Journal Articles

Submitted/Accepted Pending Revision

1) K. Hammernik, T. Kustner, B. Yaman, Z. Huang, D. Rueckert, F. Knoll and M. Akçakaya, "Physics-Driven Deep Learning for Computational Magnetic Resonance Imaging," submitted.


Published/In press (Reverse Chronological Order)


70) S. Weingärtner, O. B. Demirel, F. Gama, I. Pierce, T. A. Treibel, J. Schulz-Menger and M. Akçakaya, "Cardiac Phase-Resolved Late Gadolinium Enhancement Imaging," Frontiers in Cardiovascular Medicine, doi: 10.3389/fcvm.2022.917180.

69) O. B. Demirel, B. Yaman, C. Shenoy, S. Moeller, S. Weingärtner and M. Akçakaya, "Signal Intensity Informed Multi-Coil Encoding Operator for Physics-Guided Deep Learning Reconstruction of Highly Accelerated Myocardial Perfusion CMR," Magnetic Resonance in Medicine, 2022, doi: 10.1002/mrm.29453.

68) H. Gu, B. Yaman, K. Uğurbil, S. Moeller and M. Akçakaya, "Revisiting l1-wavelet compressed sensing MRI in the era of deep learning," Proc Natl Acad Sci USA, 119(33):e2201062119, Aug. 16, 2022.

67) B. Yaman, S. A. Hosseini, S. Moeller, J. Ellermann, K. Uğurbil and M. Akçakaya, "Multi-Mask Self-Supervised Learning for Physics-Guided Neural Networks in Highly Accelerated MRI," NMR in Biomedicine. 2022;e4798.

66) C. Zhang, S. Moeller, O. B. Demirel, K. Uğurbil and M. Akçakaya, "Residual RAKI: A Hybrid Linear and Non-Linear Approach for Scan-Specific k-space Deep Learning,” Neuroimage, 256:119248; Aug. 2022.

65) M. Akçakaya, B. Yaman, H. Chung and J. C. Ye, "Unsupervised Deep Learning Methods for Biological Image Reconstruction and Enhancement," IEEE Signal Processing Magazine, vol. 39, no. 2, pp. 28-44, March 2022.


64) L. Vizioli, S. Moeller, L. Dowdle, M. Akçakaya, F. De Martino, E. Yacoub and K Ugurbil, "Lowering the Thermal Noise Barrier in Functional Brain Mapping with Magnetic Resonance Imaging," Nature Communications, 12(1), pp. 5181, Aug. 30, 2021.

63) I. Hermann, P. Kellman, O. B. Demirel, M. Akçakaya, L. R. Schad and S. Weingärtner, "Free-breathing simultaneous T1, T2 and T2 quantification in the myocardium," Magnetic Resonance in Medicine, 86(3), pp. 1226-1240, Sept. 2021.

62) O. B. Demirel, S. Weingärtner, S. Moeller and M. Akçakaya, "Improved Simultaneous Multislice Cardiac MRI using readout concatenated k-space SPIRiT (ROCK-SPIRiT)," Magnetic Resonance in Medicine, 85(6), pp. 3036-3048, June 2021.


61) S. Moeller, P. K. Pisharady, S. Ramanna, C. Lenglet, X. Wu, E. Yacoub, K. Uğurbil and M. Akçakaya, "NOise Reduction with DIstribution Corrected (NORDIC) PCA in dMRI with complex-valued parameter-free locally low-rank processing," NeuroImage, 226:117539, Nov. 10, 2020.

60) B. Yaman, S. A. Hosseini, S. Moeller, J. Ellermann, K. Uğurbil and M. Akçakaya, "Self-Supervised Learning of Physics-Guided Reconstruction Neural Networks without Fully-Sampled Reference Data," Magnetic Resonance in Medicine, 84(6), pp. 3172-3191, Dec. 2020.

59) S. A. Hosseini, B. Yaman, S. Moeller, M. Hong and M. Akçakaya, "Dense Recurrent Neural Networks for Inverse Problems: History-Cognizant Unrolling of Optimization Algorithms," IEEE Journal on Special Topics in Signal Processing, 14(6), pp. 1280-1291, Oct. 2020.

