Two brain segmentation approaches based on Hidden Markov Models are proposed. The first approach aims to segment normal brain 3D multi-channel MR images into three tissues WM, GM, and CSF. Linear Discriminant Analysis, LDA, is applied to separate voxels belonging to different tissues as well as to reduce their features vector size. The second approach aims to detect MS lesions in Brain 3D multi-channel MR images and to label WM, GM, and CSF tissues. Preprocessing is applied in both approaches to reduce the noise level and to address sudden intensity and global intensity correction. The proposed techniques are tested using 3D images from Montereal BrainWeb data set. In the first approach, the results were numerically assessed and compared to results reported using techniques based on single channel data and applied to the same data sets. The results obtained using the multi channel HMM-based algorithm were better than the results reported for single channel data in terms of an objective measure of overlap, Dice coefficient, compared to other methods. In the second approach, the segmentation accuracy is measured using Dice coefficient and total lesions load percentage