What is an fMRI scan and how does it work?

By Megan Tung

An fMRI scan is a functional magnetic resonance imaging scan that measures and maps the brain’s activity. An fMRI scan uses the same technology as an MRI scan. An MRI is a noninvasive test that uses a strong magnetic field and radio waves to create an image of the brain. The image an MRI scan produces is just of organs/tissue, but an fMRI will produce an image showing the blood flow in the brain. By showing the blood flow it will display which parts of the brain are being stimulated.

fMRI Scanner MRI Machine (used for both MRI and fMRI scans)


In the 1930s Columbia University physicist, Isidor Isaac Rabi, discovered when a magnetic field combines with radio waves it causes the nucleus of an atom to "flip." Most of the atoms in the human body are hydrogen atoms, which have a positively-charged proton within the nucleus. When the MRI machine emits a magnetic field the protons align with the magnetic field. Radio waves then pulse into the patient's head, knocking the protons out of alignment. As the protons move back into their original position (called precession) they produce a radio signal back. The time and amount of re-alignment changes based on the thickness and hardness of the tissue. The radio waves emitted from the protons produce a clear image of the brain. In the 1900s, physicist Seiji Ogawa discovered oxygen-poor blood was affected by a magnetic field differently than oxygen-rich blood. The data showed oxygen-poor blood and oxygen-rich blood differed by 20%. The active parts of the brain contain more oxygen-rich blood, so this knowledge initiated research being done about fMRI scans.

Process the Protons Process the protons (in hydrogen atoms) go through during an MRI

How does an fMRI map the brain's activity?

As I mentioned above, the fMRI looks at blood flow in the brain to detect areas of activity. Glucose is the brain's primary source of energy, but glucose is not stored in the brain. So when parts of the brain need energy to perform an action, more blood flows in to transport glucose to the active areas, thus more oxygen-rich blood enters the area. For example, when you are speaking there is glucose and oxygen-rich blood flowing to the part of your brain designated to speaking.

During an fMRI scan the patient is asked to perform a specific task to increase oxygen-rich blood flow to a certain part of the brain. Such as tap their thumb against their fingers, look at pictures, answer questions on a screen, think about actions based off a picture (ex: they see a picture of a book and think about actions like read a book, write a book, buy a book), etc. For the tasks where the patient is asked a question, most of the time the patient is told to just think about the answer that way the speech part of the brain is not activated as well.

Hydrogen Atoms Process the protons (in hydrogen atoms) go through during an MRI

How does an fMRI help?

The primary reason for an fMRI scan is to help map a patient's brain before they go into brain surgery. Creating this map will help doctors better understand the regions of the brain linked to critical functions such as speaking, walking, sensing, or planning. The brain activity is mapped in squares called voxels, which represent thousands of neurons. Color is then added to the image to create a map of the brain.

There are clinical studies that take multiple fMRI scans to research more about the scan and data it provides. Some believe with more research and development fMRI scans will eventually allow doctors to get a look at people's mental processes (what they are thinking and feeling). If this is possible, fMRI scans could possibly be used to detect lies versus truths, which could act as more evidence in a court case. However, tons of further research needs to be done before this is actually possible.

Doctors have to be extremely cautious when operating on the brain, so an fMRI cannot be the only method to map the brain when any type of brain surgery is involved. Another method to map out the brain is called intraoperative brain mapping.** An fMRI scan is a great first step to ensuring the doctor has a deep understanding of their patient's brain prior to surgery. Typically intraoperative brain mapping is used when a tumor/part of the brain needs to be cut out. The fMRI will create a general map of the brain, but the intraoperative brain mapping will allow the doctors to know exactly what parts of the brain are surrounding the part of the brain that needs to be operated on. This method happens during a brain operation by cutting the skull open and using a small electrical probe to stimulate the brain in different ways. The doctors will place the electrode on the brain stimulating in a variety of ways depending on the location. For example, the doctor could stimulate a part of the brain and the patient might think someone is touching their arm even if nobody is near their arm. Or a part of the brain could be stimulated causing the patient to have trouble talking meaning this part of the brain is responsible for speech. The actual electrode (or its pulses) will not hurt the patient, but the electrode might stimulate a part of the brain correlated to pain. The electrode can also stimulate seizures. However, the doctors can see the patient's brainwaves, so if the doctor sees signs leading to a seizure, they will take a break from stimulating the brain. They can also give the patient anti-seizure medication. But if a seizure still does happen, cold water directly applied to the brain will almost immediately stop the seizure.

**There are various methods to map the brain, but I am just discussing one example of an invasive method and one example of a non-invasive method.

An fMRI scan is a non-invasive procedure that allows doctors to map out the brain before a surgery. This scan provides more information to the doctors about the makeup of an individual's brain to prevent serious injuries or to determine if surgery is even a possibility. Another positive is the image produced by the fMRI scan is very high resolution.

Getting an fMRI scan is a very expensive procedure (most of the time*); however, it is worth the price if the scan could prevent someone from losing a necessary function. A minor negative is the machine can only capture a clear image if the person being scanned stays completely skill, but this can be solved with braces/harnesses to hold the patient in place. Finally, researchers do not fully understand every aspect of this process. In the scan they can only look at the blood flow, not at individual neuron's activities (which is critical to mental function). When a certain area of the brain gets increased blood flow it can represent multiple different functions because it can be hard to isolate the brain performing only one specific action.

*There are clinical trials that will actually pay you money to allow them to scan your brain so they are able to gather more data.

You may also like reading:

Magnetic Fields, My Story as an MRI Tech Intern
The Powerful Magnets of an MRI Machine
Archive: How It Works
Megan Tung is a summer intern at Jameco Electronics and a freshman at University of California, Santa Barbara (UCSB). Her interests include photography, music, business, and engineering.