YAEL - Your Advanced Electrode Localizer

Create basic 3D viewer and render with colors

Electrode Localization
Featured
Author
Affiliation

Zhengjia Wang

Dept. of Neurosurgery, University of Pennsylvania

Published

October 6, 2024

Overview

Electrode localization is a critical step for getting spatial information of iEEG and DBS electrodes. YAEL (Your Advanced Electrode Localizer) provides a fully integrated pipeline that takes in raw DICOM or NIfTI images and outputs the electrode coordinates and atlas labels. The pipeline is divided into two parts:

  • Input: T1 pre-operative MRI and post-surgery CT

  • Step 1: Imaging preprocess

  • Step 2: Interactive 3D electrode localization

  • Output: electrode coordinate table and RAVE 3D viewer

For more high-level information, please check our paper. Click on the ‘Prerequisites’ button to check data and system requirements:

1. Data

The full pipeline requires T1 MRI (pre-op) and CT (post-op) with electrodes implanted. YAEL supports either DICOM or NIfTI imaging formats.

2. RAVE-Py environment

Some methods such as ANTs for CT-MR co-registration are developed in Python. We highly recommend that you run the following R command:

ravemanager::validate_python()
#> Initializing python environment: 
...
#>  ants: 0.5.3

If you see output ants: followed by a valid version number, that means ANTs is properly configured, otherwise run the following command to configure. RAVE will create an isolated Python environment that will not affect your current system.

ravemanager::configure_python()

Please make sure the computer has access to the internet.

3. FreeSurfer

FreeSurfer is highly recommended if you want to reconstruct brain surface models. The program also comes with commonly used brain parcelation and sub-cortical segmentation methods. Please check their official website on how to download and configure. Make sure you also register and download a license file (it’s free):

If you are using Windows, please consider using docker https://hub.docker.com/r/freesurfer/freesurfer to run FreeSurfer reconstruction on your own. See (TBD) for how to bring your own FreeSurfer folder to YAEL.

Step 1: Imaging Preprocess

The imaging preprocess module in YAEL contains the following two parts. If you would like to substitute any part (or even the entire module) with your existing pipelines, see ‘Alternative Preprocess’ (TBD) below.

  • T1 image preprocess
  • CT-MR co-registration

Here is a video tutorial using NIfTI T1 and CT as input:

Step 2: Interactive 3D electrode localization

Here is an introductory video of using YAEL interactive 3D viewer for electrode localization.

More videos are available here:

  • Credit: Sarah (Ivi) Fung