Graph Theory Analysis of Brain MRI Data

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Documentation for package ‘brainGraph’ version 2.7.3

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A B C D E F G H I L M N P R S V W X misc

-- A --

AAL Coordinates for data from the AAL-based atlases
aal116 Coordinates for data from the AAL-based atlases
aal2.120 Coordinates for data from the AAL-based atlases
aal2.94 Coordinates for data from the AAL-based atlases
aal90 Coordinates for data from the AAL-based atlases
analysis_random_graphs Perform an analysis with random graphs for brain MRI data
aop Approaches to estimate individual network contribution
apply_thresholds Threshold additional set of matrices

-- B --

bg_to_mediate Mediation analysis with brain graph measures as mediator variables
Bootstrapping Bootstrapping for global graph measures
brainGraph_boot Bootstrapping for global graph measures
brainGraph_GLM Fit linear models at each vertex of a graph
brainGraph_GLM_design Create a design matrix for linear model analysis
brainGraph_GLM_fit_f Fit linear models for t contrasts
brainGraph_GLM_fit_t Fit linear models for t contrasts
brainGraph_mediate Mediation analysis with brain graph measures as mediator variables
brainGraph_permute Permutation test for group difference of graph measures
brainsuite Coordinates for data from BrainSuite atlas

-- C --

centr_betw_comm Calculate communicability betweenness centrality
centr_lev Calculate a vertex's leverage centrality
coeff_var Calculate coefficient of variation
communicability Calculate communicability
contract_brainGraph Contract graph vertices based on brain lobe and hemisphere
cor.diff.test Calculate the p-value for differences in correlation coefficients
corr.matrix Calculate correlation matrix and threshold
CountEdges Count number of edges of a brain graph
count_homologous Count number of edges of a brain graph
count_inter Count number of edges of a brain graph
count_interlobar Count number of edges of a brain graph
craddock200 Coordinates for data from the Craddock200 atlas
create_mats Create connection matrices for tractography or fMRI data

-- D --

DataTables Create a data table with graph global and vertex measures
destrieux Coordinates for data from Freesurfer atlases
destrieux.scgm Coordinates for data from Freesurfer atlases
dk Coordinates for data from Freesurfer atlases
dk.scgm Coordinates for data from Freesurfer atlases
dkt Coordinates for data from Freesurfer atlases
dkt.scgm Coordinates for data from Freesurfer atlases
dosenbach160 Coordinates for data from the Dosenbach160 atlas

-- E --

edge_asymmetry Calculate an asymmetry index based on edge counts
edge_spatial_dist Calculate Euclidean distance of edges and vertices
efficiency Calculate graph global, local, or nodal efficiency
Extract.brainGraph_resids Linear model residuals in structural covariance networks

-- F --

FreesurferAtlases Coordinates for data from Freesurfer atlases

-- G --

gateway_coeff Gateway coefficient, participation coefficient, and within-mod degree z-score
get.resid Linear model residuals in structural covariance networks
GLM Fit linear models at each vertex of a graph
GLMdesign Create a design matrix for linear model analysis
GLMfit Fit linear models for t contrasts
GraphDistances Calculate Euclidean distance of edges and vertices
graph_attr_dt Create a data table with graph global and vertex measures

-- H --

hoa112 Coordinates for data from Harvard-Oxford atlas
hubness Calculate vertex hubness

-- I --

import_scn Import data for structural connectivity analysis
IndividualContributions Approaches to estimate individual network contribution

-- L --

loo Approaches to estimate individual network contribution
lpba40 Coordinates for data from the LONI probabilistic brain atlas

-- M --

make_brainGraph Create a brainGraph object
make_ego_brainGraph Create a graph of the union of multiple vertex neighborhoods
make_empty_brainGraph Create an empty graph with attributes for brainGraph
make_glm_brainGraph Create a graph with GLM-specific attributes
make_intersection_brainGraph Create the intersection of graphs based on a logical condition
make_mediate_brainGraph Create a graph with mediation-specific attributes
make_nbs_brainGraph Create a graph with NBS-specific attributes
MediationAnalysis Mediation analysis with brain graph measures as mediator variables
mtpc Multi-threshold permutation correction

-- N --

NBS Network-based statistic for brain MRI data

-- P --

part_coeff Gateway coefficient, participation coefficient, and within-mod degree z-score
plot.bg_GLM Fit linear models at each vertex of a graph
plot.brainGraph Plot a brain graph with a specific spatial layout
plot.brainGraph_boot Bootstrapping for global graph measures
plot.brainGraph_GLM Plot a graph with results from brainGraph_GLM
plot.brainGraph_mediate Plot a graph with results from a mediation analysis
plot.brainGraph_mtpc Plot a graph with results from MTPC
plot.brainGraph_NBS Plot a graph with results from the network-based statistic
plot.brainGraph_permute Permutation test for group difference of graph measures
plot.brainGraph_resids Linear model residuals in structural covariance networks
plot.IC Approaches to estimate individual network contribution
plot.mtpc Multi-threshold permutation correction
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_multi Save PNG of three views of a brain graph
plot_corr_mat Plot a correlation matrix
plot_global Plot global graph measures across densities
plot_rich_norm Plot normalized rich club coefficients against degree threshold
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

-- R --

RandomGraphs Perform an analysis with random graphs for brain MRI data
Residuals Linear model residuals in structural covariance networks
RichClub Rich club calculations
rich_club_all Rich club calculations
rich_club_attrs Assign graph attributes based on rich-club analysis
rich_club_coeff Rich club calculations
rich_club_norm Rich club calculations
rich_core Rich club calculations
robustness Analysis of network robustness

-- S --

set_brainGraph_attr Set graph, vertex, and edge attributes common in MRI analyses
sim.rand.graph.clust Perform an analysis with random graphs for brain MRI data
sim.rand.graph.par Perform an analysis with random graphs for brain MRI data
small.world Calculate graph small-worldness
summary.bg_GLM Fit linear models at each vertex of a graph
summary.bg_mediate Mediation analysis with brain graph measures as mediator variables
summary.brainGraph Create a brainGraph object
summary.brainGraph_boot Bootstrapping for global graph measures
summary.brainGraph_permute Permutation test for group difference of graph measures
summary.brainGraph_resids Linear model residuals in structural covariance networks
summary.IC Approaches to estimate individual network contribution
summary.mtpc Multi-threshold permutation correction
summary.NBS Network-based statistic for brain MRI data
symmetrize_array Create a symmetric matrix
symmetrize_mats Create a symmetric matrix
s_core Calculate the s-core of a network

-- V --

VertexRoles Gateway coefficient, participation coefficient, and within-mod degree z-score
vertex_attr_dt Create a data table with graph global and vertex measures
vertex_spatial_dist Calculate Euclidean distance of edges and vertices
vulnerability Calculate graph vulnerability

-- W --

within_module_deg_z_score Gateway coefficient, participation coefficient, and within-mod degree z-score
write_brainnet Write files to be used for visualization with BrainNet Viewer

-- X --

xfm.weights Transform edge weights

-- misc --

[.brainGraph_resids Linear model residuals in structural covariance networks