Education, tips and tricks to help you conduct better fMRI experiments.
Sure, you can try to fix it during data processing, but you're usually better off fixing the acquisition!

Saturday, February 19, 2011

Physics for understanding fMRI artifacts: Part Three

Coffee break! Time for a few tangents

In this post we're going to do a whistle-stop tour of some background concepts that you should have seen before. None of the information in today's series of videos is essential to understanding what's coming up later, when we get to k-space, the EPI pulse sequence and artifacts, but it's interesting and useful to review. Besides, these videos are well made, entertaining and are available free so we might as well use them! So, if you have the time, go grab a coffee and spend the next hour being reminded of things you probably knew at some point in a dim and distant past. You might even learn something about scanner hardware you didn't know before.

The anatomy of a miniature scanner

Don't worry too much about following every detail in today's first video, which dissects a miniature MRI scanner. It contains the same basic components as your fMRI scanner. Below, I've given a few explanatory notes on the coils and components that are most relevant to us.

Wednesday, February 9, 2011

Physics for understanding fMRI artifacts: Part Two

We continue our review of the key principles of NMR with another video courtesy of Paul Callaghan. In it, Prof Callaghan introduces the idea of bulk magnetization; the thing that you induce in your subject's brain (which is ~80% water) when you slide the subject into the magnet, and which you then manipulate to produce images.

In the video shown previously (see Part One), Prof Callaghan introduced the phenomenon of resonance and demonstrated it with a spinning wheel. In MRI the resonance frequency is governed by a simple proportionality, as given in the Larmor equation. We will use this equation later on to establish different frequencies across an object, thereby encoding spatial information and yielding, ultimately, an image of that object. We will also see how the Larmor equation is used in the k-space formalism, so make sure you have a good understanding of this deceptively simple yet intuitively valuable equation.

Sunday, February 6, 2011

Physics for understanding fMRI artifacts: Part One

This is the first in a series of posts in which I will attempt to provide you with the means to diagnose the manifold artifacts that plague fMRI. These artifacts can be inherent, e.g. distortion and dropout, or the consequences of a hardware issue, e.g. RF interference or gradient spiking, or may arise from your subject, e.g. cardiac pulsatility and head movement. However the artifacts arise, the aim is simple: by providing you the means to recognize what is going wrong in your experiment you may be able to discern the root cause, then remedy the problem and salvage your data.

It's a lot like plane spotting, only less fun.

The psychologists amongst you would be able to lecture me for days on category learning. Well, that's what this is. Except that before we can differentiate between one artifact and another we must first understand how EPI is designed to work in an ideal situation. (You don't need to know how planes fly to categorize them, apparently.) And to comprehend artifacts it's important for you to have a reasonable appreciation of the underlying physics, especially the concept of k-space. Here's the loose plan: