sorry for the delayed answer. the data preparation is described in 
Styner M., Lee J., Chin B., Chin M.S., Commowick O., Tran H., Markovic-Plese S., Jewells V., Warfield S
3D Segmentation in the Clinic: A Grand Challenge II: MS lesion segmentation. MIDAS Journal - MICCAI 2008 Workshop
http://www.midasjournal.org/browse/publi...

Best
Martin