Extraction of Structural Metrics from Crossing Fiber Models

Diffusion MRI (dMRI) measurements allow us to infer the microstructural properties of white matter and to reconstruct fiber pathways in-vivo. High angular diffusion imaging (HARDI) allows for the creation of more and more complex local models connecting the microstructure to the measured signal. One of the challenges is the derivation of meaningful metrics describing the underlying structure from the local models. The aim hereby is to increase the specificity of the widely used metric fractional anisotropy (FA) by using the additional information contained within the HARDI data. A local model which is connected directly to the underlying microstructure through the model of a single fiber population is spherical deconvolution. It produces a fiber orientation density function (fODF), which can often be interpreted as superposition of multiple peaks, each associated to one relatively coherent fiber population (bundle). Parameterizing these peaks one is able to disentangle and characterize these bundles. In this work, the fODF peaks are approximated by Bingham distributions, capturing first and second order statistics of the fiber orientations, from which metrics for the parametric quantification of fiber bundles are derived. Meaningful relationships between these measures and the underlying microstructural properties are proposed. The focus lies on metrics derived directly from properties of the Bingham distribution, such as peak length, peak direction, peak spread, integral over the peak, as well as a metric derived from the comparison of the largest peaks, which probes the complexity of the underlying microstructure. These metrics are compared to the conventionally used fractional anisotropy (FA) and it is shown how they may help to increase the specificity of the characterization of microstructural properties. Visualization of the micro-structural arrangement is another application of dMRI. This is done by using tractography to propagate the fiber layout, extracted from the local model, in each voxel. In practice most tractography algorithms use little of the additional information gained from HARDI based local models aside from the reconstructed fiber bundle directions. In this work an approach to tractography based on the Bingham parameterization of the fODF is introduced. For each of the fiber populations present in a voxel the diffusion signal and tensor are computed. Then tensor deflection tractography is performed. This allows incorporating the complete bundle information, performing local interpolation as well as using multiple directions per voxel for generating tracts. Another aspect of this work is the investigation of the spherical harmonic representation which is used most commonly for the fODF by means of the parameters derived from the Bingham distribution fit. Here a strong connection between the approximation errors in the spherical representation of the Dirac delta function and the distribution of crossing angles recovered from the fODF was discovered. The final aspect of this work is the application of the metrics derived from the Bingham fit to a number of fetal datasets for quantifying the brain’s development. This is done by introducing the Gini-coefficient as a metric describing the brain’s age

Myeloarchitecture and Intrinsic Functional Connectivity of Auditory Cortex in Musicians with Absolute Pitch

Introduction This dissertation studied structures and functions of auditory cortex in musicians with a rare auditory perception called absolute pitch (AP) using an in-vivo neuroimaging technique magnetic resonance imaging (MRI). The absolute pitch is defined as an ability to recognize pitch chroma, which is musical naming in the twelve-tone equal-temperament (12-TET) system (e.g., “C#”), of any given tonal sound without external references. It has been of interest of many psychologists since the experimental methods have been introduced in psychology over a century. Early behavioral experiments reported many findings that were validated in later studies with computerized measurement of behaviors. Over the recent two decades, in-vivo neuroimaging studies have found alteration in structures and functions of the brains of musicians with AP compared to control musicians without AP. However, quantitative models on the behaviors of neural systems behind the AP have not been suggested yet. Of