Publications

• HG Shin, W Kim, JH Lee, HS Lee, Y Nam, J Kim, X Li, PCM van Zijl, PA Calabresi, J Lee, J Jang

Association of Iron Deposition in MS Lesion with Remyelination Capacity Using Susceptibility Source Separation MRI 

NeuroImage: Clinical 2025, 45, 103748

• J Kim, M Kim, S Ji, K Min, H Jeong, HG Shin, C Oh, RJ Fox, KE Sakaie, MJ Lowe, SH Oh, S Straub, SG Kim, J Lee*

In-vivo high-resolution χ-separation at 7T

NeuroImage 2025, 308, 121060

• M Kim, S Ji, J Kim, K Min, H Jeong, J Youn, T Kim, J Jang, B Bilgic, HG Shin*, J Lee*

χ‐sepnet: Deep neural network for magnetic susceptibility source separation

Human Brain Mapping 2025, 46(2):e70136 

• Mueller J, Lu PJ, Cagol A, Probst ERJ, Shin HG, Pineda MAO, Chen X, Barakovic M, Riccardo G, Weigel M, Sabine S, Wang Y, Nguyen TD, Spincemaille P, Ludwig K, Lee J, Tsagkas H, Granziera C

Quantifying Remyelination using χ-Separation in White Matter and Cortical Multiple Sclerosis Lesions

Neurology 2024, 103:e209604

• Hong S, Bae JH, Lee J*, Chun SY*

Adaptive Selection of Sampling-Reconstruction in Fourier Compressed Sensing

European Conference on Computer Vision (ECCV) 2024

• Min K, Sohn B, Kim WJ, Park CJ, Song S, Shin DH, Chang KW, Shin NY, Kim M, Shin HG, Lee PH, Lee J*

A human brain atlas of chi-separation for normative iron and myelin distributions

NMR Biomed 2024, 37(12):e5226

• Ji S, Jang J, Kim M, Lee H, Kim W, Lee J, Shin H

Comparison between R2′-based and R2*-based χ-separation methods: A clinical evaluation in individuals with multiple sclerosis

NMR Biomed 2024, 37(9):e5167

• Lee J*, Ji S , Oh SH* 

So You Want to Image Myelin Using MRI: Magnetic Susceptibility Source Separation for Myelin Imaging

Magn Reson Med Sci 2024, 23(3):291-306 

• QSM Consensus Organization Committee, Bilgic B, Costagli M, Chan KS, Duyn J, Langkammer C, Lee J, Li X, Liu C, Marques JP, Milovic C, Robinson SD, Schweser F, Shmueli K, Spincemaille P, Straub S, Zijl P, Wang Y, ISMRM EMTP Study Group
  Recommended implementation of quantitative susceptibility mapping for clinical research in the brain: A consensus of the ISMRM electro-magnetic tissue properties study group
  Magn Res Med 2024, 91(5):1834-1862

• Kim HW, Lee S, Yang JH, Moon Y, Lee J, Moon WJ
  Cortical Iron Accumulation as an Imaging Marker for Neurodegeneration in Clinical Cognitive Impairment Spectrum: A Quantitative Susceptibility Mapping Study
  KJR  2023, 24:1131-1141

• Choi S, Kim M, Kim T, Choi EJ, Lee J, Moon SY, Cho SS, Lee J, Kwon JS
  Fronto-striato-thalamic circuit connectivity and neuromelanin in schizophrenia: an fMRI and neuromelanin-MRI study
  Schizophrenia 2023, 9:81

• Shin H, Kim T, Park J, Raj H, Jabbar MS, Abebaw ZD, Lee J, Van CC, Kim H, Shin D
  Pulmonary abnormality screening on chest x-rays from different machine specifications: a generalized AI-based image manipulation pipeline
  Eur Radiol Exp 2023, 7:68

• Jeong H, Byun H, Kang DU, Lee J*
  BlindHarmony: “Blind” Harmonization for MR Images via Flow model
  International Conference on Computer Vision (ICCV), 2023 21129-21139

• Lee S, Shin HG, Kim M, Lee J*
  Depth-wise profiles of iron and myelin in the cortex and white matter
  NeuroImage 2023 273:120058

