anatomical correlations for a hierarchical multi-atlas segmentation of the pancreas in ct images
DESCRIPTION
Many medical image analysis techniques require an initial localization and segmentation of anatomical structures. As part of the VISCERAL benchmarks on Anatomy segmentation, a hierarchical multi-atlas multi-structure segmentation approach guided by anatomical correlations is proposed. The method begins with a global alignment of the volumes and refines the alignment of the structures locally. The alignment of the bigger structures is used as reference for the smaller and harder to segment structures. The method is evaluated in the ISBI VISCERAL testset on ten anatomical structures in both contrast-enhanced and non-enhanced computed tomography scans. The proposed method obtained the highest DICE overlap score for some structures like kidneys and gallbladder. Similar segmentation accuracies compared to the highest results of the other methods proposed in the challenge are obtained for most of the other structures segmented with the method.TRANSCRIPT
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Anatomical correlations for a hierarchical multi-atlas segmentation of the pancreas in
CT images
Oscar A. Jiménez del Toro University of Applied Sciences Western Switzerland (HES-SO)
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Overview • Introduction • VISCERAL • Method
• Multi-atlas segmentation • Image registration • Hierarchical registration approach
• Pancreas segmentation • Results
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Overview • Introduction • VISCERAL • Method
• Multi-atlas segmentation • Image registration • Hierarchical registration approach
• Pancreas segmentation • Results
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Introduction • Anatomical segmentation is fundamental for
further image analysis1
• Different methods proposed2,3 (regression random forests, level set…)
• Comparison of multiple approaches for the same public dataset is uncommon
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VISual Concept Extraction challenge in RAdioLogy
• EU funded project (2012-2015) – HES-SO, ETHZ, UHD, MUW, TUW,
Gencat • Organize competitions on medical
image analysis on big data • All computation done in the cloud • Segmentation benchmark • Retrieval benchmark
• Annotation by medical doctors
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Cloud environment
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Benchmark 2 Anatomy • Automatic segmentation of
anatomical structures (20) and landmark detection
• Define challenges in large scale data (aprox. 10TB) processing
• CT and MR images (contrast-enhanced and non-enhanced)
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Overview • Introduction • VISCERAL • Method
• Multi-atlas segmentation • Image registration • Hierarchical registration approach
• Pancreas segmentation • Results
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Overview • Introduction • VISCERAL • Method
• Multi-atlas segmentation • Image registration • Hierarchical registration approach
• Pancreas segmentation • Results
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Hierarchical multi-atlas segmentation • Use multiple atlases for
the estimation on a target image
• Global and local alignment • Hierarchical selection of
the registrations improves results
• Label fusion
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Image Registration • Atlas = Patient volume + labels • Coordinate transformation
that increases spatial correlation – Affine: Rotate, translate, scale – B-spline: Non-rigid
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Right Kidney
Liver
Global alignment
Urinary Bladder Right Lung Left Lung 1st Lumbar Vertebra
Gall- bladder
Left Kidney Trachea
Spleen
2nd Local Affine
Hierarchical Registration approach
Affine
Local Affine
B-spline non-rigid
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Label fusion • Majority voting threshold
• Classification on a per-voxel basis
• Threshold optimization
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Overview • Introduction • VISCERAL • Method
• Multi-atlas segmentation • Image registration • Hierarchical registration approach
• Pancreas segmentation • Results
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Overview • Introduction • VISCERAL • Method
• Multi-atlas segmentation • Image registration • Hierarchical registration approach
• Pancreas segmentation • Results
15
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Right Kidney
Liver
Global alignment
Urinary Bladder Right Lung Left Lung 1st Lumbar Vertebra
Gall- bladder
Left Kidney Trachea
Spleen
2nd Local Affine
Pancreas segmentation Affine
Local Affine
B-spline non-rigid
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Right Kidney
Liver
Global alignment
Urinary Bladder Right Lung Left Lung 1st Lumbar Vertebra
Gall- bladder
Left Kidney Trachea
Spleen
2nd Local Affine
Affine
Local Affine
B-spline non-rigid
Liver
Right Kidney
Pancreas segmentation
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Experimental setup • VISCERAL Benchmark 1 testset • 10 contrast-enhanced CT volumes of the trunk • Added to segmentation method of 10
structures: – Liver, lungs, kidneys, gallbladder, urinary bladder,
1st lumbar vertebra, trachea and spleen • 7 independent atlases as trainingset
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Results • Average DICE score for Pancreas: 0.52
Structure DICE Rank in VISCERAL Benchmark 1
Liver 0.918 1st Right Kidney 0.913 1st Left Kidney 0.921 1st Right Lung 0.965 3rd Left Lung 0.955 3rd Spleen 0.852 3rd Trachea 0.836 2nd Gallbladder 0.566 1st Urinary bladder 0.7 3rd 1st Lumbar vertebra 0.522 2nd
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Results • Average DICE score for Pancreas: 0.52
Structure DICE Rank in VISCERAL Benchmark 1
Liver 0.918 1st Right Kidney 0.913 1st Left Kidney 0.921 1st Right Lung 0.965 3rd Left Lung 0.955 3rd Spleen 0.852 3rd Trachea 0.836 2nd Gallbladder 0.566 1st Urinary bladder 0.7 3rd 1st Lumbar vertebra 0.522 2nd
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Conclusion • Full automatic method • Requires little or no feedback from the user • Showed robustness in the segmentation of
multiple structures with high overlap • Fared well when compared to other methods
of the VISCERAL Benchmark 1 • Future work:
– Extend to method to other modalities (CTwb ISBI challenge, MR) – Test in a bigger dataset for VISCERAL Benchmark 2 Anatomy
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Sierre, Switzerland
Questions???