C-arm calibration: is it really necessary? - Ameet Kumar Jain; Michael An; Nicha Chitphakdithai; Gouthami Chintalapani; Gabor Fichtinger (Image-Guided Procedures, 2007)

Pairwise registration of images with missing correspondences due to resection. - Nicha Chitphakdithai; James S. Duncan (ISBI, 2010)

Non-rigid Registration with Missing Correspondences in Preoperative and Postresection Brain Images. - Nicha Chitphakdithai; James S. Duncan (MICCAI (1), 2010)

Non-rigid registration of longitudinal brain tumor treatment MRI. - Nicha Chitphakdithai; Veronica L. Chiang; James S. Duncan (EMBC, 2011)

Registration of brain resection MRI with intensity and location priors. - Nicha Chitphakdithai; Kenneth P. Vives; James S. Duncan (ISBI, 2011)

Tracking Metastatic Brain Tumors in Longitudinal Scans via Joint Image Registration and Labeling. - Nicha Chitphakdithai; Veronica L. Chiang; James S. Duncan (STIA, 2012)

Identifying Autism from Resting-State fMRI Using Long Short-Term Memory Networks. - Nicha C. Dvornek; Pamela Ventola; Kevin A. Pelphrey; James S. Duncan (MLMI@MICCAI, 2017)

Combining phenotypic and resting-state fMRI data for autism classification with recurrent neural networks. - Nicha C. Dvornek; Pamela Ventola; James S. Duncan (ISBI, 2018)

2-Channel convolutional 3D deep neural network (2CC3D) for fMRI analysis: ASD classification and feature learning. - Xiaoxiao Li; Nicha C. Dvornek; Xenophon Papademetris; Juntang Zhuang; Lawrence H. Staib; Pamela Ventola; James S. Duncan (ISBI, 2018)

Prediction of Pivotal response treatment outcome with task fMRI using random forest and variable selection. - Juntang Zhuang; Nicha C. Dvornek; Xiaoxiao Li; Daniel Y.-J. Yang; Pamela Ventola; James S. Duncan (ISBI, 2018)

Learning Generalizable Recurrent Neural Networks from Small Task-fMRI Datasets. - Nicha C. Dvornek; Daniel Y.-J. Yang; Pamela Ventola; James S. Duncan (MICCAI (3), 2018)

Brain Biomarker Interpretation in ASD Using Deep Learning and fMRI. - Xiaoxiao Li; Nicha C. Dvornek; Juntang Zhuang; Pamela Ventola; James S. Duncan (MICCAI (3), 2018)

Prediction of Severity and Treatment Outcome for ASD from fMRI. - Juntang Zhuang; Nicha C. Dvornek; Xiaoxiao Li; Pamela Ventola; James S. Duncan (PRIME@MICCAI, 2018)

Prediction of Autism Treatment Response from Baseline fMRI using Random Forests and Tree Bagging. - Nicha C. Dvornek; Daniel Y.-J. Yang; Archana Venkataraman; Pamela Ventola; Lawrence H. Staib; Kevin A. Pelphrey; James S. Duncan (CoRR, 2018)

Domain-Agnostic Learning With Anatomy-Consistent Embedding for Cross-Modality Liver Segmentation. - Junlin Yang; Nicha C. Dvornek; Fan Zhang 009; Juntang Zhuang; Julius Chapiro; Ming De Lin; James S. Duncan (ICCV Workshops, 2019)

Decision explanation and feature importance for invertible networks. - Juntang Zhuang; Nicha C. Dvornek; Xiaoxiao Li; Junlin Yang; James S. Duncan (ICCV Workshops, 2019)

ShelfNet for Fast Semantic Segmentation. - Juntang Zhuang; Junlin Yang; Lin Gu 003; Nicha C. Dvornek (ICCV Workshops, 2019)

Efficient Interpretation of Deep Learning Models Using Graph Structure and Cooperative Game Theory: Application to ASD Biomarker Discovery. - Xiaoxiao Li; Nicha C. Dvornek; Yuan Zhou 004; Juntang Zhuang; Pamela Ventola; James S. Duncan (IPMI, 2019)

