1. Oct 30, 2005Sylvain Jaume1 Open Topology: A Toolkit for Brain Isosurface Correction Sylvain JAUME (1), Patrice RONDAO (2), Benoit MACQ (2) (1) Kitware Inc., (2) University of Louvain

2. Oct 30, 2005Sylvain Jaume2 Visualization of the Brain Speech, vision, etc. lie in the outer layer. surface visualization

3. Oct 30, 2005Sylvain Jaume3 Visualization of the Brain 3D Image Segmentation Marching Cubes Smoothing Mesh

4. Oct 30, 2005Sylvain Jaume4 Visualization of the Brain 3D Image Segmentation Marching Cubes Smoothing Mesh

5. Oct 30, 2005Sylvain Jaume5 Visualization of the Brain 3D Image Segmentation Marching Cubes Smoothing Mesh

6. Oct 30, 2005Sylvain Jaume6 Visualization of the Brain 3D Image Segmentation Marching Cubes Smoothing Mesh with Handles

7. Oct 30, 2005Sylvain Jaume7 Visualization of the Brain 3D Image Segmentation Marching Cubes Smoothing Mesh with Handles

8. Oct 30, 2005Sylvain Jaume8 Visualization of the Brain 3D Image Segmentation Marching Cubes Smoothing Mesh with Handles

9. Oct 30, 2005Sylvain Jaume9 Visualization of the Brain 3D Image Segmentation Marching Cubes Smoothing Mesh with Handles

10. Oct 30, 2005Sylvain Jaume10 Visualization of the Brain 3D Image Segmentation Marching Cubes Smoothing Mesh with Handles

11. Oct 30, 2005Sylvain Jaume11 Visualization of the Brain Where do handles come from ? Limited resolution Scanner artifacts Segmentation errors

12. Oct 30, 2005Sylvain Jaume12 Visualization of the Brain Does it really matter ??? For 3D visualization For distance measurements For EEG source localization

13. Oct 30, 2005Sylvain Jaume13 State of the Art Image methods –Malandain 93, Shattuck 01, Kriegeskorte 01 Mesh methods –Fischl 01, Guskov 01, Wood 04, Segonne 05 Graph methods –Han 02, Segonne 03 Level-Set methods –Han 01, Bischoff 02

14. Oct 30, 2005Sylvain Jaume14 Contributions No region is left out Fast (less than 2 min) Open Source

15. Oct 30, 2005Sylvain Jaume15 Algorithm Overview Marching Cubes Handle Detection Handle Correction 3D Image Triangle Mesh Corrected 3D Image Contours

16. Oct 30, 2005Sylvain Jaume16 Algorithm Overview Marching Cubes Handle Detection Handle Correction 3D Image Triangle Mesh Contours Corrected 3D Image

17. Oct 30, 2005Sylvain Jaume17 Algorithm Overview Marching Cubes Handle Detection Handle Correction 3D Image Triangle Mesh Contours Corrected 3D Image

18. Oct 30, 2005Sylvain Jaume18 Algorithm Overview Marching Cubes Handle Detection Handle Correction 3D Image Triangle Mesh Polylines Corrected 3D Image

19. Oct 30, 2005Sylvain Jaume19 Algorithm Overview Marching Cubes Handle Detection Handle Correction 3D Image Triangle Mesh Contours Corrected 3D Image

20. Oct 30, 2005Sylvain Jaume20 Algorithm Overview Marching Cubes Handle Detection Handle Correction 3D Image Triangle Mesh Contours Corrected 3D Image

21. Oct 30, 2005Sylvain Jaume21 Algorithm Overview Marching Cubes Handle Detection Handle Correction 3D Image Triangle Mesh Contours Corrected 3D Image

22. Oct 30, 2005Sylvain Jaume22 Algorithm Overview Marching Cubes Handle Detection Handle Correction 3D Image Triangle Mesh Contours Marching CubesCorrected Mesh Corrected 3D Image

23. Oct 30, 2005Sylvain Jaume23 Algorithm Overview Marching Cubes Handle Detection Handle Correction 3D Image Triangle Mesh Contours Marching CubesCorrected Mesh Corrected 3D Image

