A method and system for medical image pre-processing at the medical image scanner that facilitates joint interpretation of the medical images by radiologists and artificial intelligence algorithms is disclosed. Raw medical image data is acquired by performing a medical image scan of a patient using a medical image scanner. Input data associated with the medical image scan of the patient and available downstream automated image analysis algorithms is acquired. A set of pre-processing algorithms to apply to the raw medical image data is selected based on the input data associated with the medical image scan of the patient and the available downstream automated image analysis algorithms using a trained machine learning based model. One or more medical images are generated from the raw medical image data by applying the selected set of pre-processing algorithms to the raw medical image data.