Myelin water fraction (MWF) mapping provides information on myelin concentration, which can be affected by neurological diseases. Most commonly, a non-negative least squares (NNLS) algorithm is used to obtain MWF. A faster alternative is the Sparsity Promoting Iterative Joint NNLS (SPIJN) algorithm. Here, we compared both methods in several brain regions from healthy participants and normal-appearing and lesion tissue from MS patients (EDSS 0-1.5). We found that NNLS-based lesion-average MWF was rather comparable to white matter while SPIJN-based MWF was lower. Thus, SPIJN could be more sensitive to demyelination in lesions but comparisons to gold standard techniques are clearly needed.