Segmentation of MRI brain scans using non-uniform partial volume densities

Abstract

We present an algorithm that provides a partial volume segmentation of a T1-weighted image of the brain into gray matter, white matter and cerebrospinal fluid. The algorithm incorporates a non-uniform partial volume density that takes the curved nature of the cortex into account. The pure gray and white matter intensities are estimated from the image, using scanner noise and cortical partial volume effects. Expected tissue fractions are subsequently computed in each voxel. The algorithm has been tested for reliability, correct estimation of the pure tissue intensities on both real (repeated) MRI data and on simulated (brain) images. Intra-class correlation coefficients (ICCs) were above 0.93 for all volumes of the three tissue types for repeated scans from the same scanner, as well as for scans with different voxel sizes from different scanners with different field strengths. The implementation of our non-uniform partial volume density provided more reliable volumes and tissue fractions, compared to a uniform partial volume density. Applying the algorithm to simulated images showed that the pure tissue intensities were estimated accurately. Variations in cortical thickness did not influence the accuracy of the volume estimates, which is a valuable property when studying (possible) group differences. In conclusion, we have presented a new partial volume segmentation algorithm that allows for comparisons over scanners and voxel sizes.