## Publications:

### Invited Talks:

**Robust Multimodal Imaging**; Talk to be presented at ISMRM Workshop on White Matter, Analysis, Translation, Experimental Validation, Evaluation & Reproducibility, 2023**High-definition MRI: tailored encoding and reconstruction across scales and field strengths**; Talk presentated at the Center for Biomedical Imaging, EPFL, 2023**Efficient MRI through Optimized Encoding and Reconstruction**; Talk presentated at the Weill Cornell Medical College, 2022**Efficient MRI through improved encoding & reconstruction**; Talk presented at the Brain Research Society, Turkey, 2022**Value of Multicontrast Techniques (Neuro)**; Educational presentation at ISMRM, 2022**Efficient MRI through Improved Encoding and Reconstruction**; Talk presented at Department of Electrical and Electronics Engineering, Bogazici University, 2021**Efficient MRI through Improved Encoding and Reconstruction**; Talk presented at King’s College London, 2021**Efficient EPI through Improved Encoding and Reconstruction**; Talk presented at Donders Institute, Radboud University, 2021**Efficient MRI through Improved Encoding and Reconstruction**; Talk presented at Department of Bioengineering, UIUC, 2021**Efficient MRI through Improved Encoding and Reconstruction**; Talk presented at UMRAM, Bilkent University, Turkey, 2021**Efficient MRI through Improved Encoding and Reconstruction**; Talk presented at Fetal Neonatal Neuroimaging and Developmental Science Center, Boston Children’s Hospital, 2020**Efficient MRI through Improved Encoding and Reconstruction**; Talk presented at Radiological Sciences Laboratory, Stanford University, 2020**Highly Efficient MRI Through Multi-shot Echo Planar Imaging**; Talk presented at the SPIE Wavelets and Sparsity XVIII conference, 2019**Wave Encoding: The Sequence, the Reconstruction & the Trade-Offs**; Talk presented at ISMRM Weekend Educational Session, 2019**QSM Tools & Their Biases**; Talk presented at ISMRM Weekend Educational Session, 2019**Basic Physics of Multiband Imaging**; Talk presented at ISMRM Weekend Educational Session, 2018**Faster MRI through Optimized Encoding and Reconstruction**; Talk presented at the Memorial Sloan Kettering Cancer Center, 2018**Faster MRI through Optimized Encoding and Reconstruction**; Talk presented at CAI2R, New York University, 2018**Faster MRI through Optimized Encoding and Reconstruction**; Talk presented at Department of Radiology, Cornell University, 2017**Faster MRI through Optimized Encoding and Reconstruction**; Talk presented at Imaging Elevated Symposium, University of Utah, 2017 [PDF]**QSM Software Demo: 2016 Reconstruction Challenge**; Talk presented at ISMRM Weekend Educational Session, 2017 [PDF] [Matlab code]**Susceptibility Weighted Imaging and Quantitative Susceptibility Mapping**; Talk presented at Neuroradiology Divison, Massachusetts General Hospital, 2016 [PDF]**Accelerated QSM**; Talk presented at Fourth International Workshop on MRI Phase Contrast & Quantitative Susceptibility Mapping, 2016 [PDF]**Advanced Parallel Imaging for Beyond Order of Magnitude Accelerated Neuroimaging**; Talk presented at the Barrow Neurological Institute, Keller Center for Imaging Innovation, 2015 [PDF]**Wave-CAIPI for Efficient TSE and QSM Acquisitions with Application in Brain Tumors**; Talk presented at ISMRM Workshop on Simultaneous Multi-Slice Imaging, 2015 [PDF]**Sparse Methods for Quantitative Susceptibility Mapping**; Talk presented at the SPIE Wavelets and Sparsity XIV conference, 2015**Simultaneous Multi-Slice Acquisition for Rapid Neuroimaging**; Talk presented at OHBM 2015 Morning Workshop: Neuroimaging Applications of Simultaneous Multi-Slice Imaging [PDF]**Susceptibility Weighted Data Acquisition and Processing**; Talk presented at MICCAI 2014 Workshop on Intelligent Imaging [PDF]**Highly Accelerated 3D Imaging**; Talk presented at 3rd Magnetic Resonance Balkan Outreach Program 2014 [PDF]**Wave-CAIPI: Highly Accelerated 3D Imaging with Reduced g-factor Penalty**; Talk presented at Boston Children's Hospital, 2014 [PDF]**MRI Image Reconstruction Algorithms: Compressed Sensing & Quantitative Susceptibility Mapping**; Talk presented at UMRAM, Bilkent University, 2011 [PDF]

### Proffered Talks:

**3D-BUDA Enables Rapid Distortion-Free QSM Acquisition**; Oral presentation at ISMRM 2020**From 2D thick slices to 3D isotropic volumetric brain MRI - a deep learning approach**; Power pitch presentation at ISMRM 2020**Robust high-quality multi-shot EPI with low-rank prior and machine learning**; Oral presentation at ISMRM 2019 [HTML]**NEATR-SMS for Highly Accelerated Multi-Shot EPI**; Oral presentation at ISMRM Workshop on Machine Learning, Part II, 2019 [PDF]**Accelerated Multi-shot EPI through Machine Learning and Joint Reconstruction**; Oral presentation at ISMRM Workshop on Machine Learning, 2018 [PDF]**Calibrationless Parallel Imaging in Multi Echo/Contrast Data**; Power pitch presentation at ISMRM 2017 [Talk] [Poster]**Joint Reconstruction of Phase-Cycled Balanced SSFP with Constrained Parallel Imaging**; Power pitch presentation at ISMRM 2017 [Talk] [Poster]**Joint Reconstruction for Phase-Cycled Balanced SSFP**; Oral presentation at NYU I2I Workshop 2016 [PDF]**Optimized CS-Wave imaging with tailored sampling and efficient reconstruction**; Oral presentation at ISMRM 2016 [PDF]**Rapid Multi-Orientation Susceptibility Mapping with Wave-CAIPI**; Oral presentation at ISMRM 2015 [PDF]**RARE/Turbo Spin Echo Imaging with Simultaneous MultiSlice Wave-CAIPI**; Oral presentation at ISMRM 2015 [PDF]**Rapid Acquisition for Multi-Orientation QSM**; Short oral presentation at 3rd QSM Workshop 2014 [PDF]**Single-Step QSM with Fast Reconstruction**; Short oral presentation at 3rd QSM Workshop 2014 [PDF]**Rapid QSM Acquisition with Wave-CAIPI**; Power poster presentation at ISMRM 2014 [Talk] [Poster]**Fast Reconstruction for Regularized Quantitative Susceptibility Mapping**; Oral presentation at ISMRM 2014 [PDF]**Fast DSI Reconstruction with Trained Dictionaries**; Oral presentation at ISMRM 2013 [PDF]**Regularized QSM in Seconds**; Oral presentation at ISMRM 2013 [PDF]**Fast Regularized Reconstruction Tools for QSM and DSI**; Oral presentation at ISMRM Workshop on Data Sampling & Image Reconstruction 2013 [PDF]**Reconstruction Algorithms for MRI**; PhD Thesis Defense [PDF]**Accelerated DSI with Compressed Sensing using Adaptive Dictionaries**; Oral presentation at MICCAI 2012 [PDF]**Joint Bayesian Compressed Sensing with Prior Estimate**; Oral presentation at ISMRM 2012 [PDF]**Joint Bayesian Compressed Sensing for Multi-contrast Reconstruction**; Oral presentation at ISMRM 2011 [PDF]**Quantitative Susceptibility Map Reconstruction with Magnitude Prior**; Oral presentation at ISMRM 2011 [PDF]

