Wiki

Welcome to the Temporal Interference Toolbox Wiki. Here you’ll find detailed guides and documentation for all aspects of the toolbox. Check out our Video Tutorials for step-by-step visual guides. Something broken? Start at the Troubleshooting Archive — 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 - Tetravox, shipped in the image and drawn in the app window
• Jobs - Every run: state, logs, artifacts, cancel and rerun
• Scripting - CLI commands, JSON config entry points, and the Python scripting API
• AI Assistant - Plugin that teaches Claude Code, Codex, Cursor and other MCP clients how to use TI-Toolbox

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

Extensions

• 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
• 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 (v3)

• Testing guide - 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.