Exploring DeepMedic for the purpose of segmenting white matter hyperintensity lesions

Fiona Lippert; Bastian Cheng; Amir Golsari; Florian Weiler; Johannes Gregori; Götz Thomalla; Jan Klein

doi:10.1117/12.2292809

27 February 2018 Exploring DeepMedic for the purpose of segmenting white matter hyperintensity lesions

Fiona Lippert, Bastian Cheng, Amir Golsari, Florian Weiler, Johannes Gregori, Götz Thomalla, Jan Klein

Proceedings Volume 10575, Medical Imaging 2018: Computer-Aided Diagnosis; 105752F (2018) https://doi.org/10.1117/12.2292809
Event: SPIE Medical Imaging, 2018, Houston, Texas, United States

Abstract

DeepMedic, an open source software library based on a multi-channel multi-resolution 3D convolutional neural network, has recently been made publicly available for brain lesion segmentations. It has already been shown that segmentation tasks on MRI data of patients having traumatic brain injuries, brain tumors, and ischemic stroke lesions can be performed very well. In this paper we describe how it can efficiently be used for the purpose of detecting and segmenting white matter hyperintensity lesions. We examined if it can be applied to single-channel routine 2D FLAIR data. For evaluation, we annotated 197 datasets with different numbers and sizes of white matter hyperintensity lesions. Our experiments have shown that substantial results with respect to the segmentation quality can be achieved. Compared to the original parametrization of the DeepMedic neural network, the timings for training can be drastically reduced if adjusting corresponding training parameters, while at the same time the Dice coefficients remain nearly unchanged. This enables for performing a whole training process within a single day utilizing a NVIDIA GeForce GTX 580 graphics board which makes this library also very interesting for research purposes on low-end GPU hardware.

Citation Download Citation

Fiona Lippert, Bastian Cheng, Amir Golsari, Florian Weiler, Johannes Gregori, Götz Thomalla, and Jan Klein "Exploring DeepMedic for the purpose of segmenting white matter hyperintensity lesions", Proc. SPIE 10575, Medical Imaging 2018: Computer-Aided Diagnosis, 105752F (27 February 2018); https://doi.org/10.1117/12.2292809

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