Phase-Based User-Steered Image Segmentation. - Lauren O'Donnell; Carl-Fredrik Westin; W. Eric L. Grimson; Juan Ruiz-Alzola; Martha Elizabeth Shenton; Ron Kikinis (MICCAI, 2001)

New Approaches to Estimation of White Matter Connectivity in Diffusion Tensor MRI: Elliptic PDEs and Geodesics in a Tensor-Warped Space. - Lauren O'Donnell; Steven Haker; Carl-Fredrik Westin (MICCAI (1), 2002)

Capturing Brain Deformation. - Simon K. Warfield; Ion-Florin Talos; Corey Kemper; Lauren O'Donnell; Carl-Fredrik Westin; William M. Wells III; Peter M. Black; Ferenc A. Jolesz; Ron Kikinis (IS4TH, 2003)

Diffusion Tensor and Functional MRI Fusion with Anatomical MRI for Image-Guided Neurosurgery. - Ion-Florin Talos; Lauren O'Donnell; Carl-Fredrik Westin; Simon K. Warfield; William M. Wells III; Seung-Schik Yoo; Lawrence P. Panych; Alexandra J. Golby; Hatsuho Mamata; Stefan S. Maier; Peter Ratiu; Charles R. G. Guttmann; et al. (MICCAI (1), 2003)

Interface Detection in Diffusion Tensor MRI. - Lauren O'Donnell; W. Eric L. Grimson; Carl-Fredrik Westin (MICCAI (1), 2004)

White Matter Tract Clustering and Correspondence in Populations. - Lauren O'Donnell; Carl-Fredrik Westin (MICCAI, 2005)

High-Dimensional White Matter Atlas Generation and Group Analysis. - Lauren O'Donnell; Carl-Fredrik Westin (MICCAI (2), 2006)

Tract-Based Morphometry. - Lauren O'Donnell; Carl-Fredrik Westin; Alexandra J. Golby (MICCAI (2), 2007)

Nonlinear Registration of Diffusion MR Images Based on Fiber Bundles. - Ulas Ziyan; Mert R. Sabuncu; Lauren O'Donnell; Carl-Fredrik Westin (MICCAI (1), 2007)

Automatic Tractography Segmentation Using a High-Dimensional White Matter Atlas. - Lauren J. O'Donnell; Carl-Fredrik Westin (IEEE Trans. Medical Imaging, 2007)

Two-tensor streamline tractography through white matter intra-voxel fiber crossings: Assessed by fMRI. - Arish A. Qazi; Gordon L. Kindlmann; Lauren O'Donnell; Sharon Peled; Alireza Radmanesh; Stephen Whalen; Alexandra J. Golby; Carl-Fredrik Westin (CVPR Workshops, 2008)

Tract-based morphometry for white matter group analysis. - Lauren J. O'Donnell; Carl-Fredrik Westin; Alexandra J. Golby (NeuroImage, 2009)

Quantitative examination of a novel clustering method using magnetic resonance diffusion tensor tractography. - Aristotle N. Voineskos; Lauren J. O'Donnell; Nancy J. Lobaugh; Douglas Markant; Stephanie Ameis; Marc Niethammer; Benoit H. Mulsant; Bruce G. Pollock; James L. Kennedy; Carl-Fredrik Westin; Martha Elizabeth Shenton (NeuroImage, 2009)

The Fiber Laterality Histogram: A New Way to Measure White Matter Asymmetry. - Lauren J. O'Donnell; Carl-Fredrik Westin; Isaiah Norton; Stephen Whalen; Laura Rigolo; Ruth E. Propper; Alexandra J. Golby (MICCAI (2), 2010)

Unbiased Groupwise Registration of White Matter Tractography. - Lauren J. O'Donnell; William M. Wells III; Alexandra J. Golby; Carl-Fredrik Westin (MICCAI (3), 2012)

fMRI-DTI modeling via landmark distance atlases for prediction and detection of fiber tracts. - Lauren J. O'Donnell; Laura Rigolo; Isaiah Norton; William M. Wells III; Carl-Fredrik Westin; Alexandra J. Golby (NeuroImage, 2012)

Fiber clustering versus the parcellation-based connectome. - Lauren J. O'Donnell; Alexandra J. Golby; Carl-Fredrik Westin (NeuroImage, 2013)

Statistical and Machine Learning Methods for Neuroimaging: Examples, Challenges, and Extensions to Diffusion Imaging Data. - Lauren J. O'Donnell; Thomas Schultz 001 (Visualization and Processing of Higher Order Descriptors for Multi-Valued Data, 2015)

