🧠 Snakemake for Neuroimaging

A Khan Lab Brainhack Tutorial

This workshop introduces you to building reproducible neuroimaging pipelines. We will use Snakemake to orchestrate a workflow that performs image resampling, thresholding, and statistical extraction using Nilearn and Nibabel.

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🚀 Quick Start: Environment Setup

1. Install Pixi

Choose the command for your operating system:

macOS / Linux / WSL2:

curl -fsSL https://pixi.sh/install.sh | bash

Windows

powershell -ExecutionPolicy Bypass -c "irm -useb https://pixi.sh/install.ps1 | iex"

2. Clone this Tutorial

git clone https://github.com/Dhananjhay/khanlab_snakemake_tutorial.git
cd khanlab_snakemake_tutorial

3. Enter the Environment

pixi shell