Research

Research Interests

Microstructure, Tractography, Harmonization, Infant Brain Development, Diffusion Model, Connectivity, Signal Representation, MR Reconstruction, Noise Mapping and Removal.

Journals

• [J7] Khoi Minh Huynh, Wei-Tang Chang, Ye Wu, and Pew-Thian Yap Optimal shrinkage denoising breaks the noise floor in high-resolution diffusion MRI, Patterns, 2024

• [J6] Wenjiao Lyu, Ye Wu, Khoi Minh Huynh, Sahar Ahmad, and Pew-Thian Yap. A multimodal submillimeter MRI atlas of the human cerebellum, Scientific Reports, 2024.

• [J5] Sang Hun Chung, Khoi Minh Huynh, Jennifer L Goralski, Yong Chen, Pew-Thian Yap, Agathe S Ceppe, Margret Z Powell, Scott H Donaldson, and Yueh Z Lee. Feasibility of free-breathing 19F MRI image acquisition to characterize ventilation defects in CF and healthy volunteers at wash-in. Magnetic Resonance in Medicine, 2023.

• [J4] Geng Chen, Yoonmi Hong, Khoi Minh Huynh, and Pew-Thian Yap. Deep learning prediction of diffusion MRI data with microstructure-sensitive loss functions. Medical Image Analysis, 2023.

• [J3] Tiantian Xu, Ye Wu, Yoonmi Hong, Sahar Ahmad, Khoi Minh Huynh, Zhixing Wang, Weili Lin, Wei-Tang Chang, and Pew-Thian Yap. Rapid Diffusion Magnetic Resonance Imaging Using Slice-Interleaved Encoding. Medical Image Analysis, 2022.

• [J2] Khoi Minh Huynh, Tiantian Xu, Ye Wu, Xifeng Wang, Geng Chen, Haiyong Wu, Kim-Han Thung, Weili Lin, Dinggang Shen, and Pew-Thian Yap. Probing Tissue Microarchitecture of the Baby Brain via Spherical Mean Spectrum Imaging. IEEE Transactions on Medical Imaging, 2020.

• [J1] Khoi Minh Huynh, Geng Chen, Ye Wu, Dinggang Shen, and Pew-Thian Yap. Multi-Site Harmonization of Diffusion MRI Data via Method of Moments. IEEE Transactions on Medical Imaging, 2019.

Conferences

• [C8] Khoi Minh Huynh, Ye Wu, Sahar Ahmad, and Pew-Thian Yap. Microstructure Fingerprinting for Heterogeneously Oriented Tissue Microenvironments. MICCAI, 2023.

• [C7] Ye Wu, Xiaoming Liu, Xinyuan Zhang, Khoi Minh Huynh, Sahar Ahmad, and Pew-Thian Yap. Relaxation-Diffusion Spectrum Imaging for Probing Tissue Microarchitecture. MICCAI, 2023.

• [C6] Khoi Minh Huynh, Wei-Tang Chang, Sang Hun Chung, Yong Chen, Yueh Lee, and Pew-Thian Yap. Noise Mapping and Removal in Complex-Valued Multi-Channel MRI via Optimal Shrinkage of Singular Values. MICCAI, 2021.

• [C5] Khoi Minh Huynh, Ye Wu, Kim-Han Thung, Sahar Ahmad, Hoyt Patrick Taylor IV, Dinggang Shen, and Pew-Thian Yap. Characterizing Intra-Soma Diffusion with Spherical Mean Spectrum Imaging. MICCAI, 2020.

• [C4] Geng Chen, Yoonmi Hong, Yongqin Zhang, Jaeil Kim, Khoi Minh Huynh, Jiquan Ma, Weili Lin, Dinggang Shen, and Pew-Thian Yap. Estimating Tissue Microstructure with Undersampled Diffusion Data via Graph Convolutional Neural Networks. MICCAI, 2020.

• [C3] Sahar Ahmad, Ye Wu, Khoi Minh Huynh, Kim-Han Thung, Weili Lin, Dinggang Shen, and Pew-Thian Yap. Fast Correction of Eddy-Current and Susceptibility-Induced Distortions Using Rotation-Invariant Contrasts. MICCAI, 2020.