Sparse Reconstruction Challenge for diffusion MRI: Validation on a physical phantom to determine which acquisition scheme and analysis method to use? - Lipeng Ning; Frederik B. Laun; Yaniv Gur; Edward V. R. DiBella; Samuel Deslauriers-Gauthier; Thinhinane Megherbi; Aurobrata Ghosh; Mauro Zucchelli; Gloria Menegaz; Rutger Fick; Samuel St-Jean; Michael Paquette; et al. (Medical Image Anal., 2015)

Fiber clustering based white matter connectivity analysis for prediction of Autism Spectrum Disorder using diffusion tensor imaging. - Fan Zhang 013; Peter Savadjiev; Tom Weidong Cai; Yang Song 001; Ragini Verma; Carl-Fredrik Westin; Lauren J. O'Donnell (ISBI, 2016)

Corticospinal tract modeling for neurosurgical planning by tracking through regions of peritumoral edema and crossing fibers using two-tensor unscented Kalman filter tractography. - Zhenrui Chen; Yanmei Tie; Olutayo I. Olubiyi; Fan Zhang 013; Alireza Mehrtash; Laura Rigolo; Pegah Kahali; Isaiah Norton; Ofer Pasternak; Yogesh Rathi; Alexandra J. Golby; Lauren J. O'Donnell (Int. J. Comput. Assist. Radiol. Surg., 2016)

Increasing the impact of medical image computing using community-based open-access hackathons: The NA-MIC and 3D Slicer experience. - Tina Kapur; Steve Pieper 001; Andriy Fedorov; Jean-Christophe Fillion-Robin; Michael Halle; Lauren O'Donnell; Andras Lasso; Tamas Ungi; Csaba Pinter; Julien Finet; Sonia Pujol; Jagadeesan Jayender; et al. (Medical Image Anal., 2016)

Q-space trajectory imaging for multidimensional diffusion MRI of the human brain. - Carl-Fredrik Westin; Hans Knutsson; Ofer Pasternak; Filip Szczepankiewicz; Evren Özarslan; Danielle van Westen; Cecilia Mattisson; Mats Bogren; Lauren J. O'Donnell; Marek Kubicki; Daniel Topgaard; Markus Nilsson (NeuroImage, 2016)

Locally-Transferred Fisher Vectors for Texture Classification. - Yang Song 001; Fan Zhang 013; Qing Li 012; Heng Huang; Lauren J. O'Donnell; Weidong Cai 001 (ICCV, 2017)

Automated connectivity-based groupwise cortical atlas generation: Application to data of neurosurgical patients with brain tumors for cortical parcellation prediction. - Fan Zhang 013; Pegah Kahali; Yannick Suter; Isaiah Norton; Laura Rigolo; Peter Savadjiev; Yang Song 001; Yogesh Rathi; Tom Weidong Cai; William M. Wells III; Alexandra J. Golby; Lauren J. O'Donnell (ISBI, 2017)

Comparison between two white matter segmentation strategies: An investigation into white matter segmentation consistency. - Fan Zhang 013; Isaiah Norton; Weidong Cai 001; Yang Song 001; William M. Wells III; Lauren J. O'Donnell (ISBI, 2017)

Reconstruction of 3D Muscle Fiber Structure Using High Resolution Cryosectioned Volume. - Yoshito Otake; Kohei Miyamoto; Axel Ollivier; Futoshi Yokota; Norio Fukuda; Lauren J. O'Donnell; Carl-Fredrik Westin; Masaki Takao; Nobuhiko Sugano; Beom Sun Chung; Jin-Seo Park; Yoshinobu Sato (MSKI@MICCAI, 2017)

Patient-Specific Skeletal Muscle Fiber Modeling from Structure Tensor Field of Clinical CT Images. - Yoshito Otake; Futoshi Yokota; Norio Fukuda; Masaki Takao; Shu Takagi; Naoto Yamamura; Lauren J. O'Donnell; Carl-Fredrik Westin; Nobuhiko Sugano; Yoshinobu Sato (MICCAI (1), 2017)

Supra-Threshold Fiber Cluster Statistics for Data-Driven Whole Brain Tractography Analysis. - Fan Zhang 013; Weining Wu; Lipeng Ning; Gloria McAnulty; Deborah P. Waber; Borjan A. Gagoski; Kiera Sarill; Hesham M. Hamoda; Yang Song 001; Weidong Cai 001; Yogesh Rathi; Lauren J. O'Donnell (MICCAI (1), 2017)

