Segmentation, Registration and Measurement of Shape Variation via Image Object Shape. - Stephen M. Pizer; Daniel S. Fritsch; Paul A. Yushkevich; Valen E. Johnson; Edward L. Chaney (IEEE Trans. Medical Imaging, 1999)

Intuitive, Localized Analysis of Shape Variability. - Paul A. Yushkevich; Stephen M. Pizer; Sarang C. Joshi; J. S. Marron (IPMI, 2001)

Multi-scale Deformable Model Segmentation and Statistical Shape Analysis Using Medial Descriptions. - Sarang C. Joshi; Stephen M. Pizer; P. Thomas Fletcher; Paul A. Yushkevich; Andrew Thall; J. S. Marron (IEEE Trans. Medical Imaging, 2002)

Feature Selection for Shape-Based Classification of Biological Objects. - Paul A. Yushkevich; Sarang C. Joshi; Stephen M. Pizer; John G. Csernansky; Lei E. Wang (IPMI, 2003)

Deformable M-Reps for 3D Medical Image Segmentation. - Stephen M. Pizer; P. Thomas Fletcher; Sarang C. Joshi; Andrew Thall; James Z. Chen; Yonatan Fridman; Daniel S. Fritsch; A. Graham Gash; John M. Glotzer; Michael R. Jiroutek; Conglin Lu; Keith E. Muller; et al. (Int. J. Comput. Vis., 2003)

Continuous medial representations for geometric object modeling in 2D and 3D. - Paul A. Yushkevich; P. Thomas Fletcher; Sarang C. Joshi; Andrew Thall; Stephen M. Pizer (Image Vis. Comput., 2003)

Registration of Diffusion Tensor Images. - Hui Zhang 005; Paul A. Yushkevich; James C. Gee (CVPR (1), 2004)

Towards Diffusion Profile Image Registration. - Hui Zhang 005; Paul A. Yushkevich; James C. Gee (ISBI, 2004)

Regional Structural Characterization of the Brain of Schizophrenia Patients. - Abraham Dubb; Paul A. Yushkevich; Zhiyong Xie; Ruben C. Gur; Raquel E. Gur; James C. Gee (MICCAI (2), 2004)

Parametric Medial Shape Representation in 3-D via the Poisson Partial Differential Equation with Non-linear Boundary Conditions. - Paul A. Yushkevich; Hui Zhang 005; James C. Gee (IPMI, 2005)

An Automated Approach to Connectivity-Based Partitioning of Brain Structures. - Philip A. Cook; Hui Zhang 005; Brian B. Avants; Paul A. Yushkevich; Daniel C. Alexander; James C. Gee; Olga Ciccarelli; Alan J. Thompson (MICCAI, 2005)

Statistical Modeling of Shape and Appearance Using the Continuous Medial Representation. - Paul A. Yushkevich; Hui Zhang 005; James C. Gee (MICCAI (2), 2005)

Deformable Registration of Diffusion Tensor MR Images with Explicit Orientation Optimization. - Hui Zhang 005; Paul A. Yushkevich; James C. Gee (MICCAI, 2005)

Anatomy-Based Visualizations of Diffusion Tensor Images of Brain White Matter. - James C. Gee; Hui Zhang 005; Abraham Dubb; Brian B. Avants; Paul A. Yushkevich; Jeffrey T. Duda (Visualization and Processing of Tensor Fields, 2006)

Efficient Generation of Shape-Based Reference Frames for the Corpus Callosum for DTI-based Connectivity Analysis. - Hui Sun; Paul A. Yushkevich; Hui Zhang 005; James C. Gee; Tony J. Simon (CVPR Workshops, 2006)

Hippocampus-Specific fMRI Group Activation Analysis with Continuous M-Reps. - Paul A. Yushkevich; John A. Detre; Kathy Z. Tang; Angela Hoang; Dawn Mechanic-Hamilton; María A. Fernández-Seara; Marc Korczykowski; Hui Zhang 005; James C. Gee (MICCAI (2), 2006)

3D Mouse Brain Reconstruction from Histology Using a Coarse-to-Fine Approach. - Paul A. Yushkevich; Brian B. Avants; Lydia Ng; Michael Hawrylycz; Pablo D. Burstein; Hui Zhang 005; James C. Gee (WBIR, 2006)

Deformable registration of diffusion tensor MR images with explicit orientation optimization. - Hui Zhang 005; Paul A. Yushkevich; Daniel C. Alexander; James C. Gee (Medical Image Anal., 2006)

User-guided 3D active contour segmentation of anatomical structures: Significantly improved efficiency and reliability. - Paul A. Yushkevich; Joseph Piven; Heather Cody Hazlett; Rachel Gimpel Smith; Sean Ho; James C. Gee; Guido Gerig (NeuroImage, 2006)

