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autoMATE - automated Multi-Atlas Tract Extraction

autoMATE (automated Multi-Atlas Tract Extraction) is a comprehensive pipeline that can generate white matter fibers from diffusion-weighted MRI and label them into coherent and anatomically meaningful major tracts. It takes advantage of the information from multiple manually constructed white matter atlases to identify more accurate and reliable tracts. Furthermore, it provides a matching scheme to establish the point-to-point correspondence between subjects over population for further statistical analysis. autoMATE can be used to examine the integrity of white matter in 3-D for large-scale population studies on neurological or neuropsychological diseases such as Alzheimer's disease and traumatic brain injury.

Code will be released shortly.

  • E.L. Dennis, F. Rashid, J. Faskowitz, Y. Jin, K.L. McMahon, G.I. de Zubicaray, N.G. Martin, I. Hickie, M.J. Wright, N. Jahanshad, and P.M. Thompson, “Mapping age effects along fiber tracts in young adults,” IEEE International Symposium on Biomedical Imaging (ISBI), Melbourne, Australia, pp. 101-104, 2017.
  • E.L. Dennis, F. Rashid, M.U. Ellis, T. Babikian, R.M. Vlasova, J.E. Villalon-Reina, Y. Jin, A. Olsen, R. Mink, C. Babbitt, J. Johnson, C.C. Giza, P.M. Thompson, and R.F. Asarnow, “Diverging white matter trajectories in children after traumatic brain injury: the RAPBI study,” Neurology, 88(15), 1392-1399, 2017.
  • Y. Jin, C. Huang, M. Daianu, L. Zhan, E.L. Dennis, R.I. Reid, C.R. Jack, Jr, H. Zhu, P.M. Thomposn, and the Alzheimer’s Disease Neuroimaging Initiative, “3D tract-specific local and global analysis of white matter integrity in Alzheimer’s disease,” Human Brain Mapping 38(3), 1191-1207, 2017.
  • M. Daianu, M.F. Mendez, V.G. Baboyan, Y. Jin, R.J. Melrose, E.E. Jimenez, and P.M. Thompson, “An advanced white matter tract analysis in frontotemporal dementia and early-onset Alzheimer’s disease,” Brain Imaging and Behavior 10(4), 1038-1053, 2016.
  • E.L. Dennis, M.U. Ellis, S.D. Marion, Y. Jin, L. Moran, A. Olsen, C. Keman, T. Babikian, R. Mink, C. Babbitt, J. Johnson, C.C. Giza, P.M. Thompson, and R.F. Asarnow, “Callosal function in pediatric traumatic brain injury linked to disrupted white matter integrity,” Journal of Neuroscience 35(28), 10202-10211, 2015.
  • E.L. Dennis, Y. Jin, C. Kernan, T. Babikian, R. Mink, C. Babbitt, J. Johnson, C.C. Giza, R.F. Asarnow, and P.M. Thompson, “White matter integrity in traumatic brain injury: effects of permissible fiber turning angle,” IEEE ISBI, New York, New York, USA, pp. 930-933, 2015.
  • Y. Jin, Y. Shi, L. Zhan, and P.M. Thompson, “Automated multi-atlas labeling of the fornix and its integrity in Alzheimer’s disease,” IEEE ISBI, New York, New York, USA, pp. 140-143, 2015.
  • E.L. Dennis, Y. Jin, J. Villalon-Reina, L. Zhan, C. Kernan, T. Babikian, R. Mink, C. Babbitt, J. Johnson, C.C. Giza, P.M. Thompson, and R. Asarnow, “White matter disruption in moderate/severe pediatric traumatic brain injury: advanced tract-based analyses,” NeuroImage: Clinical 7, 493-505, 2015.
  • Y. Jin, Y. Shi, L. Zhan, B.A. Gutman, G.I. de Zubicaray, K.L. McMahon, M.J. Wright, A.W. Toga, and P.M. Thompson, “Automatic clustering of white matter fibers in brain diffusion MRI with an application to genetics,” NeuroImage 100, 75-90, 2014.
  • Y. Jin, Y. Shi, L. Zhan, G.I. de Zubicaray, K.L. McMahon, N.G. Martin, M.J. Wright, and P.M. Thompson, “Labeling white matter tracts in HARDI by fusing multiple tract atlases with applications to genetics,” IEEE ISBI, San Francisco, California, USA, pp. 508-511, 2013.