3D Large Kernel Anisotropic Network for Brain Tumor Segmentation. - Dongnan Liu; Donghao Zhang; Yang Song 001; Fan Zhang 013; Lauren J. O'Donnell; Weidong Cai 001 (ICONIP (7), 2018)

A comparison of three fiber tract delineation methods and their impact on white matter analysis. - Valerie J. Sydnor; Ana María Rivas-Grajales; Amanda E. Lyall; Fan Zhang 013; Sylvain Bouix; Sarina Karmacharya; Martha Elizabeth Shenton; Carl-Fredrik Westin; Nikos Makris; Demian Wassermann; Lauren J. O'Donnell; Marek Kubicki (NeuroImage, 2018)

Investigation into local white matter abnormality in emotional processing and sensorimotor areas using an automatically annotated fiber clustering in major depressive disorder. - Ye Wu 001; Fan Zhang 013; Nikos Makris; Yuping Ning; Isaiah Norton; Shenglin She; Hongjun Peng; Yogesh Rathi; Yuanjing Feng; Huawang Wu; Lauren J. O'Donnell (NeuroImage, 2018)

Whole brain white matter connectivity analysis using machine learning: An application to autism. - Fan Zhang 013; Peter Savadjiev; Weidong Cai 001; Yang Song 001; Yogesh Rathi; Birkan Tunç; Drew Parker; Tina Kapur; Robert T. Schultz; Nikos Makris; Ragini Verma; Lauren J. O'Donnell (NeuroImage, 2018)

Suprathreshold fiber cluster statistics: Leveraging white matter geometry to enhance tractography statistical analysis. - Fan Zhang 013; Weining Wu; Lipeng Ning; Gloria McAnulty; Deborah P. Waber; Borjan A. Gagoski; Kiera Sarill; Hesham M. Hamoda; Yang Song 001; Weidong Cai 001; Yogesh Rathi; Lauren J. O'Donnell (NeuroImage, 2018)

An anatomically curated fiber clustering white matter atlas for consistent white matter tract parcellation across the lifespan. - Fan Zhang 013; Ye Wu 001; Isaiah Norton; Laura Rigolo; Yogesh Rathi; Nikos Makris; Lauren J. O'Donnell (NeuroImage, 2018)

Efficient 3D Depthwise and Separable Convolutions with Dilation for Brain Tumor Segmentation. - Donghao Zhang; Yang Song 001; Dongnan Liu; Chaoyi Zhang; Yicheng Wu 001; Heng Wang 007; Fan Zhang 013; Yong Xia 001; Lauren J. O'Donnell; Weidong Cai 001 (Australasian Conference on Artificial Intelligence, 2019)

Post-Traumatic Cerebral Microhemorrhages and their Effects Upon White Matter Connectivity in the Aging Human Brain. - Di Fan; Nikhil N. Chaudhari; Kenneth A. Rostowsky; Maria Calvillo; Sean K. Lee; Nahian F. Chowdhury; Fan Zhang 013; Lauren J. O'Donnell; Andrei Irimia (EMBC, 2019)

Nuclei Segmentation via a Deep Panoptic Model with Semantic Feature Fusion. - Dongnan Liu; Donghao Zhang; Yang Song 001; Chaoyi Zhang; Fan Zhang 013; Lauren O'Donnell; Weidong Cai 001 (IJCAI, 2019)

Deep White Matter Analysis: Fast, Consistent Tractography Segmentation Across Populations and dMRI Acquisitions. - Fan Zhang 013; Nico Hoffmann; Suheyla Cetin Karayumak; Yogesh Rathi; Alexandra J. Golby; Lauren J. O'Donnell (MICCAI (3), 2019)

MK-curve - Characterizing the relation between mean kurtosis and alterations in the diffusion MRI signal. - Fan Zhang 013; Lipeng Ning; Lauren J. O'Donnell; Ofer Pasternak (NeuroImage, 2019)

Unsupervised Instance Segmentation in Microscopy Images via Panoptic Domain Adaptation and Task Re-Weighting. - Dongnan Liu; Donghao Zhang; Yang Song 001; Fan Zhang 013; Lauren O'Donnell; Heng Huang; Mei Chen; Weidong Cai 001 (CVPR, 2020)

Mapping Cerebral Connectivity Changes after Mild Traumatic Brain Injury in Older Adults Using Diffusion Tensor Imaging and Riemannian Matching of Elastic Curves. - Andrei Irimia; Di Fan; Nikhil N. Chaudhari; Van Ngo; Fan Zhang 013; Shantanu H. Joshi; Lauren J. O'Donnell (ISBI, 2020)