course, neuronal modeling is a challenging problem in cognitive neuroscience studies in general. In order to generate such models to explain auditory perceptions such as AP, detailed information on structures and functions of neural systems must be obtained. In this context, we examined microarchitecture of the auditory cortex in musicians with AP using ultra- high field MRI that currently enables the highest spatial resolution of in-vivo imaging at the moment. In addition, we examined the functional connectivity between the auditory cortex and the other regions of the whole cortex. In the dissertation, detailed introduction of the pitch chroma perception is given throughout the human auditory systems from peripheral apparatus to non-primary auditory cortex in the Chapter I. In-depth discussion on the in-vivo imaging techniques, image processing, and statistical inferences focusing on the strength and potential pitfalls of the methods and their common practice in the Chapter II. In the Chapter III and IV, I explained MRI studies of the PhD project in details with discussions on the findings. Finally in the Chapter V, I summarized the major findings and discuss possible interpretation based on the framework of ‘dual auditory pathway hypothesis’. Study of Myeloarchitecture In the first study (Chapter III), a novel MRI sequence named magnetization-prepared two rapid gradient echo (MP2RAGE) was used to investigate cortical myelination. Myeloarchitecture of cerebral cortex is the one of the important histological concepts to understand organization of cortical column as well as cytoarchitecture. Neurons in the cortex are not only linked to the other distant neurons through the white matter but also connected vertically and horizontally to adjacent neurons. These short/long-distance axonal connections form myeloarchitecture of the cortex. The MP2RAGE sequence estimates a physical quantity called longitudinal relaxation rates (R1), which is sensitive to myelin concentration of the tissue. When compared to control musicians without AP, we found greater R1 in the anterior part of the right supratemporal plane in the musicians with AP. Given the finding was specific to the middle depth of cortex, the finding is unlikely related to long-distance axonal connections but likely to local connections. The precise location of the group difference was determined as the right planum polare in the template brain as well as in all individual brains. Based on the finding, I speculated that the working principles of the AP processes might be related to the dual auditory pathway hypothesis. In the theory, spatial auditory information is processed along the dorsal pathway (from the primary auditory cortex, to planum temporale, supramarginal gyrus, parietal lobules, and dorsolateral prefrontal cortex) whereas non-spatial auditory information is processed along the ventral pathway (from the primary auditory cortex to planum polare, temporal pole, anterior insular, and ventrolateral prefrontal cortex) in analogous to visual system. Because pitch chroma is spatially invariant property of an auditory object, and also it is less useful for auditory scene segregation compared to separation based on general pitch range (i.e., pitch height), I suggested the observation of cortical myelin in the anterior non-primary auditory cortex might be related to the absolute recognition of pitch chroma in AP listeners. Another potential implication of the heavy myelination is the function of myelination in neural development. In a rat model, it was demonstrated that the myelination of cortex triggers protein interactions that greatly restrict neuroplasticity after the ‘critical period’ of normal development. From genetic studies, it has been found that the onset of musical training is crucial in the acquisition of AP. Since the planum polare is related to pitch chroma processing, the increase of myelination in this region might indicate the preservation of the pitch chroma representation. Study of Intrinsic Functional Connectivity In the second study (Chapter IV), to further test the hypothesis that this highly myelinated planum polare works differently in the auditory networks, analysis of intrinsic functional connectivity using functional MRI (fMRI) measurement acquired during resting was performed. Although spontaneous neural activities during resting was once regarded as Gaussian noise without particular information, extensive researches revealed that the resting-state data (fMRI and also M/EEG) bears substantial information on the subnetworks of brain that subserve various perceptual and cognitive functions. Particularly for the perception of AP, it has been known that spontaneous and unintended recognition of pitch chroma from ambient sounds such as the siren of an ambulance. Thus it is reasonable to assume that the AP-specific network would be constantly active even at rest. From the resting-state fMRI data, greater cross-correlations between the right planum polare, which was found to be highly myelinated, and several cortical areas including the right lateral superior temporal gyrus, the anterior insula, and the left inferior frontal cortex were found in musicians with better AP performance. Moreover, greater cross-coherences between the right planum polare and the medial part of superior frontal gyrus, the anterior cingulate cortex, and the left planum polare were found in musicians with greater AP performance. As speculated, the involvement of the ventral auditory pathway in the AP-specific resting state network was strongly suggested from the tightened functional coupling between anterior supratemporal planes and the left inferior frontal cortex. Interestingly, the right planum polare exhibited greater cross-coherence with the important hub regions of the default mode network, i.e., anterior cingulate cortex and medial parts of the superior frontal cortex and the orbitofrontal cortex, implicating a link between the auditory network and default-mode network in AP listeners. This might be related to constant AP processes in AP listeners, which results in spontaneous and unintentional recognition of AP. Conclusion In the dissertation, novel MRI data from musicians with AP were provided adding knowledge of the myeloarchitectonic characteristics and related intrinsic functional connectivity of the auditory cortex to the current understanding on the neural correlates of AP. The findings were in favor of the proposed involvement of the ventral auditory pathway, which is known for processing spatially invariant properties of auditory objects. Further studies on neural behaviors of the auditory cortex in relation to the myeloarchitecture are needed in developing computational models of AP in the future.Einleitung Diese Dissertation untersucht Strukturen und Funktionen des auditorischen Kortex in Musikern mit einer seltenen auditorischen Wahrnehmen, dem absoluten Gehör (aG), mit Hilfe des in-vivo Bildgebungsfahrens der Magnetresonanztomographie (MRT). Das absolute Gehör bezeichnet die Fähigkeit die Tonklasse (z.B. „C#“) innerhalb des 12-tönigen Systems gleichmäßiger Stimmung (12-TET) ohne externe Referenz benennen zu können. Das Phänomen des absoluten Gehöres ist Gegenstand psychologischer Untersuchungen seitdem die experimentellen Methoden vor über einem Jahrhundert vorgestellt wurden. Erste behaviorale Experimente berichteten zahlreiche Ergebnisse, die später in computer-gestützten Messverfahren validiert werden konnten. In den letzten 20 Jahren konnten Studien, unter Nutzung bildgebender Verfahren, Veränderungen in der Struktur und Funktion in den Gehirnen von Musikern mit absolutem Gehör feststellen. Bisher wurden jedoch noch keine quantitativen Modelle vorgestellt, die das Verhalten neuronaler Systeme beschreiben, die dem absoluten Gehört zugrunde liegen. Die Modellierung neuronaler Systeme stellt ein anspruchsvolles Problem der gesamten kognitiven Neurowissenschaften dar. Detaillierte Informationen bezüglich der Struktur und Funktion des neuronalen Systems müssen gesammelt, um mit Hilfe von Modelle auditorische Empfindungen wie das absolute Gehör erklären zu können. In diesem Zusammenhang haben wir die Mikroarchitektur des auditorischen Kortex von Musiker mit absolutem Gehör mit Hilfe eines ultrahohem Feld-MRTs untersucht; eine Methode mit der derzeit höchsten räumlichen Auflösung aller in-vivo Bildgebungsverfahren. Außerdem wurde die funktionelle Konnektivität zwischen dem auditorischen Kortex und anderen Regionen des gesamten Kortex untersucht. In Kapitel I der Dissertation wird detailliertes Grundwissen zur Empfindung von Tonklassen, vom menschlichen auditorischen System bis zum nicht-primären auditorischen Kortex, vermittelt. Eine vertiefte Diskussion der in-vivo Bildgebungsverfahren, der Bildverarbeitung und den statistischen Rückschlüssen ist Thema von Kapitel II, mit einem Fokus auf der üblichen Verwendung, den Stärken und potentiellen Fehlern der verwendeten Methoden. In den Kapiteln III und IV habe ich die MRT-Studien der Doktorarbeit erklärt und die Ergebnisse diskutiert. Kapitel V fasst die wesentlichen Forschungsergebnisse zusammen und diskutiert eine mögliche Interpretation der Ergebnisse auf Grundlage der Dual Auditory Pathway Hypothese. Untersuchung der Myelinarchitektur In der ersten Studie (Kapitel III) wurde eine neuartige MRT Sequenz, die magnetization-prepared two rapid gradient echo (MP2RAGE) Sequenz, genutzt um die kortikale Myelinisierung zu untersuchen. Die Myelinarchitektur des zerebralen Kortex ist eine der wichtigsten histologischen Konzepte, um sowohl die Organisation einer kortikalen Kolumne als auch die Zytoarchitektur zu verstehen. Die Neuronen des Kortex sind nicht nur an entfernte Neuronen über die weiße Substanz gekoppelt, sondern auch durch vertikale und horizontale Verbindungen an unmittelbar benachbarte Neuronen. Diese kurzen und langen axonalen Verbindungen formen die Myelinarchitektur des Kortex. Die MP2RAGE Sequenz bewertet die longitudinalen Relaxations Raten (R1), welche sensitiv für die Myelinkonzentration des untersuchten Gewebes ist. Verglichen mit einer Kontrollgruppe von Musikern ohne aG konnten wir einen höheren R1- Wert im anterioren Teil der rechten supra-temporalen Ebene in Musikern mit aG feststellen. Da das Ergebnis spezifisch für eine mittlere Tiefe des Kortex war ist es wahrscheinlicher, dies auf lokale Verbindungen als auf lange axonale Verbindungen zurückzuführen. Als genauer Ort der Gruppendifferenz wurde das rechte planum polare sowohl in einem idealisierten Gehirn als auch in den individuellen Gehirnen der Probanden festgestellt. Aufgrund dieses Ergebnisses habe ich die Hypothese aufgestellt, dass die Wirkungsweise des absoluten Gehörs mit der Dual Auditory Pathway-Theorie zusammenhängt. Diese Theorie besagt, dass räumliche auditorische Information entlang einer dorsalen Bahn (vom primären auditorischen Kortex zum planum temporale, supramarginalen Gyrus, Parietallappen und dorsolateralen präfrontalen Kortex) und nicht-räumliche Informationen entlang einer ventralen Bahn (vom primären auditorischen Kortex zum planum polare, Temporalpol, anterior insular und ventrolateralen präfrontalen Kortex), ähnlich dem visuellen System, verarbeitet werden. Da die Tonklasse eine räumlich invariante Eigenschaft eines auditorischen Objektes ist und es zudem für die auditorische Szenenunterscheidung weniger bedeutsam ist als die generelle Tonhöhe, habe ich die Vermutung angestellt, dass das kortikale Myelin im anterioren nicht-primären auditorischen Kortex mit dem absoluten Gehört für die Tonklasse im Zusammenhang steht. Eine weitere Implikation der starken Myelinisierung betrifft die Funktion von Myelin in der neuronalen Entwicklung. Im Tiermodell einer Ratte konnte gezeigt werden, dass die Myelinisierung des Kortex Proteininteraktionen auslöst, die die Neuroplastizität nach einer ‚kritischen Periode‘ der normalen Entwicklung erheblich einschränkt. Genetische Studien haben gezeigt, dass der Beginn der musikalischen Ausbildung für die Entwicklung des absoluten Gehöres entscheidend ist. Da das planum polare mit der Verarbeitung von Tonklassen in Verbindung gebracht wird, könnte ein Anstieg der Myelinisierung in diesem Bereich einen Erhalt der Tonklassenrepräsentation bedeuten. Untersuchung der intrinsischen funktionellen Konnektivität In der zweiten Studie (Kapitel IV) wurde die Hypothese, dass das stark myelinisierte planum polare in den auditorischen Netzwerken verschieden wirkt, mittels funktioneller MRT (fMRT) im entspannten Wachzustand weiter untersucht. Spontane Hirnaktivität wurde lange Zeit als Gaußsches Rauschen ohne spezielle Informationen angesehen. Umfangreiche Studien konnten jedoch zeigen, dass Messungen des Ruhezustandes, sowohl fMRT als auch M/EEG, Information bezüglich der Sub-Netzwerke tragen, die Hirnfunktionen der Wahrnehmung und Kognition unterstützen. Besonders in Bezug auf die Wahrnehmung mit absolutem Gehör konnte festgestellt werden, dass Umgebungstöne wie die Sirene eines Krankenwagens unbewusst hinsichtlich der Tonklasse erkannt werden. Diese Erkenntnis stützt die Annahme, dass das aG-Netzwerk auch im Ruhezustand aktiv ist. Mit Hilfe der fMRT-Daten wurde festgestellt, dass die Kreuzkorrelation zwischen dem stark myelinisierten rechten planum polare