Learn R Programming

⚠️There's a newer version (3.1.1) of this package.Take me there.

brainGraph (version 0.48.0)

Graph Theory Analysis of Brain MRI Data

Description

A set of tools for performing graph theory analysis of brain MRI data. It is best suited to data from a Freesurfer analysis (cortical thickness, volumes, local gyrification index, surface area), but also works with e.g., tractography data from FSL. It contains a graphical user interface for graph visualization and data exploration.

Copy Link

Version

Install

install.packages('brainGraph')

Monthly Downloads

570

Version

0.48.0

License

GPL-3

Issues

Pull Requests

Stars

Forks

Repository

https://github.com/cwatson/brainGraph

Maintainer

Christopher G Watson

Last Published

December 9th, 2015

Functions in brainGraph (0.48.0)

Bootstrapping for global graph measures

Color graph edges

Give vertices in a graph a lobe attribute.

Color graph vertices

graph_neighborhood_multiple

Take the union of multiple neighborhood graphs

Coordinates for data from the Desikan-Killiany atlas

graph.contract.brain

Contract graph vertices based on brain lobe and hemisphere

Permutation test for group difference of graph vertex measures

Coordinates for data from the Desikan-Killiany-Tourville atlas

Coordinates for data from BrainSuite atlas

count_interlobar

Count number of inter-lobar connections from a given major lobe

Coordinates for data from Harvard-Oxford atlas

Coordinates for data from the Destrieux atlas

Coordinates for data from the Desikan-Killiany atlas

plot_brainGraph_list

Write PNG files for a list of graphs

graph.efficiency

Calculate graph global, local, or nodal efficiency

plot_group_means

Plot group distributions of volumetric measures for a given brain region

Linear models of columns of a data frame

Calculate correlation matrix and threshold

plot_brainGraph_gui

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

Check model residuals for each brain region

Select edges for re-wiring.

Coordinates for data from the AAl116 atlas

Calculate an asymmetry index based on edge counts

Plot a correlation matrix

Calculate graph small-worldness

Transform a vector to have a different range

Calculate graph vulnerability

set.brainGraph.attributes

Set a number of graph and vertex attributes useful in MRI analyses

plot_vertex_measures

Plot vertex-level graph measures at a single density

sim.rand.graph.par

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

Calculate Euclidean distance between vertices (MNI space)

within_module_deg_z_score

Calculate vertex within-module degree z-score

Coordinates for data from the LONI probabilistic brain atlas

plot_brainGraph

Plot a graph with a specific spatial layout

Apply a rotation matrix to a set of points

update_brainGraph_gui

Function to dynamically plot a graph

Analysis of network robustness

Calculate the normalized rich club coefficient

count_homologous

Count number of edges between homologous regions of a brain graph

plot_perm_diffs

Calculate permutation p-values and plot group differences

plot_brainGraph_mni

Draw an axial or sagittal slice of the MNI152 T1 image

Calculate the rich core of a graph

Write files to be used for visualization with BrainNet Viewer

Permutation test for group difference of graph measures

dti_create_mats

Create connection matrices for tractography analysis

brainGraph_init

Initialize variables for further use in brainGraph

Calculate vertex participation coefficient

Create a data table with graph global measures

sim.rand.graph.clust

Simulate a random graph with given degree sequence and clustering.

Coordinates for data from the Desikan-Killiany-Tourville atlas

Coordinates for data from the AAl90 atlas

group.graph.diffs

Do between-group tests at each vertex for a given graph measure

rich.club.coeff

Calculate the rich club of a graph

Calculate a vertex's leverage centrality

Create a data table with graph vertex measures