24. Oct 30, 2005Sylvain Jaume24 Key Points

25. Oct 30, 2005Sylvain Jaume25 1. Embracing the Handle

26. Oct 30, 2005Sylvain Jaume26 1. Embracing the Handle Init

27. Oct 30, 2005Sylvain Jaume27 1. Embracing the Handle Init

28. Oct 30, 2005Sylvain Jaume28 1. Embracing the Handle Init

29. Oct 30, 2005Sylvain Jaume29 1. Embracing the Handle Init

30. Oct 30, 2005Sylvain Jaume30 1. Embracing the Handle Split

31. Oct 30, 2005Sylvain Jaume31 1. Embracing the Handle Split

32. Oct 30, 2005Sylvain Jaume32 1. Embracing the Handle Split

33. Oct 30, 2005Sylvain Jaume33 1. Embracing the Handle Merge

34. Oct 30, 2005Sylvain Jaume34 1. Embracing the Handle Merge

35. Oct 30, 2005Sylvain Jaume35 1. Embracing the Handle Merge

36. Oct 30, 2005Sylvain Jaume36 1. Embracing the Handle Merge

37. Oct 30, 2005Sylvain Jaume37 1. Embracing the Handle Merge

38. Oct 30, 2005Sylvain Jaume38 1. Embracing the Handle Merge

39. Oct 30, 2005Sylvain Jaume39 1. Embracing the Handle Finalize

40. Oct 30, 2005Sylvain Jaume40 1. Embracing the Handle Finalize

41. Oct 30, 2005Sylvain Jaume41 1. Embracing the Handle Finalize

42. Oct 30, 2005Sylvain Jaume42 2. Holding it Tight Distance

43. Oct 30, 2005Sylvain Jaume43 2. Holding it Tight Distance

44. Oct 30, 2005Sylvain Jaume44 2. Holding it Tight Distance

45. Oct 30, 2005Sylvain Jaume45 2. Holding it Tight Distance

46. Oct 30, 2005Sylvain Jaume46 2. Holding it Tight Distance

47. Oct 30, 2005Sylvain Jaume47 2. Holding it Tight Distance

48. Oct 30, 2005Sylvain Jaume48 2. Holding it Tight Distance

49. Oct 30, 2005Sylvain Jaume49 2. Holding it Tight Distance

50. Oct 30, 2005Sylvain Jaume50 2. Holding it Tight Distance

51. Oct 30, 2005Sylvain Jaume51 3. Filling the Handle New pixel intensity inside the loop

52. Oct 30, 2005Sylvain Jaume52 Putting it Together 1.Handle Detection –Embracing the handle 2.Handle Localization –Holding it tight 3.Handle Correction –Filling the handle

53. Oct 30, 2005Sylvain Jaume53 Performance g: genus, i.e. number of handles V: number of vertices E: number of edges F: number of faces C: number of connected components Euler Characteristic

54. Oct 30, 2005Sylvain Jaume54 Data Structures vtkCellLinks vtkPointsvtkCellArray

55. Oct 30, 2005Sylvain Jaume55 Data Structures Edge to Start Point Edge to End Point Edge to Polygon vtkPointsvtkCellArrayHalf-Edge

56. Oct 30, 2005Sylvain Jaume56 Data Structures Edge to Reverse Edge Edge to Parent Edge vtkPointsvtkCellArrayHalf-Edge Detection Localization

57. Oct 30, 2005Sylvain Jaume57 Data Structures Edge to Contour Edge to Distance vtkPointsvtkCellArrayHalf-Edge Detection Localization

58. Oct 30, 2005Sylvain Jaume58 Data Structures Extended Half-Edge Structure: Edge to Polygon Edge to Start Point Edge to End Point Edge to Reverse Edge Edge to Parent Edge Edge to Contour Edge to Distance

59. Oct 30, 2005Sylvain Jaume59 Code vtkHandleDetection –Half-edge structure –Area growing –Shortest loop vtkHandleCorrection –Loop to image –Water-tight region

60. Oct 30, 2005Sylvain Jaume60 Goal Correct EVERY handle FAST!

61. Oct 30, 2005Sylvain Jaume61 Perspectives Visualization, measurements, source localization Benchmarking with other methods Half-Edge algorithms Integration into CARET Software

