11.2018 - SpinDoctor: a Matlab toolbox for diffusion MRI simulation
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 partial differential equation (BTPDE). A mathematical model for the time-dependent effective diffusion coefficient, called the H-ADC model, was obtained recently using homogenization techniques. The effective diffusion coefficient of the medium can be computed after solving a diffusion equation (DE) subject to a time-dependent Neumann boundary condition, under the assumption of negligible water exchange between compartments.
This project concerns a Matlab toolbox called SpinDoctor that can be used 1) to solve the BTPDE to obtain the dMRI signal; 2) to solve the DE to obtain the time-dependent effective diffusion coefficient; SpinDoctor provides build-in examples of 1) ellipsoid cells with the option of inserting a nucleus; 2) cylindrical cells with the option of including a myelin layer; 3) enclosing the cells in a computational box is also allowed. The space discretization is by P1 finite elements and the time discretiztion uses build-in Matlab routines for solving ordinary differential equations.
The intern will improve the code of this toolbox and help prepare the User Manual. The toolbox can be found at GitHub: https://github.com/jingrebeccali/SpinDoctor The class project used some code from this toolbox to solve the diffusion equation, so the intern should have some experience already with this toolbox.
Specifically: the intern will
1. run many 3-dimensional examples using this toolbox.
2. save the computational times and compute the errors of the solutions.
3. make plots and figures for the User Manual.
4. make changes to the code in order to make it more user-friendly.