Main Window and Loading Images

The main window of Lead-DBS is divided into 6 sections:

  • Data import

  • Selection of patient directory and imaging technique

  • Normalization

  • Reconstruction

  • Manual correction

  • Visualization

The button Run in the bottom right runs all processes that are checked within the main window.

To run only one specific process, please make sure that only the desired checkbox is selected. Checkboxes marked with a bold text-face address steps that actually perform an analysis themselves, other checkboxes (standard text-face) are used as options within certain processes.

Hovering over the checkboxes with the mouse will show an explanation of each element of the Main Window.

1. Selecting the file directory

By clicking on Choose Patient Directory on the top, you can browse and select the location of the image folder.

For Lead-DBS to analyze the images, it 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 may also have more views available, in which case the process of electrode localization is made easier, robust, and precise.

IMPORTANT: Images may be in DICOM or NIfTI format. If in DICOM, Lead-DBS will need to convert them into NIfTI (.nii) format using the DICOM import function. You can start by simply choosing a folder containing DICOM images in Lead-DBS and run the Import DICOM and/or assign NIfTI images function.

Finally, to process data, images must be in the *.nii file format and must have a specific naming format. For details on how to format the file names, please refer to Section 2.1.

2. Selecting the imaging technique

After the image directory has been chosen, you must select the imaging technology in the dropdown menu on the top right of the window. MR imaging is the default setting. If images are named correctly, Lead-DBS will automatically set this selection for you.