und weiteren kortikalen Arealen wie dem rechten lateral- superioren temporalen Gyrus, der anterioren insula und dem linken inferior-frontalen Kortex in Musikern mit besserer aG-Performanz erhöht ist. Weiterhin wurde eine erhöhte Kreuzkorrelation zwischen dem rechten planum polare und dem medialen Teil des superior-frontalen Gyrus, dem anterioren cingulate Kortex und dem linken planum polare in Musikern mit noch besser aG- Performanz festgestellt. Die erhöhte funktionelle Kopplung der anterioren supra-temporalen Ebene mit dem linken inferior-frontalen Kortex bekräftigt die Hypothese, dass der ventrale auditorische Pfad in dem aG- spezifischen Netzwerk des Ruhezustands beteiligt ist. Bemerkenswerterweise zeigte das rechte planum polare eine erhöhte Kreuzkorrelation mit wichtigen Hub-regionen des Default-Mode Netzwerkes, also dem anterioren cingulate Kortex und medialen Teilen des superior-frontalen Kortex, sowie dem orbito-frontalen Kortex. Dies bedeutet eine Verknüpfung des auditorischen Netzwerkes und des Default-Mode Netzwerkes in Menschen mit absolutem Gehör und könnte mit aG-Prozessen zusammenhängen, die die spontane und unbewusste Erkennung des absoluten Gehörs erlauben. Schlussfolgerung In dieser Dissertation wurden MRT-Daten von Musikern mit absolutem Gehör untersucht und damit zur Erweiterung des Wissensstandes bezüglich der Myelinarchitektur und der damit zusammenhängenden funktionellen Konnektivität des auditorischen Kortex beigetragen. Die Ergebnisse sprechen zugunsten der Einbindung des ventralen auditorischen Pfades, bekannt für die Verarbeitung räumlich-invarianter Eigenschaften auditorischer Objekte. Weitere Untersuchungen bezüglich des neuronalen Verhaltens des auditorischen Kortex in Verbindung mit der Myelinarchitektur sind notwendig, um quantitative Modelle des absoluten Gehörs entwickeln zu können

Improved Quantification of Connectivity in Human Brain Mapping

Diffusion magnetic resonance imaging (dMRI) is an advanced MRI methodology that can be used to probe the microstructure of biological tissue. dMRI can provide orientation information by modeling the process of water diffusion in white matter. This thesis presents contributions in three areas of diffusion imaging technology: diffusion reconstruction, quantification, and validation of derived metrics. It presents a novel reconstruction method by combining generalized q-sampling imaging, spherical harmonic basis functions and constrained spherical deconvolution methods to estimate the fiber orientation distribution function (ODF). This method provides improved spatial localization of brain nuclei and fiber tract separation. A novel diffusion anisotropy metric is presented that provides anatomically interpretable measurements of tracts that are robust in crossing areas of the brain. The metric, directional Axonal Volume (dAV) provides an estimate of directional water content of the tract based on the (ODF) and proton density map. dAV is a directionally sensitive metric and can separate anisotropic water content for each fiber population, providing a quantification in milliliters of water. A method is provided to map voxel-based dAV onto tracts that is not confounded by crossing areas and follows the tract morphology. This work introduces a novel textile based hollow fiber anisotropic phantom (TABIP) for validation of reconstruction and quantification methods. This provides a ground truth reference for axonal scale water tubular structures arranged in various anatomical configurations, crossing and mixing patterns. Analysis shows that: 1) the textile tracts are identifiable with scans used in human imaging and produced tracts and voxel metrics in the range of human tissue; 2) the current methods could resolve crossing at 90o and 45o but not 30o; 3) dAV/NODDI model closely matches (r=0.95) the number of fibers whereas conventional metrics poorly match (i.e., FA r=0.32). This work represents a new accurate quantification of axonal water content through diffusion imaging. dAV shows promise as a new anatomically interpretable metric of axonal connectivity that is not confounded by factors such as axon dispersion, crossing and local isotropic water content. This will provide better anatomical mapping of white matter and potentially improve the detection of axonal tract pathology

Novel mathematical methods for analysis of brain white matter fibers using diffusion MRI

White matter fibers connect and transfer information among various gray matter regions of the brain. Diffusion Magnetic Resonance Imaging (DMRI) allows in-vivo estimation of fiber orientations. From the estimated orientations, a 3D curve representation of the trajectory of fibers can be reconstructed in a process known as tractography. Automatic classification of these \tracts" into classes of anatomically known fiber bundles is a very important problem in neuroimage computing. In this thesis, three automatic fiber classification methods are proposed. The first two are based on combining neuroanatomical priors with density-based clustering. The first method includes brainstem heuristics but the second is more general and can be applied to any fiber pathway in the brain. Further, the second method introduces a novel fiber representation, Neighborhood Resolved Fiber Orientation Distribution(NRFOD), that represents a tract as a set of histograms that encode the distribution of fiber orientations in its neighborhood. The third method utilizes the NRFOD representation to directly map a tract to a probability estimate for each bundle class in a supervised classification framework. A practical training and validation set creation methodology is proposed. Additionally, the thesis includes statistical significance tests to investigate whether the structural change between pre-operative and post-operative fiber bundles after a tumor resection operation are related to the change in patient's cognitive performance scores. To this end, a fiber bundle to fiber bundle registration method and various quantitative measures of the structural change are proposed. We present results over DMRI data with clinical evaluations of 30 patients with brainstem tumors

Anatomo-functional magnetic resonance imaging of the spinal cord and its application to the characterization of spinal lesions in cats

Les lésions de la moelle épinière ont un impact significatif sur la qualité de la vie car elles peuvent induire des déficits moteurs (paralysie) et sensoriels. Ces déficits évoluent dans le temps à mesure que le système nerveux central se réorganise, en impliquant des mécanismes physiologiques et neurochimiques encore mal connus. L'ampleur de ces déficits ainsi que le processus de réhabilitation dépendent fortement des voies anatomiques qui ont été altérées dans la moelle épinière. Il est donc crucial de pouvoir attester l'intégrité de la matière blanche après une lésion spinale et évaluer quantitativement l'état fonctionnel des neurones spinaux. Un grand intérêt de l'imagerie par résonance magnétique (IRM) est qu'elle permet d'imager de façon non invasive les propriétés fonctionnelles et anatomiques du système nerveux central. Le premier objectif de ce projet de thèse a été de développer l'IRM de diffusion afin d'évaluer l'intégrité des axones de la matière blanche après une lésion médullaire. Le deuxième objectif a été d'évaluer dans quelle mesure l'IRM fonctionnelle permet de mesurer l'activité des neurones de la moelle épinière. Bien que largement appliquées au cerveau, l'IRM de diffusion et l'IRM fonctionnelle de la moelle épinière sont plus problématiques. Les difficultés associées à l'IRM de la moelle épinière relèvent de sa fine géométrie (environ 1 cm de diamètre chez l'humain), de la présence de mouvements d'origine physiologique (cardiaques et respiratoires) et de la présence d'artefacts de susceptibilité magnétique induits par les inhomogénéités de champ, notamment au niveau des disques intervertébraux et des poumons. L'objectif principal de cette thèse a donc été de développer des méthodes permettant de contourner ces difficultés. Ce développement a notamment reposé sur l'optimisation des paramètres d'acquisition d'images anatomiques, d'images pondérées en diffusion et de données fonctionnelles chez le chat et chez l'humain sur un IRM à 3 Tesla. En outre, diverses stratégies ont été étudiées afin de corriger les distorsions d'images induites par les artefacts de susceptibilité magnétique, et une étude a été menée sur la sensibilité et la spécificité de l'IRM fonctionnelle de la moelle épinière. Les résultats de ces études démontrent la faisabilité d'acquérir des images pondérées en diffusion de haute qualité, et d'évaluer l'intégrité de voies spinales spécifiques après lésion complète et partielle. De plus, l'activité des neurones spinaux a pu être détectée par IRM fonctionnelle chez des chats anesthésiés. Bien