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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  • Converting DICOM files into BIDS
  1. Lead-DBS
  2. 2. Image Import

Converting DICOM files into BIDS

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Last updated 1 year ago

Converting DICOM files into BIDS

Context

  1. Original patient imaging data are usually stored in the DICOM format. In the following steps, we will convert DICOM files into BIDS. The process is essentially similar to converting NIfTI to BIDS. However, DICOM files are first converted to NIfTI and then to BIDS.

Info panel

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

  2. Your patient’s folder should contain all the images in DICOM format (pre-operative structural T1-weighted and T2-weighted MRI and post-operative CT or MRI) (Screenshot 23).

Screenshot 23. Patient file - DICOM

How to:

  1. Select the patient that you want to convert from the main Lead DBS GUI.

    1. From the Import section, select "Import DICOM to BIDS dataset."

    2. Select the DICOM conversion tool you'd like to use.

    3. Click RUN.

  2. Lead will convert DICOM into NIfTI files, and a new window will appear. This is a new step we have not seen when converting NIfTI to BIDS (Screenshot 25)

    1. What you need to do here is to fill out the table using the drop-down menu and choose from the options (Screenshot 25B).

    2. In the Session column, choose whether the data are post-operative or pre-operative.

    3. The Type column is anat for both pre-and post-operative data.

    4. The Modality column is T1w and T2w for pre-operative data, and for post-operative data, you use CT (in this case) or MRI.

    5. The Acquisition section is filled automatically.

Screenshot 24. Import Section of the Main Lead DBS GUI

Screenshot 25. Lead-DBS to BIDS conversion

Output

  1. This time, three folders appeared in the output directory. (Screenshot 26)

  2. Source data contain the original DICOM files.

  3. Raw data contain raw NIfTI files with pre-operative and post-operative data.

  4. Derivatives folder – contains the main output from the processing tool.

Screenshot 26. Lead-DBS to BIDS conversion