CG‐SENSE revisited: Results from the first ISMRM reproducibility challenge

The aim of this work is to shed light on the issue of reproducibility in MR image reconstruction in the context of a challenge. Participants had to recreate the results of “Advances in sensitivity encoding with arbitrary k‐space trajectories" by Pruessmann et al.

[1]  Victoria Stodden,et al.  Reproducible Research , 2019, The New Statistics with R.

[2]  Tobias Knopp,et al.  MPIReco.jl: Julia Package for Image Reconstruction in MPI , 2019 .

[3]  Frank Ong,et al.  Accelerating Non-Cartesian MRI Reconstruction Convergence Using k-Space Preconditioning , 2019, IEEE Transactions on Medical Imaging.

[4]  K. Cranmer,et al.  Open is not enough , 2018, Nature Physics.

[5]  Jyh-Miin Lin,et al.  Python Non-Uniform Fast Fourier Transform (PyNUFFT): An Accelerated Non-Cartesian MRI Package on a Heterogeneous Platform (CPU/GPU) , 2018, J. Imaging.

[6]  M. Baker.  1,500 scientists lift the lid on reproducibility , 2016, Nature.

[7]  Nicolas P. Rougier,et al.  A long journey into reproducible computational neuroscience , 2015, Front. Comput. Neurosci..

[8]  Alan Edelman,et al.  Julia: A Fresh Approach to Numerical Computing , 2014, SIAM Rev..

[9]  Michael Elad,et al.  ESPIRiT—an eigenvalue approach to autocalibrating parallel MRI: Where SENSE meets GRAPPA , 2014, Magnetic resonance in medicine.

[10]  R. Peng.  Reproducible Research in Computational Science , 2011, Science.

[11]  Shuo Zhang,et al.  Nonlinear inverse reconstruction for real‐time MRI of the human heart using undersampled radial FLASH , 2010, Magnetic resonance in medicine.

[12]  K. T. Block,et al.  Advanced Methods for Radial Data Sampling in Magnetic Resonance Imaging , 2008 .

[13]  T. Hohage,et al.  Image reconstruction by regularized nonlinear inversion—Joint estimation of coil sensitivities and image content , 2008, Magnetic resonance in medicine.

[14]  Carl E. Rasmussen,et al.  The Need for Open Source Software in Machine Learning , 2007, J. Mach. Learn. Res..

[15]  Dwight G. Nishimura,et al.  Rapid gridding reconstruction with a minimal oversampling ratio , 2005, IEEE Transactions on Medical Imaging.

[16]  Eero P. Simoncelli,et al.  Image quality assessment: from error visibility to structural similarity , 2004, IEEE Transactions on Image Processing.

[17]  Jeffrey A. Fessler,et al.  Nonuniform fast Fourier transforms using min-max interpolation , 2003, IEEE Trans. Signal Process..

[18]  P. Boesiger,et al.  Advances in sensitivity encoding with arbitrary k‐space trajectories , 2001, Magnetic resonance in medicine.

[19]  D. O. Walsh,et al.  Adaptive reconstruction of phased array MR imagery , 2000, Magnetic resonance in medicine.

[20]  P. Boesiger,et al.  SENSE: Sensitivity encoding for fast MRI , 1999, Magnetic resonance in medicine.

[21]  Steven G. Johnson,et al.  FFTW: an adaptive software architecture for the FFT , 1998, Proceedings of the 1998 IEEE International Conference on Acoustics, Speech and Signal Processing, ICASSP '98 (Cat. No.98CH36181).

[22]  J. Shewchuk.  An Introduction to the Conjugate Gradient Method Without the Agonizing Pain , 1994 .

[23]  Dianne P. O'Leary,et al.  The Use of the L-Curve in the Regularization of Discrete Ill-Posed Problems , 1993, SIAM J. Sci. Comput..

[24]  Gene H. Golub,et al.  Generalized cross-validation as a method for choosing a good ridge parameter , 1979, Milestones in Matrix Computation.

[25]  L. Bluestein.  A linear filtering approach to the computation of discrete Fourier transform , 1970 .

[26]  J. Tukey,et al.  An algorithm for the machine calculation of complex Fourier series , 1965 .

[27]  Kazem Taghva,et al.  The State of Reproducible Research in Computer Science , 2020 .

[28]  J. Tukey,et al.  An Algorithm for the Machine Calculation of , 2016 .

[29]  Daniel K Sodickson,et al.  gpuNUFFT - An Open Source GPU Library for 3D Regridding with Direct Matlab Interface , 2014 .

[30]  M. Lustig,et al.  Fast Non-Cartesian Reconstruction with Pruned Fast Fourier Transform , 2014 .

[31]  Jim X. Chen,et al.  Geographic Information Systems , 2010, Computing in Science & Engineering.

[32]  Jonathan Richard Shewchuk,et al.  A Compiler for Parallel Finite Element Methods with Domain-Decomposed Unstructured Meshes , 1993 .

[33]  Jon F. Claerbout,et al.  Electronic documents give reproducible research a new meaning: 62nd Ann , 1992 .

[34]  A. Macovski,et al.  Selection of a convolution function for Fourier inversion using gridding [computerised tomography application]. , 1991, IEEE transactions on medical imaging.

[35]  P. Hansen.  Rank-Deficient and Discrete Ill-Posed Problems: Numerical Aspects of Linear Inversion , 1987 .

[36]  J. D. O'Sullivan,et al.  A Fast Sinc Function Gridding Algorithm for Fourier Inversion in Computer Tomography , 1985, IEEE Transactions on Medical Imaging.

[37]  A. N. Tikhonov,et al.  Solutions of ill-posed problems , 1977 .