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M.R.Spectroscopy
rain
A brief basic guide
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Introduction
Among the new emerging MRI techniques, brain MRS has proved to be of more interest, being
readily available & of important clinical applications.
In this simplified approach, I tried to provide the minimal required knowledge for the fellow specialist
colleagues, otherwise, MRS is a whole science by itself really worth the effort. Also, I preferred to
follow an easy-
easy-to-
to-understand & better-
better-to-
to-recall clinical approach rather than starting with the dull
sophisticated physics. Notes, illustrations, simple glossary and a list of book & internet references will help
better understanding the subject. Hoping you will enjoy as you proceed, proceed, I welcome answering any
questions by e-e-mail at amirmonirali@yahoo.com

What is MR spectroscopy?
Dr
Dr Amirmir Monir
Monir
MR spectroscopy is the use of magnetic resonance in
quantification of various metabolites (chemical
composition) and the study of their distribution in
different tissues.
Rather than displaying MRI proton signals on a gray
scale as an image depending on its relative signal strength,
MRS displays the quantities as a spectrum. The resonance
frequency of each metabolite is represented on a graph and
is expressed as parts per million (ppm). This is because the
A normal white matter spectrum demonstrating peak
resonance frequency is in MHz or 106 Hz. positions of the primary components (N-acetyl
aspartate, lipid and lactate, and choline).

MRI MRS

Compound Water (one molecule) Metabolites (various molecules)

Nucleus 1H 1H, 31P , 13C , 19F

Concentration 80 Molar Millimolar

Resonances One frequency Several frequencies (spectrum)

Contrast parameters Spin density , relaxation Chemical shift

Spatial resolution (sub-) millimeter Centimeter(s)

Temporal resolution (sub-) seconds Minutes

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 In routine MR imaging, the more edema on a T2 sequence from http://www.amirsradiology.com
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mobile protons, the brighter the signal on T2. Using MRS, the more
metabolite that is present, the taller the peak or greater the area under
the peak. Specific metabolites can be located along an x-axis. We can The different nuclei that can be used with
infer that a spectrum of the brain is “normal” from numerous years of MR spectroscopy include H 1, phosphorus 31,
studying such spectra in healthy subjects in whom peak positions and carbon 13, fluorine 19 ,and sodium 23. The
relative intensity ratios have been established. hydrogen and phosphorus concentration in
central nervous system tissue is high enough to
be useful in clinical MR spectroscopy. At this
Main metabolites time, hydrogen is best suited for MR
spectroscopy because of its:
The Good, The Bad, and The Ugly - high concentration,
- favorable relaxation time,
Although there are several metabolites included in the spectrum - high gyromagnetic ratio.
of the MRS, there are three main in the brain: N-acetyl aspartate
(NAA), choline (Cho), and the lactate and lipid groups (LL).

NAA = neuronal health (The Good)

N-acetyl aspartate is seen at 2.02 ppm and is believed to be a
marker of neuronal health. Originally, decreases in NAA were
considered to be due to neuronal destruction, since it was diminished
in cases of multiple sclerosis and following trauma. Higher peaks
indicate more normal neuronal presence, while diminished peaks
occur in situations in which neural damage or replacement has
occurred. The only condition where NAA is increased is Canavan’s
disease (genetic defect in the enzymatic breakdown of NAA).

Cho = Tumor marker or cell wall marker (The Bad)

Choline is seen at 3.22 ppm and is present in cell walls of normal brain tissue. As more brain cells are made, one
theory suggests the Cho is increased. Active tumor growth will then cause an increase in Cho, since there is above-
normal production of cells. Other processes can release or increase Cho besides tumor; multiple sclerosis or acute
infarctions will also release Cho, or cause lysis of cell walls, and increase the concentration of Cho. This can be a
transient effect, however, while tumors will demonstrate persistent Cho elevation. We call it “The Bad,” since tumors
show an increase in this metabolite.

LL = Destruction and necrosis (The Ugly)

Lactate (lactic acid) is seen as a doublet (two peaks close to one another) at 1.33
ppm and is a by-product of anaerobic metabolism. Lipids resonate at the 0.9 to 1.2
ppm range. Both are released with cell destruction or synthesized in necrosis.
Increased LL can be seen in necrotic tumors, and in stroke due to destruction of
cells, and in abscess. It can also be seen in lower concentrations in intermediate
tumors. Lactate and lipid peaks are generally present in aggressive disease
processes. Normally, lactate is not detectable on human brain MR spectroscopy.

