Diffusion simulator

Use datasynth command. Substrate can be one-diameter cylinders, gamma-dist cylinders, crossing cylinders, balls… Here you have a tuto : http://cmic.cs.ucl.ac.uk/camino/index.php?n=Tutorials.MCSimulator.

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 tuto for this option : http://cmic.cs.ucl.ac.uk/camino/index.php?n=Tutorials.MCMeshSimulation.

Advices

  • cylindersep must be at leat 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)