1. A method for assessing at least one biomarker in a region of interest of a patient and a response of the at least one biomarker to a stimulus, the method comprising: (a) obtaining at least one pre-stimulus 3D image data set in the region of interest before the stimulus is applied to the at least one biomarker; (b) obtaining at least one post-stimulus 3D image data set in the region of interest after the stimulus is applied to the at least one biomarker; and (c) extracting biomarker measurements from the at least one pre-stimulus 3D image data set and the at least one post-stimulus 3D image data set.