@article{barbosa2015quantifying,
  title={Quantifying brain iron deposition in patients with Parkinson's disease using quantitative susceptibility mapping, R2 and R2},
  author={Barbosa, Jeam Haroldo Oliveira and Santos, Antonio Carlos and Tumas, Vitor and Liu, Manju and Zheng, Weili and Haacke, E Mark and Salmon, Carlos Ernesto Garrido},
  journal={Magnetic Resonance Imaging},
  volume={33},
  number={5},
  pages={559--565},
  year={2015},
  publisher={Elsevier}
}
@article{du2016quantitative,
  title={Quantitative susceptibility mapping of the midbrain in Parkinson's disease},
  author={Du, Guangwei and Liu, Tian and Lewis, Mechelle M and Kong, Lan and Wang, Yi and Connor, James and Mailman, Richard B and Huang, Xuemei},
  journal={Movement Disorders},
  volume={31},
  number={3},
  pages={317--324},
  year={2016},
  publisher={Wiley Online Library}
}
@article{gao2021xqsm,
  title={xQSM: quantitative susceptibility mapping with octave convolutional and noise-regularized neural networks},
  author={Gao, Yang and Zhu, Xuanyu and Moffat, Bradford A and Glarin, Rebecca and Wilman, Alan H and Pike, G Bruce and Crozier, Stuart and Liu, Feng and Sun, Hongfu},
  journal={NMR in Biomedicine},
  volume={34},
  number={3},
  pages={e4461},
  year={2021},
  publisher={Wiley Online Library}
}
@article{zhang2010characterizing,
  title={Characterizing iron deposition in Parkinson's disease using susceptibility-weighted imaging: an in vivo MR study},
  author={Zhang, Jiuquan and Zhang, Yanling and Wang, Jian and Cai, Ping and Luo, Chunxia and Qian, Zhongming and Dai, Yongming and Feng, Hua},
  journal={Brain Research},
  volume={1330},
  pages={124--130},
  year={2010},
  publisher={Elsevier}
}
@article{acosta2013vivo,
  title={In vivo quantitative susceptibility mapping (QSM) in Alzheimer's disease},
  author={Acosta-Cabronero, Julio and Williams, Guy B and Cardenas-Blanco, Arturo and Arnold, Robert J and Lupson, Victoria and Nestor, Peter J},
  journal={Plos One},
  volume={8},
  number={11},
  pages={e81093},
  year={2013},
  publisher={Public Library of Science}
}
@article{langkammer2013quantitative,
  title={Quantitative susceptibility mapping in multiple sclerosis},
  author={Langkammer, Christian and Liu, Tian and Khalil, Michael and Enzinger, Christian and Jehna, Margit and Fuchs, Siegrid and Fazekas, Franz and Wang, Yi and Ropele, Stefan},
  journal={Radiology},
  volume={267},
  number={2},
  pages={551--559},
  year={2013},
  publisher={Radiological Society of North America, Inc.}
}
@article{chen2014quantitative,
  title={Quantitative susceptibility mapping of multiple sclerosis lesions at various ages},
  author={Chen, Weiwei and Gauthier, Susan A and Gupta, Ajay and Comunale, Joseph and Liu, Tian and Wang, Shuai and Pei, Mengchao and Pitt, David and Wang, Yi},
  journal={Radiology},
  volume={271},
  number={1},
  pages={183--192},
  year={2014},
  publisher={Radiological Society of North America}
}
@article{liu2009calculation,
  title={Calculation of susceptibility through multiple orientation sampling ({COSMOS}): a method for conditioning the inverse problem from measured magnetic field map to susceptibility source image in {MRI}},
  author={Liu, Tian and Spincemaille, Pascal and De Rochefort, Ludovic and et al},
  journal={Magnetic Resonance in Medicine},
  volume={61},
  number={1},
  pages={196--204},
  year={2009},
  publisher={Wiley Online Library}
}
@article{liu2010susceptibility,
  title={Susceptibility tensor imaging},
  author={Liu, Chunlei},
  journal={Magnetic Resonance in Medicine},
  volume={63},
  number={6},
  pages={1471--1477},
  year={2010},
  publisher={Wiley Online Library}
}
@article{shmueli2009magnetic,
  title={Magnetic susceptibility mapping of brain tissue in vivo using {MRI} phase data},
  author={Shmueli, Karin and de Zwart, Jacco A and van Gelderen, Peter and et al},
  journal={Magnetic Resonance in Medicine},
  volume={62},
  number={6},
  pages={1510--1522},
  year={2009},
  publisher={Wiley Online Library}
}
@article{de2008quantitative,
  title={Quantitative {MR} susceptibility mapping using piece-wise constant regularized inversion of the magnetic field},
  author={De Rochefort, Ludovic and Brown, Ryan and Prince, Martin R and et al},
  journal={Magnetic Resonance in Medicine},
  volume={60},
  number={4},
  pages={1003--1009},
  year={2008},
  publisher={Wiley Online Library}
}
@article{liu2011morphology,
  title={Morphology enabled dipole inversion ({MEDI}) from a single-angle acquisition: comparison with {COSMOS} in human brain imaging},
  author={Liu, Tian and Liu, Jing and De Rochefort, Ludovic and et al},
  journal={Magnetic Resonance in Medicine},
  volume={66},
  number={3},
  pages={777--783},
  year={2011},
  publisher={Wiley Online Library}
}
@article{liu2012accuracy,
  title={Accuracy of the morphology enabled dipole inversion (MEDI) algorithm for quantitative susceptibility mapping in MRI},
  author={Liu, Tian and Xu, Weiyu and Spincemaille, Pascal and Avestimehr, A Salman and Wang, Yi},
  journal={IEEE Transactions on Medical Imaging},
  volume={31},
  number={3},
  pages={816--824},
  year={2012},
  publisher={IEEE}
}
@article{vincent2010stacked,
  title={Stacked denoising autoencoders: Learning useful representations in a deep network with a local denoising criterion},
  author={Vincent, Pascal and Larochelle, Hugo and Lajoie, Isabelle and Bengio, Yoshua and Manzagol, Pierre-Antoine},
  journal={Journal of Machine Learning Research},
  volume={11},
  number={Dec},
  pages={3371--3408},
  year={2010}
}
@inproceedings{xie2012image,
  title={Image denoising and inpainting with deep neural networks},
  author={Xie, Junyuan and Xu, Linli and Chen, Enhong},
  booktitle={Advances in Neural Information Processing Systems},
  pages={341--349},
  year={2012}
}
@inproceedings{sun2016deep,
  title={Deep ADMM-Net for compressive sensing MRI},
  author={Sun, Jian and Li, Huibin and Xu, Zongben and others},
  booktitle={Advances in Neural Information Processing Systems},
  pages={10--18},
  year={2016}
}
@inproceedings{dong2014learning,
  title={Learning a deep convolutional network for image super-resolution},
  author={Dong, Chao and Loy, Chen Change and He, Kaiming and Tang, Xiaoou},
  booktitle={European Conference on Computer Vision},
  pages={184--199},
  year={2014},
  organization={Springer}
}
@article{wei2019learning,
  title={Learning-based single-step quantitative susceptibility mapping reconstruction without brain extraction},
  author={Wei, Hongjiang and Cao, Steven and Zhang, Yuyao and Guan, Xiaojun and Yan, Fuhua and Yeom, Kristen W and Liu, Chunlei},
  journal={NeuroImage},
  volume={202},
  pages={116064},
  year={2019},
  publisher={Elsevier}
}
@article{bollmann2019sharqnet,
  title={SHARQnet--Sophisticated harmonic artifact reduction in quantitative susceptibility mapping using a deep convolutional neural network},
  author={Bollmann, Steffen and Kristensen, Matilde Holm and Larsen, Morten Skaarup and Olsen, Mathias Vassard and Pedersen, Mads Jozwiak and {\O}stergaard, Lasse Riis and O’Brien, Kieran and Langkammer, Christian and Fazlollahi, Amir and Barth, Markus},
  journal={Zeitschrift f{\"u}r Medizinische Physik},
  volume={29},
  number={2},
  pages={139--149},
  year={2019},
  publisher={Elsevier}
}
@inproceedings{liu2019deep,
  title={Deep Gated Convolutional Neural Network for QSM Background Field Removal},
  author={Liu, Juan and Koch, Kevin M},
  booktitle={International Conference on Medical Image Computing and Computer-Assisted Intervention},
  pages={83--91},
  year={2019},
  organization={Springer}
}
@inproceedings{ronneberger2015u,
  title={U-net: Convolutional networks for biomedical image segmentation},
  author={Ronneberger, Olaf and Fischer, Philipp and Brox, Thomas},
  booktitle={International Conference on Medical Image Computing and Computer-assisted Intervention},
  pages={234--241},
  year={2015},
  organization={Springer}
}
@article{yoon2018quantitative,
  title={Quantitative susceptibility mapping using deep neural network: {QSMnet}},
  author={Yoon, Jaeyeon and Gong, Enhao and Chatnuntawech, Itthi and et al},
  journal={NeuroImage},
  year={2018},
  publisher={Elsevier}
}
@article{zhou2014background,
  title={Background field removal by solving the Laplacian boundary value problem},
  author={Zhou, Dong and Liu, Tian and Spincemaille, Pascal and Wang, Yi},
  journal={NMR in Biomedicine},
  volume={27},
  number={3},
  pages={312--319},
  year={2014},
  publisher={Wiley Online Library}
}
@inproceedings{brett2002region,
  title={Region of interest analysis using an {SPM} toolbox},
  author={Brett, Matthew and Anton, Jean-Luc and Valabregue, Romain and at al},
  booktitle={8th International Conference on Functional Mapping of the Human Brain},
  pages={497},
  year={2002},
  organization={Sendai}
}
@article{zhao2017loss,
  title={Loss functions for image restoration with neural networks},
  author={Zhao, Hang and Gallo, Orazio and Frosio, Iuri and Kautz, Jan},
  journal={IEEE Transactions on Computational Imaging},
  volume={3},
  number={1},
  pages={47--57},
  year={2017},
  publisher={IEEE}
}
@misc{MEDI_cornell_WEB,
  title = {Cornell MRI Research Lab},
