150 research outputs found

    Generalised Dice overlap as a deep learning loss function for highly unbalanced segmentations

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    Deep-learning has proved in recent years to be a powerful tool for image analysis and is now widely used to segment both 2D and 3D medical images. Deep-learning segmentation frameworks rely not only on the choice of network architecture but also on the choice of loss function. When the segmentation process targets rare observations, a severe class imbalance is likely to occur between candidate labels, thus resulting in sub-optimal performance. In order to mitigate this issue, strategies such as the weighted cross-entropy function, the sensitivity function or the Dice loss function, have been proposed. In this work, we investigate the behavior of these loss functions and their sensitivity to learning rate tuning in the presence of different rates of label imbalance across 2D and 3D segmentation tasks. We also propose to use the class re-balancing properties of the Generalized Dice overlap, a known metric for segmentation assessment, as a robust and accurate deep-learning loss function for unbalanced tasks

    A Heteroscedastic Uncertainty Model for Decoupling Sources of MRI Image Quality

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    Quality control (QC) of medical images is essential to ensure that downstream analyses such as segmentation can be performed successfully. Currently, QC is predominantly performed visually at significant time and operator cost. We aim to automate the process by formulating a probabilistic network that estimates uncertainty through a heteroscedastic noise model, hence providing a proxy measure of task-specific image quality that is learnt directly from the data. By augmenting the training data with different types of simulated k-space artefacts, we propose a novel cascading CNN architecture based on a student-teacher framework to decouple sources of uncertainty related to different k-space augmentations in an entirely self-supervised manner. This enables us to predict separate uncertainty quantities for the different types of data degradation. While the uncertainty measures reflect the presence and severity of image artefacts, the network also provides the segmentation predictions given the quality of the data. We show models trained with simulated artefacts provide informative measures of uncertainty on real-world images and we validate our uncertainty predictions on problematic images identified by human-raters

    Where is VALDO? VAscular Lesions Detection and segmentatiOn challenge at MICCAI 2021

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    Imaging markers of cerebral small vessel disease provide valuable information on brain health, but their manual assessment is time-consuming and hampered by substantial intra- and interrater variability. Automated rating may benefit biomedical research, as well as clinical assessment, but diagnostic reliability of existing algorithms is unknown. Here, we present the results of the \textit{VAscular Lesions DetectiOn and Segmentation} (\textit{Where is VALDO?}) challenge that was run as a satellite event at the international conference on Medical Image Computing and Computer Aided Intervention (MICCAI) 2021. This challenge aimed to promote the development of methods for automated detection and segmentation of small and sparse imaging markers of cerebral small vessel disease, namely enlarged perivascular spaces (EPVS) (Task 1), cerebral microbleeds (Task 2) and lacunes of presumed vascular origin (Task 3) while leveraging weak and noisy labels. Overall, 12 teams participated in the challenge proposing solutions for one or more tasks (4 for Task 1 - EPVS, 9 for Task 2 - Microbleeds and 6 for Task 3 - Lacunes). Multi-cohort data was used in both training and evaluation. Results showed a large variability in performance both across teams and across tasks, with promising results notably for Task 1 - EPVS and Task 2 - Microbleeds and not practically useful results yet for Task 3 - Lacunes. It also highlighted the performance inconsistency across cases that may deter use at an individual level, while still proving useful at a population level

    Hierarchical brain parcellation with uncertainty

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    Many atlases used for brain parcellation are hierarchically organised, progressively dividing the brain into smaller sub-regions. However, state-of-the-art parcellation methods tend to ignore this structure and treat labels as if they are `flat'. We introduce a hierarchically-aware brain parcellation method that works by predicting the decisions at each branch in the label tree. We further show how this method can be used to model uncertainty separately for every branch in this label tree. Our method exceeds the performance of flat uncertainty methods, whilst also providing decomposed uncertainty estimates that enable us to obtain self-consistent parcellations and uncertainty maps at any level of the label hierarchy. We demonstrate a simple way these decision-specific uncertainty maps may be used to provided uncertainty-thresholded tissue maps at any level of the label tree.Comment: To be published in the MICCAI 2020 workshop: Uncertainty for Safe Utilization of Machine Learning in Medical Imagin

    APOE ?4 status is associated with white matter hyperintensities volume accumulation rate independent of AD diagnosis.

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    To assess the relationship between carriage of APOE ?4 allele and evolution of white matter hyperintensities (WMHs) volume, we longitudinally studied 339 subjects from the Alzheimer's Disease Neuroimaging Initiative cohort with diagnoses ranging from normal controls to probable Alzheimer's disease (AD). A purpose-built longitudinal automatic method was used to segment WMH using constraints derived from an atlas-based model selection applied to a time-averaged image. Linear mixed models were used to evaluate the differences in rate of change across diagnosis and genetic groups. After adjustment for covariates (age, sex, and total intracranial volume), homozygous APOE ?4?4 subjects had a significantly higher rate of WMH accumulation (22.5% per year 95% CI [14.4, 31.2] for a standardized population having typical values of covariates) compared with the heterozygous (?4?3) subjects (10.0% per year [6.7, 13.4]) and homozygous ?3?3 (6.6% per year [4.1, 9.3]) subjects. Rates of accumulation increased with diagnostic severity; controls accumulated 5.8% per year 95% CI: [2.2, 9.6] for the standardized population, early mild cognitive impairment 6.6% per year [3.9, 9.4], late mild cognitive impairment 12.5% per year [8.2, 17.0] and AD subjects 14.7% per year [6.0, 24.0]. Following adjustment for APOE status, these differences became nonstatistically significant suggesting that APOE ?4 genotype is the major driver of accumulation of WMH volume rather than diagnosis of AD

