Standard algorithms provided by various MR vendors are often quite rudimentary, based on simple peak integration supplemented by minor baseline correction and fitting. There is often no correction for frequency-shifts differences of the metabolites. A spatial filter is typically applied to provide a smooth topography and avoid a pixelated appearance.
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Most vendor-supplied mapping schemes are very rudimentary and simply assign resonances based on frequency ranges. For example, NAA might be assigned 2.02 ± 0.08 ppm while Cho is defined as all pixels in the 3.24 ± 0.08 ppm range. "Concentrations" may be alternately defined as the sum, average, or peak pixel values for a given metabolite range. A rainbow color scale is commonly used for display, but the values are arbitrarily chosen and should not be used to make strong comparisons about various anatomic regions or to assess changes in metabolite levels between different studies.
Crane JC, Olson MP, Nelson SJ. SIVIC: Open-source, standards-based software for DICOM MR spectroscopy workflows. Int J Biomed Imaging 2013, Article ID 169526:1-12.
Maudsley AA, Darkazanli A, Alger JR, et al. Comprehensive processing, display, and analysis for in vivo MR spectroscopic imaging. NMR Biomed 2006; 19:492-503.
What do the peaks seen in routine brain MRS represent?