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Introduction to mrFindBorders
63
Figure 31 (top right). Deforming an atlas manually is sometimes useful before the
automatic matching process starts (to give the algorithm good starting displacement
fields), and after the matching process to manually edit the resulting deformation.
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The next commands allow creating and editing iso-angle ROIs and iso-eccentricity
ROIs (Figure 31 bottom row). The user can specify the number of angles and the num-
ber of iso-eccentricity ROIs, respectively. The created ROIs can be saved or exported
to mrLoadRet.
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Finally, the visual field sign map can be re-calculated based on the processed meas-
ured phase-wedge image and the processed measured phase-ring image, e.g., after the
coherence threshold has been changed.
Post Automatic Deformation
After the atlases have been deformed to match the corresponding measured phase images, the
visual-area ROIs can be displayed. Sometimes regions that should not have been identified are
included in the visual-area ROIs. This might be due to noise. It is possible to exclude those
regions by specifying points or polygons.
Debugging and Testing
The functions in this menu can be used to display additional information and images during
the matching process. It is also possible to record movies of how the algorithm deforms an
atlas image, and how the visual-area ROI overlay changes during the matching process. The
movies can be shown and saved from the View menu.
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