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https://github.com/lamyj/sycomore

MRI simulation toolkit
https://github.com/lamyj/sycomore

bloch-simulation configuration-mo diffusion epg extended-phase-graphs magnetization-transfer mri mri-simulation-toolkit simulation

Last synced: 2 months ago
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MRI simulation toolkit

Host: GitHub
URL: https://github.com/lamyj/sycomore
Owner: lamyj
License: mit
Created: 2019-07-29T05:36:52.000Z (over 5 years ago)
Default Branch: master
Last Pushed: 2023-12-05T10:42:12.000Z (about 1 year ago)
Last Synced: 2024-10-30T21:26:24.144Z (3 months ago)
Topics: bloch-simulation, configuration-mo, diffusion, epg, extended-phase-graphs, magnetization-transfer, mri, mri-simulation-toolkit, simulation
Language: C++
Homepage: https://sycomore.readthedocs.io/
Size: 6.87 MB
Stars: 29
Watchers: 6
Forks: 4
Open Issues: 0
Metadata Files:
- Readme: README.md
- Contributing: CONTRIBUTING.md
- License: LICENSE

Awesome Lists containing this project

README

        # Sycomore — an MRI simulation toolkit

[![Conda Version](https://img.shields.io/conda/vn/conda-forge/sycomore.svg)](https://anaconda.org/conda-forge/sycomore)

Sycomore is an MRI simulation toolkit providing [isochromat simulation](https://sycomore.readthedocs.io/en/latest/isochromat.html) and [Extended Phase Graph (EPG)](https://sycomore.readthedocs.io/en/latest/epg/index.html). 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.

```python

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

```

![T2 decay in RARE](docs/rare.png "T2 decay in RARE")

The features and data structures are described in the documentation:

- [Installing Sycomore](https://sycomore.readthedocs.io/en/latest/installation.html)

- [Common features](https://sycomore.readthedocs.io/en/latest/common_features.html)

- [Isochromat Simulation](https://sycomore.readthedocs.io/en/latest/isochromat.html)

- [Extended Phase Graph](https://sycomore.readthedocs.io/en/latest/epg/index.html)

[Anaconda]: https://anaconda.org/conda-forge/sycomore

[documentation]: https://sycomore.readthedocs.io/en/latest/installation.html

[GitHub]: https://github.com/lamyj/sycomore/

[MIT license]: https://en.wikipedia.org/wiki/MIT_License

[RARE sequence]: https://doi.org/10.1002/mrm.1910030602

[regular EPG]: https://sycomore.readthedocs.io/en/latest/epg/regular.html