Hi Eveline, 

ImageJ has a number of useful tool for doing this sort of thing. You can download it for free here: http://rsb.info.nih.gov/ij/download.html

I do the same using ImageJ or by merging the image using 3D interpolation in matlab.

Once I did some reconstruction of the image of an aortic dissection using Osirix but never attempted to do it with the brain. This may be possible, at least in the professional version.