MICCAI Grand Challenge on Neonatal Brain Segmentation (NeoBrainS12) I. Išgum 1, M.J.N.L. Benders 2,...
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![Page 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.](https://reader038.fdocuments.us/reader038/viewer/2022110116/551a7276550346545e8b6160/html5/thumbnails/1.jpg)
MICCAI Grand Challenge on Neonatal Brain Segmentation
(NeoBrainS12)
I. Išgum1, M.J.N.L. Benders2, M.A. Viergever1
1Image Sciences Institute, University Medical Center Utrecht2Department of Neonatology, University Medical Center Utrecht
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Aim
To compare the performance of (semi-)automatic algorithms for neonatal brain tissue segmentation
in T1- and T2-weighted MR scans
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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
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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
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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
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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
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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
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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
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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
Sheet 9
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Evaluation
• Dice coefficient (DC)
• Modified Hausdorff distance (MHD)– 95th-percentile Hausdorff distance
Sheet 10
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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
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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
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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
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Pre-challenge results
Sheet 14
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Set 1: Axial, 40w GA
Sheet 15
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Set 1: Overall ranking
Sheet 16
Imperial Oxford UCL UPenn FER-UMCU UMCU1*0
1
2
3
4
5
6
3
3.25
4.75
5.2
1.35
3.15
*modified version of Anbeek et al, Pediatr Res. 2008
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Set 1: Dice coefficient
Sheet 17CoGM UWM CSF CB0
0.1
0.2
0.3
0.4
0.5
0.6
0.7
0.8
0.9
1
0.830000000000001
0.89
0.760000000000001
0.840000000000001
0.88
0.720000000000001
0.830000000000001
0.870000000000001
0.710000000000001
0.8
0.850000000000001
0.610000000000001
0.850000000000001
0.91
0.770000000000001
0.830000000000001
0.88
0.730000000000001
ImperialOxfordUCLUpennFER-UMCUUMCU1
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Set 1: Dice coefficient
Sheet 18BS CB BGT0
0.1
0.2
0.3
0.4
0.5
0.6
0.7
0.8
0.9
1
0.840000000000001
0.91 0.91
0.8
0.92
0.870000000000001
0.820000000000001
0.9 0.89
0.740000000000001
0.9
0.8
0.870000000000001
0.93 0.93
0.860000000000001
0.93 0.92
ImperialOxfordUCLUpennFER-UMCUUMCU1
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Set 1: Dice coefficient
Sheet 19UWM MWM UWM+MWM0
0.1
0.2
0.3
0.4
0.5
0.6
0.7
0.8
0.9
1
0.89 0.890.88
0.43
0.880.870000000000001
0.22
0.8700000000000010.850000000000001
0.320000000000001
0.840000000000001
0.91
0.55
0.910.88
0.55
0.870000000000001
ImperialOxfordUCLUpennFER-UMCUUMCU1
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Set 1: Dice coefficient
Sheet 20CSF Vent CSF+vent0
0.1
0.2
0.3
0.4
0.5
0.6
0.7
0.8
0.9
1
0.760000000000001
0.80.770000000000001
0.720000000000001
0.850000000000001
0.7400000000000010.710000000000001
0.81
0.730000000000001
0.610000000000001
0.860000000000001
0.640000000000001
0.770000000000001
0.830000000000001
0.78
0.730000000000001
