Anatomical correlations for a hierarchical
multi-atlas segmentation of CT images
Oscar A. Jiménez del Toro
University of A...
Overview
•  Motivation
•  VISCERAL
•  Method
•  Multi-atlas segmentation
•  Image registration
•  Hierarchical registratio...
Overview
•  Motivation
•  VISCERAL
•  Method
•  Multi-atlas segmentation
•  Image registration
•  Hierarchical registratio...
Motivation
•  Anatomical segmentation is fundamental for
further image analysis and Computer-Aided
Diagnosis1
•  Manual an...
VISCERAL Benchmarks
•  Automatic segmentation of
anatomical structures (20)
– Visceral Benchmark 1: 12
ceCT test volumes*1...
Overview
•  Motivation
•  VISCERAL
•  Method
•  Multi-atlas segmentation
•  Image registration
•  Hierarchical registratio...
Overview
•  Motivation
•  VISCERAL
•  Method
•  Multi-atlas segmentation
•  Image registration
•  Hierarchical registratio...
Hierarchical multi-atlas segmentation
•  Use multiple atlases for the
estimation on a target
image
•  Global and local ali...
Image Registration
•  Atlas =
Patient volume + labels
•  Coordinate transformation
that increases spatial
correlation betw...
Affine alignment
•  Global
Affine alignment
•  Global
Affine alignment
•  Global
Affine alignment
•  Global
•  Local refinement for
independent structures
Affine alignment
•  Global
•  Local refinement for
independent structures
•  Regions of interest based on
the morphologica...
Affine alignment
•  Global
•  Local refinement for
independent structures
•  Regions of interest based on
the morphologica...
Affine alignment
•  Global
•  Local refinement for
independent structures
•  Regions of interest based on
the morphologica...
Right
Kidney
Liver
Global
alignment
Urinary
Bladder
Right
Lung
Left
Lung
1st Lumbar
Vertebra
Gall-
bladder
Left
KidneyTrac...
Non-rigid alignment
•  Non-rigid
•  B-spline
•  Multi-scale approach
•  Faster optimization
due to better initial
alignment
Label fusion
•  Majority voting threshold
•  Classification on a per-voxel
basis
•  Local registration errors are
reduced
...
Overview
•  Motivation
•  VISCERAL
•  Method
•  Multi-atlas segmentation
•  Image registration
•  Hierarchical registratio...
Overview
•  Motivation
•  VISCERAL
•  Method
•  Multi-atlas segmentation
•  Image registration
•  Hierarchical registratio...
Experimental setup
•  VISCERAL ISBI testset
•  5 contrast-enhanced CT volumes of the trunk
•  5 non-enhanced whole body CT...
Results ISBI Challenge
Structure DICE ceCT DICE wbCT
Liver 0.908 0.823
Right Kidney 0.905 0.649
Left Kidney 0.923 0.678
Ri...
Results ISBI Challenge
Structure DICE ceCT DICE wbCT
Liver 0.908 0.823
Right Kidney 0.905 0.649
Left Kidney 0.923 0.678
Ri...
Conclusion
•  Straightforward and fully automatic method
•  Showed robustness in the segmentation of
multiple structures w...
Questions???
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Anatomical correlations for a hierarchical multi-atlas segmentation of CT images

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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.

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Anatomical correlations for a hierarchical multi-atlas segmentation of CT images

