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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On this page
  • Requirements
  • Loading sample ORScene
  • Creating new ORScene
  1. Lead-OR

Imaging setup

Imaging setup to use the Lead-OR platform

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Last updated 2 years ago

Requirements

  1. 3D Slicer: (v >= 5.2.2) together with the SlicerNetstim, SlicerOpenIGTLink and SlicerIGT extensions should be installed.

  2. ORScene: An ORScene is a file that includes subject images, planning information and atlas-based segmentations ready to loaded into Slicer. It can be created from Lead-DBS and an example dataset is already included in the SlicerNetstim extension.

Loading sample ORScene

A sample ORScene is included to test the platform. To load it follow the next steps:

  1. Open Slicer.

  2. Switch to Sample Data module.

  3. Scroll down and select STN Planning.

See the following screenshots as reference:

Creating new ORScene

In order to create an ORScene follow the next steps:

  1. Process a subject in Lead-DBS with the co-registration and normalization steps.

  2. Place the surgical planning files under a leador subfolder within the subject folder.

  3. Load the subject in Lead-DBS and select Tools > Lead-OR > Create ORScene. Note that the selected atlas will be put into the scene as well.

  4. Drag and drop the ORScene.mrb file into Slicer.

See the following screenshots as reference.

3D Slicer
Step 2: Switch to Sample Data module.
Step 3: Select STN Planning ORScene.
Step 2: Lead-DBS subject processed and with Brainlab planning files in respective folder.
Step 3: Create ORScene from Lead-DBS.
Step 4: Output folder with file to load into Slicer.