Tensor scale-based image registration. - Punam K. Saha; Hui Zhang 005; Jayaram K. Udupa; James C. Gee (Image Processing, 2003)

Registration of Diffusion Tensor Images. - Hui Zhang 005; Paul A. Yushkevich; James C. Gee (CVPR (1), 2004)

Towards Diffusion Profile Image Registration. - Hui Zhang 005; Paul A. Yushkevich; James C. Gee (ISBI, 2004)

Parametric Medial Shape Representation in 3-D via the Poisson Partial Differential Equation with Non-linear Boundary Conditions. - Paul A. Yushkevich; Hui Zhang 005; James C. Gee (IPMI, 2005)

An Automated Approach to Connectivity-Based Partitioning of Brain Structures. - Philip A. Cook; Hui Zhang 005; Brian B. Avants; Paul A. Yushkevich; Daniel C. Alexander; James C. Gee; Olga Ciccarelli; Alan J. Thompson (MICCAI, 2005)

Statistical Modeling of Shape and Appearance Using the Continuous Medial Representation. - Paul A. Yushkevich; Hui Zhang 005; James C. Gee (MICCAI (2), 2005)

Deformable Registration of Diffusion Tensor MR Images with Explicit Orientation Optimization. - Hui Zhang 005; Paul A. Yushkevich; James C. Gee (MICCAI, 2005)

Anatomy-Based Visualizations of Diffusion Tensor Images of Brain White Matter. - James C. Gee; Hui Zhang 005; Abraham Dubb; Brian B. Avants; Paul A. Yushkevich; Jeffrey T. Duda (Visualization and Processing of Tensor Fields, 2006)

Efficient Generation of Shape-Based Reference Frames for the Corpus Callosum for DTI-based Connectivity Analysis. - Hui Sun; Paul A. Yushkevich; Hui Zhang 005; James C. Gee; Tony J. Simon (CVPR Workshops, 2006)

Hippocampus-Specific fMRI Group Activation Analysis with Continuous M-Reps. - Paul A. Yushkevich; John A. Detre; Kathy Z. Tang; Angela Hoang; Dawn Mechanic-Hamilton; María A. Fernández-Seara; Marc Korczykowski; Hui Zhang 005; James C. Gee (MICCAI (2), 2006)

3D Mouse Brain Reconstruction from Histology Using a Coarse-to-Fine Approach. - Paul A. Yushkevich; Brian B. Avants; Lydia Ng; Michael Hawrylycz; Pablo D. Burstein; Hui Zhang 005; James C. Gee (WBIR, 2006)

Deformable registration of diffusion tensor MR images with explicit orientation optimization. - Hui Zhang 005; Paul A. Yushkevich; Daniel C. Alexander; James C. Gee (Medical Image Anal., 2006)

Continuous Medial Representation for Anatomical Structures. - Paul A. Yushkevich; Hui Zhang 005; James C. Gee (IEEE Trans. Medical Imaging, 2006)

Structure-Specific Statistical Mapping of White Matter Tracts using the Continuous Medial Representation. - Paul A. Yushkevich; Hui Zhang 005; Tony J. Simon; James C. Gee (ICCV, 2007)

Multivariate Normalization with Symmetric Diffeomorphisms for Multivariate Studies. - Brian B. Avants; Jeffrey T. Duda; Hui Zhang 005; James C. Gee (MICCAI (1), 2007)

Fuzzy Nonparametric DTI Segmentation for Robust Cingulum-Tract Extraction. - Suyash P. Awate; Hui Zhang 005; James C. Gee (MICCAI (1), 2007)

Evaluation of Shape-Based Normalization in the Corpus Callosum for White Matter Connectivity Analysis. - Hui Sun; Paul A. Yushkevich; Hui Zhang 005; Philip A. Cook; Jeffrey T. Duda; Tony J. Simon; James C. Gee (MICCAI (2), 2007)

Unbiased White Matter Atlas Construction Using Diffusion Tensor Images. - Hui Zhang 005; Paul A. Yushkevich; Daniel Rueckert; James C. Gee (MICCAI (2), 2007)

