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README.md

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[![Build Status](https://www.travis-ci.com/mychan24/system_matrix_tools.svg?branch=master)](https://www.travis-ci.com/mychan24/system_matrix_tools)
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# System Segregation (graph measure) scripts in R and Matlab
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Scripts useful for doing Resting-state Functiaonl Correlation (RSFC) network analysis
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Scripts useful for doing Resting-state Functional Correlation (RSFC) network analysis
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**./matlab_scripts**
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* `fsLR2roizmatrix.m` - extract mean RSFC time-series from ROIs on fs_LR surfaces, outputs correlation matrix.
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* `mat2cytoscape.m` - convert correlation matrix to 3-column format used for visulization in Cytoscape.
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* `mat2cytoscape.m` - convert correlation matrix to 3-column format used for visualization in Cytoscape.
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* `segregation.m` - calculates system segregation (Chan et al. 2014).
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* `segregation_systype.m` - calculates segregation of specific system types (e.g., Sensory-motor, Association). This allows smaller systems to contribute more to the overall segregation value of that system type. This was how system-type segregation was calculated in Chan et al. (2014).
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* ./export/ - includes scripts to save node-x-node matrix as figures.
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**./R_scripts**
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* `segregation.R` - calculates system segregation (Chan et al. 2014).
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* `segregation_by_type_prcont.R` - calculates segregation of specific system types (e.g., Sensory-motor, Association), and letting system of different sizes to contribute proportionally based on their size (# of nodes). This is a similar method to `segregation.R` for whole brain system segregation.
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* `segregation_by_type_prcont.R` - calculates segregation of specific system types (e.g., Sensory-motor, Association), but first averaging within/between system connectivity for each individaul system. This allows smaller systems to contribute more to the overall segregation value of that system type. This was how system-type segregation was calculated in Chan et al. (2014).
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* `segregation_by_type_prcont.R` - calculates segregation of specific system types (e.g., Sensory-motor, Association), but first averaging within/between system connectivity for each individual system. This allows smaller systems to contribute more to the overall segregation value of that system type. This was how system-type segregation was calculated in Chan et al. (2014).
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* for visualization of matrices and networks in R, see other repository [r-for-brain-network](https://github.com/mychan24/r-for-brain-network)

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