Fast Mesh-Based Medical Image Registration

In this paper a fast triangular mesh based registration method is proposed. Having Template and Reference images as inputs, the template image is triangulated using a content adaptive mesh generation algorithm. Considering the pixel values at mesh nodes, interpolated using spline interpolation method for both of the images, the energy functional needed for image registration is minimized. The minimization process was achieved using a mesh based discretization of the distance measure and regularization term which resulted in a sparse system of linear equations, which due to the smaller size in comparison to the pixel-wise registration method, can be solved directly. Mean Squared Difference (MSD) is used as a metric for evaluating the results. Using the mesh based technique, higher speed was achieved compared to pixel-based curvature registration technique with fast DCT solver. The implementation was done in MATLAB without any specific optimization. Higher speeds can be achieved using C/C++ implementations.Comment: Accepted manuscript for ISVC'201

Anatomical Mirroring: Real-time User-specific Anatomy in Motion Using a Commodity Depth Camera

International audienceThis paper presents a mirror-like augmented reality (AR) system to display the internal anatomy of a user. Using a single Microsoft V2.0 Kinect, we animate in real-time a user-specific internal anatomy according to the user’s motion and we superimpose it onto the user’s color map. The user can visualize his anatomy moving as if he was able to look inside his own body in real-time. A new calibration procedure to set up and attach a user-specific anatomy to the Kinect body tracking skeleton is introduced. At calibration time, the bone lengths are estimated using a set of poses. By using Kinect data as input, the practical limitation of skin correspondance in prior work is overcome. The generic 3D anatomical model is attached to the internal anatomy registration skeleton, and warped on the depth image using a novel elastic deformer, subject to a closest-point registration force and anatomical constraints. The noise in Kinect outputs precludes any realistic human display. Therefore, a novel filter to reconstruct plausible motions based onfixed length bones as well as realistic angular degrees of freedom (DOFs) and limits is introduced to enforce anatomical plausibility. Anatomical constraints applied to the Kinect body tracking skeleton joints are used to maximize the physical plausibility of the anatomy motion, while minimizing the distance to the raw data. At run-time,a simulation loop is used to attract the bones towards the raw data, and skinning shaders efficiently drag the resulting anatomy to the user’s tracked motion.Our user-specific internal anatomy model is validated by comparing the skeleton with segmented MRI images. A user study is established to evaluate the believability of the animated anatomy

Unsupervised Fiber Bundles Registration using Weighted Measures Geometric Demons

International audienceBrain image registration aims at reducing anatomical variability across subjects to create a common space for group analysis. Multi-modal approaches intend to minimize cortex shape variations along with internal structures, such as fiber bundles. A di ficulty is that it requires a prior identi fication of these structures, which remains a challenging task in the absence of a complete reference atlas. We propose an extension of the log-Geometric Demons for jointly registering images and fi ber bundles without the need of point or ber correspondences. By representing fi ber bundles as Weighted Measures we can register subjects with di fferent numbers of fiber bundles. The ef ficacy of our algorithm is demonstrated by registering simultaneously T1 images and between 37 and 88 ber bundles depending on each of the ten subject used. We compare results with a multi-modal T1 + Fractional Anisotropy (FA) and a tensor-based registration algorithms and obtain superior performance with our approach

Joint T1 and Brain Fiber Log-Demons Registration Using Currents to Model Geometry

International audienceWe present an extension of the diffeomorphic Geometric Demons algorithm which combines the iconic registration with geometric constraints. Our algorithm works in the log-domain space, so that one can efficiently compute the deformation field of the geometry. We represent the shape of objects of interest in the space of currents which is sensitive to both location and geometric structure of objects. Currents provides a distance between geometric structures that can be defined without specifying explicit point-to-point correspondences. We demonstrate this framework by registering simultaneously T1 images and 65 fiber bundles consistently extracted in 12 subjects and compare it against non-linear T1, tensor, and multi-modal T1+ Fractional Anisotropy (FA) registration algorithms. Results show the superiority of the Log-domain Geometric Demons over their purely iconic counterparts

Unsupervised Probabilistic Deformation Modeling for Robust Diffeomorphic Registration

