199 research outputs found
Detecting CTP truncation artifacts in acute stroke imaging from the arterial input and the vascular output functions
Background: Current guidelines for CT perfusion (CTP) in acute stroke suggest acquiring scans with a minimal duration of 60-70 s. But even then, CTP analysis can be affected by truncation artifacts. Conversely, shorter acquisitions are still widely used in clinical practice and may, sometimes, be sufficient to reliably estimate lesion volumes. We aim to devise an automatic method that detects scans affected by truncation artifacts.
Methods: Shorter scan durations are simulated from the ISLES’18 dataset by consecutively removing the last CTP time-point until reaching a 10 s duration. For each truncated series, perfusion lesion volumes are quantified and used to label the series as unreliable if the lesion volumes considerably deviate from the original untruncated ones. Afterwards, nine features from the arterial input function (AIF) and the vascular output function (VOF) are derived and used to fit machine-learning models with the goal of detecting unreliably truncated scans. Methods are compared against a baseline classifier solely based on the scan duration, which is the current clinical standard. The ROC-AUC, precision-recall AUC and the F1-score are measured in a 5-fold cross-validation setting.
Results: The best performing classifier obtained an ROC-AUC of 0.982, precision-recall AUC of 0.985 and F1-score of 0.938. The most important feature was the AIF, measured as the time difference between the scan duration and the AIF peak. When using the AIF to build a single feature classifier, an ROC-AUC of 0.981, precision-recall AUC of 0.984 and F1-score of 0.932 were obtained. In comparison, the baseline classifier obtained an ROC-AUC of 0.954, precision-recall AUC of 0.958 and F1-Score of 0.875.
Conclusions: Machine learning models fed with AIF and VOF features accurately detected unreliable stroke lesion measurements due to insufficient acquisition duration. The AIF was the most predictive feature of truncation and identified unreliable short scans almost as good as machine learning. We conclude that AIF/VOF based classifiers are more accurate than the scans’ duration for detecting truncation. These methods could be transferred to perfusion analysis software in order to increase the interpretability of CTP outputs
AIFNet: Automatic Vascular Function Estimation for Perfusion Analysis Using Deep Learning
Perfusion imaging is crucial in acute ischemic stroke for quantifying the
salvageable penumbra and irreversibly damaged core lesions. As such, it helps
clinicians to decide on the optimal reperfusion treatment. In perfusion CT
imaging, deconvolution methods are used to obtain clinically interpretable
perfusion parameters that allow identifying brain tissue abnormalities.
Deconvolution methods require the selection of two reference vascular functions
as inputs to the model: the arterial input function (AIF) and the venous output
function, with the AIF as the most critical model input. When manually
performed, the vascular function selection is time demanding, suffers from poor
reproducibility and is subject to the professionals' experience. This leads to
potentially unreliable quantification of the penumbra and core lesions and,
hence, might harm the treatment decision process. In this work we automatize
the perfusion analysis with AIFNet, a fully automatic and end-to-end trainable
deep learning approach for estimating the vascular functions. Unlike previous
methods using clustering or segmentation techniques to select vascular voxels,
AIFNet is directly optimized at the vascular function estimation, which allows
to better recognise the time-curve profiles. Validation on the public ISLES18
stroke database shows that AIFNet reaches inter-rater performance for the
vascular function estimation and, subsequently, for the parameter maps and core
lesion quantification obtained through deconvolution. We conclude that AIFNet
has potential for clinical transfer and could be incorporated in perfusion
deconvolution software.Comment: Preprint submitted to Elsevie
Robust and parallel scalable iterative solutions for large-scale finite cell analyses
The finite cell method is a highly flexible discretization technique for
numerical analysis on domains with complex geometries. By using a non-boundary
conforming computational domain that can be easily meshed, automatized
computations on a wide range of geometrical models can be performed.
Application of the finite cell method, and other immersed methods, to large
real-life and industrial problems is often limited due to the conditioning
problems associated with these methods. These conditioning problems have caused
researchers to resort to direct solution methods, which signifi- cantly limit
the maximum size of solvable systems. Iterative solvers are better suited for
large-scale computations than their direct counterparts due to their lower
memory requirements and suitability for parallel computing. These benefits can,
however, only be exploited when systems are properly conditioned. In this
contribution we present an Additive-Schwarz type preconditioner that enables
efficient and parallel scalable iterative solutions of large-scale multi-level
hp-refined finite cell analyses.Comment: 32 pages, 17 figure
A Deep Learning Approach to Predicting Collateral Flow in Stroke Patients Using Radiomic Features from Perfusion Images
Collateral circulation results from specialized anastomotic channels which are capable of providing oxygenated blood to regions with compromised blood flow caused by ischemic injuries. The quality of collateral circulation has been established as a key factor in determining the likelihood of a favorable clinical outcome and goes a long way to determine the choice of stroke care model - that is the decision to transport or treat eligible patients immediately.
Though there exist several imaging methods and grading criteria for quantifying collateral blood flow, the actual grading is mostly done through manual inspection of the acquired images. This approach is associated with a number of challenges. First, it is time-consuming - the clinician needs to scan through several slices of images to ascertain the region of interest before deciding on what severity grade to assign to a patient. Second, there is a high tendency for bias and inconsistency in the final grade assigned to a patient depending on the experience level of the clinician.
We present a deep learning approach to predicting collateral flow grading in stroke patients based on radiomic features extracted from MR perfusion data. First, we formulate a region of interest detection task as a reinforcement learning problem and train a deep learning network to automatically detect the occluded region within the 3D MR perfusion volumes. Second, we extract radiomic features from the obtained region of interest through local image descriptors and denoising auto-encoders. Finally, we apply a convolutional neural network and other machine learning classifiers to the extracted radiomic features to automatically predict the collateral flow grading of the given patient volume as one of three severity classes - no flow (0), moderate flow (1), and good flow (2)..
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