README.md

The R1-weighted connectome: complementing brain networks with a myelin-sensitive measure

This repository contains processing scripts in support of the preprint:

Boshkovski T., Kocarev Lj., Cohen-Adad J, Mišić B., Lehéricy S., Stikov N, Mancini M., (2020). The R1-weighted connectome: complementing brain networks with a myelin-sensitive measure.

Code and Data

The main code for the connectome analysis is provided in R1-weighted_connectome.ipynb. This notebook could be used to reproduce the results in the manuscript. You can also explore some of the results via our plotly dashboard app.

Data

• group_connectivity_thr_2.mat: Group connectomes weighted with NOS, R1, and FA, thresholded with NOS<2.
• group_connectivity_thr_5.mat: Group connectomes weighted with NOS, R1, and FA, thresholded with NOS<5.
• modularity_thr_2.mat: Precomputed communities for the consensus connectomes created using NOS_threshold=2
• modularity_thr_5.mat: Precomputed communities for the consensus connectomes created using NOS_threshold=5
• atlas_names.mat: Lausanne 2008 node labels and mapping of the nodes to Yeo's and von Economo classes

Auxiliary scripts

• dwi_preprocessing.sh: Shell script used for preprocessing the diffusion data.

• medianAlongTracts.py: Script to constructs individual connectomes weighted with R1, NOS, and FA, from the diffusion tractography.