  url = {http://weill.cornell.edu/mri/pages/qsm.html},
  year={2020}
}
@misc{berkin_MIT_WEB,
  title = {Berkin Bilgic Publications},
  url = {http://martinos.org/~berkin/software.html},
  year={2019}
}

@article{1-barbosa2015quantifying,
  title={Quantifying brain iron deposition in patients with Parkinson's disease using quantitative susceptibility mapping, R2 and R2},
  author={Barbosa, Jeam Haroldo Oliveira and Santos, Antonio Carlos and Tumas, Vitor and Liu, Manju and Zheng, Weili and Haacke, E Mark and Salmon, Carlos Ernesto Garrido},
  journal={Magnetic Resonance Imaging},
  volume={33},
  number={5},
  pages={559--565},
  year={2015},
  publisher={Elsevier}
}
@article{haacke2005imaging,
  title={Imaging iron stores in the brain using magnetic resonance imaging},
  author={Haacke, E Mark and Cheng, Norman YC and House, Michael J and Liu, Qiang and Neelavalli, Jaladhar and Ogg, Robert J and Khan, Asadullah and Ayaz, Muhammad and Kirsch, Wolff and Obenaus, Andre},
  journal={Magnetic Resonance Imaging},
  volume={23},
  number={1},
  pages={1--25},
  year={2005},
  publisher={Elsevier}
}
@article{deistung2013toward,
  title={Toward in vivo histology: a comparison of quantitative susceptibility mapping (QSM) with magnitude-, phase-, and R2*-imaging at ultra-high magnetic field strength},
  author={Deistung, Andreas and Schafer, Andreas and Schweser, Ferdinand and Biedermann, Uta and Turner, Robert and Reichenbach, Jurgen R},
  journal={NeuroImage},
  volume={65},
  pages={299--314},
  year={2013},
  publisher={Elsevier}
}
@article{bilgic2012mri,
  title={MRI estimates of brain iron concentration in normal aging using quantitative susceptibility mapping},
  author={Bilgic, Berkin and Pfefferbaum, Adolf and Rohlfing, Torsten and Sullivan, Edith V and Adalsteinsson, Elfar},
  journal={NeuroImage},
  volume={59},
  number={3},
  pages={2625--2635},
  year={2012},
  publisher={Elsevier}
}
@article{zheng2013measuring,
  title={Measuring iron in the brain using quantitative susceptibility mapping and X-ray fluorescence imaging},
  author={Zheng, Weili and Nichol, Helen and Liu, Saifeng and Cheng, Yu-Chung N and Haacke, E Mark},
  journal={NeuroImage},
  volume={78},
  pages={68--74},
  year={2013},
  publisher={Elsevier}
}
@article{langkammer2012quantitative,
  title={Quantitative susceptibility mapping (QSM) as a means to measure brain iron? A post mortem validation study},
  author={Langkammer, Christian and Schweser, Ferdinand and Krebs, Nikolaus and Deistung, Andreas and Goessler, Walter and Scheurer, Eva and Sommer, Karsten and Reishofer, Gernot and Yen, Kathrin and Fazekas, Franz and others},
  journal={NeuroImage},
  volume={62},
  number={3},
  pages={1593--1599},
  year={2012},
  publisher={Elsevier}
}
@article{zhang2015quantitative,
  title={Quantitative mapping of cerebral metabolic rate of oxygen (CMRO2) using quantitative susceptibility mapping (QSM)},
  author={Zhang, Jingwei and Liu, Tian and Gupta, Ajay and Spincemaille, Pascal and Nguyen, Thanh D and Wang, Yi},
  journal={Magnetic Resonance in Medicine},
  volume={74},
  number={4},
  pages={945--952},
  year={2015},
  publisher={Wiley Online Library}
}
@article{wisnieff2015quantitative,
  title={Quantitative susceptibility mapping (QSM) of white matter multiple sclerosis lesions: interpreting positive susceptibility and the presence of iron},
  author={Wisnieff, Cynthia and Ramanan, Sriram and Olesik, John and Gauthier, Susan and Wang, Yi and Pitt, David},
  journal={Magnetic Resonance in Medicine},
  volume={74},
  number={2},
  pages={564--570},
  year={2015},
  publisher={Wiley Online Library}
}
@article{xu2015quantification,
  title={Quantification of cerebral perfusion using dynamic quantitative susceptibility mapping},
  author={Xu, Bo and Spincemaille, Pascal and Liu, Tian and Prince, Martin R and Dutruel, Silvina and Gupta, Ajay and Thimmappa, Nanda Deepa and Wang, Yi},
  journal={Magnetic Resonance in Medicine},
  volume={73},
  number={4},
  pages={1540--1548},
  year={2015},
  publisher={Wiley Online Library}
}

@article{lotfipour2012high,
  title={High resolution magnetic susceptibility mapping of the substantia nigra in Parkinson's disease},
  author={Lotfipour, Ashley K and Wharton, Samuel and Schwarz, Stefan T and Gontu, V and Sch{\"a}fer, Andreas and Peters, Andrew M and Bowtell, Richard W and Auer, Dorothee P and Gowland, Penny A and Bajaj, Nin PS},
  journal={Journal of Magnetic Resonance Imaging},
  volume={35},
  number={1},
  pages={48--55},
  year={2012},
  publisher={Wiley Online Library}
}
@article{deistung2013quantitative,
  title={Quantitative susceptibility mapping differentiates between blood depositions and calcifications in patients with glioblastoma},
  author={Deistung, Andreas and Schweser, Ferdinand and Wiestler, Benedikt and Abello, Mario and Roethke, Matthias and Sahm, Felix and Wick, Wolfgang and Nagel, Armin Michael and Heiland, Sabine and Schlemmer, Heinz-Peter and others},
  journal={Plos One},
  volume={8},
  number={3},
  pages={e57924},
  year={2013},
  publisher={Public Library of Science}
}
@article{balla2014functional,
  title={Functional quantitative susceptibility mapping (fQSM)},
  author={Balla, D{\'a}vid Z and Sanchez-Panchuelo, Rosa M and Wharton, Samuel J and Hagberg, Gisela E and Scheffler, Klaus and Francis, Susan T and Bowtell, Richard},
  journal={NeuroImage},
  volume={100},
  pages={112--124},
  year={2014},
  publisher={Elsevier}
}
@article{sharma2015quantitative,
  title={Quantitative susceptibility mapping in the abdomen as an imaging biomarker of hepatic iron overload},
  author={Sharma, Samir D and Hernando, Diego and Horng, Debra E and Reeder, Scott B},
  journal={Magnetic Resonance in Medicine},
  volume={74},
  number={3},
  pages={673--683},
  year={2015},
  publisher={Wiley Online Library}
}
@article{li2014mean,
  title={Mean magnetic susceptibility regularized susceptibility tensor imaging (MMSR-STI) for estimating orientations of white matter fibers in human brain},
  author={Li, Xu and van Zijl, Peter CM},
  journal={Magnetic Resonance in Medicine},
  volume={72},
  number={3},
  pages={610--619},
  year={2014},
  publisher={Wiley Online Library}
}
@article{salomir2003fast,
  title={A fast calculation method for magnetic field inhomogeneity due to an arbitrary distribution of bulk susceptibility},
  author={Salomir, Rares and de Senneville, Baudouin Denis and Moonen, Chrit TW},
  journal={Concepts in Magnetic Resonance Part B: Magnetic Resonance Engineering},
  volume={19},
  number={1},
  pages={26--34},
  year={2003},
  publisher={Wiley Online Library}
}
@article{marques2005application,
  title={Application of a {Fourier}-based method for rapid calculation of field inhomogeneity due to spatial variation of magnetic susceptibility},
  author={Marques, JP and Bowtell, R},
  journal={Concepts in Magnetic Resonance Part B: Magnetic Resonance Engineering},
  volume={25},
  number={1},
  pages={65--78},
  year={2005},
  publisher={Wiley Online Library}
}

@article{wharton2010susceptibility,
  title={Susceptibility mapping in the human brain using threshold-based k-space division},
  author={Wharton, Sam and Sch{\"a}fer, Andreas and Bowtell, Richard},
  journal={Magnetic Resonance in Medicine},
  volume={63},
  number={5},
  pages={1292--1304},
  year={2010},
  publisher={Wiley Online Library}
}
@article{haacke2010susceptibility,
  title={Susceptibility mapping as a means to visualize veins and quantify oxygen saturation},
  author={Haacke, EM and Tang, J and Neelavalli, J and et al},
  journal={Journal of Magnetic Resonance Imaging},
  volume={32},
  number={3},
  pages={663--676},
  year={2010},
  publisher={Wiley Online Library}
}

@article{de2010quantitative,
  title={Quantitative susceptibility map reconstruction from {MR} phase data using bayesian regularization: validation and application to brain imaging},
  author={de Rochefort, Ludovic and Liu, Tian and Kressler, Bryan and et al},
  journal={Magnetic Resonance in Medicine},
  volume={63},
  number={1},
  pages={194--206},
  year={2010},
  publisher={Wiley Online Library}
}

@article{li2015method,
  title={A method for estimating and removing streaking artifacts in quantitative susceptibility mapping},
  author={Li, Wei and Wang, Nian and Yu, Fang and Han, Hui and Cao, Wei and Romero, Rebecca and Tantiwongkosi, Bundhit and Duong, Timothy Q and Liu, Chunlei},
  journal={NeuroImage},
  volume={108},
  pages={111--122},
  year={2015},
  publisher={Elsevier}
}
@article{wang2015quantitative,
  title={Quantitative susceptibility mapping ({QSM}): decoding {MRI} data for a tissue magnetic biomarker},
  author={Wang, Yi and Liu, Tian},
  journal={Magnetic Resonance in Medicine},
  volume={73},
  number={1},
  pages={82--101},
  year={2015},
  publisher={Wiley Online Library}
}
@article{wharton2010whole,
  title={Whole-brain susceptibility mapping at high field: a comparison of multiple-and single-orientation methods},
  author={Wharton, Sam and Bowtell, Richard},
  journal={NeuroImage},
  volume={53},
  number={2},
  pages={515--525},
  year={2010},
  publisher={Elsevier}
}
@article{schenck1996role,
