In the spirit of reproducible research we try to provide source code for most of our algorithms.
Disclaimer: Please note that the source code comes without any warranty!

Berkeley Advanced Reconstruction Toolbox

Most of our software development activities are based on our BART Toolbox for image reconstruction in MRI. In the list below the color orange indicates fully reproducible numerical experiments using BART.

For the following list of reference implementations and examples please respect the copyright of the respective authors and the licence conditions. If not noted otherwise, the code ist provided for scientific use only.

SSA-FARY

Sebastian Rosenzweig, Nick Scholand, H. Christian M. Holme, Martin Uecker. Cardiac and Respiratory Self-Gating in Radial MRI using an Adapted Singular Spectrum Analysis (SSA-FARY). IEEE Transactions on Medical Imaging. 2020;39:3029-3041.

Examples for BART (by Sebastian Rosenzweig)

Introduction Video (slides) (by Sebastian Rosenzweig)

RING

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 81:1898-1906 (2019)

Examples for BART (by Sebastian Rosenzweig)

Introduction Video (slides) (by Sebastian Rosenzweig)

ESPIRiT

VCC-ESPIRiT

Martin Uecker and Michael Lustig, Estimating Absolute-Phase Maps Using ESPIRiT and Virtual Conjugate Coils, Magnetic Resonance in Medicine, 77:1201-1207 (2017)

Examples for BART (by Martin Uecker)

ESPIRiT

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)

Examples for BART (by Martin Uecker)

Matlab code (by Michael Lustig)

Nonlinear Inverse Reconstruction

Extended Nonlinear Inversion Inspired by ESPIRiT (ENLIVE)

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, Scientific Reports 9:3034 (2019) [open access] arXiv:1706.09780 [physics.med-ph]

Examples for BART (by Christian Holme)

Nonlinear Inversion for Simultaneous Multi-Slice Imaging (SMS-NLINV)

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)

Examples for BART (by Sebastian Rosenzweig)

Introduction Video (slides) (by Sebastian Rosenzweig)

Nonlinear Inversion with Total Variation (IRGNTV)

Florian Knoll, Christian Clason, Kristian Bredies, Martin Uecker, and Rudolf Stollberger, Parallel Imaging with Nonlinear Reconstruction using Variational Penalties, Magnetic Resonance in Medicine, 67:34-41 (2012)

Matlab code (by Florian Knoll and Christian Clason, TU Graz)

Nonlinear Inversion for Real-time MRI with Temporal Regularization (RT-NLINV2)

Martin Uecker, Shuo Zhang, Dirk Voit, Alexander Karaus, Klaus-Dietmar Merboldt, and Jens Frahm, Real-time magnetic resonance imaging at 20 ms resolution, NMR in Biomedicine 23:986–994 (2010)

Matlab code (by Martin Uecker)

Example: heart movie

Nonlinear Inversion for Real-time MRI (RT-NLINV)

Martin Uecker, Shuo Zhang, and Jens Frahm, Nonlinear Inverse Reconstruction for Real-time MRI of the Human Heart Using Undersampled Radial FLASH, Magnetic Resonance in Medicine 63:1456-1462 (2010)

Matlab code (by Martin Uecker)

Nonlinear Inversion (NLINV)

Martin Uecker, Thorsten Hohage, Kai Tobias Block, and Jens Frahm, Image Reconstruction by Regularized Nonlinear Inversion - Joint Estimation of Coil Sensitivities and Image Content, Magnetic Resonance in Medicine 60 (3): 674-682 (2008)

Matlab code (by Martin Uecker)

Model-based Reconstruction

Simultaneous Multi-Slice T1 Mapping with Model-Based Reconstruction

Xiaoqing Wang, Sebastian Rosenzweig, Nick Scholand, H.Christian M.Holme, Martin Uecker. Model-based Reconstruction for Simultaneous Multi-slice T1 Mapping using Single-shot Inversion-recovery Radial FLASH. Magn Reson Med. Early Access.

Examples for BART (by Xiaoqing Wang)

Model-based Reconstruction for myocardial T1 Mapping

Xiaoqing Wang, Florian Kohler, Christina Unterberg-Buchwald, Joachim Lotz, Jens Frahm, Martin Uecker. Model-based myocardial T1 mapping with sparsity constraints using single-shot inversion-recovery radial FLASH cardiovascular magnetic resonance. Journal of Cardiovascular Magnetic Resonancevolume 21:60 (2019)

Examples for BART (by Xiaoqing Wang)

Subspace reconstruction for frequency-modulated SSFP

Volkert Roeloffs, Sebastian Rosenzweig, H. Christian M. Holme, Martin Uecker, Jens Frahm. Frequency-modulated SSFP with radial sampling and subspace reconstruction: A time-efficient alternative to phase-cycled bSSFP. Magnetic Resonance in Medicine 81:1566-1579 (2019)

Examples for BART (by Volkert Roeloffs)

T2-Shuffling

Jonathan I. Tamir, Martin Uecker, Weitian Chen, Peng Lai, Marcus T. Alley, Shreyas S. Vasanawala, Michael Lustig, T2 Shuffling: Sharp, Multicontrast, Volumetric Fast Spin-Echo Imaging, Magnetic Resonance in Medicine, 77:180-195 (2017)

Matlab code (by Jonathan Tamir)

Model-based Reconstruction for T2 Mapping with a Generating Function (GF-MARTINI)

Tilman J. Sumpf, Andreas Petrovic, Martin Uecker, Florian Knoll, and Jens Frahm, Fast T2 Mapping with Improved Accuracy Using Undersampled Spin-echo MRI and Model-based Reconstructions with a Generating Function, IEEE Transactions on Medical Imaging, 33:2213-2222 (2014)

Matlab code (by Tilman J. Sumpf)

Model-based Reconstruction for T2 Mapping (MARTINI)

Tilman J Sumpf, Martin Uecker, Susann Boretius, and Jens Frahm, Model-based Nonlinear Inverse Reconstruction for T2 Mapping Using Highly Undersampled Spin-Echo MRI, Journal of Magnetic Resonance Imaging, 34:420-428 (2011)

Matlab code (by Tilman J. Sumpf)

Other Projects

Accelerated MRI Reconstruction Using Preconditioning in k-space

Frank Ong, Martin Uecker, Michael Lustig. Accelerating Non-Cartesian MRI Reconstruction Convergence using k-space Preconditioning. IEEE Transactions on Medical Imaging 39:1646-1654 (2020)

Python Notebooks (by Frank Ong)

4D-Flow Denoising Using Divergence-free Wavelets

Frank Ong, Martin Uecker, Umar Tariq, Albert Hsiao, Marcus T. Alley, Shreyas S. Vasanawala, and Michael Lustig, Robust 4D Flow Denoising using Divergence-free Wavelet Transform, Magnetic Resonance in Medicine, 73:828-842 (2015)

Matlab code (by Frank Ong)

Multi-GPU Programming Library (MGPU)

Sebastian Schätz and Martin Uecker, A Multi-GPU Programming Library for Real-Time Applications, 12th International Conference on Algorithms and Architectures for Parallel Processing (ICA3PP-2012), Fukuoka 2012, In Lecture Notes in Computer Science, 7439:114-128 (2012)

C++/CUDA code (by Sebastian Schätz)