- BART -

Uecker M, Ong F, Tamir JI, Bahri D, Virtue P, Cheng JY, Zhang T, Lustig M.
Berkeley Advanced Reconstruction Toolbox.
Annual Meeting ISMRM, Toronto 2015,
In: Proc Intl Soc Mag Reson Med 2015; 23:2486.

Uecker M, Virtue P, Ong F, Murphy MJ, Alley MT, Vasanawala SS, Lustig M.
Software Toolbox and Programming Library for Compressed Sensing and
Parallel Imaging,
ISMRM Workshop on Data Sampling and Image Reconstruction, Sedona 2013.

Tamir JI, Ong F, Cheng JY, Uecker M, Lustig M. Generalized Magnetic
Resonance Image Reconstruction using The Berkeley Advanced
Reconstruction Toolbox,
ISMRM Workshop on Data Sampling and Image Reconstruction, Sedona 2016.

Uecker M.
Machine Learning Using the BART Toolbox - Implementation of
a Deep Convolutional Neural Network for Denoising.
Joint Annual Meeting ISMRM-ESMRMB, Paris 2018,
In: Proc. Intl. Soc. Mag. Reson. Med. 2018; 26:2802.

Blumenthal M. and Uecker M.
Deep Deep Learning with BART.
ISMRM Annual Meeting 2021,
In: Proc. Intl. Soc. Mag. Reson. Med. 2021; 29:1754.

Luo G, Blumenthal M, Uecker M.
Using data-driven image priors for image reconstruction with BART.
ISMRM Annual Meeting 2021,
In: Proc. Intl. Soc. Mag. Reson. Med. 2021; 29:1756.

Holme HCM and Uecker M.
Reproducibility meets Software Testing: Automatic Tests
of Reproducible Publications Using BART.
ISMRM Annual Meeting 2021,
In: Proc. Intl. Soc. Mag. Reson. Med. 2021; 29:3768.



- reproducible publications using BART -

Uecker M, Lustig M.
Estimating Absolute-Phase Maps Using ESPIRiT and Virtual Conjugate Coils.
Magn Reson Med 2017; 77:1201-1207.
https://github.com/mrirecon/vcc-espirit

Rosenzweig S, Holme HCM, Wilke RN, Voit D, Frahm J, Uecker M.
Simultaneous Multi-Slice Reconstruction Using Regularized Nonlinear Inversion:
SMS-NLINV.
Magn Reson Med 2018; 79:2057-2066.
https://github.com/mrirecon/sms-nlinv

Rosenzweig S, Holme HCM, Uecker M.
Simple Auto-Calibrated Gradient Delay Estimation From Few Spokes Using Radial
Intersections (RING).
Magn Reson Med 2019; 81:1898-1906.
https://github.com/mrirecon/ring

Holme HCM, Rosenzweig S, Ong F, Wilke RN, Lustig M, Uecker M.
ENLIVE: An Efficient Nonlinear Method for Calibrationless and Robust Parallel
Imaging.
Scientific Reports 2019; 9:3034.
https://github.com/mrirecon/enlive

Wang X, Kohler F, Unterberg-Buchwald C, Lotz J, Frahm J, Uecker M.
Model-based myocardial T1 mapping with sparsity constraints using single-shot
inversion-recovery radial FLASH cardiovascular magnetic resonance.
J Cardioviasc Magn Reson 2019; 21:60.
https://github.com/mrirecon/myocardial-t1-mapping

Rosenzweig S, Scholand N, Holme HCM, Uecker M.
Cardiac and Respiratory Self-Gating in Radial MRI using an Adapted Singular
Spectrum Analysis (SSA-FARY).
IEEE Trans Med Imag 2020; 39:3029-3041.
https://github.com/mrirecon/SSA-FARY

Wang X, Rosenzweig S, Scholand N, Holme HCM, Uecker M.
Model-based Reconstruction for Simultaneous Multi-slice T1 Mapping using
Single-shot Inversion-recovery Radial FLASH.
Magn Reson Med 2021; 85:1258-1271.
https://github.com/mrirecon/sms-t1-mapping

