MRI Segmentation using

Dictionary Learning
-Krishna Dontaraju

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 Introduction
• Brain Tumor Segementation
– Diagnosis
– Surgery
– Radiotherapy planning
– Tumor growth Monitoring
• Manual Segmentation : 30 min – 3.5 hrs

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 Challenges
• Similar pixel intensity and texture between
normal tissue and tumor
• Variability of
– Shape
– Size
– Locations

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 Sample MRI

Visualized using MITK workbench software www.umbc.edu

 Discriminative Algorithms
• Learn to differentiate by using only training
data
– Sensitive to image acquisition protocols
vs
• Generative methods – use prior knowledge of
tumor structure and other morphologies
– Difficult to model

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 Algorithms
• Dictionary Learning
– OMP
– KSVD
• Kernal DL
– Kernal OMP
– Kernal KSVD

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Kernal KSVD

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 Dataset
• MNIST – Handwritten digits
– 60,000 training + 10,000 Testing samples
• BRATS 2012
– 30 sets of Real MRIs with 4 Modalities
• Flair, T1, T1c, T2
– 50 sets of synthetic data with 4 modalities

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 Implementation
• Datasets used
– Trainset 3 sets*
– Validation 1 set
– Test set 20000 voxels/set
• Dictionary size 500,1000
• K=3,5,10
• Voxel size =5x5x5=125
*this was still huge 158x214x174= 5,883,288 voxels per MRI
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 Tumor Ground truth
• 5 regions
– 1 for necrosis
– 2 for edema
– 3 for non-enhancing tumor
– 4 for enhancing tumor
– 0 for everything else
• 1+2+3+4 -> complete tumor
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 Results
Accuracy MNIST BRATS 2012
KSVD 96.5 51.91 (79.75,24.08)
Kernal KSVD 98.5 -

Dice score Complete tumor

Top brats performer .82
KSVD .61
23rd position .43

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Questions

Thank you!

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 References
• Lee, Jeon, et al. "Brain tumor image segmentation using kernel dictionary
learning." Engineering in Medicine and Biology Society (EMBC), 2015 37th
Annual International Conference of the IEEE. IEEE, 2015.
• Golts, Alona, and Michael Elad. "Linearized kernel dictionary
learning." IEEE Journal of Selected Topics in Signal Processing 10.4 (2016):
726-739.
• Ayache, N., N. Cordier, and H. Delingette. "The Multimodal Brain Tumor
Image Segmentation Benchmark (BRATS)." (2014).
• http://www.cs.technion.ac.il/~ronrubin/software.html

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