A medical data processing apparatus includes a memory and processing circuitry. The memory stores a learned model including an input layer to which first MR data and second MR data having the same imaging target as the first MR data and an imaging parameter different from the first MR data are inputted, an output layer from which third MR data is output with a missing portion of the first MR data restored, and at least one intermediate layer arranged between the input layer and the output layer. The processing circuitry generates third MR data relating to the subject, from the first MR data serving as a process target and relating to the subject and the second MR data relating to the subject and acquired by an imaging parameter different from the first MR data serving as the process target, in accordance with the learned model.
