Mehmet Kurt

Ezequiel de la Rosa, Ruisheng Su, Mauricio Reyes et al.

Accurate estimation of brain infarction (i.e., irreversibly damaged tissue) is critical for guiding treatment decisions in acute ischemic stroke. Reliable infarct prediction informs key clinical interventions, including the need for patient transfer to comprehensive stroke centers, the potential benefit of additional reperfusion attempts during mechanical thrombectomy, decisions regarding secondary neuroprotective treatments, and ultimately, prognosis of clinical outcomes. This work introduces the Ischemic Stroke Lesion Segmentation (ISLES) 2024 challenge, which focuses on the prediction of final infarct volumes from pre-interventional acute stroke imaging and clinical data. ISLES24 provides a comprehensive, multimodal setting where participants can leverage all clinically and practically available data, including full acute CT imaging, sub-acute follow-up MRI, and structured clinical information, across a train set of 150 cases. On the hidden test set of 98 cases, the top-performing model, a multimodal nnU-Net-based architecture, achieved a Dice score of 0.285 (+/- 0.213) and an absolute volume difference of 21.2 (+/- 37.2) mL, underlining the significant challenges posed by this task and the need for further advances in multimodal learning. This work makes two primary contributions: first, we establish a standardized, clinically realistic benchmark for post-treatment infarct prediction, enabling systematic evaluation of multimodal algorithmic strategies on a longitudinal stroke dataset; second, we analyze current methodological limitations and outline key research directions to guide the development of next-generation infarct prediction models.

Javid Abderezaei, Aymeric Pionteck, Agamdeep Chopra et al.

Deformable image registration is a key task in medical image analysis. The Brain Tumor Sequence Registration challenge (BraTS-Reg) aims at establishing correspondences between pre-operative and follow-up scans of the same patient diagnosed with an adult brain diffuse high-grade glioma and intends to address the challenging task of registering longitudinal data with major tissue appearance changes. In this work, we proposed a two-stage cascaded network based on the Inception and TransMorph models. The dataset for each patient was comprised of a native pre-contrast (T1), a contrast-enhanced T1-weighted (T1-CE), a T2-weighted (T2), and a Fluid Attenuated Inversion Recovery (FLAIR). The Inception model was used to fuse the 4 image modalities together and extract the most relevant information. Then, a variant of the TransMorph architecture was adapted to generate the displacement fields. The Loss function was composed of a standard image similarity measure, a diffusion regularizer, and an edge-map similarity measure added to overcome intensity dependence and reinforce correct boundary deformation. We observed that the addition of the Inception module substantially increased the performance of the network. Additionally, performing an initial affine registration before training the model showed improved accuracy in the landmark error measurements between pre and post-operative MRIs. We observed that our best model composed of the Inception and TransMorph architectures while using an initially affine registered dataset had the best performance with a median absolute error of 2.91 (initial error = 7.8). We achieved 6th place at the time of model submission in the final testing phase of the BraTS-Reg challenge.

Juampablo E. Heras Rivera, Dickson T. Chen, Tianyi Ren et al.

Recent advances in radiology report generation (RRG) have been driven by large paired image-text datasets; however, progress in neuro-oncology has been limited due to a lack of open paired image-report datasets. Here, we introduce BTReport, an open-source framework for brain tumor RRG that constructs natural language radiology reports using deterministically extracted imaging features. Unlike existing approaches that rely on large general-purpose or fine-tuned vision-language models for both image interpretation and report composition, BTReport performs deterministic feature extraction for image analysis and uses large language models only for syntactic structuring and narrative formatting. By separating RRG into a deterministic feature extraction step and a report generation step, the generated reports are completely interpretable and less prone to hallucinations. We show that the features used for report generation are predictive of key clinical outcomes, including survival and IDH mutation status, and reports generated by BTReport are more closely aligned with reference clinical reports than existing baselines for RRG. Finally, we introduce BTReport-BraTS, a companion dataset that augments BraTS imaging with synthetically generated radiology reports produced with BTReport. Code for this project can be found at https://github.com/KurtLabUW/BTReport.

Juampablo E. Heras Rivera, Daniel K. Low, Xavier Xiong et al.

