Hong-Hsi Lee, MD, PhD

Hong-Hsi Lee, MD, PhD

Assistant Professor at Mass General Hospital/Harvard Medical School, expert in biophysical modeling, diffusion MRI, and image processing

Posts by Collection

portfolio

publications

Along-axon diameter variation and axonal orientation dispersion revealed with 3D electron microscopy: implications for quantifying brain white matter microstructure with histology and diffusion MRI

Published in Brain Structure and Function, 2019

We developed a semi-automatic algorithm to segmented myelinated axons in the electron microscopy data of a mouse brain sample and analyzed its micro-geometry, such as axonal diameter, caliber variation, axonal undulation, and fiber orientation dispersion. The segmentation and analysis code can be downloaded here.

Recommended citation: Lee, H. H., Yaros, K., Veraart, J., et al. (2019). "Along-axon diameter variation and axonal orientation dispersion revealed with 3D electron microscopy: implications for quantifying brain white matter microstructure with histology and diffusion MRI." Brain Structure and Function, 224:1469–1488. https://doi.org/10.1007/s00429-019-01844-6

Effects of COVID-19 Prevention Measures on Other Common Infections, Taiwan

Published in Emerging Infectious Diseases, 2020

We analyzed the National Health Insurance database in Taiwan, showing that rates of other infections were significantly lower after SARS-CoV-2 prevention measures were announced. This finding can be applied to cost-effectiveness of SARS-CoV-2 prevention.

Recommended citation: Lee, H. H., & Lin, S. H. (2020). "Effects of COVID-19 prevention measures on other common infections, Taiwan." Emerging infectious diseases, 26(10), 2509. https://doi.org/10.3201/eid2610.203193

In vivo observation and biophysical interpretation of time-dependent diffusion in human cortical gray matter

Published in NeuroImage, 2020

In vivo diffusion MRI and Monte Carlo simulations indicate that the restriction along neurites is short-range disorder, and the diffusivity and kurtosis time-dependence scales as 1/√t. The 1-dimensional simulation code and power spectrum analysis can be downloaded here.

Recommended citation: Lee, H. H., Papaioannou, A., Novikov, D. S., & Fieremans, E. (2020). "In vivo observation and biophysical interpretation of time-dependent diffusion in human cortical gray matter." NeuroImage, 222, 117054. https://doi.org/10.1016/j.neuroimage.2020.117054

Realistic Microstructure Simulator (RMS): Monte Carlo simulations of diffusion in three-dimensional cell segmentations of microscopy images

Published in Journal of Neuroscience Methods, 2021

Monte Calo simulation of diffusion in voxelized micro-geometry using CUDA C++. The code for narrow pulse PGSE could be downloaded here. The code for wide pulse PGSE will be released soon.

Recommended citation: Lee, H. H., Fieremans, E., & Novikov, D. S. (2021). "Realistic Microstructure Simulator (RMS): Monte Carlo simulations of diffusion in three-dimensional cell segmentations of microscopy images." Journal of Neuroscience Methods, 350, 109018. https://doi.org/10.1016/j.jneumeth.2020.109018

The effects of axonal beading and undulation on axonal diameter estimation from diffusion MRI: Insights from simulations in human axons segmented from three-dimensional electron microscopy

Published in NMR in Biomedicine, 2024

Monte Carlo simulations of diffusion in realistic axons segmented from electron microscopy data of a human brain sample. The simulation code can be downloaded here.

Recommended citation: Lee, H. H., Tian, Q., Sheft, M., et al. (2024). "The effects of axonal beading and undulation on axonal diameter estimation from diffusion MRI: Insights from simulations in human axons segmented from three-dimensional electron microscopy." NMR in Biomedicine, e5087. https://doi.org/10.1002/nbm.5087

Age‐related alterations in human cortical microstructure across the lifespan: Insights from high‐gradient diffusion MRI

Published in Aging Cell, 2024

Soma density and radius derived from SANDI (soma and neurite density imaging) model shows significant decrease with age in human cortical gray matter in a lifespan cohort scanned on the human Connectome scanner.

Recommended citation: Lee, H., Lee, H. H., Ma, Y., Eskandarian, L., Gaudet, K., Tian, Q., ... & Huang, S. Y. (2024). "Age‐related alterations in human cortical microstructure across the lifespan: Insights from high‐gradient diffusion MRI." Aging Cell, 23(11), e14267. https://doi.org/10.1111/acel.14267

In vivo human neurite exchange time imaging at 500 mT/m diffusion gradients: Neurite exchange time imaging on Connectome 2.0

Published in Imaging Neuroscience, 2025

The NEXI (neurite exchange imaging) model fitting code can be downloaded here.

Recommended citation: Chan, K. S., Ma, Y., Lee, H., Marques, J. P., Olesen, J. L., Coelho, S., ... & Lee, H. H. (2025). "In vivo human neurite exchange time imaging at 500 mT/m diffusion gradients. " Imaging Neuroscience, 3, imag_a_00544. https://doi.org/10.1162/imag_a_00544

Ultra-high gradient connectomics and microstructure MRI scanner for imaging of human brain circuits across scales

Published in Nature Biomedical Engineering, 2025

The simulation code of pulsed-gradient sequence parameter can be downloaded here.

Recommended citation: Ramos-Llordén, G., Lee, H. H., Davids, M., Dietz, P., Krug, A., Kirsch, J. E., ... & Huang, S. Y. (2025). "Ultra-high gradient connectomics and microstructure MRI scanner for imaging of human brain circuits across scales." Nature Biomedical Engineering, 1-16. https://doi.org/10.1038/s41551-025-01457-x

talks

teaching

Teaching experience 1

Undergraduate course, University 1, Department, 2014

This is a description of a teaching experience. You can use markdown like any other post.

Teaching experience 2

Workshop, University 1, Department, 2015

This is a description of a teaching experience. You can use markdown like any other post.