Creatine
The Cr peak is located at 3.03 ppm and has contributions from Cr, Cr phosphate,
GABA, lysine and glutathione. A secondary peak for Cr is at 3.94 ppm. The Cr
compounds are involved in energy metabolism via Cr kinase reaction and probably
serve as reserves for high-energy phosphates in cell metabolism. Because the Cr
peak is relatively resistant to change during disease states when compared with other
metabolites, it is usually used in the denominator of Cho/Cr and NAA/Cr ratios. The
Cr concentration is increased in hypometabolic disease states and is decreased in
hypermetabolic disease states. 2
 The Myoinositol peak is located at 3.56 ppm and is http://www.amirsradiology.com
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known to decrease in patients with hepatic encephalopathy.
It has been suggested that mI be used as a glial cell marker
and is increased in Alzheimer’s disease and demyelinating
diseases.
The other metabolites identified at low TEs include
glutamate, glutamine and alanine. The cerebral levels of
glutamine are increased in patients with hepatic
encephalopathy and Reye’s syndrome.

Normal gray and white matter spectra. Note the

Types of MRS differences in choline concentration seen at 3.22
ppm.
Clinical proton MRS techniques include single-voxel
spectroscopy (SVS) and multi-voxel chemical shift
imaging (CSI).
Single voxel spectroscopy produces a single spectrum
from a single voxel (Fig a) that is typically 8 cm3 in
volume, whereas CSI (Fig b) measures spectra from
multiple voxels that are typically 1 cm3 1.5 cm3 in volume.
CSI data may be presented in a variety of displays
including individual spectra, spectral maps, or colored
metabolite images overlaid on anatomical images. The two
measurements yield comparable metabolic differences
between spectra from the lesion and from the surrounding b
tissue. However, the relative changes among peaks are
slightly different due to the difference in the relative
amount of healthy tissue contained in the SVS (8 cm3) and
the CSI (1.5 cm3) voxels.

Data acquisition
Once an MR image is obtained as a localizer
image, a volume of interest is selected. If a single
voxel is to be analyzed, then a single 3D region of
interest is selected.

Once the single voxel is obtained, the spectrum is collected based on the amount of protons in the
voxel. The proton signals are detected and represented as a free induction decay (FID). A Fourier
transform is applied to the FID, converting the temporal information into frequency information.
The resonant frequency is then plotted versus signal intensity on a spectrum, instead of the typical
gray-scale image. If multiple voxels are to be evaluated, then both a region of interest for evaluation
and a region of normal brain are selected for comparison. Of the single-voxel techniques, two
commonly used acquisition sequences are stimulated echo acquisition mode (STEAM) and point
resolved spectroscopy (PRESS).
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With twice the signal of STEAM, PRESS acquisitions are faster; however, spectral baselines
are better with STEAM sequences. Care must be taken when identifying voxels of interest
(especially for the “normal” brain comparisons), since significant regional differences in metabolite
distributions can be seen in both gray and white matter. Regions to be avoided when selecting
voxels include blood, bone, and cysts, since susceptibility artifacts may skew the expected normal
molecular distributions. Areas that are difficult to image include the posterior fossa and the spinal
cord (both of which encounter problems due to their proximity to bone), as well as tumors
containing cystic components, blood, or regions of calcification.
Small metabolite peaks are
not visible in the presence of
Data analysis a large water peak (left
spectrum).The effects of
inadequate water
The three-step approach to spectral analysis suppression on the spectral
Step 1: The quality assurance phase. Is it an baseline. A (sub-optimal
water suppression) and B
adequate spectrum? (adequate suppression with
Step 2: Is Hunter’s angle normal? a normalized baseline).

Step 3: Starting from the right side of the graph,

count off the location and check quantities of “The
Good, The Bad, and The Ugly.” These are located
on the x axis at 2.02 ppm, 3.22 ppm, and the area
from 0.9 to 1.33 ppm.

Quality assurance
Just as a bad image can make interpretation difficult or impossible for diagnosis, a bad MRS may
not be interpretable. Substances that are difficult for MRS to image include bone, blood, cysts, and
cerebral spinal fluid (CSF). It is difficult to obtain spectra of bone and blood due to immobile
protons (bone) and shim difficulties (blood). Both CSF and cysts can contain lactate products and,
thus, may lead to inaccurately elevated lactate or lipids as well. When performing voxel
measurements, you should stay clear of these substances in all three imaging planes. Since the area
sampled is a voxel, it acquires signal from regions above and below the box that has been placed.

