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Register a new userManifold Model for High-Resolution fMRI Joint Reconstruction and Dynamic Quantification
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Added by
Shouchang Guo
Publication date
2021
fields
Electronic Engineering
and research's language is
English
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Oscillating Steady-State Imaging (OSSI) is a recent fMRI acquisition method that exploits a large and oscillating signal, and can provide high SNR fMRI. However, the oscillatory nature of the signal leads to an increased number of acquisitions. To improve temporal resolution and accurately model the nonlinearity of OSSI signals, we build the MR physics for OSSI signal generation as a regularizer for the undersampled reconstruction rather than using subspace models that are not well suited for the data. Our proposed physics-based manifold model turns the disadvantages of OSSI acquisition into advantages and enables joint reconstruction and quantification. OSSI manifold model (OSSIMM) outperforms subspace models and reconstructs high-resolution fMRI images with a factor of 12 acceleration and without spatial or temporal resolution smoothing. Furthermore, OSSIMM can dynamically quantify important physics parameters, including $R_2^*$ maps, with a temporal resolution of 150 ms.
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Single-particle cryo-electron microscopy (cryo-EM) reconstructs the three-dimensional (3D) structure of bio-molecules from a large set of 2D projection images with random and unknown orientations. A crucial step in the single-particle cryo-EM pipeline is 3D refinement, which resolves a high-resolution 3D structure from an initial approximate volume by refining the estimation of the orientation of each projection. In this work, we propose a new approach that refines the projection angles on the continuum. We formulate the optimization problem over the density map and the orientations jointly. The density map is updated using the efficient alternating-direction method of multipliers, while the orientations are updated through a semi-coordinate-wise gradient descent for which we provide an explicit derivation of the gradient. Our method eliminates the requirement for a fine discretization of the orientation space and does away with the classical but computationally expensive template-matching step. Numerical results demonstrate the feasibility and performance of our approach compared to several baselines.
The core problem of Magnetic Resonance Imaging (MRI) is the trade off between acceleration and image quality. Image reconstruction and super-resolution are two crucial techniques in Magnetic Resonance Imaging (MRI). Current methods are designed to perform these tasks separately, ignoring the correlations between them. In this work, we propose an end-to-end task transformer network (T$^2$Net) for joint MRI reconstruction and super-resolution, which allows representations and feature transmission to be shared between multiple task to achieve higher-quality, super-resolved and motion-artifacts-free images from highly undersampled and degenerated MRI data. Our framework combines both reconstruction and super-resolution, divided into two sub-branches, whose features are expressed as queries and keys. Specifically, we encourage joint feature learning between the two tasks, thereby transferring accurate task information. We first use two separate CNN branches to extract task-specific features. Then, a task transformer module is designed to embed and synthesize the relevance between the two tasks. Experimental results show that our multi-task model significantly outperforms advanced sequential methods, both quantitatively and qualitatively.
Respiration causes time-varying frequency offsets that can result in ghosting artifacts. We propose a solution, which we term dynamic realtime z-shimming, wherein linear gradients are adjusted dynamically (slice-wise) and in real-time, to reflect magnetic field inhomogeneities that arise during image acquisition. In dynamic z-shimming, a method that is commonly used to reduce static frequency offsets in MR images of the spinal cord and brain, in-plane (static) frequency offsets are assumed to be homogeneous. Here we investigate whether or not that same assumption can be made for time-varying frequency offsets in the cervical spinal cord region. In order to explore the feasibility of dynamic realtime z-shimming, we acquired images using a pneumatic phantom setup, as well as in-vivo. We then simulated the effects of time-varying frequency offsets on MR images acquired with and without dynamic realtime z-shimming in different scenarios. We found that dynamic realtime z-shimming can reduce ghosting if the time-varying frequency offsets have an in-plane variability (standard deviation) of approximately less than 1 Hz. This scenario was achieved in our phantom setup, where we observed a 50.2% reduction in ghosting within multi-echo gradient echo images acquired with dynamic realtime z-shimming, compared to without. On the other hand, we observed that the in-plane variability of the time-varying frequency offsets is too high within the cervical spinal cord region for dynamic realtime z-shimming to be successful. These results can serve as a guideline and starting point for future dynamic realtime z-shimming experiments in which the in-plane variability of frequency offsets are minimized.
We propose a new algorithmic approach to the non-smooth and non-convex Potts problem (also called piecewise-constant Mumford-Shah problem) for inverse imaging problems. We derive a suitable splitting into specific subproblems that can all be solved efficiently. Our method does not require a priori knowledge on the gray levels nor on the number of segments of the reconstruction. Further, it avoids anisotropic artifacts such as geometric staircasing. We demonstrate the suitability of our method for joint image reconstruction and segmentation. We focus on Radon data, where we in particular consider limited data situations. For instance, our method is able to recover all segments of the Shepp-Logan phantom from $7$ angular views only. We illustrate the practical applicability on a real PET dataset. As further applications, we consider spherical Radon data as well as blurred data.
When no arterial input function is available, quantification of dynamic PET images requires a previous step devoted to the extraction of a reference time-activity curve (TAC). Factor analysis is often applied for this purpose. This paper introduces a novel approach that conducts a new kind of nonlinear factor analysis relying on a compartment model, and computes the kinetic parameters of specific binding tissues jointly. To this end, it capitalizes on data-driven parametric imaging methods to provide a physical description of the underlying PET data, directly relating the specific binding with the kinetics of the non-specific binding in the corresponding tissues. This characterization is introduced into the factor analysis formulation to yield a novel nonlinear unmixing model designed for PET image analysis. This model also explicitly introduces global kinetic parameters that allow for a direct estimation of the binding potential with respect to the free fractions in each non-specific binding tissue. The performance of the method is evaluated on synthetic and real data to demonstrate its potential interest.
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