In MRI, motion correction for fet al body poses a particular challenge due to the presence of local non-rigid transformations of organs caused by bending and stretching. The existing slice-to-volume (SVR) reconstruction methods provide efficient solution for the fet al brain that undergoes only rigid transformation or 4D fet al heart with rigid states correlated to cardiac phases. However, for fet al body reconstruction, rigid registration cannot resolve the issue of misregistrations due to deformable motion. This results in propagation of registration error to the reconstructed volume and subsequent degradation of features. We propose a novel approach for non-rigid motion correction in 3D volumes based on an extension of the classical SVR method with hierarchical deformable registration scheme and structure-based outlier rejection. Deformable SVR (DSVR) method allows high resolution reconstruction of the fet al trunk and the robust scheme for structure-based rejection of misregistered slices minimises the impact of registration error. The method performance is evaluated by comparison to the SVR and patch-to-volume registration methods for reconstruction of fet al trunk on a series of fet al MRI datasets from 28-30 weeks gestational age (GA) range with varying degree of motion corruption. An additional phantom study with simulated non-rigid motion is used for the assessment of consistency of DSVR reconstructed volumes.
The original concept of application of SVR for reconstruction of fet al brain from motion-corrupted MRI stacks was proposed in @cite_21 . It includes slice-to-volume registration interleaved with scattered data interpolation based on weighed sum of Gaussian kernels representing point spread function (PSF). During the following decade, the SVR reconstruction framework was gradually formalised and optimised with B-spline interpolation @cite_1 , SR reconstruction @cite_9 @cite_15 , edge-preserving regularisation @cite_26 , outlier rejection @cite_9 @cite_19 , intensity matching @cite_22 , total variation regularisation @cite_3 , sinc PSF model and GPU-parallelisation @cite_20 .
@cite_26 @cite_22 @cite_9 @cite_21 @cite_1 @cite_3 @cite_19 @cite_15 @cite_20
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Motion degrades magnetic resonance (MR) images and prevents acquisition of self-consistent and high-quality volume images. A novel methodology, Snapshot magnetic resonance imaging (MRI) with volume reconstruction (SVR) has been developed for imaging moving subjects at high resolution and high signal-to-noise ratio (SNR). The method combines registered 2D slices from sequential dynamic single-shot scans. The SVR approach requires that the anatomy in question is not changing shape or size and is moving at a rate that allows snapshot images to be acquired. After imaging the target volume repeatedly to guarantee sufficient sampling every where, a robust slice-to-volume registration method has been implemented that achieves alignment of each slice within 0.3 mm in the examples tested. Multilevel scattered interpolation has been used to obtain high-fidelity reconstruction with root-mean-square (rms) error that is less than the noise level in the images. The SVR method has been performed successfully for brain studies on subjects that cannot stay still, and in some cases were moving substantially during scanning. For example, awake neonates, deliberately moved adults and, especially, on fetuses, for which no conventional high-resolution 3D method is currently available. Fine structure of the in-utero fet al brain is clearly revealed for the first time and substantial SNR improvement is realized by having many individually acquired slices contribute to each voxel in the reconstructed image. Capturing an enclosing volume of moving subjects and organs using fast individual image slice acquisition has shown promise in dealing with motion artefacts. Motion between slice acquisitions results in spatial inconsistencies that can be resolved by slice-to-volume reconstruction (SVR) methods to provide high quality 3D image data. Existing algorithms are, however, typically very slow, specialised to specific applications and rely on approximations, which impedes their potential clinical use. In this paper, we present a fast multi-GPU accelerated framework for slice-to-volume reconstruction. It is based on optimised 2D 3D registration, super-resolution with automatic outlier rejection and an additional (optional) intensity bias correction. We introduce a novel and fully automatic procedure for selecting the image stack with least motion to serve as an initial registration target. We evaluate the proposed method using artificial motion corrupted phantom data as well as clinical data, including tracked freehand ultrasound of the liver and fet al Magnetic Resonance Imaging. We achieve speed-up factors greater than 30 compared to a single CPU system and greater than 10 compared to currently available state-of-the-art multi-core CPU methods. We ensure high reconstruction accuracy by exact computation of the point-spread function for every input data point, which has not previously been possible due to computational limitations. Our framework and its implementation is scalable for available computational infrastructures and tests show a speed-up factor of 1.70 for each additional GPU. This paves the way for the online application of image based reconstruction methods during clinical examinations. The source code for the proposed approach is publicly available. We propose a method for the reconstruction of volumetric fet al MRI from 2D slices, comprising super-resolution reconstruction of the volume interleaved with slice-to-volume registration to correct for the motion. The method incorporates novel intensity matching of acquired 2D slices and robust statistics which completely excludes identified misregistered or corrupted voxels and slices. The reconstruction method is applied to motion-corrupted data simulated from MRI of a preterm neonate, as well as 10 clinically acquired thick-slice fet al MRI scans and three scan-sequence optimized thin-slice fet al datasets. The proposed method produced high quality reconstruction results from all the datasets to which it was applied. Quantitative analysis performed on simulated and clinical data shows that both intensity matching and robust statistics result in statistically significant improvement of super-resolution reconstruction. The proposed novel EM-based robust statistics also improves the reconstruction when compared to previously proposed Huber robust statistics. The best results are obtained when thin-slice data and the correct approximation of the point spread function is used. This paper addresses the need for a comprehensive reconstruction algorithm of 3D fet al MRI, so far lacking in the scientific literature. In this paper, we present a novel method for the correction of motion artifacts that are present in fet al magnetic resonance imaging (MRI) scans of the whole uterus. Contrary to current slice-to-volume registration (SVR) methods, requiring an inflexible anatomical enclosure of a single investigated organ, the proposed patch-to-volume reconstruction (PVR) approach is able to reconstruct a large field of view of non-rigidly deforming structures. It relaxes rigid motion assumptions by introducing a specific amount of redundant information that is exploited with parallelized patchwise optimization, super-resolution, and automatic outlier rejection. We further describe and provide an efficient parallel implementation of PVR allowing its execution within reasonable time on commercially available graphics processing units, enabling its use in the clinical practice. We evaluate PVR’s computational overhead compared with standard methods and observe improved reconstruction accuracy in the presence of affine motion artifacts compared with conventional SVR in synthetic experiments. Furthermore, we have evaluated our method qualitatively and quantitatively on real fet al MRI data subject to maternal breathing and sudden fet al movements. We evaluate peak-signal-to-noise ratio, structural similarity index, and cross correlation with respect to the originally acquired data and provide a method for visual inspection of reconstruction uncertainty. We further evaluate the distance error for selected anatomical landmarks in the fet al head, as well as calculating the mean and maximum displacements resulting from automatic non-rigid registration to a motion-free ground truth image. These experiments demonstrate a successful application of PVR motion compensation to the whole fet al body, uterus, and placenta.