Background and Purpose: The T1-weighted dynamic contrast enhanced (DCE)-MRI is an imaging technique that provides a quantitative measure of pharmacokinetic (PK) parameters characterizing microvasculature of tissues. For the present study, we propose a new machine learning (ML) based approach to directly estimate the PK parameters from the acquired DCE-MRI image-time series that is both more robust and faster than conventional model fitting.Materials and Methods: We specifically utilize deep convolutional neural networks (CNNs) to learn the mapping between the image-time series and corresponding PK parameters. DCE-MRI datasets acquired from 15 patients with clinically evident mild ischaemic stroke were used in the experiments. Training and testing were carried out based on leave-one-patient-out cross- validation. The parameter estimates obtained by the proposed CNN model were compared against the two tracer kinetic models: (1) Patlak model, (2) Extended Tofts model, where the estimation of model parameters is done via voxelwise linear and nonlinear least squares fitting respectively.Results: The trained CNN model is able to yield PK parameters which can better discriminate different brain tissues, including stroke regions. The results also demonstrate that the model generalizes well to new cases even if a subject specific arterial input function (AIF) is not available for the new data.Conclusion: A ML-based model can be used for direct inference of the PK parameters from DCE image series. This method may allow fast and robust parameter inference in population DCE studies. Parameter inference on a 3D volume-time series takes only a few seconds on a GPU machine, which is significantly faster compared to conventional non-linear least squares fitting.
Arterial spin labeling (ASL) allows to quantify the cerebral blood flow (CBF) by magnetic labeling of the arterial blood water. ASL is increasingly used in clinical studies due to its noninvasiveness, repeatability and benefits in quantification. However, ASL suffers from an inherently low-signal-to-noise ratio (SNR) requiring repeated measurements of control/spin-labeled (C/L) pairs to achieve a reasonable image quality, which in return increases motion sensitivity. This leads to clinically prolonged scanning times increasing the risk of motion artifacts. Thus, there is an immense need of advanced imaging and processing techniques in ASL. In this paper, we propose a novel deep learning based approach to improve the perfusion-weighted image quality obtained from a subset of all available pairwise C/L subtractions. Specifically, we train a deep fully convolutional network (FCN) to learn a mapping from noisy perfusion-weighted image and its subtraction (residual) from the clean image. Additionally, we incorporate the CBF estimation model in the loss function during training, which enables the network to produce high quality images while simultaneously enforcing the CBF estimates to be as close as reference CBF values. Extensive experiments on synthetic and clinical ASL datasets demonstrate the effectiveness of our method in terms of improved ASL image quality, accurate CBF parameter estimation and considerably small computation time during testing.
Dynamic contrast-enhanced (DCE) MRI is an evolving imaging technique that provides a quantitative measure of pharmacokinetic (PK) parameters in body tissues, in which series of T1-weighted images are collected following the administration of a paramagnetic contrast agent. Unfortunately, in many applications, conventional clinical DCE-MRI suffers from low spatiotemporal resolution and insufficient volume coverage. In this paper, we propose a novel deep learning based approach to directly estimate the PK parameters from undersampled DCE-MRI data. Specifically, we design a custom loss function where we incorporate a forward physical model that relates the PK parameters to corrupted image-time series obtained due to subsampling in k-space. This allows the network to directly exploit the knowledge of true contrast agent kinetics in the training phase, and hence provide more accurate restoration of PK parameters. Experiments on clinical brain DCE datasets demonstrate the efficacy of our approach in terms of fidelity of PK parameter reconstruction and significantly faster parameter inference compared to a model-based iterative reconstruction method.
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