Ultrasound-based estimation of disease activity, such as for NAS or other activity index for NAFLD for liver disease, is provided. Ultrasound measures acoustic scatter and shear wave propagation parameters, such as measuring acoustic backscatter coefficient, shear wave velocity, and shear wave damping ratio. A score for the disease activity is determined from these scatter and shear wave propagation parameters. The physician may be assisted by relatively inexpensive and rapid ultrasound as compared to biopsy or MRI based scoring in scoring activity of a disease, such as NAFLD. Ultrasound imaging is more readily available and less expensive and MRI, and is non-invasive.