  1. 1. Anatomical correlations for a hierarchical multi-atlas segmentation of CT images Oscar A. Jiménez del Toro University of Applied Sciences Western Switzerland (HES-SO)
  2. 2. Overview •  Motivation •  VISCERAL •  Method •  Multi-atlas segmentation •  Image registration •  Hierarchical registration approach •  Experimental setup •  Results •  Conclusion 2
  3. 3. Overview •  Motivation •  VISCERAL •  Method •  Multi-atlas segmentation •  Image registration •  Hierarchical registration approach •  Experimental setup •  Results •  Conclusion 3
  4. 4. Motivation •  Anatomical segmentation is fundamental for further image analysis and Computer-Aided Diagnosis1 •  Manual annotation and visual inspection is time consuming for radiologists •  Accurate large scale data analysis techniques are needed 1 K.Doi. Current status and future potential of computer-aided diagnosis in medical imaging. British Journal of Radiology, 78:3-19, 2005. 4
  5. 5. VISCERAL Benchmarks •  Automatic segmentation of anatomical structures (20) – Visceral Benchmark 1: 12 ceCT test volumes*10 structures – ISBI challenge: 5 ceCT, 5 wbCT test volumes*10 structures •  CT and MR images (contrast-enhanced and non-enhanced)
  6. 6. Overview •  Motivation •  VISCERAL •  Method •  Multi-atlas segmentation •  Image registration •  Hierarchical registration approach •  Experimental setup •  Results •  Conclusion 6
  7. 7. Overview •  Motivation •  VISCERAL •  Method •  Multi-atlas segmentation •  Image registration •  Hierarchical registration approach •  Experimental setup •  Results •  Conclusion 7
  8. 8. Hierarchical multi-atlas segmentation •  Use multiple atlases for the estimation on a target image •  Global and local alignment •  Hierarchical selection of the registrations improves results2 •  Label fusion 2Jiménez del Toro et.al., Multi-structure Atlas-Based Segmentation using Anatomical Regions of Interest. In proceeding of: Medical Image Computing and Computer Assisted Intervention (MICCAI2013) MCV workshop, Nagoya, Japan, 2013
  9. 9. Image Registration •  Atlas = Patient volume + labels •  Coordinate transformation that increases spatial correlation between images •  Multi-scale gaussian pyramid
  10. 10. Affine alignment •  Global
  11. 11. Affine alignment •  Global
  12. 12. Affine alignment •  Global
  13. 13. Affine alignment •  Global •  Local refinement for independent structures
  14. 14. Affine alignment •  Global •  Local refinement for independent structures •  Regions of interest based on the morphologically dilated initial estimations
  15. 15. Affine alignment •  Global •  Local refinement for independent structures •  Regions of interest based on the morphologically dilated initial estimations
  16. 16. Affine alignment •  Global •  Local refinement for independent structures •  Regions of interest based on the morphologically dilated initial estimations
  17. 17. Right Kidney Liver Global alignment Urinary Bladder Right Lung Left Lung 1st Lumbar Vertebra Gall- bladder Left KidneyTrachea Spleen 2nd Local Affine Hierarchical Registration approach Affine Local Affine B-spline non- rigid
  18. 18. Non-rigid alignment •  Non-rigid •  B-spline •  Multi-scale approach •  Faster optimization due to better initial alignment
  19. 19. Label fusion •  Majority voting threshold •  Classification on a per-voxel basis •  Local registration errors are reduced •  Threshold optimization
  20. 20. Overview •  Motivation •  VISCERAL •  Method •  Multi-atlas segmentation •  Image registration •  Hierarchical registration approach •  Experimental setup •  Results •  Conclusion 20
  21. 21. Overview •  Motivation •  VISCERAL •  Method •  Multi-atlas segmentation •  Image registration •  Hierarchical registration approach •  Experimental setup •  Results •  Conclusion 21
  22. 22. Experimental setup •  VISCERAL ISBI testset •  5 contrast-enhanced CT volumes of the trunk •  5 non-enhanced whole body CT •  Applied to 10 anatomical structures: – Liver, lungs, kidneys, gallbladder, urinary bladder, 1st lumbar vertebra, trachea and spleen •  7 independent atlases as trainingset
  23. 23. Results ISBI Challenge Structure DICE ceCT DICE wbCT Liver 0.908 0.823 Right Kidney 0.905 0.649 Left Kidney 0.923 0.678 Right Lung 0.963 0.967 Left Lung 0.952 0.969 Spleen 0.859 0.677 Trachea 0.83 0.855 Gallbladder 0.4 0.271 Urinary bladder 0.68 0.616 1st Lumbar vertebra 0.472 0.44
  24. 24. Results ISBI Challenge Structure DICE ceCT DICE wbCT Liver 0.908 0.823 Right Kidney 0.905 0.649 Left Kidney 0.923 0.678 Right Lung 0.963 0.967 Left Lung 0.952 0.969 Spleen 0.859 0.677 Trachea 0.83 0.855 Gallbladder 0.4 0.271 Urinary bladder 0.68 0.616 1st Lumbar vertebra 0.472 0.44
  25. 25. Conclusion •  Straightforward and fully automatic method •  Showed robustness in the segmentation of multiple structures with high overlap for the bigger structures (e.g. kidneys, liver, lungs) •  Smaller structures fared well compared to the other approaches •  Future work: –  Extend to method to other modalities (CTwb ISBI challenge, MR) –  Improve speed of the algorithm
  26. 26. Questions???

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