How to measure cortical folding from MR images: a step-by-step tutorial to compute local gyrification index.

Cortical folding (gyrification) is determined during the first months of life, so that adverse events occurring during this period leave traces that will be identifiable at any age. As recently reviewed by Mangin and colleagues(2), several methods exist to quantify different characteristics of gyrification. For instance, sulcal morphometry can be used to measure shape descriptors such as the depth, length or indices of inter-hemispheric asymmetry(3). These geometrical properties have the advantage of being easy to interpret. However, sulcal morphometry tightly relies on the accurate identification of a given set of sulci and hence provides a fragmented description of gyrification. A more fine-grained quantification of gyrification can be achieved with curvature-based measurements, where smoothed absolute mean curvature is typically computed at thousands of points over the cortical surface(4). The curvature is however not straightforward to comprehend, as it remains unclear if there is any direct relationship between the curvedness and a biologically meaningful correlate such as cortical volume or surface. To address the diverse issues raised by the measurement of cortical folding, we previously developed an algorithm to quantify local gyrification with an exquisite spatial resolution and of simple interpretation. Our method is inspired of the Gyrification Index(5), a method originally used in comparative neuroanatomy to evaluate the cortical folding differences across species. In our implementation, which we name local Gyrification Index (lGI(1)), we measure the amount of cortex buried within the sulcal folds as compared with the amount of visible cortex in circular regions of interest. Given that the cortex grows primarily through radial expansion(6), our method was specifically designed to identify early defects of cortical development. In this article, we detail the computation of local Gyrification Index, which is now freely distributed as a part of the FreeSurfer Software (http://surfer.nmr.mgh.harvard.edu/, Martinos Center for Biomedical Imaging, Massachusetts General Hospital). FreeSurfer provides a set of automated reconstruction tools of the brain's cortical surface from structural MRI data. The cortical surface extracted in the native space of the images with sub-millimeter accuracy is then further used for the creation of an outer surface, which will serve as a basis for the lGI calculation. A circular region of interest is then delineated on the outer surface, and its corresponding region of interest on the cortical surface is identified using a matching algorithm as described in our validation study(1). This process is repeatedly iterated with largely overlapping regions of interest, resulting in cortical maps of gyrification for subsequent statistical comparisons (Fig. 1). Of note, another measurement of local gyrification with a similar inspiration was proposed by Toro and colleagues(7), where the folding index at each point is computed as the ratio of the cortical area contained in a sphere divided by the area of a disc with the same radius. The two implementations differ in that the one by Toro et al. is based on Euclidian distances and thus considers discontinuous patches of cortical area, whereas ours uses a strict geodesic algorithm and include only the continuous patch of cortical area opening at the brain surface in a circular region of interest.

An overview on the Brazilian orange juice production chain

Brazil is the world's largest producer of oranges and uses more than 70% of the harvested fruits in the production of juices. The amount of processed orange is growing about 10% per year, confirming the trend of the Brazilian citrus for juice production. This research aimed to investigate the Brazilian orange juice production chain from 2005 to 2009. Data from the amount of frozen juice produced and exported, international price of orange juice, and intermediate transactions were assessed in order to make possible selection of all interveners involved in the chain. The study using the Social Network Analysis (SNA) showed that the densest relationships in the network are from exporters to importers and from orange growers to the orange processing industry. No difference was found in the values of the network geodesic distance or the clustering coefficients from 2005 to 2009. The degree of centrality increased steadily throughout the years indicating that the processing industry attempts to minimize the risks by centralizing the actions. A decrease in export of orange juice from 2007 (2.07 10(6) t) to 2008 (2.05 10(6) t) was found, probably due to the world's financial crisis with recovery in 2009. Since 2004, there has been an increase of nearly 10% per year in the market preference of concentrate juice (OFCJ) when compared to the "not from concentrated" juice (NFC). Nowadays the NFC market represents nearly 50% of all Brazilian export which impacted in the logistic distribution and transportation issues.

New Distance Transforms for Gray Level Image Compression

This thesis deals with distance transforms which are a fundamental issue in image processing and computer vision. In this thesis, two new distance transforms for gray level images are presented. As a new application for distance transforms, they are applied to gray level image compression. The new distance transforms are both new extensions of the well known distance transform algorithm developed by Rosenfeld, Pfaltz and Lay. With some modification their algorithm which calculates a distance transform on binary images with a chosen kernel has been made to calculate a chessboard like distance transform with integer numbers (DTOCS) and a real value distance transform (EDTOCS) on gray level images. Both distance transforms, the DTOCS and EDTOCS, require only two passes over the graylevel image and are extremely simple to implement. Only two image buffers are needed: The original gray level image and the binary image which defines the region(s) of calculation. No other image buffers are needed even if more than one iteration round is performed. For large neighborhoods and complicated images the two pass distance algorithm has to be applied to the image more than once, typically 3 10 times. Different types of kernels can be adopted. It is important to notice that no other existing transform calculates the same kind of distance map as the DTOCS. All the other gray weighted distance function, GRAYMAT etc. algorithms find the minimum path joining two points by the smallest sum of gray levels or weighting the distance values directly by the gray levels in some manner. The DTOCS does not weight them that way. The DTOCS gives a weighted version of the chessboard distance map. The weights are not constant, but gray value differences of the original image. The difference between the DTOCS map and other distance transforms for gray level images is shown. The difference between the DTOCS and EDTOCS is that the EDTOCS calculates these gray level differences in a different way. It propagates local Euclidean distances inside a kernel. Analytical derivations of some results concerning the DTOCS and the EDTOCS are presented. Commonly distance transforms are used for feature extraction in pattern recognition and learning. Their use in image compression is very rare. This thesis introduces a new application area for distance transforms. Three new image compression algorithms based on the DTOCS and one based on the EDTOCS are presented. Control points, i.e. points that are considered fundamental for the reconstruction of the image, are selected from the gray level image using the DTOCS and the EDTOCS. The first group of methods select the maximas of the distance image to new control points and the second group of methods compare the DTOCS distance to binary image chessboard distance. The effect of applying threshold masks of different sizes along the threshold boundaries is studied. The time complexity of the compression algorithms is analyzed both analytically and experimentally. It is shown that the time complexity of the algorithms is independent of the number of control points, i.e. the compression ratio. Also a new morphological image decompression scheme is presented, the 8 kernels' method. Several decompressed images are presented. The best results are obtained using the Delaunay triangulation. The obtained image quality equals that of the DCT images with a 4 x 4

Ionospheric tomography using GNSS reflections

In this paper, we report a preliminary analysis of the impact of Global Navigation Satellite System Reflections (GNSS-R) data on ionospheric monitoring over the oceans. The focus will be on a single polar Low Earth Orbiter (LEO) mission exploiting GNSS-R as well as Navigation (GNSS-N) and Occultation (GNSS-O) total electron content (TEC) measurements. In order to assess impact of the data, we have simulated GNSS-R/O/N TEC data as would be measured from the LEO and from International Geodesic Service (IGS) ground stations, with an electron density (ED) field generated using a climatic ionospheric model. We have also developed a new tomographic approach inspired by the physics of the hydrogen atom and used it to effectively retrieve the ED field from the simulated TEC data near the orbital plane. The tomographic inversion results demonstrate the significant impact of GNSS-R: three-dimensional ionospheric ED fields are retrieved over the oceans quite accurately, even as, in the spirit of this initial study, the simulation and inversion approaches avoided intensive computation and sophisticated algorithmic elements (such as spatio-temporal smoothing). We conclude that GNSS-R data over the oceans can contribute significantly to a Global/GNSS Ionospheric Observation System (GIOS). Index Terms Global Navigation Satellite System (GNSS), Global Navigation Satellite System Reflections (GNSS-R), ionosphere, Low Earth Orbiter (LEO), tomography.

Représentation et détection des images et des surfaces déformables

La représentation d'une surface, son lissage et son utilisation pour l'identification, la comparaison, la classification, et l'étude des variations de volume, de courbure ou de topologie sont omniprésentes dans l'aire de la numérisation. Parmi les méthodes mathématiques, nous avons retenu les transformations difféomorphiques d'un pattern de référence. Il y a un grand intérêt théorique et numérique à approcher un difféomorphisme arbitraire par des difféomorphismes engendrés par des champs de vitesses. Sur le plan théorique la question est : "est-ce que le sous-groupe de difféomorphismes engendrés par des champs de vitesses est dense dans le groupe plus large de Micheletti pour la métrique de Courant ?" Malgré quelques progrès réalisés ici, cette question demeure ouverte. Les pistes empruntées ont alors convergé vers le sous-groupe de Azencott et de Trouvé et sa métrique dans le cadre de l'imagerie. Elle correspond à une notion de géodésique entre deux difféomorphismes dans leur sous-groupe. L'optimisation est utilisée pour obtenir un système d'équations état adjoint caractérisant la solution optimale du problème d'identification à partir des observations. Cette approche est adaptée à l'identification de surfaces obtenues par un numériseur tel que, par exemple, le scan d'un visage. Ce problème est beaucoup plus difficile que celui d'imagerie. On doit alors introduire un système de référence courbe et une surface à facettes pour les calculs. On donne la formulation du problème d'identification et du calcul du changement de volume par rapport à un scan de référence.

Reconstruction tridimensionnelle pour projection sur surfaces arbitraires.

Ce mémoire s'inscrit dans le domaine de la vision par ordinateur. Elle s'intéresse à la calibration de systèmes de caméras stéréoscopiques, à la mise en correspondance caméra-projecteur, à la reconstruction 3D, à l'alignement photométrique de projecteurs, au maillage de nuages de points, ainsi qu'au paramétrage de surfaces. Réalisé dans le cadre du projet LightTwist du laboratoire Vision3D, elle vise à permettre la projection sur grandes surfaces arbitraires à l'aide de plusieurs projecteurs. Ce genre de projection est souvent utilisé en arts technologiques, en théâtre et en projection architecturale. Dans ce mémoire, on procède au calibrage des caméras, suivi d'une reconstruction 3D par morceaux basée sur une méthode active de mise en correspondance, la lumière non structurée. Après un alignement et un maillage automatisés, on dispose d'un modèle 3D complet de la surface de projection. Ce mémoire introduit ensuite une nouvelle approche pour le paramétrage de modèles 3D basée sur le calcul efficace de distances géodésiques sur des maillages. L'usager n'a qu'à délimiter manuellement le contour de la zone de projection sur le modèle. Le paramétrage final est calculé en utilisant les distances obtenues pour chaque point du modèle. Jusqu'à maintenant, les méthodes existante ne permettaient pas de paramétrer des modèles ayant plus d'un million de points.

Convex extendable trees

The concept of convex extendability is introduced to answer the problem of finding the smallest distance convex simple graph containing a given tree. A problem of similar type with respect to minimal path convexity is also discussed.

En nombre de un amor imaginario y los orígenes de la República del Ecuador (Dossier: Bicentenario, rastros y revelaciones de la Independencia)

El autor analiza esta novela histórica de Jorge Velasco Mackenzie, en torno a los orígenes de la nación ecuatoriana, entre la historia y la fábula. Reflexiona sobre el proceso de escribir como una forma de interpelar presupuestos consagrados, valores, símbolos e identidades. Handelsman destaca que el trabajo de la Misión Geodésica Francesa, de 1736, cambió la cosmovisión de la sociedad colonial ecuatoriana, escolástica, por otra de carácter más empírico, pero que el nuevo motor del saber moderno trajo también distorsiones y omisiones de otras verdades (como el que los indígenas perdieran su protagonismo milenario como conocedores de su hábitat). Pone en relieve, igualmente, la imposibilidad de expresar en una segunda lengua lo que se vive en geografías ajenas. Personaje importante es Isabel Godin, quien no puede liberarse del mundo oscuro, complejo y ambivalente que constituye la memoria. En suma, la novela desmitifica la autoridad de las ciencias naturales y físicas, y abre la posibilidad de repensar, reescribir y resignificar la historia del país.

La muerte del cirujano. Ansiedades coloniales e identidades colectivas en Cuenca, 1739 (Estudios)

El artículo analiza las tensiones que enfrentaban a criollos y europeos en la Audiencia de Quito en el siglo XVIII, a través del caso de la muerte del cirujano Jean de Sénierges en la ciudad de Cuenca, durante la expedición geodésica a la región. El análisis de los relatos tejidos en torno al deceso del médico de la expedición muestra la progresiva consolidación de identidades políticas diferenciadas en la Colonia. Pone en evidencia, además, la importancia de analizar los motines urbanos como herramientas de acción colectiva, en las que se cristalizan estas identidades.

A comparison of extra-tropical cyclones in recent re-analyses; ERA-Interim, NASA MERRA, NCEP CFSR and JRA-25

Extra-tropical cyclones are identified and compared using data from four recent re-analyses for the winter periods in both hemispheres. Results show the largest differences occur between the older lower resolution JRA25 re-analysis when compared with the newer high resolution re-analyses, in particular in the Southern Hemisphere (SH). Spatial differences between the newest re-analyses are small in both hemispheres and generally not significant except some common regions associated with cyclogenesis close to orography. Intensities are generally related to spatial resolution except NASA-MERRA which has larger intensities for several different measures. Matching storms between re-analyses shows the number matched between ERA-Interim and the other re-analyses are similar in the Northern Hemisphere (NH). In the SH the number matched between JRA25 and ERA-Interim is lower than in the NH, but for NASA-MERRA and NCEP-CFSR the number matched is similar to the NH. The mean separation of the identically same cyclones is typically less than 20 geodesic in both hemispheres for the latest re-analyses, whereas JRA25 compared with the other re-analyses has a broader distribution in the SH indicating greater uncertainty. The instantaneous intensity differences for matched storms shows narrow distributions for pressure while for winds and vorticity the distributions are much broader indicating larger uncertainty typical of smaller scale fields. Composite cyclone diagnostics show that cyclones are very similar between the re-analyses, with differences being related to the intensities, consistent with the intensity results. Overall, results show NH cyclones correspond well between re-analyses, with a significant improvement in the SH for the latest re-analyses, indicating a convergence between re-analyses for cyclone properties.