• Kim W, Shin HG, Lee H, Park D, Kang J, Nam Y, Lee J, Jang J
  χ-separation imaging for diagnosis of multiple sclerosis versus neuromyelitis optica spectrum disorder
  Radiology 2023 307:e220941

• Ji S, Choi EJ, Sohn B, Baik K, Shin NY, Moon WJ, Park S, Song S, Lee PH, Shin DH, Oh SH, Kim EY, Lee J*
  Sandwich spatial saturation for neuromelanin-sensitive MRI: Development and multi-center trial
  NeuroImage 2022 261:119706

• Zhang Z, Cho J, Wang L, Liao C, Shin HG, Cao X, Lee J, Xu J, Zhang T, Ye H, Setsompop K, Liu H, Bilgic B
  Blip up-down acquisition for spin- and gradient-echo imaging (BUDA-SAGE) with self-supervised denoising enables efficient T2, T2*, para- and dia-magnetic susceptibility mapping
  Magn Res Med 2022 88(2):633-650

• Ji S, Yang D, Lee J, Choi SH, Kim H, Kang KM
  [REVIEW] Synthetic MRI: Technologies and applications in neuroradiology
  JMRI 2022 55(4):1013-1025

• Jung W, Steffen Bollmann, Lee J*
  [REVIEW] Overview of quantitative susceptibility mapping using deep learning – current status, challenges and opportunities
  NMR Biomed 2022 35(4) e4292

• Park J, Jung W, Choi EJ, Oh SH, Jang J, Shin D, An H, Lee J*
  DIFFnet: Diffusion parameter mapping network generalized for input diffusion gradient schemes and b-values
  IEEE Trans Medical Imaging 2022 41:491-499

• Shin D, Kim Y, Oh C, An H, Park J, Kim J, Lee J*
  Deep reinforcement learning-designed radiofrequency waveform in MRI
  Nature Machine Intelligence 2021 3:985-994   Youtube link

• Shin HG, Lee J, Yun YH, Yoo SH, Jang J, Oh SH, Nam Y, Kim S, Fukunaga M, Kim W, Choi HJ, Lee J*
  χ-separation: Magnetic susceptibility source separation toward iron and myelin mapping in the brain
  Neuroimage 2021 240:118371

• Lee S, Yoo RE, Choi SH, Oh SH, Ji S, Lee J, Huh KY, Lee JY, Hwang I, Kang KM, Yun TJ, Kim JH, Sohn CH
  Contrast-enhanced MRI T1 mapping for quantitative evaluation of putative dynamic glymphatic activity in the human brain in sleep-wake states
  Radiology 2021 300(3):661-668

• Ji S, Jeong J, Oh SH, Nam Y, Choi SH, Shin HG, Shin D, Jung W, and Lee J*
  Quad-contrast imaging: simultaneous acquisition of four contrast-weighted images (PD-weighted, T2-weighted, PD-FLAIR and T2-FLAIR images) with synthetic T1-weighted image, T1- and T2-maps
  IEEE Trans Medical Imaging 2021 40(12):3617-3626

• Lee J, Hyun JW, Lee J, Choi EJ, Shin HG, Min K, Nam Y, Kim HJ, Oh SH
  [REVIEW] So you want to image myelin using MRI: An overview and practical guide for myelin water imaging
  JMRI 2021 53(2):360-373

• Eun H+, Jeong H+, Lee J, Shin HG, and Lee J*
  A geometric approach to separate the effects of magnetic susceptibility and chemical shift/exchange in a phantom with isotropic magnetic susceptibility
  Magn Res Med 2021 85(1):281-289

• An H, Shin HG, Ji S, Jung W, Oh SH, Shin D, Park J, Lee J*,
  DeepResp: Deep learning solution for respiration-induced B0 fluctuation artifacts in multi-slice GRE
  NeuroImage 2021 224:117432

• Shin D, Ji S, Lee D, Lee J, Oh SH, Lee J*,
  Deep reinforcement learning designed Shinnar-Le Roux RF pulse using root-flipping: DeepRFSLR
  IEEE Trans Medical Imaging 2020 39(12):4391-4400

