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Joanna M. Wardlaw

Publications and source records attributed to Joanna M. Wardlaw.

12 recordsLinked to original sources

Hetero-modal learning and corruption-resistant hetero-modal inference for joint segmentation of white matter hyperintensities and ischaemic stroke lesions in MRI

White matter hyperintensities (WMH) and ischaemic stroke lesions (ISL) are visually confounding, co-occurring pathologies that require large, diverse datasets for robust deep learning segmentation. However, assembling such datasets is hindered by cohort samples that lack reference segmentations from both features and complete sets of MRI structural sequences (i.e., "modalities"). To maximise data utility, we investigate hetero-modal learning using a dataset of 206 vascular disease patients across four MRI sequences (T1-weighted, T2-weighted, fluid-attenuated inversion recovery, and diffusion-weighted imaging) with expert annotations of both WMH and ISL. We demonstrate that hetero-modal learning outperforms models trained using a single imaging modality in scenarios with substantial missing data, including a split where only 10% of the training data contains all four modalities while the remainder is uni-modal, and a split relying on a single shared "anchor" modality with zero overlap between the remaining modalities. Furthermore, models trained under this second split successfully perform inference on unseen combinations of modalities. Yet, while standard hetero-modal networks handle missing sequences, clinical deployment introduces the additional challenge of silent data degradation - where modalities are present but severely corrupted. To bridge this gap, we introduce the Multimodal Attention Router (MMAR) block. Our experiments demonstrate that, when trained with a "corruption augmentation" strategy, the MMAR effectively dynamically weights the encoded features of each modality, maintaining strong performance during hetero-modal inference even in the presence of unflagged catastrophically corrupted modalities.

eess.IV↗

Multi-task learning for the automatic grading of enlarged perivascular space burden using MRI

Enlarged perivascular spaces (PVS) visible in brain magnetic resonance imaging (MRI) are increasingly thought to be linked to poor brain health. PVS are elongated structures of less than 3 mm in diameter and can be numerous. To reflect the incidence of PVS, radiologists visually score their burden following a clinical grading scale - a task that would benefit from automation to accelerate analyses and overcome the influence of inter-observer differences. We developed and evaluated methods for training machine learning models to score PVS incidence in the basal ganglia (BG) and centrum semiovale (CSO) leveraging the Potters/Wardlaw scale. The novelty in our work lies in the use of imperfect, semi-automatically generated "silver-standard" PVS segmentation masks during training, in addition to PVS radiological scores. We comparatively evaluated a conditional convolutional neural network (CNN) which accepts PVS masks as an extra input channel, a multi-task CNN which performs both PVS segmentation and scoring, and a logistic regression model which utilises features derived from PVS masks to predict PVS scores. Multi-task learning was the most effective method, achieving a mean average precision of 64.08% compared to 60.22% for the conditional CNN, 52.11% for a baseline CNN trained only to predict PVS scores, and 49.32% for the logistic regression model. The multi-task model showed an ability to localise individual PVS not shown by the other CNNs, and behaved in a probabilistically sensible way, predicting with lower confidence on inherently harder classes. Age, sex, hypertension status, white matter hyperintensity volume, and ischaemic stroke lesion status were shown to be associated with the multi-task model's PVS score predictions and the ground truth in a similar way.

cs.CV↗

Automated Distinction of Intimal and Medial Intracranial Arterial Calcification from CT Head

Intracranial arterial calcifications (IACs) are a common finding on clinical non-contrast enhanced head CT scans and are associated with neurovascular disease. Calcifications can occur in the intimal or medial layer of the arterial wall, subtypes that differ in aetiology and may have distinct clinical relevance. These subtypes can be visually distinguished by radiologists based on the shape of the calcifications. We investigate three automated approaches for subtype classification of IAC from head CT-derived segmentation masks: (1) an automated adaptation of the established radiological visual score, (2) a sphericity-based method, and (3) a method based on shape embeddings extracted by a medical shape foundation model. All approaches use the same lightweight classification pipeline on top of the features they compute and are evaluated using 5-fold cross-validation. The three methods achieved comparable performance, with the embedding-based approach yielding the best overall results with a weighted F1 (mean $\pm$ SD) of up to 71.5 $\pm$ 3.7 for a single artery and 59.8 $\pm$ 1.7 for the joint artery classification. Performance was largely preserved when using automated instead of manual IAC segmentation masks, and we found the difference in weighted F1 not significant. Our results show that fully automated IAC subtype quantification from head CT is feasible and remains robust to the use of manual and automated IAC segmentation masks. Code at https://github.com/bjin96/iac-subtyping.

