VI 3.5 WHAT ARE FLAT MAPS? .............................................................................................................................18 3.6 ADVANTAGES OF FLAT MAPS......................................................................................................................18 3.7 CREATING FLAT MAPS ................................................................................................................................19 3.7.1 High-Resolution Anatomy Scan .............................................................................................................19 3.7.2 Low-Resolution Inplane Anatomy Scan and Functional Scan...............................................................20 3.7.3 Segmenting High-resolution Anatomical Data ......................................................................................20 3.7.4 Flattening...............................................................................................................................................22 3.7.5 Aligning..................................................................................................................................................24 3.7.6 mrLoadRet .............................................................................................................................................25 3.8 TYPES OF FLAT MAPS..................................................................................................................................29 3.8.1 Phase Maps............................................................................................................................................31 3.8.2 Coherence Maps ....................................................................................................................................34 3.8.3 Visual Field Sign Maps..........................................................................................................................34 4 INTRODUCTION TO MRFINDBORDERS..................................................................... 37 4.1 OVERVIEW ..................................................................................................................................................37 4.2 IDENTIFYING RETINOTOPIC VISUAL AREAS .................................................................................................38 4.3 STARTING THE PROGRAM............................................................................................................................41 4.4 LOADING DATA AND DISPLAYING IT ...........................................................................................................42 4.5 CREATING ATLASES ....................................................................................................................................44 4.6 DEFORMING ATLASES .................................................................................................................................49 4.7 SELECTING AND DISPLAYING RESULTS........................................................................................................49 4.8 MENUS........................................................................................................................................................54 4.8.1 File Menu...............................................................................................................................................54 4.8.2 Edit Menu...............................................................................................................................................56 4.8.3 View Menu .............................................................................................................................................58 4.8.4 Tools Menu ............................................................................................................................................60 4.8.5 Help Menu..............................................................................................................................................65 4.9 CHANGING OPTIONS AND SETTINGS ............................................................................................................65 4.9.1 Main Window Settings ...........................................................................................................................65 4.9.2 Options Menu.........................................................................................................................................66 4.9.2.1 Atlases ...........................................................................................................................................................66 4.9.2.2 Color Maps....................................................................................................................................................67 4.9.2.3 Matching........................................................................................................................................................68 5 METHODS............................................................................................................................ 72 5.1 OVERVIEW ..................................................................................................................................................72 5.2 ATLAS FITTING............................................................................................................................................74 5.2.1 Creating Initially Aligned Atlas Images.................................................................................................74 5.2.2 Representation of the Displacement Field .............................................................................................76 5.2.3 Deformation ...........................................................................................................................................80 5.2.4 Estimating Displacement Fields ............................................................................................................83