Magnetic Source Locator (MSL) is a powerful software package for 3-D integration of structural images (MRI/CT), functional images (MEG/EEG) and real time digitalization. Without sacrificing options or flexibility, MSL uniquely produces magnetic source imaging by merging MRI volume data and MEG functional data into a single environment. MSL provides capabilities for automatic registration (aligning data sets), semi-automatic segmentation (extracting structures such as brain, vessels and tumors from the data), generation of 3D surface models (for viewing the segmented structures) and quantitative analysis (measuring distances, angles, surface areas, and volumes) of various structural and functional images. The goal of developing MSL is to provide the most advanced, full-featured and easiest to use source reconstruction package ever developed for clinicians and researchers to use MEG/MRI to the maximum.