VII 5.2.5 Energy....................................................................................................................................................84 5.2.6 Optimization Techniques........................................................................................................................85 5.2.6.1 Rotating Wedge Visual Stimulus –“Grad. (Angular Dir.)”............................................................................87 5.2.6.2 Wedge and Ring Visual Stimuli –“Grad. (2 Directions)”..............................................................................89 5.2.7 Constraints.............................................................................................................................................90 5.2.8 Hierarchical Matching...........................................................................................................................92 5.2.9 Advantages of Atlas Matching ...............................................................................................................93 5.2.10   Elastic Matching ....................................................................................................................................96 5.3 MARKING VISUAL AREAS..........................................................................................................................101 5.4 QUALITY MEASURE...................................................................................................................................102 5.5 VISUALIZATION .........................................................................................................................................104 6 PROGRAM FUNCTIONS................................................................................................. 106 6.1 OVERVIEW ................................................................................................................................................106 6.2 MAIN DIRECTORY .....................................................................................................................................107 6.3 DATASTRUCTURE .....................................................................................................................................108 6.4 DISPLACEMENTFIELD................................................................................................................................109 6.5 DOCUMENTATION .....................................................................................................................................113 6.6 ENERGY ....................................................................................................................................................114 6.7 FOREIGN....................................................................................................................................................119 6.8 LOAD ........................................................................................................................................................119 6.9 MAIN.........................................................................................................................................................122 6.10 MODEL......................................................................................................................................................134 6.11 PREPROCESSING ........................................................................................................................................136 6.12 PROGRAMDATA ........................................................................................................................................137 6.13 REGISTRATION ..........................................................................................................................................138 6.14 ROI...........................................................................................................................................................139 6.15 SIGNMAP ..................................................................................................................................................142 6.16 UI .............................................................................................................................................................144 6.17 UTILITIES...................................................................................................................................................148 6.18 WARPING ..................................................................................................................................................157 6.19 MRDATA (BY ROBERT F. DOUGHERTY) ....................................................................................................159 7 RESULTS............................................................................................................................ 160 7.1 OVERVIEW ................................................................................................................................................160 7.2 ARTIFICIAL IMAGE DATA...........................................................................................................................161 7.3 MEASURED IMAGE DATA ..........................................................................................................................164 7.3.1 Data Set 1 (“Alyssa”) ..........................................................................................................................164 7.3.1.1 Options and Settings....................................................................................................................................164 7.3.1.2 Creation of Initially Aligned Atlas...............................................................................................................166 7.3.1.3 Measured Phase-wedge Images With Marked ROIs....................................................................................167 7.3.1.4 Displacement Fields and Deformed Atlas....................................................................................................169