arXiv subjects

Abdul Haseeb Ahmed

Publications and source records attributed to Abdul Haseeb Ahmed.

10 recordsLinked to original sources

arXiv2023

Prospectively accelerated dynamic speech MRI at 3 Tesla using a self-navigated spiral based manifold regularized scheme

This work proposes a self-navigated variable density spiral(VDS) based manifold regularization scheme to prospectively improve dynamic speech MRI at 3T. Short readout 1.3ms spirals were used to minimize off-resonance. A custom 16-channel speech coil was used for improved parallel imaging of vocal tract. The manifold model leveraged similarities between frames sharing similar speech postures without explicit motion binning. The self-navigating capability of VDS was leveraged to learn the Laplacian matrix of the manifold. Reconstruction was posed as a SENSE-based non-local soft weighted temporal regularization scheme. Our approach was compared against view-sharing, low-rank, finite difference, extra-dimension-based sparsity reconstruction constraints. Under-sampling experiments were conducted on five volunteers performing repetitive and arbitrary speaking tasks at different speaking rates. Quantitative evaluation in terms of mean square error over moving edges were performed in a retrospectively under-sampled data. For prospective under-sampling, blinded image quality evaluation in the categories of alias artifacts, spatial blurring, and temporal blurring were performed by three voice research experts. Region of interest analysis at articulator boundaries were performed to assess articulatory motion. Our scheme provided improved reconstruction over the others. With prospective under-sampling, a spatial resolution of 2.4mm2/pixel and a temporal resolution of 17.4 ms/frame for single slice imaging, and 52.2 ms/frame for 3-slice imaging were achieved. We demonstrated implicit motion binning by analyzing the mechanics of the Laplacian matrix. Our method demonstrated superior image quality scores in reducing spatial and temporal blurring. While it exhibited faint alias artifacts similar to temporal finite-difference, it provided statistically significant improvements over remaining constraints.

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arXiv2021

Variational manifold learning from incomplete data: application to multislice dynamic MRI

Current deep learning-based manifold learning algorithms such as the variational autoencoder (VAE) require fully sampled data to learn the probability density of real-world datasets. Once learned, the density can be used for a variety of tasks, including data imputation. However, fully sampled data is often unavailable in a variety of problems, including the recovery of dynamic and high-resolution MRI data considered in this work. To overcome this problem, we introduce a novel variational approach to learn a manifold from undersampled data. The VAE uses a decoder fed by latent vectors, drawn from a conditional density estimated from the fully sampled images using an encoder. Since fully sampled images are not available in our setting, we approximate the conditional density of the latent vectors by a parametric model whose parameters are estimated from the undersampled measurements using back-propagation. We use the framework for the joint alignment and recovery of multislice free breathing and ungated cardiac MRI data from highly undersampled measurements. Most of the current self-gating and manifold cardiac MRI approaches consider the independent recovery of images from each slice; these methods are not capable of exploiting the inter-slice redundancies in the datasets and require sophisticated post-processing or manual approaches to align the images from different slices. By contrast, the proposed scheme is able to align the multislice data and exploit the redundancies. Experimental results demonstrate the utility of the proposed scheme in dynamic imaging alignment and reconstructions.

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arXiv2021

Joint alignment and reconstruction of multislice dynamic MRI using variational manifold learning

Free-breathing cardiac MRI schemes are emerging as competitive alternatives to breath-held cine MRI protocols, enabling applicability to pediatric and other population groups that cannot hold their breath. Because the data from the slices are acquired sequentially, the cardiac/respiratory motion patterns may be different for each slice; current free-breathing approaches perform independent recovery of each slice. In addition to not being able to exploit the inter-slice redundancies, manual intervention or sophisticated post-processing methods are needed to align the images post-recovery for quantification. To overcome these challenges, we propose an unsupervised variational deep manifold learning scheme for the joint alignment and reconstruction of multislice dynamic MRI. The proposed scheme jointly learns the parameters of the deep network as well as the latent vectors for each slice, which capture the motion-induced dynamic variations, from the k-t space data of the specific subject. The variational framework minimizes the non-uniqueness in the representation, thus offering improved alignment and reconstructions.

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arXiv2021

Dynamic Imaging using Deep Bi-linear Unsupervised Regularization (DEBLUR)

Bilinear models that decompose dynamic data to spatial and temporal factors are powerful and memory-efficient tools for the recovery of dynamic MRI data. These methods rely on sparsity and energy compaction priors on the factors to regularize the recovery. The quality of the recovered images depend on the specific priors. Motivated by deep image prior, we introduce a novel bilinear model whose factors are represented using convolutional neural networks (CNNs). The CNN parameters are learned from the undersampled data off the same subject. To reduce the run time and to improve performance, we initialize the CNN parameters. We use sparsity regularization of the network parameters to minimize the overfitting of the network to measurement noise. Our experiments on free breathing and ungated cardiac cine data acquired using a navigated golden-angle gradient-echo radial sequence show the ability of our method to provide reduced spatial blurring as compared to low-rank and SToRM reconstructions.

