Segmentation of skull and scalp in 3-D human MRI using mathematical morphology

We present a new technique for segmentation of skull and scalp in T(1)-weighted magnetic resonance images (MRIs) of the human head. Our method uses mathematical morphological operations to generate realistic models of the skull, scalp, and brain that are suitable for electroencephalography (EEG) and magnetoencephalography (MEG) source modeling. We first segment the brain using our Brain Surface Extractor algorithm; using this, we can ensure that the brain does not intersect our skull segmentation. We next generate a scalp mask using a combination of thresholding and mathematical morphology. We use the scalp mask in our skull segmentation procedure, as it allows us to automatically exclude background voxels with intensities similar to those of the skull. We find the inner and outer skull boundaries using thresholding and morphological operations. Finally, we mask the results with the scalp and brain volumes to ensure closed and nonintersecting skull boundaries. Visual evaluation indicated accurate segmentations of the cranium at a gross anatomical level (other than small holes in the zygomatic bone in eight subjects) in all 44 MRI volumes processed when run using default settings. In a quantitative comparison with coregistered CT images as a gold standard, MRI skull segmentation accuracy, as measured using the Dice coefficient, was found to be similar to that which would be obtained using CT imagery with a registration error of 2-3 mm.