### Journal Publications:

*An up-to-date list can be found on [Google Scholar] and
[PubMed]*

- S. Demir, B. Clifford, W.C. Lo, A. Tabari, A.L.M. Goncalves Filho, M. Lang, S.F. Cauley, K. Setsompop,
, M.H. Lev, P.W. Schaefer, O. Rapalino, S.Y. Huang, T. Hilbert, T. Feiweier, J. Conklin;*B. Bilgic***Optimization of magnetization transfer contrast for EPI FLAIR brain imaging;**Magnetic Resonance in Medicine - B. Clifford, J. Conklin, S.Y. Huang, T. Feiweier, Z. Hosseini, A.L.M. Goncalves Filho, A. Tabari, S. Demir, W.C. Lo, M.G.F. Longo, M. Lev, P. Schaefer, O. Rapalino, K. Setsompop,
, S. Cauley;*B. Bilgic***An artificial intelligence-accelerated 2-minute multi-shot echo planar imaging protocol for comprehensive high-quality clinical brain imaging;**Magnetic Resonance in Medicine - Z. Li, Q. Tian, C. Ngamsombat, S. Cartmell, J. Conklin, A.L.M.G Filho, W.C. Lo, G. Wang, K. Ying, K. Setsompop, Q. Fan,
, S. Cauley, S.Y. Huang;*B. Bilgic***High-fidelity fast volumetric brain MRI using synergistic wave-controlled aliasing in parallel imaging and a hybrid denoising generative adversarial network (HDnGAN);**Medical Physics - Y. Arefeen, O.Beker, J. Cho, H. Yu, E. Adalsteinsson,
;*B. Bilgic***Scan-specific artifact reduction in k-space (SPARK) neural networks synergize with physics-based reconstruction to accelerate MRI;**Magnetic Resonance in Medicine [preprint] [Python code] - R. Jones, C. Maffei, J. Augustinack, B. Fischl, H. Wang,
, A. Yendiki;*B. Bilgic***High-fidelity approximation of grid- and shell-based sampling schemes from undersampled DSI using compressed sensing: Post mortem validation;**Neuroimage - F.F. Yu, S.Y. Huang, A. Kumar, T. Witzel, C. Liao, T. Duval, J. Cohen-Adad,
;*B. Bilgic***Rapid simultaneous acquisition of macromolecular tissue volume, susceptibility, and relaxometry maps;**Magnetic Resonance in Medicine - S.Y. Huang, T. Witzel, B. Keil, A. Scholz, M. Davids, P. Dietz, E. Rummert, R. Ramb, J.E. Kirsch, A. Yendiki, Q. Fan, Q. Tian, G. Ramos-Llordén, H.H. Lee, A. Nummenmaa,
, K. Setsompop, F. Wang, A.V. Avram, M. Komlosh, D. Benjamini, K.N. Magdoom, S. Pathak, W. Schneider, D.S. Novikov, E. Fieremans, S. Tounekti, C. Mekkaoui, J. Augustinack, D. Berger, A. Shapson-Coe, J. Lichtman, P.J. Basser, L.L. Wald, B.R. Rosen;*B. Bilgic***Connectome 2.0: Developing the next-generation ultra-high gradient strength human MRI scanner for bridging studies of the micro-, meso- and macro-connectome;**Neuroimage - A. Scholz, R. Etzel, M.W. May, M. Mahmutovic, Q. Tian, G. Ramos-Llordén, C. Maffei,
, T. Witzel, J.P. Stockmann, C. Mekkaoui, L.L. Wald, S.Y. Huang, A. Yendiki, B. Keil;*B. Bilgic***A 48-channel receive array coil for mesoscopic diffusion-weighted MRI of ex vivo human brain on the 3 T connectome scanner;**Neuroimage - QSM Challenge 2.0 Organization Committee,
, C. Langkammer, J.P. Marques, J. Meineke, C. Milovic, F. Schweser;*B. Bilgic***QSM reconstruction challenge 2.0: Design and report of results;**Magnetic Resonance in Medicine [PDF] [Matlab code] - M.K. Manhard, J.P. Stockmann, C. Liao, D. Park, S. Han, M. Fair, M. van den Boomen, J.R. Polimeni,
, K. Setsompop;*B. Bilgic***A multi-inversion multi-echo spin and gradient echo echo planar imaging sequence with low image distortion for rapid quantitative parameter mapping and synthetic image contrasts;**Magnetic Resonance in Medicine - C. Liao,
, Q. Tian, J.P. Stockmann, X. Cao, Q. Fan, S.S Iyer, F. Wang, C. Ngamsombat, W.C. Lo, M.K. Manhard, S.Y. Huang, L.L. Wald, K. Setsompop;*B. Bilgic***Distortion-free, high-isotropic-resolution diffusion MRI with gSlider BUDA-EPI and multicoil dynamic B0 shimming;**Magnetic Resonance in Medicine - Q. Tian, N. Zaretskaya, Q. Fan, C. Ngamsombat,
, J.R. Polimeni, S.Y. Huang;*B. Bilgic***Improved cortical surface reconstruction using sub-millimeter resolution MPRAGE by image denoising;**Neuroimage - J.P. Marques, J. Meineke, C. Milovic,
, K.S. Chan, R. Hedouin, W. van der Zwaag, C. Langkammer, F. Schweser;*B. Bilgic***QSM reconstruction challenge 2.0: A realistic in silico head phantom for MRI data simulation and evaluation of susceptibility mapping procedures;**Magnetic Resonance in Medicine - Z. Dong, F. Wang, K.S. Chan, T.G. Reese,
, J.P. Marques, K. Setsompop;*B. Bilgic***Variable flip angle echo planar time-resolved imaging (vFA-EPTI) for fast high-resolution gradient echo myelin water imaging;**Neuroimage - Q. Tian,
, Q. Fan, C. Ngamsombat, N. Zaretskaya, N.E. Fultz, N.A. Ohringer, A.S. Chaudhari, Y. Hu, T. Witzel, K. Setsompop, J.R. Polimeni, S.Y. Huang;*B. Bilgic***Improving in vivo human cerebral cortical surface reconstruction using data-driven super-resolution;**Cerebral Cortex - C. Milovic, C. Prieto,
, S. Uribe, J. Acosta-Cabronero, P. Irarrazaval, C. Tejos;*B. Bilgic***Comparison of parameter optimization methods for quantitative susceptibility mapping;**Magnetic Resonance in Medicine - Q. Tian,
, Q. Fan, C. Liao, C. Ngamsombat, Y. Hu, T. Witzel, K. Setsompop, J.R. Polimeni, S.Y. Huang;*B. Bilgic***DeepDTI: High-fidelity six-direction diffusion tensor imaging using deep learning;**Neuroimage - D. Polak, I. Chatnuntawech, J. Yoon, S.S. Iyer, J. Lee, P. Bachert, E. Adalsteinsson, K. Setsompop,
;*B. Bilgic***Nonlinear dipole inversion (NDI) enables robust quantitative susceptibility mapping (QSM);**NMR in Biomedicine [preprint] [Matlab code] - X. Cao, C. Liao, Z. Zhang, S.S. Iyer, K. Wang, H. He, H. Liu, K. Setsompop, J. Zhong,
;*B. Bilgic***Efficient T2 mapping with blip-up/down EPI and gSlider-SMS (T2-BUDA-gSlider);**Magnetic Resonance in Medicine [preprint] [Matlab code] - D. Polak, S. Cauley,
, E. Gong, P. Bachert, E. Adalsteinsson, K. Setsompop;*B. Bilgic***Joint multi-contrast Variational Network reconstruction (jVN) with application to rapid 2D and 3D imaging;**Magnetic Resonance in Medicine - Z. Dong, F. Wang, T.G. Reese,
, K. Setsompop;*B. Bilgic***Echo Planar Time-Resolved Imaging (EPTI) with Subspace Reconstruction and Optimized Spatiotemporal Encoding;**Magnetic Resonance in Medicine - C. Milovic, C. Tejos, J. Acosta-Cabronero, P.S. Özbay, F. Schwesser, J.P. Marques, P. Irarrazaval,
, C. Langkammer;*B. Bilgic***The 2016 QSM Challenge: Lessons learned and considerations for a future challenge design;**Magnetic Resonance in Medicine - S. Han, C. Liao, M.K. Manhard, D.J. Park,
, M.J. Fair, F. Wang, A.I. Blazejewska, W.A. Grissom, J.R. Polimeni, K. Setsompop;*B. Bilgic***Accelerated spin-echo functional MRI using multisection excitation by simultaneous spin-echo interleaving (MESSI) with complex-encoded generalized slice dithered enhanced resolution (cgSlider) simultaneous multislice echo-planar imaging;**Magnetic Resonance in Medicine - C. Liao, J. Stockmann, Q. Tian,
, N.S. Arango, M.K. Manhard, S.Y. Huang, W.A. Grissom, L.L. Wald, K. Setsompop;*B. Bilgic***High-fidelity, high-isotropic-resolution diffusion imaging through gSlider acquisition with B1+ and T1 corrections and integrated ΔB0 /Rx shim array;**Magnetic Resonance in Medicine - M.W. Haskell, S.F. Cauley,
, J. Hossbach, D.N. Splitthoff, J. Pfeuffer, K. Setsompop, L.L. Wald;*B. Bilgic***Network Accelerated Motion Estimation and Reduction (NAMER): Convolutional neural network guided retrospective motion correction using a separable motion model;**Magnetic Resonance in Medicine - M.K. Manhard,
, C. Liao, S.H. Han, T. Witzel, Y.F. Yen, K. Setsompop;*B. Bilgic***Accelerated whole brain perfusion imaging using a simultaneous multi-slice (SMS) spin and gradient echo (SAGE) sequence with joint-virtual coil (JVC) reconstruction;**Magnetic Resonance in Medicine , I. Chatnuntawech, M.K. Manhard, Q. Tian, C. Liao, S.F. Cauley, S.Y. Huang, J.R. Polimeni, L.L. Wald, K. Setsompop;*B. Bilgic***Highly Accelerated Multishot EPI through Synergistic Machine Learning and Joint Reconstruction;**Magnetic Resonance in Medicine [preprint] [Matlab code]- I. Chatnuntawech, K. Tantisantisom, P. Khanchaitit, T. Boonkoom,
, E. Chuangsuwanich;*B. Bilgic***Rice Classification Using Spatio-Spectral Deep Convolutional Neural Network;**arXiv preprint arXiv:1805.11491 - C. Liao, M.K. Manhard,
, an, Q. Fan, S. Han, F. Wang, D.J. Park, T. Witzel, J. Zhong, H. Wang, L.L. Wald, K. Setsompop;*B. Bilgic***Phase-matched virtual coil reconstruction for highly accelerated diffusion echo-planar imaging;**Neuroimage - D. Polak, S.F. Cauley, S.Y. Huang, M.G. Longo, J. Conklin,
, N. Ohringer, E. Raithel, P. Bachert, L.L. Wald, K. Setsompop;*B. Bilgic***Highly-accelerated volumetric brain examination using optimized wave-CAIPI encoding;**Journal of Magnetic Resonance Imaging - F. Wang, Z. Dong, T.G. Reese,
, M.K. Manhard, J. Chen, J.R. Polimeni, L.L. Wald, K. Setsompop;*B. Bilgic***Echo planar time-resolved imaging (EPTI);**Magnetic Resonance in Medicine - T.H. Kim,
, D. Polak, K. Setsompop, J.P. Haldar;*B. Bilgic***Wave-LORAKS: Combining Wave Encoding with Structured Low-Rank Matrix Modeling for More Highly Accelerated 3D Imaging;**Magnetic Resonance in Medicine - J. Yoon#, E. Gong#, I. Chatnuntawech,
, J. Lee, W. Jung, J. Ko, H. Jung, K. Setsompop, G. Zaharchuk, E.Y. Kim, J. Pauly, J. Lee;*B. Bilgic***Quantitative Susceptibility Mapping using Deep Neural Network: QSMnet;**NeuroImage