  title={The role of magnetic susceptibility in magnetic resonance imaging: MRI magnetic compatibility of the first and second kinds},
  author={Schenck, John F},
  journal={Medical Physics},
  volume={23},
  number={6},
  pages={815--850},
  year={1996},
  publisher={Wiley Online Library}
}
@article{smith2002fast,
  title={Fast robust automated brain extraction},
  author={Smith, Stephen M},
  journal={Human Brain Mapping},
  volume={17},
  number={3},
  pages={143--155},
  year={2002},
  publisher={Wiley Online Library}
}
@article{liu2011novel,
  title={A novel background field removal method for MRI using projection onto dipole fields},
  author={Liu, Tian and Khalidov, Ildar and de Rochefort, Ludovic and Spincemaille, Pascal and Liu, Jing and Tsiouris, A John and Wang, Yi},
  journal={NMR in Biomedicine},
  volume={24},
  number={9},
  pages={1129--1136},
  year={2011},
  publisher={Wiley Online Library}
}
@article{bilgic2014fast,
  title={Fast image reconstruction with {L2}-regularization},
  author={Bilgic, Berkin and Chatnuntawech, Itthi and Fan, Audrey P and et al},
  journal={Journal of Magnetic Resonance Imaging},
  volume={40},
  number={1},
  pages={181--191},
  year={2014},
  publisher={Wiley Online Library}
}
@article{liu2012morphology,
  title={Morphology enabled dipole inversion for quantitative susceptibility mapping using structural consistency between the magnitude image and the susceptibility map},
  author={Liu, Jing and Liu, Tian and de Rochefort, Ludovic and et al},
  journal={NeuroImage},
  volume={59},
  number={3},
  pages={2560--2568},
  year={2012},
  publisher={Elsevier}
}

@article{liu2013nonlinear,
  title={Nonlinear formulation of the magnetic field to source relationship for robust quantitative susceptibility mapping},
  author={Liu, Tian and Wisnieff, Cynthia and Lou, Min and et al},
  journal={Magnetic Resonance in Medicine},
  volume={69},
  number={2},
  pages={467--476},
  year={2013},
  publisher={Wiley Online Library}
}
@article{deng2015iterative,
  title={Iterative projection onto convex sets for quantitative susceptibility mapping},
  author={Deng, Weiran and Boada, Fernando and Poser, Benedikt A and Schirda, Claudiu and Stenger, Victor Andrew},
  journal={Magnetic Resonance in Medicine},
  volume={73},
  number={2},
  pages={697--703},
  year={2015},
  publisher={Wiley Online Library}
}
@article{wen2016enhancing,
  title={Enhancing k-space quantitative susceptibility mapping by enforcing consistency on the cone data (CCD) with structural priors},
  author={Wen, Yan and Wang, Yi and Liu, Tian},
  journal={Magnetic Resonance in Medicine},
  volume={75},
  number={2},
  pages={823--830},
  year={2016},
  publisher={Wiley Online Library}
}
@article{langkammer2018quantitative,
  title={Quantitative susceptibility mapping: report from the 2016 reconstruction challenge},
  author={Langkammer, Christian and Schweser, Ferdinand and Shmueli, Karin and Kames, Christian and Li, Xu and Guo, Li and Milovic, Carlos and Kim, Jinsuh and Wei, Hongjiang and Bredies, Kristian and others},
  journal={Magnetic Resonance in Medicine},
  volume={79},
  number={3},
  pages={1661--1673},
  year={2018},
  publisher={Wiley Online Library}
}
@article{bilgic2015wave,
  title={Wave-CAIPI for highly accelerated 3D imaging},
  author={Bilgic, Berkin and Gagoski, Borjan A and Cauley, Stephen F and Fan, Audrey P and Polimeni, Jonathan R and Grant, P Ellen and Wald, Lawrence L and Setsompop, Kawin},
  journal={Magnetic Resonance in Medicine},
  volume={73},
  number={6},
  pages={2152--2162},
  year={2015},
  publisher={Wiley Online Library}
}
@article{koch2018quantitative,
  title={Quantitative susceptibility mapping after sports-related concussion},
  author={Koch, Kevin M and Meier, Timothy B and Karr, Robin and Nencka, Andrew S and Muftuler, L Tugan and McCrea, Michael},
  journal={American Journal of Neuroradiology},
  volume={39},
  number={7},
  pages={1215--1221},
  year={2018},
  publisher={Am Soc Neuroradiology}
}
@article{sato2017quantitative,
  title={Quantitative susceptibility mapping using the multiple dipole-inversion combination with k-space segmentation method},
  author={Sato, Ryota and Shirai, Toru and Taniguchi, Yo and Murase, Takenori and Bito, Yoshitaka and Ochi, Hisaaki},
  journal={Magnetic Resonance in Medical Sciences},
  volume={16},
  number={4},
  pages={340--350},
  year={2017},
  publisher={Japanese Society for Magnetic Resonance in Medicine}
}
@article{kingma2014adam,
  title={Adam: A method for stochastic optimization},
  author={Kingma, Diederik P and Ba, Jimmy},
  journal={arXiv},
  year={2014}
}
@article{langkammer2015fast,
  title={Fast quantitative susceptibility mapping using 3D EPI and total generalized variation},
  author={Langkammer, Christian and Bredies, Kristian and Poser, Benedikt A and Barth, Markus and Reishofer, Gernot and Fan, Audrey Peiwen and Bilgic, Berkin and Fazekas, Franz and Mainero, Caterina and Ropele, Stefan},
  journal={NeuroImage},
  volume={111},
  pages={622--630},
  year={2015},
  publisher={Elsevier}
}
@PROCEEDINGS{gong2018qsm,
  title = {Accurate and Efficient {QSM} Reconstruction using Deep Learning},
  author = {Gong, Enhao and Bilgic, Berkin and Setsompop, Kawin and Fan, Audrey and Zaharchuk, Greg and Pauly, John},
  volume = {0189},
  publisher = {ISMRM},
  year = {2018}
}
@article{sun2014background,
  title={Background field removal using spherical mean value filtering and Tikhonov regularization},
  author={Sun, Hongfu and Wilman, Alan H},
  journal={Magnetic Resonance in Medicine},
  volume={71},
  number={3},
  pages={1151--1157},
  year={2014},
  publisher={Wiley Online Library}
}
@article{schweser2011quantitative,
  title={Quantitative imaging of intrinsic magnetic tissue properties using {MRI} signal phase: an approach to in vivo brain iron metabolism?},
  author={Schweser, Ferdinand and Deistung, Andreas and Lehr, Berengar Wendel and et al},
  journal={NeuroImage},
  volume={54},
  number={4},
  pages={2789--2807},
  year={2011},
  publisher={Elsevier}
}
@article{haacke2004susceptibility,
  title={Susceptibility weighted imaging (SWI)},
  author={Haacke, E Mark and Xu, Yingbiao and Cheng, Yu-Chung N and Reichenbach, J{\"u}rgen R},
  journal={Magnetic Resonance in Medicine},
  volume={52},
  number={3},
  pages={612--618},
  year={2004},
  publisher={Wiley Online Library}
}
@article{haacke2009susceptibility,
  title={Susceptibility-weighted imaging: technical aspects and clinical applications, part 1},
  author={Haacke, E Mark and Mittal, S and Wu, Z and Neelavalli, Jaladhar and Cheng, Y-CN},
  journal={American Journal of Neuroradiology},
  volume={30},
  number={1},
  pages={19--30},
  year={2009},
  publisher={Am Soc Neuroradiology}
}
@article{mittal2009susceptibility,
  title={Susceptibility-weighted imaging: technical aspects and clinical applications, part 2},
  author={Mittal, S and Wu, Z and Neelavalli, Jaladhar and Haacke, E Mark},
  journal={American Journal of Neuroradiology},
  volume={30},
  number={2},
  pages={232--252},
  year={2009},
  publisher={Am Soc Neuroradiology}
}
@article{sehgal2005clinical,
  title={Clinical applications of neuroimaging with susceptibility-weighted imaging},
  author={Sehgal, Vivek and Delproposto, Zachary and Haacke, E Mark and Tong, Karen A and Wycliffe, Nathaniel and Kido, Daniel K and Xu, Yingbiao and Neelavalli, Jaladhar and Haddar, Djamel and Reichenbach, J{\"u}rgen R},
  journal={Journal of Magnetic Resonance Imaging},
  volume={22},
  number={4},
  pages={439--450},
  year={2005},
  publisher={Wiley Online Library}
}
@article{nandigam2009mr,
  title={MR imaging detection of cerebral microbleeds: effect of susceptibility-weighted imaging, section thickness, and field strength},
  author={Nandigam, RNK and Viswanathan, A and Delgado, P and Skehan, ME and Smith, EE and Rosand, J and Greenberg, SM and Dickerson, BC},
  journal={American Journal of Neuroradiology},
  volume={30},
  number={2},
  pages={338--343},
  year={2009},
  publisher={Am Soc Neuroradiology}
}
@article{liu2012cerebral,
  title={Cerebral microbleeds: burden assessment by using quantitative susceptibility mapping},
  author={Liu, Tian and Surapaneni, Krishna and Lou, Min and Cheng, Liuquan and Spincemaille, Pascal and Wang, Yi},
  journal={Radiology},
  volume={262},
  number={1},
  pages={269--278},
  year={2012},
  publisher={Radiological Society of North America, Inc.}
}

@article{schweser2010differentiation,
  title={Differentiation between diamagnetic and paramagnetic cerebral lesions based on magnetic susceptibility mapping},
  author={Schweser, Ferdinand and Deistung, Andreas and Lehr, Berengar W and Reichenbach, J{\"u}rgen R},
  journal={Medical Physics},
  volume={37},
  number={10},
  pages={5165--5178},
  year={2010},
  publisher={Wiley Online Library}
}
@article{schofield2003fast,
  title={Fast phase unwrapping algorithm for interferometric applications},
  author={Schofield, Marvin A and Zhu, Yimei},
  journal={Optics Letters},
  volume={28},
  number={14},
  pages={1194--1196},
  year={2003},
  publisher={Optical Society of America}
}
@article{li2014integrated,
