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fmriPrep Workshop

This repository contains materials for an introductory workshop on fMRI preprocessing using fMRIPrep. The goal of this workshop is to provide a practical, hands-on introduction to reproducible preprocessing of fMRI data using BIDS-formatted datasets and containerized workflows.

Authors: Fabian Dorok and Sterre van de Langenberg

🧠 Workshop Content

During this workshop, participants will learn:

  • The BIDS data structure and BIDS conversion using Heudiconv
  • How to run fMRIPrep using Docker (and WSL installation for Windows Users)
  • Understanding fMRIPrep outputs
  • Quality control of fMRI preprocessing
  • Basics of reproducible neuroimaging workflows

Software Requirements

To run the pipeline locally, you will need:

  • Docker installed
  • FreeSurfer license file
  • A BIDS-formatted dataset
  • At least 8–16 GB RAM (recommended: 32 GB+)

Data

Example datasets (defaced) used in this workshop are stored in the Datasets/ folder. Unzip to your local machine before running HeuDiConv (BIDS conversion). Data can also be found here: https://drive.google.com/file/d/1niOEgwtN6ZeyWhGzxSUMYGn_NtEUdrTl/view?usp=drive_link

Code

We created a Jupyter notebook for coding along at home (as a reference after the workshop). We also uploaded a script on how to mount network drives in WSL (Scripts/ folder).