janniklasrose / rwcdti

Random Walk for cardiac Diffusion Tensor Imaging

Random Walk for cardiac Diffusion Tensor Imaging

Compiling

The code is using MATLAB, but performance-critical functions have been written in C in the form of MEX functions. They need to be compiled to be available at runtime. To do this, execute compile.m inside MATLAB.

Running a simulation

To run a simulation, it is easiest to specify all parameters using a configuration file (using the YAML format). Example configuration files are provided in the config directory.

For small scale simulations with a low number of walkers, executing on a local machine (laptop/desktop) will be sufficient. If large scale jobs are desired, parallelisation is almost certainly required. The pbs.sh file should give an indication how to run these on the HPC cluster. For storing simulation data of significant size, it is best to use the more portable HDF5 format which is generally faster than using compressed MAT files.

Publication

Citation

If this software is useful to you, please consider citing the original paper:

Rose, JN, Nielles-Vallespin, S, Ferreira, P, Firmin, DN, Scott, AD, Doorly, DJ. Novel insights into in-vivo diffusion tensor cardiovascular magnetic resonance using computational modelling and a histology‐based virtual microstructure. Magn Reson Med. 2019; 81: 2759–2773. DOI:10.1002/mrm.27561

The tagged releases are archived on Zenodo.

Dataset

Simulation data (both input geometries and results) from the MRM paper is published here.