Hippocampus-specific fMRI group activation analysis using the continuous medial representation. - Paul A. Yushkevich; John A. Detre; Dawn Mechanic-Hamilton; María A. Fernández-Seara; Kathy Z. Tang; Angela Hoang; Marc Korczykowski; Hui Zhang 005; James C. Gee (NeuroImage, 2007)

A Fuzzy, Nonparametric Segmentation Framework for DTI and MRI Analysis: With Applications to DTI-Tract Extraction. - Suyash P. Awate; Hui Zhang 005; James C. Gee (IEEE Trans. Medical Imaging, 2007)

Shape-Based Normalization of the Corpus Callosum for DTI Connectivity Analysis. - Hui Sun; Paul A. Yushkevich; Hui Zhang 005; Philip A. Cook; Jeffrey T. Duda; Tony J. Simon; James C. Gee (IEEE Trans. Medical Imaging, 2007)

High-Dimensional Spatial Normalization of Diffusion Tensor Images Improves the Detection of White Matter Differences: An Example Study Using Amyotrophic Lateral Sclerosis. - Hui Zhang 005; Brian B. Avants; Paul A. Yushkevich; John H. Woo; Sumei Wang; L. F. McCluskey; L. B. Elman; Elias R. Melhem; James C. Gee (IEEE Trans. Medical Imaging, 2007)

Multivariate analysis of thalamo-cortical connectivity loss in TBI. - Jeffrey T. Duda; Brian B. Avants; Junghoon Kim 006; Hui Zhang 005; Sunil Patel; John Whyte; James C. Gee (CVPR Workshops, 2008)

Robust regularization for the estimation of intra-voxel axon fiber orientations. - Alonso Ramirez-Manzanares; Hui Zhang 005; Mariano Rivera; James C. Gee (CVPR Workshops, 2008)

Multivariate segmentation of brain tissues by fusion of MRI and DTI data. - Suyash P. Awate; Hui Zhang 005; Tony J. Simon; James C. Gee (ISBI, 2008)

Atlas-guided probabilistic diffusion-tensor fiber tractography. - Philip A. Cook; Hui Zhang 005; Suyash P. Awate; James C. Gee (ISBI, 2008)

Surface-based modeling of white matter fasciculi with orientation encoding. - Hui Zhang 005; Paul A. Yushkevich; Tony J. Simon; James C. Gee (ISBI, 2008)

Structure-specific statistical mapping of white matter tracts. - Paul A. Yushkevich; Hui Zhang 005; Tony J. Simon; James C. Gee (NeuroImage, 2008)

Tensor-Based Morphometry of Fibrous Structures with Application to Human Brain White Matter. - Hui Zhang 005; Paul A. Yushkevich; Daniel Rueckert; James C. Gee (MICCAI (1), 2009)

High-Fidelity Meshes from Tissue Samples for Diffusion MRI Simulations. - Eleftheria Panagiotaki; Matt G. Hall; Hui Zhang 005; Bernard Siow; Mark F. Lythgoe; Daniel C. Alexander (MICCAI (2), 2010)

Axon Diameter Mapping in the Presence of Orientation Dispersion with Diffusion MRI. - Hui Zhang 005; Daniel C. Alexander (MICCAI (1), 2010)

A Computational White Matter Atlas for Aging with Surface-Based Representation of Fasciculi. - Hui Zhang 005; Paul A. Yushkevich; Daniel Rueckert; James C. Gee (WBIR, 2010)

A tract-specific framework for white matter morphometry combining macroscopic and microscopic tract features. - Hui Zhang 005; Suyash P. Awate; Sandhitsu R. Das; John H. Woo; Elias R. Melhem; James C. Gee; Paul A. Yushkevich (Medical Image Anal., 2010)

Axon Diameter Mapping in Crossing Fibers with Diffusion MRI. - Hui Zhang 005; Tim B. Dyrby; Daniel C. Alexander (MICCAI (2), 2011)

A Bayesian framework for modelling the regional variation of white matter microstructure. - Gemma Louise Morgan; Hui Zhang 005; Brandon J. Whitcher; Daniel C. Alexander (MIUA, 2011)

