An integrated approach to correction for off-resonance effects and subject movement in diffusion MR imaging

In this paper we describe a method for retrospective estimation and correction of eddy current (EC)-induced distortions and subject movement in diffusion imaging. In addition a susceptibility-induced field can be supplied and will be incorporated into the calculations in a way that accurately reflects that the two fields (susceptibility- and EC-induced) behave differently in the presence of subject movement. The method is based on registering the individual volumes to a model free prediction of what each volume should look like, thereby enabling its use on high b-value data where the contrast is vastly different in different volumes. In addition we show that the linear EC-model commonly used is insufficient for the data used in the present paper (high spatial and angular resolution data acquired with Stejskal–Tanner gradients on a 3 T Siemens Verio, a 3 T Siemens Connectome Skyra or a 7 T Siemens Magnetome scanner) and that a higher order model performs significantly better. The method is already in extensive practical use and is used by four major projects (the WU-UMinn HCP, the MGH HCP, the UK Biobank and the Whitehall studies) to correct for distortions and subject movement

Joint super-resolution and synthesis of 1 mm isotropic MP-RAGE volumes from clinical MRI exams with scans of different orientation, resolution and contrast

Most existing algorithms for automatic 3D morphometry of human brain MRI scans are designed for data with near-isotropic voxels at approximately 1 mm resolution, and frequently have contrast constraints as well-typically requiring T1-weighted images (e.g., MP-RAGE scans). This limitation prevents the analysis of millions of MRI scans acquired with large inter-slice spacing in clinical settings every year. In turn, the inability to quantitatively analyze these scans hinders the adoption of quantitative neuro imaging in healthcare, and also precludes research studies that could attain huge sample sizes and hence greatly improve our understanding of the human brain. Recent advances in convolutional neural networks (CNNs) are producing outstanding results in super-resolution and contrast synthesis of MRI. However, these approaches are very sensitive to the specific combination of contrast, resolution and orientation of the input images, and thus do not generalize to diverse clinical acquisition protocols - even within sites. In this article, we present SynthSR, a method to train a CNN that receives one or more scans with spaced slices, acquired with different contrast, resolution and orientation, and produces an isotropic scan of canonical contrast (typically a 1 mm MP-RAGE). The presented method does not require any preprocessing, beyond rigid coregistration of the input scans. Crucially, SynthSR trains on synthetic input images generated from 3D segmentations, and can thus be used to train CNNs for any combination of contrasts, resolutions and orientations without high-resolution real images of the input contrasts. We test the images generated with SynthSR in an array of common downstream analyses, and show that they can be reliably used for subcortical segmentation and volumetry, image registration (e.g., for tensor-based morphometry), and, if some image quality requirements are met, even cortical thickness morphometry. The source code is publicly available at https://github.com/BBillot/SynthSR

SurfaceAug: Closing the Gap in Multimodal Ground Truth Sampling

Despite recent advances in both model architectures and data augmentation, multimodal object detectors still barely outperform their LiDAR-only counterparts. This shortcoming has been attributed to a lack of sufficiently powerful multimodal data augmentation. To address this, we present SurfaceAug, a novel ground truth sampling algorithm. SurfaceAug pastes objects by resampling both images and point clouds, enabling object-level transformations in both modalities. We evaluate our algorithm by training a multimodal detector on KITTI and compare its performance to previous works. We show experimentally that SurfaceAug outperforms existing methods on car detection tasks and establishes a new state of the art for multimodal ground truth sampling.Comment: Contains eight pages and three figures. A version of this document was submitted to CVPR 202

Video modeling via implicit motion representations

Video modeling refers to the development of analytical representations for explaining the intensity distribution in video signals. Based on the analytical representation, we can develop algorithms for accomplishing particular video-related tasks. Therefore video modeling provides us a foundation to bridge video data and related-tasks. Although there are many video models proposed in the past decades, the rise of new applications calls for more efficient and accurate video modeling approaches.;Most existing video modeling approaches are based on explicit motion representations, where motion information is explicitly expressed by correspondence-based representations (i.e., motion velocity or displacement). Although it is conceptually simple, the limitations of those representations and the suboptimum of motion estimation techniques can degrade such video modeling approaches, especially for handling complex motion or non-ideal observation video data. In this thesis, we propose to investigate video modeling without explicit motion representation. Motion information is implicitly embedded into the spatio-temporal dependency among pixels or patches instead of being explicitly described by motion vectors.;Firstly, we propose a parametric model based on a spatio-temporal adaptive localized learning (STALL). We formulate video modeling as a linear regression problem, in which motion information is embedded within the regression coefficients. The coefficients are adaptively learned within a local space-time window based on LMMSE criterion. Incorporating a spatio-temporal resampling and a Bayesian fusion scheme, we can enhance the modeling capability of STALL on more general videos. Under the framework of STALL, we can develop video processing algorithms for a variety of applications by adjusting model parameters (i.e., the size and topology of model support and training window). We apply STALL on three video processing problems. The simulation results show that motion information can be efficiently exploited by our implicit motion representation and the resampling and fusion do help to enhance the modeling capability of STALL.;Secondly, we propose a nonparametric video modeling approach, which is not dependent on explicit motion estimation. Assuming the video sequence is composed of many overlapping space-time patches, we propose to embed motion-related information into the relationships among video patches and develop a generic sparsity-based prior for typical video sequences. First, we extend block matching to more general kNN-based patch clustering, which provides an implicit and distributed representation for motion information. We propose to enforce the sparsity constraint on a higher-dimensional data array signal, which is generated by packing the patches in the similar patch set. Then we solve the inference problem by updating the kNN array and the wanted signal iteratively. Finally, we present a Bayesian fusion approach to fuse multiple-hypothesis inferences. Simulation results in video error concealment, denoising, and deartifacting are reported to demonstrate its modeling capability.;Finally, we summarize the proposed two video modeling approaches. We also point out the perspectives of implicit motion representations in applications ranging from low to high level problems

