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Introduction to mrFindBorders
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The second component is the weight for the deformation energy. Deformation energy
defines the price (cost) that has to be paid for non-uniform deformation. The total en-
ergy will only decrease if the advantage (decrease of the other weighted energy com-
ponents) is bigger than the cost for non-uniform deformation (weighted deformation
energy). The deformation energy can ensure a smoother displacement field. However,
if the weight for the deformation energy is chosen to be too high, small local variations
might be missed. On the other hand, if the weight is too low, local noisy regions influ-
ence the result (see Figure 34 top). As a rule of thumb, the weight for the deformation
energy should be higher for data that is noisier than for data that is less noisy.
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The third weight allows using points (landmarks) that are specified by the user in the
measured phase-wedge image. These points are marked within boundaries between ad-
jacent visual areas. If the weighted point energy component is large compared to the
other energy components, it is possible to make sure that boundaries in the deformed
atlas image lie on top of specified points after deformation.
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The ring energy is a measure of how similar the measured phase-ring image is to the
corresponding atlas phase-ring image. It is calculated in the same way as the first en-
ergy component (wedge energy). The weight for the ring energy should be set to zero
if the aim is to only separate visual areas. This ensures that only the measured phase-
wedge atlas is matched to the corresponding atlas image. However, if iso-eccentricity
ROIs are to be created, the ring-energy weight should be set to a value greater than
zero.
Distance Between Adjacent Control Points
The distance between adjacent control points determines the number of control points. The
user can select from a list. If the distance is large, fewer control points are used. This leads to
a faster computation. However, the trade off is that an atlas cannot be deformed to match fine
details. The matching is done more coarsely.
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