  title={Integrated Laplacian-based phase unwrapping and background phase removal for quantitative susceptibility mapping},
  author={Li, Wei and Avram, Alexandru V and Wu, Bing and Xiao, Xue and Liu, Chunlei},
  journal={NMR in Biomedicine},
  volume={27},
  number={2},
  pages={219--227},
  year={2014},
  publisher={Wiley Online Library}
}
@article{li2011quantitative,
  title={Quantitative susceptibility mapping of human brain reflects spatial variation in tissue composition},
  author={Li, Wei and Wu, Bing and Liu, Chunlei},
  journal={NeuroImage},
  volume={55},
  number={4},
  pages={1645--1656},
  year={2011},
  publisher={Elsevier}
}


@inproceedings{bilgic2014single,
  title={Single-step {QSM} with fast reconstruction},
  author={Bilgic, Berkin and Langkammer, Christian and Wald, Lawrence L and Setsompop, Kawin},
  booktitle={Third International Workshop on MRI Phase Contrast \& Quantitative Susceptibility Mapping},
  year={2014}
}
@article{chatnuntawech2017single,
  title={Single-step quantitative susceptibility mapping with variational penalties},
  author={Chatnuntawech, Itthi and McDaniel, Patrick and Cauley, Stephen F and Gagoski, Borjan A and Langkammer, Christian and Martin, Adrian and Grant, P Ellen and Wald, Lawrence L and Setsompop, Kawin and Adalsteinsson, Elfar and others},
  journal={NMR in Biomedicine},
  volume={30},
  number={4},
  pages={e3570},
  year={2017},
  publisher={Wiley Online Library}
}
@article{liu2017preconditioned,
  title={Preconditioned total field inversion (TFI) method for quantitative susceptibility mapping},
  author={Liu, Zhe and Kee, Youngwook and Zhou, Dong and Wang, Yi and Spincemaille, Pascal},
  journal={Magnetic Resonance in Medicine},
  volume={78},
  number={1},
  pages={303--315},
  year={2017},
  publisher={Wiley Online Library}
}
@article{sun2018whole,
  title={Whole head quantitative susceptibility mapping using a least-norm direct dipole inversion method},
  author={Sun, Hongfu and Ma, Yuhan and MacDonald, M Ethan and Pike, G Bruce},
  journal={NeuroImage},
  year={2018},
  publisher={Elsevier}
}
@article{soman2018brain,
  title={Brain Injury Lesion Imaging Using Preconditioned Quantitative Susceptibility Mapping without Skull Stripping},
  author={Soman, Salil and Liu, Zhe and Kim, Geunwon and Nemec, Ursula and Holdsworth, Samantha J and Main, Keith and Lee, Bonny and Kolakowsky-Hayner, Stephanie and Selim, Magdy and Furst, Ansgar J and others},
  journal={American Journal of Neuroradiology},
  volume={39},
  number={4},
  pages={648--653},
  year={2018},
  publisher={Am Soc Neuroradiology}
}
@article{kee2018coherence,
  title={Coherence enhancement in quantitative susceptibility mapping by means of anisotropic weighting in morphology enabled dipole inversion},
  author={Kee, Youngwook and Cho, Junghun and Deh, Kofi and Liu, Zhe and Spincemaille, Pascal and Wang, Yi},
  journal={Magnetic Resonance in Medicine},
  volume={79},
  number={2},
  pages={1172--1180},
  year={2018},
  publisher={Wiley Online Library}
}


@article{wu2012whole,
  title={Whole brain susceptibility mapping using compressed sensing},
  author={Wu, Bing and Li, Wei and Guidon, Arnaud and Liu, Chunlei},
  journal={Magnetic Resonance in Medicine},
  volume={67},
  number={1},
  pages={137--147},
  year={2012},
  publisher={Wiley Online Library}
}
@article{kan2018background,
  title={Background field removal technique based on non-regularized variable kernels sophisticated harmonic artifact reduction for phase data for quantitative susceptibility mapping},
  author={Kan, Hirohito and Arai, Nobuyuki and Takizawa, Masahiro and Omori, Kazuyoshi and Kasai, Harumasa and Kunitomo, Hiroshi and Hirose, Yasujiro and Shibamoto, Yuta},
  journal={Magnetic Resonance Imaging},
  year={2018},
  publisher={Elsevier}
}
@article{ozbay2017comprehensive,
  title={A comprehensive numerical analysis of background phase correction with V-SHARP},
  author={{\"O}zbay, Pinar Senay and Deistung, Andreas and Feng, Xiang and Nanz, Daniel and Reichenbach, J{\"u}rgen Rainer and Schweser, Ferdinand},
  journal={NMR in Biomedicine},
  volume={30},
  number={4},
  pages={e3550},
  year={2017},
  publisher={Wiley Online Library}
}
@article{fang2017background,
  title={Background field removal using a region adaptive kernel for quantitative susceptibility mapping of human brain},
  author={Fang, Jinsheng and Bao, Lijun and Li, Xu and van Zijl, Peter CM and Chen, Zhong},
  journal={Journal of Magnetic Resonance},
  volume={281},
  pages={130--140},
  year={2017},
  publisher={Elsevier}
}
@article{kan2016background,
  title={Background field removal technique using regularization enabled sophisticated harmonic artifact reduction for phase data with varying kernel sizes},
  author={Kan, Hirohito and Kasai, Harumasa and Arai, Nobuyuki and Kunitomo, Hiroshi and Hirose, Yasujiro and Shibamoto, Yuta},
  journal={Magnetic Resonance Imaging},
  volume={34},
  number={7},
  pages={1026--1033},
  year={2016},
  publisher={Elsevier}
}
@article{yu2018free,
  title={Free-Form Image Inpainting with Gated Convolution},
  author={Yu, Jiahui and Lin, Zhe and Yang, Jimei and Shen, Xiaohui and Lu, Xin and Huang, Thomas S},
  journal={arXiv},
  year={2018}
}
@article{Berkin2014SingleStep,
  title={Single-Step QSM with Fast Reconstruction},
  author={Berkin, Bilgic and Christian, Langkammer and Lawrence, L Wald and Kawin, Setsompop},
  journal={ISMRM},
  year={2014},
  volume={3321}
}
@article{Kristian2014SingleStep,
  title={Single-step quantitative susceptibility mapping using total generalized variation and 3D EPI},
  author={Kristian, Bredies and Stefan, Ropele and Benedikt, A Poser and Markus, Barth and Christian, Langkammer},
  journal={ISMRM},
  year={2014},
  volume={0604}
}
@article{Tian2014Differential,
  title={Differential approach to quantitative susceptibility mapping without background field removal},
  author={Liu, Tian and Zhou, Dong and Spincemaille, Pascal and Wang, Yi},
  journal={ISMRM},
  year={2014},
  volume={0597}
}
@article{Samir2014SingleStep,
  title={ A joint background field removal and dipole deconvolution approach for quantitative susceptibility mapping in the liver},
  author={Sharma, Samir D and Hernando, Diego and Horng, Debra E and Reeder, Scott B},
  journal={ISMRM},
  year={2014},
  volume={0606}
}
@inproceedings{long2015fully,
  title={Fully convolutional networks for semantic segmentation},
  author={Long, Jonathan and Shelhamer, Evan and Darrell, Trevor},
  booktitle={Proceedings of the IEEE Conference on Computer Vision and Pattern Recognition},
  pages={3431--3440},
  year={2015}
}
@article{lecun2015deep,
  title={Deep learning},
  author={LeCun, Yann and Bengio, Yoshua and Hinton, Geoffrey},
  journal={nature},
  volume={521},
  number={7553},
  pages={436--444},
  year={2015},
  publisher={Nature Publishing Group}
}
@article{van2011computer,
  title={Computer-aided diagnosis: how to move from the laboratory to the clinic},
  author={van Ginneken, Bram and Schaefer-Prokop, Cornelia M and Prokop, Mathias},
  journal={Radiology},
  volume={261},
  number={3},
  pages={719--732},
  year={2011},
  publisher={Radiological Society of North America, Inc.}
}
@article{arimura2004automated,
  title={Automated computerized scheme for detection of unruptured intracranial aneurysms in three-dimensional magnetic resonance angiography},
  author={Arimura, Hidetaka and Li, Qiang and Korogi, Yukunori and Hirai, Toshinori and Abe, Hiroyuki and Yamashita, Yasuyuki and Katsuragawa, Shigehiko and Ikeda, Ryuji and Doi, Kunio},
  journal={Academic Radiology},
  volume={11},
  number={10},
  pages={1093--1104},
  year={2004},
  publisher={Elsevier}
}
@article{barber2015controlling,
  title={Controlling the false discovery rate via knockoffs},
  author={Barber, Rina Foygel and Cand{\`e}s, Emmanuel J and others},
  journal={The Annals of Statistics},
  volume={43},
  number={5},
  pages={2055--2085},
  year={2015},
  publisher={Institute of Mathematical Statistics}
}
@article{koch2006rapid,
  title={Rapid calculations of susceptibility-induced magnetostatic field perturbations for in vivo magnetic resonance},
  author={Koch, Kevin M and Papademetris, Xenophon and Rothman, Douglas L and de Graaf, Robin A},
  journal={Physics in Medicine \& Biology},
  volume={51},
  number={24},
  pages={6381},
  year={2006},
  publisher={IOP Publishing}
}
@article{griswold2002generalized,
  title={Generalized autocalibrating partially parallel acquisitions ({GRAPPA})},
  author={Griswold, Mark A and Jakob, Peter M and Heidemann, Robin M and Nittka, Mathias and Jellus, Vladimir and Wang, Jianmin and Kiefer, Berthold and Haase, Axel},
  journal={Magnetic Resonance in Medicine},
  volume={47},
  number={6},
  pages={1202--1210},
  year={2002},
  publisher={Wiley Online Library}
}
@article{bollmann2019sharqnet,
  title={SHARQnet--Sophisticated harmonic artifact reduction in quantitative susceptibility mapping using a deep convolutional neural network},
  author={Bollmann, Steffen and Kristensen, Matilde Holm and Larsen, Morten Skaarup and Olsen, Mathias Vassard and Pedersen, Mads Jozwiak and {\O}stergaard, Lasse Riis and O’Brien, Kieran and Langkammer, Christian and Fazlollahi, Amir and Barth, Markus},
