arXiv subjects

Yvan Gomez

Publications and source records attributed to Yvan Gomez.

5 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

Enhancing Corpus Callosum Segmentation in Fetal MRI via Pathology-Informed Domain Randomization

Accurate fetal brain segmentation is crucial for extracting biomarkers and assessing neurodevelopment, especially in conditions such as corpus callosum dysgenesis (CCD), which can induce drastic anatomical changes. However, the rarity of CCD severely limits annotated data, hindering the generalization of deep learning models. To address this, we propose a pathology-informed domain randomization strategy that embeds prior knowledge of CCD manifestations into a synthetic data generation pipeline. By simulating diverse brain alterations from healthy data alone, our approach enables robust segmentation without requiring pathological annotations. We validate our method on a cohort comprising 248 healthy fetuses, 26 with CCD, and 47 with other brain pathologies, achieving substantial improvements on CCD cases while maintaining performance on both healthy fetuses and those with other pathologies. From the predicted segmentations, we derive clinically relevant biomarkers, such as corpus callosum length (LCC) and volume, and show their utility in distinguishing CCD subtypes. Our pathology-informed augmentation reduces the LCC estimation error from 1.89 mm to 0.80 mm in healthy cases and from 10.9 mm to 0.7 mm in CCD cases. Beyond these quantitative gains, our approach yields segmentations with improved topological consistency relative to available ground truth, enabling more reliable shape-based analyses. Overall, this work demonstrates that incorporating domain-specific anatomical priors into synthetic data pipelines can effectively mitigate data scarcity and enhance analysis of rare but clinically significant malformations.

cs.CV↗

arXiv2025

Advances in Automated Fetal Brain MRI Segmentation and Biometry: Insights from the FeTA 2024 Challenge

Accurate fetal brain tissue segmentation and biometric analysis are essential for studying brain development in utero. The FeTA Challenge 2024 advanced automated fetal brain MRI analysis by introducing biometry prediction as a new task alongside tissue segmentation. For the first time, our diverse multi-centric test set included data from a new low-field (0.55T) MRI dataset. Evaluation metrics were also expanded to include the topology-specific Euler characteristic difference (ED). Sixteen teams submitted segmentation methods, most of which performed consistently across both high- and low-field scans. However, longitudinal trends indicate that segmentation accuracy may be reaching a plateau, with results now approaching inter-rater variability. The ED metric uncovered topological differences that were missed by conventional metrics, while the low-field dataset achieved the highest segmentation scores, highlighting the potential of affordable imaging systems when paired with high-quality reconstruction. Seven teams participated in the biometry task, but most methods failed to outperform a simple baseline that predicted measurements based solely on gestational age, underscoring the challenge of extracting reliable biometric estimates from image data alone. Domain shift analysis identified image quality as the most significant factor affecting model generalization, with super-resolution pipelines also playing a substantial role. Other factors, such as gestational age, pathology, and acquisition site, had smaller, though still measurable, effects. Overall, FeTA 2024 offers a comprehensive benchmark for multi-class segmentation and biometry estimation in fetal brain MRI, underscoring the need for data-centric approaches, improved topological evaluation, and greater dataset diversity to enable clinically robust and generalizable AI tools.

cs.CV↗

arXiv2023

FetMRQC: a robust quality control system for multi-centric fetal brain MRI

Fetal brain MRI is becoming an increasingly relevant complement to neurosonography for perinatal diagnosis, allowing fundamental insights into fetal brain development throughout gestation. However, uncontrolled fetal motion and heterogeneity in acquisition protocols lead to data of variable quality, potentially biasing the outcome of subsequent studies. We present FetMRQC, an open-source machine-learning framework for automated image quality assessment and quality control that is robust to domain shifts induced by the heterogeneity of clinical data. FetMRQC extracts an ensemble of quality metrics from unprocessed anatomical MRI and combines them to predict experts' ratings using random forests. We validate our framework on a pioneeringly large and diverse dataset of more than 1600 manually rated fetal brain T2-weighted images from four clinical centers and 13 different scanners. Our study shows that FetMRQC's predictions generalize well to unseen data while being interpretable. FetMRQC is a step towards more robust fetal brain neuroimaging, which has the potential to shed new insights on the developing human brain.

eess.IV↗

arXiv2023

FetMRQC: Automated Quality Control for fetal brain MRI

Quality control (QC) has long been considered essential to guarantee the reliability of neuroimaging studies. It is particularly important for fetal brain MRI, where large and unpredictable fetal motion can lead to substantial artifacts in the acquired images. Existing methods for fetal brain quality assessment operate at the \textit{slice} level, and fail to get a comprehensive picture of the quality of an image, that can only be achieved by looking at the \textit{entire} brain volume. In this work, we propose FetMRQC, a machine learning framework for automated image quality assessment tailored to fetal brain MRI, which extracts an ensemble of quality metrics that are then used to predict experts' ratings. Based on the manual ratings of more than 1000 low-resolution stacks acquired across two different institutions, we show that, compared with existing quality metrics, FetMRQC is able to generalize out-of-domain, while being interpretable and data efficient. We also release a novel manual quality rating tool designed to facilitate and optimize quality rating of fetal brain images. Our tool, along with all the code to generate, train and evaluate the model is available at https://github.com/Medical-Image-Analysis-Laboratory/fetal_brain_qc/ .

eess.IV↗