Accurate brain tumor typing requires integrating heterogeneous clinical evidence, including magnetic resonance imaging (MRI), histopathology, and pathology reports, which are often incomplete at the time of diagnosis. We introduce CoRe-BT, a cross-modal radiology-pathology-text benchmark for brain tumor typing, designed to study robust multimodal learning under missing modality conditions. The dataset comprises 310 patients with multi-sequence brain MRI (T1, T1c, T2, FLAIR), including 95 cases with paired H&E-stained whole-slide pathology images and pathology reports. All cases are annotated with tumor type and grade, and MRI volumes include expert-annotated tumor masks, enabling both region-aware modeling and auxiliary learning tasks. Tumors are categorized into six clinically relevant classes capturing the heterogeneity of common and rare glioma subtypes. We evaluate tumor typing under variable modality availability by comparing MRI-only models with multimodal approaches that incorporate pathology information when present. Baseline experiments demonstrate the feasibility of multimodal fusion and highlight complementary modality contributions across clinically relevant typing tasks. CoRe-BT provides a grounded testbed for advancing multimodal glioma typing and representation learning in realistic scenarios with incomplete clinical data.

Agamdeep S. Chopra, Caitlin Neher, Tianyi Ren et al.

Tau positron emission tomography (tau-PET) provides an in vivo marker of Alzheimer's disease pathology, but cost and limited availability motivate MRI-based alternatives. We introduce DisQ-HNet (DQH), a framework that synthesizes tau-PET from paired T1-weighted and FLAIR MRI while exposing how each modality contributes to the prediction. The method combines (i) a Partial Information Decomposition (PID)-guided, vector-quantized encoder that partitions latent information into redundant, unique, and complementary components, and (ii) a Half-UNet decoder that preserves anatomical detail using pseudo-skip connections conditioned on structural edge cues rather than direct encoder feature reuse. Across multiple baselines (VAE, VQ-VAE, and UNet), DisQ-HNet maintains reconstruction fidelity and better preserves disease-relevant signal for downstream AD tasks, including Braak staging, tau localization, and classification. PID-based Shapley analysis provides modality-specific attribution of synthesized uptake patterns.

Tianyi Ren, Daniel Low, Pittra Jaengprajak et al.

Segmentation is the identification of anatomical regions of interest, such as organs, tissue, and lesions, serving as a fundamental task in computer-aided diagnosis in medical imaging. Although deep learning models have achieved remarkable performance in medical image segmentation, the need for explainability remains critical for ensuring their acceptance and integration in clinical practice, despite the growing research attention in this area. Our approach explored the use of contrast-level Shapley values, a systematic perturbation of model inputs to assess feature importance. While other studies have investigated gradient-based techniques through identifying influential regions in imaging inputs, Shapley values offer a broader, clinically aligned approach, explaining how model performance is fairly attributed to certain imaging contrasts over others. Using the BraTS 2024 dataset, we generated rankings for Shapley values for four MRI contrasts across four model architectures. Two metrics were proposed from the Shapley ranking: agreement between model and ``clinician" imaging ranking, and uncertainty quantified through Shapley ranking variance across cross-validation folds. Higher-performing cases (Dice \textgreater0.6) showed significantly greater agreement with clinical rankings. Increased Shapley ranking variance correlated with decreased performance (U-Net: $r=-0.581$). These metrics provide clinically interpretable proxies for model reliability, helping clinicians better understand state-of-the-art segmentation models.

Tianyi Ren, Ethan Honey, Harshitha Rebala et al.

Tumor segmentation from multi-modal brain MRI images is a challenging task due to the limited samples, high variance in shapes and uneven distribution of tumor morphology. The performance of automated medical image segmentation has been significant improvement by the recent advances in deep learning. However, the model predictions have not yet reached the desired level for clinical use in terms of accuracy and generalizability. In order to address the distinct problems presented in Challenges 1, 2, and 3 of BraTS 2023, we have constructed an optimization framework based on a 3D U-Net model for brain tumor segmentation. This framework incorporates a range of techniques, including various pre-processing and post-processing techniques, and transfer learning. On the validation datasets, this multi-modality brain tumor segmentation framework achieves an average lesion-wise Dice score of 0.79, 0.72, 0.74 on Challenges 1, 2, 3 respectively.

Juampablo E. Heras Rivera, Agamdeep S. Chopra, Tianyi Ren et al.