International audienceWe propose a deformable registration algorithm based on unsupervised learning of a low-dimensional probabilistic parameterization of deformations. We model registration in a probabilistic and generative fashion, by applying a conditional variational autoencoder (CVAE) network. This model enables to also generate normal or pathological deformations of any new image based on the probabilistic latent space. Most recent learning-based registration algorithms use supervised labels or deformation models, that miss important properties such as diffeomorphism and sufficiently regular deformation fields. In this work, we constrain transformations to be diffeomorphic by using a differentiable exponentiation layer with a symmetric loss function. We evaluated our method on 330 cardiac MR sequences and demonstrate robust intra-subject registration results comparable to two state-of-the-art methods but with more regular deformation fields compared to a recent learning-based algorithm. Our method reached a mean DICE score of 78.3% and a mean Hausdorff distance of 7.9mm. In two preliminary experiments, we illustrate the model's abilities to transport pathological deformations to healthy subjects and to cluster five diseases in the unsupervised deformation encoding space with a classification performance of 70%

Variational Registration of Multiple Images with the SVD based SqN Distance Measure

Image registration, especially the quantification of image similarity, is an important task in image processing. Various approaches for the comparison of two images are discussed in the literature. However, although most of these approaches perform very well in a two image scenario, an extension to a multiple images scenario deserves attention. In this article, we discuss and compare registration methods for multiple images. Our key assumption is, that information about the singular values of a feature matrix of images can be used for alignment. We introduce, discuss and relate three recent approaches from the literature: the Schatten q-norm based SqN distance measure, a rank based approach, and a feature volume based approach. We also present results for typical applications such as dynamic image sequences or stacks of histological sections. Our results indicate that the SqN approach is in fact a suitable distance measure for image registration. Moreover, our examples also indicate that the results obtained by SqN are superior to those obtained by its competitors.Comment: 12 pages, 5 figures, accepted at the conference "Scale Space and Variational Methods" in Hofgeismar, Germany 201

Using synthetic MR images for distortion correction

Functional MRI (fMRI) data acquired using echo-planar imaging (EPI) are highly distorted by magnetic field inhomogeneities. Distortion and differences in image contrast between EPI and T1-weighted and T2-weighted (T1w/T2w) images makes their alignment a challenge. Typically, field map data are used to correct EPI distortions. Alignments achieved with field maps can vary greatly and depends on the quality of field map data. However, many public datasets lack field map data entirely. Additionally, reliable field map data is often difficult to acquire in high-motion pediatric or developmental cohorts. To address this, we developed Synth, a software package for distortion correction and cross-modal image registration that does not require field map data. Synth combines information from T1w and T2w anatomical images to construct an idealized undistorted synthetic image with similar contrast properties to EPI data. This synthetic image acts as an effective reference for individual-specific distortion correction. Using pediatric (ABCD: Adolescent Brain Cognitive Development) and adult (MSC: Midnight Scan Club; HCP: Human Connectome Project) data, we demonstrate that Synth performs comparably to field map distortion correction approaches, and often outperforms them. Field map-less distortion correction with Synth allows accurate and precise registration of fMRI data with missing or corrupted field map information

Characterizing Heterogeneity in Neuroimaging, Cognition, Clinical Symptoms, and Genetics Among Patients With Late-Life Depression