• Polak D, Chatnuntawech I, Yoon J, Iyer SS, Milovic C, Lee J, Bachert P, Adalsteinsson E, Setsompop K, Bilgic B
  Nonlinear dipole inversion (NDI) enables robust quantitative susceptibility mapping (QSM)
  NMR in Biomed 2020, 33(12):e4271

• Jung W, Yoon J, Ji S, Choi JY, Kim JM, Nam Y, Kim EY, Lee J*
  Exploring linearity of deep neural network trained QSM: QSMnet+
  Neuroimage 2020 211:116619

• Lee J, Lee D, Choi JY, Shin D, Shin HG, Lee J*
  Artificial neural network for myelin water imaging
  Magn Res Med 2020 83(5):1875-1883

• Choi JY, Hart T, Whyte J, Rabinowitz AR, Oh SH, Lee J*, Kim JJ*
  Myelin water imaging of moderate to severe diffuse traumatic brain injury
  NeuroImage in Clinic 2019 22:101785

• Shin HG, Oh SH, Fukunaga M, Nam Y, Lee D, Jung W, Jo M, Ji S, Choi JY, Lee J*
  Advances in gradient echo myelin water imaging at 3T and 7T
  NeuroImage 2019 188:835-844

• Kim JY, Yoon JM, Park JE, Choi EJ, Lee JH, Kim HS
  Radiomics in peritumoral non-enhancing regions: fractional anisotropy and cerebral blood volume improve prediction of local progression and overall survival in patients with glioblastoma
  Neuroradiology 2019 61:1261–1272

• Sung YH, Lee J, Nam Y, Shin HG, Noh Y, Hwang KH, Lee H, Kim EY,
  Initial diagnostic workup of Parkinsonism: dopamine transporter positron emission tomography versus susceptibility map-weighted imaging at 3T
  Parkinsonism & Related Disorders 2019 62:171-178

• Choi JY, Lee J, Nam Y, Lee J, Oh SH
  Improvement of reproducibility in quantitative susceptibility mapping (QSM) and transverse relaxation rates (R2*) after physiological noise correction
  JMRI 2019 49(6):1769-1776

• Choi JY+, Jeong IH+, Oh SH, Oh CH, Kim HJ*, Lee J*
  Evaluation of normal-appearing white matter in multiple sclerosis using ViSTa myelin water imaging and GRASE myelin water imaging
  JMRI 2019 49(4):1091-1098

• Kim EY, Sung YH, Lee J
  Nigrosome 1 imaging: technical considerations and clinical applications
  British Journal of Radiology, 2019, 92:20180842

• Lee LE, Ljungberg E, Shin D, Figley CR, Vavasour IM, Rauscher A, Cohen-Adad J, Li DKB, Traboulsee AL, MacKay AL, Lee J, Kolind SH
  Inter-vendor reproducibility of myelin water imaging using a 3D gradient and spin echo sequence
  Frontiers in Neuroscience 2018 12:854

• Yoon J, Gong E, Chatnuntawech I, Bilgic B, Lee J, Jung W, Ko J, Jung H, Setsompop K, Zaharchuk G, Kim EY, Pauly J, Lee J*
  Quantitative susceptibility mapping using deep neural network: QSMnet
  NeuroImage 2018 179:199-206

• Lee DH, Lee JG, Lee J, Nam Y
  Single-scan z-shim method for reducing susceptibility artifacts in gradient echo myelin water imaging
  Magn Res Med 2018 80(3):1101-1109

• Sung YH, Lee J, Nam Y, Shin HG, Noh Y, Shin DH, Kim EY
  Differential involvement of nigral subregions in idiopathic Parkinson’s disease,
  Human Brain Mapping 2018 39(1):542-553

• Oh SH, Sin WY, Lee J, Lowe MJ
  Variable density magnetization transfer (vdMT) imaging for 7 tesla MR imaging
  NeuroImage 2018 168:242-249

• Jung WJ, Lee J, Shin HG, Nam Y, H Zhang, Oh SH, Lee J*
  Whole brain g-ratio mapping using myelin water imaging (MWI) and neurite orientation dispersion and density imaging (NODDI),
  NeuroImage 2018 182:379-388