Continuous Medial Representation for Anatomical Structures. - Paul A. Yushkevich; Hui Zhang 005; James C. Gee (IEEE Trans. Medical Imaging, 2006)

Structure-Specific Statistical Mapping of White Matter Tracts using the Continuous Medial Representation. - Paul A. Yushkevich; Hui Zhang 005; Tony J. Simon; James C. Gee (ICCV, 2007)

Non-Uniform Smoothing in Hippocampus-Specific Group Fmri Analysis. - Paul A. Yushkevich; John A. Detre; James C. Gee (ISBI, 2007)

Evaluation of Shape-Based Normalization in the Corpus Callosum for White Matter Connectivity Analysis. - Hui Sun; Paul A. Yushkevich; Hui Zhang 005; Philip A. Cook; Jeffrey T. Duda; Tony J. Simon; James C. Gee (MICCAI (2), 2007)

Unbiased White Matter Atlas Construction Using Diffusion Tensor Images. - Hui Zhang 005; Paul A. Yushkevich; Daniel Rueckert; James C. Gee (MICCAI (2), 2007)

Hippocampus-specific fMRI group activation analysis using the continuous medial representation. - Paul A. Yushkevich; John A. Detre; Dawn Mechanic-Hamilton; María A. Fernández-Seara; Kathy Z. Tang; Angela Hoang; Marc Korczykowski; Hui Zhang 005; James C. Gee (NeuroImage, 2007)

Neuroinformatics for Genome-Wide 3-D Gene Expression Mapping in the Mouse Brain. - Lydia Ng; Sayan D. Pathak; Chihchau Kuan; Christopher Lau; Hong-wei Dong; Andrew Sodt; Chinh Dang; Brian B. Avants; Paul A. Yushkevich; James C. Gee; David R. Haynor; Ed S. Lein; et al. (IEEE ACM Trans. Comput. Biol. Bioinform., 2007)

Shape-Based Normalization of the Corpus Callosum for DTI Connectivity Analysis. - Hui Sun; Paul A. Yushkevich; Hui Zhang 005; Philip A. Cook; Jeffrey T. Duda; Tony J. Simon; James C. Gee (IEEE Trans. Medical Imaging, 2007)

High-Dimensional Spatial Normalization of Diffusion Tensor Images Improves the Detection of White Matter Differences: An Example Study Using Amyotrophic Lateral Sclerosis. - Hui Zhang 005; Brian B. Avants; Paul A. Yushkevich; John H. Woo; Sumei Wang; L. F. McCluskey; L. B. Elman; Elias R. Melhem; James C. Gee (IEEE Trans. Medical Imaging, 2007)

Synthesis, Deformation, and Statistics of 3D Objects via M-Reps. - Stephen M. Pizer; Qiong Han; Sarang C. Joshi; P. Thomas Fletcher; Paul A. Yushkevich; Andrew Thall (Medial Representations, 2008)

Introduction. - Stephen M. Pizer; Kaleem Siddiqi; Paul A. Yushkevich (Medial Representations, 2008)

Spatial correspondence based asymmetry analysis in FMRI. - Sandhitsu R. Das; Dawn Mechanic-Hamilton; Marc Korczykowski; Brian B. Avants; John A. Detre; James C. Gee; Paul A. Yushkevich (ISBI, 2008)

Branching medial models for cardiac shape representation. - Hui Sun; Brian B. Avants; Alejandro F. Frangi; Sebastián Ordas; James C. Gee; Paul A. Yushkevich (ISBI, 2008)

Building an atlas of hippocampal subfields using postmortem MRI. - Paul A. Yushkevich; Brian B. Avants; John Pluta; David Minkoff; Stephen Pickup; Weixia Liu; John A. Detre; Murray Grossman; James C. Gee (ISBI, 2008)

Surface-based modeling of white matter fasciculi with orientation encoding. - Hui Zhang 005; Paul A. Yushkevich; Tony J. Simon; James C. Gee (ISBI, 2008)

3D Cerebral Cortical Morphometry in Autism: Increased Folding in Children and Adolescents in Frontal, Parietal, and Temporal Lobes. - Suyash P. Awate; Lawrence Win; Paul A. Yushkevich; Robert T. Schultz; James C. Gee (MICCAI (1), 2008)

Cardiac Medial Modeling and Time-Course Heart Wall Thickness Analysis. - Hui Sun; Brian B. Avants; Alejandro F. Frangi; Federico Sukno; James C. Gee; Paul A. Yushkevich (MICCAI (2), 2008)

Shape-Based Alignment of Hippocampal Subfields: Evaluation in Postmortem MRI. - Paul A. Yushkevich; Brian B. Avants; John Pluta; David Minkoff; John A. Detre; Murray Grossman; James C. Gee (MICCAI (1), 2008)

Structure-specific statistical mapping of white matter tracts. - Paul A. Yushkevich; Hui Zhang 005; Tony J. Simon; James C. Gee (NeuroImage, 2008)

