Final infarct prediction in acute ischemic stroke

This article focuses on the control center of each human body: the brain. We will point out the pivotal role of the cerebral vasculature and how its complex mechanisms may vary between subjects. We then emphasize a specific acute pathological state, i.e., acute ischemic stroke, and show how medical imaging and its analysis can be used to define the treatment. We show how the core-penumbra concept is used in practice using mismatch criteria and how machine learning can be used to make predictions of the final infarct, either via deconvolution or convolutional neural networks.Comment: 17 pages, 5 figures, part of PhD thesis KU Leuven 2022 "Understanding Final Infarct Prediction in Acute Ischemic Stroke Using Convolutional Neural Networks

Theoretical analysis and experimental validation of volume bias of soft Dice optimized segmentation maps in the context of inherent uncertainty

The clinical interest is often to measure the volume of a structure, which is typically derived from a segmentation. In order to evaluate and compare segmentation methods, the similarity between a segmentation and a predefined ground truth is measured using popular discrete metrics, such as the Dice score. Recent segmentation methods use a differentiable surrogate metric, such as soft Dice, as part of the loss function during the learning phase. In this work, we first briefly describe how to derive volume estimates from a segmentation that is, potentially, inherently uncertain or ambiguous. This is followed by a theoretical analysis and an experimental validation linking the inherent uncertainty to common loss functions for training CNNs, namely cross-entropy and soft Dice. We find that, even though soft Dice optimization leads to an improved performance with respect to the Dice score and other measures, it may introduce a volume bias for tasks with high inherent uncertainty. These findings indicate some of the method's clinical limitations and suggest doing a closer ad-hoc volume analysis with an optional re-calibration step.Comment: 18 pages, 7 figures, 3 tables, published in Elsevier Medical Image Analysis (2021

Dice Semimetric Losses: Optimizing the Dice Score with Soft Labels

The soft Dice loss (SDL) has taken a pivotal role in many automated segmentation pipelines in the medical imaging community. Over the last years, some reasons behind its superior functioning have been uncovered and further optimizations have been explored. However, there is currently no implementation that supports its direct use in settings with soft labels. Hence, a synergy between the use of SDL and research leveraging the use of soft labels, also in the context of model calibration, is still missing. In this work, we introduce Dice semimetric losses (DMLs), which (i) are by design identical to SDL in a standard setting with hard labels, but (ii) can be used in settings with soft labels. Our experiments on the public QUBIQ, LiTS and KiTS benchmarks confirm the potential synergy of DMLs with soft labels (e.g. averaging, label smoothing, and knowledge distillation) over hard labels (e.g. majority voting and random selection). As a result, we obtain superior Dice scores and model calibration, which supports the wider adoption of DMLs in practice. Code is available at \href{https://github.com/zifuwanggg/JDTLosses}{https://github.com/zifuwanggg/JDTLosses}.Comment: Submitted to MICCAI2023. Code is available at https://github.com/zifuwanggg/JDTLosse

Theoretical analysis and experimental validation of volume bias of soft Dice optimized segmentation maps in the context of inherent uncertainty

The clinical interest is often to measure the volume of a structure, which is typically derived from a segmentation. In order to evaluate and compare segmentation methods, the similarity between a segmentation and a predefined ground truth is measured using popular discrete metrics, such as the Dice score. Recent segmentation methods use a differentiable surrogate metric, such as soft Dice, as part of the loss function during the learning phase. In this work, we first briefly describe how to derive volume estimates from a segmentation that is, potentially, inherently uncertain or ambiguous. This is followed by a theoretical analysis and an experimental validation linking the inherent uncertainty to common loss functions for training CNNs, namely cross-entropy and soft Dice. We find that, even though soft Dice optimization leads to an improved performance with respect to the Dice score and other measures, it may introduce a volume bias for tasks with high inherent uncertainty. These findings indicate some of the method’s clinical limitations and suggest doing a closer ad-hoc volume analysis with an optional re-calibration step.NEXIS (www.nexis-project.eu), a project that has received funding from the European Union’s Horizon 2020 Research and Innovations Programme and an innovation mandate of Flanders Innovation and Entrepreneurship (VLAIO).http://www.elsevier.com/locate/mediahj2022Anatom

