Welcome to our recent research on brain connectivity:
The functional brain favours segregated modular connectivity at old age unless targeted by neurodegeneration
by Peraza LR, O'Brien JT, Blamire A, Kaiser M and Taylor J-P.
This manuscript is currently under review, but here we are providing custom software, data sharing and links to increase reproducibility of our results. A tutorial is available at https://github.com/LuisPerazaRo/modulardissociation.
Software and algorithms
The following table shows all software used in this investigation and links are provided. With the exception of Matlab, all tools are free and the Matlab toolboxes are free and open source.
Modular dissociation and network construction by local threshold (Matlab code): www.lewybodylab.org/research/modulardissociation
Brain Connectivity Toolbox (BCT): https://sites.google.com/site/bctnet
MIT Matlab Tools for Network Analysis for the MST: http://strategic.mit.edu/downloads.php?page=matlab_networks
Network Community Toolbox (NCT) – Consensus community: http://commdetect.weebly.com
BrainNet Viewer: https://www.nitrc.org/projects/bnv
FMRIB Software Library (FSL) v5.0: https://fsl.fmrib.ox.ac.uk
BrainWavelet Toolbox: http://www.brainwavelet.org
Anatomical location of regions in MNI coordinates; cuixufindstructure.m (Matlab): http://www.alivelearn.net/
Diverging colour maps for visualization: http://www.kennethmoreland.com/
pyClusterROI for functional atlases from fMRI: http://ccraddock.github.io/cluster_roi
Matlab 2017a, Mathworks, Inc: https://uk.mathworks.com
Python 2.7.12: https://www.python.org
The connectivity matrices from the NKI database are now stored in Figshare: https://figshare.com/s/7057a9ac73458c3ebbcc
This repository comprises all raw matrices from the NKI, MNI coordinates, functional atlases and participant codes. Please refer to the PDF describing the variable content.
Tutorial for modular dissociation estimation
We have prepared the GitHub tutorial with Matlab code and instructions about how to estimate MD, and use the data repository from Figshare: