TMS_ElectricField_Group_Simulation

Introduction

The induced electric field strength at targeted cortical regions (by transcranial magnetic stimulation) is influenced by various biophysical parameters including tissue density (e.g., scalp, skull, meninges, and CSF), scalp-cortex distance, gyral patterns, and tissue conductivity.

In the context of neuromodulation research and clinical applications, understanding the magnitude and distribution of these induced electric fields is vital. It aids in making informed decisions regarding the stimulation protocols and understanding the effects and safety of the procedure.

Group Analysis with SimNIBS

This repository contains a Python script to perform group analysis of TMS simulations using SimNIBS for specific subjects, both pre and post some treatment.

Description

The script is tailored to run simulations for TMS (Transcranial Magnetic Stimulation) by setting up a coil in the C3 position. The coil used in the simulation is Magstim_70mm_Fig8.nii.gz, but this can be changed based on available coil definitions in SimNIBS.

Subjects are labeled with an ID followed by either _pre or _post indicating pre-intervention and post-intervention status, respectively.

Requirements

• Python (version as per SimNIBS compatibility)
• SimNIBS 4.0 installed and set up

Instructions

1. Setup: Ensure you have SimNIBS 4.0 and the required dependencies installed.
2. Data: Ensure your subject data is structured correctly, especially the naming conventions. The script assumes names like 'sub-011_pre', 'sub-011_post', etc.
3. Parameters: The script currently uses the Magstim_70mm_Fig8.nii.gz coil at position C3 with an orientation of [0, 0, 1]. Adjust these parameters in the script if necessary.
4. Running the Script: Execute the script in the environment where SimNIBS is set up. It will simulate the electric fields for all the specified subjects and save the results in the Remy_TBS_group_analysis directory.

Folder Structure

The results will be saved in a directory named Remy_TBS_group_analysis. Inside this directory, there will be individual directories for each subject, labeled by their ID and status, e.g., sub-011_pre.

Note

1. Ensure you have enough computational resources, as TMS simulations can be computationally intensive.
2. Ensure backup of any previous simulations as this script might overwrite the results if executed multiple times.
3. Adjust coil parameters (didt, pos, moments) as per your requirements.

References

• SimNIBS documentation
• TMS coil definitions in SimNIBS