Deformable Atlases for the Segmentation of Internal Brain Nuclei in Magnetic Resonance Imaging
Keywords:
MRI, brain, deep grey matter nuclei, atlas, image normalisation, registration, segmentationAbstract
Magnetic resonance imaging (MRI) is commonly employed for the depiction of soft tissues, most notably the human brain. Computer-aided image analysis techniques lead to image enhancement and automatic detection of anatomical structures. However, the information contained in images does not often offer enough contrast to robustly obtain a good detection of all internal brain structures, not least the deep grey matter nuclei. We propose a method that incorporates prior anatomical knowledge in the shape of digital atlases that deform to fit the image data to be analysed. Our technique is based on a combination of rigid, affine and non-rigid registration, segmentation of key anatomical landmarks and propagation of the information of the atlas to detect deep grey matter nuclei. The Montreal Neurological Institute (MNI) and Zubal atlases are employed. Results show that detecting important structures such as the ventricles and brain outlines greatly improves the results. Our method is fully automatic.References
J. Ashburner, K.J. Friston, "Voxel-Based Morphometry - The Methods", NeuroImage, 11:805-821, 2000. http://dx.doi.org/10.1006/nimg.2000.0582
M A. Brown, R.C. Semelka, "MR Imaging Abbreviations, Definitions, and Descriptions: A Review", Radiology, 213:647-662, 1999. http://dx.doi.org/10.1148/radiology.213.3.r99dc18647
P. Cachier, E. Bardinet, D. Dormont, X. Pennec, N. Ayache, "Iconic Feature-based Nonrigid Registration: The PASHA Algorithm", CVIU - Special Issue on Nonrigid Registration, 89(2-3):272-298, 2003.
D.L. Collins, A.P. Zijdenbos, V. Kollokian, J.G. Sled, N.J. Kabani, C.J. Holmes, A.C. Evans, "Design and Construction of a Realistic Digital Brain Phantom", IEEE Transactions on Medical Imaging, 17(3):463-468, 1998. http://dx.doi.org/10.1109/42.712135
J. Duncan, N. Ayache, "Medical Image Analysis: Progress over Two Decades and the Challenges Ahead", IEEE Transactions on Pattern Analysis and Machine Intelligence, 22(1):85-106, 2000. http://dx.doi.org/10.1109/34.824822
M. A. González Ballester, A. Zisserman, M. Brady, "Estimation of the Partial Volume Effect in MRI", Medical Image Analysis, 6(4):389-405, 2002. http://dx.doi.org/10.1016/S1361-8415(02)00061-0
J P. Hornak, "The Basics of MRI", http://www.cis.rit.edu/htbooks/mri/.
M.G. Linguraru, M.A. Gonzales Ballester, E. Bardinet, D. Galanaud, D. Dormont, J.P. Brandel, N. Ayache, "Automated Analysis of Basal Ganglia Intensity Distribution in Multisequence MRI of the Brain - Application to Creutzfeldt-Jakob Disease", Rapport de Recherche, INRIA, 2004.
J.C. Mazziotta, A.W. Toga, A.C. Evans, P.T. Fox, J. Lancaster, K. Zilles, R.P. Woods, T. Paus, G. Simpson, B. Pike, C.J. Holmes, D.L. Collins, P.M. Thompson, D. MacDonald, M. Iacoboni, T. Schormann, K. Amunts, N. Palomero-Gallagher, S. Geyer, L. Parsors, K.L. Narr, N. Kabani, G. Le Goualher, M. Boomsma, T. Cannon, R. Kawashima, B. Mazoyer, "A Probabilistic Atlas and Reference System for the Human Brain: International Consortium for Brain Mapping (ICBM)", Philosophical Transactions of the Royal Society of London, Series B (Biological Sciences), 356(1412):1293-1322, Appendix II, 2001.
S. Ourselin, "Recalage d'Images Médicales par Appariement de Régions - Application à la Construction d'Atlas Histologiques 3D" , PhD thesis, Université de Nice - Sophia Antipolis, 2002.
S. Ourselin, A. Roche, S. Prima, N. Ayache, "Block Matching: A General Framework to Improve Robustness of Rigid Registration of Medical Images", in A.M. DiGioia and S. Delp (eds.) Medical Robotics, Imaging and Computer Assisted Surgery (MICCAI 2000), volume 1935 of Lectures Notes in Computer Science, Springer, 557-566, 2000. http://dx.doi.org/10.1007/978-3-540-40899-4_57
D.D. Stark, W.G. Bradley, W.G. Jr. Bradley, "Magnetic Resonance Imaging", Mosby, 1999.
J. Talairach, P. Tournoux, "Co-Planar Stereotaxic Atlas of the Human Brain", Thieme Medical Publishers, 1988.
K. Van Leemput, F. Maes, D. Vandermeulen, A. Colchester, P. Suetens, "Automated Segmentation of Multiple Sclerosis Lesions by Model Outlier Detection", IEEE Transactions on Medical Imaging, 20(8):677-688, 2001. http://dx.doi.org/10.1109/42.938237
I.G. Zubal, C.R. Harrell, E.O. Smith, Z. Rattner, G. Gindi, P.B. Hoffer, "Computerized Threedimensional Segmented Human Anatomy", Medical Physics, 21:299-302, 1994 http://dx.doi.org/10.1118/1.597290
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