Neuroimaging Workflow (skeleton)

This repository is a lightweight skeleton for neuroimaging analyses inspired by brainGraph, fsbrain, and threeBrain.

What you'll find:

• R/ — reusable R functions for loading data, computing network measures, and generating figures.
• pipelines/ — separate pipeline stages: preprocessing, analysis, plotting.
• scripts/ — small CLI wrappers to run pipeline stages (R and PowerShell-friendly).
• figures/ — output folder for generated figures.
• data/ — place example or small test datasets here (no large data committed).
• tests/ — minimal tests using testthat to validate basic pipeline wiring.

Quick start

1. Install recommended packages in R (example):

install.packages(c("igraph", "ggplot2", "dplyr", "testthat"))
# optionally: devtools::install_github("cwatson/brainGraph")

2. Run a pipeline stage (from repo root) in R:

# Preprocess
Rscript scripts/run_pipeline.R --stage preprocess

# Analysis
Rscript scripts/run_pipeline.R --stage analyze

# Plots
Rscript scripts/run_pipeline.R --stage plots

Or in PowerShell:

.\scripts\run_pipeline.ps1 -Stage preprocess

How to extend

• Replace the placeholder functions in R/analysis.R and R/figures.R with your real processing steps.
• Add real data under data/ (do not commit large raw files; use data/README.md to document acquisition).
• Optionally convert pipelines to targets, drake, or snakemake for reproducible DAGs.