58) C. Shenoy, S. Romano, A. Hughes, O. Okasha, P. S. Nijjar, P. Velangi, C. M. Martin, M. Akçakaya and A. Farzaneh-Far, "Cardiac Magnetic Resonance Feature Tracking Global Longitudinal Strain and Prognosis After Heart Transplantation," JACC Cardiovasc Imaging, 13(9), pp. 193401942, Sep. 2020.

57) S. Moeller, P. K. Pisharady, J. Andersson, M. Akçakaya, N. Harel, R. Ma, X. Wu, E. Yacoub, C. Lenglet and K. Uğurbil, "Diffusion Imaging in the Post-HCP Era," Journal of Magnetic Resonance Imaging, in press.

56) I. Hermann, T. Uhrig, J. Chacon-Caldera, M. Akçakaya, L. Schad and S. Weingärtner, "Towards measuring the effect of flow in blood T1 assessed in a flow phantom and in vivo," Physics in Medicine and Biology, 65(9):095001, Apr. 28, 2020.

55) R. Ma, M. Akçakaya, S. Moeller, E. Auerbach, K. Uğurbil and P.-F. van de Moortele, "Effective Correction of Eddy Current Induced Artifacts in Human Connectome Project-style Multiband Diffusion MRI at 7T Using a Multi-probe Field Monitoring Camera," NeuroImage, 216:116861, Aug. 1, 2020.

54) S. Moeller, S. Ramanna, C. Lenglet, P. Pisharady, E. Auerbach, L. DelaBarre, X. Wu, M. Akçakaya and K. Uğurbil, "Self-navigation for 3D multi-shot EPI with data-reference," Magnetic Resonance in Medicine, 84(5), pp. 1747-1762, Oct. 2020.

53) P. S. Velangi, K. A. Chen, F. Kazmirczak, O. Okasha, L. von Wald, H. Roukoz, A. Farzaneh-Far, J. Markowitz, P. S. Nijjar, M. Bhargava, D. Perlman, M. Akçakaya and C. Shenoy, "Right Ventricular Abnormalities on Cardiovascular Magnetic Resonance Imaging in Patients With Sarcoidosis," JACC Cardiovasc Imaging, 13(6), pp. 1395-1405, June 2020.

52) S. A. Hosseini, C. Zhang, S. Weingärtner, S. Moeller, M. Stuber, K. Uğurbil and M. Akçakaya, "Accelerated Coronary MRI with sRAKI: A Database-Free Self-Consistent Neural Network k-space Reconstruction for Arbitrary Undersampling," PLoS One, 15(2):e0229418, Feb 21, 2020.

51) F. Knoll, K. Hammernik, C. Zhang, S. Moeller, T. Pock, D. K. Sodickson and M. Akçakaya, "Deep Learning Methods for Parallel Magnetic Resonance Imaging Reconstruction," IEEE Signal Processing Magazine, 37(1), pp. 128-140, Jan. 2020.


50) C. Zhang, S. A. Hosseini, S. Weingärtner, S. Moeller, K. Uğurbil and M. Akçakaya, "Optimized Fast GPU Implementation of Robust Artificial-neural-networks for k-space Interpolation (RAKI) Reconstruction," PLoS One, 14(10):e0223315, Oct. 23, 2019.

49) P. S. Velangi, C. Choo, K. A. Chen, F. Kazmirczak, P. S. Nijjar, A. Farzaneh-Far, O. Okasha, M. Akçakaya, J. W. Weinsaft and C. Shenoy, "Long-term Embolic Outcomes after Detection of Left Ventricular Thrombus by Late Gadolinium Enhancement Cardiovascular Magnetic Resonance Imaging: A Matched Cohort Study," Circulation: Cardiovascular Imaging, 12(11):e009723, Nov 2019.

48) A. Hughes, O. Okasha, A. Farzaneh-Far, F. Kazmirczak, P. S. Nijjar, P. S. Velangi, M. Akçakaya, C. M. Martin and C. Shenoy, "Myocardial Fibrosis and Prognosis in Heart Transplant Recipients," Circulation: Cardiovascular Imaging, 12(10):e009060, Oct 2019.

