Finding the Brain Cortex Using Fuzzy Segmentation, Isosurfaces, and Deformable Surface Models. - Chenyang Xu 001; Dzung L. Pham; Jerry L. Prince (IPMI, 1997)

An Automated Technique for Statistical Characterization of Brain Tissues in Magnetic Resonance Imaging. - Dzung L. Pham; Jerry L. Prince; Chenyang Xu 001; Azar P. Dagher (Int. J. Pattern Recognit. Artif. Intell., 1997)

Partial Volume Estimation and the Fuzzy C-means Algorithm. - Dzung L. Pham; Jerry L. Prince (ICIP (3), 1998)

Reconstruction of the Central Layer of the Human Cerebral Cortex from MR Images. - Chenyang Xu 001; Dzung L. Pham; Jerry L. Prince; Maryam E. Etemad; Daphne N. Yu (MICCAI, 1998)

Adaptive fuzzy c-means algorithm for image segmentation in the presence of intensity inhomogeneities. - Dzung L. Pham; Jerry L. Prince (Image Processing, 1998)

An Adaptive Fuzzy Segmentation Algorithm for Three-Dimensional Magnetic Resonance Images. - Dzung L. Pham; Jerry L. Prince (IPMI, 1999)

Automated Segmentation of Sulcal Regions. - Maryam E. Rettmann; Chenyang Xu 001; Dzung L. Pham; Jerry L. Prince (MICCAI, 1999)

An adaptive fuzzy C-means algorithm for image segmentation in the presence of intensity inhomogeneities. - Dzung L. Pham; Jerry L. Prince (Pattern Recognit. Lett., 1999)

Adaptive Fuzzy Segmentation of Magnetic Resonance Images. - Dzung L. Pham; Jerry L. Prince (IEEE Trans. Medical Imaging, 1999)

Reconstruction of the Human Cerebral Cortex from Magnetic Resonance Images. - Chenyang Xu 001; Dzung L. Pham; Maryam E. Rettmann; Daphne N. Yu; Jerry L. Prince (IEEE Trans. Medical Imaging, 1999)

Edge-Adaptive Clustering for Unsupervised Image Segmentation. - Dzung L. Pham (ICIP, 2000)

Quantitative validation of a deformable cortical surface model. - Daphne N. Yu; Chenyang Xu 001; Maryam E. Rettmann; Dzung L. Pham; Jerry L. Prince (Image Processing, 2000)

Robust Fuzzy Segmentation of Magnetic Resonance Images. - Dzung L. Pham (CBMS, 2001)

Spatial Models for Fuzzy Clustering. - Dzung L. Pham (Comput. Vis. Image Underst., 2001)

Fuzzy clustering with spatial constraints. - Dzung L. Pham (ICIP (2), 2002)

Automatic segmentation of white matter lesions in T1-weighted brain MR images. - Songyang Yu; Dzung L. Pham; Dinggang Shen; Edward Herskovits; Susan M. Resnick; Christos Davatzikos (ISBI, 2002)

New approaches for measuring changes in the cortical surface using an automatic reconstruction algorithm. - Dzung L. Pham; Xiao Han 007; Maryam E. Rettmann; Chenyang Xu 001; Duygu Tosun; Susan M. Resnick; Jerry L. Prince (Image Processing, 2002)

Automatic classification of sulcal regions of the human brain cortex using pattern recognition. - Kirsten Judith Behnke; Maryam E. Rettmann; Dzung L. Pham; Dinggang Shen; Susan M. Resnick; Christos Davatzikos; Jerry L. Prince (Image Processing, 2003)

Integrating Intensity and Boundary Information for Tissue Classification. - Dzung L. Pham (CBMS, 2004)

Robust Unsupervised Tissue Classification in MR Images. - Dzung L. Pham; Jerry L. Prince (ISBI, 2004)

Topology Smoothing for Segmentation and Surface Reconstruction. - Pierre-Louis Bazin; Dzung L. Pham (MICCAI (1), 2004)

Simultaneous Boundary and Partial Volume Estimation in Medical Images. - Dzung L. Pham; Pierre-Louis Bazin (MICCAI (1), 2004)

