The different areas of the brain do not work in isolation. Instead they operate as integrated systems. These systems can be identified because areas within the same system have a similar, though not identical, pattern of connections. Because the areas are also interconnected, the activations of areas within a system tend to covary over time, whether the subject is at rest or engaged in a task. Thus the different systems can be identified on the basis of the degree to which they covary or are activated independently. There are two aims in studying functional systems. One is to identify the nature of information that flows from one area to another. The other is to characterize the causal structure of the system. Several methods are available to do this, and these have been particularly useful for studying top-down effects, as in the voluntary control of attention.
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