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***Brain-Graph-Tools Manual***
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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