Kevin Keraudren started a PhD in 2011 on organ localization in fetal MRI. His own research includes developing a 2D detector for fetal heads in MRI images and detecting eyes. Future plans are to validate current detectors, target other organs, and improve visualization of fetal MRI data through semi-automatic organ cataloguing.

1. Organ localisation in Fetal MRI
PhD started in October 2011
Kevin Keraudren
Steiner Unit, Hammersmith Hospital
June 8th , 2012

2. Introduction
What about fetuses?
1
What about fetuses?
3
Own research
2D detector for fetal heads
Eye detection
4
Future plans
Introduction
2
Own research
Future plans
K. Keraudren (ICL)
Organ localisation in Fetal MRI
June 8th , 2012
2 / 31

3. Introduction
What about fetuses?
1
What about fetuses?
3
Own research
4
Future plans
Introduction
2
Own research
Future plans
K. Keraudren (ICL)
Organ localisation in Fetal MRI
June 8th , 2012
3 / 31

4. Introduction
What about fetuses?
Own research
Future plans
Organ localisation
What?
Automatic detection of organs: center, bounding box or rough
segmentation.
Why?
Segmentation, measurements, optimised or standardised
visualisations, browsable body (keyword queries), tagging...
How?
Machine Learning methods, trained on relevant Training Data.
K. Keraudren (ICL)
Organ localisation in Fetal MRI
June 8th , 2012
4 / 31

5. Introduction
What about fetuses?
Own research
Future plans
Adults?
2 main groups on this subject:
Microsoft (A. Criminisi)
Siemens (D. Comaniciu)
Main focus on CT data from adults:
Modality
Subject
CT on adult
intensities directly related to
tissues
lay still, can hold breath,
aligned with the scanner
K. Keraudren (ICL)
MRI on fetus
relative values and field inhomogeneities
movement, random orientation and position of the
limbs, bending of the spine
Organ localisation in Fetal MRI
June 8th , 2012
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6. Introduction
What about fetuses?
Own research
Future plans
Siemens:
“Hierarchical Parsing and Semantic Navigation of Full Body CT
Data”, Seifert et al. (2009)
Slice detection
K. Keraudren (ICL)
Landmark detection
Organ localisation in Fetal MRI
Object detection
+ shape refinement
June 8th , 2012
6 / 31

7. Introduction
What about fetuses?
Own research
Future plans
Microsoft:
“Regression Forests for Efficient Anatomy Detection and
Localization in CT Studies”, Criminisi et al. (2011)
Automatic organ detection, repositioning of the 3D camera
and selection of the best colour transfer function
K. Keraudren (ICL)
Organ localisation in Fetal MRI
June 8th , 2012
7 / 31

8. Introduction
What about fetuses?
1
What about fetuses?
3
Own research
4
Future plans
Introduction
2
Own research
Future plans
K. Keraudren (ICL)
Organ localisation in Fetal MRI
June 8th , 2012
8 / 31

9. Introduction
What about fetuses?
Own research
Future plans
“Automatic Segmentation of Head Structures on Fetal MRI”, Anquez et
al. (2009) [FEMONUM]
Modeling the eyes for
template matching:
real eye, model and template
24 MRI volumes,
30-35 gestational weeks,
0.94 × 0.94 × 4 mm3
no motion
K. Keraudren (ICL)
Organ localisation in Fetal MRI
June 8th , 2012
9 / 31

10. Introduction
What about fetuses?
Own research
Future plans
“Automatic Segmentation of Head Structures on Fetal MRI”, Anquez et
al. (2009) [FEMONUM]
Graph-cut segmentation
of the brain, with rotated
template around eyes
center
24 MRI volumes,
30-35 gestational weeks,
0.94 × 0.94 × 4 mm3
no motion
K. Keraudren (ICL)
Organ localisation in Fetal MRI
June 8th , 2012
10 / 31

11. Introduction
What about fetuses?
Own research
Future plans
“Segmentation of the Fetal Envelope on Ante-Natal MRI”, Anquez et al.
(2010)
Semi-automated
registration of a
simplified skeleton
K. Keraudren (ICL)
Mean shape, graphcut initialisation and
resulting segmentation
Organ localisation in Fetal MRI
June 8th , 2012
11 / 31

12. Introduction
What about fetuses?
Own research
Future plans
“Detection of Fetal Anatomies from Ultrasound Images using a
Constrained Probabilistic Boosting Tree”, Carneiro et al. (2008)
From an annotated database,
learn to detect organs
Head and whole body
K. Keraudren (ICL)
Organ localisation in Fetal MRI
June 8th , 2012
12 / 31

13. Introduction
What about fetuses?
1
What about fetuses?
3
Own research
2D detector for fetal heads
Eye detection
4
Future plans
Introduction
2
Own research
Future plans
K. Keraudren (ICL)
Organ localisation in Fetal MRI
June 8th , 2012
13 / 31

14. Introduction
What about fetuses?
Own research
Future plans
2D detector for fetal heads
Sagittal head detector
Training data (Thanks Vanessa!)
Average image
303 tightly cropped images
K. Keraudren (ICL)
Organ localisation in Fetal MRI
June 8th , 2012
14 / 31