Multivariate High-Dimensional Cortical Folding Analysis, Combining Complexity and Shape, in Neonates with Congenital Heart Disease. - Suyash P. Awate; Paul A. Yushkevich; Zhuang Song; Daniel J. Licht; James C. Gee (IPMI, 2009)

Ventricular Wall Thickness Analysis in Acute Myocardial Infarction and Hypertrophic Cardiomyopathy. - Hui Sun; Catalina Tobon-Gomez; Sandhitsu R. Das; Marina Huguet; Paul A. Yushkevich; Alejandro F. Frangi (ISBI, 2009)

Gender Differences in Cerebral Cortical Folding: Multivariate Complexity-Shape Analysis with Insights into Handling Brain-Volume Differences. - Suyash P. Awate; Paul A. Yushkevich; Daniel J. Licht; James C. Gee (MICCAI (1), 2009)

Tensor-Based Morphometry of Fibrous Structures with Application to Human Brain White Matter. - Hui Zhang 005; Paul A. Yushkevich; Daniel Rueckert; James C. Gee (MICCAI (1), 2009)

Continuous medial representation of brain structures using the biharmonic PDE. - Paul A. Yushkevich (NeuroImage, 2009)

A high-resolution computational atlas of the human hippocampus from postmortem magnetic resonance imaging at 9.4 T. - Paul A. Yushkevich; Brian B. Avants; John Pluta; Sandhitsu R. Das; David Minkoff; Dawn Mechanic-Hamilton; Simon Glynn; Stephen Pickup; Weixia Liu; James C. Gee; Murray Grossman; John A. Detre (NeuroImage, 2009)

Shape-based semi-automatic hippocampal subfield segmentation with learning-based bias removal. - Hongzhi Wang 002; Sandhitsu R. Das; John Pluta; Caryne Craige; Murat Altinay; Michael Weiner 001; Susanne G. Mueller; Paul A. Yushkevich (ISBI, 2010)

Automatic Cardiac MRI Segmentation Using a Biventricular Deformable Medial Model. - Hui Sun; Alejandro F. Frangi; Hongzhi Wang 002; Federico Sukno; Catalina Tobon-Gomez; Paul A. Yushkevich (MICCAI (1), 2010)

Standing on the Shoulders of Giants: Improving Medical Image Segmentation via Bias Correction. - Hongzhi Wang 002; Sandhitsu R. Das; John Pluta; Caryne Craige; Murat Altinay; Brian B. Avants; Michael Weiner 001; Susanne G. Mueller; Paul A. Yushkevich (MICCAI (3), 2010)

A Computational White Matter Atlas for Aging with Surface-Based Representation of Fasciculi. - Hui Zhang 005; Paul A. Yushkevich; Daniel Rueckert; James C. Gee (WBIR, 2010)

A tract-specific framework for white matter morphometry combining macroscopic and microscopic tract features. - Hui Zhang 005; Suyash P. Awate; Sandhitsu R. Das; John H. Woo; Elias R. Melhem; James C. Gee; Paul A. Yushkevich (Medical Image Anal., 2010)

The optimal template effect in hippocampus studies of diseased populations. - Brian B. Avants; Paul A. Yushkevich; John Pluta; David Minkoff; Marc Korczykowski; John A. Detre; James C. Gee (NeuroImage, 2010)

Cerebral cortical folding analysis with multivariate modeling and testing: Studies on gender differences and neonatal development. - Suyash P. Awate; Paul A. Yushkevich; Zhuang Song; Daniel J. Licht; James C. Gee (NeuroImage, 2010)

Bias in estimation of hippocampal atrophy using deformation-based morphometry arises from asymmetric global normalization: An illustration in ADNI 3 T MRI data. - Paul A. Yushkevich; Brian B. Avants; Sandhitsu R. Das; John Pluta; Murat Altinay; Caryne Craige (NeuroImage, 2010)

Nearly automatic segmentation of hippocampal subfields in in vivo focal T2-weighted MRI. - Paul A. Yushkevich; Hongzhi Wang 002; John Pluta; Sandhitsu R. Das; Caryne Craige; Brian B. Avants; Michael W. Weiner; Susanne G. Mueller (NeuroImage, 2010)

N4ITK: Improved N3 Bias Correction. - Nicholas J. Tustison; Brian B. Avants; Philip A. Cook; Yuanjie Zheng; Alexander Egan; Paul A. Yushkevich; James C. Gee (IEEE Trans. Medical Imaging, 2010)

Regression-based label fusion for multi-atlas segmentation. - Hongzhi Wang 002; Jung Wook Suh; Sandhitsu R. Das; John Pluta; Murat Altinay; Paul A. Yushkevich (CVPR, 2011)

Optimal Weights for Multi-atlas Label Fusion. - Hongzhi Wang 002; Jung Wook Suh; John Pluta; Murat Altinay; Paul A. Yushkevich (IPMI, 2011)