47) S.-W. Chieh, M. Kaveh, M. Akçakaya and S. Moeller, "Self-calibrated interpolation of non-Cartesian data with GRAPPA in parallel imaging," Magnetic Resonance in Medicine, 83(5):1837-1850, 2020.

46) C. I. Kanatsoulis, X. Fu, N. D. Sidiropoulos and M. Akçakaya, "Tensor Completion from Regular Sub-Nyquist Samples," IEEE Trans. on Signal Processing, 68(1), pp. 1-16, 2020.

45) B. Yaman, S. Weingärtner, N. Kargas, N. D. Sidiropoulos and M. Akçakaya, "Low-Rank Tensor Models for Improved Multi-Dimensional MRI: Application to Dynamic Cardiac T1 Mapping," IEEE Trans. on Computational Imaging, 6(1), pp. 194-207, 2020.

44) F. Kazmirczak, P. S. Nijjar, L. Zhang, A. Hughes, K. A. Chen, O. Okasha, C. M. Martin, M. Akçakaya, A. Farzaneh-Far and C. Shenoy, "Safety and prognostic value of regadenoson stress cardiovascular magnetic resonance imaging in heart transplant recipients," Journal of Cardiovascular Magnetic Resonance, 21(1):9, 2019.  (pdf)

43) M. Akçakaya, S. Moeller, S. Weingärtner and K. Ugurbil, "Scan-specific Robust Artificial-neural-networks for k-space Interpolation (RAKI) Reconstruction: Database-free Deep Learning for Fast Imaging," Magnetic Resonance in Medicine, 81(1), pp. 439-453, Jan. 2019. (pdf) (code)


42) L. Q. Lin, F. Kazmirczak, K. A. Chen, O. Okasha, P. S. Nijjar, C. M. Martin, M. Akçakaya, A. Farzaneh-Far and C. Shenoy, "Impact of Cardiovascular Magnetic Resonance Imaging on Identifying the Etiology of Cardiomyopathy in Patients Undergoing Cardiac Transplantation," Nature Scientific Reports, 8(1):16212, Nov 1, 2018. (pdf)

41) S. A. H. Hosseini, A. Sohrabpour, M. Akçakaya and B. He, "Electromagnetic Brain Source Imaging by Means of a Robust Minimum Variance Beamformer," IEEE Trans. on Biomedical Engineering, 65(10): 2365-2374, Oct 2018. (pdf)

40) B. Rieger, M. Akçakaya, J. C. Pariente, S. Llufriu, E. Martinez-Heras, S. Weingärtner and L. R. Schad, "Time Efficient Whole-Brain Coverage with MR Fingerprinting using Slice-Interleaved Echo-Planar-Imaging," Nature Scientific Reports, 8(1):6667, April 27, 2018. (pdf)

39) G. Wang, L. Zhang, G. B. Giannakis, M. Akçakaya and J. Chen, "Sparse Phase Retrieval via Truncated Amplitude Flow," IEEE Trans. on Signal Processing, 66(2), pp. 479-491, Jan. 2018. (pdf)

38) S. Weingärtner, C. Shenoy, B. Rieger, L. R. Schad, J. Schulz-Menger and M. Akçakaya, "TempOrally-resolved Parametric Asssessment of Z-magnetization recovery (TOPAZ): Dynamic Myocardial T1 Mapping using a Cine Steady-State Look-Locker Approach," Magnetic Resonance in Medicine, 79(4), pp. 2087-2100, Apr. 2018. (pdf)


37) S. Weingärtner, S. Moeller, S. Schmitter, E. Auerbach, P. Kellman, C. Shenoy and M. Akçakaya, "Simultaneous Multi-Slice Imaging for Native Myocardial T1 Mapping: Improved Spatial Coverage in a Single Breath-Hold," Magnetic Resonance in Medicine, 78(2), pp. 462-471, Aug. 2017. (pdf)

36) T. A. Basha, M. Akçakaya, C. Liew, C. Tsao, F. N. Delling, W. J. Manning and R. Nezafat, "Clinical Performance of High-Resolution Late Gadolinium Enhancement Imaging with Compressed Sensing," Journal of Magnetic Resonance Imaging, 46(6):1829-1838, Dec. 2017. (pdf)

