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

1. Load Patient Folder

PreviousSelf-Tutoring with Lead-TutorNextImporting a classic Lead-DBS dataset to BIDS version

Last updated 1 year ago

Click on Choose Dataset Directory at the top of the main window to select the folder you would like to save your data to.

The name of this dataset directory should contain ONLY alphanumeric characters, but NO special characters, including underscores. It is also strongly recommended to not use reserved words such as leaddbs, lead_group,derivatives as the name of the dataset directory.

The name should reflect the project you are working on. You can use a folder already in BIDS format or select an empty folder. If you select an empty folder, Lead-DBS will automatically create 3 subfolders (derivatives, rawdata, sourcedata) and a json file (dataset_description.json) within that folder. The resulting dataset folder should look like this:

To add patients to your dataset, click on the button shown below. Select the patient folder you want to add from the pop-up window. It is possible to hold shift and select multiple patients to import. Patient folders should contain preoperative and postoperative brain images. These files can be in DICOM, nifti or BIDS format.

You can use the additional buttons shown below to remove patients, rename patients and to add additional nifti or DICOM images to the patients folder.

If your images are not in BIDS format, the folder will be highlighted in red as shown below. You need to convert the patient files to BIDS format from 0. Import section, which is explained in the next section.

In the dropdown menu, select the electrode model and the number of electrodes. By default, R and Lare selected, i.e., a bilateral implantation in the right and left hemispheres is assumed. For some applications such as epilepsy, more electrodes may be applicable.

To analyze images, Lead-DBS needs at least the following views:

  • for MR images, a post-operative image (at least a transversal view)

  • for CT images, a post-operative acquisition plus a pre-operative MR image.

You can use the up and down arrows in this part to select the previous or next patient folder. For instance, you may have a folder cohortwith patient folders patient001through to patient010and would like to move up or down between patient folders. The dropdown menu Recent patients provides quick access to recently analyzed patient folders.

These images should be in the selected patient folder. You may have more views and sequences available, in which case electrode localization is made easier, more robust and more precise. These images can be in DICOM or NIfTI format. Lead-DBS needs to convert DICOM images into NIfTI (.nii) format as described in the .

The indicator at the bottom notifies whether a postoperative MR or CT image was detected. This can be changed with the after importing and renaming images.

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An example folder in BIDS format.
Add patients
Patient selection - it is possible to select multiple patients to import.