Hippocampus segmentation using a stable maximum likelihood classifier ensemble algorithm. - Hongzhi Wang 002; Jung Wook Suh; Sandhitsu R. Das; Murat Altinay; John Pluta; Paul A. Yushkevich (ISBI, 2011)

Heterogeneity of functional activation during memory encoding across hippocampal subfields in temporal lobe epilepsy. - Sandhitsu R. Das; Dawn Mechanic-Hamilton; John Pluta; Marc Korczykowski; John A. Detre; Paul A. Yushkevich (NeuroImage, 2011)

A learning-based wrapper method to correct systematic errors in automatic image segmentation: Consistently improved performance in hippocampus, cortex and brain segmentation. - Hongzhi Wang 002; Sandhitsu R. Das; Jung Wook Suh; Murat Altinay; John Pluta; Caryne Craige; Brian B. Avants; Paul A. Yushkevich (NeuroImage, 2011)

Spatial bias in multi-atlas based segmentation. - Hongzhi Wang 002; Paul A. Yushkevich (CVPR, 2012)

From label fusion to correspondence fusion: A new approach to unbiased groupwise registration. - Paul A. Yushkevich; Hongzhi Wang 002; John Pluta; Brian B. Avants (CVPR, 2012)

Reconstruction of the human hippocampus in 3D from histology and high-resolution ex-vivo MRI. - Daniel H. Adler; Alex Yang Liu; John Pluta; Salmon Kadivar; Sylvia Orozco; Hongzhi Wang 002; James C. Gee; Brian B. Avants; Paul A. Yushkevich (ISBI, 2012)

Dependency prior for multi-atlas label fusion. - Hongzhi Wang 002; Paul A. Yushkevich (ISBI, 2012)

Guiding Automatic Segmentation with Multiple Manual Segmentations. - Hongzhi Wang 002; Paul A. Yushkevich (MICCAI (2), 2012)

Measuring longitudinal change in the hippocampal formation from in vivo high-resolution T2-weighted MRI. - Sandhitsu R. Das; Brian B. Avants; John Pluta; Hongzhi Wang 002; Jung Wook Suh; Michael W. Weiner; Susanne G. Mueller; Paul A. Yushkevich (NeuroImage, 2012)

Multi-atlas Segmentation with Robust Label Transfer and Label Fusion. - Hongzhi Wang 002; Alison M. Pouch; Manabu Takabe; Benjamin M. Jackson; Joseph H. Gorman III; Robert C. Gorman; Paul A. Yushkevich (IPMI, 2013)

Deformable Modeling Using a 3D Boundary Representation with Quadratic Constraints on the Branching Structure of the Blum Skeleton. - Paul A. Yushkevich; Hui Gary Zhang (IPMI, 2013)

Automated Segmentation and Geometrical Modeling of the Tricuspid Aortic Valve in 3D Echocardiographic Images. - Alison M. Pouch; Hongzhi Wang 002; Manabu Takabe; Benjamin M. Jackson; Chandra M. Sehgal; Joseph H. Gorman III; Robert C. Gorman; Paul A. Yushkevich (MICCAI (1), 2013)

Groupwise Segmentation with Multi-atlas Joint Label Fusion. - Hongzhi Wang 002; Paul A. Yushkevich (MICCAI (1), 2013)

Multi-atlas Segmentation without Registration: A Supervoxel-Based Approach. - Hongzhi Wang 002; Paul A. Yushkevich (MICCAI (3), 2013)

Multi-atlas segmentation with joint label fusion and corrective learning - an open source implementation. - Hongzhi Wang 002; Paul A. Yushkevich (Frontiers Neuroinformatics, 2013)

Multi-Atlas Segmentation with Joint Label Fusion. - Hongzhi Wang 002; Jung Wook Suh; Sandhitsu R. Das; John Pluta; Caryne Craige; Paul A. Yushkevich (IEEE Trans. Pattern Anal. Mach. Intell., 2013)

Segmentation of the Aortic Valve Apparatus in 3D Echocardiographic Images: Deformable Modeling of a Branching Medial Structure. - Alison M. Pouch; Sijie Tian; Manabu Takabe; Hongzhi Wang 002; Jiefu Yuan; Albert T. Cheung; Benjamin M. Jackson; Joseph H. Gorman III; Robert C. Gorman; Paul A. Yushkevich (STACOM, 2014)

Automatic Clustering and Thickness Measurement of Anatomical Variants of the Human Perirhinal Cortex. - Long Xie; John Pluta; Hongzhi Wang 002; Sandhitsu R. Das; Lauren Mancuso; Dasha Kliot; Brian B. Avants; Song-Lin Ding; David A. Wolk; Paul A. Yushkevich (MICCAI (3), 2014)

