lamyj / sycomore

MRI simulation toolkit

Sycomore — an MRI simulation toolkit

Sycomore is an MRI simulation toolkit providing isochromat simulation and Extended Phase Graph (EPG). Sycomore is a Python packge in which all computationnaly-intensive operations are run by a C++ backend, providing a very fast runtime.

Sycomore is free software, released under the MIT license, and its source code is available on GitHub.

Installation

Packaged versions of Sycomore are available on Anaconda for Linux, macOS and Windows.

To install from Anaconda, type conda install -c conda-forge sycomore. Additional details, including building from source, are provided in the documentation.

Usage

The following code simulates a single repetition of a simple RARE sequence using regular EPG and plots the transverse magnetization of each echo.

import numpy
import sycomore
from sycomore.units import *

species = sycomore.Species(1000*ms, 100*ms)
TE = 4*ms
train_length = 40

model = sycomore.epg.Regular(species)
signal = numpy.zeros(train_length, dtype=complex)

model.apply_pulse(90*deg)
for echo in range(train_length):
    model.apply_time_interval(TE/2)
    model.apply_pulse(180*deg)
    model.apply_time_interval(TE/2)
    
    signal[echo] = model.echo

The features and data structures are described in the documentation:

• Installing Sycomore
• Common features
• Isochromat Simulation
• Extended Phase Graph