DDEvENet: Evidence-based ensemble learning for uncertainty-aware brain parcellation using diffusion MRI. - Li, Chenjun; Yang, Dian; Yao, Shun; Wang, Shuyue; Wu, Ye; Zhang, Le; Li, Qiannuo; Cho, Kang Ik Kevin; Seitz-Holland, Johanna; Ning, Lipeng; Legarreta, Jon Haitz; Rathi, Yogesh; 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. - Chen, Yuqian; Zhang, Fan; Wang, Meng; Zekelman, Leo R.; Karayumak, Suheyla Cetin; Xue, Tengfei; Zhang, Chaoyi; Song, Yang; Rushmore, Jarrett; Makris, Nikos; Rathi, Yogesh; Cai, Weidong; et al. (Medical Image Anal., 2025)

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

A Deep Network for Explainable Prediction of Non-Imaging Phenotypes using Anatomical Multi-View Data. - Wei, Yuxiang; Chen, Yuqian; Xue, Tengfei; Zekelman, Leo R.; Makris, Nikos; Rathi, Yogesh; Cai, Tom Weidong; Zhang, Fan; O'Donnell, Lauren J. (CoRR, 2024)

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

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

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

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

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

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

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

DINeuro: Distilling Knowledge from 2D Natural Images via Deformable Tubular Transferring Strategy for 3D Neuron Reconstruction. - Cheng, Yik San; Zhao, Runkai; Wang, Heng; Peng, Hanchuan; Lo, Yui; Chen, Yuqian; O'Donnell, Lauren J.; Cai, Weidong (CoRR, 2024)

TractShapeNet: Efficient Multi-Shape Learning with 3D Tractography Point Clouds. - Lo, Yui; Chen, Yuqian; Liu, Dongnan; Legarreta, Jon Haitz; Zekelman, Leo R.; Zhang, Fan; Rushmore, Jarrett; Rathi, Yogesh; Makris, Nikos; Golby, Alexandra J.; Cai, Weidong; O'Donnell, Lauren J. (CoRR, 2024)

A Novel Deep Learning Tractography Fiber Clustering Framework for Functionally Consistent White Matter Parcellation Using Multimodal Diffusion MRI and Functional MRI. - Wang, Jin; Guo, Bocheng; Li, Yijie; Wang, Junyi; Chen, Yuqian; Rushmore, Jarrett; Makris, Nikos; Rathi, Yogesh; O'Donnell, Lauren J.; Zhang, Fan (CoRR, 2024)

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. - Xue, Tengfei; Zhang, Fan; Zhang, Chaoyi; Chen, Yuqian; Song, Yang; Golby, Alexandra J.; Makris, Nikos; Rathi, Yogesh; Cai, Weidong; O'Donnell, Lauren J. (Medical Image Anal., 2023)

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

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

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

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

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

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

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

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

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

TractGraphCNN: anatomically informed graph CNN for classification using diffusion MRI tractography. - Chen, Yuqian; Zhang, Fan; Zekelman, Leo R.; Xue, Tengfei; Zhang, Chaoyi; Song, Yang; Makris, Nikos; Rathi, Yogesh; Cai, Tom Weidong; O'Donnell, Lauren J. (CoRR, 2023)

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

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

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

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

TractGeoNet: A geometric deep learning framework for pointwise analysis of tract microstructure to predict language assessment performance. - Chen, Yuqian; Zekelman, Leo R.; Zhang, Chaoyi; Xue, Tengfei; Song, Yang; Makris, Nikos; Rathi, Yogesh; Golby, Alexandra J.; Cai, Weidong; Zhang, Fan; O'Donnell, Lauren J. (CoRR, 2023)

TractCloud: Registration-free tractography parcellation with a novel local-global streamline point cloud representation. - Xue, Tengfei; Chen, Yuqian; Zhang, Chaoyi; Golby, Alexandra J.; Makris, Nikos; Rathi, Yogesh; Cai, Weidong; Zhang, Fan; O'Donnell, Lauren J. (CoRR, 2023)

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

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

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

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

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

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

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

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

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

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

Model and predict age and sex in healthy subjects using brain white matter features: A deep learning approach. - He, Hao; Zhang, Fan; Pieper, Steve; Makris, Nikos; Rathi, Yogesh; Wells, William M., III; O'Donnell, Lauren J. (CoRR, 2022)

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

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

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

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. - Xue, Tengfei; Zhang, Fan; Zhang, Chaoyi; Chen, Yuqian; Song, Yang; Golby, Alexandra J.; Makris, Nikos; Rathi, Yogesh; Cai, Weidong; O'Donnell, Lauren J. (CoRR, 2022)

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

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

DeepRGVP: A Novel Microstructure-Informed Supervised Contrastive Learning Framework for Automated Identification Of The Retinogeniculate Pathway Using dMRI Tractography. - Li, Sipei; He, Jianzhong; Xue, Tengfei; Xie, Guoqiang; Yao, Shun; Chen, Yuqian; Torio, Erickson F.; Feng, Yuanjing; Bastos, Dhiego Chaves de Almeida; Rathi, Yogesh; Makris, Nikos; Kikinis, Ron; et al. (CoRR, 2022)

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

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

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

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

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

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

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

CellTrack R-CNN: A Novel End-To-End Deep Neural Network for Cell Segmentation and Tracking in Microscopy Images. - Chen, Yuqian; Song, Yang; Zhang, Chaoyi; Zhang, Fan; O'Donnell, Lauren; Chrzanowski, Wojciech; Cai, Weidong (CoRR, 2021)

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

DSNet: A Dual-Stream Framework for Weakly-Supervised Gigapixel Pathology Image Analysis. - Xiang, Tiange; Song, Yang; Zhang, Chaoyi; Liu, Dongnan; Chen, Mei; Zhang, Fan; Huang, Heng; O'Donnell, Lauren; Cai, Weidong (CoRR, 2021)

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

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

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

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

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

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

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

FiberStars: Visual Comparison of Diffusion Tractography Data between Multiple Subjects. - Franke, Loraine; Weidele, Daniel Karl I.; Zhang, Fan; Karayumak, Suheyla Cetin; Pieper, Steve; O'Donnell, Lauren J.; Rathi, Yogesh; Haehn, Daniel (CoRR, 2020)

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Corticospinal tract modeling for neurosurgical planning by tracking through regions of peritumoral edema and crossing fibers using two-tensor unscented Kalman filter tractography. - Chen, Zhenrui; Tie, Yanmei; Olubiyi, Olutayo I.; Zhang, Fan; Mehrtash, Alireza; Rigolo, Laura; Kahali, Pegah; Norton, Isaiah; Pasternak, Ofer; Rathi, Yogesh; Golby, Alexandra J.; O'Donnell, Lauren J. (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. - Kapur, Tina; Pieper, Steve; Fedorov, Andriy; Fillion-Robin, Jean-Christophe; Halle, Michael; O'Donnell, Lauren; Lasso, Andras; Ungi, Tamas; Pinter, Csaba; Finet, Julien; Pujol, Sonia; Jayender, Jagadeesan; et al. (Medical Image Anal., 2016)

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

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

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

Statistical and Machine Learning Methods for Neuroimaging: Examples, Challenges, and Extensions to Diffusion Imaging Data. - O'Donnell, Lauren J.; Schultz, Thomas (2015)

Computational Diffusion MRI and Brain Connectivity, MICCAI Workshops CDMRI/MMBC, Nagoya, Japan, September 22nd, 2013 (Springer, 2014)

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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