Anatomically Targeted-Automated Tractography (AT-AT)

Developed by: [email protected]

Introduction

Anatomically Targeted-Automated Tractography (AT-AT) is a collection of bash scripts designed to perform tractography based on the anatomical terminations of fibre bundles. The tractography is constrained by data from 10 healthy control subjects with 7T diffusion MRI scans from the Human Connectome Project (HCP).

Available Bundles

• Arcuate Fasciculus (3 sub-fasciculi as per https://academic.oup.com/brain/article/145/4/1242/6526361?login=false)
• Arcuate Fasciculus posterior

Requirements

• Operating System: Mac or Linux
• Freesurfer: Version 7.4 or higher
• MRtrix3: Installed
• Python: Installed

Installation

1. Download the repository and place it in a desired directory. For example, you can place it at /Users/lawrence/ (this path will be referred to as <path>).

2. Set the script path: After downloading the repository, you need to add the path to the scripts directory in your bashrc (LINUX). If you're on MacOS you'll need to either update your bash_profile or zshrc depending on if you're using bash or zsh in the terminl window. By default, mac uses zshrc. Replace bashrc in the following code with the desired shell target. Replace <path> with the actual path where the software is installed:

echo 'export PATH="<path>/AT-AT/scripts:$PATH"' >> ~/.bashrc

For example, if you installed the software in /Users/lawrence/:

echo 'export PATH="/Users/lawrence/AT-AT/scripts:$PATH"' >> ~/.bashrc

Source the updated bashrc: To apply the changes, either close and reopen your terminal or run:

source ~/.bashrc

Install the required Python packages: Navigate to the repository directory and install the required Python dependencies via pip:

pip install -r requirements.txt

This will install all necessary packages for running the scripts.

Usage

Once everything is set up, you can call the scripts directly from your terminal. Here’s an example:

ATAT_AF.sh -gif gif_parc.nii.gz -T1 T1.nii.gz -fivett 5tt_hsvs.nii.gz -FOD wm.mif -out_dir ATAT2_Tractography/

Available Scripts The scripts currently available in this release (as of 27/02/2025) include:

• ATAT_AF.sh
• ATAT_AFp.sh

Script Options These are the available options for running the scripts:

• -gif: Input GIF parcellation (REQUIRED)
• -T1: Input T1 parcellation (REQUIRED)
• -fivett: Input 5tt image (REQUIRED)
• -FOD: Input CSD image (REQUIRED)
• -out_dir: Output folder for all preprocessing and tracts (REQUIRED)
• -roi_dir: Output folder for tract ROIs (OPTIONAL)
• -niftyReg: Use NiftyReg instead of easyReg registration tract mask (OPTIONAL)
• -alg: Select default algorithm: det or prob (default=prob) (OPTIONAL)
• -threads: Select the number of threads for easyReg to use (default=10) (OPTIONAL)

Example Commands

An example showing all options and their usage:

ATAT_AF.sh -gif gif_parc.nii.gz -T1 T1.nii.gz -fivett 5tt_hsvs.nii.gz -FOD wm.mif -out_dir ATAT2_Tractography/ -roi_dir ATAT2_Tractography/roi/ -niftyReg -alg det -threads 15

Output

Based on the basic commands, there will be .tck files present in ATAT2_Tractography/ which you can use for analysis.