this is a very commonly used technique. but at the moment the solely way to do this is by using the basic image processing and to conduct a multiplication of the original and the binary image. this simple function could be provided by the segmentation bundle
Isn't this what the AutoCrop action does?
-> When you create a new segmentation and draw some contours then right click on the segmentation node. There will be an "Auto Crop" entry.
There is also a bug concerning the auto crop function: T11213.
Currently MITK crashes if you try that :-) but Stefan and I are working on this bug.