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©
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
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
- Contents
- 1 A. Overview
- 1. Introduction
- 2. Background
- 3. Starting and Running BioImage Suite
- 4. Application Structure
- 5. Looking At Images
- 6. Advanced Image Visualization
- 2 B. Anatomical Image Analysis
- 7. The Image Processing and Histogram Tools
- 8. The Interactive Segmentation Tools
- 9. Tissue Classification
- 10. Linear Registration
- 11. Non Linear Registration
- 11.1 Introduction
- 11.2 Visualizing NonLinear Transformations
- 11.3 Nonrigid Registration (Intensity Based)
- 11.4 Distortion Correction (Single Axis Distortion)
- 11.5 Batch Mode Registration
- 11.6 Example: Co-register reference 3D brain with individual 3D brain
- 11.7 Checking 3D to Reference non-linear registrations
- 11.8 Remarks
- 12. Landmarks, Surfaces and Point-based Registration
- 3 C. Functional MRI Analysis
- 4 D. Multi Subject/Multi Image Analysis
- 14. The Multi-Subject Control
- 14.1 Introduction
- 14.2 Setup File Format
- 14.3 The Multisubject Tool Graphical User Interface
- 14.4 Examples
- 14.4.1 How to Overlay Activation Maps onto Anatomical Images
- (a) Overlaying Common Space Tmaps onto Reference Image
- (b) Overlaying Individual Tmaps onto Individual 2D Anatomical
- 14.4.2 Generating Across Subjects Composite Maps
- (a) Single Group Composite Maps.
- (b) Two Group T-test Comparisons
- 14.4.3 Creating Multi-Slice Image Displays
- 14.4.4 Warping single subject data to Common Space
- 14.5 The new SimpleViewer Tool
- 15. The Data Tree Manager
- 14. The Multi-Subject Control
- 5 E. Diffusion Weighted Image Analysis
- 6 F. Neurosurgery Tools
- 19. Intracranial Electrode Localization
- 20. The VVLink Tool
- 21. The Differential SPECT Tool
- 21.1 Introduction
- 21.2 Interfacing with the Data Tree Manager
- 21.3 Ictal-Interictal Subtraction Analysis by SPM
- 21.4 Ictal-Interictal Subtraction Analysis by Bioimage Suite
- 21.5 Subtraction Processing
- 21.6 Rejoining Blobs
- 21.7 Cluster Level Statistics
- 21.8 EXAMPLE: Running ISAS and ISAB
- 21.9 EXAMPLE: Using the Utilities Tab
- 7 G. Cardiovascular Image Analysis
- 22. 4D Surface Editor
- 23. Estimation of LV Deformation
- Step 1: The Input Surfaces
- Step 2: Creating Triangulated Surfaces
- Step 2b: Renaming the frames
- Step 3: Running the Shape-Tracking Algorithm
- Step 4: Generating the initial solid
- Step 5: Running the Finite Element Process
- Step 6: Generating Average Strain Values (Pies) for analysis
- Additional Visualization Tools
- 24. Angiography Tools
- 25. Processing Mouse Hindlimb SPECT/CT Images
- 8 Additional/Miscellaneous Topics
- 9 Appendices
- Bibliography
- About this document ...