115 research outputs found
Cross-Subject Image Analysis in Diffusion Brain MRI
As our life expectancy continues to rise, the prevalence of diseases associated with aging increases correspondingly. For Alzheimer’s disease, this implies that the number of persons affected, directly or indirectly, will rise dramatically. Early diagnosis, intervention, and ultimately prevention of Alzheimer’s disease are therefore ever more urgent research aims. Advanced neuroimaging techniques such as diffusion MRI, which provides non-invasive insight into brain changes at the microstructural level, are promising for the identification of changes that relate to the early stages of the disease. Disentangling these early pathological changes from those in ‘normal’ brain aging however requires more insight in the broad spectrum o
Reproducible White Matter Tract Segmentation Using 3D U-Net on a Large-scale DTI Dataset
Tract-specific diffusion measures, as derived from brain diffusion MRI, have
been linked to white matter tract structural integrity and neurodegeneration.
As a consequence, there is a large interest in the automatic segmentation of
white matter tract in diffusion tensor MRI data. Methods based on the
tractography are popular for white matter tract segmentation. However, because
of the limited consistency and long processing time, such methods may not be
suitable for clinical practice. We therefore developed a novel convolutional
neural network based method to directly segment white matter tract trained on a
low-resolution dataset of 9149 DTI images. The method is optimized on input,
loss function and network architecture selections. We evaluated both
segmentation accuracy and reproducibility, and reproducibility of determining
tract-specific diffusion measures. The reproducibility of the method is higher
than that of the reference standard and the determined diffusion measures are
consistent. Therefore, we expect our method to be applicable in clinical
practice and in longitudinal analysis of white matter microstructure.Comment: Machine Learning in Medical Imaging (MLMI), 201
A hybrid deep learning framework for integrated segmentation and registration: evaluation on longitudinal white matter tract changes
To accurately analyze changes of anatomical structures in longitudinal
imaging studies, consistent segmentation across multiple time-points is
required. Existing solutions often involve independent registration and
segmentation components. Registration between time-points is used either as a
prior for segmentation in a subsequent time point or to perform segmentation in
a common space. In this work, we propose a novel hybrid convolutional neural
network (CNN) that integrates segmentation and registration into a single
procedure. We hypothesize that the joint optimization leads to increased
performance on both tasks. The hybrid CNN is trained by minimizing an
integrated loss function composed of four different terms, measuring
segmentation accuracy, similarity between registered images, deformation field
smoothness, and segmentation consistency. We applied this method to the
segmentation of white matter tracts, describing functionally grouped axonal
fibers, using N=8045 longitudinal brain MRI data of 3249 individuals. The
proposed method was compared with two multistage pipelines using two existing
segmentation methods combined with a conventional deformable registration
algorithm. In addition, we assessed the added value of the joint optimization
for segmentation and registration separately. The hybrid CNN yielded
significantly higher accuracy, consistency and reproducibility of segmentation
than the multistage pipelines, and was orders of magnitude faster. Therefore,
we expect it can serve as a novel tool to support clinical and epidemiological
analyses on understanding microstructural brain changes over time.Comment: MICCAI 2019 (oral presentation
MisMatch: Calibrated Segmentation via Consistency on Differential Morphological Feature Perturbations with Limited Labels
Semi-supervised learning (SSL) is a promising machine learning paradigm to
address the issue of label scarcity in medical imaging. SSL methods were
originally developed in image classification. The state-of-the-art SSL methods
in image classification utilise consistency regularisation to learn unlabelled
predictions which are invariant to input level perturbations. However, image
level perturbations violate the cluster assumption in the setting of
segmentation. Moreover, existing image level perturbations are hand-crafted
which could be sub-optimal. Therefore, it is a not trivial to straightforwardly
adapt existing SSL image classification methods in segmentation. In this paper,
we propose MisMatch, a semi-supervised segmentation framework based on the
consistency between paired predictions which are derived from two differently
learnt morphological feature perturbations. MisMatch consists of an encoder and
two decoders. One decoder learns positive attention for foreground on
unlabelled data thereby generating dilated features of foreground. The other
decoder learns negative attention for foreground on the same unlabelled data
thereby generating eroded features of foreground. We first develop a 2D U-net
based MisMatch framework and perform extensive cross-validation on a CT-based
pulmonary vessel segmentation task and show that MisMatch statistically
outperforms state-of-the-art semi-supervised methods when only 6.25\% of the
total labels are used. In a second experiment, we show that U-net based
MisMatch outperforms state-of-the-art methods on an MRI-based brain tumour
segmentation task. In a third experiment, we show that a 3D MisMatch
outperforms a previous method using input level augmentations, on a left atrium
segmentation task. Lastly, we find that the performance improvement of MisMatch
over the baseline might originate from its better calibration
Neuro4Neuro: A neural network approach for neural tract segmentation using large-scale population-based diffusion imaging
Subtle changes in white matter (WM) microstructure have been associated with
normal aging and neurodegeneration. To study these associations in more detail,
it is highly important that the WM tracts can be accurately and reproducibly
characterized from brain diffusion MRI. In addition, to enable analysis of WM
tracts in large datasets and in clinical practice it is essential to have
methodology that is fast and easy to apply. This work therefore presents a new
approach for WM tract segmentation: Neuro4Neuro, that is capable of direct
extraction of WM tracts from diffusion tensor images using convolutional neural
network (CNN). This 3D end-to-end method is trained to segment 25 WM tracts in
aging individuals from a large population-based study (N=9752, 1.5T MRI). The
proposed method showed good segmentation performance and high reproducibility,
i.e., a high spatial agreement (Cohen's kappa, k = 0.72 ~ 0.83) and a low
scan-rescan error in tract-specific diffusion measures (e.g., fractional
anisotropy: error = 1% ~ 5%). The reproducibility of the proposed method was
higher than that of a tractography-based segmentation algorithm, while being
orders of magnitude faster (0.5s to segment one tract). In addition, we showed
that the method successfully generalizes to diffusion scans from an external
dementia dataset (N=58, 3T MRI). In two proof-of-principle experiments, we
associated WM microstructure obtained using the proposed method with age in a
normal elderly population, and with disease subtypes in a dementia cohort. In
concordance with the literature, results showed a widespread reduction of
microstructural organization with aging and substantial group-wise
microstructure differences between dementia subtypes. In conclusion, we
presented a highly reproducible and fast method for WM tract segmentation that
has the potential of being used in large-scale studies and clinical practice.Comment: Preprint to be published in NeuroImag
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Quantifying disease activity in rheumatoid arthritis with the TSPO PET ligand 18 F-GE-180 and comparison with 18 F-FDG and DCE-MRI
Abstract: Purpose: While the aetiology of rheumatoid arthritis (RA) remains unclear, many of the inflammatory components are well characterised. For diagnosis and therapy evaluation, in vivo insight into these processes would be valuable. Various imaging probes have shown value including dynamic contrast-enhanced (DCE) MRI and PET/CT using 18F-fluorodeoxyglucose (18F-FDG) or tracers targeting the translocator protein (TSPO). To evaluate 18F-GE-180, a novel TSPO PET tracer, for detecting and quantifying disease activity in RA, we compared 18F-GE-180 uptake with that of 18F-FDG and DCE-MRI measures of inflammation. Methods: Eight RA patients with moderate-to-high, stable disease activity and active disease in at least one wrist were included in this study (NCT02350426). Participants underwent PET/CT examinations with 18F-GE-180 and 18F-FDG on separate visits, covering the shoulders and from the pelvis to the feet, including hands and wrists. DCE-MRI was performed on one affected hand. Uptake was compared visually between tracers as judged by an experienced radiologist and quantitatively using the maximum standardised uptake value (SUVmax). Uptake for both tracers was correlated with DCE-MRI parameters of inflammation, including the volume transfer coefficient Ktrans using Pearson correlation (r). Results: PET/CT imaging with 18F-GE-180 in RA patients showed marked extra-synovial uptake around the affected joints. Overall sensitivity for detecting clinically affected joints was low (14%). 18F-GE-180 uptake did not or only weakly correlate with DCE-MRI parameters in the wrist (r = 0.09–0.31). 18F-FDG showed higher sensitivity for detecting symptomatic joints (34%), as well as strong positive correlation with DCE-MRI parameters (SUVmax vs. Ktrans: r = 0.92 for wrist; r = 0.68 for metacarpophalangeal joints). Conclusions: The correlations between DCE-MRI parameters and 18F-FDG uptake support use of this PET tracer for quantification of inflammatory burden in RA. The TSPO tracer 18F-GE-180, however, has shown limited use for the investigation of RA due to its poor sensitivity and ability to quantify disease activity in RA
Where is VALDO? VAscular Lesions Detection and segmentatiOn challenge at MICCAI 2021
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 VAscular Lesions DetectiOn and Segmentation (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
Recent smell loss is the best predictor of COVID-19 among individuals with recent respiratory symptoms
In a preregistered, cross-sectional study we investigated whether olfactory loss is a reliable predictor of COVID-19 using a crowdsourced questionnaire in 23 languages to assess symptoms in individuals self-reporting recent respiratory illness. We quantified changes in chemosensory abilities during the course of the respiratory illness using 0-100 visual analog scales (VAS) for participants reporting a positive (C19+; n=4148) or negative (C19-; n=546) COVID-19 laboratory test outcome. Logistic regression models identified univariate and multivariate predictors of COVID-19 status and post-COVID-19 olfactory recovery. Both C19+ and C19- groups exhibited smell loss, but it was significantly larger in C19+ participants (mean±SD, C19+: -82.5±27.2 points; C19-: -59.8±37.7). Smell loss during illness was the best predictor of COVID-19 in both univariate and multivariate models (ROC AUC=0.72). Additional variables provide negligible model improvement. VAS ratings of smell loss were more predictive than binary chemosensory yes/no-questions or other cardinal symptoms (e.g., fever). Olfactory recovery within 40 days of respiratory symptom onset was reported for ~50% of participants and was best predicted by time since respiratory symptom onset. We find that quantified smell loss is the best predictor of COVID-19 amongst those with symptoms of respiratory illness. To aid clinicians and contact tracers in identifying individuals with a high likelihood of having COVID-19, we propose a novel 0-10 scale to screen for recent olfactory loss, the ODoR-19. We find that numeric ratings ≤2 indicate high odds of symptomatic COVID-19 (4<10). Once independently validated, this tool could be deployed when viral lab tests are impractical or unavailable
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