• [C2] Khoi Minh Huynh, Tiantian Xu, Ye Wu, Geng Chen, Kim-Han Thung, Haiyong Wu, Weili Lin, Dinggang Shen, and Pew-Thian Yap, for the UNC/UMN Baby Connectome Project Consortium. Probing Brain Micro-Architecture by Orientation Distribution Invariant Identification of Diffusion Compartments. MICCAI, 2019.

• [C1] Khoi Minh Huynh, Tiantian Xu, Ye Wu, Kim-Han Thung, Geng Chen, Weili Lin, Dinggang Shen, and Pew-Thian Yap. Characterizing Non-Gaussian Diffusion in Heterogeneously Oriented Tissue Microenvironments. MICCAI, 2019.

Preprints

• Wei-Tang Chang, Stephanie Langella, Min Sung Seo, Khoi Huynh, Pew-Thian Yap, Weili Lin, Kelly Giovanello. Cross-layer Balance of Visuo-hippocampal Functional Connectivity Is Associated With Episodic Memory Recognition Accuracy 2020.

• Wei-Tang Chang, Khoi Minh Huynh, Pew-Thian Yap, and Weili Lin. Navigator-Free Submillimeter Diffusion Imaging using Multishot-encoded Simultaneous Multi-slice (MUSIUM) 2020.

Workshops

• [W3] Hoyt Patrick Taylor IV, Sahar Ahmad, Ye Wu, Khoi Minh Huynh, Zhen Zhou, Zhengwang Wu, Weili Lin, Li Wang, Gang Li, Han Zhang, and Pew-Thian Yap. Longitudinal Parcellation of the Infant Cortex Using Multi-modal Connectome Harmonics. CDMRI, 2020.
• [W2] Tiantian Xu, Ye Wu, Yoonmi Hong, Khoi Minh Huynh, Weili Lin, Wei-Tang Chang, and Pew-Thian Yap. Image Reconstruction from Accelerated Slice-Interleaved Diffusion Encoding Data. CDMRI, 2020.
• [W1] Khoi Minh Huynh, Geng Chen, Ye Wu, Dinggang Shen, and Pew-Thian Yap. Longitudinal Harmonization for Improving Tractography in Baby Diffusion MRI. CDMRI, 2018.

Abstracts

• [A26] Khoi Minh Huynh, Sahar Ahmad, Kim-Han Thung, and Pew-Thian Yap. Cell radius and membrane permeability in the developing brain. ISMRM, 2024.

• [A25] Truc Nguyen, Khoi Minh Huynh, Sang Hun Chung, Pew-Thian Yap, and Yueh Z Lee. Temporal profile block-matching denoising enables free-breathing dynamic 19F lung MRI with sub 0.5 second acquisition time. ISMRM, 2024.

• [A24] Wenjiao Lyu, Ye Wu, Khoi Minh Huynh, Sahad Ahmad, and Pew-Thian Yap. A Multimodal Atlas of the Human Cerebellum at 760 micron Resolution. OHBM, 2023.

• [A23] Khoi Minh Huynh, Sahad Ahmad, Kim-Han Thung, Weili Lin, and Pew-Thian Yap. Longitudinal atlases of cortical and subcortical tissue microstructure in the early developing brain. OHBM, 2023.

• [A22] Sang Hun Chung, Khoi Minh Huynh, Yong Chen, Pew-Thian Yap, Jennifer Goralski, Scott Donaldson, and Yueh Z Lee. Lung Multi-Breath Wash in/out MRI with 19F with Sub 0.5 Second Scan Time. ISMRM, 2023.

• [A21] Khoi Minh Huynh, Sang Hun Chung, Yueh Lee, and Pew-Thian Yap. Multidimensional optimal denoising with block matching is robust to misalignment and contrast changes. ISMRM, 2023.

• [A20] Sang Hun Chung, Khoi Minh Huynh, Yong Chen, Pew-Thian Yap, Jennifer L Goralski, Scott H Donaldson, and Yueh Z Lee. Ventilation defect percentage comparison between spiral with post-acquisition denoising and cartesian acquisition for 19F lung magnetic resonance imaging,. Journal of Cystic Fibrosis, 2022.

