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Tools for data mining of brain graphs. Related publication: http://dx.doi.org/10.1007/s11571-017-9445-1
kerepesi/Brain-Graph-Tools
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**************************** ***Brain-Graph-Tools Manual*** **************************** Copyright by Csaba Kerepesi, 2015 ***LICENCE*** - Brain-Graph-Tools are free software: you may redistribute it and/or modify its under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or any later version. - Brain-Graph-Tools are distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details (http://www.gnu.org/licenses/). - For any other inquiries send an Email to Csaba Kerepesi: kerepesi@caesar.elte.hu ***CITATION*** - When publishing work that is based on the results from RefBrainGraph.pl please cite: B. Szalkai, C. Kerepesi, B. Varga, V. Grolmusz The Budapest Reference Connectome Server v2.0 Neuroscience Letters, Volume 595, Pages 60–62 (2015). http://dx.doi.org/10.1016/j.neulet.2015.03.071 - When publishing work that is based on the results from BrainDiversity.pl please cite: C. Kerepesi, B. Szalkai, B. Varga, V. Grolmusz Comparative Connectomics: Mapping the Inter-Individual Variability of Connections within the Regions of the Human Brain arXiv, arXiv:1507.00327 (2015). http://arxiv.org/abs/1507.00327v1 - When publishing work that is based on the results from BrainDiversity.pl please cite: C. Kerepesi, B. Szalkai, B. Varga, V. Grolmusz Does the Budapest Reference Connectome Server Shed Light to the Development of the Connections of the Human Brain? arXiv, arXiv:1509.05703v1 (2015). http://arxiv.org/abs/1509.05703v1 ***PREREQUISITES*** - Linux OS - Perl v5.14.2 or later - Download the brain graphs from http://braingraph.org/download-pit-group-connectomes/ - copy 100307_connectome_scale500.graphml file to the directory of RefBrainGraph.pl ***BUDAPEST REFERENCE CONNECTOME WORKFLOW*** Version 1.0: - download the 6 brain graphs and unzip them: http://www.cmtk.org/datasets/homo_sapiens_01.cff - copy the brain graphs (graphml files) to the 6_BrainGraphs directory - download all the files of the Brain-Graph-Tools and copy them to the directory where the 6_BrainGraphs directory is - perl RefBrainGraph.pl -MinC 3 -MinStr 0 -StrMerge avg -Out graphml -Project 1.0 > 6_BrainGraphs-RefBrainGraph-C3.graphml Version 2.0: - download the partial set, 96 brain graphs from http://braingraph.org/download-pit-group-connectomes/ and unzip them - copy the brain graphs (graphml files) to the 96_BrainGraphs directory - download all files of Brain-Graph-Tools and copy them to the directory where the 96_BrainGraphs directory is - all: perl RefBrainGraph.pl -MinC 48 -MinStr 0 -StrMerge avg -Out graphml -Project 2.0 > 96-all-RefBrainGraph-C48.graphml - female: perl RefBrainGraph.pl -MinC 26 -MinStr 0 -StrMerge avg -Out graphml -Project 2.0-F > 52-F-RefBrainGraph-C26.graphml - male: perl RefBrainGraph.pl -MinC 22 -MinStr 0 -StrMerge avg -Out graphml -Project 2.0-M > 44-M-RefBrainGraph-C22.graphml ***BRAIN DIVERSITY WORKFLOW*** - download the full set, 392 brain graphs from http://braingraph.org/download-pit-group-connectomes/ and unzip them - create a 392_BrainGraphs directory (mkdir 392_BrainGraphs) and copy the brain graphs to it - download all files of Brain-Graph-Tools and copy them to the directory where the 392_BrainGraphs directory is Generate input graph list: - cd 392_BrainGraph - ls *_connectome_scale500.graphml > ../all_392_scale500.list - cd .. Prefiles: - perl -w GenPreFile.pl 1 100 all_392_scale500.list 392_BrainGraphs Compute brain diversity: - perl -w BrainDiversity.pl all_392_scale500.list-GenPreFile-1.csv 392 0 lobes distr_func ***BRAIN EVOLUTION WORKFLOW*** - download the partial set, 96 brain graphs from http://braingraph.org/download-pit-group-connectomes/ and unzip them - create a 96_BrainGraphs directory (mkdir 96_BrainGraphs) and copy the brain graphs to it - download all files of Brain-Graph-Tools and copy them to the directory where the 96_BrainGraphs directory is Generate input graph list: - cd 96_BrainGraph - ls *_connectome_scale500.graphml > ../all_96_scale500.list - cd .. Prefile: - perl -w GenPreFile.pl 1 100 all_96_scale500.list 96_BrainGraphs/ Compute brain evolution: - perl -w BrainEvolution.pl results/all_96_scale500.list-GenPreFile-1.csv 96 1015
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Tools for data mining of brain graphs. Related publication: http://dx.doi.org/10.1007/s11571-017-9445-1
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