Software

Programming Library and Software Toolbox 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_v0.1.7.tgz

Examples: examples_2013-07-07.tgz (5.4 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. Epub (2013)

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!

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)