Examples of an adequate spectrum include good water suppression; otherwise the water peak on
the MRS spectrum is so abundant, it will overshadow the other metabolites. The normal water
concentration is 100,000 times the concentration of other metabolites. To detect these metabolites
successfully, the signal from water must be suppressed adequately. The water peak located at the far
left of the spectrum at 4.7 ppm can be suppressed using chemical shift selective excitation (CHESS)
or water elimination Fourier transform technique.

At present, CHESS is the most frequently used technique and involves presaturation of water
signal using one or more 90° presaturation pulses centered over the water resonance frequency.
Using this technique, the water signal can be suppressed by a factor of up to 1000. In contrast,
water elimination Fourier transform technique involves a 180° pulse centered over water and is less
efficient than CHESS for water suppression.
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Hunter’s angle is a term coined from a neurosurgeon, Hunter
Sheldon. Instead of doing complex ratios and analysis of the
spectra, he simply used his pocket comb. He placed his comb on
Hunter’s angle
the spectrum at approximately a 45˚ angle and connected several
of the peaks. If the angle and peaks roughly corresponded to the
45˚ angle, the curve was probably normal (Fig). If the peaks
strayed off the comb’s angle, the curve was abnormal (Fig). This
is a quick, useful method to read MRS and determine normal from
abnormal. It is important to remember, however, that this angle
was used with STEAM spectra from the brain only.
Examples of abnormal spectra. Note that
Hunter’s angle is seen to be ≠ 45° slope in all
cases. This aids in the evaluation of normal
versus abnormal, though it is not specific for
a pathologic diagnosis. The spectra (from left
to right), respectively, correspond to a
glioblastoma multiforme, a low-grade
astrocytoma, stroke, and multiple sclerosis.

The Good, The Bad, and The Ugly

We can look at NAA, Cho, and LL in a more simplified
pattern. First, the zero point on the curve is located at the far
right of the x-axis in spectral analysis. N-acetyl aspartate is a
neuronal marker, thus making it a high, plentiful peak on the
curve in normal brain tissue. We can call this “The Good”
marker. If the neuronal health is good, this peak will be the
highest peak. It is located at 2.02 ppm on the x-axis.
Elevations do not occur (except in patients with Canavans
disease). Decreased NAA can be due to replacement with
other metabolites (ie, tumor cell walls) or due to unhealthy High-grade tumor. Increased lipid and
neurons, as in diffuse axonal injury, multiple sclerosis, or lactate as well as choline in the presence
infarction. It can be reversible of decreased N-acetyl aspartate is
indicative of a high grade tumor with
Next, we moved left on the spectrum to 3.22 ppm on the x- increased cell walls and necrosis.
axis, the location of the Cho peak. Remember, we termed Cho
“The Bad” because excess amounts can indicate cell
destruction and release of cell walls, or an increase in cell
wall synthesis. Excess Cho is an indicator of tumor. It can
also be elevated in early phases of cellular destruction and
lysis, as in multiple sclerosis and stroke. These can therefore
mimic tumor in their early phases.
Finally, there are the LL peaks located between 0.9 and
1.33 ppm. This is termed “The Ugly” because it is an
extremely dreadful finding. Lactate and lipid peaks occur
when necrosis and a sizeable amount of cell death occurs. It Low- to intermediate-grade tumor.
Elevated choline due to cell wall synthesis
will be the highest peak on the spectrum in most high-grade in the absence of significant necrosis
tumors with marked depression of the NAA peak. Another (lipid and lactate) elevation.
cause of increased LL peaks occurs with cellular destruction
such as stroke. 5
High-grade tumor: Predominantly “The Bad and The
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Ugly.” There is abundant LL and Cho. N-acetyl aspartate
is depressed from replacement of neurons with cell wall
synthesis and necrosis (Fig).
Lower-grade tumor: Predominantly “The Bad.” There is
elevated Cho from tumor cell wall synthesis, but not
marked elevation in LL from necrosis. Some NAA
depression is present (Fig).

The MR spectroscopy spectra of metastases shows

increased Cho/Cr and decreased NAA/Cr ratios. The
Stroke. Decreased N-acetyl aspartate (neuronal
lactate and lipid levels are more likely to be elevated in health) and choline (cell walls) with elevation of
metastases than in primary brain neoplasms. lipid and lactate from cell destruction.
A typical cerebellopontine angle schwannoma will show
the absence of NAA along with elevation of
phosphoinositide peak at 3.6 ppm.
The absence of NAA along with elevation of alanine
peak (1.3 to 1.4 ppm) is often seen in meningiomas.

