1. Volume Flow Determination by QMRA / 2008/02/15 Page 1 of 64 Volume Flow Determination in the Cranial Vessel Tree Based on Quantitative Magnetic Resonance Data Supervisor (TUM): Supervisors (BrainLAB): Andreas Keil Thomas Seiler, Fritz Vollmer Advisor:Prof. Dr. Navab by Jürgen Sotke

2. Volume Flow Determination by QMRA / 2008/02/15 Page 2 of 64 Goal Quantitative Magnetic Resonance Angiography (QMRA) State of the Art New Approach Results Agenda

3. Volume Flow Determination by QMRA / 2008/02/15 Page 3 of 64 Goal

4. Volume Flow Determination by QMRA / 2008/02/15 Page 4 of 64 Quantitative information about volume flow rates (either abstract or graphicaly) Purposes: Diagnosis (stenosis, ischemia) Review of operation results Goal

5. Volume Flow Determination by QMRA / 2008/02/15 Page 5 of 64 QMRA

6. Volume Flow Determination by QMRA / 2008/02/15 Page 6 of 64 So far there exists only one MR technique which allows to directly measure flow velocities: In a phase contrast image, the grey level is linearly dependent to the velocity of the blood. Phase Contrast Image: bright = high velocities in the direction of the scan dark = high velociteis in the opposite direction phase contrast MR QMRA

7. Volume Flow Determination by QMRA / 2008/02/15 Page 7 of 64 Two undesired effects: 1. Limited velocity range 2. Works only for blood flow in one given direction QMRA Lotz J., Meir C., Leppert A. et al.: “Cardiovascular Flow Meaurement with Phase-Contrast MR Imaging: Basic Facts and Implementation”, RSNA, 2002

8. Volume Flow Determination by QMRA / 2008/02/15 Page 8 of 64 State of the Art or... State of the Art

9. Volume Flow Determination by QMRA / 2008/02/15 Page 9 of 64 State of the Art http://www.youtube.com/watch?v=a7rBJWhCkF8&feature=related http://www.vassolinc.com/QuickTourNOVA.cfm Visite or for a video about the current use of QMRA.

10. Volume Flow Determination by QMRA / 2008/02/15 Page 10 of 64 Pre-planed slices - inefficient workflow - requires registration - only flow information for a few samples State of the Art http://www.vassolinc.com

11. Volume Flow Determination by QMRA / 2008/02/15 Page 11 of 64 Agenda Goal QMRA State of the Art The New Approach Results

12. Volume Flow Determination by QMRA / 2008/02/15 Page 12 of 64 Combining an abstract model of the vessel tree with flow information. New Approach

13. Volume Flow Determination by QMRA / 2008/02/15 Page 13 of 64 Agenda Goal QMRA State of the Art The New Approach Results 1.Data Acquisition 2.Segmentation 3.Creation of an Abstract Model of the Vessel Tree 4.Adding Flow Information to the Abstract Tree 5.Improving Flow Information by the Use of Topological Information

14. Volume Flow Determination by QMRA / 2008/02/15 Page 14 of 64 Data Acquisition New Approach/Data Acquisition

15. Volume Flow Determination by QMRA / 2008/02/15 Page 15 of 64 Only one session with PCA scans in at least three orientations over the whole volume. New Approach/Data Acquisition

16. Volume Flow Determination by QMRA / 2008/02/15 Page 16 of 64 Because of pulsatile fluctuations, some kind of averaging over the heart beat is necessary: Each plane consist of a set of PCA slices depicting flow during different intervals of the (ECG-triggered) heart beat cycle. New Approach/Data Acquisition

17. Volume Flow Determination by QMRA / 2008/02/15 Page 17 of 64 Agenda Goal QMRA State of the Art The New Approach Results 1.Data Acquisition 2.Segmentation 3.Creation of an Abstract Model of the Vessel Tree 4.Adding Flow Information to the Abstract Tree 5.Improving Flow Information by the Use of Topological Information New Approach/Segmentation

18. Volume Flow Determination by QMRA / 2008/02/15 Page 18 of 64 Segmentation directly from the phase contrast data requires combining the three orthogonal scans due to the directional sensitivity of phase contrast MR. New Approach/Segmentation Phase contrast images only depict vessels which run roughly parallel to the scan direction

19. Volume Flow Determination by QMRA / 2008/02/15 Page 19 of 64 1.Combining PC-images 2.Region Growing 3.Closing Three major segmentation steps New Approach/Segmentation Eiho, Sekiguchi, S.H., Sugimoto, N. et al.: “Branch-Based Region Growing Method For Blood Vessel Segmentation”, Systems and Computers in Japan, 2005

20. Volume Flow Determination by QMRA / 2008/02/15 Page 20 of 64 Segmentation Result New Approach/Segmentation

21. Volume Flow Determination by QMRA / 2008/02/15 Page 21 of 64 Agenda Goal QMRA State of the Art The New Approach Results 1.Data Acquisition 2.Segmentation 3.Creation of an Abstract Model of the Vessel Tree 4.Adding Flow Information to the Abstract Tree 5.Improving Flow Information by the Use of Topological Information