CRUISE: Cortical reconstruction using implicit surface evolution. - Xiao Han 007; Dzung L. Pham; Duygu Tosun; Maryam E. Rettmann; Chenyang Xu 001; Jerry L. Prince (NeuroImage, 2004)

Topology Preserving Tissue Classification with Fast Marching and Topology Templates. - Pierre-Louis Bazin; Dzung L. Pham (IPMI, 2005)

Topology Correction Using Fast Marching Methods and Its Application to Brain Segmentation. - Pierre-Louis Bazin; Dzung L. Pham (MICCAI (2), 2005)

Super-resolved multi-channel fuzzy segmentation of MR brain images. - Ying Bai; Xiao Han 007; Dzung L. Pham; Jerry L. Prince (Image Processing, 2005)

Free software tools for atlas-based volumetric neuroimage analysis. - Pierre-Louis Bazin; Dzung L. Pham; William Gandler; Matthew J. McAuliffe (Image Processing, 2005)

TOADS: topology-preserving, anatomy-driven segmentation. - Pierre-Louis Bazin; Dzung L. Pham (ISBI, 2006)

Simultaneous registration and tissue classification using clustering algorithms. - Dzung L. Pham; Pierre-Louis Bazin (ISBI, 2006)

Digital Homeomorphisms in Deformable Registration. - Pierre-Louis Bazin; Lotta Maria Ellingsen; Dzung L. Pham (IPMI, 2007)

Statistical and Topological Atlas Based Brain Image Segmentation. - Pierre-Louis Bazin; Dzung L. Pham (MICCAI (1), 2007)

Topology correction of segmented medical images using a fast marching algorithm. - Pierre-Louis Bazin; Dzung L. Pham (Comput. Methods Programs Biomed., 2007)

Topology-Preserving Tissue Classification of Magnetic Resonance Brain Images. - Pierre-Louis Bazin; Dzung L. Pham (IEEE Trans. Medical Imaging, 2007)

Fuzzy c-means with variable compactness. - Snehashis Roy; Harsh K. Agarwal; Aaron Carass; Ying Bai; Dzung L. Pham; Jerry L. Prince (ISBI, 2008)

Homeomorphic brain image segmentation with topological and statistical atlases. - Pierre-Louis Bazin; Dzung L. Pham (Medical Image Anal., 2008)

Automated Reconstruction of the Cerebral Cortex in Multiple Sclerosis Patients. - Navid Shiee; Pierre-Louis Bazin; Daniel S. Reich; Dzung L. Pham (ISBI, 2009)

Belief Propagation Based Segmentation of White Matter Tracts in DTI. - Pierre-Louis Bazin; John A. Bogovic; Daniel S. Reich; Jerry L. Prince; Dzung L. Pham (MICCAI (1), 2009)

MR contrast synthesis for lesion segmentation. - Snehashis Roy; Aaron Carass; Navid Shiee; Dzung L. Pham; Jerry L. Prince (ISBI, 2010)

A topology-preserving approach to the segmentation of brain images with multiple sclerosis lesions. - Navid Shiee; Pierre-Louis Bazin; Arzu Ozturk; Daniel S. Reich; Peter A. Calabresi; Dzung L. Pham (NeuroImage, 2010)

The Java Image Science Toolkit (JIST) for Rapid Prototyping and Publishing of Neuroimaging Software. - Blake C. Lucas; John A. Bogovic; Aaron Carass; Pierre-Louis Bazin; Jerry L. Prince; Dzung L. Pham; Bennett A. Landman (Neuroinformatics, 2010)

Erratum to: The Java Image Science Toolkit (JIST) for Rapid Prototyping and Publishing of Neuroimaging Software. - Blake C. Lucas; John A. Bogovic; Aaron Carass; Pierre-Louis Bazin; Jerry L. Prince; Dzung L. Pham; Bennett A. Landman (Neuroinformatics, 2010)

Digital Topology in Brain Imaging. - Dzung L. Pham; Pierre-Louis Bazin; Jerry L. Prince (IEEE Signal Process. Mag., 2010)

Segmentation of Brain Images Using Adaptive Atlases with Application to Ventriculomegaly. - Navid Shiee; Pierre-Louis Bazin; Jennifer L. Cuzzocreo; Ari Blitz; Dzung L. Pham (IPMI, 2011)

