Methods for analyzing retinal tomography maps to detect patterns of optic nerve diseases such as glaucoma, optic neuritis, anterior ischemic optic neuropathy are disclosed in this invention. The areas of mapping include the macula centered on the fovea, and the region centered on the optic nerve head. The retinal layers that are analyzed include the nerve fiber, ganglion cell, inner plexiform and inner nuclear layers and their combinations. The overall retinal thickness can also be analyzed. Pattern analysis are applied to the maps to create single parameter for diagnosis and progression analysis of glaucoma and optic neuropathy.