brainGraph: Graph Theory Analysis of Brain MRI Data

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.

AuthorChristopher G. Watson <>
Date of publication2016-10-10 18:18:43
MaintainerChristopher G. Watson <>

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Man pages

aal116: Coordinates for data from the AAl116 atlas

aal2.120: Coordinates for data from the AAL2 atlas

aal2.94: Coordinates for data from the AAL2 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...

assign_lobes: Give vertices in a graph a _lobe_ attribute.

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

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

cor.diff.test: Calculate the p-value for differences in correlation...

corr.matrix: Calculate correlation matrix and threshold

count_homologous: Count number of edges between homologous regions of a brain...

count_interlobar: Count number of inter-lobar connections from a given major...

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...

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

dosenbach160: Coordinates for data from the Dosenbach160 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_attr_dt: Create a data table with graph global measures

graph.contract.brain: Contract graph vertices based on brain lobe and hemisphere

graph.efficiency: Calculate graph global, local, or nodal efficiency

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...

lpba40: Coordinates for data from the LONI probabilistic brain atlas

make_empty_brainGraph: Create an empty graph with attributes for brainGraph

NBS: Network-based statistic for brain MRI data

part.coeff: Calculate vertex participation coefficient Permutation test for group difference of graph measures Permutation test for group difference of graph measures

plot_boot: Plot global graph measures with shaded regions calculated...

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...

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...

plot_perm_diffs: Calculate permutation p-values and plot group differences

plot_rich_norm: Plot normalized rich club coefficients against degree...

plot_vertex_measures: Plot vertex-level graph measures at a single density or... Assign graph attributes based on rich-club analysis Calculate the rich club of a graph 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...

sim.rand.graph.clust: Simulate a random graph with given degree sequence and...

sim.rand.graph.par: Simulate N random graphs w/ same clustering and degree... Calculate graph small-worldness

SPM: Perform between-group tests at each vertex for a given vertex...

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


aal116 Man page
aal2.120 Man page
aal2.94 Man page
aal90 Man page
analysis_random_graphs Man page
aop Man page
assign_lobes Man page
auc_diff Man page
boot_global Man page
brainGraph_init Man page
brainsuite Man page
centr_lev Man page
check.resid Man page
choose.edges Man page
color.edges Man page
color.vertices Man page
cor.diff.test Man page
corr.matrix Man page
count_homologous Man page
count_interlobar Man page
destrieux Man page
destrieux.scgm Man page
dk Man page
dk.scgm Man page
dkt Man page
dkt.scgm Man page
dosenbach160 Man page
dti_create_mats Man page
edge_asymmetry Man page
edge_spatial_dist Man page
get.resid Man page
graph_attr_dt Man page
graph.contract.brain Man page
graph.efficiency Man page
graph_neighborhood_multiple Man page
hoa112 Man page
loo Man page
lpba40 Man page
make_empty_brainGraph Man page
NBS Man page
part.coeff Man page Man page Man page
plot_boot Man page
plot_brainGraph Man page
plot_brainGraph_gui Man page
plot_brainGraph_list Man page
plot_brainGraph_mni Man page
plot_corr_mat Man page
plot_global Man page
plot_group_means Man page
plot_perm_diffs Man page
plot_rich_norm Man page
plot_vertex_measures Man page Man page Man page Man page
rich.core Man page
robustness Man page
rotation Man page
set.brainGraph.attributes Man page
sim.rand.graph.clust Man page
sim.rand.graph.par Man page Man page
SPM Man page
update_brainGraph_gui Man page
vec.transform Man page
vertex_attr_dt Man page
vertex_spatial_dist Man page
vulnerability Man page
within_module_deg_z_score Man page
write.brainnet Man page


