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How Does Functional Magnetic Resonance Imaging Work?

Looking into Functional Neuroimaging


Updated November 25, 2012

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How Does Functional Magnetic Resonance Imaging Work?

A researcher looks at a functional magnetic resonance image.


Magnetic Resonance Imaging (MRI) has given doctors very good pictures of the structures of the brain. A newer technique called functional MRI can go even further by indirectly measuring brain activity as well. While most of the time these techniques are just used in research studies, they’re becoming more common in medical practice.

You’ve probably come across images made using functional MRI at some point. The images show a brain with colored areas lighting up areas of the brain associated with some function like language or movement. These studies are very popular: Hundreds of scientific articles using this technology are published every month, many of which are also mentioned in lay press. But how are these images made, and what do they actually represent?

How Functional MRI Works

Functional MRI makes use of a special signal called blood oxygen level dependent (BOLD) contrast. Blood flowing through the brain carries oxygen on molecules called hemoglobin. Hemoglobin molecules also carry iron, and so have a magnetic signal. It turns out that hemoglobin molecules have different magnetic properties when they are attached to oxygen than when they are not carrying oxygen, and this small difference can be detected with an MRI machine.

When an area of the brain is more active, it initially uses up a lot of oxygen in the blood. Shortly afterwards, the brain dilates local blood vessels in order to restore the oxygen supply. The brain may even do this job a little too well, so that more oxygenated blood goes into the area than what was initially used. The MRI machine can detect the difference in signal that results from this increase in blood oxygen.

So functional MRI studies are not actually looking at neuronal activity directly, but are looking at how blood oxygen levels change, and assuming that this is connected to nerves firing. Studies have shown that this assumption is usually correct, although sometimes you need to interpret the studies carefully if you think that the blood flow may not be as tightly coupled to nervous activity as usual. Diseases like vascular malformations, tumors, and even normal aging can change the relationship between neural activity and the local blood flow that results in BOLD signal.

How Can Doctors Use Functional MRI?

Because it is a newer technology and because other techniques can answer similar questions that fMRI could, fMRI is not commonly used in clinical or hospital settings. However, it can be used to help plan important brain surgeries. For example, if a neurosurgeon wants to remove a brain tumor that sits close to the language centers of the brain, they may order an fMRI study to help show exactly what areas of the brain are involved with language. This helps the neurosurgeon avoid damaging those regions while performing surgery. However, the most common use of fMRI is in medical research.

What Types of Research Is Done Using fMRI?

There are two main ways of looking at brain function using fMRI. One method focuses on finding specific areas of the brain that respond to some task or stimulus. For example, the person in the MRI scanner might be shown a flashing checkerboard at some points, and other times a blank screen. They may be asked to push a button whenever they see the flashing checkerboard. The signal during the task will then be compared to the signal when the task isn’t being done, and the result will be a kind of picture of what brain regions were involved with seeing a flashing checkerboard and then pushing a button.

The other way fMRI can be used is to evaluate neural networks. This involves figuring out what areas of the brain are talking to each other. If one area of the brain usually lights up at the same time as another, these two areas of the brain may be connected. No task may even be needed in order to do this kind of study. For this reason, these studies are sometimes called “resting state functional magnetic resonance imaging.”

The information that comes from functional MRI studies is very complicated, and requires a lot of statistical analysis to become meaningful. This initially led many people to mistrust the results of functional MRI studies, as it seemed there were many possible opportunities for error in the analysis. However, as both researchers and reviewers have become more familiar with the new technology, results are becoming both more trusted and trustworthy.

What Does the Future Hold for Functional MRI?

Functional MRI studies have already shown many different things about the brain, in addition to confirming what we already knew about neural pathways and localization. While it is difficult to say whether fMRI will ever be commonly used in a clinical setting, its popularity and effectiveness as a research tool alone makes it important for both doctors and laypeople to have a basic understanding of how this tool works.


Pressman P, Gitelman D. Functional MRI: A primer for neurology residents. Neurology 2012 March 06, 78 (10) e68-e71

Faro SH, Mohamed FB, Haughton V. Functional MRI: Basic Principles and Clinical Applications: Oxford Univrsity Press, USA, 2006.

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