Abstract: In this paper an algorithm for fully automatic segmentation of the cortex from T1-weighted axial or sagittal MRI data is presented. When analysing 3D MRI images of the brain it is often important to segment the brain from non-brain tissue such as eyes and membranes of the brain. The segmentation algorithm uses a histogram-based method to find accurate threshold values. Four initial masks are created; first two thresholded masks from the original volume, background and brain tissue, then a third mask thresholded from a 3D grey-level eroded version of the volume, brain tissue, and lastly a fourth mask thresholded from a 3D grey-level dilated version of the volume, containing surrounding fat. On the start slice of these masks, binary morphological operations and logical operations are used. Then the rest of the slices are segmented using information from the previous slice combined with the other masks. Information from earlier slices is propagated to keep the segmented volume from leaking into non-brain tissue.