Prediction of Treatment Outcome for Autism from Structure of the Brain Based On Sure Independence Screening. - Juntang Zhuang; Nicha C. Dvornek; Qingyu Zhao; Xiaoxiao Li; Pamela Ventola; James S. Duncan (ISBI, 2019)

Jointly Discriminative and Generative Recurrent Neural Networks for Learning from fMRI. - Nicha C. Dvornek; Xiaoxiao Li; Juntang Zhuang; James S. Duncan (MLMI@MICCAI, 2019)

Graph Neural Network for Interpreting Task-fMRI Biomarkers. - Xiaoxiao Li; Nicha C. Dvornek; Yuan Zhou 004; Juntang Zhuang; Pamela Ventola; James S. Duncan (MICCAI (5), 2019)

Unsupervised Domain Adaptation via Disentangled Representations: Application to Cross-Modality Liver Segmentation. - Junlin Yang; Nicha C. Dvornek; Fan Zhang 009; Julius Chapiro; Ming De Lin; James S. Duncan (MICCAI (2), 2019)

Invertible Network for Classification and Biomarker Selection for ASD. - Juntang Zhuang; Nicha C. Dvornek; Xiaoxiao Li; Pamela Ventola; James S. Duncan (MICCAI (3), 2019)

Hepatocellular Carcinoma Intra-arterial Treatment Response Prediction for Improved Therapeutic Decision-Making. - Junlin Yang; Nicha C. Dvornek; Fan Zhang 009; Julius Chapiro; Ming De Lin; Aaron Abajian; James S. Duncan (CoRR, 2019)

Adaptive Checkpoint Adjoint Method for Gradient Estimation in Neural ODE. - Juntang Zhuang; Nicha C. Dvornek; Xiaoxiao Li; Sekhar Tatikonda; Xenophon Papademetris; James S. Duncan (ICML, 2020)

Estimating Reproducible Functional Networks Associated with Task Dynamics Using Unsupervised LSTMS. - Nicha C. Dvornek; Pamela Ventola; James S. Duncan (ISBI, 2020)

Graph embedding using Infomax for ASD classification and brain functional difference detection. - Xiaoxiao Li; Nicha C. Dvornek; Juntang Zhuang; Pamela Ventola; James S. Duncan (Biomedical Applications in Molecular, Structural, and Functional Imaging, 2020)

Demographic-Guided Attention in Recurrent Neural Networks for Modeling Neuropathophysiological Heterogeneity. - Nicha C. Dvornek; Xiaoxiao Li; Juntang Zhuang; Pamela Ventola; James S. Duncan (MLMI@MICCAI, 2020)

Efficient Shapley Explanation for Features Importance Estimation Under Uncertainty. - Xiaoxiao Li; Yuan Zhou 004; Nicha C. Dvornek; Yufeng Gu; Pamela Ventola; James S. Duncan (MICCAI (1), 2020)

Pooling Regularized Graph Neural Network for fMRI Biomarker Analysis. - Xiaoxiao Li; Yuan Zhou 004; Nicha C. Dvornek; Muhan Zhang; Juntang Zhuang; Pamela Ventola; James S. Duncan (MICCAI (7), 2020)

Cross-Modality Segmentation by Self-supervised Semantic Alignment in Disentangled Content Space. - Junlin Yang; Xiaoxiao Li; Daniel H. Pak; Nicha C. Dvornek; Julius Chapiro; Ming De Lin; James S. Duncan (DART/DCL@MICCAI, 2020)

AdaBelief Optimizer: Adapting Stepsizes by the Belief in Observed Gradients. - Juntang Zhuang; Tommy Tang; Yifan Ding; Sekhar Tatikonda; Nicha C. Dvornek; Xenophon Papademetris; James S. Duncan (NeurIPS, 2020)

