Novel Methods for the Visualization and Analysis of Functional Maps in Cortex

Introduction to mrFindBorders 65 4.8.5 Help Menu mrFindBorders opens a browser window with help if the user chooses the Help function from the Help menu (Figure 32). Information about mrFindBorders can be displayed, also in a browser window, by selecting “About”. Finally, this document is available in PDF (Adobe’s Portable Document Format) format. 4.9 Changing Options and Settings Although options have to be changed before the atlas is deformed to match the measured data, the Options menu is explained here so that the reader can better understand it. 4.9.1 Main Window Settings Figure 19 shows mrFindBorders’ main window. Setting a coherence threshold allows exclud- ing phase values with a low coherence value, i.e., with a low signal-to-noise ratio. Phase val- ues that have a coherence value below the set threshold are set to NaN. Regions that are NaN do not lead to an increased energy in the matching process. Therefore, noisy regions can be reduced. More details are presented later. Figure 32: mrFindBorders Help menu See text for details