Diffusion MRI data acquisition and preprocessing

Diffusion MRI images (repetition time: 7748 ms, echo time: 86 ms, flip angle: 90°, field of view: 224 × 224 mm, resolution: 2 mm isotropic, 64 directions, b-values: 0, 1000 s/mm², 75 axial slices) were collected from each participant. FSL (fsl.fmrib.ox.ac.uk) was used for all diffusion MRI data analyses (Smith et al., 2004; Woolrich et al., 2009; Jenkinson et al., 2012). The diffusion data were first corrected for eddy currents, then for head motion using an affine registration, then the brain was extracted (Smith et al., 2004). This was then used as input in two different procedures: (i) DTIFIT to calculate fractional anisotropy maps; and (ii) custom written MATLAB (R2013a, The Mathworks, Natick, MA, USA) code (Pasternak et al., 2009) to calculate free water and free-water-corrected fractional anisotropy maps (FA_T), which was consistent with prior work (Pasternak et al., 2009; Ofori et al., 2015). To obtain a standardized space representation of the free water and FA_T maps, the original fractional anisotropy map was registered to the FMRIB FA template in standard space (1 mm isotropic) by a non-linear warp using the Advanced Normalization Tools (ANTs) package (Avants et al., 2008).