Brain Imaging Alphabetical Soup: Making Sense of CAT, PET, MRI, fMRI, SPECT: fMRI

This article will focus on fMRI imaging.

fMRI, or functional magnetic resonance imaging, uses MRI equipment. fMRI is sensitive to the amount of deoxyhemoglobin in the blood. We know that when neurons consume oxygen, the neurons convert oxyhemoglobin to deoxyhemoglobin. Now, deoxyhemoglobin has magnetic properties, and these magnetic properties therefore introduce distortions in the local magnetic field. This distortion can be measured, and the measurement therefore gives an indication of how much deoxyhemoglobin in is in the blood. This technique is termed BOLD, for blood oxygen-level-dependent contrast.

The BOLD signal evolves over time in response to an increase in neural activity. This is called the hemodynamic response time, or HRF. HRF has three phases:


  1. The initial dip: as neurons consume oxygen, there is a small rise in deoxyhemoglobin, which results in a reduction of the BOLD signal.
  2. Overcompensation: in response to the increased consumption of oxygen, blood to a brain region increases. The increase in blood flow is greater than the increase in blood consumption, and therefore, the BOLD signal increases. This is the component that the fMRI normally measures.
  3. Undershoot: Blood flow and oxygen consumption dip before returning back to original levels.


The temporal resolution of fMRI is several seconds. This is better than PET scans, but it is still slow compared to the speeds at which cognitive processes take place.


Brain Imaging Alphabetical Soup: Making Sense of CAT, PET, MRI, fMRI, SPECT: MRI

I started this mini-series with the articles on how imaging got started, and on CT scans. Now we’ll move on to MRI scans.

MRI, or magnetic resonance imaging, is used to create images of the body’s tissues, specifically of the soft tissues, like organs. X-rays pass through soft tissues undistorted and relatively easily. Now, most human tissue is water-based (which makes sense considering we’re 70% water).  The amount of water in tissues differ. So different tissues will behave differently. These differences can then be used to construct a 3D image.

MRI scans are constructed by applying a strong magnetic field around the body. In water, you can find single protons (Hydrogen atoms, like H20). In MRI scans, it is the H nuclei that create the signal.

So, initially, the fields are randomly oriented. When a strong external magnetic field is applied, a fraction will organize themselves, and align themselves with the external field. This external field is applied in a constant manner throughout the scanning session.

Now, when the protons are aligned, a brief radio frequency is applied. This radio frequency then knocks the protons out of alignment by 90 degrees to their original orientation. So now the protons are spinning in this new state, and as they do this, they produce a detectable change in the magnetic field. This then is what forms the MRI signal.

Eventually, the protons are pulled back into their original alignment (they “relax”). The MRI scanner then repeats the process by sending the radio frequency to excite the protons in different slices of the brain that is being scanned.

Now there are different types of MRI scans, including the T1 and T2 scans.

T1-weighted images are used for structural imaging of the brain. In a T1-weighted image, gray matter looks gray, and white matter looks white. Pretty simple to distinguish.

When the protons are misaligned at 90 degrees to the magnetic field, the MRI signal decays because of interactions with other nearby molecules. This is the T2 image.