Fully automatic segmentation of the mitral leaflets in 3D transesophageal echocardiographic images using multi-atlas joint label fusion and deformable medial modeling. - Alison M. Pouch; Hongzhi Wang 002; Manabu Takabe; Benjamin M. Jackson; Joseph H. Gorman III; Robert C. Gorman; Paul A. Yushkevich; Chandra M. Sehgal (Medical Image Anal., 2014)

Histology-derived volumetric annotation of the human hippocampal subfields in postmortem MRI. - Daniel H. Adler; John Pluta; Salmon Kadivar; Caryne Craige; James C. Gee; Brian B. Avants; Paul A. Yushkevich (NeuroImage, 2014)

Multi-atlas label fusion with augmented atlases for fast and accurate segmentation of cardiac MR images. - Long Xie; Suman Sedai; Xi Liang 001; Colin B. Compas; Hongzhi Wang 002; Paul A. Yushkevich; Tanveer F. Syeda-Mahmood (ISBI, 2015)

Medially constrained deformable modeling for segmentation of branching medial structures: Application to aortic valve segmentation and morphometry. - Alison M. Pouch; Sijie Tian; Manabu Takabe; Jiefu Yuan; Robert C. Gorman Jr.; Albert T. Cheung; Hongzhi Wang 002; Benjamin M. Jackson; Joseph H. Gorman III; Robert C. Gorman; Paul A. Yushkevich (Medical Image Anal., 2015)

Assessing atrophy measurement techniques in dementia: Results from the MIRIAD atrophy challenge. - David M. Cash; Chris Frost 001; Leonardo O. Iheme; Devrim Ünay; Melek Kandemir; Jurgen Fripp; Olivier Salvado; Pierrick Bourgeat; Martin Reuter 001; Bruce Fischl; Marco Lorenzi; Giovanni B. Frisoni; et al. (NeuroImage, 2015)

Quantitative comparison of 21 protocols for labeling hippocampal subfields and parahippocampal subregions in in vivo MRI: Towards a harmonized segmentation protocol. - Paul A. Yushkevich; Robert S. C. Amaral; Jean C. Augustinack; Andrew R. Bender; Jeffrey D. Bernstein; Marina Boccardi; Martina Bocchetta; Alison C. Burggren; Valerie A. Carr; M. Mallar Chakravarty; Gaël Chételat; Ana M. Daugherty; et al. (NeuroImage, 2015)

ITK-SNAP: An interactive tool for semi-automatic segmentation of multi-modality biomedical images. - Paul A. Yushkevich; Yang Gao 031; Guido Gerig (EMBC, 2016)

A framework for informing segmentation of in vivo MRI with information derived from ex vivo imaging: Application in the medial temporal lobe. - Paul A. Yushkevich; Laura E. M. Wisse; Daniel H. Adler; Ranjit Ittyerah; John Pluta; John L. Robinson; Theresa Schuck; John Q. Trojanowski; Murray Grossman; John A. Detre; Mark A. Elliott; Jon B. Toledo; et al. (EMBC, 2016)

Probabilistic Atlas of the Human Hippocampus Combining Ex Vivo MRI and Histology. - Daniel H. Adler; Ranjit Ittyerah; John Pluta; Stephen Pickup; Weixia Liu; David A. Wolk; Paul A. Yushkevich (MICCAI (3), 2016)

Globally Optimal Label Fusion with Shape Priors. - Ipek Oguz; Satyananda Kashyap; Hongzhi Wang 002; Paul A. Yushkevich; Milan Sonka (MICCAI (2), 2016)

Accounting for the Confound of Meninges in Segmenting Entorhinal and Perirhinal Cortices in T1-Weighted MRI. - Long Xie; Laura E. M. Wisse; Sandhitsu R. Das; Hongzhi Wang 002; David A. Wolk; José V. Manjón; Paul A. Yushkevich (MICCAI (2), 2016)

Supervoxel-Based Hierarchical Markov Random Field Framework for Multi-atlas Segmentation. - Ning Yu; Hongzhi Wang 002; Paul A. Yushkevich (Patch-MI@MICCAI, 2016)

Image Segmentation and Modeling of the Pediatric Tricuspid Valve in Hypoplastic Left Heart Syndrome. - Alison M. Pouch; Ahmed H. Aly; Andras Lasso; Alexander V. Nguyen; Adam B. Scanlan; Francis X. McGowan; Gabor Fichtinger; Robert C. Gorman; Joseph H. Gorman III; Paul A. Yushkevich; Matthew A. Jolley (FIMH, 2017)

Multiple Sclerosis Lesion Segmentation Using Joint Label Fusion. - Mengjin Dong; Ipek Oguz; Nagesh Subbana; Peter A. Calabresi; Russell T. Shinohara; Paul A. Yushkevich (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)

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)

Gradient Boosted Trees for Corrective Learning. - Baris U. Oguz; Russell T. Shinohara; Paul A. Yushkevich; Ipek Oguz (MLMI@MICCAI, 2017)

