F. M. Kirby Research Center for Functional Brain Imaging
At the Kennedy Krieger Institute

Scientific Overview

How to Image the Brain

Magnetic Resonance Imaging (MRI) is an exciting, non-invasive technique for brain imaging. Since the mid-1980s, standard MRI techniques have been used to generate high-quality anatomical images of normal and abnormal brain structures. Functional MRI allows us to measure brain metabolism through the main connections in the brain.

Below, we have listed a few categories related to research on the brain:

  • Watching the Brain at Work
    How the brain functions is dependent on several factors, especially fuel and oxygen. This section describes how we measure oxygen metabolism and produce an image in fMRI.
  • Brain Chemistry
    Magnetic Resonance Spectroscopy and Spectroscopic Imaging are two techniques that evaluate the chemical components of the brain.
  • Tracing Neuronal Connections
    Communications between nerve cells in the brain are essential for normal brain activity. Diffusion Tensor Imaging (DTI) techniques are being developed to generate 3-D pictures of the communication pathways in the brain.
  • Brain Anatomy
    Studies to visualize the brain structures in multi-dimensional maps allow us to validate location of various brain functions.
Combining all of these technologies yields informative images.

This image shows neuronal connections in the brain.

Citation: H. Huang, J. L. Prince, A. Carass, B. Landman, P. C. van Zijl, and S. Mori. "Cortico-cortical connectivity revealed by DTI-based tractography." ISMRM, 2006.

Watching the Brain at Work

An fMRI showing brain activity, mapped onto structural images.

We use strong magnets to create high quality pictures of the brain. A strong magnetic field, combined with radio frequency waves (such as those detected by your FM radio), create detectable "echoes" from water molecules within brain tissue. From these "echoes," we can reconstruct a picture of the brain tissues themselves. This non-invasive technique is called "Magnetic Resonance Imaging" (MRI). Over the past decade, MRI has become an invaluable tool for diagnosing various medical conditions.

The brain is a collection of nerve cells, called "neurons." These neurons do all of the work we associate the brain, including seeing, feeling, and thinking.

To work properly, neurons need a constant supply of fuel and oxygen. Blood vessels transport these necessary chemicals to all of the brain cells. When the brain is working on a task, a particular set of neurons associated with that particular task work harder than the rest of the brain cells. These neurons require more nutrients and oxygen; therefore, the blood supply to them increases. Then, fuel and oxygen move from the blood into the cells, which changes the magnetic properties of the blood. We can use fMRI to measure these changes in magnetic properties.

fMRI techniques are often used to characterize memory. For example, if you were told to dial a particular number, a part of your brain would work harder to keep that number in your memory. This part of your brain would require more oxygen and nutrients. We can then use fMRI to image the changes in blood supply, pinpointing the location of those neurons in the brain.

[Adapted from the work of J. Pekar and P. Barker, 1999.]


Brain Chemistry

Several spectra from Magnetic Resonance Spectroscopic imaging.

Magnetic Resonance Spectroscopy (MRS) is a technique that allows us to evaluate the naturally-occurring chemicals in brain cells over time. We can detect and monitor these chemicals during different brain activities, which allows us to characterize normal and abnormal functionality in the brain.

Some examples of the chemicals we examine in MRS include: sources of energy for the cells, molecules that are found only on neurons, or products of metabolic reactions. The presence or absence of these molecules indicates the level of cellular activity within the neurons.

MRS Imaging (MRSI) is a closely-related technique that compiles the spectroscopy information from MRS, and puts it into an image format. This image is used to link anatomical information with function.

[Adapted from the work of P. Barker, 1999.]


Tracing Neuronal Connections


Diffusion tensor imaging allows us to create images of fiber tracts, which relay information throughout the nervous system.
Citation: S. Wakana, H. Jiang, L.M. Nagae-Poetscher, P.C.M. van Zijl, and S. Mori, "Fiber-tract Based Atlas of Human White Matter Anatomy", Radiology, 230, 77-87 (2004).

Each neuron has two distinct parts: the cell body, and a long extension called an "axon." The axons are important for communication between the distinct areas of the brain.

Overall, the brain is organized in the following manner: the cell bodies (known as "gray matter") are located in the outermost area, and the axons (known as "white matter") project inward. Diffusion Tensor Imaging (DTI) can be used to evaluate how well the neurons communicate with each other along their axons.

DTI detects the movement of water along these axons. We can then project this activity onto two-dimensional or three-dimensional models. Many clinical disorders are caused by the abnormal function of these communication pathways. DTI allows us to visualize the structural integrity of axonal pathways, allowing us to generate images for individual subjects under a variety of conditions.

[Adapted from the work of S. Mori, 1999.]


Brain Anatomy

T1-weighted image of a healthy volunteer

A structural image of the brain, using T1-weighted contrast. This type of image is typically used in studying brain anatomy.

MRI has many sources of contrast, which arise from specific properties in each tissue. The brain consists of neuronal cell bodies ("gray matter"), connected via axonal fibers ("white matter"), surrounded by cerebro-spinal fluid (CSF).

Two particular parameters, called "relaxation times," are "T1" and "T2." In a "T1-weighted" image, white matter appears bright, and CSF appears dark. In a "T2-weighted" image, white matter appears dark, and CSF appears bright.

This is also an image of an axial slice of the brain. MRI can produce images in any orientation. Usually, we analyze images in three planes, as if "slicing" the brain in three directions.

  • "Axial" slices are horizontal slices through the brain, as if we were slicing from the nose to the back of the head. In this picture, the top of the image corresponds to the front of the person's head, and the bottom of the images corresponds to the back of the person's head.
  • "Coronal" slices are vertical slices through the brain, as if we were looking at a person's face, then slicing from the top of the head to the bottom of the head.
  • "Sagittal" slices are also vertical slices through the brain, but are positioned as if we were looking at a person's ear, then slicing from the top of the head to the bottom of the head.