arXiv subjects

Hassan Rivaz

Publications and source records attributed to Hassan Rivaz.

At least 73 records · Page 4Linked to original sources

arXiv2022

DiffeoRaptor: Diffeomorphic Inter-modal Image Registration using RaPTOR

Purpose: Diffeomorphic image registration is essential in many medical imaging applications. Several registration algorithms of such type have been proposed, but primarily for intra-contrast alignment. Currently, efficient inter-modal/contrast diffeomorphic registration, which is vital in numerous applications, remains a challenging task. Methods: We proposed a novel inter-modal/contrast registration algorithm that leverages Robust PaTch-based cOrrelation Ratio (RaPTOR) metric to allow inter-modal/contrast image alignment and bandlimited geodesic shooting demonstrated in Fourier Approximated Lie Algebras (FLASH) algorithm for fast diffeomorphic registration. Results: The proposed algorithm, named DiffeoRaptor, was validated with three public databases for the tasks of brain and abdominal image registration while comparing the results against three state-of-the-art techniques, including FLASH, NiftyReg, and Symmetric image normalization (SyN). Conclusions: Our results demonstrated that DiffeoRaptor offered comparable or better registration performance in terms of registration accuracy. Moreover, DiffeoRaptor produces smoother deformations than SyN in inter-modal and contrast registration. The code for DiffeoRaptor is publicly available at https://github.com/nimamasoumi/DiffeoRaptor.

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arXiv2022

A Unifying Approach to Inverse Problems of Ultrasound Beamforming and Deconvolution

Beamforming is an essential step in the ultrasound image formation pipeline and has recently attracted growing interest. An important goal of beamforming is to increase the image spatial resolution, or in other words to narrow down the system point spread function. In parallel to beamforming approaches, deconvolution methods have also been explored in ultrasound imaging to mitigate the adverse effects of PSF. Unfortunately, these two steps have only been considered separately in a sequential approach. Herein, a novel framework for unifying beamforming and deconvolution in ultrasound image reconstruction is introduced. More specifically, the proposed formulation is a regularized inverse problem including two linear models for beamforming and deconvolution plus additional sparsity constraint. We take advantage of the alternating direction method of multipliers algorithm to find the solution of the joint optimization problem. The performance evaluation is presented on a set of publicly available simulations, real phantoms, and in vivo data. Furthermore, the superiority of the proposed approach in comparison with the sequential approach as well as each of the other beamforming and deconvolution approaches alone is also shown. Results demonstrate that our approach combines the advantages of both methods and offers ultrasound images with superior resolution and contrast.

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arXiv2022

Physics-Inspired Regularized Pulse-Echo Quantitative Ultrasound: Efficient Optimization with ADMM

Pulse-echo Quantitative ultrasound (PEQUS), which estimates the quantitative properties of tissue microstructure, entails estimating the average attenuation and the backscatter coefficient (BSC). Growing recent research has focused on the regularized estimation of these parameters. Herein, we make two contributions to this field: First, we consider the physics of the average attenuation and backscattering to devise regularization terms accordingly. More specifically, since the average attenuation gradually alters in different parts of the tissue while BSC can vary markedly from tissue to tissue, we apply L2 and L1 norms for the average attenuation and the BSC, respectively. Second, we multiply different frequencies and depths of the power spectra with different weights according to their noise levels. Our rationale is that the high-frequency contents of the power spectra at deep regions have a low signal-to-noise ratio. We exploit the alternating direction method of multipliers (ADMM) for optimizing the cost function. Qualitative and quantitative evaluation of bias and variance exhibit that our proposed algorithm substantially improves the estimations of the average attenuation and the BSC.

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arXiv2022

Inverse Problem of Ultrasound Beamforming with Denoising-Based Regularized Solutions

During the past few years, inverse problem formulations of ultrasound beamforming have attracted a growing interest. They usually pose beamforming as a minimization problem of a fidelity term resulting from the measurement model plus a regularization term that enforces a certain class on the resulting image. Herein, we take advantages of alternating direction method of multipliers to propose a flexible framework in which each term is optimized separately. Furthermore, the proposed beamforming formulation is extended to replace the regularization term by a denoising algorithm, based on the recent approaches called plug-and-play (PnP) and regularization by denoising (RED). Such regularizations are shown in this work to better preserve speckle texture, an important feature in ultrasound imaging, than sparsity-based approaches previously proposed in the literature. The efficiency of proposed methods is evaluated on simulations, real phantoms, and \textit{in vivo} data available from a plane-wave imaging challenge in medical ultrasound. Furthermore, a comprehensive comparison with existing ultrasound beamforming methods is also provided. These results show that the RED algorithm gives the best image quality in terms of contrast index while preserving the speckle statistics.

