Wiki

Welcome to the Temporal Interference Toolbox Wiki. Here you’ll find detailed guides and documentation for all aspects of the toolbox. The Video Tutorials were recorded with v2, so the interface differs from v3. Something broken? Start at Troubleshooting — the maintainer-verified list of known problems and fixes.

The application

The v3 desktop app is one window with a workflow-ordered rail. These pages describe what each row of that rail does; see Desktop Application for how the app, the container and the server fit together.

• Overview - Welcome, project opening and switching, then the project at a glance
• Pre-processing - Structural MRI preparation and head-model generation
  • FastSurfer / FreeSurfer - Segmentation, reconstruction and GPU setup
  • QSIPrep / QSIRecon - Diffusion processing and conductivity tensors
• Simulator - One row per simulation job, with free-hand electrode placement on the subject’s own scalp
• Flex Search - The Optimizer’s Flex method: differential-evolution electrode optimization
• Ex Search - The Optimizer’s Ex method: exhaustive search over a leadfield matrix
• Analyzer - Field analysis in mesh and voxel space, one target per job row
• Notebooks - Jupyter on the container’s SimNIBS Python, inside the app
• Results - Every output a subject has, with reports rendered in place
• Viewer - Opens your project’s scenes in the separate TetraVox desktop app, which TI-Toolbox installs and manages
• Jobs - Every run: state, logs, artifacts, cancel and rerun
• Scripting - CLI commands, JSON config entry points, and the Python scripting API
• Example Data - Public example heads (raw scans and ready-made head models) to try every page
• AI Assistant - Plugin that teaches Claude Code, Codex, Cursor and other MCP clients how to use TI-Toolbox
• Telemetry & Privacy - What opt-in usage telemetry sends, and how to control it

Embedded Tools

• Reports - The HTML report each head model, DTI step, simulation and search writes
• Logging - Comprehensive logging system documentation
• Brain Atlases - The MNI-space atlases shipped with TI-Toolbox, the subject-space parcellations built during pre-processing, and atlas resampling
• Montage Visualizer - Electrode montage visualization on head
• Electrode Mapping - Optimal electrode position mapping to EEG nets

Optional Tools

• Optional Tools - The panels you switch on in Settings ▸ Extensions
• 3D Visual Exporter - PLY/GLB/Blender exports of regions, vectors and montages
• Free Electrode Placement - Clicking electrodes onto the scalp, now part of the Simulator
• Nilearn Visuals - Publication-ready brain visualizations
• EEG Caps - Apply MNI electrode caps to an existing head model and inspect nets on the scalp
• Cluster-Based Permutation Testing - Non-parametric statistical analysis (the Permutation Analysis extension)
• Quick Notes - An autosaving project notepad with optional timestamps
• NIfTI Group Averaging - Group analysis and comparison tools
• Tissue Analyzer - Volume and thickness assessment for CSF, bone, and skin (part of pre-processing)

Development & Testing

• Development & Testing - Current test strategy, commands, fixtures, and verification limits
• Python Environment - Managing the SimNIBS Python environment and dependencies
• Desktop Application - Electron app, container lifecycle and the server it talks to
• Agent Plugin Internals - Skills, MCP server architecture, and tests behind the AI assistant integration
• API Reference - Complete Python API documentation (auto-generated from docstrings)

Legacy versions

Still using v2? See the brief legacy-version notice for version-specific documentation and migration information.