From 3D magnetic resonance images to structural representations of the cortex topography using topology preserving deformations

Abstract

Abstract.We propose an algorithm allowing the construction of a structural representation of the cortical topography from a Tl-weighted 3D MR image. This representation is an attributed relational graph (ARG) inferred from the 3D skeleton of the object made up of the union of gray matter and cerebro-spinal fluid enclosed in the brain hull. In order to increase the robustness of the skeletonization, topological and regularization constraints are included in the segmentation process using an original method: the homotopically deformable regions. This method is halfway between deformable contour and Markovian segmentation approaches. The 3D skeleton is segmented in simple surfaces (SSs) constituting the ARG nodes (mainly cortical folds). The ARG relations are of two types: first, the SS pairs connected in the skeleton; second, the SS pairs delimi6ng a gyrus. The described algorithm has been developed in the frame of a project aiming at the automatic detection and recognition of the main cortical sulci. Indeed, the ARG is a synthetic representation of all the information required by the sulcus identification. This project will contribute to the development of new methodologies for human brain functional mapping and neurosurgery operation planning.

CRUISE: Cortical reconstruction using implicit surface evolution

“…Many approaches have been proposed in the literature for the reconstruction of the cortex from MR brain images (Dale et al, 1999;Davatzikos and Bryan, 1996;Joshi et al, 1999;Kriegeskorte and Goebel, 2001;MacDonald et al, 2000;Mangin et al, 1995;Sandor and Leahy, 1997;Shattuck and Leahy, 2002;Teo et al, 1997;Zeng et al, 1999;Xu et al, 1999). These approaches differ in their ability to capture the convoluted cortical geometry, reconstruction accuracy, robustness against imaging artifacts, computation time, topological correctness, and self-intersection avoidance.…”

“…We now give a brief survey of several of these methods, and compare them to CRUISE. Mangin et al (1995) introduced a homotopically deformable region method to construct a topographical map of the cortex that preserved the correct topology. A major shortcoming of this method is that its accuracy is limited to the voxel level, and thus the method is not well suited for finding the pial surface.…”

A comparison of voxel and surface based cortical thickness estimation methods

“…This may be partly due to long running software efforts, producing accessible software packages such as BrainSuite 1 Leahy, 2001, 2002), BrainVISA 2 (Mangin et al, 1995) and FreeSurfer 3 Fischl et al, 1999;Fischl and Dale, 2000). Of these, FreeSurfer is the most widely used (Nakamura et al, 2010), and the FreeSurfer wiki lists many references on both the methodology and clinical studies.…”

A framework based on spin glass models for the inference of anatomical connectivity from diffusion‐weighted MR data – a technical review

“…Using high-resolution anatomical images provides the assurance that no spurious voxels link two different white matter gyri throughout the separating sulcus. 31 Once the fascicle map domain has been defined, a representation has to be devised for the local pieces of fascicles. Each piece will have some degrees of freedom, which will lead to set out the inverse problem as an optimization driven issue.…”

“…44 This sulcus labeling can be used further to split the cortical surface into gyri defined by several limiting sulci using geodesic distance-based Voronoï diagrams. 31 Hence, the numerous putative Ufascicles passing under the sulci will be sorted according to the locations of their extremities in order to fill a gyrus connectivity matrix (Fig. 10).…”