BrainVoyager v23.0

Overview of Useful Tools

This chapter describes several useful tools that are essential to work efficiently with BrainVoyager. These tools usually perform a single function that could (and probably will in the future) also be described in other contexts; they are presented here so that they may be discovered more quickly when users look for useful tools.

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
- Group-GLM Statistics Workflow
Data Preprocessing
- Functional and Anatomical Preprocessing
- Preprocessing of Functional Data
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
- 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
- Fixed Effects, Random Effects, Mixed Effects
- Fixed Effects Group Analysis
  - Fixed Effects (FFX) Group Analysis
- Random Effects Group Analysis
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
- Advanced Segmentation Tools
- Automatic Cortex Segmentation for BBR
- Manual Segmentation Tools
- Reconstructing Edited Brain Volumes
- Deep Neural Network Segmentation
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)
- Inter-Subject Correlation (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
- TMS Neuronavigation