Iterative training of robust k-space interpolation networks for improved image reconstruction with limited scan specific training samples
University of Würzburg（维尔茨堡大学）；Fraunhofer Institute for Integrated Circuits IIS（弗劳恩霍夫集成电路研究所IIS）；University Hospital Würzburg（维尔茨堡大学医院）；Research Centre for Natural Sciences（自然科学研究中心）
Peter Dawood, Felix Breuer, Paul R. Burd, István Homolya, Johannes Oberberger, Peter M. Jakob, Martin Blaimer
Purpose: To evaluate an iterative learning approach for enhanced performance of Robust Artificial-neural-networks for K-space Interpolation (RAKI), when only a limited amount of training data (auto-calibration signals, ACS) are available for accelerated standard 2D imaging. Methods: In a first step, the RAKI model was optimized for the case of strongly limited training data amount. In the iterative learning approach (termed iterative RAKI), the optimized RAKI model is initially trained using original and augmented ACS obtained from a linear parallel imaging reconstruction. Subsequently, the RAKI convolution filters are refined iteratively using original and augmented ACS extracted from the previous RAKI reconstruction. Evaluation was carried out on 200 retrospectively undersampled in-vivo datasets from the fastMRI neuro database with different contrast settings. Results: For limited training data (18 and 22 ACS lines for R=4 and R=5, respectively), iterative RAKI outperforms standard RAKI by reducing residual artefacts and yields strong noise suppression when compared to standard parallel imaging, underlined by quantitative reconstruction quality metrics. In combination with a phase constraint, further reconstruction improvements can be achieved. Additionally, iterative RAKI shows better performance than both GRAPPA and RAKI in case of pre-scan calibration with varying contrast between training- and undersampled data. Conclusion: The iterative learning approach with RAKI benefits from standard RAKIs well known noise suppression feature but requires less original training data for the accurate reconstruction of standard 2D images thereby improving net acceleration.
Informed Sinogram Interpolation for Sparse View Reconstruction
Technische Universität München（慕尼黑工业大学）；Waygate Technologies, Baker Hughes Digital Solutions GmbH（韦盖特技术，贝克休斯数字解决方案有限公司）；Technische Universität Darmstadt（达姆施塔特工业大学）；Munich Center for Machine Learning (MCML)（慕尼黑机器学习中心）
The University of Maryland, College Park（马里兰大学帕克分校）；University of Rochester（罗切斯特大学）；Chinese Academy of Sciences（中国科学院）；Peng Cheng Laboratory（鹏城实验室）
We propose a marginal super-resolution (MSR) approach based on 2D convolutional neural networks (CNNs) for interpolating an anisotropic brain magnetic resonance scan along the highly under-sampled direction, which is assumed to axial without loss of generality. Previous methods for slice interpolation only consider data from pairs of adjacent 2D slices. The possibility of fusing information from the direction orthogonal to the 2D slices remains unexplored. Our approach performs MSR in both sagittal and coronal directions, which provides an initial estimate for slice interpolation. The interpol…
With the recent introduction of CT scanners with large cone angles, wide coverage detectors now provide a desirable scanning platform for cardiac CT that allows whole heart imaging in a single rotation. On these scanners, while half-scan data is strictly sufficient to produce images with the best temporal resolution, acquiring a full 360 degree rotation worth of data is beneficial for wide-cone image reconstruction at negligible additional radiation dose. Applying Model-Based Iterative Reconstruction (MBIR) algorithm to the heart has shown to yield significant enhancement in image quality for …
Image inpainting is a restoration process which has numerous applications. Restoring of scanned old images with scratches, or removing objects in images are some of inpainting applications. Different approaches have been used for implementation of inpainting algorithms. Interpolation approaches only consider one direction for this purpose. In this paper we present a new perspective to image inpainting. We consider multiple directions and apply both one-dimensional and two-dimensional bicubic interpolations. Neighboring pixels are selected in a hyperbolic formation to better preserve corner pix…
The key aspect of parallel-beam X-ray CT is forward and back projection, but its computational burden continues to be an obstacle for applications. We propose a method to improve the performance of related algorithms by calculating the Gram filter exactly and interpolating the sinogram signal optimally. In addition, the detector blur effect can be included in our model efficiently. The improvements in speed and quality for back projection and iterative reconstruction are shown in our experiments on both analytical phantoms and real CT images.
