mychan24 / system-segregation-and-graph-tools

System segregation (see Chan et al. 2014 PNAS) and RSFC brain network tools

System Segregation (graph measure) scripts in R and MATLAB

Scripts useful for doing Resting-state Functional Correlation (RSFC) network analysis

Segregation calculations in R and MATLAB

./R or ./MATLAB

• segregation.R/.m - calculates system segregation (Chan et al. 2014).
• segregation_by_type_prcont.R/.m - 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/.m for whole brain system segregation.
• segregation_by_type_eqcont.R/.m - 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).

Utility

./MATLAB

• fsLR2roizmatrix.m - extract mean RSFC time-series from ROIs on fs_LR surfaces, outputs correlation matrix.

• mat2cytoscape.m - convert correlation matrix to 3-column format used for visualization in Cytoscape.

• ./export/ - includes scripts to save node-x-node matrix as figures.

• for visualization of matrices and networks in R, see other repository r-for-brain-network

system-segregation-and-graph-tools's Issues

Add a na2zero flag

Flag to enable turning NA/NaN to 0, default = F

Question consultation

Dear authors:
Recently I have looking your this project and feel interested in it !could have a introduction, like paper or tutorial of this project? Thanks a lot! I am looking forward to your reply Sincerely!

Best regards.