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arXiv2022

RESECT-SEG: Open access annotations of intra-operative brain tumor ultrasound images

Purpose: Registration and segmentation of magnetic resonance (MR) and ultrasound (US) images play an essential role in surgical planning and resection of brain tumors. However, validating these techniques is challenging due to the scarcity of publicly accessible sources with high-quality ground truth information. To this end, we propose a unique annotation dataset of tumor tissues and resection cavities from the previously published RESECT dataset (Xiao et al. 2017) to encourage a more rigorous assessments of image processing techniques. Acquisition and validation methods: The RESECT database consists of MR and intraoperative US (iUS) images of 23 patients who underwent resection surgeries. The proposed dataset contains tumor tissues and resection cavity annotations of the iUS images. The quality of annotations were validated by two highly experienced neurosurgeons through several assessment criteria. Data format and availability: Annotations of tumor tissues and resection cavities are provided in 3D NIFTI formats. Both sets of annotations are accessible online in the \url{https://osf.io/6y4db}. Discussion and potential applications: The proposed database includes tumor tissue and resection cavity annotations from real-world clinical ultrasound brain images to evaluate segmentation and registration methods. These labels could also be used to train deep learning approaches. Eventually, this dataset should further improve the quality of image guidance in neurosurgery.

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arXiv2022

Physically Inspired Constraint for Unsupervised Regularized Ultrasound Elastography

Displacement estimation is a critical step of virtually all Ultrasound Elastography (USE) techniques. Two main features make this task unique compared to the general optical flow problem: the high-frequency nature of ultrasound radio-frequency (RF) data and the governing laws of physics on the displacement field. Recently, the architecture of the optical flow networks has been modified to be able to use RF data. Also, semi-supervised and unsupervised techniques have been employed for USE by considering prior knowledge of displacement continuity in the form of the first- and second-derivative regularizers. Despite these attempts, no work has considered the tissue compression pattern, and displacements in axial and lateral directions have been assumed to be independent. However, tissue motion pattern is governed by laws of physics in USE, rendering the axial and the lateral displacements highly correlated. In this paper, we propose Physically Inspired ConsTraint for Unsupervised Regularized Elastography (PICTURE), where we impose constraints on the Poisson's ratio to improve lateral displacement estimates. Experiments on phantom and in vivo data show that PICTURE substantially improves the quality of the lateral displacement estimation.

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arXiv2022

Deep Estimation of Speckle Statistics Parametric Images

Quantitative Ultrasound (QUS) provides important information about the tissue properties. QUS parametric image can be formed by dividing the envelope data into small overlapping patches and computing different speckle statistics such as parameters of the Nakagami and Homodyned K-distributions (HK-distribution). The calculated QUS parametric images can be erroneous since only a few independent samples are available inside the patches. Another challenge is that the envelope samples inside the patch are assumed to come from the same distribution, an assumption that is often violated given that the tissue is usually not homogenous. In this paper, we propose a method based on Convolutional Neural Networks (CNN) to estimate QUS parametric images without patching. We construct a large dataset sampled from the HK-distribution, having regions with random shapes and QUS parameter values. We then use a well-known network to estimate QUS parameters in a multi-task learning fashion. Our results confirm that the proposed method is able to reduce errors and improve border definition in QUS parametric images.

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arXiv2022

Incorporating Gradient Similarity for Robust Time Delay Estimation in Ultrasound Elastography

Energy-based ultrasound elastography techniques minimize a regularized cost function consisting of data and continuity terms to obtain local displacement estimates based on the local time-delay estimation (TDE) between radio-frequency (RF) frames. The data term associated with the existing techniques takes only the amplitude similarity into account and hence is not sufficiently robust to the outlier samples present in the RF frames under consideration. This drawback creates noticeable artifacts in the strain image. To resolve this issue, we propose to formulate the data function as a linear combination of the amplitude and gradient similarity constraints. We estimate the adaptive weight concerning each similarity term following an iterative scheme. Finally, we optimize the non-linear cost function in an efficient manner to convert the problem to a sparse system of linear equations which are solved for millions of variables. We call our technique rGLUE: robust data term in GLobal Ultrasound Elastography. rGLUE has been validated using simulation, phantom, in vivo liver, and breast datasets. In all of our experiments, rGLUE substantially outperforms the recent elastography methods both visually and quantitatively. For simulated, phantom, and in vivo datasets, respectively, rGLUE achieves 107%, 18%, and 23% improvements of signal-to-noise ratio (SNR) and 61%, 19%, and 25% improvements of contrast-to-noise ratio (CNR) over GLUE, a recently-published elastography algorithm.