0.81
0.750000000000001
ImperialOxfordUCLUpennFER-UMCUUMCU1
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Set 1: MHD
Sheet 21CoGM UWM CSF CB0
0.5
1
1.5
2
2.5
3
0.7300000000000010.630000000000001
1.68
0.6100000000000010.700000000000001
2.03
0.730000000000001
0.99
2.18
1.01
1.68
2.64
0.52
0.4
1.53
0.660000000000001
1.03
2.14
ImperialOxfordUCLUpennFER-UMCUUMCU1
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Set 1: MHD
Sheet 22BS CB BGT0
0.5
1
1.5
2
2.5
3
3.5
4
4.5
1.04
0.7000000000000010.8
1.24
0.630000000000001
1.321.3
0.92
1.29
1.96
0.850000000000001
4.18
0.52
0.35 0.35
0.750000000000001
0.35 0.4
ImperialOxfordUCLUpennFER-UMCUUMCU1
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Set 1: MHD
Sheet 23UWM MWM UWM+MWM0
5
10
15
20
25
30
35
0.630000000000001 0.7000000000000010.700000000000001
4.41
0.7500000000000010.99
29.38
1.031.68
17.07
1.79
0.4
4.36
0.41.03
8.9
1.07
ImperialOxfordUCLUpennFER-UMCUUMCU1
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Set 1: MHD
Sheet 24CSF Vent CSF+vent0
2
4
6
8
10
12
14
1.68
11.74
1.552.03
1.18
1.812.18
1.53
2.06
2.64
0.720000000000001
2.46
1.53
2.86
1.49
2.14
1.36
2
ImperialOxfordUCLUpennFER-UMCUUMCU1
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Set 2: Coronal, 30w GA
Sheet 25
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Set 2: Overall ranking
Sheet 26
Imperial UCL Upenn UMCU20
0.5
1
1.5
2
2.5
3
3.5
1.892
3.1
1.8
*Chita et al, submitted to a conference
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Set 2: Dice coefficient
Sheet 27CoGM UWM CSF CB0.00
0.10
0.20
0.30
0.40
0.50
0.60
0.70
0.80
0.90
1.00
0.70
0.91
0.84
0.71
0.90
0.76
0.60
0.87
0.63
0.70
0.94
0.85
ImperialUCLUpennUMCU2
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Set 2: Dice coefficient
Sheet 28BS CB BGT0.00
0.10
0.20
0.30
0.40
0.50
0.60
0.70
0.80
0.90
1.00
0.75
0.87
0.82
0.73
0.87
0.84
0.65
0.85
0.74
ImperialUCLUpenn
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Set 2: Dice coefficient
Sheet 29UWM MWM UWM+MWM0.00
0.10
0.20
0.30
0.40
0.50
0.60
0.70
0.80
0.90
1.00
0.90563 0.9054210.90
0.16
0.900.87
0.69
0.87
0.938652 0.938443
ImperialUCLUpennUMCU2
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Set 2: Dice coefficient
Sheet 30CSF Vent CSF+vent0.00
0.10
0.20
0.30
0.40
0.50
0.60
0.70
0.80
0.90
1.00
0.840.86 0.85
0.76
0.86
0.78
0.63
0.87
0.66
0.846348
0.79
ImperialUCLUpennUMCU2
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Set 2: MHD
Sheet 31CoGM UWM CSF CB0.00
0.50
1.00
1.50
2.00
2.50
1.00
0.50
1.32
0.91
0.75
1.15
1.90
0.83
2.11
1.11
0.34
0.94
ImperialUCLUpennUMCU2
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Set 2: MHD
Sheet 32BS CB BGT0.00
0.50
1.00
1.50
2.00
2.50
3.00
3.50
4.00
4.50
3.03
0.81
2.01
3.27
0.82
2.01
3.45
1.17
3.97
ImperialUCLUpenn
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Set 2: MHD
Sheet 33UWM MWM UWM+MWM0.00
5.00
10.00
15.00
20.00
25.00
0.498195 0.4982130.75
22.76
0.750.83 0.61 0.830.338562000000001 0.338562333333334
ImperialUCLUpennUMCU2
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Set 2: MHD
Sheet 34CSF Vent CSF+vent0.00
0.50
1.00
1.50
2.00
2.50
3.00
3.50
1.321.43
0.81
1.15
0.90
1.03
2.11
1.28
2.05
0.94332
3.03
ImperialUCLUpennUMCU2
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Set 3: Coronal, 40w GA
Sheet 35
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Set 3: Overall ranking
Sheet 36
Imperial Geneva UCL UPenn0.0
0.5
1.0
1.5
2.0
2.5
3.0
3.5
1.7
2.3
2.7
2.9
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Set 3: Dice coefficient
Sheet 37CoGM UWM CSF CB0.00
0.10
0.20
0.30
0.40
0.50
0.60
0.70
0.80
0.90
1.00
0.76
0.89
0.67
0.75
0.86
0.750.73
0.84
0.58
0.69
0.83
0.71
GenevaImperialUCLUpenn
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Set 3: Dice coefficient
Sheet 38BS CB BGT0.00
0.10
0.20
0.30
0.40
0.50
0.60
0.70
0.80
0.90
1.00
0.71
0.89
0.85
0.73
0.92
0.86
0.73
0.92
0.85
0.36
