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brainGraph (version 0.72.0)

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.

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Install

install.packages('brainGraph')

Monthly Downloads

487

Version

0.72.0

License

GPL-3

Issues

10

Pull Requests

1

Stars

187

Forks

54

Maintainer

Christopher G Watson

Last Published

October 10th, 2016

Functions in brainGraph (0.72.0)

boot_global

Bootstrapping for global graph measures
aal116

Coordinates for data from the AAl116 atlas
aal2.120

Coordinates for data from the AAL2 atlas
brainGraph_init

Initialize variables for further use in brainGraph
aop

"Add-one-patient" approach to estimate individual network contribution
analysis_random_graphs

Perform an analysis with random graphs for brain MRI data
assign_lobes

Give vertices in a graph a lobe attribute.
auc_diff

Difference in the area-under-the-curve of two vectors
aal2.94

Coordinates for data from the AAL2 atlas
aal90

Coordinates for data from the AAl90 atlas
brainsuite

Coordinates for data from BrainSuite atlas
color.vertices

Color graph vertices
cor.diff.test

Calculate the p-value for differences in correlation coefficients
count_homologous

Count number of edges between homologous regions of a brain graph
choose.edges

Select edges for re-wiring.
color.edges

Color graph edges
count_interlobar

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

Coordinates for data from the Destrieux atlas
check.resid

Check model residuals for each brain region
corr.matrix

Calculate correlation matrix and threshold
get.resid

Linear model residuals across brain regions
destrieux.scgm

Coordinates for data from the Destrieux atlas
dk.scgm

Coordinates for data from the Desikan-Killiany atlas
dkt

Coordinates for data from the Desikan-Killiany-Tourville atlas
dkt.scgm

Coordinates for data from the Desikan-Killiany-Tourville atlas
edge_spatial_dist

Calculate Euclidean distance of edges
graph_attr_dt

Create a data table with graph global measures
dti_create_mats

Create connection matrices for tractography analysis
dosenbach160

Coordinates for data from the Dosenbach160 atlas
dk

Coordinates for data from the Desikan-Killiany atlas
lpba40

Coordinates for data from the LONI probabilistic brain atlas
make_empty_brainGraph

Create an empty graph with attributes for brainGraph
graph.contract.brain

Contract graph vertices based on brain lobe and hemisphere
hoa112

Coordinates for data from Harvard-Oxford atlas
NBS

Network-based statistic for brain MRI data
permute.group

Permutation test for group difference of graph measures
permute.group.auc

Permutation test for group difference of graph measures
graph_neighborhood_multiple

Take the union of multiple neighborhood graphs
plot_boot

Plot global graph measures with shaded regions calculated from bootstrapping
loo

"Leave-one-out" approach to estimate individual network contribution
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
plot_corr_mat

Plot a correlation matrix
plot_global

Plot global graph measures across densities
plot_brainGraph_mni

Draw an axial or sagittal slice of the MNI152 T1 image
plot_brainGraph

Plot a brain graph with a specific spatial layout
plot_rich_norm

Plot normalized rich club coefficients against degree threshold
plot_brainGraph_gui

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

Plot vertex-level graph measures at a single density or threshold
sim.rand.graph.par

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

Write PNG files for a list of graphs
small.world

Calculate graph small-worldness
vec.transform

Transform a vector to have a different range
vertex_attr_dt

Create a data table with graph vertex measures
set.brainGraph.attributes

Set a number of graph and vertex attributes useful in MRI analyses
sim.rand.graph.clust

Simulate a random graph with given degree sequence and clustering.
rich.club.norm

Calculate the normalized rich club coefficient
write.brainnet

Write files to be used for visualization with BrainNet Viewer
rich.core

Calculate the rich core of a graph
rich.club.coeff

Calculate the rich club of a graph
rich.club.attrs

Assign graph attributes based on rich-club analysis
SPM

Perform between-group tests at each vertex for a given vertex measure
update_brainGraph_gui

Function to dynamically plot a graph
vertex_spatial_dist

Calculate average Euclidean distance for each vertex
vulnerability

Calculate graph vulnerability
robustness

Analysis of network robustness
rotation

Apply a rotation matrix to a set of points