Fiber tractogrophy and tract segmentation in multiple sclerosis lesions. - Navid Shiee; Pierre-Louis Bazin; Peter A. Calabresi; Daniel S. Reich; Dzung L. Pham (ISBI, 2011)

Editorial. - Jerry L. Prince; Dzung L. Pham; Kyle J. Myers (Medical Image Anal., 2011)

Direct segmentation of the major white matter tracts in diffusion tensor images. - Pierre-Louis Bazin; Chuyang Ye; John A. Bogovic; Navid Shiee; Daniel S. Reich; Jerry L. Prince; Dzung L. Pham (NeuroImage, 2011)

Intensity standardization of longitudinal images using 4D clustering. - Qing He; Navid Shiee; Daniel S. Reich; Peter A. Calabresi; Dzung L. Pham (ISBI, 2013)

Longitudinal intensity normalization in the presence of multiple sclerosis lesions. - Snehashis Roy; Aaron Carass; Navid Shiee; Dzung L. Pham; Peter A. Calabresi; Daniel S. Reich; Jerry L. Prince (ISBI, 2013)

Voxel-wise displacement as independent features in classification of multiple sclerosis. - Min Chen 006; Aaron Carass; Daniel S. Reich; Peter A. Calabresi; Dzung L. Pham; Jerry L. Prince (Image Processing, 2013)

Clustering of High Dimensional Longitudinal Imaging Data. - Seonjoo Lee; Vadim Zipunnikov; Navid Shiee; Ciprian M. Crainiceanu; Brian S. Caffo; Dzung L. Pham (PRNI, 2013)

Automatic magnetic resonance spinal cord segmentation with topology constraints for variable fields of view. - Min Chen 006; Aaron Carass; Jiwon Oh; Govind Nair; Dzung L. Pham; Daniel S. Reich; Jerry L. Prince (NeuroImage, 2013)

System for Integrated Neuroimaging Analysis and Processing of Structure. - Bennett A. Landman; John A. Bogovic; Aaron Carass; Min Chen 006; Snehashis Roy; Navid Shiee; Zhen Yang 002; Bhaskar Kishore; Dzung L. Pham; Pierre-Louis Bazin; Susan M. Resnick; Jerry L. Prince (Neuroinformatics, 2013)

Random forest FLAIR reconstruction from T1, T2, and PD-weighted MRI. - Amod Jog; Aaron Carass; Dzung L. Pham; Jerry L. Prince (ISBI, 2014)

Subject Specific Sparse Dictionary Learning for Atlas Based Brain MRI Segmentation. - Snehashis Roy; Aaron Carass; Jerry L. Prince; Dzung L. Pham (MLMI, 2014)

Example based lesion segmentation. - Snehashis Roy; Qing He; Aaron Carass; Amod Jog; Jennifer L. Cuzzocreo; Daniel S. Reich; Jerry L. Prince; Dzung L. Pham (Image Processing, 2014)

Tree-Encoded Conditional Random Fields for Image Synthesis. - Amod Jog; Aaron Carass; Dzung L. Pham; Jerry L. Prince (IPMI, 2015)

Longitudinal Patch-Based Segmentation of Multiple Sclerosis White Matter Lesions. - Snehashis Roy; Aaron Carass; Jerry L. Prince; Dzung L. Pham (MLMI, 2015)

Multi-output decision trees for lesion segmentation in multiple sclerosis. - Amod Jog; Aaron Carass; Dzung L. Pham; Jerry L. Prince (Image Processing, 2015)

Cerebral microbleed segmentation from susceptibility weighted images. - Snehashis Roy; Amod Jog; Elizabeth M. Sweeney; John A. Butman; Dzung L. Pham (Image Processing, 2015)

Intraparenchymal hemorrhage segmentation from clinical head CT of patients with traumatic brain injury. - Snehashis Roy; Sean Wilkes; Ramon Diaz-Arrastia; John A. Butman; Dzung L. Pham (Image Processing, 2015)

MR image synthesis by contrast learning on neighborhood ensembles. - Amod Jog; Aaron Carass; Snehashis Roy; Dzung L. Pham; Jerry L. Prince (Medical Image Anal., 2015)

