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 <cgwatson@bu.edu>
Date of publication2016-10-10 18:18:43
MaintainerChristopher G. Watson <cgwatson@bu.edu>
LicenseGPL-3
Version0.72.0
https://github.com/cwatson/brainGraph

View on CRAN

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

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

permute.group.auc: 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...

rich.club.attrs: Assign graph attributes based on rich-club analysis

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...

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...

small.world: 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

Files in this package

brainGraph
brainGraph/inst
brainGraph/inst/extdata
brainGraph/inst/extdata/brainGraph_icon.png
brainGraph/NAMESPACE
brainGraph/data
brainGraph/data/dosenbach160.rda
brainGraph/data/dk.rda
brainGraph/data/destrieux.rda
brainGraph/data/dk.scgm.rda
brainGraph/data/brainsuite.rda
brainGraph/data/aal116.rda
brainGraph/data/lpba40.rda
brainGraph/data/hoa112.rda
brainGraph/data/aal2.94.rda
brainGraph/data/aal2.120.rda
brainGraph/data/dkt.scgm.rda
brainGraph/data/aal90.rda
brainGraph/data/dkt.rda
brainGraph/data/destrieux.scgm.rda
brainGraph/R
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/sysdata.rda
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/MD5
brainGraph/DESCRIPTION
brainGraph/man
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/rich.club.norm.Rd brainGraph/man/plot_global.Rd brainGraph/man/permute.group.auc.Rd 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/permute.group.Rd 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/rich.club.attrs.Rd 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/small.world.Rd 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/rich.club.coeff.Rd 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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