BMCTool 0.3.0

A python tool to perform Bloch-McConnell (BMC) simulations.

Bloch-McConnell (BMC) Simulation Tool

This repository contains a purely python-based Bloch-McConnell (BMC) simulation tool that can be used to simulate the evolution of the magnetization in various (exchanging) magnetic environments ('pools') under arbitrary radio-frequency (RF) irradiation. The tool was developed to simulate Chemical Exchange Saturation Transfer (CEST) or related spectra, but can be used for many other MR simulations as well.

The BMCTool utilizes the pulseq open file format to define and store all events (RF pulses, gradients, delays, ADCs) that shall be simulated. The scanner settings and characteristic properties of the magnetic environments (relaxation times, pool size fractions, exchange rates) are defined and stored in config-files in the YAML file format.

Every simulation requires exactly one seq-file (containing all events) and at least one config-file.

Installation

The BMCTool can be installed from PyPi using

pip install bmctool

Please keep in mind that the BMCTool is still in it's initial development and changes to the code might happen quite often. Thus, for the moment, we recommend cloning the latest version from the BMCTool GitHub repository using

git clone https://github.com/schuenke/BMCTool.git

and carefully tracking any changes/commits.

Initial Test

To make sure that the installation was successful, you can run an example simulation that is provided with both, the installation using pip and GitHub. To run the simulation, simply execute the simulate.py file or run the following code:

from bmctool.simulate import simulate
simulate()

When no *.seq and *.yaml files are defined, the simulation uses the WASABI.seq and config_wasabi.yaml example files. The generated plot should look like this:

(CEST) Config and Seq-File Library

All simulations using the BMCTool (or the pulseq-cest project) require a yaml file that includes all simulation settings and a seq file, which defines the events to be simulated. An example seq-file and an example yaml file can be found in the library subfolder. The BMCTool GitHub repository further contains some example files to create your own seq-files.

Pulseq-CEST Project

The BMCTool was developed in parallel to the pulseq-cest project that aims to provide published and approved CEST saturation blocks in the pulseq open file format to enable an exact comparison of CEST saturation blocks with newly developed or adapted saturation blocks for reproducible research. The pulseq-cest project provides a MATLAB implementation and a python implementation that both use the same Bloch-McConnell equation solver implemented in C++.

Pulseq-CEST Library

You will find several pre-defined and approved CEST pre-saturation schemes and simulation configs in the pulseq-cest-library GitHub repository. You can clone the library using

git clone https://github.com/kherz/pulseq-cest-library.git

or directly download the latest version as a ZIP file.