Stroke or radiation necrosis: Predominately “The

Ugly.” There are decreased NAA and Cho peaks with
elevation of LL from destruction (Fig).
Multiple sclerosis (MS). Decreased N-acetyl
Multiple sclerosis: Loss of “The Good.” There is loss of aspartate without elevation of the lipid and
NAA peak height, but not much elevation in Cho or LL lactate peaks or choline (a finding of chronic MS
on MRS). In early or acute MS, both lipid and
chronically. Early on, both Cho and LL can be elevated lactate, as well as choline, can be elevated.
(Fig) and can mimic tumor. A follow-up MRS will
usually demonstrate change.

Epilepsy: The MR spectroscopy detection of a decrease in NAA coupled with an occasional

increase in lactate is useful in detection of the seizure focus in patients with temporal lobe epilepsy.
The decrease in NAA corresponds to neuronal loss on histology in these patients. The localization
of the seizure focus is helpful in the surgical planning of temporal lobectomy in patients with
intractable seizure disorder.

Radiation necrosis versus recurrent tumor. (A) Tumor recurrence. There is elevation of choline as well as lipid and lactate.
The choline elevation raises our suspicion of tumor. Note that the baseline water suppression has been altered to ease
interpretation. (B) Radiation necrosis. There is elevation only in the lipid lactate area. If the patient has the proper clinical
history and the time frame is correct, this is consistent with radiation necrosis and not recurrent tumor. We may elect to
follow this with additional MRS and MRI evaluations.
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75-year-old woman. (A) The T2-weighted image
shows acute hematoma (arrow) with associated
edema. (B) The proton magnetic resonance
spectroscopy shows a single lipid peak (arrow), which
was interpreted as no evidence of neoplasm. There
are no discernable N-acetylaspartate and choline
peaks seen because of magnetic field inhomogeneity
induced by paramagnetic blood products. Acquisition
parameters: Long echo-time spin-echo (point
resolved spectroscopy) sequence with repetition
time/echo time = 1500 ms/135 ms.

Other diseases
In patients with Alzheimer’s disease, there is a decrease in
NAA levels and hippocampus atrophy, which may be useful in
distinguishing this disease from normal aging.
There are reports of a decrease in NAA levels and an increase in mI in patients with Alzheimer’s
disease. In patients with hepatic encephalopathy, there is an increase in glutamine, a decrease in
Cho, and a decrease in mI concentration. In Parkinson’s disease, NAA, Cr, and Cho levels are
unchanged but lactate levels are elevated. The MR spectroscopy feature of brain abscess includes
increased acetate and succinate levels at 1.92 and 2.42 ppm, respectively.

Brain abscess in a 59-year-old man. (A) The post-

contrast T1-weighted image shows a focal necrotic
space-occupying lesion in the left temporal lobe
with peripheral rim enhancement. (B) The proton
magnetic resonance spectroscopy of this lesion
shows elevated acetate and succinate levels at 1.92
ppm and 2.42 ppm, respectively (arrows). These
are key markers for brain abscess identification
(arrows). The broad peak between 1.0 to 1.5 ppm is
related to lipid and/or amino acids. Acquisition
parameters: Long echo-time spin-echo (point
resolved spectroscopy) sequence with repetition
time/echo time = 1500 ms/135 ms.