TRAKO: Efficient Transmission of Tractography Data for Visualization. - Daniel Haehn; Loraine Franke; Fan Zhang 013; Suheyla Cetin Karayumak; Steve Pieper 001; Lauren J. O'Donnell; Yogesh Rathi (MICCAI (7), 2020)

Deep white matter analysis (DeepWMA): Fast and consistent tractography segmentation. - Fan Zhang 013; Suheyla Cetin Karayumak; Nico Hoffmann; Yogesh Rathi; Alexandra J. Golby; Lauren J. O'Donnell (Medical Image Anal., 2020)

Creation of a novel trigeminal tractography atlas for automated trigeminal nerve identification. - Fan Zhang 013; Guoqiang Xie; Laura Leung; Michael A. Mooney; Lorenz Epprecht; Isaiah Norton; Yogesh Rathi; Ron Kikinis; Ossama Al-Mefty; Nikos Makris; Alexandra J. Golby; Lauren J. O'Donnell (NeuroImage, 2020)

FiberStars: Visual Comparison of Diffusion Tractography Data between Multiple Subjects. - Loraine Franke; Daniel Karl I. Weidele; Fan Zhang 013; Suheyla Cetin Karayumak; Steve Pieper 001; Lauren J. O'Donnell; Yogesh Rathi; Daniel Haehn (PacificVis, 2021)

Celltrack R-CNN: A Novel End-To-End Deep Neural Network For Cell Segmentation And Tracking In Microscopy Images. - Yuqian Chen; Yang Song 001; Chaoyi Zhang; Fan Zhang 013; Lauren O'Donnell; Wojciech Chrzanowski; Weidong Cai 001 (ISBI, 2021)

Deep Fiber Clustering: Anatomically Informed Unsupervised Deep Learning for Fast and Effective White Matter Parcellation. - Yuqian Chen; Chaoyi Zhang; Yang Song 001; Nikos Makris; Yogesh Rathi; Weidong Cai 001; Fan Zhang 013; Lauren J. O'Donnell (MICCAI (7), 2021)

Image registration: Maximum likelihood, minimum entropy and deep learning. - Alireza Sedghi; Lauren J. O'Donnell; Tina Kapur; Erik G. Learned-Miller; Parvin Mousavi; William M. Wells III (Medical Image Anal., 2021)

Tractography dissection variability: What happens when 42 groups dissect 14 white matter bundles on the same dataset? - Kurt G. Schilling; François Rheault; Laurent Petit; Colin B. Hansen; Vishwesh Nath; Fang-Cheng Yeh; Gabriel Girard; Muhamed Barakovic; Jonathan Rafael-Patino; Thomas Yu; Elda Fischi Gomez; Marco Pizzolato; et al. (NeuroImage, 2021)

Deep learning based segmentation of brain tissue from diffusion MRI. - Fan Zhang 013; Anna Breger; Kang Ik Kevin Cho; Lipeng Ning; Carl-Fredrik Westin; Lauren J. O'Donnell; Ofer Pasternak (NeuroImage, 2021)

PDAM: A Panoptic-Level Feature Alignment Framework for Unsupervised Domain Adaptive Instance Segmentation in Microscopy Images. - Dongnan Liu; Donghao Zhang; Yang Song 001; Fan Zhang 013; Lauren O'Donnell; Heng Huang; Mei Chen; Weidong Cai 001 (IEEE Trans. Medical Imaging, 2021)

Model and Predict Age and Sex in Healthy Subjects Using Brain White Matter Features: A Deep Learning Approach. - Hao He; Fan Zhang 013; Steve Pieper 001; Nikos Makris; Yogesh Rathi; William M. Wells III; Lauren J. O'Donnell (ISBI, 2022)

Supwma: Consistent and Efficient Tractography Parcellation of Superficial White Matter with Deep Learning. - Tengfei Xue; Fan Zhang 013; Chaoyi Zhang; Yuqian Chen; Yang Song 001; Nikos Makris; Yogesh Rathi; Weidong Cai 001; Lauren J. O'Donnell (ISBI, 2022)

White Matter Tracts are Point Clouds: Neuropsychological Score Prediction and Critical Region Localization via Geometric Deep Learning. - Yuqian Chen; Fan Zhang 013; Chaoyi Zhang; Tengfei Xue; Leo R. Zekelman; Jianzhong He; Yang Song 001; Nikos Makris; Yogesh Rathi; Alexandra J. Golby; Weidong Cai 001; Lauren J. O'Donnell (MICCAI (1), 2022)

