A structural tissue water fraction phantom derived from electron microscopy for simulation-based evaluation in MRI

Quantifying myelin is essential for understanding demyelinating disease, yet myelin water fraction (MWF) varies across studies due to sequence choice, acquisition parameters, and field inhomogeneities. A major limitation is the lack of a phantom with a known structural reference. This study aimed to develop an electron microscopy (EM)-derived numerical MRI phantom representing structural tissue water fractions and to evaluate how acquisition and field conditions influence simulated MWF estimates. Here, simulated MWF refers to the short-T₂ component recovered from EM-derived structural fractions and should be distinguished from in-vivo biological MWF.

EM images of CNS tissue were segmented into myelin, axons, and intra-/extracellular water (29%, 41%, 30%). Relaxation times were assigned from the literature, and simulated MWF was defined as the short-T₂ component estimated using non-negative least squares. Multi-echo spoiled gradient echo signals were simulated across TR, flip angle, and synthetic B₀/B₁ inhomogeneity.

The phantom produced compartment-specific decay curves and enabled controlled evaluation of acquisition-dependent behavior. MWF increased with flip angle, decreased with longer TR, and showed systematic bias under B₀/B₁ variation. The framework further visualized mixing among compartments and sensitivity to relaxation- and field-driven changes.

This tissue water fraction phantom provides a structural ground truth for reproducible evaluation of simulated MWF and supports optimization and future methodological standardization of quantitative MRI.