Subject-Specific Sparse Dictionary Learning for Atlas-Based Brain MRI Segmentation. - Snehashis Roy; Qing He; Elizabeth M. Sweeney; Aaron Carass; Daniel S. Reich; Jerry L. Prince; Dzung L. Pham (IEEE J. Biomed. Health Informatics, 2015)

Quantification of traumatic meningeal injury using dynamic contrast enhanced (DCE) fluid-attenuated inversion recovery (FLAIR) imaging. - Marcelo Adrián Castro; Joshua P. Williford; Martin R. Cota; Judy M. MacLaren; Bernard J. Dardzinski; Lawrence L. Latour; Dzung L. Pham; John A. Butman (Biomedical Applications in Molecular, Structural, and Functional Imaging, 2016)

Patch Based Synthesis of Whole Head MR Images: Application To EPI Distortion Correction. - Snehashis Roy; Yi-Yu Chou; Amod Jog; John A. Butman; Dzung L. Pham (SASHIMI@MICCAI, 2016)

Incompressible Phase Registration for Motion Estimation from Tagged Magnetic Resonance Images. - Fangxu Xing; Jonghye Woo; Arnold D. Gomez; Dzung L. Pham; Philip V. Bayly; Maureen L. Stone; Jerry L. Prince (RAMBO+HVSMR@MICCAI, 2016)

Segmentation and labeling of the ventricular system in normal pressure hydrocephalus using patch-based tissue classification and multi-atlas labeling. - Lotta Maria Ellingsen; Snehashis Roy; Aaron Carass; Ari Blitz; Dzung L. Pham; Jerry L. Prince (Image Processing, 2016)

Combining multi-atlas segmentation with brain surface estimation. - Yuankai Huo; Aaron Carass; Susan M. Resnick; Dzung L. Pham; Jerry L. Prince; Bennett A. Landman (Image Processing, 2016)

Consistent cortical reconstruction and multi-atlas brain segmentation. - Yuankai Huo; Andrew J. Plassard; Aaron Carass; Susan M. Resnick; Dzung L. Pham; Jerry L. Prince; Bennett A. Landman (NeuroImage, 2016)

Automatic falx cerebri and tentorium cerebelli segmentation from magnetic resonance images. - Jeffrey Glaister; Aaron Carass; Dzung L. Pham; John A. Butman; Jerry L. Prince (Biomedical Applications in Molecular, Structural, and Functional Imaging, 2017)

Whole Brain Parcellation with Pathology: Validation on Ventriculomegaly Patients. - Aaron Carass; Muhan Shao; Xiang Li 063; Blake Dewey; Ari Blitz; Snehashis Roy; Dzung L. Pham; Jerry L. Prince; Lotta Maria Ellingsen (Patch-MI@MICCAI, 2017)

Joint Intensity Fusion Image Synthesis Applied to Multiple Sclerosis Lesion Segmentation. - Greg M. Fleishman; Alessandra Valcarcel; Dzung L. Pham; Snehashis Roy; Peter A. Calabresi; Paul A. Yushkevich; Russell T. Shinohara; Ipek Oguz (BrainLes@MICCAI, 2017)

Falx Cerebri Segmentation via Multi-atlas Boundary Fusion. - Jeffrey Glaister; Aaron Carass; Dzung L. Pham; John A. Butman; Jerry L. Prince (MICCAI (1), 2017)

Dice Overlap Measures for Objects of Unknown Number: Application to Lesion Segmentation. - Ipek Oguz; Aaron Carass; Dzung L. Pham; Snehashis Roy; Nagesh Subbana; Peter A. Calabresi; Paul A. Yushkevich; Russell T. Shinohara; Jerry L. Prince (BrainLes@MICCAI, 2017)

Synthesizing CT from Ultrashort Echo-Time MR Images via Convolutional Neural Networks. - Snehashis Roy; John A. Butman; Dzung L. Pham (SASHIMI@MICCAI, 2017)

Random forest regression for magnetic resonance image synthesis. - Amod Jog; Aaron Carass; Snehashis Roy; Dzung L. Pham; Jerry L. Prince (Medical Image Anal., 2017)

Robust skull stripping using multiple MR image contrasts insensitive to pathology. - Snehashis Roy; John A. Butman; Dzung L. Pham (NeuroImage, 2017)

