Imaging module

Introduction

Spinach contains a very general implementation of the Fokker-Planck formalism that is able to treat 3D diffusion and hydrodynamics simultaneously with Liouville-space spin dynamics, relaxation and chemical kinetics. This is a result of our in-house research, and it is dictated by the direction in which the field is moving: many emerging magnetic resonance methods (ultrafast NMR, singlet state imaging, spatially encoded NMR, metabolite-selective MRI, catalyst MRI, hyperpolarised imaging, etc.) fall in between the established simulation frameworks: on the one hand, they require accurate simulation of three-dimensional diffusion, hydrodynamics and chemical processes; on the other, it is essential that the spin evolution in every molecule is treated quantum mechanically in a way that accurately describes spin relaxation processes. At the same time, sophisticated spatially and temporally modulated radiofrequency pulses must be accounted for. Within the Fokker-Planck formalism, things like three-dimensional diffusion, hydrodynamics and off-resonance radiofrequency appear in a very simple way – each of these is just another constant matrix to add to the background evolution Hamiltonian.

Setting up the imaging context

{:imaging.m}

Pre-programmed pulse sequences

basic_1d_hard.m - basic 1D imaging with a hard pulse and a gradient

cpmg_dec.m - CPMG echo train epi_2d.m - 2D (spatial) echo planar imaging sequence

epi_3d.m - Diffusion weighted 3D echo planar imaging pulse sequence.

fse.m - 2D (spatial) fast spin echo sequence

grad_echo.m - simple gradient echo pulse sequence

phase_enc_2d.m - 2D (spatial) phase encoded imaging.

phase_enc_3d.m - 3D (spatial) imaging with slice selection followed by phase-encoded acquisition

press_1d.m - 1D (spatial) PRESS sequence

press_2d.m - 2D (spatial) PRESS sequence

press_voxel_1d.m - voxel selection diagnostics for 1D (spatial) PRESS pulse sequence

press_voxel_2d.m - voxel selection diagnostics for 2D (spatial) PRESS pulse sequence

press_voxel_3d.m - voxel selection diagnostics for 2D (spatial) PRESS pulse sequence

slice_select_1d.m - slice selection diagnostics

spin_echo.m - simple spin echo pulse sequence

spiral.m - 2D (spatial) imaging with spiral readout

udd_dec.m - Uhrig Dynamic Decoupling (UDD) echo train

uhrig_times.m - timing sequence for UDD echo train

Other relevant functions

hydrodynamics.m - first derivative operators with respect to spatial coordinates.

ngridpts.m - estimates the minimum number of spatial grid points necessary to have a valid treatment of gradient driven experiments with explicit digitization of spatial dimensions.

v2fplanck.m - converts diffusion and velocity fields into Fokker-Planck operators.

Version 2.1, authors: Ilya Kuprov, Ahmed Allami, Maria Grazia Concilio