    Common infections and neuroimaging markers of dementia in three UK cohort studies

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    INTRODUCTION: We aimed to investigate associations between common infections and neuroimaging markers of dementia risk (brain volume, hippocampal volume, white matter lesions) across three population-based studies. METHODS: We tested associations between serology measures (pathogen serostatus, cumulative burden, continuous antibody responses) and outcomes using linear regression, including adjustments for total intracranial volume and scanner/clinic information (basic model), age, sex, ethnicity, education, socioeconomic position, alcohol, body mass index, and smoking (fully adjusted model). Interactions between serology measures and apolipoprotein E (APOE) genotype were tested. Findings were meta-analyzed across cohorts (Nmain ¬†=¬†2632; NAPOE-interaction ¬†=¬†1810). RESULTS: Seropositivity to John Cunningham virus associated with smaller brain volumes in basic models (ő≤¬†=¬†-3.89¬†mL [-5.81, -1.97], Padjusted ¬†<¬†0.05); these were largely attenuated in fully adjusted models (ő≤¬†=¬†-1.59¬†mL [-3.55, 0.36], P¬†=¬†0.11). No other relationships were robust to multiple testing corrections and sensitivity analyses, but several suggestive associations were observed. DISCUSSION: We did not find clear evidence for relationships between common infections and markers of dementia risk. Some suggestive findings warrant testing for replication

    Courage in decision-making:A mixed-methods study of COVID-19 vaccine uptake in women of reproductive age in the UK

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    COVID-19 vaccination rates are lower in women of reproductive age (WRA), including preg-nant/postpartum women despite their poorer COVID-19-related outcomes. We evaluated vac-cination experiences of 3,568 UK WRA, including 1,983 women (55.6%) experiencing a pandemic pregnancy, recruited through the ZOE COVID Symptom Study app. Two staggered online ques-tionnaires (Oct-Dec 2021: 3,453 responders; Aug-Sept 2022: 2,129 responders) assessed reproductive status, COVID-19 status, vaccination, and attitudes for/against vaccination. Descriptive analyses included vaccination type(s), timing relative to age-based eligibility and reproductive status, vaccination delay (first vaccination &gt;28 days from eligibility), and rationale, with content analysis of free-text comments. Most responders (3,392/3,453, 98.2%) were vaccinated by Dec 2021, motivated by: altruism, vaccination supportiveness in general, low-risk, and COVID-19 concerns. Few declined vaccination (by Sept/2022: 20/2,129, 1.0%), citing: risks (pregnancy-specific and longer-term), pre-existing immunity, and personal/philosophical reasons. Few women de-layed vaccination, although pregnant/postpartum women (vs. other WRA), received vaccination later (median 3 vs. 0 days after eligibility, p&lt;0.0001). Despite high uptake, concerns included: adverse effects; misinformation (including from healthcare providers); ever-changing govern-ment advice; and complex decision-making. In summary, most women in this large WRA cohort were promptly vaccinated, including pregnant/post-partum women. Altruism and community benefit superseded personal benefit as reasons for vaccination. Nevertheless, responders expe-rienced angst, and received vaccine-related misinformation and discouragement. These findings should inform vaccination strategies in WRA

    Automated White Matter Hyperintensity Segmentation Using Bayesian Model Selection: Assessment and Correlations with Cognitive Change.

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    Accurate, automated white matter hyperintensity (WMH) segmentations are needed for large-scale studies to understand contributions of WMH to neurological diseases. We evaluated Bayesian Model Selection (BaMoS), a hierarchical fully-unsupervised model selection framework for WMH segmentation. We compared BaMoS segmentations to semi-automated segmentations, and assessed whether they predicted longitudinal cognitive change in control, early Mild Cognitive Impairment (EMCI), late Mild Cognitive Impairment (LMCI), subjective/significant memory concern (SMC) and Alzheimer's (AD) participants. Data were downloaded from the Alzheimer's disease Neuroimaging Initiative (ADNI). Magnetic resonance images from 30 control and 30¬†AD participants were selected to incorporate multiple scanners, and were semi-automatically segmented by 4 raters and BaMoS. Segmentations were assessed using volume correlation, Dice score, and other spatial metrics. Linear mixed-effect models were fitted to 180 control, 107 SMC, 320 EMCI, 171 LMCI and 151¬†AD participants separately in each group, with the outcomes being cognitive change (e.g. mini-mental state examination; MMSE), and BaMoS WMH, age, sex, race and education used as predictors. There was a high level of agreement between BaMoS' WMH segmentation volumes and a consensus of rater segmentations, with a median Dice score of 0.74 and correlation coefficient of 0.96. BaMoS WMH predicted cognitive change in: control, EMCI, and SMC groups using MMSE; LMCI using clinical dementia rating scale; and EMCI using Alzheimer's disease assessment scale-cognitive subscale (p¬†<‚ÄČ0.05, all tests). BaMoS compares well to semi-automated segmentation, is robust to different WMH loads and scanners, and can generate volumes which predict decline. BaMoS can be applicable to further large-scale studies
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