Diffusion tensor magnetic resonance imaging (DTI) has the ability to provide non-invasive information on tissue microstructure not available in routine clinical MRI images. This includes information regarding the degree of anisotropy as well as the direction of the diffusion of water molecules within the tissues. Since white matter areas of the brain have an ordered structure (due to the myelination and directionality of axons) and thus a high degree of anisotropy, the ability to detect changes in anisotropy can be extremely useful in the study of diseases such as multiple sclerosis (MS), which involves the demyelination of axons. Several studies have used DTI to investigate well defined MS lesions as well as normal appearing white matter (NAWM) lesions not seen in conventional MR images. These studies have typically used region of interest (ROI) based approaches to analyze the data. However, studies using ROI based analysis techniques have several drawbacks. These include the time required to draw ROIs, the reproducibility of these ROIs, and the accuracy of placement of these ROIs, especially in NAWM regions where there is no a priori knowledge of the presence or absence of MS lesions. In this study, we have demonstrated the utilization of a semi-automated method for performing a voxelwise analysis in the detection of MS lesions.