The Brownian traveller on manifolds

We study the inuence of the intrinsic curvature on the large time behaviour of the heat equation in a tubular neighbourhood of an unbounded geodesic in a two-dimensional Riemannian manifold. Since we consider killing boundary conditions, there is always an exponential-type decay for the heat semigroup. We show that this exponential-type decay is slower for positively curved manifolds comparing to the at case. As the main result, we establish a sharp extra polynomial-type decay for the heat semigroup on negatively curved manifolds comparing to the at case. The proof employs the existence of Hardy-type inequalities for the Dirichlet Laplacian in the tubular neighbourhoods on negatively curved manifolds and the method of self-similar variables and weighted Sobolev spaces for the heat equation.

Results of Joint Experiments and other IAEA activities on research using small tokamaks

This paper presents an overview of the results obtained during the Joint Experiments organized in the framework of the IAEA Coordinated Research Project on `Joint Research Using Small Tokamaks` that have been carried out on the tokamaks CASTOR at IPP Prague, Czech Republic (2005), T-10 at RRC `Kurchatov Institute`, Moscow, Russia (2006), and the most recent one at ISTTOK at IST, Lisbon, Portugal, in 2007. Experimental programmes were aimed at diagnosing and characterizing the core and the edge plasma turbulence in a tokamak in order to investigate correlations between the occurrence of transport barriers, improved confinement, electric fields and electrostatic turbulence using advanced diagnostics with high spatial and temporal resolution. On CASTOR and ISTTOK, electric fields were generated by biasing an electrode inserted into the edge plasma and an improvement of the global particle confinement induced by the electrode positive biasing has been observed. Geodesic acoustic modes were studied using heavy ion beam diagnostics on T-10 and ISTTOK and correlation reflectometry on T-10. ISTTOK is equipped with a gallium jet injector and the technical feasibility of gallium jets interacting with plasmas has been investigated in pulsed and ac operation. The first Joint Experiments have clearly demonstrated that small tokamaks are suitable for broad international cooperation to conduct dedicated joint research programmes. Other activities within the IAEA Coordinated Research Project on Joint Research Using Small Tokamaks are also overviewed.

Genericity of Nondegeneracy for Light Rays in Stationary Spacetimes

Given a Lorentzian manifold (M, g), an event p and an observer U in M, then p and U are light conjugate if there exists a lightlike geodesic gamma : [0, 1] -> M joining p and U whose endpoints are conjugate along gamma. Using functional analytical techniques, we prove that if one fixes p and U in a differentiable manifold M, then the set of stationary Lorentzian metrics in M for which p and U are not light conjugate is generic in a strong sense. The result is obtained by reduction to a Finsler geodesic problem via a second order Fermat principle for light rays, and using a transversality argument in an infinite dimensional Banach manifold setup.

Spectral flow and iteration of closed semi-Riemannian geodesics

We introduce the notion of spectral flow along a periodic semi-Riemannian geodesic, as a suitable substitute of the Morse index in the Riemannian case. We study the growth of the spectral flow along a closed geodesic under iteration, determining its asymptotic behavior.

Iteration of closed geodesics in stationary Lorentzian manifolds

Following the lines of Bott in (Commun Pure Appl Math 9:171-206, 1956), we study the Morse index of the iterates of a closed geodesic in stationary Lorentzian manifolds, or, more generally, of a closed Lorentzian geodesic that admits a timelike periodic Jacobi field. Given one such closed geodesic gamma, we prove the existence of a locally constant integer valued map Lambda(gamma) on the unit circle with the property that the Morse index of the iterated gamma(N) is equal, up to a correction term epsilon(gamma) is an element of {0,1}, to the sum of the values of Lambda(gamma) at the N-th roots of unity. The discontinuities of Lambda(gamma) occur at a finite number of points of the unit circle, that are special eigenvalues of the linearized Poincare map of gamma. We discuss some applications of the theory.