Probabilistic Atlas of the Human Hippocampus Combining Ex Vivo MRI and Histology
Abstract
The human hippocampus is a complex structure consisting of multiple anatomically and functionally distinct subfields. Obtaining subfield-specific measures from in vivo MRI is challenging, and can benefit from a detailed 3D anatomical reference. This paper builds a computational atlas of the hippocampus from high-resolution ex vivo MRI of 26 specimens using groupwise deformable registration. A surface-based approach based on the explicit segmentation and geometric modeling of hippocampal layers is used to initialize deformable registration of ex vivo MRI scans. This initialization improves of groupwise registration quality, as measured in terms of similarity metrics and qualitatively. The resulting atlas, which also includes annotations mapped from histology, is a unique resource for describing variability in hippocampal anatomy.
References
- 1.Adler, D.H., Pluta, J., Kadivar, S., Craige, C., Gee, J.C., Avants, B.B., Yushkevich, P.A.: Histology-derived volumetric annotation of the human hippocampal subfields in postmortem MRI. Neuroimage 84, 505–523 (2014)CrossRefGoogle Scholar
- 2.Avants, B., Epstein, C., Grossman, M., Gee, J.: Symmetric diffeomorphic image registration with cross-correlation: evaluating automated labeling of elderly and neurodegenerative brain. Med. Image Anal. 12, 26–41 (2008)CrossRefGoogle Scholar
- 3.Breiman, L.: Random forests. Mach. Learn. 45(1), 5–32 (2001)CrossRefGoogle Scholar
- 4.Chung, M.K., Worsley, K.J., Nacewicz, B.M., Dalton, K.M., Davidson, R.J.: General multivariate linear modeling of surface shapes using surfstat. Neuroimage 53(2), 491–505 (2010)CrossRefGoogle Scholar
- 5.de Flores, R., La Joie, R., Chételat, G.: Structural imaging of hippocampal subfields in healthy aging and Alzheimer’s disease. Neuroscience 309, 29–50 (2015)CrossRefGoogle Scholar
- 6.Frangi, A.F., Niessen, W.J., Vincken, K.L., Viergever, M.A.: Multiscale vessel enhancement filtering. In: Wells, W.M., Colchester, A., Delp, S. (eds.) MICCAI 1998. LNCS, vol. 1496, pp. 130–137. Springer, Heidelberg (1998). doi: 10.1007/BFb0056195CrossRefGoogle Scholar
- 7.Iglesias, J.E., Augustinack, J.C., Nguyen, K., Player, C.M., Player, A., Wright, M., Roy, N., Frosch, M.P., McKee, A.C., Wald, L.L., Fischl, B., Van Leemput, K.: Alzheimer’s disease neuroimaging initiative: a computational atlas of the hippocampal formation using ex vivo, ultra-high resolution MRI: Application to adaptive segmentation of in vivo MRI. Neuroimage 115, 117–137 (2015)CrossRefGoogle Scholar
- 8.Jones, S.E., Buchbinder, B.R., Aharon, I.: Three-dimensional mapping of cortical thickness using laplace’s equation. Hum. Brain Mapp. 11(1), 12–32 (2000)CrossRefGoogle Scholar
- 9.Joshi, S., Davis, B., Jomier, M., Gerig, G.: Unbiased diffeomorphic atlas construction for computational anatomy. Neuroimage 23(Suppl 1), S151–S160 (2004)CrossRefGoogle Scholar
- 10.Small, S., Schobel, S., Buxton, R., Witter, M., Barnes, C.: A pathophysiological framework of hippocampal dysfunction in ageing and disease. Nat. Rev. Neurosci. 12(10), 585–601 (2011)CrossRefGoogle Scholar
- 11.van Strien, N.M., Widerøe, M., van de Berg, W.D.J., Uylings, H.B.M.: Imaging hippocampal subregions with in vivo MRI: advances and limitations. Nat. Rev. Neurosci. 13(1), 70 (2012)CrossRefGoogle Scholar
- 12.Todd, M.J., Yıldırım, E.A.: On khachiyan’s algorithm for the computation of minimum-volume enclosing ellipsoids. Discrete Appl. Math. 155(13), 1731–1744 (2007)MathSciNetCrossRefGoogle Scholar
- 13.Wang, H., Suh, J.W., Das, S.R., Pluta, J., Craige, C., Yushkevich, P.A.: Multi-atlas segmentation with joint label fusion. IEEE Trans. Pattern Anal. Mach. Intell. 35(3), 611–623 (2013)CrossRefGoogle Scholar
- 14.Winterburn, J.L., Pruessner, J.C., Chavez, S., Schira, M.M., Lobaugh, N.J., Voineskos, A.N., Chakravarty, M.M.: A novel in vivo atlas of human hippocampal subfields using high-resolution 3 T magnetic resonance imaging. Neuroimage 74, 254–265 (2013)CrossRefGoogle Scholar
- 15.Yushkevich, P.A., Avants, B.B., Pluta, J., Das, S., Minkoff, D., Mechanic-Hamilton, D., Glynn, S., Pickup, S., Liu, W., Gee, J.C., Grossman, M., Detre, J.A.: A high-resolution computational atlas of the human hippocampus from postmortem magnetic resonance imaging at 9.4 t. Neuroimage 44(2), 385–398 (2009)CrossRefGoogle Scholar
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