Clonal analysis with the MARCM (mosaic analysis with a repressible cell marker) system can be used for studying cell lineage, development, and anatomy in the Drosophila olfactory system and other parts of the fly brain. To compare confocal images of labeled neurons in different brains, it may be desirable to register them to a template or standard brain. There are various image registration approaches available. Some depend on manually specifying landmarks on the brains to be registered. Others depend only on the grayscale intensity value of one of the channels in the confocal image. Another important difference between registration approaches is whether they apply linear or nonlinear (warping) transformations. Linear transformations typically include translation, rotation, and scaling along each axis. Nonlinear transformations are much more computationally intensive, but are required to register brains with different shapes. Here we describe the practical steps required for an intensity-based nonlinear registration that has been used to map the higher olfactory centers of the Drosophila brain using the staining for the presynaptic marker Bruchpilot (nc82). This registration is in fact a two-step process. The first step is a linear transformation that roughly aligns the two brains, followed by a second nonlinear step that allows different parts of the brain to move in slightly different directions.