Wang X, Tan Z, Scholand N, Roeloffs V, Uecker M.
Physics-based Reconstruction Methods for Magnetic Resonance Imaging.
Philos. Trans. R. Soc. A. 2021; 379:20200196.
https://github.com/mrirecon/physics-recon



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


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

Pruessmann KP, Weiger M, Scheidegger MB, Boesiger P.
SENSE: Sensitivity encoding for fast MRI.
Magn Reson Med 1999; 42:952-962.

Pruessmann KP, Weiger M, Boernert P, Boesiger P.
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 -
(commands: fft, nufft, pics)


O’Sullivan JD.
A fast sinc function gridding algorithm for Fourier inversion in
computer tomography.
IEEE Trans Med Imaging 1985; 4:200-207.

Jackson JI, Meyer CH, Nishimura DG, Macovski A.
Selection of a convolution function for Fourier inversion using gridding.
IEEE Trans Med Imaging 1991; 3:473-478.

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

Frigo M, Johnson SG.
The Design and Implementation of FFTW3.
Proc IEEE 2005; 93:216-231.

Uecker M, Zhang S, Frahm J.
Nonlinear Inverse Reconstruction for Real-time MRI of the
Human Heart Using Undersampled Radial FLASH.
Magn Reson Med 2010; 63:1456-1462.

Ong F, Uecker M, Jiang W, Lustig M.
Fast Non-Cartesian Reconstruction with Pruned Fast Fourier Transform.
Annual Meeting ISMRM, Toronto 2015,
In: Proc Intl Soc Mag Reson Med 2015; 23:3639.




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


Walsh DO, Gmitro AF, Marcellin MW.
Adaptive reconstruction of phased array MR imagery.
Magn Reson Med 2000; 43:682-690.

Griswold M, Walsh D, Heidemann R, Haase A, Jakob A.
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 2002; 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.

Uecker M, Virtue P, Vasanawala SS, Lustig M.
ESPIRiT Reconstruction Using Soft SENSE.
Annual Meeting ISMRM, Salt Lake City 2013,
In: Proc Intl Soc Mag Reson Med 2013; 21:127.

Uecker M, Lai P, Murphy MJ, Virtue P, Elad M, Pauly JM, Vasanawala SS,
Lustig M.
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)


Uecker M, Hohage T, Block KT, Frahm J.
Image reconstruction by regularized nonlinear inversion-joint estimation
of coil sensitivities and image content.
Magn Reson Med 2008; 60:674-682.

Bi Z, Uecker M, Jiang D, Lustig M, Ying K.
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 2013; 21:2584.

Shin PJ, Larson PEZ, Ohliger MA, Elad M, Pauly JM, Vigneron DB, Lustig M.
Calibrationless Parallel Imaging Reconstruction Based on Structured
Low-Rank Matrix Completion.
Magn Reson Med 2014; 72:959-970.

Holme HCM, Rosenzweig S, Ong F, Wilke RN, Lustig M, Uecker M.
ENLIVE: An Efficient Nonlinear Method for Calibrationless and Robust Parallel
Imaging.
Scientific Reports 2019; 9:3034.





- coil compression -
(command: cc)


Buehrer M, Pruessmann KP, Boesiger P, Kozerke S.
Array compression for MRI with large coil arrays.
Magn Reson Med 2007, 57:1131-1139.

Huang F, Vijayakumar S, Li Y, Hertel S, Duensing GR.
A software channel compression technique for faster reconstruction
with many channels.
Magn Reson Imaging 2008; 26:133-141.

Zhang T, Pauly JM, Vasanawala SS, Lustig M.
Coil compression for accelerated imaging with cartesian sampling.
Magn Reson Med 2013; 69:571-582.

