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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).

MR spectroscopy spectrum
MR spectroscopy spectrum

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


MetaboliteFrequency (ppm)RoleClinical relevance
mIMyoinositol3,6Glial markerRaised in gliomas and MS


Reduced in herpetic encephalitis

ChoCholine3,2Cell membrane and metabolism markerRaised in tumours and demyelination
CrCreatine3,0Energy metabolism markerConstant peak
GlxGABA, glutamine, glutamate2,1 – 2,5Intracellular neuronal transmitterRaised in hepatic encephalopathy
NAAN-Acetyl-Aspartate2,0Healthy neuronal markerRaised in Canavan’s disease


Reduced in any condition resulting in loss of neurons

LacLactate1,3 doubletAnaerobic respirationRaised in ischaemia, seizures, tumours, mitochondrial disorders
LipLipids0,9 and 1,4 Raised in necrotic tumours
aaAminoacids0,97 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
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
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).

Written by radiologists, for radiologists with plenty of easy-to-follow diagrams to explain complicated concepts. An excellent resource for radiology physics revision.

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