Automated template-based brain localization and extraction for fetal brain MRI reconstruction.

Most fetal brain MRI reconstruction algorithms rely only on brain tissue-relevant voxels of low-resolution (LR) images to enhance the quality of inter-slice motion correction and image reconstruction. Consequently the fetal brain needs to be localized and extracted as a first step, which is usually a laborious and time consuming manual or semi-automatic task. We have proposed in this work to use age-matched template images as prior knowledge to automatize brain localization and extraction. This has been achieved through a novel automatic brain localization and extraction method based on robust template-to-slice block matching and deformable slice-to-template registration. Our template-based approach has also enabled the reconstruction of fetal brain images in standard radiological anatomical planes in a common coordinate space. We have integrated this approach into our new reconstruction pipeline that involves intensity normalization, inter-slice motion correction, and super-resolution (SR) reconstruction. To this end we have adopted a novel approach based on projection of every slice of the LR brain masks into the template space using a fusion strategy. This has enabled the refinement of brain masks in the LR images at each motion correction iteration. The overall brain localization and extraction algorithm has shown to produce brain masks that are very close to manually drawn brain masks, showing an average Dice overlap measure of 94.5%. We have also demonstrated that adopting a slice-to-template registration and propagation of the brain mask slice-by-slice leads to a significant improvement in brain extraction performance compared to global rigid brain extraction and consequently in the quality of the final reconstructed images. Ratings performed by two expert observers show that the proposed pipeline can achieve similar reconstruction quality to reference reconstruction based on manual slice-by-slice brain extraction. The proposed brain mask refinement and reconstruction method has shown to provide promising results in automatic fetal brain MRI segmentation and volumetry in 26 fetuses with gestational age range of 23 to 38 weeks

Real-Time Automatic Fetal Brain Extraction in Fetal MRI by Deep Learning

Brain segmentation is a fundamental first step in neuroimage analysis. In the case of fetal MRI, it is particularly challenging and important due to the arbitrary orientation of the fetus, organs that surround the fetal head, and intermittent fetal motion. Several promising methods have been proposed but are limited in their performance in challenging cases and in real-time segmentation. We aimed to develop a fully automatic segmentation method that independently segments sections of the fetal brain in 2D fetal MRI slices in real-time. To this end, we developed and evaluated a deep fully convolutional neural network based on 2D U-net and autocontext, and compared it to two alternative fast methods based on 1) a voxelwise fully convolutional network and 2) a method based on SIFT features, random forest and conditional random field. We trained the networks with manual brain masks on 250 stacks of training images, and tested on 17 stacks of normal fetal brain images as well as 18 stacks of extremely challenging cases based on extreme motion, noise, and severely abnormal brain shape. Experimental results show that our U-net approach outperformed the other methods and achieved average Dice metrics of 96.52% and 78.83% in the normal and challenging test sets, respectively. With an unprecedented performance and a test run time of about 1 second, our network can be used to segment the fetal brain in real-time while fetal MRI slices are being acquired. This can enable real-time motion tracking, motion detection, and 3D reconstruction of fetal brain MRI.Comment: This work has been submitted to ISBI 201

Volumetric MRI Reconstruction from 2D Slices in the Presence of Motion

Despite recent advances in acquisition techniques and reconstruction algorithms, magnetic resonance imaging (MRI) remains challenging in the presence of motion. To mitigate this, ultra-fast two-dimensional (2D) MRI sequences are often used in clinical practice to acquire thick, low-resolution (LR) 2D slices to reduce in-plane motion. The resulting stacks of thick 2D slices typically provide high-quality visualizations when viewed in the in-plane direction. However, the low spatial resolution in the through-plane direction in combination with motion commonly occurring between individual slice acquisitions gives rise to stacks with overall limited geometric integrity. In further consequence, an accurate and reliable diagnosis may be compromised when using such motion-corrupted, thick-slice MRI data. This thesis presents methods to volumetrically reconstruct geometrically consistent, high-resolution (HR) three-dimensional (3D) images from motion-corrupted, possibly sparse, low-resolution 2D MR slices. It focuses on volumetric reconstructions techniques using inverse problem formulations applicable to a broad field of clinical applications in which associated motion patterns are inherently different, but the use of thick-slice MR data is current clinical practice. In particular, volumetric reconstruction frameworks are developed based on slice-to-volume registration with inter-slice transformation regularization and robust, complete-outlier rejection for the reconstruction step that can either avoid or efficiently deal with potential slice-misregistrations. Additionally, this thesis describes efficient Forward-Backward Splitting schemes for image registration for any combination of differentiable (not necessarily convex) similarity measure and convex (not necessarily smooth) regularization with a tractable proximal operator. Experiments are performed on fetal and upper abdominal MRI, and on historical, printed brain MR films associated with a uniquely long-term study dating back to the 1980s. The results demonstrate the broad applicability of the presented frameworks to achieve robust reconstructions with the potential to improve disease diagnosis and patient management in clinical practice

Computerized Analysis of Magnetic Resonance Images to Study Cerebral Anatomy in Developing Neonates