62. Oct 30, 2005Sylvain Jaume62 MICCAI Open Source Workshop "Open Topology: A Toolkit for Brain Isosurface Correction", Jaume, Rondao, Macq, MICCAI WS 2005. Article Code Data Demo

63. Oct 30, 2005Sylvain Jaume63 www.OpenTopology.org Algorithm Source code Documentation Data Updates

64. Oct 30, 2005Sylvain Jaume64 Acknowledgements Special thanks to M. Ferrant, S.K. Warfield, A.H. Barr, and many others at UCL-Belgium, CalTech, SPL, MIT, INRIA and VTK mailing list. Thank you for your interest!

65. Oct 30, 2005Sylvain Jaume65 References I Segonne, Florent and Grimson, W. Eric L and Fischl, Bruce, A Genetic Algorithm for the Topology Correction of Cortical Surfaces, IPMI 2005. Bischoff, Stefan and Kobbelt, Leif, Sub-Voxel Topology Control for Level-Set Surfaces},Computer Graphics Forum 2003. Stephan Bischoff, Leif Kobbelt, Parameterization-free active contour models with topology control, The Visual Computer 2004. Aktouf, Zouina and Bertrand, Gilles and Perroton, Laurent, A three-dimensional holes closing algorithm, Pattern Recognition Letters 2002. Bertrand, Gilles, Simple Points, topological numbers and geodesic neighborhood in cubic grids, Pattern Recognition Letters 1994. Bertrand, Gilles, A boolean characterization of three-dimensional simple points, Pattern Recognition Letters 1996. G. Bertrand and G. Malandain, A New Characterization of Three-Dimensional Simple Points, Pattern Recognition Letters 1994

66. Oct 30, 2005Sylvain Jaume66 References II Fischl, B. and Liu, A. and Dale, A. M., Automated Manifold Surgery: Constructing Geometrically Accurate and Topologically Correct Models of the Human Cerebral Cortex, IEEE Transactions on Medical Imaging. Han, X., Xu, C., Braga-Neto, U., Prince, J., Topology Correction in Brain Cortex Segmentation Using a Multiscale Graph-based Algorithm, IEEE Transactions on Medical Imaging 2002. X. Han, C. Xu, D. Tosun, and J. L. Prince, Cortical Surface Reconstruction Using a Topology Preserving Geometric Deformable Model, MMBIA 2001. Kriegeskorte, N. and Goebel, R., An Efficient Algorithm for Topologically Correct Segmentation of the Cortical Sheet in Anatomical MR Volumes, NeuroImage, 2001. Shattuck, D. W. and Leahy, R. M., Automated Graph-based Analysis and Correction of Cortical Volume Topology, IEEE Transactions on Medical Imaging, 2001. Bischoff, S. and Kobbelt, L., Isosurface Reconstruction with Topology Control, Pacific Graphics Proceedings, 2002.

67. Oct 30, 2005Sylvain Jaume67 References III Bischoff, Stephan and Kobbelt, Leif, Topologically Correct Extraction of the Cortical Surface of a Brain Using Level-Set Methods, Bildverarbeitung fuer die Medizin, 2004. Malandain, Grégoire and Bertrand, Gilles and Ayache, Nicholas, Topological Segmentation of Discrete Surfaces, International Journal of Computer Vision, 1993. Zeng, X. and Staib, L. H. and Schultz, R. T. and Duncan, J. S., Segmentation and Measurement of the Cortex from 3D MR Images Using Coupled Surfaces Propagation, IEEE Transactions on Medical Imaging, 1999. Ségonne, F. and Fischl, B. and Grimson, E., Topology correction of Subcortical Structures, Medical Image Computing and Computer-Assisted Intervention (MICCAI) 2003. Guskov, I. and Wood, Z., Topological Noise Removal, Graphics Interface, 2001. Wood, Z. J. and Hoppe, H. and Desbrun, M. and Schröder, P., Removing Excess Topology from Isosurfaces, ACM Transactions on Graphics, 2004.

68. Oct 30, 2005Sylvain Jaume68 State of the Art Image methods –Can miss large regions Mesh methods –Self-intersections Graph methods –Computationally intensive Level-Set methods –Controlled with heuristics