0.91
0.79
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Set 3: Dice coefficient
Sheet 39UWM MWM UWM+MWM0.00
0.10
0.20
0.30
0.40
0.50
0.60
0.70
0.80
0.90
1.00
0.88764 0.8794160.855914 0.8469300000000010.84
0.08
0.830.83
0.07
0.82
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Set 3: Dice coefficient
Sheet 40CSF Vent CSF+vent0.00
0.10
0.20
0.30
0.40
0.50
0.60
0.70
0.80
0.90
0.669200000000002
0.710988
0.75
0.82
0.77
0.58
0.70
0.61
0.71
0.84
0.72
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Set 3: MHD
Sheet 41CoGM UWM CSF CB0.00
0.50
1.00
1.50
2.00
2.50
3.00
3.50
4.00
0.83
0.57
3.61
0.860.95
2.24
1.01
1.23
2.96
1.17 1.12
2.72
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Set 3: MHD
Sheet 42BS CB BGT0.00
0.50
1.00
1.50
2.00
2.50
3.00
3.50
4.00
4.50
1.83
0.73
1.16
1.65
0.52
1.15
1.37
0.45
1.35
3.91
0.70
3.51
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Set 3: MHD
Sheet 43UWM MWM UWM+MWM0.00
5.00
10.00
15.00
20.00
25.00
30.00
35.00
0.565854 0.7308070.945071 1.122171.23
23.52
1.301.12
33.23
1.20
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Set 3: MHD
Sheet 44CSF Vent CSF+vent0.00
2.00
4.00
6.00
8.00
10.00
12.00
14.00
3.61137
2.445212.24
12.22
1.81
2.96
1.88
2.692.72
0.99
2.40
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CoGM: Sulci segmentation (40w)
Sheet 45
T2w Manual segmentationAutomatic 1 Automatic 2 Automatic 3 Automatic 4
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CoGM: Sulci segmentation (30w)
Sheet 46
T2wManual segmentation
Automatic 1 Automatic 2 Automatic 3 Automatic 4
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CoGM: Oversegmentation in CB
Sheet 47
T2w Manual segmentation
Automatic 1
Automatic 2
Automatic 3
Automatic 4
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UWM: False positives in CSF
Sheet 48
T2wManual segmentation
Automatic 1 Automatic 2 Automatic 3 Automatic 4
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CSF: sulci
Sheet 49
T2wManual segmentation
Automatic 1 Automatic 2 Automatic 3 Automatic 4
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T2w Manual segmentation
Ventricles
Sheet 50Automatic 1 Automatic 2 Automatic 3 Automatic 4
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CB: oversegmentation
Sheet 51
T2w Manual segmentation
Automatic 1
Automatic 2
Automatic 3
Automatic 4
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BGT-BS-MWM
Sheet 52Automatic 1 Automatic 2 Automatic 3 Automatic 4
T2wManual segmentation
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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
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Set 1: Combinations
Sheet 54CoGM UWM CSF CB0
0.1
0.2
0.3
0.4
0.5
0.6
0.7
0.8
0.9
1
0.850000000000001
0.91
0.770000000000001
0.85
0.89
0.78
0.86
0.91
0.79
FER-UMCUImperialOxfordUCLUpennUMCU1MVWMV
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Set 1: Combinations
Sheet 55BS CB BGT0.650000000000002
0.700000000000002
0.750000000000002
0.800000000000002
0.850000000000002
0.900000000000002
0.950000000000002
1
0.870000000000001
0.93 0.93
0.86
0.94
0.91
0.87
0.93
0.91
0.93
FER-UMCUImperialOxfordUCLUpennUMCU1MVWMV
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Set 1: Combinations
Sheet 56UWM MWM UWM+MWM0.2
0.3
0.4
0.5
0.6
0.7
0.8
0.9
1
0.91
0.55
0.910.89
0.38
0.890.91
0.46
0.90
0.55
FER-UMCUImperialOxfordUCLUpennUMCU1MVWMV
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Set 1: Combinations
Sheet 57CSF Vent CSF+vent0.5
0.55
0.6
0.65
0.7
0.75
0.8
0.85
0.9
0.95
0.7700000000000020.780.78
0.88
0.790.79
0.88
0.80
0.860000000000001
FER-UMCUImperialOxfordUCLUpennUMCU1MVWMV
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• All NeoBrains12 teams
• Christian Mol• Karina Kersbergen• Linda de Vries• Floris Groenendal• Pim Moeskops
Acknowledgement
Sheet 58
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Questions?
Sheet 59