The reconstruction of gap-free signals from observation data is a critical challenge for numerous application domains, such as geoscience and space-based earth observation, when the available sensors or the data collection processes lead to irregularly-sampled and noisy observations. Optimal interpolation (OI), also referred to as kriging, provides a theoretical framework to solve interpolation problems for Gaussian processes (GP). The associated computational complexity being rapidly intractable for n-dimensional tensors and increasing numbers of observations, a rich literature has emerged to…
Resting-state functional Magnetic Resonance Imaging (fMRI) is a powerful imaging technique for studying functional development of the brain in utero. However, unpredictable and excessive movement of fetuses have limited its clinical applicability. Previous studies have focused primarily on the accurate estimation of the motion parameters employing a single step 3D interpolation at each individual time frame to recover a motion-free 4D fMRI image. Using only information from a 3D spatial neighborhood neglects the temporal structure of fMRI and useful information from neighboring timepoints. Her…
University of Ottawa（渥太华大学）；the Korea University Anam Hospital（高丽大学安岩医院）
Image interpolation in medical area is of high importance as most 3D biomedical volume images are sampled where the distance between consecutive slices significantly greater than the in-plane pixel size due to radiation dose or scanning time. Image interpolation creates a number of new slices between known slices in order to obtain an isotropic volume image. The results can be used for the higher quality of 3D reconstruction and visualization of human body structures. Semantic interpolation on the manifold has been proved to be very useful for smoothing image interpolation. Nevertheless, all p…
Recently, a number of approaches to low-dose computed tomography (CT) have been developed and deployed in commercialized CT scanners. Tube current reduction is perhaps the most actively explored technology with advanced image reconstruction algorithms. Sparse data sampling is another viable option to the low-dose CT, and sparse-view CT has been particularly of interest among the researchers in CT community. Since analytic image reconstruction algorithms would lead to severe image artifacts, various iterative algorithms have been developed for reconstructing images from sparsely view-sampled pr…
4D iterative reconstruction of brain fMRI in the moving fetus
Computational Imaging Research Lab（计算成像研究实验室）；Medical University of Vienna（维也纳医科大学）；Lausanne University Hospital (CHUV)（洛桑大学医院（CHUV））；University of Lausanne (UNIL)（洛桑大学（UNIL））；CIBM Center for Biomedical Imaging（CIBM生物医学成像中心）
Amsterdam University Medical Centers（阿姆斯特丹大学医学中心）；University of Amsterdam（阿姆斯特丹大学）；Amsterdam Cardiovascular Sciences（阿姆斯特丹心血管科学研究所）；Informatics Institute, University of Amsterdam（阿姆斯特丹大学信息学研究所）
High-resolution medical images are beneficial for analysis but their acquisition may not always be feasible. Alternatively, high-resolution images can be created from low-resolution acquisitions using conventional upsampling methods, but such methods cannot exploit high-level contextual information contained in the images. Recently, better performing deep-learning based super-resolution methods have been introduced. However, these methods are limited by their supervised character, i.e. they require high-resolution examples for training. Instead, we propose an unsupervised deep learning semanti…
Non-regular sampling can reduce aliasing at the expense of noise. Recently, it has been shown that non-regular sampling can be carried out using a conventional regular imaging sensor when the surface of its individual pixels is partially covered. This technique is called quarter sampling (also 1/4 sampling), since only one quarter of each pixel is sensitive to light. For this purpose, the choice of a proper sampling mask is crucial to achieve a high reconstruction quality. In the scope of this work, we present an iterative algorithm to improve an arbitrary quarter sampling mask which results i…
University of Bremen（不来梅大学）；Fraunhofer Institute for Digital Medicine MEVIS（弗劳恩霍夫数字医学研究所MEVIS）；Radboud UMC（拉德堡德大学医学中心）
Convolutional neural networks have not only been applied for classification of voxels, objects, or images, for instance, but have also been proposed as a bodypart regressor. We pick up this underexplored idea and evaluate its value for registration: A CNN is trained to output the relative height within the human body in axial CT scans, and the resulting scores are used for quick alignment between different timepoints. Preliminary results confirm that this allows both fast and robust prealignment compared with iterative approaches.
