SpinDoctor：扩散模拟的Matlab工具箱MRI
SpinDoctor: a Matlab toolbox for diffusion MRI simulation
摘要：
非均匀介质中扩散编码磁场梯度脉冲作用下水质子的复杂横向磁化可以用多室Bloch-Torrey偏微分方程（BTPDE）来模拟。利用均匀化技术，在BTPDE上建立了一个与时间相关的表观扩散系数（ADC）的数学模型，称为H-ADC模型。在假设隔室之间的水交换可忽略不计的情况下，H-ADC模型从受时间依赖的Neumann边界条件约束的扩散方程（DE）的解产生扩散介质的ADC。本文描述了一个名为SpinDoctor的公开可用Matlab工具箱，可用于1）求解BTPDE以获得dMRI信号（该工具箱提供了一种稳健拟合dMRI信号以获得拟合ADC的方法）; 2）求解H-ADC模型的DE以获得ADC; 3）工具箱中还包括ADC的短时近似公式，用于与模拟ADC进行比较。偏微分方程的P1有限元求解结合内置的Matlab程序求解常微分方程。有限元网格生成使用工具箱中包含的称为Tetgen的外部软件包执行。SpinDoctor提供了内置选项，包括1）具有细胞核的球形细胞; 2）具有髓鞘层的圆柱形细胞; 3）封闭在a）盒子中或b）紧紧包裹细胞的细胞外空间（ECS）; 4）通过弯曲和扭曲变形典型细胞。5)BT-PDE的渗透膜（H-ADC假设渗透性可忽略不计）。内置扩散编码脉冲序列包括脉冲梯度自旋回波和振荡梯度自旋回波。
英文摘要：
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 apparent diffusion coefficient (ADC), called the H-ADC model, was obtained recently using homogenization techniques on the BTPDE. Under the assumption of negligible water exchange between compartments, the H-ADC model produces the ADC of a diffusion medium from the solution of a diffusion equation (DE) subject to a time-dependent Neumann boundary condition. This paper describes a publicly available Matlab toolbox called SpinDoctor that can be used 1) to solve the BTPDE to obtain the dMRI signal (the toolbox provides a way of robustly fitting the dMRI signal to obtain the fitted ADC); 2) to solve the DE of the H-ADC model to obtain the ADC; 3) a short-time approximation formula for the ADC is also included in the toolbox for comparison with the simulated ADC. The PDEs are solved by P 1 finite elements combined with build-in Matlab routines for solving ordinary differential equations. The finite element mesh generation is performed using an external package called Tetgen that is included in the toolbox. SpinDoctor provides built-in options of including 1) spherical cells with a nucleus; 2) cylindrical cells with a myelin layer; 3) an extra-cellular space (ECS) enclosed either a) in a box or b) in a tight wrapping around the cells; 4) deformation of canonical cells by bending and twisting. 5) permeable membranes for the BT-PDE (the H-ADC assumes negligible permeability). Built-in diffusion-encoding pulse sequences include the Pulsed Gradient Spin Echo and the Oscilating Gradient Spin Echo.
机构、总结、中文摘要均由AI分析而来，可能存在错误，请以论文正文为准。
