ITK Meets the Virtual Soldier GE Global Research Bill Lorensen, Jim Miller Dirk Padfield, James Ross Wes Turner [email_add...
Outline <ul><li>Atlas Quality Control </li></ul><ul><li>Model Generation </li></ul><ul><li>Implicit Anatomical Modeling </...
Activities <ul><li>Atlas from NLM </li></ul><ul><li>Reconciled labels </li></ul><ul><li>Registered slices </li></ul><ul><l...
Atlas Quality Control <ul><li>Thorax Atlas consists of 411 70mm camera cryo-section slices and corresponding segmentation ...
Atlas Quality Control <ul><li>Labeled 407 structures </li></ul><ul><li>Registered 70mm film images </li></ul><ul><li>Recon...
Overlay.tcl
Atlas Quality Control Left Sixth Rib Segmentation Dust removed via “voting”
Model Generation <ul><li>Generated four types of models from segmentation labels </li></ul>Discrete Decimated (90%) Colore...
Model Generation
Model Generation
VHM Thorax Models
Implicit Anatomical Modeling <ul><li>Label = f(X,Y,Z) </li></ul>X,Y,Z I,J,K Label
Implicit Anatomical Modeling 0 mm: right_ventricle 2 mm: pericardium 3 mm: left_ventricle 52 mm: mediastinum 53 mm: left_u...
Implicit Anatomical Modeling
RGB to CT Registration
RGB to CT Registration
Deformable Registration
Model Refinement Using LevelSets
 
 
LevelSet Model Refinement <ul><li>Powerful technique to track the evolution of surfaces using image based constraints and ...
Load Sharing Facility <ul><li>256 3.2 Ghz Dual Processor Xeon </li></ul><ul><li>2 gig of memory each </li></ul><ul><li>Job...
LSF Toolkit
Laplacian LevelSet DOE Threshold Advection Curvature 1000 runs in 50 minutes!
Threshold Advection Curvature
LS Threshold Selection using IsolatedConnected Initial Using Threshold LS Using  IsolatedConnected LS
ThresholdLevelSet
3D IsolatedConnected LS Model vs. Initial Model Left ventricle and ascending aorta Pulmonary Trunk
ITK Meets the Virtual Soldier GE Global Research Bill Lorensen, Jim Miller Dirk Padfield, James Ross Wes Turner [email_add...
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ITK Tutorial Presentation Slides-951

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http://hdl.handle.net/1926/161

Published in: Technology, Business
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ITK Tutorial Presentation Slides-951

  1. 1. ITK Meets the Virtual Soldier GE Global Research Bill Lorensen, Jim Miller Dirk Padfield, James Ross Wes Turner [email_address]
  2. 2. Outline <ul><li>Atlas Quality Control </li></ul><ul><li>Model Generation </li></ul><ul><li>Implicit Anatomical Modeling </li></ul><ul><li>Registration </li></ul><ul><li>Model Refinement Usinig Level Sets </li></ul>
  3. 3. Activities <ul><li>Atlas from NLM </li></ul><ul><li>Reconciled labels </li></ul><ul><li>Registered slices </li></ul><ul><li>Computed bounding boxes </li></ul><ul><li>Calculated adjacencies </li></ul><ul><li>Generated models using vtkDiscreteMarchingCubes </li></ul><ul><li>Colored models </li></ul><ul><li>Registered atlas to CT </li></ul><ul><li>Atlas as seed for level sets </li></ul><ul><li>Deformation of man to woman </li></ul>
  4. 4. Atlas Quality Control <ul><li>Thorax Atlas consists of 411 70mm camera cryo-section slices and corresponding segmentation label maps </li></ul>Slice Resolution: 2048 x 1350
  5. 5. Atlas Quality Control <ul><li>Labeled 407 structures </li></ul><ul><li>Registered 70mm film images </li></ul><ul><li>Reconciled labels throughout entire volume </li></ul><ul><li>Computed bounding boxes for all labels </li></ul><ul><li>Removed some “dusty” structures </li></ul><ul><ul><li>Automatic reassignment </li></ul></ul>
  6. 6. Overlay.tcl
  7. 7. Atlas Quality Control Left Sixth Rib Segmentation Dust removed via “voting”
  8. 8. Model Generation <ul><li>Generated four types of models from segmentation labels </li></ul>Discrete Decimated (90%) Colored Smoothed
  9. 9. Model Generation
  10. 10. Model Generation
  11. 11. VHM Thorax Models
  12. 12. Implicit Anatomical Modeling <ul><li>Label = f(X,Y,Z) </li></ul>X,Y,Z I,J,K Label
  13. 13. Implicit Anatomical Modeling 0 mm: right_ventricle 2 mm: pericardium 3 mm: left_ventricle 52 mm: mediastinum 53 mm: left_upper_lobe_of_lung 66 mm: superior_lingular_branch_left_pulmonary 68 mm: left_upper_lobe_of_lung 107 mm: unknown 112 mm: left_fourth_rib 117 mm: serratus_anterior_muscle 123 mm: unknown 186 mm: pectoralis_minor_muscle 191 mm: deltoid_muscle 259 mm: unknown 261 mm: subcutaneous_tissue_of_trunk 271 mm: skin_of_trunk
  14. 14. Implicit Anatomical Modeling
  15. 15. RGB to CT Registration
  16. 16. RGB to CT Registration
  17. 17. Deformable Registration
  18. 18. Model Refinement Using LevelSets
  19. 21. LevelSet Model Refinement <ul><li>Powerful technique to track the evolution of surfaces using image based constraints and forces </li></ul><ul><li>Three techniques investigated </li></ul><ul><ul><li>Threshold Level Set </li></ul></ul><ul><ul><li>Laplacian Level Set </li></ul></ul><ul><ul><li>Canny Level Set </li></ul></ul><ul><li>All techniques are part of Insight Toolkit (itk) </li></ul>But: Algorithm parameter space is high!
  20. 22. Load Sharing Facility <ul><li>256 3.2 Ghz Dual Processor Xeon </li></ul><ul><li>2 gig of memory each </li></ul><ul><li>Jobs scheduled with Load Sharing Facility (LSF) </li></ul><ul><ul><li>Platform Computing Corporation </li></ul></ul><ul><li>LSF Toolkit </li></ul><ul><ul><li>GE Research front-end and monitoring </li></ul></ul>
  21. 23. LSF Toolkit
  22. 24. Laplacian LevelSet DOE Threshold Advection Curvature 1000 runs in 50 minutes!
  23. 25. Threshold Advection Curvature
  24. 26. LS Threshold Selection using IsolatedConnected Initial Using Threshold LS Using IsolatedConnected LS
  25. 27. ThresholdLevelSet
  26. 28. 3D IsolatedConnected LS Model vs. Initial Model Left ventricle and ascending aorta Pulmonary Trunk
  27. 29. ITK Meets the Virtual Soldier GE Global Research Bill Lorensen, Jim Miller Dirk Padfield, James Ross Wes Turner [email_address]
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