Phase Vector Incompressible Registration Algorithm for Motion Estimation From Tagged Magnetic Resonance Images. - Fangxu Xing; Jonghye Woo; Arnold D. Gomez; Dzung L. Pham; Philip V. Bayly; Maureen L. Stone; Jerry L. Prince (IEEE Trans. Medical Imaging, 2017)

Deep learning of resting state networks from independent component analysis. - Yi-Yu Chou; Snehashis Roy; Catie Chang; John A. Butman; Dzung L. Pham (ISBI, 2018)

TBI contusion segmentation from MRI using convolutional neural networks. - Snehashis Roy; John A. Butman; Leighton Chan; Dzung L. Pham (ISBI, 2018)

A deep learning framework for brain extraction in humans and animals with traumatic brain injury. - Snehashis Roy; Andrew K. Knutsen; Alexandru Korotcov; Asamoah Bosomtwi; Bernard Dardzinski; John A. Butman; Dzung L. Pham (ISBI, 2018)

Alternating segmentation and simulation for contrast adaptive tissue classification. - Dzung L. Pham; Snehashis Roy (Biomedical Applications in Molecular, Structural, and Functional Imaging, 2018)

Classifying magnetic resonance image modalities with convolutional neural networks. - Samuel Remedios; Dzung L. Pham; John A. Butman; Snehashis Roy (Computer-Aided Diagnosis, 2018)

A Deep Learning Based Anti-aliasing Self Super-Resolution Algorithm for MRI. - Can Zhao 001; Aaron Carass; Blake E. Dewey; Jonghye Woo; Jiwon Oh; Peter A. Calabresi; Daniel S. Reich; Pascal Sati; Dzung L. Pham; Jerry L. Prince (MICCAI (1), 2018)

Multiple Sclerosis Lesion Segmentation from Brain MRI via Fully Convolutional Neural Networks. - Snehashis Roy; John A. Butman; Daniel S. Reich; Peter A. Calabresi; Dzung L. Pham (CoRR, 2018)

Cascaded convolutional neural networks for spine chordoma tumor segmentation from MRI. - Syed M. S. Reza; Snehashis Roy; Deric M. Park; Dzung L. Pham; John A. Butman (Biomedical Applications in Molecular, Structural, and Functional Imaging, 2019)

Distributed deep learning for robust multi-site segmentation of CT imaging after traumatic brain injury. - Samuel Remedios; Snehashis Roy; Justin A. Blaber; Camilo Bermudez; Vishwesh Nath; Mayur B. Patel; John A. Butman; Bennett A. Landman; Dzung L. Pham (Image Processing, 2019)

3-D Measurements of Acceleration-Induced Brain Deformation via Harmonic Phase Analysis and Finite-Element Models. - Arnold D. Gomez; Andrew K. Knutsen; Fangxu Xing; Yuan-Chiao Lu; Deva Chan; Dzung L. Pham; Philip V. Bayly; Jerry L. Prince (IEEE Trans. Biomed. Eng., 2019)

Contrast Adaptive Tissue Classification by Alternating Segmentation and Synthesis. - Dzung L. Pham; Yi-Yu Chou; Blake E. Dewey; Daniel S. Reich; John A. Butman; Snehashis Roy (SASHIMI@MICCAI, 2020)

Federated Gradient Averaging for Multi-Site Training with Momentum-Based Optimizers. - Samuel W. Remedios; John A. Butman; Bennett A. Landman; Dzung L. Pham (DART/DCL@MICCAI, 2020)

AdaBoosted Deep Ensembles: Getting Maximum Performance Out of Small Training Datasets. - Syed M. S. Reza; John A. Butman; Deric M. Park; Dzung L. Pham; Snehashis Roy (MLMI@MICCAI, 2020)

Extracting 2D weak labels from volume labels using multiple instance learning in CT hemorrhage detection. - Samuel Remedios; Zihao Wu 003; Camilo Bermudez; Cailey I. Kerley; Snehashis Roy; Mayur B. Patel; John A. Butman; Bennett A. Landman; Dzung L. Pham (Image Processing, 2020)

