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Introduction to mrFindBorders
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image and the corresponding atlas image. A high total energy means a bad deformation, a low
total energy a good deformation. A good deformation is expected to yield a good fit between
deformed atlas image and the corresponding measured image. Therefore, by minimizing the
total energy, the fit can be improved. An optimization technique does this. It estimates the
displacement fields, which define the deformation, so that the total energy becomes low. Once
the atlas matches the measured image well enough, the visual areas in the measured image can
be inferred from the atlas annotations.
First, this chapter motivates why it is useful to identify visual areas. Then, a quick tour of
how to produce some results with mrFindBorders is given, followed by a more detailed expla-
nation of its menus. Finally, the settings and options that can be changed in the main and op-
tions windows are discussed.
4.2 Identifying Retinotopic Visual Areas
It is useful to determine the locations of the visual areas or the boundaries between adjacent
visual areas. Some reasons are listed next (compare with [Wandell, 1999 #16]):
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In general, localizing functional regions in the brain is an important step on the way to
understand brain function. Once certain functionally specialized regions have been
identified, further quantitative investigation can take place [Khan, 1999 #33].
·
In the case of visual areas, brain mapping helps to understand the mechanisms of hu-
man vision. Understanding the functional specializations of the different visual areas is
an important first step towards understanding human vision.
·
The visual areas give a useful coordinate system that helps to identify locations within
cortex. This is useful to make comparisons between normal persons and persons with
various kinds of disabilities, e.g., deaf persons or persons with retina defects. It is also
useful for surgeons.
·
Identifying visual areas can help to make comparisons between brains at different
times in one subject (e.g., if brain changes due to a tumor or an injury) and between
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