Neuropsychiatric Disease Classification Using Functional Connectomics - Results of the Connectomics in NeuroImaging Transfer Learning Challenge. - Markus D. Schirmer; Archana Venkataraman; Islem Rekik; Minjeong Kim; Stewart Mostofsky; Mary Beth Nebel; Keri Rosch; Karen Seymour; Deana Crocetti; Hassna Irzan; Michael Hütel; Sébastien Ourselin; et al. (CoRR, 2020)

Multi-site fMRI analysis using privacy-preserving federated learning and domain adaptation: ABIDE results. - Xiaoxiao Li; Yufeng Gu; Nicha C. Dvornek; Lawrence H. Staib; Pamela Ventola; James S. Duncan (Medical Image Anal., 2020)

Layer Embedding Analysis in Convolutional Neural Networks for Improved Probability Calibration and Classification. - Fan Zhang 009; Nicha C. Dvornek; Junlin Yang; Julius Chapiro; Jim Duncan 001 (IEEE Trans. Medical Imaging, 2020)

MALI: A memory efficient and reverse accurate integrator for Neural ODEs. - Juntang Zhuang; Nicha C. Dvornek; Sekhar Tatikonda; James S. Duncan (ICLR, 2021)

Multiple-Shooting Adjoint Method for Whole-Brain Dynamic Causal Modeling. - Juntang Zhuang; Nicha C. Dvornek; Sekhar Tatikonda; Xenophon Papademetris; Pamela Ventola; James S. Duncan (IPMI, 2021)

A Metamodel Structure For Regression Analysis: Application To Prediction Of Autism Spectrum Disorder Severity. - Shiyu Wang; Nicha C. Dvornek (ISBI, 2021)

Momentum Centering and Asynchronous Update for Adaptive Gradient Methods. - Juntang Zhuang; Yifan Ding; Tommy Tang; Nicha C. Dvornek; Sekhar Tatikonda; James S. Duncan (NeurIPS, 2021)

BrainGNN: Interpretable Brain Graph Neural Network for fMRI Analysis. - Xiaoxiao Li; Yuan Zhou 004; Nicha C. Dvornek; Muhan Zhang; Siyuan Gao; Juntang Zhuang; Dustin Scheinost; Lawrence H. Staib; Pamela Ventola; James S. Duncan (Medical Image Anal., 2021)

Neuropsychiatric disease classification using functional connectomics - results of the connectomics in neuroimaging transfer learning challenge. - Markus D. Schirmer; Archana Venkataraman; Islem Rekik; Minjeong Kim; Stewart H. Mostofsky; Mary Beth Nebel; Keri Rosch; Karen Seymour; Deana Crocetti; Hassna Irzan; Michael Hütel; Sébastien Ourselin; et al. (Medical Image Anal., 2021)

Automatic Inter-Frame Patient Motion Correction for Dynamic Cardiac PET Using Deep Learning. - Luyao Shi; Yihuan Lu; Nicha C. Dvornek; Christopher A. Weyman; Edward J. Miller; Albert J. Sinusas; Chi Liu 001 (IEEE Trans. Medical Imaging, 2021)

Surrogate Gap Minimization Improves Sharpness-Aware Training. - Juntang Zhuang; Boqing Gong; Liangzhe Yuan; Yin Cui; Hartwig Adam; Nicha C. Dvornek; Sekhar Tatikonda; James S. Duncan; Ting Liu 005 (ICLR, 2022)

MCP-Net: Inter-frame Motion Correction with Patlak Regularization for Whole-body Dynamic PET. - Xueqi Guo; Bo Zhou 009; Xiongchao Chen; Chi Liu 001; Nicha C. Dvornek (MICCAI (4), 2022)

Early Disease Stage Characterization in Parkinson's Disease from Resting-state fMRI Data Using a Long Short-term Memory Network. - Xueqi Guo; Sule Tinaz; Nicha C. Dvornek (CoRR, 2022)

