Multiple Sclerosis Lesion Segmentation in Brain MRI Using Inception Modules Embedded in a Convolutional Neural Network

Abstract

Multiple sclerosis (MS) is a chronic and autoimmune disease that forms lesions in the central nervous system. Quantitative analysis of these lesions has proved to be very useful in clinical trials for therapies and assessing disease prognosis. However, the efficacy of these quantitative analyses greatly depends on how accurately the MS lesions have been identified and segmented in brain MRI. This is usually carried out by radiologists who label 3D MR images slice by slice using commonly available segmentation tools. However, such manual practices are time consuming and error prone. To circumvent this problem, several automatic segmentation techniques have been investigated in recent years. In this paper, we propose a new framework for automatic brain lesion segmentation that employs a novel convolutional neural network (CNN) architecture. In order to segment lesions of different sizes, we have to pick a specific filter or size 3 $\times$ 3 or 5 $\times$ 5. Sometimes, it is hard to decide which filter will work better to get the best results. Google Net has solved this problem by introducing an inception module. An inception module uses $3\times 3$ , $5\times 5$ , $1\times 1$ and max pooling filters in parallel fashion. Results show that incorporating inception modules in a CNN has improved the performance of the network in the segmentation of MS lesions. We compared the results of the proposed CNN architecture for two loss functions: binary cross entropy (BCE) and structural similarity index measure (SSIM) using the publicly available ISBI-2015 challenge dataset. A score of 93.81 which is higher than the human rater with BCE loss function is achieved.