Spatiotemporal Segmentation and Modeling of the Mitral Valve in Real-Time 3D Echocardiographic Images. - Alison M. Pouch; Ahmed H. Aly; Eric Lai; Natalie Yushkevich; Rutger H. Stoffers; Joseph H. Gorman IV; Albert T. Cheung; Joseph H. Gorman III; Robert C. Gorman; Paul A. Yushkevich (MICCAI (1), 2017)

A tract-specific approach to assessing white matter in preterm infants. - Diliana Pecheva; Paul A. Yushkevich; Dafnis Batalle; Emer J. Hughes; Paul Aljabar; Julia Wurie; Joseph V. Hajnal; A. David Edwards; Daniel C. Alexander; Serena J. Counsell; Hui Zhang 005 (NeuroImage, 2017)

Multi-template analysis of human perirhinal cortex in brain MRI: Explicitly accounting for anatomical variability. - Long Xie; John Pluta; Sandhitsu R. Das; Laura E. M. Wisse; Hongzhi Wang 002; Lauren Mancuso; Dasha Kliot; Brian B. Avants; Song-Lin Ding; José V. Manjón; David A. Wolk; Paul A. Yushkevich (NeuroImage, 2017)

Semi-automated Image Segmentation of the Midsystolic Left Ventricular Mitral Valve Complex in Ischemic Mitral Regurgitation. - Ahmed H. Aly; Abdullah H. Aly; Mahmoud Elrakhawy; Kirlos Haroun; Luis Prieto-Riascos; Robert C. Gorman Jr.; Natalie Yushkevich; Yoshiaki Saito; Joseph H. Gorman III; Robert C. Gorman; Paul A. Yushkevich; Alison M. Pouch (STACOM@MICCAI, 2018)

Combining Deep Learning and Multi-atlas Label Fusion for Automated Placenta Segmentation from 3DUS. - Baris U. Oguz; Jiancong Wang; Natalie Yushkevich; Alison M. Pouch; James C. Gee; Paul A. Yushkevich; Nadav Schwartz; Ipek Oguz (DATRA/PIPPI@MICCAI, 2018)

Characterizing Anatomical Variability and Alzheimer's Disease Related Cortical Thinning in the Medial Temporal Lobe Using Graph-Based Groupwise Registration and Point Set Geodesic Shooting. - Long Xie; Laura E. M. Wisse; Sandhitsu R. Das; Ranjit Ittyerah; Jiancong Wang; David A. Wolk; Paul A. Yushkevich (ShapeMI@MICCAI, 2018)

Characterizing the human hippocampus in aging and Alzheimer's disease using a computational atlas derived from ex vivo MRI and histology. - Daniel H. Adler; Laura E. M. Wisse; Ranjit Ittyerah; John Pluta; Song-Lin Ding; Long Xie; Jiancong Wang; Salmon Kadivar; John L. Robinson; Theresa Schuck; John Q. Trojanowski; Murray Grossman; et al. (Proc. Natl. Acad. Sci. USA, 2018)

The Cancer Imaging Phenomics Toolkit (CaPTk): Technical Overview. - Sarthak Pati; Ashish Singh; Saima Rathore; Aimilia Gastounioti; Mark Bergman; Phuc Ngo; Sung Min Ha; Dimitrios Bounias; James Minock; Grayson Murphy; Hongming Li; Amit Bhattarai; et al. (BrainLes@MICCAI (2), 2019)

Diffeomorphic Medial Modeling. - Paul A. Yushkevich; Ahmed H. Aly; Jiancong Wang; Long Xie; Robert C. Gorman; Laurent Younes; Alison M. Pouch (IPMI, 2019)

Facilitating Manual Segmentation of 3D Datasets Using Contour And Intensity Guided Interpolation. - Sadhana Ravikumar; Laura E. M. Wisse; Yang Gao 031; Guido Gerig; Paul A. Yushkevich (ISBI, 2019)

Improving Multi-atlas Segmentation by Convolutional Neural Network Based Patch Error Estimation. - Long Xie; Jiancong Wang; Mengjin Dong; David A. Wolk; Paul A. Yushkevich (MICCAI (3), 2019)

Accurate and Robust Alignment of Variable-stained Histologic Images Using a General-purpose Greedy Diffeomorphic Registration Tool. - Ludovic Venet; Sarthak Pati; Paul A. Yushkevich; Spyridon Bakas (CoRR, 2019)

Barnes-Hut Approximation for Point SetGeodesic Shooting. - Jiancong Wang; Long Xie; Paul A. Yushkevich; James C. Gee (CoRR, 2019)

User-Guided Segmentation of Multi-modality Medical Imaging Datasets with ITK-SNAP. - Paul A. Yushkevich; Artem Pashchinskiy; Ipek Oguz; Suyash Mohan; J. Eric Schmitt; Joel M. Stein; Dzenan Zukic; Jared Vicory; Matthew McCormick 001; Natalie Yushkevich; Nadav Schwartz; Yang Gao 031; et al. (Neuroinformatics, 2019)

