Effect of framework soldering on the deformation of implant abutments after framework seating: a study with strain gauges

Introduction: Passive fit has been considered an important requirement for the longevity of implant-supported prostheses. Among the different steps of prostheses construction, casting is a feature that can influence the precision of fit and consequently the uniformity of possible deformation among abutments upon the framework connection. Purpose: This study aimed at evaluating the deformation of abutments after the connection of frameworks either cast in one piece or after soldering. Materials and Methods: A master model was used to simulate a human mandible with 5 implants. Ten frameworks were fabricated on cast models and divided into 2 groups. Strain gauges were attached to the mesial and distal sides of the abutments to capture their deformation after the framework’s screw retentions were tightened to the abutments. Results: The mean values of deformation were submitted to a 3-way analysis of variance that revealed significant differences between procedures and the abutment side. The results showed that none of the frameworks presented a complete passive fit. Conclusion: The soldering procedure led to a better although uneven distribution of compression strains on the abutments.

Shallow and deep deformation in northern Apennines region using seismological data

For its particular position and the complex geological history, the Northern Apennines has been considered as a natural laboratory to apply several kinds of investigations. By the way, it is complicated to joint all the knowledge about the Northern Apennines in a unique picture that explains the structural and geological emplacement that produced it. The main goal of this thesis is to put together all information on the deformation - in the crust and at depth - of this region and to describe a geodynamical model that takes account of it. To do so, we have analyzed the pattern of deformation in the crust and in the mantle. In both cases the deformation has been studied using always information recovered from earthquakes, although using different techniques. In particular the shallower deformation has been studied using seismic moment tensors information. For our purpose we used the methods described in Arvidsson and Ekstrom (1998) that allowing the use in the inversion of surface waves [and not only of the body waves as the Centroid Moment Tensor (Dziewonski et al., 1981) one] allow to determine seismic source parameters for earthquakes with magnitude as small as 4.0. We applied this tool in the Northern Apennines and through this activity we have built up the Italian CMT dataset (Pondrelli et al., 2006) and the pattern of seismic deformation using the Kostrov (1974) method on a regular grid of 0.25 degree cells. We obtained a map of lateral variations of the pattern of seismic deformation on different layers of depth, taking into account the fact that shallow earthquakes (within 15 km of depth) in the region occur everywhere while most of events with a deeper hypocenter (15-40 km) occur only in the outer part of the belt, on the Adriatic side. For the analysis of the deep deformation, i.e. that occurred in the mantle, we used the anisotropy information characterizing the structure below the Northern Apennines. The anisotropy is an earth properties that in the crust is due to the presence of aligned fluid filled cracks or alternating isotropic layers with different elastic properties while in the mantle the most important cause of seismic anisotropy is the lattice preferred orientation (LPO) of the mantle minerals as the olivine. This last is a highly anisotropic mineral and tends to align its fast crystallographic axes (a-axis) parallel to the astenospheric flow as a response to finite strain induced by geodynamic processes. The seismic anisotropy pattern of a region is measured utilizing the shear wave splitting phenomenon (that is the seismological analogue to optical birefringence). Here, to do so, we apply on teleseismic earthquakes recorded on stations located in the study region, the Sileny and Plomerova (1996) approach. The results are analyzed on the basis of their lateral and vertical variations to better define the earth structure beneath Northern Apennines. We find different anisotropic domains, a Tuscany and an Adria one, with a pattern of seismic anisotropy which laterally varies in a similar way respect to the seismic deformation. Moreover, beneath the Adriatic region the distribution of the splitting parameters is so complex to request an appropriate analysis. Therefore we applied on our data the code of Menke and Levin (2003) which allows to look for different models of structures with multilayer anisotropy. We obtained that the structure beneath the Po Plain is probably even more complicated than expected. On the basis of the results obtained for this thesis, added with those from previous works, we suggest that slab roll-back, which created the Apennines and opened the Tyrrhenian Sea, evolved in the north boundary of Northern Apennines in a different way from its southern part. In particular, the trench retreat developed primarily south of our study region, with an eastward roll-back. In the northern portion of the orogen, after a first stage during which the retreat was perpendicular to the trench, it became oblique with respect to the structure.

Estimating crustal deformation from geodetic data

By the end of the 19th century, geodesy has contributed greatly to the knowledge of regional tectonics and fault movement through its ability to measure, at sub-centimetre precision, the relative positions of points on the Earth’s surface. Nowadays the systematic analysis of geodetic measurements in active deformation regions represents therefore one of the most important tool in the study of crustal deformation over different temporal scales [e.g., Dixon, 1991]. This dissertation focuses on motion that can be observed geodetically with classical terrestrial position measurements, particularly triangulation and leveling observations. The work is divided into two sections: an overview of the principal methods for estimating longterm accumulation of elastic strain from terrestrial observations, and an overview of the principal methods for rigorously inverting surface coseismic deformation fields for source geometry with tests on synthetic deformation data sets and applications in two different tectonically active regions of the Italian peninsula. For the long-term accumulation of elastic strain analysis, triangulation data were available from a geodetic network across the Messina Straits area (southern Italy) for the period 1971 – 2004. From resulting angle changes, the shear strain rates as well as the orientation of the principal axes of the strain rate tensor were estimated. The computed average annual shear strain rates for the time period between 1971 and 2004 are γ˙1 = 113.89 ± 54.96 nanostrain/yr and γ˙2 = -23.38 ± 48.71 nanostrain/yr, with the orientation of the most extensional strain (θ) at N140.80° ± 19.55°E. These results suggests that the first-order strain field of the area is dominated by extension in the direction perpendicular to the trend of the Straits, sustaining the hypothesis that the Messina Straits could represents an area of active concentrated deformation. The orientation of θ agree well with GPS deformation estimates, calculated over shorter time interval, and is consistent with previous preliminary GPS estimates [D’Agostino and Selvaggi, 2004; Serpelloni et al., 2005] and is also similar to the direction of the 1908 (MW 7.1) earthquake slip vector [e.g., Boschi et al., 1989; Valensise and Pantosti, 1992; Pino et al., 2000; Amoruso et al., 2002]. Thus, the measured strain rate can be attributed to an active extension across the Messina Straits, corresponding to a relative extension rate ranges between < 1mm/yr and up to ~ 2 mm/yr, within the portion of the Straits covered by the triangulation network. These results are consistent with the hypothesis that the Messina Straits is an important active geological boundary between the Sicilian and the Calabrian domains and support previous preliminary GPS-based estimates of strain rates across the Straits, which show that the active deformation is distributed along a greater area. Finally, the preliminary dislocation modelling has shown that, although the current geodetic measurements do not resolve the geometry of the dislocation models, they solve well the rate of interseismic strain accumulation across the Messina Straits and give useful information about the locking the depth of the shear zone. Geodetic data, triangulation and leveling measurements of the 1976 Friuli (NE Italy) earthquake, were available for the inversion of coseismic source parameters. From observed angle and elevation changes, the source parameters of the seismic sequence were estimated in a join inversion using an algorithm called “simulated annealing”. The computed optimal uniform–slip elastic dislocation model consists of a 30° north-dipping shallow (depth 1.30 ± 0.75 km) fault plane with azimuth of 273° and accommodating reverse dextral slip of about 1.8 m. The hypocentral location and inferred fault plane of the main event are then consistent with the activation of Periadriatic overthrusts or other related thrust faults as the Gemona- Kobarid thrust. Then, the geodetic data set exclude the source solution of Aoudia et al. [2000], Peruzza et al. [2002] and Poli et al. [2002] that considers the Susans-Tricesimo thrust as the May 6 event. The best-fit source model is then more consistent with the solution of Pondrelli et al. [2001], which proposed the activation of other thrusts located more to the North of the Susans-Tricesimo thrust, probably on Periadriatic related thrust faults. The main characteristics of the leveling and triangulation data are then fit by the optimal single fault model, that is, these results are consistent with a first-order rupture process characterized by a progressive rupture of a single fault system. A single uniform-slip fault model seems to not reproduce some minor complexities of the observations, and some residual signals that are not modelled by the optimal single-fault plane solution, were observed. In fact, the single fault plane model does not reproduce some minor features of the leveling deformation field along the route 36 south of the main uplift peak, that is, a second fault seems to be necessary to reproduce these residual signals. By assuming movements along some mapped thrust located southward of the inferred optimal single-plane solution, the residual signal has been successfully modelled. In summary, the inversion results presented in this Thesis, are consistent with the activation of some Periadriatic related thrust for the main events of the sequence, and with a minor importance of the southward thrust systems of the middle Tagliamento plain.

