fMRI-Based Cognitive Neuroscience for Beginners

A complete course to learn both practical skills and theory involved in fMRI research.

By Sam Rosenberg

With contributions from Cory McCabe

What Is This Course?

I am creating this “course” for someone new to/interested in this field to be able to both:

1. Gain practical skills to use for research
2. Learn theory behind some of the analyses

I have not been involved much in data acquisition, so sadly, no information on data acquisition is included. Instead, this is more focused on the data management, processing, and analysis side to provide information on everything to do once the data is on a server.

What You Should Know

(The answer is yes, you all do)

If you have made it this far, congratulations on getting through the hardest part - starting! For this course, I am going to assume you have some basic, and I mean very basic, knowledge of anatomy and statistics(probably high school level, but there’s some very impressive high schools out there so I don’t know how much this will help). If you feel that you do not fit in this category, do not worry! You can easily teach yourself whatever information you feel you are missing as you go through each module. The internet in 2024 is a goldmine of free knowledge, just a goldmine that has several obstacles in the way of the gold and lot’s of fools gold mixed in. That’s why this guide sticks to reputable sources and makes your life less stressful.

Overview

This “course” is split into both theory and practical knowledge. You do not need to go through all the theory to understand the majority of the practical knowledge/skills, but in the practical knowledge I will use terminology introduced in the theory material (it is written expecting you, the reader, to know the terms or look up the terms and teach yourself as you go (which you can all do, there’s nothing too mind bending in this introductory course).

For each section, you should go through each page in order for the best experience, but if you are already an expert in a certain topic, you don’t waste your time reviewing the basics.

If doing both sections(which I highly highly recommend - so much so that I intentionally used highly twice), then I would recommend that you go through each module in the following order:

1. Theory Modules 1+2+3 (Understanding what MRI data is)
2. Practical Knowledge/Skills Modules 1+2+3+4+5 (A handful of skills for interacting with MRI data)
3. Practical Knowledge/Skills Module 6 (Statistics is the backbone of research, hence this module getting its own line)
4. Theory Modules 4+5+6 (How we analyze the data and a neuroanatomy intro)
5. Practical Knowledge Modules 7+8 (Running fMRI analysis and more advanced skills, aka coding)

Theory and application are both useful skills, but each theory has no use if it can’t applied and skills have no use if one doesn’t know what they’re doing. By going through both sections at the same time as I have outlined above, it will allow you to better see how theory and application connect to each other(which isn’t always as intuitive as it seems).

Course Pages

Theory

1. How an MRI works
2. fMRI/The BOLD Signal
3. HRF (Hemodynamic Response Function)
4. GLM (General Linear Model)
5. Neuroanatomy
6. More General Methods Background

Practical Knowledge/Skills

1. What is neuroimaging data?
2. Unix Basics
   • File Permissions
   • Transferring Files Between Servers
3. Viewing Data/Drawing VOIs/Lesions
4. Preprocessing Data
5. Data Management Basics
6. Statistics
7. Introduction To fMRI Analysis Programs
   • Troubleshooting
8. Useful Coding Skills