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. Appendix
  2. Command line interface

Command line options

Option
Description

-dicomcheck

Import DICOM series

-coreg_checkbox

Run coregistration

-coregctmethod

CT to MRI coregistration method

-coregmrpopup

MRI to MRI coregistration method

-normalize_checkbox

Run normalization

-normmethod

Normalization method

1: SPM SHOOT

2: SPM Segment

3: SPM Dartel

4: three step affine

5: MaGeT Brain like segmentation

6: MaGet Brain like normalization

7: FSL FNIRT

8: Re-Apply

9: ANTs (default)

-scrf

Run Brain Shift Correction

-scrfmask

Brain Shift Correction method

-extractsurface

Run extract surface

-surcafemethod

Extract surface method

-doreconstruction_checkbox

Run pre-Recontruct algorithm

-reconmethod

pre-Recontruct method

-manualheight_checkbox

Manual localization of DBS electrodes

-render_checkbox

Open 3D viewer

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Last updated 3 years ago