Joint Image and Label Self-super-Resolution. - Samuel W. Remedios; Shuo Han 001; Blake E. Dewey; Dzung L. Pham; Jerry L. Prince; Aaron Carass (SASHIMI@MICCAI, 2021)

SMORE: A Self-Supervised Anti-Aliasing and Super-Resolution Algorithm for MRI Using Deep Learning. - Can Zhao 001; Blake E. Dewey; Dzung L. Pham; Peter A. Calabresi; Daniel S. Reich; Jerry L. Prince (IEEE Trans. Medical Imaging, 2021)

Relationship between cerebral vasculature and brain stiffness measured using MR elastography. - Ahmed Alshareef; Curtis L. Johnson; Aaron Carass; Andrew K. Knutsen; Peyton L. Delgorio; Grace McIlvain; Alexa M. Diano; K. T. Ramesh; Philip V. Bayly; Dzung L. Pham; Jerry L. Prince (Biomedical Applications in Molecular, Structural, and Functional Imaging, 2022)

Multiple Sclerosis brain lesion segmentation with different architecture ensembles. - Pouria Tohidi; Samuel W. Remedios; Danielle L. Greenman; Muhan Shao; Shuo Han 001; Blake E. Dewey; Jacob C. Reinhold; Yi-Yu Chou; Dzung L. Pham; Jerry L. Prince; Aaron Carass (Biomedical Applications in Molecular, Structural, and Functional Imaging, 2022)

Deep Filter Bank Regression for Super-Resolution of Anisotropic MR Brain Images. - Samuel W. Remedios; Shuo Han 001; Yuan Xue 002; Aaron Carass; Trac D. Tran; Dzung L. Pham; Jerry L. Prince (MICCAI (6), 2022)

Bi-directional Synthesis of Pre- and Post-contrast MRI via Guided Feature Disentanglement. - Yuan Xue 002; Blake E. Dewey; Lianrui Zuo; Shuo Han 001; Aaron Carass; Peiyu Duan; Samuel W. Remedios; Dzung L. Pham; Shiv Saidha; Peter A. Calabresi; Jerry L. Prince (SASHIMI@MICCAI, 2022)

Automatic classification of MRI contrasts using a deep Siamese network and one-shot learning. - Yi-Yu Chou; Samuel W. Remedios; John A. Butman; Dzung L. Pham (Image Processing, 2022)

Self-Supervised Super-Resolution for Anisotropic MR Images with and Without Slice Gap. - Samuel W. Remedios; Shuo Han 001; Lianrui Zuo; Aaron Carass; Dzung L. Pham; Jerry L. Prince; Blake E. Dewey (SASHIMI@MICCAI, 2023)

A deep generative prior for high-resolution isotropic MR head slices. - Samuel W. Remedios; Blake E. Dewey; Aaron Carass; Dzung L. Pham; Jerry L. Prince (Image Processing, 2023)

Towards an Accurate and Generalizable Multiple Sclerosis Lesion Segmentation Model Using Self-Ensembled Lesion Fusion. - Jinwei Zhang; Lianrui Zuo; Blake E. Dewey; Samuel W. Remedios; Dzung L. Pham; Aaron Carass; Jerry L. Prince (ISBI, 2024)

Is Registering Raw Tagged-MR Enough for Strain Estimation in the Era of Deep Learning? - Zhangxing Bian; Ahmed Alshareef; Shuwen Wei; Junyu Chen 002; Yuli Wang; Jonghye Woo; Dzung L. Pham; Jiachen Zhuo; Aaron Carass; Jerry L. Prince (CoRR, 2024)

Brightness-Invariant Tracking Estimation in Tagged MRI. - Zhangxing Bian; Shuwen Wei; Xiao Liang; Yuan-Chiao Lu; Samuel W. Remedios; Fangxu Xing; Jonghye Woo; Dzung L. Pham; Aaron Carass; Philip V. Bayly; Jiachen Zhuo; Ahmed Alshareef; et al. (IPMI (2), 2025)

ECLARE: Efficient cross-planar learning for anisotropic resolution enhancement. - Samuel W. Remedios; Shuwen Wei; Shuo Han 001; Jinwei Zhang; Aaron Carass; Kurt G. Schilling; Dzung L. Pham; Jerry L. Prince; Blake E. Dewey (CoRR, 2025)