• Kim EY, Sung YH, Shin HG, Noh Y, Nam Y*, Lee J*
  Diagnosis of early-stage idiopathic Parkinson’s disease using high-resolution quantitative susceptibility mapping with histogram analysis in the substantia nigra at 3T
  J Clin Neurol 2018 14(1):90-97

• Lee J, Shin HG, Jung WJ, Nam Y, Oh SH, Lee J*
  An R2* model of white matter for fiber orientation and myelin concentration
  NeuroImage 2017 162:269-275

• Nam Y, Gho SM, Kim DH, Kim EY*, Lee J*
  Imaging of nigrosome 1 in substantia nigra at 3T using multiecho susceptibility map-weighted imaging (SMWI)
  JMRI 2017 46(2):528-536

• Jeong IH+, Choi JY+, Kim SH, Hyun JW, Joung AR, Lee J*, Kim HJ*
  Normal appearing white matter demyelination in neuromyelitis optica spectrum disorder
  Eur J Neurol 2017 24(4):652-658

• Lee J*, Nam Y, Choi JY, Kim EY, Oh SH, Kim DH*
  [REVIEW] Mechanisms of T2* anisotropy and gradient echo myelin water imaging
  NMR Biomed 2017 30(4):e3513

• Stafford RB, Woo MK, Oh SE, Dolui S, Zhao T, Kim YB, Detre JA, Cho ZH*, Lee J*
  An actively decoupled dual transceiver coil system for continuous ASL at 7 T
  International Journal of Imaging Systems and Technology 2016 26:106-115

• Jeong IH+, Choi JY+, Kim SH, Hyun JW, Joung A, Lee J*, Kim HJ*
  Comparison of myelin water fraction values in periventricular white matter lesions between multiple sclerosis and neuromyelitis optica spectrum disorder
  Multiple Sclerosis 2016 22(12):1616-1620

• Sung YH, Noh Y, Lee J, Kim EY
  Drug-induced Parkinsonism versus idiopathic Parkinson disease
  Radiology 2016 279:849-858

• Woo MK, Hong SM, Lee J, Kang CK, Park SY, Son YD, Kim YB, Cho ZH
  Extended monopole antenna array with individual shield (EMAS) coil – an improved monopole antenna design for brain imaging at 7T MRI
  Magn Res Med 2016 75:2566-2572

• Nam YH, Kim DH, Lee J*
  Physiological noise compensation in gradient-echo myelin water imaging
  NeuroImage 2015 120:345-349

• Noh Y, Sung Y, Lee J, Kim EY
  Nigrosome 1 imaging at 3T MRI for the diagnosis of early-stage idiopathic Parkinson’s disease: assessment of diagnostic accuracy and agreement on imaging asymmetry and clinical laterality
  AJNR 2015 36:2010-2016

• Nam YH, Lee J*, Hwang D, Kim DH*
  Improved estimation of myelin water fraction using complex model fitting
  NeuroImage 2015 116:214-221

• Kim D, Lee HM, Oh SH, Lee J*
  Probing signal phase in direct visualization of short transverse relaxation time component (ViSTa)
  Magn Res Med 2015 74:499-505

• Sullivan S, Eucker SA, Gabrieli D, Bradfield C, Coats B, Maltese MR, Lee J, Smith C, Margulies SS
  White matter tract-oriented deformation predicts traumatic axonal brain injury and reveals rotational direction-specific vulnerabilities
  Biomech Model Mechanobiol 2015 14:877-896

• SS Oh, Y Han, J Lee, Yun SD, JK Kang, EM Lee, HW Yoon, JY Chung, HW Park
  A pulsed artifact removal method considering artifact variations in the simultaneous recording of EEG and fMRI.
  Neurosci Res 2014 81-82:42-50

• SS Oh, SH Oh, Y Nam, D Han, RB Stafford, J Hwang, DH Kim, HW Park, J Lee*
  An improved susceptibility weighted imaging method using multi-echo acquisition.
  Magn Res Med 2014 72:452-458

