From 1d7503c82ae27cbafa654dfb3634c08e6f35b8c1 Mon Sep 17 00:00:00 2001 From: Micaela Chan <4413270+mychan24@users.noreply.github.com> Date: Tue, 15 Mar 2022 10:33:34 -0500 Subject: [PATCH] Update README and cahnge file structurte (remove _script) --- .../export/colormap_roi.m | 0 .../export/colormap_roi_meta.m | 0 {matlab_scripts => MATLAB}/fsLR2roizmat.m | 0 {matlab_scripts => MATLAB}/map_to_gii.m | 0 {matlab_scripts => MATLAB}/mat2cytoscape.m | 0 {matlab_scripts => MATLAB}/segregation.m | 0 .../segregation_by_type_eqcont.m | 0 .../segregation_by_type_prcont.m | 0 {R_scripts => R}/segregation.R | 0 {R_scripts => R}/segregation_by_type_eqcont.R | 0 {R_scripts => R}/segregation_by_type_prcont.R | 0 README.md | 18 ++++++++++-------- 12 files changed, 10 insertions(+), 8 deletions(-) rename {matlab_scripts => MATLAB}/export/colormap_roi.m (100%) rename {matlab_scripts => MATLAB}/export/colormap_roi_meta.m (100%) rename {matlab_scripts => MATLAB}/fsLR2roizmat.m (100%) rename {matlab_scripts => MATLAB}/map_to_gii.m (100%) rename {matlab_scripts => MATLAB}/mat2cytoscape.m (100%) rename {matlab_scripts => MATLAB}/segregation.m (100%) rename {matlab_scripts => MATLAB}/segregation_by_type_eqcont.m (100%) rename {matlab_scripts => MATLAB}/segregation_by_type_prcont.m (100%) rename {R_scripts => R}/segregation.R (100%) rename {R_scripts => R}/segregation_by_type_eqcont.R (100%) rename {R_scripts => R}/segregation_by_type_prcont.R (100%) diff --git a/matlab_scripts/export/colormap_roi.m b/MATLAB/export/colormap_roi.m similarity index 100% rename from matlab_scripts/export/colormap_roi.m rename to MATLAB/export/colormap_roi.m diff --git a/matlab_scripts/export/colormap_roi_meta.m b/MATLAB/export/colormap_roi_meta.m similarity index 100% rename from matlab_scripts/export/colormap_roi_meta.m rename to MATLAB/export/colormap_roi_meta.m diff --git a/matlab_scripts/fsLR2roizmat.m b/MATLAB/fsLR2roizmat.m similarity index 100% rename from matlab_scripts/fsLR2roizmat.m rename to MATLAB/fsLR2roizmat.m diff --git a/matlab_scripts/map_to_gii.m b/MATLAB/map_to_gii.m similarity index 100% rename from matlab_scripts/map_to_gii.m rename to MATLAB/map_to_gii.m diff --git a/matlab_scripts/mat2cytoscape.m b/MATLAB/mat2cytoscape.m similarity index 100% rename from matlab_scripts/mat2cytoscape.m rename to MATLAB/mat2cytoscape.m diff --git a/matlab_scripts/segregation.m b/MATLAB/segregation.m similarity index 100% rename from matlab_scripts/segregation.m rename to MATLAB/segregation.m diff --git a/matlab_scripts/segregation_by_type_eqcont.m b/MATLAB/segregation_by_type_eqcont.m similarity index 100% rename from matlab_scripts/segregation_by_type_eqcont.m rename to MATLAB/segregation_by_type_eqcont.m diff --git a/matlab_scripts/segregation_by_type_prcont.m b/MATLAB/segregation_by_type_prcont.m similarity index 100% rename from matlab_scripts/segregation_by_type_prcont.m rename to MATLAB/segregation_by_type_prcont.m diff --git a/R_scripts/segregation.R b/R/segregation.R similarity index 100% rename from R_scripts/segregation.R rename to R/segregation.R diff --git a/R_scripts/segregation_by_type_eqcont.R b/R/segregation_by_type_eqcont.R similarity index 100% rename from R_scripts/segregation_by_type_eqcont.R rename to R/segregation_by_type_eqcont.R diff --git a/R_scripts/segregation_by_type_prcont.R b/R/segregation_by_type_prcont.R similarity index 100% rename from R_scripts/segregation_by_type_prcont.R rename to R/segregation_by_type_prcont.R diff --git a/README.md b/README.md index 99db2c3..7602d8b 100755 --- 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)