Diffusion Simulator

Use datasynth command. Substrate can be one-diameter cylinders, gamma-dist cylinders, crossing cylinders, balls. Here you have a tutorial: Monte Carlo Diffusion Simulator.

Basic commands:

datasynth -walkers 50000 -tmax 2000 -voxels 1 -p 0.0 -schemefile /home/django/tanguy/data/simulations/bvecs/patient_1.scheme  -initial uniform -substrate cylinder -packing hex -cylinderrad 2E-6 -cylindersep 4.1 > Diffusion.img
analyzeheader -datadims 1 1 1 -nimages 16 -voxeldims 1 1 1 -datatype float -outputfile Diffusion.hdr
fslchfiletype NIFTI Diffusion.img

You can choose the permeability of the barriers via p but not the thickness.

However, you can also build any kind of shape using a PLY file (3D object file). Here is a tutorial for this option: Monte-Carlo Mesh Simulation.

Recommendations

• cylindersep must be at least twice as big as cylinderrad (cylinders mustn’t overlap)

• Be very careful at high q-values (>0.14 um-1). You need lots of walkers (200 000), and time steps (-tmax 3000)