A computer-implemented method for automatically identifying subjects at risk of Multiple Sclerosis (MS) includes acquiring a plurality of images of a subject's brain using a Magnetic Resonance Imaging (MRI) scanner. A contrast enhancement process is applied to each image to generate a plurality of contrast-enhanced images. An automated lesion detection algorithm is applied to detect one or more lesions present in the contrast-enhanced images. An automated central vein detection algorithm is applied to detect one or more central veins present in the contrast-enhanced images. An automated paramagnetic rim detection algorithm is applied to detect one or more paramagnetic rims present in the contrast-enhanced images. The patient's risk for MS may then be determined based on the one or more of the lesions, central veins, and paramagnetic rims present in the contrast-enhanced images.