qu'encourageants, ces résultats mettent en lumière la nécessité de développer davantage ces nouvelles techniques. L'existence d'un outil de neuroimagerie fiable et robuste, capable de confirmer les paramètres cliniques, permettrait d'améliorer le diagnostic et le pronostic chez les patients atteints de lésions médullaires. Un des enjeux majeurs serait de suivre et de valider l'effet de diverses stratégies thérapeutiques. De telles outils représentent un espoir immense pour nombre de personnes souffrant de traumatismes et de maladies neurodégénératives telles que les lésions de la moelle épinière, les tumeurs spinales, la sclérose en plaques et la sclérose latérale amyotrophique.Spinal cord injury has a significant impact on quality of life since it can lead to motor (paralysis) and sensory deficits. These deficits evolve in time as reorganisation of the central nervous system occurs, involving physiological and neurochemical mechanisms that are still not fully understood. Given that both the severity of the deficit and the successful rehabilitation process depend on the anatomical pathways that have been altered in the spinal cord, it may be of great interest to assess white matter integrity after a spinal lesion and to evaluate quantitatively the functional state of spinal neurons. The great potential of magnetic resonance imaging (MRI) lies in its ability to investigate both anatomical and functional properties of the central nervous system non invasively. To address the problem of spinal cord injury, this project aimed to evaluate the benefits of diffusion-weighted MRI to assess the integrity of white matter axons that remain after spinal cord injury. The second objective was to evaluate to what extent functional MRI can measure the activity of neurons in the spinal cord. Although widely applied to the brain, diffusion-weighted MRI and functional MRI of the spinal cord are not straightforward. Various issues arise from the small cross-section width of the cord, the presence of cardiac and respiratory motions, and from magnetic field inhomogeneities in the spinal region. The main purpose of the present thesis was therefore to develop methodologies to circumvent these issues. This development notably focused on the optimization of acquisition parameters to image anatomical, diffusion-weighted and functional data in cats and humans at 3T using standard coils and pulse sequences. Moreover, various strategies to correct for susceptibility-induced distortions were investigated and the sensitivity and specificity in spinal cord functional MRI was studied. As a result, acquisition of high spatial and angular diffusion-weighted images and evaluation of the integrity of specific spinal pathways following spinal cord injury was achieved. Moreover, functional activations in the spinal cord of anaesthetized cats was detected. Although encouraging, these results highlight the need for further technical and methodological development in the near-future. Being able to develop a reliable neuroimaging tool for confirming clinical parameters would improve diagnostic and prognosis. It would also enable to monitor the effect of various therapeutic strategies. This would certainly bring hope to a large number of people suffering from trauma and neurodegenerative diseases such as spinal cord injury, tumours, multiple sclerosis and amyotrophic lateral sclerosis

Imagerie de diffusion en temps-réel (correction du bruit et inférence de la connectivité cérébrale)

La plupart des constructeurs de systèmes d'imagerie par résonance magnétique (IRM) proposent un large choix d'applications de post-traitement sur les données IRM reconstruites a posteriori, mais très peu de ces applications peuvent être exécutées en temps réel pendant l'examen. Mises à part certaines solutions dédiées à l'IRM fonctionnelle permettant des expériences relativement simples ainsi que d'autres solutions pour l'IRM interventionnelle produisant des scans anatomiques pendant un acte de chirurgie, aucun outil n'a été développé pour l'IRM pondérée en diffusion (IRMd). Cependant, comme les examens d'IRMd sont extrêmement sensibles à des perturbations du système hardware ou à des perturbations provoquées par le sujet et qui induisent des données corrompues, il peut être intéressant d'investiguer la possibilité de reconstruire les données d'IRMd directement lors de l'examen. Cette thèse est dédiée à ce projet innovant. La