Motion-compensated image reconstruction for improved kidney function assessment using dynamic contrast-enhanced MRI.

Accurately measuring renal function is crucial for pediatric patients with kidney conditions. Traditional methods have limitations, but dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI) provides a safe and efficient approach for detailed anatomical evaluation and renal function assessment. However, motion artifacts during DCE-MRI can degrade image quality and introduce misalignments, leading to unreliable results. This study introduces a motion-compensated reconstruction technique for DCE-MRI data acquired using golden-angle radial sampling. Our proposed method achieves three key objectives: (1) identifying and removing corrupted data (outliers) using a Gaussian process model fitting with a k -space center navigator, (2) efficiently clustering the data into motion phases and performing interphase registration, and (3) utilizing a novel formulation of motion-compensated radial reconstruction. We applied the proposed motion correction (MoCo) method to DCE-MRI data affected by varying degrees of motion, including both respiratory and bulk motion. We compared the outcomes with those obtained from the conventional radial reconstruction. Our evaluation encompassed assessing the quality of images, concentration curves, and tracer kinetic model fitting, and estimating renal function. The proposed MoCo reconstruction improved the temporal signal-to-noise ratio for all subjects, with a 21.8% increase on average, while total variation values of the aorta, right, and left kidney concentration were improved for each subject, with 32.5%, 41.3%, and 42.9% increases on average, respectively. Furthermore, evaluation of tracer kinetic model fitting indicated that the median standard deviation of the estimated filtration rate ( σ F T ), mean normalized root-mean-squared error (nRMSE), and chi-square goodness-of-fit of tracer kinetic model fit were decreased from 0.10 to 0.04, 0.27 to 0.24, and, 0.43 to 0.27, respectively. The proposed MoCo technique enabled more reliable renal function assessment and improved image quality for detailed anatomical evaluation in the case of bulk and respiratory motion during the acquisition of DCE-MRI.

Learning the Regularization in DCE-MR Image Reconstruction for Functional Imaging of Kidneys.

Kidney DCE-MRI aims at both qualitative assessment of kidney anatomy and quantitative assessment of kidney function by estimating the tracer kinetic (TK) model parameters. Accurate estimation of TK model parameters requires an accurate measurement of the arterial input function (AIF) with high temporal resolution. Accelerated imaging is used to achieve high temporal resolution, which yields under-sampling artifacts in the reconstructed images. Compressed sensing (CS) methods offer a variety of reconstruction options. Most commonly, sparsity of temporal differences is encouraged for regularization to reduce artifacts. Increasing regularization in CS methods removes the ambient artifacts but also over-smooths the signal temporally which reduces the parameter estimation accuracy. In this work, we propose a single image trained deep neural network to reduce MRI under-sampling artifacts without reducing the accuracy of functional imaging markers. Instead of regularizing with a penalty term in optimization, we promote regularization by generating images from a lower dimensional representation. In this manuscript we motivate and explain the lower dimensional input design. We compare our approach to CS reconstructions with multiple regularization weights. Proposed approach results in kidney biomarkers that are highly correlated with the ground truth markers estimated using the CS reconstruction which was optimized for functional analysis. At the same time, the proposed approach reduces the artifacts in the reconstructed images.

Stopping Criterion Design for Recursive Bayesian Classification: Analysis and Decision Geometry.

Systems that are based on recursive Bayesian updates for classification limit the cost of evidence collection through certain stopping/termination criteria and accordingly enforce decision making. Conventionally, two termination criteria based on pre-defined thresholds over (i) the maximum of the state posterior distribution; and (ii) the state posterior uncertainty are commonly used. In this paper, we propose a geometric interpretation over the state posterior progression and accordingly we provide a point-by-point analysis over the disadvantages of using such conventional termination criteria. For example, through the proposed geometric interpretation we show that confidence thresholds defined over maximum of the state posteriors suffer from stiffness that results in unnecessary evidence collection whereas uncertainty based thresholding methods are fragile to number of categories and terminate prematurely if some state candidates are already discovered to be unfavorable. Moreover, both types of termination methods neglect the evolution of posterior updates. We then propose a new stopping/termination criterion with a geometrical insight to overcome the limitations of these conventional methods and provide a comparison in terms of decision accuracy and speed. We validate our claims using simulations and using real experimental data obtained through a brain computer interfaced typing system.

