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Training deep ConvNets requires large labeled datasets. However, collecting pixel-level labels for medical image segmentation is very expensive and requires a high level of expertise. In addition, most existing segmentation masks provided by clinical experts focus on specific anatomical structures. In this paper, we propose a method dedicated to handle such partially labeled medical image datasets. We propose a strategy to identify pixels for which labels are correct, and to train Fully Convolutional Neural Networks with a multi-label