To perform Dixon MRI, generate multi-contrast images, and extract multi-parametric maps, this invention presents a multi-echo
gradient echo protocol with two sets of echo trains. An example implementation of the invention at 3 T acquires a short-TE
train (ΔTE˜1.2 ms, TE <10 ms), which is used to map B0 inhomogeneity and
proton density fat fraction (FF), and a second—susceptibility sensitive—long-TE
train (16 ms<TE<45 ms) will enable quantification of local
frequency shift (LFS) and susceptibility. The presented pipeline automatically generates co-registered images and maps with / without fat-suppressed, including magnitude- and complex-based FF map, B0 map, anatomical images, brain
mask, R2* map, unwrapped phase maps for each echo, susceptibility-sensitive images (SWI, LFS and quantitative susceptibility) for each echo, mean susceptibility-sensitive images for each echo-
train. The invention is directly applicable to whole head / neck, liver, knee or even
whole body scans with sliding table.