NBS                     Network-based statistic for brain MRI data
SPM                     Perform between-group tests at each vertex for
                        a given vertex measure
aal116                  Coordinates for data from the AAl116 atlas
aal90                   Coordinates for data from the AAl90 atlas
analysis_random_graphs
                        Perform an analysis with random graphs for
                        brain MRI data
aop                     "Add-one-patient" approach to estimate
                        individual network contribution
assign_lobes            Give vertices in a graph a _lobe_ attribute.
boot_global             Bootstrapping for global graph measures
brainGraph_init         Initialize variables for further use in
                        brainGraph
brainsuite              Coordinates for data from BrainSuite atlas
centr_lev               Calculate a vertex's leverage centrality
check.resid             Check model residuals for each brain region
choose.edges            Select edges for re-wiring.
color.edges             Color graph edges
color.vertices          Color graph vertices
corr.matrix             Calculate correlation matrix and threshold
count_homologous        Count number of edges between homologous
                        regions of a brain graph
count_interlobar        Count number of inter-lobar connections from a
                        given major lobe
destrieux               Coordinates for data from the Destrieux atlas
destrieux.scgm          Coordinates for data from the Destrieux atlas
dk                      Coordinates for data from the Desikan-Killiany
                        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
dti_create_mats         Create connection matrices for tractography
                        analysis
edge_asymmetry          Calculate an asymmetry index based on edge
                        counts
edge_spatial_dist       Calculate Euclidean distance of edges
get.resid               Linear model residuals across brain regions
graph.contract.brain    Contract graph vertices based on brain lobe and
                        hemisphere
graph.efficiency        Calculate graph global, local, or nodal
                        efficiency
graph_attr_dt           Create a data table with graph global measures
graph_neighborhood_multiple
                        Take the union of multiple neighborhood graphs
hoa112                  Coordinates for data from Harvard-Oxford atlas
loo                     "Leave-one-out" approach to estimate individual
                        network contribution
lpba40                  Coordinates for data from the LONI
                        probabilistic brain atlas
make_empty_brainGraph   Create an empty graph with attributes for
                        brainGraph
part.coeff              Calculate vertex participation coefficient
permute.group           Permutation test for group difference of graph
                        measures
plot_boot               Plot global graph measures with shaded regions
                        calculated from bootstrapping
plot_brainGraph         Plot a 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_mni     Draw an axial or sagittal slice of the MNI152
                        T1 image
plot_corr_mat           Plot a correlation matrix
plot_global             Plot global graph measures across densities
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_rich_norm          Plot normalized rich club coefficients against
                        degree threshold
plot_vertex_measures    Plot vertex-level graph measures at a single
                        density
rich.club.coeff         Calculate the rich club of a graph
rich.club.norm          Calculate the normalized rich club coefficient
rich.core               Calculate the rich core of a graph
robustness              Analysis of network robustness
rotation                Apply a rotation matrix to a set of points
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.
sim.rand.graph.par      Simulate N random graphs w/ same clustering and
                        degree sequence as the input.
small.world             Calculate graph small-worldness
update_brainGraph_gui   Function to dynamically plot a graph
vec.transform           Transform a vector to have a different range
vertex_attr_dt          Create a data table with graph vertex measures
vertex_spatial_dist     Calculate average Euclidean distance for each
                        vertex
vulnerability           Calculate graph vulnerability
within_module_deg_z_score
                        Calculate vertex within-module degree z-score
write.brainnet          Write files to be used for visualization with
                        BrainNet Viewer