Unsupervised inter-frame motion correction for whole-body dynamic PET using convolutional long short-term memory in a convolutional neural network. - Xueqi Guo; Bo Zhou 009; David Pigg; Bruce Spottiswoode; Michael E. Casey; Chi Liu 001; Nicha C. Dvornek (Medical Image Anal., 2022)

Copy Number Variation Informs fMRI-Based Prediction of Autism Spectrum Disorder. - Nicha C. Dvornek; Catherine Sullivan; James S. Duncan; Abha R. Gupta (MLCN@MICCAI, 2023)

TAI-GAN: Temporally and Anatomically Informed GAN for Early-to-Late Frame Conversion in Dynamic Cardiac PET Motion Correction. - Xueqi Guo; Luyao Shi; Xiongchao Chen; Bo Zhou 009; Qiong Liu; Huidong Xie; Yi-Hwa Liu; Richard Palyo; Edward J. Miller; Albert J. Sinusas; Bruce Spottiswoode; Chi Liu 001; et al. (SASHIMI@MICCAI, 2023)

Learning Sequential Information in Task-Based fMRI for Synthetic Data Augmentation. - Jiyao Wang; Nicha C. Dvornek; Lawrence H. Staib; James S. Duncan (MLCN@MICCAI, 2023)

FedNI: Federated Graph Learning With Network Inpainting for Population-Based Disease Prediction. - Liang Peng; Nan Wang; Nicha C. Dvornek; Xiaofeng Zhu 001; Xiaoxiao Li (IEEE Trans. Medical Imaging, 2023)

MCP-Net: Introducing Patlak Loss Optimization to Whole-Body Dynamic PET Inter-Frame Motion Correction. - Xueqi Guo; Bo Zhou 009; Xiongchao Chen; Ming-Kai Chen; Chi Liu 001; Nicha C. Dvornek (IEEE Trans. Medical Imaging, 2023)

SIFT-DBT: Self-Supervised Initialization and Fine-Tuning for Imbalanced Digital Breast Tomosynthesis Image Classification. - Yuexi Du; Regina J. Hooley; John Lewin; Nicha C. Dvornek (ISBI, 2024)

Spectral Brain Graph Neural Network for Prediction of Anxiety in Children with Autism Spectrum Disorder. - Peiyu Duan; Nicha C. Dvornek; Jiyao Wang; Jeffrey Eilbott; Yuexi Du; Denis G. Sukhodolsky; James S. Duncan (ISBI, 2024)

CLEFT: Language-Image Contrastive Learning with Efficient Large Language Model and Prompt Fine-Tuning. - Yuexi Du; Brian Chang; Nicha C. Dvornek (MICCAI (12), 2024)

Self-supervised Pre-training Tasks for an fMRI Time-Series Transformer in Autism Detection. - Yinchi Zhou; Peiyu Duan; Yuexi Du; Nicha C. Dvornek (MLCN@MICCAI, 2024)

Prior knowledge-guided vision-transformer-based unsupervised domain adaptation for intubation prediction in lung disease at one week. - Junlin Yang; John Anderson Garcia Henao; Nicha C. Dvornek; Jianchun He; Danielle V. Bower; Arno Depotter; Herkus Bajercius; Aurélie Pahud de Mortanges; Chenyu You; Christopher Gange; Roberta Eufrasia Ledda; Mario Silva; et al. (Comput. Medical Imaging Graph., 2024)

STNAGNN: Spatiotemporal Node Attention Graph Neural Network for Task-based fMRI Analysis. - Jiyao Wang; Nicha C. Dvornek; Peiyu Duan; Lawrence H. Staib; Pamela Ventola; James S. Duncan (CoRR, 2024)

TAI-GAN: A Temporally and Anatomically Informed Generative Adversarial Network for early-to-late frame conversion in dynamic cardiac PET inter-frame motion correction. - Xueqi Guo; Luyao Shi; Xiongchao Chen; Qiong Liu; Bo Zhou 009; Huidong Xie; Yi-Hwa Liu; Richard Palyo; Edward J. Miller; Albert J. Sinusas; Lawrence H. Staib; Bruce Spottiswoode; et al. (Medical Image Anal., 2024)

