Normative neurodevelopment

This repository includes code used to analyze the relationship between dimensional psychopathology phenotypes and deviations from normative neurodevelopment in the Philadelphia Neurodevelopmental Cohort.

Code

In the code subdirectory you will find the following Jupyter notebooks and .py scripts:

1. Pre-normative modeling scripts:

• get_train_test.ipynb
  • Performs initial ingest of PNC demographic data, participant exclusion based on various quality control.
  • Produces Figures 2A and 2B.
  • Designates train/test split.
• compute_node_metrics.ipynb
  • Reads in neuroimaging data.
  • Sets up feature table of regional brain features.
• clean_node_metrics.ipynb
  • Performs nuisance regression on feature table.
• prepare_normative.ipynb
  • Prepares input files for normative modeling.

2. Run normative modeling:

• run_normative_local.py
  • Runs primary normative models on local machine.
• cluster/run_normative_perm.sh
  • Submits each of the permuted normative models to the cluster as a separate job

3. Results:

• results_s1.ipynb
  • Produces Figure 2C
• results_s2.ipynb
  • Produces Figures 3 and 4
• results_s3.ipynb
  • Produces Figure 5