Spinverse: Differentiable Physics for Permeability-Aware Microstructure Reconstruction from Diffusion MRI

Diffusion MRI (dMRI) is sensitive to microstructural barriers, yet most existing methods either assume impermeable boundaries or estimate voxel-level parameters without recovering explicit interfaces. We present Spinverse, a permeability-aware reconstruction method that inverts dMRI measurements through a fully differentiable Bloch-Torrey simulator. Spinverse represents tissue on a fixed tetrahedral grid and treats each interior face permeability as a learnable parameter; low-permeability faces act as diffusion barriers, so microstructural boundaries whose topology is not fixed a priori (up to the resolution of the ambient mesh) emerge without changing mesh connectivity or vertex positions. Given a target signal, we optimize face permeabilities by backpropagating a signal-matching loss through the PDE forward model, and recover an interface by thresholding the learned permeability field. To mitigate the ill-posedness of permeability inversion, we use mesh-based geometric priors; to avoid local minima, we use a staged multi-sequence optimization curriculum. Across a collection of synthetic voxel meshes, Spinverse reconstructs diverse geometries and demonstrates that sequence scheduling and regularization are critical to avoid outline-only solutions while improving both boundary accuracy and structural validity.