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brainGraph (version 0.55.0)

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

570

Version

0.55.0

License

GPL-3

Issues

10

Pull Requests

1

Stars

191

Forks

54

Maintainer

Christopher G Watson

Last Published

December 24th, 2015

Functions in brainGraph (0.55.0)

dti_create_mats

Create connection matrices for tractography analysis
plot_brainGraph

Plot a graph with a specific spatial layout
color.edges

Color graph edges
graph_attr_dt

Create a data table with graph global measures
centr_lev

Calculate a vertex's leverage centrality
plot_corr_mat

Plot a correlation matrix
aal90

Coordinates for data from the AAl90 atlas
choose.edges

Select edges for re-wiring.
group.graph.diffs

Do between-group tests at each vertex for a given graph measure
sim.rand.graph.par

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

Count number of edges between homologous regions of a brain graph
lpba40

Coordinates for data from the LONI probabilistic brain atlas
part.coeff

Calculate vertex participation coefficient
dkt.scgm

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

Function to dynamically plot a graph
plot_rich_norm

Plot normalized rich club coefficients against degree threshold
color.vertices

Color graph vertices
count_interlobar

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

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

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

Take the union of multiple neighborhood graphs
rich.club.norm

Calculate the normalized rich club coefficient
vec.transform

Transform a vector to have a different range
dk.scgm

Coordinates for data from the Desikan-Killiany atlas
rich.club.coeff

Calculate the rich club of a graph
dkt

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

Plot global graph measures with shaded regions calculated from bootstrapping
edge_asymmetry

Calculate an asymmetry index based on edge counts
permute.group

Permutation test for group difference of graph measures
brainGraph_init

Initialize variables for further use in brainGraph
aal116

Coordinates for data from the AAl116 atlas
brainsuite

Coordinates for data from BrainSuite atlas
plot_perm_diffs

Calculate permutation p-values and plot group differences
loo

"Leave-one-out" approach to estimate individual network contribution
get.resid

Linear model residuals across brain regions
boot_global

Bootstrapping for global graph measures
check.resid

Check model residuals for each brain region
plot_brainGraph_list

Write PNG files for a list of graphs
plot_brainGraph_gui

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

Plot group distributions of volumetric measures for a given brain region
dk

Coordinates for data from the Desikan-Killiany atlas
plot_vertex_measures

Plot vertex-level graph measures at a single density
robustness

Analysis of network robustness
small.world

Calculate graph small-worldness
permute.vertex

Permutation test for group difference of graph vertex measures
within_module_deg_z_score

Calculate vertex within-module degree z-score
rich.core

Calculate the rich core of a graph
sim.rand.graph.clust

Simulate a random graph with given degree sequence and clustering.
rotation

Apply a rotation matrix to a set of points
vertex_attr_dt

Create a data table with graph vertex measures
vulnerability

Calculate graph vulnerability
write.brainnet

Write files to be used for visualization with BrainNet Viewer
corr.matrix

Calculate correlation matrix and threshold
destrieux

Coordinates for data from the Destrieux atlas
spatial.dist

Calculate Euclidean distance between vertices (MNI space)
graph.contract.brain

Contract graph vertices based on brain lobe and hemisphere
assign_lobes

Give vertices in a graph a lobe attribute.
hoa112

Coordinates for data from Harvard-Oxford atlas
graph.efficiency

Calculate graph global, local, or nodal efficiency
set.brainGraph.attributes

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