fMRI Resources

The following section will provide with useful resources when starting with fMRI analyses. Mostly, links to tutorials, lectures and relevant software for the different analysis.

The main software used by the members of the Predictive Brain Lab to do fMRI analysis is the following:

You can ask other lab members if they have pro’s and con’s regarding their software selection before deciding what to use. It may be the case that specific software is better for some analysis compared to others.

General Resources

Toolbox

  • The Donders Institute offers hands-on annual courses to get acquainted with some of the most recent neuroimaging techniques. Experts on the field working at the insitute guide these several day workshops. You can find the current schedule here.

Ask other lab members for their experience with these courses. Additionally, you might want to consider looking at the software being used during these toolkits as it might not match with your experience or goals.

Books

  • If you are completely unfamiliar with fMRI analysis, a great starter point is the book by Poldrack, Mumford and Nichols - Handbook of Functional fMRI Analysis. It provides thorough explanations concerning all the steps necessary to process this type of data. You might be able to find this online or checking the Radboud University Library.

Video Series

  • One of the authors of the Handbook of Functional fMRI Analysis book, Jeanette Mumford, has also made a video lecture series covering a wide of topics regarding the analysis of fMRI data. They provide intuitive easy to follow explanations for how fMRI analysis work. You can find her channel here (it is recommended to have a basic level of linear algebra to follow her explanations).

  • Another video lecture series that has now been transformed into a Coursera Course by Martin Lindquist and Tor Wager can be found here. The link for the Coursera crash course is here

  • Rebecca Saxe’s Bootcamp on fMRI (Conceptual) - This short video series focuses on getting a proper understanding of the concepts behind fMRI analysis.

Courses

  • FSL is a comprehensive library of analysis tools for FMRI, MRI and diffusion brain imaging data. The creators of this library often offer an in-person course on how to use it. However, more relevant for us, they also have the materials and lectures for this course online. For almost all studies the following tutorials of the 2018 Course are useful: (1) Brain Extraction, Registration, Motion Correction and EPI Distortion. (3) FMRI Preprocessing and Model-Based Analysis. In case you have any questions, they also have their own WIKI. Lastly, Jeanette Mumford also has a series of Youtube videos for FSL for task MRI.
    • Andy’s Brain Book - A tutorial online for beginners on how to perform fMRI analysis with FSL.

  • Lukas Snoek developed a tutorial series for the research master’s students of the University of Amsterdam to get introduced to fMRI analysis and pattern-analysis with this type of data. The courses are free and open-source. They contain extensive computer labs/tutorials. The purpose of this course is to teach you the basic concepts and methodology of functional MRI (fMRI) research. This is a great resource to get hands-on with fMRI analysis right away. They make use of Jupyter Notebooks (Python) and FSL. You can find the link here

  • This is a course to give users and introduction to using FreeSurfer, as well as get you acquainted with the concepts needed to perform its various modes of analysis and processing of MRI data. You can find the link here

  • NiLearn While this is not specifically a course, NiLearn provides very clear documentation on the different types of analysis you can perform on fMRI as well as information on the different assumptions made when working with this type of data. We recommend to use this resource when you already have prior experience with fMRI data or when you are feeling ready to dive directly on some more advance code

Lists

  • Jonathan Peelle MRI resources especially helpful for beginners - A common way of starting to do neuroimaging analysis is through a mixture of self-directed study, research, and asking other experts around you for help. A great place to start is by looking at the great material available online (such as the resources highlighted in this wiki), as it can give you a great overview of what can be done. This list here, provides some other resources that Jonathan Peelle from Northeastern University put together to do this type of analysis.
    • Linked to these resources is also this very helpful reading list for understanding the analysis options you have when using this type of data: MRI Reading List Johnathan Peelle

Specific Resources

  • Design Efficiency in fMRI - This page addresses the question of how to design fMRI experiments that are sensitive to a specific hypothesis.