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brainGraph (version 1.0.0)

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 and fMRI data from DPABI. It contains a graphical user interface for graph visualization and data exploration and several functions for generating useful figures.

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install.packages('brainGraph')

Monthly Downloads

543

Version

1.0.0

License

GPL-3

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Repository

https://github.com/cwatson/brainGraph

Maintainer

Christopher G Watson

Last Published

April 10th, 2017

Functions in brainGraph (1.0.0)

Coordinates for data from the AAl90 atlas

analysis_random_graphs

Perform an analysis with random graphs for brain MRI data

Coordinates for data from the AAL2 atlas

Select edges for re-wiring.

Color graph vertices and edges

Coordinates for data from the AAL2 atlas

Calculate a vertex's leverage centrality

Check model residuals for each brain region

Network-based statistic for brain MRI data

Coordinates for data from the AAl116 atlas

Coordinates for data from the Craddock200 atlas

Create connection matrices for tractography or fMRI data

contract_brainGraph

Contract graph vertices based on brain lobe and hemisphere

Calculate the p-value for differences in correlation coefficients

delete_all_attr

Delete all attributes of a graph

Coordinates for data from the Destrieux atlas

Coordinates for data from Harvard-Oxford atlas

IndividualContributions

Approaches to estimate individual network contribution

Plot a correlation matrix

Plot global graph measures across densities

rich_club_attrs

Assign graph attributes based on rich-club analysis

rich_club_coeff

Calculate the rich club of a graph

Transform a vector to have a different range

Give vertices in a graph a

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

brainGraph_GLM_design

Create a design matrix for linear model analysis

brainGraph_GLM_fit

Fit linear models and calculate statistics

Permutation test for group difference of graph measures

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

Calculate graph vulnerability

Create a data table with graph vertex measures

Write files to be used for visualization with BrainNet Viewer

make_empty_brainGraph

Create an empty graph with attributes for brainGraph

Bootstrapping for global graph measures

Run linear models at each vertex of a graph

brainGraph_init

Initialize variables for further use in brainGraph

Coordinates for data from BrainSuite atlas

Coordinates for data from the Destrieux atlas

Coordinates for data from the Desikan-Killiany atlas

Coordinates for data from the LONI probabilistic brain atlas

Coordinates for data from the Desikan-Killiany atlas

Coordinates for data from the Desikan-Killiany-Tourville atlas

Linear model residuals across brain regions

Create a data table with graph global measures

Calculate an asymmetry index based on edge counts

Calculate graph global, local, or nodal efficiency

Plot global graph measures with shaded regions calculated from bootstrapping

plot_brainGraph

Plot a brain graph with a specific spatial layout

plot_brainGraph_mni

Draw an axial or sagittal slice of the MNI152 T1 image

plot_brainGraph_multi

Save PNG of three views of a brain graph

Plot normalized rich club coefficients against degree threshold

plot_vertex_measures

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

Calculate correlation matrix and threshold

Count number of edges of a brain graph

Coordinates for data from the Desikan-Killiany-Tourville atlas

Coordinates for data from the Dosenbach160 atlas

Analysis of network robustness

Apply a rotation matrix to a set of points

set_brainGraph_attr

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

sim.rand.graph.clust

Simulate a random graph with given degree sequence and clustering.

Calculate the normalized rich club coefficient

Calculate the rich core of a graph

sim.rand.graph.par

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

Calculate graph small-worldness

make_ego_brainGraph

Create a graph of the union of multiple vertex neighborhoods

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_group_means

Plot group distributions of volumetric measures for a given brain region

plot_perm_diffs

Calculate permutation p-values and plot group differences

Calculate Euclidean distance of edges and vertices

update_brainGraph_gui

Function to dynamically plot a graph