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Bioimagesuite Manual 95522 2

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Bioimagesuite Manual 95522 2 v2.6 c Copyright 2008 X. Papademetris, M. Jackowski, N. Rajeevan, R.T. Constable, and L.H Staib. Section of Bioimaging Sciences, Dept. of Diagnostic Radiology, Yale School of Medicine. All Rights Reserved ii Draft July 18, 2008 v2.6 Contents I A. Overview 1 1. Introduction 2 1.1. BioImage Suite Functionality . 3 1.2. BioImage Suite Software Infrastructure . 4 1.3. A Brief History . 4 2. Background 6 2.1. Applications of Medical Imaging Analysis: A Brief Overview . 6 2.2. Medical Image Processing & Analysis . 8 2.3. Software Development Related to Medical Image Analysis . 9 2.4. 3D Graphics and Volume Rendering . 11 3. Starting and Running BioImage Suite 18 3.1. Installation Overview . 18 3.2. Installation Instructions . 19 3.3. The Main BioImage Suite Menu . 22 3.4. Preferences Editor . 23 4. Application Structure 26 4.1. Application Structure Overview . 26 4.2. The File Menu . 27 4.3. The Display Menu . 31 5. Looking At Images 32 5.1. Image Formats . 32 5.2. The Viewers . 33 5.3. The Colormap Editor . 37 5.4. Coordinates for NeuroImaging . 39 5.5. Atlas Tools . 44 6. Advanced Image Visualization 47 6.1. 4D Images . 47 6.2. 3D Rendering Controls . 48 6.3. Volume Rendering . 48 6.4. Oblique Slices . 53 6.5. The Animation Tool . 54 iii Draft July 18, 2008 CONTENTS v2.6 II B. Anatomical Image Analysis 59 7. The Image Processing and Histogram Tools 60 7.1. Introduction . 60 7.2. “Image” and “Results” . 61 7.3. Histogram Control . 62 7.4. The Image Processing Control . 64 7.5. EXAMPLE:Reorientation of Images . 69 8. The Interactive Segmentation Tools 71 8.1. Introduction . 71 8.2. The Objectmap Editor Tools . 73 8.3. The Surface Editor . 74 8.4. Delineating a surface: a step-by-step recipe. 83 9. Tissue Classification 84 9.1. Accessing the Segmentation Tool . 84 9.2. Math Morphology . 85 9.3. Histogram Segmentation . 87 9.4. FSL Brain Extraction Tool . 88 9.5. Grey/White Segmentation – using FSL Fast . 92 9.6. Bias Field Correction . 93 9.7. Appendix: A Little bit of Theory . 97 10.Linear Registration 99 10.1. Accessing the Registration Tools . 100 10.2. Registration — Transformation . 102 10.3. Manual Registration . 107 10.4. Linear Registration (Intensity Based) . 109 10.5. Functional Overlay . 110 10.6. Image Compare . 113 10.7. EXAMPLE: Interactive Registration Tools . 114 10.8. Linear Transformations Theory: . 120 11.Non Linear Registration 122 11.1. Introduction . 122 11.2. Visualizing NonLinear Transformations . 122 11.3. Nonrigid Registration (Intensity Based) . 124 11.4. Distortion Correction (Single Axis Distortion) . 125 11.5. Batch Mode Registration . 125 11.6. Example: Co-register reference 3D brain with individual 3D brain . 132 11.7. Checking 3D to Reference non-linear registrations . 134 11.8. Remarks . 135 12.Landmarks, Surfaces and Point-based Registration 136 12.1. Introduction . 136 12.2. Acquiring Landmarks . 136 12.3. The Surface Control and the Surface Objectmap Control . 140 12.4. Point-based Registration Tools . 145 iv Draft July 18, 2008 CONTENTS v2.6 12.5. Appendix: An Overview of Robust Point Matching . 147 III C. Functional MRI Analysis 150 13.The Single Subject fMRI Tool 151 13.1. Introduction . 151 13.2. The fMRI Tool User Interface . 151 IV D. Multi Subject/Multi Image Analysis 162 14.The Multi-Subject Control 163 14.1. Introduction . 163 14.2. Setup File Format . 164 14.3. The Multisubject Tool Graphical User Interface . 167 14.4. Examples . 174 14.5. The new SimpleViewer Tool . 183 15.The Data Tree Manager 185 15.1. Introduction . 185 15.2. The Tree . 185 15.3. Space, Anatomical, and Functional Images . 192 15.4. The Overlay Tab . 195 15.5. Multiple Image Calculations . 195 15.6. Functionality for Intracranial Electrode Attributes . 197 15.7. Options . 200 V E. Diffusion Weighted Image Analysis 202 16.Diffusion Tensor Image Analysis 203 16.1. Introduction . 203 16.2. Accessing the Diffusion Tool . 204 16.3. Tensor Utility . 204 16.4. Loading diffusion-weighted images (DWI) . 204 16.5. Specifying gradient directions . 205 16.6. Loading a mask . 206 16.7. Computing the tensor . 207 16.8. Tensor transformations . 207 17.Diffusion Tensor Analysis 210 17.1. Introduction . 210 17.2. Loading the diffusion tensor . 210 17.3. Results . 211 17.4. Statistics . 211 17.5. Visualization . 212 17.6. Transformations . 215 v Draft July 18, 2008 CONTENTS v2.6 18.Fiber Tracking 216 18.1. Introduction . ..
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