MR spectrum – normal

The normal MR spectrum

  • observed spectra varies with echo time (TE) used in acquiring them.
  • short (20-30 ms), intermediate (135-144 ms) or long (270-288 ms).
  • more peaks in short TE.
  • long TE typically detects peaks for 4 compounds
    1. NAA (N-acetylaspartate)
    2. choline
    3. creatine (Cr)
    4. lactate
  • different areas of brain have different concentrations of metabolites.
  • concentration varies with brain maturation.
  • Infants
    • high choline, myoinositol
    • low Cr, NAA
Screen Shot 2016-07-08 at 07.48.18
1- lactate, 2-NAA, 7-creatine, 8-choline, 10-inositol

N-acetyl aspartate (NAA)

  • most obvious peak
  • at 2.01 ppm
  • reference for chemical shift determination
  • contributions from NAA, N-acetylaspartate glutamate, glycoproteins, amino acid residues in peptides.
  • two functions in adult brain
    • precursor of brain lipids
    • involved in coenzyme A interactions
    • alternate suggestion of it being an osmolyte – neurotransmitter / neuromodulator precursor
  • higher in cortex than in white matter
  • located in neurons and its branches
  • low concentration in mature glia
  • reduced in neurodegenerative diseases
  • absolute or relative decrease in relation to Cr peak suggests axonal / neuronal damage
  • transient reduction – energy depletion as synthesis of NAA occurs in mitochondria.
  • in infants – concentration is same in gray and white matter
    • indicator of normal oligodendroglial development


  • trimethylamine peak
  • 3.21 ppm
  • choline, betaine, carnitine, myo-inositol and taurine
  • contains phosphoryl choline, phosphorylethanolamine, glycerophosphorylchlorine, glycerophosphorylethanolamine and free choline
  • phosphorylethanolamine dominates in neonates; decreases with age with phosphoryl choline
  • glycerophosphorylchlorine, glycerophosphorylethanolamine increase with age
  • choline reflects structural components of cell membranes (myelin sheaths)
  • membrane bound choline not visualized in MR
  • increased in highly cellular processes – high grade tumors, neurodegenerative disorders
  • focal inflammation -> marked local cellularity -> cell membrane breakdown -> elevated choline
  • seen higher in thalami and cerebellum > cerebral white matter > cerebral cortex

Creatine (Cr)

  • 3.03 ppm
  • methyl protons of creatine and phosphocreatine
  • minor contributions from gamma-amino butyrate, lysine and glutathione
  • second smaller peak at 3.94ppm
  • maintenance of energy dependent systems in all brain cells
  • cerebellum > thalami > basal ganglia > cortical gray matter > cortical white matter
  • stable in most situations; hence used as a standard for other metabolites


  • two peaks 3.56 ppm and 4.06 ppm
  • storage pool for membrane phosphoinositides – involved in hormonal systems and enzyme regulation
  • essential growth factor – precursor of phosphatidylinositol
  • located primary in glial cells – specific marker
  • osmoregulation, cell nutrition, detoxification
  • 3.56 ppm peak gets minor contributions from glycine and inositol-1-phosphate


  • singlet peak at 3.35 ppm
  • not from taurine as previously described

Cerebral glucose

  • singlet peak at 3.43 ppm with short TE
  • area under peak used as gross measurement of glucose concentration in brain


  • doublet peak 1.3 ppm (1.27 and 1.36 ppm)
  • trace amounts in appropriate for gestational age term neonates
  • more than trace amounts in first few hours of life indicate some form of brain injury
  • normal findings in CSF of premature and term neonates; concentration up to 2.7 mm/L
  • exclusion of CSF important to rule out false positivity in encephalopathy
  • propan-1,2-diol mimics doublet peak – it’s a solvent used in anti epileptics


  • 2.1 – 2.4 ppm region
  • second peak at 3.75 ppm alpha -CH moiety
  • excitatory neurotransmitter
  • seen in hypoxia, seizures, possible trauma
  • difficult to identify as it overlaps with NAA and Cr peaks; improves in higher magnetic fields

Macromolecular peaks

  • typical in short echo spectra in infants
  • between 0.5 and 1.0 ppm and between 1.0 and 1.6 ppm
  • methylene and methyl protons
  • no clinical significance if less than half peak of NAA
  • when large peaks – degenerative process
  • inborn errors of metabolism, child abuse in normal infants

Phosphodiester and phosphomonoesters

  • progressive decrease – good marker of infant brain development
  • high in preterm infants

Key spectral variations in different brain regions

  • NAA/Cr
    • brain stem and cerebellum > cerebral hemispheres
    • cerebral white matter > basal nuclei
    • frontal white matter > parietal white matter
  • Choline/Cr
    • Choline > Cr in white matter
    • Cr > choline in gray matter


Brain maturation and spectral variations

  • decreasing phosphomonoester peak
  • increasing phosphocreatine and phosphodiester peaks
  • increase in NAA relative to choline and creatine phosphocreatine peaks
  • diminishing myo-inositol peak
  • scyllo-inositol highest at birth
*adapted from pediatric neuroimaging textbook – Barkowich