<commit_before>

SENSE:

<NAME>, <NAME>, <NAME>, <NAME>. SENSE: Sensitivity
encoding for fast MRI. Magn Reson Med 1999; 42:952-962.

<NAME>, <NAME>, <NAME>, <NAME>. Advances in sensitivity
encoding with arbitrary k-space trajectories. 
Magn Reson Med 2001; 46:638-651.



compressed sensing:

<NAME>, <NAME> and <NAME>, Sparse MRI: The application of
compressed sensing for rapid MR imaging. Magn Reson Med 2007,
58: 1182–1195.

Block KT, <NAME>, and <NAME>. Undersampled radial MRI with
multiple coils. Iterative image reconstruction using a total
variation constraint. Magn Reson Med 2007, 57: 1086-1098.




direct calibration:

<NAME>, <NAME>, <NAME>, Price MD, <NAME>.
Self-calibrating parallel imaging with automatic coil sensitivity
extraction. Magn Reson Med 2002; 47:529-538.


ESPIRiT:

<NAME>, <NAME>, <NAME>, <NAME>, <NAME>, <NAME>, <NAME>,
<NAME>. ESPIRiT - An Eigenvalue Approach to  Autocalibrating Parallel
MRI: Where SENSE meets GRAPPA. Magn Reson Med 2014; 71: 990-1001.


nonlinear inversion:

<NAME>, <NAME>, Block KT, <NAME>. Image reconstruction by
regularized nonlinear inversion—joint estimation of coil sensitivities
and image content. Magn Reson Med 2008; 60:674-682.


SAKE:

<NAME>, <NAME>, <NAME>, <NAME>, <NAME>, <NAME>,
Lustig M. Calibrationless Parallel Imaging Reconstruction Based on
Structured Low-Rank Matrix Completion. Magn Reson Med 2014; Epub

<NAME>, <NAME>, <NAME>, <NAME>, <NAME>. Robust Low-rank Matrix
Completion for sparse motion correction in auto calibration PI.
Annual Meeting ISMRM, Salt Lake City 2013,
In: Proc Intl Soc Mag Reson Med 21;2584


coil compression:

<NAME>, <NAME>, <NAME>, <NAME>, Du<NAME>. A software channel
compression technique for faster reconstruction with many channels.
Magn Reson Imaging 2008; 26:133-141.

<NAME>, <NAME>, <NAME>, <NAME>. Array compression for
MRI with large coil arrays. Magn Reson Med 2007, 57:1131-1139.

<NAME>, <NAME>, Vasanawala SS, <NAME>. Coil compression for
accelerated imaging with cartesian sampling. Magn Reson Med 2013;
69:571-582.

<NAME>, <NAME>, <NAME>. ESPIRiT-Based Coil Compression for
Cartesian Sampling,  Annual Meeting ISMRM, Salt Lake City 2013,
In: Proc Intl Soc Mag Reson Med 21:2657


divergence-free wavelets:

<NAME>, <NAME>, <NAME>, <NAME>, <NAME>, Vasanawala SS, <NAME>.
Robust 4D Flow Denoising using Divergence-free Wavelet Transform, 
Magn Reson Med 2015; 73: 828-842.

<commit_msg>references<commit_after>

- BART -

<NAME>, <NAME>, <NAME>, <NAME>, <NAME>, <NAME>, <NAME>, <NAME>.
Berkeley Advanced Reconstruction Toolbox.
Annual Meeting ISMRM, Toronto 2015,
In: Proc Intl Soc Mag Reson Med 23; 2486.

<NAME>, <NAME>, <NAME>, <NAME>, <NAME>, <NAME>, <NAME>.
Software Toolbox and Programming Library for Compressed Sensing and
Parallel Imaging,
ISMRM Workshop on Data Sampling and Image Reconstruction, Sedona 2013.




- sensitivity-encoded parallel imaging -
(commands: itsense, pocsense, bpsense, rsense, pics)


Ra JB and Rim CY.
Fast imaging using subencoding data sets from multiple detectors.
Magn Reson Med 1993; 30:142-145.

<NAME>, <NAME>, <NAME>, <NAME>.
SENSE: Sensitivity encoding for fast MRI.
Magn Reson Med 1999; 42:952-962.

<NAME>, <NAME>, <NAME>, <NAME>.
Advances in sensitivity encoding with arbitrary k-space trajectories.
Magn Reson Med 2001; 46:638-651.

Samsonov AA, Kholmovski EG, Parker DL, Johnson CR.
POCSENSE: POCS-based reconstruction for sensitivity encoded magnetic
resonance imaging.
Magn Reson Med 2004; 52:1397-1406.




