Journal of Biomedical Engineering Research (대한의용생체공학회:의공학회지)

The Korean Society of Medical and Biological Engineering (대한의용생체공학회)
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Co-registration of Multiple Postmortem Brain Slices to Corresponding MRIs Using Voxel Similarity Measures and Slice-to-Volume Transformation

  • Kim Tae-Seong (Department of Biomedical Engineering, College of Electronics and Information, Kyung Hee University)
  • Published : 2005.08.01
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Abstract

New methods to register multiple hemispheric slices of the postmortem brain to anatomically corresponding in-vivo MRI slices within a 3D volumetric MRI are presented. Gel-embedding and fiducial markers are used to reduce geometrical distortions in the postmortem brain volume. The registration algorithm relies on a recursive extraction of warped MRI slices from the reference MRI volume using a modified non-linear polynomial transformation until matching slices are found. Eight different voxel similarity measures are tested to get the best co-registration cost and the results show that combination of two different similarity measures shows the best performance. After validating the implementation and approach through simulation studies, the presented methods are applied to real data. The results demonstrate the feasibility and practicability of the presented co­registration methods, thus providing a means of MR signal analysis and histological examination of tissue lesions via co­registered images of postmortem brain slices and their corresponding MRI sections. With this approach, it is possible to investigate the pathology of a disease through both routinely acquired MRls and postmortem brain slices, thus improving the understanding of the pathological substrates and their progression.