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arXiv2022

Investigating Shift-Variance of Convolutional Neural Networks in Ultrasound Image Segmentation

While accuracy is an evident criterion for ultrasound image segmentation, output consistency across different tests is equally crucial for tracking changes in regions of interest in applications such as monitoring the patients' response to treatment, measuring the progression or regression of the disease, reaching a diagnosis, or treatment planning. Convolutional neural networks (CNNs) have attracted rapidly growing interest in automatic ultrasound image segmentation recently. However, CNNs are not shift-equivariant, meaning that if the input translates, e.g., in the lateral direction by one pixel, the output segmentation may drastically change. To the best of our knowledge, this problem has not been studied in ultrasound image segmentation or even more broadly in ultrasound images. Herein, we investigate and quantify the shift-variance problem of CNNs in this application and further evaluate the performance of a recently published technique, called BlurPooling, for addressing the problem. In addition, we propose the Pyramidal BlurPooling method that outperforms BlurPooling in both output consistency and segmentation accuracy. Finally, we demonstrate that data augmentation is not a replacement for the proposed method. Source code is available at https://git.io/pbpunet and http://code.sonography.ai.

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arXiv2022

Bi-Directional Semi-Supervised Training of Convolutional Neural Networks for Ultrasound Elastography Displacement Estimation

The performance of ultrasound elastography (USE) heavily depends on the accuracy of displacement estimation. Recently, Convolutional Neural Networks (CNN) have shown promising performance in optical flow estimation and have been adopted for USE displacement estimation. Networks trained on computer vision images are not optimized for USE displacement estimation since there is a large gap between the computer vision images and the high-frequency Radio Frequency (RF) ultrasound data. Many researchers tried to adopt the optical flow CNNs to USE by applying transfer learning to improve the performance of CNNs for USE. However, the ground truth displacement in real ultrasound data is unknown, and simulated data exhibits a domain shift compared to the real data and is also computationally expensive to generate. To resolve this issue, semi-supervised methods have been proposed wherein the networks pre-trained on computer vision images are fine-tuned using real ultrasound data. In this paper, we employ a semi-supervised method by exploiting the first and second-order derivatives of the displacement field for the regularization. We also modify the network structure to estimate both forward and backward displacements, and propose to use consistency between the forward and backward strains as an additional regularizer to further enhance the performance. We validate our method using several experimental phantom and in vivo data. We also show that the network fine-tuned by our proposed method using experimental phantom data performs well on in vivo data similar to the network fine-tuned on in vivo data. Our results also show that the proposed method outperforms current deep learning methods and is comparable to computationally expensive optimization-based algorithms.

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arXiv2022

Robust Scatterer Number Density Segmentation of Ultrasound Images

Quantitative UltraSound (QUS) aims to reveal information about the tissue microstructure using backscattered echo signals from clinical scanners. Among different QUS parameters, scatterer number density is an important property that can affect estimation of other QUS parameters. Scatterer number density can be classified into high or low scatterer densities. If there are more than 10 scatterers inside the resolution cell, the envelope data is considered as Fully Developed Speckle (FDS) and otherwise, as Under Developed Speckle (UDS). In conventional methods, the envelope data is divided into small overlapping windows (a strategy here we refer to as patching), and statistical parameters such as SNR and skewness are employed to classify each patch of envelope data. However, these parameters are system dependent meaning that their distribution can change by the imaging settings and patch size. Therefore, reference phantoms which have known scatterer number density are imaged with the same imaging settings to mitigate system dependency. In this paper, we aim to segment regions of ultrasound data without any patching. A large dataset is generated which has different shapes of scatterer number density and mean scatterer amplitude using a fast simulation method. We employ a convolutional neural network (CNN) for the segmentation task and investigate the effect of domain shift when the network is tested on different datasets with different imaging settings. Nakagami parametric image is employed for the multi-task learning to improve the performance. Furthermore, inspired by the reference phantom methods in QUS, A domain adaptation stage is proposed which requires only two frames of data from FDS and UDS classes. We evaluate our method for different experimental phantoms and in vivo data.

