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: