Jean-Marie Favreau

Cortical surface mapping using topology correction, partial flattening and 3D shape context-based non-rigid registration for use in quantifying atrophy in Alzheimer's disease

Magnetic resonance (MR) provides a non-invasive way to investigate changes in the brain resulting from aging or neurodegenerative disorders such as Alzheimers disease (AD). Performing accurate analysis for population studies is challenging because of the interindividual anatomical variability. A large set of tools is found to perform studies of brain anatomy and population analysis (FreeSurfer, SPM, FSL). In this paper we present a newly developed surface-based processing pipeline (MILXCTE) that allows accurate vertex-wise statistical comparisons of brain modifications, such as cortical thickness (CTE). The brain is first segmented into the three main tissues: white matter, gray matter and cerebrospinal fluid, after CTE is computed, a topology corrected mesh is generated. Partial inflation and non-rigid registration of cortical surfaces to a common space using shape context are then performed. Each of the steps was firstly validated using MR images from the OASIS database. We then applied the pipeline to a sample of individuals randomly selected from the AIBL study on AD and compared with FreeSurfer. For a population of 50 individuals we found correlation of cortical thickness in all the regions of the brain (average r=0.62 left and r=0.64 right hemispheres). We finally computed changes in atrophy in 32 AD patients and 81 healthy elderly individuals. Significant differences were found in regions known to be affected in AD. We demonstrated the validity of the method for use in clinical studies which provides an alternative to well established techniques to compare different imaging biomarkers for the study of neurodegenerative diseases.

A Tool for Topographic Analysis of Electrode Contacts in Human Cortical Stimulation

Electric chronic stimulation of the human motor cortex (ECSM) has been reported to alleviate chronic severe pain. However the mechanism of action of ECSM is still hypothetical. This is due mainly to the poor knowledge of 1) the electric diffusion through the multiple structures beneath the epidural contacts (i.e. dura matter, cerebrospinal fluid space, arachnoid membrane, grey and white matter layers, pie mere and vascular tree), 2) the absence of consensus concerning the stimulation parameters (mono versus bipolar stimulation, cathodic or anodic current) and 3) the detailed cortical topography of the contacts. In this study we focused on the precise identification of the cortical areas covered by the electric contacts in a series of twelve patients operated on for ECSM. We propose a new automatic tool for topographic analysis able to compute 2D maps from the 3D anatomic MRI with bijective transformation (point- to-point correspondance). Anatomical regions of interest (AROIs) were visually identified, manually outlined and extracted (Iplan, BrainLab, Germany) for further analysis: 1) for the anatomic structures, on pre operative Tl-weigthed magnetic resonance imaging (MRI), the frontal (superior or Fl, intermediate or F2 and inferior or F3), the pre central and the post central gyrus; 2) for the electrode contacts (Resume, Medtronic, USA), on post operative computerized tomography (CT). After getting white and gray matter membership maps by automatic segmentation, we produced a cortical mask to build a triangular mesh. We defined a homeomorphism between the 3D mesh and a subset of R2 and could apply in consequence the circle packing algorithm. We built depth maps (distance to the skull), distance- to-contact maps (distance to a given electrode contact) and anatomic structure maps. Results showed that it was easier to accurately define the location of the contact projection on the cortex allowing physicians to correlate the benefit with the topography. In particular, because of the unfolding, it was easier to integrate the cytoarchitectonics (i.e. the manually identified AROIs) knowledge in the analysis. Beyond the better understanding of ECSM and indirectly of the pathophysiologic process of chronic pain, this new tool might be used in the future for image guided electrode positioning.

A novel Computer-Aided Tree Species Identification method based on Burst Wind Segmentation of 3D bark textures

Terrestrial Laser Scanning (TLS) systems have gained increasing popularity in the forestry domain and are today widely used for the automatic measurement of forest inventory attributes. Nevertheless, to the best of our knowledge the problem of tree species recognition from TLS data has received very little attention from the scientific community. It is in this context that we present a novel Computer-Aided Tree Species Identification method based on 3D bark texture analysis. The novelty of our approach resides in the following three key points: (1) 3D salient regions extraction using a new morphological segmentation method that we have called Burst Wind Segmentation, (2) the extraction and pre-annotation of a collection of typical 3D bark patterns, known as scars, from each of the tree species. The pre-annotated scars are stored in a dictionary that we have called ScarBook and they are used as a reference for the comparison of the 3D salient segmented regions, (3) a wide variety of advanced shape, saliency, curvature and roughness features are extracted from the 3D salient segmented regions. To study the performance of our method, an experiment has been carried out on a dataset composed of 969 patches which correspond to 30xa0cm long segments of the trunk at breast height. Six species among the most dominant species in European forests have been tested with patches of different diameter at breast height values so as to study the identification accuracy with respect to age. The results obtained are very encouraging and promising and they confirm the possibility of identifying tree species using TLS data.