contribution majeure de cette thèse a consisté en des solutions de débruitage des données d'IRMd en temps réel. En effet, le signal pondéré en diffusion peut être corrompu par un niveau élevé de bruit qui n'est plus gaussien, mais ricien ou chi non centré. Après avoir réalisé un état de l'art détaillé de la littérature sur le bruit en IRM, nous avons étendu l'estimateur linéaire qui minimise l'erreur quadratique moyenne (LMMSE) et nous l'avons adapté à notre cadre de temps réel réalisé avec un filtre de Kalman. Nous avons comparé les performances de cette solution à celles d'un filtrage gaussien standard, difficile à implémenter car il nécessite une modification de la chaîne de reconstruction pour y être inséré immédiatement après la démodulation du signal acquis dans l'espace de Fourier. Nous avons aussi développé un filtre de Kalman parallèle qui permet d'appréhender toute distribution de bruit et nous avons montré que ses performances étaient comparables à celles de notre méthode précédente utilisant un filtre de Kalman non parallèle. Enfin, nous avons investigué la faisabilité de réaliser une tractographie en temps-réel pour déterminer la connectivité structurelle en direct, pendant l'examen. Nous espérons que ce panel de développements méthodologiques permettra d'améliorer et d'accélérer le diagnostic en cas d'urgence pour vérifier l'état des faisceaux de fibres de la substance blanche.Most magnetic resonance imaging (MRI) system manufacturers propose a huge set of software applications to post-process the reconstructed MRI data a posteriori, but few of them can run in real-time during the ongoing scan. To our knowledge, apart from solutions dedicated to functional MRI allowing relatively simple experiments or for interventional MRI to perform anatomical scans during surgery, no tool has been developed in the field of diffusion-weighted MRI (dMRI). However, because dMRI scans are extremely sensitive to lots of hardware or subject-based perturbations inducing corrupted data, it can be interesting to investigate the possibility of processing dMRI data directly during the ongoing scan and this thesis is dedicated to this challenging topic. The major contribution of this thesis aimed at providing solutions to denoise dMRI data in real-time. Indeed, the diffusion-weighted signal may be corrupted by a significant level of noise which is not Gaussian anymore, but Rician or noncentral chi. After making a detailed review of the literature, we extended the linear minimum mean square error (LMMSE) estimator and adapted it to our real-time framework with a Kalman filter. We compared its efficiency to the standard Gaussian filtering, difficult to implement, as it requires a modification of the reconstruction pipeline to insert the filter immediately after the demodulation of the acquired signal in the Fourier space. We also developed a parallel Kalman filter to deal with any noise distribution and we showed that its efficiency was quite comparable to the non parallel Kalman filter approach. Last, we addressed the feasibility of performing tractography in real-time in order to infer the structural connectivity online. We hope that this set of methodological developments will help improving and accelerating a diagnosis in case of emergency to check the integrity of white matter fiber bundles.PARIS11-SCD-Bib. électronique (914719901) / SudocSudocFranceF

Group-wise analysis on myelination profiles of cerebral cortex using the second eigenvector of Laplace-Beltrami operator

Myeloarchitecture of cerebral cortex has crucial implication on the function of cortical columnar modules. Based on the recent development of high-field magnetic resonance imaging (MRI), it was demonstrated that it is possible to individually reconstruct such intracortical microstructures. However, there is a scarcity of publicly available frameworks to perform group-wise statistical inferences on high resolution data. In this paper, we present a novel framework that parameterizes curved brain structures in order to construct correspondences across subjects without deforming individual geometry. We use the second Laplace-Beltrami eigenfunction to build such a parameterization, which is known to monotonically increase along the longest geodesic distance on an arbitrary manifold. To demonstrate our framework, a study on the lateralization of Heschl’s gyrus is presented with multiple comparison correction