Update README and cahnge file structurte (remove _script)

mychan24 · Mar 15, 2022 · 1d7503c · 1d7503c
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diff --git a/matlab_scripts/export/colormap_roi.m → MATLAB/export/colormap_roi.m b/matlab_scripts/export/colormap_roi.m → MATLAB/export/colormap_roi.m
diff --git a/matlab_scripts/export/colormap_roi_meta.m → MATLAB/export/colormap_roi_meta.m b/matlab_scripts/export/colormap_roi_meta.m → MATLAB/export/colormap_roi_meta.m
diff --git a/matlab_scripts/fsLR2roizmat.m → MATLAB/fsLR2roizmat.m b/matlab_scripts/fsLR2roizmat.m → MATLAB/fsLR2roizmat.m
diff --git a/matlab_scripts/map_to_gii.m → MATLAB/map_to_gii.m b/matlab_scripts/map_to_gii.m → MATLAB/map_to_gii.m
diff --git a/matlab_scripts/mat2cytoscape.m → MATLAB/mat2cytoscape.m b/matlab_scripts/mat2cytoscape.m → MATLAB/mat2cytoscape.m
diff --git a/matlab_scripts/segregation.m → MATLAB/segregation.m b/matlab_scripts/segregation.m → MATLAB/segregation.m
diff --git a/matlab_scripts/segregation_by_type_eqcont.m → MATLAB/segregation_by_type_eqcont.m b/matlab_scripts/segregation_by_type_eqcont.m → MATLAB/segregation_by_type_eqcont.m
diff --git a/matlab_scripts/segregation_by_type_prcont.m → MATLAB/segregation_by_type_prcont.m b/matlab_scripts/segregation_by_type_prcont.m → MATLAB/segregation_by_type_prcont.m
diff --git a/R_scripts/segregation.R → R/segregation.R b/R_scripts/segregation.R → R/segregation.R
diff --git a/R_scripts/segregation_by_type_eqcont.R → R/segregation_by_type_eqcont.R b/R_scripts/segregation_by_type_eqcont.R → R/segregation_by_type_eqcont.R
diff --git a/R_scripts/segregation_by_type_prcont.R → R/segregation_by_type_prcont.R b/R_scripts/segregation_by_type_prcont.R → R/segregation_by_type_prcont.R
diff --git a/README.md b/README.md
@@ -1,18 +1,20 @@
 [![Build Status](https://www.travis-ci.com/mychan24/system_matrix_tools.svg?branch=master)](https://www.travis-ci.com/mychan24/system_matrix_tools) [![DOI](https://img.shields.io/badge/DOI-10.1073%2Fpnas.1415122111-purple)](https://doi.org/10.1073/pnas.1415122111)
 
-# System Segregation (graph measure) scripts in R and Matlab
+# System Segregation (graph measure) scripts in R and MATLAB
 
 Scripts useful for doing Resting-state Functional Correlation (RSFC) network analysis
 
-**./matlab_scripts**
+## 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.
-*  `segregation.m`  -  calculates system segregation (Chan et al. 2014). 
-*  `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). 
 *  ./export/ - includes scripts to save node-x-node matrix as figures.
 
-**./R_scripts**
-*  `segregation.R`  -  calculates system segregation (Chan et al. 2014). 
-*  `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. 
-*  `segregation_by_type_eqcont.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). 
+
 *  for visualization of matrices and networks in R, see other repository [r-for-brain-network](https://github.com/mychan24/r-for-brain-network)