Abstract: A computer implemented method for training a whole medical image foundation model, including: receiving a plurality of medical image datasets; extracting local sections of image data from the plurality of medical image datasets; obtaining one or more causal variables associated with the local sections and/or patient; training one or more self-supervised learning models based on the local sections of image data and the causal variables; combining the one or more trained self-supervised learning models with a deep learning network configured to combine a latent representation of the local sections of image data from the one or more trained self-supervised learning models into a patient-level representation; and combining, with the one or more trained self-supervised learning models and the deep learning network, at least one further network or function configured to accept the patient-level representation as input, the at least one further network or function operable to perform one or more patient-specific pre