BrainVoyager QX v2.8

BrainVoyager QX User's Guide

Welcome to BrainVoyager QX, the comprehensive, powerful, cross-platform neuroimaging tool. To get started, follow one of the links below:

• Getting started
  Here you find help on how to quickly learn to use basic features of BrainVoyager QX.
• General overview
  Here you find a description of the overall structure of this guide.
• What's new
  This section describes new features introduced in the current version (2.8.4) and major features introduced in previous releases.

Note that you can also use the most recent version of the User's Guide online.

Copyright © 2014 Rainer Goebel. All rights reserved.

• BrainVoyager QX User's Guide
• General Information
  • Getting Started
  • General Overview
  • Installation
  • Credits
  • What's New
  • Platform-Specific Tips
• Basic (f)MRI Data Analysis
  • Overview of Basic (f)MRI Data Analysis
  • Preprocessing
    • Preprocessing of Functional Data
    • Slice Scan Time Correction
    • Motion Detection and Correction
    • Temporal High-Pass Filtering
  • Coregistration
    • Coregistration of Functional and Anatomical Data Sets
    • Initial Alignment (IA) Step
    • IA Using Header-Based Coregistration
    • IA Using Corresponding Points
    • Fine-Tuning Alignment (FA) Step
    • FA Using Gradient-Driven Affine Transformations
    • FA Using Intensity-Driven Rigid Transformations
  • Brain Normalization
    • Automatic ACPC and Talairach Transformation
    • Manual ACPC and Talairach Transformation
  • Creation of Volume Time Course Data
    • Introduction to VTC/VDW Creation
    • VTC Data in Talairach Space
    • VTC Data in Native and ACPC Space
    • VTC Data In FMR Space
• Statistical Data Analysis
  • Overview of Statistical Data Analysis
  • Basic Statistical Principles
  • The General Linear Model (GLM)
  • Time Course Normalization
  • From Single Voxels to Statistical Maps
  • The Multiple Comparisons Problem
  • Single-Subject Analysis
    • GLM Analysis
    • Adding High-Pass Filter Confound Predictors
    • High-Pass Filtering of Design Matrix
    • Single-Subject, Multi-Run Analysis
  • Fixed Effects, Random Effects, Mixed Effects
  • Fixed Effects Group Analysis
    • Fixed Effects (FFX) Group Analysis
  • Random Effects Group Analysis
    • Random Effects (RFX) Group Analysis
    • Multi-Subject RFX GLM
    • Principles of ANCOVA Modelling
    • Creation and Test of ANCOVA Models
    • Single-Factor Repeated Measures ANOVA
    • Two-Factors Repeated Measures ANOVA
    • Three-Factors Repeated Measures ANOVA
    • Single-Factor ANOVA
    • ANOVA with 1 Within- and 1 Between-Subjects Factor
    • ANOVA with 2 Within- and 1 Between-Subjects Factor
    • Single-Factor ANCOVA
• Brain and Cortex Segmentation
  • Overview
  • Head Skin Segmentation and Reconstruction
  • Intensity Inhomogeneity Correction
  • Cortex Segmentation and Reconstruction
    • Overview
    • The Automatic Cortex Segmentation Pipeline
    • Tissue Contrast Enhancement
    • Mask-Based Removal of Non-Cortical Structures
    • Intensity Histogram Analysis
    • Labeling White Matter Using Region Growing
    • Morphological Operations
    • Segregation of Hemispheres
    • Creation of Topologically Correct Cortex Segmentations
    • Surface Reconstruction of the Cortical Sheet
    • Verification of Segmentation Results
  • Advanced Segmentation Tools
    • Overview
    • Preparatory Steps
    • Segmentation of the WM-GM Boundary
    • Segmentation of the GM-CSF Boundary
    • Reconstruction of Cortex Hemispheres
• Cortex-Based Alignment
  • Overview
  • Preparing a Mesh for CBA
  • Morphing Cortex to a Sphere
  • Mapping Standard Sphere to Morphed Sphere