TractoFormer: A Novel Fiber-Level Whole Brain Tractography Analysis Framework Using Spectral Embedding and Vision Transformers. - Fan Zhang 013; Tengfei Xue; Weidong Cai 001; Yogesh Rathi; Carl-Fredrik Westin; Lauren J. O'Donnell (MICCAI (1), 2022)

DFC: Anatomically Informed Fiber Clustering with Self-supervised Deep Learning for Fast and Effective Tractography Parcellation. - Yuqian Chen; Chaoyi Zhang; Tengfei Xue; Yang Song 001; Nikos Makris; Yogesh Rathi; Tom Weidong Cai; Fan Zhang 013; Lauren J. O'Donnell (CoRR, 2022)

A Novel Supervised Contrastive Regression Framework for Prediction of Neurocognitive Measures Using Multi-Site Harmonized Diffusion MRI Tractography. - Tengfei Xue; Fan Zhang 013; Leo R. Zekelman; Chaoyi Zhang; Yuqian Chen; Suheyla Cetin Karayumak; Steven D. Pieper; William M. Wells III; Yogesh Rathi; Nikos Makris; Weidong Cai 001; Lauren J. O'Donnell (CoRR, 2022)

Age Prediction Performance Varies Across Deep, Superficial, and Cerebellar White Matter Connections. - Yuxiang Wei 004; Tengfei Xue; Yogesh Rathi; Nikos Makris; Fan Zhang 013; Lauren J. O'Donnell (CoRR, 2022)

White matter association tracts underlying language and theory of mind: An investigation of 809 brains from the Human Connectome Project. - Leo R. Zekelman; Fan Zhang 013; Nikos Makris; Jianzhong He; Yuqian Chen; Tengfei Xue; Daniela Liera; Daniel L. Drane; Yogesh Rathi; Alexandra J. Golby; Lauren J. O'Donnell (NeuroImage, 2022)

Quantitative mapping of the brain's structural connectivity using diffusion MRI tractography: A review. - Fan Zhang 013; Alessandro Daducci; Yong He; Simona Schiavi; Caio Seguin; Robert E. Smith 002; Chun-Hung Yeh; Tengda Zhao; Lauren J. O'Donnell (NeuroImage, 2022)

How Machine Learning is Powering Neuroimaging to Improve Brain Health. - Nalini M. Singh; Jordan B. Harrod; Sandya Subramanian; Mitchell B. Robinson; Ken Chang; Suheyla Cetin Karayumak; Adrian Vasile Dalca; Simon B. Eickhoff; Michael Fox; Loraine Franke; Polina Golland; Daniel Haehn; et al. (Neuroinformatics, 2022)

DSNet: A Dual-Stream Framework for Weakly-Supervised Gigapixel Pathology Image Analysis. - Tiange Xiang; Yang Song 001; Chaoyi Zhang; Dongnan Liu; Mei Chen; Fan Zhang 013; Heng Huang; Lauren O'Donnell; Weidong Cai 001 (IEEE Trans. Medical Imaging, 2022)

Deep Diffusion MRI Registration (DDMReg): A Deep Learning Method for Diffusion MRI Registration. - Fan Zhang 013; William M. Wells III; Lauren J. O'Donnell (IEEE Trans. Medical Imaging, 2022)

Tractgraphcnn: Anatomically Informed Graph CNN for Classification Using Diffusion MRI Tractography. - Yuqian Chen; Fan Zhang 013; Leo R. Zekelman; Tengfei Xue; Chaoyi Zhang; Yang Song 001; Nikos Makris; Yogesh Rathi; Weidong Cai 001; Lauren J. O'Donnell (ISBI, 2023)

DEEPRGVP: A novel microstructure-informed supervised contrastive learning framework for automated identification of the retinogeniculate pathway using dMRI tractography. - Sipei Li; Jianzhong He; Tengfei Xue; Guoqiang Xie; Shun Yao; Yuqian Chen; Erickson F. Torio; Yuanjing Feng; Dhiego Chaves de Almeida Bastos; Yogesh Rathi; Nikos Makris; Ron Kikinis; et al. (ISBI, 2023)

GeoLab: Geometry-Based Tractography Parcellation of Superficial White Matter. - Nabil Vindas; Nicole Labra Avila; Fan Zhang 013; Tengfei Xue; Lauren J. O'Donnell; Jean-François Mangin (ISBI, 2023)

Tractography-Based Parcellation of Cerebellar Dentate Nuclei via a Deep Nonnegative Matrix Factorization Clustering Method. - Xiao Xu; Yuqian Chen; Leo R. Zekelman; Yogesh Rathi; Nikos Makris; Fan Zhang 013; Lauren J. O'Donnell (ISBI, 2023)