Cascaded Multi-path Shortcut Diffusion Model for Medical Image Translation. - Yinchi Zhou; Tianqi Chen; Jun Hou; Huidong Xie; Nicha C. Dvornek; S. Kevin Zhou; David L. Wilson; James S. Duncan; Chi Liu 001; Bo Zhou 009 (Medical Image Anal., 2024)

Mine yOur owN Anatomy: Revisiting Medical Image Segmentation With Extremely Limited Labels. - Chenyu You; Weicheng Dai; Fenglin Liu; Yifei Min; Nicha C. Dvornek; Xiaoxiao Li; David A. Clifton; Lawrence H. Staib; James S. Duncan (IEEE Trans. Pattern Anal. Mach. Intell., 2024)

Multi-view and Multi-scale Alignment for Contrastive Language-Image Pre-training in Mammography. - Yuexi Du; John A. Onofrey; Nicha C. Dvornek (IPMI (2), 2025)

SRE-CONV: Symmetric Rotation Equivariant Convolution for Biomedical Image Classification. - Yuexi Du; Jiazhen Zhang; Tal Zeevi; Nicha C. Dvornek; John A. Onofrey (ISBI, 2025)

Causal Modeling of FMRI Time-Series for Interpretable Autism Spectrum Disorder Classification. - Peiyu Duan; Nicha C. Dvornek; Jiyao Wang; Lawrence H. Staib; James S. Duncan (ISBI, 2025)

Towards Zero-Shot Task-Generalizable Learning on FMRI. - Jiyao Wang; Nicha C. Dvornek; Peiyu Duan; Lawrence H. Staib; James S. Duncan (ISBI, 2025)

Improved Vessel Segmentation with Symmetric Rotation-Equivariant U-Net. - Jiazhen Zhang; Yuexi Du; Nicha C. Dvornek; John A. Onofrey (ISBI, 2025)

Style mixup enhanced disentanglement learning for unsupervised domain adaptation in medical image segmentation. - Zhuotong Cai; Jingmin Xin; Chenyu You; Peiwen Shi; Siyuan Dong; Nicha C. Dvornek; Nanning Zheng 001; James S. Duncan (Medical Image Anal., 2025)

CXR-LT 2024: A MICCAI challenge on long-tailed, multi-label, and zero-shot disease classification from chest X-ray. - Mingquan Lin; Gregory Holste; Song Wang 026; Yiliang Zhou; Yishu Wei; Imon Banerjee; Pengyi Chen; Tianjie Dai; Yuexi Du; Nicha C. Dvornek; Yuyan Ge; Zuwei Guo; et al. (Medical Image Anal., 2025)

Fed-NDIF: A Noise-Embedded Federated Diffusion Model For Low-Count Whole-Body PET Denoising. - Yinchi Zhou; Huidong Xie; Menghua Xia; Qiong Liu; Bo Zhou 009; Tianqi Chen; Jun Hou; Liang Guo; Xinyuan Zheng; Hanzhong Wang; Biao Li; Axel Rominger; et al. (CoRR, 2025)

GMR-Conv: An Efficient Rotation and Reflection Equivariant Convolution Kernel Using Gaussian Mixture Rings. - Yuexi Du; Jiazhen Zhang; Nicha C. Dvornek; John A. Onofrey (CoRR, 2025)

Equivariant Imaging Biomarkers for Robust Unsupervised Segmentation of Histopathology. - Fuyao Chen; Yuexi Du; Tal Zeevi; Nicha C. Dvornek; John A. Onofrey (CoRR, 2025)

CXR-LT 2024: A MICCAI challenge on long-tailed, multi-label, and zero-shot disease classification from chest X-ray. - Mingquan Lin; Gregory Holste; Song Wang 026; Yiliang Zhou; Yishu Wei; Imon Banerjee; Pengyi Chen; Tianjie Dai; Yuexi Du; Nicha C. Dvornek; Yuyan Ge; Zuowei Guo; et al. (CoRR, 2025)