2. dMRI Tractography & Atlasing

Diffusion magnetic resonance imaging (dMRI) tractography is an advanced imaging method that uniquely enables in vivo mapping of the brain’s white matter connections at macro scale. Over the last two decades, the study of the human brain using dMRI tractography has played a prominent role in the neuroimaging research landscape. Dr. Zhang and his colleagues have developed novel computational tools for tractography analysis with a focus on improving our understanding of brain structure and function mapping. In particular, they have provided a data-driven tractography atlas, which for the first time enables consistent identification of white matter tracts across the lifespan and across different disease populations. The atlas and the related computational tools are publicly available, which are currently being used by many local, national and international institutions in their research projects.

Selected publications:

review Fan Zhang, Alessandro Daducci, Yong He, Simona Schiavi, Caio Seguin, Robert Smith, Chun-Hung Yeh, Tengda Zhao, and Lauren J O'Donnell.
Quantitative mapping of the brain's structural connectivity using diffusion MRI tractography: a review.
NeuroImage. 2022.
Publisher's Version
Invited Review

Fan Zhang, Ye Wu, Isaiah Norton, Yogesh Rathi, Nikos Makris, and Lauren J. O'Donnell.
An anatomically curated fiber clustering white matter atlas for consistent white matter tract parcellation across the lifespan.
NeuroImage, 179, Pp. 429-447. 2018.
Publisher's Version, Website, Tutorial, Software/Code (Atlaswhitematteranalysis, UKF, SlicerDMRI), Suppl Video 1, Suppl Vidoe 2

Fan Zhang, Ye Wu, Isaiah Norton, Yogesh Rathi, Alexandra J Golby, and Lauren J O'Donnell.
Test–retest reproducibility of white matter parcellation using diffusion MRI tractography fiber clustering.
Human Brain Mapping, 40, 10, Pp. 3041–3057. 2019.
Publisher's Version


Fan Zhang, Thomas Noh, Parikshit Juvekar, Sarah F. Frisken, Laura Rigolo, Isaiah Norton, Tina Kapur, Sonia Pujol, William Wells, Alex Yarmarkovich, Gordon Kindlmann, Demian Wassermann, Raul San Jose Estepar, Yogesh Rathi, Ron Kikinis, Hans J. Johnson, Carl-Fredrik Westin, Steve Pieper, Alexandra J. Golby, and Lauren J. O'Donnell.
SlicerDMRI: Diffusion MRI and Tractography Research Software for Brain Cancer Surgery Planning and Visualization.
JCO Clinical Cancer Informatics, 4, Pp. 299–309. 2020.
Publisher's Version

Isaiah Norton, Ibn Essayed, Fan Zhang, Sonia Pujol, Alex Yarmarkovich, Alexandra Golby, Gordon Kindlmann, Demian Wasserman, Raul San José Estepar, Yogesh Rathi, Steve Pieper, Ron Kikinis, Hans Johnson, Carl-Fredrik Westin, and Lauren J. O'Donnell. .
SlicerDMRI: Open Source Diffusion MRI Software for Brain Cancer Research.
Cancer Research, 77, 21, Pp. e101–103. 2017.
Publisher's Version

cranial nerves

Fan Zhang, Guoqiang Xie, Laura Leung, Michael Mooney, Lorenz Epprecht, Isaiah Norton, Yogesh Rathi, Ron Kikinis, Ossama Al-Mefty, Nikos Makris, Alexandra J. Golbya, and Lauren J. O’Donnell.
Creation of a novel trigeminal tractography atlas for automated trigeminal nerve identification.
NeuroImage, 220, Pp. 117063. 2020.
Publisher's Version

Guoqiang Xie*, Fan Zhang*(co-first), Laura Leung, Michael A Mooney, Lorenz Epprecht, Isaiah Norton, Yogesh Rathi, Ron Kikinis, Ossama Al-Mefty, Nikos Makris, Alexandra J Golby, and Lauren J O'Donnell.
Anatomical assessment of trigeminal nerve tractography using diffusion MRI: A comparison of acquisition b-values and single-and multi-fiber tracking strategies.
NeuroImage: Clinical, 25, Pp. 102160. 2020.
Publisher's Version

Jianzhong He*, Fan Zhang*(co-first), Guoqiang Xie, Shun Yao, Yuanjing Feng, Dhiego CA Bastos, Yogesh Rathi, Nikos Makris, Ron Kikinis, Alexandra J Golby, and Lauren J. O'Donnell.
Comparison of multiple tractography methods for reconstruction of the retinogeniculate visual pathway using diffusion MRI.
Human Brain Mapping, 42, 12, Pp. 3887-3904. 2021.
Publisher's Version