35) S. Weingärtner, F. Zimmer, G. J. Metzger, K. Uğurbil, P.-F. van de Moortele and M. Akçakaya, "Motion-Robust Cardiac B1+ Mapping at 3T using Interleaved Bloch-Siegert Shifts," Magnetic Resonance in Medicine, 78(2), pp. 670-677, Aug. 2017. (pdf)

34) S. Weingärtner, N. M. Meßner, F. G. Zöllner, M. Akçakaya and L. R. Schad, "Black-Blood Native T1 Mapping: Blood Signal Suppression for Reduced Partial-Voluming in the Myocardium" Magnetic Resonance in Medicine, 78(2), pp. 484-493, Aug. 2017. (pdf)


33) M. Akçakaya, S. Weingärtner, T. A. Basha, S. Roujol, S. Bellm and R. Nezafat, "Joint Myocardial T1 and T2 Mapping Using a Combination of Saturation Recovery and T2-preparation," Magnetic Resonance in Medicine, 76(3), pp. 888-896, Sept. 2016. (pdf)

2015 and earlier

32) M. Akçakaya and V. Tarokh, “Sparse Signal Recovery from a Mixture of Linear and Magnitude-Only Measurements,” IEEE Signal Processing Letters, 22(9), pp. 1220-1223, Sept. 2015. (pdf)

31) S. Roujol, T. A. Basha, S. Weingärtner, M. Akçakaya, S. J. Berg, W. J. Manning and R. Nezafat, "Impact of Motion Correction on Reproducibility and Spatial Variability of Quantitative Myocardial T2 Mapping," Journal of Cardiovascular Magnetic Resonance, 17:46, 2015.  (pdf)

30) M. Akçakaya*, T. A. Basha*, S. Weingärtner, S. Roujol, S. Berg and R. Nezafat, "Improved Quantitative Myocardial T2 Mapping," Magnetic Resonance in Medicine, 74(1), pp. 93-105, July 2015. (*: denotes co-first authorship). (pdf)

29) M. Akçakaya, S. Nam, T. A. Basha, K. Kawaji, V. Tarokh and R. Nezafat, “An Augmented Lagrangian Based Compressed Sensing Reconstruction for Non-Cartesian Magnetic Resonance Imaging without Gridding and Regridding at Every Iteration,” PLoS ONE, 9(9):e107107, Sept. 12, 2014. (pdf)

28) S. Weingärtner, M. Akçakaya, S. Roujol, T. A. Basha, C. Tschabrunn, S. Berg, E. Anter and R. Nezafat, “Free-breathing Combined 3D Late Gadolinium Enhancement and T1 Mapping for Myocardial Tissue Characterization,” Magnetic Resonance in Medicine, 74(4), pp. 1032-1041, Oct. 2015. (pdf)

27) T. A. Basha, M. Akçakaya, B. Goddu, S. Berg and R. Nezafat, “Accelerated 3D Cine Phase Contrast Imaging using Randomly Undersampled Echo Planar Imaging with Compressed Sensing Reconstruction,” NMR Biomedicine, 28(1), pp. 30-39, Jan. 2015. (pdf)

26) S. Roujol, M. Foppa, T. A. Basha, M. Akçakaya, B. Goddu, S. Berg and R. Nezafat, “Highly Accelerated Free-Breathing ECG-Triggered Contrast-Enhanced Pulmonary Vein MRA,” Journal of Cardiovascular Magnetic Resonance, 16:91, 2014. (pdf)

25) K. Kawaji, M. Foppa, S. Roujol, M. Akçakaya and R. Nezafat, "Whole Heart Coronary Imaging with Flexible Acquisition Window and Trigger Delay," PLoS ONE, 10(2):e0112020, Feb. 26, 2015. (pdf)

24) M. Akçakaya, S. Weingärtner, S. Roujol and R. Nezafat, “On the Selection of Sampling Points for Myocardial T1 Mapping,” Magnetic Resonance in Medicine, 73(5), pp. 1741-1753, May 2015. (pdf)

23) S. Weingärtner, S. Roujol, M. Akçakaya, T. A. Basha, W. J. Manning and R. Nezafat, “Free-Breathing Multi-Slice Native Myocardial T1 Mapping using the Slice-Interleaved T1 (STONE) Sequence,” Magnetic Resonance in Medicine, 74(1), pp. 115-214, July 2015. (pdf)

