When loading a multilabel segmentation (just a 'short' image with label values: 0, 1, 2, 3...) MITK will not automatically assign the multilabel colormap. Instead it uses binary segmentation color map, meaning that everything !=0 is white. That should be changed
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How does this image look like? What type of image is it? How do you think will MITK decide if the given image is a multilabel segmentation?