6.2019 - Implementing the HEART Module in SpinDoctor (a Matlab toolbox for diffusion MRI simulation)

The complex transverse water proton magnetization subject to diffusion-encoding magnetic field gradient pulses in a heterogeneous medium can be modeled by the multiple compartment Bloch-Torrey equation. The total magnetization in a voxel is the diffusion MRI signal. We have developed a Matlab toolbox called SpinDoctor that solves the Bloch-Torrey equation; the space discretization uses P1 finite elements and the time discretiztion uses build-in Matlab routines for solving ordinary differential equations.

SpinDoctor was developed for modeling diffusion MRI for the brain. The modeling of diffusion MRI for moving and deforming organs such as the heart is more challenging due to significant motion and deformation of the imaged medium during the signal acquisition. Recently, a mathematical formulation of the Bloch-Torrey equation that accounts for motion and deformation was published and we have implemented the numerical solution of this new equation using finite elements.

The intern will
1. Improve an existing code that solves the Bloch-Torrey equation in moving and deforming domains;
2. Publish the above code as the HEART Module inside SpinDoctor on GibHub;
3. Help prepare the User Manual for the HEART Module;
4. Help prepare a scientific article about the HEART Module;