Connectome 3t mr scanner

To observe the directionally averaged signal decay versus diffusion weighting b, simulations in realistic IAS are performed by applying 2.27 × 10⁷ random walkers in total diffusing over 1 × 10⁶ steps with a duration 2 × 10⁻⁴ and a length 0.049μm. The diffusion and gradient pulse width (t, δ) = (20. 7.1). (30,13) and (50.9,35.1) ms are chosen to match the experiments performed on animal 16.4T MR scanner (Bruker BioSpin), clinical 3T MR scanner (Siemens Prisma), and Siemens Connectome 3T MR scanner (Veraart et al., 2020 (link)). Diffusion signals are calculated based on the accumulated diffusional phase for each of 18 b-values =16–100 ms/μm² along 30 uniformly distributed directions for each b-shell. Total calculation time is ~ 2 days.
Directionally averaged signal ${\overline{S}}_i$ for individual axon was calculated by averaging diffusion signals of all directions for each b-shell, and the volume-weighted sum of all axons was also calculated:
$$\overline{S}=\frac{\sum _i{f}_i\cdot {\overline{S}}_i}{\sum _i{f}_i}.$$
The RD, D_⊥(t, δ), was estimated by fitting Eq. (27) to simulated ${\overline{S}}_i$ and $\overline{S}$ over the range b=55–100 ms/μm² for individual axons and for all axons, and the effective radius of wide pulse, r_{eff, WP}, was calculated based on estimated D_⊥ and Eq. (22) and compared with theoretical predictions in Eq. (23).