22. Volume Flow Determination by QMRA / 2008/02/15 Page 22 of 64 Creation of an Abstract Model of the Vessel Tree New Approach/Abstract Tree Model Segmentation resultTopological Model

23. Volume Flow Determination by QMRA / 2008/02/15 Page 23 of 64 3.1) Topological Structure of the Vessel Tree { { Skeleton { Centerline New Approach/Abstract Tree Model

24. Volume Flow Determination by QMRA / 2008/02/15 Page 24 of 64 3.1) Topological Structure of the Vessel Tree => Centerline-Extraction Two common techniques: Distance based approaches Thinning New Approach/Abstract Tree Model/Topological Structure

25. Volume Flow Determination by QMRA / 2008/02/15 Page 25 of 64 Distance-Transform-Map 2D-object minimal distance of the pixel to the object‘s bounds 0 1 2 New Approach/Abstract Tree Model/Topological Structure/Distance Maps Distance Based Centerline Extraction In the case of symmetrical 2D-objects the maxima of the DTM already pose the centerline pixels.

26. Volume Flow Determination by QMRA / 2008/02/15 Page 26 of 64 Distance Based Centerline Extraction New Approach/Abstract Tree Model/Topological Structure/Distance Maps Not radially symmetrical objects possess multiple local maxima in their distance maps, which cannot be connected in a well defined way. In 3D only radially symmetrical objects pose such distinct maxima of the distance map.

27. Volume Flow Determination by QMRA / 2008/02/15 Page 27 of 64 New Approach/Abstract Tree Model/Topological Structure/Distance Maps Multiple Maxima in the DTM

28. Volume Flow Determination by QMRA / 2008/02/15 Page 28 of 64 New Approach/Abstract Tree Model/Topological Structure/Distance Maps Multiple Maxima in the DTM

29. Volume Flow Determination by QMRA / 2008/02/15 Page 29 of 64 Multiple Maxima in the DTM New Approach/Abstract Tree Model/Topological Structure/Distance Maps …can be avoided by filtering the DTM

30. Volume Flow Determination by QMRA / 2008/02/15 Page 30 of 64 …can be avoided by filtering the DTM, but this causes a loss of connectivity in thin vessel segments. Multiple Maxima in the DTM New Approach/Abstract Tree Model/Topological Structure/Distance Maps

31. Volume Flow Determination by QMRA / 2008/02/15 Page 31 of 64 Thinning … works by removing the voxels at the object bounds… … layer… … by layer… …until the remaining object poses only a thickness of one voxel.

32. Volume Flow Determination by QMRA / 2008/02/15 Page 32 of 64 Thinning Result New Approach/Abstract Tree Model/Topological Structure/Thinning Lamy, J.: “Integrating digital topology in image-processing libraries”, Elsevier Ireland Ltd, 2005

33. Volume Flow Determination by QMRA / 2008/02/15 Page 33 of 64 Centerline Extraction Distance based approach Thinning + correctness - bad connectivity + high connectivity - faulty New Approach/Abstract Tree Model/Topological Structure => combined approach using centerline voxels from thinning to connect local maxima from distance transform

34. Volume Flow Determination by QMRA / 2008/02/15 Page 34 of 64 Centerline Extraction: combined approach New Approach/Abstract Tree Model/Topological Structure/Combined Approach

35. Volume Flow Determination by QMRA / 2008/02/15 Page 35 of 64 3.2) Assignment of Volumetric Information to the Abstract Model α α 1 2 New Approach/Abstract Tree Model/Assignment of Volumetric Information A voxel in the vicinity of a centerline segment is added to the assigned volume, if the two intersection angles in the image are smaller then 90°.

36. Volume Flow Determination by QMRA / 2008/02/15 Page 36 of 64 Agenda Goal A little bit of MR-Physics State of the Art The New Approach Results 1.Data Acquisition 2.Segmentation 3.Creation of an Abstract Model of the Vessel Tree 4.Adding Flow Information to the Abstract Tree 5.Improving Flow Information by the Use of Topological Information

37. Volume Flow Determination by QMRA / 2008/02/15 Page 37 of 64 New Approach/Abstract Tree Model/Adding Flow Information Since the three phase contrast scans are orthogonal, they can be considered as the three components of a velocity vector.

38. Volume Flow Determination by QMRA / 2008/02/15 Page 38 of 64 Flow Velocities in all Vessel Segments New Approach/Abstract Tree Model/Adding Flow Information Total flow velocities in the vessel tree.

39. Volume Flow Determination by QMRA / 2008/02/15 Page 39 of 64 Intersection area New Approach/Abstract Tree Model/Adding Flow Information The knowledge of length and volume of all segments of the abstract vessel tree allows to compute the average intersection angle in all of these segments.

