PADDIT: Probabilistic Augmentation of Data using Diffeomorphic Image Transformation

Mauricio Orbes-Arteaga; Lauge Sørensen; Jorge Cardoso; Marc Modat; Sebastien Ourselin; Stefan Sommer; Mads Nielsen; Christian Igel; Akshay Pai

doi:10.1117/12.2512520

15 March 2019 PADDIT: Probabilistic Augmentation of Data using Diffeomorphic Image Transformation

Mauricio Orbes-Arteaga, Lauge Sørensen, Jorge Cardoso, Marc Modat, Sebastien Ourselin, Stefan Sommer, Mads Nielsen, Christian Igel , Akshay Pai

Author Affiliations +

Proceedings Volume 10949, Medical Imaging 2019: Image Processing; 109490S (2019) https://doi.org/10.1117/12.2512520
Event: SPIE Medical Imaging, 2019, San Diego, California, United States

Abstract

For proper generalization performance of convolutional neural networks (CNNs) in medical image segmentation, the learnt features should be invariant under particular non-linear shape variations of the input. To induce invariance in CNNs to such transformations, we propose Probabilistic Augmentation of Data using Diffeomorphic Image Transformation (PADDIT) – a systematic framework for generating realistic transformations that can be used to augment data for training CNNs. The main advantage of PADDIT is the ability to produce transformations that capture the morphological variability in the training data. To this end, PADDIT constructs a mean template which represents the main shape tendency of the training data. A Hamiltonian Monte Carlo(HMC) scheme is used to sample transformations which warp the training images to the generated mean template. Augmented images are created by warping the training images using the sampled transformations. We show that CNNs trained with PADDIT outperforms CNNs trained without augmentation and with generic augmentation (0.2 and 0.15 higher dice accuracy respectively) in segmenting white matter hyperintensities from T1 and FLAIR brain MRI scans.

Conference Presentation

Citation Download Citation

Mauricio Orbes-Arteaga, Lauge Sørensen, Jorge Cardoso, Marc Modat, Sebastien Ourselin, Stefan Sommer, Mads Nielsen, Christian Igel , and Akshay Pai "PADDIT: Probabilistic Augmentation of Data using Diffeomorphic Image Transformation", Proc. SPIE 10949, Medical Imaging 2019: Image Processing, 109490S (15 March 2019); https://doi.org/10.1117/12.2512520

ACCESS THE FULL ARTICLE

INSTITUTIONAL
Select your institution to access the SPIE Digital Library.

SELECT YOUR INSTITUTION

PERSONAL
Sign in with your SPIE account to access your personal subscriptions or to use specific features such as save to my library, sign up for alerts, save searches, etc.

PERSONAL SIGN IN

No SPIE Account? Create one

PURCHASE THIS CONTENT

SUBSCRIBE TO DIGITAL LIBRARY

50 downloads per 1-year subscription

Members: $195

Non-members: $335 ADD TO CART

25 downloads per 1 - year subscription

Members: $145

Non-members: $250 ADD TO CART

PURCHASE SINGLE ARTICLE

Includes PDF, HTML & Video, when available