BrainVoyager v23.0
Patches-Of-Interest (POIs)
Coming soon...
Copyright © 2023 Rainer Goebel. All rights reserved.
BrainVoyager User's Guide
What's New
General Information
Overview
Main Features
Installation
Installing and Enabling Python
Platform-Specific Tips
What's New - Archive
Credits
Getting Started
Launching BrainVoyager
The Graphical User Interface
Opening and Saving Documents
Scene Files
DICOM to Documents
Creating Functional Documents
Creating Anatomical Documents
Creating Diffusion-Weighted Documents
DICOM to NIfTI and BIDS
NIfTI Sidecar Files - JSON and TSV
Anonymization and Defacing
The 3D Viewer
Coordinates and Transformations
Spatial Transformation Matrices
Coordinate Systems
NIfTI Files
4D NIfTI Time Course Files
NIfTI Volume Map Files
Scripts and Plugins
Overview
Scripting and Automation
The Script Development Window
Developing User Interfaces
Python Scripting and Development
Plugins
Plugin Development
BV Notebooks
Introduction
User Interface
Python Code Cells
Markdown Cellls
Image Cells
Image Annotator
Animation Cells
Embedded Viewers
From GUI to Code
Data Analysis Manager
Reproducible Analysis Pipelines
BIDS Compatibility
Create New Project
Add Subject to Project
Adding NIfTI and DICOM Datasets
Workflows
Inspecting Workflow Reports
Data Flow Visualization
Preprocessing Pipelines
Preprocessing Workflows
Anatomical Preprocessing
Anatomical Normalization
Functional Preprocessing
Coregistration
Functional Normalization
Group-GLM Statistics Workflow
Data Preprocessing
Functional and Anatomical Preprocessing
Preprocessing of Functional Data
Overview
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
IIHC of Functional Volume
Fine-Tuning Alignment (FA) Step
FA Using Gradient-Driven Affine Transformations
Boundary-Based Registration (BBR)
FA Using Boundary-Based Registration
Manual IA Using Corresponding Points
FA Using Intensity-Driven Rigid Transformations
Transformation to Normalized Space
Overview of Brain Normalization
MNI 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
VMR to FMR-VTC Space Alignment Using BBR
Creation of Mesh Time Course Data
From Volume to Mesh Time Courses
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
Overlaying Volume Maps
Overlaying Surface Maps on Cortex Meshes
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
Two-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
Removing MP2Rage Background Noise
PD-Based Intensity Inhomogeneity Correction
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
Automatic Cortex Segmentation for BBR
Manual Segmentation Tools
Reconstructing Edited Brain Volumes
Deep Neural Network Segmentation
Background
Tissue Classification
Postprocessing
Regions-Of-Interest
Introduction
Volumes-Of-Interest (VOIs)
VOIs from Numerical Region Labels
Patches-Of-Interest (POIs)
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
Pairwise Source to Target Alignment
Group Alignment
Visualizing Group Results
CBA Transformation of POIs
CBA Transformation of SMPs
Functionally Informed CBA
Probabilistic Maps and Atlas Creation
Introduction
Probabilistic Maps from Volume Maps
Probabilistic Maps from Surface Maps
Probabilistic Maps and MPMs from VOIs
Probabilistic Maps and MPMs from POIs
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
Representational Similarity Analysis
Overview
First-Level RSA
Second-Level RSA
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
Decoding pRF Models
Functional Connectivity Analysis
Independent Component Analysis (ICA)
Single-Subject ICA
IC Fingerprints
Group-Level ICA
Inter-Subject Correlation (ISC) Analysis
Overview
While-Brain ISC Analysis
ROI ISC Analysis
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
Laminar and Columnar Analysis
Overview
Using PD Scans for Inhomogeneity Correction
Creation of High-Resolution VTCs
VTC-VTC Alignment of Multiple Runs
Spatial Transformation of VTC Data
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
Equi-Volume Depth Modelling
Depth Grids as Flattened Volumes
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
Useful Tools
Overview
Multi-Subject Contrast Maps from GLMs
Creating VTC Masks from Statistical Maps
Cross-VTC Intersubject Correlation
Projecting a Mesh in a VMR
Projecting a Mesh as Filled Volume
Drawing POIs
POI Path Tools
Shortest Path Creation
Creating Sulcal Depth Maps
Quality Assurance Tools
Overview of Tools
Verification of Functional Brain Coverage
Volume Rendering
Introduction
Anatomical Data
Slice Cuts
Lighting
Volume Maps
Volumes-Of-Interest
Settings and Options
High-Resolution Grid Data
Movie Studio
Introduction
From States to Movies
Editing Movies
Mesh Morphing Movies
Surface Maps for Activation Movies
Adding Images
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
TMS Neuronavigation