BrainVoyager is a highly optimized and user friendly software system for the analysis and visualization of functional and anatomical magnetic resonance imaging data. It combines surface-based and volume-based tools to study the structure and function of the human brain.

 The power and speed of BrainVoyager offers you an exciting opportunity to explore the secrets of the active brain.The latest edition of BrainVoyager comes with a Diffusor Tension Imaging (DTI) module that allows for the analysis of diffusion-weighted MRI data.

 The comprehensive and powerful neuroimaging tool contains many exciting new features. New, highly efficient analysis tools including statistical, numerical, and image processing routines allow you to break down your data sets into even more meaningful and insightful figures.

Major advancements in segmentation methods and surface reconstruction techniques enable you to easily create far more detailed reconstructions in really beautiful, figures and movies.

BrainVoyager is the only complete solution that runs on all major platforms at high speed with the ability to simply and reliably exchange data, figures and movie between them.

Add-ons and extra software!

• Share the high quality figures and movies that you create with colleagues. Simply download BrainVoyager Viewer for free and see the results of your analyses on any other computer as you would using BrainVoyager.

• BrainVoyager connects with BESA (Brain Electrical Source Analysis) for a really easy way to combine MEG, EEG and fMRI data. For more information about BESA, click here.

• When purchased with the TMS Neuronavigator Module, it enables the precise and individual navigation of a TMS coil to a specific anatomical area of the brain. For more information about BrainVoyager TMS Neuronavigator, click here.

• BrainVoyager is really simple and easy to use, and a free educational software program, Brain Tutor, can be downloaded to help get the most from BrainVoyager. Training courses held throughout the year are also a really helpful addition to your BrainVoyager education.

BrainVoyager is designed for high performance, ease of use and flexible data processing. BrainVoyager offers a comprehensive set of analysis and visualization tools which start their operation on raw data (2D structural and functional matrices) and produce beautiful visualizations of the obtained results.

Project Creation

BrainVoyager starts by automatically assembling images into 2D and 3D functional and anatomical multi-slice projects.

Diffusor Tension Imaging (DTI) module to analyze diffusion-weighted MRI data including calculation of FA maps, fiber tracking and FA group comparisons.

Data Analysis

Data analysis includes preprocessing, correlation analysis, determination of Talairach coordinates, volume rendering, surface rendering and cortex flattening.

Preprocessing

Preprocessing includes motion correction, Gaussian spatial and temporal data smoothing, linear trend removal and filtering in the frequency domain.

Statistical Analysis

BrainVoyager performs a wide range of statistical analyses including; parametrical mapping, contribution maps, Independent Component Analysis (ICA), Region-of-interest analysis and Event-related fMRI analysis. specifications.

Analysis tools, modules and plugins

• ANCOVA module: allows import and analyses of multi-subject data sets.

• Self-Organizing Group ICA Plugin: allows group level ICA by analyzing the spatial similarity of independent components across subjects.

• Group Data Simulator Plugin: creates multi-subject data sets allowing to test new analysis tools as well as to learn how to analyze planned fMRI experiments.

• Fuzzy Clustering of Time Courses Plugin: allows clustering voxels of VTC data sets with respect to the similarity of their time courses.

• Group-level cortical thickness analysis (CTA): can now be performed using cortically aligned brains.

• Granger Causality Mapping: to estimate influences between brain areas

• Multiple Comparison Correction: using a cluster-size threshold

• BOLD Latency Mapping

Visualization Tools

Parametric and non-parametric statistical maps may be superimposed both on the original functional scans as well as onto T1-weighted 2D or 3D anatomical reference scans. Time courses of selected regions-of-interest (ROIs) are available both in 2D and 3D representations. Statistical maps may be computed either in the 2D or 3D representation since structural as well as functional 4D data (space x time) are transformed into Talairach space. This allows you to compare activated brain regions across different experiments and across different subjects

Segmentation

Segmentation of tissue (e.g., isolating the brain, differentiating gray and white matter) is performed using region-growing methods, filter operations as well as the application of 3D templates. Using the mouse it is very easy to explore a 3D volume with superimposed pseudocolor-coded statistical maps in a four-window representation showing a sagittal, coronal, transversal and oblique section. Based on a (segmented) 3D data set a three-dimensional reconstruction of the subjects' head and brain can be calculated and displayed from any specified viewpoint using volume or surface rendering.

