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Advanced fMRI Analysis Workflows in BrainVoyager QX

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BrainVoyager QX: A Beginner’s Guide to Installation and First StepsBrainVoyager QX is a comprehensive software package for analyzing structural and functional magnetic resonance imaging (MRI) data. It’s widely used in cognitive neuroscience for preprocessing, statistical analysis, visualization, and surface-based work. This guide walks you through obtaining and installing BrainVoyager QX, setting up a basic project, and performing the first preprocessing and inspection steps on structural and functional datasets. It also highlights useful tips, common pitfalls, and next steps for deeper analysis.

Before you begin — system requirements and licensing

  • BrainVoyager QX runs on Windows and macOS. Check the latest system compatibility on the BrainVoyager website before installing.
  • Ensure you have sufficient RAM (at least 8–16 GB recommended) and disk space for MRI datasets (several GBs per subject depending on scan protocols).
  • BrainVoyager is commercial software and requires a license. Academic labs typically obtain institutional licenses; individuals may request trial licenses from the vendor. Verify your license type and any node-locking or floating license server details before installation.

Downloading BrainVoyager QX

  1. Visit the BrainVoyager website (BrainVoyager.com) and navigate to the downloads section.
  2. Choose the appropriate installer for your operating system (Windows or macOS).
  3. If required, log into your account or provide license information to access the download.
  4. Save the installer to a location you can easily access (Downloads folder or a dedicated neuroimaging software directory).

Installation steps

Windows:

  1. Double-click the downloaded .exe installer.
  2. Follow the installer prompts: accept license agreement, choose installation folder, and select components (typical install is usually fine for most users).
  3. If your license uses a license file (.lic) or license server, note the location and configuration steps required after installation.
  4. Finish and launch BrainVoyager QX from the Start Menu or desktop shortcut.

macOS:

  1. Open the downloaded .dmg file and drag the BrainVoyager QX application into your Applications folder.
  2. If macOS blocks opening the app (from an unidentified developer), go to System Preferences → Security & Privacy → General and allow the app to open.
  3. Configure license settings if prompted (license file or server).

License activation:

  • If you were provided a license file, follow Help → License Manager (or similar) within BrainVoyager to load the file.
  • For floating licenses, you may need to enter a license server address. Confirm details with your administrator.

Organizing your data and setting up a project

Before importing data, organize your files. A clear folder structure reduces mistakes and makes analyses reproducible.

Suggested structure:

  • ProjectRoot/
    • subject01/
      • anat/ (structural T1)
      • func/ (functional runs)
      • dicom/ (raw DICOMs)
    • subject02/
    • scripts/ (processing logs or custom scripts)
    • derivatives/ (outputs)

BrainVoyager accepts DICOM, NIfTI, and its own VMR/VMR/DMR formats. If your data are in DICOMs, you can import per-subject directories directly; if they’re in NIfTI, ensure consistent orientation and header integrity.

First launch and interface tour

When you open BrainVoyager QX for the first time:

  • Familiarize yourself with the main windows: 3D Viewer, Slice Viewer, and Project Explorer.
  • The Menu provides access to preprocessing, statistical tools, and visualization modules.
  • The Project Explorer is where subjects, scans, and data files are listed and managed.

Spend a few minutes opening example datasets (often included) to explore how volumes and surfaces are displayed.

Importing and converting data

  1. Create a new subject entry in the Project Explorer (File → New Project / New Subject).
  2. Import structural (T1) scans first. For DICOMs, choose Import → DICOM. For NIfTI, use Import → Volume and select the .nii/.nii.gz file.
  3. Verify that the anatomical volume displays correctly (orientation, complete brain coverage). If not, consider re-exporting DICOMs or reorienting NIfTI headers using tools like FSL’s fslreorient2std (outside BrainVoyager).
  4. Import functional runs similarly. After import, BrainVoyager may convert volumes to its internal formats (VMR for structural, VTC for functional time courses).

Basic preprocessing pipeline

A typical minimal preprocessing workflow in BrainVoyager QX includes:

  • Slice timing correction — aligns slices in each volume to a common acquisition time.
  • Motion correction (realignment) — corrects head movement across volumes, producing motion parameters you should inspect.
  • Coregistration — aligns functional data to the structural scan.
  • Spatial smoothing (optional for first steps) — applies a Gaussian kernel (e.g., 4–8 mm FWHM) to improve SNR and satisfy GLM assumptions.
  • Temporal filtering — high-pass filter to remove slow drifts; optionally low-pass filtering depending on analysis.

Step-by-step:

  1. Open your functional dataset (VTC) in the Slice Viewer.
  2. Run Slice Timing Correction (Process → Slice Time Correction), selecting the correct acquisition order (ascending, descending, interleaved). If uncertain, check DICOM headers or scanner protocol.
  3. Run Motion Correction (Process → Motion Correction). Inspect the motion plots—look for sudden jumps > 2–3 mm or degrees. Excessive motion may require excluding volumes or subjects.
  4. Coregistration: Use the automatic or manual alignment tools (Volume-Based Alignment) to align VTC to the VMR. Verify by overlaying functional activation or mean functional image on structural slices.
  5. Apply spatial smoothing (Volume → Spatial Smoothing) with a kernel appropriate to your study and voxel size.
  6. Save processed files in a derivatives/ folder and document settings.

Quality control checks

  • Visual inspection: scroll through motion-corrected time volumes to spot residual artifacts.
  • Motion parameters: plot translations and rotations; note runs with spikes.
  • Mean functional image: check for brain coverage and signal dropout (especially near sinuses).
  • Coregistration: overlay functional mean on anatomical and inspect multiple planes.

Keep a QC log noting any excluded runs or problematic subjects.

First statistical analysis (GLM) — very basic

  1. Define the experimental design: create an STC (stimulus timing) file or set up conditions/events within BrainVoyager.
  2. Precompute predictors by convolving event timings with the canonical hemodynamic response.
  3. Run the General Linear Model (GLM) on the preprocessed VTC. Include motion parameters as regressors of no interest.
  4. Inspect single-subject statistical maps (t maps) in the 3D or slice viewer.
  5. For group analysis, export single-subject maps (e.g., beta or contrast maps) and use BrainVoyager’s multi-subject GLM tools or export to other packages for mixed-effects analysis.

Visualization basics

  • Surface reconstruction: create cortical surfaces from the structural VMR (Mesh → Create Cortical Mesh). This enables surface-based visualization and mapping of functional data onto the cortical sheet.
  • Flattening and ROI tools: you can flatten regions for visualization, draw ROIs manually, or import ROIs from other tools.
  • Overlay statistical maps on surfaces and threshold interactively to explore activations.

Common pitfalls and quick troubleshooting

  • Incorrect slice acquisition order causes poor slice timing correction—confirm sequence details.
  • Misoriented NIfTI headers lead to flipped brains—use external tools to fix orientation before importing.
  • Excessive motion: consider scrubbing volumes, using motion regressors, or excluding runs.
  • License issues: ensure your license file/server details are correct if the application won’t start fully.

Next steps and learning resources

  • Practice with example datasets and replicate published pipelines.
  • Explore advanced features: surface-based analysis, ROI statistics, connectivity analyses, retinotopic mapping tools.
  • Read the BrainVoyager manual and tutorials on the vendor site and check community forums for tips.

BrainVoyager QX is powerful but has a learning curve. Starting with careful data organization, basic preprocessing, and methodical QC will get you reliable first results and prepare you to explore the software’s advanced capabilities.

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