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 |

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_GLM | Run 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 and calculate statistics |

brainGraph_init | Initialize variables for further use in brainGraph |

brainsuite | Coordinates for data from BrainSuite atlas |

centr_betw_comm | Calculate communicability betweenness centrality |

centr_lev | Calculate a vertex's leverage centrality |

check.resid | Check model residuals for each brain region |

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 |

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 |

graph_attr_dt | Create a data table with graph global measures |

hoa112 | Coordinates for data from Harvard-Oxford atlas |

individ_contrib | Approaches to estimate individual network contribution |

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

make_ego_brainGraph | Create a graph of the union of multiple vertex neighborhoods |

make_empty_brainGraph | Create an empty graph with attributes for brainGraph |

mtpc | Multi-threshold permutation correction |

NBS | Network-based statistic for brain MRI data |

permute.group | 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_brainGraph_multi | Save PNG of three views of a brain graph |

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 |

s_core | Calculate the s-core of a network |

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

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 |

spatial_dist | Calculate Euclidean distance of edges and vertices |

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_attr_dt | Create a data table with graph vertex measures |

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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