Automated Meshing of Anatomical Shapes for Deformable Medial Modeling: Application to the Placenta in 3D Ultrasound. - Alison M. Pouch; Paul A. Yushkevich; Abdullah H. Aly; Alexander H. F. Woltersom; Edidiong Okon; Ahmed H. Aly; Natalie Yushkevich; Shobhana Parameshwaran; Jiancong Wang; Baris U. Oguz; James C. Gee; Ipek Oguz; et al. (ISBI, 2020)

Building an Ex Vivo Atlas of the Earliest Brain Regions Affected by Alzheimer's Disease Pathology. - Sadhana Ravikumar; Laura E. M. Wisse; Ranjit Ittyerah; Sydney Lim; Madigan Lavery; Long Xie; John L. Robinson; Theresa Schuck; Murray Grossman; Edward B. Lee; M. Dylan Tisdall; Karthik Prabhakaran; et al. (ISBI, 2020)

3D Mapping of TAU Neurofibrillary Tangle Pathology in the Human Medial Temporal Lobe. - Paul A. Yushkevich; Maria Mercedes Iñiguez de Onzoño Martin; Ranjit Ittyerah; Sydney Lim; Madigan Lavery; Jiancong Wang; Alex Ling Yu Hung; Nicolas Vergnet; Sadhana Ravikumar; Long Xie; Mengjin Dong; Robin DeFlores; et al. (ISBI, 2020)

Domain Generalizer: A Few-Shot Meta Learning Framework for Domain Generalization in Medical Imaging. - Pulkit Khandelwal; Paul A. Yushkevich (DART/DCL@MICCAI, 2020)

DeepAtrophy: Teaching a Neural Network to Differentiate Progressive Changes from Noise on Longitudinal MRI in Alzheimer's Disease. - Mengjin Dong; Long Xie; Sandhitsu R. Das; Jiancong Wang; Laura E. M. Wisse; Robin DeFlores; David A. Wolk; Paul A. Yushkevich (CoRR, 2020)

ANHIR: Automatic Non-Rigid Histological Image Registration Challenge. - Jirí Borovec; Jan Kybic; Ignacio Arganda-Carreras; Dmitry V. Sorokin; Gloria Bueno; Alexander V. Khvostikov; Spyridon Bakas; Eric I-Chao Chang; Stefan Heldmann; Kimmo Kartasalo; Leena Latonen; Johannes Lotz 002; et al. (IEEE Trans. Medical Imaging, 2020)

Deep Label Fusion: A 3D End-To-End Hybrid Multi-atlas Segmentation and Deep Learning Pipeline. - Long Xie; Laura E. M. Wisse; Jiancong Wang; Sadhana Ravikumar; Trevor Glenn; Anica Luther; Sydney Lim; David A. Wolk; Paul A. Yushkevich (IPMI, 2021)

Unfolding the Medial Temporal Lobe Cortex to Characterize Neurodegeneration Due to Alzheimer's Disease Pathology Using Ex vivo Imaging. - Sadhana Ravikumar; Laura E. M. Wisse; Sydney Lim; David J. Irwin; Ranjit Ittyerah; Long Xie; Sandhitsu R. Das; Edward B. Lee; M. Dylan Tisdall; Karthik Prabhakaran; John A. Detre; Gabor Mizsei; et al. (MLCN@MICCAI, 2021)

Deformable Image Registration using Neural ODEs. - Yifan Wu; Tom Z. Jiahao; Jiancong Wang; Paul A. Yushkevich; James C. Gee; M. Ani Hsieh (CoRR, 2021)

Gray Matter Segmentation in Ultra High Resolution 7 Tesla ex vivo T2w MRI of Human Brain Hemispheres. - Pulkit Khandelwal; Shokufeh Sadaghiani; Sadhana Ravikumar; Sydney Lim; Sanaz Arezoumandan; Claire Peterson; Eunice Chung; Madigan L. Bedard; Noah Capp; Ranjit Ittyerah; Elyse Migdal; Grace Choi; et al. (CoRR, 2021)

DeepAtrophy: Teaching a neural network to detect progressive changes in longitudinal MRI of the hippocampal region in Alzheimer's disease. - Mengjin Dong; Long Xie; Sandhitsu R. Das; Jiancong Wang; Laura E. M. Wisse; Robin DeFlores; David A. Wolk; Paul A. Yushkevich (NeuroImage, 2021)

NODEO: A Neural Ordinary Differential Equation Based Optimization Framework for Deformable Image Registration. - Yifan Wu; Tom Z. Jiahao; Jiancong Wang; Paul A. Yushkevich; M. Ani Hsieh; James C. Gee (CVPR, 2022)

