In the current MITK version the segmentation utilities can be used with both unsigned char ('normal' segmentation) AND unsigned short (multilabel segmentations) images. Other types are not supported (filtered) due to inconsistencies with the mitk segmentations. In general it is of course possible to allow all data types but we think this would be not very intuitive.

A hint: A colleague once stumbled upon this issue as well. He was confused that there was no message telling him that. He was loading an .mhd file with a different data type. So please make sure that an appropriate error message is printed and it doesn't lead to a crash.
Can't reproduce it myself currently because of timing issues...
Best, Ingmar