22) S. Pflugi, S. Roujol, M. Akçakaya, K. Kawaji, M. Foppa, B. Heydari, B. Goddu, K. V. Kissinger, S. Berg, W. J. Manning, S. Kozerke and R. Nezafat, “Accelerated Cardiac MR Stress Perfusion with Radial Sampling After Physical Exercise with an MR-compatible Supine Bicycle Ergometer,” Magnetic Resonance in Medicine, 74(2), pp. 384-395, Aug. 2015. (pdf)

21) M. Akçakaya, T. A. Basha, S. Pflugi, M. Foppa, K. V. Kissinger, T. H. Hauser and R. Nezafat, “Localized Spatio-Temporal Constraints for Accelerated CMR Perfusion,” Magnetic Resonance in Medicine, 72(3), pp. 629-639, Sept. 2014. (pdf)

20) S. Weingärtner, M. Akçakaya, S. Roujol, T. A. Basha, C. Stehning, K. V. Kissinger, B. Goddu, S. Berg, W. J. Manning and R. Nezafat, “Free-Breathing Post-Contrast Three-dimensional T1 Mapping: Volumetric Assessment of Myocardial T1 Values,” Magnetic Resonance in Medicine, 73(1): pp. 214-222, Jan. 2015. (pdf)

19) S. Roujol, T. A. Basha, M. Akçakaya, M. Foppa, R. H. Chan, K. V. Kissinger, B. Goddu, S. Berg, W. J. Manning and R. Nezafat, “3D Late Gadolinium Enhancement in a Single Prolonged Breath-hold using Supplemental Oxygenation and Hyperventilation,” Magnetic Resonance in Medicine, 72(3), pp. 850-857, Sept. 2014. (pdf)

18) M. Akçakaya, P. Gulaka, T. A. Basha, L. H. Ngo, W. J. Manning and R. Nezafat, “Free-Breathing Phase Contrast MRI with Near 100% Respiratory Navigator Efficiency using k-space Dependent Respiratory Gating,” Magnetic Resonance in Medicine, 71(6), pp. 2172-2179, June 2014. (pdf)

17) M. Akçakaya, T. A. Basha, R. H. Chan, W. J. Manning and R. Nezafat, “Accelerated Isotropic Sub-Millimeter Whole-Heart Coronary MRI: Compressed Sensing versus Parallel Imaging,” Magnetic Resonance in Medicine, 71(2), pp. 815-822, Feb. 2014 . (pdf)

16) S. Weingärtner, M. Akçakaya, K. V. Kissinger, B. Goddu, S. Berg, W. J. Manning, R. Nezafat, “Combined Saturation/Inversion Recovery Sequences for Improved Evaluation of Scar and Diffuse Fibrosis in Patients with Arrhythmia or Heart Rate Variability,” Magnetic Resonance in Medicine, 71(3), pp. 1024-1034, March 2014. (pdf)

15) S. Nam, S. Hong, M. Akçakaya, Y. Kwak, B. Goddu, K. V. Kissinger, W. J. Manning, V. Tarokh, R. Nezafat, "Compressed Sensing Reconstruction for Undersampled Breath-Hold Radial Cine Imaging with Auxiliary Free-Breathing Data," Journal of Magnetic Resonance Imaging, 39(1), pp. 179-188, Jan. 2014. (pdf)

14) M. Akçakaya, J. L. Shaw, T. H. Hauser and R. Nezafat, "Utility of Respiratory-Navigator-Rejected k-space Lines for Improved Signal-to-Noise Ratio in 3D Cardiac MR," Magnetic Resonance in Medicine, 70(5), pp. 1332-1339, Nov. 2013 . (pdf)

13) Y. Kwak, S. Nam, M. Akçakaya, T. A. Basha, B. Goddu, W. J. Manning, V. Tarokh, R. Nezafat, "Accelerated Aortic Flow Assessment with Compressed Sensing With and Without Use of the Sparsity of the Complex Difference Image," Magnetic Resonance in Medicine, 70(3), pp. 851-858, Sept. 2013. (pdf)

