A dual-channel 3D MRI segmentation technique based on Grouping Artificial Immune Networks (GAIN) is introduced to detect MS lesion in MR images. The technique demonstrates the ability of artificial immune networks to handle MS lesions detection in T1- and T2-weighted brain MRI. The GAIN-based MRI segmentation technique was evaluated using simulated MS brain images from the McConnell Brain Imaging Centre, Montreal Neurological Institute of McGill University. 3D anisotropic filtering is used to handle noise artifacts in the simulated 3D MRI data sets. Experimental results demonstrated that dual channel MS segmentation approach exhibited high accuracy in segmenting the simulated MS brain data and an even higher accuracy when compared to techniques based on single channel 3D MRI data sets in terms of the Dice coefficient, an objective measure of overlap.