412 research outputs found
Automatic C-Plane Detection in Pelvic Floor Transperineal Volumetric Ultrasound
Transperineal volumetric ultrasound (US) imaging has become routine practice for diagnosing pelvic floor disease (PFD). Hereto, clinical guidelines stipulate to make measurements in an anatomically defined 2D plane within a 3D volume, the so-called C-plane. This task is currently performed manually in clinical practice, which is labour-intensive and requires expert knowledge of pelvic floor anatomy, as no computer-aided C-plane method exists. To automate this process, we propose a novel, guideline-driven approach for automatic detection of the C-plane. The method uses a convolutional neural network (CNN) to identify extreme coordinates of the symphysis pubis and levator ani muscle (which define the C-plane) directly via landmark regression. The C-plane is identified in a postprocessing step. When evaluated on 100 US volumes, our best performing method (multi-task regression with UNet) achieved a mean error of 6.05 mm and 4.81 â and took 20 s. Two experts blindly evaluated the quality of the automatically detected planes and manually defined the (gold standard) C-plane in terms of their clinical diagnostic quality. We show that the proposed method performs comparably to the manual definition. The automatic method reduces the average time to detect the C-plane by 100 s and reduces the need for high-level expertise in PFD US assessment
Automatic Extraction of Hiatal Dimensions in 3-D Transperineal Pelvic Ultrasound Recordings
The aims of this work were to create a robust automatic software tool for measurement of the levator hiatal area on transperineal ultrasound (TPUS) volumes and to measure the potential reduction in variability and time taken for analysis in a clinical setting. The proposed tool automatically detects the C-plane (i.e., the plane of minimal hiatal dimensions) from a 3-D TPUS volume and subsequently uses the extracted plane to automatically segment the levator hiatus, using a convolutional neural network. The automatic pipeline was tested using 73 representative TPUS volumes. Reference hiatal outlines were obtained manually by two experts and compared with the pipeline's automated outlines. The Hausdorff distance, area, a clinical quality score, C-plane angle and C-plane Euclidean distance were used to evaluate C-plane detection and quantify levator hiatus segmentation accuracy. A visual Turing test was created to compare the performance of the software with that of the expert, based on the visual assessment of C-plane and hiatal segmentation quality. The overall time taken to extract the hiatal area with both measurement methods (i.e., manual and automatic) was measured. Each metric was calculated both for computerâobserver differences and for inter-and intra-observer differences. The automatic method gave results similar to those of the expert when determining the hiatal outline from a TPUS volume. Indeed, the hiatal area measured by the algorithm and by an expert were within the intra-observer variability. Similarly, the method identified the C-plane with an accuracy of 5.76 ± 5.06° and 6.46 ± 5.18 mm in comparison to the inter-observer variability of 9.39 ± 6.21° and 8.48 ± 6.62 mm. The visual Turing test suggested that the automatic method identified the C-plane position within the TPUS volume visually as well as the expert. The average time taken to identify the C-plane and segment the hiatal area manually was 2 min and 35 ± 17 s, compared with 35 ± 4 s for the automatic result. This study presents a method for automatically measuring the levator hiatal area using artificial intelligence-based methodologies whereby the C-plane within a TPUS volume is detected and subsequently traced for the levator hiatal outline. The proposed solution was determined to be accurate, relatively quick, robust and reliable and, importantly, to reduce time and expertise required for pelvic floor disorder assessment
Segmenting white matter hyperintensities on isotropic three-dimensional Fluid Attenuated Inversion Recovery magnetic resonance images: Assessing deep learning tools on a Norwegian imaging database
An important step in the analysis of magnetic resonance imaging (MRI) data for neuroimaging is the automated segmentation of white matter hyperintensities (WMHs). Fluid Attenuated Inversion Recovery (FLAIR-weighted) is an MRI contrast that is particularly useful to visualize and quantify WMHs, a hallmark of cerebral small vessel disease and Alzheimer's disease (AD). In order to achieve high spatial resolution in each of the three voxel dimensions, clinical MRI protocols are evolving to a three-dimensional (3D) FLAIR-weighted acquisition. The current study details the deployment of deep learning tools to enable automated WMH segmentation and characterization from 3D FLAIR-weighted images acquired as part of a national AD imaging initiative. Based on data from the ongoing Norwegian Disease Dementia Initiation (DDI) multicenter study, two 3D models-one