12) S. Nam, M. Akçakaya, T. A. Basha, C. Stehning, W. J. Manning, V. Tarokh and R. Nezafat, “Compressed Sensing Reconstruction for Whole Heart Imaging with 3D Radial Trajectories: A GPU Implementation,” Magnetic Resonance in Medicine, 69(1), pp. 91–102, Jan. 2013. (pdf)

11) M. Akçakaya, H. Rayatzadeh, T. A. Basha, S. N. Hong, R. H. Chan, K. V. Kissinger, T. H. Hauser, M, E. Josephson, W. J. Manning and R. Nezafat, “Accelerated Late Gadolinium Enhancement Cardiac MRI with Isotropic Spatial Resolution Using Compressed Sensing: Initial Experience,” Radiology, 264(3):691-699, Sept. 2012. (pdf)

10) M. Akçakaya*, T. A. Basha*, R. H. Chan, H. Rayatzadeh, K. V. Kissinger, B. Goddu, L. A. Goepfert, W. J. Manning and R. Nezafat, "Accelerated Contrast-Enhanced Whole Heart Coronary MRI using Low-dimensional-Structure Self-learning and Thresholding (LOST)," Magnetic Resonance in Medicine, 67(5), pp. 1434-1443, May 2012. (*: denotes co-first authorship). (pdf) (cover image)

9) M. H. Moghari, M. Akçakaya, A. O'Connor, T. A. Basha, M. Casanova, L. Goepfert, K. V. Kissinger, B. Goddu, M. L. Chuang, V. Tarokh, W. J. Manning and R. Nezafat, "Compressed-Sensing Motion Compensation (CosMo): A Joint Prospective-Retrospective Respiratory Navigator for Coronary MRI," Magnetic Resonance in Medicine, 66(6), pp. 1674-1681, Dec. 2011. (pdf)

8) M. Akçakaya, T. A. Basha, B. Goddu, L. A. Goepfert, K. V. Kissinger, V. Tarokh, W. J. Manning and R. Nezafat, "Low-dimensional-Structure Self-Learning and Thresholding (LOST): Regularization Beyond Compressed Sensing for MRI Reconstruction," Magnetic Resonance in Medicine, 66(3), pp. 756–767, Sept. 2011. (pdf) ISMRM I. I. Rabi Young Investigator Award Finalist

7) M. Akçakaya, J. Park and V. Tarokh, "A Coding Theory Approach to Noisy Compressive Sensing Using Low Density Frames," IEEE Trans. on Signal Processing, 59(11), pp. 5369-5379, Nov. 2011. (pdf)

6) M. Akçakaya, P. Hu, M. L. Chuang, T. H. Hauser, L. H. Ngo, W. J. Manning, V. Tarokh and R. Nezafat, "Accelerated Non-Contrast Enhanced Pulmonary Vein MRA with Distributed Compressed Sensing,'' Journal of Magnetic Resonance Imaging, 33(5), pp. 1248-1255, May 2011. (pdf)

5) M. Akçakaya, S. Nam, P. Hu, M. H. Moghari, L. H. Ngo, V. Tarokh, W. J. Manning and R. Nezafat, "Compressed Sensing with Wavelet Domain Dependencies for Coronary MRI: A Retrospective Study," IEEE Trans. on Medical Imaging, 30(5), pp. 1090-1099, May 2011. (pdf)

4) M. Akçakaya and V. Tarokh, "Shannon Theoretic Limits on Noisy Compressive Sampling," IEEE Trans. on Information Theory, 56(1), pp. 492-504, Jan. 2010. (pdf)

3) M. Akçakaya and V. Tarokh, "A Frame Construction and A Universal Distortion Bound for Sparse Representations," IEEE Trans. on Signal Processing, 56(6), pp. 2443-2450, June 2008. (pdf)

2) M. Akçakaya and V. Tarokh, "Performance of Sparse Representation Algorithms Using Randomly Generated Frames," IEEE Signal Processing Letters, 14(11), pp. 777-780, Nov. 2007. (pdf)

1) N. Mysore, J. Bajcsy, M. Akçakaya and H. Kobayashi, "A New Performance Evaluation Technique for Iteratively Decoded Magnetic Recording Systems," IEEE Trans. on Magnetics, 41(10), pp. 2986-2988, Oct. 2005. (pdf)