CATNUS: Coordinate-Aware Thalamic Nuclei Segmentation Using T1-Weighted MRI

Anqi Feng; Zhangxing Bian; Samuel W. Remedios; Savannah P. Hays; Blake E. Dewey; Alexa Colinco; Jiachen Zhuo; Dan Benjamini; Jerry L. Prince

arXiv · 2512.05329

CATNUS: Coordinate-Aware Thalamic Nuclei Segmentation Using T1-Weighted MRI

Anqi Feng·Zhangxing Bian·Samuel W. Remedios·Savannah P. Hays·Blake E. Dewey·Alexa Colinco·Jiachen Zhuo·Dan Benjamini·Jerry L. Prince

View original source ↗Read source document ↗Export metadata ↓

Abstract

Accurate segmentation of thalamic nuclei from magnetic resonance images is important due to the distinct roles of these nuclei in overall brain function and to their differential involvement in neurological and psychiatric disorders. However, segmentation remains challenging given the small size of many nuclei, limited intrathalamic contrast and image resolution, and inter-subject anatomical variability. In this work, we present CATNUS (Coordinate-Aware Thalamic Nuclei Segmentation), segmenting 13 thalamic nuclei (or nuclear groups) using a 3D U-Net architecture enhanced with coordinate convolution layers, which provide more precise localization of both large and small nuclei. To support broad clinical applicability, we provide pre-trained model variants that can operate on quantitative T1 maps as well as on widely used magnetization-prepared rapid gradient echo (MPRAGE) and fast gray matter acquisition T1 inversion recovery (FGATIR) sequences. We benchmarked CATNUS against established methods, including FreeSurfer, THOMAS and HIPS-THOMAS, demonstrating improved segmentation accuracy and robust test-retest reliability across multiple nuclei. Furthermore, CATNUS demonstrated strong out-of-distribution generalization on traveling-subject datasets spanning multiple scanners, field strengths, and vendors, producing reliable and anatomically coherent segmentations across diverse acquisition conditions. Overall, CATNUS provides an accurate and generalizable solution for thalamic nuclei segmentation, with strong potential to facilitate large-scale neuroimaging studies and support real-world clinical assessment.

Explore related subjects

eess.IV physics.med-ph

Keep this discovery

BibTeX RIS

Anqi Feng, Zhangxing Bian, Samuel W. Remedios, Savannah P. Hays, Blake E. Dewey, Alexa Colinco, Jiachen Zhuo, Dan Benjamini, Jerry L. Prince. 2025-12-05. CATNUS: Coordinate-Aware Thalamic Nuclei Segmentation Using T1-Weighted MRI. https://arxiv.org/abs/2512.05329

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related papers

arXiv2026

Exponential Pixelating Integral transform with dual fractal features for enhanced chest X-ray abnormality detection

The heightened prevalence of respiratory disorders, particularly exacerbated by a significant upswing in fatalities due to the novel coronavirus, underscores the critical need for early detection and timely intervention. This imperative is paramount, possessing the potential to profoundly impact and safeguard numerous lives. Medically, chest radiography stands out as an essential and economically viable medical imaging approach for diagnosing and assessing the severity of diverse Respiratory Disorders. However, their detection in Chest X-Rays is a cumbersome task even for well-trained radiologists owing to low contrast issues, overlapping of the tissue structures, subjective variability, and the presence of noise. To address these issues, a novel analytical model termed Exponential Pixelating Integral is introduced for the automatic detection of infections in Chest X-Rays in this work. Initially, the presented Exponential Pixelating Integral enhances the pixel intensities to overcome the low-contrast issues that are then polar-transformed followed by their representation using the locally invariant Mandelbrot and Julia fractal geometries for effective distinction of structural features. The collated features labeled Exponential Pixelating Integral with dually characterized fractal features are then classified by the non-parametric multivariate adaptive regression splines to establish an ensemble model between each pair of classes for effective diagnosis of diverse diseases. Rigorous analysis of the proposed classification framework on large medical benchmarked datasets showcases its superiority over its peers by registering a higher classification accuracy and F1 scores ranging from 98.46 to 99.45% and 96.53-98.10% respectively, making it a precise and interpretable automated system for diagnosing respiratory disorders.

eess.IV↗

arXiv2026

Myocardial Strain Drift Correction in Deep Learning Based Ultrasound Tracking

Myocardial strain from echocardiography is a key biomarker for cardiac function. Recent deep learning methods show strong performance for myocardial motion tracking but often lack physiological constraints, leading to temporal drift across the cardiac cycle. Consequently, tracked points may not return to their relative initial positions at the end of each cardiac cycle, producing inaccurate strain estimates and even divergence in some cases. We propose a deep learning framework that compensates for drift during myocardial tracking. We extend a state-of-the-art echocardiographic tracking method (TAS-Net) with persistent memory tokens that share information across sliding windows over full cardiac cycles. A teacher-student fine-tuning strategy on real echocardiographic data then enforces physiologically consistent cyclic motion while preserving tracking accuracy. Experiments show reduced global and regional strain drift, improved agreement with clinical references, and better test-retest reproducibility, supporting more reliable myocardial strain estimation in clinical practice.

eess.IV↗

arXiv2026

Morphological Decoupling-Based Skeletal Classification for Clinical Assessment of Malocclusion

Malocclusion skeletal grading is a fundamental task in orthodontics, critical for diagnosis and treatment planning. Traditionally, cone-beam computed tomography (CBCT) is used for visual measurement, and the reconstructed lateral cephalograms are handed over to expert dentists for diagnosis. However, manual review is time-consuming, labor-intensive, and subject to inter-operator variability. Therefore, an automatic CBCT-based system is needed for reliable malocclusion skeletal grading. In this case, we develop TeethGNN, a novel graph-based framework designed to combine CBCT image features with morphological information for accurate and efficient malocclusion grading. TeethGNN utilizes a decoupled learnable decoder to directly predict key morphological indicators from CBCT images, eliminating the need for manual measurements. These morphological features are then fused with image features using a graph neural network (GNN), which effectively models the relationships between the modalities. To further enhance robustness and calibration, we introduce a collaborative calibration strategy. This strategy combines multi-scale graph adversarial perturbation for explicit calibration and nonlinear topological graph calibration for implicit confidence adjustment. Extensive experiments and ablation studies on our collected clinical dataset demonstrate that our malocclusion measurement system achieves 77.08\% in accuracy and 89.61\% in AUC, outperforming the compared state-of-the-art methods. These results validate the effectiveness of graph-based multimodal fusion and collaborative calibration in improving malocclusion grading performance. Our system shows strong potential for advancing computer-aided orthodontic diagnosis, providing an accurate and reliable solution for vision-based clinical measurement and diagnosis.

eess.IV↗