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Data
Implementation
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README.md

README.md

Estimating Brain Connectivity Networks With Additional Knowledge

This repository provides the data and an implementation of the algorithms described in the paper Integrating Additional Knowledge Into the Estimation of Graphical Models for Brain Connectivity Networks by Yunqi Bu and Johannes Lederer.

Usage

The file Implementation/graph_estimation.R contains a function GraphEstimation to estimate a connectivity network using the SI method described in the paper.

In order to use this function, one needs a matrix of fMRI data and a matrix containing pairwise distances between the brain regions.

An exemplary matrix of fMRI data (preprocessed data for one subject) and the distance matrix for the regions can be found in this repository under Implementation/ExampleData/example_fMRI.csv and Implementation/ExampleData/distance_matrix.csv, respectively.

A program that uses these matrices and produces an image of the resulting connectivity network can be found in Implementation/example.R.

Detailed descriptions on the fMRI preprocessing procedure can be found under Data/preprocessing_documentation.md.

Preprocessed data for all 37 patients in the study can be found under Data/PreprocessedData. The brain region names, the lobe that each region belongs to, and the 42 regions of interest indicator is given in Data/brain_regions.csv.

The coding invokes Google's style guide for R.

Repository Authors

  • Yunqi Bu — Graduate student in Biostatistics, University of Washington — methodology and R implementation
  • Johannes Lederer — Assistant Professor in Statistics, University of Washington — methodology and R implementation
  • Benjamin J. Phillips — Undergraduate student in Mathematics, University of Washington — revision of R implementation.

Acknowledgements

The raw fMRI data was collected and provided by Dr. Dantao Peng, Dr. Yanlei Mu, and Dr. Xiao Zhang. The data preprocessing was conducted by Dr. Min Zhang.

Reference

Integrating Additional Knowledge Into the Estimation of Graphical Models for Brain Connectivity Networks

Cite as "Bu and Lederer, Integrating Additional Knowledge Into the Estimation of Graphical Models for Brain Connectivity Networks, arXiv:1704.02739, 2017"