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MICCAI Grand Challenge on Neonatal Brain Segmentation (NeoBrainS12)

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. Aim.

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MICCAI Grand Challenge on Neonatal Brain Segmentation (NeoBrainS12)

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  1. MICCAI Grand Challenge on Neonatal Brain Segmentation (NeoBrainS12) I. Išgum1, M.J.N.L. Benders2, M.A. Viergever1 1Image Sciences Institute, University Medical Center Utrecht 2Department 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: • axial scans acquired at 40 weeks corrected gestational age • coronal scans acquired at 30 weeks corrected gestational age • coronal scans acquired 40 weeks corrected gestational age

  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

  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

  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

  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

  8. Task • To segment • cortical grey matter (CoGM) • basal ganglia and thalami (BGT) • unmyelinated white matter (UWM) • myelinated white matter (MWM) • brainstem (BS) • cerebellum (CB) • ventricles (Vent) • cerebrospinal fluid in the extracerebral space (CSF)

  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.nl

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

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

  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

  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

  14. Pre-challenge results

  15. Set 1: Axial, 40w GA

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

  17. Set 1: Dice coefficient

  18. Set 1: Dice coefficient

  19. Set 1: Dice coefficient

  20. Set 1: Dice coefficient

  21. Set 1: MHD

  22. Set 1: MHD

  23. Set 1: MHD

  24. Set 1: MHD

  25. Set 2: Coronal, 30w GA

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

  27. Set 2: Dice coefficient

  28. Set 2: Dice coefficient

  29. Set 2: Dice coefficient

  30. Set 2: Dice coefficient

  31. Set 2: MHD

  32. Set 2: MHD

  33. Set 2: MHD

  34. Set 2: MHD

  35. Set 3: Coronal, 40w GA

  36. Set 3: Overall ranking

  37. Set 3: Dice coefficient

  38. Set 3: Dice coefficient

  39. Set 3: Dice coefficient

  40. Set 3: Dice coefficient

  41. Set 3: MHD

  42. Set 3: MHD

  43. Set 3: MHD

  44. Set 3: MHD

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

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

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

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

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

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

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