# Equal contribution - G.C. Ngo,
, B.A. Gagoski, B.P. Sutton;*B. Bilgic***Correction of Magnetic Field Inhomogeneity Effects for Fast Quantitative Susceptibility Mapping;**Magnetic Resonance in Medicine - C. Milovic,
, B. Zhao, C. Langkammer, C. Tejos, J. Acosta-Cabronero;*B. Bilgic***Weak-harmonic regularization for quantitative susceptibility mapping (WH-QSM);**Magnetic Resonance in Medicine - Z. Dong, F. Wang, T.G. Reese, M.K. Manhard,
, L.L. Wald, H. Guo, K. Setsompop;*B. Bilgic***Tilted-CAIPI for Highly Accelerated Distortion-Free EPI with Point Spread Function (PSF) Encoding;**Magnetic Resonance in Medicine - F.F. Yu, F. Chiang, N. Stephens, B. Tantiwongkosi,
, S.Y. Huang, R. Romero;*B. Bilgic***Characterization of normal-appearing white matter in multiple sclerosis using quantitative susceptibility mapping in conjunction with diffusion tensor imaging;**Neuroradiology - F. Wang,
, Z. Dong, M.K. Manhard, N. Ohringer, B. Zhao, M. Haskell, S.F. Cauley, Q. Fan, T. Witzel, E. Adalsteinsson, L.L. Wald, K. Setsompop;*B. Bilgic***Motion-robust sub-millimeter isotropic diffusion imaging through motion corrected generalized slice dithered enhanced resolution (MC-gSlider) acquisition;**Magnetic Resonance in Medicine - Z. Wu#,
#, H. He, Y. Sun, Y. Du, K. Setsompop, J. Zhong;*B. Bilgic***Wave-CAIPI ViSTa: Highly Accelerated Whole-Brain Direct Myelin Water Imaging with Zero-Padding Reconstruction;**Magnetic Resonance in Medicine

# Equal contribution #, T.H. Kim#, C. Liao, M.K. Manhard, L.L. Wald, J. Haldar, K. Setsompop;*B. Bilgic***Improving Parallel Imaging by Jointly Reconstructing Multi-Contrast Data;**Magnetic Resonance in Medicine [PDF] [Matlab code]

# Equal contribution- C. Milovic,
, B. Zhao, J. Acosta-Cabronero, C. Tejos;*B. Bilgic***Fast Nonlinear Susceptibility Inversion with Variational Regularization;**Magnetic Resonance in Medicine [Matlab code] - C. Liao#,
#, M.K. Manhard, B. Zhao, X. Cao, J. Zhong, L.L. Wald, K. Setsompop;*B. Bilgic***3D MR fingerprinting with accelerated stack-of-spirals and hybrid sliding-window and GRAPPA reconstruction;**NeuroImage [PDF]

# Equal contribution - C. Langkammer#, F. Schweser#, K. Shmueli#, C. Kames, X. Li, L. Guo, C. Milovic, J. Kim, H. Wei, K. Bredies, S. Buch, Y. Guo, Z. Liu, J. Meineke, A. Rauscher, J.P. Marques,
>#;*B. Bilgic***Quantitative Susceptibility Mapping: Report from the 2016 Reconstruction Challenge;**Magnetic Resonance in Medicine [PDF]

# Equal contribution #, H. Ye#, L.L. Wald, K. Setsompop;*B. Bilgic***Simultaneous Time Interleaved MultiSlice (STIMS) for Rapid Susceptibility Weighted Acquisition;**NeuroImage [PDF] [Matlab code]

# Equal contribution- S. Soman, J.A. Bregni,
, U. Nemec, A.P. Fan, Z. Liu, R.L. Barry, J. Du, M. Moseley, Y. Wang;*B. Bilgic***Susceptibility Based Neuroimaging: Standard Methods, Clinical Applications and Future Directions;**Current Radiology Reports,*review article* - K. Setsompop, Q. Fan,
, J. Stockmann, S. Huang, S.F. Cauley, A. Nummenmaa, Y. Rathi, T. Witzel, L.L. Wald;*B. Bilgic***High-resolution In Vivo Diffusion Imaging of the Human Brain with Generalized SLIce Dithered Enhanced Resolution Simultaneous MultiSlice (gSlider-SMS);**Magnetic Resonance in Medicine - D. Polak, K. Setsompop, S.F. Cauley, B.A. Gagoski, F. Maier, P. Bachert, L.L. Wald,
;*B. Bilgic***Wave-CAIPI for Highly Accelerated MP-RAGE Imaging;**Magnetic Resonance in Medicine [PDF] - U. Yarach, M.H. In, I. Chatnuntawech,
, F. Godenschweger, H. Mattern, A. Sciarra, O. Speck;*B. Bilgic***Model-based Iterative Reconstruction for Single-shot EPI at 7T;**Magnetic Resonance in Medicine - S.F. Cauley, K. Setsompop,
, H. Bhat, B.A. Gagoski, L.L. Wald;*B. Bilgic***Auto-calibrated Wave-CAIPI Reconstruction; Joint Optimization of K-space Trajectory and Parallel Imaging Reconstruction;**Magnetic Resonance in Medicine - H. Ye, S.F. Cauley, B.A. Gagoski,
, D. Ma, Y. Jiang, Y. Du, M.A. Griswold, L.L. Wald, K. Setsompop;*B. Bilgic***Simultaneous Multi-Slice Magnetic Resonance Fingerprinting (SMS-MRF) with Direct-spiral Slice- GRAPPA (ds-SG) Reconstruction**; Magnetic Resonance in Medicine - I. Chatnuntawech, P. McDaniel, S.F. Cauley, B.A. Gagoski, C. Langkammer, A. Martin, P.E. Grant, L.L. Wald, K. Setsompop, E. Adalsteinsson,
;*B. Bilgic***TGV-Regularized Single-Step Quantitative Susceptibility Mapping**; NMR in Biomedicine [PDF] [Matlab code] - P. McDaniel,
, A.P. Fan, J. Stout, E. Adalsteinsson;*B. Bilgic***Mitigation of Partial-Volume Effects in Susceptibility-Based Oxygenation Measurements by Joint Utilization of Magnitude and Phase (JUMP)**; Magnetic Resonance in Medicine - I. Chatnuntawech#, A. Martin#,
, K. Setsompop, E. Adalsteinsson, E. Schiavi;*B. Bilgic***Vectorial Total Generalized Variation for Accelerated Multi-Channel Multi-Contrast MRI**; Magnetic Resonance Imaging

# Equal contribution , L. Xie, R. Dibb, C. Langkammer, A. Mutluay, H. Ye, J.R. Polimeni, C. Liu, L.L. Wald, K. Setsompop;*B. Bilgic***Rapid Multi-Orientation Quantitative Susceptibility Mapping**; NeuroImage [PDF] [Matlab code]- C. Langkammer, K. Bredies, B.A. Poser, M. Barth, G. Reishofer, A.P. Fan,
, F. Fazekas, C. Mainero, S. Ropele;*B. Bilgic***Fast Quantitative Susceptibility Mapping using 3D EPI and Total Generalized Variation**; NeuroImage - B. Gagoski#,
#, C. Eichner, H. Bhat, P.E. Grant, L.L. Wald, K. Setsompop;*B. Bilgic***RARE/Turbo Spin Echo Imaging with Simultaneous MultiSlice Wave-CAIPI**; Magnetic Resonance in Medicine [PDF] [Matlab code]

# Equal contribution , B. Gagoski, S.F. Cauley, A.P. Fan, J.R. Polimeni, P.E. Grant, L.L. Wald, K. Setsompop;*B. Bilgic***Wave-CAIPI for Highly Accelerated 3D Imaging**; Magnetic Resonance in Medicine [PDF] [Matlab code]

