Typical diffusion-weighted imaging (DWI) is susceptible to partial volume effects: different types of tissue that reside in the same voxel are inextricably mixed. For instance, in regions near the cerebral ventricles or parenchyma, fractional anisotropy (FA) from diffusion tensor imaging (DTI) may be underestimated, due to partial volumes of cerebral spinal fluid (CSF). Free-water can be suppressed by adding parameters to diffusion MRI models. For example, the DTI model can be extended to separately take into account the contributions of tissue and CSF, by representing the tissue compartment with an anisotropic diffusion tensor and the CSF compartment as an isotropic free water diffusion coefficient. Recently, two procedures were proposed to fit this two-compartment model to diffusion-weighted data acquired for at least two different non-zero diffusion MRI b-values. In this work, the first open-source reference implementation of these procedures is provided. In addition to presenting some methodological improvements that increase model fitting robustness, the free water DTI procedures are re-evaluated using Monte-Carlo multicompartmental simulations. Analogous to previous studies, our results show that the free water elimination DTI model is able to remove confounding effects of fast diffusion for typical FA values of brain white matter. In addition, this study confirms that for a fixed scanning time the fwDTI fitting procedures have better performance when data is acquired for diffusion gradient direction evenly distributed along two b-values of 500 and 1500 s/mm2.
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