BrainVoyager QX v2.8
Single-Subject, Multi-Run Analysis
[coming soon]
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