eess.IV↗

Comparative evaluation of training strategies using partially labelled datasets for segmentation of white matter hyperintensities and stroke lesions in FLAIR MRI

White matter hyperintensities (WMH) and ischaemic stroke lesions (ISL) are key imaging biomarkers of cerebral small vessel disease (SVD) detectable on magnetic resonance imaging (MRI). The development of robust deep learning models to automatically segment and differentiate these pathologies remains challenging. Specifically, WMH and ISL frequently co-occur within the same subject and present as visually confounding hyperintensities on fluid-attenuated inversion recovery (FLAIR) sequences, complicating their accurate delineation. To address the scarcity of fully annotated cohorts, we systematically evaluated six accessible strategies for training a joint WMH and ISL segmentation model using partially labelled data. We aggregated privately held and publicly available datasets to curate a large-scale cohort of 2,052 MRI volumes, of which 1341 and 1152 volumes contained ground truth annotations for WMH and ISL, respectively. Our analysis indicates that multiple strategies effectively leverage partially labelled data to enhance overall model performance, with pseudolabelling emerging as the most effective approach. This model exhibited a consistent WMH segmentation policy and successfully detected the majority of FLAIR-positive ISL. These findings demonstrate the viability of using partially labelled data to develop reliable automated segmentation tools, which can support ongoing SVD monitoring and high-throughput biomarker extraction for large-scale clinical research.

cs.CV↗

Subcortical Shape Variations and Their Associations with Cognition Across the 8th Decade of Life. A Study in the Lothian Birth Cohort 1936

The study of brain morphology changes in normal individuals may capture aspects of functionally-relevant brain aging not fully indicated by gross volumetry. Despite the important role of subcortical brain structures in cognition, the associations between their morphological trajectories and cognitive changes in aging have not been documented. We use neuroimaging, demographic, and cognitive data from a large longitudinal study of cognitive aging, the Lothian Birth Cohort 1936, to explore shape changes in subcortical brain structures of community-dwelling individuals across their 8th decade of life. We investigate the association of these changes with cognitive aging using ANCOVA and mixed linear model analyses. Subcortical shape changes were heterogeneous, with varied atrophy patterns across whole period. The hippocampus and the ventral DC experienced varied morphological deformations (from its baseline point) different in left and right hemispheres, while the thalami and globus pallidi shapes, for example, experienced a more uniform volume contraction, nearly symmetrical throughout different timelines. Changes in general cognition were mainly associated with inwards and outwards vertex displacements between the time-points.

q-bio.NC↗

Standardized Evaluation of Automatic Methods for Perivascular Spaces Segmentation in MRI -- MICCAI 2024 Challenge Results

Perivascular spaces (PVS), when abnormally enlarged and visible in magnetic resonance imaging (MRI) structural sequences, are important imaging markers of cerebral small vessel disease and potential indicators of neurodegenerative conditions. Despite their clinical significance, automatic enlarged PVS (EPVS) segmentation remains challenging due to their small size, variable morphology, similarity with other pathological features, and limited annotated datasets. This paper presents the EPVS Challenge organized at MICCAI 2024, which aims to advance the development of automated algorithms for EPVS segmentation across multi-site data. We provided a diverse dataset comprising 100 training, 50 validation, and 50 testing scans collected from multiple international sites (UK, Singapore, and China) with varying MRI protocols and demographics. All annotations followed the STRIVE protocol to ensure standardized ground truth and covered the full brain parenchyma. Seven teams completed the full challenge, implementing various deep learning approaches primarily based on U-Net architectures with innovations in multi-modal processing, ensemble strategies, and transformer-based components. Performance was evaluated using dice similarity coefficient, absolute volume difference, recall, and precision metrics. The winning method employed MedNeXt architecture with a dual 2D/3D strategy for handling varying slice thicknesses. The top solutions showed relatively good performance on test data from seen datasets, but significant degradation of performance was observed on the previously unseen Shanghai cohort, highlighting cross-site generalization challenges due to domain shift. This challenge establishes an important benchmark for EPVS segmentation methods and underscores the need for the continued development of robust algorithms that can generalize in diverse clinical settings.

