Update README.md

Add toolbox versions and example input/output data details.

README.md

@@ -6,11 +6,15 @@ This repo contains code accompanying the manuscript [Functional brain network co
 We provide two freely available partitions (assignments of regions to communities, also sometimes called networks), that were estimated using data from children ages 9-11. For more details, see the [preprint](https://www.biorxiv.org/content/10.1101/2021.01.21.427677v1)!
 
 
-## Code
+## Requirements
 
-Preprocessing was conducted using fMRIprep ([link](https://fmriprep.org/en/stable/)) and xcpEngine ([link](https://xcpengine.readthedocs.io/)). 
+Preprocessing was conducted using fMRIprep v. 1.4.1 ([link](https://fmriprep.org/en/stable/)) and xcpEngine version 1.0 ([link](https://xcpengine.readthedocs.io/)) on a high-performance computing cluster running CentOS 6.9. See [preprint](https://www.biorxiv.org/content/10.1101/2021.01.21.427677v1) methods for all software version specifications.
 
-Code used in this repo depends heavily on that of the Computational Brain Imaging Group (found [here](https://github.com/ThomasYeoLab/CBIG)), which must be set up to run functions in the `code/yeo_networks` folder. The weighted stochastic block model (WSBM, `code/wsbm`) was run using code from Aicher et al. (2015), found [here](https://aaronclauset.github.io/wsbm/).
+Code used in this repo depends heavily on that of the Computational Brain Imaging Group (v0.17.0, found [here](https://github.com/ThomasYeoLab/CBIG)). This must be installed to run functions in the `code/yeo_networks` folder. 
+
+The weighted stochastic block model (WSBM, `code/wsbm`) was run using v1.2 code from Aicher et al. (2015), found [here](https://aaronclauset.github.io/wsbm/), which must be installed for MATLAB to run the WSBM. The Network Community Toolbox ([here](http://commdetect.weebly.com/)) and GenLouvain 2.1 [code](http://netwiki.amath.unc.edu/GenLouvain/GenLouvain) must also be in your MATLAB path to use the iterative WSBM consensus partitioning algorithm.
+
+Numerals at the beginning of scripts indicate the order in which they were used. In some cases (e.g. in MATLAB), you must modify the script name to remove the number, as filenames cannot start with numeric values.
 
 ## Partitions
 
@@ -20,6 +24,12 @@ Both the developmental clustering partition and the developmental WSBM are provi
 
 The WSBM partition is also provided as a vector of assignments for the Schaefer 400-region parcellation, available from the CBIG group [here](https://github.com/ThomasYeoLab/CBIG/tree/master/stable_projects/brain_parcellation/Schaefer2018_LocalGlobal).
 
+## Data
+
+The developmental clustering partition was generated using code from the [CBIG](https://github.com/ThomasYeoLab/CBIG/tree/master/stable_projects/brain_parcellation/Yeo2011_fcMRI_clustering). To run the clustering algorithm, use `code/yeo_networks/1_yeo_clustering_n670_1000x.csh`. Example inputs and expected outputs are provided in the [CBIG repository](https://github.com/ThomasYeoLab/CBIG/tree/master/stable_projects/brain_parcellation/Yeo2011_fcMRI_clustering/examples).
+
+The developmental WSBM partition was generated using code from [Aaron Clauset](https://aaronclauset.github.io/wsbm/). To run the WSBM algorithm, use `code/wsbm/1_zscore_and_wsbm_training_sample.m`. An example script and example inputs and outputs is available in `data/example`([here](https://github.com/utooley/Tooley_2021_child_functional_comms/tree/master/data/example)).
+
 ## Manuscript
 
 Statistics and data that are directly imported into the manuscript live in this folder.