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Bug 3047 - update Brain Connectivity Toolbox to latest version

Reported 2016-01-18 16:10:00 +0100
Modified 2016-05-05 20:31:34 +0200
Product: FieldTrip
Component: external
Version: unspecified
Hardware: PC
Operating System: Mac OS
Importance: P5 normal
Assigned to: Jan-Mathijs Schoffelen
Depends on:
See also:

Robert Oostenveld - 2016-01-18 16:10:44 +0100

On 17 Jan 2016, at 20:55, Mikail Rubinov wrote: Dear Colleague, I am contacting you because your software resource utilizes code from the Brain Connectivity Toolbox (BCT). We have just updated the BCT with important bug fixes and several new functions. See the attached release notes for details. Please let me know if you need any additional information. Best regards, Mika Rubinov, on behalf of all BCT Contributors

Robert Oostenveld - 2016-01-18 16:12:09 +0100

Here are the release notes. ----------------------------------- Contents Version 2016-16-01: Major update Version 2015-25-01: Major update Version 2014-04-05: Minor update Version 2016-16-01: Major update New network models generative_model.m: Implements more than 10 generative network models. evaluate_generative_model.m: Implements and evaluates the accuracy of more than 10 generative network models. demo_generative_models_geometric.m and demo_generative_models_neighbors.m: Demonstrate the capabilities of the new generative model functions. New network measures clustering_coef_wu_sign.m: Multiple generalizations of the clustering coefficient for networks with positive and negative weights. core_periphery_dir.m: Optimal core structure and core-ness statistic. gateway_coef_sign.m: Gateway coefficient (a variant of the participation coefficient) for networks with positive and negative weights. local_assortativity_sign.m: Local (nodal) assortativity for networks with positive and negative weights. randmio_dir_signed.m: Random directed graph with preserved signed in- and out- degree distribution. Removed network measures modularity_louvain_und_sign.m, modularity_finetune_und_sign.m: This functionality is now provided by community_louvain.m. modularity_probtune_und_sign.m: Similar functionality is provided by consensus_und.m Bug fixes and/or code improvements and/or documentation improvements charpath.m: Changed default behavior, such that infinitely long paths (i.e. paths between disconnected nodes) are now included in computations by default, but may be excluded manually. community_louvain.m: Included generalization for negative weights, enforced binary network input for Potts-model Hamiltonian, streamlined code. eigenvector_centrality_und.m: Ensured the use of leading eigenvector for computations of eigenvector centrality. modularity_und.m, modularity_dir.m: Enforced single node moves during fine-tuning step. null_model_und_sign.m and null_model_dir_sign.m: Fixed preservation of negative degrees in sparse networks with negative weights. randmio_und_signed.m: Now allows unbiased exploration of all network configurations. transitivity_bd.m, transitivity_wu.m, transitivity_wd.m: removed tests for absence of nodewise 3-cycles. Expanded documentation. clustering_coef_wu.m, clustering_coef_wd.m: Expanded documentation. motif3-m and motif4-m functions: Expanded documentation. rich_club_wu.m, rich_club_wd.m. Expanded documentation. Cosmetic and MATLAB code analyzer (mlint) improvements to many other functions Version 2015-25-01: Major update Includes two new community-detection scripts and multiple improvements New community detection scripts: 1. community_louvain.m (supersedes modularity_louvain.m and modularity_finetune.m scripts); 2. link_communities.m. added autofix flag to weight_conversion.m for fixing common weight problems. other function improvements: participation_coef.m, charpath.m, reorder_mod.m. bug fixes: modularity_finetune_und_sign.m, modularity_probtune_und_sign.m, threshold_proportional.m changed help files: assortativity_wei.m, distance_wei.m Version 2014-04-05: Minor update consensus_und.m is now a self-contained function headers in charpath.m and in threshold_proportional.m have been corrected Published with MATLABĀ® R2015b

