Systems and methods are provided for synthesizing protocol independent magnetic resonance images. A patient is scanned by a magnetic resonance imaging system to acquire magnetic resonance data. The magnetic resonance data is input to a machine learnt generator network trained to extract features from input magnetic resonance data and synthesize protocol independent images using the extracted features. The machine learnt generator network generates a protocol independent segmented magnetic resonance image from the input magnetic resonance data. The protocol independent magnetic resonance image is displayed.