Virtual Brain Inference (VBI)¶

The Virtual Brain Inference (VBI) toolkit is an open-source, flexible solution tailored for probabilistic inference on virtual brain models. It integrates computational models with personalized anatomical data to deepen the understanding of brain dynamics and neurological processes. VBI supports fast simulations, comprehensive feature extraction, and employs deep neural density estimators to handle various neuroimaging data types. Its goal is to bridge the gap in solving the inverse problem of identifying control parameters that best explain observed data, thereby making these models applicable for clinical settings. VBI leverages high-performance computing through GPU acceleration and C++ code to ensure efficiency in processing.

Workflow¶

Installation¶

Quick Start:

First, create a conda environment:

conda create --name vbi python=3.10
conda activate vbi

Then install VBI:

pip install vbi                    # Light version (CPU only)
pip install vbi[inference]         # With parameter inference
pip install vbi[inference-gpu]     # Full functionality with GPU

Verify Installation:

import vbi
vbi.tests()
vbi.test_imports()

Complete Installation Guide:

For detailed instructions including Docker, platform-specific guides (Windows, Google Colab, EBRAINS), troubleshooting, and installation from source, see our comprehensive Installation Guide guide.

import vbi vbi.tests() vbi.test_imports()

Example output for full installation:

Dependency Check

Package      Version       Status
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━
vbi          v0.2.1        ✅ Available
numpy        1.24.4        ✅ Available
scipy        1.10.1        ✅ Available
matplotlib   3.7.5         ✅ Available
sbi          0.22.0        ✅ Available
torch        2.4.1+cu121   ✅ Available
cupy         12.3.0        ✅ Available

Torch GPU available: True
Torch device count: 1
Torch CUDA version: 12.1
CuPy GPU available: True
CuPy device count: 1

Example output for light version:

Dependency Check

Package      Version       Status
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━
vbi          v0.2.1        ✅ Available
numpy        1.24.4        ✅ Available
scipy        1.10.1        ✅ Available
matplotlib   3.7.5         ✅ Available
sbi          -             ❌ Not Found
torch        -             ❌ Not Found
cupy         -             ❌ Not Found

Note: Missing packages are expected for light installation.
Install vbi[inference] or vbi[inference-gpu] for additional functionality.