Scanner upgrades are a persistent but important problem when conducting MRI research studies. Systematic differences introduced by a scanner upgrade can have undesirable effects on the conclusions of a study. Quantitative tissue microstructure measurements by diffuson tensor imaging (DTI) can be affected by systematic differences in noise floor effects. Noise floor effects are due to rectification of signal by magnitude reconstruction than can, in turn, bias microstructure measurements. A retrospective correction that accounts for noise statistics is proposed to limit systematic differences in DTI measurements across scanner upgrades. A practical measure, signal to noise floor ratio (SNFR) is proposed to determine the conditions under which the retrospective correction works effectively.