A new framework for assessing subject-specific whole brain circulation and perfusion using MRI-based measurements and a multi-scale continuous flow model

A large variety of severe medical conditions involve alterations in microvascular circulation. Hence, measurements or simulation of circulation and perfusion has considerable clinical value and can be used for diagnostics, evaluation of treatment efficacy, and for surgical planning. However, the accuracy of traditional tracer kinetic one-compartment models is limited due to scale dependency. As a remedy, we propose a scale invariant mathematical framework for simulating whole brain perfusion. The suggested framework is based on a segmentation of anatomical geometry down to imaging voxel resolution. Large vessels in the arterial and venous network are identified from time-of-flight (ToF) and quantitative susceptibility mapping (QSM). Macro-scale flow in the large-vessel-network is accurately modelled using the Hagen-Poiseuille equation, whereas capillary flow is treated as two-compartment porous media flow. Macro-scale flow is coupled with micro-scale flow by a spatially distributing support function in the terminal endings. Perfusion is defined as the transition of fluid from the arterial to the venous compartment. We demonstrate a whole brain simulation of tracer propagation on a realistic geometric model of the human brain, where the model comprises distinct areas of grey and white matter, as well as large vessels in the arterial and venous vascular network. Our proposed framework is an accurate and viable alternative to traditional compartment models, with high relevance for simulation of brain perfusion and also for restoration of field parameters in clinical brain perfusion applications.publishedVersio

Memento: Localized time‐warping for spatio‐temporal selection

Interaction techniques for temporal data are often focused on affecting the spatial aspects of the data, for instance through the use of transfer functions, camera navigation or clipping planes. However, the temporal aspect of the data interaction is often neglected. The temporal component is either visualized as individual time steps, an animation or a static summary over the temporal domain. When dealing with streaming data, these techniques are unable to cope with the task of re‐viewing an interesting local spatio‐temporal event, while continuing to observe the rest of the feed. We propose a novel technique that allows users to interactively specify areas of interest in the spatio‐temporal domain. By employing a time‐warp function, we are able to slow down time, freeze time or even travel back in time, around spatio‐temporal events of interest. The combination of such a (pre‐defined) time‐warp function and brushing directly in the data to select regions of interest allows for a detailed review of temporally and spatially localized events, while maintaining an overview of the global spatio‐temporal data. We demonstrate the utility of our technique with several usage scenarios

Memento: Localized time‐warping for spatio‐temporal selection

Interaction techniques for temporal data are often focused on affecting the spatial aspects of the data, for instance through the use of transfer functions, camera navigation or clipping planes. However, the temporal aspect of the data interaction is often neglected. The temporal component is either visualized as individual time steps, an animation or a static summary over the temporal domain. When dealing with streaming data, these techniques are unable to cope with the task of re‐viewing an interesting local spatio‐temporal event, while continuing to observe the rest of the feed. We propose a novel technique that allows users to interactively specify areas of interest in the spatio‐temporal domain. By employing a time‐warp function, we are able to slow down time, freeze time or even travel back in time, around spatio‐temporal events of interest. The combination of such a (pre‐defined) time‐warp function and brushing directly in the data to select regions of interest allows for a detailed review of temporally and spatially localized events, while maintaining an overview of the global spatio‐temporal data. We demonstrate the utility of our technique with several usage scenarios

A new framework for assessing subject-specific whole brain circulation and perfusion using MRI-based measurements and a multi-scale continuous flow model

A large variety of severe medical conditions involve alterations in microvascular circulation. Hence, measurements or simulation of circulation and perfusion has considerable clinical value and can be used for diagnostics, evaluation of treatment efficacy, and for surgical planning. However, the accuracy of traditional tracer kinetic one-compartment models is limited due to scale dependency. As a remedy, we propose a scale invariant mathematical framework for simulating whole brain perfusion. The suggested framework is based on a segmentation of anatomical geometry down to imaging voxel resolution. Large vessels in the arterial and venous network are identified from time-of-flight (ToF) and quantitative susceptibility mapping (QSM). Macro-scale flow in the large-vessel-network is accurately modelled using the Hagen-Poiseuille equation, whereas capillary flow is treated as two-compartment porous media flow. Macro-scale flow is coupled with micro-scale flow by a spatially distributing support function in the terminal endings. Perfusion is defined as the transition of fluid from the arterial to the venous compartment. We demonstrate a whole brain simulation of tracer propagation on a realistic geometric model of the human brain, where the model comprises distinct areas of grey and white matter, as well as large vessels in the arterial and venous vascular network. Our proposed framework is an accurate and viable alternative to traditional compartment models, with high relevance for simulation of brain perfusion and also for restoration of field parameters in clinical brain perfusion applications

