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9 Summary
The visual cortex, which can be found in the occipital lobe, can be subdivided into different
visual areas. The visual areas are an important part of cortex organization. Among others, the
areas V1, V2, and V3 are retinotopically organized, i.e., adjacent points in the visual field map
onto adjacent points in the retinotopically organized visual cortex.
To improve the visualization, the cortical surface can be flattened. Functional magnetic
resonance imaging data, which is recorded from the cortical gray matter while a certain visual
stimulus is presented to a subject, can be displayed in two-space. Based on the resulting func-
tional flat maps, retinotopically organized visual areas can be identified. Often this is done
manually. The developed tool, called mrFindBorders, uses functional flat maps to segregate
retinotopic visual areas with only little user interaction. Such a semi automatic approach is not
only less user-time consuming, it is also more systematic, i.e., the results do not depend as
much on the performance of the user as in manual identification.
The program creates labeled atlas images, which are initially aligned with their corre-
sponding measured flat maps. The atlases show expected pattern of brain activity. The align-
ment can be improved by deforming the atlases. In the current implementation, the deforma-
tion is defined by pixel displacement fields. Displacement values are only assigned to a subset
of all pixels to reduce the degrees of freedom. This yields faster computation and smoother
deformations. The displacement values for the other pixels are calculated based on the dis-
placement values for the subset of pixels by interpolation. Once the atlas images have been
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