40. Volume Flow Determination by QMRA / 2008/02/15 Page 40 of 64 Flow Rates in all Vessel Segments New Approach/Abstract Tree Model/Adding Flow Information With knowledge of the intersection areas, flow rates can be computed for all segments of the abstract tree.

41. Volume Flow Determination by QMRA / 2008/02/15 Page 41 of 64 Agenda Goal A little bit of MR-Physics State of the Art The New Approach Results 1.Data Acquisition 2.Segmentation 3.Creation of an Abstract Model of the Vessel Tree 4.Adding Flow Information to the Abstract Tree 5.Improving Flow Information by the Use of Topological Information

42. Volume Flow Determination by QMRA / 2008/02/15 Page 42 of 64 or generating an intelligently weighted combination of the data from different slices Angular information allows selecting the most suitable PC-slice in order to improve flow information. Angle between sagittal plane and vessel segment 3 Angle between coronal plane and vessel segment 3 New Approach/Improving Flow Information

43. Volume Flow Determination by QMRA / 2008/02/15 Page 43 of 64 232 ? 448 51 ? 42 ? ? 50 48 232 216 448 181 51 72 42 30 98 50 48 ? - - + 109 - - + - + + - - - - + - Substitution of Unreliable Data in the Abstract Vessel Tree New Approach/Improving Flow Information

44. Volume Flow Determination by QMRA / 2008/02/15 Page 44 of 64 Summary QMRA poses technical limitations which so far compelled an inefficient workflow requiring patient or image registration and supplying only flow information for a few selected slices. The new approach might allow to acquire the necessary data in a one-step workflow without the need for patient or image registration that supplies flow information for all parts of the vessel tree with an accuracy (nearly) equal to that of pre-planed slices.

45. Volume Flow Determination by QMRA / 2008/02/15 Page 45 of 64 Results

46. Volume Flow Determination by QMRA / 2008/02/15 Page 46 of 64 Segmentation from PC-Data yespossible? advisable? depends… mutual improvement:future work? QMRA-Software would allow to detect and correct segmentation faults Improved segmentation would lead to improved abstract model. Results

47. Volume Flow Determination by QMRA / 2008/02/15 Page 47 of 64 Visualizing Flow yespossible? visualizing in the abstract treefuture work? Results

48. Volume Flow Determination by QMRA / 2008/02/15 Page 48 of 64 Substituting “unreliable” data in the vessel tree not provedpossible? would require better datafuture work? Results

49. Volume Flow Determination by QMRA / 2008/02/15 Page 49 of 64 Finding a corrective factor/function not provedpossible? would require more datafuture work? Results

50. Volume Flow Determination by QMRA / 2008/02/15 Page 50 of 64 Appendix

51. Volume Flow Determination by QMRA / 2008/02/15 Page 51 of 64 A little bit of MR-Physics

52. Volume Flow Determination by QMRA / 2008/02/15 Page 52 of 64 MRI is all about... the angular moment (spin) of protons.

53. Volume Flow Determination by QMRA / 2008/02/15 Page 53 of 64 These protons prefer to align with the external magnetic field of the scanner but can be “persuaded” (excited) to “anti-align” for a short moment.

54. Volume Flow Determination by QMRA / 2008/02/15 Page 54 of 64 When the protons “fall back” to the parallel state, after they were excited, they emit radio waves…

55. Volume Flow Determination by QMRA / 2008/02/15 Page 55 of 64 The strength of the external field has influence on how easily the protons can be excited.

56. Volume Flow Determination by QMRA / 2008/02/15 Page 56 of 64 The Physics of Phase Contrast

57. Volume Flow Determination by QMRA / 2008/02/15 Page 57 of 64

58. Volume Flow Determination by QMRA / 2008/02/15 Page 58 of 64

59. Volume Flow Determination by QMRA / 2008/02/15 Page 59 of 64 Image Plane phase shift moving proton field gradient slower proton

60. Volume Flow Determination by QMRA / 2008/02/15 Page 60 of 64 Two undesired effects: 1. Only 180° to encode all velocities 2. Works only for blood flow in the direction of the gradient  limited velocity range

61. Volume Flow Determination by QMRA / 2008/02/15 Page 61 of 64 Multiple Maxima in the DTM How to get rid of them? Averaging over close neighbors / by clusters? => many undesired effects Better: preventing them by filtering

62. Volume Flow Determination by QMRA / 2008/02/15 Page 62 of 64 Preventing multiple maxima by filtering Distance maps after applying a Gaussian filter

63. Volume Flow Determination by QMRA / 2008/02/15 Page 63 of 64 Multiple Maxima in the DTM

64. Volume Flow Determination by QMRA / 2008/02/15 Page 64 of 64 Thinning Thinning must take the topology of the object before removing voxels. Only voxels which are not important to preserve the objects topology are allowed to be deleted.