off-the-shelf from the NVIDIA nnU-Net framework and the other internally developed-were trained, validated, and tested. A third cutting-edge Deep Bayesian network model (HyperMapp3r) was implemented without any de-novo tuning to serve as a comparison architecture. The 2.5D in-house developed and 3D nnU-Net models were trained and validated in-house across five national collection sites among 441 participants from the DDI study, of whom 194 were men and whose average age was (64.91 +/- 9.32) years. Both an external dataset with 29 cases from a global collaborator and a held-out subset of the internal data from the 441 participants were used to test all three models. These test sets were evaluated independently. The ground truth human-in-the-loop segmentation was compared against five established WMH performance metrics. The 3D nnU-Net had the highest performance out of the three tested networks, outperforming both the internally developed 2.5D model and the SOTA Deep Bayesian network with an average dice similarity coefficient score of 0.76 +/- 0.16. Our findings demonstrate that WMH segmentation models can achieve high performance when trained exclusively on FLAIR input volumes that are 3D volumetric acquisitions. Single image input models are desirable for ease of deployment, as reflected in the current embedded clinical research project. The 3D nnU-Net had the highest performance, which suggests a way forward for our need to automate WMH segmentation while also evaluating performance metrics during on-going data collection and model retraining
Leveraging Ellipsoid Bounding Shapes and Fast R-CNN for Enlarged Perivascular Spaces Detection and Segmentation
Enlarged perivascular spaces (EPVS) are small fluid-filled spaces surrounding blood vessels in the brain. They have been found to be important in the development and progression of cerebrovascular disease, including stroke, dementia, and cerebral small vessel disease. Their accurate detection and quantification are crucial for early diagnosis and better management of these diseases. In recent years, object detection techniques such as Mask R-CNN approach have been widely used to automate the detection and segmentation of small objects. To account for the tubular shape of these markers we use ellipsoid shapes instead of bounding boxes to express the location of individual elements in the implementation of the Fast R-CNN. We investigate the performance of this model under different modality combinations and find that the T2 modality alone, as well as the combination of T1+T2, deliver better performance
Longitudinal structural and perfusion MRI enhanced by machine learning outperforms standalone modalities and radiological expertise in high-grade glioma surveillance
PURPOSE: Surveillance of patients with high-grade glioma (HGG) and identification of disease progression remain a major challenge in neurooncology. This study aimed to develop a support vector machine (SVM) classifier, employing combined longitudinal structural and perfusion MRI studies, to classify between stable disease, pseudoprogression and progressive disease (3-class problem). METHODS: Study participants were separated into two groups: group I (total cohort: 64 patients) with a single DSC time point and group II (19 patients) with longitudinal DSC time points (2-3). We retrospectively analysed 269 structural MRI and 92 dynamic susceptibility contrast perfusion (DSC) MRI scans. The SVM classifier was trained using all available MRI studies for each group. Classification accuracy was assessed for different feature dataset and time point combinations and compared to radiologistsâ classifications. RESULTS: SVM classification based on combined perfusion and structural features outperformed radiologistsâ classification across all groups. For the identification of progressive disease, use of combined features and longitudinal DSC time points improved classification performance (lowest error rate 1.6%). Optimal performance was observed in group II (multiple time points) with SVM sensitivity/specificity/accuracy of 100/91.67/94.7% (first time point analysis) and 85.71/100/94.7% (longitudinal analysis), compared to 60/78/68% and 70/90/84.2% for the respective radiologist classifications. In group I (single time point), the SVM classifier also outperformed radiologistsâ classifications with sensitivity/specificity/accuracy of 86.49/75.00/81.53% (SVM) compared to 75.7/68.9/73.84% (radiologists). CONCLUSION: Our results indicate that utilisation of a machine learning (SVM) classifier based on analysis of longitudinal perfusion time points and combined structural and perfusion features significantly enhances classification outcome (p value= 0.0001)
Let's Agree to Disagree: Learning Highly Debatable Multirater Labelling
