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
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  1. Lead-OR

Using the platform

PreviousElectrophysiology setupNextCode Backbone

Last updated 2 years ago

This page shows an overview of the Lead-OR platform using the sample data mentioned in the imaging and electrophysiology setup pages.

  1. Open Slicer and load the sample STN planning as mentioned in the page.

  2. Open OpenEphys and build a signal chain as mentioned in the page.

  3. In Slicer, switch to the Lead-OR module, create a new IGTLConnector and set it to active. Select the Planning transform node.

  1. In OpenEphys, select IGTLink from the Lead-OR module and connect. Click on Start acquisition.

  1. Signal streaming will start and will be processed through the different plug-ins. The Lead-OR module in OpenEphys will send the distance to target, together with processed features to Slicer. In Slicer, recording channels will appear and they should be linked to their respective trajectories. This is done by first clicking the channel name and then the desired trajectory.

  1. The features sent by OpenEphys also appear in Slicer, where they can be set to map to the Tube's radius and/or color.

That's all! A few more tips:

  • Use the Reslice driver button next to distance to target transform selector to set the view inplane with the trajectory.

  • Explore different trajectory visualizations: model, line and tip.

  • When created by Lead-DBS different planning transforms will be available to select.

imaging setup
electrophysiology setup