Automated segmentation of endometrial cancer on MR images using deep learning

Preoperative MR imaging in endometrial cancer patients provides valuable information on local tumor extent, which routinely guides choice of surgical procedure and adjuvant therapy. Furthermore, whole-volume tumor analyses of MR images may provide radiomic tumor signatures potentially relevant for better individualization and optimization of treatment. We apply a convolutional neural network for automatic tumor segmentation in endometrial cancer patients, enabling automated extraction of tumor texture parameters and tumor volume. The network was trained, validated and tested on a cohort of 139 endometrial cancer patients based on preoperative pelvic imaging. The algorithm was able to retrieve tumor volumes comparable to human expert level (likelihood-ratio test, p=0.06). The network was also able to provide a set of segmentation masks with human agreement not different from inter-rater agreement of human experts (Wilcoxon signed rank test, p=0.08, p=0.60, and p=0.05). An automatic tool for tumor segmentation in endometrial cancer patients enables automated extraction of tumor volume and whole-volume tumor texture features. This approach represents a promising method for automatic radiomic tumor profiling with potential relevance for better prognostication and individualization of therapeutic strategy in endometrial cancer

Automated segmentation of endometrial cancer on MR images using deep learning

Preoperative MR imaging in endometrial cancer patients provides valuable information on local tumor extent, which routinely guides choice of surgical procedure and adjuvant therapy. Furthermore, whole-volume tumor analyses of MR images may provide radiomic tumor signatures potentially relevant for better individualization and optimization of treatment. We apply a convolutional neural network for automatic tumor segmentation in endometrial cancer patients, enabling automated extraction of tumor texture parameters and tumor volume. The network was trained, validated and tested on a cohort of 139 endometrial cancer patients based on preoperative pelvic imaging. The algorithm was able to retrieve tumor volumes comparable to human expert level (likelihood-ratio test, p=0.06). The network was also able to provide a set of segmentation masks with human agreement not different from inter-rater agreement of human experts (Wilcoxon signed rank test, p=0.08, p=0.60, and p=0.05). An automatic tool for tumor segmentation in endometrial cancer patients enables automated extraction of tumor volume and whole-volume tumor texture features. This approach represents a promising method for automatic radiomic tumor profiling with potential relevance for better prognostication and individualization of therapeutic strategy in endometrial cancer

Automated segmentation of endometrial cancer on MR images using deep learning

Preoperative MR imaging in endometrial cancer patients provides valuable information on local tumor extent, which routinely guides choice of surgical procedure and adjuvant therapy. Furthermore, whole-volume tumor analyses of MR images may provide radiomic tumor signatures potentially relevant for better individualization and optimization of treatment. We apply a convolutional neural network for automatic tumor segmentation in endometrial cancer patients, enabling automated extraction of tumor texture parameters and tumor volume. The network was trained, validated and tested on a cohort of 139 endometrial cancer patients based on preoperative pelvic imaging. The algorithm was able to retrieve tumor volumes comparable to human expert level (likelihood-ratio test, p=0.06). The network was also able to provide a set of segmentation masks with human agreement not different from inter-rater agreement of human experts (Wilcoxon signed rank test, p=0.08, p=0.60, and p=0.05). An automatic tool for tumor segmentation in endometrial cancer patients enables automated extraction of tumor volume and whole-volume tumor texture features. This approach represents a promising method for automatic radiomic tumor profiling with potential relevance for better prognostication and individualization of therapeutic strategy in endometrial cancer