GitHub

Check out our GitHub for script examples and other helpful information.

Tutorials

Feel free to browse our collection of tutorials and other learning materials!

These tutorials created by core staff describe how to implement different neuroimaging platforms and analysis pipelines on OSCAR, Brown’s supercomputer cluster. These are living documents! If something is out of date, or you find a more efficient way to do the job, let us know. We’d love to share your knowledge with the broader DPHB imaging community, and of course, credit your contributions!

 

Introduction to functional neuroimaging

MRI Fundamentals

fMRI Analysis Software

Shell basics and using Brown’s high performance computing cluster

Shell Basics

Introduction to CCV and Oscar

Oscar Accounts

XNAT

Organizing and naming your data according to the Brain Imaging Data Standard

Introducing BIDS-Part I

Introducing BIDS-Part II

Heudiconv

BIDS Validation

Quality control

MRIQC – Part 1: Intro and How to Run

MRIQC – Part 2: IQMs

MRIQC – Part 3: Artifacts

MRIQC – Part 4: Interpreting Results

Preprocessing

Preprocessing

Preprocessing with fMRIPrep

Diffusion Preprocessing

Spectroscopy Data Collection & Preprocessing with Osprey

MRS_Protocol_MAG_website_2.27.24