The integration of machine learning in magnetic resonance imaging (MRI), specifically in neuroimaging, is proving to be incredibly effective, leading to better diagnostic accuracy, accelerated image analysis, and data-driven insights, which can potentially transform patient care. Deep learning models utilize multiple layers of processing to capture intricate details of complex data, which can then be used on a variety of tasks, including brain tumor classification, segmentation, image synthesis, and registration. Previous research demonstrates high accuracy in tumor segmentation using various model architectures, including nn-UNet and Swin-UNet. U-Mamba, which uses state space modeling, also achieves high accuracy in medical image segmentation. To leverage these models, we propose a deep learning framework that ensembles these state-of-the-art architectures to achieve accurate segmentation and produce finely synthesized images.

Tianyi Ren, Juampablo E. Heras Rivera, Hitender Oswal et al.

Stroke is among the top three causes of death worldwide, and accurate identification of stroke lesion boundaries is critical for diagnosis and treatment. Supervised deep learning methods have emerged as the leading solution for stroke lesion segmentation but require large, diverse, and annotated datasets. The ISLES'24 challenge addresses this need by providing longitudinal stroke imaging data, including CT scans taken on arrival to the hospital and follow-up MRI taken 2-9 days from initial arrival, with annotations derived from follow-up MRI. Importantly, models submitted to the ISLES'24 challenge are evaluated using only CT inputs, requiring prediction of lesion progression that may not be visible in CT scans for segmentation. Our winning solution shows that a carefully designed preprocessing pipeline including deep-learning-based skull stripping and custom intensity windowing is beneficial for accurate segmentation. Combined with a standard large residual nnU-Net architecture for segmentation, this approach achieves a mean test Dice of 28.5 with a standard deviation of 21.27.

Tianyi Ren, Juampablo Heras Rivera, Hitender Oswal et al.

Deep learning has been successfully applied to medical image segmentation, enabling accurate identification of regions of interest such as organs and lesions. This approach works effectively across diverse datasets, including those with single-image contrast, multi-contrast, and multimodal imaging data. To improve human understanding of these black-box models, there is a growing need for Explainable AI (XAI) techniques for model transparency and accountability. Previous research has primarily focused on post hoc pixel-level explanations, using methods gradient-based and perturbation-based apporaches. These methods rely on gradients or perturbations to explain model predictions. However, these pixel-level explanations often struggle with the complexity inherent in multi-contrast magnetic resonance imaging (MRI) segmentation tasks, and the sparsely distributed explanations have limited clinical relevance. In this study, we propose using contrast-level Shapley values to explain state-of-the-art models trained on standard metrics used in brain tumor segmentation. Our results demonstrate that Shapley analysis provides valuable insights into different models' behavior used for tumor segmentation. We demonstrated a bias for U-Net towards over-weighing T1-contrast and FLAIR, while Swin-UNETR provided a cross-contrast understanding with balanced Shapley distribution.

Juampablo E. Heras Rivera, Caitlin M. Neher, Mehmet Kurt

$\textbf{Purpose:}$ To develop and evaluate an operator learning framework for nonlinear inversion (NLI) of brain magnetic resonance elastography (MRE) data, which enables real-time inversion of elastograms with comparable spatial accuracy to NLI. $\textbf{Materials and Methods:}$ In this retrospective study, 3D MRE data from 61 individuals (mean age, 37.4 years; 34 female) were used for development of the framework. A predictive deep operator learning framework (oNLI) was trained using 10-fold cross-validation, with the complex curl of the measured displacement field as inputs and NLI-derived reference elastograms as outputs. A structural prior mechanism, analogous to Soft Prior Regularization in the MRE literature, was incorporated to improve spatial accuracy. Subject-level evaluation metrics included Pearson's correlation coefficient, absolute relative error, and structural similarity index measure between predicted and reference elastograms across brain regions of different sizes to understand accuracy. Statistical analyses included paired t-tests comparing the proposed oNLI variants to the convolutional neural network baselines. $\textbf{Results:}$ Whole brain absolute percent error was 8.4 $\pm$ 0.5 ($μ'$) and 10.0 $\pm$ 0.7 ($μ''$) for oNLI and 15.8 $\pm$ 0.8 ($μ'$) and 26.1 $\pm$ 1.1 ($μ''$) for CNNs. Additionally, oNLI outperformed convolutional architectures as per Pearson's correlation coefficient, $r$, in the whole brain and across all subregions for both the storage modulus and loss modulus (p < 0.05). $\textbf{Conclusion:}$ The oNLI framework enables real-time MRE inversion (30,000x speedup), outperforming CNN-based approaches and maintaining the fine-grained spatial accuracy achievable with NLI in the brain.