brainGraph/R/graph_contract_brain.R brainGraph/R/cor_diff_test.R brainGraph/R/choose_edges.R brainGraph/R/rich_club_attrs.R brainGraph/R/plot_brainGraph_list.R brainGraph/R/count_interlobar.R brainGraph/R/robustness.R brainGraph/R/plot_brainGraph_gui.R brainGraph/R/graph_neighborhood_multiple.R brainGraph/R/plot_group_means.R brainGraph/R/count_homologous.R brainGraph/R/plot_rich_norm.R brainGraph/R/centr_lev.R brainGraph/R/update_brainGraph_gui.R brainGraph/R/sim_rand_graph_par.R brainGraph/R/color_edges.R brainGraph/R/within_module_degree_z_score.R brainGraph/R/set_brainGraph_attributes.R brainGraph/R/check_resid.R
brainGraph/R/part_coeff.R brainGraph/R/small_world.R brainGraph/R/sim_rand_graph_clust.R brainGraph/R/get_resid.R brainGraph/R/vec_transform.R brainGraph/R/rich_club_norm.R brainGraph/R/SPM.R brainGraph/R/plot_global.R brainGraph/R/dti_create_mats.R brainGraph/R/NBS.R brainGraph/R/plot_brainGraph.R brainGraph/R/boot_global.R brainGraph/R/vertex_attr_dt.R brainGraph/R/graph_efficiency.R brainGraph/R/plot_vertex_measures.R brainGraph/R/color_vertices.R brainGraph/R/corr_matrix.R brainGraph/R/permute_group_auc.R brainGraph/R/permute_group.R brainGraph/R/plot_boot.R brainGraph/R/graph_attr_dt.R brainGraph/R/write_brainnet.R brainGraph/R/auc_diff.R brainGraph/R/brainGraph_init.R brainGraph/R/plot_brainGraph_mni.R brainGraph/R/analysis_random_graphs.R brainGraph/R/rich_core.R brainGraph/R/rotation.R brainGraph/R/plot_perm_diffs.R brainGraph/R/vulnerability.R brainGraph/R/make_empty_brainGraph.R brainGraph/R/edge_asymmetry.R brainGraph/R/individ_contrib.R brainGraph/R/assign_lobes.R brainGraph/R/plot_corr_mat.R brainGraph/R/rich_club_coeff.R brainGraph/R/spatial_dist.R
brainGraph/man/boot_global.Rd brainGraph/man/aal2.94.Rd brainGraph/man/loo.Rd brainGraph/man/lpba40.Rd brainGraph/man/assign_lobes.Rd brainGraph/man/set.brainGraph.attributes.Rd brainGraph/man/centr_lev.Rd brainGraph/man/cor.diff.test.Rd brainGraph/man/aal90.Rd brainGraph/man/ brainGraph/man/plot_global.Rd brainGraph/man/ brainGraph/man/plot_boot.Rd brainGraph/man/update_brainGraph_gui.Rd brainGraph/man/get.resid.Rd brainGraph/man/aal116.Rd brainGraph/man/destrieux.scgm.Rd brainGraph/man/vertex_spatial_dist.Rd brainGraph/man/auc_diff.Rd brainGraph/man/dosenbach160.Rd brainGraph/man/vertex_attr_dt.Rd brainGraph/man/plot_vertex_measures.Rd brainGraph/man/plot_group_means.Rd brainGraph/man/plot_brainGraph_list.Rd brainGraph/man/ brainGraph/man/plot_corr_mat.Rd brainGraph/man/brainGraph_init.Rd brainGraph/man/within_module_deg_z_score.Rd brainGraph/man/check.resid.Rd brainGraph/man/ brainGraph/man/dk.Rd brainGraph/man/make_empty_brainGraph.Rd brainGraph/man/robustness.Rd brainGraph/man/count_homologous.Rd brainGraph/man/part.coeff.Rd brainGraph/man/dkt.scgm.Rd brainGraph/man/dti_create_mats.Rd brainGraph/man/destrieux.Rd brainGraph/man/corr.matrix.Rd brainGraph/man/SPM.Rd brainGraph/man/plot_brainGraph_mni.Rd brainGraph/man/aal2.120.Rd brainGraph/man/edge_asymmetry.Rd brainGraph/man/choose.edges.Rd brainGraph/man/hoa112.Rd brainGraph/man/graph_neighborhood_multiple.Rd brainGraph/man/graph.efficiency.Rd brainGraph/man/graph.contract.brain.Rd brainGraph/man/plot_perm_diffs.Rd brainGraph/man/sim.rand.graph.par.Rd brainGraph/man/aop.Rd brainGraph/man/rich.core.Rd brainGraph/man/ brainGraph/man/write.brainnet.Rd brainGraph/man/color.vertices.Rd brainGraph/man/sim.rand.graph.clust.Rd brainGraph/man/vec.transform.Rd brainGraph/man/vulnerability.Rd brainGraph/man/ brainGraph/man/dkt.Rd brainGraph/man/NBS.Rd brainGraph/man/brainsuite.Rd brainGraph/man/plot_rich_norm.Rd brainGraph/man/edge_spatial_dist.Rd brainGraph/man/rotation.Rd brainGraph/man/color.edges.Rd brainGraph/man/analysis_random_graphs.Rd brainGraph/man/graph_attr_dt.Rd brainGraph/man/dk.scgm.Rd brainGraph/man/count_interlobar.Rd brainGraph/man/plot_brainGraph.Rd brainGraph/man/plot_brainGraph_gui.Rd

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