• SH Oh, M Bilello, M Schindler, CE Markowitz, JA Detre, J Lee*
  Direct visualization of short transverse relaxation time component (ViSTa).
  NeuroImage 2013 83:485-92

• SH Oh, YB Kim, ZH Cho, J Lee*
  Origin of B0 orientation dependent R2* (=1/T2*) in white matter.
  NeuroImage 2013 73:71-9

• R Datta, J Lee, BB Avants, CH Vite, B Tseng, JC Gee, GD Aguirre, GK Aguirre
  A digital atlas of the dog brain.
  PLOS ONE 2012 7:e52140

• J Lee*, K Shmueli, B-T Kang, B Yao, M Fukunaga, P van Gelderen, S Palumbo, F Bosetti, AC Silva, JH Duyn
  The contribution of myelin to magnetic susceptibilty-weighted contrasts in high-field MRI of the brain.
  Neuroimage 2012 59:3967-75

• TS Kim, J Lee*, JH Lee, GH Glover, JH Pauly
  Analysis of the BOLD characteristics in pass-band bSSFP fMRI.
  International Journal of Imaging Systems and Technology 2012 22:23-32

• GT Buracas, Y Jung, J Lee, RB Buxton, EC Wong, TT Liu
  On multiple alternating steady states induced by periodic spin phase perturbation waveforms.
  Magn Reson Med 2012 67:1412-8

• P van Gelderen, JA de Zwart, J Lee, P Sati, DS Reich, JH Duyn
  Nonexponential T2* decay in white matter.
  Magn Reson Med 2012 67:110-7

• J Lee*, P van Gelderen, LW Kuo, H Merkle, AC Silva, JH Duyn
  T2*-based fiber orientation mapping.
  Neuroimage 2011 57:225-34

• J Lee*, M Fukunaga, JH Duyn
  Improving contrast to noise ratio of resonance frequency contrast images (phase images) using balanced steady-state free precession.
  Neuroimage 2011 54:2779-88

• J Lee*, K Shmueli, M Fukunaga, P van Gelderen, H Merkle, AC Silva, JH Duyn
  Sensitivity of MRI resonance frequency to the orientation of brain tissue microstructure.
  PNAS 2010 107:5130-5

• M Fukunaga, T-Q Li, P van Gelderen, Y de Zwart, K Shmueli, B Yao, J Lee, D Maric, M Aronova, G Zhang, R Leapman, J Schenck, H Merkle, JH Duyn
  Layer-specific variation of iron content in cerebral cortex as a source of MRI contrast.
  PNAS 2010 1073834-9

• J Lee*, Y Hirano, M Fukunaga, AC Silva, JH Duyn
  On the contribution of deoxyhemoglobin to MRI gray-white matter phase contrast at high field.
  Neuroimage 2010 49:193-8

• L Qin, P van Gelderen, JA Derbyshire, F Jin, J Lee, JA de Zwart, Y Tao, JH Duyn
  Prospective head movement correction for high resolution MRI using an in-bore optical tracking system.
  Magn Reson Med 2009 62:924-34

• J Lee*, M Lustig, DH Kim, JM Pauly
  Improved shim methods based on the minimization of the maximum off-resonance frequency for balanced SSFP.
  Magn Reson Med 2009 61:1500-6

• A Schwartzman, RF Dougherty, J Lee, D Ghahremani, JE Taylor
  Empirical null and false discovery rate analysis in neuroimaging.
  Neuroimage 2009 44:71-82

• J Lee*, M Shahram, A Schwartzman, JM Pauly
  Complex data analysis in high-resolution SSFP fMRI.
  Magn Reson Med 2007 57:905-17

• J Lee*, JM Santos, SM Conolly, KL Miller, BA Hargreaves, JM Pauly
  Respiration-induced B0 field fluctuation compensation in balanced SSFP: real-time approach for transition-band SSFP fMRI.
  Magn Reson Med 2006 55:1197-201

• KL Miller, BA Hargreaves, J Lee, D Ress, RC deCharms, JM Pauly
  Functional brain imaging using a blood oxygenation sensitive steady state.
  Magn Reson Med 2003 50:675-83