Lesionometry

Simple Tractometry-based metrics for characterizing white matter lesions within fibre pathways. This repository contains the scripts used in Chamberland et al. 2020 and Winter et al. 2021. If using, please cite the following paper:

Mia Winter, Emma C Tallantyre, Thomas AW Brice, Neil P Robertson, Derek K Jones, and Maxime Chamberland. 
Tract-specific MRI measures explain learning and recall differences in multiple sclerosis.
Brain Communications, 2021;, fcab065, https://doi.org/10.1093/braincomms/fcab065

Install

This package requires Mrtrix 3.

J.-D. Tournier, R. E. Smith, D. Raffelt, R. Tabbara, T. Dhollander, M. Pietsch, D. Christiaens, B. Jeurissen, C.-H. Yeh, and A. Connelly. 
MRtrix3: A fast, flexible and open software framework for medical image processing and visualisation. 
NeuroImage, 202 (2019), pp. 116–37.

git clone https://github.com/chamberm/Lesionometry

python setup.py install
or
pip install -e .

Usage

Calculate Lesion Load

compute_LL.py lesions.nii.gz brain.nii.gz -s SubjectID -o OutputDirectory

Calculate Tractogram Load

compute_TL.py lesions.nii.gz tractogram.tck -s SubjectID -o OutputDirectory

Calculate Bundle Load

compute_BL.py lesions.nii.gz bundle.tck -s SubjectID -o OutputDirectory

Author

Maxime Chamberland Website