A Registration- and Uncertainty-Based Framework for White Matter Tract Segmentation with Only One Annotated Subject. - Hao Xu 042; Tengfei Xue; Dongnan Liu; Fan Zhang 013; Carl-Fredrik Westin; Ron Kikinis; Lauren J. O'Donnell; Weidong Cai 001 (ISBI, 2023)

A Deep Learning Framework for Estimating Multi-Fiber PICASO Model Parameters of Tissue Microstructure Using Diffusion MRI. - Tengfei Xue; Hazhar Sufi Karimi; William Consagra; Fan Zhang 013; Weidong Cai 001; Lauren J. O'Donnell; Lipeng Ning; Yogesh Rathi (ISBI, 2023)

A Deep Network for Explainable Prediction of Non-imaging Phenotypes Using Anatomical Multi-view Data. - Yuxiang Wei 004; Yuqian Chen; Tengfei Xue; Leo R. Zekelman; Nikos Makris; Yogesh Rathi; Weidong Cai 001; Fan Zhang 013; Lauren J. O'Donnell (CDMRI@MICCAI, 2023)

TractCloud: Registration-Free Tractography Parcellation with a Novel Local-Global Streamline Point Cloud Representation. - Tengfei Xue; Yuqian Chen; Chaoyi Zhang; Alexandra J. Golby; Nikos Makris; Yogesh Rathi; Weidong Cai 001; Fan Zhang 013; Lauren J. O'Donnell (MICCAI (8), 2023)

Fiber Tract Shape Measures Inform Prediction of Non-Imaging Phenotypes. - Wan Liu 001; Yuqian Chen; Chuyang Ye; Nikos Makris; Yogesh Rathi; Weidong Cai 001; Fan Zhang 013; Lauren J. O'Donnell (CoRR, 2023)

Reconstructing the somatotopic organization of the corticospinal tract remains a challenge for modern tractography methods. - Jianzhong He; Fan Zhang 013; Yiang Pan; Yuanjing Feng; Jarrett Rushmore; Erickson Torio; Yogesh Rathi; Nikos Makris; Ron Kikinis; Alexandra J. Golby; Lauren J. O'Donnell (CoRR, 2023)

Superficial white matter analysis: An efficient point-cloud-based deep learning framework with supervised contrastive learning for consistent tractography parcellation across populations and dMRI acquisitions. - Tengfei Xue; Fan Zhang 013; Chaoyi Zhang; Yuqian Chen; Yang Song 001; Alexandra J. Golby; Nikos Makris; Yogesh Rathi; Weidong Cai 001; Lauren J. O'Donnell (Medical Image Anal., 2023)

Deep fiber clustering: Anatomically informed fiber clustering with self-supervised deep learning for fast and effective tractography parcellation. - Yuqian Chen; Chaoyi Zhang; Tengfei Xue; Yang Song 001; Nikos Makris; Yogesh Rathi; Tom Weidong Cai; Fan Zhang 013; Lauren J. O'Donnell (NeuroImage, 2023)

A Novel Deep Clustering Framework for Fine-Scale Parcellation of Amygdala Using DMRI Tractography. - Haolin He; Ce Zhu; Le Zhang 001; Yipeng Liu 001; Xiao Xu; Yuqian Chen; Leo R. Zekelman; Jarrett Rushmore; Yogesh Rathi; Nikos Makris; Lauren J. O'Donnell; Fan Zhang 013 (ISBI, 2024)

Cross-Domain Fiber Cluster Shape Analysis for Language Performance Cognitive Score Prediction. - Yui Lo; Yuqian Chen; Dongnan Liu; Wan Liu 001; Leo R. Zekelman; Fan Zhang 013; Yogesh Rathi; Nikos Makris; Alexandra J. Golby; Weidong Cai 001; Lauren J. O'Donnell (CDMRI@MICCAI, 2024)

SAT-Morph: Unsupervised Deformable Medical Image Registration Using Vision Foundation Models with Anatomically Aware Text Prompt. - Hao Xu 042; Tengfei Xue; Dongnan Liu; Fan Zhang 013; Carl-Fredrik Westin; Ron Kikinis; Lauren J. O'Donnell; Weidong Cai 001 (MedAGI@MICCAI, 2024)

When Diffusion MRI Meets Diffusion Model: A Novel Deep Generative Model for Diffusion MRI Generation. - Xi Zhu; Wei Zhang; Yijie Li; Lauren J. O'Donnell; Fan Zhang 013 (MICCAI (2), 2024)

