The techniques available for the interrogation and analysis of neuroimaging data have a large influence in determining the flexibility, sensitivity and scope of neuroimaging experiments. The development of such methodologies has allowed investigators to address scientific questions which could not previously be answered and, as such, has become an important research area in its own right.In this paper, we present a review of the research carried out by the Analysis Group at the Oxford Centre for Functional MRI of the Brain (FMRIB). This research has focussed on the development of new methodologies for the analysis of both structural and functional magnetic resonance imaging data . The majority of the research laid out in this paper has been implemented as freely available software tools within FMRIB's Software Library (FSL).

A fundamental issue in neuroscience is the relation between structure and function. However, gross landmarks do not correspond well to microstructural borders and cytoarchitecture cannot be visualized in a living brain used for functional studies. Here, we used diffusion-weighted and functional MRI to test structurefunction relations directly. Distinct neocortical regions were defined as volumes having similar connectivity profiles and borders identified where connectivity changed. Without using prior information, we found an abrupt profile change where the border between supplementary motor area (SMA) and pre-SMA is expected. Consistent with this anatomical assignment, putative SMA and pre-SMA connected to motor and prefrontal regions, respectively. Excellent spatial correlations were found between volumes defined by using connectivity alone and volumes activated during tasks designed to involve SMA or pre-SMA selectively. This finding demonstrates a strong relationship between structure and function in medial frontal cortex and offers a strategy for testing such correspondences elsewhere in the brain.S ince early attempts to parcellate human and nonhuman cortex into structurally distinct subdivisions, the hypothesis that structural borders correspond to functional borders has been widely held (1-3). However, this hypothesis has been tested only rarely. Structural features such as sulci and gyri are commonly used to define anatomical regions in functional imaging, neurophysiology, and lesion studies, yet they have only a limited correspondence to more fine-grained structural organization such as cytoarchitecture (4-6). Microstructural borders based, for example, on measurements of cyto-, myelo-, or receptor architecture (7-9), can only be defined post mortem, and the methodological demands of such studies preclude investigation of the regional functional specializations in the same animals. Detailed testing of the relationship between these anatomicallybased measures and function based on comparisons between subjects is limited by the apparently substantial interindividual variations in microstructural anatomical boundaries (4-6).A structural feature that has not previously been used to define areal boundaries in the human neocortex is connectivity to other brain regions. Whereas features such as cytoarchitecture, myeloarchitecture, and receptor distributions distinguish the processing capabilities of a region, connectional anatomy constrains the nature of the information available to a region and the influence that it can exert over other regions in a distributed network. Therefore, not only does structural variation reflect functional organization, but local structural organization also determines local functional specialization. Data on brain connectivity in macaque monkeys show that cytoarchitectonically and functionally distinct regions of prefrontal cortex have distinct connectivity ''fingerprints'' (10). Differences in connectivity that parallel differences in cytoarchitecture have been used to define su...