This repository contains the analysis code used in the above report. It was conducted on a pair of datasets: the locally held TOPSY dataset recruited in London, Ontario, Canada, and the open access Human Connectome Project - Early Psychosis. Data was preprocessed with the following Snakemake pipelines:
- snakedwi: Preprocessing, image correction, and registration of diffusion weighted imaging
- snaketract: mrtrix-based pipeline deriving tractography from diffusion weighted images.
- snakeanat: Wrapping fastsurfer and ciftify to calculate the cortical mesh and HCP preprocessing derivatives
- templategen: Uses greedy for rapid calculation of a common template space
- snakemodel: Incorporation of TBSS and (NBS)[https://www.nitrc.org/projects/nbs] into a snakemake pipeline
The snakemake workflow in the workflow directly calculates the graph-theory parameters used in the study. The primary file is notebooks/paper-fep-sc-disruption.ipynb
, which contains all the code used to generate figures for the manuscript.