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Introduction to mrFindBorders
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4.5 Creating Atlases
For the task of finding the boundaries between adjacent retinotopic visual areas, functional
data is used. As explained before, the functional data is transformed to two-dimensional flat
maps. When the same visual stimulus, e.g., a flickering rotating wedge stimulus, is used, the
pattern found in the corresponding flat maps are similar across different subjects and at differ-
ent times. It is possible to create an atlas, which can be seen as a model of the expected pattern
of measured activity. Therefore, for this project, two-dimensional atlases that represent the
pattern of activity that is expected to be found in measured functional flat maps are of interest.
An atlas can be created in different ways. For example, an atlas can be based on data that
was measured from a single subject. Since brains are different due to the variability across in-
dividuals, a single representative brain does not exist. Deformable (adaptable) atlases are use-
ful to represent the functional pattern of different subjects. A registration algorithm can esti-
mate a two-dimensional displacement field to register the atlas data set with a measured data
set.
Measured functional flat maps from a single scan show high levels of noise. Therefore,
instead of using data recorded from a single subject or multiple subjects directly, it is possible
to create an abstraction of the measured images, i.e., a cartoon atlas. This is done in a way so
that the atlas shows the general pattern of activity that is theoretically expected in brains from
different subjects.
Because of many monkey studies and many human subjects that have been scanned, re-
searchers have a strong prediction of the expected pattern in functional flat maps produced
with standard wedge and ring stimuli. The atlases used in this project are cartoon atlases that
can be locally deformed to more closely match the measured data.
At first, atlas images are created so that they are initially (coarsely) aligned with the indi-
vidual measured phase data. After the button “1. Create Atlases” in the main window has been
pressed, the user can choose between two ways to create these atlases. He or she can specify
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