Importance: Late-life depression (LLD) is characterized by considerable heterogeneity in clinical manifestation. Unraveling such heterogeneity might aid in elucidating etiological mechanisms and support precision and individualized medicine. Objective: To cross-sectionally and longitudinally delineate disease-related heterogeneity in LLD associated with neuroanatomy, cognitive functioning, clinical symptoms, and genetic profiles. Design, Setting, and Participants: The Imaging-Based Coordinate System for Aging and Neurodegenerative Diseases (iSTAGING) study is an international multicenter consortium investigating brain aging in pooled and harmonized data from 13 studies with more than 35 000 participants, including a subset of individuals with major depressive disorder. Multimodal data from a multicenter sample (N = 996), including neuroimaging, neurocognitive assessments, and genetics, were analyzed in this study. A semisupervised clustering method (heterogeneity through discriminative analysis) was applied to regional gray matter (GM) brain volumes to derive dimensional representations. Data were collected from July 2017 to July 2020 and analyzed from July 2020 to December 2021. Main Outcomes and Measures: Two dimensions were identified to delineate LLD-associated heterogeneity in voxelwise GM maps, white matter (WM) fractional anisotropy, neurocognitive functioning, clinical phenotype, and genetics. Results: A total of 501 participants with LLD (mean [SD] age, 67.39 [5.56] years; 332 women) and 495 healthy control individuals (mean [SD] age, 66.53 [5.16] years; 333 women) were included. Patients in dimension 1 demonstrated relatively preserved brain anatomy without WM disruptions relative to healthy control individuals. In contrast, patients in dimension 2 showed widespread brain atrophy and WM integrity disruptions, along with cognitive impairment and higher depression severity. Moreover, 1 de novo independent genetic variant (rs13120336; chromosome: 4, 186387714; minor allele, G) was significantly associated with dimension 1 (odds ratio, 2.35; SE, 0.15; P = 3.14 ×10⁸) but not with dimension 2. The 2 dimensions demonstrated significant single-nucleotide variant–based heritability of 18% to 27% within the general population (N = 12 518 in UK Biobank). In a subset of individuals having longitudinal measurements, those in dimension 2 experienced a more rapid longitudinal change in GM and brain age (Cohen ƒ² = 0.03; P = .02) and were more likely to progress to Alzheimer disease (Cohen ƒ² = 0.03; P = .03) compared with those in dimension 1 (N = 1431 participants and 7224 scans from the Alzheimer’s Disease Neuroimaging Initiative [ADNI], Baltimore Longitudinal Study of Aging [BLSA], and Biomarkers for Older Controls at Risk for Dementia [BIOCARD] data sets). Conclusions and Relevance: This study characterized heterogeneity in LLD into 2 dimensions with distinct neuroanatomical, cognitive, clinical, and genetic profiles. This dimensional approach provides a potential mechanism for investigating the heterogeneity of LLD and the relevance of the latent dimensions to possible disease mechanisms, clinical outcomes, and responses to interventions

Biomechanics-informed Neural Networks for Myocardial Motion Tracking in MRI

Image registration is an ill-posed inverse problem which often requires regularisation on the solution space. In contrast to most of the current approaches which impose explicit regularisation terms such as smoothness, in this paper we propose a novel method that can implicitly learn biomechanics-informed regularisation. Such an approach can incorporate application-specific prior knowledge into deep learning based registration. Particularly, the proposed biomechanics-informed regularisation leverages a variational autoencoder (VAE) to learn a manifold for biomechanically plausible deformations and to implicitly capture their underlying properties via reconstructing biomechanical simulations. The learnt VAE regulariser then can be coupled with any deep learning based registration network to regularise the solution space to be biomechanically plausible. The proposed method is validated in the context of myocardial motion tracking on 2D stacks of cardiac MRI data from two different datasets. The results show that it can achieve better performance against other competing methods in terms of motion tracking accuracy and has the ability to learn biomechanical properties such as incompressibility and strains. The method has also been shown to have better generalisability to unseen domains compared with commonly used L2 regularisation schemes.Comment: The paper is early accepted by MICCAI 202

Deep Group-wise Variational Diffeomorphic Image Registration

Deep neural networks are increasingly used for pair-wise image registration. We propose to extend current learning-based image registration to allow simultaneous registration of multiple images. To achieve this, we build upon the pair-wise variational and diffeomorphic VoxelMorph approach and present a general mathematical framework that enables both registration of multiple images to their geodesic average and registration in which any of the available images can be used as a fixed image. In addition, we provide a likelihood based on normalized mutual information, a well-known image similarity metric in registration, between multiple images, and a prior that allows for explicit control over the viscous fluid energy to effectively regularize deformations. We trained and evaluated our approach using intra-patient registration of breast MRI and Thoracic 4DCT exams acquired over multiple time points. Comparison with Elastix and VoxelMorph demonstrates competitive quantitative performance of the proposed method in terms of image similarity and reference landmark distances at significantly faster registration