Editor's pick June 2015- I. Chatnuntawech, B. Gagoski,
, S.F. Cauley, K. Setsompop, E. Adalsteinsson;*B. Bilgic***Accelerated MRSI Using Randomly Undersampled Spiral-Based k-Space Trajectories**; Magnetic Resonance in Medicine - S.F. Cauley, Y. Xi,
, J. Xia, E. Adalsteinsson, V. Balakrishnan, L.L. Wald, K. Setsompop;*B. Bilgic***Fast reconstruction for multichannel compressed sensing using a hierarchically semiseparable solver**; Magnetic Resonance in Medicine , A.P. Fan, J.R. Polimeni, S.F. Cauley, M. Bianciardi, E. Adalsteinsson, L.L. Wald, K. Setsompop;*B. Bilgic***Fast Quantitative Susceptibility Mapping with L1-Regularization and Automatic Parameter Selection**; Magnetic Resonance in Medicine [PDF] [Matlab code]- A.P. Fan,
, L. Gagnon, T. Witzel, H. Bhat, B.R. Rosen, E. Adalsteinsson;*B. Bilgic***Quantitative Oxygenation Venography from MRI Phase**; Magnetic Resonance in Medicine , I. Chatnuntawech, A.P. Fan, K. Setsompop, S.F. Cauley, L.L. Wald, E. Adalsteinsson;*B. Bilgic***Fast Image Reconstruction with L2-Regularization**; Journal of Magnetic Resonance Imaging [PDF] [Matlab code], I. Chatnuntawech, K. Setsompop, S.F. Cauley, L.L. Wald, E. Adalsteinsson;*B. Bilgic***Fast Diffusion Spectrum Imaging Reconstruction with Trained Dictionaries**; IEEE Transactions on Medical Imaging, [PDF] [Revised Matlab code], K. Setsompop, J. Cohen-Adad, A. Yendiki, L.L. Wald, E. Adalsteinsson;*B. Bilgic***Accelerated Diffusion Spectrum Imaging with Compressed Sensing using Adaptive Dictionaries**; Magnetic Resonance in Medicine, [PDF] [Matlab code]

Cover article December 2012, B. Gagoski, T. Kok, E. Adalsteinsson;*B. Bilgic***Lipid Suppression in CSI with Spatial Priors and Highly Undersampled Peripheral k-space**; Magnetic Resonance in Medicine, [PDF] [Matlab code]-
, A. Pfefferbaum, T. Rohlfing, E.V. Sullivan, E. Adalsteinsson;*B. Bilgic***MRI Estimates of Brain Iron Concentration in Normal Aging Using Quantitative Susceptibility Mapping**; NeuroImage, [PDF] [Matlab code] -
, V.K. Goyal, E. Adalsteinsson;*B. Bilgic***Multi-contrast Reconstruction with Bayesian Compressed Sensing**; Magnetic Resonance in Medicine, [PDF] [Matlab code]

MIT News article: New algorithm could substantially speed up MRI scans

### Conference Papers:

- Z. Zhang, H. Ye, M. Li, H. Liu,
;*B. Bilgic***Liver-BUDA-SAGE: Simultaneous whole liver T2 and T2* mapping in one breath-hold**; International Symposium on Biomedical Imaging: Kolkata, India, 2022 - C Liao, X Cao, J Cho, Z Zhang, K Setsompop,
;*B. Bilgic***Highly efficient MRI through multi-shot echo planar imaging**; Wavelets and Sparsity XVIII, SPIE 2019 [PDF] - B. Zhao,
, E. Adalsteinsson, M.A. Griswold, L.L. Wald, K. Setsompop;*B. Bilgic***Simultaneous multislice magnetic resonance fingerprinting with low-rank and subspace modeling**; EMBC 2017 - S. Cetin,
, A.P. Fan, S.J. Holdsworth, G. Unal;*B. Bilgic***Vessel Orientation Constrained Quantitative Susceptibility Mapping (QSM) Reconstruction**; MICCAI 2016 , I. Chatnuntawech, C. Langkammer, K. Setsompop;*B. Bilgic***Sparse Methods for Quantitative Susceptibility Mapping**; Wavelets and Sparsity XIV, SPIE 2015 [PDF] [Matlab code]- I. Chatnuntawech,
, A. Martin, K. Setsompop, E. Adalsteinsson;*B. Bilgic***Fast Reconstruction for Accelerated Multi-Slice Multi-Contrast MRI**; International Symposium on Biomedical Imaging: From Nano to Macro, 2015 - B. Zhao, F. Lam,
, H. Ye, K. Setsompop;*B. Bilgic***Maximum Likelihood Reconstruction for Magnetic Resonance Fingerprinting**; International Symposium on Biomedical Imaging: From Nano to Macro, 2015 - F. Yanez, A.P. Fan,
, C. Milovic, E. Adalsteinsson, P. Irarrazaval;*B. Bilgic***Quantitative Susceptibility Map Reconstruction via Total Generalized Variation Regularization**; 3rd International Workshop on Pattern Recognition in NeuroImaging , K. Setsompop, J. Cohen-Adad, V. Wedeen, L. Wald, E. Adalsteinsson;*B. Bilgic***Accelerated Diffusion Spectrum Imaging with Compressed Sensing using Adaptive Dictionaries**; MICCAI 2012, [PDF] [Matlab code]

MICCAI Young Scientist Award Finalist, B.K.P. Horn, I. Masaki;*B. Bilgic***Fast Human Detection with Cascaded Ensembles on the GPU**; IEEE Intelligent Vehicles Symposium, 2010, Pages: 325 - 332 [PDF], B.K.P. Horn, I. Masaki;*B. Bilgic***Efficient Integral Image Computation on the GPU**; IEEE Intelligent Vehicles Symposium, 2010, Pages: 528 - 533 [PDF]

### Conference Abstracts:

#### 2020:

- W-C Lo, B. Clifford, S. Bollmann, T. Feiweier, S. Giri, C. Liao, J. Cho, S. Cauley, K. Setsompop,
; 2-minute Comprehensive Brain Exam Using Multi-Shot EPI with Synergistic Model-Based & Deep Learning Reconstruction; ISMRM Workshop on MData Sampling & Image Reconstruction, Sedona, AZ, USA, 2020*B. Bilgic* - W. Lee, S. So, J. Cho, C. Liao, Q. Tian, H. Park, E. Adalsteinsson, K. Setsompop,
; Rapid Distortion Free Diffusion Imaging Using Joint k/q-Space Reconstruction & Tailored Acquisition; ISMRM Workshop on MData Sampling & Image Reconstruction, Sedona, AZ, USA, 2020*B. Bilgic* - Q. Tian,
, Q. Fan, C. Liao, C. Ngamsombat, Y. Hu, T. Witzel, K. Setsompop, J. Polimeni, S. Huang; High-fidelity diffusion tensor MRI with six diffusion-weighted images using optimized q-space sampling and deep learning; ISMRM Workshop on MData Sampling & Image Reconstruction, Sedona, AZ, USA, 2020*B. Bilgic*

