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.

Author
Christopher G. Watson <cgwatson@bu.edu>
Date of publication
2016-10-10 18:18:43
Maintainer
Christopher G. Watson <cgwatson@bu.edu>
License
GPL-3
Version
0.72.0
URLs

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