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-DBS

3. Volume Registrations

First steps in the LEAD-DBS pipeline.

PreviousConverting DICOM files into BIDSNextCoregister Volumes

Last updated 1 year ago

First, Lead-DBS coregisters preoperative and postoperative images. MR images are coregistered to MR images by default with SPM. Postoperative CT images are coregistered to preoperative MR images with ANTs (red arrow number 1).

Second, you can choose to normalize the volumes to the MNI nonlinear 2009b space with ANTs (red arrow 2). The ANTs settings are optimized for the subcortex, see . With a multi-core computer, you can increase the number of threads to reduce computation time. To do this, click on Settings. Find more information about . For more information about templates and other normalization methods, see .

Third, brainshift correction is recommended to improve lead localization (red arrow 3). Due to the lead implantation, brain shift is highly likely, i.e., the brain moves with respect to the skull. More information about the correction is on.

The following subpages provide more technical detail.

Finally, you can approve, recalculate or reject the registration and normalization results visually by ticking Check Results. Warp Drive allows for fine manual adjustments to better match, for instance, an atlas fit of the subthalamic nucleus with the patient-specific nucleus (red arrows 4 & 5). See for more information on WarpDrive.

here
Ewert et al. (2019)
MNI spaces here
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