PVR: Patch-to-Volume Reconstruction for Large Area Motion Correction of Fetal MRI

In this paper we present a novel method for the correction of motion artifacts that are present in fetal 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 patch-wise 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 (GPU), enabling its use in the clinical practice. We evaluate PVR's computational overhead compared to standard methods and observe improved reconstruction accuracy in presence of affine motion artifacts of approximately 30% compared to conventional SVR in synthetic experiments. Furthermore, we have evaluated our method qualitatively and quantitatively on real fetal MRI data subject to maternal breathing and sudden fetal movements. We evaluate peak-signal-to-noise ratio (PSNR), structural similarity index (SSIM), and cross correlation (CC) with respect to the originally acquired data and provide a method for visual inspection of reconstruction uncertainty. With these experiments we demonstrate successful application of PVR motion compensation to the whole uterus, the human fetus, and the human placenta.Comment: 10 pages, 13 figures, submitted to IEEE Transactions on Medical Imaging. v2: wadded funders acknowledgements to preprin

Numerical methods for coupled reconstruction and registration in digital breast tomosynthesis.

Digital Breast Tomosynthesis (DBT) provides an insight into the fine details of normal fibroglandular tissues and abnormal lesions by reconstructing a pseudo-3D image of the breast. In this respect, DBT overcomes a major limitation of conventional X-ray mam- mography by reducing the confounding effects caused by the superposition of breast tissue. In a breast cancer screening or diagnostic context, a radiologist is interested in detecting change, which might be indicative of malignant disease. To help automate this task image registration is required to establish spatial correspondence between time points. Typically, images, such as MRI or CT, are first reconstructed and then registered. This approach can be effective if reconstructing using a complete set of data. However, for ill-posed, limited-angle problems such as DBT, estimating the deformation is com- plicated by the significant artefacts associated with the reconstruction, leading to severe inaccuracies in the registration. This paper presents a mathematical framework, which couples the two tasks and jointly estimates both image intensities and the parameters of a transformation. Under this framework, we compare an iterative method and a simultaneous method, both of which tackle the problem of comparing DBT data by combining reconstruction of a pair of temporal volumes with their registration. We evaluate our methods using various computational digital phantoms, uncom- pressed breast MR images, and in-vivo DBT simulations. Firstly, we compare both iter- ative and simultaneous methods to the conventional, sequential method using an affine transformation model. We show that jointly estimating image intensities and parametric transformations gives superior results with respect to reconstruction fidelity and regis- tration accuracy. Also, we incorporate a non-rigid B-spline transformation model into our simultaneous method. The results demonstrate a visually plausible recovery of the deformation with preservation of the reconstruction fidelity

Automatic landmark annotation and dense correspondence registration for 3D human facial images

Dense surface registration of three-dimensional (3D) human facial images holds great potential for studies of human trait diversity, disease genetics, and forensics. Non-rigid registration is particularly useful for establishing dense anatomical correspondences between faces. Here we describe a novel non-rigid registration method for fully automatic 3D facial image mapping. This method comprises two steps: first, seventeen facial landmarks are automatically annotated, mainly via PCA-based feature recognition following 3D-to-2D data transformation. Second, an efficient thin-plate spline (TPS) protocol is used to establish the dense anatomical correspondence between facial images, under the guidance of the predefined landmarks. We demonstrate that this method is robust and highly accurate, even for different ethnicities. The average face is calculated for individuals of Han Chinese and Uyghur origins. While fully automatic and computationally efficient, this method enables high-throughput analysis of human facial feature variation.Comment: 33 pages, 6 figures, 1 tabl

A Deep Learning Framework for Unsupervised Affine and Deformable Image Registration

Image registration, the process of aligning two or more images, is the core technique of many (semi-)automatic medical image analysis tasks. Recent studies have shown that deep learning methods, notably convolutional neural networks (ConvNets), can be used for image registration. Thus far training of ConvNets for registration was supervised using predefined example registrations. However, obtaining example registrations is not trivial. To circumvent the need for predefined examples, and thereby to increase convenience of training ConvNets for image registration, we propose the Deep Learning Image Registration (DLIR) framework for \textit{unsupervised} affine and deformable image registration. In the DLIR framework ConvNets are trained for image registration by exploiting image similarity analogous to conventional intensity-based image registration. After a ConvNet has been trained with the DLIR framework, it can be used to register pairs of unseen images in one shot. We propose flexible ConvNets designs for affine image registration and for deformable image registration. By stacking multiple of these ConvNets into a larger architecture, we are able to perform coarse-to-fine image registration. We show for registration of cardiac cine MRI and registration of chest CT that performance of the DLIR framework is comparable to conventional image registration while being several orders of magnitude faster.Comment: Accepted: Medical Image Analysis - Elsevie

Grid simulation services for the medical community

The first part of this paper presents a selection of medical simulation applications, including image reconstruction, near real-time registration for neuro-surgery, enhanced dose distribution calculation for radio-therapy, inhaled drug delivery prediction, plastic surgery planning and cardio-vascular system simulation. The latter two topics are discussed in some detail. In the second part, we show how such services can be made available to the clinical practitioner using Grid technology. We discuss the developments and experience made during the EU project GEMSS, which provides reliable, efficient, secure and lawful medical Grid services

EchoFusion: Tracking and Reconstruction of Objects in 4D Freehand Ultrasound Imaging without External Trackers

Ultrasound (US) is the most widely used fetal imaging technique. However, US images have limited capture range, and suffer from view dependent artefacts such as acoustic shadows. Compounding of overlapping 3D US acquisitions into a high-resolution volume can extend the field of view and remove image artefacts, which is useful for retrospective analysis including population based studies. However, such volume reconstructions require information about relative transformations between probe positions from which the individual volumes were acquired. In prenatal US scans, the fetus can move independently from the mother, making external trackers such as electromagnetic or optical tracking unable to track the motion between probe position and the moving fetus. We provide a novel methodology for image-based tracking and volume reconstruction by combining recent advances in deep learning and simultaneous localisation and mapping (SLAM). Tracking semantics are established through the use of a Residual 3D U-Net and the output is fed to the SLAM algorithm. As a proof of concept, experiments are conducted on US volumes taken from a whole body fetal phantom, and from the heads of real fetuses. For the fetal head segmentation, we also introduce a novel weak annotation approach to minimise the required manual effort for ground truth annotation. We evaluate our method qualitatively, and quantitatively with respect to tissue discrimination accuracy and tracking robustness.Comment: MICCAI Workshop on Perinatal, Preterm and Paediatric Image analysis (PIPPI), 201