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Introduction to mrFindBorders
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The phase offset is a constant phase value that is added to all pixels of a measured phase im-
age. For the measured phase-wedge image, it is automatically determined after the data has
been loaded so that phases in atlas and measured image match. In the case of the measured
phase-ring image, it is automatically calculated after the atlas images have been created.
The user can also set the phase offset manually by changing the position of the appropri-
ate slider. To re-estimate the phase offset automatically, one of the buttons below the sliders
can be pressed. This is useful after changing the coherence threshold, or after setting regions
in the measured phase-wedge image to NaN. The reason for this is that the phase offset is cal-
culated based on the processed data and not based on the original, loaded data.
4.9.2 Options Menu
Options can be changed in the options menu after data have been loaded. In the top menu, se-
lect Edit-Options to open the options window. A figure like the one in Figure 33 is shown. In
many cases, the shown default options, which are saved in the file vSetUdDefault.m, have not
to be changed for a new data set.
4.9.2.1 Atlases
The radial length of the wedge in the atlas image can be changed. If the radius factor is one,
then the radius that is calculated by the program is used without modification. The ring atlas is
also influenced by the specified radius factor. In addition, a fovea offset (for the wedge atlas)
can be specified. This is the distance between the center of the wedge and the expected center
of the fovea. A fovea offset of zero creates an atlas where all iso-angle lines would end up in
one point. This is usually not a good model for the measured phase-wedge image.
Both parameters, the atlas radius and the fovea offset, are calculated automatically if the
user decides to specify a polygon with four points instead of 3 points in the boundaries when
creating the atlases. Therefore, if the polygon method is used, the parameters specified in the
options menu do not influence the atlas creation process.
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