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Common analysis methods model the data as a linear combination of metabolite basis spectra. This large\u2010scale multi\u2010site study compares the levels of the four major metabolite complexes in short\u2010TE spectra estimated by three linear\u2010combination modeling (LCM) algorithms. 277 medial parietal lobe short\u2010TE PRESS spectra (TE = 35 ms) from a recent 3 T multi\u2010site study were preprocessed with the Osprey software. The resulting spectra were modeled with Osprey, Tarquin and LCModel, using the same three vendor\u2010specific basis sets (GE, Philips and Siemens) for each algorithm. Levels of total N\u2010acetylaspartate (tNAA), total choline (tCho), myo\u2010inositol (mI) and glutamate + glutamine (Glx) were quantified with respect to total creatine (tCr). Group means and coefficient of variations of metabolite estimates agreed well for tNAA and tCho across vendors and algorithms, but substantially less so for Glx and mI, with mI systematically estimated as lower by Tarquin. The cohort mean coefficient of determination for all pairs of LCM algorithms across all datasets and metabolites was \n<jats:inline-graphic xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" xlink:href=\"graphic\/nbm4482-math-0001.png\" xlink:title=\"urn:x-wiley:09523480:media:nbm4482:nbm4482-math-0001\"\/>= 0.39, indicating generally only moderate agreement of individual metabolite estimates between algorithms. There was a significant correlation between local baseline amplitude and metabolite estimates (cohort mean \n<jats:inline-graphic xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" xlink:href=\"graphic\/nbm4482-math-0002.png\" xlink:title=\"urn:x-wiley:09523480:media:nbm4482:nbm4482-math-0002\"\/>= 0.10).<\/jats:p><jats:p>While mean estimates of major metabolite complexes broadly agree between linear\u2010combination modeling algorithms at group level, correlations between algorithms are only weak\u2010to\u2010moderate, despite standardized preprocessing, a large sample of young, healthy and cooperative subjects, and high spectral quality. These findings raise concerns about the comparability of MRS studies, which typically use one LCM software and much smaller sample sizes.<\/jats:p>","DOI":"10.1002\/nbm.4482","type":"journal-article","created":{"date-parts":[[2021,2,6]],"date-time":"2021-02-06T02:53:13Z","timestamp":1612579993000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":86,"title":["Comparison of different linear\u2010combination modeling algorithms for short\u2010TE proton spectra"],"prefix":"10.1002","volume":"34","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-7148-292X","authenticated-orcid":false,"given":"Helge J.","family":"Z\u00f6llner","sequence":"first","affiliation":[{"name":"Russell H. Morgan Department of Radiology and Radiological Science The Johns Hopkins University School of Medicine  Baltimore Maryland USA"},{"name":"F. M. 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