All code for this project can be found in the src directory. Let's go through
each component of the source code of this study individually:
The src/preprocessing directory contains all code related to preprocessing the
functional connectomes used in this study. This preprocessing was performed
using junifer. The src/preprocessing/yamls
directory contains all the junifer yaml files used to define the individual preprocessing
pipelines, and the src/preprocessing/junifer_jobs directory contains all
configuration, submit, and log files related to each pipeline that was created and run.
The src/pipeline directory contains each of the individual pipeline components
used to get the main results of this study. The contents of this directory
are essentially python scripts that accept a number of arguments for configuration
of the pipeline component. The filenames are numbered in the order in which the
pipeline components should be executed. Each script is meant to be run using
src/pipeline as a working directory and may not work if run from elsewhere.
Each of them use the ArgumentParser
to parse command line arguments so you can run the -h, --help option to learn
more about how to use them.
Unsurprisingly, the src/plotting directory contains all scripts that create
plots used to present the results of this project. Similarly to the src/pipeline,
the scripts in src/plotting are roughly numbered in order of appearance.
The directories results, logs, data, and figures contain all study input
and output data, not all of which are pushed to the repository to protect confidential
data.
The conda environment used in this project can be recreated using the
environment.yaml file in the root of the project.