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  • About Me
  • Real-time MRI
  • Image Reconstruction
  • Software
  • Publications
  • Software

    Software Toolbox and Programming Library for Compressed Sensing and Parallel Imaging

    Martin Uecker, Patrick Virtue, Frank Ong, Mark J. Murphy, Marcus T. Alley, Shreyas S. Vasanawala, Michael Lustig

    The high complexity of advanced algorithms presents challenges for research and clinical application of new reconstruction methods. While researchers need flexible and interactive tools, clinical evaluation and application require robust and highly efficient implementations. Here, we present a framework for image reconstruction which 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 selected iterative optimization algorithms. The command-line tools provide direct access to basic operations on multi-dimensional arrays as well as efficient implementations of selected iterative reconstruction algorithms.

    Figure: Sagittal section of a human knee acquired with an 3D-FSE sequence and reconstructed with L1-ESPIRiT.

    Usage Examples

    The toolbox can be used in combination with Matlab/Octave. In our examples the tools are called directly from Matlab which is used for image display.

    Download

    C/C++ source code (for Linux and MacOS X): recon_v0.1.10.tgz

    Examples: examples_2014-04-23.tgz (5.5 MB)

    References

    Martin Uecker, Patrick Virtue, Frank Ong, Mark J. Murphy, Marcus T. Alley, Shreyas S. Vasanawala, 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)

    Nonlinear Inversion and Real-time MRI

    Unless otherwise noted, the following source code was written by me while working at the Biomedizinische NMR Forschungs GmbH. It is provided here for scientific use only. Please note that the source code comes without any warranty!

    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: NLINV

    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 (6): 1456-1462 (2010)

    Matlab code: RTNLINV

    Nonlinear Inversion for Real-time MRI with Temporal Regularization

    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: RTNLINV2 Example: heart movie

    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: IRGNTV (by Florian Knoll and Christian Clason, TU Graz)

    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: MARTINI (by Tilman J. Sumpf)

    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) arXiv:1301.1215 [cs.DC]

    C++/CUDA code: MGPU (by Sebastian Schätz)

    Related Software Projects

    Other image reconstruction software and related projects:

    Michael Lustig's Software

    Jeffrey A. Fessler's Image Reconstruction Toolbox

    AGILE - Library for GPU accelerated reconstruction problems in medical imaging

    MRI Unbound - MRI Pulse sequence design and reconstruction source code

    Gadgetron - Framework for medical image reconstruction

    Codeare - MRI image reconstruction and sequence runtime interaction

    IMPATIENT - Iterative MR image reconstruction using Graphics Processing Units

    BiomedNMR - Technical developments