Keywords

References

  1. H. M. Wisniewski and J. Wegiel, 'Neuropathology of Alzheimer's disease', Neuroimaging Clin. N. Am., Vol. 5, pp.45-57, 1995
  2. S. Grafton, M. Sumi, G. K Stimac, E. C. Alvord, C. M. Shaw, and D. Nochlin, 'Comparison of postmortem magnetic resonance imaging and neuropathologic findings in the cerebral white matter', Arch. Neurol., Vol. 48, pp. 293-298, 1991 https://doi.org/10.1001/archneur.1991.00530150061019
  3. G. W. E. Englund, E. M. Larsson, A. Brun, S. Cronqvist, and B. Persson, 'Proton magnetic resonance relaxation times $T_1$ and $T_2$ related to postmortem interval: An investigation on porcine brain tissue', Acta. Radiol. Diagnosis, Vol. 27, pp. 115, 1986
  4. T. Schormann, A. Dabringhaus, and K. Zilles, 'Statistics of Deformations in Histology and Application to Improve Alignment with MRI', IEEE Trans. Med. Imag., Vol. 14, No.1, pp. 25-35, 1995 https://doi.org/10.1109/42.370399
  5. M. R Grafe, G. A. Press, D. P. Berthoty, J. R Hesselink, and C. A. Wiley, 'Abnormalities of the brain in AIDS patients: Correlation of postmortem MRI findings with neuropathology', A. J. N. R, Vol. 11, pp. 905-911, 1990
  6. P. L. McGeer, H. Kamo, R Harrop, E. G. McGeer, W. R. W. Martin, B. D. Pate, and D. K. B. Li, 'Comparision of PET, MRI, and CT with pathology in a proven case of Alzheimer's disease', Neurology, Vol. 36, pp. 1569-1574, 1986 https://doi.org/10.1212/WNL.36.12.1569
  7. J. R. Nixon, G. M. Miller, H. Okazaki, and M. R. Gomez, 'Cerebral tuberous sclerosis: Postmortem magnetic resonance imaging and pathologic anatomy', Mayo Clin. Proc., Vol. 64, pp. 305-311, 1989
  8. A. W. Toga, An Introduction to Brain Warping. In Brain Warping. Academic Press, San Diego, 1-26, 1999
  9. R. P. Woods, S. T. Grafton, C. J. Holmes, S. R. Cheery, and J. C. Mazziotta, 'Automated Image Registration: I. General Methods and Intrasubject, Intramodality Validation', J. Comp. Assisted Tomogr., Vol. 22, No.1, pp. 139-152, 1998 https://doi.org/10.1097/00004728-199801000-00027
  10. P. A. Freeborough, R. P. Woods RP, and N. C. Fox, 'Accurate Registration of Serial 3D MR Brain Images and Its Application to Visualizing Change in Neurodegenerative Disorders', J. Comp. Assisted Tomogr., Vol. 20, No.6, pp. 1012-1022, 1996 https://doi.org/10.1097/00004728-199611000-00030
  11. U. Kjems, S. C. Strother, J. Anderson, I. Law, and L. K. Hansen, 'Enhancing the Multivariate Signal of $[^{15}O]$ Water PET Studies with a New Nonlinear Neuroanatomical Registration Algorithm', IEEE Trans. Med. Imag., Vol. 8, No.4,pp. 306-319, 1999
  12. C. Studholme, E. Novotny, R. Stokking, J. S. Duncan, I. G. Zubal, and D. Spencer D, 'Alignment of Functional Data Acquired Before and After Intra-Cranial Electrode Implantation Using Non-Rigid Anatomical MRI Registration', Proc. Intl. Soc. Mag. Reson. Med., Vol. 8, pp.585, 2000
  13. C. Studholme, R. T. Constable, and J. S. Duncan, 'Accurate Alignment of Functional EPI Data to Anatomical MRI Using a Physics-Based Distortion Model', IEEE Trans. Med. Imag., Vol. 19, No. 11, pp. 1115-1127, 2000 https://doi.org/10.1109/42.896788
  14. C. Zarow, T.-S. Kim, M. Singh, and H. Chui, 'A Standarized Method for Brain Cutting Suitable for Both Stereology and MRI-Brain Coregistration', J. Neurosci. Methods, Vol. 139, No.2, pp. 209-215, 2004 https://doi.org/10.1016/j.jneumeth.2004.04.034
  15. T.-S. Kim, M. Singh, W. Sungkarat, C. Zarow, and H. Chui, 'Registration of In-Vivo MRI to Postmortem Brain Photographs', Proc. Intl. Soc. Mag. Res. Med., Vol.8, pp.677, 2000
  16. T.-S. Kim, M. Singh, W. Sungkarat, C. Zarow, and H. Chui, 'Automatic Registration of Postmortem Brain Slices to MRI Reference Volume', IEEE Trans. Nucl. Sci., Vol. 47, No. 4, pp. 1607-1613, 2000 https://doi.org/10.1109/23.873023
  17. T.-S. Kim, M. Singh, S. Kim, C. Zarow, W. G. Ellis, and H. Chui, 'MRI-Guided Histological Analysis of Postmortem Brain Slices', Proc. Intl, Soc. Mag. Res. Med., Vol. 11, pp.2255, 2003
  18. T.-S. Kim, M. Singh, S. Kim, C. Zarow, and H. Chui, 'Simultaneous Registration of Multiple Postmortem Bran Slice Images to their Corresponding MRIs', Proc. Intl. Soc. Mag. Res. Med., Vol. 10, 2002
