Torsten is the right person to respond here and you may need to give an example e.g. some small input images and an output image if debugging is required.

Assuming that you have used the default behaviour of average_images, I believe it should just calculate the simple mean of the input images. What format are they in? Is it possible that they have some kind of calibration (which could be stored in a nii file).

You could show stack histograms from ImageJ or use the cmtk histogram tool to show full histogram inc min / max information for your inputs and outputs.

Best,

Greg.