In this study, we proposed a pipeline to locate subcortical structures in patients with deep gray matter lesions using clinical brain MRI images. Due to altered signal intensity profile caused by lesions and high slice thickness (~5mm), segmentation of clinical MRI images provide challenges for state-of-the-art algorithms. Our proposed pipeline generates better subcortical structure segmentations, including better lesion coverage and more reliable segmentations than other widely used algorithms. The proposed pipeline may have help in automating the diagnosis of subcortical lesions, potentially improving current clinical practice.
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