q-bio.QM↗

Calibrated Self-supervised Vision Transformers Improve Intracranial Arterial Calcification Segmentation from Clinical CT Head Scans

Vision Transformers (ViTs) have gained significant popularity in the natural image domain but have been less successful in 3D medical image segmentation. Nevertheless, 3D ViTs are particularly interesting for large medical imaging volumes due to their efficient self-supervised training within the masked autoencoder (MAE) framework, which enables the use of imaging data without the need for expensive manual annotations. Intracranial arterial calcification (IAC) is an imaging biomarker visible on routinely acquired CT scans linked to neurovascular diseases such as stroke and dementia, and automated IAC quantification could enable their large-scale risk assessment. We pre-train ViTs with MAE and fine-tune them for IAC segmentation for the first time. To develop our models, we use highly heterogeneous data from a large clinical trial, the third International Stroke Trial (IST-3). We evaluate key aspects of MAE pre-trained ViTs in IAC segmentation, and analyse the clinical implications. We show: 1) our calibrated self-supervised ViT beats a strong supervised nnU-Net baseline by 3.2 Dice points, 2) low patch sizes are crucial for ViTs for IAC segmentation and interpolation upsampling with regular convolutions is preferable to transposed convolutions for ViT-based models, and 3) our ViTs increase robustness to higher slice thicknesses and improve risk group classification in a clinical scenario by 46%. Our code is available online.

cs.CV↗

Uncertainty quantification for White Matter Hyperintensity segmentation detects silent failures and improves automated Fazekas quantification

White Matter Hyperintensities (WMH) are key neuroradiological markers of small vessel disease present in brain MRI. Assessment of WMH is important in research and clinics. However, WMH are challenging to segment due to their high variability in shape, location, size, poorly defined borders, and similar intensity profile to other pathologies (e.g stroke lesions) and artefacts (e.g head motion). In this work, we assess the utility and semantic properties of the most effective techniques for uncertainty quantification (UQ) in segmentation for the WMH segmentation task across multiple test-time data distributions. We find UQ techniques reduce 'silent failure' by identifying in UQ maps small WMH clusters in the deep white matter that are unsegmented by the model. A combination of Stochastic Segmentation Networks with Deep Ensembles also yields the highest Dice and lowest Absolute Volume Difference % (AVD) score and can highlight areas where there is ambiguity between WMH and stroke lesions. We further demonstrate the downstream utility of UQ, proposing a novel method for classification of the clinical Fazekas score using spatial features extracted from voxelwise WMH probability and UQ maps. We show that incorporating WMH uncertainty information improves Fazekas classification performance and calibration. Our model with (UQ and spatial WMH features)/(spatial WMH features)/(WMH volume only) achieves a balanced accuracy score of 0.74/0.67/0.62, and root brier score of 0.65/0.72/0.74 in the Deep WMH and balanced accuracy of 0.74/0.73/0.71 and root brier score of 0.64/0.66/0.68 in the Periventricular region. We further demonstrate that stochastic UQ techniques with high sample diversity can improve the detection of poor quality segmentations.

eess.IV↗

Automated neuroradiological support systems for multiple cerebrovascular disease markers -- A systematic review and meta-analysis

Cerebrovascular diseases (CVD) can lead to stroke and dementia. Stroke is the second leading cause of death world wide and dementia incidence is increasing by the year. There are several markers of CVD that are visible on brain imaging, including: white matter hyperintensities (WMH), acute and chronic ischaemic stroke lesions (ISL), lacunes, enlarged perivascular spaces (PVS), acute and chronic haemorrhagic lesions, and cerebral microbleeds (CMB). Brain atrophy also occurs in CVD. These markers are important for patient management and intervention, since they indicate elevated risk of future stroke and dementia. We systematically reviewed automated systems designed to support radiologists reporting on these CVD imaging findings. We considered commercially available software and research publications which identify at least two CVD markers. In total, we included 29 commercial products and 13 research publications. Two distinct types of commercial support system were available: those which identify acute stroke lesions (haemorrhagic and ischaemic) from computed tomography (CT) scans, mainly for the purpose of patient triage; and those which measure WMH and atrophy regionally and longitudinally. In research, WMH and ISL were the markers most frequently analysed together, from magnetic resonance imaging (MRI) scans; lacunes and PVS were each targeted only twice and CMB only once. For stroke, commercially available systems largely support the emergency setting, whilst research systems consider also follow-up and routine scans. The systems to quantify WMH and atrophy are focused on neurodegenerative disease support, where these CVD markers are also of significance. There are currently no openly validated systems, commercially, or in research, performing a comprehensive joint analysis of all CVD markers (WMH, ISL, lacunes, PVS, haemorrhagic lesions, CMB, and atrophy).

