I have written a plugin for ImageJ/Fiji which does fusion between PET or SPECT images and CT or MRI.
It is in partial use at Beth Israel Hospital in Boston Mass.
The software is located at
http://sourceforge.net/projects/bifijiplugins/There are 2 main plugins:
1) Read the Beth Israel database - of interest only in the hospital.
2) PetCtViewer - the program which is hopefully of more general interest.
3) PluginsUpdater - for automatic update of one or both of the above.
If you need help setting up the above, please contact me: ilan.tal-at-gmail.com
Ilan