Fully Automated 3D Segmentation and Diffeomorphic Medial Modeling of the Left Ventricle Mitral Valve Complex in Ischemic Mitral Regurgitation. - Ahmed H. Aly; Pulkit Khandelwal; Abdullah H. Aly; Takayuki Kawashima; Kazuki Mori; Yoshiaki Saito; Judy Hung; Joseph H. Gorman III; Alison M. Pouch; Robert C. Gorman; Paul A. Yushkevich (Medical Image Anal., 2022)

Improved Segmentation of Deep Sulci in Cortical Gray Matter Using a Deep Learning Framework Incorporating Laplace's Equation. - Sadhana Ravikumar; Ranjit Ittyerah; Sydney Lim; Long Xie; Sandhitsu R. Das; Pulkit Khandelwal; Laura E. M. Wisse; Madigan L. Bedard; John L. Robinson; Terry Schuck; Murray Grossman; John Q. Trojanowski; et al. (IPMI, 2023)

Image-to-Image Translation Between Tau Pathology and Neuronal Metabolism PET in Alzheimer Disease with Multi-domain Contrastive Learning. - Michael Tran Duong; Sandhitsu R. Das; Pulkit Khandelwal; Xueying Lyu; Long Xie; Paul A. Yushkevich; David A. Wolk; Ilya M. Nasrallah (MLCN@MICCAI, 2023)

Integrating color deconvolution thresholding and weakly supervised learning for automated segmentation of neurofibrillary tangle and neuropil threads. - Hyung S. Roh; David J. Irwin; Mónica Muñoz López; Maria Mercedes Iñiguez de Onzoño Martin; Ranjit Ittyerah; Sydney Lim; Madigan L. Bedard; John L. Robinson; Theresa Schuck; Emilio Artacho-Pérula; María del Mar Arroyo Jiménez; Maria del Pilar Marcos Rabal; et al. (Digital and Computational Pathology, 2023)

Automated deep learning segmentation of high-resolution 7 T ex vivo MRI for quantitative analysis of structure-pathology correlations in neurodegenerative diseases. - Pulkit Khandelwal; Michael Tran Duong; Shokufeh Sadaghiani; Sydney Lim; Amanda Denning; Eunice Chung; Sadhana Ravikumar; Sanaz Arezoumandan; Claire Peterson; Madigan L. Bedard; Noah Capp; Ranjit Ittyerah; et al. (CoRR, 2023)

Regional Deep Atrophy: a Self-Supervised Learning Method to Automatically Identify Regions Associated With Alzheimer's Disease Progression From Longitudinal MRI. - Mengjin Dong; Long Xie; Sandhitsu R. Das; Jiancong Wang; Laura E. M. Wisse; Robin DeFlores; David A. Wolk; Paul A. Yushkevich (CoRR, 2023)

Deep label fusion: A generalizable hybrid multi-atlas and deep convolutional neural network for medical image segmentation. - Long Xie; Laura E. M. Wisse; Jiancong Wang; Sadhana Ravikumar; Pulkit Khandelwal; Trevor Glenn; Anica Luther; Sydney Lim; David A. Wolk; Paul A. Yushkevich (Medical Image Anal., 2023)

Surface-Based Parcellation and Vertex-wise Analysis of Ultra High-resolution ex vivo 7 tesla MRI in Alzheimer's disease and related dementias. - Pulkit Khandelwal; Michael Tran Duong; Lisa Levorse; Constanza Fuentes; Amanda Denning; Winifred Trotman; Ranjit Ittyerah; Alejandra Bahena; Theresa Schuck; Marianna Gabrielyan; Karthik Prabhakaran; Daniel T. Ohm; et al. (MLCN@MICCAI, 2024)

Surface-based parcellation and vertex-wise analysis of ultra high-resolution ex vivo 7 tesla MRI in neurodegenerative diseases. - Pulkit Khandelwal; Michael Tran Duong; Constanza Fuentes; Amanda Denning; Winifred Trotman; Ranjit Ittyerah; Alejandra Bahena; Theresa Schuck; Marianna Gabrielyan; Karthik Prabhakaran; Daniel T. Ohm; Gabor Mizsei; et al. (CoRR, 2024)

Streamlining 4D Cardiac Image Workflows: Open-Source Tools for Segmentation, Registration, and Visualization. - Jilei Hao; Paul A. Yushkevich; Ningjun J. Dong; Silvani Amin; Zaiyang Guo; Natalie Yushkevich; Ankush Aggarwal; Alison M. Pouch (FIMH (2), 2025)

Nearly isotropic segmentation for medial temporal lobe subregions in multi-modality MRI. - Yue Li; Pulkit Khandelwal; Long Xie; Laura E. M. Wisse; Nidhi Mundada; Christopher A. Brown; Emily McGrew; Amanda Denning; Sandhitsu R. Das; David A. Wolk; Paul A. Yushkevich (CoRR, 2025)