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
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 .
compute_LL.py lesions.nii.gz brain.nii.gz -s SubjectID -o OutputDirectory
compute_TL.py lesions.nii.gz tractogram.tck -s SubjectID -o OutputDirectory
compute_BL.py lesions.nii.gz bundle.tck -s SubjectID -o OutputDirectory
Maxime Chamberland Website