Jan-Mathijs Schoffelen - 2016-01-19 15:57:07 +0100

[jansch@mentat001 external]$ svn commit -m "enhancement - updated to the most recent version of the software" bct/* Adding (bin) bct/Coactivation_matrix.mat Adding (bin) bct/GroupAverage_rsfMRI_matrix.mat Sending bct/README Adding bct/adjacency_plot_und.m Adding bct/agreement.m Adding bct/agreement_weighted.m Adding bct/align_matrices.m Adding bct/assortativity_bin.m Adding bct/assortativity_wei.m Adding bct/backbone_wu.m Sending bct/betweenness_bin.m Sending bct/betweenness_wei.m Sending bct/breadth.m Sending bct/cat.mat Sending bct/charpath.m Sending bct/clustering_coef_bd.m Sending bct/clustering_coef_bu.m Sending bct/clustering_coef_wd.m Sending bct/clustering_coef_wu.m Adding bct/clustering_coef_wu_sign.m Adding bct/community_louvain.m Adding bct/consensus_und.m Adding bct/core_periphery_dir.m Adding (bin) bct/demo_generative_models_data.mat Adding bct/demo_generative_models_geometric.m Adding bct/demo_generative_models_neighbors.m Sending bct/distance_bin.m Sending bct/distance_wei.m Sending bct/diversity_coef_sign.m Sending bct/edge_betweenness_bin.m Sending bct/edge_betweenness_wei.m Adding bct/edge_nei_overlap_bd.m Adding bct/edge_nei_overlap_bu.m Adding bct/efficiency_bin.m Adding bct/efficiency_wei.m Adding bct/eigenvector_centrality_und.m Sending bct/erange.m Adding bct/evaluate_generative_model.m Sending bct/find_motif34.m Sending bct/findpaths.m Adding bct/flow_coef_bd.m Adding bct/gateway_coef_sign.m Adding bct/generative_model.m Adding bct/get_components.m Adding bct/grid_communities.m Adding bct/gtom.m Adding bct/kcore_bd.m Adding bct/kcore_bu.m Adding bct/kcoreness_centrality_bd.m Adding bct/kcoreness_centrality_bu.m Sending bct/latmio_dir.m Sending bct/latmio_dir_connected.m Sending bct/latmio_und.m Sending bct/latmio_und_connected.m Adding bct/link_communities.m Adding bct/local_assortativity_wu_sign.m Sending bct/make_motif34lib.m Sending bct/makeevenCIJ.m Sending bct/makefractalCIJ.m Sending bct/makelatticeCIJ.m Sending bct/makeringlatticeCIJ.m Sending bct/maketoeplitzCIJ.m Adding bct/matching_ind_und.m Sending bct/modularity_dir.m Sending bct/modularity_und.m Sending bct/module_degree_zscore.m Sending bct/motif3funct_bin.m Sending bct/motif3funct_wei.m Sending bct/motif3struct_bin.m Sending bct/motif3struct_wei.m Sending bct/motif4funct_bin.m Sending bct/motif4funct_wei.m Sending bct/motif4struct_bin.m Sending bct/motif4struct_wei.m Adding bct/null_model_dir_sign.m Sending bct/null_model_und_sign.m Adding bct/pagerank_centrality.m Sending bct/participation_coef.m Sending bct/participation_coef_sign.m Sending bct/partition_distance.m Sending bct/randmio_dir.m Sending bct/randmio_dir_connected.m Adding bct/randmio_dir_signed.m Sending bct/randmio_und.m Sending bct/randmio_und_connected.m Sending bct/randmio_und_signed.m Adding bct/randomize_graph_partial_und.m Sending bct/randomizer_bin_und.m Adding bct/release_notes.m Sending bct/rentian_scaling.m Sending bct/reorderMAT.m Adding bct/reorder_matrix.m Sending bct/reorder_mod.m Adding bct/rich_club_bd.m Adding bct/rich_club_bu.m Adding bct/rich_club_wd.m Adding bct/rich_club_wu.m Adding bct/score_wu.m Sending bct/strengths_und_sign.m Adding bct/subgraph_centrality.m Sending bct/threshold_proportional.m Sending bct/transitivity_bd.m Sending bct/transitivity_wd.m Sending bct/transitivity_wu.m Adding bct/weight_conversion.m Sending bct/writetoPAJ.m Transmitting file data .......................................................................................................... Committed revision 11086. Thanks for letting us know Mika!