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Introduction to mrFindBorders
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4.3 Starting the Program
In mrFindBorders’ main directory resides a file called README.txt. Every user should read
this file at the beginning. Then, before the program can be started, the MATLAB paths have to
be set. This is done automatically by the MATLAB file mrFindBordersPath.m in the main di-
rectory of mrFindBorders. Not only the mrFindBorders paths need to be set up, but also those
of other tools like mrLoadRet. After the paths have been set, mrFindBorders can be started by
entering “mrFindBorders” in the MATLAB command window.
Figure 17 shows the main window after start-up. A wedge atlas with annotations for vis-
ual areas and fovea is displayed. A color bar showing the color map legend can be seen at the
right of the image. It shows the colors in the color map. The corresponding phase values in
radians are given. The atlas that is created by the algorithm has two additional areas beyond
V3 for better matching (see Figure 21). However, only areas V3d, V2d, V1, V2v, and V3v as
in Figure 17 are overlaid onto measured phase images in mrFindBorders for viewing pur-
poses.
The main window of mrFindBorders, shown in Figure 17, allows performing many tasks.
The commands to start those tasks can be given by choosing from the menu at the top. It is
also possible to activate or change different items in the main window, i.e., by pressing a but-
ton, by selecting from a list box, or by changing the position of a slider.
Figure 18 shows a sequence of steps to produce results with mrFindBorders. After the
program has been started, data has to be loaded. Then, the options are set. The options are ex-
plained later in this chapter after some more fundamental explanations have been given so that
the options explanations are easier to understand. New users who would like to get a quick
start can leave the options unchanged and create atlases right after loading data (press button
labeled “1. Create Atlases”). Then, to deform the created initially aligned atlases, the atlas can
be deformed (press button labeled “2. Deform Atlases”). After the automatic registration
(matching) has finished, the wanted visual areas can be marked by selecting from the corre-
sponding list box in the main window. The next sections describe these steps in more detail.
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