  journal={Zeitschrift f{\"u}r Medizinische Physik},
  volume={29},
  number={2},
  pages={139--149},
  year={2019},
  publisher={Elsevier}
}
@article{chen2019qsmgan,
  title={{QSMGAN}: Improved Quantitative Susceptibility Mapping using 3D Generative Adversarial Networks with Increased Receptive Field},
  author={Chen, Yicheng and Jakary, Angela and Avadiappan, Sivakami and et al},
  journal={NeuroImage},
  pages={116389},
  year={2019},
  publisher={Elsevier}
}
@inproceedings{goodfellow2014generative,
  title={Generative adversarial nets},
  author={Goodfellow, Ian and Pouget-Abadie, Jean and Mirza, Mehdi and et al},
  booktitle={Advances in neural information processing systems},
  pages={2672--2680},
  year={2014}
}
@inproceedings{arjovsky2017wasserstein,
  title={Wasserstein generative adversarial networks},
  author={Arjovsky, Martin and Chintala, Soumith and Bottou, L{\'e}on},
  booktitle={International conference on machine learning},
  pages={214--223},
  year={2017}
}
@article{jung2020exploring,
  title={Exploring linearity of deep neural network trained {QSM}: {QSMnet+}},
  author={Jung, Woojin and Yoon, Jaeyeon and Ji, Sooyeon and et al},
  journal={NeuroImage},
  volume={211},
  pages={116619},
  year={2020},
  publisher={Elsevier}
}
@article{wei2019learning,
  title={Learning-based Single-step Quantitative Susceptibility Mapping Reconstruction Without Brain Extraction},
  author={Wei, Hongjiang and Cao, Steven and Zhang, Yuyao and Guan, Xiaojun and Yan, Fuhua and Yeom, Kristen W and Liu, Chunlei},
  journal={arXiv preprint arXiv:1905.05953},
  year={2019}
}
@article{zhang2019fidelity,
  title={Fidelity Imposed Network Edit (FINE) for Solving Ill-Posed Image Reconstruction},
  author={Zhang, Jinwei and Liu, Zhe and Zhang, Shun and Zhang, Hang and Spincemaille, Pascal and Nguyen, Thanh D and Sabuncu, Mert R and Wang, Yi},
  journal={arXiv preprint arXiv:1905.07284},
  year={2019}
}
@article{bilgic2014fastL2,
  title={Fast image reconstruction with L2-regularization},
  author={Bilgic, Berkin and Chatnuntawech, Itthi and Fan, Audrey P and Setsompop, Kawin and Cauley, Stephen F and Wald, Lawrence L and Adalsteinsson, Elfar},
  journal={Journal of magnetic resonance imaging},
  volume={40},
  number={1},
  pages={181--191},
  year={2014},
  publisher={Wiley Online Library}
}
@article{wei2015streaking,
  title={Streaking artifact reduction for quantitative susceptibility mapping of sources with large dynamic range},
  author={Wei, Hongjiang and Dibb, Russell and Zhou, Yan and Sun, Yawen and Xu, Jianrong and Wang, Nian and Liu, Chunlei},
  journal={NMR in Biomedicine},
  volume={28},
  number={10},
  pages={1294--1303},
  year={2015},
  publisher={Wiley Online Library}
}
@article{chavhan2009principles,
  title={Principles, techniques, and applications of T2*-based MR imaging and its special applications},
  author={Chavhan, Govind B and Babyn, Paul S and Thomas, Bejoy and Shroff, Manohar M and Haacke, E Mark},
  journal={Radiographics},
  volume={29},
  number={5},
  pages={1433--1449},
  year={2009},
  publisher={Radiological Society of North America}
}
@article{bilgic2016rapid,
  title={Rapid multi-orientation quantitative susceptibility mapping},
  author={Bilgic, Berkin and Xie, Luke and Dibb, Russell and Langkammer, Christian and Mutluay, Aysegul and Ye, Huihui and Polimeni, Jonathan R and Augustinack, Jean and Liu, Chunlei and Wald, Lawrence L and others},
  journal={NeuroImage},
  volume={125},
  pages={1131--1141},
  year={2016},
  publisher={Elsevier}
}
@article{tamir2019unsupervised,
  title={Unsupervised Deep Basis Pursuit: Learning inverse problems without ground-truth data},
  author={Tamir, Jonathan I and Yu, Stella X and Lustig, Michael},
  journal={arXiv preprint arXiv:1910.13110},
  year={2019}
}
@inproceedings{michailovich2019self,
  title={Self-supervised Learning of Inverse Problem Solvers in Medical Imaging},
  author={Michailovich, Oleg and Zibulevsky, Michael},
  booktitle={Domain Adaptation and Representation Transfer and Medical Image Learning with Less Labels and Imperfect Data},
  volume={11795},
  pages={111},
  year={2019},
  organization={Springer Nature}
}
@article{yaman2019self,
  title={Self-Supervised Physics-Based Deep Learning MRI Reconstruction Without Fully-Sampled Data},
  author={Yaman, Burhaneddin and Hosseini, Seyed Amir Hossein and Moeller, Steen and Ellermann, Jutta and Uǧurbil, K{\^a}mil and Ak{\c{c}}akaya, Mehmet},
  journal={arXiv preprint arXiv:1910.09116},
  year={2019}
}
@article{torop2019deep,
  title={Deep learning using a biophysical model for Robust and Accelerated Reconstruction (RoAR) of quantitative and artifact-free R2* images},
  author={Torop, Max and Kothapalli, Satya and Sun, Yu and Liu, Jiaming and Kahali, Sayan and Yablonskiy, Dmitriy A and Kamilov, Ulugbek S},
  journal={arXiv preprint arXiv:1912.07087},
  year={2019}
}
@article{kwon2020unsupervised,
  title={Unsupervised learning of a deep neural network for metal artifact correction using dual-polarity readout gradients},
  author={Kwon, Kinam and Kim, Dongchan and Kim, Byungjai and Park, HyunWook},
  journal={Magnetic Resonance in Medicine},
  volume={83},
  number={1},
  pages={124--138},
  year={2020},
  publisher={Wiley Online Library}
}
@article{liao2019artifact,
  title={Artifact Disentanglement Network for Unsupervised Metal Artifact Reduction},
  author={Liao, Haofu and Lin, Wei-An and Zhou, S Kevin and Luo, Jiebo},
  journal={arXiv preprint arXiv:1906.01806},
  year={2019}
}
@inproceedings{balakrishnan2018unsupervised,
  title={An unsupervised learning model for deformable medical image registration},
  author={Balakrishnan, Guha and Zhao, Amy and Sabuncu, Mert R and Guttag, John and Dalca, Adrian V},
  booktitle={Proceedings of the IEEE Conference on Computer Vision and Pattern Recognition},
  pages={9252--9260},
  year={2018}
}
@article{batson2019noise2self,
  title={Noise2self: Blind denoising by self-supervision},
  author={Batson, Joshua and Royer, Loic},
  journal={arXiv preprint arXiv:1901.11365},
  year={2019}
}
@inproceedings{krull2019noise2void,
  title={Noise2void-learning denoising from single noisy images},
  author={Krull, Alexander and Buchholz, Tim-Oliver and Jug, Florian},
  booktitle={Proceedings of the IEEE Conference on Computer Vision and Pattern Recognition},
  pages={2129--2137},
  year={2019}
}
@inproceedings{ulyanov2018deep,
  title={Deep image prior},
  author={Ulyanov, Dmitry and Vedaldi, Andrea and Lempitsky, Victor},
  booktitle={Proceedings of the IEEE CVPR},
  pages={9446--9454},
  year={2018}
}
@article{milovic2018fast,
  title={Fast nonlinear susceptibility inversion with variational regularization},
  author={Milovic, Carlos and Bilgic, Berkin and Zhao, Bo and et al},
  journal={Magnetic Resonance in Medicine},
  volume={80},
  number={2},
  pages={814--821},
  year={2018},
  publisher={Wiley Online Library}
}
@article{uecker2014espirit,
  title={{ESPIRiT}—an eigenvalue approach to autocalibrating parallel MRI: where SENSE meets {GRAPPA}},
  author={Uecker, Martin and Lai, Peng and Murphy, Mark J and et al},
  journal={Magnetic Resonance in Medicine},
  volume={71},
  number={3},
  pages={990--1001},
  year={2014},
  publisher={Wiley Online Library}
}
@article{schweser2017illustrated,
  title={An illustrated comparison of processing methods for phase MRI and QSM: removal of background field contributions from sources outside the region of interest},
  author={Schweser, Ferdinand and Robinson, Simon Daniel and de Rochefort, Ludovic and Li, Wei and Bredies, Kristian},
  journal={NMR in Biomedicine},
  volume={30},
  number={4},
  pages={e3604},
  year={2017},
  publisher={Wiley Online Library}
}
@inproceedings{fischer2003flirt,
  title={FLIRT: A flexible image registration toolbox},
  author={Fischer, Bernd and Modersitzki, Jan},
  booktitle={International Workshop on Biomedical Image Registration},
  pages={261--270},
  year={2003},
  organization={Springer}
}
@article{Bollmann2019SHARPQnet,
  title={SHARQnet--Sophisticated harmonic artifact reduction in quantitative susceptibility mapping using a deep convolutional neural network},
  author={Bollmann, Steffen and Kristensen, Matilde Holm and Larsen, Morten Skaarup and Olsen, Mathias Vassard and Pedersen, Mads Jozwiak and {\O}stergaard, Lasse Riis and O’Brien, Kieran and Langkammer, Christian and Fazlollahi, Amir and Barth, Markus},
  journal={Zeitschrift f{\"u}r Medizinische Physik},
  volume={29},
  number={2},
  pages={139--149},
  year={2019},
  publisher={Elsevier}
}
@article{bollmann2019deepqsm,
  title={{DeepQSM}-using deep learning to solve the dipole inversion for quantitative susceptibility mapping},
  author={Bollmann, Steffen and Rasmussen, Kasper Gade B{\o}tker and Kristensen, Mads and et al},
  journal={NeuroImage},
  volume={195},
  pages={373--383},
  year={2019},
  publisher={Elsevier}
}
@article{schweser2018quantitative,
  title={Quantitative susceptibility mapping ({QSM}) with an extended physical model for {MRI} frequency contrast in the brain: a proof-of-concept of quantitative susceptibility and residual ({QUASAR}) mapping},
  author={Schweser, Ferdinand and Zivadinov, Robert},
