This section presents an overview of our research into the analysis of structural MRI data. The tools resulting from this research provide the means for making quantitative measurements of physiologically or clinically relevant parameters. For example, the combination in SIENA of brain extraction (BET), tissue-type segmentation (FAST) and robust affine registration (FLIRT) allows for the accurate measurement of temporal brain-volume change. However, these tools are also of crucial importance in the processing stream in functional neuroimaging experiments. BET and FLIRT not only allow functional results to be interpreted in the context of the anatomy visible in structural images, but also allow data from different individuals and groups of individuals to be compared directly.