Center for Functional MRI In the Department of Radiology

Structural MRI Imaging

Structural MRI provides information to qualitatively and quantitatively describe the shape, size, and integrity of gray and white matter structures in the brain. Broadly speaking, MRI signal varies across tissue types because gray matter contains more cell bodies (e.g., neurons and glial cells) than white matter, which is primarily composed of long-range nerve fibers (myelinated axons), along with supporting glial cells. Morphometric techniques measure the volume or shape of gray matter structures, such as subcortical nuclei or the hippocampus, and the volume, thickness, or surface area of the cerebral neocortex. Macrostructural white matter integrity can also be measured using volumes of normal and abnormal white matter, providing indications of inflammation, edema, or demyelination, complementing microstructural diffusion weighted MRI to provide a comprehensive picture of white matter integrity.

Since brain function depends to some extent on the integrity of brain structure, measures that characterize the underlying tissue integrity also allow one to examine the impact of tissue loss or damage on functional signals. Furthermore, structural MRI provides an anatomical reference for visualization of activation patterns and regions of interest to extract functional signal information.

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Many pulse sequences are available, emphasizing different aspects of normal and abnormal brain tissue. By modifying sequence parameters such as repetition time (TR) and echo time (TE), for example, anatomical images can emphasize contrast between gray and white matter (e.g., T1-weighted with short TR and short TE) or between brain tissue and cerebrospinal fluid (e.g., T2-weighted with long TR and long TE). Sequences vary in the information they provide and, of course, how long they take to acquire. Different image processing approaches often require specific types of sequences and may recommend specifically tuned sequences to provide the best results.

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Provides good contrast between gray matter (dark gray) and white matter (lighter gray) tissues, while CSF is void of signal (black).


  • Water, such as CSF, as well as dense bone and air appear dark.
  • Fat, such as lipids in the myelinated white matter, appears bright.
  • Contrast between the neocortex and white matter is best.
  • Contrast between some subcortical gray matter nuclei and white matter is fine but not as good as between cortex and white matter. These nuclei, such as the caudate and putamen, tend to have more white matter fibers and vascular infrastructure than other gray matter regions, increasing the brightness (i.e., lighter gray, more similar to white matter).
  • Pathological processes, such as demyelination or inflammation, often increase water content in tissues, which decreases the signal on T1; white matter disease often shows up as darker areas in the lighter gray-colored white matter. (Extensive white matter disease on T1 (left); Moderate white matter disease on T1 (left)) Due to a better measure of water content, T2-weighted images are more sensitive to subtle white matter alterations.
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Provides good contrast between CSF (bright) and brain tissue (dark). Some T2 sequences demonstrate additional contrast between gray matter (lighter gray) and white matter (darker gray).


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Provides good contrast between gray (bright) and white (darker gray) matter, with little contrast between brain and CSF.


  • Water varies in signal, with CSF often gray while other fluids may be of higher signal intensity; air appears dark.
  • Fat, such as lipids in the white matter, is relatively bright, although gray matter appears brighter than white matter.
  • Subcortical nuclei and neocortex tend to be more similar in intensity than on T1.
  • Pathological processes, such as demyelination or inflammation, often increase water content in tissues, which increases signal on PD; white matter disease often shows up as brighter areas but with signal different from CSF, unlike T2 (Moderate white matter disease on PD (right)) .
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  • T1 (left) and T2 (right) axial sections from an older individual with severe white matter disease.
  • T1 (left) and T2 (middle) and PD (right) axial sections from an older individual with moderate white matter disease.

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