TractGraphFormer: Anatomically Informed Hybrid Graph CNN-Transformer Network for Classification from Diffusion MRI Tractography. - Yuqian Chen; Fan Zhang 013; Meng Wang; Leo R. Zekelman; Suheyla Cetin Karayumak; Tengfei Xue; Chaoyi Zhang; Yang Song 001; Nikos Makris; Yogesh Rathi; Tom Weidong Cai; Lauren J. O'Donnell (CoRR, 2024)

Deep multimodal saliency parcellation of cerebellar pathways: linking microstructure and individual function through explainable multitask learning. - Ari Tchetchenian; Leo R. Zekelman; Yuqian Chen; Jarrett Rushmore; Fan Zhang 013; Edward H. Yeterian; Nikos Makris; Yogesh Rathi; Erik Meijering; Yang Song 001; Lauren J. O'Donnell (CoRR, 2024)

White Matter Geometry-Guided Score-Based Diffusion Model for Tissue Microstructure Imputation in Tractography Imaging. - Yui Lo; Yuqian Chen; Fan Zhang 013; Dongnan Liu; Leo R. Zekelman; Suheyla Cetin Karayumak; Yogesh Rathi; Tom Weidong Cai; Lauren J. O'Donnell (CoRR, 2024)

EVENet: Evidence-based Ensemble Learning for Uncertainty-aware Brain Parcellation Using Diffusion MRI. - Chenjun Li; Dian Yang; Shun Yao; Shuyue Wang; Ye Wu 001; Le Zhang 001; Qiannuo Li; Kang Ik Kevin Cho; Johanna Seitz-Holland; Lipeng Ning; Jon Haitz Legarreta; Yogesh Rathi; et al. (CoRR, 2024)

The shape of the brain's connections is predictive of cognitive performance: an explainable machine learning study. - Yui Lo; Yuqian Chen; Dongnan Liu; Wan Liu 001; Leo R. Zekelman; Jarrett Rushmore; Fan Zhang 013; Yogesh Rathi; Nikos Makris; Alexandra J. Golby; Weidong Cai 001; Lauren J. O'Donnell (CoRR, 2024)

TractGeoNet: A geometric deep learning framework for pointwise analysis of tract microstructure to predict language assessment performance. - Yuqian Chen; Leo R. Zekelman; Chaoyi Zhang; Tengfei Xue; Yang Song 001; Nikos Makris; Yogesh Rathi; Alexandra J. Golby; Weidong Cai 001; Fan Zhang 013; Lauren J. O'Donnell (Medical Image Anal., 2024)

DDParcel: Deep Learning Anatomical Brain Parcellation From Diffusion MRI. - Fan Zhang 013; Kang Ik Kevin Cho; Johanna Seitz-Holland; Lipeng Ning; Jon Haitz Legarreta; Yogesh Rathi; Carl-Fredrik Westin; Lauren J. O'Donnell; Ofer Pasternak (IEEE Trans. Medical Imaging, 2024)

Medical Image Registration Meets Vision Foundation Model: Prototype Learning and Contour Awareness. - Hao Xu 042; Tengfei Xue; Jianan Fan; Dongnan Liu; Yuqian Chen; Fan Zhang 013; Carl-Fredrik Westin; Ron Kikinis; Lauren J. O'Donnell; Weidong Cai 001 (IPMI (1), 2025)

Dineuro: Distilling Knowledge from 2D Natural Images via Deformable Tubular Transferring Strategy for 3D Neuron Reconstruction. - Yik San Cheng; Runkai Zhao; Heng Wang 007; Hanchuan Peng; Yui Lo; Yuqian Chen; Lauren J. O'Donnell; Weidong Cai 001 (ISBI, 2025)

TractShapeNet: Efficient Multi-Shape Learning with 3D Tractography Point Clouds. - Yui Lo; Yuqian Chen; Dongnan Liu; Jon Haitz Legarreta; Leo R. Zekelman; Fan Zhang 013; Jarrett Rushmore; Yogesh Rathi; Nikos Makris; Alexandra J. Golby; Tom Weidong Cai; Lauren J. O'Donnell (ISBI, 2025)

A Novel Deep Learning Tractography Fiber Clustering Framework for Functionally Consistent White Matter Parcellation Using Multimodal Diffusion MRI and Functional MRI. - Jin Wang; Bocheng Guo; Yijie Li; Junyi Wang; Yuqian Chen; Jarrett Rushmore; Nikos Makris; Yogesh Rathi; Lauren J. O'Donnell; Fan Zhang 013 (ISBI, 2025)