Advanced segmentation tool means even higher quality segmentation of grey and white matter and boundaries.

Volume Rendering

Volume rendering is performed with a very fast ray casting algorithm; lightning calculations are based on Phong-shading. Surface rendering of reconstructed surfaces is performed using OpenGL. Using texture mapping, a reconstructed surface (e.g., head or brain) may be sliced in real time, showing both surface and volume data at the same time. Initial polygon meshes serve as the basis for surface finding, cortex inflation and cortex flattening computations.

Talairach Tools

Talairach transformation is performed in two steps. The first step consists of rotating the 3D data set for each subject to be aligned with the stereotaxic axes. For this step the location of the anterior commissure (AC) and the posterior commissure (PC) as well as two rotation parameters for midsagittal alignment has to be specified interactively. In the second step the extreme points of the cerebrum are specified. These points together with the AC and PC coordinates are then used to scale the 3D data sets into the dimensions of the standard brain of the Talairach and Tournaux atlas.

Surface Reconstruction

The surface reconstruction procedure starts with a sphere (recursively tesselated icosahedron) or a rectangle, which slowly wraps around a (segmented) volume data set. In order to avoid topological defects and to let the surface smoothly grow into deep sulci, a dynamic mesh algorithm was developed which automatically invents new polygons on the fly at places where they are needed. A reconstructed cortical surface may be inflated, cut interactively and slowly unfolded minimizing areal distortions. Statistical 3D maps may be superimposed on reconstructed, inflated or flattened cortex. Signal time courses may be invoked by simply pointing to any region of a visualized surface.

Mesh Manipulation

Fast and interactive surface slicing, cortex inflation and unfolding in real-time.

Display Utlities

Visualization consists of color-coded displays, point models, wire frames, shaded surfaces, transparent rendering, scene animation. Scene viewing conditions can be saved and loaded and 2D/3D images can be exported, movie files, meshes etc.

UPDATE! The "NIfTI-1 Converter Plugin", implemented by Hester Breman, allows to exchange data with other fMRI software packages.

Coregistration of MRI with EEG & MEG

For an easy superposition of the results of source analysis with individual EEG and MEG data, BrainVoyager provides an interactive link to BESA (Brain Electrical Source Analysis). The bidirectional connection of the two programs allows for source seeding from fMRI clusters with one mouse click.

Supported raw data formats

• Siemens IMA, GE Image, Philips PAR/RED, MR; Bruker, ACR/NEMA, DICOM, ANALYZE

Data preprocessing

• Inter-slice scan time correction (important for event-related fMRI)

• 2D and 3D motion detection and correction

• Spatial and temporal bandpass filtering in frequency space

• Gaussian smoothing in space/time domain

• Removal of linear and higher-order trends in time course data

Statistical analysis

• Parametrical statistical mapping: linear correlation, cross-correlation, General Linear Model (GLM)

• GLM contrasts (t-maps), model comparisons (F-maps)

• Colour-coded relative contribution maps

• Factorial design builder, conjunction analysis, random effects analysis

• Cortex-based fixed – and random-effects GLM

• Volume and Cortex-based Independent Component Analysis (ICA)

• Correction for serial correlations and multiple comparisons, Bonferoni correction, False discovery rate (FDR) correction.