Juampablo E. Heras Rivera, Hitender Oswal, Tianyi Ren et al.

Stroke is among the top three causes of death worldwide, and accurate identification of ischemic stroke lesion boundaries from imaging is critical for diagnosis and treatment. The main imaging modalities used include magnetic resonance imaging (MRI), particularly diffusion weighted imaging (DWI), and computed tomography (CT)-based techniques such as non-contrast CT (NCCT), contrast-enhanced CT angiography (CTA), and CT perfusion (CTP). DWI is the gold standard for the identification of lesions but has limited applicability in low-resource settings due to prohibitive costs. CT-based imaging is currently the most practical imaging method in low-resource settings due to low costs and simplified logistics, but lacks the high specificity of MRI-based methods in monitoring ischemic insults. Supervised deep learning methods are the leading solution for automated ischemic stroke lesion segmentation and provide an opportunity to improve diagnostic quality in low-resource settings by incorporating insights from DWI when segmenting from CT. Here, we develop a series of models which use CT images taken upon arrival as inputs to predict follow-up lesion volumes annotated from DWI taken 2-9 days later. Furthermore, we implement clinically motivated preprocessing steps and show that the proposed pipeline results in a 38% improvement in Dice score over 10 folds compared to a nnU-Net model trained with the baseline preprocessing. Finally, we demonstrate that through additional preprocessing of CTA maps to extract vessel segmentations, we further improve our best model by 21% over 5 folds.

Tianyi Ren, Abhishek Sharma, Juampablo Heras Rivera et al.

Identification of tumor margins is essential for surgical decision-making for glioblastoma patients and provides reliable assistance for neurosurgeons. Despite improvements in deep learning architectures for tumor segmentation over the years, creating a fully autonomous system suitable for clinical floors remains a formidable challenge because the model predictions have not yet reached the desired level of accuracy and generalizability for clinical applications. Generative modeling techniques have seen significant improvements in recent times. Specifically, Generative Adversarial Networks (GANs) and Denoising-diffusion-based models (DDPMs) have been used to generate higher-quality images with fewer artifacts and finer attributes. In this work, we introduce a framework called Re-Diffinet for modeling the discrepancy between the outputs of a segmentation model like U-Net and the ground truth, using DDPMs. By explicitly modeling the discrepancy, the results show an average improvement of 0.55\% in the Dice score and 16.28\% in HD95 from cross-validation over 5-folds, compared to the state-of-the-art U-Net segmentation model.

Bhakti Baheti, Satrajit Chakrabarty, Hamed Akbari et al.

Registration of longitudinal brain MRI scans containing pathologies is challenging due to dramatic changes in tissue appearance. Although there has been progress in developing general-purpose medical image registration techniques, they have not yet attained the requisite precision and reliability for this task, highlighting its inherent complexity. Here we describe the Brain Tumor Sequence Registration (BraTS-Reg) challenge, as the first public benchmark environment for deformable registration algorithms focusing on estimating correspondences between pre-operative and follow-up scans of the same patient diagnosed with a diffuse brain glioma. The BraTS-Reg data comprise de-identified multi-institutional multi-parametric MRI (mpMRI) scans, curated for size and resolution according to a canonical anatomical template, and divided into training, validation, and testing sets. Clinical experts annotated ground truth (GT) landmark points of anatomical locations distinct across the temporal domain. Quantitative evaluation and ranking were based on the Median Euclidean Error (MEE), Robustness, and the determinant of the Jacobian of the displacement field. The top-ranked methodologies yielded similar performance across all evaluation metrics and shared several methodological commonalities, including pre-alignment, deep neural networks, inverse consistency analysis, and test-time instance optimization per-case basis as a post-processing step. The top-ranked method attained the MEE at or below that of the inter-rater variability for approximately 60% of the evaluated landmarks, underscoring the scope for further accuracy and robustness improvements, especially relative to human experts. The aim of BraTS-Reg is to continue to serve as an active resource for research, with the data and online evaluation tools accessible at https://bratsreg.github.io/.