Towards fully automated third molar development staging in panoramic radiographs

Staging third molar development is commonly used for age assessment in sub-adults. Current staging techniques are, at most, semi-automated and rely on manual interactions prone to operator variability. The aim of this study was to fully automate the staging process by employing the full potential of deep learning, using convolutional neural networks (CNNs) in every step of the procedure. The dataset used to train the CNNs consisted of 400 panoramic radiographs (OPGs), with 20 OPGs per developmental stage per sex, staged in consensus between three observers. The concepts of transfer learning, using pre-trained CNNs, and data augmentation were used to mitigate the issues when dealing with a limited dataset. In this work, a three-step procedure was proposed and the results were validated using fivefold cross-validation. First, a CNN localized the geometrical center of the lower left third molar, around which a square region of interest (ROI) was extracted. Second, another CNN segmented the third molar within the ROI. Third, a final CNN used both the ROI and the segmentation to classify the third molar into its developmental stage. The geometrical center of the third molar was found with an average Euclidean distance of 63 pixels. Third molars were segmented with an average Dice score of 93%. Finally, the developmental stages were classified with an accuracy of 54%, a mean absolute error of 0.69 stages, and a linear weighted Cohen’s kappa coefficient of 0.79. The entire automated workflow on average took 2.72 s to compute, which is substantially faster than manual staging starting from the OPG. Taking into account the limited dataset size, this pilot study shows that the proposed fully automated approach shows promising results compared with manual staging.Internal Funds KU Leuvenhttp://link.springer.com/journal/4142021-04-01hj2020Anatom

Optimization with soft Dice can lead to a volumetric bias

status: Published onlin

DeepVoxNet: voxel‐wise prediction for 3D images

Several important medical image analysis tasks can be cast as a voxel-wise prediction: e.g. segmentation of structures of interest or regression of a new modality from others. Convolutional neural networks (CNNs) are the state-of-the-art approach for voxel-wise prediction and high-quality software such as Keras is available to define, train and use them. To harness them in the context of medical image analysis problems, additional components are necessary to handle the memory requirements of 3D processing, the various image modalities that are typically combined and the appropriate data augmentation. We have created DeepVoxNet to provide these components, and let researchers and developers quickly use CNNs on medical image analysis problems in an efficient and flexible fashion.status: Published onlin

Effect of lower third molar segmentations on automated tooth development staging using a convolutional neural network

Staging third molar development is commonly used for age estimation in subadults. Automated developmental stage allocation to the mandibular left third molar in panoramic radiographs has been examined in a pilot study. This method used an AlexNet Deep Convolutional Neural Network (CNN) approach to stage lower left third molars, which had been selected by manually drawn bounding boxes around them. This method (bounding box AlexNet = BA) still contained parts of surrounding structures which may have affected the automated stage allocation performance. We hypothesize that segmenting only the third molar could further improve the automated stage allocation performance. Therefore, the current study aimed to determine and validate the effect of lower third molar segmentations on automated tooth development staging. Retrospectively, 400 panoramic radiographs were collected, processed and segmented in three ways: bounding box (BB), rough (RS), and full (FS) tooth segmentation. A DenseNet201 CNN was used for automated stage allocation. Automated staging results were compared with reference stages - allocated by human observers - overall and per stage. FS rendered the best results with a stage allocation accuracy of 0.61, a mean absolute difference of 0.53 stages and a Cohen's linear kappa of 0.84. Misallocated stages were mostly neighboring stages, and DenseNet201 rendered better results than AlexNet by increasing the percentage of correctly allocated stages by 3% (BA compared to BB). FS increased the percentage of correctly allocated stages by 7% compared to BB. In conclusion, full tooth segmentation and a DenseNet CNN optimize automated dental stage allocation for age estimation