#### 2019:

- J. Cho, H. Park, K. Setsompop,
; Multi-shot Echo-planar Imaging with Simultaneous MultiSlice Wave-Encoding; International Society for Magnetic Resonance in Medicine 27th Scientific Meeting, Montreal, 2019*B. Bilgic* - D. Polak, I. Chatnuntawech, J. Yoon, S.S. Iyer, K. Setsompop,
; VaNDI: Variational Nonlinear Dipole Inversion enables QSM without free parameters; International Society for Magnetic Resonance in Medicine 27th Scientific Meeting, Montreal, 2019 [Matlab code]*B. Bilgic* ; C. Liao, M.K. Manhard, Q. Tian, I. Chatnuntawech, S.S. Iyer, S.F. Cauley, T. Feiweier, S. Giri, Y. Hu, S. Huang, J. Polimeni, L.L. Wald, K. Setsompop; Robust high-quality multi-shot EPI with low-rank prior and machine learning; International Society for Magnetic Resonance in Medicine 27th Scientific Meeting, Montreal, 2019 [HTML] [Matlab code]*B. Bilgic*- X. Cao, C. Liao, S.S. Iyer, H. He, K. Setsompop, J. Zhong,
; T2-gSlider: rapid high resolution T2 mapping with generalized SLIce Dithered Enhanced Resolution and model-based reconstruction; International Society for Magnetic Resonance in Medicine 27th Scientific Meeting, Montreal, 2019 [Matlab code]*B. Bilgic* - M.K. Manhard, C. Liao, J. Stockmann, D. Park, S. Han, J. Polimeni,
, JK. Setsompop; Combined T1, T2, and T2* mapping using a multi-inversion multi-echo spin and gradient echo EPI sequence; International Society for Magnetic Resonance in Medicine 27th Scientific Meeting, Montreal, 2019*B. Bilgic* - R. Jones, G. Grisot, J. Augustinack, D. Boas, B. Fischl, H. Wang,
, A. Yendiki; Validation of DSI compressed sensing reconstruction in ex vivo human brain; International Society for Magnetic Resonance in Medicine 27th Scientific Meeting, Montreal, 2019*B. Bilgic* - J. Marques,
, J. Maineke, C. Milovic, K-S Chan, W. van der Zwaag, R. Hedouin, C. Langkammer, F. Schweser; Towards QSM Challenge 2.0: Creation and Evaluation of a Realistic Magnetic Susceptibility Phantom; International Society for Magnetic Resonance in Medicine 27th Scientific Meeting, Montreal, 2019*B. Bilgic* - Q. Tian,
, Q. Fan, C. Ngamsombat, A. Chaudhari, N. Ohringer, Y. Hu, T. Witzel, K. Setsompop, J. Polimeni, S. Huang; SuperSurfer: Cortical surface reconstruction using super-resolution anatomical MR images synthesized by deep learning; International Society for Magnetic Resonance in Medicine 27th Scientific Meeting, Montreal, 2019*B. Bilgic* - Q. Tian,
, Q. Fan, C. Ngamsombat, C. Liao, Y. Hu, T. Witzel, K. Setsompop, J. Polimeni, S. Huang; Six-direction diffusion tensor MRI using a convolutional neural network; International Society for Magnetic Resonance in Medicine 26th Scientific Meeting, Montreal, 2019*B. Bilgic* - S.S. Iyer, D. Polak, C. Liao, S.F. Cauley,
, K. Setsompop; Rapid, Time-Resolved Brain Imaging with Multiple Clinical Contrasts using Wave-Shuffling; International Society for Magnetic Resonance in Medicine 26th Scientific Meeting, Montreal, 2019*B. Bilgic* - M. Fair, F. Wang, Z. Dong,
, T. Reese, K. Setsompop, L.L. Wald; Propeller Echo-Planar Time-resolved Imaging with Dynamic Encoding (PEPTIDE); International Society for Magnetic Resonance in Medicine 26th Scientific Meeting, Montreal, 2019*B. Bilgic* - M. Haskell, S.F. Cauley,
, J. Hossbach, J. Pfeuffer, K. Setsompop, L.L. Wald; Network Accelerated Motion Estimation and Reduction (NAMER): Accelerating forward model based retrospective motion correction using a convolutional neural network; International Society for Magnetic Resonance in Medicine 26th Scientific Meeting, Montreal, 2019*B. Bilgic* - D. Polak, S.F. Cauley,
, E. Raithel, P. Bachert, E. Adalsteinsson, K. Setsompop; Joint multi-contrast Variational Network reconstruction (jVN) with application to Wave-CAIPI acquisition for rapid imaging; International Society for Magnetic Resonance in Medicine 26th Scientific Meeting, Montreal, 2019*B. Bilgic* - C. Liao, J. Stockmann, Q. Tian,
, M.K. Manhard, L.L. Wald, K. Setsompop; High-fidelity, high-isotropic resolution diffusion imaging through gSlider acquisition with B1+ & T1 corrections and multi-coil B0 shim array; International Society for Magnetic Resonance in Medicine 26th Scientific Meeting, Montreal, 2019*B. Bilgic* - S.F. Cauley, D. Polak, W. Liu,
, B. Gagoski, P.E. Grant, J. Conklin, J. Kirsch, S. Huang, K. Setsompop, L.L. Wald; Geometric Coil Mixing (GCM) to Dampen Confounding Signals in MRI Reconstruction; International Society for Magnetic Resonance in Medicine 26th Scientific Meeting, Montreal, 2019*B. Bilgic* - Q. Tian, C. Ngamsombat,
, Q. Fan, Y. Hu, J. McNab, T. Witzel, K. Setsompop, J. Polimeni, S. Huang; Creating a diffusion tractography-based atlas of human thalamic ventral intermediate nucleus aided by deep learning; International Society for Magnetic Resonance in Medicine 26th Scientific Meeting, Montreal, 2019*B. Bilgic* - F. Wang, Z. Dong, T. Reese,
, M.K. Manhard, J. Chen, J. Polimeni, L.L. Wald, K. Setsompop; Echo Planar Time-Resolved Imaging (EPTI); International Society for Magnetic Resonance in Medicine 26th Scientific Meeting, Montreal, 2019*B. Bilgic* - Z. Dong, F. Wang, T. Reese,
, K. Setsompop; Echo Planar Time-Resolved Imaging (EPTI) with subspace constraint and optimized k-t trajectory; International Society for Magnetic Resonance in Medicine 26th Scientific Meeting, Montreal, 2019*B. Bilgic*

#### 2018:

, I. Chatnuntawech, S.F. Cauley, M.K. Manhard, L.L. Wald, K. Setsompop;*B. Bilgic***Accelerated Multi-shot EPI through Machine Learning and Joint Reconstruction**; ISMRM Workshop on Machine Learning, Pacific Grove, CA, USA, 2018,*oral presentation*[PDF] [Data & Python code for Keras]- J. Yoon, E. Gong, G. Zaharchuk, J. Pauly,
, J. Lee, J. Ko, H. Jung, J. Lee; QSM with deep neural network; ISMRM Workshop on Machine Learning, Pacific Grove, CA, USA, 2018*B. Bilgic* - D. Polak, E. Gong, S.F. Cauley,
, E. Raithel, G. Zaharchuk, J. Pauly, Kawin Setsompop; Faster 3D brain scans using Wave-CAIPI encoding and Deep Learning denoising; ISMRM Workshop on Machine Learning, Pacific Grove, CA, USA, 2018*B. Bilgic* - B. Zhu,
, C. Liao, B.R. Rosen, M.S. Rosen; Deep learning MR reconstruction with Automated Transform by Manifold Approximation (AUTOMAP) in real-world acquisitions with imperfect training: simulation and in-vivo experiments; ISMRM Workshop on Machine Learning, Pacific Grove, CA, USA, 2018*B. Bilgic* , S.F. Cauley, L.L. Wald, K. Setsompop; Joint SENSE Reconstruction for Faster Multi-Contrast Wave Encoding; International Society for Magnetic Resonance in Medicine 26th Scientific Meeting, Paris, 2018 [Matlab code] [PDF]*B. Bilgic*- F.F. Yu, S.Y. Huang, T. Duval, J. Cohen-Adad,
; Rapid simultaneous acquisition of QSM and MTV; International Society for Magnetic Resonance in Medicine 26th Scientific Meeting, Paris, 2018*B. Bilgic* , S.F. Cauley, I. Chatnuntawech, M.K. Manhard, F. Wang, M. Haskell, C. Liao, L.L. Wald, K. Setsompop; Combining MR-Physics and Machine Learning to Address Intractable Reconstruction Problems; International Society for Magnetic Resonance in Medicine 26th Scientific Meeting, Paris, 2018 [PDF] [Data & Python code for Keras]*B. Bilgic*- T.H. Kim,
, C. Liao, M.K. Manhard, L.L. Wald, J.P. Haldar, K. Setsompop; Improving Parallel Imaging by Jointly Reconstructing Multi-Contrast Data; International Society for Magnetic Resonance in Medicine 26th Scientific Meeting, Paris, 2018*B. Bilgic* - C. Milovic,
, B. Zhao, C. Langkammer, J. Acosta-Cabronero, C. Tejos; Nonlinear projection onto dipole fields with preconditioning (nPDF); International Society for Magnetic Resonance in Medicine 26th Scientific Meeting, Paris, 2018*B. Bilgic* - S. Han, C. Liao, M.K. Manhard,
, F. Wang, A.I. Blazejewska, M. van den Boomen, W.A. Grissom, J.R. Polimeni, K. Setsompop; Accelerated spin-echo fMRI using generalized SLIce Dithered Enhanced Resolution Simultaneous MultiSlice (gSlider-SMS) with 'complex-basis' RF-encoding; International Society for Magnetic Resonance in Medicine 26th Scientific Meeting, Paris, 2018*B. Bilgic* - M.K. Manhard,
, C. Liao, S. Han, T. Witzel, Y.F. Yen, K. Setsompop; Accelerated dynamic quantitative perfusion imaging using an optimized simultaneous multi-slice (SMS) spin and gradient echo (SAGE) sequence with joint-virtual coil (JVC) reconstruction; International Society for Magnetic Resonance in Medicine 26th Scientific Meeting, Paris, 2018*B. Bilgic* -
A.S. Kanaan, A. Anwander, R. Metere, A. Schafer, T. Schlumm, J. Near,
, K. Muller-Wahl H. Moller; Iron-related gene expression associated with magnetic susceptibility reductions: Application to the pathophysiology of a movement disorder population; International Society for Magnetic Resonance in Medicine 26th Scientific Meeting, Paris, 2018*B. Bilgic* -
F. Wang, Z. Dong, T.G. Reese,
, M.K. Manhard, L.L. Wald, K. Setsompop; Echo Planar Time-resolved Imaging (EPTI); International Society for Magnetic Resonance in Medicine 26th Scientific Meeting, Paris, 2018*B. Bilgic* -
F. Wang,
, Z. Dong, M.K. Manhard, N. Ohringer, B. Zhao, M. Haskell, S.F. Cauley, Q. Fan, T. Witzel, E. Adalsteinsson, L.L. Wald, K. Setsompop; Motion-robust sub-millimeter isotropic diffusion imaging through Motion Corrected Generalized Slice Dithered Enhanced Resolution (MC-gSlider) acquisition; International Society for Magnetic Resonance in Medicine 26th Scientific Meeting, Paris, 2018*B. Bilgic* -
Y.V. Chang, S.F. Cauley, W. Liu, D. Polak, B.A. Gagoski,
, K. Setsompop, J.R. Polimeni; Quantitative assessment of automatic cortical surface reconstructions from Wave-CAIPI MPRAGE: A validation study; International Society for Magnetic Resonance in Medicine 26th Scientific Meeting, Paris, 2018*B. Bilgic* -
E. Gong,
, K. Setsompop, A.P. Fan, G. Zaharchuk, J. Pauly; Accurate and Efficient QSM Reconstruction using Deep Learning; International Society for Magnetic Resonance in Medicine 26th Scientific Meeting, Paris, 2018*B. Bilgic* -
C. Liao, M.K. Manhard,
, Q. Fan, H. Wang, S. Han, D.J. Park, F. Wang, J. Zhong, L.L. Wald, K. Setsompop; Joint Virtual Coil Reconstruction with Background Phase Matching for Highly Accelerated Diffusion Echo-Planar Imaging; International Society for Magnetic Resonance in Medicine 26th Scientific Meeting, Paris, 2018*B. Bilgic* -
B. Zhu,
, C. Liao, B.R. Rosen, M.S. Rosen; Deep learning MR reconstruction with Automated Transform by Manifold Approximation (AUTOMAP) in real-world acquisitions with imperfect training; International Society for Magnetic Resonance in Medicine 26th Scientific Meeting, Paris, 2018*B. Bilgic* -
J. Yoon, J. Ko, J. Lee, H. Jung,
, K. Setsompop, J. Lee; Quantitative Susceptibility Mapping using Deep Neural Network; International Society for Magnetic Resonance in Medicine 26th Scientific Meeting, Paris, 2018*B. Bilgic* -
S. Lala, B.A. Gagoski, J.N. Stout, B. Zhao,
, P.E. Grant, P. Golland, E. Adalsteinsson; A Machine Learning Approach for Mitigating Artifacts in Fetal Imaging due to an Undersampled HASTE Sequence; International Society for Magnetic Resonance in Medicine 26th Scientific Meeting, Paris, 2018*B. Bilgic* -
C. Milovic,
, B. Zhao, C. Langkammer, C. Tejos, J. Acosta-Cabronero; Weak-harmonic regularization for quantitative susceptibility mapping (WH-QSM); International Society for Magnetic Resonance in Medicine 26th Scientific Meeting, Paris, 2018*B. Bilgic* -
D. Polak, S.F. Cauley, S.Y. Huang, M.G. Longo,
, E. Rathiel, L.L. Wald, K. Setsompop; Highly-accelerated volumetric brain protocol using optimized Wave-CAIPI encoding; International Society for Magnetic Resonance in Medicine 26th Scientific Meeting, Paris, 2018*B. Bilgic* -
H. Wei,
, K. Setsompop, B. Keil, D. Feinberg, C. Liu; Imaging Human Brain Cortical Substructure with Quantitative Susceptibility Mapping at 7 T; International Society for Magnetic Resonance in Medicine 26th Scientific Meeting, Paris, 2018*B. Bilgic* -
Z. Dong, F. Wang, T.G. Reese, M.K. Manhard,
, L.L. Wald, H. Guo, K. Setsompop; Fast Distortion-Free Diffusion Imaging using “tilted-CAIPI” PSF-EPI; International Society for Magnetic Resonance in Medicine 26th Scientific Meeting, Paris, 2018*B. Bilgic* -
Z. Dong, F. Wang, T.G. Reese, M.K. Manhard,
, L.L. Wald, H. Guo, K. Setsompop; Tilted-CAIPI for Highly Accelerated Distortion-Free EPI with Point Spread Function (PSF) Encoding; International Society for Magnetic Resonance in Medicine 26th Scientific Meeting, Paris, 2018*B. Bilgic* -
Z. Wu,
, H. He, Y. Sun, Y. Du, K. Setsompop, J. Zhong; Zero-padding reconstruction for wave-CAIPI images with improved accuracy, and its application in ViSTa myelin water images; International Society for Magnetic Resonance in Medicine 26th Scientific Meeting, Paris, 2018*B. Bilgic* -
S.S. Iyer,
, K. Setsompop; Faster T2 Shuffling with Wave-encoding; International Society for Magnetic Resonance in Medicine 26th Scientific Meeting, Paris, 2018*B. Bilgic* -
A. Tamanti, K. Bredies, M. Castellaro, S. Ropele,
, C. Langkammer; Structure tensor enhanced quantitative susceptibility mapping (ST-QSM); International Society for Magnetic Resonance in Medicine 26th Scientific Meeting, Paris, 2018*B. Bilgic* -
C. Liao,
, M.K. Manhard, X. Cao, J. Zhong, L.L. Wald, K. Setsompop; Optimized 3D Stack-of-Spirals MR Fingerprinting with Hybrid Sliding-Window and GRAPPA Reconstruction; International Society for Magnetic Resonance in Medicine 26th Scientific Meeting, Paris, 2018*B. Bilgic*