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arXiv2022

Deep Ultrasound Denoising Without Clean Data

On one hand, the transmitted ultrasound beam gets attenuated as propagates through the tissue. On the other hand, the received Radio-Frequency (RF) data contains an additive Gaussian noise which is brought about by the acquisition card and the sensor noise. These two factors lead to a decreasing Signal to Noise Ratio (SNR) in the RF data with depth, effectively rendering deep regions of B-Mode images highly unreliable. There are three common approaches to mitigate this problem. First, increasing the power of transmitted beam which is limited by safety threshold. Averaging consecutive frames is the second option which not only reduces the framerate but also is not applicable for moving targets. And third, reducing the transmission frequency, which deteriorates spatial resolution. Many deep denoising techniques have been developed, but they often require clean data for training the model, which is usually only available in simulated images. Herein, a deep noise reduction approach is proposed which does not need clean training target. The model is constructed between noisy input-output pairs, and the training process interestingly converges to the clean image that is the average of noisy pairs. Experimental results on real phantom as well as ex vivo data confirm the efficacy of the proposed method for noise cancellation.

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arXiv2022

Second-Order Ultrasound Elastography with L1-norm Spatial Regularization

Time delay estimation (TDE) between two radio-frequency (RF) frames is one of the major steps of quasi-static ultrasound elastography, which detects tissue pathology by estimating its mechanical properties. Regularized optimization-based techniques, a prominent class of TDE algorithms, optimize a non-linear energy functional consisting of data constancy and spatial continuity constraints to obtain the displacement and strain maps between the time-series frames under consideration. The existing optimization-based TDE methods often consider the L2-norm of displacement derivatives to construct the regularizer. However, such a formulation over-penalizes the displacement irregularity and poses two major issues to the estimated strain field. First, the boundaries between different tissues are blurred. Second, the visual contrast between the target and the background is suboptimal. To resolve these issues, herein, we propose a novel TDE algorithm where instead of L2-, L1-norms of both first- and second-order displacement derivatives are taken into account to devise the continuity functional. We handle the non-differentiability of L1-norm by smoothing the absolute value function's sharp corner and optimize the resulting cost function in an iterative manner. We call our technique Second-Order Ultrasound eLastography with L1-norm spatial regularization (L1-SOUL). In terms of both sharpness and visual contrast, L1-SOUL substantially outperforms GLUE, OVERWIND, and SOUL, three recently published TDE algorithms in all validation experiments performed in this study. In cases of simulated, phantom, and in vivo datasets, respectively, L1-SOUL achieves 67.8%, 46.81%, and 117.35% improvements of contrast-to-noise ratio (CNR) over SOUL. The L1-SOUL code can be downloaded from http://code.sonography.ai.

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arXiv2021

Fast Strain Estimation and Frame Selection in Ultrasound Elastography using Machine Learning

Ultrasound Elastography aims to determine the mechanical properties of the tissue by monitoring tissue deformation due to internal or external forces. Tissue deformations are estimated from ultrasound radio frequency (RF) signals and are often referred to as time delay estimation (TDE). Given two RF frames I1 and I2, we can compute a displacement image which shows the change in the position of each sample in I1 to a new position in I2. Two important challenges in TDE include high computational complexity and the difficulty in choosing suitable RF frames. Selecting suitable frames is of high importance because many pairs of RF frames either do not have acceptable deformation for extracting informative strain images or are decorrelated and deformation cannot be reliably estimated. Herein, we introduce a method that learns 12 displacement modes in quasi-static elastography by performing Principal Component Analysis (PCA) on displacement fields of a large training database. In the inference stage, we use dynamic programming (DP) to compute an initial displacement estimate of around 1% of the samples, and then decompose this sparse displacement into a linear combination of the 12 displacement modes. Our method assumes that the displacement of the whole image could also be described by this linear combination of principal components. We then use the GLobal Ultrasound Elastography (GLUE) method to fine-tune the result yielding the exact displacement image. Our method, which we call PCA-GLUE, is more than 10 times faster than DP in calculating the initial displacement map while giving the same result. Our second contribution in this paper is determining the suitability of the frame pair I1 and I2 for strain estimation, which we achieve by using the weight vector that we calculated for PCA-GLUE as an input to a multi-layer perceptron (MLP) classifier.

