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Automated Topology Correction for Human Brain Segmentation

  • Lin Chen
  • Gudrun Wagenknecht
Part of the Lecture Notes in Computer Science book series (LNCS, volume 4191)

Abstract

We describe a new method to reconstruct human brain structures from 3D magnetic resonance brain images. Our method provides a fully automatic topology correction mechanism, thus avoiding tedious manual correction. Topological correctness is important because it is an essential prerequisite for brain atlas deformation and surface flattening. Our method uses an axis-aligned sweep through the volume to locate handles. Handles are detected by successively constructing and analyzing a directed graph. A multiple local region-growing process is used which simultaneously acts on the foreground and the background to isolate handles and tunnels. The sizes of handles and tunnels are measured, then handles are removed or tunnels filled based on their sizes. This process was used for 256 T1-weighted MR volumes.

Keywords

Directed Graph Connectivity Graph Simple Point Human Cerebral Cortex Border Point 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

References

  1. 1.
    Xu, C., Pham, D.L., Rettmann, M.E., Yu, D.N., Prince, J.L.: Reconstruction of the human cerebral cortex from magnetic resonance images. IEEE Trans. Med. Imag. 18(6), 467–480 (1999)CrossRefGoogle Scholar
  2. 2.
    Kriegeskorte, N., Goebel, R.: An efficient algorithm for topologically correct segmentation of the cortical sheet in anatomical mr volumes. NeuroImage 14, 329–346 (2001)CrossRefGoogle Scholar
  3. 3.
    Dale, A.M., Fischl, B., Sereno, M.I.: Cortical surface-based analysis i: Segmentation and surface reconstruction. NeuroImage 9, 179–194 (1999)CrossRefGoogle Scholar
  4. 4.
    Fischl, B., Liu, A., Dale, M.: Automated mainfold surgery: Constructing geometrically accurate and topologically correct methods of the human cerebral cortex. IEEE Trans. Med. Imag. 20, 70–80 (2001)CrossRefGoogle Scholar
  5. 5.
    Shattuck, D., Leahy, M.: Automated graph-based analysis and correction of cortical volume topology. IEEE Trans. Med. Imag. 20(11), 1167–1177 (2001)CrossRefGoogle Scholar
  6. 6.
    Han, X., Xu, C., Neto, U., Prince, J.: Topology correction in brain cortex segmentation using a multiscale, graph-based algorithm. IEEE Trans. Med. Imag. 21(2), 109–121 (2002)CrossRefGoogle Scholar
  7. 7.
    Wood, Z., Hoppe, H., Desbrun, M., Schroeder, P.: Removing excess topology from isosurfaces. ACM Transactions on graphics 23, 190–208 (2004)CrossRefGoogle Scholar
  8. 8.
    Bertrand, G.: Simple points, topological numbers and geodesic neighborhoods in cubic grids. Pattern Recognition Letters 15, 1028–1032 (1994)Google Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2006

Authors and Affiliations

  • Lin Chen
    • 1
  • Gudrun Wagenknecht
    • 1
  1. 1.Central Institute for ElectronicsResearch Center JuelichJuelichGermany

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