In recent years, there have been multiple works of literature reviewing methods for automatically segmenting multiple sclerosis (MS) lesions. However, there is no literature systematically and individually review deep learning-based MS lesion segmentation methods. Although the previous review also included methods based on deep learning, there are some methods based on deep learning that they did not review. In addition, their review of deep learning methods did not go deep into the specific categories of Convolutional Neural Network (CNN). They only reviewed these methods in a generalized form, such as supervision strategy, input data handling strategy, etc. This paper presents a systematic review of the literature in automated multiple sclerosis lesion segmentation based on deep learning. Algorithms based on deep learning reviewed are classified into two categories through their CNN style, and their strengths and weaknesses will also be given through our investigation and analysis. We give a quantitative comparison of the methods reviewed through two metrics: Dice Similarity Coefficient (DSC) and Positive Predictive Value (PPV). Finally, the future direction of the application of deep learning in MS lesion segmentation will be discussed.

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