This is the repo for code and data imported directly into the manuscript:
Tooley, U. A., Bassett, D. S. & Mackey, A. P. (2022). Functional brain network community structure in childhood: Unfinished territories and fuzzy boundaries. NeuroImage, 118843. https://doi.org/10.1016/j.neuroimage.2021.118843
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 manuscript!
Preprocessing was conducted using fMRIprep v. 1.4.1 (link) and xcpEngine version 1.0 (link) on a high-performance computing cluster running CentOS 6.9. See Methods for all software version specifications.
Code used in this repo depends heavily on that of the Computational Brain Imaging Group (v0.17.0, found here). 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, which must be installed for MATLAB to run the WSBM. The Network Community Toolbox (here) and GenLouvain 2.1 code must also be in your MATLAB path to use the iterative WSBM consensus partitioning algorithm.
Numbers 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.
Both the developmental clustering partition and the developmental WSBM are provided in fsaverage6, MNI152, and fs_LR 32k space in the partitions folder. The adult clustering partition was estimated by Yeo et al. in their 2011 paper, and is available from the CBIG group here.
The WSBM partition is also provided as a vector of assignments for the Schaefer 400-region parcellation, available from the CBIG group here.
The developmental clustering partition was generated using code from the CBIG. 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.
The developmental WSBM partition was generated using code from Aaron Clauset. To run the WSBM algorithm, use code/wsbm/1_zscore_and_wsbm_main_sample.m. An example script and example inputs and outputs is available in data/example(here).
Statistics and data that are directly imported into the manuscript live in this folder.