Constrained parameterization with applications to graphics and image processing.

Surface parameterization is to establish a transformation that maps the points on a surface to a specified parametric domain. It has been widely applied to computer graphics and image processing fields. The challenging issue is that the usual positional constraints always result in triangle flipping in parameterizations (also called foldovers). Additionally, distortion is inevitable in parameterizations. Thus the rigid constraint is always taken into account. In general, the constraints are application-dependent. This thesis thus focuses on the various constraints depended on applications and investigates the foldover-free constrained parameterization approaches individually. Such constraints usually include, simple positional constraints, tradeoff of positional constraints and rigid constraint, and rigid constraint. From the perspective of applications, we aim at the foldover-free parameterization methods with positional constraints, the as-rigid-as-possible parameterization with positional constraints, and the well-shaped well-spaced pre-processing procedure for low-distortion parameterizations in this thesis. The first contribution of this thesis is the development of a RBF-based re-parameterization algorithm for the application of the foldover-free constrained texture mapping. The basic idea is to split the usual parameterization procedure into two steps, 2D parameterization with the constraints of convex boundaries and 2D re-parameterization with the interior positional constraints. Moreover, we further extend the 2D re-parameterization approach with the interior positional constraints to high dimensional datasets, such as, volume data and polyhedrons. The second contribution is the development of a vector field based deformation algorithm for 2D mesh deformation and image warping. Many presented deformation approaches are used to employ the basis functions (including our proposed RBF-based re-parameterization algorithm here). The main problem is that such algorithms have infinite support, that is, any local deformation always leads to small changes over the whole domain. Our presented vector field based algorithm can effectively carry on the local deformation while reducing distortion as much as possible. The third contribution is the development of a pre-processing for surface parameterization. Except the developable surfaces, the current parameterization approaches inevitably incur large distortion. To reduce distortion, we proposed a pre-processing procedure in this thesis, including mesh partition and mesh smoothing. As a result, the resulting meshes are partitioned into a set of small patches with rectangle-like boundaries. Moreover, they are well-shaped and well-spaced. This pre-processing procedure can evidently improve the quality of meshes for low-distortion parameterizations

Fast and Accurate 3D Face Recognition Using Registration to an Intrinsic Coordinate System and Fusion of Multiple Region classifiers

In this paper we present a new robust approach for 3D face registration to an intrinsic coordinate system of the face. The intrinsic coordinate system is defined by the vertical symmetry plane through the nose, the tip of the nose and the slope of the bridge of the nose. In addition, we propose a 3D face classifier based on the fusion of many dependent region classifiers for overlapping face regions. The region classifiers use PCA-LDA for feature extraction and the likelihood ratio as a matching score. Fusion is realised using straightforward majority voting for the identification scenario. For verification, a voting approach is used as well and the decision is defined by comparing the number of votes to a threshold. Using the proposed registration method combined with a classifier consisting of 60 fused region classifiers we obtain a 99.0% identification rate on the all vs first identification test of the FRGC v2 data. A verification rate of 94.6% at FAR=0.1% was obtained for the all vs all verification test on the FRGC v2 data using fusion of 120 region classifiers. The first is the highest reported performance and the second is in the top-5 of best performing systems on these tests. In addition, our approach is much faster than other methods, taking only 2.5 seconds per image for registration and less than 0.1 ms per comparison. Because we apply feature extraction using PCA and LDA, the resulting template size is also very small: 6 kB for 60 region classifiers

Processing strategies for functional magnetic resonance imaging data sets

Thesis (Ph.D.)--Harvard--Massachusetts Institute of Technology Division of Health Sciences and Technology, 1999.Includes bibliographical references (leaves 108-118).by Luis Carlos Maas, III.Ph.D