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arXiv2021

Plane-Wave Ultrasound Beamforming: A Deep Learning Approach

Medical ultrasound provides images which are the spatial map of the tissue echogenicity. Unfortunately, an ultrasound image is a low-quality version of the expected Tissue Reflectivity Function (TRF) mainly due to the non-ideal Point Spread Function (PSF) of the imaging system. This paper presents a novel beamforming approach based on deep learning to get closer to the ideal PSF in Plane-Wave Imaging (PWI). The proposed approach is designed to reconstruct the desired TRF from echo traces acquired by transducer elements using only a single plane-wave transmission. In this approach, first, an ideal model for the TRF is introduced by setting the imaging PSF as a sharp Gaussian function. Then, a mapping function between the pre-beamformed Radio-Frequency (RF) channel data and the proposed TRF is constructed using deep learning. Network architecture contains multi-resolution decomposition and reconstruction using wavelet transform for effective recovery of high-frequency content of the desired TRF. Inspired by curriculum learning, we exploit step by step training from coarse (mean square error) to fine ($\ell_{0.2}$) loss functions. The proposed method is trained on a large number of simulation ultrasound data with the ground-truth echogenicity map extracted from real photographic images. The performance of the trained network is evaluated on the publicly available simulation and \textit{in vivo} test data without any further fine-tuning. Simulation test results confirm that the proposed method reconstructs images with a high quality in terms of resolution and contrast, which are also visually similar to the proposed ground-truth image. Furthermore, \textit{in vivo} results show that the trained mapping function preserves its performance in the new domain. Therefore, the proposed approach maintains high resolution, contrast, and framerate simultaneously.

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arXiv2021

Estimation of the Scatterer Size Distributions in Quantitative Ultrasound Using Constrained Optimization

Quantitative ultrasound (QUS) parameters such as the effective scatterer diameter (ESD) reveal tissue properties by analyzing ultrasound backscattered echo signal. ESD can be attained through parametrizing backscatter coefficient using form factor models. However, reporting a single scatterer size cannot accurately characterize a tissue, particularly when the media contains scattering sources with a broad range of sizes. Here we estimate the probability of contribution of each scatterer size by modeling the measured form factor as a linear combination of form factors from individual sacatterer sizes. We perform the estimation using two novel techniques. In the first technique, we cast scatterer size distribution as an optimization problem, and efficiently solve it using a linear system of equations. In the second technique, we use the solution of this system of equations to constrain the optimization function, and solve the constrained problem. The methods are evaluated in simulated backscattered coefficients using Faran theory. We evaluate the robustness of the proposed techniques by adding Gaussian noise. The results show that both methods can accurately estimate the scatterer size distribution, and that the second method outperforms the first one.

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arXiv2021

Ultrasound Domain Adaptation Using Frequency Domain Analysis

A common issue in exploiting simulated ultrasound data for training neural networks is the domain shift problem, where the trained models on synthetic data are not generalizable to clinical data. Recently, Fourier Domain Adaptation (FDA) has been proposed in the field of computer vision to tackle the domain shift problem by replacing the magnitude of the low-frequency spectrum of a synthetic sample (source) with a real sample (target). This method is attractive in ultrasound imaging given that two important differences between synthetic and real ultrasound data are caused by unknown values of attenuation and speed of sound (SOS) in real tissues. Attenuation leads to slow variations in the amplitude of the B-mode image, and SOS mismatch creates aberration and subsequent blurring. As such, both domain shifts cause differences in the low-frequency components of the envelope data, which are replaced in the proposed method. We demonstrate that applying the FDA method to the synthetic data, simulated by Field II, obtains an 3.5\% higher Dice similarity coefficient for a breast lesion segmentation task.

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arXiv2021

An Ultra-Fast Method for Simulation of Realistic Ultrasound Images

Convolutional neural networks (CNNs) have attracted a rapidly growing interest in a variety of different processing tasks in the medical ultrasound community. However, the performance of CNNs is highly reliant on both the amount and fidelity of the training data. Therefore, scarce data is almost always a concern, particularly in the medical field, where clinical data is not easily accessible. The utilization of synthetic data is a popular approach to address this challenge. However, but simulating a large number of images using packages such as Field II is time-consuming, and the distribution of simulated images is far from that of the real images. Herein, we introduce a novel ultra-fast ultrasound image simulation method based on the Fourier transform and evaluate its performance in a lesion segmentation task. We demonstrate that data augmentation using the images generated by the proposed method substantially outperforms Field II in terms of Dice similarity coefficient, while the simulation is almost 36000 times faster (both on CPU).

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