MR spectroscopy

MR spectroscopy counts as a molecular imaging technique because it can measure the concentration of certain molecules within the imaged region. Different nuclei can be targeted such as carbon-13 and phosphorous-31. However, hydrogen-1 (protons) are the most commonly used due to the high sensitivity of the nuclei, the 100% availability of the isotope and the abundant presence of protons in most metabolites creating a larger signal.

  • Advantages of MRS:
    • Can identify concentration of metabolites in imaged tissue
  • Disadvantages of MRS:
    • Low resolution
    • Very susceptible to local magnetic field heterogeneity. This is very noticeable when imaging close to bone, calcium and blood. Shimming (homogenisation) of the field can improve artifacts.
    • Can only image limited area


MRS utilises the fact that each metabolite will have a very slightly different Larmour frequency. The frequencies of the returned signals are plotted in units of parts per million (ppm) along with the strength of the signal (i.e. the concentration of the metabolite).


MRS spectrum


The most common metabolites detected and their clinical relevance are outlined below.


Metabolite Frequency (ppm) Role Clinical relevance
mI Myoinositol 3,6 Glial marker

Raised in gliomas and MS

Reduced in herpetic encephalitis

Cho Choline 3,2 Cell membrane and metabolism marker Raised in tumours and demyelination
Cr Creatine 3,0 Energy metabolism marker Constant peak
Glx GABA, glutamine, glutamate 2,1 - 2,5 Intracellular neuronal transmitter Raised in hepatic encephalopathy
NAA N-Acetyl-Aspartate 2,0 Healthy neuronal marker

Raised in Canavan's disease

Reduced in any condition resulting in loss of neurons

Lac Lactate 1,3 doublet Anaerobic respiration Raised in ischaemia, seizures, tumours, mitochondrial disorders
Lip Lipids 0,9 and 1,4   Raised in necrotic tumours
aa Aminoacids 0,97   Raised in pyogenic abscesses


Performing MRS


MRS can be single voxel or multivoxel

Single voxel spectroscopy (SVS): a single voxel is selected and analysed.

  • Advantages:
    • High signal-to-noise ratio
    • No spectral contamination
    • Short scan times
  • Disadvantages:
    • Very small coverage
    • Low resolution


Single voxel spectroscopy


Multi-voxel chemical shift imaging (CSI): multiple voxels in a 1D, 2D or 3D array are selected and a spectrum is produced for each voxel.

  • Advantages:
    • Larger total coverage
    • Higher resolution
  • Disadvantages:
    • Longer imaging time
    • More likely to have magnetic field inhomogeneities
    • Lower signal-to-noise ratio
    • Spectral contamination from adjacent voxels


Multi voxel spectroscopy



1. Suppress water signal

Water contains a large quantity of hydrogen nuclei which masks the small spectroscopic signal from other metabolites. This is usually done with a CHEmical Shift Selective (CHESS) sequence which saturates out the water signal.

2. Select voxel or voxels of interest

With SVS this is done with successive RF pulses in three orthogonal planes which intersect at the voxel of interest. With CSI,phase-encoding steps are used to image multiple voxels.

3. Acquire spectrum

Several sequences can be used to acquire the spectrum including Point RESolved Spectroscopy (PRESS) and Stimulated Echo Acquisition Mode (STEAM).


Σ  Summary
  • MRS utilises different Larmour frequencies based on metabolite composition
  • Most often uses protons (1H) but can use 13C or 31P
  • Forms spectrum of frequencies present and strength of signal (concentration)
  • MRS is low resolution and very susceptible to local magnetic field inhomogeneities
  1. Suppress water signal
    • e.g. with CHESS sequence
    • Very high proton count in water masks other weaker signals
  2. Select voxel / voxels of interest
    • Single-voxel: quicker, better signal to noise ratio
    • Multi-voxel: better resolution, image larger area
  3. Acquire spectrum
    • PRESS and STEAM most common

Next page: MR angiography

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