15. Introduction
What about fetuses?
Own research
Future plans
2D detector for fetal heads
Sagittal head detector
Viola&Jones detector from
OpenCV
Local Binary Pattern (LBP)
features
Exhaustive search by
rotating/mirroring new image
K. Keraudren (ICL)
Organ localisation in Fetal MRI
June 8th , 2012
15 / 31

16. Introduction
What about fetuses?
Own research
Future plans
2D detector for fetal heads
LBP features
1
2
5
4
6
3
7
8
black if
∑ Neighbour < ∑ Middle
else white
K. Keraudren (ICL)
Organ localisation in Fetal MRI
June 8th , 2012
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17. Introduction
What about fetuses?
Own research
Future plans
2D detector for fetal heads
LBP features
First tests of the detection process
K. Keraudren (ICL)
Organ localisation in Fetal MRI
June 8th , 2012
17 / 31

18. Introduction
What about fetuses?
Own research
Future plans
2D detector for fetal heads
Detection result
5min for a 1◦ rotation step,
less than 1min if 8◦ rotation step.
K. Keraudren (ICL)
Organ localisation in Fetal MRI
June 8th , 2012
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19. Introduction
What about fetuses?
Own research
Future plans
2D detector for fetal heads
Coronal head detector
Training data
Average image
666 tightly cropped images
K. Keraudren (ICL)
Organ localisation in Fetal MRI
June 8th , 2012
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20. Introduction
What about fetuses?
Own research
Future plans
2D detector for fetal heads
Transverse head detector
Training data
Average image
246 tightly cropped images + mirrored
K. Keraudren (ICL)
Organ localisation in Fetal MRI
June 8th , 2012
20 / 31

21. Introduction
What about fetuses?
Own research
Future plans
2D detector for fetal heads
Neck region darker than the brain
Influence of background
K. Keraudren (ICL)
Organ localisation in Fetal MRI
June 8th , 2012
21 / 31

22. Introduction
What about fetuses?
Own research
Future plans
2D detector for fetal heads
Detection result
In volumes, multiple detections increase confidence
Movie as example of true and false detection
K. Keraudren (ICL)
Organ localisation in Fetal MRI
June 8th , 2012
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23. Introduction
What about fetuses?
Own research
Future plans
2D detector for fetal heads
Room for improvement
Specific task, specific training data: no universal detector
Need for more testing, better separation of training and testing
data
Confidence score, and combining 3 detectors into a classifier
Combine with other detectors (eyes?) to increase confidence and
orientation
K. Keraudren (ICL)
Organ localisation in Fetal MRI
June 8th , 2012
23 / 31

24. Introduction
What about fetuses?
Own research
Future plans
Eye detection
Eye detection pipeline
1
Slice by slice:
1
2
2
Canny edge detection + template matching
Intensity filtering
For the whole volume:
1
2
3
4
Grouping candidate circles
Forming candidate pairs (25 mm ≤ d ≤ 39 mm)
Chan&Vese Level Sets segmentation + shape
checking
Grouping candidate pairs
K. Keraudren (ICL)
Organ localisation in Fetal MRI
June 8th , 2012
24 / 31

25. Introduction
What about fetuses?
Own research
Future plans
Eye detection
K. Keraudren (ICL)
Organ localisation in Fetal MRI
June 8th , 2012
25 / 31

26. Introduction
What about fetuses?
Own research
Future plans
Eye detection
Problem of motion (here 1.3mm spacing)
Several results returned, ranked by number of detection
Is it worth having a more complex pipeline than FEMONUM?
K. Keraudren (ICL)
Organ localisation in Fetal MRI
June 8th , 2012
26 / 31

27. Introduction
What about fetuses?
1
What about fetuses?
3
Own research
4
Future plans
Introduction
2
Own research
Future plans
K. Keraudren (ICL)
Organ localisation in Fetal MRI
June 8th , 2012
27 / 31

28. Introduction
What about fetuses?
Own research
Future plans
Future plans
Validate and integrate current detectors
Target other organs: dataset of 50 fetuses with lungs, heart,
kidneys, liver and whole body (Damodaram et al., 2012)
Regression Forests, multi-organs detection
Long-term goals:
Improve visualisation of fetal MRI data
(Semi-)Automatic building of catalogues of organs
K. Keraudren (ICL)
Organ localisation in Fetal MRI
June 8th , 2012
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29. Introduction
What about fetuses?
Own research
Future plans
Thanks!
K. Keraudren (ICL)
Organ localisation in Fetal MRI
June 8th , 2012
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30. Introduction
What about fetuses?
Own research
Future plans
Questions?
K. Keraudren (ICL)
Organ localisation in Fetal MRI
June 8th , 2012
30 / 31

31. Introduction
What about fetuses?
Own research
Future plans
Manual segmentation with OpenCV Grabcut
20min for 30 slices
K. Keraudren (ICL)
Organ localisation in Fetal MRI
June 8th , 2012
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