- implementation of the non-uniform FFT -
(command: nufft, pics)


<NAME>.
A fast sinc function gridding algorithm for Fourier inversion in
computer tomography.
IEEE Trans Med Imaging 1985; 4:200-207.

<NAME>, <NAME>, <NAME>, <NAME>.
Selection of a convolution function for Fourier inversion using gridding.
IEEE Trans Med Imaging 1991; 3:473-478.

<NAME> and <NAME>.
Major speedup of reconstruction for sensitivity­encoding with arbitrary
trajectories.
Annual Meeting of the ISMRM, Glasgow 2001,
In: Proc Intl Soc Mag Reson Med 9; 767.

<NAME>, <NAME>, <NAME>, <NAME>.
Fast Non-Cartesian Reconstruction with Pruned Fast Fourier Transform.
Annual Meeting ISMRM, Toronto 2015,
In: Proc Intl Soc Mag Reson Med 23; 3639.




- methods for sensitivity calibration -
(commands: walsh, caldir, ecalib, ecaltwo)


<NAME>, <NAME>, <NAME>.
Adaptive reconstruction of phased array MR imagery.
Magn Reson Med 2000, 43:682-690.

<NAME>, <NAME>, <NAME>, <NAME>, <NAME>.
The Use of an Adaptive Reconstruction for Array Coil Sensitivity
Mapping and Intensity Normalization
Annual Meetig ISMRM, Honolulu 2002,
In: Proc Intl Soc Mag Reson Med 10; 2410.

McKenzie CA, Yeh EN, Ohliger MA, Price MD, Sodickson DK.
Self-calibrating parallel imaging with automatic coil sensitivity
extraction.
Magn Reson Med 2002; 47:529-538.

<NAME>, <NAME>, <NAME>, <NAME>.
ESPIRiT Reconstruction Using Soft SENSE.
Annual Meeting ISMRM, Salt Lake City 2013,
In: Proc Intl Soc Mag Reson Med 21; 127.

<NAME>, <NAME>, <NAME>, <NAME>, <NAME>, <NAME>, <NAME>,
<NAME>.
ESPIRiT - An Eigenvalue Approach to  Autocalibrating Parallel MRI:
Where SENSE meets GRAPPA.
Magn Reson Med 2014; 71:990-1001.




- joint estimation: nonlinear inversion, calibrationless -
(commands: nlinv, sake)


<NAME>, <NAME>, <NAME>, <NAME>.
Image reconstruction by regularized nonlinear inversion-joint estimation
of coil sensitivities and image content.
Magn Reson Med 2008; 60:674-682.

<NAME>, <NAME>, <NAME>, <NAME>, <NAME>.
Robust Low-rank Matrix Completion for sparse motion correction in auto
calibration PI.
Annual Meeting ISMRM, Salt Lake City 2013,
In: Proc Intl Soc Mag Reson Med 21; 2584.

<NAME>, <NAME>, <NAME>, <NAME>, <NAME>, <NAME>, <NAME>.
Calibrationless Parallel Imaging Reconstruction Based on Structured
Low-Rank Matrix Completion.
Magn Reson Med 2014; 72:959-970.




- coil compression -
(command: cc)


<NAME>, <NAME>, <NAME>, <NAME>.
Array compression for MRI with large coil arrays.
Magn Reson Med 2007, 57:1131-1139.

<NAME>, <NAME>, <NAME>, <NAME>, Du<NAME>.
A software channel compression technique for faster reconstruction
with many channels.
Magn Reson Imaging 2008; 26:133-141.

<NAME>, <NAME>, Vasanawala SS, <NAME>.
Coil compression for accelerated imaging with cartesian sampling.
Magn Reson Med 2013; 69:571-582.

<NAME>, <NAME>, <NAME>.
ESPIRiT-Based Coil Compression for Cartesian Sampling,
Annual Meeting ISMRM, Salt Lake City 2013,
In: Proc Intl Soc Mag Reson Med 21; 2657.




- compressed sensing MRI -
(commands: pocsense, rsense, pics)


<NAME>, <NAME>, and <NAME>.
Undersampled radial MRI with multiple coils. Iterative image
reconstruction using a total variation constraint.
Magn Reson Med 2007; 57:1086-1098.

<NAME>, <NAME> and <NAME>.
Sparse MRI: The application of compressed sensing for rapid MR imaging.
Magn Reson Med 2007; 58:1182-1195.

<NAME>, <NAME>, <NAME>, <NAME>, <NAME>, <NAME>.
Regularized sensitivity encoding (SENSE) reconstruction using
Bregman iterations.
Magn Reson Med 2009; 61:145-152.