  journal={NMR in Biomedicine},
  volume={31},
  number={12},
  pages={e3999},
  year={2018},
  publisher={Wiley Online Library}
}
@article{zhang2020fidelity,
  title={Fidelity imposed network edit (FINE) for solving ill-posed image reconstruction},
  author={Zhang, Jinwei and Liu, Zhe and Zhang, Shun and Zhang, Hang and Spincemaille, Pascal and Nguyen, Thanh D and Sabuncu, Mert R and Wang, Yi},
  journal={NeuroImage},
  volume={211},
  pages={116579},
  year={2020},
  publisher={Elsevier}
}
@article{tieleman2012lecture,
  title={Lecture 6.5-rmsprop: Divide the gradient by a running average of its recent magnitude},
  author={Tieleman, Tijmen and Hinton, Geoffrey},
  journal={COURSERA: Neural networks for machine learning},
  volume={4},
  number={2},
  pages={26--31},
  year={2012}
}
@article{ashburner2005unified,
  title={Unified segmentation},
  author={Ashburner, John and Friston, Karl J},
  journal={NeuroImage},
  volume={26},
  number={3},
  pages={839--851},
  year={2005},
  publisher={Elsevier}
}
@article{li2014integrate,
  title={Integrated Laplacian-based phase unwrapping and background phase removal for quantitative susceptibility mapping},
  author={Li, Wei and Avram, Alexandru V and Wu, Bing and Xiao, Xue and Liu, Chunlei},
  journal={NMR in Biomedicine},
  volume={27},
  number={2},
  pages={219--227},
  year={2014},
  publisher={Wiley Online Library}
}
@article{liu2019quantitative,
  title={Quantitative susceptibility inversion through parcellated multiresolution neural networks and k-space substitution},
  author={Liu, Juan and Nencka, Andrew S and Muftuler, L Tugan and Swearingen, Brad and Karr, Robin and Koch, Kevin M},
  journal={arXiv preprint arXiv:1903.04961},
  year={2019}
}
@article{polak2020nonlinear,
  title={Nonlinear dipole inversion ({NDI}) enables robust quantitative susceptibility mapping ({QSM})},
  author={Polak, Daniel and Chatnuntawech, Itthi and Yoon, Jaeyeon and et al},
  journal={NMR in Biomedicine},
  pages={e4271},
  year={2020},
  publisher={Wiley Online Library}
}
@article{zhang2016quantitative,
  title={Quantitative susceptibility mapping and R2* measured changes during white matter lesion development in multiple sclerosis: myelin breakdown, myelin debris degradation and removal, and iron accumulation},
  author={Zhang, Y and Gauthier, SA and Gupta, Ajay and Chen, Weiwei and Comunale, Joseph and Chiang, GC-Y and Zhou, D and Askin, G and Zhu, W and Pitt, D and others},
  journal={American Journal of Neuroradiology},
  volume={37},
  number={9},
  pages={1629--1635},
  year={2016},
  publisher={Am Soc Neuroradiology}
}
@article{langley2009unwrapping,
  title={Unwrapping magnetic resonance phase maps with Chebyshev polynomials},
  author={Langley, Jason and Zhao, Qun},
  journal={Magnetic Resonance Imaging},
  volume={27},
  number={9},
  pages={1293--1301},
  year={2009},
  publisher={Elsevier}
}
@article{liu20123d,
  title={3D fiber tractography with susceptibility tensor imaging},
  author={Liu, Chunlei and Li, Wei and Wu, Bing and Jiang, Yi and Johnson, G Allan},
  journal={Neuroimage},
  volume={59},
  number={2},
  pages={1290--1298},
  year={2012},
  publisher={Elsevier}
}
@article{abdul2007fast,
  title={Fast and robust three-dimensional best path phase unwrapping algorithm},
  author={Abdul-Rahman, Hussein S and Gdeisat, Munther A and Burton, David R and Lalor, Michael J and Lilley, Francis and Moore, Christopher J},
  journal={Applied Optics},
  volume={46},
  number={26},
  pages={6623--6635},
  year={2007},
  publisher={Optical Society of America}
}
@article{cusack2002new,
  title={New robust 3-D phase unwrapping algorithms: application to magnetic field mapping and undistorting echoplanar images},
  author={Cusack, R and Papadakis, N},
  journal={Neuroimage},
  volume={16},
  number={3},
  pages={754--764},
  year={2002},
  publisher={Elsevier}
}
@article{spoorthi2020phasenet,
  title={PhaseNet 2.0: Phase Unwrapping of Noisy Data Based on Deep Learning Approach},
  author={Spoorthi, GE and Gorthi, Rama Krishna Sai Subrahmanyam and Gorthi, Subrahmanyam},
  journal={IEEE Transactions on Image Processing},
  volume={29},
  pages={4862--4872},
  year={2020},
  publisher={IEEE}
}
@article{zhang2019rapid,
  title={Rapid and robust two-dimensional phase unwrapping via deep learning},
  author={Zhang, Teng and Jiang, Shaowei and Zhao, Zixin and Dixit, Krishna and Zhou, Xiaofei and Hou, Jia and Zhang, Yongbing and Yan, Chenggang},
  journal={Optics express},
  volume={27},
  number={16},
  pages={23173--23185},
  year={2019},
  publisher={Optical Society of America}
}
@article{spoorthi2018phasenet,
  title={Phasenet: A deep convolutional neural network for two-dimensional phase unwrapping},
  author={Spoorthi, GE and Gorthi, Subrahmanyam and Gorthi, Rama Krishna Sai Subrahmanyam},
  journal={IEEE Signal Processing Letters},
  volume={26},
  number={1},
  pages={54--58},
  year={2018},
  publisher={IEEE}
}
@article{yang2017dagan,
  title={DAGAN: Deep de-aliasing generative adversarial networks for fast compressed sensing MRI reconstruction},
  author={Yang, Guang and Yu, Simiao and Dong, Hao and Slabaugh, Greg and Dragotti, Pier Luigi and Ye, Xujiong and Liu, Fangde and Arridge, Simon and Keegan, Jennifer and Guo, Yike and others},
  journal={IEEE Transactions on Medical Imaging},
  volume={37},
  number={6},
  pages={1310--1321},
  year={2017},
  publisher={IEEE}
}
@article{quan2018compressed,
  title={Compressed sensing MRI reconstruction using a generative adversarial network with a cyclic loss},
  author={Quan, Tran Minh and Nguyen-Duc, Thanh and Jeong, Won-Ki},
  journal={IEEE Transactions on Medical Imaging},
  volume={37},
  number={6},
  pages={1488--1497},
  year={2018},
  publisher={IEEE}
}
@article{zhao2019applications,
  title={Applications of a deep learning method for anti-aliasing and super-resolution in MRI},
  author={Zhao, Can and Shao, Muhan and Carass, Aaron and Li, Hao and Dewey, Blake E and Ellingsen, Lotta M and Woo, Jonghye and Guttman, Michael A and Blitz, Ari M and Stone, Maureen and others},
  journal={Magnetic resonance imaging},
  volume={64},
  pages={132--141},
  year={2019},
  publisher={Elsevier}
}
@article{meuree2019patch,
  title={Patch-based super-resolution of arterial spin labeling magnetic resonance images},
  author={Meur{\'e}e, C{\'e}dric and Maurel, Pierre and Ferr{\'e}, Jean-Christophe and Barillot, Christian},
  journal={Neuroimage},
  volume={189},
  pages={85--94},
  year={2019},
  publisher={Elsevier}
}
@article{lehtinen2018noise2noise,
  title={Noise2noise: Learning image restoration without clean data},
  author={Lehtinen, Jaakko and Munkberg, Jacob and Hasselgren, Jon and Laine, Samuli and Karras, Tero and Aittala, Miika and Aila, Timo},
  journal={arXiv preprint arXiv:1803.04189},
  year={2018}
}
@article{sharma2017mri,
  title={MRI-based quantitative susceptibility mapping (QSM) and R2* mapping of liver iron overload: Comparison with SQUID-based biomagnetic liver susceptometry},
  author={Sharma, Samir D and Fischer, Roland and Schoennagel, Bjoern P and Nielsen, Peter and Kooijman, Hendrik and Yamamura, Jin and Adam, Gerhard and Bannas, Peter and Hernando, Diego and Reeder, Scott B},
  journal={Magnetic Resonance in Medicine},
  volume={78},
  number={1},
  pages={264--270},
  year={2017},
  publisher={Wiley Online Library}
}
@article{haacke2005imaging,
  title={Imaging iron stores in the brain using magnetic resonance imaging},
  author={Haacke, E Mark and Cheng, Norman YC and House, Michael J and Liu, Qiang and Neelavalli, Jaladhar and Ogg, Robert J and Khan, Asadullah and Ayaz, Muhammad and Kirsch, Wolff and Obenaus, Andre},
  journal={Magnetic Resonance Imaging},
  volume={23},
  number={1},
  pages={1--25},
  year={2005},
  publisher={Elsevier}
}
@article{haacke2007establishing,
  title={Establishing a baseline phase behavior in magnetic resonance imaging to determine normal vs. abnormal iron content in the brain},
  author={Haacke, E Mark and Ayaz, Muhammad and Khan, Asadullah and Manova, Elena S and Krishnamurthy, Bharani and Gollapalli, Lakshman and Ciulla, Carlo and Kim, I and Petersen, Floyd and Kirsch, Wolff},
  journal={Journal of Magnetic Resonance Imaging},
  volume={26},
  number={2},
  pages={256--264},
  year={2007},
  publisher={Wiley Online Library}
}
@article{fatemi2009identification,
  title={Identification of breast calcification using magnetic resonance imaging},
  author={Fatemi-Ardekani, Ali and Boylan, Colm and Noseworthy, Michael D},
  journal={Medical Physics},
  volume={36},
  number={12},
  pages={5429--5436},
  year={2009},
  publisher={Wiley Online Library}
}
@article{lee2012contribution,
  title={The contribution of myelin to magnetic susceptibility-weighted contrasts in high-field MRI of the brain},
  author={Lee, Jongho and Shmueli, Karin and Kang, Byeong-Teck and Yao, Bing and Fukunaga, Masaki and Van Gelderen, Peter and Palumbo, Sara and Bosetti, Francesca and Silva, Afonso C and Duyn, Jeff H},
  journal={Neuroimage},
  volume={59},
  number={4},
  pages={3967--3975},
  year={2012},
  publisher={Elsevier}
}
@article{barbosa2015quantifying,
