The AFI sequence is a robust flip angle mapping method and is used within quantitative MRI protocols. AFI is a modified spoiled gradient echo (SPGR) sequence, employing interleaved TR times of different lengths. It is well known that SPGR signal behaviour is sensitive to Magnetization Transfer effects, so in this work we used a two-pool model to derive signal equations for AFI that include MT. We found that MT will lead to an underestimation of flip angle by up to 6% in white matter and that longer TR and lower RF energy lead to larger bias.
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