#### 2017:

, B. Zhao, I. Chatnuntawech, L.L. Wald, K. Setsompop;*B. Bilgic***Calibrationless Parallel Imaging in Multi Echo/Contrast Data**; International Society for Magnetic Resonance in Medicine 25th Scientific Meeting, Hawaii,*Power Pitch presentation*[HTML] [Matlab code], T. Witzel, H. Bhat, L.L. Wald, K. Setsompop;*B. Bilgic***Joint Reconstruction of Phase-Cycled Balanced SSFP with Constrained Parallel Imaging**; International Society for Magnetic Resonance in Medicine 25th Scientific Meeting, Hawaii,*Power Pitch presentation*[HTML] [Matlab code]- D. Polak, K. Setsompop, S.F. Cauley, B.A. Gagoski, H. Bhat, F. Maier, L.L. Wald,
;*B. Bilgic***Wave-CAIPI for Highly Accelerated MP-RAGE Imaging**; International Society for Magnetic Resonance in Medicine 25th Scientific Meeting, Hawaii,*Power Pitch presentation*

Magna Cum Laude Award -
B. Zhao,
, J. Stockmann, L.L. Wald, K. Setsompop;*B. Bilgic***A Maximum Likelihood Approach to Simultaneous Multislice Magnetic Resonance Fingerprinting**; International Society for Magnetic Resonance in Medicine 25th Scientific Meeting, Hawaii -
B.A. Poser,
, B.A. Gagoski, K. Uludag, V.A Stenger, L.L. Wald, K. Setsompop;*B. Bilgic***Echo-planar imaging with wave-CAIPI acquisition and reconstruction**; International Society for Magnetic Resonance in Medicine 25th Scientific Meeting, Hawaii -
T.H. Kim,
, D. Polak, K. Setsompop, J.P. Haldar;*B. Bilgic***Wave-LORAKS for faster Wave-CAIPI MRI**; International Society for Magnetic Resonance in Medicine 25th Scientific Meeting, Hawaii -
Z. Wu,
, H. He, Y. Sun, K. Setsompop, J. Zhong;*B. Bilgic***Wave-CAIPI ViSTa: Accelerated mapping for direct visualization of myelin water**; International Society for Magnetic Resonance in Medicine 25th Scientific Meeting, Hawaii -
G-C Ngo,
, B. Gagoski, B.P. Sutton; Incorporating macroscale susceptibility in QSM reconstruction with 3D spiral acquisition; International Society for Magnetic Resonance in Medicine 25th Scientific Meeting, Hawaii*B. Bilgic* -
C. Milovic,
, B. Zhao, J. Acosta-Cabronero, C. Tejos;*B. Bilgic***A Fast Algorithm for Nonlinear QSM Reconstruction**; International Society for Magnetic Resonance in Medicine 25th Scientific Meeting, Hawaii -
C.S. Aigner, A. Rund,
, B.A. Gagoski, K. Setsompop, K. Kunisch, R. Stollberger;*B. Bilgic***Application of time-optimal simultaneous multi-slice refocusing to TSE/RARE**; International Society for Magnetic Resonance in Medicine 25th Scientific Meeting, Hawaii -
H. Wang, J.R. Polimeni,
, L.L. Wald, K. Setsompop;*B. Bilgic***Analytical G-factor Calculation for Slice-GRAPPA with Odd-even Kernels (SG-OK)**; International Society for Magnetic Resonance in Medicine 25th Scientific Meeting, Hawaii -
H. Ye, C. Liao, Q. Li, Xiaozhi Cao, B. Zhao,
, K. Setsompop, H. He, H. Liu, J. Zhong;*B. Bilgic***Spiral-out and -in Double Echoes (SOIDE) Magnetic Resonance Fingerprinting with Improved T2 Mapping**; International Society for Magnetic Resonance in Medicine 25th Scientific Meeting, Hawaii -
A.S. Kanaan, A. Anwander, A. Schäfer,
, T. Schlumm, J. Near, K. Müller-Vahl2, H.E. Möller;*B. Bilgic***QSM meets MRS: The influence of subcortical iron on glutamatergic neurotransmission in a movement disorder population**; International Society for Magnetic Resonance in Medicine 25th Scientific Meeting, Hawaii -
B. Keil, C. Sappo,
, J.R. Polimeni, L. Golestani, R. Etzel, L.L Wald, D.A. Feinberg, K. Setsompop;*B. Bilgic***Sub-Millimeter Cortical Imaging at 7T using a High-Density Motor-Cortex 32-Channel Array Coil**; International Society for Magnetic Resonance in Medicine 25th Scientific Meeting, Hawaii -
R. Metere, A.S. Kanaan,
, T. Schlumm, H.E. Möller;*B. Bilgic***Effects of coil combination algorithms on Quantitative Susceptibility Mapping**; International Society for Magnetic Resonance in Medicine 25th Scientific Meeting, Hawaii -
S.D. Robinson, K. Eckstein, J.P. Marques,
, S. Trattnig, F. Schweser;*B. Bilgic***A comprehensive assessment of methods for combining phase data from array radio-frequency coils at 7T**; International Society for Magnetic Resonance in Medicine 25th Scientific Meeting, Hawaii

#### 2016:

, T. Witzel, H. Bhat, L.L. Wald, K. Setsompop*B. Bilgic***; Joint Reconstruction for Phase-Cycled Balanced SSFP**;

