Analysis code for: "Examining Relationships between Functional and Structural Brain Network Architecture, Age, and Attention Skills in Early Childhood"

This repository contains the code used for analyses in:

Rokos, L., Bray, S.L., Neudorf, J., Samson, A.D., Shen, K., & McIntosh, A.R. (2024). "Examining Relationships between Functional and Structural Brain Network Architecture, Age, and Attention skills in Early Childhood"

Overall Workflow

1. Clone the Repository

   • Clone this repository to your local computer.

2. PLS MATLAB Code

   • Clone the PLS repository or download the PLS MATLAB code from McIntosh Lab PLS GitHub to your local computer.

For the scripts in: ~/Rokos2024_SCFC_NetworkAnalyses/1.compute_metrics, ~/Rokos2024_SCFC_NetworkAnalyses/2.analyses_contrasts/ and ~/Rokos2024_SCFC_NetworkAnalyses/3.visualise_brainplots/, you will need to modify paths, file names, and the variables of interest within the scripts first. "%MODIFY" in those scripts indicates where needs to be changed.

3. Compute Graph Theory Metrics

   • In MATLAB, run the Compute_GraphTheory_Metrics.m script located at ~/Rokos2024_SCFC_NetworkAnalyses/1.compute_metrics/ to compute and save the necessary graph theory metrics.

4. Run Mean-Centered PLS Analyses

   • In MATLAB, run the Figure_2_Mean_Centered_PLS.m script located at ~/Rokos2024_SCFC_NetworkAnalyses/2.analyses_contrasts/ to obtain results for Figure 2.

5. Run Behavioural PLS (bPLS) Analyses

   • In MATLAB, run one of the following scripts located at ~/Rokos2024_SCFC_NetworkAnalyses/2.analyses_contrasts/:
     • For Figure 3: Run Figure_3_Behavioural_PLS.m
     • For Figure 4: Run the Figure_4A_Behavioural_PLS.m and Figure_4B_Behavioural_PLS.m scripts
     • For Figure 5: Run Figure_5_Behavioural_PLS.m
     • For Figure 6: Run Figure_6_SCFC_Coupling_Combined_bPLS.m
     • Note: These scripts include code to run the behavioural PLS analyses and to plot the contrasts.

6. Visualize Results in R

   • In R, run the Brain_Plots.r script located at ~/Rokos2024_SCFC_NetworkAnalyses/3.visualise_brainplots/ to plot the bootstrap ratios on a brain.
   • Note: The exact BSRs may be slightly different than in the paper because of resampling

Necessary Tools

• MATLAB PLS Code: McIntosh Lab PLS GitHub
• R Packages: ggseg and ggsegSchaefer
• Brain Connectivity Toolbox: BCT Website (Required functions are located in ~/Rokos2024_SCFC_NetworkAnalyses/1.compute_metrics/functions)