Michigan Neuroimaging Initiative

Tutorial materials

This is intended to be a collection of links to helpful tutorial resources. If you have comments about the resources, whether they were helpful or not, are the links dead, etc, please let us know at michigan-nii@umich.edu.

Nipype Beginner’s Guide

While mainly in introduction to the Python-based Nipype software, Michael Notter’s Nipype Beginner’s Guide also has a very good summary of neuroimaging data, its collection, and the flow through the various processing steps.

Berkeley Functional MRI methods course

For those seriously interested in Python-based fMRI analysis, the web site for UC Berkeley’s web site for their Psychology 214, Functional MRI methods course is a must see.

Organizing data and workflow

There is a very good article on organizing neuroimaging data and workflow in Frontiers in Neuroinformatics, “Using Make for Reproducible and Parallel Neuroimaging Workflow and Quality-Assurance”, Askren, McAllister-Day, Koh, et al.

The IBIC Using GNU Make for Neuroimaging Workflow manual, by Askren, Mcallister-Day, Koh, et al., is available from the IBIC web site. We can make the examples and data available on any YBRC Brainbox. Other users should get the material from the NITRC Using Make for Neuroimaging Workflow: Manual and Examples web page. (NOTE: The manual provided by the link above is more recent than that at the NITRC website.)

Local copies on this server are at
Askren, et al., article
IBIC Manual

Psychiatry Methods Core tutorials

The Psychiatry Methods Core has created a series of videos and PDF documents that cover a variety of topics on their scripts and processing stream. The list can be found on the Psychiatry Methods Core Support page.

R programming

In the summer of 2017, Nick Michalak and Iris Wang taught a workshop “R Programming for Research”. The workshop was based around Hadley Wickham's “Tidyverse” and his notion of tidy data. Additionally, graphical techniques using the “Grammar of Graphics”, largely formulated by Leland Wilkinson, were introduced.

R Programming for Research GitHub repository. You can read about it here, and exercises and examples are available for download.


The Linux Command Line: Fifth Internet Edition, William E Schott, Version 19.01, Jan 2019. http://linuxcommand.org/

The .pdf version of The Linux Command Line is a good starting point for people new to Linux and has some useful things even for those with a good deal of experience. The basic functionality of the command line has been remarkably stable for the last decade; sure, there have been additions, but what used to work in 2010, or even 2001, still works. Investing in learning these tools will pay off in the long run. Really.