Bahri D, Uecker M, Lustig M.
ESPIRiT-Based Coil Compression for Cartesian Sampling.
Annual Meeting ISMRM, Salt Lake City 2013,
In: Proc Intl Soc Mag Reson Med 2013; 21:2657.




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


Block KT, Uecker M, Frahm J.
Undersampled radial MRI with multiple coils. Iterative image
reconstruction using a total variation constraint.
Magn Reson Med 2007; 57:1086-1098.

Lustig M, Donoho D, Pauly JM.
Sparse MRI: The application of compressed sensing for rapid MR imaging.
Magn Reson Med 2007; 58:1182-1195.

Liu B, King K, Steckner M, Xie J, Sheng J, Ying L.
Regularized sensitivity encoding (SENSE) reconstruction using
Bregman iterations.
Magn Reson Med 2009; 61:145-152.




- non-linear model-based reconstruction -
(commands: moba)


Block KT, Uecker M, Frahm J.
Model-Based Iterative Reconstruction for Radial Fast Spin-Echo MRI.
IEEE Trans Med Imag 2009; 28:1759-1769.

Wang X, Roeloffs V, Klosowski J, Tan Z, Voit D, Uecker M, Frahm J.
Model-based T1 Mapping with Sparsity Constraints Using Single-Shot
Inversion-Recovery Radial FLASH.
Magn Reson Med 2018; 79:730-740.

Wang X, Kohler F, Unterberg-Buchwald C, Lotz J, Frahm J, Uecker M.
Model-based myocardial T1 mapping with sparsity constraints using single-shot
inversion-recovery radial FLASH cardiovascular magnetic resonance.
J Cardioviasc Magn Reson 2019; 21:60.

Tan Z, Voit D, Kollmeier J, Uecker M, Frahm J.
Dynamic Water/Fat Separation and B0 Inhomogeneity Mapping -- Joint Estimation
Using Undersampled Triple-Echo Multi-Spoke Radial FLASH.
Magn Reson Med 2019; 82:1000-1011.

Wang X, Rosenzweig S, Scholand N, Holme HCM, Uecker M.
Model-based Reconstruction for Simultaneous Multi-slice T1 Mapping using
Single-shot Inversion-recovery Radial FLASH.
Magn Reson Med 2021; 85:1258-1271.



- subspace reconstruction -
(commands: pics, signal, svd)


Liang Z, Spatiotemporal Imaging with partially separable functions.
4th IEEE International Symposium on Biomedical Imaging: From Nano to Macro,
2007; 988-991.

Petzschner FH, Ponce IP, Blaimer M, Jakob PM, Breuer FA.
Fast MR parameter mapping using k‐t principal component analysis.
Magn Reson Med 2011; 66;706-716.

Mani M, Jacob M, Magnotta V, Zhong J.
Fast iterative algorithm for the reconstruction of multishot non-cartesian
diffusion data.
Magn Reson Med 2015; 74:1086–1094.




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


Rudin LI, Osher S, Fatemi E.
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.

Ong F, Uecker M, Tariq U, Hsiao A, Alley MT, Vasanawala SS, Lustig M.
Robust 4D Flow Denoising using Divergence-free Wavelet Transform, 
Magn Reson Med 2015; 73:828-842.

Ong F, Lustig M.
Beyond low rank + sparse: Multi-scale low rank matrix decomposition,
IEEE J Sel Topics Signal Process 2016; 10:672-687.

Bredies K, Kunisch K, Pock T.
Total generalized variation.
SIAM Journal on Imaging Sciences 2010; 3:492-526.

Luo G, Zhao N, Jiang W, Hui ES, Cao P.
MRI reconstruction using deep Bayesian estimation.
Magn Reson Med 2020; 84:2246-2261.

Knoll F, Bredies K, Pock T, Stollberger R.
Second order total generalized variation (TGV) for MRI.
Magn Reson Med 2010; 65:480-491.




- sampling schemes -
(commands: traj, poisson, wave, wavepsf)


Winkelmann S, Schaeffter T, Koehler T, Eggers H, Doessel O.
An optimal radial profile order based on the Golden Ratio
for time-resolved MRI.
IEEE Trans Med Imaging 2007; 26:68-76.

