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Despite several automated strategies for identification/segmentation of Multiple Sclerosis (MS) lesions in Magnetic Resonance Imaging (MRI) being developed, they consistently fall short when compared to the performance of human experts. This emphasizes the unique skills and expertise of human professionals in dealing with the uncertainty resulting from the vagueness and variability of MS, the lack of specificity of MRI concerning MS, and the inherent instabilities of MRI. Physicians manage this uncertainty in part by relying on their radiological, clinical, and anatomical experience. We have developed an automated framework for identifying and segmenting MS lesions in MRI scans by introducing a novel approach to replicating human diagnosis, a significant advancement in the field. This framework has the potential to revolutionize the way MS lesions are identified and segmented, being based on three main concepts: (1) Modeling the uncertainty; (2) Use of separately trained Convolutional Neural Networks (CNNs) optimized for detecting lesions, also considering their context in the brain, and to ensure spatial continuity; (3) Implementing an ensemble classifier to combine information from these CNNs. The proposed framework has been trained, validated, and tested on a single MRI modality, the FLuid-Attenuated Inversion Recovery (FLAIR) of the MSSEG benchmark public data set containing annotated data from seven expert radiologists and one ground truth. The comparison with the ground truth and each of the seven human raters demonstrates that it operates similarly to human raters. At the same time, the proposed model demonstrates more stability, effectiveness and robustness to biases than any other state-of-the-art model though using just the FLAIR modality.