• Region-of interest analysis tool

• Event-related fMRI analysis tools and display

• Granger causality mapping

Utility functions and visualisation tools

• Creation of stimulation protocols; graphical specification of statistical tests; condition-based segmentation and visualization of time course plots

• Simultaneous display of reference function and time course plot

• Protocol-based automatic generation of event-related averaging files

• Display of original data values or percent signal change

• Tabular output for ROI-based GLM analysis

• Loading and display of multiple statistical maps with appropriate map intersection colouring

• Interactive editing of look-up colour tables

• Labeling of anatomical and functional regions

Segmentation and volumetry

• Automatic brain segmentation from 3D data sets using three-dimensional intensity inhomogeneity correction, Talairach templates, histogram analysis, and region growing

• Determination of the volume (mm3) of anatomical regions and functional clusters

• 3D filtering (e.g. Gaussian smoothing) in space or frequency domain

Talairach tools

• Interactive transformation of 3D data sets into Talairach space with visualization of full or partial Talairach grid and coordinates of a selected voxel or the center of gravity of a functional cluster

• Functional 4D time course data in Talairach space allowing: display of time courses of selected voxels or clusters; the computation of statistical 3D maps; inter-subject averaging of 3D anatomical data sets, 4D time courses and 3D statistical maps

Spatial transformation and registration

• Automatic co-registration of functional and anatomical data sets

• Rigid body 3D alignment, 3D motion correction

• Talairach transformation

• Tri-linear and sinc, and cubic spline interpolation

• Interactive multi-modal co-registration (MRI, fMRI, PET, EEG/MEG)

Surface reconstruction

• Head reconstruction with deformable models (i.e. sphere)

• Automatic polygon mesh reconstruction of the segmented cortex along the white/grey matter boundary and the pial surface

• Automatic correction of topological errors in the cortical surface

• Creation and display of multiple surfaces (i.e. scenes composed of cortical hemisphere and transparently rendered head)

• Colouring of convex/concave curvature, sulcal depth and statistical maps

• Automatic cortical volume and cortical thickness analysis

Mesh manipulation

• Interactive real-time slicing through head and brain meshes

• Combined display of multiple cut planes

• Automatic inflation, cutting and flattening of reconstructed cortical hemispheres

• Specification of parameters for various deformation forces

• Reference between 3D coordinates of morphed mesh (e.g. flattened cortex) to original mesh (e.g. folded cortex)

• Display of statistical 3D maps on inflated or flattened surface

• Immediate access and display of time course data for any surface patch

• Surface-based inter-subject alignment

Display utilities

• Simultanous colour-coded display of statistical surface maps or ICA component maps

• Meshes as point models, wire frames, shaded surfaces

• Transparent rendering of selected meshes

• Visualization of MEG/EEG multiple dipole models and waveforms

• Specification of mesh colours and multiple light sources

• Scene antialiasing; scene animation

• Saving and loading of scene viewing conditions

• Creation and display of fMRI and MEG activation movies on slices and meshes

• Export of current 2D or 3D view as 8-bit PNG/GIF/BMP or 24-bit BMP/JPEG file

• Export of dynamic processes as AVI/MNG movie files

• Export of statistical maps merged with 3D structural images as DICOM Exports as .DXF,. VRML or STL polygon meshes (i.e. prototyping, physical brain models)

Coregistration of fMRI with EEG and MEG

• Coregistration of coordinate systems by fiducials and / or surface points

• Direct projection of BESA source models into the individual MRI via interactive link with BV

• Projection of BESA source models into the individual MRI in BESA

• Direct imaging of 3D source images in the individual MRI

• Minimum norm current image based on individual gray/white matter boundary

• Seeding of sources into BESA from anatomical 2D or 3D MR images or from fMRI BOLD clusters in BV via interactive link

• Overlapped display of fMRI and EEG / MEG sources in BV

Hardware requirements

• PC with Intel Pentium II/III/IV, AMD Athlon

• Power Mac G4, G5, Power Book G4, iBook G4

• Unix Workstation (i.e. Sun Solaris)

• Open GL graphics board (i.e. NVIDIA GeForce, ATI Radeon)

• 512 MB RAM

Note: BrainVoyager QX requires a for a single computer or a network dongle providing "floating" licenses. The HASP license system allows you to use the program on Windows, Linux and Mac OS X. With your purchase of BrainVoyager QX, you will receive executables for all these platforms. If you want to use BrainVoyager QX on Unix (i.e. Sun Solaris), please send us an email and we will send you further information about availability of BrainVoyager QX for Unix platforms.