  19. M. Singh, W. Frei, and T. Shibata, 'A digital technique for accurate change detection in nuclear medicine images with applications to myocardial perfusion studies using thallium-201', IEEE Trans. Nucl. Sci., Vol. 26, pp. 565-575, 1979 https://doi.org/10.1109/TNS.1979.4329692
  20. S. Sandor and R. Leahy, 'Surface-Based Labeling of Cortical Anatomy Using a Deformable Atlas', IEEE Trans. Med. Imag., Vol. 16, No. 1, pp. 41-54, 1997 https://doi.org/10.1109/42.552054
  21. T.-S. Kim, M. Singh, N. Ghugre, S. Kim, C. Zarow, and H. Chui, 'Registration of Postmortem Brain Slices to Matching MR Slices within 3D Reference MRI', Proc. Intl. Soc. Mag. Res. Med., 814, 2001
  22. M. Holden, D. L. G. Hill, E. R. E. Denton, J. M. Jarosz, T. C. S. Cox, T. Rohlfing, J. Goodey, and D. J. Hawkes, 'Pixel Similarity Measures for 3-D Serial MR Brain Image Registration', IEEE Trans. Med. Imag., Vol. 19, No.2, pp. 94-102, 2000 https://doi.org/10.1109/42.836369
  23. J. V. Hajnal, N. Saeed, E. J. Soar, A. Oatridge, I. R. Young, and G. M. Bydder, 'A registration and interpolation procedure for subpixel matching of serially acquired MR images', J. Comp. Assisted Tomogr., Vol. 19, No. 289-296, 1995
  24. P. A. Viola, Alignment by maximization of mutual information, Ph.D. thesis, Massachusetts Inst. Technol., Cambridge, 1995
  25. L. Lemieux, U. C. Wieshmann, N. F. Moran, D. R. Fish, and S. D. Shoovon, 'The detection and significance of subtle changes in mixed-signal brain lesions by serial MRI scan matching and spatial normalization', Med. Image Anal., Vol. 2, No.3, pp. 227-242.1998 https://doi.org/10.1016/S1361-8415(98)80021-2
  26. F. Maes, A. Collignon, D. Vandermeulen, G. Marchal, and P. Suetens, 'Multimodality Image Registration by Maximization of Mutual Information', IEEE Trans. Med. Imag., Vol. 16, No.2, pp. 187-198, 1997 https://doi.org/10.1109/42.563664
  27. B. Kim, J. L. Boes, P. H. Bland, T. L. Chenevert, and C. R. Meyer, ' Motion Correction in fMRI via Registration of Individual Slices Into an Anatomical Volume', Mag. Res. Med., Vol. 41, pp. 96-972, 1999
  28. B. Kim, J. L. Boes, K. A. Frey, and C. R. Meyer, 'Mutual information for automated unwarping of rat brain autoradiography', Neuroimage, Vol. 5, No.1, pp. 31-40, 1997 https://doi.org/10.1006/nimg.1996.0251
  29. C. Studholme, Measures of 3D medical image alignment, Ph.D. thesis, University of London, London, 1997
  30. T. M. Buzug, J. Weese, C. Fassnacht, and C. Lorenz, 'Image Registration: Convex Weighting Functions for Histogram-Based Similarity Measures', Lecture Notes in Computer Science, Berlin, Germany, Speringer-Verlag, pp. 203-212, 1997
  31. M. Singh, L. Al-Dayeh, P. Patel, T.-S. Kim, C. Guclu, and O. Nalcioglu, 'Correction. of Head Movements in Multi-Slice EPI and Single-Slice Gradient-Echo Functional MRI', IEEE Trans. Nucl. Sci., Vol. 45, pp. 2162-2167, 1998 https://doi.org/10.1109/23.708332
  32. J. Weese, G. P. Penney, P. Desmedt, and T. M. Buzug, 'Pixel-Based 2D/3D Registration of Fluoroscopy Images and CT Scans for Image-Guided Surgery', IEEE Trans. Inform. Technol. Biomed., Vol. 1, No.4, pp. 284-293, 1997 https://doi.org/10.1109/4233.681173
  33. L. Freire, A. Roche, and J.-F. Mangin, 'What is the Best Similarity Measure for Motion Correction in 'fMRI Time Series?', IEEE Trans. Med. Imag., Vol. 21, No.5, pp. 470-484, 2002 https://doi.org/10.1109/TMI.2002.1009383
  34. W. H. Press, S. A. Teukolsky, W. T. Vetterling, and B. P. Flannery, Numerical Recipes in C: The Art of Scientific Computing. Cambridge Press, Cambridge, 1992
  35. G. K. Kanji, 100 Statistical Tests. SAGE Publications, Great Britain, 1993
  36. R. A. Schowengerdt, Techniques for image processing and classification in remote sensing: Academic Press, New York, pp. 106-116, 1983
  37. P. Cachier and X. Pennec, '2D Non-Rigid Registration by Gradient Descent on a Gaussin-Windowed Similarity Measure using Convolutions', IEEE Proc. Math. Methods in Biomed. Image Analysis, pp. 182-189, 2000