  • Creating Curvature Maps for Alignment
  • CBA Transformation of POIs
  • CBA Transformation of SMPs
  • Functionally Informed CBA
• Probabilistic Maps
  • Introduction
  • Probabilistic Maps from Volume Maps
  • Probabilistic Maps from Surface Maps
  • Probabilistic Maps from Volumes-Of-Interest
  • Probabilistic Maps from Surface Patches-Of-Interest
• Multi-Voxel Pattern Analysis (MVPA)
  • Overview
  • Basic Concepts
  • Trial Estimation
  • Support Vector Machines (SVMs)
  • Applying SVMs to ROIs
  • Assessing the Significance of SVMs
  • ROI-SVM Batch Processing
  • Recursive Feature Elimination (RFE)
  • Multivariate Searchlight Mapping
• Population Receptive Field Analysis
  • Introduction to pRF Analysis
  • Generating Binary Stimulus Frames
  • Creating pRF Model Time Courses
  • pRF Estimation in Volume Space
  • pRF Estimation in Cortical Surface Space
• Independent Component Analysis (ICA)
  • Single-Subject ICA
  • IC Fingerprints
  • Group-Level ICA
• Cortical Thickness Analysis
  • Overview
  • Measuring Cortical Thickness in Volume Space
  • Measuring Cortical Thickness in Cortex Space
  • Group Analysis of Cortical Thickness Maps
  • ROI Analysis of Cortical Thickness Maps
• Diffusion-Weighted Imaging Analysis
  • Overview
  • DMR Project Creation
  • Diffusion Tensor Estimation
  • ADC and FA Maps on Measured Slices
  • From Measured Slices to 3D Space
  • Diffusion Tensor Estimation in 3D Space
  • ADC, FA and Color Direction Maps
  • Diffusion Tensor Visualization
  • Interactive Fiber Tracking
  • VOI-Based Fiber Tracking
  • Editing Properties of Fiber Bundles
  • Group Analysis of FA Maps
• EEG/MEG Analysis: The EMEG Suite
  • Overview of EEG/MEG Distributed Source Analysis
  • EEG/MEG Forward Models
  • EEG/MEG Channel Data Preparation and Preprocessing
  • EEG/MEG Channel Data Covariance Calculation
  • EEG/MEG Inverse Models
  • EEG/MEG Source Time Course Reconstruction
  • EEG/MEG Continous Wavelet Filtering
  • EEG/MEG Source Imaging and Analysis
  • EEG Source Analysis with EEG-fMRI Coupling
  • EEG/MEG File Formats
  • EEG and MEG Channel Configurations
  • EEG and MEG Raw Data Import
  • EEG/MEG Channel Data Filtering
  • EEG/MEG Temporal Independent Component Analysis
  • Simultaneous EEG-fMRI: FMRI Artifact Detection and Removal
• Miscellaneous Tools
  • Overview
  • Multi-Subject t and Beta Maps from GLMs
  • Creating VTC Masks from Statistical Maps
  • Cross-VTC Intersubject Correlation
  • POI Path Tools
  • Shortest Path Creation
  • Creating Sulcal Depth Maps
• Tools for High-Resolution MRI Data
  • Overview
  • Using PD Scans for Inhomogeneity Correction
  • Creation of High-Resolution VTCs
  • Whole-Mesh Cortical Depth Sampling
  • Issues with the Whole-Mesh Sampling Approach
  • Regular 2D Grids At Different Cortical Depth Levels
  • Visualization of Depth Grids and Sampled Data
• Quality Assurance Tools
  • Overview of Tools
  • Verification of Functional Brain Coverage
• Volume Rendering
  • Introduction
  • Real-Time Volume Rendering
  • Multiple Anatomical Data Sets
  • Inclusion of Statistical Data Sets
  • Masking and Cutting
  • Rendering Options
• Movie Studio
  • Introduction
  • From States to Movies
  • Editing Movies
  • Surface Maps for Activation Movies
  • Adding Bitmaps
  • Exporting Movies
• Additional Documentation
  • Additional Documentation
  • Exploiting the Power of GP-GPUs
  • Analysis of Retinotopic Mapping Experiments
    • Retinotopic Mapping of Early Visual Areas
    • Cross-Correlation Analysis of Phase-Encoded Stimuli
    • Mirror Representations and Field Sign Maps
  • Scripting and Automation
  • Plugins
  • Plugin Development
  • TMS Neuronavigation