DTI registration in atlas based fiber analysis of infantile Krabbe disease. - Yi Wang 069; Aditya Gupta; Zhexing Liu; Hui Zhang 005; Maria L. Escolar; John H. Gilmore; Sylvain Gouttard; Pierre Fillard; Eric A. Maltbie; Guido Gerig; Martin Styner (NeuroImage, 2011)

Axon diameter mapping in the presence of orientation dispersion with diffusion MRI. - Hui Zhang 005; Penny L. Hubbard; Geoffrey J. M. Parker; Daniel C. Alexander (NeuroImage, 2011)

NODDI: Practical in vivo neurite orientation dispersion and density imaging of the human brain. - Hui Zhang 005; Torben Schneider; Claudia A. M. Wheeler-Kingshott; Daniel C. Alexander (NeuroImage, 2012)

A diffusion tensor brain template for Rhesus Macaques. - Nagesh Adluru; Hui Zhang 005; Andrew S. Fox; Steven E. Shelton; Chad M. Ennis; Anne M. Bartosic; Jonathan A. Oler; Do P. M. Tromp; Elizabeth Zakszewski; James C. Gee; Ned H. Kalin; Andrew L. Alexander (NeuroImage, 2012)

Beyond Crossing Fibers: Tractography Exploiting Sub-voxel Fibre Dispersion and Neighbourhood Structure. - Matthew C. Rowe; Hui Gary Zhang; Neil Oxtoby; Daniel C. Alexander (IPMI, 2013)

Deformable Modeling Using a 3D Boundary Representation with Quadratic Constraints on the Branching Structure of the Blum Skeleton. - Paul A. Yushkevich; Hui Gary Zhang (IPMI, 2013)

Ranking diffusion-MRI models with in-vivo human brain data. - Uran Ferizi; Torben Schneider; Eleftheria Panagiotaki; Gemma L. Nedjati-Gilani; Hui Gary Zhang; Claudia A. M. Wheeler-Kingshott; Daniel C. Alexander (ISBI, 2013)

Tract-oriented statistical group comparison of diffusion in sheet-like white matter. - Mark Lyksborg; Tim Bjørn Dyrby; Per Soelberg Sørensen; Morten Blinkenberg; Hartwig Roman Siebner; Daniel C. Alexander; Rasmus Larsen 001; Hui Zhang 005 (ISBI, 2013)

The Importance of Being Dispersed: A Ranking of Diffusion MRI Models for Fibre Dispersion Using In Vivo Human Brain Data. - Uran Ferizi; Torben Schneider; Maira Tariq; Claudia A. M. Wheeler-Kingshott; Hui Gary Zhang; Daniel C. Alexander (MICCAI (1), 2013)

Registration of Prone and Supine CT Colonography Datasets with Differing Endoluminal Distension. - Holger Roth; Jamie McClelland; Thomas Hampshire; Darren Boone; Yipeng Hu; Marc Modat; Hui Zhang 005; Sébastien Ourselin; Steve Halligan; David J. Hawkes (Abdominal Imaging, 2013)

Model-Based Super-Resolution of Diffusion MRI. - Alexandra Tobisch; Peter F. Neher; Matthew C. Rowe; Klaus H. Maier-Hein; Hui Zhang 005 (CDMRI/MMBC@MICCAI, 2013)

Effects of DTI spatial normalization on white matter tract reconstructions. - Nagesh Adluru; Hui Zhang 005; Do P. M. Tromp; Andrew L. Alexander (Image Processing, 2013)

An unbiased longitudinal analysis framework for tracking white matter changes using diffusion tensor imaging with application to Alzheimer's disease. - Shiva Keihaninejad; Hui Zhang 005; Natalie S. Ryan; Ian B. Malone; Marc Modat; Manuel Jorge Cardoso; David M. Cash; Nick C. Fox; Sébastien Ourselin (NeuroImage, 2013)

Image Quality Transfer via Random Forest Regression: Applications in Diffusion MRI. - Daniel C. Alexander; Darko Zikic; Jiaying Zhang 001; Hui Zhang 005; Antonio Criminisi (MICCAI (3), 2014)

