The Berkeley Advanced Reconstruction Toolbox (BART) toolbox is a free and open-source image-reconstruction
framework for Computational Magnetic Resonance Imaging
developed by the research groups of
(Göttingen University) and
It consists of a programming library and a toolbox of command-line programs. The library provides common operations on multi-dimensional
arrays, Fourier and wavelet transforms, as well as generic implementations of iterative optimization algorithms.
The command-line tools provide direct access to basic operations on multi-dimensional arrays as well
as efficient implementations of many calibration and reconstruction algorithms for parallel imaging and compressed sensing
Figure: l1-ESPIRiT reconstruction of a human abdomen (variable-density Poisson-disc
sampling, R=7, RF-spoiled 3D-FLASH, B0 = 3T TR/TE = 4.3/1.0ms, partial echo .6, matrix: 320x256x184, 32 channels)
Total reconstruction time: 51s including compression (14s), calibration (9s), iterative reconstruction (12s),
and other processing steps (16s) on a multi-GPU system.
List of Features
- basic features:
- runs on Linux and Mac OS X
- multi-dimensional operations on arrays
- fast non-uniform Fourier Transform (nuFFT and convolution-based method)
- multi-dimensional (divergence-free) wavelet transform
- parallel computation on multiple cores and with Graphical Processing Units (GPU)
- iterative methods:
- Conjugate Gradients (CG)
- (Fast) Iterative Soft-Thresholding Algorithm (ISTA and FISTA)
- Normalized iterative hard thresholding (NIHT)
- Alternating Direction Method of Multipliers (ADMM)
- Iteratively Regularized Gauss-Newton Method (IRGNM)
- Chambolle-Pock primal-dual algorithm
- calibration methods:
- direct calibration of coil sensitivities from k-space center
- Walsh's method for calibration of coil sensitivities
- (geometric) channel compression and whitening
- RING: estimation of gradient delays for radial MRI
- reconstruction methods for MRI:
- iterative parallel imaging reconstruction: POCSENSE, SENSE
- compressed sensing and parallel imaging
- calibration-less parallel imaging: NLINV and ENLIVE (non-linear optimization) and SAKE (structured low-rank matrix completion)
- regularization (in arbitrary dimensions):
- total variation
- (multi-scale) low-rank
Perform ESPIRiT calibration and image reconstruction with
$ bart ecalib kspace sensitivities
$ bart pics -l1 -r0.001 kspace sensitivities image_out
A python-based image viewer (bartview.py) which can read the
BART data format is included in the source repository.
An image viewer for Linux and Mac OS X can be found
Please direct all questions or comments to the public mailing list:
mrirecon list (public)
(or contact the main author: martin.uecker at med.uni-goettingen.de)
Note: The software is intended for research use only
and NOT FOR DIAGNOSTIC USE. It comes without any
warranty (see LICENSE for details).
It is recommended to download the latest release. All releases can be found here.
BART has also been included in Debian GNU/Linux (and Ubuntu). The
Debian binary package can be reproducibly built
from the source code (as distributed by Debian) and can be downloaded from here. There is also a package for the image viewer.
Please note that running BART on Windows is not supported. Nevertheless, some versions of BART are reported to work on Windows using WSL or Cygwin.
For developers: the C source code can be found in the GitHub repository
Installation of the required libraries, downloading and unpacking of the archive, and
compilation on Linux is usually as simple as typing the following commands:
$ sudo apt-get install make gcc libfftw3-dev liblapacke-dev libpng-dev libopenblas-dev
$ wget https://github.com/mrirecon/bart/archive/vX.Y.ZZ.tar.gz
$ tar xzvf vX.YY.ZZ.tar.gz
$ cd bart-X.YY.ZZ
See the README file included with the source code for further instructions and for Mac OS X and Windows.
If you are a Docker user you can also start with this extremely simple Dockerfile.
Matlab Interface and Examples
The toolbox can also be used in combination with Matlab/Octave.
>> sensitivities = bart('ecalib', kspace);
>> image_out = bart('pics -l1 -r0.001', kspace, sensitivities);
More examples where the tools are called
directly from Matlab can be found here.
Matlab code and data: GitHub repository
A Matlab-based image viewer which works well with BART is arrayShow by Tilman Sumpf.
Workshop Materials with Examples
The toolbox was presented at the ISMRM 2016 Data Sampling and Image Reconstruction Workshop. This material was created for BART version 0.3.00 and later versions might have minor differences. Please check the README included with each release for up-to-date installation instructions.
Demo code and data: GitHub repository
This is a list of research paper which can be fully reproduced using BART.
- Sebastian Rosenzweig, H. Christian M. Holme, Martin Uecker. Simple Auto-Calibrated Gradient Delay Estimation From Few Spokes Using Radial Intersections (RING). Magnetic Resonance in Medicine, DOI:10.1002/mrm.27506 (2018) GitHub repository
- H. Christian M. Holme, Sebastian Rosenzweig, Frank Ong, Robin N. Wilke, Michael Lustig, Martin Uecker.
ENLIVE: An Efficient Nonlinear Method for Calibrationless and Robust Parallel Imaging. submitted 2017, arXiv:1706.09780 [physics.med-ph] GitHub repository
- Sebastian Rosenzweig, H. Christian M. Holme, Robin N. Wilke, Dirk Voit, Jens Frahm, Martin Uecker. Simultaneous Multi-Slice Reconstruction Using Regularized Nonlinear Inversion: SMS-NLINV. Magnetic Resonance in Medicine 79:2057-2066 (2018) GitHub repository
- Martin Uecker and Michael Lustig. Estimating Absolute-Phase Maps Using ESPIRiT and Virtual Conjugate Coils. Magnetic Resonance in Medicine 77:1201-1207 (2017) GitHub repository
A a generic reference (all versions): BART Toolbox for Computational Magnetic Resonance Imaging, DOI: 10.5281/zenodo.592960
- Martin Uecker. Machine Learning Using the BART Toolbox - Implementation of a Deep Convolutional Neural Network for Denoising. Joint Annual Meeting ISMRM-ESMRMB, Paris 2018, In Proc. Intl. Soc. Mag. Reson. Med. 26;2802
- Jonathan I Tamir, Frank Ong, Joseph Y Cheng, Martin Uecker, and Michael Lustig. Generalized Magnetic Resonance Image Reconstruction using The Berkeley Advanced Reconstruction Toolbox. ISMRM Workshop on Data Sampling and Image Reconstruction, Sedona 2016
- Martin Uecker, Frank Ong, Jonathan I Tamir, Dara Bahri, Patrick Virtue, Joseph Y Cheng, Tao Zhang, and Michael Lustig.
Berkeley Advanced Reconstruction Toolbox. Annual Meeting ISMRM, Toronto 2015, In Proc. Intl. Soc. Mag. Reson. Med. 23:2486
- Martin Uecker, Patrick Virtue, Frank Ong, Mark J. Murphy, Marcus T. Alley, Shreyas S. Vasanawala, and Michael Lustig. Software Toolbox and Programming Library for Compressed Sensing and Parallel Imaging. ISMRM Workshop on Data Sampling and Image Reconstruction, Sedona 2013
- Martin Uecker, Peng Lai, Mark J. Murphy, Patrick Virtue, Michael Elad, John M. Pauly, Shreyas S. Vasanawala, and Michael Lustig. ESPIRiT - An Eigenvalue Approach to Autocalibrating Parallel MRI: Where SENSE meets GRAPPA. Magnetic Resonance in Medicine, 71:990-1001 (2014)