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arXiv2021

Dynamic imaging using a deep generative SToRM (Gen-SToRM) model

We introduce a generative smoothness regularization on manifolds (SToRM) model for the recovery of dynamic image data from highly undersampled measurements. The model assumes that the images in the dataset are non-linear mappings of low-dimensional latent vectors. We use the deep convolutional neural network (CNN) to represent the non-linear transformation. The parameters of the generator as well as the low-dimensional latent vectors are jointly estimated only from the undersampled measurements. This approach is different from traditional CNN approaches that require extensive fully sampled training data. We penalize the norm of the gradients of the non-linear mapping to constrain the manifold to be smooth, while temporal gradients of the latent vectors are penalized to obtain a smoothly varying time-series. The proposed scheme brings in the spatial regularization provided by the convolutional network. The main benefit of the proposed scheme is the improvement in image quality and the orders-of-magnitude reduction in memory demand compared to traditional manifold models. To minimize the computational complexity of the algorithm, we introduce an efficient progressive training-in-time approach and an approximate cost function. These approaches speed up the image reconstructions and offers better reconstruction performance.

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arXiv2021

Deep Generative SToRM model for dynamic imaging

We introduce a novel generative smoothness regularization on manifolds (SToRM) model for the recovery of dynamic image data from highly undersampled measurements. The proposed generative framework represents the image time series as a smooth non-linear function of low-dimensional latent vectors that capture the cardiac and respiratory phases. The non-linear function is represented using a deep convolutional neural network (CNN). Unlike the popular CNN approaches that require extensive fully-sampled training data that is not available in this setting, the parameters of the CNN generator as well as the latent vectors are jointly estimated from the undersampled measurements using stochastic gradient descent. We penalize the norm of the gradient of the generator to encourage the learning of a smooth surface/manifold, while temporal gradients of the latent vectors are penalized to encourage the time series to be smooth. The main benefits of the proposed scheme are (a) the quite significant reduction in memory demand compared to the analysis based SToRM model, and (b) the spatial regularization brought in by the CNN model. We also introduce efficient progressive approaches to minimize the computational complexity of the algorithm.

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arXiv2020

Free-breathing and ungated cardiac cine using navigator-less spiral SToRM

We introduce a kernel low-rank algorithm to recover free-breathing and ungated dynamic MRI from spiral acquisitions without explicit k-space navigators. It is often challenging for low-rank methods to recover free-breathing and ungated images from undersampled measurements; extensive cardiac and respiratory motion often results in the Casorati matrix not being sufficiently low-rank. Therefore, we exploit the non-linear structure of the dynamic data, which gives the low-rank kernel matrix. Unlike prior work that rely on navigators to estimate the manifold structure, we propose a kernel low-rank matrix completion method to directly fill in the missing k-space data from variable density spiral acquisitions. We validate the proposed scheme using simulated data and in-vivo data. Our results show that the proposed scheme provides improved reconstructions compared to the classical methods such as low-rank and XD-GRASP. The comparison with breath-held cine data shows that the quantitative metrics agree, whereas the image quality is marginally lower.

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arXiv2019

Dynamic MRI using deep manifold self-learning

We propose a deep self-learning algorithm to learn the manifold structure of free-breathing and ungated cardiac data and to recover the cardiac CINE MRI from highly undersampled measurements. Our method learns the manifold structure in the dynamic data from navigators using autoencoder network. The trained autoencoder is then used as a prior in the image reconstruction framework. We have tested the proposed method on free-breathing and ungated cardiac CINE data, which is acquired using a navigated golden-angle gradient-echo radial sequence. Results show the ability of our method to better capture the manifold structure, thus providing us reduced spatial and temporal blurring as compared to the SToRM reconstruction.

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arXiv2019

Motion correction in cardiac perfusion data by using robust matrix decomposition

Motion free reconstruction of compressively sampled cardiac perfusion MR images is a challenging problem. It is due to the aliasing artifacts and the rapid contrast changes in the reconstructed perfusion images. In addition to the reconstruction limitations, many registration algorithms under perform in the presence of the rapid intensity changes. In this paper, we propose a novel motion correction method that reconstructs the motion free image series from the undersampled cardiac perfusion MR data. The motion correction method uses the novel robust principal component analysis based reconstruction along with the periodic decomposition to separate the respiratory motion component that can be registered, from the contrast intensity variations. It is tested on simulated data and the clinically acquired data. The performance of the method is qualitatively assessed and compared with the existing motion correction methods. The proposed method is validated by comparing manually acquired time-intensity curves of the myocardial sectors to automatically generated curves before and after registration.

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arXiv2019

Efficient Reconstruction of Free Breathing Under-Sampled Cardiac Cine MRI

Respiratory motion can cause strong blurring artifacts in the reconstructed image during MR acquisition. These artifacts become more prominent when use in the presence of undersampled data. Recently, compressed sensing (CS) is developed as an MR reconstruction technique, to recover good quality images from the compressive k-space samples. To maximize the benefits of CS in free breathing data, it is understandable to use CS with the motion corrected images. In this paper, we have developed a new CS based motion corrected image reconstruction technique. In this two-stage technique, we use similarity measure to sort the motion corrupted data into different respiratory states. Then, we use a new reconstruction algorithm, which iteratively performs reconstruction and motion correction. The performance of the proposed method is qualitatively and quantitively evaluated using simulated data and clinical data. Results depict that this method performs the better reconstruction of respiratory motion corrected cardiac cine images as compared to the CS based reconstruction method.

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