BrainViz DK

Overview

BrainViz DK is a comprehensive brain visualization toolkit developed by Dilanjan DK, designed to provide advanced visualization capabilities for neuroimaging data analysis. This toolkit offers interactive 3D brain rendering, comprehensive visualization tools, and seamless integration with popular neuroimaging analysis workflows.

Key Features

Installation

pip install brainviz-dk

git clone https://github.com/DilanjanDK7/brainviz_dk.git
cd brainviz_dk
pip install -e .

git clone https://github.com/DilanjanDK7/brainviz_dk.git
cd brainviz_dk
pip install -e .[dev]

pip install brainviz-dk[plotly]

pip install brainviz-dk[templateflow]

python -c "import brainviz_dk; print('BrainViz DK installed successfully!')"

Quick Start Guide

Basic Surface Plotting

import brainviz_dk as bv

# Single view plot
bv.plot_surface('path/to/surface_data.nii.gz')

# Multiple views
bv.plot_surface('path/to/surface_data.nii.gz', views=['lateral', 'medial', 'dorsal'])

Quality Presets

# Draft quality (fast preview)
bv.plot_surface('data.nii.gz', quality='draft')

# Publication quality
bv.plot_surface('data.nii.gz', quality='publication')

Volumetric Visualization

# Orthogonal slices
bv.plot_volume('path/to/volume_data.nii.gz', view_type='ortho')

# Glass brain
bv.plot_volume('path/to/volume_data.nii.gz', view_type='glass')

# Mosaic view
bv.plot_volume('path/to/volume_data.nii.gz', view_type='mosaic')

Command-Line Interface

Basic Usage

# Surface plotting
brainviz-dk surface data.nii.gz --output plot.png

# Volume plotting
brainviz-dk volume data.nii.gz --view-type ortho --output plot.png

# List available templates
brainviz-dk templates list

Advanced CLI Examples

# Custom quality settings
brainviz-dk surface data.nii.gz --quality publication --dpi 300 --output high_res.png

# Thresholded statistical maps
brainviz-dk surface stats.nii.gz --threshold 3.0 --colormap hot --output stats.png

# Batch processing
brainviz-dk surface *.nii.gz --output-dir plots/ --quality standard

Quality Presets

BrainViz DK offers several quality presets optimized for different use cases. Choose the right preset based on your needs:

Brain Templates

BrainViz DK supports multiple standardized brain templates for consistent visualization across studies:

# List available templates
import brainviz_dk as bv
bv.list_templates()

# Load specific template
template = bv.load_template('MNI152')

Advanced Usage

Custom Figure Sizes

bv.plot_surface('data.nii.gz', figsize=(12, 8), quality='publication')

Threshold and Colormap Adjustments

bv.plot_surface('stats.nii.gz', 
                threshold=2.3, 
                colormap='hot', 
                vmin=2.3, 
                vmax=6.0)

ROI Overlays

bv.plot_surface('data.nii.gz', 
                roi_overlay='roi_mask.nii.gz',
                roi_colors=['red', 'blue', 'green'])

Applications

• fMRI data visualization and analysis
• Structural MRI brain mapping
• Connectivity analysis visualization
• Statistical brain mapping
• Research presentation and publication graphics
• Educational neuroimaging demonstrations
• Quality control and data inspection
• Group analysis reports

Performance Considerations

• Memory Usage: High-resolution templates may require significant RAM
• Processing Time: Publication quality settings take longer but produce better results
• Disk Space: Template downloads require several GB of storage
• GPU Acceleration: Available for large datasets and complex visualizations

Documentation & Resources

• Official Documentation (ReadTheDocs)
• GitHub Repository
• README & Installation Guide
• Usage Examples
• PyPI Package

Troubleshooting

Common Issues

• Missing Dependencies: Ensure all required packages are installed
• Template Download Problems: Check internet connection and disk space
• Memory Concerns: Use lower resolution templates for large datasets
• Platform-Specific Issues: See documentation for OS-specific guidance

Contact

For questions, collaboration, or feature requests, contact Dilanjan DK at [email protected].