  title={Quantifying brain iron deposition in patients with Parkinson's disease using quantitative susceptibility mapping, R2 and R2},
  author={Barbosa, Jeam Haroldo Oliveira and Santos, Antonio Carlos and Tumas, Vitor and Liu, Manju and Zheng, Weili and Haacke, E Mark and Salmon, Carlos Ernesto Garrido},
  journal={Magnetic Resonance Imaging},
  volume={33},
  number={5},
  pages={559--565},
  year={2015},
  publisher={Elsevier}
}
@article{li2012reducing,
  title={Reducing the object orientation dependence of susceptibility effects in gradient echo MRI through quantitative susceptibility mapping},
  author={Li, Jianqi and Chang, Shixin and Liu, Tian and Wang, Qianfeng and Cui, Deqi and Chen, Xiaoyue and Jin, Moonsoo and Wang, Baocheng and Pei, Mengchao and Wisnieff, Cynthia and others},
  journal={Magnetic Resonance in Medicine},
  volume={68},
  number={5},
  pages={1563--1569},
  year={2012},
  publisher={Wiley Online Library}
}
@article{schafer2009using,
  title={Using magnetic field simulation to study susceptibility-related phase contrast in gradient echo MRI},
  author={Sch{\"a}fer, Andreas and Wharton, Sam and Gowland, Penny and Bowtell, Richard},
  journal={Neuroimage},
  volume={48},
  number={1},
  pages={126--137},
  year={2009},
  publisher={Elsevier}
}
@article{langkammer2016quantitative,
  title={Quantitative susceptibility mapping in Parkinson's disease},
  author={Langkammer, Christian and Pirpamer, Lukas and Seiler, Stephan and Deistung, Andreas and Schweser, Ferdinand and Franthal, Sebastian and Homayoon, Nina and Katschnig-Winter, Petra and Koegl-Wallner, Mariella and Pendl, Tamara and others},
  journal={PLoS One},
  volume={11},
  number={9},
  year={2016},
  publisher={Public Library of Science}
}
@article{zhang2018longitudinal,
  title={Longitudinal atlas for normative human brain development and aging over the lifespan using quantitative susceptibility mapping},
  author={Zhang, Yuyao and Wei, Hongjiang and Cronin, Matthew J and He, Naying and Yan, Fuhua and Liu, Chunlei},
  journal={Neuroimage},
  volume={171},
  pages={176--189},
  year={2018},
  publisher={Elsevier}
}
@article{pfefferbaum2009mri,
  title={MRI estimates of brain iron concentration in normal aging: comparison of field-dependent (FDRI) and phase (SWI) methods},
  author={Pfefferbaum, Adolf and Adalsteinsson, Elfar and Rohlfing, Torsten and Sullivan, Edith V},
  journal={Neuroimage},
  volume={47},
  number={2},
  pages={493--500},
  year={2009},
  publisher={Elsevier}
}
@article{van2016quantitative,
  title={Quantitative susceptibility mapping suggests altered brain iron in premanifest Huntington disease},
  author={Van Bergen, Jiri MG and Hua, Jun and Unschuld, Paul G and Lim, Issel Anne L and Jones, Craig K and Margolis, Russell L and Ross, Christopher A and Van Zijl, Peter CM and Li, Xu},
  journal={American journal of neuroradiology},
  volume={37},
  number={5},
  pages={789--796},
  year={2016},
  publisher={Am Soc Neuroradiology}
}
@article{sun2018quantitative,
  title={Quantitative susceptibility mapping for following intracranial hemorrhage},
  author={Sun, Hongfu and Klahr, Ana C and Kate, Mahesh and Gioia, Laura C and Emery, Derek J and Butcher, Kenneth S and Wilman, Alan H},
  journal={Radiology},
  volume={288},
  number={3},
  pages={830--839},
  year={2018},
  publisher={Radiological Society of North America}
}
@article{chen2014intracranial,
  title={Intracranial calcifications and hemorrhages: characterization with quantitative susceptibility mapping},
  author={Chen, Weiwei and Zhu, Wenzhen and Kovanlikaya, IIhami and Kovanlikaya, Arzu and Liu, Tian and Wang, Shuai and Salustri, Carlo and Wang, Yi},
  journal={Radiology},
  volume={270},
  number={2},
  pages={496--505},
  year={2014},
  publisher={Radiological Society of North America}
}
@inproceedings{schweser2011quan,
  title={Quantitative magnetic susceptibility mapping (QSM) in breast disease reveals additional information for MR-based characterization of carcinoma and calcification},
  author={Schweser, Ferdinand and Herrmann, KH and Deistung, A and Atterbury, M and Baltzer, PA and Burmeister, HP and Kaiser, WA and Reichenbach, J{\"u}rgen Rainer},
  booktitle={Proceedings of the International Society for Magnetic Resonance in Medicine},
  year={2011}
}
@article{lustig2007sparse,
  title={Sparse MRI: The application of compressed sensing for rapid MR imaging},
  author={Lustig, Michael and Donoho, David and Pauly, John M},
  journal={Magnetic Resonance in Medicine: An Official Journal of the International Society for Magnetic Resonance in Medicine},
  volume={58},
  number={6},
  pages={1182--1195},
  year={2007},
  publisher={Wiley Online Library}
}
@article{hammernik2018learning,
  title={Learning a variational network for reconstruction of accelerated MRI data},
  author={Hammernik, Kerstin and Klatzer, Teresa and Kobler, Erich and Recht, Michael P and Sodickson, Daniel K and Pock, Thomas and Knoll, Florian},
  journal={Magnetic Resonance in Medicine},
  volume={79},
  number={6},
  pages={3055--3071},
  year={2018},
  publisher={Wiley Online Library}
}
@inproceedings{krizhevsky2012imagenet,
  title={Imagenet classification with deep convolutional neural networks},
  author={Krizhevsky, Alex and Sutskever, Ilya and Hinton, Geoffrey E},
  booktitle={Advances in neural information processing systems},
  pages={1097--1105},
  year={2012}
}
@inproceedings{he2016deep,
  title={Deep residual learning for image recognition},
  author={He, Kaiming and Zhang, Xiangyu and Ren, Shaoqing and Sun, Jian},
  booktitle={Proceedings of the IEEE conference on computer vision and pattern recognition},
  pages={770--778},
  year={2016}
}
@article{zhu2018image,
  title={Image reconstruction by domain-transform manifold learning},
  author={Zhu, Bo and Liu, Jeremiah Z and Cauley, Stephen F and Rosen, Bruce R and Rosen, Matthew S},
  journal={Nature},
  volume={555},
  number={7697},
  pages={487--492},
  year={2018},
  publisher={Nature Publishing Group}
}
@inproceedings{deng2009imagenet,
  title={Imagenet: A large-scale hierarchical image database},
  author={Deng, Jia and Dong, Wei and Socher, Richard and Li, Li-Jia and Li, Kai and Fei-Fei, Li},
  booktitle={2009 IEEE conference on computer vision and pattern recognition},
  pages={248--255},
  year={2009},
  organization={Ieee}
}
@article{lecun1998gradient,
  title={Gradient-based learning applied to document recognition},
  author={LeCun, Yann and Bottou, L{\'e}on and Bengio, Yoshua and Haffner, Patrick},
  journal={Proceedings of the IEEE},
  volume={86},
  number={11},
  pages={2278--2324},
  year={1998},
  publisher={Ieee}
}
@book{goodfellow2016deep,
  title={Deep learning},
  author={Goodfellow, Ian and Bengio, Yoshua and Courville, Aaron},
  year={2016},
  publisher={MIT press}
}
@article{lecun1989backpropagation,
  title={Backpropagation applied to handwritten zip code recognition},
  author={LeCun, Yann and Boser, Bernhard and Denker, John S and Henderson, Donnie and Howard, Richard E and Hubbard, Wayne and Jackel, Lawrence D},
  journal={Neural computation},
  volume={1},
  number={4},
  pages={541--551},
  year={1989},
  publisher={MIT Press}
}
@article{liu2015susceptibility,
  title={Susceptibility-weighted imaging and quantitative susceptibility mapping in the brain},
  author={Liu, Chunlei and Li, Wei and Tong, Karen A and Yeom, Kristen W and Kuzminski, Samuel},
  journal={Journal of magnetic resonance imaging},
  volume={42},
  number={1},
  pages={23--41},
  year={2015},
  publisher={Wiley Online Library}
}
@article{haacke2015quantitative,
  title={Quantitative susceptibility mapping: current status and future directions},
  author={Haacke, E Mark and Liu, Saifeng and Buch, Sagar and Zheng, Weili and Wu, Dongmei and Ye, Yongquan},
  journal={Magnetic resonance imaging},
  volume={33},
  number={1},
  pages={1--25},
  year={2015},
  publisher={Elsevier}
}
@article{liu2010unambiguous,
  title={Unambiguous identification of superparamagnetic iron oxide particles through quantitative susceptibility mapping of the nonlinear response to magnetic fields},
  author={Liu, Tian and Spincemaille, Pascal and de Rochefort, Ludovic and Wong, Richard and Prince, Martin and Wang, Yi},
  journal={Magnetic Resonance Imaging},
  volume={28},
  number={9},
  pages={1383--1389},
  year={2010},
  publisher={Elsevier}
}
@article{mamisch2012t2,
  title={T2 star relaxation times for assessment of articular cartilage at 3 T: a feasibility study},
  author={Mamisch, Tallal Charles and Hughes, Timothy and Mosher, Timothy J and Mueller, Christoph and Trattnig, Siegfried and Boesch, Chris and Welsch, Goetz Hannes},
  journal={Skeletal Radiology},
  volume={41},
  number={3},
  pages={287--292},
  year={2012},
  publisher={Springer}
}
@article{huisman2005intracranial,
  title={Intracranial hemorrhage: ultrasound, CT and MRI findings},
  author={Huisman, Thierry AGM},
  journal={European Radiology},
  volume={15},
  number={3},
  pages={434--440},
  year={2005},
  publisher={Springer}
}
@article{makariou2009intracranial,
  title={Intracranial calcifications},
  author={Makariou, Erini and Patsalides, Athos D},
  journal={Applied Radiology},
  volume={38},
  number={11},
  pages={48},
