Core functionality of MRzero

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  • License: GNU Affero General Public License v3
  • Author: Jonathan Endres
  • Requires: Python >=3.10
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Project description

PyPI - Version

MRzero Core

The MRzero Core contains the core functionality of MRzero like MRI sequence building, simulation and reconstruction. MRzero Core does not force you to take any particular approach to e.g., reconstruction, as it targets easy integration in existing projects. Nevertheless, more tools can be added in the future if they helpful for the general application space.

🎉 1.0 release

Version 1.0 adds Pulseq 1.5 support and flips the sign convention of the simulated signal, so that it is now the complex conjugate of what previous versions returned. Reconstruction accordingly switches from fft to ifft.

See the FFT sign conventions page for details, and the CHANGELOG for the full list of changes. If anything else broke, please open an issue.

Usage

MRzero Core is written in Python, heavily relying on PyTorch for fast (GPU-) Tensor calculations. To improve performance, parts of the simulation are written in Rust and compiled for x86 Windows and Linux, other platforms are currently not supported.

Install with pip:

pip install MRzeroCore

The typical way of using it is like the following:

import MRzeroCore as mr0

Examples on how to use MR-zero can be found in the Playground.

Pulseq Integration

MRzero Core makes Pulseq simulation incredibly easy - simulate any .seq file in just one line:

import MRzeroCore as mr0

# Simulate any Pulseq file
seq = mr0.Sequence.import_file("your_sequence.seq")
signal = mr0.util.simulate(seq)  # That's it!

Key Features:

  • One-line simulation of any Pulseq .seq file
  • PyPulseq integration - write sequences in Python, simulate with MR-zero
  • Google Colab ready - 13+ ready-to-run examples
  • MATLAB ↔ Python workflow - create in MATLAB Pulseq, simulate in Python
  • No dependencies - fully self-contained Pulseq parser included
  • Scanner-ready export - export MR-zero sequences as .seq files

Try it now: Open In Colab

Links

Building from source

This assumes windows as host operating system. For building the python wheel, you need:

Building for Windows

maturin build --interpreter python

Building for Linux

docker run --rm -v <path-to-repo>/MRzero-Core:/io ghcr.io/pyo3/maturin build

Building the documentation

Install newest (beta) version of mdBook:

cargo install --git https://github.com/rust-lang/mdBook.git mdbook

Run a live-preview server:

# in the root directory:
mdbook serve documentation

Official builds

The python wheels hosted by PyPI is built as described above, and uploaded as following:

maturin upload target/wheels/MRzeroCore-{ version }-cp37-abi3-win_amd64.whl target/wheels/MRzeroCore-{ version }-cp37-abi3-manylinux_2_17_x86_64.manylinux2014_x86_64.whl -u <pypi-user> -p <pypi-pwd>

The documentation is built using readthedocs, which works the same as described above.

Project details

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  • License: GNU Affero General Public License v3
  • Author: Jonathan Endres
  • Requires: Python >=3.10
  • Provides-Extra: pp15
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