Classification and differentiation of small pathological objects may greatly vary among human raters due to differences in training, expertise and their consistency over time. In a radiological setting, objects commonly have high within-class appearance variability whilst sharing certain characteristics across different classes, making their distinction even more difficult. As an example, markers of cerebral small vessel disease, such as enlarged perivascular spaces (EPVS) and lacunes, can be very varied in their appearance while exhibiting high inter-class similarity, making this task highly challenging for human raters. In this work, we investigate joint models of individual rater behaviour and multi-rater consensus in a deep learning setting, and apply it to a brain lesion object-detection task. Results show that jointly modelling both individual and consensus estimates leads to significant improvements in performance when compared to directly predicting consensus labels, while also allowing the characterization of human-rater consistency
Optimizing the Dice Score and Jaccard Index for Medical Image Segmentation: Theory & Practice
The Dice score and Jaccard index are commonly used metrics for the evaluation
of segmentation tasks in medical imaging. Convolutional neural networks trained
for image segmentation tasks are usually optimized for (weighted)
cross-entropy. This introduces an adverse discrepancy between the learning
optimization objective (the loss) and the end target metric. Recent works in
computer vision have proposed soft surrogates to alleviate this discrepancy and
directly optimize the desired metric, either through relaxations (soft-Dice,
soft-Jaccard) or submodular optimization (Lov\'asz-softmax). The aim of this
study is two-fold. First, we investigate the theoretical differences in a risk
minimization framework and question the existence of a weighted cross-entropy
loss with weights theoretically optimized to surrogate Dice or Jaccard. Second,
we empirically investigate the behavior of the aforementioned loss functions
w.r.t. evaluation with Dice score and Jaccard index on five medical
segmentation tasks. Through the application of relative approximation bounds,
we show that all surrogates are equivalent up to a multiplicative factor, and
that no optimal weighting of cross-entropy exists to approximate Dice or
Jaccard measures. We validate these findings empirically and show that, while
it is important to opt for one of the target metric surrogates rather than a
cross-entropy-based loss, the choice of the surrogate does not make a
statistical difference on a wide range of medical segmentation tasks.Comment: MICCAI 201
Exploring Campylobacter seasonality across Europe (2008-2016) using The European Surveillance System TESSy
Background: Campylobacteriosis is the most commonly reported food-borne infection in the European Union, with an annual number of cases estimated at around 9 million. In many countries, campylobacteriosis has a striking seasonal peak during early/ mid-summer. In the early 2000s, several publications reported on campylobacteriosis seasonality across Europe and associations with temperature and precipitation. Subsequently, many European countries have introduced new measures against this foodborne disease. Aim: To examine how the seasonality of campylobacteriosis varied across Europe from 2008â16, to explore associations with temperature and precipitation, and to compare these results with previous studies. We also sought to assess the utility of the European Surveillance System TESSy for cross-European seasonal analysis of campylobacteriosis. Methods: Wardâs Minimum Variance Clustering was used to group countries with similar seasonal patterns of campylobacteriosis. A two-stage multivariate meta-analysis methodology was used to explore associations with temperature and precipitation. Results: Nordic countries had a pronounced seasonal campylobacteriosis peak in mid-to late summer (weeks 29â32), while most other European countries had a less pronounced peak earlier in the year. The United Kingdom, Ireland, Hungary and Slovakia had a slightly earlier peak (week 24). Campylobacteriosis cases were positively associated with temperature and, to a lesser degree, precipitation. Conclusion: Across Europe, the strength and timing of campylobacteriosis peaks have remained similar to those observed previously. In addition, TESSy is a useful resource for cross-Euro-pean seasonal analysis of infectious diseases such as campylobacteriosis, but its utility depends upon each countryâs reporting infrastructure
Functional connectivity measured with magnetoencephalography identifies persons with HIV disease
There is need for a valid and reliable biomarker for HIV Associated Neurocognitive Disorder (HAND). The purpose of the present study was to provide preliminary evidence of the potential utility of neuronal functional connectivity measures obtained using magnetoencephalography (MEG) to identify HIV-associated changes in brain function. Resting state, eyes closed, MEG data from 10 HIV-infected individuals and 8 seronegative controls were analyzed using mutual information (MI) between all pairs of MEG sensors to ..
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