Cortical Surface Reconstruction with SurfRelax

A Brief Introduction and Tutorial

Jonas Larsson, jonas.larsson [at] rhul.ac.uk

1. General information and system requirements

• 1.1 Introduction
• 1.2 Copyright notice and disclaimer
• 1.3 What is the latest version, and where can I get it?
• 1.4 What operating systems are supported? What other software is required?
• 1.5 Where can I found more documentation?

2. Getting started

• 2.1 Installation
• 2.2 Settings
• 2.3 Troubleshooting
• 2.4 Directory structure

3. Surface based analysis with SurfRelax

• 3.1 What is it?
• 3.2 Common applications
• 3.3 When should it not be used?
• 3.4 Why use SurfRelax?
• 3.5 Input and output
• 3.6 File formats
• 3.7 Basic steps
• 3.8 Overview of programs, scripts, and files
• 3.9 Screenshots
• 3.10 Warning

4. Tutorial (warning: large document with many images)

• 4.1 Using the GUI: SurfRelax.tcl
• 4.2 Before you start
• 4.3 Image preprocessing
• 4.4 Automated surface extraction
• 4.5 Intensity normalization (inhomogeneity correction) and skull stripping
• 4.6 White matter filling
• 4.7 Hemisphere segmentation
• 4.8 Surface extraction
• 4.9 Surface editing
• 4.10 Surface optimization
• 4.11 Surface inflation
• 4.12 Surface flattening
• 4.13 Using surfaces for visualization
• 4.14 Using surfaces for data analysis
• 4.15 Troubleshooting

5. VolumeViewer

• 5.1 Supported file formats
• 5.2 Loading images
• 5.3 Editing images
• 5.4 Overlaying surfaces
• 5.5 Aligning surfaces to functional data
• 5.6 Other options

6. SurfaceViewer

• 6.1 Supported file formats
• 6.2 Loading surfaces
• 6.3 Overlaying data
• 6.4 Main window options
• 6.5 Visualization window options
• 6.6 Editing surfaces
• 6.7 Creating and displaying surface ROIs

7. Auxiliary programs

• 7.1 Programs for operations on surfaces
• 7.2 Programs for operations on images
• 7.3 Programs for operations on surface ROIs
• 7.4 Conversion programs
• 7.5 External programs used in the package
• 7.6 Other useful programs

8. Using SurfRelax with other image analysis packages

• 8.1 Exporting segmentations and flat maps to mrLoadRet
• 8.2 Exporting ROIs to mrLoadRet
• 8.3 Displaying mrLoadRet functional data in VolumeViewer and SurfaceViewer
• 8.4 Viewing functional data from SPM/FSL with VolumeViewer and SurfaceViewer

9. References

• 9.1 Further reading
• 9.2 Other packages
• 9.3 Acknowledgements