• [A19] Khoi Minh Huynh, Sahad Ahmad, Kim-Han Thung, Zhengwang Wu, Weili Lin, Li Wang, Gang Li, and Pew-Thian Yap. Evolution of Cortical Microstructure Across the Human Lifespan. OHBM, 2022.

• [A18] Sang Hun Chung, Khoi Minh Huynh, Yong Chen, Pew-Thian Yap, Jennifer L. Goralski, Scott H. Donaldson, and Yueh Lee. Feasibility of VDP Calculation using 19F Free Breathing Spiral Ac- quisition with Post-Acquisition Denoising. ISMRM, 2022.

• [A17] Jelle Veraart, Daan Christiaens, Erpeng Dai, Luke J. Edwards, Vladimir Golkov, Siawoosh Mohammadi, Kurt G. Schilling, Mohammad Hadi Aarabi, Benjamin Ades-Aron, Nagesh Adluru, Sahar Ahmad, Santiago Aja-Fernandez, Andrew L. Alexander, Mariam Andersson, Elixabete Ansorena, Fakhereh Movahedian Attar, Arnaud Attye, Dogu Baran Aydogan, Steven H. Baete, Gianpaolo Antonio Basile, Giulia Berto, Ahmad Beyh, Alberto Cacciola, Maxime Chamberland, Fernando Calamante, Jenny Chen, Jian Chen, Shin Tai Chong, Santiago Coelho, Luis Concha, Ricardo Coronado-Leija, Michiel Cottaar, Daniel Cremers, Szabolcs David, Alberto De Luca, Flavio Dell’Acqua, Thijs Dhollander, Jason Druzgal, Tim B. Dyrby, Hernandez-Torres Enedino, Oscar Esteban, Els Fieremans, Leon Fonville, Bjorn Fricke, Martijn Froeling, Ian Galea, Gabriel Girard, Francesco Grussu, Chin-Chin Heather Hsu, Yung-Chin Hsu, Khoi Huynh, Matilde Inglese, Heide Johansen-berg, Derek K Jones, Kouhei Kamiya, Claire Kelly, Ahmad Raza Khan, Ali Khan, Yi-Chia Kung, Alberto Lazari, Alexander Leemans, Laura Mancini, Ivan I. Maximov, Harri Merisaari, Malwina Molendowska, Benjamin T. Newman, Michael D. Noseworthy, Dmitry S. Novikov, Raquel Perez-Lopez, Franco Pestili, Tomasz Pieciak, Marco Pizzolato, Alvaro Planchuelo-Gomez, Paul Polak, Erika P. Raven, Ricardo Rios-Carrillo, Viljami Sairanen, Simona Schiavi, Pohchoo Seow, Dmitri Shastin, Yao-Chia Shih, Lucas Soustelle, Yue Sun, Karsten Tabelow, Chantal MW Tax, Guillaume Theaud, Sjoerd B. Vos, Ryckie G. Wade, Li Wang, Limei Wang, Thomas Welton, Lars T. Westlye, Stefan Winzeck, Joseph Yuan-Mou Yang, Pew-Thian Yap, Yukai Zou, Jennifer A. McNab, Bennett A. Landman, Nikolaus Weiskopf, and Maxime Descoteaux. A data-driven variability assessment of brain diffusion MRI preprocessing pipelines. ISMRM, 2022.

• [A16] Ye Wu, Sahar Ahmad, Khoi Minh Huynh, Tiantian Xu, and Pew-Thian Yap. COMEDI: A Toolkit for Lifespan Computational Diffusion MRI. ISMRM, 2022.

• [A15] Wei-Tang Chang, Stephanie Langella, Khoi Minh Huynh, Min Sung Seo, Pew-Thian Yap, Weili Lin, and Kelly S. Giovanello. Investigation of brainwide functional networks associated with hippocampal subfields during memory encoding and retrieval using fMRI with 1-mm isotropic resolution. ISMRM, 2022.

