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
  • Explore Stats
  • Calculate Distance Between VTA and an Anatomical Atlas Structure
  • Correlate Variable and VTA Intersection
  1. Lead-Group

Calculate VTA and Stats

PreviousGroup VisualizationNextSweetspot Explorer

Last updated 1 year ago

To Calculate stats and VTA, click "Calculate stats & VTA" in the main GUI.

This will calculate the VTAs and electrical fields for both hemispheres for each patient, in native and in MNI space. The generated files will be stored under "stimulations" folder of each patient. An example of the folder structure is displayed below:

Explore Stats

After calculating VTA and stats, Lead Group provides statistical tests for group comparison. It is possible to see which electrode contacts reside within an anatomical atlas structure, to calculate the distance of contacts to an anatomical atlas structure, to generate correlation plots between a clinical variable and the intersection of contacts with a structure.

Calculate Distance Between VTA and an Anatomical Atlas Structure

  1. Click "Explore Stats" under Calculate Stats & VTA section in the main GUI.

  2. From the window that pops up(Fig.3), choose the subcortical region you're interested in. If the structure you're interested in is not on the list, you can change the subcortical atlas from the main GUI under "General Settings."

  3. From the "Activated regions" menu, choose VTAs or E-fields.

  4. Click on "Generate Target Report". From the pop-up window, select the threshold you want to use in mm's.

  5. Two windows will pop up, one showing the distances of electrode centers to the nearest voxel of the target and one showing electrode centers residing in the target structure based on the selected threshold. Active contacts will be highlighted in red.

Since the distance to the closest voxel of a target is rendered, even if the electrode contact is in the middle of the target structure, the distance to the shell of the target will be listed. Thus, a visual check of the contact positions is recommended!

Correlate Variable and VTA Intersection

  1. Click "Explore Stats" under Calculate Stats & VTA section in the main GUI.

  2. From the window that pops up(Fig.3), choose the variable and subcortical region of your interest. If the structure you're interested in is not on the list, you can change the subcortical atlas from the main GUI under "General Settings."

  3. From the "Activated regions" menu, choose VTAs or E-fields.

  4. Click on "Correlate Variable and VTA Intersection". This will generate correlation plots(Fig. 4), showing the correlation between VTA and target intersection and the clinical variable of choice.

Figure 3: Explore Stats

Figure 4