Pitfalls
MR spectroscopy is a technically demanding investigation and produces low SNR. The possible
causes of poor spectral quality on MR spectroscopy include hemorrhage, postoperative changes,
less than 200 acquisitions, small voxel size, and automatic shimming. These causes either result in
poor homogenity of the magnetic field or poor SNR, making the interpretation of spectroscopy data
unreliable. The presence of hemorrhage and postoperative changes within the volume of interest
often leads to poor-quality measurements due to susceptibility effects caused by hemosiderin. The
cortical brain lesions located close to the calvaria are often difficult to image on MR spectroscopy
because of susceptibility artifacts and contamination from lipids located outside the dura.
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A little bite of physics (only if interested)
Chemical shift….what does it mean?
Individual nuclei of the same isotope in a molecule have transition frequencies that differ
depending on their chemical environment. This phenomenon, called chemical shift, occurs because
the effective magnetic field at a particular nucleus in a molecule is less than the applied magnetic
field due to shielding by electrons. So, chemical shift is defined as nuclear shielding / applied
magnetic field.
An example of resonance chemical shift is observed in
the 1H nuclear magnetic resonance spectrum of ethyl
acetate (CH3COOCH2CH3; Fig). Resonances at several
frequencies are observed in this spectrum. The methylene
(CH2) protons are affected by the electron-withdrawing
oxygen atoms of the neighboring ester group, and as a result
the chemical shift of the methylene proton resonance is
significantly different from the chemical shift of the
resonances of the protons of the methyl (CH3) groups of
ethyl acetate. The two methyl groups are in different
chemical environments and therefore give rise to resonances
that have different chemical shifts.
Because of the dependence of the transition frequency of a nucleus on its chemical environment,
chemical shift is diagnostic of the functional group containing the nucleus of interest.
The chemical shift (either in hertz or ppm) of a resonance is assigned relative to the chemical
shift of a standard reference material. The nuclear magnetic resonance community has agreed to
set the chemical shift of certain standard compounds to 0 ppm. For 1H nuclear magnetic
resonance, the accepted standard is tetramethylsilane, which is defined to have a chemical shift
of 0 ppm.

Some useful definitions

Magnetic resonance (MR) :Absorption or emission
of electromagnetic energy by atomic nuclei in a static
magnetic field, after excitation by electromagnetic RF
radiation at resonant frequency.
Fourier transform : Mathematical procedure for
reconstructing images from raw data.

Voxel: Volume element of the sample to be

examined. Voxel size = slice thickness X pixel size

Shim : Correction of magnetic field inhomogeneity caused by the magnet itself, ferromagnetic
objects, or the patient's body. The basic shim usually involves the introduction of small iron pieces
in the magnet. The patient related fine shim is software-controlled and performed using a shim
coil.
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References

1. Constantinidis I. MRS methodology. Adv Neurol. 2000;83:235-246.

2. Ballestero J. Essentials of proton magnetic resonance spectroscopy and applications in
spaceoccupying lesions of the brain. A Radiol. 2001;30(4):55-63.
3. Danielsen ER, Ross B. Magnetic Resonance Spectroscopy Diagnosis of Neurological Disease.
New York: Marcel Dekker, Inc.; 1999.
4. Wiedermann D, Schuff N, Matson GB, et al. Short echo time multi-slice proton magnetic
resonance spectroscopic imaging in human brain: Metabolite distributions and reliability. Magn
Reson Imaging. 2001;19:1073-1080.
5. Ross B, Bluml S. Magnetic resonance spectroscopy of the human brain. Anat Rec. 2001;265:54-
84.
6. Marshall I, Wardlaw J, Cannon J, et al. Reproducibility of metabolite peak areas in 1H-MRS of the
brain. Magn Reson Imaging. 1996;14:281-292.
7. Michael et al. Magnetic resonance spectroscopy: A basic guide to data acquisition and
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8. Frahm J, Bruhn H, Gyngell ML, et al. Localized high resolution proton NMR spectroscopy using
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9. Miller BL. A review of chemical issues in 1H NMR spectroscopy: N-acetyl-L-aspartate, creatine
and choline. NMR Biomed. 1991;4:47-52.
10. Kreis R, Ernst T, Ross BD. Development of the human brain: In vivo quantification of metabolite
and water content with proton magnetic resonance spectroscopy. Magn Reson Med. 1993;30:424-
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11. Flogel U, Willker W, Leibfritz D. Regulation of intracellular pH in neuronal and glial tumor
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12. Jarvik JG, Lenkinski RE, Grossman RI, et al. Proton MR spectroscopy of HIV-infected patients:
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13. Chang L, Miller BL, Mcbride D, et al. Brain lesions in patients with AIDS: H-1 MR
spectroscopy. Radiology. 1995;197:525-531.
14. Gillard JH, Barker PB, van Zijl PCM, et al. Proton MR spectroscopy in acute middle cerebral
artery stroke. AJNR Am J Neuroradiol. 1996;17:873-886.
15. Miller BL, Moats RA, Shonk T, et al. Alzheimer disease: Depiction of increased myoinositol
with proton MR spectroscopy. Radiology. 1993;187:433-437.
16. Shonk TK, Moats RA, Giffored P, et al. Probable Alzheimer disease: Diagnosis with proton MR
spectroscopy.
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18. http://www.spectroscopynow.com
19. http://www.siemensmedicalsystems.com
20. http://www.rsna.org Dr Amir Monir 9