README.md

iEEG Electrode Visualization and FreeSurfer Pipeline

This repository contains two primary scripts: one for running the recon-all pipeline on T1-weighted MRI images and another for visualizing intracranial EEG (iEEG) electrodes in native space using FreeView.

Scripts Overview

1. 1-recon-all.py

A script to guide you through the process of running the recon-all command on T1-weighted MRI images. The steps include:

• Installing FreeSurfer.
• Setting up the FreeSurfer environment.
• Running the recon-all command.
• Visualizing the results using FreeView.

2. 2-visualize-electrodes.py

This script provides instructions for plotting iEEG electrodes in native space using FreeView. Key steps include:

• Preparing the electrode coordinate data.
• Loading the MRI image in FreeView.
• Adding and customizing electrode coordinates.
• Verifying electrode locations to ensure accuracy.

Figures

1. Subcortical Structures Visualization

2. White Matter and Pial Surfaces

3. Brain Surface Reconstruction