A method of generating biomarker parameters includes acquiring imaging data depicting a patient using a MRI system. The imaging data is acquired for a plurality of contrasts resulting from application of a pulse on the patient's anatomy. A process is executed to generate a MoCoAve image for each contrast. This process includes dividing the imaging data for the contrast into bins corresponding to one of a plurality of respiratory motion phases, and reconstructing the imaging data in each bin to yield bin images. The process further includes selecting a reference bin image from the bin images, and warping the bin images based on the reference bin image. The warped bin images and the reference bin image are averaged to generate the MoCoAve image for the contrast. One or more biomarker parameter maps are calculated based on the MoCoAve images generated for the contrasts.