ESMRMB 33rd Scientific Meeting,

NYU Innovation to Implementation in Imaging Workshop [PDF] [Matlab code], J.P. Marques, L.L. Wald, K. Setsompop*B. Bilgic***; Block Coil Compression for Virtual Body Coil without Phase Singularities**; Fourth International Workshop on MRI Phase Contrast & Quantitative Susceptibility Mapping [PDF] [Matlab code], S.F. Cauley, H. Ye, C. Langkammer, B.A. Poser, K. Setsompop*B. Bilgic***; Accelerated QSM**; Fourth International Workshop on MRI Phase Contrast & Quantitative Susceptibility Mapping,*invited abstract*[PDF]- C. Milovic,
, B. Zhao, J. Acosta-Cabronero, C. Tejos*B. Bilgic***; A Fast Algorithm for Nonlinear QSM Reconstruction with Variational Penalties**; Fourth International Workshop on MRI Phase Contrast & Quantitative Susceptibility Mapping - R. Metere, A.S. Kanaan, A. Schäfer,
, T. Schlumm, H.E. Möller*B. Bilgic***; Effects of different coil reconstruction algorithms on QSM results**; Fourth International Workshop on MRI Phase Contrast & Quantitative Susceptibility Mapping - J. Kim, S. Bollmann, C. Langkammer,
; GPU-accelerated Quantitative Susceptibility Map Reconstruction with Total Generalized Variation Regularization; Fourth International Workshop on MRI Phase Contrast & Quantitative Susceptibility Mapping*B. Bilgic* , H. Ye, L.L. Wald, K. Setsompop;*B. Bilgic***Optimized CS-Wave imaging with tailored sampling and efficient reconstruction**; International Society for Magnetic Resonance in Medicine 24th Scientific Meeting,*oral presentation*[HTML]

Summa Cum Laude Award- I. Chatnuntawech, P. McDaniel, S.F. Cauley, B.A. Gagoski, C. Langkammer, A. Martin, P.E. Grant, L.L. Wald, K. Setsompop, E. Adalsteinsson,
*B. Bilgic***; TGV-Regularized Single-Step Quantitative Susceptibility Mapping**; International Society for Magnetic Resonance in Medicine 24th Scientific Meeting,*oral presentation*[HTML] [Matlab code] , J.R. Polimeni, L.L. Wald, K. Setsompop;*B. Bilgic***Automated tissue phase and QSM estimation from multichannel data**; International Society for Magnetic Resonance in Medicine 24th Scientific Meeting,*e-poster presentation*[HTML] [Matlab code]- P. McDaniel,
, A.P. Fan, J. Stout, E. Adalsteinsson;*B. Bilgic***Simultaneous Quantification of Blood Vessel Caliber and Oxygenation via Multi-Voxel Joint Utilization of Magnitude and Phase (MV-JUMP)**; International Society for Magnetic Resonance in Medicine 24th Scientific Meeting,*e-poster presentation* - S.F. Cauley, K. Setsompop,
, H. Bhat, B. Gagoski, T. Witzel, L.L. Wald;*B. Bilgic***Joint K-space Trajectory and Parallel Imaging Optimization for Auto-calibrated Image Reconstruction**; International Society for Magnetic Resonance in Medicine 24th Scientific Meeting,*power pitch presentation* - H. Ye,
, S.F. Cauley, B. Gagoski, J. Zhong, Y. Du, L.L. Wald, K. Setsompop;*B. Bilgic***Echo-Shift wave-CAIPI with Simultaneous MultiSlice for rapid susceptibility weighted FLASH imaging**; International Society for Magnetic Resonance in Medicine 24th Scientific Meeting,*e-poster presentation*

- H. Ye, B. Gagoski,
, S.F. Cauley, D. Ma, Y. Du, L.L. Wald, K. Setsompop;*B. Bilgic***Simultaneous Multi-Slice MR Fingerprinting with slice-GRAPPA reconstruction**; ISMRM Workshop on Simultaneous Multi-Slice Imaging, 2015 - B. Gagoski†,
†, C. Eichner, H. Bhat, P.E. Grant, L.L. Wald, K. Setsompop;*B. Bilgic***RARE/Turbo Spin Echo Imaging with Simultaneous MultiSlice Wave-CAIPI**; International Society for Magnetic Resonance in Medicine 23rd Scientific Meeting,*oral presentation*[PDF] [Matlab code]

† These authors contributed equally to this work

Summa Cum Laude Award , L. Xie, R. Dibb, C. Langkammer, A. Mutluay, H. Ye, J.R. Polimeni, C. Liu, L.L. Wald, K. Setsompop;*B. Bilgic***Rapid Multi-Orientation Susceptibility Mapping with Wave-CAIPI**; International Society for Magnetic Resonance in Medicine 23rd Scientific Meeting,*oral presentation*[PDF] [Matlab code]

Summa Cum Laude Award

White Matter Study Group student research competition finalist- K. Setsompop,
, A. Nummenmaa, Q. Fan, S.F. Cauley, S. Haung, I. Chatnuntawech, Y. Rathi, T. Witzel, L.L. Wald;*B. Bilgic***700 μm isotropic diffusion imaging at 3T using SLIDER-SMS with ZOOPPA**; International Society for Magnetic Resonance in Medicine 23rd Scientific Meeting - K. Jafari-Khouzani,
, J. Kalpathy-Cramer, K. Setsompop;*B. Bilgic***Fast non-local means reconstruction for multi-contrast compressed sensing**; International Society for Magnetic Resonance in Medicine 23rd Scientific Meeting - P. McDaniel, A.P. Fan,
, J. Stout, E. Adalsteinsson;*B. Bilgic***Improved Accuracy in Susceptibility-based OEF Measurements by Mitigation of Partial-Volume Effects via Combined Magnitude and Phase Reconstruction**; International Society for Magnetic Resonance in Medicine 23rd Scientific Meeting - S. Cetin, A.P. Fan,
, K. Setsompop, G. Unal;*B. Bilgic***Semi-automated visualization and segmentation of cerebral veins from QSM**; International Society for Magnetic Resonance in Medicine 23rd Scientific Meeting - I. Chatnuntawech,
, A. Martin, K. Setsompop, E. Adalsteinsson;*B. Bilgic***A Fast Reconstruction Algorithm for Accelerated Multi-Contrast MRI**; International Society for Magnetic Resonance in Medicine 23rd Scientific Meeting - A. Martin, I. Chatnuntawech,
, K. Setsompop, E. Adalsteinsson, E. Schiavi;*B. Bilgic***Total Generalized Variation for Joint Multi-Contrast Parallel Imaging Reconstruction of Undersampled k-space Data**; International Society for Magnetic Resonance in Medicine 23rd Scientific Meeting - C. Langkammer,
, C. Louapre, S. Govindarajan, C. Gianni, K. Setsompop, C. Mainero;*B. Bilgic***Wave-CAIPI and TGV-QSM for fast sub-millimeter QSM at 7 Tesla**; International Society for Magnetic Resonance in Medicine 23rd Scientific Meeting - H. Ye, B. Gagoski,
, S.F. Cauley, D. Ma, Y. Du, M.A. Griswold, L.L. Wald, K. Setsompop;*B. Bilgic***Simultaneous Multi-Slice Magnetic Resonance Fingerprinting Reconstruction using GROG+GRAPPA (GG)**; International Society for Magnetic Resonance in Medicine 23rd Scientific Meeting - Y. Jiang, H. Ye,
, D. Ma, T. Witzel, S.F. Cauley, E. Adalsteinsson, K. Setsompop, M.A. Griswold, L.L. Wald;*B. Bilgic***Simultaneous T1 and T2 quantitation of the Human Brain at 7 Tesla by MR Fingerprinting**; International Society for Magnetic Resonance in Medicine 23rd Scientific Meeting

#### 2015:

#### 2014:

, C. Langkammer, A. Mutluay, L.L. Wald, K. Setsompop;*B. Bilgic***Rapid Acquisition for Multi-Orientation QSM**; Third International Workshop on MRI Phase Contrast & Quantitative Susceptibility Mapping,*talk & poster presentation*[PDF]

Honorable mention for best poster award, C. Langkammer, L.L. Wald, K. Setsompop;*B. Bilgic***Single-Step QSM with Fast Reconstruction**; Third International Workshop on MRI Phase Contrast & Quantitative Susceptibility Mapping,*talk & poster presentation*[PDF] [Matlab code], B. Gagoski, S.F. Cauley, A.P. Fan, J.R. Polimeni, P.E. Grant, L.L. Wald, K. Setsompop;*B. Bilgic***Wave-CAIPI Enables Highly Accelerated 3D MRI**; 40th Annual Northeast Bioengineering Conference,*poster presentation*[PDF], A.P. Fan K. Setsompop, C. Eichner, S.F. Cauley, J.R. Polimeni, M. Bianciardi, E. Adalsteinsson, L.L. Wald, K. Setsompop;*B. Bilgic***Fast Reconstruction for Regularized Quantitative Susceptibility Mapping**; International Society for Magnetic Resonance in Medicine 22nd Scientific Meeting,*oral presentation*[PDF] [Matlab code]

Summa Cum Laude Award, B. Gagoski, S.F. Cauley, A.P. Fan, J.R. Polimeni, P.E. Grant, L.L. Wald, K. Setsompop;*B. Bilgic***Rapid QSM Acquisition with Wave-CAIPI**; International Society for Magnetic Resonance in Medicine 22nd Scientific Meeting,*power poster presentation*[PDF] [Matlab code]

