Table 1: Input parameters of RMS.

The guideline of setting up simulation parameters is based on (Fieremans and Lee, 2018). MT: magnetization transfer, PG: pulsed-gradient, t: diffusion time, δ: gradient pulse width, S/V: surface-to-volume ratio.

Voxel size	lp	< length scale in cell geometry (e.g., axon diameter, cell body size)
Intrinsic diffusivity	D0	~ 2 − 3 μm2/ms in vivo
Time for each step	δt	small enough such that P1→2 ⪡ 1, PMT ⪡ 1, and δs < lp
Total time	Tmax	> t for narrow PG, > (t + δ) for wide PG
Number of steps	Nstep	= ⌈Tmax/δt⌉, at least 1000 steps to lower discretization error
Number of particles	Npar	as many as possible within the given calculation time
Step size	δs	= $\sqrt{2d{D}_0\cdot \delta t}$, d = dimension (typically, d = 3)
Optional
Diffusion gradient	g(τ)	limited by maximal gradient strength, slew rate, and b-value
Permeability	κ
Surface relaxivity	ϱ
MT exchange rate	R	= ϱ · S/V
Relaxation time	T1/T2	~ 800/80 ms in brain white matter at 3T