Abstract

Skull stripping is an important image processing step in many neuroimaging studies. In this paper, a comparison of three brain extraction algorithms is done, namely Brain Surface Extractor (BSE), skull stripping algorithm using Geodesic Active Contour (GAC), and skull stripping using active contours without edges. The comparison is done with respect to accuracy of the three algorithms. The results provided by the three algorithms are compared against the processed results available in the OASIS dataset. A comparison of the three algorithms shows that BSE provides the best results with respect to the percentage of non-brain matter contained in the final segmented output. The algorithm using GAC produces a conservative result containing some amount of non-brain matter that can be removed using morphological operator. The algorithm using active contours without edges produces segmentation results containing some amount of brain matter removed from the result. This is mainly due to the sensitivity of the active contour to intensity values in the sulci present in the brain magnetic resonance image.

References

• H. H. Zhuang, D. J. Valentino, and A. W. Toga, "Skull-stripping magnetic resonance images using a model-based level set," NeuroImage, vol. 32, pp. 79 – 82, 2006.
• C. DeCarli, J. Maisog, D. G. M. Murphy, D. Teichberg, S. I. Rapoport, and B. Horwitz, "Method for quantification of brain ventricular and subarachnoid CSF volumes from MR images," J. Comput. Assist. Tomogr. , vol. 16, no. 2, pp. 274 – 284, 1992
• C. Lee, S. Huh, T. A. Keller, and M. Unser, "Unsupervised connectivity-based thresholding segmentation of midsaggital brain MR images," Comput. Biol. Med. , vol. 28, pp. 309 – 338, 1998
• S. Huh, T. A. Keller, K. H. Sohn, and C. Lee, "Automated cerebrum segmentation from 3-D saggital brain MR images," Comput. Biol. Med. , vol. 32, pp. 311 – 328, 2002
• D. W. Shuttuck, S. R. Sandor-Leahy, K. A. Schaper, D. A. Rottenburg, and R. M. Leahy, "Magnetic resonance image tissue classification using a partial volume model," NeuroImage, vol. 13, pp. 856 – 876, 2001
• G. B. Aboutanos, J. Nikanne, N. Watkins, and B. M. Dawant, "Model creation and deformation for the automatic segmentation of the brain in MR images," IEEE Trans. Biomed. Engg. , vol. 46, no. 11, pp. 1346 – 1356, 1999
• X. Zeng, L. H. Staib, R. T. Schultz, and J. S. Duncan, "Segmentation and measurement of the cortex from 3-D MR images using coupled-surfaces propagation," IEEE Trans. Med. Imag. , vol. 18, no. 10, pp. 927 – 937, 1999
• J. S. Suri, "Two-dimensional fast magnetic resonance brain segmentation," IEEE Trans. Med. Biol. , pp. 84 – 95, 2001
• C. Baillard, P. Hellier, and C. Barillot, "Segmentation of brain 3D MR images using level sets and dense registration," Med. Image Anal. , vol. 5, pp. 185 – 194, 2001
• S. M. Smith, "Fast robust automated brain extraction," Hum. Brain Mapp. , vol. 17, pp. 143 – 155, 2002
• H. Rifai, I. Bloch, S. Hutchinson, J. Wiart, and L. Garnero, "Segmentation of the skull in MRI volumes using deformable model and taking the partial volume effect into account," Med. Image Anal. , vol. 4, pp. 219 – 233, 2000
• S. Shah and A. Ross, "Iris segmentation using geodesic active contours," IEEE Trans. Inf. Foren. & Sec. , vol. 4, no. 4, pp. 824 – 836, 2009
• J. A. Sethian, "A review of recent numerical algorithms for hypersurfaces moving with curvature dependent speed," J. Different. Geometry, vol. 31, pp. 131 – 161, 1989
• R. Malladi, J. A. Sethian, and B. C. Vemuri, "Shape modeling with front propagation: a level set approach," IEEE Trans. Pattern Anal. , Mach. Intell. , vol. 17, no. 2, pp. 125 – 133, 1995
• T. F. Chan and L. A. Vese, "Active contours without edges," IEEE Trans. Image Process. , vol. 10, no. 2, pp. 266 – 277, 2001
• P. Perona and J. Malik, "Scale-space and edge detection using anisotropic diffusion," IEEE Trans. Pattern Anal. Mach. Intell. , vol. 12, no. 7, pp. 629 – 639, 1990
• M. Sussman, P. Smereka, and S. Osher, "A level set approach for computing solutions to incompressible two-phase flow," J. Comput. Phys. , vol. 114, pp. 146 – 159, 1994
• S. Osher and J. A. Sethian, "Fronts propagating with curvature-dependent speed: Algorithms based on Hamilton-Jacobi Formulation," J. Comput. Phys. , vol. 79, pp. 12 – 49, 1988