Lead-DBS User Guide
  • Introduction
  • How to contribute to Lead-DBS
  • Installation
  • Lead-DBS
    • Overview
    • Self-Tutoring with Lead-Tutor
    • 1. Load Patient Folder
      • Importing a classic Lead-DBS dataset to BIDS version
    • 2. Image Import
      • Converting NIfTI-images into BIDS
      • Converting DICOM files into BIDS
    • 3. Volume Registrations
      • Coregister Volumes
      • Normalizing the Images
      • Brainshift Correction
      • Checking the Coregistration and Normalization
    • 4. (optional) Surface Reconstruction
    • 5. (optional) Reconstruction of Electrode Trajectories
      • Orientation of Directional Leads
        • Prerequisites
        • Automatic Algorithm
        • Possible Problems with the Automatic Algorithm
        • User-Assisted Algorithm (Manual Refine)
      • TRAC/CORE Details
      • Manual Reconstruction
      • Reconstruction File
    • 6. (optional) Perform Connectivity Analysis
    • 7. Visualization
      • MER Analysis
    • Reconstruction Statistics
  • Lead-Group
    • Group analyses with Lead-DBS
    • Setup Analysis
    • General Settings
    • Group Visualization
    • Calculate VTA and Stats
    • Sweetspot Explorer
  • Connectomics
    • Connectomics
      • Diffusion MRI: Patient Specific Processing
      • fMRI-Analysis: Patient Specific Processing
      • Using Normative Connectomes
      • Network Mapping Explorer
      • Fiber Filtering Explorer
    • Lead Connectome Mapper
  • Lead-OR
    • Imaging setup
    • Electrophysiology setup
    • Using the platform
  • Appendix
    • Code Backbone
    • Acquiring and Installing Atlases
      • Customizing Atlas Visualization
    • Troubleshooting / Specific Help
      • Adding Fortran dependencies for VTA modeling
      • VTA Calculation Troubleshoot
    • Command line interface
      • Command line options
    • Matlab scripting examples
      • Installing an atlas from an online repository
      • Warping a normative connectome to native subject space
    • Using Slicer
      • Sweet-sour spot
Powered by GitBook
On this page
  • Key Features
  • Dependencies

Introduction

NextHow to contribute to Lead-DBS

Last updated 3 months ago

Lead-DBS is an open-source, MATLAB-based toolbox to localize and visualize electrodes in patients treated with deep brain stimulation. Importantly, the toolbox is intended for research and not for clinical use. First, this user guide focuses on Lead-DBS and single patient analysis with co-registration, normalization and reconstruction. Second, the user guide covers group analyses with Lead-Group.

This user guide is intended to cover most use cases. For troubleshooting or other questions, the Lead-DBS community offers great support on the .

Quick history: Lead-DBS was initially developed at the , Department of Neurology, Charité – University Medicine (CCM), Berlin, Germany. Since 2019, the has been coordinating the development.

Other useful links: , ,

If you are new to Lead-DBS, also check out .

Key Features

  • Linear and nonlinear registration of MRI and CT images

  • Reconstruction of the electrode trajectories

  • Manual correction of the electrode localization

  • Visualization of results in 2D slice views

  • Visualization of a 3D model showing DBS electrodes and their target areas

  • Calculation of the Volume of Activated Tissue (VAT) and visualization of the structural connectivity from the VAT to other brain areas

  • Group analysis

Dependencies

Lead-DBS is a collection of tools for the purpose of DBS electrode reconstructions and related processing. The core job of our development team is to find and integrate the best neuroimaging tools available within the open-source community and develop our own code where no good code can be found. Thus, Lead-DBS heavily depends on other tools that should be referenced properly if used for research projects. Please find a list of tools used by Lead-DBS .

Slack user channel
Movement Disorders Unit of Andrea Kühn
Network Stimulation Laboratory of Andreas Horn
Lead-DBS website
Lead-DBS on GitHub
Lead-DBS on Bluesky
our resources for self-tutoring Lead-DBS using Lead Tutor here
here