Graph Theory Analysis of Brain MRI Data

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 |

apply_thresholds | Threshold additional set of matrices |

args_as_list | Convert arguments into a single list |

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

bg_to_mediate | Convert brainGraph results to "mediate" object |

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 | Fit linear models for t contrasts |

brainGraph_init | Initialize variables for further use in brainGraph |

brainGraph_mediate | Mediation analysis with brain graph measures as mediator... |

brainGraph_permute | Permutation test for group difference of graph measures |

brainsuite | Coordinates for data from BrainSuite atlas |

centr_betw_comm | Calculate communicability betweenness centrality |

centr_lev | Calculate a vertex's leverage centrality |

choose.edges | Select edges for re-wiring. |

coeff_var | Calculate coefficient of variation |

color_vertices_edges | Color graph vertices and edges |

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... |

corr.matrix | Calculate correlation matrix and threshold |

count_edges | 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 |

data_tables | Create a data table with graph global and vertex measures |

delete_all_attr | Delete all attributes of a graph |

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 |

edge_asymmetry | Calculate an asymmetry index based on edge counts |

efficiency | Calculate graph global, local, or nodal efficiency |

get.resid | Linear model residuals across brain regions |

glm_fit_helper | Helper function for GLM fitting |

hoa112 | Coordinates for data from Harvard-Oxford atlas |

individ_contrib | Approaches to estimate individual network contribution |

is.brainGraph | Determine whether x is a brainGraph object |

lpba40 | Coordinates for data from the LONI probabilistic brain atlas |

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... |

make_mediate_brainGraph | Create a graph with mediation-specific attributes |

make_nbs_brainGraph | Create a graph with NBS-specific attributes |

mtpc | Multi-threshold permutation correction |

NBS | Network-based statistic for brain MRI data |

partition | Partition a design matrix into columns of interest and... |

plot.bg_GLM | Plot GLM diagnostics for a brain network |

plot.brainGraph | Plot a brain graph with a specific spatial layout |

plot.brainGraph_boot | Plot bootstrap output of global graph measures across... |

plot.brainGraph_GLM | Plot a graph with results from brainGraph_GLM |

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_mediate | Plot a graph with results from a mediation analysis |

plot.brainGraph_mtpc | Plot a graph with results from MTPC |

plot_brainGraph_multi | Save PNG of three views of a brain graph |

plot.brainGraph_NBS | Plot a graph with results from the network-based statistic |

plot.brainGraph_permute | Plot results from permutation testing |

plot.brainGraph_resids | Plot model residuals for each brain region |

plot_corr_mat | Plot a correlation matrix |

plot_global | Plot global graph measures across densities |

plot.mtpc | Plot statistics from an MTPC analysis |

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

plot_vertex_measures | Plot vertex-level graph measures at a single density or... |

plot_volumetric | Plot group distributions of volumetric measures for a given... |

random_graphs | Simulate N random graphs w/ same clustering and degree... |

randomise | Randomize and fit a model and find the maximum statistic |

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 |

rstudent_mat | Calculate studentized residuals with matrix input |

s_core | Calculate the s-core of a network |

set_brainGraph_attr | Set graph, vertex, and edge attributes common in MRI analyses |

setup_glm | Helper function to set-up for GLM analyses |

setup_randomise | Helper function to setup for randomise |

small.world | Calculate graph small-worldness |

spatial_dist | Calculate Euclidean distance of edges and vertices |

subset_graph | Subset graphs based on a given logical condition |

summary.bg_GLM | Print a summary from brainGraph_GLM analysis |

summary.bg_mediate | Print a summary from a brainGraph mediation analysis |

summary.brainGraph | Print a summary of a brainGraph object |

summary.brainGraph_boot | Print a summary from a bootstrap analysis |

summary.brainGraph_permute | Print a summary from a permutation analysis |

summary.brainGraph_resids | Print a summary of residuals for structural covariance data |

summary.mtpc | Print a summary of MTPC results |

summary.NBS | Print a summary of NBS analysis |

symmetrize_mats | Create a symmetric matrix |

update_brainGraph_gui | Function to dynamically plot a graph |

vec.transform | Transform a vector to have a different range |

vertex_roles | Gateway coefficient, participation coefficient, and... |

vulnerability | Calculate graph vulnerability |

write_brainnet | Write files to be used for visualization with BrainNet Viewer |

xfm.weights | Transform edge weights |

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