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
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.
Linux
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.