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4 Introduction to mrFindBorders
4.1 Overview
The name of the developed tool is "mrFindBorders". This name was selected because the tool
belongs to a group of tools that handle MRI data ("mr") and because it can be used to find the
borders between adjacent retinotopic visual areas ("FindBorders"). The prefix "mr" is spoken
"mister" rather than "mr”. In this chapter, an introduction to mrFindBorders is presented. It
can be a user’s guide for learning to work with the program. Since this is an introduction, not
all concepts may become clear immediately. The reader is referred to later chapters that de-
scribe in detail the methods that are only sketched here.
The different retinotopic visual areas can be segregated from certain flattened phase maps
manually (see section 3.8). mrFindBorders' aim is it to simplify the task by making the proce-
dure more automatic. The results are also more systematic and do not depend as much on the
performance of the user as in manual segregation. The procedure is as follows. The program
creates initially aligned labeled atlases based on a theoretical, parameterized model of the ex-
pected activity. Some user input is required at this stage. In the atlases, the different visual ar-
eas are known. The atlases can be fit to the data by deformation using spline-based displace-
ment fields. A total energy is calculated, which is a weighted sum of currently four compo-
nents. For example, one component is a distance measure between the measured phase-wedge
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