DDEvENet: Evidence-based ensemble learning for uncertainty-aware brain parcellation using diffusion MRI. - Chenjun Li; Dian Yang; Shun Yao; Shuyue Wang; Ye Wu 001; Le Zhang 001; Qiannuo Li; Kang Ik Kevin Cho; Johanna Seitz-Holland; Lipeng Ning; Jon Haitz Legarreta; Yogesh Rathi; et al. (Comput. Medical Imaging Graph., 2025)

TractGraphFormer: Anatomically informed hybrid graph CNN-transformer network for interpretable sex and age prediction from diffusion MRI tractography. - Yuqian Chen; Fan Zhang 013; Meng Wang; Leo R. Zekelman; Suheyla Cetin Karayumak; Tengfei Xue; Chaoyi Zhang; Yang Song 001; Jarrett Rushmore; Nikos Makris; Yogesh Rathi; Weidong Cai 001; et al. (Medical Image Anal., 2025)

DeepNuParc: A novel deep clustering framework for fine-scale parcellation of brain nuclei using diffusion MRI tractography. - Haolin He; Ce Zhu; Le Zhang 001; Yipeng Liu 001; Xiao Xu; Yuqian Chen; Leo R. Zekelman; Jarrett Rushmore; Yogesh Rathi; Nikos Makris; Lauren J. O'Donnell; Fan Zhang 013 (NeuroImage, 2025)

Deep diffusion MRI template (DDTemplate): A novel deep learning groupwise diffusion MRI registration method for brain template creation. - Junyi Wang; Xi Zhu; Wei Zhang; Mubai Du; William M. Wells; Lauren J. O'Donnell; Fan Zhang 013 (NeuroImage, 2025)

TractCloud-FOV: Deep Learning-based Robust Tractography Parcellation in Diffusion MRI with Incomplete Field of View. - Yuqian Chen; Leo R. Zekelman; Yui Lo; Suheyla Cetin Karayumak; Tengfei Xue; Yogesh Rathi; Nikos Makris; Fan Zhang 013; Tom Weidong Cai; Lauren J. O'Donnell (CoRR, 2025)

A Novel Streamline-based diffusion MRI Tractography Registration Method with Probabilistic Keypoint Detection. - Junyi Wang; Mubai Du; Ye Wu 001; Yijie Li; William M. Wells III; Lauren J. O'Donnell; Fan Zhang 013 (CoRR, 2025)

DDCSR: A Novel End-to-End Deep Learning Framework for Cortical Surface Reconstruction from Diffusion MRI. - Chengjin Li; Yuqian Chen; Nir A. Sochen; Wei Zhang; Carl-Fredrik Westin; Yogesh Rathi; Lauren J. O'Donnell; Ofer Pasternak; Fan Zhang 013 (CoRR, 2025)

MultiCo3D: Multi-Label Voxel Contrast for One-Shot Incremental Segmentation of 3D Neuroimages. - Hao Xu 042; Tengfei Xue; Dongnan Liu; Yuqian Chen; Fan Zhang 013; Carl-Fredrik Westin; Ron Kikinis; Lauren J. O'Donnell; Weidong Cai 001 (CoRR, 2025)

A Multimodal Deep Learning Approach for White Matter Shape Prediction in Diffusion MRI Tractography. - Yui Lo; Yuqian Chen; Dongnan Liu; Leo R. Zekelman; Jarrett Rushmore; Yogesh Rathi; Nikos Makris; Alexandra J. Golby; Fan Zhang 013; Tom Weidong Cai; Lauren J. O'Donnell (CoRR, 2025)

DeepMultiConnectome: Deep Multi-Task Prediction of Structural Connectomes Directly from Diffusion MRI Tractography. - Marcus J. Vroemen; Yuqian Chen; Yui Lo; Tengfei Xue; Tom Weidong Cai; Fan Zhang 013; Josien P. W. Pluim; Lauren J. O'Donnell (CoRR, 2025)

AGFS-Tractometry: A Novel Atlas-Guided Fine-Scale Tractometry Approach for Enhanced Along-Tract Group Statistical Comparison Using Diffusion MRI Tractography. - Ruixi Zheng; Wei Zhang; Yijie Li; Xi Zhu; Zhou Lan; Jarrett Rushmore; Yogesh Rathi; Nikos Makris; Lauren J. O'Donnell; Fan Zhang 013 (CoRR, 2025)

DDTracking: A Deep Generative Framework for Diffusion MRI Tractography with Streamline Local-Global Spatiotemporal Modeling. - Yijie Li; Wei Zhang; Xi Zhu; Ye Wu 001; Yogesh Rathi; Lauren J. O'Donnell; Fan Zhang 013 (CoRR, 2025)