The study of cerebral anatomy in developing neonates is of great importance for the understanding of brain development during the early period of life. This dissertation therefore focuses on three challenges in the modelling of cerebral anatomy in neonates during brain development. The methods that have been developed all use Magnetic Resonance Images (MRI) as source data. To facilitate study of vascular development in the neonatal period, a set of image analysis algorithms are developed to automatically extract and model cerebral vessel trees. The whole process consists of cerebral vessel tracking from automatically placed seed points, vessel tree generation, and vasculature registration and matching. These algorithms have been tested on clinical Time-of- Flight (TOF) MR angiographic datasets. To facilitate study of the neonatal cortex a complete cerebral cortex segmentation and reconstruction pipeline has been developed. Segmentation of the neonatal cortex is not effectively done by existing algorithms designed for the adult brain because the contrast between grey and white matter is reversed. This causes pixels containing tissue mixtures to be incorrectly labelled by conventional methods. The neonatal cortical segmentation method that has been developed is based on a novel expectation-maximization (EM) method with explicit correction for mislabelled partial volume voxels. Based on the resulting cortical segmentation, an implicit surface evolution technique is adopted for the reconstruction of the cortex in neonates. The performance of the method is investigated by performing a detailed landmark study. To facilitate study of cortical development, a cortical surface registration algorithm for aligning the cortical surface is developed. The method first inflates extracted cortical surfaces and then performs a non-rigid surface registration using free-form deformations (FFDs) to remove residual alignment. Validation experiments using data labelled by an expert observer demonstrate that the method can capture local changes and follow the growth of specific sulcus

Novel Image Processing Methods for Improved Fetal Brain MRI

Fetal magnetic resonance imaging (MRI) has been increasingly used as a powerful complement imaging modality to ultrasound imaging (US) for the clinical evaluation of prenatal abnormalities. Specifically, clinical application of fetal MRI has been significantly improved in the nineties by hardware and software advances with the development of ultrafast multi-slice T2-weighted (T2w) acquisition sequences able to freeze the unpredictable fetal motion and provide excellent soft-tissue contrast. Fetal motion is indeed the major challenge in fetal MRI and slice acquisition time should be kept as short as possible. As a result, typical fetal MRI examination involves the acquisition of a set of orthogonally planned scans of thick two-dimensional slices, largely free of intra-slice motion artifacts. The poor resolution in the slice-select dimension as well as possible motion occurring between slices limits further quantitative data analysis, which is the key for a better understanding of the developing brain but also the key for the determination of operator-independent biomarkers that might significantly facilitate fetal diagnosis and prognosis. To this end, several research groups have developed in the past ten years advanced image processing methods, often denoted by motion-robust super-resolution (SR) techniques, to reconstruct from a set of clinical low-resolution (LR) scans, a high-resolution (HR) motion-free volume. SR problem is usually modeled as a linear inverse problem describing the imaging degradation due to acquisition and fetal motion. Typically, such approaches consist in iterating between slice motion estimation that estimates the motion parameters and SR that recovers the HR image given the estimated degradation model. This thesis focuses on the development of novel advanced image processing methods, which have enabled the design of a completely automated reconstruction pipeline for fetal MRI. The proposed techniques help in improving state-of-the-art fetal MRI reconstruction in terms of efficiency, robustness and minimized user-interactions, with the ultimate goal of being translated to the clinical environment. The first part focuses on the development of a more efficient Total Variation (TV)-regularized optimization algorithm for the SR problem. The algorithm uses recent advances in convex optimization with a novel adaptive regularization strategy to offer simultaneously fast, accurate and robust solutions to the fetal image recovery problem. Extensive validations on both simulated fetal and real clinical data show the proposed algorithm is highly robust in front of motion artifacts and that it offers the best trade-off between speed and accuracy for fetal MRI recovery as in comparison with state-of-the art methods. The second part focuses on the development of a novel automatic brain localization and extraction approach based on template-to-slice block matching and deformable slice-totemplate registration. Asmost fetal brain MRI reconstruction algorithms rely only on brain tissue-relevant voxels of low-resolution (LR) images to enhance the quality of inter-slice motion correction and image reconstruction, the fetal brain needs to be localized and extracted as a first step. These tasks generally necessitate user interaction, manually or semi-automatically done. Our methods have enabled the design of completely automated reconstruction pipeline that involves intensity normalization, inter-slice motion estimation, and super-resolution. Quantitative evaluation on clinical MRI scans shows that our approach produces brain masks that are very close to manually drawn brain masks, and ratings performed by two expert observers show that the proposed pipeline achieves similar reconstruction quality to reference reconstruction based on manual slice-by-slice brain extraction without any further effort. The third part investigates the possibility of automatic cortical folding quantification, one of the best biomarkers of brain maturation, by combining our automatic reconstruction pipeline with a state-of-the-art fetal brain tissue segmentation method and existing automated tools provided for adult brain’s cortical folding quantification. Results indicate that our reconstruction pipeline can provide HR MR images with sufficient quality that enable the use of surface tessellation and active surface algorithms similar to those developed for adults to extract meaningful information about fetal brain maturation. Finally, the last part presents new methodological improvements of the reconstruction pipeline aiming at improving the quality of the image for quantitative data analysis, whose accuracy is highly dependent on the quality and resolution of the reconstructed image. In particular, it presents a more consistent and global magnetic bias field correction method which takes advantage of the super-resolution framework to provide a final reconstructed image quasi free of the smooth bias field. Then, it presents a new TV SR algorithm that uses the Huber norm in the data fidelity term to be more robust to non-Gaussian outliers. It also presents the design of a novel joint reconstruction-segmentation framework and the development of a novel TV SR algorithm driven by segmentation to produce images with enhanced edge information that could ultimately improve their segmentation. Finally, it preliminary investigates the capability of increasing the resolution in the in-plane dimensions using SR to ultimately reduce the partial volume effect

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