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brainGraph (version 2.0.2)

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

581

Version

2.0.2

License

GPL-3

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Repository

https://github.com/cwatson/brainGraph

Maintainer

Christopher G Watson

Last Published

February 23rd, 2018

Functions in brainGraph (2.0.2)

apply_thresholds

Threshold additional set of matrices

Coordinates for data from the AAl116 atlas

Network-based statistic for brain MRI data

brainGraph_mediate

Mediation analysis with brain graph measures as mediator variables

brainGraph_permute

Permutation test for group difference of graph measures

Coordinates for data from the Craddock200 atlas

Coordinates for data from BrainSuite atlas

Create connection matrices for tractography or fMRI data

Select edges for re-wiring.

Calculate coefficient of variation

Create a data table with graph global and vertex measures

delete_all_attr

Delete all attributes of a graph

Coordinates for data from the Desikan-Killiany-Tourville atlas

Helper function for GLM fitting

Multi-threshold permutation correction

Coordinates for data from Harvard-Oxford atlas

Coordinates for data from the Desikan-Killiany-Tourville atlas

make_ego_brainGraph

Create a graph of the union of multiple vertex neighborhoods

make_empty_brainGraph

Create an empty graph with attributes for brainGraph

Plot GLM diagnostics for a brain network

plot.brainGraph_boot

Plot bootstrap output of global graph measures across densities

Partition a design matrix into columns of interest and nuisance

plot.brainGraph

Plot a brain graph with a specific spatial layout

plot_brainGraph_gui

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

plot_brainGraph_list

Write PNG files for a list of graphs

plot.brainGraph_mediate

Plot a graph with results from a mediation analysis

plot_vertex_measures

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

plot_volumetric

Plot group distributions of volumetric measures for a given brain region

Calculate studentized residuals with matrix input

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

Calculate the s-core of a network

Randomize and fit a model and find the maximum statistic

Analysis of network robustness

summary.brainGraph_boot

Print a summary from a bootstrap analysis

Apply a rotation matrix to a set of points

summary.brainGraph_permute

Print a summary from a permutation analysis

Transform a vector to have a different range

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

Print a summary of NBS analysis

Print a summary from brainGraph_GLM analysis

Coordinates for data from the AAL2 atlas

Coordinates for data from the AAL2 atlas

centr_betw_comm

Calculate communicability betweenness centrality

Calculate a vertex's leverage centrality

Color graph vertices and edges

communicability

Calculate communicability

Coordinates for data from the Destrieux atlas

Coordinates for data from the Destrieux atlas

Calculate graph global, local, or nodal efficiency

Linear model residuals across brain regions

make_glm_brainGraph

Create a graph with GLM-specific attributes

make_intersection_brainGraph

Create the intersection of graphs based on a logical condition

plot.brainGraph_resids

Plot model residuals for each brain region

Plot statistics from an MTPC analysis

Calculate the normalized rich club coefficient

Calculate the rich core of a graph

Coordinates for data from the AAl90 atlas

Fit linear models at each vertex of a graph

analysis_random_graphs

Perform an analysis with random graphs for brain MRI data

Calculate Euclidean distance of edges and vertices

brainGraph_GLM_design

Create a design matrix for linear model analysis

Calculate correlation matrix and threshold

Count number of edges of a brain graph

Coordinates for data from the Desikan-Killiany atlas

Coordinates for data from the Desikan-Killiany atlas

Subset graphs based on a given logical condition

Coordinates for data from the LONI probabilistic brain atlas

summary.bg_mediate

Print a summary from a brainGraph mediation analysis

summary.brainGraph

Print a summary of a brainGraph object

Transform edge weights

make_brainGraph

Create a brainGraph object

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

Plot a correlation matrix

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

Plot global graph measures across densities

Plot normalized rich club coefficients against degree threshold

set_brainGraph_attr

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

Convert brainGraph results to "mediate" object

Helper function to set-up for GLM analyses

symmetrize_mats

Create a symmetric matrix

Fit linear models for t contrasts

update_brainGraph_gui

Function to dynamically plot a graph

Calculate graph vulnerability

brainGraph_boot

Bootstrapping for global graph measures

Write files to be used for visualization with BrainNet Viewer

contract_brainGraph

Contract graph vertices based on brain lobe and hemisphere

Calculate the p-value for differences in correlation coefficients

Coordinates for data from the Dosenbach160 atlas

Calculate an asymmetry index based on edge counts

IndividualContributions

Approaches to estimate individual network contribution

Determine whether x is a brainGraph object

make_mediate_brainGraph

Create a graph with mediation-specific attributes

make_nbs_brainGraph

Create a graph with NBS-specific attributes

plot.brainGraph_mtpc

Plot a graph with results from MTPC

plot.brainGraph_permute

Plot results from permutation testing

rich_club_attrs

Assign graph attributes based on rich-club analysis

rich_club_coeff

Calculate the rich club of a graph

Calculate graph small-worldness

setup_randomise

Helper function to setup for randomise

summary.brainGraph_resids

Print a summary of residuals for structural covariance data

Print a summary of MTPC results

Convert arguments into a single list

brainGraph_init

Initialize variables for further use in brainGraph