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brainGraph (version 2.2.0)

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.packages('brainGraph')

Monthly Downloads

568

Version

2.2.0

License

GPL-3

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Repository

https://github.com/cwatson/brainGraph

Maintainer

Christopher G Watson

Last Published

May 29th, 2018

Functions in brainGraph (2.2.0)

brainGraph_boot

Bootstrapping for global graph measures

contract_brainGraph

Contract graph vertices based on brain lobe and hemisphere

Calculate the p-value for differences in correlation coefficients

Calculate an asymmetry index based on edge counts

Create connection matrices for tractography or fMRI data

Plot GLM diagnostics for a brain network

IndividualContributions

Approaches to estimate individual network contribution

Plot statistics from an MTPC analysis

Calculate graph small-worldness

plot_brainGraph_gui

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

Color graph vertices and edges

Coordinates for data from the Craddock200 atlas

Partition a design matrix into columns of interest and nuisance

Coordinates for data from the Dosenbach160 atlas

setup_randomise

Helper function to setup for randomise

Coordinates for data from Harvard-Oxford atlas

Rich club calculations

plot.brainGraph

Plot a brain graph with a specific spatial layout

Coordinates for data from the Desikan-Killiany atlas

Coordinates for data from the Desikan-Killiany atlas

communicability

Calculate communicability

Create a data table with graph global and vertex measures

Calculate Euclidean distance of edges and vertices

plot.brainGraph_GLM

Plot a graph with results from brainGraph_GLM

Calculate correlation matrix and threshold

Write files to be used for visualization with BrainNet Viewer

Select edges for re-wiring.

Coordinates for data from BrainSuite atlas

Transform edge weights

Calculate coefficient of variation

make_ego_brainGraph

Create a graph of the union of multiple vertex neighborhoods

plot.brainGraph_mediate

Plot a graph with results from a mediation analysis

make_brainGraph

Create a brainGraph object

rich_club_attrs

Assign graph attributes based on rich-club analysis

Coordinates for data from the Destrieux atlas

Get some variables for LM

Coordinates for data from the Destrieux atlas

Helper function to set-up for GLM analyses

Analysis of network robustness

delete_all_attr

Delete all attributes of a graph

Count number of edges of a brain graph

Calculate the s-core of a network

Determine whether x is a brainGraph object

set_brainGraph_attr

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

Coordinates for data from the LONI probabilistic brain atlas

Coordinates for data from the Desikan-Killiany-Tourville atlas

plot.brainGraph_mtpc

Plot a graph with results from MTPC

Simulate N random graphs w/ same clustering and degree sequence as the input.

plot.brainGraph_permute

Plot results from permutation testing

make_empty_brainGraph

Create an empty graph with attributes for brainGraph

plot_volumetric

Plot group distributions of volumetric measures for a given brain region

plot.brainGraph_resids

Plot model residuals for each brain region

make_glm_brainGraph

Create a graph with GLM-specific attributes

Coordinates for data from the Desikan-Killiany-Tourville atlas

make_nbs_brainGraph

Create a graph with NBS-specific attributes

Subset graphs based on a given logical condition

Multi-threshold permutation correction

Plot a correlation matrix

Plot global graph measures across densities

Apply a rotation matrix to a set of points

Print a summary from brainGraph_GLM analysis

symmetrize_mats

Create a symmetric matrix

summary.brainGraph_permute

Print a summary from a permutation analysis

plot_brainGraph_multi

Save PNG of three views of a brain graph

plot_brainGraph_list

Write PNG files for a list of graphs

Calculate graph global, local, or nodal efficiency

make_intersection_brainGraph

Create the intersection of graphs based on a logical condition

Linear model residuals in structural covariance networks

make_mediate_brainGraph

Create a graph with mediation-specific attributes

Calculate studentized residuals with matrix input

plot.brainGraph_NBS

Plot a graph with results from the network-based statistic

plot_vertex_measures

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

plot.brainGraph_boot

Plot bootstrap output of global graph measures across densities

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

Calculate graph vulnerability

Plot normalized rich club coefficients against degree threshold

summary.bg_mediate

Print a summary from a brainGraph mediation analysis

summary.brainGraph

Print a summary of a brainGraph object

update_brainGraph_gui

Function to dynamically plot a graph

Transform a vector to have a different range

apply_thresholds

Threshold additional set of matrices

analysis_random_graphs

Perform an analysis with random graphs for brain MRI data

Coordinates for data from the AAl90 atlas

Coordinates for data from the AAl116 atlas

Coordinates for data from the AAL2 atlas

Coordinates for data from the AAL2 atlas

Convert arguments into a single list

Convert brainGraph results to "mediate" object

Network-based statistic for brain MRI data

Fit linear models at each vertex of a graph

brainGraph_permute

Permutation test for group difference of graph measures

Fit linear models for t contrasts

brainGraph_GLM_design

Create a design matrix for linear model analysis

Calculate a vertex's leverage centrality

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

centr_betw_comm

Calculate communicability betweenness centrality

brainGraph_init

Initialize variables for further use in brainGraph

brainGraph_mediate

Mediation analysis with brain graph measures as mediator variables