Combined Volumetric and Surface (CVS) Registration

1. Combined Volumetric and Surface (CVS) Registration Gheorghe Postelnicu, Lilla Zöllei, Bruce Fischl A.A. Martinos Center for Biomedical Imaging, MGH FS workshop

2. Introduction and motivation • Surface-based (2D) registration does an excellent job of aligning cortical folds, but doesn’t apply to non-cortical structures (e.g. basal ganglia). • Volumetric (3D) registration applies to the entire brain but doesn’t in general align folding patterns. • Solution: integrate them

3. Why Aligning Folds in the Volume is Hard! Affine transform of surfaces from one subject mapped to another.

4. pial surface WM surface Template Affine Nonlinear

5. Outline • Proposed Framework: • Automated Surface-based registration • Initialization via an Elastic Transform • Intensity-based Volumetric Registration • Experiments • Validation

6. Surface-based registration • accurate, topologically correct reconstructions of the cortical surfaces (L/R white/pial) • registration in the spherical space  1-to-1 mapping Data term Topology preservation Metric distortion

7. Reconstruction of cortical surfaces

8. Template Registered Source Source Surface Morph • spherical registration for each of the hemispheres independently Sulcal pattern projected on the sphere

9. Surface Morph

10. Elastic morph • to diffuse vector field from the cortical surfaces to the rest of the volume • regularity constraint: • elastic deformation, i.e. a smooth, orientation-preserving deformation satisfying • our choice: Navier operator from the linear elasticity theory + finite element method (FEM)

11. Elastic Morph • Iterate for i=1:n • create mesh • set up BC’s from surface • setup linear elastic system • solve system • solve topology problems Tetrahedral mesh used for one iteration of the elastic solver. Notice how the mesh is denser near the input surfaces

12. Example of Morph Dynamics

13. Results – Elastic Morph Template Affine HAMMER Elastic

14. Intensity-based registration • Nonlinear optical flow intensity based registration [Fischl, NeuroImage04] GI: intensity term GT: topology constraining term GS: smoothness term

15. Resulting Morph Template Elastic CVS Template

16. Step 2: Elastic deformation

17. Step 3: Intensity deformation

18. Experimental setup • Compare: FLIRT, HAMMER, CVS • Template: single, randomly selected scan; rest in the data set is registered to it • Accuracy: Generalized Jaccard overlap metric

19. Experiments • Adult brain inter-subject [R. Buckner]: • 40 subjects (66 cortical+21subcortical manually segmented labels) • IBSR dataset, CMA, MGH (http://www.cma.mgh.harvard.edu/ibsr/) • 10 subjects • 15 GM/WM structures; mostly sub-cortical • common with Joshi

20. The last column of the cortical measures represents the overlap measure computed in the surface space. The vertical lines represent the standard error of the mean of the measurement. 2

21. TEMPLATE

22. FLIRT

23. HAMMER

24. ELASTIC

25. CVS

26. TEMPLATE

27. TEMPLATE

28. FLIRT

29. HAMMER

30. ELASTIC

31. CVS

32. TEMPLATE

33. 3 Overlap measure: Jaccard In figures: mean and standard error

34. Template 3

35. FLIRT 3

36. HAMMER 3

37. CVS 3

38. Template HAMMER FLIRT CVS 3

39. CVS registration script mri_cvs_register --template $template --mov $subjid USAGE: mri_cvs_register Required Arguments: --mov subjid : subjid for subject to be moved / registered --template subjid : subjid for subject to be kept fixed (template)** Optional Arguments --outdir directory : output directory where all the results are written (default is SUBJECTS_DIR/mov/cvs) --noaseg : do not use aseg volumes in the registration pipeline (default is 0) --nocleanup : do not delete temporary files (default is 0) --nolog : do not produce a log file (default is 0) --version : print version and exit --help : print help and exit

40. Applications to tractography • Goal: fiber bundle alignment • Study: compare CVS to methods directly aligning DWI-derived scalar volumes • Conclusion: high accuracy cross-subject registration based on structural MRI images can provide improved alignment • Zöllei, Stevens, Huber, Kakunoori, Fischl: “Improved Tractography Alignment Using Combined Volumetric and Surface Registration”,  NeuroImage 51 (2010), 206-213

41. CST ILF UNCINATE Mean Hausdorff distance measures for three fiber bundles

42. FLIRT FA-FNIRT CVS Average tracts after registration mapped to the template displayed with iso-surfaces

43. FLIRT FA-FNIRT CVS Average tracts after registration mapped to the template displayed with morphed tracks

44. FLIRT FA-FNIRT CVS Average tracts after registration mapped to the template displayed with morphed tracks

45. Ongoing development • Improve CVS capability to register ex-vivo to in-vivo acquisitions • Implemented MI-based volumetric registration (for CVS step 3) to accommodate intensity profile differences • Qualitative preliminary results on 4 subjects • L. Zöllei, Allison Stevens, Bruce Fischl: Non-linear Registration of Intra-subject Ex-vivo and In-vivo Brain Acquisitions, Human Brain Mapping, June 2010

46. Target (in-vivo) Masked target 2-step CVS CVS with MI Subject 1

47. Target (in-vivo) Masked target 2-step CVS CVS with MI Subject 2

48. Target (in-vivo) Masked target 2-step CVS CVS with MI Subject 3

49. Target (in-vivo) Masked target 2-step CVS CVS with MI Subject 4