Geometric Analysis of Uncertainty Sampling for Dense Neural Network Layer.

For model adaptation of fully connected neural network layers, we provide an information geometric and sample behavioral active learning uncertainty sampling objective analysis. We identify conditions under which several uncertainty-based methods have the same performance and show that such conditions are more likely to appear in the early stages of learning. We define riskier samples for adaptation, and demonstrate that, as the set of labeled samples increases, margin-based sampling outperforms other uncertainty sampling methods by preferentially selecting these risky samples. We support our derivations and illustrations with experiments using Meta-Dataset, a benchmark for few-shot learning. We compare uncertainty-based active learning objectives using features produced by SimpleCNAPS (a state-of-the-art few-shot classifier) as input for a fully-connected adaptation layer. Our results indicate that margin-based uncertainty sampling achieves similar performance as other uncertainty based sampling methods with fewer labelled samples as discussed in the novel geometric analysis.

INCORPORATING TEMPORAL DEPENDENCY ON ERP BASED BCI.

In brain computer interface (BCI) systems based on event related potentials (ERPs), a windowed electroencephalography (EEG) signal is taken into consideration for the assumed duration of the ERP potential. In BCI applications inter stimuli interval is shorter than the ERP duration. This causes temporal dependencies over observation potentials thus disallows taking the data into consideration independently. However, conventionally the data is assumed to be independent for decreasing complexity. In this paper we propose a graphical model which covers the temporal dependency into consideration by labeling each time sample. We also propose a formulation to exploit the time series structure of the EEG.

Optimal Query Selection Using Multi-Armed Bandits.

Query selection for latent variable estimation is conventionally performed by opting for observations with low noise or optimizing information theoretic objectives related to reducing the level of estimated uncertainty based on the current best estimate. In these approaches, typically the system makes a decision by leveraging the current available information about the state. However, trusting the current best estimate results in poor query selection when truth is far from the current estimate, and this negatively impacts the speed and accuracy of the latent variable estimation procedure. We introduce a novel sequential adaptive action value function for query selection using the multi-armed bandit (MAB) framework which allows us to find a tractable solution. For this adaptive-sequential query selection method, we analytically show: (i) performance improvement in the query selection for a dynamical system, (ii) the conditions where the model outperforms competitors. We also present favorable empirical assessments of the performance for this method, compared to alternative methods, both using Monte Carlo simulations and human-in-the-loop experiments with a brain computer interface (BCI) typing system where the language model provides the prior information.

On Analysis of Active Querying for Recursive State Estimation.

In stochastic linear/non-linear active dynamic systems, states are estimated with the evidence through recursive measurements in response to queries of the system about the state to be estimated. Therefore, query selection is essential for such systems to improve state estimation accuracy and time. Query selection is conventionally achieved by minimization of the evidence variance or optimization of various information theoretic objectives. It was shown that optimization of mutual information-based objectives and variance-based objectives arrive at the same solution. However, existing approaches optimize approximations to the intended objectives rather than solving the exact optimization problems. To overcome these shortcomings, we propose an active querying procedure using mutual information maximization in recursive state estimation. First we show that mutual information generalizes variance based query selection methods and show the equivalence between objectives if the evidence likelihoods have unimodal distributions. We then solve the exact optimization problem for query selection and propose a query (measurement) selection algorithm. We specifically formulate the mutual information maximization for query selection as a combinatorial optimization problem and show that the objective is sub-modular, therefore can be solved efficiently with guaranteed convergence bounds through a greedy approach. Additionally, we analyze the performance of the query selection algorithm by testing it through a brain computer interface typing system.