In vivo Estimation of Dispersion Anisotropy of Neurites Using Diffusion MRI. - Maira Tariq; Torben Schneider; Daniel C. Alexander; Claudia A. M. Wheeler-Kingshott; Hui Zhang 005 (MICCAI (3), 2014)

Assessing white matter microstructure of the newborn with multi-shell diffusion MRI and biophysical compartment models. - Nicolas Kunz; Hui Zhang 005; Lana Vasung; Kieran O'Brien; Yaniv Assaf; François Lazeyras; Daniel C. Alexander; Petra S. Hüppi (NeuroImage, 2014)

A Simulation Framework for Quantitative Validation of Artefact Correction in Diffusion MRI. - Mark S. Graham; Ivana Drobnjak; Hui Zhang 005 (IPMI, 2015)

Accelerated Microstructure Imaging via Convex Optimization (AMICO) from diffusion MRI data. - Alessandro Daducci; Erick Jorge Canales-Rodríguez; Hui Zhang 005; Tim B. Dyrby; Daniel C. Alexander; Jean-Philippe Thiran (NeuroImage, 2015)

White matter compartment models for in vivo diffusion MRI at 300 mT/m. - Uran Ferizi; Torben Schneider; Thomas Witzel; Lawrence L. Wald; Hui Zhang 005; Claudia A. M. Wheeler-Kingshott; Daniel C. Alexander (NeuroImage, 2015)

Neurite orientation dispersion and density imaging of the healthy cervical spinal cord in vivo. - Francesco Grussu; Torben Schneider; Hui Zhang 005; Daniel C. Alexander; Claudia A. M. Wheeler-Kingshott (NeuroImage, 2015)

Application of neurite orientation dispersion and density imaging (NODDI) to a tau pathology model of Alzheimer's disease. - Niall Colgan; Bernard Siow; James M. O'Callaghan; Ian F. Harrison; Jack A. Wells; Holly E. Holmes; Ozama Ismail; Simon Richardson; Daniel C. Alexander; Emily C. Collins 002; Elizabeth M. C. Fisher; Ross A. Johnson; et al. (NeuroImage, 2016)

Realistic simulation of artefacts in diffusion MRI for validating post-processing correction techniques. - Mark S. Graham; Ivana Drobnjak; Hui Zhang 005 (NeuroImage, 2016)

Bingham-NODDI: Mapping anisotropic orientation dispersion of neurites using diffusion MRI. - Maira Tariq; Torben Schneider; Daniel C. Alexander; Claudia A. M. Wheeler-Kingshott; Hui Zhang 005 (NeuroImage, 2016)

Image quality transfer and applications in diffusion MRI. - Daniel C. Alexander; Darko Zikic; Aurobrata Ghosh; Ryutaro Tanno; Viktor Wottschel; Jiaying Zhang 001; Enrico Kaden; Tim B. Dyrby; Stamatios N. Sotiropoulos; Hui Zhang 005; Antonio Criminisi (NeuroImage, 2017)

Towards a comprehensive framework for movement and distortion correction of diffusion MR images: Within volume movement. - Jesper L. R. Andersson; Mark S. Graham; Ivana Drobnjak; Hui Zhang 005; Nicola Filippini; Matteo Bastiani (NeuroImage, 2017)

Improved tractography using asymmetric fibre orientation distributions. - Matteo Bastiani; Michiel Cottaar; Krikor Dikranian; Aurobrata Ghosh; Hui Zhang 005; Daniel C. Alexander; Tim E. J. Behrens; Saâd Jbabdi; Stamatios N. Sotiropoulos (NeuroImage, 2017)

Early development of structural networks and the impact of prematurity on brain connectivity. - Dafnis Batalle; Emer J. Hughes; Hui Zhang 005; Jacques-Donald Tournier; Nora Tusor; Paul Aljabar; Luqman Wali; Daniel C. Alexander; Joseph V. Hajnal; Chiara Nosarti; A. David Edwards; Serena J. Counsell (NeuroImage, 2017)

