A method and system for automatic MR brain scan planning is disclosed. The method utilizes a set of 2D orthogonal localizer images to determine scanning planes for 3D diagnostic MR scans. A location of the mid-sagittal plane (MSP) is detected in each of a transversal localizer image and a coronal localizer image. A sagittal scanning plane is determined based on the location of the MSP in the transversal and coronal localizer images. A diagnostic sagittal MR scan is then acquired based on the sagittal scanning plane. The corpus callosum CC is segmented in a sagittal MR image slice resulting from the diagnostic sagittal MR scan. A transversal scanning plane can be determined based on a location of the CC in the sagittal MR image slice and the location of the MSP in the coronal localizer image, and a coronal scanning plane can be determined based on the location of the CC in the sagittal MR image slice and the location of the MSP in the transversal localizer image.
System and method for magnetic resonance brain scan planning