- sparsity transforms, variational penalties, regularization -
(commands: cdf97, rof, lrmatrix, pocsense, rsense, pics)


<NAME>, <NAME>, <NAME>.
Nonlinear total variation based noise removal algorithms,
Physica D: Nonlinear Phenomena 1992; 60:259-268.

Figueiredo MAT and Nowak RD.
An EM algorithm for wavelet-based image restoration
IEEE Trans Image Process 2003; 12:906-916.

<NAME>, <NAME>, <NAME>, <NAME>, <NAME>, Vasanawala SS, <NAME>.
Robust 4D Flow Denoising using Divergence-free Wavelet Transform, 
Magn Reson Med 2015; 73:828-842.

<NAME>, <NAME>.
Beyond low rank + sparse: Multi-scale low rank matrix decomposition,
preprint 2015; arXiv:1507.08751.




- sampling schemes -
(commands: traj, poisson)


<NAME>, <NAME>, <NAME>, <NAME>, <NAME>.
An optimal radial profile order based on the Golden Ratio
for time-resolved MRI.
IEEE Trans Med Imaging 2007; 26:68-76.

<NAME>, <NAME>, <NAME>, <NAME>, <NAME>.
L1 SPIR-iT: Autocalibrating Parallel Imaging Compressed Sensing
Annual Meeting ISMRM, Honolulu 2009,
In: Proc Intl Soc Mag Reson Med 17; 379.




- acceleration with graphical processing units -
(commands: pocsense, rsense, nufft, pics)


<NAME>, <NAME>, <NAME>.
Nonlinear Inverse Reconstruction for Real-time MRI of the Human Heart
Using Undersampled Radial FLASH.
Magn Reson Med 2010; 63:1456-1462.

<NAME>, <NAME>, <NAME>, <NAME>, <NAME>, <NAME>.
Fast ℓ1-SPIRiT Compressed Sensing Parallel Imaging MRI: Scalable
Parallel Implementation and Clinically Feasible Runtime.
IEEE Trans Med Imaging 2012; 31:1250-1262.




- numerical phantoms -
(command: phantom)


Shepp LA, Logan BF.
The Fourier reconstruction of a head section
IEEE T Nucl Sci 1974; 21:21-43.

<NAME>, <NAME>, <NAME>, <NAME>,
Realistic Analytical Phantoms for Parallel Magnetic Resonance Imaging
IEEE Trans Med Imaging 2012; 31:626-636.




- applications -

Hollingsworth KG, Higgins DM, McCallum M, <NAME>, Coombs A, Straub V.
Investigating the quantitative fidelity of prospectively undersampled
chemical shift imaging in muscular dystrophy with compressed sensing
and parallel imaging reconstruction.
Magn Reson Med 2014; 72: 1610-1619.

<NAME>, <NAME>, <NAME>, <NAME>, <NAME>, <NAME>, <NAME>,
<NAME>, Vasanawala SS.
Fast Pediatric 3D Free Breathing Abdominal Dynamic Contrast Enhanced MRI
with a High Spatiotemporal Resolution,
J Magn Reson Imaging 2015; 41:460-473.

Addy NO, Ingle RR, Wu HH, Hu BS, Nishimura DG.
High-resolution variable-density 3D cones coronary MRA.
Magn Reson Med 2015; 74: 614-621.

<NAME>, <NAME>, <NAME>, <NAME>, <NAME>, <NAME>,
<NAME>, Vasanawala SS.
Free-Breathing Pediatric MRI with Nonrigid Motion Correction and Acceleration,
J Magn Reson Imaging 2015; 42:407-420.

<NAME>, <NAME>, <NAME>.
Parallel Magnetic Resonance Imaging as Approximation in a
Reproducing Kernel Hilbert Space,
Inverse Problems 2015; 31:045008.

<NAME>, <NAME>, <NAME>, <NAME>, <NAME>, <NAME>,
<NAME>, <NAME>.
Accelerating MR Imaging Liver Steatosis Measurement Using Combined
Compressed Sensing and Parallel Imaging: A Quantitative Evaluation,
Radiology 2016; 278:245-256.

<NAME>, <NAME>, <NAME>, <NAME>, <NAME>, <NAME>, <NAME>,
<NAME>, <NAME>, Vasanawala SS.
Comprehensive Motion-Compensated Highly-Accelerated 4D Flow MRI with
Ferumoxytol Enhancement for Pediatric Congenital Heart Disease,
J Magn Reson Imaging, Epub (2015)

<NAME>, <NAME>, <NAME>, <NAME>, <NAME>, Vasanawala SS, <NAME>.
T2-Shuffling: Sharp, Multi-Contrast, Volumetric Fast Spin-Echo Imaging
Magn Recon Med; in press (2015).

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