  year={2009},
  publisher={Anderson Publishing Ltd.}
}
@article{pruessmann1999sense,
  title={SENSE: sensitivity encoding for fast MRI},
  author={Pruessmann, Klaas P and Weiger, Markus and Scheidegger, Markus B and Boesiger, Peter},
  journal={Magnetic Resonance in Medicine},
  volume={42},
  number={5},
  pages={952--962},
  year={1999},
  publisher={Wiley Online Library}
}
@article{wisnieff2013magnetic,
  title={Magnetic susceptibility anisotropy: cylindrical symmetry from macroscopically ordered anisotropic molecules and accuracy of MRI measurements using few orientations},
  author={Wisnieff, Cynthia and Liu, Tian and Spincemaille, Pascal and Wang, Shuai and Zhou, Dong and Wang, Yi},
  journal={Neuroimage},
  volume={70},
  pages={363--376},
  year={2013},
  publisher={Elsevier}
}
@article{odena2016deconvolution,
  title={Deconvolution and checkerboard artifacts},
  author={Odena, Augustus and Dumoulin, Vincent and Olah, Chris},
  journal={Distill},
  volume={1},
  number={10},
  pages={e3},
  year={2016}
}
@inproceedings{abadi2016tensorflow,
  title={Tensorflow: A system for large-scale machine learning},
  author={Abadi, Mart{\'\i}n and Barham, Paul and Chen, Jianmin and Chen, Zhifeng and Davis, Andy and Dean, Jeffrey and Devin, Matthieu and Ghemawat, Sanjay and Irving, Geoffrey and Isard, Michael and others},
  booktitle={12th $\{$USENIX$\}$ Symposium on Operating Systems Design and Implementation ($\{$OSDI$\}$ 16)},
  pages={265--283},
  year={2016}
}
@inproceedings{snell2017prototypical,
  title={Prototypical networks for few-shot learning},
  author={Snell, Jake and Swersky, Kevin and Zemel, Richard},
  booktitle={Advances in neural information processing systems},
  pages={4077--4087},
  year={2017}
}
@inproceedings{zhou2017unsupervised,
  title={Unsupervised learning of depth and ego-motion from video},
  author={Zhou, Tinghui and Brown, Matthew and Snavely, Noah and Lowe, David G},
  booktitle={Proceedings of the IEEE Conference on Computer Vision and Pattern Recognition},
  pages={1851--1858},
  year={2017}
}
@inproceedings{sung2018learning,
  title={Learning to compare: Relation network for few-shot learning},
  author={Sung, Flood and Yang, Yongxin and Zhang, Li and Xiang, Tao and Torr, Philip HS and Hospedales, Timothy M},
  booktitle={Proceedings of the IEEE Conference on Computer Vision and Pattern Recognition},
  pages={1199--1208},
  year={2018}
}
@article{jing2020self,
  title={Self-supervised visual feature learning with deep neural networks: A survey},
  author={Jing, Longlong and Tian, Yingli},
  journal={IEEE Transactions on Pattern Analysis and Machine Intelligence},
  year={2020},
  publisher={IEEE}
}
@article{bauer2011comparingparameter,
  title={Comparingparameter choice methods for regularization of ill-posed problems},
  author={Bauer, Frank and Lukas, Mark A},
  journal={Mathematics and Computers in Simulation},
  volume={81},
  number={9},
  pages={1795--1841},
  year={2011},
  publisher={Elsevier}
}
@book{engl1996regularization,
  title={Regularization of inverse problems},
  author={Engl, Heinz Werner and Hanke, Martin and Neubauer, Andreas},
  volume={375},
  year={1996},
  publisher={Springer Science \& Business Media}
}
@inproceedings{buciluǎ2006model,
  title={Model compression},
  author={Buciluǎ, Cristian and Caruana, Rich and Niculescu-Mizil, Alexandru},
  booktitle={Proceedings of the 12th ACM SIGKDD international conference on Knowledge discovery and data mining},
  pages={535--541},
  year={2006}
}
@inproceedings{zhu2017unpaired,
  title={Unpaired image-to-image translation using cycle-consistent adversarial networks},
  author={Zhu, Jun-Yan and Park, Taesung and Isola, Phillip and Efros, Alexei A},
  booktitle={Proceedings of the IEEE international conference on computer vision},
  pages={2223--2232},
  year={2017}
}
@article{long2015learning,
  title={Learning transferable features with deep adaptation networks},
  author={Long, Mingsheng and Cao, Yue and Wang, Jianmin and Jordan, Michael I},
  journal={arXiv preprint arXiv:1502.02791},
  year={2015}
}
@inproceedings{tzeng2017adversarial,
  title={Adversarial discriminative domain adaptation},
  author={Tzeng, Eric and Hoffman, Judy and Saenko, Kate and Darrell, Trevor},
  booktitle={Proceedings of the IEEE conference on computer vision and pattern recognition},
  pages={7167--7176},
  year={2017}
}
@inproceedings{zou2018unsupervised,
  title={Unsupervised domain adaptation for semantic segmentation via class-balanced self-training},
  author={Zou, Yang and Yu, Zhiding and Vijaya Kumar, BVK and Wang, Jinsong},
  booktitle={Proceedings of the European conference on computer vision (ECCV)},
  pages={289--305},
  year={2018}
}
@article{hoffman2017cycada,
  title={Cycada: Cycle-consistent adversarial domain adaptation},
  author={Hoffman, Judy and Tzeng, Eric and Park, Taesung and Zhu, Jun-Yan and Isola, Phillip and Saenko, Kate and Efros, Alexei A and Darrell, Trevor},
  journal={arXiv preprint arXiv:1711.03213},
  year={2017}
}
@article{wang2018deep,
  title={Deep visual domain adaptation: A survey},
  author={Wang, Mei and Deng, Weihong},
  journal={Neurocomputing},
  volume={312},
  pages={135--153},
  year={2018},
  publisher={Elsevier}
}
@article{bilgic2020qsm,
  title={QSM Reconstruction Challenge 2.0: Design and Report of Results},
  author={Bilgic, Berkin and Langkammer, Christian and Marques, Jos{\'e} P and Meineke, Jakob and Milovic, Carlos and Schweser, Ferdinand and QSM Challenge 2.0 Organization Committee and others},
  journal={bioRxiv},
  year={2020},
  publisher={Cold Spring Harbor Laboratory}
}
@inproceedings{liu2020weakly,
  title={Weakly-Supervised Learning for Single-Step Quantitative Susceptibility Mapping},
  author={Liu, Juan and Koch, Kevin M},
  booktitle={International Workshop on Machine Learning for Medical Image Reconstruction},
  pages={70--81},
  year={2020},
  organization={Springer}
}
@inproceedings{liu2020model,
  title={Model-Based Learning for Quantitative Susceptibility Mapping},
  author={Liu, Juan and Koch, Kevin M},
  booktitle={International Workshop on Machine Learning for Medical Image Reconstruction},
  pages={48--59},
  year={2020},
  organization={Springer}
}
@article{marques2021qsm,
  title={QSM Reconstruction Challenge 2.0: a realistic in silico head phantom for MRI data simulation and evaluation of susceptibility mapping procedures},
  author={Marques, Jos{\'e} P and Meineke, Jakob and Milovic, Carlos and Bilgic, Berkin and Chan, Kwok-Shing and Hedouin, Renaud and vand der Zwaag, Wietske and Langkammer, Christian and Schweser, Ferdinand},
  journal={Biorxiv},
  pages={2020--09},
  year={2021},
  publisher={Cold Spring Harbor Laboratory}
}
@article{gao2020xqsm,
  title={xQSM: quantitative susceptibility mapping with octave convolutional and noise-regularized neural networks},
  author={Gao, Yang and Zhu, Xuanyu and Moffat, Bradford A and Glarin, Rebecca and Wilman, Alan H and Pike, G Bruce and Crozier, Stuart and Liu, Feng and Sun, Hongfu},
  journal={NMR in Biomedicine},
  pages={e4461},
  year={2020},
  publisher={Wiley Online Library}
}
@inproceedings{zou2018unsupervised,
  title={Unsupervised domain adaptation for semantic segmentation via class-balanced self-training},
  author={Zou, Yang and Yu, Zhiding and Vijaya Kumar, BVK and Wang, Jinsong},
  booktitle={Proceedings of the European conference on computer vision (ECCV)},
  pages={289--305},
  year={2018}
}
@inproceedings{atapour2018real,
  title={Real-time monocular depth estimation using synthetic data with domain adaptation via image style transfer},
  author={Atapour-Abarghouei, Amir and Breckon, Toby P},
  booktitle={Proceedings of the IEEE Conference on Computer Vision and Pattern Recognition},
  pages={2800--2810},
  year={2018}
}
@article{ganin2016domain,
  title={Domain-adversarial training of neural networks},
  author={Ganin, Yaroslav and Ustinova, Evgeniya and Ajakan, Hana and Germain, Pascal and Larochelle, Hugo and Laviolette, Fran{\c{c}}ois and Marchand, Mario and Lempitsky, Victor},
  journal={The Journal of Machine Learning Research},
  volume={17},
  number={1},
  pages={2096--2030},
  year={2016},
  publisher={JMLR. org}
}
@article{jenkinson2002improved,
  title={Improved optimization for the robust and accurate linear registration and motion correction of brain images},
  author={Jenkinson, Mark and Bannister, Peter and Brady, Michael and et al},
  journal={Neuroimage},
  volume={17},
  number={2},
  pages={825--841},
  year={2002},
  publisher={Academic Press}
}
@article{jenkinson2001global,
  title={A global optimisation method for robust affine registration of brain images},
  author={Jenkinson, Mark and Smith, Stephen},
  journal={Medical image analysis},
  volume={5},
  number={2},
  pages={143--156},
  year={2001},
  publisher={Elsevier}
}
@article{tzeng2014deep,
  title={Deep domain confusion: Maximizing for domain invariance},
  author={Tzeng, Eric and Hoffman, Judy and Zhang, Ning and Saenko, Kate and Darrell, Trevor},
  journal={arXiv preprint arXiv:1412.3474},
  year={2014}
}
@misc{QSMnet_github,
  title = {QSMnet Code},
  url = {https://github.com/SNU-LIST/QSMnet},
  year={2020}
}
