Image registration with anatomical modalities, such as CT and MRI, facilitates the anatomical identification and localization in the interpretation of nuclear medicine images that lack anatomical information. The implementation of Functional Image Registration (FIRE), an operating system (OS) and platform independent multimodal image registration software is reported. In order to register the images without an operator's interaction, several automatic algorithms were implemented. These include principal axes matching and maximization of the mutual information methods. The user interface was designed to support the manual registration of the images. Fused images were composed by overlaying one image with the other one transparently, in which the opacity of the overlaid image was interactively controlled. FIRE was successfully applied to many clinical cases for which automatic and/or manual registration was required. An OS and platform independent program for image registration developed in this study will be useful for the clinical application of image registration techniques.