Shanghai Jiao Tong University（上海交通大学）；University of Sydney（悉尼大学）
Dynamic medical imaging is usually limited in application due to the large radiation doses and longer image scanning and reconstruction times. Existing methods attempt to reduce the dynamic sequence by interpolating the volumes between the acquired image volumes. However, these methods are limited to either 2D images and/or are unable to support large variations in the motion between the image volume sequences. In this paper, we present a spatiotemporal volumetric interpolation network (SVIN) designed for 4D dynamic medical images. SVIN introduces dual networks: first is the spatiotemporal mot…
Objective: Quantitative technique based on In-line phase-contrast computed tomography with single scanning attracts more attention in application due to the flexibility of the implementation. However, the quantitative results usually suffer from artifacts and noise, since the phase retrieval and reconstruction are independent ("two-steps") without feedback from the original data. Our goal is to develop a method for material quantitative imaging based on a priori information specifically for the single-scanning data. Method: An iterative method that directly reconstructs the refractive index de…
Deep learning-based single image super-resolution (SISR) methods face various challenges when applied to 3D medical volumetric data (i.e., CT and MR images) due to the high memory cost and anisotropic resolution, which adversely affect their performance. Furthermore, mainstream SISR methods are designed to work over specific upsampling factors, which makes them ineffective in clinical practice. In this paper, we introduce a Spatially Aware Interpolation NeTwork (SAINT) for medical slice synthesis to alleviate the memory constraint that volumetric data poses. Compared to other super-resolution …
Purpose, To develop a high scanning efficiency, motion corrected imaging strategy for free-breathing pulmonary MRI by combining a motion compensation reconstruction with a UTE acquisition, called iMoCo UTE. Methods, An optimized golden angle ordering radial UTE sequence was used to continuously acquire data for 5 minutes. All readouts were grouped to different respiratory motion states based on self-navigator signals, then motion resolved data was reconstructed by XD Golden angle RAdial Sparse Parallel reconstruction (XD GRASP). One state from the motion resolved images was selected as a refer…
Purdue University（普渡大学）；Lawrence Berkeley National Laboratory（劳伦斯伯克利国家实验室）；Los Alamos National Laboratory（洛斯阿拉莫斯国家实验室）；Air Force Research Laboratory（美国空军研究实验室）
Many material and biological samples in scientific imaging are characterized by non-local repeating structures. These are studied using scanning electron microscopy and electron tomography. Sparse sampling of individual pixels in a 2D image acquisition geometry, or sparse sampling of projection images with large tilt increments in a tomography experiment, can enable high speed data acquisition and minimize sample damage caused by the electron beam. In this paper, we present an algorithm for electron tomographic reconstruction and sparse image interpolation that exploits the non-local redundanc…
Parallel imaging is widely used in magnetic resonance imaging as an acceleration technology. Traditional linear reconstruction methods in parallel imaging often suffer from noise amplification. Recently, a non-linear robust artificial-neural-network for k-space interpolation (RAKI) exhibits superior noise resilience over other linear methods. However, RAKI performs poorly at high acceleration rates, and needs a large amount of autocalibration signals as the training samples. In order to tackle these issues, we propose a multi-weight method that implements multiple weighting matrices on the und…
Magnetic Resonance Fingerprinting (MRF) reconstructs tissue maps based on a sequence of very highly undersampled images. In order to be able to perform MRF reconstruction, state-of-the-art MRF methods rely on priors such as the MR physics (Bloch equations) and might also use some additional low-rank or spatial regularization. However to our knowledge these three regularizations are not applied together in a joint reconstruction. The reason is that it is indeed challenging to incorporate effectively multiple regularizations in a single MRF optimization algorithm. As a result most of these metho…
Magnetic resonance imaging with hyperpolarized contrast agents can provide unprecedented \textit{in-vivo} measurements of metabolism, but yields images that are lower resolution than that achieved with proton anatomical imaging. In order to spatially localize the metabolic activity, the metabolic image must be interpolated to the size of the proton image. The most common methods for choosing the unknown values rely exclusively on values of the original un-interpolated image. In this work, we present an alternative method that uses the higher-resolution proton image to provide additional spatia…
In order to determine the 3D structure of a thick sample, researchers have recently combined ptychography (for high resolution) and tomography (for 3D imaging) in a single experiment. 2-step methods are usually adopted for reconstruction, where the ptychography and tomography problems are often solved independently. In this paper, we provide a novel model and ADMM-based algorithm to jointly solve the ptychography-tomography problem iteratively, also employing total variation regularization. The proposed method permits large scan stepsizes for the ptychography experiment, requiring less measure…
