Enhanced cortical thickness measurements for rodent brains via Lagrangian-based RK4 streamline computation

The cortical thickness of the mammalian brain is an important morphological characteristic that can be used to investigate and observe the brain's developmental changes that might be caused by biologically toxic substances such as ethanol or cocaine. Although various cortical thickness analysis methods have been proposed that are applicable for human brain and have developed into well-validated open-source software packages, cortical thickness analysis methods for rodent brains have not yet become as robust and accurate as those designed for human brains. Based on a previously proposed cortical thickness measurement pipeline for rodent brain analysis,1 we present an enhanced cortical thickness pipeline in terms of accuracy and anatomical consistency. First, we propose a Lagrangian-based computational approach in the thickness measurement step in order to minimize local truncation error using the fourth-order Runge-Kutta method. Second, by constructing a line object for each streamline of the thickness measurement, we can visualize the way the thickness is measured and achieve sub-voxel accuracy by performing geometric post-processing. Last, with emphasis on the importance of an anatomically consistent partial differential equation (PDE) boundary map, we propose an automatic PDE boundary map generation algorithm that is specific to rodent brain anatomy, which does not require manual labeling. The results show that the proposed cortical thickness pipeline can produce statistically significant regions that are not observed in the previous cortical thickness analysis pipeline

Geometric Shape Features Extraction Using a Steady State Partial Differential Equation System

A unified method for extracting geometric shape features from binary image data using a steady state partial differential equation (PDE) system as a boundary value problem is presented in this paper. The PDE and functions are formulated to extract the thickness, orientation, and skeleton simultaneously. The main advantages of the proposed method is that the orientation is defined without derivatives and thickness computation is not imposed a topological constraint on the target shape. A one-dimensional analytical solution is provided to validate the proposed method. In addition, two-dimensional numerical examples are presented to confirm the usefulness of the proposed method.Comment: 31 pages, 10 figure

Modelos Deformáveis em Imagem Médica

Modelos deformáveis são actualmente bastante utilizados em imagem médica pois, através da utilização de princípios físicos, simulam de forma bastante satisfatória o comportamento dos objectos reais.Basicamente os modelos deformáveis são inicializados junto dos objectos a considerar, por processos automáticos ou semi-automáticos, e a aproximação para a posição final desejada é conseguida através de um processo de minimização de energia. Esta minimização de energia é verificada quando o modelo atinge o equilíbrio, entre as suas forças internas e as forças externas originadas pelos dados e por eventuais forças impostas pelo utilizador.Neste relatório são apresentados os fundamentos dos modelos deformáveis e indicados alguns exemplos de aplicação em imagem médica, nomeadamente na segmentação, no emparelhamento, no alinhamento e na reconstrução de dados 2D e 3D.Palavras-chave: Contornos activos, imagem médica, modelos deformáveis.Deformable models are currently very used in medical image since, through the use of physical principles, they simulate quite satisfactory the real objects behavior.Basically the deformable models are placed in the image near to the objects to be considered, by automatic or semi-automatic processes, and the approach to the desired final position is obtained through an energy minimization process. This energy minimization is verified when the model reaches the equilibrium, between its internal forces and the external forces originated by the data and eventual forces imposed by the user.In this report are presented the deformable models fundaments and indicated some application examples in medical imaging field, namely in segmentation, matching, alignment and in the reconstruction of 2D and 3D data.Keywords: Active contours, deformable models, medical image

Imaging Informatics and the Human Brain Project: the Role of Structure, Review

(no abstract

JOSA: Joint surface-based registration and atlas construction of brain geometry and function

Surface-based cortical registration is an important topic in medical image analysis and facilitates many downstream applications. Current approaches for cortical registration are mainly driven by geometric features, such as sulcal depth and curvature, and often assume that registration of folding patterns leads to alignment of brain function. However, functional variability of anatomically corresponding areas across subjects has been widely reported, particularly in higher-order cognitive areas. In this work, we present JOSA, a novel cortical registration framework that jointly models the mismatch between geometry and function while simultaneously learning an unbiased population-specific atlas. Using a semi-supervised training strategy, JOSA achieves superior registration performance in both geometry and function to the state-of-the-art methods but without requiring functional data at inference. This learning framework can be extended to any auxiliary data to guide spherical registration that is available during training but is difficult or impossible to obtain during inference, such as parcellations, architectonic identity, transcriptomic information, and molecular profiles. By recognizing the mismatch between geometry and function, JOSA provides new insights into the future development of registration methods using joint analysis of the brain structure and function.Comment: A. V. Dalca and B. Fischl are co-senior authors with equal contribution. arXiv admin note: text overlap with arXiv:2303.0159

3D Brain Segmentation Using Dual-Front Active Contours with Optional User Interaction

Important attributes of 3D brain cortex segmentation algorithms include robustness, accuracy, computational efficiency, and facilitation of user interaction, yet few algorithms incorporate all of these traits. Manual segmentation is highly accurate but tedious and laborious. Most automatic techniques, while less demanding on the user, are much less accurate. It would be useful to employ a fast automatic segmentation procedure to do most of the work but still allow an expert user to interactively guide the segmentation to ensure an accurate final result. We propose a novel 3D brain cortex segmentation procedure utilizing dual-front active contours which minimize image-based energies in a manner that yields flexibly global minimizers based on active regions. Region-based information and boundary-based information may be combined flexibly in the evolution potentials for accurate segmentation results. The resulting scheme is not only more robust but much faster and allows the user to guide the final segmentation through simple mouse clicks which add extra seed points. Due to the flexibly global nature of the dual-front evolution model, single mouse clicks yield corrections to the segmentation that extend far beyond their initial locations, thus minimizing the user effort. Results on 15 simulated and 20 real 3D brain images demonstrate the robustness, accuracy, and speed of our scheme compared with other methods

Constructing morphometric profiles along the human brain cortex using in vivo Magnetic Resonance Imaging (MRI)

The geometry of the brain cortex is comprised of gyri (outward folds) and sulci (inward folds). Several biological properties about the anatomy and physiology of the brain cortex have been measured at the top of the sulci and at the bottom of the gyri; however, no one has yet measured how the values of these properties (called biomarkers) change along the path joining the top of the sulci and the bottom of the gyri. In this work, a methodology to display that information is shown, using different modalities of MRI images as input. There are four main steps to the methodology: the first two consist on obtaining the lines that run on top of the gyri and at the bottom of the sulci, while the next two make use of these lines to create a geodesic path between the top of the gyri and the bottom of the sulci and assigning biomarker values to each point of this geodesic path. The results of this work are composed of the validation of the methodology and three examples of possible applications of the methodology. These applications could be applied in future work to improve the detection and study the neurodevelopment of neurodegenerative diseases.Ingeniería Biomédic