• [A14] Wei-Tang Chang, Khoi Minh Huynh, Pew-Thian Yap, and Weili Lin. Navigator-Free Submillimeter Diffusion MRI using Multishot-encoded Simultaneous Multi-slice (MUSIUM) Imaging. ISMRM, 2021.

• [A13] Khoi Minh Huynh, Wei-Tang Chang, and Pew-Thian Yap. Reducing Noise in Complex-Valued Multi-Channel Diffusion- Weighted Data via Optimal Shrinkage of Singular Values. ISMRM, 2021.

• [A12] Khoi Minh Huynh, Ye Wu, and Pew-Thian Yap. Quantifying Cell Size and Membrane Permeability with Microstructure Fingerprinting. ISMRM, 2021.

• [A11] Ye Wu, Sahar Ahmad, Khoi Minh Huynh, Siyuan Liu, Kim-Han Thung, Weili Lin, and Pew-Thian Yap, for the UNC/UMN Baby Connectome Project Consortium. An Automated Processing Pipeline for Diffusion MRI in the Baby Connectome Project. ISMRM, 2021.

• [A10] Khoi Minh Huynh, Ye Wu, Kim-Han Thung, Sahar Ahmad, Zhengwang Wu, Weili Lin, Han Zhang, Li Wang, Gang Li, and Pew-Thian Yap. Dense Temporal Mapping of Cortical Microstructure in the Early Developing Brain. OHBM, 2020.

• [A9] Khoi Minh Huynh, Sahar Ahmad, Ye Wu, Kim-Han Thung, Zhengwang Wu, Weili Lin, Han Zhang, Li Wang, Gang Li, and Pew-Thian Yap. Correlation of Myelin Content and Neurite Density in the Early Developing Human Cortex. OHBM, 2020.

• [A8] Khoi Minh Huynh, Ye Wu, Kim-Han Thung, Sahar Ahmad, Hoyt Patrick Taylor IV, Weili Lin, and Pew-Thian Yap. Multivariate Quantification of Brain Development During the First Two Years of Life. OHBM, 2020.

• [A7] Khoi Minh Huynh, Ye Wu, Hoyt Patrick Taylor IV, Weili Lin, and Pew-Thian Yap. Tackling Degeneracy in Linear Tensor Encoding Diffusion MRI. ISMRM, 2020.

• [A6] Khoi Minh Huynh, Ye Wu, Kim-Han Thung, Sahar Ahmad, Hoyt Patrick Taylor IV, Weili Lin, and Pew-Thian Yap. Quantifying Intra-Soma Diffusion Properties via Spherical Mean Spectrum Imaging. ISMRM, 2020.

• [A5] Khoi Minh Huynh, Ye Wu, Geng Chen, Kim-Han Thung, Weili Lin, Dinggang Shen, and Pew-Thian Yap. Quantifying Tissue Microstructure Non-Gaussianity in the Presence of Fiber Dispersion. RSNA, 2019.

• [A4] Khoi Minh Huynh, Ye Wu, Kim-Han Thung, Geng Chen, Weili Lin, Dinggang Shen, and Pew-Thian Yap, for the UNC/UMN Baby Connectome Project Consortium. Dense Mapping of Microstructural Development in the Human Brain During the First Two Years of Life. OHBM, 2019.

• [A3] Khoi Minh Huynh, Ye Wu, Kim-Han Thung, Geng Chen, Weili Lin, Dinggang Shen, and Pew-Thian Yap, for the UNC/UMN Baby Connectome Project Consortium. Biases of Microstructure Models in Baby Diffusion MRI. ISMRM, 2019.

• [A2] Khoi Minh Huynh, Jaeil Kim, Geng Chen, Dinggang Shen, and Pew-Thian Yap. Longitudinal Harmonization of Baby Diffusion MRI Data. OHBM, 2018.

• [A1] Khoi Minh Huynh, Geng Chen, Wei-Tang Chang, Weili Lin, Dinggang Shen, and Pew-Thian Yap. Spatially Varying Signal-Drift Correction in Diffusion MRI. ISMRM, 2018.