more modules which express activities of a specific brain network among a plurality of modules by evaluating correlation between the feature value for each module and the image feature value for each brain network.
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