arXiv subjects

Busra Bulut

Publications and source records attributed to Busra Bulut.

4 recordsLinked to original sources

arXiv2026

PRIME-SVR: Physics-infoRmed Implicit Multi-Echo Slice-to-Volume Reconstruction for Fetal T2 mapping

Slice-to-volume reconstruction (SVR) is the standard method for obtaining high-resolution (HR) 3D fetal brain volumes from motion-corrupted 2D MRI slice stacks acquired in multiple orientations. Existing SVR methods are optimized and validated only for clinical-range echo times (TEs), limiting their use at non-clinical TEs and making them incompatible with quantitative T2 mapping, a protocol- and center-independent biomarker of fetal brain maturation requiring HR reconstructions across multiple TEs. We present PRIME-SVR, the first implicit neural representation (INR) framework for joint HR reconstruction from multi-echo MRI. A single fully connected network models a continuous function from spatial coordinates to signal intensities across TEs, while a second network estimates slice-specific acquisition degradations. Cross-TE coherence is enforced via a Bloch equation-derived regularization penalizing deviations from expected T2 decay, with adaptive weighting that strengthens coupling for degraded stacks. The method is fully self-supervised. We validate PRIME-SVR on 39 in vivo fetal acquisitions (13 subjects x 3 TEs) from two centers, two vendors, and two field strengths (1.5 T and 0.55 T). Compared to state-of-the-art SVR, PRIME-SVR improves reconstruction sharpness by 47%, anatomical accuracy by 30%, and cross-TE structural consistency by 14%. It enables reconstruction at late TEs previously inaccessible to SVR, yielding the first 0.8 mm isotropic T2 maps at 0.55 T and the first T2 maps derived from INR-based SVR. PRIME-SVR also accelerates quantitative imaging by reducing the data needed for multi-TE reconstruction, cutting acquisition from 15 to 10 minutes while keeping T2 accuracy within 1.7% in white and deep gray matter, or to 5 minutes with a mean T2 error of 2.3% for high-quality acquisitions.

physics.med-ph↗

arXiv2025

T2 mapping at 0.55 T using Ultra-Fast Spin Echo MRI

Low-field T2 mapping MRI can democratize neuropediatric imaging by improving accessibility and providing quantitative biomarkers of brain development. \textbf{Purpose:} To evaluate the feasibility of high-resolution T2 mapping using a single-shot fast spin-echo (SS-FSE) sequence at 0.55~T in a healthy control cohort. \textbf{Study Type:} Prospective single-center study. \textbf{Population:} In vivo: ten healthy adults (18--43~years, 5 females/5 males). In vitro: NIST Phantom. \textbf{Field strength/sequence:} Multi-echo ultra-fast spin-echo at 0.55~T and 1.5~T. \textbf{Assessment:} Feasibility was first assessed in vitro using the NIST Phantom, comparing T2 relaxation times to spectrometer references at 0.55~T. Acquisition and T2-fitting parameters optimized in vitro were applied in vivo. Repeatability was evaluated by atlas-based analysis of white matter (WM) and cortical grey matter (GM) regions. Coefficients of variation (CoV) were computed across runs, sessions, and subjects. \textbf{Statistical Tests:} Wilcoxon signed-rank test with Bonferroni correction ($\alpha = 0.05/n_{ROI}$) assessed CoV differences. Pearson correlation coefficients quantified T2 associations. \textbf{Results:} In vitro, mono-exponential fitting under Gaussian--Rician noise yielded deviations $<12\%$ from reference values. In vivo, inter-subject CoV was 5.2\% (WM) and 17.7\% (GM), comparable to 1.5~T. Mean T2 times were 118~ms (WM) and 188~ms (GM) at 0.55~T, with a 16.5-minute acquisition. \textbf{Conclusion:} A rapid, robust high-resolution T2 mapping protocol at 0.55~T for HASTE MRI is presented, employing Gaussian noise-based fitting. We report the first normative T2 values for healthy adult brains at 0.55~T, demonstrating technical feasibility and reliability.

physics.app-ph↗

arXiv2025

Physics-Informed Joint Multi-TE Super-Resolution with Implicit Neural Representation for Robust Fetal T2 Mapping

T2 mapping in fetal brain MRI has the potential to improve characterization of the developing brain, especially at mid-field (0.55T), where T2 decay is slower. However, this is challenging as fetal MRI acquisition relies on multiple motion-corrupted stacks of thick slices, requiring slice-to-volume reconstruction (SVR) to estimate a high-resolution (HR) 3D volume. Currently, T2 mapping involves repeated acquisitions of these stacks at each echo time (TE), leading to long scan times and high sensitivity to motion. We tackle this challenge with a method that jointly reconstructs data across TEs, addressing severe motion. Our approach combines implicit neural representations with a physics-informed regularization that models T2 decay, enabling information sharing across TEs while preserving anatomical and quantitative T2 fidelity. We demonstrate state-of-the-art performance on simulated fetal brain and in vivo adult datasets with fetal-like motion. We also present the first in vivo fetal T2 mapping results at 0.55T. Our study shows potential for reducing the number of stacks per TE in T2 mapping by leveraging anatomical redundancy.

cs.CV↗

arXiv2024

Evaluating Synthetic Data Generation for Domain Generalization in Fetal Brain MRI Segmentation

Fetal brain tissue segmentation from magnetic resonance imaging (MRI) is crucial for studying neurodevelopment, but remains challenging due to data heterogeneity and limited annotations. Domain randomization (DR) has recently emerged as a promising strategy for single-source domain generalization by synthesizing training images with randomized artifacts, contrast, and resolution. In this work, we investigate how to maximize the out-of-domain (OOD) generalization of DR-based methods. We evaluate several synthetic data generation strategies for DR, with a particular focus on our recently proposed framework, FetalSynthSeg. We show that simple Gaussian mixture-based intensity modeling outperforms more complex physics-based simulations, and that intensity clustering (subdividing tissue classes based on intensity) improves OOD robustness. Evaluated on 348 fetal subjects from four sites spanning 0.55-3T and both T1w and T2w contrasts, FetalSynthSeg reaches state-of-the-art performance on several FeTA 2024 testing datasets (80-85 Dice score) and, for the first time, offers robust segmentation on modalities other than T2w for fetal brain segmentation (80 Dice on dHCP-T1w dataset). Compared with state-of-the-art methods such as BOUNTI, nnU-Net ensemble, and the FeTA 2024 winner, FetalSynthSeg delivers comparable or superior accuracy while maintaining strong robustness across domain shifts. Our code, model weights, and Docker image ready for easy inference are available at https://hub.docker.com/r/vzalevskyi/fetalsynthseg.

eess.IV↗