1. MICCAI Grand Challenge on Neonatal Brain Segmentation (NeoBrainS12) I. Išgum 1, M.J.N.L. Benders 2, M.A. Viergever 1 1 Image Sciences Institute, University Medical Center Utrecht 2 Department of Neonatology, University Medical Center Utrecht

2. Aim To compare the performance of (semi-)automatic algorithms for neonatal brain tissue segmentation in T1- and T2-weighted MR scans

3. Data Three different image sets of pre-term born infants are available: 1.axial scans acquired at 40 weeks corrected gestational age 2.coronal scans acquired at 30 weeks corrected gestational age 3.coronal scans acquired 40 weeks corrected gestational age Sheet 3

4. Patient population No brain pathology was visible 15 months follow-up normal according to Griffith's assessment test All scans acquired on a Philips 3T system Sheet 4

5. Protocol: axial scans, 40 w 3DT1-weighted: TR=9.4 ms; TE=4.6 ms; scan time=3.44 min, FOV=180x180; reconstruction matrix=512x512; consecutive sections with thickness=2.0 mm; number of sections=50, in-plane resolution 0.35 mm x 0.35 mm; T2-weighted: TR=6293 ms; TE=120 ms; scan time=5.40 min; FOV=180x180; reconstruction matrix=512x512; consecutive sections with thickness=2.0 mm; number of sections=50, in-plane resolution 0.35 mm x 0.35 mm Sheet 5

6. Protocol: coronal scans, 30 w 3DT1-weighted: TR=9.4 ms; TE=4.6 ms; scan time=4.44 min, FOV=130x100; reconstruction matrix=384x384; consecutive sections with thickness=2.0 mm; number of sections=50, in-plane resolution 0.34 mm x 0.34 mm; T2-weighted: TR=10085 ms; TE=120 ms; scan time=6.23 min; FOV=130x100; reconstruction matrix=384x384; consecutive sections with thickness=2.0 mm; number of sections=50, in-plane resolution 0.34 mm x 0.34 mm Sheet 6

7. Protocol: coronal scans, 40 w 3DT1-weighted: TR=9.5 ms; TE=4.6 ms; scan time=7.02 min, FOV=200x200; reconstruction matrix=256x256; consecutive sections with thickness=1.2 mm; number of sections=110, in-plane resolution 0.78 mm x 0.78 mm; T2-weighted: TR=4847 ms; TE=150 ms; scan time=5.05 min; FOV=180x180; reconstruction matrix=512x512; consecutive sections with thickness=1.2 mm; number of sections=110, in-plane resolution 0.35 mm x 0.35 mm Sheet 7

8. Task To segment 1.cortical grey matter (CoGM) 2.basal ganglia and thalami (BGT) 3.unmyelinated white matter (UWM) 4.myelinated white matter (MWM) 5.brainstem (BS) 6.cerebellum (CB) 7.ventricles (Vent) 8.cerebrospinal fluid in the extracerebral space (CSF) Sheet 8

9. Reference standard Manual segmentations were performed by trained observers The segmentations were verified independently by three neonatologists In case of disagreement, the decision was made in a consensus meeting Protocol: http://neobrains12.isi.uu.nlhttp://neobrains12.isi.uu.nl Sheet 9

10. Evaluation Dice coefficient (DC) Modified Hausdorff distance (MHD) –95th-percentile Hausdorff distance Sheet 10

11. Ranking Per set ranking –based on per tissue rankings Per tissue rankings –for the eight tissue classes –unmyelinated + myelinated white matter –cerebrospinal fluid in the extracerebral space + ventricles Rankings based on –Dice coefficient –modified Hausdorff distance Sheet 11

12. Overall rankings The overall per tissue ranking –average of per tissue rankings based on the DC and based on the MHD The overall per set ranking –Average of overall per tissue rankings within the data set Sheet 12

13. Winners One winner per set will be announced To qualify –a team must be ranked in at least three overall per tissue rankings for the given set –the segmentation method needs to be automatic –team had no other data from the segmented sets but those provided by the challenge Sheet 13

14. Pre-challenge results Sheet 14

15. Set 1: Axial, 40w GA Sheet 15

16. Set 1: Overall ranking Sheet 16 *modified version of Anbeek et al, Pediatr Res. 2008

17. Set 1: Dice coefficient Sheet 17

18. Set 1: Dice coefficient Sheet 18

19. Set 1: Dice coefficient Sheet 19

20. Set 1: Dice coefficient Sheet 20

21. Set 1: MHD Sheet 21

22. Set 1: MHD Sheet 22

23. Set 1: MHD Sheet 23

24. Set 1: MHD Sheet 24

25. Set 2: Coronal, 30w GA Sheet 25

26. Set 2: Overall ranking Sheet 26 *Chita et al, submitted to a conference

27. Set 2: Dice coefficient Sheet 27

28. Set 2: Dice coefficient Sheet 28

29. Set 2: Dice coefficient Sheet 29

30. Set 2: Dice coefficient Sheet 30

31. Set 2: MHD Sheet 31

32. Set 2: MHD Sheet 32

33. Set 2: MHD Sheet 33

34. Set 2: MHD Sheet 34

35. Set 3: Coronal, 40w GA Sheet 35

36. Set 3: Overall ranking Sheet 36

37. Set 3: Dice coefficient Sheet 37

38. Set 3: Dice coefficient Sheet 38

39. Set 3: Dice coefficient Sheet 39

40. Set 3: Dice coefficient Sheet 40

41. Set 3: MHD Sheet 41

42. Set 3: MHD Sheet 42

43. Set 3: MHD Sheet 43

44. Set 3: MHD Sheet 44

45. CoGM: Sulci segmentation (40w) Sheet 45 T2w Manual segmentation Automatic 1Automatic 2Automatic 3Automatic 4

46. CoGM: Sulci segmentation (30w) Sheet 46 T2w Manual segmentation Automatic 1Automatic 2Automatic 3Automatic 4

47. CoGM: Oversegmentation in CB Sheet 47 T2w Manual segmentation Automatic 1 Automatic 2 Automatic 3 Automatic 4

48. UWM: False positives in CSF Sheet 48 T2w Manual segmentation Automatic 1Automatic 2Automatic 3Automatic 4

49. CSF: sulci Sheet 49 T2w Manual segmentation Automatic 1Automatic 2Automatic 3Automatic 4

50. T2w Manual segmentation Ventricles Sheet 50 Automatic 1Automatic 2Automatic 3Automatic 4

51. CB: oversegmentation Sheet 51 T2wManual segmentation Automatic 1 Automatic 2 Automatic 3 Automatic 4

52. BGT-BS-MWM Sheet 52 Automatic 1Automatic 2Automatic 3Automatic 4 T2w Manual segmentation

53. Combination of methods Majority voting with all submitted methods Weighted majority voting of all methods –Based on a dice coefficient –Leave-one-out experiments Sheet 53

54. Set 1: Combinations Sheet 54

55. Set 1: Combinations Sheet 55

56. Set 1: Combinations Sheet 56

57. Set 1: Combinations Sheet 57

58. All NeoBrains12 teams Christian Mol Karina Kersbergen Linda de Vries Floris Groenendal Pim Moeskops Acknowledgement Sheet 58

59. Questions? Sheet 59