There is disclosed a novel system and method for improving MRI and DWI image quality and tissue detail and contrast is introduced and referred to in this disclosure as “compensated magnetic resonance imaging” or CMRI in which a compensation function and noise scale factor are determined during a calibration process by acquiring one or more test signals on the MRI system to determine a compensation function and noise scale factor, and signal acquisitions are conducted from a subject, and the signals are then used to reconstruct MRI images by maximizing a quality metric that takes the acquired signals, compensation function, and noise scale factor as part of the input parameters. Advantageously, by taking into a compensation function and a noise scale factor, CMRI can provide significantly improved MRI image quality and tissue detail and contrast.