arXiv subjects

Jenny Crinion

Publications and source records attributed to Jenny Crinion.

4 recordsLinked to original sources

arXiv2025

Unified 3D MRI Representations via Sequence-Invariant Contrastive Learning

Self-supervised deep learning has accelerated 2D natural image analysis but remains difficult to translate into 3D MRI, where data are scarce and pre-trained 2D backbones cannot capture volumetric context. We present a \emph{sequence-invariant} self-supervised framework leveraging quantitative MRI (qMRI). By simulating multiple MRI contrasts from a single 3D qMRI scan and enforcing consistent representations across these contrasts, we learn anatomy-centric rather than sequence-specific features. The result is a single 3D encoder that excels across tasks and protocols. Experiments on healthy brain segmentation (IXI), stroke lesion segmentation (ARC), and MRI denoising show significant gains over baseline SSL approaches, especially in low-data settings (up to +8.3\% Dice, +4.2 dB PSNR). It also generalises to unseen sites, supporting scalable clinical use. Code and trained models are publicly available at https://github.com/liamchalcroft/contrast-squared

cs.CV↗

arXiv2025

Domain-Agnostic Stroke Lesion Segmentation Using Physics-Constrained Synthetic Data

Segmenting stroke lesions in MRI is challenging due to diverse acquisition protocols that limit model generalisability. In this work, we introduce two physics-constrained approaches to generate synthetic quantitative MRI (qMRI) images that improve segmentation robustness across heterogeneous domains. Our first method, $\texttt{qATLAS}$, trains a neural network to estimate qMRI maps from standard MPRAGE images, enabling the simulation of varied MRI sequences with realistic tissue contrasts. The second method, $\texttt{qSynth}$, synthesises qMRI maps directly from tissue labels using label-conditioned Gaussian mixture models, ensuring physical plausibility. Extensive experiments on multiple out-of-domain datasets show that both methods outperform a baseline UNet, with $\texttt{qSynth}$ notably surpassing previous synthetic data approaches. These results highlight the promise of integrating MRI physics into synthetic data generation for robust, generalisable stroke lesion segmentation. Code is available at https://github.com/liamchalcroft/qsynth

eess.IV↗

arXiv2024

Estimating the construct validity of Principal Components Analysis

In many scientific disciplines, the features of interest cannot be observed directly, so must instead be inferred from observed behaviour. Latent variable analyses are increasingly employed to systematise these inferences, and Principal Components Analysis (PCA) is perhaps the simplest and most popular of these methods. Here, we examine how the assumptions that we are prepared to entertain, about the latent variable system, mediate the likelihood that PCA-derived components will capture the true sources of variance underlying data. As expected, we find that this likelihood is excellent in the best case, and robust to empirically reasonable levels of measurement noise, but best-case performance is also: (a) not robust to violations of the method's more prominent assumptions, of linearity and orthogonality; and also (b) requires that other subtler assumptions be made, such as that the latent variables should have varying importance, and that weights relating latent variables to observed data have zero mean. Neither variance explained, nor replication in independent samples, could reliably predict which (if any) PCA-derived components will capture true sources of variance in data. We conclude by describing a procedure to fit these inferences more directly to empirical data, and use it to find that components derived via PCA from two different empirical neuropsychological datasets, are less likely to have meaningful referents in the brain than we hoped.

stat.ME↗

arXiv2021

NUVA: A Naming Utterance Verifier for Aphasia Treatment

Anomia (word-finding difficulties) is the hallmark of aphasia, an acquired language disorder most commonly caused by stroke. Assessment of speech performance using picture naming tasks is a key method for both diagnosis and monitoring of responses to treatment interventions by people with aphasia (PWA). Currently, this assessment is conducted manually by speech and language therapists (SLT). Surprisingly, despite advancements in automatic speech recognition (ASR) and artificial intelligence with technologies like deep learning, research on developing automated systems for this task has been scarce. Here we present NUVA, an utterance verification system incorporating a deep learning element that classifies 'correct' versus' incorrect' naming attempts from aphasic stroke patients. When tested on eight native British-English speaking PWA the system's performance accuracy ranged between 83.6% to 93.6%, with a 10-fold cross-validation mean of 89.5%. This performance was not only significantly better than a baseline created for this study using one of the leading commercially available ASRs (Google speech-to-text service) but also comparable in some instances with two independent SLT ratings for the same dataset.

cs.CL↗