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brainGraph (version 2.7.3)

Graph Theory Analysis of Brain MRI Data

Description

A set of tools for performing graph theory analysis of brain MRI data. It works with data from a Freesurfer analysis (cortical thickness, volumes, local gyrification index, surface area), diffusion tensor tractography data (e.g., from FSL) and resting-state fMRI data (e.g., from DPABI). It contains a graphical user interface for graph visualization and data exploration, along with several functions for generating useful figures.

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Install

install.packages('brainGraph')

Monthly Downloads

736

Version

2.7.3

License

GPL-3

Issues

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Repository

https://github.com/cwatson/brainGraph

Maintainer

Christopher G Watson

Last Published

November 7th, 2019

Functions in brainGraph (2.7.3)

Coordinates for data from BrainSuite atlas

Calculate coefficient of variation

Select edges for re-wiring.

Coordinates for data from the Craddock200 atlas

Apply a rotation matrix to a set of points

Difference in the area-under-the-curve of two vectors

centr_betw_comm

Calculate communicability betweenness centrality

Convert arguments into a single list

Create connection matrices for tractography or fMRI data

Calculate a vertex's leverage centrality

FreesurferAtlases

Coordinates for data from Freesurfer atlases

Check for edge weights

delete_all_attr

Delete all attributes of a graph

Create a data table with graph global and vertex measures

Check for presence of a strength attribute

Check for presence of a degree attribute

Coordinates for data from the AAL-based atlases

make_brainGraph

Create a brainGraph object

communicability

Calculate communicability

Import data for structural connectivity analysis

IndividualContributions

Approaches to estimate individual network contribution

Calculate graph global, local, or nodal efficiency

Coordinates for data from Harvard-Oxford atlas

apply_thresholds

Threshold additional set of matrices

make_ego_brainGraph

Create a graph of the union of multiple vertex neighborhoods

plot_brainGraph_list

Write PNG files for a list of graphs

brainGraph_permute

Permutation test for group difference of graph measures

Calculate the p-value for differences in correlation coefficients

Fit linear models at each vertex of a graph

contract_brainGraph

Contract graph vertices based on brain lobe and hemisphere

Get some variables for LM

make_intersection_brainGraph

Create the intersection of graphs based on a logical condition

plot.brainGraph_mtpc

Plot a graph with results from MTPC

Symmetrize a matrix with the mean of off-diagonal elements

plot_volumetric

Plot group distributions of volumetric measures for a given brain region

plot_brainGraph_gui

GUI for plotting graphs overlaid on an MNI152 image or in a circle.

Calculate vertex hubness

make_mediate_brainGraph

Create a graph with mediation-specific attributes

Perform an analysis with random graphs for brain MRI data

Fit linear models for t contrasts

symmetrize_mats

Create a symmetric matrix

Transform edge weights

Linear model residuals in structural covariance networks

update_brainGraph_gui

Function to dynamically plot a graph

Coordinates for data from the LONI probabilistic brain atlas

update_fs_names

Update column names in a Freesurfer table

MediationAnalysis

Mediation analysis with brain graph measures as mediator variables

make_nbs_brainGraph

Create a graph with NBS-specific attributes

Determine whether x is a brainGraph object

setup_randomise

Helper function to setup for randomise

make_empty_brainGraph

Create an empty graph with attributes for brainGraph

Color graph vertices and edges

Count number of edges of a brain graph

make_glm_brainGraph

Create a graph with GLM-specific attributes

plot.brainGraph

Plot a brain graph with a specific spatial layout

rich_club_attrs

Assign graph attributes based on rich-club analysis

Rich club calculations

plot.brainGraph_GLM

Plot a graph with results from brainGraph_GLM

plot.brainGraph_NBS

Plot a graph with results from the network-based statistic

plot_brainGraph_multi

Save PNG of three views of a brain graph

Calculate studentized residuals with matrix input

Bootstrapping for global graph measures

Network-based statistic for brain MRI data

plot.brainGraph_mediate

Plot a graph with results from a mediation analysis

Partition a design matrix into columns of interest and nuisance

Calculate the s-core of a network

Calculate correlation matrix and threshold

Calculate Euclidean distance of edges and vertices

Multi-threshold permutation correction

set_brainGraph_attr

Set graph, vertex, and edge attributes common in MRI analyses

Analysis of network robustness

Calculate graph small-worldness

Transform a vector to have a different range

Create a design matrix for linear model analysis

Gateway coefficient, participation coefficient, and within-mod degree z-score

Calculate an asymmetry index based on edge counts

Subset graphs based on a given logical condition

Coordinates for data from the Dosenbach160 atlas

Plot a correlation matrix

Helper function to set-up for GLM analyses

Plot global graph measures across densities

Calculate graph vulnerability

Plot normalized rich club coefficients against degree threshold

plot_vertex_measures

Plot vertex-level graph measures at a single density or threshold

Write files to be used for visualization with BrainNet Viewer