imgDilated = imdilate( img, structuringElement )
If you use a 3D array as a structuring element (for example, ones(3,3,3)), imdilate will work on 3D images (see http://www.mathworks.com/matlabcentral/newsreader/view_thread/66040).
I don't know whether it is possible to create a structuring element in 3D using the function strel. This is not in the documentation, so I doubt it. But it's not very difficult to make your own '3D-ball-shaped' structuring element. (Please note that strel('ball',N,R) is not a 3D-ball in this sense: it just refers to the fact that the generated structuring element is not 'flat', but has height differences).
Mark