A tract-specific approach to assessing white matter in preterm infants. - Diliana Pecheva; Paul A. Yushkevich; Dafnis Batalle; Emer J. Hughes; Paul Aljabar; Julia Wurie; Joseph V. Hajnal; A. David Edwards; Daniel C. Alexander; Serena J. Counsell; Hui Zhang 005 (NeuroImage, 2017)

Image processing and Quality Control for the first 10, 000 brain imaging datasets from UK Biobank. - Fidel Alfaro-Almagro; Mark Jenkinson; Neal K. Bangerter; Jesper L. R. Andersson; Ludovica Griffanti; Gwenaëlle Douaud; Stamatios N. Sotiropoulos; Saâd Jbabdi; Moisés Hernández-Fernández; Emmanuel Vallée; Diego Vidaurre; Matthew A. Webster; et al. (NeuroImage, 2018)

Susceptibility-induced distortion that varies due to motion: Correction in diffusion MR without acquiring additional data. - Jesper L. R. Andersson; Mark S. Graham; Ivana Drobnjak; Hui Zhang 005; Jon Campbell (NeuroImage, 2018)

Neurite imaging reveals microstructural variations in human cerebral cortical gray matter. - Hikaru Fukutomi; Matthew F. Glasser; Hui Zhang 005; Joonas A. A. Autio; Timothy S. Coalson; Tomohisa Okada; Kaori Togashi; David C. Van Essen; Takuya Hayashi 002 (NeuroImage, 2018)

A supervised learning approach for diffusion MRI quality control with minimal training data. - Mark S. Graham; Ivana Drobnjak; Hui Zhang 005 (NeuroImage, 2018)

Whole brain g-ratio mapping using myelin water imaging (MWI) and neurite orientation dispersion and density imaging (NODDI). - Woojin Jung; Jin-Gu Lee; Hyeong-Geol Shin; Yoonho Nam; Hui Zhang 005; Se-Hong Oh 001; Jongho Lee 003 (NeuroImage, 2018)

Contextual Fibre Growth to Generate Realistic Axonal Packing for Diffusion MRI Simulation. - Ross Callaghan; Daniel C. Alexander; Hui Zhang 005; Marco Palombo (IPMI, 2019)

Different patterns of cortical maturation before and after 38 weeks gestational age demonstrated by diffusion MRI in vivo. - Dafnis Batalle; Jonathan O'Muircheartaigh; Antonios Makropoulos; Christopher J. Kelly; Ralica Dimitrova; Emer J. Hughes; Joseph V. Hajnal; Hui Zhang 005; Daniel C. Alexander; A. David Edwards; Serena J. Counsell (NeuroImage, 2019)

A generative model of realistic brain cells with application to numerical simulation of the diffusion-weighted MR signal. - Marco Palombo; Daniel C. Alexander; Hui Zhang 005 (NeuroImage, 2019)

ConFiG: Contextual Fibre Growth to generate realistic axonal packing for diffusion MRI simulation. - Ross Callaghan; Daniel C. Alexander; Marco Palombo; Hui Zhang 005 (NeuroImage, 2020)

SANDI: A compartment-based model for non-invasive apparent soma and neurite imaging by diffusion MRI. - Marco Palombo; Andrada Ianus; Michele Guerreri; Daniel Nunes; Daniel C. Alexander; Noam Shemesh; Hui Zhang 005 (NeuroImage, 2020)

Machine learning based white matter models with permeability: An experimental study in cuprizone treated in-vivo mouse model of axonal demyelination. - Ioana Hill; Marco Palombo; Mathieu D. Santin; Francesca Branzoli; Anne-Charlotte Philippe; Demian Wassermann; Marie-Stephane Aigrot; Bruno Stankoff; Anne Baron-Van Evercooren; Mehdi Felfli; Dominique Langui; Hui Zhang 005; et al. (NeuroImage, 2021)

Mapping complex cell morphology in the grey matter with double diffusion encoding MR: A simulation study. - Andrada Ianus; Daniel C. Alexander; Hui Zhang 005; Marco Palombo (NeuroImage, 2021)

