About MR Spectroscopy

Excerpt reproduced from the American Society of Neuroradiology Advanced Imaging Symposium 2000:29-36.

Spectroscopy can be performed with a large number of isotopes. However, for all practical purposes, we focus on hydrogen nuclei.

Basics of MRS

Conventional MR imaging measures signals emitted by hydrogen (proton) nuclei from small pixels that have been selected by spatial variations in frequency and phase. This spatial mapping enables the signal to be formed into images. However, when using frequency changes for spatial encoding, we lose our ability to discriminate much of the important information about chemical environment among the nuclei. Water, fat and other chemicals, typically amino acids, combine to produce a single net signal from each pixel. We have limited ability to distinguish relative contributions in MRI. Magnetic Resonance Spectroscopy (MRS) can extract information about the chemicals that reside on the frequency scale between water and fat in both a qualitative and quantitative manner. MRS uses the same principles as Magnetic Resonance Imaging (MRI) but rather than generating an image, a plot representing chemical composition of a region is generated.

In vivo spectroscopy is similar to the NMR spectroscopy one learns in organic chemistry. A rf pulse is applied to the sample. The signal from the sample is measured and Fourier transformed. The primary differences between analytical NMR spectroscopy and in vivo MRS are the composition of the sample and the acquisition technique. Analytic and in vivo spectroscopy both use position, signal intensity and linewidth along with spectral patterns to display chemical information. A "ppm scale" describes the "position" of the peaks or resonances on the x-axis. The parts per million or ppm refer to the unit of measure used to identify a peak location. The ppm is calculated by dividing the difference in frequency (in Hertz) of two peaks (with one peak being the reference) by the operating frequency of the MR scanner (in Hertz). This makes comparison of a peak location found on the spectrum of a 1.5T scanner comparable to that found at that location on a 4.0T MR scanner. An example of this is the methyl resonance on the acetyl group of N-acetyl aspartate appears at 2.0 ppm whether it was measured on a 1.0 T, 1.5T, 3T or a 4T scanner. The signal intensity (amplitude on the y-axis) and linewidth provide the "area" which can be used to quantitate the amount of the observed chemical. The concentration threshold for detection is much higher with in vivo MRS than with analytical NMR. Specifically, in vivo MRS requires the neurochemicals to be at a level of 0.5mM for recognition. Typically, the neurochemicals observed range in concentration from 0.5 to 10 mM. The spectral patterns arising from interactions of bonding electrons within the chemical molecule can be exploited to distinguish and identify the chemicals. This spin coupling property is most often appreciated for distinguishing lactate.

Basic In Vivo Localization Techniques

While analytical NMR can use simple one pulse experiments, basic in vivo MRS uses multiple rf pulses to localize on a given region of the body. There are two basic types of in vivo spectroscopy: single voxel and multi-voxel. The single voxel techniques generate a cubic or rectangular based volume element (voxel) for a region to be sampled with MRS. There are variations for the multi-voxel techniques that allow one, two and 3 dimensional acquisition of multiple voxels in single or multiple slices which are also referred to as chemical shift imaging (CSI). Either type of spectroscopy can use variations of the two pulse sequences currently serving as standards for proton MRS localization techniques. For simplicity, these localization sequences are described in terms of single voxel MRS. Both localization techniques use three orthogonal slices intersecting to create a voxel. The STEAM (STimulated Echo Acquisition Mode) technique(1) generates a cubic or rectangular voxel by the acquisition of three orthogonal slice selective 90-degree pulses. By using 90-degree pulses, a well-delineated voxel is created within the sample. This technique minimizes signal contamination from outside the region of interest. The second technique, PRESS (Point RESolved Spectroscopy)(2), also generates a cubic or rectangular voxel by the acquisition of three orthogonal slice selective pulses, differing by using a 90-degree pulse followed by two 180-degree pulses. The voxel generated by PRESS is not as precisely defined as that of STEAM, however, the signal to noise gained by using PRESS is twice as large over STEAM.

Both STEAM and PRESS need a technique to suppress the water signal found in their voxels. Water has a concentration level on the order of 110 M while most metabolites of interest are at the 1-10 mM level. A commonly used technique, CHEmically Selective Saturation (CHESS), is applied prior to the selected localization technique. Three frequency selective pulses are applied along with a dephasing gradient to suppress the water. Most prescan failure arises from inadequate water suppression. This often arises while sampling inhomogeneous regions. MRS is more sensitive than MRI to nonuniformities in the magnetic field. MRS requires using a process known as shimming to improve the global and/or local magnetic field. Upon shimming effectively, the water linewidth is sufficiently narrow for the CHESS sequence to null the signal. Large water resonances due to inhomogeneities within the region of interest are often unsuppressable. Also, the linewidths of the metabolite peaks can not be distinguished. As shimming improves the field homogeneity, linewidths become smaller and the resolution is enhanced. Automatic Prescanning has enabled clinical MRS to be performed in a reasonable amount of time by shimming, setting the observed frequency, optimizing the suppression and localization pulses, and setting the transmitter power and the receivers.

  1. Frahm J, Bruhn H, Gyngell ML. Localized high resolution proton NMR spectroscopy using stimulated echoes: initial applications to human brain in vivo. Magn Reson Med 1989;9: 79.
  2. Bottomley PA. Selective volume method for performing localized NMR spectroscopy. US Patent 1984.

Abbreviations: CNS central nervous system, MRI Magnetic resonance imaging, MRS Magnetic resonance spectroscopy, NAA N-acetylaspartate, TR Repetition time, TE Echo time, TM Mixing time, PRESS Point resolved spectroscopy, STEAM Stimulated-echo acquisition mode, VOI Voxel of interest, Cr Creatine and phosphocreatine, Cho Choline containing compounds, mI Myo-inositol.