Summa Cum Laude Award- I. Chatnuntawech, B. Gagoski,
, S.F. Cauley, P.E. Grant, K. Setsompop, E. Adalsteinsson;*B. Bilgic***Accelerated MRSI Using Randomly Undersampled Spiral-Based K-Space Trajectories**; International Society for Magnetic Resonance in Medicine 22nd Scientific Meeting - C. Eichner,
, M. Bianciardi, J.R. Polimeni, R. Turner, J. Schulz, D. Norris, L.L. Wald, K. Setsompop;*B. Bilgic***Acquisition and Processing Pipeline for Multi-Contrast fMRI Multi-Echo SMS (MESMS) GE-EPI at 7T**; International Society for Magnetic Resonance in Medicine 22nd Scientific Meeting - M. Bianciardi, J.R. Polimeni, K. Setsompop, C. Eichner,
, L.L. Wald;*B. Bilgic***Evaluation of Dynamic Off-Resonance Correction of Respiratory Instability in MRI Signals for High-Order Spherical Harmonic Basis Set and Multivariate Modeling of Respiratory Sources**; International Society for Magnetic Resonance in Medicine 22nd Scientific Meeting - S.F. Cauley,
, J.R. Polimeni, H. Bhat, L.L. Wald, K. Setsompop;*B. Bilgic***A General Hierarchical Mapping Framework (HMF) for Coil Compression**; International Society for Magnetic Resonance in Medicine 22nd Scientific Meeting - S.F. Cauley, M. Lustig,
, H. Bhat, L.L. Wald, K. Setsompop;*B. Bilgic***Geometric-Decomposition Coil Compression for Real-Time Simultaneous MultiSlice EPI Reconstruction at High MultiBand Factors**; International Society for Magnetic Resonance in Medicine 22nd Scientific Meeting - P. Montesinos, J.R. Polimeni,
, S.F. Cauley, M. Desco, R. Nezafat, L.L. Wald, E. Adalsteinsson, D.E. Sosnovik;*B. Bilgic***High Resolution Inner Volume Imaging of Human Coronary Atherosclerotic Plaque: Impact and Limits of Parallel Acquisition**; International Society for Magnetic Resonance in Medicine 22nd Scientific Meeting

#### 2013:

, I. Chatnuntawech, K. Setsompop, S.F. Cauley, L.L. Wald, E. Adalsteinsson;*B. Bilgic***Fast Regularized Reconstruction Tools for QSM and DSI**; ISMRM Workshop on Data Sampling & Image Reconstruction 2013,*oral presentation*[PDF] [QSM Matlab code] [DSI Matlab code], I. Chatnuntawech, K. Setsompop, S.F. Cauley, L.L. Wald, E. Adalsteinsson;*B. Bilgic***Fast DSI Reconstruction with Trained Dictionaries**; International Society for Magnetic Resonance in Medicine 21st Scientific Meeting,*oral presentation*[PDF] c

Magna Cum Laude Award, I. Chatnuntawech, A.P. Fan, E. Adalsteinsson;*B. Bilgic***Regularized QSM in Seconds**; International Society for Magnetic Resonance in Medicine 21st Scientific Meeting,*oral presentation*[PDF] [Matlab code]

Summa Cum Laude Award- S.F. Cauley, Y. Xi,
, K. Setsompop, J. Xia, E. Adalsteinsson, V.R. Balakrishnan, L.L. Wald;*B. Bilgic***Scalable and Accurate Variance Estimation (SAVE) for Joint Bayesian Compressed Sensing**; International Society for Magnetic Resonance in Medicine 21st Scientific Meeting - S.F. Cauley, O.A. Abuhashem, I. Chatnuntawech,
, K. Setsompop, L.L. Wald, E. Adalsteinsson;*B. Bilgic***Low-Rank Basis Smoothing for the Denoising of Diffusion Weighted Images**; International Society for Magnetic Resonance in Medicine 21st Scientific Meeting - I. Chatnuntawech,
, E. Adalsteinsson;*B. Bilgic***Undersampled Spectroscopic Imaging with Model-based Reconstruction**; International Society for Magnetic Resonance in Medicine 21st Scientific Meeting - I. Chatnuntawech,
, B. Gagoski, T. Kok, A.P. Fan, E. Adalsteinsson;*B. Bilgic***Metabolite Map Estimation from Undersampled Spectroscopic Imaging Data using N-Compartment Model**; International Society for Magnetic Resonance in Medicine 21st Scientific Meeting - S.Y. Huang, E. Adalsteinsson,
, S. Foong, L.L. Wald;*B. Bilgic***Localized Electrical Property Retrieval - Theories and Numerical Examples**; International Society for Magnetic Resonance in Medicine 21st Scientific Meeting - A.P. Fan,
, L. Gagnon, T. Witzel, H. Bhat, B.R. Rosen, E. Adalsteinsson;*B. Bilgic***Quantitative Oxygenation Venogram from MR Phase**; International Society for Magnetic Resonance in Medicine 21st Scientific Meeting

#### 2012:

, E. Adalsteinsson;*B. Bilgic***Joint Bayesian Compressed Sensing with Prior Estimate**; International Society for Magnetic Resonance in Medicine 20th Scientific Meeting,*oral presentation*[PDF] [Matlab code], B. Gagoski, E. Adalsteinsson;*B. Bilgic***Lipid Suppression in CSI with Highly-Undersampled Peripheral K-Space and Spatial Priors**; International Society for Magnetic Resonance in Medicine 20th Scientific Meeting,*e-poster presentation*[PDF] [Matlab code]- O. A. Abuhashem,
, E. Adalsteinsson;*B. Bilgic***GPU Accelerated Quantitative Susceptibility Mapping**; International Society for Magnetic Resonance in Medicine 20th Scientific Meeting - B. Gagoski,
, T. Kok, E. Adalsteinsson;*B. Bilgic***Accelerated Spiral Chemical Shift Imaging with Compressed Sensing**; International Society for Magnetic Resonance in Medicine 20th Scientific Meeting - T. Kok,
, B. Gagoski, E. Adalsteinsson;*B. Bilgic***Lipid Artifact Suppression for Detection of Cortical Metabolites in High-Resolution CTPRESS**; International Society for Magnetic Resonance in Medicine 20th Scientific Meeting - A. P. Fan,
, K. A. Heberlein, B. R. Rosen, E. Adalsteinsson;*B. Bilgic***Quantification of the Cerebral Metabolic Rate of Oxygen (CMRO2) Across the Cortex Using Phase-Based Regional Oxygen Metabolism (PROM) MRI**; International Society for Magnetic Resonance in Medicine 20th Scientific Meeting - K. Setsompop,
, J. Cohen-Adad, M. D. Tisdall, B. Keil, T. Witzel, Y. Rathi, V. J. Wedeen, E. Adalsteinsson, L. L. Wald ;*B. Bilgic***Whole-Brain DSI in 4 Minutes: Sparse Sampling in Q-Space with Simultaneous Multi-Slice Acquisition**; International Society for Magnetic Resonance in Medicine 20th Scientific Meeting

#### 2011:

, V.K. Goyal, E. Adalsteinsson;*B. Bilgic***Joint Bayesian Compressed Sensing for Multi-contrast Reconstruction**; International Society for Magnetic Resonance in Medicine 19th Scientific Meeting,*oral presentation*[PDF] [Matlab code], A.P. Fan, E. Adalsteinsson;*B. Bilgic***Quantitative Susceptibility Map Reconstruction with Magnitude Prior**; International Society for Magnetic Resonance in Medicine 19th Scientific Meeting,*oral presentation*[PDF]- T. Kok,
, and E. Adalsteinsson;*B. Bilgic***Multi Task Bayesian Compressed Sensing in Sparse 2D Spectroscopy**; International Society for Magnetic Resonance in Medicine 19th Scientific Meeting - P. Fan,
, T. Benner, B. R. Rosen, E. Adalsteinsson;*B. Bilgic***Regularized Quantitative Susceptibility Mapping for Phase-based Regional Oxygen Metabolism (PROM) at 7T**; International Society for Magnetic Resonance in Medicine 19th Scientific Meeting

### Theses:

;*B. Bilgic***Reconstruction Algorithms for MRI**; Ph.D. thesis, Massachusetts Institute of Technology, Department of Electrical Engineering and Computer Science, February 2013 [PDF];*B. Bilgic***Fast Human Detection with Cascaded Ensembles**; S.M. thesis, Massachusetts Institute of Technology, Department of Electrical Engineering and Computer Science, February 2010 [PDF]

### Patents:

- S.F. Cauley,
, K. Setsompop, L.L. Wald;*B. Bilgic***Systems and Methods For Fast Magnetic Resonance Image Reconstruction Using A Hierarchically Semiseparable Solver**; patent pending. , K. Setsompop, B.A. Gagoski, L.L. Wald;*B. Bilgic***Rapid Gradient Echo Imaging with Echo-Shifted Wave-CAIPI**; patent pending., K. Setsompop, L.L. Wald;*B. Bilgic***Simultaneous Multi-Slice (SMS) Imaging with Random Gradient Blip Scheme**; patent pending., K. Setsompop;*B. Bilgic***Fast Quantitative Susceptibility Mapping with L1-Regularization and Automatic Parameter Selection**; patent pending., E. Adalsteinsson;*B. Bilgic***Joint Bayesian Compressed Sensing with Applications in MRI**; WIPO Patent No. WO/2012/037067, 2012.