Lustig M, Alley M, Vasanawala S, Donoho DL, Pauly JM.
L1 SPIR-iT: Autocalibrating Parallel Imaging Compressed Sensing
Annual Meeting ISMRM, Honolulu 2009,
In: Proc Intl Soc Mag Reson Med 2009; 17:379.

Bilgic B, Gagoski BA, Cauley SF, Fan AP, Polimeni JR, Grant PE,
Wald LL, Setsompop K. Wave-CAIPI for highly accelerated 3D
imaging.
Magn Reson Med 2014; 73:2152-2162.

Wundrak S, Paul J, Ulrici J, Hell E, Geibel M-A, Bernhardt P, Rottbauer W,
Rasche V.
Golden ratio sparse MRI using tiny golden angles.
Magn Reson Med 2016; 75:2372-2378.




- trajectory correction -
(commands: estdelay)


Block KT, Uecker M.
Simple Method for Adaptive Gradient-Delay Compensation in Radial MRI.
Annual Meeting ISMRM, Montreal 2011,
In: Proc. Intl. Soc. Mag. Reson. Med 2011; 19:2816.

Rosenzweig S, Holme HCM, Uecker M.
Simple Auto-Calibrated Gradient Delay Estimation From Few Spokes Using Radial
Intersections (RING).
Magn Reson Med 2019; 81:1898-1906.




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


Uecker M, Zhang S, Frahm J.
Nonlinear Inverse Reconstruction for Real-time MRI of the Human Heart
Using Undersampled Radial FLASH.
Magn Reson Med 2010; 63:1456-1462.

Murphy M, Alley M, Demmel J, Keutzer K, Vasanawala S, Lustig M.
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 and signals -
(commands: phantom, signal)


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

Koay CG, Sarlls JE, Özarslan E.
Three-Dimensional Analytical Magnetic Resonance
Imaging Phantom in the Fourier Domain.
Magn Reson Med 2007; 58:430-436.

Guerquin-Kern M, Lejeune L, Pruessmann KP, M Unser M,
Realistic Analytical Phantoms for Parallel Magnetic Resonance Imaging.
IEEE Trans Med Imaging 2012; 31:626-636.

Look DC, Locker DR.
Time Saving in Measurement of NMR and EPR Relaxation Times.
Review of Scientific Instruments 1970; 41:250.

Schmitt P, Griswold MA, Jakob PM, Kotas M, Gulani V, Flentje M, Haase A.
Inversion recovery TrueFISP: Quantification of T1, T2, and spin density.
Magn Reson Med 2004; 51:661-667.

Hamilton G, Yokoo T, Bydder M, Cruite I, Schroeder ME, Sirlin CB, Middleton MS.
In vivo characterization of the liver fat 1H MR spectrum.
NMR Biomed 2011; 24:784-790.

Assländer J, Novikov DS, Lattanzi R, Sodickson DK, Cloos MA.
Hybrid-state free precession in nuclear magnetic resonance.
Communications Physics. 2019; 2:73.



- machine learning -
(command: reconet)


Hammernik K, Klatzer T, Kobler E, Recht MP, Sodickson DK, Pock T, Knoll F.
Learning a variational network for reconstruction of accelerated MRI data.
Magn Reson Med 2018; 79:3055-3071.

Aggarwal HK, Mani MP, Jacob M.
MoDL: Model-Based Deep Learning Architecture for Inverse Problems.
IEEE Trans Med Imaging 2019; 38:394--405.

Pock T and Sabach S.
Inertial Proximal Alternating Linearized Minimization (iPALM) for Nonconvex
and Nonsmooth Problems.
SIAM J Imaging Sci 2016; 9:1756--1787.

Kingma DP and Ba J.
Adam: A Method for Stochastic Optimization.
arXiv preprint 2014, arXiv:1412.6980