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, Cervenansky,
F., Yang, X., Heng, P. A., ... & Sanroma, G.
(2018). Deep learning techniques for
automatic mri cardiac multi-structures
segmentation and diagnosis: Is the problem
solved?. IEEE transactions on medical imaging,
37(11), 2514-2525.
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Agenda
- What is CMRI?
- challenges related to CMRI
- The Purpose of the paper
- Machine learning techniques for CMRI from 2009-2015
- Challenges
- Non deep Learning approach
- Deep Learning approach
- Evaluation Framework
- Evaluated architecture
- Results
- Clinical applications
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What is CMRI?
The analysis require accurate delineation of the left and right ventricular
endocardium and epicardium, for both end diastolic (ED) and end systolic (ES)
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Challenges related to CMRI Segmentation
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Purpose of the paper
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Machine learning techniques for CMRI from 2009-2015: challenges
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Machine learning techniques for CMRI from 2009-2015: non deep learning
techniques
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Machine learning techniques for CMRI from 2009-2015: deep learning techniques
● patch-based CNN
● 2D convolutional neural networks (CNNs)
● Deep learning frameworks
Dozen of papers
Not used before LV segmentation
published in the
2013 ● combined approach between CNN and multi-atlas
subject ● automatic combined deep-learning and deformable
model approach
● Recurrent Fully-Convolutional Network (RFCN) for both
LV and RV
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Evaluation Framework dataset: Patients selection
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Evaluation Framework dataset:
Acquisition protocol
6 years
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Evaluation Framework dataset: Training and testing dataset
The data for each subject was converted to a general 4D image representation
format (nifti) without loss of resolution.
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Evaluation Framework: Reference segmentation and contouring protocol
Geometrical metrics:
3D Hausdorff distance which is the greatest of all the distances from a point in
one set to the closest point in the other set. allows an intrinsic management of
the missing segmentation problem on the end slices.
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Evaluation Framework:Evaluation metrics(2)
Clinical performance:
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Evaluation Framework:Evaluation metrics (3)
Classification performance:
● Accuracy: For the whole examinations of the testing database and per
disease
● Confusion matrix (Precision, Recall, F-score)
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For segmentation For classification
2D U-Net SVM
Dense U-Net 2D Random forest
3D U-Net
2D+3D U-Net
2D M-Net
2D Grid-Net
SVF-Net
Levelset+MRF
Dilated CNN
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EVALUATED ARCHITECTURES
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A. Architectures for cardiac multi-structure segmentation :
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. B.Solutions for automatic cardiac diagnosis:
● · Isensee et al. extracted a series of instants and dynamic features from the
segmentation maps and used an ensemble of 50 multilayer perceptrons
(MLP) and a random forest to perform classification.
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● Wolterink et al. extracted 14 features (12 from the segmentation maps +
patient weight and height) and used a five-class random forest classifier with
1,000 decision trees.
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The best performing method
They computed 567 features including physiological features (e.g. height
and weight) and radiomic features such as shapebased features, intensity
statistics, and various texture features.
From these results, one can see that the 2D-3D U-Net ensemble model
proposed by Isensee et al. is overall the top performing method for
segmentation .
As we had 50 patients . Khened et al. obtained nearly perfect results with
48 patients correctly classified.(96% AUC ) with random forest algorithm.
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Discussion
Where do methods fail?
· Images from healthy subjects (NOR) are not easier to segment than
those from pathological cases as the scores relative to this group get the
largest Hausdorff distances for the LV-ED and LV-ES.
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...
○ Another hypothesis commonly accepted in the community is that slices
next to the valves and/or the apex of the ventricle are more difficult to
segment due to partial volume effect with surrounding structures.
○Finally, it is worth pointing that the use of a larger database than the one
involved in this project might help in resolving the listed remaining issues.
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CONCLUSIONS
There is a need of a new metric because the fact that clinical and geometrical
metrics used to assess results have important limits and that methods within the
inter-observer variability may still be error-prone.
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...
We believe that some other pathologies such as inflammatory
cardiomyopathy could be successfully diagnosed with the proposed
machine learning methods, other (yet more complex) diseases such as
congenital heart diseases or heart defect, would need dedicated studies.
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