We propose a new similarity measure, Combined Connectivity and Spatial Adjacency (CCSA), to be used in hierarchical agglomerative clustering (HAC) for automated segmentation of Self-Organizing Maps (SOMs, Kohonen ). The CCSA measure is specifically designed to assist segmentation of large, complex, functional image data by exploiting general spatial characteristics of such data. The proposed CCSA measure is constructed from two strong indicators of cluster structure: the degree of localization of data points in physical space and the degree of connectivity of SOM prototypes (as defined by Tasdemir and Merényi ). The new measure is expected to enhance cluster capture in large functional image data cubes such as hyperspectral imagery or fMRI brain images, where many relevant clusters exist with widely varying statistical properties and in complex relationships both in feature space and in physical (image) space. We demonstrate the effectiveness of our approach using the CCSA measure on progressively complex synthetic spatial data and on real fMRI brain data.