Ultrasound system for precise neuromodulation of human deep brain circuits

MR and CT image processing tools for targeting and registration

This repository contains scripts and utilities for processing MR and CT images used with our advanced transcranial ultrasound system, a 256-element array designed for precise deep brain neuromodulation in humans. These tools were written by Bradley Treeby, University College London.

Overview

The tools in this repository support a complete workflow for:

• Converting DICOM to NIfTI format
• Registering brain and positioning images to the helmet reference frame
• Processing planning images for transducer targeting
• Real-time replanning between sessions to maintain targeting accuracy
• Segmenting thalamic nuclei using FreeSurfer
• Computing targeting shifts for re-registration

Research Publication

These scripts were developed for and used in the neuromodulation system described in the paper:

Martin, E., Roberts, M., Grigoras, I.F., Wright, O., Nandi, T., Rieger, S.W., Campbell, J., den Boer, T., Cox, B.T., Stagg, C.J. and Treeby, B.E., "Ultrasound system for precise neuromodulation of human deep brain circuits." bioRxiv, https://doi.org/10.1101/2024.06.08.597305, 2024.

If you find these tools useful for your reserach, please consider citing our paper.

Repository Structure

• Bash Scripts: Collection of shell scripts for image processing and registration

  • convertDicoms.sh - Convert DICOM images to NIfTI format
  • registerWithHelmet.sh - Register T1 images with the helmet reference image
  • registerWithHelmetSaveAll.sh - Register T1 images with additional outputs
  • segmentThalamus.sh - Extract thalamic nuclei maps using FreeSurfer
  • computeTargetShift.sh - Calculate shifts in target position
  • processImagesForPlanning.sh - Main workflow script for image processing

• MATLAB Functions: Support functions for image processing

  • resliceImageToRAS.m - Reslice and pad NIfTI images
  • extractTransducerPosition.m - Generate transformations for k-Plan
  • computeRigidTransform.m - Compute transformations between coordinate systems

Documentation

• Setup and Installation - How to install required software and set up scripts
• Image Conversion - Converting DICOM images to NIfTI format
• Processing Planning Images - Detailed workflow for planning
• k-Plan Simulations - Setting up k-Plan simulations
• Real-Time Replanning - Protocol for between-session adjustments

Requirements

• FSL (FMRIB Software Library)
• FreeSurfer
• 3D Slicer
• MATLAB (for some processing steps)
• dcm2niix (for DICOM conversion)

For complete setup instructions, see the Setup and Installation guide.

Usage

A typical workflow involves:

1. Converting DICOM images using convertDicoms.sh
2. Segmenting thalamic nuclei with segmentThalamus.sh
3. Creating a subject-specific script based on processImagesForPlanningS00X.sh
4. Running the processing script to generate targeting data
5. Using computeTargetShift.sh for between-session replanning

See Processing Planning Images for detailed instructions.