Eddy-current (EC) and motion effects in diffusion-tensor imaging (DTI) bias the estimation of quantitative diffusion indices, such as the fractional anisotropy. Both effects can be retrospectively corrected by registering the strongly distorted diffusion-weighted images to less-distorted T2-weighted images acquired without diffusion weighting. Two different affine spatial transformations are usually employed for this correction: slicewise and whole-brain transformations. However, a relation between estimated transformation parameters and EC distortions has not been established yet for the latter approach. In this study, a novel diffusion-gradient-direction-independent estimation of the EC field is proposed based solely on affine whole-brain registration parameters. Using this model, it is demonstrated that a more distinct evaluation of the whole-brain EC effects is possible if the through-plane distortion was considered in addition to the well-known in-plane distortions. Moreover, a comparison of different whole-brain registrations relative to a slicewise approach is performed, in terms of the relative tensor error. Our findings suggest that for appropriate intersubject comparison of DTI data, a whole-brain registration containing nine affine parameters provides comparable performance (between 0 and 3%) to slicewise methods and can be performed in a fraction of the time.