physics.med-ph↗

Pre-processing and quality control of large clinical CT head datasets for intracranial arterial calcification segmentation

As a potential non-invasive biomarker for ischaemic stroke, intracranial arterial calcification (IAC) could be used for stroke risk assessment on CT head scans routinely acquired for other reasons (e.g. trauma, confusion). Artificial intelligence methods can support IAC scoring, but they have not yet been developed for clinical imaging. Large heterogeneous clinical CT datasets are necessary for the training of such methods, but they exhibit expected and unexpected data anomalies. Using CTs from a large clinical trial, the third International Stroke Trial (IST-3), we propose a pipeline that uses as input non-enhanced CT scans to output regions of interest capturing selected large intracranial arteries for IAC scoring. Our method uses co-registration with templates. We focus on quality control, using information presence along the z-axis of the imaging to group and apply similarity measures (structural similarity index measure) to triage assessment of individual image series. Additionally, we propose superimposing thresholded binary masks of the series to inspect large quantities of data in parallel. We identify and exclude unrecoverable samples and registration failures. In total, our pipeline processes 10,659 CT series, rejecting 4,322 (41%) in the entire process, 1,450 (14% of the total) during quality control, and outputting 6,337 series. Our pipeline enables effective and efficient region of interest localisation for targeted IAC segmentation.

eess.IV↗

Direct Estimation of Pharmacokinetic Parameters from DCE-MRI using Deep CNN with Forward Physical Model Loss

Dynamic contrast-enhanced (DCE) MRI is an evolving imaging technique that provides a quantitative measure of pharmacokinetic (PK) parameters in body tissues, in which series of T1-weighted images are collected following the administration of a paramagnetic contrast agent. Unfortunately, in many applications, conventional clinical DCE-MRI suffers from low spatiotemporal resolution and insufficient volume coverage. In this paper, we propose a novel deep learning based approach to directly estimate the PK parameters from undersampled DCE-MRI data. Specifically, we design a custom loss function where we incorporate a forward physical model that relates the PK parameters to corrupted image-time series obtained due to subsampling in k-space. This allows the network to directly exploit the knowledge of true contrast agent kinetics in the training phase, and hence provide more accurate restoration of PK parameters. Experiments on clinical brain DCE datasets demonstrate the efficacy of our approach in terms of fidelity of PK parameter reconstruction and significantly faster parameter inference compared to a model-based iterative reconstruction method.

cs.CV↗

Perivascular Spaces Segmentation in Brain MRI Using Optimal 3D Filtering

Perivascular Spaces (PVS) are a recently recognised feature of Small Vessel Disease (SVD), also indicating neuroinflammation, and are an important part of the brain's circulation and glymphatic drainage system. Quantitative analysis of PVS on Magnetic Resonance Images (MRI) is important for understanding their relationship with neurological diseases. In this work, we propose a segmentation technique based on the 3D Frangi filtering for extraction of PVS from MRI. Based on prior knowledge from neuroradiological ratings of PVS, we used ordered logit models to optimise Frangi filter parameters in response to the variability in the scanner's parameters and study protocols. We optimized and validated our proposed models on two independent cohorts, a dementia sample (N=20) and patients who previously had mild to moderate stroke (N=48). Results demonstrate the robustness and generalisability of our segmentation method. Segmentation-based PVS burden estimates correlated with neuroradiological assessments (Spearman's $ρ$ = 0.74, p $<$ 0.001), suggesting the great potential of our proposed method

cs.CV↗