A method to automatically align magnetic resonance (MR) brain scans for diagnostic scan planning, including: acquiring a three-dimensional (3D) localizer image of a patient; selecting a two-dimensional (2D) coronal view and a 2D transverse view from the localizer image; identifying a mid-sagittal plane (MSP) line in each of the coronal and transverse views and calculating a 3D MSP based on the MSP lines; reconstructing the localizer image based on an equation for the 3D MSP to obtain an image of the MSP of the patient's brain; identifying crista galli (CG) and tip of the occipital bone (TOB) in the image of the MSP of the patient's brain; calculating a transformation matrix based on the MSP, CG and TOB in the image and using the transformation matrix to obtain a scan plan for the patient; and outputting the scan plan for the patient.