Multi-layer Ontologies for Integrated 3D Shape Segmentation and Annotation

Mesh segmentation and semantic annotation are used as preprocessing steps for many applications, including shape retrieval, mesh abstraction, and adap-tive simplification. In current practice, these two steps are done sequentially: a purely geometrical analysis is employed to extract the relevant parts, and then these parts are annotated. We introduce an original framework where annotation and seg-mentation are performed simultaneously, so that each of the two steps can take advantage of the other. Inspired by existing methods used in image processing, we employ an experts knowledge of the context to drive the process while minimizing the use of geometric analysis. For each specific context a multi-layer ontology can be designed on top of a basic knowledge layer which conceptualizes 3D object features from the point of view of their geometry, topology, and possible attributes. Each feature is associated with an elementary algorithm for its detection. An expert can define the upper layers of the ontology to conceptualize a specific domain without the need to reconsider the elementary algorithms. This approach has a twofold advantage: on one hand it allows to leverage domain knowledge from experts even if they have limited or no skills in geometry processing and computer program-Thomas Dietenbeck Sorbonne Universites, UPMC Univ Paris 06, INSERM UMRS 1146, CNRS UMR 7371, Labora-toire dImagerie Biomedicale, F-75013,

Tight bounds in the quadtree complexity theorem and the maximal number of pixels crossed by a curve of given length

The main purpose of this work is to determine the exact maximum number of pixels (a bi-dimensional sequence of unit squares tiling a plane) that a rectifiable curve of given length l can cross. In other words, given lR, we provide the value N(l) of the maximal cardinality of the digital cover of a rectifiable curve of length l. The optimal curves are polygonal curves with integer vertices, 0, 1 or 2 vertical or horizontal steps and an arbitrary number of diagonal steps. We also report the properties of the staircase function N(l), which is affinely periodic in the sense that N(l+2)=N(l)+3 and a bound N(l)4+32l.Our second aim is to look at the restricted class of closed curves and offer some conjectures on the maximum number Nclosed(l) of pixels that a closed curve of length l can cross.This work finds its application in the quadtree complexity theorem. This well-known result bounds the number of quads with a shape of perimeter p by 16q11+16p. However, this linear bound is not tight. From our new upper bound Nclosed(l)N(l)4+32l we derive a new improved multiresolution complexity theorem: Number(quads)16q11+62p. Lastly, we show that this new bound is tight up to a maximal error of 16(q1).

Technical Section: Tiling surfaces with cylinders using n-loops

Subdividing surfaces into cylindrers is a significant question in various applications. Even if specific approaches have been described in several domains, most of the time topological properties are not explicitly handled, and the segmentation remains mainly driven by geometry. We present here an original approach to describe the topological and combinatorial nature of a tiling with cylinders. We first introduce m-cellular complexes, a framework allowing the flexible description of cuttings and tilings. Then we describe n-loops, an extension of the loops for producing tilings with cylinders. Computational issues of n-loops are then addressed, using both topological and geometrical properties of the surface. Finally, we propose two applications, first tiling a surface with large quadrangles patches, and then segmenting surfaces with possible protrusions.

A combined voxel and surface based method for topology correction of brain surfaces

Brain surfaces provide a reliable representation for cortical mapping. The construction of correct surfaces from magnetic resonance images (MRI) segmentation is a challenging task, especially when genus zero surfaces are required for further processing such as parameterization, partial inflation and registration. The generation of such surfaces has been approached either by correcting a binary image as part of the segmentation pipeline or by modifying the mesh representing the surface. During this task, the preservation of the structure may be compromised because of the convoluted nature of the brain and noisy/imperfect segmentations. In this paper, we propose a combined, voxel and surfacebased, topology correction method which preserves the structure of the brain while yielding genus zero surfaces. The topology of the binary segmentation is first corrected using a set of topology preserving operators applied sequentially. This results in a white matter/gray matter binary set with correct sulci delineation, homotopic to a filled sphere. Using the corrected segmentation, a marching cubes mesh is then generated and the tunnels and handles resulting from the meshing are finally removed with an algorithm based on the detection of nonseparating loops. The approach was validated using 20 young individuals MRI from the OASIS database, acquired at two different time-points. Reproducibility and robustness were evaluated using global and local criteria such as surface area, curvature and point to point distance. Results demonstrated the method capability to produce genus zero meshes while preserving geometry, two fundamental properties for reliable and accurate cortical mapping and further clinical studies.

Industrial Phase-Shifting Profilometry in Motion

Phase-Shift Profilometry (PSP) provides a means for dense high-quality surface scanning. However it imposes a staticity constraint: The scene is required to remain still during the acquisition of multiple images. PSP is also not applicable to dynamic scenes. On the other hand, there exist active stereo techniques which overcome these constraints but impose other limitations, for instance on the surface’s continuity or texture, or by significantly reducing the reconstruction’s resolution.

Tiling Surfaces with Cylinders Using n-loops

Subdividing surfaces into cylindrers is a significant question in various applications. Even if specific approaches have been described in several domains, most of the time topological properties are not explicitly handled, and the segmentation remains mainly driven by geometry. We present here an original approach to describe the topological and combinatorial nature of a tiling with cylinders. We first introduce m-cellular complexes, a framework allowing the flexible description of cuttings and tilings. Then we describe n-loops, an extension of the loops for producing tilings with cylinders. Computational issues of n-loops are then addressed, using both topological and geometrical properties of the surface. Finally, we propose two applications, first tiling a surface with large quadrangles patches, and then segmenting surfaces with possible protrusions.