A new insight in stress recovery tecniques and hessian reconstruction methods

Stress recovery techniques have been an active research topic in the last few years since, in 1987, Zienkiewicz and Zhu proposed a procedure called Superconvergent Patch Recovery (SPR). This procedure is a last-squares fit of stresses at super-convergent points over patches of elements and it leads to enhanced stress fields that can be used for evaluating finite element discretization errors. In subsequent years, numerous improved forms of this procedure have been proposed attempting to add equilibrium constraints to improve its performances. Later, another superconvergent technique, called Recovery by Equilibrium in Patches (REP), has been proposed. In this case the idea is to impose equilibrium in a weak form over patches and solve the resultant equations by a last-square scheme. In recent years another procedure, based on minimization of complementary energy, called Recovery by Compatibility in Patches (RCP) has been proposed in. This procedure, in many ways, can be seen as the dual form of REP as it substantially imposes compatibility in a weak form among a set of self-equilibrated stress fields. In this thesis a new insight in RCP is presented and the procedure is improved aiming at obtaining convergent second order derivatives of the stress resultants. In order to achieve this result, two different strategies and their combination have been tested. The first one is to consider larger patches in the spirit of what proposed in [4] and the second one is to perform a second recovery on the recovered stresses. Some numerical tests in plane stress conditions are presented, showing the effectiveness of these procedures. Afterwards, a new recovery technique called Last Square Displacements (LSD) is introduced. This new procedure is based on last square interpolation of nodal displacements resulting from the finite element solution. In fact, it has been observed that the major part of the error affecting stress resultants is introduced when shape functions are derived in order to obtain strains components from displacements. This procedure shows to be ultraconvergent and is extremely cost effective, as it needs in input only nodal displacements directly coming from finite element solution, avoiding any other post-processing in order to obtain stress resultants using the traditional method. Numerical tests in plane stress conditions are than presented showing that the procedure is ultraconvergent and leads to convergent first and second order derivatives of stress resultants. In the end, transverse stress profiles reconstruction using First-order Shear Deformation Theory for laminated plates and three dimensional equilibrium equations is presented. It can be seen that accuracy of this reconstruction depends on accuracy of first and second derivatives of stress resultants, which is not guaranteed by most of available low order plate finite elements. RCP and LSD procedures are than used to compute convergent first and second order derivatives of stress resultants ensuring convergence of reconstructed transverse shear and normal stress profiles respectively. Numerical tests are presented and discussed showing the effectiveness of both procedures.

Shape fabric development during progressive deformation

Zusammenfassung:Das Ziel dieser Arbeit ist ein besseres Verständnis von der Art und Weise wie sich Formregelungsgefüge entwicklen. Auf dieser Basis wird der Nutzen von Formregelungsgefügen für die Geologie evaluiert. Untersuchungsmethoden sind Geländearbeit und -auswertung, numerische Simulationen und Analogexperimente. Untersuchungen an Formregelungsgefügen in Gesteinen zeigen, daß ein Formregelungsgefüge nur zu einem begrenzten Grad als Anzeiger für die Stärke der Verformung benutzt werden kann. Der angenommene Grund hierfür ist der Einfluß des Verhältnisses von ursprünglicher zu rekristallisierter Korngröße auf die Gefügeentwicklung und von der Art und Weise wie dynamische Rekristallisation ein Gefüge verändert. Um diese Beobachtung zu evaluieren, wurden verschiedene numerische Simulationen von dynamischer Rekristallisation durchgeführt. Ein neuer Deformationsapparat, mit dem generelle Fließregime modelliert werden können, wurde entwickelt. Die rheologischen Eigenschaften von Materialien, die für solche Experimente benutzt werden, wurden untersucht und diskutiert. Ergebnisse von Analogexperimenten zeigen, daß die Intensität eines Formregelungsgefüges positiv mit der Abnahme der 'kinematic vorticity number' und einem nicht-Newtonianischen, 'power law' Verhalten des Materixmaterials korreliert ist. Experimente, in denen die Formveränderung von viskosen Einschlüssen während der progressiven Verformung modelliert werden, zeigen, daß verschiedene Viskositätskontraste zwischen Matrix- und Einschlußmaterial in charakteristische Formgefüge resultieren.

Finite element models of coseismic deformation due to the 2009 L'Aquila (Italy) and 2008 Wenchuan(China) earthquakes

The topic of my Ph.D. thesis is the finite element modeling of coseismic deformation imaged by DInSAR and GPS data. I developed a method to calculate synthetic Green functions with finite element models (FEMs) and then use linear inversion methods to determine the slip distribution on the fault plane. The method is applied to the 2009 L’Aquila Earthquake (Italy) and to the 2008 Wenchuan earthquake (China). I focus on the influence of rheological features of the earth's crust by implementing seismic tomographic data and the influence of topography by implementing Digital Elevation Models (DEM) layers on the FEMs. Results for the L’Aquila earthquake highlight the non-negligible influence of the medium structure: homogeneous and heterogeneous models show discrepancies up to 20% in the fault slip distribution values. Furthermore, in the heterogeneous models a new area of slip appears above the hypocenter. Regarding the 2008 Wenchuan earthquake, the very steep topographic relief of Longmen Shan Range is implemented in my FE model. A large number of DEM layers corresponding to East China is used to achieve the complete coverage of the FE model. My objective was to explore the influence of the topography on the retrieved coseismic slip distribution. The inversion results reveals significant differences between the flat and topographic model. Thus, the flat models frequently adopted are inappropriate to represent the earth surface topographic features and especially in the case of the 2008 Wenchuan earthquake.

Spatial and temporal characterisation of ground deformation recorded by geodetic techniques

A critical point in the analysis of ground displacements time series is the development of data driven methods that allow the different sources that generate the observed displacements to be discerned and characterised. A widely used multivariate statistical technique is the Principal Component Analysis (PCA), which allows reducing the dimensionality of the data space maintaining most of the variance of the dataset explained. Anyway, PCA does not perform well in finding the solution to the so-called Blind Source Separation (BSS) problem, i.e. in recovering and separating the original sources that generated the observed data. This is mainly due to the assumptions on which PCA relies: it looks for a new Euclidean space where the projected data are uncorrelated. The Independent Component Analysis (ICA) is a popular technique adopted to approach this problem. However, the independence condition is not easy to impose, and it is often necessary to introduce some approximations. To work around this problem, I use a variational bayesian ICA (vbICA) method, which models the probability density function (pdf) of each source signal using a mix of Gaussian distributions. This technique allows for more flexibility in the description of the pdf of the sources, giving a more reliable estimate of them. Here I present the application of the vbICA technique to GPS position time series. First, I use vbICA on synthetic data that simulate a seismic cycle (interseismic + coseismic + postseismic + seasonal + noise) and a volcanic source, and I study the ability of the algorithm to recover the original (known) sources of deformation. Secondly, I apply vbICA to different tectonically active scenarios, such as the 2009 L'Aquila (central Italy) earthquake, the 2012 Emilia (northern Italy) seismic sequence, and the 2006 Guerrero (Mexico) Slow Slip Event (SSE).

Simultaneous Multiscale Polyaffine Registration by Incorporating Deformation Statistics

Locally affine (polyaffine) image registration methods capture intersubject non-linear deformations with a low number of parameters, while providing an intuitive interpretation for clinicians. Considering the mandible bone, anatomical shape differences can be found at different scales, e.g. left or right side, teeth, etc. Classically, sequential coarse to fine registration are used to handle multiscale deformations, instead we propose a simultaneous optimization of all scales. To avoid local minima we incorporate a prior on the polyaffine transformations. This kind of groupwise registration approach is natural in a polyaffine context, if we assume one configuration of regions that describes an entire group of images, with varying transformations for each region. In this paper, we reformulate polyaffine deformations in a generative statistical model, which enables us to incorporate deformation statistics as a prior in a Bayesian setting. We find optimal transformations by optimizing the maximum a posteriori probability. We assume that the polyaffine transformations follow a normal distribution with mean and concentration matrix. Parameters of the prior are estimated from an initial coarse to fine registration. Knowing the region structure, we develop a blockwise pseudoinverse to obtain the concentration matrix. To our knowledge, we are the first to introduce simultaneous multiscale optimization through groupwise polyaffine registration. We show results on 42 mandible CT images.

A three-dimensional histological atlas of the human basal ganglia. II. Atlas deformation strategy and evaluation in deep brain stimulation for Parkinson disease

OBJECT: The localization of any given target in the brain has become a challenging issue because of the increased use of deep brain stimulation to treat Parkinson disease, dystonia, and nonmotor diseases (for example, Tourette syndrome, obsessive compulsive disorders, and depression). The aim of this study was to develop an automated method of adapting an atlas of the human basal ganglia to the brains of individual patients. METHODS: Magnetic resonance images of the brain specimen were obtained before extraction from the skull and histological processing. Adaptation of the atlas to individual patient anatomy was performed by reshaping the atlas MR images to the images obtained in the individual patient using a hierarchical registration applied to a region of interest centered on the basal ganglia, and then applying the reshaping matrix to the atlas surfaces. RESULTS: Results were evaluated by direct visual inspection of the structures visible on MR images and atlas anatomy, by comparison with electrophysiological intraoperative data, and with previous atlas studies in patients with Parkinson disease. The method was both robust and accurate, never failing to provide an anatomically reliable atlas to patient registration. The registration obtained did not exceed a 1-mm mismatch with the electrophysiological signatures in the region of the subthalamic nucleus. CONCLUSIONS: This registration method applied to the basal ganglia atlas forms a powerful and reliable method for determining deep brain stimulation targets within the basal ganglia of individual patients.

Quantification of Popliteal Artery Deformation During Leg Flexion in Subjects With Peripheral Artery Disease: A Pilot Study

Purpose: To quantify the in vivo deformations of the popliteal artery during leg flexion in subjects with clinically relevant peripheral artery disease (PAD). Methods: Five patients (4 men; mean age 69 years, range 56–79) with varying calcification levels of the popliteal artery undergoing endovascular revascularization underwent 3-dimensional (3D) rotational angiography. Image acquisition was performed with the leg straight and with a flexion of 70°/20° in the knee/hip joints. The arterial centerline and the corresponding branches in both positions were segmented to create 3D reconstructions of the arterial trees. Axial deformation, twisting, and curvatures were quantified. Furthermore, the relationships between the calcification levels and the deformations were investigated. Results: An average shortening of 5.9%±2.5% and twist rate of 3.8±2.2°/cm in the popliteal artery were observed. Maximal curvatures in the straight and flexed positions were 0.12±0.04 cm−1 and 0.24±0.09 cm−1, respectively. As the severity of calcification increased, the maximal curvature in the straight position increased from 0.08 to 0.17 cm−1, while an increase from 0.17 to 0.39 cm−1 was observed for the flexed position. Axial elongations and arterial twisting were not affected by the calcification levels. Conclusion: The popliteal artery of patients with symptomatic PAD is exposed to significant deformations during flexion of the knee joint. The severity of calcification directly affects curvature, but not arterial length or twisting angles. This pilot study also showed the ability of rotational angiography to quantify the 3D deformations of the popliteal artery in patients with various levels of calcification.

Characterization of granite matrix porosity and pore-space geometry by in situ and laboratory methods

Most available studies of interconnected matrix porosity of crystalline rocks are based on laboratory investigations; that is, work on samples that have undergone stress relaxation and were affected by drilling and sample preparation. The extrapolation of the results to in situ conditions is therefore associated with considerable uncertainty, and this was the motivation to conduct the ‘in situ Connected Porosity’ experiment at the Grimsel Test Site (Central Swiss Alps). An acrylic resin doped with fluorescent agents was used to impregnate the microporous granitic matrix in situ around an injection borehole, and samples were obtained by overcoring. The 3-D structure of the porespace, represented by microcracks, was studied by U-stage fluorescence microscopy. Petrophysical methods, including the determination of porosity, permeability and P -wave velocity, were also applied. Investigations were conducted both on samples that were impregnated in situ and on non-impregnated samples, so that natural features could be distinguished from artefacts. The investigated deformed granites display complex microcrack populations representing a polyphase deformation at varying conditions. The crack population is dominated by open cleavage cracks in mica and grain boundary cracks. The porosity of non-impregnated samples lies slightly above 1 per cent, which is 2–2.5 times higher than the in situ porosity obtained for impregnated samples. Measurements of seismic velocities (Vp ) on spherical rock samples as a function of confining pressure, spatial direction and water saturation for both non-impregnated and impregnated samples provide further constraints on the distinction between natural and induced crack types. The main conclusions are that (1) an interconnected network of microcracks exists in the whole granitic matrix, irrespective of the distance to ductile and brittle shear zones, and (2) conventional laboratory methods overestimate the matrix porosity. Calculations of contaminant transport through fractured media often rely on matrix diffusion as a retardation mechanism.

Simulation-based evaluation of susceptibility distortion correction methods in diffusion MRI for connectivity analysis

Connectivity analysis on diffusion MRI data of the whole-brain suffers from distortions caused by the standard echo-planar imaging acquisition strategies. These images show characteristic geometrical deformations and signal destruction that are an important drawback limiting the success of tractography algorithms. Several retrospective correction techniques are readily available. In this work, we use a digital phantom designed for the evaluation of connectivity pipelines. We subject the phantom to a “theoretically correct” and plausible deformation that resembles the artifact under investigation. We correct data back, with three standard methodologies (namely fieldmap-based, reversed encoding-based, and registration- based). Finally, we rank the methods based on their geometrical accuracy, the dropout compensation, and their impact on the resulting connectivity matrices.

A gradient-enhanced large-deformation continuum damage model for fibre-reinforced materials

A non-local gradient-based damage formulation within a geometrically non-linear setting is presented. The hyperelastic constitutive response at local material point level is governed by a strain energy which is additively composed of an isotropic matrix and of an anisotropic fibre-reinforced material, respectively. The inelastic constitutive response is governed by a scalar [1–d]-type damage formulation, where only the anisotropic elastic part is assumed to be affected by the damage. Following the concept in Dimitrijević and Hackl [28], the local free energy function is enhanced by a gradient-term. This term essentially contains the gradient of the non-local damage variable which, itself, is introduced as an additional independent variable. In order to guarantee the equivalence between the local and non-local damage variable, a penalisation term is incorporated within the free energy function. Based on the principle of minimum total potential energy, a coupled system of Euler–Lagrange equations, i.e., the balance of linear momentum and the balance of the non-local damage field, is obtained and solved in weak form. The resulting coupled, highly non-linear system of equations is symmetric and can conveniently be solved by a standard incremental-iterative Newton–Raphson-type solution scheme. Several three-dimensional displacement- and force-driven boundary value problems—partially motivated by biomechanical application—highlight the mesh-objective characteristics and constitutive properties of the model and illustratively underline the capabilities of the formulation proposed

Numerical methods in Nonlinear Analysis of shell structures

The design of shell and spatial structures represents an important challenge even with the use of the modern computer technology.If we concentrate in the concrete shell structures many problems must be faced,such as the conceptual and structural disposition, optimal shape design, analysis, construction methods, details etc. and all these problems are interconnected among them. As an example the shape optimization requires the use of several disciplines like structural analysis, sensitivity analysis, optimization strategies and geometrical design concepts. Similar comments can be applied to other space structures such as steel trusses with single or double shape and tension structures. In relation to the analysis the Finite Element Method appears to be the most extended and versatile technique used in the practice. In the application of this method several issues arise. First the derivation of the pertinent shell theory or alternatively the degenerated 3-D solid approach should be chosen. According to the previous election the suitable FE model has to be adopted i.e. the displacement,stress or mixed formulated element. The good behavior of the shell structures under dead loads that are carried out towards the supports by mainly compressive stresses is impaired by the high imperfection sensitivity usually exhibited by these structures. This last effect is important particularly if large deformation and material nonlinearities of the shell may interact unfavorably, as can be the case for thin reinforced shells. In this respect the study of the stability of the shell represents a compulsory step in the analysis. Therefore there are currently very active fields of research such as the different descriptions of consistent nonlinear shell models given by Simo, Fox and Rifai, Mantzenmiller and Buchter and Ramm among others, the consistent formulation of efficient tangent stiffness as the one presented by Ortiz and Schweizerhof and Wringgers, with application to concrete shells exhibiting creep behavior given by Scordelis and coworkers; and finally the development of numerical techniques needed to trace the nonlinear response of the structure. The objective of this paper is concentrated in the last research aspect i.e. in the presentation of a state-of-the-art on the existing solution techniques for nonlinear analysis of structures. In this presentation the following excellent reviews on this subject will be mainly used.

Image processing methods for human brain connectivity analysis from in-vivo diffusion MRI

The structural connectivity of the brain is considered to encode species-wise and subject-wise patterns that will unlock large areas of understanding of the human brain. Currently, diffusion MRI of the living brain enables to map the microstructure of tissue, allowing to track the pathways of fiber bundles connecting the cortical regions across the brain. These bundles are summarized in a network representation called connectome that is analyzed using graph theory. The extraction of the connectome from diffusion MRI requires a large processing flow including image enhancement, reconstruction, segmentation, registration, diffusion tracking, etc. Although a concerted effort has been devoted to the definition of standard pipelines for the connectome extraction, it is still crucial to define quality assessment protocols of these workflows. The definition of quality control protocols is hindered by the complexity of the pipelines under test and the absolute lack of gold-standards for diffusion MRI data. Here we characterize the impact on structural connectivity workflows of the geometrical deformation typically shown by diffusion MRI data due to the inhomogeneity of magnetic susceptibility across the imaged object. We propose an evaluation framework to compare the existing methodologies to correct for these artifacts including whole-brain realistic phantoms. Additionally, we design and implement an image segmentation and registration method to avoid performing the correction task and to enable processing in the native space of diffusion data. We release PySDCev, an evaluation framework for the quality control of connectivity pipelines, specialized in the study of susceptibility-derived distortions. In this context, we propose Diffantom, a whole-brain phantom that provides a solution to the lack of gold-standard data. The three correction methodologies under comparison performed reasonably, and it is difficult to determine which method is more advisable. We demonstrate that susceptibility-derived correction is necessary to increase the sensitivity of connectivity pipelines, at the cost of specificity. Finally, with the registration and segmentation tool called regseg we demonstrate how the problem of susceptibility-derived distortion can be overcome allowing data to be used in their original coordinates. This is crucial to increase the sensitivity of the whole pipeline without any loss in specificity.