A method of analyzing medical image data to measure brain atrophy and determine the severity and progression of multiple sclerosis or other condition which leads to neurodegeneration or axonal damage is provided. Magnetic resonance image data representing a brain of a subject is provided and a brain surface contour is automatically identified by separating the brain from other connected structures in the image data. A total volume within the brain surface contour is calculated. A brain volume is then determined within the surface contour which excludes fluid filled regions and accounts for partial volume effects. The brain volume is then normalized by the total contour volume which generates a brain parenchymal fraction. The brain parenchymal fraction serves as a reliable measurement of brain atrophy and assists in determining the severity and progression of multiple sclerosis or other condition which leads to neurodegeneration or axonal damage.
Method and system for brain volume analysis