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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  2. 2. Image Import

Converting NIfTI-images into BIDS

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Last updated 1 year ago

Context

  1. In the following steps, Lead DBS converts the legacy NIfTI-images into Brain Imaging Data Structure (BIDS) images.

  2. BIDS is a data structure for neuroimaging and behavioural data used in the imaging domain.

  3. This step is necessary to re-assure that the lead-DBS will be able to work with data. Moreover, using BIDS is an easy way to store and re-use the data between various toolboxes.

Info panel

  1. Make sure that one folder stores all of your patient data, that data are in NIfTI format, and the file names do not contain any spaces or special characters.

  2. The folder should contain pre-operative anat files and post-operative postop files.

  3. CT files cannot be used as pre-operative data, MRI files are used instead.

Screenshot 1. Patient file - NIfTI

To start the importing process, simply select "Import NIfTI to BIDS dataset" and click "RUN". It is possible to import multiple patient files by holding shift and selecting multiple patients.

A window will pop up where you need to specify the session (preop or postop), type (anat, functional, dwi), modality and acquisition (sag, cor, axial, iso)

Here is another example with postoperative CT scans.

Output

  • After Lead migrated all NIfTI files into BIDS format, you can find them in the selected output folder/dataset directory. In our case, the folder’s name was “Directory”

  • The folder contains three main sub-folders: “derivatives”, “raw data” and "source data". Each of these files contains data about our patients. The raw images that we have just converted will be stored under the "rawdata/sub-[PATIENTNAME]” folder. The Lead will use these data for further analysis.

  • “Dataset_description” file contains information about your dataset.