![][julia-19] [![][gh-actions-komamri]][gh-actions-url] [![][buildkite-badge]][buildkite-url] [![][codecov-komamri]][codecov-url] [![][license]][license-url] [![][julia-blue]][julia-blue-url] [![][total-downloads-komamri]][downloads-komamri-url]
[![][docr-img]][docr-url] [![][docd-img]][docd-url] [![][paper-img]][paper-url]
KomaMRI.jl is a Julia package for highly efficient β‘ MRI simulations. KomaMRI was built from the ground up to be: easy to use, extensible, cross-platform, and powered by open-source community standards.
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Features: |
- Fast simulations with CPU/GPU parallelization ππ¨
- Extensible, so anyone can include new features π
- Supports community-standards [π€](## "Pulseq and ISMRMRD")
- Interactive visualizations using PlotlyJS.jl π²
- Cross-platform (Windows, Mac & Linux) π
- Friendly GUI (using web technologies) π
- Compatible with modern notebooks [π](## "Pluto and Jupyter")
- Flexible API for advanced users π¨βπ»
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| **Packages** | **Stable Version** | **Build Status** | **Code Coverage** | **Downloads** |
|:------------------------------------------- |:---------------------------------------------|:--------------------------------------------|:--------------------------------------|:----------------------------------------------------|
| π¦ [KomaMRI.jl](## "User Interface") | [![][komamri-version]][komamri-juliahub] | [![][gh-actions-komamri]][gh-actions-url] | [![][codecov-komamri]][codecov-url] | [![][downloads-komamri]][downloads-komamri-url] |
| β π¦ [KomaMRIBase.jl](## "Custom Types") | [![][komabase-version]][komabase-juliahub] | [![][gh-actions-komabase]][gh-actions-url] | [![][codecov-komabase]][codecov-url] | [![][downloads-komabase]][downloads-komabase-url] |
| β π¦ [KomaMRICore.jl](## "Simulation") | [![][komacore-version]][komacore-juliahub] | [![][gh-actions-komacore]][gh-actions-url] | [![][codecov-komacore]][codecov-url] | [![][downloads-komacore]][downloads-komacore-url] |
| β π¦ [KomaMRIFiles.jl](## "Input/Output") | [![][komafiles-version]][komafiles-juliahub] | [![][gh-actions-komafiles]][gh-actions-url] | [![][codecov-komafiles]][codecov-url] | [![][downloads-komafiles]][downloads-komafiles-url] |
| β π¦ [KomaMRIPlots.jl](## "Plots") | [![][komaplots-version]][komaplots-juliahub] | [![][gh-actions-komaplots]][gh-actions-url] | [![][codecov-komaplots]][codecov-url] | [![][downloads-komaplots]][downloads-komaplots-url] |
News
☰ Roadmap
v1.0:
- [x] Phantom and Sequence data types,
- [x] Spin precession in gradient-only blocks (simulation optimization),
- [x] GPU acceleration using CUDA.jl,
- [x] RF excitation,
- [x] GPU accelaration of RF excitation,
- [x] Scanner data-type:
, etc.,
- [x] [Pulseq](https://github.com/imr-framework/pypulseq) IO,
- [x] Signal "Raw Output" dictionary ([ISMRMRD](https://ismrmrd.github.io/)),
- [x] [MRIReco.jl](https://magneticresonanceimaging.github.io/MRIReco.jl/latest/) for the reconstruciton,
- [ ] Documentation,
- [ ] [Auxiliary Pulseq functions](https://github.com/imr-framework/pypulseq/tree/master/pypulseq),
- [ ] Coil sensitivities,
- [ ] Cardiac phantoms and triggers.
- [ ]
decay,
Next:
- [ ] Diffusion models with Laplacian Eigen Functions,
- [ ] Magnetic susceptibility,
- [ ] Use [PackageCompiler.jl](https://julialang.github.io/PackageCompiler.jl/dev/apps.html) to build a ditributable core or app.
Installation
To install, just type ] add KomaMRI
in the Julia REPL or copy-paste the following into the Julia REPL:
pkg> add KomaMRI
For more information about installation instructions, refer to the section Getting Started of the documentation.
First run
KomaMRI.jl features a convenient GUI with predefined simulation inputs (i.e. Sequence
, Phantom
, and Scanner
). To launch the GUI, use the following command:
using KomaMRI
KomaUI()
Press the button that says "Simulate!" to do your first simulation :). Then, a notification will emerge telling you that the simulation was successful. In this notification, you can either select to (1) see the Raw Data or (2) to proceed with the reconstruction.
How to Contribute
KomaMRI exists thanks to all our contributors:
Want to be highlighted here? We welcome contributions from the community! If you're interested in contributing, please read our Contribution Guidelines for details on how to get started.
How to Cite
If you use this package, please cite our paper.
Plain Text:
Castillo-Passi, C, Coronado, R, Varela-Mattatall, G, Alberola-LΓ³pez, C, Botnar, R, Irarrazaval, P. KomaMRI.jl: An open-source framework for general MRI simulations with GPU acceleration. Magn Reson Med. 2023; 1- 14. doi: 10.1002/mrm.29635
BibTex:
@article{https://doi.org/10.1002/mrm.29635,
author = {Castillo-Passi, Carlos and Coronado, Ronal and Varela-Mattatall, Gabriel and Alberola-LΓ³pez, Carlos and Botnar, RenΓ© and Irarrazaval, Pablo},
title = {KomaMRI.jl: An open-source framework for general MRI simulations with GPU acceleration},
journal = {Magnetic Resonance in Medicine},
keywords = {Bloch equations, GPU, GUI, Julia, open source, simulation},
doi = {https://doi.org/10.1002/mrm.29635},
url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/mrm.29635},
eprint = {https://onlinelibrary.wiley.com/doi/pdf/10.1002/mrm.29635},
}
Tested compatibility
All parallel backends are tested on Linux (besides Apple silicon) using the latest stable release, Julia 1 (stable), and Julia 1.9 (compat).
| KomaMRICore | CPU | GPU (Nvidia) | GPU (AMD) | GPU (Apple) | GPU (Intel) |
|:---------------------|:-----------------------------------:|:-----------------------------------:|:--------------------------------:|:----------------------------------:|:----------------------------------:|
| Julia 1.9 | [![][cpu-compat]][buildkite-url] | [![][nvidia-compat]][buildkite-url] | [![][amd-compat]][buildkite-url] | [![][apple-compat]][buildkite-url] | [![][intel-compat]][buildkite-url] |
| Julia 1 | [![][cpu-stable]][buildkite-url] | [![][nvidia-stable]][buildkite-url] | [![][amd-stable]][buildkite-url] | [![][apple-stable]][buildkite-url] | [![][intel-stable]][buildkite-url] |
Single-threaded compatibility is tested in all major operating systems (OS).
| KomaMRI | CPU (single-threaded) |
|:---------------------|:-----------------------------------------:|
| Julia 1.9 (Windows) | [![][gh-actions-komamri]][gh-actions-url] |
| Julia 1.9 (Linux) | [![][gh-actions-komamri]][gh-actions-url] |
| Julia 1.9 (Mac OS) | [![][gh-actions-komamri]][gh-actions-url] |
| Julia 1 (Windows) | [![][gh-actions-komamri]][gh-actions-url] |
| Julia 1 (Linux) | [![][gh-actions-komamri]][gh-actions-url] |
| Julia 1 (Mac OS) | [![][gh-actions-komamri]][gh-actions-url] |
If you see any problem with this information, please let us know in a GitHub issue.