Comparative analysis of signal models for microscopic fractional anisotropy estimation using q-space trajectory encoding. - Leevi Kerkelä; Fabio Nery; Ross Callaghan; Fenglei Zhou; Noemi G. Gyori; Filip Szczepankiewicz; Marco Palombo; Geoff J. M. Parker; Hui Zhang 005; Matt G. Hall; Chris A. Clark (NeuroImage, 2021)

On the generalizability of diffusion MRI signal representations across acquisition parameters, sequences and tissue types: Chronicles of the MEMENTO challenge. - Alberto De Luca; Andrada Ianus; Alexander Leemans; Marco Palombo; Noam Shemesh; Hui Zhang 005; Daniel C. Alexander; Markus Nilsson; Martijn Froeling; Geert Jan Biessels; Mauro Zucchelli; Matteo Frigo; et al. (NeuroImage, 2021)

Corrigendum to "SANDI: A compartment-based model for non-invasive apparent soma and neurite imaging by diffusion MRI" [Neuroimage 215 (2020), 116835]. - Marco Palombo; Andrada Ianus; Michele Guerreri; Daniel Nunes; Daniel C. Alexander; Noam Shemesh; Hui Zhang 005 (NeuroImage, 2021)

Not all voxels are created equal: Reducing estimation bias in regional NODDI metrics using tissue-weighted means. - Christopher S. Parker; Tom Veale; Martina Bocchetta; C. F. Slattery; Ian B. Malone; David L. Thomas; Jonathan M. Schott; David M. Cash; Hui Zhang 005 (NeuroImage, 2021)

How Can Spherical CNNs Benefit ML-Based Diffusion MRI Parameter Estimation? - Tobias Goodwin-Allcock; Jason D. McEwen; Robert J. Gray; Parashkev Nachev; Hui Zhang 005 (CDMRI@MICCAI, 2022)

Correction of Susceptibility Distortion in EPI: A Semi-supervised Approach with Deep Learning. - Antoine Legouhy; Mark S. Graham; Michele Guerreri; Whitney Stee; Thomas Villemonteix; Philippe Peigneux; Hui Zhang 005 (CDMRI@MICCAI, 2022)

Choice of training label matters: how to best use deep learning for quantitative MRI parameter estimation. - Sean C. Epstein; Timothy J. P. Bray; Margaret A. Hall-Craggs; Hui Zhang 005 (CoRR, 2022)

Resolving Quantitative MRI Model Degeneracy with Machine Learning via Training Data Distribution Design. - Michele Guerreri; Sean C. Epstein; Hojjat Azadbakht; Hui Zhang 005 (IPMI, 2023)

POLAFFINI: Efficient Feature-Based Polyaffine Initialization for Improved Non-linear Image Registration. - Antoine Legouhy; Ross Callaghan; Hojjat Azadbakht; Hui Zhang 005 (IPMI, 2023)

Rician likelihood loss for quantitative MRI using self-supervised deep learning. - Christopher S. Parker; Anna Schroder; Sean C. Epstein; James Cole; Daniel C. Alexander; Hui Zhang 005 (CoRR, 2023)

Eddeep: Fast Eddy-Current Distortion Correction for Diffusion MRI with Deep Learning. - Antoine Legouhy; Ross Callaghan; Whitney Stee; Philippe Peigneux; Hojjat Azadbakht; Hui Zhang 005 (MICCAI (2), 2024)

SCREENER: A general framework for task-specific experiment design in quantitative MRI. - Tianshu Zheng; Zican Wang; Timothy J. P. Bray; Daniel C. Alexander; Dan Wu; Hui Zhang 005 (CoRR, 2024)

Resolving Quantitative MRI Model Degeneracy in Self-supervised Machine Learning. - Giulio V. Minore; Louis Dwyer-Hemmings; Timothy J. P. Bray; Hui Zhang 005 (IPMI (2), 2025)

An extragradient and noise-tuning adaptive iterative network for diffusion MRI-based microstructural estimation. - Tianshu Zheng; Chuyang Ye; Zhaopeng Cui; Hui Zhang 005; Daniel C. Alexander; Dan Wu (Medical Image Anal., 2025)