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Getting Started

Get up and running with BrainSuite and its related programs SVReg (integrated into the GUI) and BDP.

• Installation: How to set up BrainSuite, SVReg, and BrainSuite Diffusion Pipeline (BDP) after download
• Quick Start: Cortical Surface Extraction Sequence (CSE): Basic instructions on how to create a 3D model of a brain from MRI images using BrainSuite.
• Quick Start: Surface/Volume Registration (SVReg): Basic instructions on how to register and automatically label the surfaces and volumes created by BrainSuite using SVReg.
• Quick Start: BrainSuite Diffusion Pipeline (BDP): Align diffusion data to an anatomical scan, correct for distortion, generate tracts, and automatically analyze connectivity of labeled brain regisions using BDP and BrainSuite.
• Tutorials: Step-by-step instructions on processing an example dataset
  • Extract a Brain
  • Register/Label a Brain
  • Diffusion Imaging
• FAQ: Frequently asked questions about BrainSuite, SVReg, and BDP.

Processing

Detailed documentation about each stage of the Cortical Surface Extraction sequence in BrainSuite as well as SVReg and BDP. Provides descriptions of inputs, command-line flags, output files, and information on how each program works.

• Cortical Surface Extraction:
  • Overview:
  • Skull Stripping (BSE):
    • Overview
    • Anisotropic Diffusion Filter
    • Edge Detection
    • Finding the Brain
    • Finish Brain
    • Tuning the BSE Parameters
  • Bias Field Correction:
    • Overview
    • Initialization
    • Compute Bias Points
    • Compute Splines
    • Remove Bias
  • Tissue Classification:
    • Overview
    • Tissue Classification
    • MAP Classification
  • Cerebrum Labeling:
    • Overview
    • Initialization
    • Align Linear
    • Align Warp
    • Label Lobes
  • Cortex Mask Selection
  • Scrub Mask
  • Topology Correction
  • Wisp Removal
  • Inner Cortical Surface
  • Pial Surface Generation
  • Split Hemipsheres
  • Output Files
• Surface/Volume Registration:
  • Overview
  • Usage
  • Output Files
  • Analyzing With MATLAB
• BrainSuite Diffusion Pipeline:
  • Overview
  • Requirements
  • Setup
  • Usage
  • Flags
  • Output Files
  • File Formats
• Additional Tools:

Interface

Information on interacting with BrainSuite’s graphical user interface, including keyboard shortcuts.

• Controls:
  • Overview
  • Keyboard Shortcuts
• Delineation:
  • Sulcal Curve Delineation
  • ROI Delineation:
    • Masking
    • Label Painter Tool
• Visualization:
  • Tractography Visualization

Formats

Information on file formats used by BrainSuite.

• DFS: File-format used by BrainSuite for surfaces
• BST: Plain-text file format that lets you load volumes, surfaces, labels, fiber tracts, and other files at once. Useful if you will be opening the same set of files mutliple times.

Publications

List of papers describing and validating the methods used by BrainSuite

News

Short posts of news relating to BrainSuite (such as new releases)

About

Information about the people behind BrainSuite and its supporting grants.

• Software Download:
• BrainSuite Support Forums:

FAQ

Frequently asked questions about BrainSuite, SVReg, and BDP.